Preparation of a novel dual-function strong cation exchange/hydrophobic interaction chromatography stationary phase for protein separation.

Science.gov (United States)

Zhao, Kailou; Yang, Li; Wang, Xuejiao; Bai, Quan; Yang, Fan; Wang, Fei

2012-08-30

We have explored a novel dual-function stationary phase which combines both strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC) characteristics. The novel dual-function stationary phase is based on porous and spherical silica gel functionalized with ligand containing sulfonic and benzyl groups capable of electrostatic and hydrophobic interaction functionalities, which displays HIC character in a high salt concentration, and IEC character in a low salt concentration in mobile phase employed. As a result, it can be employed to separate proteins with SCX and HIC modes, respectively. The resolution and selectivity of the dual-function stationary phase were evaluated under both HIC and SCX modes with standard proteins and can be comparable to that of conventional IEC and HIC columns. More than 96% of mass and bioactivity recoveries of proteins can be achieved in both HIC and SCX modes, respectively. The results indicated that the novel dual-function column could replace two individual SCX and HIC columns for protein separation. Mixed retention mechanism of proteins on this dual-function column based on stoichiometric displacement theory (SDT) in LC was investigated to find the optimal balance of the magnitude of electrostatic and hydrophobic interactions between protein and the ligand on the silica surface in order to obtain high resolution and selectivity for protein separation. In addition, the effects of the hydrophobicity of the ligand of the dual-function packings and pH of the mobile phase used on protein separation were also investigated in detail. The results show that the ligand with suitable hydrophobicity to match the electrostatic interaction is very important to prepare the dual-function stationary phase, and a better resolution and selectivity can be obtained at pH 6.5 in SCX mode. Therefore, the dual-function column can replace two individual SCX and HIC columns for protein separation and be used to set up two-dimensional liquid

Mixed-matrix membrane adsorbers for protein separation

NARCIS (Netherlands)

Avramescu, M.E.; Borneman, Z.; Wessling, M.

2003-01-01

The separation of two similarly sized proteins, bovine serum albumin (BSA) and bovine hemoglobin (Hb) was carried out using a new type of ion-exchange mixed-matrix adsorber membranes. The adsorber membranes were prepared by incorporation of various types of Lewatit ion-exchange resins into an

Fractionation separation of human plasma proteins using HPLC with a homemade iron porphyrin based monolithic column.

Science.gov (United States)

Zhang, Doudou; Zhao, Yu; Lan, Dandan; Pang, Xiaomin; Bai, Ligai; Liu, Haiyan; Yan, Hongyuan

2017-11-15

In this work a polymer monolithic column was fabricated within the confines of a stainless steel column (50×4.6mm i.d.) via radical polymerization by using iron porphyrin and butyl methacrylate as co-monomers, ethylene glycol dimethacrylate as crosslinking agent, ethylene glycol, isopropyl alcohol and N, N-dimethylformamide as tri-porogens, benzoyl peroxide and N,N-dimethylaniline as initiators. The resulting monolithic column was characterized by elemental analysis, scanning electron microscopy, nitrogen adsorption BET surface area, and mercury intrusion porosimetry, respectively. Results showed that the homemade monolith occupied relatively uniform pore structure, low back pressure, and enhanced selectivity for proteins in complex bio-samples. The present work described a simple and efficient method for "fractionation separation" of human plasma proteins, and it is a promising separation method for complex bio-samples in proteomic research. Copyright © 2017 Elsevier B.V. All rights reserved.

Tandem assays of protein and glucose with functionalized core/shell particles based on magnetic separation and surface-enhanced Raman scattering.

Science.gov (United States)

Kong, Xianming; Yu, Qian; Lv, Zhongpeng; Du, Xuezhong

2013-10-11

Tandem assays of protein and glucose in combination with mannose-functionalized Fe3 O4 @SiO2 and Ag@SiO2 tag particles have promising potential in effective magnetic separation and highly sensitive and selective SERS assays of biomaterials. It is for the first time that tandem assay of glucose is developed using SERS based on the Con A-sandwiched microstructures between the functionalized magnetic and tag particles. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid detection and purification of sequence specific DNA binding proteins using magnetic separation

Directory of Open Access Journals (Sweden)

TIJANA SAVIC

2006-02-01

Full Text Available In this paper, a method for the rapid identification and purification of sequence specific DNA binding proteins based on magnetic separation is presented. This method was applied to confirm the binding of the human recombinant USF1 protein to its putative binding site (E-box within the human SOX3 protomer. It has been shown that biotinylated DNA attached to streptavidin magnetic particles specifically binds the USF1 protein in the presence of competitor DNA. It has also been demonstrated that the protein could be successfully eluted from the beads, in high yield and with restored DNA binding activity. The advantage of these procedures is that they could be applied for the identification and purification of any high-affinity sequence-specific DNA binding protein with only minor modifications.

SURVEY REGARDING THE ULTRAFILTRATION OF PROTEINES THROUGH MEMBRANE BASED PROCEDURES

Directory of Open Access Journals (Sweden)

CAMELIA HODOSAN

2008-05-01

Full Text Available This work is based on examples that emphasize the complexity of the proteins ultrafiltration process, pointing out the first 10-15 minutes of ultrafiltration. The knowledgement of the factors that influence the separation through ultrafiltration of proteins will allow to choose the right type of membrane, the frequent use of the same membrane and the operation in mechanical and chemical conditions adequate to the ultrafiltration system, when it is separated a protein with certain molecular weight.

Artificial receptor-functionalized nanoshell: facile preparation, fast separation and specific protein recognition

Science.gov (United States)

Ouyang, Ruizhuo; Lei, Jianping; Ju, Huangxian

2010-05-01

This work combined molecular imprinting technology with superparamagnetic nanospheres as the core to prepare artificial receptor-functionalized magnetic nanoparticles for separation of homologous proteins. Using dopamine as a functional monomer, novel surface protein-imprinted superparamagnetic polydopamine (PDA) core-shell nanoparticles were successfully prepared in physiological conditions, which could maintain the natural structure of a protein template and achieved the development of molecularly imprinted polymers (MIPs) from one dimension to zero dimension for efficient recognition towards large biomolecules. The resultant nanoparticles could be used for convenient magnetic separation of homologous proteins with high specificity. The nanoparticles possessed good monodispersibility, uniform surface morphology and high saturation magnetization value. The bound amounts of template proteins measured by both indirect and direct methods were in good agreement. The maximum number of imprinted cavities on the surface of the bovine hemoglobin (Hb)-imprinted nanoshell was 2.21 × 1018 g - 1, which well matched their maximum binding capacity toward bovine Hb. Both the simple method for preparation of MIPs and the magnetic nanospheres showed good application potential in fast separation, effective concentration and selective biosensing of large protein molecules.

Artificial receptor-functionalized nanoshell: facile preparation, fast separation and specific protein recognition

Energy Technology Data Exchange (ETDEWEB)

Ouyang, Ruizhuo; Lei Jianping; Ju Huangxian, E-mail: jpl@nju.edu.cn, E-mail: hxju@nju.edu.cn [Key Laboratory of Analytical Chemistry for Life Science (Education Ministry of China), Department of Chemistry, Nanjing University, Nanjing 210093 (China)

2010-05-07

This work combined molecular imprinting technology with superparamagnetic nanospheres as the core to prepare artificial receptor-functionalized magnetic nanoparticles for separation of homologous proteins. Using dopamine as a functional monomer, novel surface protein-imprinted superparamagnetic polydopamine (PDA) core-shell nanoparticles were successfully prepared in physiological conditions, which could maintain the natural structure of a protein template and achieved the development of molecularly imprinted polymers (MIPs) from one dimension to zero dimension for efficient recognition towards large biomolecules. The resultant nanoparticles could be used for convenient magnetic separation of homologous proteins with high specificity. The nanoparticles possessed good monodispersibility, uniform surface morphology and high saturation magnetization value. The bound amounts of template proteins measured by both indirect and direct methods were in good agreement. The maximum number of imprinted cavities on the surface of the bovine hemoglobin (Hb)-imprinted nanoshell was 2.21 x 10{sup 18} g{sup -1}, which well matched their maximum binding capacity toward bovine Hb. Both the simple method for preparation of MIPs and the magnetic nanospheres showed good application potential in fast separation, effective concentration and selective biosensing of large protein molecules.

Interrogation of an autofluorescence-based method for protein fingerprinting.

Science.gov (United States)

Siddaramaiah, Manjunath; Rao, Bola Sadashiva S; Joshi, Manjunath B; Datta, Anirbit; Sandya, S; Vishnumurthy, Vasudha; Chandra, Subhash; Nayak, Subramanya G; Satyamoorthy, Kapaettu; Mahato, Krishna K

2018-03-14

In the present study, we have designed a laser-induced fluorescence (LIF) based instrumentation and developed a sensitive methodology for the effective separation, visualization, identification and analysis of proteins on a single platform. In this method, intrinsic fluorescence spectra of proteins were detected after separation on 1 or 2 dimensional Sodium Dodecyl Sulfate-Tris(2-carboxyethyl)phosphine (SDS-TCEP) polyacrylamide gel electrophoresis (PAGE) and the data were analyzed. The MATLAB assisted software was designed for the development of PAGE fingerprint for the visualization of protein after 1- and 2-dimensional protein separation. These provided objective parameters of intrinsic fluorescence intensity, emission peak, molecular weight and isoelectric point using a single platform. Further, the current architecture could differentiate the overlapping proteins in the PAGE gels which otherwise were not identifiable by conventional staining, imaging and tagging methods. Categorization of the proteins based on the presence or absence of tyrosine or tryptophan residues and assigning the corresponding emission peaks (309-356 nm) with pseudo colors allowed the detection of proportion of proteins within the given spectrum. The present methodology doesn't use stains or tags, hence amenable to couple with mass spectroscopic measurements. This technique may have relevance in the field of proteomics that is used for innumerable applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ndj1, a telomere-associated protein, regulates centrosome separation in budding yeast meiosis

Science.gov (United States)

Li, Ping; Shao, Yize; Jin, Hui

2015-01-01

Yeast centrosomes (called spindle pole bodies [SPBs]) remain cohesive for hours during meiotic G2 when recombination takes place. In contrast, SPBs separate within minutes after duplication in vegetative cells. We report here that Ndj1, a previously known meiosis-specific telomere-associated protein, is required for protecting SPB cohesion. Ndj1 localizes to the SPB but dissociates from it ∼16 min before SPB separation. Without Ndj1, meiotic SPBs lost cohesion prematurely, whereas overproduction of Ndj1 delayed SPB separation. When produced ectopically in vegetative cells, Ndj1 caused SPB separation defects and cell lethality. Localization of Ndj1 to the SPB depended on the SUN domain protein Mps3, and removal of the N terminus of Mps3 allowed SPB separation and suppressed the lethality of NDJ1-expressing vegetative cells. Finally, we show that Ndj1 forms oligomeric complexes with Mps3, and that the Polo-like kinase Cdc5 regulates Ndj1 protein stability and SPB separation. These findings reveal the underlying mechanism that coordinates yeast centrosome dynamics with meiotic telomere movement and cell cycle progression. PMID:25897084

Protein-protein interaction network-based detection of functionally similar proteins within species.

Science.gov (United States)

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

An investigation of paper based microfluidic devices for size based separation and extraction applications.

Science.gov (United States)

Zhong, Z W; Wu, R G; Wang, Z P; Tan, H L

2015-09-01

Conventional microfluidic devices are typically complex and expensive. The devices require the use of pneumatic control systems or highly precise pumps to control the flow in the devices. This work investigates an alternative method using paper based microfluidic devices to replace conventional microfluidic devices. Size based separation and extraction experiments conducted were able to separate free dye from a mixed protein and dye solution. Experimental results showed that pure fluorescein isothiocyanate could be separated from a solution of mixed fluorescein isothiocyanate and fluorescein isothiocyanate labeled bovine serum albumin. The analysis readings obtained from a spectrophotometer clearly show that the extracted tartrazine sample did not contain any amount of Blue-BSA, because its absorbance value was 0.000 measured at a wavelength of 590nm, which correlated to Blue-BSA. These demonstrate that paper based microfluidic devices, which are inexpensive and easy to implement, can potentially replace their conventional counterparts by the use of simple geometry designs and the capillary action. These findings will potentially help in future developments of paper based microfluidic devices. Copyright © 2015 Elsevier B.V. All rights reserved.

Polymethacrylate-based monoliths as stationary phases for separation of biopolymers and immobilization of enzymes.

Science.gov (United States)

Martinović, Tamara; Josić, Djuro

2017-11-01

The experiences in the production and application of polymethacrylate-based monolithic supports, since their development almost thirty years ago, are presented. The main driving force for the development of new chromatographic supports was the necessity for the isolation and separation of physiologically active biopolymers and their use for therapeutic purposes. For this sake, a development of a method for fast separation, preventing denaturation and preserving their biological activity was necessary. Development of polysaccharide-based supports, followed by the introduction of polymer-based chromatographic media, is shortly described. This development was followed by the advances in monolithic media that are now used for both large- and small-scale separation of biopolymers and nanoparticles. Finally, a short overview is given about the applications of monoliths for sample displacement chromatography, resulting in isolation of physiologically active biomolecules, such as proteins, protein complexes, and nucleic acid, as well as high-throughput sample preparation for proteomic investigations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations.

Science.gov (United States)

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C; Landes, Christy F

2014-02-11

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally.

Separation techniques: Chromatography

Science.gov (United States)

Coskun, Ozlem

2016-01-01

Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorption, partition, and size exclusion. Other chromatography techniques are based on the stationary bed, including column, thin layer, and paper chromatography. Column chromatography is one of the most common methods of protein purification. PMID:28058406

Bacterial surface layer proteins as a novel capillary coating material for capillary electrophoretic separations

Energy Technology Data Exchange (ETDEWEB)

Moreno-Gordaliza, Estefanía, E-mail: emorenog@ucm.es [Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Universiteit Leiden, Einsteinweg 55, 2300, RA, Leiden (Netherlands); Department of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid (Spain); Stigter, Edwin C.A. [Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Universiteit Leiden, Einsteinweg 55, 2300, RA, Leiden (Netherlands); Department of Molecular Cancer Research, Universitair Medisch Centrum Utrecht, Wilhelmina Kinder Ziekenhuis, Lundlaan 6, 3584, EA Utrecht (Netherlands); Lindenburg, Petrus W.; Hankemeier, Thomas [Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Universiteit Leiden, Einsteinweg 55, 2300, RA, Leiden (Netherlands)

2016-06-07

A novel concept for stable coating in capillary electrophoresis, based on recrystallization of surface layer proteins on hydrophobized fused silica capillaries, was demonstrated. Surface layer protein A (SlpA) from Lactobacillus acidophilus bacteria was extracted, purified and used for coating pre-silanized glass substrates presenting different surface wettabilities (either hydrophobic or hydrophilic). Contact angle determination on SlpA-coated hydrophobic silica slides showed that the surfaces turned to hydrophilic after coating (53 ± 5°), due to a protein monolayer formation by protein-surface hydrophobic interactions. Visualization by atomic force microscopy demonstrated the presence of a SlpA layer on methylated silica slides displaying a surface roughness of 0.44 ± 0.02 nm. Additionally, a protein layer was visualized by fluorescence microscopy in methylated silica capillaries coated with SlpA and fluorescein isothiocyanate-labeled. The SlpA-coating showed an outstanding stability, even after treatment with 20 mM NaOH (pH 12.3). The electroosmotic flow in coated capillaries showed a partial suppression at pH 7.50 (3.8 ± 0.5 10{sup −9} m{sup 2} V{sup −1} s{sup −1}) when compared with unmodified fused silica (5.9 ± 0.1 10{sup −8} m{sup 2} V{sup −1} s{sup −1}). To demonstrate the potential of this novel coating, the SlpA-coated capillaries were applied for the first time for electrophoretic separation, and proved to be very suitable for the isotachophoretic separation of lipoproteins in human serum. The separations showed a high degree of repeatability (absolute migration times with 1.1–1.8% coefficient-of-variation (CV) within a day) and 2–3% CV inter-capillary reproducibility. The capillaries were stable for more than 100 runs at pH 9.40, and showed to be an exceptional alternative for challenging electrophoretic separations at long-term use. - Highlights: • New coating using recrystallized surface-layer proteins on

A simple immunoblotting method after separation of proteins in agarose gel

DEFF Research Database (Denmark)

Koch, C; Skjødt, K; Laursen, I

1985-01-01

A simple and sensitive method for immunoblotting of proteins after separation in agarose gels is described. It involves transfer of proteins onto nitrocellulose paper simply by diffusion through pressure, a transfer which only takes about 10 min. By this method we have demonstrated the existence ...

Microphase Separation Controlled beta-Sheet Crystallization Kinetics in Fibrous Proteins

International Nuclear Information System (INIS)

Hu, X.; Lu, Q.; Kaplan, D.; Cebe, P.

2009-01-01

Silk is a naturally occurring fibrous protein with a multiblock chain architecture. As such, it has many similarities with synthetic block copolymers, including the possibility for e-sheet crystallization restricted within the crystallizable blocks. The mechanism of isothermal crystallization kinetics of e-sheet crystals in silk multiblock fibrous proteins is reported in this study. Kinetics theories, such as Avrami analysis which was established for studies of synthetic polymer crystal growth, are for the first time extended to investigate protein self-assembly in e-sheet rich Bombyx mori silk fibroin samples, using time-resolved Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and synchrotron real-time wide-angle X-ray scattering (WAXS). The Avrami exponent, n, was close to 2 for all methods and crystallization temperatures, indicating formation of e-sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in synthetic polymers. Observations by scanning electron microscopy support the view that the protein structures vary during the different stages of crystal growth, and show a microphase separation pattern after chymotrypsin enzyme biodegradation. We present a model to explain the crystallization of the multiblock silk fibroin protein, by analogy to block copolymers: crystallization of e-sheets occurs under conditions of geometrical restriction caused by phase separation of the crystallizable and uncrystallizable blocks. This crystallization model could be widely applicable in other proteins with multiblock (i.e., crystallizable and noncrystallizable) domains.

Integration of carboxyl modified magnetic particles and aqueous two-phase extraction for selective separation of proteins.

Science.gov (United States)

Gai, Qingqing; Qu, Feng; Zhang, Tao; Zhang, Yukui

2011-07-15

Both of the magnetic particle adsorption and aqueous two-phase extraction (ATPE) were simple, fast and low-cost method for protein separation. Selective proteins adsorption by carboxyl modified magnetic particles was investigated according to protein isoelectric point, solution pH and ionic strength. Aqueous two-phase system of PEG/sulphate exhibited selective separation and extraction for proteins before and after magnetic adsorption. The two combination ways, magnetic adsorption followed by ATPE and ATPE followed by magnetic adsorption, for the separation of proteins mixture of lysozyme, bovine serum albumin, trypsin, cytochrome C and myloglobin were discussed and compared. The way of magnetic adsorption followed by ATPE was also applied to human serum separation. Copyright © 2011 Elsevier B.V. All rights reserved.

Protein-based stable isotope probing.

Science.gov (United States)

Jehmlich, Nico; Schmidt, Frank; Taubert, Martin; Seifert, Jana; Bastida, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Vogt, Carsten

2010-12-01

We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.

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

International Nuclear Information System (INIS)

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

2013-01-01

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

Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter

Directory of Open Access Journals (Sweden)

Klaubert Dieter H

2008-04-01

Full Text Available Abstract Background The ability to specifically label proteins within living cells can provide information about their dynamics and function. To study a membrane protein, we fused a multi-functional reporter protein, HaloTag®, to the extracellular domain of a truncated integrin. Results Using the HaloTag technology, we could study the localization, trafficking and processing of an integrin-HaloTag fusion, which we showed had cellular dynamics consistent with native integrins. By labeling live cells with different fluorescent impermeable and permeable ligands, we showed spatial separation of plasma membrane and internal pools of the integrin-HaloTag fusion, and followed these protein pools over time to study bi-directional trafficking. In addition to combining the HaloTag reporter protein with different fluorophores, we also employed an affinity tag to achieve cell capture. Conclusion The HaloTag technology was used successfully to study expression, trafficking, spatial separation and real-time translocation of an integrin-HaloTag fusion, thereby demonstrating that this technology can be a powerful tool to investigate membrane protein biology in live cells.

Poly(norepinephrine)-coated open tubular column for the separation of proteins and recombination human erythropoietin by capillary electrochromatography.

Science.gov (United States)

Xiao, Xue; Zhang, Yamin; Wu, Jia; Jia, Li

2017-12-01

Recombinant human erythropoietin is an important therapeutic protein with high economic interest due to the benefits provided by its clinical use for the treatment of anemias associated with chronic renal failure and chemotherapy. In this work, a poly(norepinephrine)-coated open tubular column was successfully prepared based on the self-polymerization of norepinephrine under mild alkaline condition, the favorable film forming and easy adhesive properties of poly(norepinephrine). The poly(norepinephrine) coating was characterized by scanning electron microscopy and measurement of the electro-osmotic flow. The thickness of the coating was about 431 nm. The electrochromatographic performance of the poly(norepinephrine)-coated open tubular column was evaluated by separation of proteins. Some basic and acidic proteins including two variants of bovine serum albumin and two variants of β-lactoglobulin achieved separation in the poly(norepinephrine)-coated open tubular column. More importantly, the column demonstrated separation ability for the glycoforms of recombinant human erythropoietin. In addition, the column demonstrated good repeatability with the run-to-run, day-to-day, and column-to-column relative standard deviations of migration times of proteins less than 3.40%. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Novel, In-solution Separation of Endogenous Cardiac Sarcomeric Proteins and Identification of Distinct Charged Variants of Regulatory Light Chain*

Science.gov (United States)

Scruggs, Sarah B.; Reisdorph, Rick; Armstrong, Mike L.; Warren, Chad M.; Reisdorph, Nichole; Solaro, R. John; Buttrick, Peter M.

2010-01-01

The molecular conformation of the cardiac myosin motor is modulated by intermolecular interactions among the heavy chain, the light chains, myosin binding protein-C, and titin and is governed by post-translational modifications (PTMs). In-gel digestion followed by LC/MS/MS has classically been applied to identify cardiac sarcomeric PTMs; however, this approach is limited by protein size, pI, and difficulties in peptide extraction. We report a solution-based work flow for global separation of endogenous cardiac sarcomeric proteins with a focus on the regulatory light chain (RLC) in which specific sites of phosphorylation have been unclear. Subcellular fractionation followed by OFFGEL electrophoresis resulted in isolation of endogenous charge variants of sarcomeric proteins, including regulatory and essential light chains, myosin heavy chain, and myosin-binding protein-C of the thick filament. Further purification of RLC using reverse-phase HPLC separation and UV detection enriched for RLC PTMs at the intact protein level and provided a stoichiometric and quantitative assessment of endogenous RLC charge variants. Digestion and subsequent LC/MS/MS unequivocally identified that the endogenous charge variants of cardiac RLC focused in unique OFFGEL electrophoresis fractions were unphosphorylated (78.8%), singly phosphorylated (18.1%), and doubly phosphorylated (3.1%) RLC. The novel aspects of this study are that 1) milligram amounts of endogenous cardiac sarcomeric subproteome were focused with resolution comparable with two-dimensional electrophoresis, 2) separation and quantification of post-translationally modified variants were achieved at the intact protein level, 3) separation of intact high molecular weight thick filament proteins was achieved in solution, and 4) endogenous charge variants of RLC were separated; a novel doubly phosphorylated form was identified in mouse, and singly phosphorylated, singly deamidated, and deamidated/phosphorylated forms were

Mesoporous Silica Thin Membranes with Large Vertical Mesochannels for Nanosize-Based Separation.

Science.gov (United States)

Liu, Yupu; Shen, Dengke; Chen, Gang; Elzatahry, Ahmed A; Pal, Manas; Zhu, Hongwei; Wu, Longlong; Lin, Jianjian; Al-Dahyan, Daifallah; Li, Wei; Zhao, Dongyuan

2017-09-01

Membrane separation technologies are of great interest in industrial processes such as water purification, gas separation, and materials synthesis. However, commercial filtration membranes have broad pore size distributions, leading to poor size cutoff properties. In this work, mesoporous silica thin membranes with uniform and large vertical mesochannels are synthesized via a simple biphase stratification growth method, which possess an intact structure over centimeter size, ultrathin thickness (≤50 nm), high surface areas (up to 1420 m 2 g -1 ), and tunable pore sizes from ≈2.8 to 11.8 nm by adjusting the micelle parameters. The nanofilter devices based on the free-standing mesoporous silica thin membranes show excellent performances in separating differently sized gold nanoparticles (>91.8%) and proteins (>93.1%) due to the uniform pore channels. This work paves a promising way to develop new membranes with well-defined pore diameters for highly efficient nanosize-based separation at the macroscale. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic algorithm based separation cascade optimization

International Nuclear Information System (INIS)

Mahendra, A.K.; Sanyal, A.; Gouthaman, G.; Bera, T.K.

2008-01-01

The conventional separation cascade design procedure does not give an optimum design because of squaring-off, variation of flow rates and separation factor of the element with respect to stage location. Multi-component isotope separation further complicates the design procedure. Cascade design can be stated as a constrained multi-objective optimization. Cascade's expectation from the separating element is multi-objective i.e. overall separation factor, cut, optimum feed and separative power. Decision maker may aspire for more comprehensive multi-objective goals where optimization of cascade is coupled with the exploration of separating element optimization vector space. In real life there are many issues which make it important to understand the decision maker's perception of cost-quality-speed trade-off and consistency of preferences. Genetic algorithm (GA) is one such evolutionary technique that can be used for cascade design optimization. This paper addresses various issues involved in the GA based multi-objective optimization of the separation cascade. Reference point based optimization methodology with GA based Pareto optimality concept for separation cascade was found pragmatic and promising. This method should be explored, tested, examined and further developed for binary as well as multi-component separations. (author)

LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

Directory of Open Access Journals (Sweden)

Di Nicola Marta

2007-03-01

Full Text Available Abstract Background Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances. Results LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples. Conclusion The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.

Using Biomolecules to Separate Plutonium

Science.gov (United States)

Gogolski, Jarrod

Used nuclear fuel has traditionally been treated through chemical separations of the radionuclides for recycle or disposal. This research considers a biological approach to such separations based on a series of complex and interdependent interactions that occur naturally in the human body with plutonium. These biological interactions are mediated by the proteins serum transferrin and the transferrin receptor. Transferrin to plutonium in vivo and can deposit plutonium into cells after interacting with the transferrin receptor protein at the cell surface. Using cerium as a non-radioactive surrogate for plutonium, it was found that cerium(IV) required multiple synergistic anions to bind in the N-lobe of the bilobal transferrin protein, creating a conformation of the cerium-loaded protein that would be unable to interact with the transferrin receptor protein to achieve a separation. The behavior of cerium binding to transferrin has contributed to understanding how plutonium(IV)-transferrin interacts in vivo and in biological separations.

Nanoparticle-based capillary electroseparation of proteins in polymer capillaries under physiological conditions

DEFF Research Database (Denmark)

Nilsson, C.; Harwigsson, I.; Becker, K.

2010-01-01

Totally porous lipid-based liquid crystalline nanoparticles were used as pseudostationary phase for capillary electroseparation with LIF detection of proteins at physiological conditions using unmodified cyclic olefin copolymer capillaries (Topas (R), 6.7 cm effective length). In the absence of n...... at protein friendly conditions. The developed capillary-based method facilitates future electrochromatography of proteins on polymer-based microchips under physiological conditions and enables the initial optimization of separation conditions in parallel to the chip development....

New Developments in Membrane-Based Chemical Separations

National Research Council Canada - National Science Library

Jirage, Kshama

1998-01-01

Membrane based chemical separations is an emerging field of research. This is because membrane-based separations are potentially less energy intensive and more cost effective than competing separation methods...

Protein-Based Nanoparticle Preparation via Nanoprecipitation Method

Directory of Open Access Journals (Sweden)

Mohamad Tarhini

2018-03-01

Full Text Available Nanoparticles are nowadays largely investigated in the field of drug delivery. Among nanoparticles, protein-based particles are of paramount importance since they are natural, biodegradable, biocompatible, and nontoxic. There are several methods to prepare proteins containing nanoparticles, but only a few studies have been dedicated to the preparation of protein- based nanoparticles. Then, the aim of this work was to report on the preparation of bovine serum albumin (BSA-based nanoparticles using a well-defined nanoprecipitation process. Special attention has been dedicated to a systematic study in order to understand separately the effect of each operating parameter of the method (such as protein concentration, solvent/non-solvent volume ratio, non-solvent injection rate, ionic strength of the buffer solution, pH, and cross-linking on the colloidal properties of the obtained nanoparticles. In addition, the mixing processes (batch or drop-wise were also investigated. Using a well-defined formulation, submicron protein-based nanoparticles have been obtained. All prepared particles have been characterized in terms of size, size distribution, morphology, and electrokinetic properties. In addition, the stability of nanoparticles was investigated using Ultraviolet (UV scan and electrophoresis, and the optimal conditions for preparing BSA nanoparticles by the nanoprecipitation method were concluded.

Optimal protein library design using recombination or point mutations based on sequence-based scoring functions.

Science.gov (United States)

Pantazes, Robert J; Saraf, Manish C; Maranas, Costas D

2007-08-01

In this paper, we introduce and test two new sequence-based protein scoring systems (i.e. S1, S2) for assessing the likelihood that a given protein hybrid will be functional. By binning together amino acids with similar properties (i.e. volume, hydrophobicity and charge) the scoring systems S1 and S2 allow for the quantification of the severity of mismatched interactions in the hybrids. The S2 scoring system is found to be able to significantly functionally enrich a cytochrome P450 library over other scoring methods. Given this scoring base, we subsequently constructed two separate optimization formulations (i.e. OPTCOMB and OPTOLIGO) for optimally designing protein combinatorial libraries involving recombination or mutations, respectively. Notably, two separate versions of OPTCOMB are generated (i.e. model M1, M2) with the latter allowing for position-dependent parental fragment skipping. Computational benchmarking results demonstrate the efficacy of models OPTCOMB and OPTOLIGO to generate high scoring libraries of a prespecified size.

A Two-Week Guided Inquiry Protein Separation and Detection Experiment for Undergraduate Biochemistry

Science.gov (United States)

Carolan, James P.; Nolta, Kathleen V.

2016-01-01

A laboratory experiment for teaching protein separation and detection in an undergraduate biochemistry laboratory course is described. This experiment, performed in two, 4 h laboratory periods, incorporates guided inquiry principles to introduce students to the concepts behind and difficulties of protein purification. After using size-exclusion…

A general model for membrane-based separation processes

DEFF Research Database (Denmark)

Soni, Vipasha; Abildskov, Jens; Jonsson, Gunnar Eigil

2009-01-01

behaviour will play an important role. In this paper, modelling of membrane-based processes for separation of gas and liquid mixtures are considered. Two general models, one for membrane-based liquid separation processes (with phase change) and another for membrane-based gas separation are presented....... The separation processes covered are: membrane-based gas separation processes, pervaporation and various types of membrane distillation processes. The specific model for each type of membrane-based process is generated from the two general models by applying the specific system descriptions and the corresponding...

A Chip-Capillary Hybrid Device for Automated Transfer of Sample Pre-Separated by Capillary Isoelectric Focusing to Parallel Capillary Gel Electrophoresis for Two-Dimensional Protein Separation

Science.gov (United States)

Lu, Joann J.; Wang, Shili; Li, Guanbin; Wang, Wei; Pu, Qiaosheng; Liu, Shaorong

2012-01-01

In this report, we introduce a chip-capillary hybrid device to integrate capillary isoelectric focusing (CIEF) with parallel capillary sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS-PAGE) or capillary gel electrophoresis (CGE) toward automating two-dimensional (2D) protein separations. The hybrid device consists of three chips that are butted together. The middle chip can be moved between two positions to re-route the fluidic paths, which enables the performance of CIEF and injection of proteins partially resolved by CIEF to CGE capillaries for parallel CGE separations in a continuous and automated fashion. Capillaries are attached to the other two chips to facilitate CIEF and CGE separations and to extend the effective lengths of CGE columns. Specifically, we illustrate the working principle of the hybrid device, develop protocols for producing and preparing the hybrid device, and demonstrate the feasibility of using this hybrid device for automated injection of CIEF-separated sample to parallel CGE for 2D protein separations. Potentials and problems associated with the hybrid device are also discussed. PMID:22830584

Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

International Nuclear Information System (INIS)

Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

2016-01-01

A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q_m_a_x) and dissociation constant (K_L) were analyzed by Langmuir isotherms (R"2 = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

Energy Technology Data Exchange (ETDEWEB)

Liu, Yanjin [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Dai, Qingzhou [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Zhou, Yigang [Department of Microbiology, College of Basic Medicine, Central South University, Changsha, 410083 (China)

2016-09-14

A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q{sub max}) and dissociation constant (K{sub L}) were analyzed by Langmuir isotherms (R{sup 2} = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

Metal–organic frameworks based membranes for liquid separation

KAUST Repository

Li, Xin

2017-11-07

Metal-organic frameworks (MOFs) represent a fascinating class of solid crystalline materials which can be self-assembled in a straightforward manner by the coordination of metal ions or clusters with organic ligands. Owing to their intrinsic porous characteristics, unique chemical versatility and abundant functionalities, MOFs have received substantial attention for diverse industrial applications, including membrane separation. Exciting research activities ranging from fabrication strategies to separation applications of MOF-based membranes have appeared. Inspired by the marvelous achievements of MOF-based membranes in gas separations, liquid separations are also being explored for the purpose of constructing continuous MOFs membranes or MOF-based mixed matrix membranes. Although these are in an emerging stage of vigorous development, most efforts are directed towards improving the liquid separation efficiency with well-designed MOF-based membranes. Therefore, as an increasing trend in membrane separation, the field of MOF-based membranes for liquid separation is highlighted in this review. The criteria for judicious selection of MOFs in fabricating MOF-based membranes are given. Special attention is paid to rational design strategies for MOF-based membranes, along with the latest application progress in the area of liquid separations, such as pervaporation, water treatment, and organic solvent nanofiltration. Moreover, some attractive dual-function applications of MOF-based membranes in the removal of micropollutants, degradation, and antibacterial activity are also reviewed. Finally, we define the remaining challenges and future opportunities in this field. This Tutorial Review provides an overview and outlook for MOF-based membranes for liquid separations. Further development of MOF-based membranes for liquid separation must consider the demands of strict separation standards and environmental safety for industrial application.

Metal-organic frameworks based membranes for liquid separation.

Science.gov (United States)

Li, Xin; Liu, Yuxin; Wang, Jing; Gascon, Jorge; Li, Jiansheng; Van der Bruggen, Bart

2017-11-27

Metal-organic frameworks (MOFs) represent a fascinating class of solid crystalline materials which can be self-assembled in a straightforward manner by the coordination of metal ions or clusters with organic ligands. Owing to their intrinsic porous characteristics, unique chemical versatility and abundant functionalities, MOFs have received substantial attention for diverse industrial applications, including membrane separation. Exciting research activities ranging from fabrication strategies to separation applications of MOF-based membranes have appeared. Inspired by the marvelous achievements of MOF-based membranes in gas separations, liquid separations are also being explored for the purpose of constructing continuous MOFs membranes or MOF-based mixed matrix membranes. Although these are in an emerging stage of vigorous development, most efforts are directed towards improving the liquid separation efficiency with well-designed MOF-based membranes. Therefore, as an increasing trend in membrane separation, the field of MOF-based membranes for liquid separation is highlighted in this review. The criteria for judicious selection of MOFs in fabricating MOF-based membranes are given. Special attention is paid to rational design strategies for MOF-based membranes, along with the latest application progress in the area of liquid separations, such as pervaporation, water treatment, and organic solvent nanofiltration. Moreover, some attractive dual-function applications of MOF-based membranes in the removal of micropollutants, degradation, and antibacterial activity are also reviewed. Finally, we define the remaining challenges and future opportunities in this field. This Tutorial Review provides an overview and outlook for MOF-based membranes for liquid separations. Further development of MOF-based membranes for liquid separation must consider the demands of strict separation standards and environmental safety for industrial application.

A reassessment of synchronous fluorescence in the separation of Trp and Tyr contributions in protein emission and in the determination of conformational changes

DEFF Research Database (Denmark)

Bobone, Sara; van de Weert, Marco; Stella, Lorenzo

2014-01-01

solvents, as well as a real protein (bovine serum albumin). Unfortunately, synchronous spectra were found to be unreliable in the separation of Trp and Tyr emission components in proteins. A simple alternative approach based on the deconvolution of emission spectra is presented. In addition, an equation...

Preparative isoelectric focusing in a cellulose-based separation medium

Czech Academy of Sciences Publication Activity Database

Šalplachta, Jiří; Horká, Marie; Šlais, Karel

2017-01-01

Roč. 40, č. 11 (2017), s. 2498-2505 ISSN 1615-9306 R&D Projects: GA MZd(CZ) NV16-29916A; GA ČR(CZ) GA16-03749S; GA MV(CZ) VI20172020069 Institutional support: RVO:68081715 Keywords : isoelectric focusing * preparative * proteins * separation Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 2.557, year: 2016

Whey protein isolate gel for separation: A formation, characterization, and application study

Science.gov (United States)

Teo, Jiunn Yeong

performance of WPI monolith for continuous bed chromatography. Nonetheless the WPI monolith may be used to separate different protein molecules based on protein-protein interaction between WPI and protein molecules to be separated.

Nanocapillaries for Open Tubular Chromatographic Separations of Proteins in Femtoliter to Picoliter Samples

Science.gov (United States)

Wang, Xiayan; Cheng, Chang; Wang, Shili; Zhao, Meiping; Dasgupta, Purnendu K.; Liu, Shaorong

2009-01-01

We have recently examined the potential of bare nanocapillaries for free solution DNA separations and demonstrated efficiencies exceeding 106 theoretical plates/m. In the present work, we demonstrate the use of bare and hydroxypropylcellulose (HPC) coated open tubular nanocapillaries for protein separations. Using 1.5 μm inner diameter (i.d.) capillary columns, hydrodynamically injecting femto to picoliter (fL-pL) volumes of fluorescent or fluorescent dye labeled protein samples, utilizing a pneumatically pressurized chamber containing 1.0 mM sodium tetraborate solution eluent (typ. 200 psi) as the pump and performing on-column detection using a simple laser-induced fluorescence detector, we demonstrate efficiencies of close to a million theoretical plates/m while generating single digit μL volumes of waste for a complete chromatographic run. We achieve baseline resolution for a protein mixture consisting of transferrin, α-lactalbumin, insulin, and α -2-macroglobulin. PMID:19663450

Hepatitis C Virus E1 and E2 Proteins Used as Separate Immunogens Induce Neutralizing Antibodies with Additive Properties.

Directory of Open Access Journals (Sweden)

Elodie Beaumont

Full Text Available Various strategies involving the use of hepatitis C virus (HCV E1 and E2 envelope glycoproteins as immunogens have been developed for prophylactic vaccination against HCV. However, the ideal mode of processing and presenting these immunogens for effective vaccination has yet to be determined. We used our recently described vaccine candidate based on full-length HCV E1 or E2 glycoproteins fused to the heterologous hepatitis B virus S envelope protein to compare the use of the E1 and E2 proteins as separate immunogens with their use as the E1E2 heterodimer, in terms of immunogenetic potential and the capacity to induce neutralizing antibodies. The specific anti-E1 and anti-E2 antibody responses induced in animals immunized with vaccine particles harboring the heterodimer were profoundly impaired with respect to those in animals immunized with particles harboring E1 and E2 separately. Moreover, the anti-E1 and anti-E2 antibodies had additive neutralizing properties that increase the cross-neutralization of heterologous strains of various HCV genotypes, highlighting the importance of including both E1 and E2 in the vaccine for an effective vaccination strategy. Our study has important implications for the optimization of HCV vaccination strategies based on HCV envelope proteins, regardless of the platform used to present these proteins to the immune system.

Carbon nanotubes-assisted polyacrylamide gel electrophoresis for enhanced separation of human serum proteins and application in liverish diagnosis.

Science.gov (United States)

Jiang, Fubin; Wang, Yanan; Hu, Xinfang; Shao, Na; Na, Na; Delanghe, Joris R; Ouyang, Jin

2010-11-01

The application of pore-gradient polyacrylamide gel electrophoresis (PG-PAGE) incorporated with carbon nanotube modified by Triton X-100 and carboxylation so as to improve the separation of human serum proteins is reported. The novel PG-PAGE was made by adding water-soluble single-walled carbon nanotubes (CNTs) when preparing the polyacrylamide gel. Significant improvements in separation of complement C3 protein and haptoglobin (Hp) in human serum were achieved. It was estimated that the interactions between the hydrophilic groups on the proteins and the surface of the CNTs result in different adsorption kinetics of complement C3 and Hp subtype on the nanoparticles incorporated in the gel, thus enhancing the separation of the two proteins in serum. This new CNT matrix-assisted PG-PAGE method for enhanced separation of complement C3 and Hp in human serum was successfully applied to distinguish the samples from liverish patients and healthy people.

Separators - Technology review: Ceramic based separators for secondary batteries

Energy Technology Data Exchange (ETDEWEB)

Nestler, Tina; Schmid, Robert; Münchgesang, Wolfram; Bazhenov, Vasilii; Meyer, Dirk C. [Technische Universität Bergakademie Freiberg, Institut für Experimentelle Physik, Leipziger Str. 23, 09596 Freiberg (Germany); Schilm, Jochen [Fraunhofer-Institut für Keramische Technologien und Systeme IKTS, Winterbergstraße 28, 01277 Dresden (Germany); Leisegang, Tilmann [Fraunhofer-Technologiezentrum Halbleitermaterialien THM, Am St.-Niclas-Schacht 13, 09599 Freiberg (Germany)

2014-06-16

Besides a continuous increase of the worldwide use of electricity, the electric energy storage technology market is a growing sector. At the latest since the German energy transition ('Energiewende') was announced, technological solutions for the storage of renewable energy have been intensively studied. Storage technologies in various forms are commercially available. A widespread technology is the electrochemical cell. Here the cost per kWh, e. g. determined by energy density, production process and cycle life, is of main interest. Commonly, an electrochemical cell consists of an anode and a cathode that are separated by an ion permeable or ion conductive membrane - the separator - as one of the main components. Many applications use polymeric separators whose pores are filled with liquid electrolyte, providing high power densities. However, problems arise from different failure mechanisms during cell operation, which can affect the integrity and functionality of these separators. In the case of excessive heating or mechanical damage, the polymeric separators become an incalculable security risk. Furthermore, the growth of metallic dendrites between the electrodes leads to unwanted short circuits. In order to minimize these risks, temperature stable and non-flammable ceramic particles can be added, forming so-called composite separators. Full ceramic separators, in turn, are currently commercially used only for high-temperature operation systems, due to their comparably low ion conductivity at room temperature. However, as security and lifetime demands increase, these materials turn into focus also for future room temperature applications. Hence, growing research effort is being spent on the improvement of the ion conductivity of these ceramic solid electrolyte materials, acting as separator and electrolyte at the same time. Starting with a short overview of available separator technologies and the separator market, this review focuses on ceramic-based

Separators - Technology review: Ceramic based separators for secondary batteries

Science.gov (United States)

Nestler, Tina; Schmid, Robert; Münchgesang, Wolfram; Bazhenov, Vasilii; Schilm, Jochen; Leisegang, Tilmann; Meyer, Dirk C.

2014-06-01

Besides a continuous increase of the worldwide use of electricity, the electric energy storage technology market is a growing sector. At the latest since the German energy transition ("Energiewende") was announced, technological solutions for the storage of renewable energy have been intensively studied. Storage technologies in various forms are commercially available. A widespread technology is the electrochemical cell. Here the cost per kWh, e. g. determined by energy density, production process and cycle life, is of main interest. Commonly, an electrochemical cell consists of an anode and a cathode that are separated by an ion permeable or ion conductive membrane - the separator - as one of the main components. Many applications use polymeric separators whose pores are filled with liquid electrolyte, providing high power densities. However, problems arise from different failure mechanisms during cell operation, which can affect the integrity and functionality of these separators. In the case of excessive heating or mechanical damage, the polymeric separators become an incalculable security risk. Furthermore, the growth of metallic dendrites between the electrodes leads to unwanted short circuits. In order to minimize these risks, temperature stable and non-flammable ceramic particles can be added, forming so-called composite separators. Full ceramic separators, in turn, are currently commercially used only for high-temperature operation systems, due to their comparably low ion conductivity at room temperature. However, as security and lifetime demands increase, these materials turn into focus also for future room temperature applications. Hence, growing research effort is being spent on the improvement of the ion conductivity of these ceramic solid electrolyte materials, acting as separator and electrolyte at the same time. Starting with a short overview of available separator technologies and the separator market, this review focuses on ceramic-based separators

ATPS: "Aqueous two-phase System" as the "Answer to Protein Separation" for protein-processing Food Industry.

Science.gov (United States)

Khan, Bilal Muhammad; Liu, Zhi-Cong; Shi, Fu-Lin; Cheong, Kit-Leong; Liu, Yang

2018-06-08

Every individual needs food for its nutritional value and flavor while the economic growth of a nation depends on a thriving profit-generating industry. The food industry caters to both needs in an efficient manner. Proteins can rightly be considered as the driving force behind the overwhelming success of this industry. However, purification of proteins is not an easy undertaking due to their intricate nature while presently employed procedures for this purpose, regrettably, are both costly, and labor- and time-intensive in addition to being unsettling on proteins structural conformity. ATPS has accumulated a lot of interest from the scientific community due to its mild operating conditions, high recovery yield, ease of scaling it up, and its cost-effective and environment friendly nature. This review tries to amass some accounts concerning the utility of ATPS for the separation and purification of proteins. Some auspicious clues in this regard can be witnessed along with a few loopholes which need to be addressed before this technique can truly demonstrate its potential vis-à-vis industrial protein purification. Overall, a polymer - salt (citrates in particular) ATPS with an added inert supplementary salt can be regarded as a better option for purifying proteins.

Separations Science Data Base: an abstractor's manual

International Nuclear Information System (INIS)

Roddy, J.W.; McDowell, W.J.; Michelson, D.C.

1981-07-01

The Separations Science Data Base, designed specifically for the retrieval of information needed in chemical separations problems (i.e., how to perform a given separation under given conditions), is described. The procedure for entering records into the data base is given. The initial entries are concerned primarily with liquid-liquid extraction and liquid-solid ion exchange methods for metal ions and salts; however, the data base is constructed so that almost any separations process can be accommodated. Each record is indexed with information provided under the following fields: author; title; publication source; date of publication; organization performing and/or sponsoring the work; brief abstract of the work; abstract number if the work has been so referenced, and/or abstractor's initials; type of separation system used (e.g., flotation); specific or generic name of the separation agent used (e.g., acetylacetone); list of substances separated (e.g., gold, copper); qualitative description of the supporting medium or matrix containing the substances before separation (e.g., nitrate); type of literature where the article was printed (e.g., book); and type of information that the article contains. Each of these fields may be searched independently of the others (or in combination), and the last six fields contain specific key words that are listed on the input form. Definitions are provided for the 39 information terms

Continuous flow electrophoretic separation of proteins and cells from mammalian tissues

Science.gov (United States)

Hymer, W. C.; Barlow, Grant H.; Blaisdell, Steven J.; Cleveland, Carolyn; Farrington, Mary Ann; Feldmeier, Mary; Hatfield, J. Michael; Lanham, J. Wayne; Grindeland, Richard; Snyder, Robert S.

1987-01-01

This paper describes an apparatus for continuous flow electrophoresis (CFE), designed to separate macromolecules and cells at conditions of microgravity. In this CFE, buffer flows upward in a 120-cm long flow chamber, which is 16-cm wide x 3.0-mm thick in the microgravity version (and 6-cm wide x 1.5-mm thick in the unit-gravity laboratory version). Ovalbumin and rat serum albumin were separated in space (flight STS-4) with the same resolution of the two proteins achieved at 25 percent total w/v concentration that was obtained in the laboratory at 0.2 percent w/v concentration. Rat anterior pituitary cells, cultured human embryonic kidney cells, and canine Langerhans cells were separated into subpopulations (flight STS-8) more effectively than in unit gravity, with comparable resolution having been achieved at 100 times the concentration possible on earth.

Acetonitrile as a buffer additive for free zone capillary electrophoresis separation and characterization of maize (Zeamays L. ) and sorghum (Sorghum bicolor L. Moench) storage proteins.

Science.gov (United States)

Bean, S R; Lookhart, G L; Bietz, J A

2000-02-01

An improved method for separating and characterizing maize (Zea mays L.) and sorghum (Sorghum bicolor L. Moench) storage proteins by free zone capillary electrophoresis (FZCE) was developed. Previous electrophoretic methods for analyzing these proteins required high concentrations of urea to maintain protein solubility during separation. To overcome disadvantages of urea, we developed a FZCE method that mimicked reversed-phase high-performance liquid chromatography (RP-HPLC) in that it used high levels of acetonitrile (ACN) at low pH. The optimized FZCE buffer system consisted of 80 mM phosphate-glycine buffer, nominal pH 2.5, containing 60% ACN and a cellulose derivative to dynamically coat capillary walls. Resolution was similar to or higher than that previously achieved by FZCE buffers utilizing 8 M urea as a buffer additive. ACN concentrations of at least 50% were necessary to achieve acceptable separations; this ACN concentration is approximately that necessary to extract these storage proteins. ACN was equally effective as traditional ethanol solvents and 8 M urea for solubilizing maize and sorghum proteins. The ACN-based FZCE buffer system gave high repeatability (buffers. This FZCE method may be applicable for the analysis of other hydrophobic proteins without the use of urea.

Facilitating the Hyphenation of CIEF and MALDI-MS for Two-Dimensional Separation of Proteins

Science.gov (United States)

Cheng, Chang; Lu, Joann J.; Wang, Xiayan; Roberts, Jonathan; Liu, Shaorong

2011-01-01

Both CIEF and MALDI-MS are frequently used in protein analysis, but hyphenation of the two is not investigated proportionally. One of the major reasons is that the additives (such as carrier ampholytes and detergent) in CIEF severely suppress the MALDI-MS signal, which hampers the hyphenation of the two. In this paper, we develop a simple means to alleviate the above signal-suppressing effect. We first deposit 1 µL of water onto a MALDI-MS target, deliver a fraction of CIEF-separated protein (~0.1 µL) to the water droplet, evaporate the solvent, add 0.5 µL of MALDI matrix to the sample spot, dry the matrix, and move the target plate to a MALDI-TOF-MS for mass spectrum measurement. We optimize the droplet volume and the laser-ablation region. Under the optimized conditions, we improve the signal to noise ratio by 2–10 fold. We also apply this method for two-dimensional separations of standard proteins and Apolipoprotein A-I, a membrane protein expressed in E. Coli cells. PMID:20603827

Transient isotachophoresis in carrier ampholyte-based capillary electrophoresis for protein analysis

Czech Academy of Sciences Publication Activity Database

Busnel, J. M.; Descroix, S.; Godfrin, D.; Hennion, M. C.; Kašička, Václav; Peltre, G.

2006-01-01

Roč. 27, č. 18 (2006), s. 3591-3598 ISSN 0173-0835 Institutional research plan: CEZ:AV0Z40550506 Keywords : carrier ampholyte-based capillary electrophoresis * transient isotachophoresis * proteins Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.101, year: 2006

Active and separate secretion of fiber and penton base during the early phase of Ad2 or Ad5 infection

Energy Technology Data Exchange (ETDEWEB)

Yan, Yuhua; Zhang, Bo; Hou, Weihong; Lin, Hongyu [Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing (China); Rebetz, Johan [The Rausing Laboratory, Department of Neurosurgery, Lund University, Lund (Sweden); Hong, Saw-See [Viral Infections & Comparative Pathology, UMR-754 UCBL-INRA-EPHE, Université Lyon 1, Lyon Cedex 07 (France); Wang, Youjun; Ran, Liang [Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing (China); Fan, Xiaolong, E-mail: XFan@bnu.edu.cn [Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing (China)

2017-05-15

Fiber and penton base overproduced in adenovirus (Ad) infected cells can be secreted prior to progeny release and thereby regulate progeny spread. We aimed to investigate the mechanisms of fiber and penton base secretion in Ad2- or Ad5-infected A549 cells. Our flow cytometry analyses detected abundant surface fiber molecules, but little penton base molecules at 12 h post infection. Immunogold staining combined with transmission electron microscopic analyses revealed separate, non-co-localized release of fiber and penton base in the proximity of the plasma membrane. Depolymerization of microtubule and actin cytoskeletons, and inhibition of Rock kinase and myosin II activity together demonstrated cytoskeletal network-dependent fiber secretion. Inhibition of intracellular calcium [Ca{sup 2+}]{sub i} signaling caused diminished fiber secretion, which was associated with diminished progeny production. Thus, fiber and penton base are actively and separately secreted during the early stages of Ad2 or Ad5 infection, their secretion may play important role in Ad life cycle. - Highlights: •Excessive production of structural proteins is common to viral infection, which may regulate the host-virus equilibrium and the spreading of viruses. •The adenovirus (Ad) structural proteins, fiber and penton base, are respectively important for Ad binding to its receptor and subsequent internalization in host cells. In Ad infected cells, these two structural proteins are excessively produced. •The mechanisms underlying the release of fiber and penton base molecules at the early phase of Ad infection is yet poorly understood. •Our studies show that in Ad5 or Ad2 infected A549 cells, fiber and penton base molecules are actively and separately secreted. •Fiber secretion is dependent on cytoskeleton-mediated protein traffic. •Inhibition of myosin II motor and Ca{sup 2+} signaling activity significantly diminishes fiber secretion. •These findings could contribute to our

Active and separate secretion of fiber and penton base during the early phase of Ad2 or Ad5 infection

International Nuclear Information System (INIS)

Yan, Yuhua; Zhang, Bo; Hou, Weihong; Lin, Hongyu; Rebetz, Johan; Hong, Saw-See; Wang, Youjun; Ran, Liang; Fan, Xiaolong

2017-01-01

Fiber and penton base overproduced in adenovirus (Ad) infected cells can be secreted prior to progeny release and thereby regulate progeny spread. We aimed to investigate the mechanisms of fiber and penton base secretion in Ad2- or Ad5-infected A549 cells. Our flow cytometry analyses detected abundant surface fiber molecules, but little penton base molecules at 12 h post infection. Immunogold staining combined with transmission electron microscopic analyses revealed separate, non-co-localized release of fiber and penton base in the proximity of the plasma membrane. Depolymerization of microtubule and actin cytoskeletons, and inhibition of Rock kinase and myosin II activity together demonstrated cytoskeletal network-dependent fiber secretion. Inhibition of intracellular calcium [Ca 2+ ] i signaling caused diminished fiber secretion, which was associated with diminished progeny production. Thus, fiber and penton base are actively and separately secreted during the early stages of Ad2 or Ad5 infection, their secretion may play important role in Ad life cycle. - Highlights: •Excessive production of structural proteins is common to viral infection, which may regulate the host-virus equilibrium and the spreading of viruses. •The adenovirus (Ad) structural proteins, fiber and penton base, are respectively important for Ad binding to its receptor and subsequent internalization in host cells. In Ad infected cells, these two structural proteins are excessively produced. •The mechanisms underlying the release of fiber and penton base molecules at the early phase of Ad infection is yet poorly understood. •Our studies show that in Ad5 or Ad2 infected A549 cells, fiber and penton base molecules are actively and separately secreted. •Fiber secretion is dependent on cytoskeleton-mediated protein traffic. •Inhibition of myosin II motor and Ca 2+ signaling activity significantly diminishes fiber secretion. •These findings could contribute to our understanding of Ad

Recent applications of capillary electromigration methods to separation and analysis of proteins

Czech Academy of Sciences Publication Activity Database

Štěpánová, Sille; Kašička, Václav

2016-01-01

Roč. 933, Aug 24 (2016), s. 23-42 ISSN 0003-2670 R&D Projects: GA ČR(CZ) GA15-01948S Institutional support: RVO:61388963 Keywords : affinity electrophoresis * capillary electrophoresis * isoelectric focusing * isotachophoresis * proteins * review Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.950, year: 2016

Use of electrophoretically separated serum protein fractions for the diagnosis of cardiomyopathy

International Nuclear Information System (INIS)

Siddiqui, Z.H.; Cheema, A.M.

2011-01-01

In an investigation of molecular pathogenesis in cardiovascular diseases, the blood samples of the patients diagnosed for cardiomyopathy (CMP) were obtained from the Punjab Institute of Cardiology, Lahore. Blood samples of the healthy subjects of comparable age group without any history of cardiac ailment were also collected for the control comparisons. The sera of CMP were separated and used for the study of the protein profiles with sodium dodecyle sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in first dimension. Quantification of various protein fractions done by Gene Genius Bio-imaging Gel Documentation System that provide the data of molecular weights and the percent raw volume covered by each of the fractions. The protein fractions that showed significant variation were separated by using the technique of electro blotting and electro elution and run on isoelectric focusing (IEF) in second dimension to determine their isoelectric points. The most pertinent results in the comparison were the significant increase in apolipoprotein B, Ceruloplasmin, apolipoprotein A-I and transthyretin in the sera of patients of CMP compared to healthy subjects. These results show that level of apolipoprotein B, Ceruloplasmin, apolipoprotein A-I and transthyretin are strong predictor of CMP and can also be used for the diagnosis of CMP. (author)

In situ photo-immobilised pH gradient isoelectric focusing and zone electrophoresis integrated two-dimensional microfluidic chip electrophoresis for protein separation

International Nuclear Information System (INIS)

Lin, Fengmin; Yu, Shiyong; Gu, Le; Zhu, Xuetao; Wang, Jianshe; Zhu, Han; Lu, Yi; Wang, Yihua; Deng, Yulin; Geng, Lina

2015-01-01

A method is introduced for open-column photo-induced site-selective immobilization of pH gradients in a layer of PEG-methacrylate in a multi-dimensional microfluidic chip for use in electrophoresis. It has several attractive features: (a) mixtures of fluorescently labelled proteins carbonic anhydrase, catalase and myoglobin in their native state can be separated by pH-gradient isoelectric focusing (IEF) and zone electrophoresis (CZE) using integrated 2D chip electrophoresis; (b) compared to strip packing or monolithic photo-immobilization, it overcomes the shortcomings of free carrier ampholyte-based 2D chip electrophoresis in an easy way; (c) larger amount of sample can be loaded into the open column-mode electrophoresis (d) immobilized pH gradients can be re-used and the chip can be recycled; (e) a multilayer 3D pH gradient is established by a layer-by-layer assembly technique to further increase the separation capacity. In our perception, this strategy has a large potential in microfluidic chip-based separation schemes because of its simplicity, separation power, re-usability, and separation capacity. (author)

A cost-effective device for the rapid transfer of gel-separated proteins onto membranes.

Science.gov (United States)

Tam, Hann W; Huang, Yu-Chen; Tam, Ming F

2009-03-01

We describe here the fabrication of a cost-effective semi-dry blotting apparatus for the transfer of proteins onto membranes. Graphite sheets were used as electrodes. Protein mixtures were separated on NuPAGE 4% to 12% polyacrylamide gradient gels. With a Tris-bicine buffer, we demonstrated that close to 80% of the proteins with apparent molecular mass of 80kDa or less were removed from the gels after 8min of blotting. The process is much faster than the techniques reported previously in the literature.

Engineering protein scaffolds for protein separation, biocatalysis and nanotechnology applications

Science.gov (United States)

Liu, Fang

Globally, there is growing appreciation for developing a sustainable economy that uses eco-efficient bio-processes. Biotechnology provides an increasing range of tools for industry to help reduce cost and improve environmental performance. Inspired by the naturally evolved machineries of protein scaffolds and their binding ligands, synthetic protein scaffolds were engineered based on cohesin-dockerin interactions and metal chelating peptides to tackle the challenges and make improvements in three specific areas: (1) protein purification, (2) biofuel cells, and (3) nanomaterial synthesis. The first objective was to develop efficient and cost-effective non-chromatographic purification processes to purify recombinant proteins in an effort to meet the dramatically growing market of protein drugs. In our design, the target protein was genetically fused with a dockerin domain from Clostridium thermocellum and direct purification and recovery was achieved using thermo-responsive elastin-like polypeptide (ELP) scaffold containing the cohesin domain from the same species. By exploiting the highly specific interaction between the dockerin and cohesin domain and the reversible aggregation property of ELP, highly purified and active dockerin-tagged proteins, such as endoglucanase CelA, chloramphenicol acetyl transferase (CAT) and enhanced green fluorescence protein (EGFP), were recovered directly from crude cell extracts in a single purification step with yields achieving over 90%. Incorporation of a self-cleaving intein domain enabled rapid removal of the affinity tag from the target proteins by another cycle of thermal precipitation. The purification cost can be further reduced by regenerating and recycling the ELP-cohesin capturing scaffolds. However, due to the high binding affinity between cohesin and dockerin domains, the bound dockerin-intein tag cannot be completely disassociated from ELP-cohesin scaffold after binding. Therefore, a truncated dockerin with the calcium

Open-tubular capillary electrochromatography with bare gold nanoparticles-based stationary phase applied to separation of trypsin digested native and glycated proteins

Czech Academy of Sciences Publication Activity Database

Mikšík, Ivan; Lacinová, Kateřina; Zmatlíková, Zdeňka; Sedláková, Pavla; Král, V.; Sýkora, D.; Řezanka, P.; Kašička, Václav

2012-01-01

Roč. 35, č. 8 (2012), s. 994-1002 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/09/0675; GA ČR(CZ) GA203/08/1428 Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z40550506 Keywords : capillary electrochromatography * gold nanoparticles * glycation * peptide maps * proteins Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.591, year: 2012

Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response

Energy Technology Data Exchange (ETDEWEB)

Riback, Joshua A.; Katanski, Christopher D.; Kear-Scott, Jamie L.; Pilipenko, Evgeny V.; Rojek, Alexandra E.; Sosnick, Tobin R.; Drummond, D. Allan

2017-03-01

In eukaryotic cells, diverse stresses trigger coalescence of RNA-binding proteins into stress granules. In vitro, stress-granule-associated proteins can demix to form liquids, hydrogels, and other assemblies lacking fixed stoichiometry. Observing these phenomena has generally required conditions far removed from physiological stresses. We show that poly(A)-binding protein (Pab1 in yeast), a defining marker of stress granules, phase separates and forms hydrogels in vitro upon exposure to physiological stress conditions. Other RNA-binding proteins depend upon low-complexity regions (LCRs) or RNA for phase separation, whereas Pab1’s LCR is not required for demixing, and RNA inhibits it. Based on unique evolutionary patterns, we create LCR mutations, which systematically tune its biophysical properties and Pab1 phase separation in vitro and in vivo. Mutations that impede phase separation reduce organism fitness during prolonged stress. Poly(A)-binding protein thus acts as a physiological stress sensor, exploiting phase separation to precisely mark stress onset, a broadly generalizable mechanism.

Polydopamine-coated open tubular column for the separation of proteins by capillary electrochromatography.

Science.gov (United States)

Xiao, Xing; Wang, Wentao; Chen, Jia; Jia, Li

2015-08-01

The separation and determination of proteins in food is an important aspect in food industry. Inspired by the self-polymerization of dopamine under alkaline conditions and the natural adhesive properties of polydopamine, in this paper, a simple and economical method was developed for the preparation of polydopamine-coated open tubular column, in which ammonium persulfate was used as the source of oxygen to induce and facilitate the polymerization of dopamine to form polydopamine. In comparison with a naked fused-silica capillary, the direction and magnitude of the electro-osmotic flow of the as-prepared polydopamine-coated open tubular column could be manipulated by varying the pH values of background solutions due to the existence of amine and phenolic hydroxyl groups on polydopamine coating. The surface morphology of the polydopamine-coated open tubular column was studied by scanning electron microscopy, and the thickness of polydopamine coating was 106 nm. The performance of the polydopamine-coated open tubular column was validated by analysis of proteins. The relative standard deviations of migration times of proteins representing run-to-run, day-to-day, and column-to-column were less than 3.5%. In addition, the feasibility of the polydopamine-coated open tubular column for real samples was verified by the separation of proteins in chicken egg white and pure milk. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Separation Systems Data Base: a users' manual

International Nuclear Information System (INIS)

Roddy, J.W.; McDowell, W.J.

1978-11-01

A data base designed specifically for the retrieval of information needed in chemical separations problems is described. Included are descriptions of the basic methods of searching and retrieving information from the data base, the procedure for entering records into the data base, a listing of additional references concerning the computer information process and an example of a typical record. The initial entries are concerned primarily with liquid-liquid extraction methods for metal ions and salts. However, the data base is constructed so that almost any separation process can be accommodated

Suitability of two-dimensional electrophoretic protein separations for quantitative detection of mutations

International Nuclear Information System (INIS)

Taylor, J.; Anderson, N.L.; Anderson, N.G.; Gemmell, A.; Giometti, C.S.; Nance, S.L.; Tollaksen, S.L.

1986-01-01

Separation of proteins by two-dimensional electrophoresis (2DE) provides a powerful method for mutagenesis studies, since hundreds of proteins can be monitored simultaneously. In previous mutation studies in which 2DE has been used, only qualitative protein differences were monitored; quantitative protein variations were not evaluated. Although significant differences in protein abundance can be detected by eye, the large number of protein spots present in 2DE patterns together with the large number of individual patterns required for a mutagenesis study would necessitate the use of a computerized analysis system to detect the rare quantitative protein changes indicative of gene deletions or inactivation of genes by point mutations in regulatory genes. A pilot study to search for heritable mutations induced by treatment of mice with either ethylnitrosourea or gamma radiation is underway. Samples are being monitored for quantitative changes that reduce the amount of protein by about 50%. The results of this study indicate that the key methods to improve the application of 2DE to mutation screening are to increase the number of measurable spots (i.e., improve stain sensitivity) and to decrease the spread of values for the volume measurements. Even small improvements in these areas could greatly increase the number of monitorable spots. 9 refs., 4 figs

Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

Science.gov (United States)

Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

2013-12-19

To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

Conceptual design of distillation-based hybrid separation processes.

Science.gov (United States)

Skiborowski, Mirko; Harwardt, Andreas; Marquardt, Wolfgang

2013-01-01

Hybrid separation processes combine different separation principles and constitute a promising design option for the separation of complex mixtures. Particularly, the integration of distillation with other unit operations can significantly improve the separation of close-boiling or azeotropic mixtures. Although the design of single-unit operations is well understood and supported by computational methods, the optimal design of flowsheets of hybrid separation processes is still a challenging task. The large number of operational and design degrees of freedom requires a systematic and optimization-based design approach. To this end, a structured approach, the so-called process synthesis framework, is proposed. This article reviews available computational methods for the conceptual design of distillation-based hybrid processes for the separation of liquid mixtures. Open problems are identified that must be addressed to finally establish a structured process synthesis framework for such processes.

Preparation and characterization of monodisperse large-porous silica microspheres as the matrix for protein separation.

Science.gov (United States)

Xia, Hongjun; Wan, Guangping; Zhao, Junlong; Liu, Jiawei; Bai, Quan

2016-11-04

High performance liquid chromatography (HPLC) is a kind of efficient separation technology and has been used widely in many fields. Micro-sized porous silica microspheres as the most popular matrix have been used for fast separation and analysis in HPLC. In this paper, the monodisperse large-porous silica microspheres with controllable size and structure were successfully synthesized with polymer microspheres as the templates and characterized. First, the poly(glycidyl methacrylate-co-ethyleneglycol dimethacrylate) microspheres (P GMA-EDMA ) were functionalized with tetraethylenepentamine (TEPA) to generate amino groups which act as a catalyst in hydrolysis of tetraethyl orthosilicate (TEOS) to form Si-containing low molecular weight species. Then the low molecular weight species diffused into the functionalized P GMA-EDMA microspheres by induction force of the amino groups to form polymer/silica hybrid microspheres. Finally, the organic polymer templates were removed by calcination, and the large-porous silica microspheres were obtained. The compositions, morphology, size distribution, specific surface area and pore size distribution of the porous silica microspheres were characterized by infrared analyzer, scanning-electron microscopy, dynamic laser scattering, the mercury intrusion method and thermal gravimetric analysis, respectively. The results show that the agglomeration of the hybrid microspheres can be overcome when the templates were functionalized with TEPA as amination reagent, and the yield of 95.7% of the monodisperse large-porous silica microspheres can be achieved with high concentration of polymer templates. The resulting large-porous silica microspheres were modified with octadecyltrichlorosilane (ODS) and the chromatographic evaluation was performed by separating the proteins and the digest of BSA. The baseline separation of seven kinds of protein standards was achieved, and the column delivered a better performance when separating BSA digests

Determination of total antioxidant capacity of milk by CUPRAC and ABTS methods with separate characterisation of milk protein fractions.

Science.gov (United States)

Çekiç, Sema Demirci; Demir, Aslı; Başkan, Kevser Sözgen; Tütem, Esma; Apak, Reşat

2015-05-01

Most milk-applied antioxidant assays in literature are based on the isolation and quantification of individual antioxidative compounds, whereas total antioxidant capacity (TAC) gives a more holistic picture due to cooperative action of antioxidants. Recently, the cupric reducing antioxidant capacity (CUPRAC) method has been modified to measure the antioxidant capacities of thiol-containing proteins, where the classical ammonium acetate buffer - that may otherwise precipitate proteins- was replaced with concentrated urea buffer (able to expose embedded thiol groups of proteins to oxidative attack) adjusted to pH 7.0. Thus, antioxidant capacity of milk was investigated with two competing TAC assays, namely CUPRAC and ABTS (2,2'-azinobis(3-ethylbenzothiazoline-6-sulphonic acid))/persulphate, because only these assays were capable of evaluating protein contribution to the observed TAC value. As milk fat caused turbidity, experiments were carried out with skim milk or defatted milk samples. To determine TAC, modified CUPRAC method was applied to whole milk, separated and redissolved protein fractions, and the remaining liquid phase after necessary operations. Both TAC methods were investigated for their dilution sensitivity and antioxidant power assessment of separate milk fractions such as casein and whey. Proteins like β-lactoglobulin and casein (but not simple thiols) exhibited enhanced CUPRAC reactivity with surfactant (SDS) addition. Addition of milk protein fractions to whole skim milk produced significant 'negative-biased' deviations (up to -26% relative standard error) from TAC absorbance additivity in the application of the ABTS method, as opposed to that of the CUPRAC method less affected by chemical deviations from Beer's law thereby producing much smaller deviations from additivity (i.e. the property of additivity is valid when the measured TAC of a mixture is equal to the sum of individual antioxidant capacities of its constituents).

Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

Directory of Open Access Journals (Sweden)

Peng Liu

2015-01-01

Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

Development in electrophoresis: instrumentation for two-dimensional gel electrophoresis of protein separation and application of capillary electrophoresis in micro-bioanalysis

Energy Technology Data Exchange (ETDEWEB)

Xu, Aoshuang [Iowa State Univ., Ames, IA (United States)

2008-01-01

This dissertation begins with a general introduction of topics related to this work. The following chapters contain three scientific manuscripts, each presented in a separate chapter with accompanying tables, figures, and literature citations. The final chapter summarizes the work and provides some prospective on this work. This introduction starts with a brief treatment of the basic principles of electrophoresis separation, followed by a discussion of gel electrophoresis and particularly polyacrylamide gel electrophoresis for protein separation, a summary of common capillary electrophoresis separation modes, and a brief treatment of micro-bioanalysis application of capillary electrophoresis, and ends with an overview of protein conformation and dynamics.

Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection.

Science.gov (United States)

Chen, Yifei; Sun, Yuxing; Han, Bing-Qing

2015-01-01

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.

Separations systems data base: a users' manual. Revision I

International Nuclear Information System (INIS)

Roddy, J.W.; McDowell, W.J.

1981-01-01

A separations systems data base (SEPSYS), designed specifically for the retrieval of information needed in chemical separations problems (i.e., how to perform a given separation under given conditions), is described. Included are descriptions of the basic methods of searching and retrieving information from the data base, the procedure for entering records into the data base, a listing of additional references concerning the computer information process, and an example of a typical record. The initial entries are concerned primarily with liquid-liquid extraction and liquid-solid ion exchange methods for metal ions and salts; however, the data base is constructed so that almost any separation process can be accommodated. Each record is indexed with information provided under the following fields: author; title; publication source; data of publication; organization sponsoring the work; brief abstract of the work; abstract number if the work has been so referenced, and/or abstractors initials; type of separation system used (e.g., flotation); specific or generic name of the separation agent used (e.g., acetylacetone); list of substances separated (e.g., gold, copper); qualitative description of the supporting medium or matrix containing the substances before separation (e.g., nitrate); type of literature where the record was printed (e.g., book); and type of information that the article contains. Each of these fields may be searched independently of the others (or in combination), and the last six fields contain specific key words that are listed in the report. Definitions are provided for the 36 information terms

Biomimetic membranes for sensor and separation applications

CERN Document Server

2012-01-01

This book addresses the possibilities and challenges in mimicking biological membranes and creating membrane-based sensor and separation devices. It covers recent advances in developing biomimetic membranes for technological applications with a focus on the use of integral membrane protein mediated transport. It describes the fundamentals of biosensing as well as separation and shows how the two processes work together in biological systems. The book provides an overview of the current state of the art, points to areas that need further investigation and anticipates future directions in the field. Biomimetics is a truly cross-disciplinary approach and this is exemplified by the challenges in mimicking osmotic processes as they occur in nature using aquaporin protein water channels as central building blocks. In the development of a biomimetic sensor/separation technology, both channel and carrier proteins are important and examples of how these may be reconstituted and controlled in biomimetic membranes are ...

Development of green betaine-based deep eutectic solvent aqueous two-phase system for the extraction of protein.

Science.gov (United States)

Li, Na; Wang, Yuzhi; Xu, Kaijia; Huang, Yanhua; Wen, Qian; Ding, Xueqin

2016-05-15

Six kinds of new type of green betaine-based deep eutectic solvents (DESs) have been synthesized. Deep eutectic solvent aqueous two-phase systems (DES-ATPS) were established and successfully applied in the extraction of protein. Betaine-urea (Be-U) was selected as the suitable extractant. Single factor experiments were carried out to determine the optimum conditions of the extraction process, such as the salt concentration, the mass of DES, the separation time, the amount of protein, the temperature and the pH value. The extraction efficiency could achieve to 99.82% under the optimum conditions. Mixed sample and practical sample analysis were discussed. The back extraction experiment was implemented and the back extraction efficiency could reach to 32.66%. The precision experiment, repeatability experiment and stability experiment were investigated. UV-vis, FT-IR and circular dichroism (CD) spectra confirmed that the conformation of protein was not changed during the process of extraction. The mechanisms of extraction were researched by dynamic light scattering (DLS), the measurement of the conductivity and transmission electron microscopy (TEM). DES-protein aggregates and embraces phenomenon play considerable roles in the separation process. All of these results indicated that betaine-based DES-ATPS may provide a potential substitute new method for the separation of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

An electronic channel switching-based aptasensor for ultrasensitive protein detection

Energy Technology Data Exchange (ETDEWEB)

Li Hongbo; Wang Cui [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Wu Zaisheng, E-mail: wuzaisheng@163.com [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Lu Limin; Qiu Liping; Zhou Hui; Shen Guoli [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Yu Ruqin, E-mail: rqyu@hnu.edu.cn [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China)

2013-01-03

Highlights: Black-Right-Pointing-Pointer Target IgE is successfully designed to serve as a barrier to separate enzyme from its substrate. Black-Right-Pointing-Pointer This sensing platform of electronic channel switching-based aptasensor can be simply manipulated. Black-Right-Pointing-Pointer The stable hairpin structure of anti-IgE aptamer is utilized to detect target IgE. Black-Right-Pointing-Pointer The sensor is ultrasensitive sensitivity, excellent selectivity and small volume of sample. Black-Right-Pointing-Pointer It is a powerful platform to be further expanded to detect more kinds of proteins and even cells. - Abstract: Due to the ubiquity and essential of the proteins in all living organisms, the identification and quantification of disease-specific proteins are particularly important. Because the conformational change of aptamer upon its target or probe/target/probe sandwich often is the primary prerequisite for the design of an electrochemical aptameric assay system, it is extremely difficult to construct the electrochemical aptasensor for protein assay because the corresponding aptamers cannot often meet the requirement. To circumvent the obstacles mentioned, an electronic channel switching-based (ECS) aptasensor for ultrasensitive protein detection is developed. The essential achievement made is that an innovative sensing concept is proposed: the hairpin structure of aptamer is designed to pull electroactive species toward electrode surface and makes the surface-immobilized IgE serve as a barrier that separates enzyme from its substrate. It seemingly ensures that the ECS aptasensor exhibits most excellent assay features, such as, a detection limit of 4.44 Multiplication-Sign 10{sup -6} {mu}g mL{sup -1} (22.7 fM, 220 zmol in 10-{mu}L sample) (demonstrating a 5 orders of magnitude improvement in detection sensitivity compared with classical electronic aptasensors) and dynamic response range from 4.44 Multiplication-Sign 10{sup -6} to 4.44 Multiplication

Protein unfolding versus β-sheet separation in spider silk nanocrystals

International Nuclear Information System (INIS)

Alam, Parvez

2014-01-01

In this communication a mechanism for spider silk strain hardening is proposed. Shear failure of β-sheet nanocrystals is the first failure mode that gives rise to the creation of smaller nanocrystals, which are of higher strength and stiffness. β-sheet unfolding requires more energy than nanocrystal separation in a shear mode of failure. As a result, unfolding occurs after the nanocrystals separate in shear. β-sheet unfolding yields a secondary strain hardening effect once the β-sheet conformation is geometrically stable and acts like a unidirectional fibre in a fibre reinforced composite. The mechanism suggested herein is based on molecular dynamics calculations of residual inter-β-sheet separation strengths against residual intra-β-sheet unfolding strengths. (paper)

preservation of irradiated mechanically separated turkey hen meat based Vienna sausages

International Nuclear Information System (INIS)

Ben Abderabba, N.

1996-01-01

This study evaluates the influence of growing doses of irradiation on the microbiological quality (pathogenic bacteria, faecal contaminants, total germs) and the physical and chemical characteristics (pH, humidity, total free fat materials, chloride and protein) of mechanically separated turkey hen meat. This study also permitted the measuring of the effects of incorporation of mechanical y separated turkey hen meat irradiated at 5 KGy on the microbiological, physical, chemical and structural qualities of Vienna sausages, as manufactured in a private company in Tunis (author)

Chromatographic Separations of Enantiomers and Underivatized Oligosaccharides

Energy Technology Data Exchange (ETDEWEB)

Liu, Ying [Iowa State Univ., Ames, IA (United States)

2004-01-01

My graduate research has focused on separation science and bioanalytical analysis, which emphasized in method development. It includes three major areas: enantiomeric separations using high performance liquid chromatography (HPLC), Super/subcritical fluid chromatography (SFC), and capillary electrophoresis (CE); drug-protein binding behavior studies using CE; and carbohydrate analysis using liquid chromatograph-electrospray ionization mass spectrometry (LC-ESI-MS). Enantiomeric separations continue to be extremely important in the pharmaceutical industry. An in-depth evaluation of the enantiomeric separation capabilities of macrocyclic glycopeptides CSPs with SFC mobile phases was investigated using a set of over 100 chiral compounds. It was found that the macrocyclic based CSPs were able to separate enantiomers of various compounds with different polarities and functionalities. Seventy percent of all separations were achieved in less than 4 min due to the high flow rate (4.0 ml/min) that can be used in SFC. Drug-protein binding is an important process in determining the activity and fate of a drug once it enters the body. Two drug/protein systems have been studied using frontal analysis CE method. More sensitive fluorescence detection was introduced in this assay, which overcame the problem of low sensitivity that is common when using UV detection for drug-protein studies. In addition, the first usage of an argon ion laser with 257 nm beam coupled with CCD camera as a frontal analysis detection method enabled the simultaneous observation of drug fluorescence as well as the protein fluorescence. LC-ESI-MS was used for the separation and characterization of underivatized oligosaccharide mixtures. With the limits of detection as low as 50 picograms, all individual components of oligosaccharide mixtures (up to 11 glucose-units long) were baseline resolved on a Cyclobond I 2000 column and detected using ESI-MS. This system is characterized by high chromatographic

Chromatographic Separations of Enantiomers and Underivatized Oligosaccharides

International Nuclear Information System (INIS)

Ying Liu

2004-01-01

My graduate research has focused on separation science and bioanalytical analysis, which emphasized in method development. It includes three major areas: enantiomeric separations using high performance liquid chromatography (HPLC), Super/subcritical fluid chromatography (SFC), and capillary electrophoresis (CE); drug-protein binding behavior studies using CE; and carbohydrate analysis using liquid chromatograph-electrospray ionization mass spectrometry (LC-ESI-MS). Enantiomeric separations continue to be extremely important in the pharmaceutical industry. An in-depth evaluation of the enantiomeric separation capabilities of macrocyclic glycopeptides CSPs with SFC mobile phases was investigated using a set of over 100 chiral compounds. It was found that the macrocyclic based CSPs were able to separate enantiomers of various compounds with different polarities and functionalities. Seventy percent of all separations were achieved in less than 4 min due to the high flow rate (4.0 ml/min) that can be used in SFC. Drug-protein binding is an important process in determining the activity and fate of a drug once it enters the body. Two drug/protein systems have been studied using frontal analysis CE method. More sensitive fluorescence detection was introduced in this assay, which overcame the problem of low sensitivity that is common when using UV detection for drug-protein studies. In addition, the first usage of an argon ion laser with 257 nm beam coupled with CCD camera as a frontal analysis detection method enabled the simultaneous observation of drug fluorescence as well as the protein fluorescence. LC-ESI-MS was used for the separation and characterization of underivatized oligosaccharide mixtures. With the limits of detection as low as 50 picograms, all individual components of oligosaccharide mixtures (up to 11 glucose-units long) were baseline resolved on a Cyclobond I 2000 column and detected using ESI-MS. This system is characterized by high chromatographic

Fractionation of Exosomes and DNA using Size-Based Separation at the Nanoscale

Science.gov (United States)

Wunsch, Benjamin; Smith, Joshua; Wang, Chao; Gifford, Stacey; Brink, Markus; Bruce, Robert; Solovitzky, Gustavo; Austin, Robert; Astier, Yann

Exosomes, a key target of ``liquid biopsies'', are nano-vesicles found in nearly all biological fluids. Exosomes are secreted by eukaryotic and prokaryotic cells alike, and contain information about their originating cells, including surface proteins, cytoplasmic proteins, and nucleic acids. One challenge in studying exosome morphology is the difficulty of sorting exosomes by size and surface markers. Common separation techniques for exosomes include ultracentrifugation and ultrafiltration, for preparation of large volume samples, but these techniques often show contamination and significant heterogeneity between preparations. To date, deterministic lateral displacement (DLD) pillar arrays in silicon have proven an efficient technology to sort, separate, and enrich micron-scale particles including human parasites, eukaryotic cells, blood cells, and circulating tumor cells in blood; however, the DLD technology has never been translated to the true nanoscale, where it could function on bio-colloids such as exosomes. We have fabricated nanoscale DLD (nanoDLD) arrays capable of rapidly sorting colloids down to 20 nm in continuous flow, and demonstrated size sorting of individual exosome vesicles and dsDNA polymers, opening the potential for on-chip biomolecule separation and diagnosti

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

Science.gov (United States)

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Effect of acid- and alkaline-aided extractions on functional and rheological properties of proteins recovered from mechanically separated turkey meat (MSTM).

Science.gov (United States)

Hrynets, Yuliya; Omana, Dileep A; Xu, Yan; Betti, Mirko

2010-09-01

Functional and rheological characteristics of acid- and alkali-extracted proteins from mechanically separated turkey meat (MSTM) have been investigated. Extractions were carried out at 4 pH values (2.5, 3.5, 10.5, and 11.5). The study demonstrated that alkali and acid extractions resulted in significant (P hardness, chewiness, springiness, and cohesiveness) of recovered proteins were found to be unaffected (P > 0.05) by different extraction pH. The protein extracted at pH 3.5 formed a highly viscoelastic gel network as evidenced by storage modulus (G') values, whereas the gel formed from proteins extracted at pH 10.5 was found to be the weakest. The work also revealed that acid treatments were more effective for removal of total heme pigments from MSTM. Color characteristics of protein isolates were markedly improved compared to the initial material and tended to be better when subjected to acid extractions. Mechanically separated meat is one of the cheapest sources of protein obtained by grinding meat and bones together and forcing the mixture through a perforated drum. The use of mechanically separated turkey meat (MSTM) for the production of further processed poultry products is limited due to its undesirable color and textural properties. Recovery of proteins from MSTM using pH shifting process will help the poultry processors to get better returns and also create opportunity to produce functional food ingredients.

A green deep eutectic solvent-based aqueous two-phase system for protein extracting

International Nuclear Information System (INIS)

Xu, Kaijia; Wang, Yuzhi; Huang, Yanhua; Li, Na; Wen, Qian

2015-01-01

Highlights: • A strategy for the protein purification with a deep eutectic solvent(DES)-based aqueous two-phase system. • Choline chloride-glycerin DES was selected as the extraction solvent. • Bovine serum albumin and trypsin were used as the analytes. • Aggregation phenomenon was detected in the mechanism research. - Abstract: As a new type of green solvent, deep eutectic solvent (DES) has been applied for the extraction of proteins with an aqueous two-phase system (ATPS) in this work. Four kinds of choline chloride (ChCl)-based DESs were synthesized to extract bovine serum albumin (BSA), and ChCl-glycerol was selected as the suitable extraction solvent. Single factor experiments have been done to investigate the effects of the extraction process, including the amount of DES, the concentration of salt, the mass of protein, the shaking time, the temperature and PH value. Experimental results show 98.16% of the BSA could be extracted into the DES-rich phase in a single-step extraction under the optimized conditions. A high extraction efficiency of 94.36% was achieved, while the conditions were applied to the extraction of trypsin (Try). Precision, repeatability and stability experiments were studied and the relative standard deviations (RSD) of the extraction efficiency were 0.4246% (n = 3), 1.6057% (n = 3) and 1.6132% (n = 3), respectively. Conformation of BSA was not changed during the extraction process according to the investigation of UV–vis spectra, FT-IR spectra and CD spectra of BSA. The conductivity, dynamic light scattering (DLS) and transmission electron microscopy (TEM) were used to explore the mechanism of the extraction. It turned out that the formation of DES–protein aggregates play a significant role in the separation process. All the results suggest that ChCl-based DES-ATPS are supposed to have the potential to provide new possibilities in the separation of proteins

Ionic-Liquid Based Separation of Azeotropic Mixtures

DEFF Research Database (Denmark)

Kulajanpeng, Kusuma; Suriyapraphadilok, Uthaiporn; Gani, Rafiqul

2014-01-01

methodology for the screening of ionic liquids (ILs) as entrainers for ILs-based separation processes in binary aqueous azeotropic systems (e.g., water + ethanol and water + isopropanol) is presented. Ionic liquids as entrainers were first screened based on a combination of criteria such as stabi......methodology for the screening of ionic liquids (ILs) as entrainers for ILs-based separation processes in binary aqueous azeotropic systems (e.g., water + ethanol and water + isopropanol) is presented. Ionic liquids as entrainers were first screened based on a combination of criteria...... [C1MIM][DMP]. For the final evaluation, the best candidates for aqueous systems were used as entrainers, and then the vapor-liquid equilibrium (VLE) of the ternary systems containing ILs was predicted by the Non Random Two Liquids (NRTL) model to confirm the breaking of the azeotrope. Based...... on minimum concentration of the ILs required to break the given azeotrope, the best ILs as entrainers for water + ethanol and water + isopropanol azeotropic mixtures were [C1MIM][DMP] and [C2MIM][N(CN)2], respectively....

Metal–organic frameworks based membranes for liquid separation

KAUST Repository

Li, Xin; Liu, Yuxin; Wang, Jing; Gascon, Jorge; Li, Jiansheng; Van der Bruggen, Bart

2017-01-01

, the field of MOF-based membranes for liquid separation is highlighted in this review. The criteria for judicious selection of MOFs in fabricating MOF-based membranes are given. Special attention is paid to rational design strategies for MOF-based membranes

Multistage Magnetic Separator of Cells and Proteins

Science.gov (United States)

Barton, Ken; Ainsworth, Mark; Daily, Bruce; Dunn, Scott; Metz, Bill; Vellinger, John; Taylor, Brock; Meador, Bruce

2005-01-01

The multistage electromagnetic separator for purifying cells and magnetic particles (MAGSEP) is a laboratory apparatus for separating and/or purifying particles (especially biological cells) on the basis of their magnetic susceptibility and magnetophoretic mobility. Whereas a typical prior apparatus based on similar principles offers only a single stage of separation, the MAGSEP, as its full name indicates, offers multiple stages of separation; this makes it possible to refine a sample population of particles to a higher level of purity or to categorize multiple portions of the sample on the basis of magnetic susceptibility and/or magnetophoretic mobility. The MAGSEP includes a processing unit and an electronic unit coupled to a personal computer. The processing unit includes upper and lower plates, a plate-rotation system, an electromagnet, an electromagnet-translation system, and a capture-magnet assembly. The plates are bolted together through a roller bearing that allows the plates to rotate with respect to each other. An interface between the plates acts as a seal for separating fluids. A lower cuvette can be aligned with as many as 15 upper cuvette stations for fraction collection during processing. A two-phase stepping motor drives the rotation system, causing the upper plate to rotate for the collection of each fraction of the sample material. The electromagnet generates a magnetic field across the lower cuvette, while the translation system translates the electromagnet upward along the lower cuvette. The current supplied to the electromagnet, and thus the magnetic flux density at the pole face of the electromagnet, can be set at a programmed value between 0 and 1,400 gauss (0.14 T). The rate of translation can be programmed between 5 and 2,000 m/s so as to align all sample particles in the same position in the cuvette. The capture magnet can be a permanent magnet. It is mounted on an arm connected to a stepping motor. The stepping motor rotates the arm to

A Protein-Based Ferritin Bio-Nanobattery

Directory of Open Access Journals (Sweden)

Gerald D. Watt

2012-01-01

Full Text Available Nanostructured materials are increasingly important for the construction of electrochemical energy storage devices that will meet the needs of portable nanodevices. Here we describe the development of a nanoenergy storage system based on inorganic mineral phases contained in ferritin proteins. The electrochemical cell consists of an anode containing ~2000 iron atoms as Fe(OH2 in the hollow protein interior of ferritin and a cathode containing ~2000 of Co(OH3 in a separate ferritin molecule. The achieved initial voltage output from a combination of Fe2+- and Co3+-ferritins adsorbed on gold electrodes was ~500 mV, while a combination of Fe2+- and Co3+-ferritins immobilized on gold produced a voltage of 350–405 mV. When fully discharged, Fe(OH3 and Co(OH2 are the products of a single electron transfer per metal atom from anode to cathode. The spent components can be regenerated by chemical or electrochemical methods restoring battery function. The properties of ferritins are presented and their unique characteristics are described, which have led to the development of a functional bio-nanobattery.

Diagnostic use of electrophoretically separated serum protein fractions in the patients of angina pectoris

International Nuclear Information System (INIS)

Siddiqui, Z.H.; Cheema, A.M.

2010-01-01

The understanding of molecular pathogenesis of clinical states enables for diagnosis and effective management of the diseases. In an investigation of molecular pathogenesis or adaptation in cardiovascular diseases, the blood samples of the patients diagnosed for angina pectoris (AP) were obtained from the Punjab Institute of Cardiology, Lahore. Blood samples of the healthy subjects of comparable age group without any history of cardiac ailment were also collected for the control comparisons. The sera of AP were separated and used for the study of the protein profiles with sodium dodecyles sulfate polyacrylamide gel electrophoresis (SDS-PAGE)in first dimension. Quantification of various protein fractions done by Gene Genius Bio-imaging Gel Documentation System that provide the data of molecular weights and the percent raw volume covered. by each of the fractions. The protein fractions that showed significant variation were separated by using the technique of electro blotting and electro elution and run on isoelectric focusing (IEF) in second dimension to determine their isoelectric points. The most pertinent results in the comparison were the significant increase in apolipoprotein B, marked decrease in apolipoprotein A-I and high apolipoprotein B/apolipoprotein A-I ratio in the sera of patients of AP compared to healthy subjects. These results show that level of apolipoprotein A-I, apolipoprotein B and the apolipoprotein B/apolipoprotein A-I ratio are strong predictor of AP and can also be used for the diagnosis of AP. (author)

Assessment of parameters of gas centrifuge and separation cascade basing on integral characteristics of separation plant

Energy Technology Data Exchange (ETDEWEB)

Borisevich, Valentin, E-mail: VDBorisevich@mephi.ru [National Research Nuclear University MEPhI, Kashirskoe Shosse 31, Moscow 115409 (Russian Federation); National Research Center “Kurchatov Institute”, Kurchatov Square 1, Moscow 123182 (Russian Federation); Borshchevskiy, Michael, E-mail: Michael_mephi@mail.ru [National Research Nuclear University MEPhI, Kashirskoe Shosse 31, Moscow 115409 (Russian Federation); Andronov, Igor, E-mail: andronov@imp.kiae.ru [National Research Center “Kurchatov Institute”, Kurchatov Square 1, Moscow 123182 (Russian Federation); Senchenkov, Sergey, E-mail: senchenkov@imp.kiae.ru [National Research Center “Kurchatov Institute”, Kurchatov Square 1, Moscow 123182 (Russian Federation)

2013-12-15

Highlights: • We developed the calculation method to assess a feed flow rate into a gas centrifuge. • It is based on the knowledge of the integral characteristics of a separation plant. • Our method is verified by comparison with the results of the independent one. • The method also allows to specify other features of the separation cascade work. - Abstract: A calculation technique to assess a feed flow rate into a single GC, a total number of centrifuges in a separation cascade and to determine its likely configurations basing on the known integral characteristics of a centrifugal plant is developed. Evaluation of characteristics of the industrial gas centrifuge TC-12 and separation cascades of the NEF plant performed by two independent calculation techniques demonstrates their satisfactory agreement. This methodology would help to some extent the nuclear inspectors in evaluating and assessing the capability of an enrichment facility, and discovering any use for undeclared purposes.

Membrane-based ethylene/ethane separation: The upper bound and beyond

KAUST Repository

Rungta, Meha

2013-08-02

Ethylene/ethane separation via cryogenic distillation is extremely energy-intensive, and membrane separation may provide an attractive alternative. In this paper, ethylene/ethane separation performance using polymeric membranes is summarized, and an experimental ethylene/ethane polymeric upper bound based on literature data is presented. A theoretical prediction of the ethylene/ethane upper bound is also presented, and shows good agreement with the experimental upper bound. Further, two ways to overcome the ethylene/ethane upper bound, based on increasing the sorption or diffusion selectivity, is also discussed, and a review on advanced membrane types such as facilitated transport membranes, zeolite and metal organic framework based membranes, and carbon molecular sieve membranes is presented. Of these, carbon membranes have shown the potential to surpass the polymeric ethylene/ethane upper bound performance. Furthermore, a convenient, potentially scalable method for tailoring the performance of carbon membranes for ethylene/ethane separation based on tuning the pyrolysis conditions has also been demonstrated. © 2013 American Institute of Chemical Engineers.

Drop Size Distribution - Based Separation of Stratiform and Convective Rain

Science.gov (United States)

Thurai, Merhala; Gatlin, Patrick; Williams, Christopher

2014-01-01

For applications in hydrology and meteorology, it is often desirable to separate regions of stratiform and convective rain from meteorological radar observations, both from ground-based polarimetric radars and from space-based dual frequency radars. In a previous study by Bringi et al. (2009), dual frequency profiler and dual polarization radar (C-POL) observations in Darwin, Australia, had shown that stratiform and convective rain could be separated in the log10(Nw) versus Do domain, where Do is the mean volume diameter and Nw is the scaling parameter which is proportional to the ratio of water content to the mass weighted mean diameter. Note, Nw and Do are two of the main drop size distribution (DSD) parameters. In a later study, Thurai et al (2010) confirmed that both the dual-frequency profiler based stratiform-convective rain separation and the C-POL radar based separation were consistent with each other. In this paper, we test this separation method using DSD measurements from a ground based 2D video disdrometer (2DVD), along with simultaneous observations from a collocated, vertically-pointing, X-band profiling radar (XPR). The measurements were made in Huntsville, Alabama. One-minute DSDs from 2DVD are used as input to an appropriate gamma fitting procedure to determine Nw and Do. The fitted parameters - after averaging over 3-minutes - are plotted against each other and compared with a predefined separation line. An index is used to determine how far the points lie from the separation line (as described in Thurai et al. 2010). Negative index values indicate stratiform rain and positive index indicate convective rain, and, moreover, points which lie somewhat close to the separation line are considered 'mixed' or 'transition' type precipitation. The XPR observations are used to evaluate/test the 2DVD data-based classification. A 'bright-band' detection algorithm was used to classify each vertical reflectivity profile as either stratiform or convective

Prospects of Source-Separation-Based Sanitation Concepts: A Model-Based Study

Directory of Open Access Journals (Sweden)

Cees Buisman

2013-07-01

Full Text Available Separation of different domestic wastewater streams and targeted on-site treatment for resource recovery has been recognized as one of the most promising sanitation concepts to re-establish the balance in carbon, nutrient and water cycles. In this study a model was developed based on literature data to compare energy and water balance, nutrient recovery, chemical use, effluent quality and land area requirement in four different sanitation concepts: (1 centralized; (2 centralized with source-separation of urine; (3 source-separation of black water, kitchen refuse and grey water; and (4 source-separation of urine, feces, kitchen refuse and grey water. The highest primary energy consumption of 914 MJ/capita(cap/year was attained within the centralized sanitation concept, and the lowest primary energy consumption of 437 MJ/cap/year was attained within source-separation of urine, feces, kitchen refuse and grey water. Grey water bio-flocculation and subsequent grey water sludge co-digestion decreased the primary energy consumption, but was not energetically favorable to couple with grey water effluent reuse. Source-separation of urine improved the energy balance, nutrient recovery and effluent quality, but required larger land area and higher chemical use in the centralized concept.

Laser-based optical activity detection of amino acids and proteins

Energy Technology Data Exchange (ETDEWEB)

Reitsma, B.H.

1987-01-01

The optical activity detector (OAD) for HPLC is a selective detector for optically active substances including amino acids and proteins. This study illustrates the use of the OAD in three related areas. Section I illustrates the separation of four free amino acids using cation-exchange chromatography. Detection by coupling the OAD to a refractive index detector (RI) for proline and threonine and the OAD to an ultraviolet absorbance detector (UV) for tyrosine and phenylalanine allows the calculation of enantiomeric (D/L) ratios of these amino acids without physical separation. Specific rotations of these four amino acids are also reported. Section II illustrates the separation of 16 dansyl-L-amino acids by RP-HPLC with detection by OA/UV. Section III illustrates the RP-HPLC separation of conformers of soybean trypsin inhibitor. Detection by OA/UV provides insights from the chromatogram unavailable for UV absorbance detection alone. In addition, identification of impurities is simplified with OA/UV. Specific rotations of the separated protein fractions show no significant change accompanying change in conformation.

Composite separators and redox flow batteries based on porous separators

Science.gov (United States)

Li, Bin; Wei, Xiaoliang; Luo, Qingtao; Nie, Zimin; Wang, Wei; Sprenkle, Vincent L.

2016-01-12

Composite separators having a porous structure and including acid-stable, hydrophilic, inorganic particles enmeshed in a substantially fully fluorinated polyolefin matrix can be utilized in a number of applications. The inorganic particles can provide hydrophilic characteristics. The pores of the separator result in good selectivity and electrical conductivity. The fluorinated polymeric backbone can result in high chemical stability. Accordingly, one application of the composite separators is in redox flow batteries as low cost membranes. In such applications, the composite separator can also enable additional property-enhancing features compared to ion-exchange membranes. For example, simple capacity control can be achieved through hydraulic pressure by balancing the volumes of electrolyte on each side of the separator. While a porous separator can also allow for volume and pressure regulation, in RFBs that utilize corrosive and/or oxidizing compounds, the composite separators described herein are preferable for their robustness in the presence of such compounds.

Laser-based optical activity detection of amino acids and proteins

Energy Technology Data Exchange (ETDEWEB)

Reitsma, B.H.

1987-08-01

The optical activity detector (OAD) for HPLC is a selective detector for optically active substances including amino acids and proteins. Four free amino acids were resolved using cation-exchange chromatography followed by detection with refractive index detector (RI) for proline and threonine and the OAD to an ultraviolet absorbance detector (uv) for tyrosine and phenylalanine. Amino acid detection by refractive index is not sensitive and uv absorbance detects only three amino acids. Derivatization of amino acids to make them detectable by uv absorbance enhances the applicability of OA/uv for the determination of enantiomeric ratios. The separation of 16 dansyl-L-amino acids by RP-HPLC with detection by OA/uv is illustrated. Calculation of the specific rotation of 22 dansyl-L-amino acids shows that derivatization enhances the OA detectability of some amino acids but degrades that of others. RP-HPLC of proteins is a rapidly developing technique. Several researchers have reported the detection of multiple peaks when a pure protein is subjected to HPLC under certain conditions. These multiple peaks have been determined to be different conformations of the same protein. Since proteins are optically active, OA is a suitable detector. The RP-HPLC separation of conformers of soybean trypsin inhibitor is illustrated. Detection by OA/uv provides insights from the chromatogram unavailable from uv absorbance detection alone. In addition, identification of impurities is simplified with OA/uv. Specific rotations of the separated protein fractions show no significant change accompanying change in conformation. 163 refs., 13 figs., 9 tabs.

Tunable separations based on a molecular size effect for biomolecules by poly(ethylene glycol) gel-based capillary electrophoresis.

Science.gov (United States)

Kubo, Takuya; Nishimura, Naoki; Furuta, Hayato; Kubota, Kei; Naito, Toyohiro; Otsuka, Koji

2017-11-10

We report novel capillary gel electrophoresis (CGE) with poly(ethylene glycol) (PEG)-based hydrogels for the effective separations of biomolecules containing sugars and DNAs based on a molecular size effect. The gel capillaries were prepared in a fused silica capillary modified with 3-(trimethoxysilyl)propylmethacrylate using a variety of the PEG-based hydrogels. After the fundamental evaluations in CGE regarding the separation based on the molecular size effect depending on the crosslinking density, the optimized capillary provided the efficient separation of glucose ladder (G1 to G20). In addition, another capillary showed the successful separation of DNA ladder in the range of 10-1100 base pair, which is superior to an authentic acrylamide-based gel capillary. For both glucose and DNA ladders, the separation ranges against the molecular size were simply controllable by alteration of the concentration and/or units of ethylene oxide in the PEG-based crosslinker. Finally, we demonstrated the separations of real samples, which included sugars carved out from monoclonal antibodies, mAbs, and then the efficient separations based on the molecular size effect were achieved. Copyright © 2017 Elsevier B.V. All rights reserved.

A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

DEFF Research Database (Denmark)

Blagoev, B.; Kratchmarova, I.; Ong, S.E.

2003-01-01

Mass spectrometry-based proteomics can reveal protein-protein interactions on a large scale, but it has been difficult to separate background binding from functionally important interactions and still preserve weak binders. To investigate the epidermal growth factor receptor (EGFR) pathway, we em...

The Effect of Column and Eluent Fluorination on the Retention and Separation of non-Fluorinated Amino Acids and Proteins by HPLC

Science.gov (United States)

Joyner, Katherine; Wang, Weizhen; Yu, Yihua Bruce

2011-01-01

The effect of column and eluent fluorination on the retention and separation of non-fluorinated amino acids and proteins in HPLC is investigated. A side-by-side comparison of fluorocarbon column and eluents (F-column and F-eluents) with their hydrocarbon counterparts (H-column and H-eluents) in the separation of a group of 33 analytes, including 30 amino acids and 3 proteins, is conducted. The H-column and the F-column contain the n-C8H17 group and n-C8F17 group, respectively, in their stationary phases. The H-eluents include ethanol (EtOH) and isopropanol (ISP) while the F-eluents include trifluoroethanol (TFE) and hexafluorosopropanol (HFIP). The 2 columns and 4 eluents generated 8 (column, eluent) pairs that produce 264 retention time data points for the 33 analytes. A statistical analysis of the retention time data reveals that although the H-column is better than the F-column in analyte separation and H-eluents are better than F-eluents in analyte retention, the more critical factor is the proper pairing of column with eluent. Among the conditions explored in this project, optimal retention and separation is achieved when the fluorocarbon column is paired with ethanol, even though TFE is the most polar one among the 4 eluents. This result shows fluorocarbon columns have much potential in chromatographic analysis and separation of non-fluorinated amino acids and proteins. PMID:21318121

Boronic Acid-Based Approach for Separation and Immobilization of Glycoproteins and Its Application in Sensing

Directory of Open Access Journals (Sweden)

Lin Liu

2013-10-01

Full Text Available Glycoproteins influence a broad spectrum of biological processes including cell-cell interaction, host-pathogen interaction, or protection of proteins against proteolytic degradation. The analysis of their glyco-structures and concentration levels are increasingly important in diagnosis and proteomics. Boronic acids can covalently react with cis-diols in the oligosaccharide chains of glycoproteins to form five- or six-membered cyclic esters. Based on this interaction, boronic acid-based ligands and materials have attracted much attention in both chemistry and biology as the recognition motif for enrichment and chemo/biosensing of glycoproteins in recent years. In this work, we reviewed the progress in the separation, immobilization and detection of glycoproteins with boronic acid-functionalized materials and addressed its application in sensing.

Separation of both fibrous and globular proteins on the basis of molecular weight using high-performance size exclusion chromatography.

Science.gov (United States)

Barden, J A

1983-11-01

A high-performance size exclusion liquid chromatographic system has been used to separate proteins with different shapes solely on the basis of their molecular weights. After the effects of ionic and hydrophobic interactions with the stationary phase have been overcome, protein elution is normally governed by their effective size in solution. Conditions are described under which proteins, with isoelectric points within the normal operating pH range of the columns, are eluted independent of their Stokes' radii. Even fibrous proteins with axial ratios of 50 elute according to their known molecular weights over the range 2000-2,000,000.

Projective synchronization based on suitable separation

International Nuclear Information System (INIS)

Li Guohui; Xiong Chuan; Sun Xiaonan

2007-01-01

A new approach for constructing a projective-synchronized chaotic slave system is proposed in this paper. This method is based on suitable separation by decomposing the system as the linear part and the nonlinear one. From matrix measure theory, some simple but efficient criteria are derived for projective synchronization of chaotic system. Numerical simulations for the Lorenz system show that this control method works very well

A green deep eutectic solvent-based aqueous two-phase system for protein extracting.

Science.gov (United States)

Xu, Kaijia; Wang, Yuzhi; Huang, Yanhua; Li, Na; Wen, Qian

2015-03-15

As a new type of green solvent, deep eutectic solvent (DES) has been applied for the extraction of proteins with an aqueous two-phase system (ATPS) in this work. Four kinds of choline chloride (ChCl)-based DESs were synthesized to extract bovine serum albumin (BSA), and ChCl-glycerol was selected as the suitable extraction solvent. Single factor experiments have been done to investigate the effects of the extraction process, including the amount of DES, the concentration of salt, the mass of protein, the shaking time, the temperature and PH value. Experimental results show 98.16% of the BSA could be extracted into the DES-rich phase in a single-step extraction under the optimized conditions. A high extraction efficiency of 94.36% was achieved, while the conditions were applied to the extraction of trypsin (Try). Precision, repeatability and stability experiments were studied and the relative standard deviations (RSD) of the extraction efficiency were 0.4246% (n=3), 1.6057% (n=3) and 1.6132% (n=3), respectively. Conformation of BSA was not changed during the extraction process according to the investigation of UV-vis spectra, FT-IR spectra and CD spectra of BSA. The conductivity, dynamic light scattering (DLS) and transmission electron microscopy (TEM) were used to explore the mechanism of the extraction. It turned out that the formation of DES-protein aggregates play a significant role in the separation process. All the results suggest that ChCl-based DES-ATPS are supposed to have the potential to provide new possibilities in the separation of proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

Pepsin Digested Oat Bran Proteins: Separation, Antioxidant Activity, and Identification of New Peptides

Directory of Open Access Journals (Sweden)

Ariane Vanvi

2016-01-01

Full Text Available The aim of this study was to determine pepsin hydrolysis conditions to produce digested oat bran proteins with higher radical scavenging activities and separate and identify peptides. Isolated proteins were then digested with different concentrations of pepsin and incubation times. Hydrolysates produced with 1 : 30 enzyme substrate (E/S ratio and 2 h possessed the highest peroxyl radical scavenging activity, 608 ± 17 µM TE/g (compared to 456–474 µM TE/g for other digests, and was therefore subsequently fractionated into eight fractions (F1–F8 by high performance liquid chromatography (HPLC. F1 and F2 had little activity because of their low protein contents. Activities of F3–F8 were 447–874 µM TE/g, 20–36%, and 10–14% in the peroxyl, superoxide anion, and hydroxyl radical tests, respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS was used to identify a total of fifty peptides that may have contributed to the activity of F3, a fraction that better scavenged radicals.

Covalently coating dextran on macroporous polyglycidyl methacrylate microsphere enabled rapid protein chromatographic separation

International Nuclear Information System (INIS)

Zhang, Rongyue; Li, Qiang; Li, Juan; Zhou, Weiqing; Ye, Peili; Gao, Yang; Ma, Guanghui; Su, Zhiguo

2012-01-01

Protein denaturation and nonspecific adsorption on polymer media as a chromatographic support have been a problem which needs to be overcome. Macroporous poly(glycidyl methacrylate–divinylbezene) (PGMA–DVB) microspheres prepared in this study were firstly covalently coated with dextran through a three-step method. The dextran was firstly adsorbed onto the microspheres and then covalently bound to the PGMA–DVB microsphere through ether bonds which were formed by hydroxyl group reacting with epoxy group at the presence of 4-(Dimethylamino) pyridine. Finally, the coating dextran layer was crosslinked by ethylene glycol diglycidyl ether to form the continuous network coating. The coated microspheres were characterized by Fourier transform infrared spectra, scanning electron microscope, mercury porosimetry measurements, laser scanning confocal microscope, and protein adsorption experiments. Results showed that PGMA–DVB microspheres coated with dextran successfully maintained the macroporous structure and high permeability. The backpressure was only 1.69 MPa at a high flow rate of 2891 cm/h. Consequently, the hydrophilicity and biocompatibility of modified microspheres were greatly improved, and the contact angle decreased from 184° to 13°, and nonspecific adsorption of proteins was decreased to little or none. The clad dextran coating with large amounts of hydroxyl group was easily derived to be various functional groups. The derived media have great potential applications in rapid protein chromatography. - Highlights: ► Macroporous PGMA–DVB microspheres were covalently coated with dextran. ► The hydrophilicity of the coated microspheres was significantly improved. ► The irreversible adsorption of proteins was reduced to zero. ► The coated microspheres can maintain the macropore structure. ► The coated microspheres were applied to rapid protein separation.

Modeling Protein Structures in Feed and Seed Tissues Using Novel Synchrotron-Based Analytical Technique

International Nuclear Information System (INIS)

Yu, P.

2008-01-01

Traditional 'wet' chemical analyses usually looks for a specific known component (such as protein) through homogenization and separation of the components of interest from the complex tissue matrix. Traditional 'wet' chemical analyses rely heavily on the use of harsh chemicals and derivatization, therefore altering the native feed protein structures and possibly generating artifacts. The objective of this study was to introduce a novel and non-destructive method to estimate protein structures in feed and seeds within intact tissues using advanced synchrotron-based infrared microspectroscopy (SFTIRM). The experiments were performed at the National Synchrotron Light Source in Brookhaven National Laboratory (US Dept. of Energy, NY). The results show that with synchrotron-based SFTIRM, we are able to localize relatively 'pure' protein without destructions of the feed and seed tissues and qualify protein internal structures in terms of the proportions and ratios of a-helix, β-sheet, random coil and β-turns on a relative basis using multi-peak modeling procedures. These protein structure profile (a-helix, β-sheet, etc.) may influence protein quality and availability in animals. Several examples of feed and seeds were provided. The implications of this study are that we can use this new method to compare internal protein structures between feeds and between seed verities. We can also use this method to detect heat-induced the structural changes of protein in feeds.

An Improved CO2 Separation and Purification System Based on Cryogenic Separation and Distillation Theory

Directory of Open Access Journals (Sweden)

Gang Xu

2014-05-01

Full Text Available In this study, an improved CO2 separation and purification system is proposed based on in-depth analyses of cryogenic separation and distillation theory as well as the phase transition characteristics of gas mixtures containing CO2. Multi-stage compression, refrigeration, and separation are adopted to separate the majority of the CO2 from the gas mixture with relatively low energy penalty and high purity. Subsequently, the separated crude liquid CO2 is distilled under high pressure and near ambient temperature conditions so that low energy penalty purification is achieved. Simulation results indicate that the specific energy consumption for CO2 capture is only 0.425 MJ/kgCO2 with 99.9% CO2 purity for the product. Techno-economic analysis shows that the total plant investment is relatively low. Given its technical maturity and great potential in large-scale production, compared to conventional MEA and SelexolTM absorption methods, the cost of CO2 capture of the proposed system is reduced by 57.2% and 45.9%, respectively. The result of this study can serve as a novel approach to recovering CO2 from high CO2 concentration gas mixtures.

Halloysite-based dopamine-imprinted polymer for selective protein capture.

Science.gov (United States)

Zhu, Xiaohong; Li, Hui; Liu, Hui; Peng, Wei; Zhong, Shian; Wang, Yan

2016-06-01

We describe a facile, general, and highly efficient approach to obtain polydopamine-coated molecularly imprinted polymer based on halloysite nanotubes for bovine serum albumin. The method combined surface molecular imprinting and one-step immobilized template technique. Hierarchically structured polymer was prepared in physiological conditions adopting dopamine as functional monomer. A thin layer of polydopamine can be coated on the surface of amino-modified halloysite nanotubes by self-polymerization, and the thickness of the imprinted shells can be controlled by the mass ratio of matrix and dopamine. The polymer was characterized by Fourier transform infrared spectrometry, transmission electron microscopy, and thermogravimetric analysis. The prepared material showed high binding capacity (45.4 mg/g) and specific recognition behavior toward the template protein. In addition, stability and regeneration analyses indicated that the imprinted polymer exhibited excellent reusability (relative standard deviation < 9% for batch-to-batch evaluation). Therefore, the developed polymer is effective for protein recognition and separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening.

Science.gov (United States)

Bozóki, Beáta; Gazda, Lívia; Tóth, Ferenc; Miczi, Márió; Mótyán, János András; Tőzsér, József

2018-01-01

In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection. Copyright © 2017 Elsevier Inc. All rights reserved.

Recent developments in membrane-based separations in biotechnology processes: review.

Science.gov (United States)

Rathore, A S; Shirke, A

2011-01-01

Membrane-based separations are the most ubiquitous unit operations in biotech processes. There are several key reasons for this. First, they can be used with a large variety of applications including clarification, concentration, buffer exchange, purification, and sterilization. Second, they are available in a variety of formats, such as depth filtration, ultrafiltration, diafiltration, nanofiltration, reverse osmosis, and microfiltration. Third, they are simple to operate and are generally robust toward normal variations in feed material and operating parameters. Fourth, membrane-based separations typically require lower capital cost when compared to other processing options. As a result of these advantages, a typical biotech process has anywhere from 10 to 20 membrane-based separation steps. In this article we review the major developments that have occurred on this topic with a focus on developments in the last 5 years.

Partitioning the proteome: phase separation for targeted analysis of membrane proteins in human post-mortem brain.

Directory of Open Access Journals (Sweden)

Jane A English

Full Text Available Neuroproteomics is a powerful platform for targeted and hypothesis driven research, providing comprehensive insights into cellular and sub-cellular disease states, Gene × Environmental effects, and cellular response to medication effects in human, animal, and cell culture models. Analysis of sub-proteomes is becoming increasingly important in clinical proteomics, enriching for otherwise undetectable proteins that are possible markers for disease. Membrane proteins are one such sub-proteome class that merit in-depth targeted analysis, particularly in psychiatric disorders. As membrane proteins are notoriously difficult to analyse using traditional proteomics methods, we evaluate a paradigm to enrich for and study membrane proteins from human post-mortem brain tissue. This is the first study to extensively characterise the integral trans-membrane spanning proteins present in human brain. Using Triton X-114 phase separation and LC-MS/MS analysis, we enriched for and identified 494 membrane proteins, with 194 trans-membrane helices present, ranging from 1 to 21 helices per protein. Isolated proteins included glutamate receptors, G proteins, voltage gated and calcium channels, synaptic proteins, and myelin proteins, all of which warrant quantitative proteomic investigation in psychiatric and neurological disorders. Overall, our sub-proteome analysis reduced sample complexity and enriched for integral membrane proteins by 2.3 fold, thus allowing for more manageable, reproducible, and targeted proteomics in case vs. control biomarker studies. This study provides a valuable reference for future neuroproteomic investigations of membrane proteins, and validates the use Triton X-114 detergent phase extraction on human post mortem brain.

Protein-Based Drug-Delivery Materials

Directory of Open Access Journals (Sweden)

Dave Jao

2017-05-01

Full Text Available There is a pressing need for long-term, controlled drug release for sustained treatment of chronic or persistent medical conditions and diseases. Guided drug delivery is difficult because therapeutic compounds need to survive numerous transport barriers and binding targets throughout the body. Nanoscale protein-based polymers are increasingly used for drug and vaccine delivery to cross these biological barriers and through blood circulation to their molecular site of action. Protein-based polymers compared to synthetic polymers have the advantages of good biocompatibility, biodegradability, environmental sustainability, cost effectiveness and availability. This review addresses the sources of protein-based polymers, compares the similarity and differences, and highlights characteristic properties and functionality of these protein materials for sustained and controlled drug release. Targeted drug delivery using highly functional multicomponent protein composites to guide active drugs to the site of interest will also be discussed. A systematical elucidation of drug-delivery efficiency in the case of molecular weight, particle size, shape, morphology, and porosity of materials will then be demonstrated to achieve increased drug absorption. Finally, several important biomedical applications of protein-based materials with drug-delivery function—including bone healing, antibiotic release, wound healing, and corneal regeneration, as well as diabetes, neuroinflammation and cancer treatments—are summarized at the end of this review.

Combination of Complex-Based and Magnitude-Based Multiecho Water-Fat Separation for Accurate Quantification of Fat-Fraction

Science.gov (United States)

Yu, Huanzhou; Shimakawa, Ann; Hines, Catherine D. G.; McKenzie, Charles A.; Hamilton, Gavin; Sirlin, Claude B.; Brittain, Jean H.; Reeder, Scott B.

2011-01-01

Multipoint water–fat separation techniques rely on different water–fat phase shifts generated at multiple echo times to decompose water and fat. Therefore, these methods require complex source images and allow unambiguous separation of water and fat signals. However, complex-based water–fat separation methods are sensitive to phase errors in the source images, which may lead to clinically important errors. An alternative approach to quantify fat is through “magnitude-based” methods that acquire multiecho magnitude images. Magnitude-based methods are insensitive to phase errors, but cannot estimate fat-fraction greater than 50%. In this work, we introduce a water–fat separation approach that combines the strengths of both complex and magnitude reconstruction algorithms. A magnitude-based reconstruction is applied after complex-based water–fat separation to removes the effect of phase errors. The results from the two reconstructions are then combined. We demonstrate that using this hybrid method, 0–100% fat-fraction can be estimated with improved accuracy at low fat-fractions. PMID:21695724

Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

DEFF Research Database (Denmark)

Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V

1998-01-01

Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross...

Covalently coating dextran on macroporous polyglycidyl methacrylate microsphere enabled rapid protein chromatographic separation

Energy Technology Data Exchange (ETDEWEB)

Zhang, Rongyue; Li, Qiang; Li, Juan; Zhou, Weiqing; Ye, Peili; Gao, Yang; Ma, Guanghui, E-mail: ghma@home.ipe.ac.cn; Su, Zhiguo

2012-12-01

were applied to rapid protein separation.

In Situ Magnetic Separation for Extracellular Protein Production

DEFF Research Database (Denmark)

Kappler, T.; Cerff, Martin; Ottow, Kim Ekelund

2009-01-01

A new approach for in situ product removal from bioreactors is presented in which high-gradient magnetic separation is used. This separation process was used for the adsorptive removal of proteases secreted by Bacillus licheniformis. Small, non-porous bacitracin linked magnetic adsorbents were...... was not influenced by the in situ product removal step. Protease production also remained the same after the separation step. Furthermore, degradation of the protease, which followed first order kinetics, was reduced by using the method. Using a theoretical modeling approach, we Could show that protease yield...... in total was enhanced by using in situ magnetic separation. The process described here is a promising technique to improve overall yield in No production processes which are often limited due to weak downstream operations, Potential limitations encountered during a bioprocess can be overcome...

Citrate based ''TALSPEAK'' lanthanide-actinide separation process

International Nuclear Information System (INIS)

Del Cul, G.D.; Bond, W.D.; Toth, L.M.; Davis, G.D.; Dai, S.; Metcalf, D.H.

1994-09-01

The potential hazard posed to future generations by long-lived radionuclides such as the transuranic elements (TRU) is perceived as a major problem associated with the use of nuclear power. TRU wastes have to remain isolated from the environment for ''geological'' periods of time. The costs of building, maintaining, and operating a ''geological TRU repository'' can be very high. Therefore, there are significant economical advantages in segregating the relatively low volume of TRU wastes from other nuclear wastes. The chemical behavior of lanthanides and actinides, 4f and 5f elements respectively, is rather similar. As a consequence, the separation of these two groups is difficult. The ''TALSPEAK'' process (Trivalent Actinide Lanthanide Separations by Phosphorus-reagent Extraction from Aqueous Complexes) is one of the few means available to separate the trivalent actinides from the lanthanides. The method is based on the preferential complexation of the trivalent actinides by an aminopolyacetic acid. Cold experiments showed that by using citric acid the deleterious effects produced by impurities such as zirconium are greatly reduced

Membrane manufacture for peptide separations

KAUST Repository

Kim, Dooli; Salazar Moya, Octavio Ruben; Nunes, Suzana Pereira

2016-01-01

Nanostructured polymeric membranes are key tools in biomedical applications such as hemodialysis, protein separations, in the food industry, and drinking water supply from seawater. Despite of the success in different separation processes, membrane manufacture itself is at risk, since the most used solvents are about to be banned in many countries due to environmental and health issues. We propose for the first time the preparation of polyethersulfone membranes based on dissolution in the ionic liquid 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DEP). We obtained a series of membranes tailored for separation of solutes with molecular weight of 30, 5, 1.3, and 1.25 kg mol-1 with respective water permeances of 140, 65, 30 and 20 Lm-2h-1bar-1. We demonstrate their superior efficiency in the separation of complex mixtures of peptides with molecular weights in the range of 800 to 3500 gmol-1. Furthermore, the thermodynamics and kinetics of phase separation leading to the pore formation in the membranes were investigated. The rheology of the solutions and the morphology of the prepared membranes were examed and compared to those of polyethersulfone in organic solvents currently used for membrane manufacture.

Membrane manufacture for peptide separations

KAUST Repository

Kim, Dooli

2016-06-07

Nanostructured polymeric membranes are key tools in biomedical applications such as hemodialysis, protein separations, in the food industry, and drinking water supply from seawater. Despite of the success in different separation processes, membrane manufacture itself is at risk, since the most used solvents are about to be banned in many countries due to environmental and health issues. We propose for the first time the preparation of polyethersulfone membranes based on dissolution in the ionic liquid 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DEP). We obtained a series of membranes tailored for separation of solutes with molecular weight of 30, 5, 1.3, and 1.25 kg mol-1 with respective water permeances of 140, 65, 30 and 20 Lm-2h-1bar-1. We demonstrate their superior efficiency in the separation of complex mixtures of peptides with molecular weights in the range of 800 to 3500 gmol-1. Furthermore, the thermodynamics and kinetics of phase separation leading to the pore formation in the membranes were investigated. The rheology of the solutions and the morphology of the prepared membranes were examed and compared to those of polyethersulfone in organic solvents currently used for membrane manufacture.

DTFP-Growth: Dynamic Threshold-Based FP-Growth Rule Mining Algorithm Through Integrating Gene Expression, Methylation, and Protein-Protein Interaction Profiles.

Science.gov (United States)

Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan; Mallik, Saurav; Bhadra, Tapas; Mukherji, Ayan

2018-04-01

Association rule mining is an important technique for identifying interesting relationships between gene pairs in a biological data set. Earlier methods basically work for a single biological data set, and, in maximum cases, a single minimum support cutoff can be applied globally, i.e., across all genesets/itemsets. To overcome this limitation, in this paper, we propose dynamic threshold-based FP-growth rule mining algorithm that integrates gene expression, methylation and protein-protein interaction profiles based on weighted shortest distance to find the novel associations among different pairs of genes in multi-view data sets. For this purpose, we introduce three new thresholds, namely, Distance-based Variable/Dynamic Supports (DVS), Distance-based Variable Confidences (DVC), and Distance-based Variable Lifts (DVL) for each rule by integrating co-expression, co-methylation, and protein-protein interactions existed in the multi-omics data set. We develop the proposed algorithm utilizing these three novel multiple threshold measures. In the proposed algorithm, the values of , , and are computed for each rule separately, and subsequently it is verified whether the support, confidence, and lift of each evolved rule are greater than or equal to the corresponding individual , , and values, respectively, or not. If all these three conditions for a rule are found to be true, the rule is treated as a resultant rule. One of the major advantages of the proposed method compared with other related state-of-the-art methods is that it considers both the quantitative and interactive significance among all pairwise genes belonging to each rule. Moreover, the proposed method generates fewer rules, takes less running time, and provides greater biological significance for the resultant top-ranking rules compared to previous methods.

Blind Source Separation Based on Covariance Ratio and Artificial Bee Colony Algorithm

Directory of Open Access Journals (Sweden)

Lei Chen

2014-01-01

Full Text Available The computation amount in blind source separation based on bioinspired intelligence optimization is high. In order to solve this problem, we propose an effective blind source separation algorithm based on the artificial bee colony algorithm. In the proposed algorithm, the covariance ratio of the signals is utilized as the objective function and the artificial bee colony algorithm is used to solve it. The source signal component which is separated out, is then wiped off from mixtures using the deflation method. All the source signals can be recovered successfully by repeating the separation process. Simulation experiments demonstrate that significant improvement of the computation amount and the quality of signal separation is achieved by the proposed algorithm when compared to previous algorithms.

A novel multimodal chromatography based single step purification process for efficient manufacturing of an E. coli based biotherapeutic protein product.

Science.gov (United States)

Bhambure, Rahul; Gupta, Darpan; Rathore, Anurag S

2013-11-01

Methionine oxidized, reduced and fMet forms of a native recombinant protein product are often the critical product variants which are associated with proteins expressed as bacterial inclusion bodies in E. coli. Such product variants differ from native protein in their structural and functional aspects, and may lead to loss of biological activity and immunogenic response in patients. This investigation focuses on evaluation of multimodal chromatography for selective removal of these product variants using recombinant human granulocyte colony stimulating factor (GCSF) as the model protein. Unique selectivity in separation of closely related product variants was obtained using combined pH and salt based elution gradients in hydrophobic charge induction chromatography. Simultaneous removal of process related impurities was also achieved in flow-through leading to single step purification process for the GCSF. Results indicate that the product recovery of up to 90.0% can be obtained with purity levels of greater than 99.0%. Binding the target protein at pHproduct variants using the combined pH and salt based elution gradient and removal of the host cell impurities in flow-through are the key novel features of the developed multimodal chromatographic purification step. Copyright © 2013 Elsevier B.V. All rights reserved.

Dynamic light scattering study on phase separation of a protein-water mixture: Application on cold cataract development in the ocular lens

Science.gov (United States)

Petta, V.; Pharmakakis, N.; Papatheodorou, G. N.; Yannopoulos, S. N.

2008-06-01

We present a detailed dynamic light scattering study of the phase separation in the ocular lens emerging during cold cataract development. Cold cataract is a phase separation effect that proceeds via spinodal decomposition of the lens cytoplasm with cooling. The intensity autocorrelation functions of the lens protein content are analyzed with the aid of two methods, providing information on the populations and dynamics of the scattering elements associated with cold cataract. It is found that the temperature dependence of many measurable parameters changes appreciably at the characteristic temperature ˜16±1°C which is associated with the onset of cold cataract. By extending the temperature range of this work to previously inaccessible regimes, i.e., well below the phase separation or coexistence curve at Tcc , we have been able to accurately determine the temperature dependence of the collective and self-diffusion coefficients of proteins near the spinodal. The analysis showed that the dynamics of proteins bears some resemblance to the dynamics of structural glasses, where the apparent activation energy for particle diffusion increases below Tcc , indicating a highly cooperative motion. Application of ideas developed for studying the critical dynamics of binary protein-solvent mixtures, as well as the use of a modified Arrhenius equation, enabled us to estimate the spinodal temperature Tsp of the lens nucleus. The applicability of dynamic light scattering as a noninvasive, early-diagnostic tool for ocular diseases is also demonstrated in light of the findings of the present paper.

Prospects of Source-Separation-Based Sanitation Concepts: A Model-Based Study

NARCIS (Netherlands)

Tervahauta, T.H.; Trang Hoang,; Hernández, L.; Zeeman, G.; Buisman, C.J.N.

2013-01-01

Separation of different domestic wastewater streams and targeted on-site treatment for resource recovery has been recognized as one of the most promising sanitation concepts to re-establish the balance in carbon, nutrient and water cycles. In this study a model was developed based on literature data

Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of [35S]methionine-labeled proteins

International Nuclear Information System (INIS)

Tabaqchali, S.; O'Farrell, S.; Holland, D.; Silman, R.

1986-01-01

A typing method for Clostridium difficile based on the incorporation of [ 35 S]methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile

Emitter signal separation method based on multi-level digital channelization

Science.gov (United States)

Han, Xun; Ping, Yifan; Wang, Sujun; Feng, Ying; Kuang, Yin; Yang, Xinquan

2018-02-01

To solve the problem of emitter separation under complex electromagnetic environment, a signal separation method based on multi-level digital channelization is proposed in this paper. A two-level structure which can divide signal into different channel is designed first, after that, the peaks of different channels are tracked using the track filter and the coincident signals in time domain are separated in time-frequency domain. Finally, the time domain waveforms of different signals are acquired by reverse transformation. The validness of the proposed method is proved by experiment.

Permission-Based Separation Logic for Multithreaded Java Programs

NARCIS (Netherlands)

Haack, Christian; Huisman, Marieke; Hurlin, C.

2011-01-01

This paper motivates and presents a program logic for reasoning about multithreaded Java-like programs with concurrency primitives such as dynamic thread creation, thread joining and reentrant object monitors. The logic is based on concurrent separation logic. It is the first detailed adaptation of

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis.

Science.gov (United States)

Masso, Majid; Vaisman, Iosif I

2008-09-15

Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function. Such models are also valuable for the design and engineering of new proteins. Previously described methods have utilized properties of protein sequence or structure to predict the free energy change of mutants due to thermal (DeltaDeltaG) and denaturant (DeltaDeltaG(H2O)) denaturations, as well as mutant thermal stability (DeltaT(m)), through the application of either computational energy-based approaches or machine learning techniques. However, accuracy associated with applying these methods separately is frequently far from optimal. We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential. For any mutation due to a single amino acid replacement in a protein, the method provides an empirical normalized measure of the ensuing environmental perturbation occurring at every residue position. A feature vector is generated for the mutant by considering perturbations at the mutated position and it's ordered six nearest neighbors in the 3-dimensional (3D) protein structure. These predictors of stability change are evaluated by applying machine learning tools to large training sets of mutants derived from diverse proteins that have been experimentally studied and described. Predictive models based on our combined approach are either comparable to, or in many cases significantly outperform, previously published results. A web server with supporting documentation is available at http://proteins.gmu.edu/automute.

Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

Directory of Open Access Journals (Sweden)

Jung Me Hwang

2011-12-01

Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

Analytical modal diffusion theory based on flux separability

International Nuclear Information System (INIS)

Segev, M.

1987-01-01

The theory provides for an iterative solution of the mathematical problem of generating the assembly-wise power distribution in a LWR through the solution of the 2-group, multidimensional, diffusion equation. The companion problems of assembly pre-homogenization and of pin power reconstruction are of no direct concern presently. The theoretical development stems from the assumption of flux separability in X, Y and Z. The assumption derives from the notion that separability holds in a great part of the interior of a LWR assembly. More important, well accurate power maps are generated with a code based on the theoretical develpment yielded by the basic assumption

Partial separation of platelet and placental adenosine receptors from adenosine A2-like binding protein

International Nuclear Information System (INIS)

Zolnierowicz, S.; Work, C.; Hutchison, K.; Fox, I.H.

1990-01-01

The ubiquitous adenosine A2-like binding protein obscures the binding properties of adenosine receptors assayed with 5'-N-[ 3 H]ethylcarboxamidoadenosine [( 3 H]NECA). To solve this problem, we developed a rapid and simple method to separate adenosine receptors from the adenosine A2-like binding protein. Human platelet and placental membranes were solubilized with 1% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. The soluble platelet extract was precipitated with polyethylene glycol and the fraction enriched in adenosine receptors was isolated from the precipitate by differential centrifugation. The adenosine A2-like binding protein was removed from the soluble placental extract with hydroxylapatite and adenosine receptors were precipitated with polyethylene glycol. The specificity of the [ 3 H]NECA binding is typical of an adenosine A2 receptor for platelets and an adenosine A1 receptor for placenta. This method leads to enrichment of adenosine A2 receptors for platelets and adenosine A1 receptors for placenta. This provides a useful preparation technique for pharmacologic studies of adenosine receptors

Synthesis and characterization of recombinant abductin-based proteins.

Science.gov (United States)

Su, Renay S-C; Renner, Julie N; Liu, Julie C

2013-12-09

Recombinant proteins are promising tools for tissue engineering and drug delivery applications. Protein-based biomaterials have several advantages over natural and synthetic polymers, including precise control over amino acid composition and molecular weight, modular swapping of functional domains, and tunable mechanical and physical properties. In this work, we describe recombinant proteins based on abductin, an elastomeric protein that is found in the inner hinge of bivalves and functions as a coil spring to keep shells open. We illustrate, for the first time, the design, cloning, expression, and purification of a recombinant protein based on consensus abductin sequences derived from Argopecten irradians . The molecular weight of the protein was confirmed by mass spectrometry, and the protein was 94% pure. Circular dichroism studies showed that the dominant structures of abductin-based proteins were polyproline II helix structures in aqueous solution and type II β-turns in trifluoroethanol. Dynamic light scattering studies illustrated that the abductin-based proteins exhibit reversible upper critical solution temperature behavior and irreversible aggregation behavior at high temperatures. A LIVE/DEAD assay revealed that human umbilical vein endothelial cells had a viability of 98 ± 4% after being cultured for two days on the abductin-based protein. Initial cell spreading on the abductin-based protein was similar to that on bovine serum albumin. These studies thus demonstrate the potential of abductin-based proteins in tissue engineering and drug delivery applications due to the cytocompatibility and its response to temperature.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Membrane-based, sedimentation-assisted plasma separator for point-of-care applications.

Science.gov (United States)

Liu, Changchun; Mauk, Michael; Gross, Robert; Bushman, Frederic D; Edelstein, Paul H; Collman, Ronald G; Bau, Haim H

2013-11-05

Often, high-sensitivity, point-of-care (POC) clinical tests, such as HIV viral load, require large volumes of plasma. Although centrifuges are ubiquitously used in clinical laboratories to separate plasma from whole blood, centrifugation is generally inappropriate for on-site testing. Suitable alternatives are not readily available to separate the relatively large volumes of plasma from milliliters of blood that may be needed to meet stringent limit-of-detection specifications for low-abundance target molecules. We report on a simple-to-use, low-cost, pump-free, membrane-based, sedimentation-assisted plasma separator capable of separating a relatively large volume of plasma from undiluted whole blood within minutes. This plasma separator consists of an asymmetric, porous, polysulfone membrane housed in a disposable chamber. The separation process takes advantage of both gravitational sedimentation of blood cells and size exclusion-based filtration. The plasma separator demonstrated a "blood in-plasma out" capability, consistently extracting 275 ± 33.5 μL of plasma from 1.8 mL of undiluted whole blood within less than 7 min. The device was used to separate plasma laden with HIV viruses from HIV virus-spiked whole blood with recovery efficiencies of 95.5% ± 3.5%, 88.0% ± 9.5%, and 81.5% ± 12.1% for viral loads of 35,000, 3500, and 350 copies/mL, respectively. The separation process is self-terminating to prevent excessive hemolysis. The HIV-laden plasma was then injected into our custom-made microfluidic chip for nucleic acid testing and was successfully subjected to reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP), demonstrating that the plasma is sufficiently pure to support high-efficiency nucleic acid amplification.

Chemical structure, comparison antioxidant capacity and separation antioxidant of hen, duck and quail egg white protein hydrolysate

Science.gov (United States)

Fatah, A.; Meihu, M.; Ning, Q.; Setiani, B. E.; Bintoro, V. P.

2018-01-01

Amino acid linkages as proteins are nutritional substance which important for diet intake. Purification protein procesing undergo heating procedure process followed by additional of proteolytic enzymes or acid had been resulting in protein hydrolysates. A protein hydrolysate describe as many free amino acids bound together through a complex mixture of peptides. Egg white protein hydrolysates is one of subject interested to study for human health or industry product. The objectives of the research are to determine and identification the antioxidant derived from egg white hydrolysate protein. Identification of chemical structure of albumen and albumen protein hydrolysate was examine using IR Spectrophotometry. While comparison of antioxidant capacity and antioxidant separation egg albumen was also investigate using FTIR method (Fourier Transform Infrared Spectroscopy). Hen, duck and quail albumen egg white and on hydrolisate form were used as research materials. The results were showing that different time and enzyme of hydrolysis were not influence at secondary structure of hydrolysate albumen protein. Phytochemical content such as alcohol and hydroxyl compound which have potential as functional group of antioxidant were detected in all of the samples. Their results of radical scavenging activities samples hydrolyzed by pepsin were respectively 89.40%, 50.25% and 85.13%. Whereas the radical scavenging activities of hydrolysates hydrolyzed by papain were 72.85%, 61% and 76.45% respectively.

Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

International Nuclear Information System (INIS)

Yang Jianyi; Yu Zuguo; Anh, Vo

2009-01-01

The Schneider and Wrede hydrophobicity scale of amino acids and the 6-letter model of protein are proposed to study the relationship between the primary structure and the secondary structural classification of proteins. Two kinds of multifractal analyses are performed on the two measures obtained from these two kinds of data on large proteins. Nine parameters from the multifractal analyses are considered to construct the parameter spaces. Each protein is represented by one point in these spaces. A procedure is proposed to separate large proteins in the α, β, α + β and α/β structural classes in these parameter spaces. Fisher's linear discriminant algorithm is used to assess our clustering accuracy on the 49 selected large proteins. Numerical results indicate that the discriminant accuracies are satisfactory. In particular, they reach 100.00% and 84.21% in separating the α proteins from the {β, α + β, α/β} proteins in a parameter space; 92.86% and 86.96% in separating the β proteins from the {α + β, α/β} proteins in another parameter space; 91.67% and 83.33% in separating the α/β proteins from the α + β proteins in the last parameter space.

Advances in microscale separations towards nanoproteomics applications

Energy Technology Data Exchange (ETDEWEB)

Yi, Lian; Piehowski, Paul D.; Shi, Tujin; Smith, Richard D.; Qian, Wei-Jun

2017-11-01

Microscale separations (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. While significant advances have been achieved in MS-based proteomics, the current platforms still face a significant challenge in overall sensitivity towards nanoproteomics (i.e., with less than 1 g total amount of proteins available) applications such as cellular heterogeneity in tissue pathologies. Herein, we review recent advances in microscale separation techniques and integrated sample processing systems that improve the overall sensitivity and coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.

Comparison of different base flow separation methods in a lowland catchment

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S. Uhlenbrook

2009-11-01

Full Text Available Assessment of water resources available in different storages and moving along different pathways in a catchment is important for its optimal use and protection, and also for the prediction of floods and low flows. Moreover, understanding of the runoff generation processes is essential for assessing the impacts of climate and land use changes on the hydrological response of a catchment. Many methods for base flow separation exist, but hardly one focuses on the specific behaviour of temperate lowland areas. This paper presents the results of a base flow separation study carried out in a lowland area in the Netherlands. In this study, field observations of precipitation, groundwater and surface water levels and discharges, together with tracer analysis are used to understand the runoff generation processes in the catchment. Several tracer and non-tracer based base flow separation methods were applied to the discharge time series, and their results are compared.

The results show that groundwater levels react fast to precipitation events in this lowland area with shallow groundwater tables. Moreover, a good correlation was found between groundwater levels and discharges suggesting that most of the measured discharge also during floods comes from groundwater storage. It was estimated using tracer hydrological approaches that approximately 90% of the total discharge is groundwater displaced by event water mainly infiltrating in the northern part of the catchment, and only the remaining 10% is surface runoff. The impact of remote recharge causing displacement of near channel groundwater during floods could also be motivated with hydraulic approximations. The results show further that when base flow separation is meant to identify groundwater contributions to stream flow, process based methods (e.g. the rating curve method; Kliner and Knezek, 1974 are more reliable than other simple non-tracer based methods. Also, the recursive filtering method

HPLC separation of human serum albumin isoforms based on their isoelectric points

Science.gov (United States)

Bonilla, Lucía; Torres, María José; Schopfer, Francisco; Freeman, Bruce A.; Armas, Larissa; Ricciardi, Alejandro; Alvarez, Beatriz; Radi, Rafael

2014-01-01

Human serum albumin (HSA) is the most abundant protein in plasma. Cys34, the only free Cys residue, is the predominant plasma thiol and a relevant sacrificial antioxidant. Both in vivo circulating HSA and pharmaceutical preparations are heterogeneous with respect to the oxidation state of Cys34. In this work, we developed an external pH gradient chromatofocusing procedure that allows the analysis of the oxidation status of HSA in human plasma and biopharmaceutical products based on the different apparent isoelectric points and chemical properties of the redox isoforms. Specifically, reduced-mercury blocked HSA (HSA–SHg+), HSA with Cys34 oxidized to sulfenic acid (HSA–SOH) and HSA oxidized to sulfinate anion (HSA–SO2−) can be separated with resolutions of 1.4 and 3.1 (first and last pair) and hence quantified and purified. In addition, an N-terminally degraded isoform (HSA3–585) in different redox states can be resolved as well. Confirmation of the identity of the chromatofocusing isolated isoforms was achieved by high resolution whole protein MS. It is proposed that the chromatofocusing procedure can be used to produce more exact and complete descriptions of the redox status of HSA in vivo and in vitro. Finally, the scalability capabilities of the chromatofocusing procedure allow for the preparation of highly pure standards of several redox isoforms of HSA PMID:24316526

Blind Separation of Nonstationary Sources Based on Spatial Time-Frequency Distributions

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Zhang Yimin

2006-01-01

Full Text Available Blind source separation (BSS based on spatial time-frequency distributions (STFDs provides improved performance over blind source separation methods based on second-order statistics, when dealing with signals that are localized in the time-frequency (t-f domain. In this paper, we propose the use of STFD matrices for both whitening and recovery of the mixing matrix, which are two stages commonly required in many BSS methods, to provide robust BSS performance to noise. In addition, a simple method is proposed to select the auto- and cross-term regions of time-frequency distribution (TFD. To further improve the BSS performance, t-f grouping techniques are introduced to reduce the number of signals under consideration, and to allow the receiver array to separate more sources than the number of array sensors, provided that the sources have disjoint t-f signatures. With the use of one or more techniques proposed in this paper, improved performance of blind separation of nonstationary signals can be achieved.

Structure based alignment and clustering of proteins (STRALCP)

Science.gov (United States)

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of (/sup 35/S)methionine-labeled proteins

Energy Technology Data Exchange (ETDEWEB)

Tabaqchali, S.; O' Farrell, S.; Holland, D.; Silman, R.

1986-01-01

A typing method for Clostridium difficile based on the incorporation of (/sup 35/S)methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile.

Bioengineered protein-based nanocage for drug delivery.

Science.gov (United States)

Lee, Eun Jung; Lee, Na Kyeong; Kim, In-San

2016-11-15

Nature, in its wonders, presents and assembles the most intricate and delicate protein structures and this remarkable phenomenon occurs in all kingdom and phyla of life. Of these proteins, cage-like multimeric proteins provide spatial control to biological processes and also compartmentalizes compounds that may be toxic or unstable and avoids their contact with the environment. Protein-based nanocages are of particular interest because of their potential applicability as drug delivery carriers and their perfect and complex symmetry and ideal physical properties, which have stimulated researchers to engineer, modify or mimic these qualities. This article reviews various existing types of protein-based nanocages that are used for therapeutic purposes, and outlines their drug-loading mechanisms and bioengineering strategies via genetic and chemical functionalization. Through a critical evaluation of recent advances in protein nanocage-based drug delivery in vitro and in vivo, an outlook for de novo and in silico nanocage design, and also protein-based nanocage preclinical and future clinical applications will be presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Selective separation and concentration of antihypertensive peptides from rapeseed protein hydrolysate by electrodialysis with ultrafiltration membranes.

Science.gov (United States)

He, Rong; Girgih, Abraham T; Rozoy, Elodie; Bazinet, Laurent; Ju, Xing-Rong; Aluko, Rotimi E

2016-04-15

Rapeseed protein isolate was subjected to alcalase digestion to obtain a protein hydrolysate that was separated into peptide fractions using electrodialysis with ultrafiltration membrane (EDUF) technology. The EDUF process (6h duration) led to isolation of three peptide fractions: anionic (recovered in KCl-1 compartment), cationic (recovered in KCl-2 compartment), and those that remained in the feed compartment, which was labeled final rapeseed protein hydrolysate (FRPH). As expected the KCl-1 peptides were enriched in negatively-charged (43.57%) while KCl-2 contained high contents of positively-charged (28.35%) amino acids. All the samples inhibited angiotensin converting enzyme (ACE) and renin activities in dose-dependent manner with original rapeseed protein hydrolysate having the least ACE-inhibitory IC50 value of 0.0932±0.0037 mg/mL while FRPH and KCl-2 had least renin-inhibitory IC50 values of 0.47±0.05 and 0.55±0.06 mg/mL, respectively. Six hours after oral administration (100 mg/kg body weight) to spontaneously hypertensive rats, the FRPH produced the maximum systolic blood pressure reduction of -51 mmHg. Copyright © 2015 Elsevier Ltd. All rights reserved.

Competitive binding thyroid assay with improved bound-free separation step

International Nuclear Information System (INIS)

1979-01-01

A competitive binding assay is described for serum thyroid hormone using 125 I-labelled thyroid hormone and exogenous thyroid hormone binding protein. The unbound thyroid hormone is separated from thyroid hormone bound to thyroid hormone binding protein using an intermediate base anion exchange resin. This resin comprises tertiary and quaternary amine groups on a polyalkyleneamine lattice and is compressed with microcrystalline cellulose in a tablet form. The assay technique of the present invention employing an intermediate base anion resin was found to give superior results compared with alternative assay techniques used in serum thyroid hormone estimation. (UK)

An incentive-based source separation model for sustainable municipal solid waste management in China.

Science.gov (United States)

Xu, Wanying; Zhou, Chuanbin; Lan, Yajun; Jin, Jiasheng; Cao, Aixin

2015-05-01

Municipal solid waste (MSW) management (MSWM) is most important and challenging in large urban communities. Sound community-based waste management systems normally include waste reduction and material recycling elements, often entailing the separation of recyclable materials by the residents. To increase the efficiency of source separation and recycling, an incentive-based source separation model was designed and this model was tested in 76 households in Guiyang, a city of almost three million people in southwest China. This model embraced the concepts of rewarding households for sorting organic waste, government funds for waste reduction, and introducing small recycling enterprises for promoting source separation. Results show that after one year of operation, the waste reduction rate was 87.3%, and the comprehensive net benefit under the incentive-based source separation model increased by 18.3 CNY tonne(-1) (2.4 Euros tonne(-1)), compared to that under the normal model. The stakeholder analysis (SA) shows that the centralized MSW disposal enterprises had minimum interest and may oppose the start-up of a new recycling system, while small recycling enterprises had a primary interest in promoting the incentive-based source separation model, but they had the least ability to make any change to the current recycling system. The strategies for promoting this incentive-based source separation model are also discussed in this study. © The Author(s) 2015.

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

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Vakser Ilya A

2011-07-01

Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

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Li Min

2012-03-01

Full Text Available Abstract Background Identification of essential proteins is always a challenging task since it requires experimental approaches that are time-consuming and laborious. With the advances in high throughput technologies, a large number of protein-protein interactions are available, which have produced unprecedented opportunities for detecting proteins' essentialities from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. However, the network topology-based centrality measures are very sensitive to the robustness of network. Therefore, a new robust essential protein discovery method would be of great value. Results In this paper, we propose a new centrality measure, named PeC, based on the integration of protein-protein interaction and gene expression data. The performance of PeC is validated based on the protein-protein interaction network of Saccharomyces cerevisiae. The experimental results show that the predicted precision of PeC clearly exceeds that of the other fifteen previously proposed centrality measures: Degree Centrality (DC, Betweenness Centrality (BC, Closeness Centrality (CC, Subgraph Centrality (SC, Eigenvector Centrality (EC, Information Centrality (IC, Bottle Neck (BN, Density of Maximum Neighborhood Component (DMNC, Local Average Connectivity-based method (LAC, Sum of ECC (SoECC, Range-Limited Centrality (RL, L-index (LI, Leader Rank (LR, Normalized α-Centrality (NC, and Moduland-Centrality (MC. Especially, the improvement of PeC over the classic centrality measures (BC, CC, SC, EC, and BN is more than 50% when predicting no more than 500 proteins. Conclusions We demonstrate that the integration of protein-protein interaction network and gene expression data can help improve the precision of predicting essential proteins. The new centrality measure, PeC, is an effective essential protein discovery method.

Protein-protein docking using region-based 3D Zernike descriptors

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Sael Lee

2009-12-01

Full Text Available Abstract Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for

The bacterial defensin resistance protein MprF consists of separable domains for lipid lysinylation and antimicrobial peptide repulsion.

Directory of Open Access Journals (Sweden)

Christoph M Ernst

2009-11-01

Full Text Available Many bacterial pathogens achieve resistance to defensin-like cationic antimicrobial peptides (CAMPs by the multiple peptide resistance factor (MprF protein. MprF plays a crucial role in Staphylococcus aureus virulence and it is involved in resistance to the CAMP-like antibiotic daptomycin. MprF is a large membrane protein that modifies the anionic phospholipid phosphatidylglycerol with l-lysine, thereby diminishing the bacterial affinity for CAMPs. Its widespread occurrence recommends MprF as a target for novel antimicrobials, although the mode of action of MprF has remained incompletely understood. We demonstrate that the hydrophilic C-terminal domain and six of the fourteen proposed trans-membrane segments of MprF are sufficient for full-level lysyl-phosphatidylglycerol (Lys-PG production and that several conserved amino acid positions in MprF are indispensable for Lys-PG production. Notably, Lys-PG production did not lead to efficient CAMP resistance and most of the Lys-PG remained in the inner leaflet of the cytoplasmic membrane when the large N-terminal hydrophobic domain of MprF was absent, indicating a crucial role of this protein part. The N-terminal domain alone did not confer CAMP resistance or repulsion of the cationic test protein cytochrome c. However, when the N-terminal domain was coexpressed with the Lys-PG synthase domain either in one protein or as two separate proteins, full-level CAMP resistance was achieved. Moreover, only coexpression of the two domains led to efficient Lys-PG translocation to the outer leaflet of the membrane and to full-level cytochrome c repulsion, indicating that the N-terminal domain facilitates the flipping of Lys-PG. Thus, MprF represents a new class of lipid-biosynthetic enzymes with two separable functional domains that synthesize Lys-PG and facilitate Lys-PG translocation. Our study unravels crucial details on the molecular basis of an important bacterial immune evasion mechanism and it may help

Protein-Based Drug-Delivery Materials

OpenAIRE

Jao, Dave; Xue, Ye; Medina, Jethro; Hu, Xiao

2017-01-01

There is a pressing need for long-term, controlled drug release for sustained treatment of chronic or persistent medical conditions and diseases. Guided drug delivery is difficult because therapeutic compounds need to survive numerous transport barriers and binding targets throughout the body. Nanoscale protein-based polymers are increasingly used for drug and vaccine delivery to cross these biological barriers and through blood circulation to their molecular site of action. Protein-based pol...

Protein complex prediction based on k-connected subgraphs in protein interaction network

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Habibi Mahnaz

2010-09-01

Full Text Available Abstract Background Protein complexes play an important role in cellular mechanisms. Recently, several methods have been presented to predict protein complexes in a protein interaction network. In these methods, a protein complex is predicted as a dense subgraph of protein interactions. However, interactions data are incomplete and a protein complex does not have to be a complete or dense subgraph. Results We propose a more appropriate protein complex prediction method, CFA, that is based on connectivity number on subgraphs. We evaluate CFA using several protein interaction networks on reference protein complexes in two benchmark data sets (MIPS and Aloy, containing 1142 and 61 known complexes respectively. We compare CFA to some existing protein complex prediction methods (CMC, MCL, PCP and RNSC in terms of recall and precision. We show that CFA predicts more complexes correctly at a competitive level of precision. Conclusions Many real complexes with different connectivity level in protein interaction network can be predicted based on connectivity number. Our CFA program and results are freely available from http://www.bioinf.cs.ipm.ir/softwares/cfa/CFA.rar.

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

HomPPI: a class of sequence homology based protein-protein interface prediction methods

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Dobbs Drena

2011-06-01

Full Text Available Abstract Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i NPS-HomPPI (Non partner-specific HomPPI, which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii PS-HomPPI (Partner-specific HomPPI, which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of

Protein-protein docking using region-based 3D Zernike descriptors.

Science.gov (United States)

Venkatraman, Vishwesh; Yang, Yifeng D; Sael, Lee; Kihara, Daisuke

2009-12-09

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-alphaRMSD 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods.

Jammer Suppression in DS-CDMA Communications using Parafac-based Blind Separation

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Xu Lingyun

2016-01-01

Full Text Available In this paper we propose to apply parafac-based source separation techniques for jammer suppression in direct spread spectrum communication systems. The jammer excision is formulated as an optimization problem and a new algorithm is presented which is based on the parafac tri-iterative least square algorithm. By jointly diagonalizing the time delay correlation matrix of the observed signals and using the new proposed method, a better solution is achieved. The proposed algorithm can successfully separate communication signals and jamming signals. Simulation results reveal that our proposed algorithm has the better blind signal separation performance than joint diagonalization method. Our proposed algorithm doesn’t require whitening processing. Moreover our proposed algorithm works well in the underdetermined condition, where the number of sources exceeds than the number of antennas.

Physical stage of photosynthesis charge separation

Science.gov (United States)

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

2016-06-01

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

Calculations of helium separation via uniform pores of stanene-based membranes

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Guoping Gao

2015-12-01

Full Text Available The development of low energy cost membranes to separate He from noble gas mixtures is highly desired. In this work, we studied He purification using recently experimentally realized, two-dimensional stanene (2D Sn and decorated 2D Sn (SnH and SnF honeycomb lattices by density functional theory calculations. To increase the permeability of noble gases through pristine 2D Sn at room temperature (298 K, two practical strategies (i.e., the application of strain and functionalization are proposed. With their high concentration of large pores, 2D Sn-based membrane materials demonstrate excellent helium purification and can serve as a superior membrane over traditionally used, porous materials. In addition, the separation performance of these 2D Sn-based membrane materials can be significantly tuned by application of strain to optimize the He purification properties by taking both diffusion and selectivity into account. Our results are the first calculations of He separation in a defect-free honeycomb lattice, highlighting new interesting materials for helium separation for future experimental validation.

Protein complex prediction based on k-connected subgraphs in protein interaction network

OpenAIRE

Habibi, Mahnaz; Eslahchi, Changiz; Wong, Limsoon

2010-01-01

Abstract Background Protein complexes play an important role in cellular mechanisms. Recently, several methods have been presented to predict protein complexes in a protein interaction network. In these methods, a protein complex is predicted as a dense subgraph of protein interactions. However, interactions data are incomplete and a protein complex does not have to be a complete or dense subgraph. Results We propose a more appropriate protein complex prediction method, CFA, that is based on ...

Effects of Proteoliposome Composition and Draw Solution Types on Separation Performance of Aquaporin-Based Proteoliposomes

DEFF Research Database (Denmark)

Zhao, Yang; Vararattanavech, Ardcharaporn; Li, Xuesong

2013-01-01

Escherichia coli cells, and their separation properties were characterized by stopped-flow measurements. The current study systematically investigated the effect of proteoliposome composition (lipid type, protein-to-lipid ratio (PLR), and the addition of cholesterol) on water permeability and NaCl retention......Aquaporins are a large family of water transport proteins in cell membranes. Their high water permeability and solute rejection make them potential building blocks for high-performance biomimetic membranes for desalination. In the current study, proteoliposomes were prepared using AquaporinZ from...

Fullerene and dendrimer based nano-composite gas separation membranes

NARCIS (Netherlands)

Sterescu, D.M.

2007-01-01

This thesis describes the development of new materials for membrane based gas separation processes. Long-term stable, loosely packed (high free volume) amorphous polymer films were prepared by introduction of super-molecular pendant groups, which possess hardsphere properties to avoid dense

Structure-based barcoding of proteins.

Science.gov (United States)

Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

2014-01-01

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods

Directory of Open Access Journals (Sweden)

Pontil Massimiliano

2009-10-01

Full Text Available Abstract Background Alanine scanning mutagenesis is a powerful experimental methodology for investigating the structural and energetic characteristics of protein complexes. Individual amino-acids are systematically mutated to alanine and changes in free energy of binding (ΔΔG measured. Several experiments have shown that protein-protein interactions are critically dependent on just a few residues ("hot spots" at the interface. Hot spots make a dominant contribution to the free energy of binding and if mutated they can disrupt the interaction. As mutagenesis studies require significant experimental efforts, there is a need for accurate and reliable computational methods. Such methods would also add to our understanding of the determinants of affinity and specificity in protein-protein recognition. Results We present a novel computational strategy to identify hot spot residues, given the structure of a complex. We consider the basic energetic terms that contribute to hot spot interactions, i.e. van der Waals potentials, solvation energy, hydrogen bonds and Coulomb electrostatics. We treat them as input features and use machine learning algorithms such as Support Vector Machines and Gaussian Processes to optimally combine and integrate them, based on a set of training examples of alanine mutations. We show that our approach is effective in predicting hot spots and it compares favourably to other available methods. In particular we find the best performances using Transductive Support Vector Machines, a semi-supervised learning scheme. When hot spots are defined as those residues for which ΔΔG ≥ 2 kcal/mol, our method achieves a precision and a recall respectively of 56% and 65%. Conclusion We have developed an hybrid scheme in which energy terms are used as input features of machine learning models. This strategy combines the strengths of machine learning and energy-based methods. Although so far these two types of approaches have mainly been

Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

Directory of Open Access Journals (Sweden)

Lei Yang

2014-01-01

Full Text Available Cliques (maximal complete subnets in protein-protein interaction (PPI network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning.

A new protein-protein interaction sensor based on tripartite split-GFP association.

Science.gov (United States)

Cabantous, Stéphanie; Nguyen, Hau B; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A; Favre, Gilles; Terwilliger, Thomas C; Waldo, Geoffrey S

2013-10-04

Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.

Selective binding and magnetic separation of His-tagged proteins using Fe3O4/PAM/NTA-Ni2+ Magnetic Nanoparticles

Science.gov (United States)

Guo, Huiling; Li, Mengyun; Tu, Shu; Sun, Honghao

2018-03-01

Fe3O4 nanoparticles coated with polyacrylamide (PAM) were synthesized. The magnetic core, with an average hydrodynamic size of 235.5 nm, allowed the magnetic nanoparticles (MNPs) rapid separation from solutions under an external magnetic field. NTA-Ni2+ was modified on the surface of Fe3O4/PAM MNPs to selectively trap his-tagged green fluorescent protein (GFP). The results showed that Fe3O4/PAM/NTA-Ni2+ MNPs exhibited remarkable capability of selective binding and separating his-tagged GFP. The adsorption efficiency was 93.37%.

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

NARCIS (Netherlands)

Xue, Li C; Garcia Lopes Maia Rodrigues, João; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2016-01-01

Although many advanced and sophisticatedab initioapproaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to

Microparticle Separation by Cyclonic Separation

Science.gov (United States)

Karback, Keegan; Leith, Alexander

2017-11-01

The ability to separate particles based on their size has wide ranging applications from the industrial to the medical. Currently, cyclonic separators are primarily used in agriculture and manufacturing to syphon out contaminates or products from an air supply. This has led us to believe that cyclonic separation has more applications than the agricultural and industrial. Using the OpenFoam computational package, we were able to determine the flow parameters of a vortex in a cyclonic separator in order to segregate dust particles to a cutoff size of tens of nanometers. To test the model, we constructed an experiment to separate a test dust of various sized particles. We filled a chamber with Arizona test dust and utilized an acoustic suspension technique to segregate particles finer than a coarse cutoff size and introduce them into the cyclonic separation apparatus where they were further separated via a vortex following our computational model. The size of the particles separated from this experiment will be used to further refine our model. Metropolitan State University of Denver, Colorado University of Denver, Dr. Randall Tagg, Dr. Richard Krantz.

Major Intrinsic Proteins in Biomimetic Membranes

DEFF Research Database (Denmark)

Helix Nielsen, Claus

2010-01-01

or as sensor devices based on e.g., the selective permeation of metalloids. In principle a MIP based membrane sensor/separation device requires the supporting biomimetic matrix to be virtually impermeable to anything but water or the solute in question. In practice, however, a biomimetic support matrix....../separation technology, a unique class of membrane transport proteins is especially interesting the major intrinsic proteins (MIPs). Generally, MIPs conduct water molecules and selected solutes in and out of the cell while preventing the passage of other solutes, a property critical for the conservation of the cells...... internal pH and salt concentration. Also known as water channels or aquaporins they are highly efficient membrane pore proteins some of which are capable of transporting water at very high rates up to 109 molecules per second. Some MIPs transport other small, uncharged solutes, such as glycerol and other...

Permission-based separation logic for multi-threaded Java programs

NARCIS (Netherlands)

Amighi, A.; Haack, Christian; Huisman, Marieke; Hurlin, C.

This paper presents a program logic for reasoning about multithreaded Java-like programs with concurrency primitives such as dynamic thread creation, thread joining and reentrant object monitors. The logic is based on concurrent separation logic. It is the first detailed adaptation of concurrent

A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli.

Science.gov (United States)

Smith, Corey L; Matheson, Timothy D; Trombly, Daniel J; Sun, Xiaoming; Campeau, Eric; Han, Xuemei; Yates, John R; Kaufman, Paul D

2014-09-15

Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element-containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus. © 2014 Smith et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Twist on protein microarrays: layering wax-patterned nitrocellulose to create customizable and separable arrays of multiplexed affinity columns.

Science.gov (United States)

de Lange, Victoria; Vörös, János

2014-05-06

We developed the simple and inexpensive FoRe microarray to simultaneously test several 1 μL samples for multiple proteins. By combining forward and reverse phase microarrays into an innovative three-dimensional format, the FoRe array exploits the advantages and eliminates several drawbacks of the traditional approaches (i.e., large sample volumes, protein loss, and cross-reactivity between detection antibodies). Samples are pipetted into an array of separable, multiplexed affinity columns. Several nitrocellulose membranes, each functionalized with a different capture antibody, are stacked to create a customizable affinity column. The nitrocellulose is patterned with wax to form 25 isolated microspots on each layer, allowing us to analyze multiple samples in parallel. After running the immunoassay, the stacks are quickly disassembled, revealing 2D microarrays of different fractions from multiple samples. By combining the stack-and-separate technique with wax patterning, we keep the arrays low cost and easily tailored to a variety of applications. We successfully performed 3D multiplexing using a model system with mouse and rabbit IgG. Binding proved to be independent of the position in the stack, and the limit of detection for a mouse IgG sandwich assay was 7.3 pM in BSA and 15 pM in human plasma. The FoRe microarray makes it possible to identify protein expression patterns across several minute volume samples; for example, it could be used to analyze cell lysate in drug response studies or pricks of blood from small animal studies.

In-capillary enrichment, proteolysis and separation using capillary electrophoresis with discontinuous buffers: application on proteins with moderately acidic and basic isoelectric points.

Science.gov (United States)

Nesbitt, Chandra A; Yeung, Ken K-C

2009-01-01

Advances in mass spectrometry and capillary-format separation continue to improve the sensitivity of protein analysis. Of equal importance is the miniaturization of sample pretreatment such as enrichment and proteolysis. In a previous report (Nesbitt et al., Electrophoresis, 2008, 29, 466-474), nanoliter-volume protein enrichment, tryptic digestion, and partial separation was demonstrated in capillary electrophoresis followed by MALDI mass spectral analysis. A discontinuous buffer system, consisting of ammonium (pH 10) and acetate (pH 4), was used to create a pH junction inside the capillary, trapping a protein with a neutral isoelectric point, myoglobin (pI 7.2). Moreover, co-enrichment of myoglobin with trypsin led to an in-capillary digestion. In this paper, the ability of this discontinuous buffer system to perform similar in-capillary sample pretreatment on proteins with moderately acidic and basic pI was studied and reported. Lentil lectin (pI 8.6) and a multi-phosphorylated protein, beta-casein (pI 5.1), were selected as model proteins. In addition to the previously shown tryptic digestion, proteolysis with endoproteinase Asp-N was also performed. Digestion of these acidic and basic pI proteins produced a few peptides with extreme pI values lying outside the trapping range of the discontinuous buffer. An alteration in the peptide trapping procedure was made to accommodate these analytes. Offline MALDI mass spectral analysis confirmed the presence of the expected peptides. The presented miniaturized sample pretreatment methodology was proven to be applicable on proteins with a moderately wide range of pI. Flexibility in the choice of protease was also evident.

Ultra-microporous triptycene-based polyimide membranes for high-performance gas separation

KAUST Repository

Ghanem, Bader

2014-03-11

A highly permeable and highly selective polyimide of intrinsic microporosity is prepared using a 9,10-diisopropyl-triptycene contortion center. The three-dimensionality and shape-persistence of triptycene afford exceptional sieving-based gas separation performance transcending the latest permeability/selectivity trade-offs for industrial gas separations involving oxygen and hydrogen. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultra-microporous triptycene-based polyimide membranes for high-performance gas separation

KAUST Repository

Ghanem, Bader; Swaidan, Raja; Litwiller, Eric; Pinnau, Ingo

2014-01-01

A highly permeable and highly selective polyimide of intrinsic microporosity is prepared using a 9,10-diisopropyl-triptycene contortion center. The three-dimensionality and shape-persistence of triptycene afford exceptional sieving-based gas separation performance transcending the latest permeability/selectivity trade-offs for industrial gas separations involving oxygen and hydrogen. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential Precipitation and Solubilization of Proteins.

Science.gov (United States)

Ryan, Barry J; Kinsella, Gemma K

2017-01-01

Differential protein precipitation is a rapid and economical step in protein purification and is based on exploiting the inherent physicochemical properties of the polypeptide. Precipitation of recombinant proteins, lysed from the host cell, is commonly used to concentrate the protein of choice before further polishing steps with more selective purification columns (e.g., His-Tag, Size Exclusion, etc.). Recombinant proteins can also precipitate naturally as inclusion bodies due to various influences during overexpression in the host cell. Although this phenomenon permits easier initial separation from native proteins, these inclusion bodies must carefully be differentially solubilized so as to reform functional, correctly folded proteins. Here, appropriate bioinformatics tools to aid in understanding a protein's propensity to aggregate and solubilize are explored as a backdrop for a typical protein extraction, precipitation, and selective resolubilization procedure, based on a recombinantly expressed protein.

Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

Directory of Open Access Journals (Sweden)

Donald Adjeroh

2018-03-01

Full Text Available In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI. In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences, and structure information (protein and RNA secondary structures. This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.

Base-catalyzed depolymerization of lignin : separation of monomers

Energy Technology Data Exchange (ETDEWEB)

Vigneault, A. [Sherbrooke Univ., PQ (Canada). Dept. of Chemical Engineering; Johnson, D.K. [National Renewable Energy Laboratory, Golden, CO (United States); Chornet, E. [Sherbrooke Univ., PQ (Canada). Dept. of Chemical Engineering; National Renewable Energy Laboratory, Golden, CO (United States)

2007-12-15

Biofuels produced from residual lignocellulosic biomass range from ethanol to biodiesel. The use of lignin for the production of alternate biofuels and green chemicals has been studied with particular emphasis on the structure of lignin and its oxyaromatic nature. In an effort to fractionate lignocellulosic biomass and valorize specific constitutive fractions, the authors developed a strategy for the separation of 12 added value monomers produced during the hydrolytic base catalyzed depolymerization (BCD) of a Steam Exploded Aspen Lignin. The separation strategy was similar to vanillin purification to obtain pure monomers, but combining more steps after the lignin depolymerization such as acidification, batch liquid-liquid-extraction (LLE), followed by vacuum distillation, liquid chromatography (LC) and crystallization. The purpose was to develop basic data for an industrial size process flow diagram, and to evaluate both the monomer losses during the separation and the energy requirements. Experimentally testing of LLE, vacuum distillation and flash LC in the laboratory showed that batch vacuum distillation produced up to 4 fractions. Process simulation revealed that a series of 4 vacuum distillation columns could produce 5 distinct monomer streams, of which 3 require further chromatography and crystallization operations for purification. 22 refs., 4 tabs., 8 figs.

Protein bioseparation using ultrafiltration: theory, applications and new developments

National Research Council Canada - National Science Library

Ghosh, Raja

2003-01-01

... membrane-based separation process. This book discusses how ultrafiltration could be used for protein bioseparation. There are several good books on protein bioseparation and indeed several others on ultrafiltration. However, there are relatively fewer books dealing specifically with protein bioseparation using ultrafiltration, in spite of this being an a...

Bio-Inspired Protein-Based Nanoformulations for Cancer Theranostics

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Yi Gou

2018-04-01

Full Text Available Over the past decade, more interests have been aroused in engineering protein-based nanoformulations for cancer treatment. This excitement originates from the success of FDA approved Abraxane (Albumin-based paclitaxel nanoparticles in 2005. The new generation of biocompatible endogenous protein-based nanoformulations is currently constructed through delivering cancer therapeutic and diagnostic agents simultaneously, as named potential theranostics. Protein nanoformulations are commonly incorporated with dyes, contrast agents, drug payloads or inorganic nanoclusters, serving as imaging-guided combinatorial cancer therapeutics. Employing the nature identity of proteins, the theranostics, escape the clearance by reticuloendothelial cells and have a long blood circulation time. The nanoscale sizet allows them to be penetrated deeply into tumor tissues. In addition, stimuli release and targeted molecules are incorporated to improve the delivery efficiency. The ongoing advancement of protein-based nanoformulations for cancer theranostics in recent 5 years is reviewed in this paper. Fine-designed nanoformulations based on albumin, ferritin, gelatin, and transferrin are highlighted from the literature. Finally, the current challenges are identified in translating protein-based nanoformulations from laboratory to clinical trials.

Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.

Directory of Open Access Journals (Sweden)

Wan Li

Full Text Available The cardiomyopathies are a group of heart muscle diseases which can be inherited (familial. Identifying potential disease-related proteins is important to understand mechanisms of cardiomyopathies. Experimental identification of cardiomyophthies is costly and labour-intensive. In contrast, bioinformatics approach has a competitive advantage over experimental method. Based on "guilt by association" analysis, we prioritized candidate proteins involving in human cardiomyopathies. We first built weighted human cardiomyopathy-specific protein-protein interaction networks for three subtypes of cardiomyopathies using the known disease proteins from Online Mendelian Inheritance in Man as seeds. We then developed a method in prioritizing disease candidate proteins to rank candidate proteins in the network based on "guilt by association" analysis. It was found that most candidate proteins with high scores shared disease-related pathways with disease seed proteins. These top ranked candidate proteins were related with the corresponding disease subtypes, and were potential disease-related proteins. Cross-validation and comparison with other methods indicated that our approach could be used for the identification of potentially novel disease proteins, which may provide insights into cardiomyopathy-related mechanisms in a more comprehensive and integrated way.

Neonatal maternal separation up-regulates protein signalling for cell survival in rat hypothalamus.

Science.gov (United States)

Irles, Claudine; Nava-Kopp, Alicia T; Morán, Julio; Zhang, Limei

2014-05-01

We have previously reported that in response to early life stress, such as maternal hyperthyroidism and maternal separation (MS), the rat hypothalamic vasopressinergic system becomes up-regulated, showing enlarged nuclear volume and cell number, with stress hyperresponsivity and high anxiety during adulthood. The detailed signaling pathways involving cell death/survival, modified by adverse experiences in this developmental window remains unknown. Here, we report the effects of MS on cellular density and time-dependent fluctuations of the expression of pro- and anti-apoptotic factors during the development of the hypothalamus. Neonatal male rats were exposed to 3 h-daily MS from postnatal days 2 to 15 (PND 2-15). Cellular density was assessed in the hypothalamus at PND 21 using methylene blue staining, and neuronal nuclear specific protein and glial fibrillary acidic protein immunostaining at PND 36. Expression of factors related to apoptosis and cell survival in the hypothalamus was examined at PND 1, 3, 6, 9, 12, 15, 20 and 43 by Western blot. Rats subjected to MS exhibited greater cell-density and increased neuronal density in all hypothalamic regions assessed. The time course of protein expression in the postnatal brain showed: (1) decreased expression of active caspase 3; (2) increased Bcl-2/Bax ratio; (3) increased activation of ERK1/2, Akt and inactivation of Bad; PND 15 and PND 20 were the most prominent time-points. These data indicate that MS can induce hypothalamic structural reorganization by promoting survival, suppressing cell death pathways, increasing cellular density which may alter the contribution of these modified regions to homeostasis.

Origins and Evolution of Inorganic-Based and MOF-Based Mixed-Matrix Membranes for Gas Separations

Directory of Open Access Journals (Sweden)

Edson V. Perez

2016-09-01

Full Text Available Gas separation for industrial, energy, and environmental applications requires low energy consumption and small footprint technology to minimize operating and capital costs for the processing of large volumes of gases. Among the separation methods currently being used, like distillation, amine scrubbing, and pressure and temperature swing adsorption, membrane-based gas separation has the potential to meet these demands. The key component, the membrane, must then be engineered to allow for high gas flux, high selectivity, and chemical and mechanical stability at the operating conditions of feed composition, pressure, and temperature. Among the new type of membranes studied that show promising results are the inorganic-based and the metal-organic framework-based mixed-matrix membranes (MOF-MMMs. A MOF is a unique material that offers the possibility of tuning the porosity of a membrane by introducing diffusional channels and forming a compatible interface with the polymer. This review details the origins of these membranes and their evolution since the first inorganic/polymer and MOF/polymer MMMs were reported in the open literature. The most significant advancements made in terms of materials, properties, and testing conditions are described in a chronological fashion.

PARTITION EFFICIENCY OF NEWLY DESIGNED LOCULAR MULTILAYER COIL FOR COUNTERCURRENT CHROMATOGRAPHIC SEPARATION OF PROTEINS USING SMALL-SCALE CROSS-AXIS COIL PLANET CENTRIFUGE WITH AQUEOUS-AQUEOUS POLYMER PHASE SYSTEMS.

Science.gov (United States)

Shinomiya, Kazufusa; Ito, Yoichiro

2009-01-01

Countercurrent chromatographic performance of the locular multilayer coil separation column newly designed in our laboratory was evaluated in terms of theoretical plate number, peak resolution and retention of the stationary phase in protein separation with an aqueous polymer phase system using the small-scale cross-axis coil planet centrifuge (X-axis CPC) fabricated in our laboratory. The locular column was made from 1.0 mm I.D., 2.0 mm O.D. or 1.5 mm I.D., 2.5 mm O.D. PTFE tubing compressed with a pair of hemostat at 2 or 4 cm intervals. The protein separation was performed using a set of stable proteins including cytochrome C, myoglobin and lysozyme with the 12.5% (w/w) polyethylene glycol 1000 and 12.5% (w/w) dibasic potassium phosphate system under 1000 rpm of column revolution. The 1.5 mm I.D., 2.5 mm O.D. locular tubing compressed at 2 cm intervals yielded better partition efficiencies than the non-clamped tubing using both lower and upper mobile phases with satisfactory retention of the stationary phase. The overall results suggest that the newly designed locular multilayer coil is useful to the preparative separation of proteins with aqueous-aqueous polymer phase system using our small-scale X-axis CPC.

Extraction and separation of water soluble proteins from Bacillus thuringiensis-transgenic and non-transgenic maize species by CZE

Czech Academy of Sciences Publication Activity Database

Sázelová, Petra; Kašička, Václav; Ibanez, E.; Cifuentes, A.

2009-01-01

Roč. 32, č. 21 (2009), s. 3801-3808 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/08/1428 Grant - others:GA ČR(CZ) GA203/09/0675 Program:GA Institutional research plan: CEZ:AV0Z40550506 Keywords : Bacillus thuringiensis -transgenic maize * CZE-UV profiling * Maize proteins Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.551, year: 2009

A new affinity-HPLC packing for protein separation: Cibacron blue attached uniform porous poly(HEMA-co-EDM) beads.

Science.gov (United States)

Unsal, Ender; Durdu, Aysun; Elmas, Begum; Tuncel, Murvet; Tuncel, Ali

2005-11-01

In this study, a new affinity high-performance liquid chromatography (HPLC) stationary phase suitable for protein separation was synthesized. In the first stage of the synthesis, uniform porous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate), poly(HEMA-co-EDM), beads 6.2 mum in size were obtained. Homogeneous distribution of hydroxyl groups in the bead interior was confirmed by confocal laser scanning microscopy. The plain poly(HEMA-co-EDM) particles gave very low non-specific protein adsorption with albumin. The selected dye ligand Cibacron blue F3G-A (CB F3G-A) was covalently linked onto the beads via hydroxyl groups. In the batch experiments, albumin adsorption up to 60 mg BSA/g particles was obtained with the CB F3G-A carrying poly(HEMA-co-EDM) beads. The affinity-HPLC of selected proteins (albumin and lysozyme) was investigated in a 25 mm x 4.0-mm inner diameter column packed with CB F3G-A carrying beads and both proteins were successfully resolved. By a single injection, 200 mug of protein was loaded and quantitatively eluted from the column. The protein recovery increased with increasing flow rate and salt concentration of the elution buffer and decreased with the increasing protein feed concentration. During the albumin elution, theoretical plate numbers up to 30,000 plates/m were achieved by increasing the salt concentration.

Cyanobacterial flv4-2 Operon-Encoded Proteins Optimize Light Harvesting and Charge Separation in Photosystem II.

Science.gov (United States)

Chukhutsina, Volha; Bersanini, Luca; Aro, Eva-Mari; van Amerongen, Herbert

2015-05-01

Photosystem II (PSII) complexes drive the water-splitting reaction necessary to transform sunlight into chemical energy. However, too much light can damage and disrupt PSII. In cyanobacteria, the flv4-2 operon encodes three proteins (Flv2, Flv4, and Sll0218), which safeguard PSII activity under air-level CO2 and in high light conditions. However, the exact mechanism of action of these proteins has not been clarified yet. We demonstrate that the PSII electron transfer properties are influenced by the flv4-2 operon-encoded proteins. Accelerated secondary charge separation kinetics was observed upon expression/overexpression of the flv4-2 operon. This is likely induced by docking of the Flv2/Flv4 heterodimer in the vicinity of the QB pocket of PSII, which, in turn, increases the QB redox potential and consequently stabilizes forward electron transfer. The alternative electron transfer route constituted by Flv2/Flv4 sequesters electrons from QB(-) guaranteeing the dissipation of excess excitation energy in PSII under stressful conditions. In addition, we demonstrate that in the absence of the flv4-2 operon-encoded proteins, about 20% of the phycobilisome antenna becomes detached from the reaction centers, thus decreasing light harvesting. Phycobilisome detachment is a consequence of a decreased relative content of PSII dimers, a feature observed in the absence of the Sll0218 protein. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Ionic liquid-based materials: a platform to design engineered CO2 separation membranes.

Science.gov (United States)

Tomé, Liliana C; Marrucho, Isabel M

2016-05-21

During the past decade, significant advances in ionic liquid-based materials for the development of CO2 separation membranes have been accomplished. This review presents a perspective on different strategies that use ionic liquid-based materials as a unique tuneable platform to design task-specific advanced materials for CO2 separation membranes. Based on compilation and analysis of the data hitherto reported, we provide a judicious assessment of the CO2 separation efficiency of different membranes, and highlight breakthroughs and key challenges in this field. In particular, configurations such as supported ionic liquid membranes, polymer/ionic liquid composite membranes, gelled ionic liquid membranes and poly(ionic liquid)-based membranes are detailed, discussed and evaluated in terms of their efficiency, which is attributed to their chemical and structural features. Finally, an integrated perspective on technology, economy and sustainability is provided.

A domain-based approach to predict protein-protein interactions

Directory of Open Access Journals (Sweden)

Resat Haluk

2007-06-01

Full Text Available Abstract Background Knowing which proteins exist in a certain organism or cell type and how these proteins interact with each other are necessary for the understanding of biological processes at the whole cell level. The determination of the protein-protein interaction (PPI networks has been the subject of extensive research. Despite the development of reasonably successful methods, serious technical difficulties still exist. In this paper we present DomainGA, a quantitative computational approach that uses the information about the domain-domain interactions to predict the interactions between proteins. Results DomainGA is a multi-parameter optimization method in which the available PPI information is used to derive a quantitative scoring scheme for the domain-domain pairs. Obtained domain interaction scores are then used to predict whether a pair of proteins interacts. Using the yeast PPI data and a series of tests, we show the robustness and insensitivity of the DomainGA method to the selection of the parameter sets, score ranges, and detection rules. Our DomainGA method achieves very high explanation ratios for the positive and negative PPIs in yeast. Based on our cross-verification tests on human PPIs, comparison of the optimized scores with the structurally observed domain interactions obtained from the iPFAM database, and sensitivity and specificity analysis; we conclude that our DomainGA method shows great promise to be applicable across multiple organisms. Conclusion We envision the DomainGA as a first step of a multiple tier approach to constructing organism specific PPIs. As it is based on fundamental structural information, the DomainGA approach can be used to create potential PPIs and the accuracy of the constructed interaction template can be further improved using complementary methods. Explanation ratios obtained in the reported test case studies clearly show that the false prediction rates of the template networks constructed

Blind Separation of Acoustic Signals Combining SIMO-Model-Based Independent Component Analysis and Binary Masking

Directory of Open Access Journals (Sweden)

Hiekata Takashi

2006-01-01

Full Text Available A new two-stage blind source separation (BSS method for convolutive mixtures of speech is proposed, in which a single-input multiple-output (SIMO-model-based independent component analysis (ICA and a new SIMO-model-based binary masking are combined. SIMO-model-based ICA enables us to separate the mixed signals, not into monaural source signals but into SIMO-model-based signals from independent sources in their original form at the microphones. Thus, the separated signals of SIMO-model-based ICA can maintain the spatial qualities of each sound source. Owing to this attractive property, our novel SIMO-model-based binary masking can be applied to efficiently remove the residual interference components after SIMO-model-based ICA. The experimental results reveal that the separation performance can be considerably improved by the proposed method compared with that achieved by conventional BSS methods. In addition, the real-time implementation of the proposed BSS is illustrated.

Quantification of trace elements in protein bands by synchrotron radiation x-ray fluorescence after isoelectric focusing separation of human hemoglobin

International Nuclear Information System (INIS)

Gao Yuxi; Chen Chunying; Li Bai; He Wei; Huang Yuying; Chai Zhifang

2005-01-01

The role and effects of a trace element in a particular organism strongly depend on its particular chemical forms in which the element is present. Therefore, the bulk content or concentration of an element in the organism of interest is often meaningless in judging its biological significance. To understand bioavailability, transportation, cell uptake, metabolism, toxicity, and other biological behaviors of trace elements in the body, information is needed about speciation of trace element, especially about distribution of metal-containing proteins. Development of appropriate methods for speciation analysis is therefore required. Synchrotron radiation x-ray fluorescence (SRXRF) is a sensitive method for multielemental analysis with detection limit of 10 ng/g. It has been successfully used for imaging and quantifying trace elements in various pathological and healthy tissues, even in a single cell, to help understand the mechanism of diseases and the biochemistry of elements. In our previous work, the technique was combined with electrophoresis to study distribution of metalloproteins in biological samples, but the quantitative analysis of trace elements in protein bands after electrophoresis was still unrealized. In this study, a procedure has been proposed for quantification of Fe, Cu, and Zn in protein bands with SRXRF analysis after isoelectric focusing (IEF) separation. Calibration standards were prepared by adding certain amounts of metal ions and free-metal proteins to electrophoresis gel. Human hemoglobin was separated with IEF, and Fe, Cu, and Zn in protein bands were analyzed by SRXRF. The calibration curves can be obtained in a range of 0-8 mg/kg metals and a linear relationship between dosage of metals and fluorescent intensity can be observed (r 2 > 0.99). The method provides the detection limits of 2.43, 1.12, and 0.96 mg/kg for Fe, Cu and Zn, and the recoveries of 90.4 and 115.7 % for Fe and Zn, respectively. The hyphenated technique of SRXRF and IEF

Phylogenetic relationship among five geckos from Egypt based on RAPD-PCR and protein electrophoresis (SDS–PAGE

Directory of Open Access Journals (Sweden)

Nadia H.M. Sayed

2012-05-01

Full Text Available Genetic variations between five gekkonid species from Egypt; Tropiocolotes tripolitanus, Tropiocolotes steudneri, Tropiocolotes nattereri, Tarentola mauritanica and Tarentola annularis were analyzed by SDS–PAGE for water soluble proteins and random amplified polymorphic DNA (RAPD analysis. Based on SDS–PAGE of water soluble proteins for all species, the obtained results revealed a total of 17 bands at molecular weights that ranged from 95 to 16 kDa. The polymorphic bands among species were 11 (64.7% and the mean similarity matrix value between them was 70.7%. Using RAPD-PCR, the results showed eight total amplified bands at molecular weights that ranged from 1408 to 360 bp. The polymorphic bands between species were 7 (87.5% and the mean similarity matrix between them was 44.6%. The dendrogram showed that, the five gekkonid species are separated from each other into two clusters. The first cluster contains three species of the genus Tropiocolotes. The second cluster includes the two species of the genus Tarentola. Based on SDS–PAGE and RAPD-PCR results, T. nattereri is sister to T. steudneri with higher genetic similarity than with T. tripolitanus. It is concluded that, the similarity coefficient and the genetic distance values between the five gekkonid species indicate that the five gekkonid species are not identical and are separated from each other. From these results, it is indicated that the protein and RAPD analysis are useful molecular tools to indicate genetic variation between the species in the same genus or in the different genera.

Two-Dimensional Metal-Organic Framework Nanosheets for Membrane-Based Gas Separation.

Science.gov (United States)

Peng, Yuan; Li, Yanshuo; Ban, Yujie; Yang, Weishen

2017-08-07

Metal-organic framework (MOF) nanosheets could serve as ideal building blocks of molecular sieve membranes owing to their structural diversity and minimized mass-transfer barrier. To date, discovery of appropriate MOF nanosheets and facile fabrication of high performance MOF nanosheet-based membranes remain as great challenges. A modified soft-physical exfoliation method was used to disintegrate a lamellar amphiprotic MOF into nanosheets with a high aspect ratio. Consequently sub-10 nm-thick ultrathin membranes were successfully prepared, and these demonstrated a remarkable H 2 /CO 2 separation performance, with a separation factor of up to 166 and H 2 permeance of up to 8×10 -7  mol m -2  s -1  Pa -1 at elevated testing temperatures owing to a well-defined size-exclusion effect. This nanosheet-based membrane holds great promise as the next generation of ultrapermeable gas separation membrane. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Energy Technology Data Exchange (ETDEWEB)

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

2008-06-27

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

Novel Fission-Product Separation Based on Room-Temperature Ionic Liquids

International Nuclear Information System (INIS)

Rogers, Robin D.

2004-01-01

This project has demonstrated that Sr2+ and Cs+ can be selectively extracted from aqueous solutions into ionic liquids using crown ethers and that unprecedented large distribution coefficients can be achieved for these fission products. The volume of secondary wastes can be significantly minimized with this new separation technology. Through the current EMSP funding, the solvent extraction technology based on ionic liquids has been shown to be viable and can potentially provide the most efficient separation of problematic fission products from high level wastes. The key results from the current funding period are the development of highly selective extraction process for cesium ions based on crown ethers and calixarenes, optimization of selectivities of extractants via systematic change of ionic liquids, and investigation of task-specific ionic liquids incorporating both complexant and solvent characteristics

Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

DEFF Research Database (Denmark)

Sikder, K. U.; Stone, K. A.; Kumar, P. B. S.

2014-01-01

We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that mic......We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find...... that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells. (C) 2014 AIP Publishing LLC....

Estimation on separation efficiency of aluminum from base-cap of spent fluorescent lamp in hammer crusher unit.

Science.gov (United States)

Rhee, Seung-Whee

2017-09-01

In order to separate aluminum from the base-cap of spent fluorescent lamp (SFL), the separation efficiency of hammer crusher unit is estimated by introducing a binary separation theory. The base-cap of SFL is composed by glass fragment, binder, ferrous metal, copper and aluminum. The hammer crusher unit to recover aluminum from the base-cap consists of 3stages of hammer crusher, magnetic separator and vibrating screen. The optimal conditions of rotating speed and operating time in the hammer crusher unit are decided at each stage. At the optimal conditions, the aluminum yield and the separation efficiency of hammer crusher unit are estimated by applying a sequential binary separation theory at each stage. And the separation efficiency between hammer crusher unit and roll crush system is compared to show the performance of aluminum recovery from the base-cap of SFL. Since the separation efficiency can be increased to 99% at stage 3, from the experimental results, it is found that aluminum from the base-cap can be sufficiently recovered by the hammer crusher unit. Copyright © 2017. Published by Elsevier Ltd.

Electrokinetic characterization of whey protein separation

DEFF Research Database (Denmark)

Keiding, Kristian; Stougård, Anders; Christensen, Morten Lykkegaard

Cross flow filtration of whey protein has been performed on 3 different membranes. The rejections have been determined by HPLC analysis of the feed and permeate. The pure membranes as well as the fouled membranes have been characterized by measurements of the streaming potential along the membrane...

Separation of piracetam derivatives on polysaccharide-based chiral stationary phases.

Science.gov (United States)

Kažoka, H; Koliškina, O; Veinberg, G; Vorona, M

2013-03-15

High-performance liquid chromatography was used for the enantiomeric separation of two chiral piracetam derivatives. The suitability of six commercially available polysaccharide-based chiral stationary phases (CSPs) under normal phase mode for direct enantioseparation has been investigated. The influence of the CSPs as well the nature and content of an alcoholic modifier in the mobile phase on separation and elution order was studied. It was established that CSP Lux Amylose-2 shows high chiral recognition ability towards 4-phenylsubstituted piracetam derivatives. Copyright © 2013 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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

2010-09-01

Plasma acute-phase proteins (APPs) glyco-isoforms are important biomarkers of inflammatory processes such as those occurring in multiple sclerosis (MS). Specific analysis of these proteins is often hampered by sample biochemical complexity. The aim of our study was to set up a method to accurately visualize, identify and quantify APPs glyco-isoforms in human serum. An enrichment strategy based on affinity chromatography using the carbohydrate-binding proteins concanavalin A (ConA) and erythrina cristagalli lectin (ECL) was applied to pooled serum samples from 15 patients and 9 healthy individuals. Image analysis of 2-DE detected 30 spots with a fold change higher than 1.5. A total of 14 were statistically significant (p valuewell known. Performing galectin-3 binding and Western blotting, we were able to demonstrate a correlation between hybrid type glyco-isoforms of β-haptoglobin and MS. In conclusion, although the patho-physiological role of the identified species still remains unclear and further validations are needed, these findings may have a relevant impact on disease-specific marker identification approaches.

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

Science.gov (United States)

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

Audio Source Separation in Reverberant Environments Using β-Divergence-Based Nonnegative Factorization

DEFF Research Database (Denmark)

Fakhry, Mahmoud; Svaizer, Piergiorgio; Omologo, Maurizio

2017-01-01

-maximization algorithm and used to separate the signals by means of multichannel Wiener filtering. We propose to estimate these parameters by applying nonnegative factorization based on prior information on source variances. In the nonnegative factorization, spectral basis matrices can be defined as the prior...... information. The matrices can be either extracted or indirectly made available through a redundant library that is trained in advance. In a separate step, applying nonnegative tensor factorization, two algorithms are proposed in order to either extract or detect the basis matrices that best represent......In Gaussian model-based multichannel audio source separation, the likelihood of observed mixtures of source signals is parametrized by source spectral variances and by associated spatial covariance matrices. These parameters are estimated by maximizing the likelihood through an expectation...

Fluorescence-Based Multiplex Protein Detection Using Optically Encoded Microbeads

Directory of Open Access Journals (Sweden)

Dae Hong Jeong

2012-03-01

Full Text Available Potential utilization of proteins for early detection and diagnosis of various diseases has drawn considerable interest in the development of protein-based multiplex detection techniques. Among the various techniques for high-throughput protein screening, optically-encoded beads combined with fluorescence-based target monitoring have great advantages over the planar array-based multiplexing assays. This review discusses recent developments of analytical methods of screening protein molecules on microbead-based platforms. These include various strategies such as barcoded microbeads, molecular beacon-based techniques, and surface-enhanced Raman scattering-based techniques. Their applications for label-free protein detection are also addressed. Especially, the optically-encoded beads such as multilayer fluorescence beads and SERS-encoded beads are successful for generating a large number of coding.

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

Science.gov (United States)

Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

2017-11-01

Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common

In vivo collection of rare proteins using kinesin-based "nano-harvesters".

Energy Technology Data Exchange (ETDEWEB)

Bachand, Marlene; Bachand, George David; Greene, Adrienne Celeste; Carroll-Portillo, Amanda

2008-11-01

In this project, we have developed a novel platform for capturing, transport, and separating target analytes using the work harnessed from biomolecular transport systems. Nanoharvesters were constructed by co-organizing kinesin motor proteins and antibodies on a nanocrystal quantum dot (nQD) scaffold. Attachment of kinesin and antibodies to the nQD was achieved through biotin-streptavidin non-covalent bonds. Assembly of the nanoharvesters was characterized using a modified enzyme-linked immunosorbent assay (ELISA) that confirmed attachment of both proteins. Nanoharvesters selective against tumor necrosis factor-{alpha} (TNF-{alpha}) and nuclear transcription factor-{kappa}B (NF-{kappa}B) were capable of detecting target antigens at <100 ng/mL in ELISAs. A motility-based assay was subsequently developed using an antibody-sandwich approach in which the target antigen (TNF-{alpha}) formed a sandwich with the red-emitting nanoharvester and green-emitting detection nQD. In this format, successful sandwich formation resulted in a yellow emission associated with surface-bound microtubules. Step-wise analysis of sandwich formation suggested that the motility function of the kinesin motors was not adversely affected by either antigen capture or the subsequent binding of the detection nQDs. TNF-{alpha} was detected as low as {approx}1.5 ng/mL TNF-{alpha}, with 5.2% of the nanoharvesters successfully capturing the target analyte and detection nQDs. Overall, these results demonstrate the ability to capture target protein analytes in vitro using the kinesin-based nanoharvesters in nanofluidic environments. This system has direct relevance for lab-on-a-chip applications where pressure-driven or electrokinetic movement of fluids is impractical, and offers potential application for in vivo capture of rare proteins within the cytoplasmic domain of live cells.

Ionic-Liquid-Mediated Extraction and Separation Processes for Bioactive Compounds: Past, Present, and Future Trends.

Science.gov (United States)

Ventura, Sónia P M; E Silva, Francisca A; Quental, Maria V; Mondal, Dibyendu; Freire, Mara G; Coutinho, João A P

2017-05-24

Ionic liquids (ILs) have been proposed as promising media for the extraction and separation of bioactive compounds from the most diverse origins. This critical review offers a compilation on the main results achieved by the use of ionic-liquid-based processes in the extraction and separation/purification of a large range of bioactive compounds (including small organic extractable compounds from biomass, lipids, and other hydrophobic compounds, proteins, amino acids, nucleic acids, and pharmaceuticals). ILs have been studied as solvents, cosolvents, cosurfactants, electrolytes, and adjuvants, as well as used in the creation of IL-supported materials for separation purposes. The IL-based processes hitherto reported, such as IL-based solid-liquid extractions, IL-based liquid-liquid extractions, IL-modified materials, and IL-based crystallization approaches, are here reviewed and compared in terms of extraction and separation performance. The key accomplishments and future challenges to the field are discussed, with particular emphasis on the major lacunas found within the IL community dedicated to separation processes and by suggesting some steps to overcome the current limitations.

Tapered Microfluidic for Continuous Micro-Object Separation Based on Hydrodynamic Principle.

Science.gov (United States)

Ahmad, Ida Laila; Ahmad, Mohd Ridzuan; Takeuchi, Masaru; Nakajima, Masahiro; Hasegawa, Yasuhisa

2017-12-01

Recent advances in microfluidic technologies have created a demand for a simple and efficient separation intended for various applications such as food industries, biological preparation, and medical diagnostic. In this paper, we report a tapered microfluidic device for passive continuous separation of microparticles by using hydrodynamic separation. By exploiting the hydrodynamic properties of the fluid flow and physical characteristics of micro particles, effective size based separation is demonstrated. The tapered microfluidic device has widening geometries with respect to specific taper angle which amplify the sedimentation effect experienced by particles of different sizes. A mixture of 3-μm and 10-μm polystyrene microbeads are successfully separated using 20° and 25° taper angles. The results obtained are in agreement with three-dimensional finite element simulation conducted using Abaqus 6.12. Moreover, the feasibility of this mechanism for biological separation is demonstrated by using polydisperse samples consists of 3-μm polystyrene microbeads and human epithelial cervical carcinoma (HeLa) cells. 98% of samples purity is recovered at outlet 1 and outlet 3 with flow rate of 0.5-3.0 μl/min. Our device is interesting despite adopting passive separation approach. This method enables straightforward, label-free, and continuous separation of multiparticles in a stand-alone device without the need for bulky apparatus. Therefore, this device may become an enabling technology for point of care diagnosis tools and may hold potential for micrototal analysis system applications.

A universal DNA-based protein detection system.

Science.gov (United States)

Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan

2013-09-25

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.

Magnetic separations in biotechnology.

Science.gov (United States)

Borlido, L; Azevedo, A M; Roque, A C A; Aires-Barros, M R

2013-12-01

Magnetic separations are probably one of the most versatile separation processes in biotechnology as they are able to purify cells, viruses, proteins and nucleic acids directly from crude samples. The fast and gentle process in combination with its easy scale-up and automation provide unique advantages over other separation techniques. In the midst of this process are the magnetic adsorbents tailored for the envisioned target and whose complex synthesis spans over multiple fields of science. In this context, this article reviews both the synthesis and tailoring of magnetic adsorbents for bioseparations as well as their ultimate application. Copyright © 2013 Elsevier Inc. All rights reserved.

Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease.

Science.gov (United States)

Gable, Jonathan E; Lee, Gregory M; Acker, Timothy M; Hulce, Kaitlin R; Gonzalez, Eric R; Schweigler, Patrick; Melkko, Samu; Farady, Christopher J; Craik, Charles S

2016-04-19

Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Capillary electrophoresis separation of neutral organic compounds, pharmaceutical drugs, proteins and peptides, enantiomers, and anions

Energy Technology Data Exchange (ETDEWEB)

Ding, Wei -Liang [Iowa State Univ., Ames, IA (United States)

1999-02-12

Addition of a novel anionic surfactant, namely lauryl polyoxyethylene sulfate, to an aqueous-acetonitrile electrolyte makes it possible to separate nonionic organic compounds by capillary electrophoresis. Separation is based on differences in the association between analytes and the surfactant. Highly hydrophobic compounds such as polyaromatic hydrocarbons are well separated by this new surfactant. Migration times of analytes can be readily changed over an unusually large range by varying the additive concentration and the proportion of acetonitrile in the electrolyte. Several examples are given, including the separation of four methylbenz[a]anthracene isomers and the separation of normal and deuterated acetophenone. The effect of adding this new surfactant to the acidic electrolyte was also investigated. Incorporation of cetyltrimethylammonium bromide in the electrolyte is shown to dynamically coat the capillary and reverse electroosmotic flow. Chiral recognition mechanism is studied using novel synthetic surfactants as chiral selectors, which are made from amino acids reacting with alkyl chloroformates. A satisfactory separation of both inorganic and organic anions is obtained using electrolyte solutions as high as 5 M sodium chloride using direct photometric detection. The effect of various salts on electrophoretic and electroosmotic mobility is further discussed. Several examples are given under high-salt conditions.

Fragment-based quantum mechanical calculation of protein-protein binding affinities.

Science.gov (United States)

Wang, Yaqian; Liu, Jinfeng; Li, Jinjin; He, Xiao

2018-04-29

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Nanochemistry of protein-based delivery agents

Science.gov (United States)

Rajendran, Subin; Udenigwe, Chibuike; Yada, Rickey

2016-07-01

The past decade has seen an increased interest in the conversion of food proteins into functional biomaterials, including their use for loading and delivery of physiologically active compounds such as nutraceuticals and pharmaceuticals. Proteins possess a competitive advantage over other platforms for the development of nanodelivery systems since they are biocompatible, amphipathic, and widely available. Proteins also have unique molecular structures and diverse functional groups that can be selectively modified to alter encapsulation and release properties. A number of physical and chemical methods have been used for preparing protein nanoformulations, each based on different underlying protein chemistry. This review focuses on the chemistry of the reorganization and/or modification of proteins into functional nanostructures for delivery, from the perspective of their preparation, functionality, stability and physiological behavior.

Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

Science.gov (United States)

Zhang, Shu-Bo; Tang, Qiang-Rong

2016-07-21

Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful indicators for protein interaction. However, conventional methods based on GO similarity fail to take advantage of the specificity of GO terms in the ontology graph. We proposed a GO-based method to predict protein-protein interaction by integrating different kinds of similarity measures derived from the intrinsic structure of GO graph. We extended five existing methods to derive the semantic similarity measures from the descending part of two GO terms in the GO graph, then adopted a feature integration strategy to combines both the ascending and the descending similarity scores derived from the three sub-ontologies to construct various kinds of features to characterize each protein pair. Support vector machines (SVM) were employed as discriminate classifiers, and five-fold cross validation experiments were conducted on both human and yeast protein-protein interaction datasets to evaluate the performance of different kinds of integrated features, the experimental results suggest the best performance of the feature that combines information from both the ascending and the descending parts of the three ontologies. Our method is appealing for effective prediction of protein-protein interaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Single channel blind source separation based on ICA feature extraction

Institute of Scientific and Technical Information of China (English)

无

2007-01-01

A new technique is proposed to solve the blind source separation (BSS) given only a single channel observation. The basis functions and the density of the coefficients of source signals learned by ICA are used as the prior knowledge. Based on the learned prior information the learning rules of single channel BSS are presented by maximizing the joint log likelihood of the mixed sources to obtain source signals from single observation,in which the posterior density of the given measurements is maximized. The experimental results exhibit a successful separation performance for mixtures of speech and music signals.

Avaliação funcional de bases proteicas desidratadas de anchoita (Engraulis anchoita Functional evaluation of two dehydrated anchovy (Engraulis anchoita Protein bases

Directory of Open Access Journals (Sweden)

Liziane Garcia-Torchelsen

2011-12-01

Full Text Available Considerou-se neste trabalho a avaliação funcional de bases proteicas desidratadas de anchoita (Engraulis anchoita foi considerada neste trabalho. A polpa do pescado foi separada mecanicamente e submetida à lavagem com dois solventes, água e ácido fosfórico. A secagem em camada delgada das bases proteicas foi conduzida em temperaturas de 40, 60 e 70°C e espessuras de amostra de 5mm. O produto foi avaliado considerando a determinação de proteínas solúveis, composição centesimal e propriedades funcionais, expressas pela solubilidade protéica, capacidade de retenção de água, capacidade de retenção de gordura e capacidade emulsificante. Os resultados indicaram que a obtenção da base proteica de anchoita usando ácido fosfórico como solvente de lavagem apresentou melhores características, se consideradas as operações de extração de proteínas solúveis, secagem e propriedades funcionais do produto final. Com relação à secagem, verificou-se que esta operação origina um produto com melhores características funcionais quando são empregadas temperaturas de 40 e 60°C.The functional evaluation of two dehydrated anchovy (Engraulis anchoita protein bases was considered in this work. The fish meat was mechanically separated and subjected to washing with two solvents, water and phosphoric acid, to obtain the protein bases. Thin layer drying of the protein bases was carried out at temperatures of 40, 60 and 70 °C, with a sample thickness of 5mm. The products were evaluated considering the determinations of the soluble proteins, proximate composition and the functional properties such as protein solubility, water holding capacity, fat holding capacity and emulsifying capacity. The results indicated that obtaining the anchovy protein base using phosphoric acid as the washing solvent resulted in better characteristics, when considering the operations of extracting and drying the soluble proteins and the functional properties of

Elucidating the weak protein-protein interaction mechanisms behind the liquid-liquid phase separation of a mAb solution by different types of additives.

Science.gov (United States)

Wu, Guoliang; Wang, Shujing; Tian, Zhou; Zhang, Ning; Sheng, Han; Dai, Weiguo; Qian, Feng

2017-11-01

Liquid-liquid phase separation (LLPS) has long been observed during the physical stability investigation of therapeutic protein formulations. The buffer conditions and the presence of various excipients are thought to play important roles in the formulation development of monoclonal antibodies (mAbs). In this study, the effects of several small-molecule excipients (histidine, alanine, glycine, sodium phosphate, sodium chloride, sorbitol and sucrose) with diverse physical-chemical properties on LLPS of a model IgG1 (JM2) solutions were investigated by multiple techniques, including UV-vis spectroscopy, circular dichroism, differential scanning calorimetry/fluorimetry, size exclusion chromatography and dynamic light scattering. The LLPS of JM2 was confirmed to be a thermodynamic equilibrium process with no structural changes or irreversible aggregation of proteins. Phase diagrams of various JM2 formulations were constructed, suggesting that the phase behavior of JM2 was dependent on the solution pH, ionic strength and the presence of other excipients such as glycine, alanine, sorbitol and sucrose. Furthermore, we demonstrated that for this mAb, the interaction parameter (k D ) determined at low protein concentration appeared to be a good predictor for the occurrence of LLPS at high concentration. Copyright © 2017 Elsevier B.V. All rights reserved.

Ion-Exchange Membrane Chromatography as an Alternative Method of Separation of Potato y Virus

Directory of Open Access Journals (Sweden)

Treder Krzysztof

2015-12-01

Full Text Available Procedures of separation of virus particles from a plant material are multistage. Furthermore often they are difficult in terms of methodology and require use of expensive, highly specialist equipment and yield of separation is often low. The antigen obtained is often degraded and contains admixtures of other proteins. Therefore, generation of high quality and specificity antibodies based on such antigen is very difficult and quality of the antibodies has impact on reliability, sensitivity and unambiguity of results of immunodiagnostic tests (e.g. ELISA that are currently conventionally used to detect vegetable viruses. In this study three conventionally-performed methods of separation of potato virus Y (PVY were compared and a method of separation based on membrane chromatography, as an alternative separation technique, has been presented. It has been demonstrated that in proper process conditions good quality virus preparation can be obtained.

In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

Directory of Open Access Journals (Sweden)

Laura Acevedo-Pacheco

2016-10-01

Full Text Available Background: One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective: The aim was to determine and compare the essential amino acid (EAA scores, protein digestibility corrected amino acid scores (PDCAAS, and in vivo protein quality (protein digestibility, protein efficiency ratio (PER, biological values (BV, and net protein utilization (NPU values of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design: To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results: The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions: The proposed enrichment of cereal-based foods with soybean proteins greatly

A PC based control system for the CERN ISOLDE separators

International Nuclear Information System (INIS)

Billinge, R.; Bret, A.; Deloose, I.; Pace, A.; Shering, G.

1992-01-01

The control system of the two isotope separators of CERN, named ISOLDE, is being completely redesigned with the goal of having a flexible, high performance and inexpensive system. A new architecture that makes heavy use of the commercial software and hardware available for the huge Personal Computer (PC) market is being implemented on the 1700 geographically distributed control channels of the separators. 8 MS-DOS TM i386-based PCs with about 80 acquisition/control boards are used to access the equipments while 3 other PCs running Microsoft Windows TM and Microsoft Excel TM are used as consoles, the whole through a Novell TM Local Area Network with a PC Disk Server used as a database. This paper describes the interesting solutions found and discusses the reduced programming work load and costs that are expected to build the system before the start of the separators in March 1992. (author)

Detection of vegetation LUE based on chlorophyll fluorescence separation algorithm from Fraunhofer line

Science.gov (United States)

Liu, Liangyun; Zhang, Bing

2009-09-01

Photosynthetic efficiency is very important, and not yet generally assessable by remote sensing. Much research has proved the possibility of the separation of solar-induced chlorophyll fluorescence (ChlF) from the reflected hyperspectral data. As the 'probe' of plant photosynthesis, it is possible to detect photosynthetic light use efficiency (LUE) by the separated solar-induced ChlF. A diurnal experiment was carried out on winter wheat on Apr. 18, 2008, and the canopy radiance spectra and leaf LUE data were measured synchronously. The solar-induced chlorophyll fluorescence signals at 760nm and 688nm were separated from the reflected radiance spectral based on Fraunhofer lines in two oxygen absorption bands. The result showed that LUE was negatively correlated to the separated chlorophyll signals. The statistical models for LUE based on the solar-induced chlorophyll fluorescence values at 688 nm and 760 nm bands had correlation coefficients (R2) of 0.64 and 0.78, respectively. In addition, photochemical reflectance index (PRI) was also linked to LUE, and a statistical model for LUE based on PRI has a correlation coefficient (R2) of 0.66. The presented method provides a novel solution for monitoring LUE from remote sensing data.

Insect-based protein: future promising protein source for fish cultured

Science.gov (United States)

Nugroho, R. A.; Nur, F. M.

2018-04-01

As one of the vital component feed used in fisheries, fishmeal (FM) is generally added to the fish diet to enhance fish growth, digestive performance and absorption of nutrients. This addition contributes significantly to the variable production cost in the aquaculture industry. Expanded production of carnivorous species requiring high protein, high-energy feeds will further tax global fish meal. Thus, research based on the low-cost budget for feed operating cost should be strategized to assist aquaculturists in enhancing fish productivity. Moreover, suitable alternative feed ingredients will have to be utilized to provide the essential nutrients and energy needed to fuel the growth of aquaculture production. To this effect, the use of insect-based protein sources to replace FM that often scarce, expensive, limited availability, and leads to high fish production costs is alternative ways and has been gaining momentum. Currently, Insects have been proposed as one of the potential future protein sources of protein because of the production of insects is highly sustainable. Farming insects is characterized by higher food conversion efficiencies, lower environmental impact, and higher potential to be grown on waste streams.

Ceria Based Composite Membranes for Oxygen Separation

DEFF Research Database (Denmark)

Gurauskis, Jonas; Ovtar, Simona; Kaiser, Andreas

2014-01-01

Mixed ionic-electronic conducting membranes for oxygen gas separation are attracting a lot of interest due to their promising potential for the pure oxygen and the syngas production. Apart from the need for a sufficiently high oxygen permeation fluxes, the prolonged stability of these membranes...... under the large oxygen potential gradients at elevated temperatures is decisive for the future applications. The gadolinium doped cerium oxide (CGO) based composite membranes are considered as promising candidates due to inherent stability of CGO phase. The CGO matrix is a main oxygen ion transporter......; meanwhile the primary role of a secondary phase in this membrane is to compensate the low electronic conductivity of matrix at intended functioning conditions. In this work thin film (15-20 μm) composite membranes based on CGO matrix and LSF electronic conducting phase were fabricated and evaluated...

Nanochemistry of protein-based delivery agents

Directory of Open Access Journals (Sweden)

Subin R.C.K. Rajendran

2016-07-01

Full Text Available The past decade has seen an increased interest in the conversion of food proteins into functional biomaterials, including their use for loading and delivery of physiologically active compounds such as nutraceuticals and pharmaceuticals. Proteins possess a competitive advantage over other platforms for the development of nanodelivery systems since they are biocompatible, amphipathic, and widely available. Proteins also have unique molecular structures and diverse functional groups that can be selectively modified to alter encapsulation and release properties. A number of physical and chemical methods have been used for preparing protein nanoformulations, each based on different underlying protein chemistry. This review focuses on the chemistry of the reorganization and/or modification of proteins into functional nanostructures for delivery, from the perspective of their preparation, functionality, stability and physiological behavior.

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Cytocompatible and water stable ultrafine protein fibers for tissue engineering

Science.gov (United States)

Jiang, Qiuran

This dissertation proposal focuses on the development of cytocompatible and water stable protein ultrafine fibers for tissue engineering. The protein-based ultrafine fibers have the potential to be used for biomedicine, due to their biocompatibility, biodegradability, similarity to natural extracellular matrix (ECM) in physical structure and chemical composition, and superior adsorption properties due to their high surface to volume ratio. However, the current technologies to produce the protein-based ultrafine fibers for biomedical applications still have several problems. For instance, the current electrospinning and phase separation technologies generate scaffolds composed of densely compacted ultrafine fibers, and cells can spread just on the surface of the fiber bulk, and hardly penetrate into the inner sections of scaffolds. Thus, these scaffolds can merely emulate the ECM as a two dimensional basement membrane, but are difficult to mimic the three dimensional ECM stroma. Moreover, the protein-based ultrafine fibers do not possess sufficient water stability and strength for biomedical applications, and need modifications such as crosslinking. However, current crosslinking methods are either high in toxicity or low in crosslinking efficiency. To solve the problems mentioned above, zein, collagen, and gelatin were selected as the raw materials to represent plant proteins, animal proteins, and denatured proteins in this dissertation. A benign solvent system was developed specifically for the fabrication of collagen ultrafine fibers. In addition, the gelatin scaffolds with a loose fibrous structure, high cell-accessibility and cell viability were produced by a novel ultralow concentration phase separation method aiming to simulate the structure of three dimensional (3D) ECM stroma. Non-toxic crosslinking methods using citric acid as the crosslinker were also developed for electrospun or phase separated scaffolds from these three proteins, and proved to be

Microfluidic emulsion separation-simultaneous separation and sensing by multilayer nanofilm structures

Energy Technology Data Exchange (ETDEWEB)

Uhlmann, P; Truman, P; Stamm, M [Leibniz-Institut fuer Polymerforschung Dresden e V, Hohe Strasse 6, 01069 Dresden (Germany); Varnik, F; Zikos, G [Ruhr Universitaet Bochum, Stiepeler Strasse 129, 44801 Bochum (Germany); Moulin, J-F; Mueller-Buschbaum, P, E-mail: uhlmannp@ipfdd.de [Technische Universitaet Muenchen, Physik-Department, LS E13, James-Franck-Strasse 1, 85748 Garching (Germany)

2011-05-11

Emulsion separation is of high relevance for filtration applications, liquid-liquid-partitioning of biomolecules like proteins and recovery of products from droplet microreactors. Selective interaction of various components of an emulsion with substrates is used to design microfluidic flow chambers for efficient separation of emulsions into their individual components. Our lab-on-a-chip device consists of an emulsion separation cell with an integrated silicon sensor chip, the latter allowing the detection of liquid motion via the field-effect signal. Thus, within our lab-on-a-chip device, emulsions can be separated while the separation process is monitored simultaneously. For emulsion separation a surface energy step gradient, namely a sharp interface between the hydrophobic and hydrophilic parts of the separation chamber, is used. The key component of the lab-on-a-chip system is a multilayer and multifunctional nanofilm structure which not only provides the surface energy step gradient for emulsion separation but also constitutes the functional parts of the field-effect transistors. The proof-of-principle was performed using a model emulsion consisting of immiscible aqueous and organic solvent components. Droplet coalescence was identified as a key aspect influencing the separation process, with quite different effects during separation on open surfaces as compared to slit geometry. For a detailed description of this observation, an analytical model was derived and lattice Boltzmann computer simulations were performed. By use of grazing incidence small angle x-ray scattering (GISAXS) interfacial nanostructures during gold nanoparticle deposition in a flow field were probed to demonstrate the potential of GISAXS for in situ investigations during flow.

Weak cation magnetic separation technology and MALDI-TOF-MS in screening serum protein markers in primary type I osteoporosis.

Science.gov (United States)

Shi, X L; Li, C W; Liang, B C; He, K H; Li, X Y

2015-11-30

We investigated weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of primary type I osteoporosis. We selected 16 postmenopausal women with osteoporosis and nine postmenopausal women as controls to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were obtained from controls and patients. Serum protein was extracted with the WCX protein chip system; protein fingerprints were examined using MALDI-TOF-MS. The preprocessed and model construction data were handled by the ProteinChip system. The diagnostic models were established using a genetic arithmetic model combined with a support vector machine (SVM). The SVM model with the highest Youden index was selected. Combinations with the highest accuracy in distinguishing different groups of data were selected as potential biomarkers. From the two groups of serum proteins, 123 cumulative MS protein peaks were selected. Significant intensity differences in the protein peaks of 16 postmenopausal women with osteoporosis were screened. The difference in Youden index between the four groups of protein peaks showed that the highest peaks had mass-to-charge ratios of 8909.047, 8690.658, 13745.48, and 15114.52. A diagnosis model was established with these four markers as the candidates, and the model specificity and sensitivity were found to be 100%. Two groups of specimens in the SVM results on the scatterplot were distinguishable. We established a diagnosis model, and provided a new serological method for screening and diagnosis of osteoporosis with high sensitivity and specificity.

SEPHYDRO: An Integrated Multi-Filter Web-Based Tool for Baseflow Separation

Science.gov (United States)

Serban, D.; MacQuarrie, K. T. B.; Popa, A.

2017-12-01

Knowledge of baseflow contributions to streamflow is important for understanding watershed scale hydrology, including groundwater-surface water interactions, impact of geology and landforms on baseflow, estimation of groundwater recharge rates, etc. Baseflow (or hydrograph) separation methods can be used as supporting tools in many areas of environmental research, such as the assessment of the impact of agricultural practices, urbanization and climate change on surface water and groundwater. Over the past few decades various digital filtering and graphically-based methods have been developed in an attempt to improve the assessment of the dynamics of the various sources of streamflow (e.g. groundwater, surface runoff, subsurface flow); however, these methods are not available under an integrated platform and, individually, often require significant effort for implementation. Here we introduce SEPHYDRO, an open access, customizable web-based tool, which integrates 11 algorithms allowing for separation of streamflow hydrographs. The streamlined interface incorporates a reference guide as well as additional information that allows users to import their own data, customize the algorithms, and compare, visualise and export results. The tool includes one-, two- and three-parameter digital filters as well as graphical separation methods and has been successfully applied in Atlantic Canada, in studies dealing with nutrient loading to fresh water and coastal water ecosystems. Future developments include integration of additional separation algorithms as well as incorporation of geochemical separation methods. SEPHYDRO has been developed through a collaborative research effort between the Canadian Rivers Institute, University of New Brunswick (Fredericton, New Brunswick, Canada), Agriculture and Agri-Food Canada and Environment and Climate Change Canada and is currently available at http://canadianriversinstitute.com/tool/

Graphene based integrated tandem supercapacitors fabricated directly on separators

KAUST Repository

Chen, Wei

2015-04-09

It is of great importance to fabricate integrated supercapacitors with extended operation voltages as high energy density storage devices. In this work, we develop a novel direct electrode deposition on separator (DEDS) process to fabricate graphene based integrated tandem supercapacitors for the first time. The DEDS process generates compact graphene-polyaniline electrodes directly on the separators to form integrated supercapacitors. The integrated graphene-polyaniline tandem supercapacitors demonstrate ultrahigh volumetric energy density of 52.5 Wh L^(−1) at power density of 6037 W L^(−1) and excellent gravimetric energy density of 26.1 Wh kg^(−1) at power density of 3002 W kg^(−1) with outstanding electrochemical stability for over 10000 cycles. This study show great promises for the future development of integrated energy storage devices.

Designing protein-based biomaterials for medical applications.

Science.gov (United States)

Gagner, Jennifer E; Kim, Wookhyun; Chaikof, Elliot L

2014-04-01

Biomaterials produced by nature have been honed through billions of years, evolving exquisitely precise structure-function relationships that scientists strive to emulate. Advances in genetic engineering have facilitated extensive investigations to determine how changes in even a single peptide within a protein sequence can produce biomaterials with unique thermal, mechanical and biological properties. Elastin, a naturally occurring protein polymer, serves as a model protein to determine the relationship between specific structural elements and desirable material characteristics. The modular, repetitive nature of the protein facilitates the formation of well-defined secondary structures with the ability to self-assemble into complex three-dimensional architectures on a variety of length scales. Furthermore, many opportunities exist to incorporate other protein-based motifs and inorganic materials into recombinant protein-based materials, extending the range and usefulness of these materials in potential biomedical applications. Elastin-like polypeptides (ELPs) can be assembled into 3-D architectures with precise control over payload encapsulation, mechanical and thermal properties, as well as unique functionalization opportunities through both genetic and enzymatic means. An overview of current protein-based materials, their properties and uses in biomedicine will be provided, with a focus on the advantages of ELPs. Applications of these biomaterials as imaging and therapeutic delivery agents will be discussed. Finally, broader implications and future directions of these materials as diagnostic and therapeutic systems will be explored. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simulation of Protein and Peptide-Based Biomaterials

National Research Council Canada - National Science Library

Daggett, Valerie

2002-01-01

The overall goal of the proposed research is to pursue realistic molecular modeling studies of the stability, dynamics, structure, function, and folding of proteins and protein-based biomaterials in solution...

Developing Novel Protein-based Materials using Ultrabithorax: Production, Characterization, and Functionalization

Science.gov (United States)

Huang, Zhao

2011-12-01

Compared to 'conventional' materials made from metal, glass, or ceramics, protein-based materials have unique mechanical properties. Furthermore, the morphology, mechanical properties, and functionality of protein-based materials may be optimized via sequence engineering for use in a variety of applications, including textile materials, biosensors, and tissue engineering scaffolds. The development of recombinant DNA technology has enabled the production and engineering of protein-based materials ex vivo. However, harsh production conditions can compromise the mechanical properties of protein-based materials and diminish their ability to incorporate functional proteins. Developing a new generation of protein-based materials is crucial to (i) improve materials assembly conditions, (ii) create novel mechanical properties, and (iii) expand the capacity to carry functional protein/peptide sequences. This thesis describes development of novel protein-based materials using Ultrabithorax, a member of the Hox family of proteins that regulate developmental pathways in Drosophila melanogaster. The experiments presented (i) establish the conditions required for the assembly of Ubx-based materials, (ii) generate a wide range of Ubx morphologies, (iii) examine the mechanical properties of Ubx fibers, (iv) incorporate protein functions to Ubx-based materials via gene fusion, (v) pattern protein functions within the Ubx materials, and (vi) examine the biocompatibility of Ubx materials in vitro. Ubx-based materials assemble at mild conditions compatible with protein folding and activity, which enables Ubx chimeric materials to retain the function of appended proteins in spatial patterns determined by materials assembly. Ubx-based materials also display mechanical properties comparable to existing protein-based materials and demonstrate good biocompatibility with living cells in vitro. Taken together, this research demonstrates the unique features and future potential of novel Ubx-based

Bioorthogonal chemistry: applications in activity-based protein profiling.

Science.gov (United States)

Willems, Lianne I; van der Linden, Wouter A; Li, Nan; Li, Kah-Yee; Liu, Nora; Hoogendoorn, Sascha; van der Marel, Gijs A; Florea, Bogdan I; Overkleeft, Herman S

2011-09-20

of chemical biology research include contributions from many areas of the multifaceted discipline of chemistry, and particularly from organic chemistry. Researchers apply knowledge inherent to organic chemistry, such as reactivity and selectivity, to the manipulation of specific biomolecules in biological samples (cell extracts, living cells, and sometimes even animal models) to gain insight into the biological phenomena in which these molecules participate. In this Account, we highlight some of the recent developments in chemical biology research driven by organic chemistry, with a focus on bioorthogonal chemistry in relation to activity-based protein profiling. The rigorous demands of bioorthogonality have not yet been realized in a truly bioorthogonal reagent pair, but remarkable progress has afforded a range of tangible contributions to chemical biology research. Activity-based protein profiling, which aims to obtain information on the workings of a protein (or protein family) within the larger context of the full biological system, has in particular benefited from these advances. Both activity-based protein profiling and bioorthogonal chemistry have been around for approximately 15 years, and about 8 years ago the two fields very profitably intersected. We expect that each discipline, both separately and in concert, will continue to make important contributions to chemical biology research. © 2011 American Chemical Society

Carbon Molecular Sieve Membranes Derived from Tröger's Base-Based Microporous Polyimide for Gas Separation.

Science.gov (United States)

Wang, Zhenggong; Ren, Huiting; Zhang, Shenxiang; Zhang, Feng; Jin, Jian

2018-03-09

Carbon molecular sieve (CMS)-based membranes have attracted great attention because of their outstanding gas-separation performance. The polymer precursor is a key point for the preparation of high-performance CMS membranes. In this work, a microporous polyimide precursor containing a Tröger's base unit was used for the first time to prepare CMS membranes. By optimizing the pyrolysis procedure and the soaking temperature, three TB-CMS membranes were obtained. Gas-permeation tests revealed that the comprehensive gas-separation performance of the TB-CMS membranes was greatly enhanced relative to that of most state-of-the-art CMS membranes derived from polyimides reported so far. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer

Science.gov (United States)

CHEN, CHEN; SHEN, HONG; ZHANG, LI-GUO; LIU, JIAN; CAO, XIAO-GE; YAO, AN-LIANG; KANG, SHAO-SAN; GAO, WEI-XING; HAN, HUI; CAO, FENG-HONG; LI, ZHI-GUO

2016-01-01

Currently, using human prostate cancer (PCa) tissue samples to conduct proteomics research has generated a large amount of data; however, only a very small amount has been thoroughly investigated. In this study, we manually carried out the mining of the full text of proteomics literature that involved comparisons between PCa and normal or benign tissue and identified 41 differentially expressed proteins verified or reported more than 2 times from different research studies. We regarded these proteins as seed proteins to construct a protein-protein interaction (PPI) network. The extended network included one giant network, which consisted of 1,264 nodes connected via 1,744 edges, and 3 small separate components. The backbone network was then constructed, which was derived from key nodes and the subnetwork consisting of the shortest path between seed proteins. Topological analyses of these networks were conducted to identify proteins essential for the genesis of PCa. Solute carrier family 2 (facilitated glucose transporter), member 4 (SLC2A4) had the highest closeness centrality located in the center of each network, and the highest betweenness centrality and largest degree in the backbone network. Tubulin, beta 2C (TUBB2C) had the largest degree in the giant network and subnetwork. In addition, using module analysis of the whole PPI network, we obtained a densely connected region. Functional annotation indicated that the Ras protein signal transduction biological process, mitogen-activated protein kinase (MAPK), neurotrophin and the gonadotropin-releasing hormone (GnRH) signaling pathway may play an important role in the genesis and development of PCa. Further investigation of the SLC2A4, TUBB2C proteins, and these biological processes and pathways may therefore provide a potential target for the diagnosis and treatment of PCa. PMID:27121963

Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations

NARCIS (Netherlands)

Astefanei, A.; Dapic, I.; Camenzuli, M.

The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms

Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

OpenAIRE

Wang, Liwen; Chance, Mark R.

2011-01-01

Structural MS is a rapidly growing field with many applications in basic research and pharmaceutical drug development. In this feature article the overall technology is described and several examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate protein structure, and identify ligand dependent conformational changes in proteins are described.

High-Throughput Genetic Analysis and Combinatorial Chiral Separations Based on Capillary Electrophoresis

Energy Technology Data Exchange (ETDEWEB)

Zhong, Wenwan [Iowa State Univ., Ames, IA (United States)

2003-01-01

Capillary electrophoresis (CE) offers many advantages over conventional analytical methods, such as speed, simplicity, high resolution, low cost, and small sample consumption, especially for the separation of enantiomers. However, chiral method developments still can be time consuming and tedious. They designed a comprehensive enantioseparation protocol employing neutral and sulfated cyclodextrins as chiral selectors for common basic, neutral, and acidic compounds with a 96-capillary array system. By using only four judiciously chosen separation buffers, successful enantioseparations were achieved for 49 out of 54 test compounds spanning a large variety of pKs and structures. Therefore, unknown compounds can be screened in this manner to identify optimal enantioselective conditions in just one rn. In addition to superior separation efficiency for small molecules, CE is also the most powerful technique for DNA separations. Using the same multiplexed capillary system with UV absorption detection, the sequence of a short DNA template can be acquired without any dye-labels. Two internal standards were utilized to adjust the migration time variations among capillaries, so that the four electropherograms for the A, T, C, G Sanger reactions can be aligned and base calling can be completed with a high level of confidence. the CE separation of DNA can be applied to study differential gene expression as well. Combined with pattern recognition techniques, small variations among electropherograms obtained by the separation of cDNA fragments produced from the total RNA samples of different human tissues can be revealed. These variations reflect the differences in total RNA expression among tissues. Thus, this Ce-based approach can serve as an alternative to the DNA array techniques in gene expression analysis.

Prediction of Protein-Protein Interactions by NanoLuc-Based Protein-Fragment Complementation Assay | Office of Cancer Genomics

Science.gov (United States)

The CTD2 Center at Emory has developed a new NanoLuc®-based protein-fragment complementation assay (NanoPCA) which allows the detection of novel protein-protein interactions (PPI). NanoPCA allows the study of PPI dynamics with reversible interactions.  Read the abstract. Experimental Approaches Read the detailed Experimetnal Approaches. 

A protein-based hydrogel for in vitro expansion of mesenchymal stem cells.

Directory of Open Access Journals (Sweden)

Jingyu Wang

Full Text Available Hydrogels are widely used as scaffolds in tissue engineering because they can provide excellent environments for bioactive components including growth factors and cells. We reported in this study on a physical hydrogel formed by a specific protein-peptide interaction, which could be used for the three dimensional (3D cell culture of murine mesenchymal stem cells (mMSC. The mMSC kept dividing during the 7-day culture period and the metabolic-active cell number at day 7 was 359% more than that at day 1. This kind of physical hydrogel could be converted to a homogeneous solution by firstly adding an equal volume of culture medium and then pipeting for several times. Therefore, mMSC post culture could be easily separated from cell-gel constructs. We believed that the protein-based hydrogel system in this study could be developed into a promising scaffold for in vitro expansion of stem cells and cell therapy. This work would be in the general interests of researchers in the fields of biomaterials and supramolecular chemistry.

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

KAUST Repository

Cui, Xuefeng

2016-06-15

Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

Separation in Data Mining Based on Fractal Nature of Data

Czech Academy of Sciences Publication Activity Database

Jiřina, Marcel; Jiřina jr., M.

2013-01-01

Roč. 3, č. 1 (2013), s. 44-60 ISSN 2225-658X Institutional support: RVO:67985807 Keywords : nearest neighbor * fractal set * multifractal * IINC method * correlation dimension Subject RIV: JC - Computer Hardware ; Software http://sdiwc.net/digital-library/separation-in-data-mining-based-on-fractal-nature-of-data.html

Optimization of elution salt concentration in stepwise elution of protein chromatography using linear gradient elution data. Reducing residual protein A by cation-exchange chromatography in monoclonal antibody purification.

Science.gov (United States)

Ishihara, Takashi; Kadoya, Toshihiko; Endo, Naomi; Yamamoto, Shuichi

2006-05-05

Our simple method for optimization of the elution salt concentration in stepwise elution was applied to the actual protein separation system, which involves several difficulties such as detection of the target. As a model separation system, reducing residual protein A by cation-exchange chromatography in human monoclonal antibody (hMab) purification was chosen. We carried out linear gradient elution experiments and obtained the data for the peak salt concentration of hMab and residual protein A, respectively. An enzyme-linked immunosorbent assay was applied to the measurement of the residual protein A. From these data, we calculated the distribution coefficient of the hMab and the residual protein A as a function of salt concentration. The optimal salt concentration of stepwise elution to reduce the residual protein A from the hMab was determined based on the relationship between the distribution coefficient and the salt concentration. Using the optimized condition, we successfully performed the separation, resulting in high recovery of hMab and the elimination of residual protein A.

Systematic screening methodology and energy efficient design of ionic liquid-based separation processes

DEFF Research Database (Denmark)

Kulajanpeng, Kusuma; Suriyapraphadilok, Uthaiporn; Gani, Rafiqul

2016-01-01

in size of the target solute was investigated using the same separation process and IL entrainer to obtain the same product purity. The proposed methodology has been evaluated through a case study of binary alcoholic aqueous azeotropic separation: water+ethanol and water+isopropanol.......A systematic methodology for the screening of ionic liquids (ILs) as entrainers and for the design of ILs-based separation processes in various homogeneous binary azeotropic mixtures has been developed. The methodology focuses on the homogeneous binary aqueous azeotropic systems (for example, water...

Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate.

Science.gov (United States)

Zhang, Xueru; McGown, Linda B

2013-06-01

DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Designing coarse grained-and atom based-potentials for protein-protein docking

Directory of Open Access Journals (Sweden)

Tobi Dror

2010-11-01

Full Text Available Abstract Background Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results Using a linear programming (LP technique, we developed two types of potentials: (i Side chain-based and (ii Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys, based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked structure, a potential energy lower than those of any of the non-native (misdocked structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atom-based potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.

Renewable and superior thermal-resistant cellulose-based composite nonwoven as lithium-ion battery separator.

Science.gov (United States)

Zhang, Jianjun; Liu, Zhihong; Kong, Qingshan; Zhang, Chuanjian; Pang, Shuping; Yue, Liping; Wang, Xuejiang; Yao, Jianhua; Cui, Guanglei

2013-01-01

A renewable and superior thermal-resistant cellulose-based composite nonwoven was explored as lithium-ion battery separator via an electrospinning technique followed by a dip-coating process. It was demonstrated that such nanofibrous composite nonwoven possessed good electrolyte wettability, excellent heat tolerance, and high ionic conductivity. The cells using the composite separator displayed better rate capability and enhanced capacity retention, when compared to those of commercialized polypropylene separator under the same conditions. These fascinating characteristics would endow this renewable composite nonwoven a promising separator for high-power lithium-ion battery.

Isobaric Tags for Relative and Absolute Quantification (iTRAQ)-Based Untargeted Quantitative Proteomic Approach To Identify Change of the Plasma Proteins by Salbutamol Abuse in Beef Cattle.

Science.gov (United States)

Zhang, Kai; Tang, Chaohua; Liang, Xiaowei; Zhao, Qingyu; Zhang, Junmin

2018-01-10

Salbutamol, a selective β 2 -agonist, endangers the safety of animal products as a result of illegal use in food animals. In this study, an iTRAQ-based untargeted quantitative proteomic approach was applied to screen potential protein biomarkers in plasma of cattle before and after treatment with salbutamol for 21 days. A total of 62 plasma proteins were significantly affected by salbutamol treatment, which can be used as potential biomarkers to screen for the illegal use of salbutamol in beef cattle. Enzyme-linked immunosorbent assay measurements of five selected proteins demonstrated the reliability of iTRAQ-based proteomics in screening of candidate biomarkers among the plasma proteins. The plasma samples collected before and after salbutamol treatment were well-separated by principal component analysis (PCA) using the differentially expressed proteins. These results suggested that an iTRAQ-based untargeted quantitative proteomic strategy combined with PCA pattern recognition methods can discriminate differences in plasma protein profiles collected before and after salbutamol treatment.

Recyclability of PET/WPI/PE Multilayer Films by Removal of Whey Protein Isolate-Based Coatings with Enzymatic Detergents

Directory of Open Access Journals (Sweden)

Patrizia Cinelli

2016-06-01

Full Text Available Multilayer plastic films provide a range of properties, which cannot be obtained from monolayer films but, at present, their recyclability is an open issue and should be improved. Research to date has shown the possibility of using whey protein as a layer material with the property of acting as an excellent barrier against oxygen and moisture, replacing petrochemical non-recyclable materials. The innovative approach of the present research was to achieve the recyclability of the substrate films by separating them, with a simple process compatible with industrial procedures, in order to promote recycling processes leading to obtain high value products that will beneficially impact the packaging and food industries. Hence, polyethyleneterephthalate (PET/polyethylene (PE multi-layer film was prepared based on PET coated with a whey protein layer, and then the previous structure was laminated with PE. Whey proteins, constituting the coating, can be degraded by enzymes so that the coating films can be washed off from the plastic substrate layer. Enzyme types, dosage, time, and temperature optima, which are compatible with procedures adopted in industrial waste recycling, were determined for a highly-efficient process. The washing of samples based on PET/whey and PET/whey/PE were efficient when performed with enzymatic detergent containing protease enzymes, as an alternative to conventional detergents used in recycling facilities. Different types of enzymatic detergents tested presented positive results in removing the protein layer from the PET substrate and from the PET/whey/PE multilayer films at room temperature. These results attested to the possibility of organizing the pre-treatment of the whey-based multilayer film by washing with different available commercial enzymatic detergents in order to separate PET and PE, thus allowing a better recycling of the two different polymers. Mechanical properties of the plastic substrate, such as stress at

Recyclability of PET/WPI/PE Multilayer Films by Removal of Whey Protein Isolate-Based Coatings with Enzymatic Detergents

Science.gov (United States)

Cinelli, Patrizia; Schmid, Markus; Bugnicourt, Elodie; Coltelli, Maria Beatrice; Lazzeri, Andrea

2016-01-01

Multilayer plastic films provide a range of properties, which cannot be obtained from monolayer films but, at present, their recyclability is an open issue and should be improved. Research to date has shown the possibility of using whey protein as a layer material with the property of acting as an excellent barrier against oxygen and moisture, replacing petrochemical non-recyclable materials. The innovative approach of the present research was to achieve the recyclability of the substrate films by separating them, with a simple process compatible with industrial procedures, in order to promote recycling processes leading to obtain high value products that will beneficially impact the packaging and food industries. Hence, polyethyleneterephthalate (PET)/polyethylene (PE) multi-layer film was prepared based on PET coated with a whey protein layer, and then the previous structure was laminated with PE. Whey proteins, constituting the coating, can be degraded by enzymes so that the coating films can be washed off from the plastic substrate layer. Enzyme types, dosage, time, and temperature optima, which are compatible with procedures adopted in industrial waste recycling, were determined for a highly-efficient process. The washing of samples based on PET/whey and PET/whey/PE were efficient when performed with enzymatic detergent containing protease enzymes, as an alternative to conventional detergents used in recycling facilities. Different types of enzymatic detergents tested presented positive results in removing the protein layer from the PET substrate and from the PET/whey/PE multilayer films at room temperature. These results attested to the possibility of organizing the pre-treatment of the whey-based multilayer film by washing with different available commercial enzymatic detergents in order to separate PET and PE, thus allowing a better recycling of the two different polymers. Mechanical properties of the plastic substrate, such as stress at yield, stress and

Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.

Science.gov (United States)

Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

2015-02-01

We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. Copyright © 2014 Elsevier Inc. All rights reserved.

Membrane-based technologies for biogas separations.

Science.gov (United States)

Basu, Subhankar; Khan, Asim L; Cano-Odena, Angels; Liu, Chunqing; Vankelecom, Ivo F J

2010-02-01

Over the past two decades, membrane processes have gained a lot of attention for the separation of gases. They have been found to be very suitable for wide scale applications owing to their reasonable cost, good selectivity and easily engineered modules. This critical review primarily focuses on the various aspects of membrane processes related to the separation of biogas, more in specific CO(2) and H(2)S removal from CH(4) and H(2) streams. Considering the limitations of inorganic materials for membranes, the present review will only focus on work done with polymeric materials. An overview on the performance of commercial membranes and lab-made membranes highlighting the problems associated with their applications will be given first. The development studies carried out to enhance the performance of membranes for gas separation will be discussed in the subsequent section. This review has been broadly divided into three sections (i) performance of commercial polymeric membranes (ii) performance of lab-made polymeric membranes and (iii) performance of mixed matrix membranes (MMMs) for gas separations. It will include structural modifications at polymer level, polymer blending, as well as synthesis of mixed matrix membranes, for which addition of silane-coupling agents and selection of suitable fillers will receive special attention. Apart from an overview of the different membrane materials, the study will also highlight the effects of different operating conditions that eventually decide the performance and longevity of membrane applications in gas separations. The discussion will be largely restricted to the studies carried out on polyimide (PI), cellulose acetate (CA), polysulfone (PSf) and polydimethyl siloxane (PDMS) membranes, as these membrane materials have been most widely used for commercial applications. Finally, the most important strategies that would ensure new commercial applications will be discussed (156 references).

New Liquid Phases for the Gas Chromatographic Separation of Strong Bases on Capillary Columns

OpenAIRE

Grob, K.

2017-01-01

The current practice of pretreating the solid support with free alkali to increase separation efficiency for basic compounds proved to be unsuitable for capillary columns. Instead of this, homogenous organic materials of high base strength are required. We found polyethylene imine (PEI) and polypropylene imine (PPI) to be very efficient as liquid phases of capillary columns for the separation of bases. The preparation of polymers is mentioned. Silanization or acetylation of the free hydroxyl ...

A method based on a separation of variables in magnetohydrodynamics (MHD); Une methode de separation des variables en magnetohydrodynamique

Energy Technology Data Exchange (ETDEWEB)

Cessenat, M.; Genta, P.

1996-12-31

We use a method based on a separation of variables for solving a system of first order partial differential equations, in a very simple modelling of MHD. The method consists in introducing three unknown variables {phi}1, {phi}2, {phi}3 in addition of the time variable {tau} and then searching a solution which is separated with respect to {phi}1 and {tau} only. This is allowed by a very simple relation, called a `metric separation equation`, which governs the type of solutions with respect to time. The families of solutions for the system of equations thus obtained, correspond to a radial evolution of the fluid. Solving the MHD equations is then reduced to find the transverse component H{sub {Sigma}} of the magnetic field on the unit sphere {Sigma} by solving a non linear partial differential equation on {Sigma}. Thus we generalize ideas due to Courant-Friedrichs and to Sedov on dimensional analysis and self-similar solutions. (authors).

Temperature-responsive chromatography for the separation of biomolecules.

Science.gov (United States)

Kanazawa, Hideko; Okano, Teruo

2011-12-09

Temperature-responsive chromatography for the separation of biomolecules utilizing poly(N-isopropylacrylamide) (PNIPAAm) and its copolymer-modified stationary phase is performed with an aqueous mobile phase without using organic solvent. The surface properties and function of the stationary phase are controlled by external temperature changes without changing the mobile-phase composition. This analytical system is based on nonspecific adsorption by the reversible transition of a hydrophilic-hydrophobic PNIPAAm-grafted surface. The driving force for retention is hydrophobic interaction between the solute molecules and the hydrophobized polymer chains on the stationary phase surface. The separation of the biomolecules, such as nucleotides and proteins was achieved by a dual temperature- and pH-responsive chromatography system. The electrostatic and hydrophobic interactions could be modulated simultaneously with the temperature in an aqueous mobile phase, thus the separation system would have potential applications in the separation of biomolecules. Additionally, chromatographic matrices prepared by a surface-initiated atom transfer radical polymerization (ATRP) exhibit a strong interaction with analytes, because the polymerization procedure forms a densely packed polymer, called a polymer brush, on the surfaces. The copolymer brush grafted surfaces prepared by ATRP was an effective tool for separating basic biomolecules by modulating the electrostatic and hydrophobic interactions. Applications of thermally responsive columns for the separations of biomolecules are reviewed here. Copyright © 2011 Elsevier B.V. All rights reserved.

Microarray-based screening of heat shock protein inhibitors.

Science.gov (United States)

Schax, Emilia; Walter, Johanna-Gabriela; Märzhäuser, Helene; Stahl, Frank; Scheper, Thomas; Agard, David A; Eichner, Simone; Kirschning, Andreas; Zeilinger, Carsten

2014-06-20

Based on the importance of heat shock proteins (HSPs) in diseases such as cancer, Alzheimer's disease or malaria, inhibitors of these chaperons are needed. Today's state-of-the-art techniques to identify HSP inhibitors are performed in microplate format, requiring large amounts of proteins and potential inhibitors. In contrast, we have developed a miniaturized protein microarray-based assay to identify novel inhibitors, allowing analysis with 300 pmol of protein. The assay is based on competitive binding of fluorescence-labeled ATP and potential inhibitors to the ATP-binding site of HSP. Therefore, the developed microarray enables the parallel analysis of different ATP-binding proteins on a single microarray. We have demonstrated the possibility of multiplexing by immobilizing full-length human HSP90α and HtpG of Helicobacter pylori on microarrays. Fluorescence-labeled ATP was competed by novel geldanamycin/reblastatin derivatives with IC50 values in the range of 0.5 nM to 4 μM and Z(*)-factors between 0.60 and 0.96. Our results demonstrate the potential of a target-oriented multiplexed protein microarray to identify novel inhibitors for different members of the HSP90 family. Copyright © 2014 Elsevier B.V. All rights reserved.

Preparation of functional lupine protein fractions by dry separation

NARCIS (Netherlands)

Pelgrom, P.J.M.; Berghout, J.A.M.; Goot, van der A.J.; Boom, R.M.; Schutyser, M.A.I.

2014-01-01

Lupine protein concentrate is a promising ingredient that can be obtained by a combination of milling and air classification, generally called dry fractionation. This is a more sustainable route than conventional wet extraction and delivers a protein concentrate with native functional properties.

Quantum modeling of ultrafast photoinduced charge separation

Science.gov (United States)

Rozzi, Carlo Andrea; Troiani, Filippo; Tavernelli, Ivano

2018-01-01

Phenomena involving electron transfer are ubiquitous in nature, photosynthesis and enzymes or protein activity being prominent examples. Their deep understanding thus represents a mandatory scientific goal. Moreover, controlling the separation of photogenerated charges is a crucial prerequisite in many applicative contexts, including quantum electronics, photo-electrochemical water splitting, photocatalytic dye degradation, and energy conversion. In particular, photoinduced charge separation is the pivotal step driving the storage of sun light into electrical or chemical energy. If properly mastered, these processes may also allow us to achieve a better command of information storage at the nanoscale, as required for the development of molecular electronics, optical switching, or quantum technologies, amongst others. In this Topical Review we survey recent progress in the understanding of ultrafast charge separation from photoexcited states. We report the state-of-the-art of the observation and theoretical description of charge separation phenomena in the ultrafast regime mainly focusing on molecular- and nano-sized solar energy conversion systems. In particular, we examine different proposed mechanisms driving ultrafast charge dynamics, with particular regard to the role of quantum coherence and electron-nuclear coupling, and link experimental observations to theoretical approaches based either on model Hamiltonians or on first principles simulations.

Protein methylation reactions in intact pea chloroplasts

International Nuclear Information System (INIS)

Niemi, K.J.

1989-01-01

Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ( 3 H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented

Process for the separation of proteins from acid whey

Energy Technology Data Exchange (ETDEWEB)

Mirabel, B

1980-01-01

Acid whey from cheese or casein manufacture (pH less than 4.6) and containing about 5.2 g protein/l is passed through a cation exchange resin (of silica coated with a copolymer of styrene/vinyltriethoxysilane carrying SO/sub 3/H functional groups). The proteins adsorbed on the resin (alpha-lactalbumin, beta-lactoglobulin, serum albumin and immunoglobulins) are eluated with an 0.1 M ammonia solution, concentrated under vacuum and freeze-dried, obtaining a final product with 88% undenatured protein. The products are for use in the food and pharmaceutical industries and for dietetic and veterinary purposes.

Tröger’s Base Ladder Polymer for Membrane-Based Hydrocarbon Separation

KAUST Repository

Alhazmi, Abdulrahman

2017-05-01

The use of polymeric membranes for natural gas separation has rapidly increased during the past three decades, particularly for carbon dioxide separation from natural gas. Another valuable application is the separation of heavy hydrocarbons from methane (fuel gas conditioning), more importantly for remote area and off-shore applications. A new potential polymeric membrane that might be utilized for natural gas separations is a Tröger’s base ladder polymer (PIM-Trip-TB-2). This glassy polymeric membrane was synthesized by the polymerization reaction of 9, 10-dimethyl-2,6 (7) diaminotriptycene with dimethoxymethane. In this research, the polymer was selected due to its high surface area and highly interconnected microporous structure. Sorption isotherms of nitrogen (N2), oxygen (O¬2), methane (CH4), carbon dioxide (CO2), ethane (C2H6), propane (C3H8), and n-butane (n-C4H10) were measured at 35 °C over a range of pressures using a Hiden Intelligent Gravimetric Analyzer, IGA. The more condensable gases (C2H6, CO2, C3H8, and n-C4H10) showed high solubility due to their high affinity to the polymer matrix. The permeation coefficients were determined for various gases at 35 °C and pressure difference of 5 bar via the constant-pressure/variable-volume method. The PIM-Trip-TB-2 film exhibited high performance for several high-impact applications, such as O2/N2, H2/N2 and H2/CH4. Also, physical aging for several gases was examined by measuring the permeability coefficients at different periods of time. Moreover, a series of mixed-gas permeation tests was performed using 2 vol.% n-C4H10/98 vol.% CH4 and the results showed similar transport characteristics to other microporous polymers with pores of less than 2 nm. The work performed in this research suggested that PIM-Trip-TB-2 is suitable for the separation of: (i) higher hydrocarbons from methane and (ii) small, non-condensable gases such as O2/N2 and H2/CH4.

A probabilistic fragment-based protein structure prediction algorithm.

Directory of Open Access Journals (Sweden)

David Simoncini

Full Text Available Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].

Gearbox Fault Diagnosis in a Wind Turbine Using Single Sensor Based Blind Source Separation

Directory of Open Access Journals (Sweden)

Yuning Qian

2016-01-01

Full Text Available This paper presents a single sensor based blind source separation approach, namely, the wavelet-assisted stationary subspace analysis (WSSA, for gearbox fault diagnosis in a wind turbine. Continuous wavelet transform (CWT is used as a preprocessing tool to decompose a single sensor measurement data into a set of wavelet coefficients to meet the multidimensional requirement of the stationary subspace analysis (SSA. The SSA is a blind source separation technique that can separate the multidimensional signals into stationary and nonstationary source components without the need for independency and prior information of the source signals. After that, the separated nonstationary source component with the maximum kurtosis value is analyzed by the enveloping spectral analysis to identify potential fault-related characteristic frequencies. Case studies performed on a wind turbine gearbox test system verify the effectiveness of the WSSA approach and indicate that it outperforms independent component analysis (ICA and empirical mode decomposition (EMD, as well as the spectral-kurtosis-based enveloping, for wind turbine gearbox fault diagnosis.

Processing and characteristics of canola protein-based biodegradable packaging: A review.

Science.gov (United States)

Zhang, Yachuan; Liu, Qiang; Rempel, Curtis

2018-02-11

Interest increased recently in manufacturing food packaging, such as films and coatings, from protein-based biopolymers. Among various protein sources, canola protein is a novel source for manufacturing polymer films. It can be concentrated or isolated by aqueous extraction technology followed by protein precipitation. Using this procedure, it was claimed that more than 99% of protein was extracted from the defatted canola meal, and protein recovery was 87.5%. Canola protein exhibits thermoplastic properties when plasticizers are present, including water, glycerol, polyethylene glycol, and sorbitol. Addition of these plasticizers allows the canola protein to undergo glass transition and facilitates deformation and processability. Normally, canola protein-based bioplastics showed low mechanical properties, which had tensile strength (TS) of 1.19 to 4.31 MPa. So, various factors were explored to improve it, including blending with synthetic polymers, modifying protein functionality through controlled denaturation, and adding cross-linking agents. Canola protein-based bioplastics were reported to have glass transition temperature, T g , below -50°C but it highly depends on the plasticizer content. Canola protein-based bioplastics have demonstrated comparable mechanical and moisture barrier properties compared with other plant protein-based bioplastics. They have great potential in food packaging applications, including their use as wraps, sacks, sachets, or pouches.

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

Science.gov (United States)

Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

2014-04-08

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both

Separation of large DNA molecules by applying pulsed electric field to size exclusion chromatography-based microchip

Science.gov (United States)

Azuma, Naoki; Itoh, Shintaro; Fukuzawa, Kenji; Zhang, Hedong

2018-02-01

Through electrophoresis driven by a pulsed electric field, we succeeded in separating large DNA molecules with an electrophoretic microchip based on size exclusion chromatography (SEC), which was proposed in our previous study. The conditions of the pulsed electric field required to achieve the separation were determined by numerical analyses using our originally proposed separation model. From the numerical results, we succeeded in separating large DNA molecules (λ DNA and T4 DNA) within 1600 s, which was approximately half of that achieved under a direct electric field in our previous study. Our SEC-based electrophoresis microchip will be one of the effective tools to meet the growing demand of faster and more convenient separation of large DNA molecules, especially in the field of epidemiological research of infectious diseases.

The Skeletal Muscle Anabolic Response to Plant- versus Animal-Based Protein Consumption.

Science.gov (United States)

van Vliet, Stephan; Burd, Nicholas A; van Loon, Luc J C

2015-09-01

Clinical and consumer market interest is increasingly directed toward the use of plant-based proteins as dietary components aimed at preserving or increasing skeletal muscle mass. However, recent evidence suggests that the ingestion of the plant-based proteins in soy and wheat results in a lower muscle protein synthetic response when compared with several animal-based proteins. The possible lower anabolic properties of plant-based protein sources may be attributed to the lower digestibility of plant-based sources, in addition to greater splanchnic extraction and subsequent urea synthesis of plant protein-derived amino acids compared with animal-based proteins. The latter may be related to the relative lack of specific essential amino acids in plant- as opposed to animal-based proteins. Furthermore, most plant proteins have a relatively low leucine content, which may further reduce their anabolic properties when compared with animal proteins. However, few studies have actually assessed the postprandial muscle protein synthetic response to the ingestion of plant proteins, with soy and wheat protein being the primary sources studied. Despite the proposed lower anabolic properties of plant vs. animal proteins, various strategies may be applied to augment the anabolic properties of plant proteins. These may include the following: 1) fortification of plant-based protein sources with the amino acids methionine, lysine, and/or leucine; 2) selective breeding of plant sources to improve amino acid profiles; 3) consumption of greater amounts of plant-based protein sources; or 4) ingesting multiple protein sources to provide a more balanced amino acid profile. However, the efficacy of such dietary strategies on postprandial muscle protein synthesis remains to be studied. Future research comparing the anabolic properties of a variety of plant-based proteins should define the preferred protein sources to be used in nutritional interventions to support skeletal muscle mass gain

Sludge Water Characteristics Under Different Separation Methods from a Membrane Bioreactor

KAUST Repository

Wei, Chunhai

2013-11-22

The concept of sludge water was proposed to integrate the relative terminologies and its characteristics under different separation methods from a membrane bioreactor (MBR) were investigated in this study. Based on chemical oxygen demand (COD) and three-dimensional fluorescence excitation-emission matrix (F-EEM), and compared with the control (gravitational sedimentation), some suspended particulate organics or biopolymer clusters (mainly proteins) were released from sludge flocs into the supernatant after centrifugation under low to middle centrifugal forces (10-4000 g) and then aggregated into a pellet under high centrifugal forces (10000-20000 g). Filtration (1.2 μm glass fiber filter) produced sludge water with a lower biopolymers concentration than the control (gravitational sedimentation followed by filtration) due to cake layer formation during filtration. As for centrifugation followed by filtration, low to middle centrifugal forces did not significantly affect sludge water characteristics but high centrifugal forces reduced the concentrations of some proteins in sludge water from advanced analytical protocols including F-EEM and liquid chromatography with on-line organic carbon detection (LC-OCD), demonstrating a low to middle centrifugal force suitable for MBR sludge water separation. From LC-OCD, the main fractions of sludge water were humic substances and building blocks, low molecular weight neutrals and biopolymers (mainly proteins rather than polysaccharides). Supplemental materials are available for this article. Go to the publisher\\'s online edition of Separation Science and Technology to view the supplemental file. © 2013 Copyright Taylor and Francis Group, LLC.

Sludge Water Characteristics Under Different Separation Methods from a Membrane Bioreactor

KAUST Repository

Wei, Chunhai; Amy, Gary L.

2013-01-01

The concept of sludge water was proposed to integrate the relative terminologies and its characteristics under different separation methods from a membrane bioreactor (MBR) were investigated in this study. Based on chemical oxygen demand (COD) and three-dimensional fluorescence excitation-emission matrix (F-EEM), and compared with the control (gravitational sedimentation), some suspended particulate organics or biopolymer clusters (mainly proteins) were released from sludge flocs into the supernatant after centrifugation under low to middle centrifugal forces (10-4000 g) and then aggregated into a pellet under high centrifugal forces (10000-20000 g). Filtration (1.2 μm glass fiber filter) produced sludge water with a lower biopolymers concentration than the control (gravitational sedimentation followed by filtration) due to cake layer formation during filtration. As for centrifugation followed by filtration, low to middle centrifugal forces did not significantly affect sludge water characteristics but high centrifugal forces reduced the concentrations of some proteins in sludge water from advanced analytical protocols including F-EEM and liquid chromatography with on-line organic carbon detection (LC-OCD), demonstrating a low to middle centrifugal force suitable for MBR sludge water separation. From LC-OCD, the main fractions of sludge water were humic substances and building blocks, low molecular weight neutrals and biopolymers (mainly proteins rather than polysaccharides). Supplemental materials are available for this article. Go to the publisher's online edition of Separation Science and Technology to view the supplemental file. © 2013 Copyright Taylor and Francis Group, LLC.

Tröger’s Base Ladder Polymer for Membrane-Based Hydrocarbon Separation

KAUST Repository

Alhazmi, Abdulrahman

2017-01-01

The use of polymeric membranes for natural gas separation has rapidly increased during the past three decades, particularly for carbon dioxide separation from natural gas. Another valuable application is the separation of heavy hydrocarbons from

Chitosan-based delivery systems for protein therapeutics and antigens

NARCIS (Netherlands)

Amidi, M.; Mastrobattista, E.; Jiskoot, W.; Hennink, W.E.

Therapeutic peptides/proteins and protein-based antigens are chemically and structurally labile compounds, which are almost exclusively administered by parenteral injections. Recently, non-invasive mucosal routes have attracted interest for administration of these biotherapeutics. Chitosan-based

Immunomagnetic cell separation, imaging, and analysis using Captivate ferrofluids

Science.gov (United States)

Jones, Laurie; Beechem, Joseph M.

2002-05-01

We have developed applications of CaptivateTM ferrofluids, paramagnetic particles (approximately 200 nm diameter), for isolating and analyzing cell populations in combination with fluorescence-based techniques. Using a microscope-mounted magnetic yoke and sample insertion chamber, fluorescent images of magnetically captured cells were obtained in culture media, buffer, or whole blood, while non-magnetically labeled cells sedimented to the bottom of the chamber. We combined this immunomagnetic cell separation and imaging technique with fluorescent staining, spectroscopy, and analysis to evaluate cell surface receptor-containing subpopulations, live/dead cell ratios, apoptotic/dead cell ratios, etc. The acquired images were analyzed using multi-color parameters, as produced by nucleic acid staining, esterase activity, or antibody labeling. In addition, the immunomagnetically separated cell fractions were assessed through microplate analysis using the CyQUANT Cell Proliferation Assay. These methods should provide an inexpensive alternative to some flow cytometric measurements. The binding capacities of the streptavidin- labled Captivate ferrofluid (SA-FF) particles were determined to be 8.8 nmol biotin/mg SA-FF, using biotin-4- fluorescein, and > 106 cells/mg SA-FF, using several cell types labeled with biotinylated probes. For goat anti- mouse IgG-labeled ferrofluids (GAM-FF), binding capacities were established to be approximately 0.2 - 7.5 nmol protein/mg GAM-FF using fluorescent conjugates of antibodies, protein G, and protein A.

Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

Science.gov (United States)

Sikder, Md. Kabir Uddin; Stone, Kyle A.; Kumar, P. B. Sunil; Laradji, Mohamed

2014-01-01

We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells. PMID:25106608

S-Layer Protein-Based Biosensors

Directory of Open Access Journals (Sweden)

Bernhard Schuster

2018-04-01

Full Text Available The present paper highlights the application of bacterial surface (S- layer proteins as versatile components for the fabrication of biosensors. One technologically relevant feature of S-layer proteins is their ability to self-assemble on many surfaces and interfaces to form a crystalline two-dimensional (2D protein lattice. The S-layer lattice on the surface of a biosensor becomes part of the interface architecture linking the bioreceptor to the transducer interface, which may cause signal amplification. The S-layer lattice as ultrathin, highly porous structure with functional groups in a well-defined special distribution and orientation and an overall anti-fouling characteristics can significantly raise the limit in terms of variety and the ease of bioreceptor immobilization, compactness of bioreceptor molecule arrangement, sensitivity, specificity, and detection limit for many types of biosensors. The present paper discusses and summarizes examples for the successful implementation of S-layer lattices on biosensor surfaces in order to give a comprehensive overview on the application potential of these bioinspired S-layer protein-based biosensors.

S-Layer Protein-Based Biosensors.

Science.gov (United States)

Schuster, Bernhard

2018-04-11

The present paper highlights the application of bacterial surface (S-) layer proteins as versatile components for the fabrication of biosensors. One technologically relevant feature of S-layer proteins is their ability to self-assemble on many surfaces and interfaces to form a crystalline two-dimensional (2D) protein lattice. The S-layer lattice on the surface of a biosensor becomes part of the interface architecture linking the bioreceptor to the transducer interface, which may cause signal amplification. The S-layer lattice as ultrathin, highly porous structure with functional groups in a well-defined special distribution and orientation and an overall anti-fouling characteristics can significantly raise the limit in terms of variety and the ease of bioreceptor immobilization, compactness of bioreceptor molecule arrangement, sensitivity, specificity, and detection limit for many types of biosensors. The present paper discusses and summarizes examples for the successful implementation of S-layer lattices on biosensor surfaces in order to give a comprehensive overview on the application potential of these bioinspired S-layer protein-based biosensors.

Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes.

Directory of Open Access Journals (Sweden)

Jiawei Luo

Full Text Available Computational approaches aided by computer science have been used to predict essential proteins and are faster than expensive, time-consuming, laborious experimental approaches. However, the performance of such approaches is still poor, making practical applications of computational approaches difficult in some fields. Hence, the development of more suitable and efficient computing methods is necessary for identification of essential proteins.In this paper, we propose a new method for predicting essential proteins in a protein interaction network, local interaction density combined with protein complexes (LIDC, based on statistical analyses of essential proteins and protein complexes. First, we introduce a new local topological centrality, local interaction density (LID, of the yeast PPI network; second, we discuss a new integration strategy for multiple bioinformatics. The LIDC method was then developed through a combination of LID and protein complex information based on our new integration strategy. The purpose of LIDC is discovery of important features of essential proteins with their neighbors in real protein complexes, thereby improving the efficiency of identification.Experimental results based on three different PPI(protein-protein interaction networks of Saccharomyces cerevisiae and Escherichia coli showed that LIDC outperformed classical topological centrality measures and some recent combinational methods. Moreover, when predicting MIPS datasets, the better improvement of performance obtained by LIDC is over all nine reference methods (i.e., DC, BC, NC, LID, PeC, CoEWC, WDC, ION, and UC.LIDC is more effective for the prediction of essential proteins than other recently developed methods.

Citrate-based open-quotes Talspeakclose quotes actinide-lanthanide separation process

International Nuclear Information System (INIS)

Del Cul, G.D.; Toth, L.M.; Bond, W.D.

1997-01-01

Lanthanide elements are produced in relatively high yield by fission of 235 U. Almost all the lanthanide isotopes decay to stable nonradioactive lanthanide isotopes in a relatively short time. Consequently, it is highly advantageous to separate the relatively small actinide fraction from the relatively large quantities of lanthanide isotopes. The TALSPEAK process (Trivalent Actinide Lanthanide Separations by Phosphorus-reagent Extraction from Aqueous Complexes) is one of the few means available to separate the trivalent actinides from the lanthanides. Previous work based on the use of lactic or glycolic acid has shown deleterious effects of some impurity ions such as zirconium(IV), even at concentrations on the order of 10 -4 M. Other perceived problems were the need to maintain the pH and reagent concentrations within a narrow range and a significant solubility of the organic phase at high carboxylic acid concentrations. The authors' cold experiments showed that replacing the traditional extractants glycolic or lactic acid with citric acid eliminates or greatly reduces the deleterious effects produced by impurities such as zirconium. An extensive series of batch tests was done using a wide range of reagent concentrations at different pH values, temperatures, and contact times. The results demonstrated that the citrate-based TALSPEAK can tolerate appreciable changes in pH and reagent concentrations while maintaining an adequate lanthanide extraction. Experiments using a three-stage glass mixer-settler showed a good lanthanide extraction, appropriate phase disengagement, no appreciable deleterious effects due to the presence of impurities such as zirconium, excellent pH buffering, and no significant loss of organic phase

[Adsorption characteristics of proteins on membrane surface and effect of protein solution environment on permeation behavior of berberine].

Science.gov (United States)

Li, Yi-Qun; Xu, Li; Zhu, Hua-Xu; Tang, Zhi-Shu; Li, Bo; Pan, Yong-Lan; Yao, Wei-Wei; Fu, Ting-Ming; Guo, Li-Wei

2017-10-01

In order to explore the adsorption characteristics of proteins on the membrane surface and the effect of protein solution environment on the permeation behavior of berberine, berberine and proteins were used as the research object to prepare simulated solution. Low field NMR, static adsorption experiment and membrane separation experiment were used to study the interaction between the proteins and ceramic membrane or between the proteins and berberine. The static adsorption capacity of proteins, membrane relative flux, rejection rate of proteins, transmittance rate of berberine and the adsorption rate of proteins and berberine were used as the evaluation index. Meanwhile, the membrane resistance distribution, the particle size distribution and the scanning electron microscope (SEM) were determined to investigate the adsorption characteristics of proteins on ceramic membrane and the effect on membrane separation process of berberine. The results showed that the ceramic membrane could adsorb the proteins and the adsorption model was consistent with Langmuir adsorption model. In simulating the membrane separation process, proteins were the main factor to cause membrane fouling. However, when the concentration of proteins was 1 g•L⁻¹, the proteins had no significant effect on membrane separation process of berberine. Copyright© by the Chinese Pharmaceutical Association.

A fluorescent-based HPLC assay for quantification of cysteine and cysteamine adducts in Escherichia coli-derived proteins.

Science.gov (United States)

Soriano, Brian D; Tam, Lei-Ting T; Lu, Hsieng S; Valladares, Violeta G

2012-01-01

Recombinant proteins expressed in Escherichia coli are often produced as unfolded, inactive forms accumulated in inclusion bodies. Redox-coupled thiols are typically employed in the refolding process in order to catalyze the formation of correct disulfide bonds at maximal folding efficiency. These thiols and the recombinant proteins can form mixed disulfide bonds to generate thiol-protein adducts. In this work, we apply a fluorescent-based assay for the quantification of cysteine and cysteamine adducts as observed in E. coli-derived proteins. The thiols are released by reduction of the adducted protein, collected and labeled with a fluorescent reagent, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. The derivatized thiols are separated by reversed-phase HPLC and can be accurately quantified after method optimization. The estimated thiol content represents total amount of adducted forms present in the analyzed samples. The limit of quantification (LOQ) was established; specifically, the lowest amount of quantifiable cysteine adduction is 30 picograms and the lowest amount of quantifiable cysteamine adduction is 60 picograms. The assay is useful for quantification of adducts in final purified products as well as in-process samples from various purification steps. The assay indicates that the purification process accomplishes a decrease in cysteine adduction from 0.19 nmol adduct/nmol protein to 0.03 nmol adduct/nmol protein as well as a decrease in cysteamine adduction from 0.24 nmol adduct/nmol protein to 0.14 nmol adduct/nmol protein. Copyright © 2011. Published by Elsevier B.V.

Magnetic separation techniques in sample preparation for biological analysis: a review.

Science.gov (United States)

He, Jincan; Huang, Meiying; Wang, Dongmei; Zhang, Zhuomin; Li, Gongke

2014-12-01

Sample preparation is a fundamental and essential step in almost all the analytical procedures, especially for the analysis of complex samples like biological and environmental samples. In past decades, with advantages of superparamagnetic property, good biocompatibility and high binding capacity, functionalized magnetic materials have been widely applied in various processes of sample preparation for biological analysis. In this paper, the recent advancements of magnetic separation techniques based on magnetic materials in the field of sample preparation for biological analysis were reviewed. The strategy of magnetic separation techniques was summarized. The synthesis, stabilization and bio-functionalization of magnetic nanoparticles were reviewed in detail. Characterization of magnetic materials was also summarized. Moreover, the applications of magnetic separation techniques for the enrichment of protein, nucleic acid, cell, bioactive compound and immobilization of enzyme were described. Finally, the existed problems and possible trends of magnetic separation techniques for biological analysis in the future were proposed. Copyright © 2014 Elsevier B.V. All rights reserved.

Feature-based attentional modulation increases with stimulus separation in divided-attention tasks.

Science.gov (United States)

Sally, Sharon L; Vidnyánsky, Zoltán; Papathomas, Thomas V

2009-01-01

Attention modifies our visual experience by selecting certain aspects of a scene for further processing. It is therefore important to understand factors that govern the deployment of selective attention over the visual field. Both location and feature-specific mechanisms of attention have been identified and their modulatory effects can interact at a neural level (Treue and Martinez-Trujillo, 1999). The effects of spatial parameters on feature-based attentional modulation were examined for the feature dimensions of orientation, motion and color using three divided-attention tasks. Subjects performed concurrent discriminations of two briefly presented targets (Gabor patches) to the left and right of a central fixation point at eccentricities of +/-2.5 degrees , 5 degrees , 10 degrees and 15 degrees in the horizontal plane. Gabors were size-scaled to maintain consistent single-task performance across eccentricities. For all feature dimensions, the data show a linear increase in the attentional effects with target separation. In a control experiment, Gabors were presented on an isoeccentric viewing arc at 10 degrees and 15 degrees at the closest spatial separation (+/-2.5 degrees ) of the main experiment. Under these conditions, the effects of feature-based attentional effects were largely eliminated. Our results are consistent with the hypothesis that feature-based attention prioritizes the processing of attended features. Feature-based attentional mechanisms may have helped direct the attentional focus to the appropriate target locations at greater separations, whereas similar assistance may not have been necessary at closer target spacings. The results of the present study specify conditions under which dual-task performance benefits from sharing similar target features and may therefore help elucidate the processes by which feature-based attention operates.

A method based on a separation of variables in magnetohydrodynamics (MHD)

International Nuclear Information System (INIS)

Cessenat, M.; Genta, P.

1996-01-01

We use a method based on a separation of variables for solving a system of first order partial differential equations, in a very simple modelling of MHD. The method consists in introducing three unknown variables φ1, φ2, φ3 in addition of the time variable τ and then searching a solution which is separated with respect to φ1 and τ only. This is allowed by a very simple relation, called a 'metric separation equation', which governs the type of solutions with respect to time. The families of solutions for the system of equations thus obtained, correspond to a radial evolution of the fluid. Solving the MHD equations is then reduced to find the transverse component H Σ of the magnetic field on the unit sphere Σ by solving a non linear partial differential equation on Σ. Thus we generalize ideas due to Courant-Friedrichs and to Sedov on dimensional analysis and self-similar solutions. (authors)

Nanostructured Membranes Functionalized with Gold Nanoparticles for Separation and Recovery of Monoclonal Antibodies

KAUST Repository

Soldan, Giada

2017-11-01

The need of purified biomolecules, such as proteins or antibodies, has required the biopharmaceutical industries to look for new recovering solutions to reduce time and costs of bioseparations. In the last decade, the emergent field of membrane chromatography has gained attention as possible substituent of the common used protein A affinity chromatography for bioseparations. In this scenario, gold nanoparticles can be used as means for offering affinity, mainly because of their biocompatible and reversible binding behavior, together with their high surface area-to-volume ratio, which offers a large number of binding sites. This work introduces a new procedure for purification of monoclonal antibodies based on polymeric membranes functionalized with gold nanoparticles. This novel approach shortens the process of purification by promoting selective binding of antibodies, while separating a mixture of biomolecules during a filtration process. The effects of gold nanoparticles and the surrounding ligand on the proteins adsorption and filtration are investigated. The results confirm that the functionalization helps in inducing a selective binding, preventing the non-selective one, and it also improves the selectivity of the separation process.

Entropy-based automated classification of independent components separated from fMCG

International Nuclear Information System (INIS)

Comani, S; Srinivasan, V; Alleva, G; Romani, G L

2007-01-01

Fetal magnetocardiography (fMCG) is a noninvasive technique suitable for the prenatal diagnosis of the fetal heart function. Reliable fetal cardiac signals can be reconstructed from multi-channel fMCG recordings by means of independent component analysis (ICA). However, the identification of the separated components is usually accomplished by visual inspection. This paper discusses a novel automated system based on entropy estimators, namely approximate entropy (ApEn) and sample entropy (SampEn), for the classification of independent components (ICs). The system was validated on 40 fMCG datasets of normal fetuses with the gestational age ranging from 22 to 37 weeks. Both ApEn and SampEn were able to measure the stability and predictability of the physiological signals separated with ICA, and the entropy values of the three categories were significantly different at p <0.01. The system performances were compared with those of a method based on the analysis of the time and frequency content of the components. The outcomes of this study showed a superior performance of the entropy-based system, in particular for early gestation, with an overall ICs detection rate of 98.75% and 97.92% for ApEn and SampEn respectively, as against a value of 94.50% obtained with the time-frequency-based system. (note)

Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins.

Science.gov (United States)

Dzuricky, Michael; Roberts, Stefan; Chilkoti, Ashutosh

2018-05-01

A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.

Initial investigation of dietitian perception of plant-based protein quality.

Science.gov (United States)

Hughes, Glenna J; Kress, Kathleen S; Armbrecht, Eric S; Mukherjea, Ratna; Mattfeldt-Beman, Mildred

2014-07-01

Interest in plant-based diets is increasing, evidenced by scientific and regulatory recommendations, including Dietary Guidelines for Americans. Dietitians provide guidance in dietary protein selection but little is known about how familiar dietitians are with the quality of plant versus animal proteins or methods for measuring protein quality. Likewise, there is a need to explore their beliefs related to dietary recommendations. The aim of this study was to assess dietitians' perceptions of plant-based protein quality and to determine if these are affected by demographic factors such as age and dietary practice group (DPG) membership. This was a cross-sectional design using an online survey. The survey was sent to all members of the Missouri Dietetic Association. All completed surveys (136) were analyzed. The main outcome measures were responses to belief and knowledge questions about the protein quality of plant-based diets, along with demographic information including age and DPG membership. Descriptive statistics and frequencies were determined, and chi-square analysis was used to determine the associations between belief and knowledge responses and demographic characteristics. Responses to belief statements suggested a high level of support for plant-based diets. No associations were found between any of the belief questions and demographic factors. A majority of respondents were not familiar with protein quality determination methods that are currently recognized by global regulatory and advisory agencies. Potential barriers identified in shifting to a more plant-based diet were lack of interest and perceived difficulty. Knowledge among dietitians of plant-based protein quality in general, and methods of protein quality measurement more specifically, needs to be addressed to enhance their knowledge base for making dietary protein recommendations. Two potential avenues for training are university curricula and continuing education opportunities provided to

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

Directory of Open Access Journals (Sweden)

Ulf Hensen

Full Text Available Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.

Complete chromogen separation and analysis in double immunohistochemical stains using Photoshop-based image analysis.

Science.gov (United States)

Lehr, H A; van der Loos, C M; Teeling, P; Gown, A M

1999-01-01

Simultaneous detection of two different antigens on paraffin-embedded and frozen tissues can be accomplished by double immunohistochemistry. However, many double chromogen systems suffer from signal overlap, precluding definite signal quantification. To separate and quantitatively analyze the different chromogens, we imported images into a Macintosh computer using a CCD camera attached to a diagnostic microscope and used Photoshop software for the recognition, selection, and separation of colors. We show here that Photoshop-based image analysis allows complete separation of chromogens not only on the basis of their RGB spectral characteristics, but also on the basis of information concerning saturation, hue, and luminosity intrinsic to the digitized images. We demonstrate that Photoshop-based image analysis provides superior results compared to color separation using bandpass filters. Quantification of the individual chromogens is then provided by Photoshop using the Histogram command, which supplies information on the luminosity (corresponding to gray levels of black-and-white images) and on the number of pixels as a measure of spatial distribution. (J Histochem Cytochem 47:119-125, 1999)

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

Science.gov (United States)

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

2017-07-03

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

π-Extended triptycene-based material for capillary gas chromatographic separations.

Science.gov (United States)

Yang, Yinhui; Wang, Qinsi; Qi, Meiling; Huang, Xuebin

2017-10-02

Triptycene-based materials feature favorable physicochemical properties and unique molecular recognition ability that offer good potential as stationary phases for capillary gas chromatography (GC). Herein, we report the investigation of utilizing a π-extended triptycene material (denoted as TQPP) for GC separations. As a result, the TQPP capillary column exhibited high column efficiency of 4030 plates m -1 and high-resolution performance for a wide range of analytes, especially structural and positional isomers. Interestingly, the TQPP stationary phase showed unique shape selectivity for alkanes isomers and preferential retention for analytes with halogen atoms and H-bonding nature mainly through their halogen-bonding and H-bonding interactions. In addition, the TQPP column had good repeatability and reproducibility with the RSD values of 0.02-0.34% for run-to-run, 0.09-0.80% for day-to-day and 1.4-5.2% for column-to-column, respectively, and favorable thermal stability up to 280 °C. This work demonstrates the promising future of triptycene-based materials as a new class of stationary phases for GC separations. Copyright © 2017 Elsevier B.V. All rights reserved.

Sorbent application on the base of chitosan for radionuclides separation

International Nuclear Information System (INIS)

Pivarciova, L.

2016-01-01

Radioactive waste contains enormous amounts of radionuclides, which pollute the environment and can cause serious chemical and radiological toxicity threats to lower and higher living organism. Alternative process for the removal of heavy metal ions and radionuclides is sorption, which utilizes various certain natural materials of biological origin. Amino-polysaccharide-based sorbents e.g. chitosan represent suitable materials for binding of metal oxo-anion species because of numerous functional groups -OH and -NH_2 because of their suitable H-bond donor and acceptor sites. The sorbents on the base chitosan prepared through chemical modification were used for removal and separation certain radionuclides from aqueous media. The aim of this work was the study of physicochemical properties of prepared sorbents. The specific surface of sorbents was characterized with BET methods. Point of zero charge was identified with potentiometric titration. The size of particles and shape of sorbents were determined by scanning electron microscope. The sorption experiments for selected radionuclides were conducted under static and dynamic conditions. The effect of various parameters on the sorption "9"9"mTc, "6"0Co and the effect of pH on the separation of radionuclide mixture in the solution were studied. (author)

The microstructure and rheology of homogeneous and phase separated gelatine gels

NARCIS (Netherlands)

Ersch, C.; Linden, E. van der; Venema, P.; Martin, A.

2016-01-01

The gelation of gelatine in mixtures of gelatine (type A or type B) and globular proteins (Whey Protein Isolate (WPI), Whey Protein Aggregates (WPA) and Soy Protein Isolate (SPI)) was studied with a focus on their phase separation during gelation. Confocal laser scanning microscopy, visual

Protein-Based Urine Test Predicts Kidney Transplant Outcomes

Science.gov (United States)

... News Releases News Release Thursday, August 22, 2013 Protein-based urine test predicts kidney transplant outcomes NIH- ... supporting development of noninvasive tests. Levels of a protein in the urine of kidney transplant recipients can ...

A force-based protein biochip

Science.gov (United States)

Blank, K.; Mai, T.; Gilbert, I.; Schiffmann, S.; Rankl, J.; Zivin, R.; Tackney, C.; Nicolaus, T.; Spinnler, K.; Oesterhelt, F.; Benoit, M.; Clausen-Schaumann, H.; Gaub, H. E.

2003-09-01

A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.

Whole Protein Native Fitness Potentials

Science.gov (United States)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

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

Exploration of zwitterionic cellulose acetate antifouling ultrafiltration membrane for bovine serum albumin (BSA) separation.

Science.gov (United States)

Liu, Yang; Huang, Haitao; Huo, Pengfei; Gu, Jiyou

2017-06-01

This study focused on the preparation of a new kind of membrane material, zwitterionic cellulose acetate (ZCA), via a three-step procedure consist of oxidization, Schiff base and quaternary amination reaction, and the fabrication of antifouling ZCA ultrafiltration membrane by the non-solvent-induced phase separation method (NIPS). The morphologies, surface chemical structures and compositions of the obtained CA and ZCA membranes were thoroughly characterized by field emission scanning electron microscopy (FE-SEM) with energy dispersive X-ray (EDX) spectroscopy, Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), respectively. Meanwhile, the thermal stability, porosity and average pore size of two investigated membranes were also studied. As a result, the ZCA membrane displayed significantly improved hydrophilicity and water permeability compared with those of the reference CA membrane, despite a slight decrease in the protein rejection ratio. According to the cycle ultrafiltration performance of bovine serum albumin (BSA) solution and protein adsorption experiment, ZCA membrane exhibited better flux recovery property and fouling resistant ability, especially irreversible fouling resistant ability, suggesting superior antifouling performance. This new approach gives polymer-based membrane a long time life and excellent ultrafiltration performance, and seems promising for potential applications in the protein separation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-05-25

The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

Electrophoretic separation of proteins in space

Science.gov (United States)

Brown, R. K.

1976-01-01

Commercially available and synthetic wide range and short range ampholytes used in the isoelectric focusing of proteins was analyzed by ion exchange chromatography. A pH gradient over the pH range 3.8 to 11.0 was used to elute the ampholytes from a column of a sulfonated polystyrene resin. The wide range ampholytes were resolved into some 60 to 70 ninhydrin positive components. The recovery obtained with the method was quantitative. Acid short range ampholytes have approximately 35 components which elute readily from the ion exchange resin. Basic short range ampholytes gave about 50 components, most of which eluted at alkaline pH.

The microstructure and rheology of homogeneous and phase separated gelatine gels

NARCIS (Netherlands)

Ersch, Carsten; Linden, van der Erik; Venema, Paul; Martin, Anneke

2016-01-01

The gelation of gelatine in mixtures of gelatine (type A or type B) and globular proteins (Whey Protein Isolate (WPI), Whey Protein Aggregates (WPA) and Soy Protein Isolate (SPI)) was studied with a focus on their phase separation during gelation. Confocal laser scanning microscopy, visual

Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction.

Science.gov (United States)

Wang, Yijie; Qian, Xiaoning

2017-03-14

Intuitively, proteins in the same protein complexes should highly interact with each other but rarely interact with the other proteins in protein-protein interaction (PPI) networks. Surprisingly, many existing computational algorithms do not directly detect protein complexes based on both of these topological properties. Most of them, depending on mathematical definitions of either "modularity" or "conductance", have their own limitations: Modularity has the inherent resolution problem ignoring small protein complexes; and conductance characterizes the separability of complexes but fails to capture the interaction density within complexes. In this paper, we propose a two-step algorithm FLCD (Finding Low-Conductance sets with Dense interactions) to predict overlapping protein complexes with the desired topological structure, which is densely connected inside and well separated from the rest of the networks. First, FLCD detects well-separated subnetworks based on approximating a potential low-conductance set through a personalized PageRank vector from a protein and then solving a mixed integer programming (MIP) problem to find the minimum-conductance set within the identified low-conductance set. At the second step, the densely connected parts in those subnetworks are discovered as the protein complexes by solving another MIP problem that aims to find the dense subnetwork in the minimum-conductance set. Experiments on four large-scale yeast PPI networks from different public databases demonstrate that the complexes predicted by FLCD have better correspondence with the yeast protein complex gold standards than other three state-of-the-art algorithms (ClusterONE, LinkComm, and SR-MCL). Additionally, results of FLCD show higher biological relevance with respect to Gene Ontology (GO) terms by GO enrichment analysis.

Computational Screening of MOF-Based Mixed Matrix Membranes for CO2/N2 Separations

Directory of Open Access Journals (Sweden)

Zeynep Sumer

2016-01-01

Full Text Available Atomically detailed simulations were used to examine CO2/N2 separation potential of metal organic framework- (MOF- based mixed matrix membranes (MMMs in this study. Gas permeability and selectivity of 700 new MMMs composed of 70 different MOFs and 10 different polymers were calculated for CO2/N2 separation. This is the largest number of MOF-based MMMs for which computational screening is done to date. Selecting the appropriate MOFs as filler particles in polymers resulted in MMMs that have higher CO2/N2 selectivities and higher CO2 permeabilities compared to pure polymer membranes. We showed that, for polymers that have low CO2 permeabilities but high CO2 selectivities, the identity of the MOF used as filler is not important. All MOFs enhanced the CO2 permeabilities of this type of polymers without changing their selectivities. Several MOF-based MMMs were identified to exceed the upper bound established for polymers. The methods we introduced in this study will create many opportunities to select the MOF/polymer combinations with useful properties for CO2 separation applications.

Magnetic separations: From steel plants to biotechnology

Energy Technology Data Exchange (ETDEWEB)

Cafer T. Yavuz; Arjun Prakash; J.T. Mayo; Vicki L. Colvin [Rice University, Houston, TX (United States). Department of Chemistry

2009-05-15

Magnetic separations have for decades been essential processes in diverse industries ranging from steel production to coal desulfurization. In such settings magnetic fields are used in continuous flow processes as filters to remove magnetic impurities. High gradient magnetic separation (HGMS) has found even broader use in wastewater treatment and food processing. Batch scale magnetic separations are also relevant in industry, particularly biotechnology where fixed magnetic separators are used to purify complex mixtures for protein isolation, cell separation, drug delivery, and biocatalysis. In this review, we introduce the basic concepts behind magnetic separations and summarize a few examples of its large scale application. HGMS systems and batch systems for magnetic separations have been developed largely in parallel by different communities. However, in this work we compare and contrast each approach so that investigators can approach both key areas. Finally, we discuss how new advances in magnetic materials, particularly on the nanoscale, as well as magnetic filter design offer new opportunities for industries that have challenging separation problems.

Assessment of Carbon- and Metal-Based Nanoparticle DNA Damage with Microfluidic Electrophoretic Separation Technology.

Science.gov (United States)

Schrand, Amanda M; Powell, Thomas; Robertson, Tiffany; Hussain, Saber M

2015-02-01

In this study, we examined the feasibility of extracting DNA from whole cell lysates exposed to nanoparticles using two different methodologies for evaluation of fragmentation with microfluidic electrophoretic separation. Human lung macrophages were exposed to five different carbon- and metal-based nanoparticles at two different time points (2 h, 24 h) and two different doses (5 µg/ml, 100 µg/ml). The primary difference in the banding patterns after 2 h of nanoparticle exposure is more DNA fragmentation at the higher NP concentration when examining cells exposed to nanoparticles of the same composition. However, higher doses of carbon and silver nanoparticles at both short and long dosing periods can contribute to erroneous or incomplete data with this technique. Also comparing DNA isolation methodologies, we recommend the centrifugation extraction technique, which provides more consistent banding patterns in the control samples compared to the spooling technique. Here we demonstrate that multi-walled carbon nanotubes, 15 nm silver nanoparticles and the positive control cadmium oxide cause similar DNA fragmentation at the short time point of 2 h with the centrifugation extraction technique. Therefore, the results of these studies contribute to elucidating the relationship between nanoparticle physicochemical properties and DNA fragmentation results while providing the pros and cons of altering the DNA isolation methodology. Overall, this technique provides a high throughput way to analyze subcellular alterations in DNA profiles of cells exposed to nanomaterials to aid in understanding the consequences of exposure and mechanistic effects. Future studies in microfluidic electrophoretic separation technologies should be investigated to determine the utility of protein or other assays applicable to cellular systems exposed to nanoparticles.

Soft inertial microfluidics for high throughput separation of bacteria from human blood cells

Energy Technology Data Exchange (ETDEWEB)

Wu, Zhigang; Willing, Ben; Bjerketorp, Joakim; Jansson, Janet K.; Hjort, Klas

2009-01-05

We developed a new approach to separate bacteria from human blood cells based on soft inertial force induced migration with flow defined curved and focused sample flow inside a microfluidic device. This approach relies on a combination of an asymmetrical sheath flow and proper channel geometry to generate a soft inertial force on the sample fluid in the curved and focused sample flow segment to deflect larger particles away while the smaller ones are kept on or near the original flow streamline. The curved and focused sample flow and inertial effect were visualized and verified using a fluorescent dye primed in the device. First the particle behavior was studied in detail using 9.9 and 1.0 {micro}m particles with a polymer-based prototype. The prototype device is compact with an active size of 3 mm{sup 2}. The soft inertial effect and deflection distance were proportional to the fluid Reynolds number (Re) and particle Reynolds number (Re{sub p}), respectively. We successfully demonstrated separation of bacteria (Escherichia coli) from human red blood cells at high cell concentrations (above 10{sup 8}/mL), using a sample flow rate of up to 18 {micro}L/min. This resulted in at least a 300-fold enrichment of bacteria at a wide range of flow rates with a controlled flow spreading. The separated cells were proven to be viable. Proteins from fractions before and after cell separation were analyzed by gel electrophoresis and staining to verify the removal of red blood cell proteins from the bacterial cell fraction. This novel microfluidic process is robust, reproducible, simple to perform, and has a high throughput compared to other cell sorting systems. Microfluidic systems based on these principles could easily be manufactured for clinical laboratory and biomedical applications.

Preliminary study on chicken feather protein-based wood adhesives

Science.gov (United States)

Zehui Jiang; Daochun Qin; Chung-Yun Hse; Monlin Kuo; Zhaohui Luo; Ge Wang; Yan Yu

2008-01-01

The objective of this preliminary study was to partially replace phenol in the synthesis of phenol-formaldehyde resin with feather protein. Feather protein–based resins, which contained one part feather protein and two parts phenol, were formulated under the conditions of two feather protein hydrolysis methods (with and without presence of phenol during...

Structural determination of intact proteins using mass spectrometry

Science.gov (United States)

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

A genetically modified protein-based hydrogel for 3D culture of AD293 cells.

Directory of Open Access Journals (Sweden)

Xiao Du

Full Text Available Hydrogels have strong application prospects for drug delivery, tissue engineering and cell therapy because of their excellent biocompatibility and abundant availability as scaffolds for drugs and cells. In this study, we created hybrid hydrogels based on a genetically modified tax interactive protein-1 (TIP1 by introducing two or four cysteine residues in the primary structure of TIP1. The introduced cysteine residues were crosslinked with a four-armed poly (ethylene glycol having their arm ends capped with maleimide residues (4-armed-PEG-Mal to form hydrogels. In one form of the genetically modification, we incorporated a peptide sequence 'GRGDSP' to introduce bioactivity to the protein, and the resultant hydrogel could provide an excellent environment for a three dimensional cell culture of AD293 cells. The AD293 cells continued to divide and displayed a polyhedron or spindle-shape during the 3-day culture period. Besides, AD293 cells could be easily separated from the cell-gel constructs for future large-scale culture after being cultured for 3 days and treating hydrogel with trypsinase. This work significantly expands the toolbox of recombinant proteins for hydrogel formation, and we believe that our hydrogel will be of considerable interest to those working in cell therapy and controlled drug delivery.

Sequence-based prediction of protein protein interaction using a deep-learning algorithm.

Science.gov (United States)

Sun, Tanlin; Zhou, Bo; Lai, Luhua; Pei, Jianfeng

2017-05-25

Protein-protein interactions (PPIs) are critical for many biological processes. It is therefore important to develop accurate high-throughput methods for identifying PPI to better understand protein function, disease occurrence, and therapy design. Though various computational methods for predicting PPI have been developed, their robustness for prediction with external datasets is unknown. Deep-learning algorithms have achieved successful results in diverse areas, but their effectiveness for PPI prediction has not been tested. We used a stacked autoencoder, a type of deep-learning algorithm, to study the sequence-based PPI prediction. The best model achieved an average accuracy of 97.19% with 10-fold cross-validation. The prediction accuracies for various external datasets ranged from 87.99% to 99.21%, which are superior to those achieved with previous methods. To our knowledge, this research is the first to apply a deep-learning algorithm to sequence-based PPI prediction, and the results demonstrate its potential in this field.

Phase separation in lipid bilayers triggered by low pH

International Nuclear Information System (INIS)

Suresh, Swetha; Edwardson, J. Michael

2010-01-01

Research highlights: → Lipid bilayers have been imaged by atomic force microscopy (AFM). → At pH 5 phase separation occurs in lipid bilayers containing mixed acyl chains. → Phase separation does not occur when lipids have only unsaturated chains. → Phase separation might drive protein clustering during endocytosis. -- Abstract: Endocytosis involves the capture of membrane from the cell surface in the form of vesicles, which become rapidly acidified to about pH 5. Here we show using atomic force microscopy (AFM) imaging that this degree of acidification triggers phase separation in lipid bilayers containing mixed acyl chains (e.g. palmitoyl/oleoyl) or complex mixtures (e.g. total brain extract) but not in bilayers containing only lipids with unsaturated chains (e.g. dioleoyl). Since mixed-chain lipids are major constituents of the outer leaflet of the plasma membrane, the type of phase separation reported here might support protein clustering and signaling during endocytosis.

Synthetic Polymer Affinity Ligand for Bacillus thuringiensis ( Bt) Cry1Ab/Ac Protein: The Use of Biomimicry Based on the Bt Protein-Insect Receptor Binding Mechanism.

Science.gov (United States)

Liu, Mingming; Huang, Rong; Weisman, Adam; Yu, Xiaoyang; Lee, Shih-Hui; Chen, Yalu; Huang, Chao; Hu, Senhua; Chen, Xiuhua; Tan, Wenfeng; Liu, Fan; Chen, Hao; Shea, Kenneth J

2018-05-24

We report a novel strategy for creating abiotic Bacillus thuringiensis ( Bt) protein affinity ligands by biomimicry of the recognition process that takes place between Bt Cry1Ab/Ac proteins and insect receptor cadherin-like Bt-R 1 proteins. Guided by this strategy, a library of synthetic polymer nanoparticles (NPs) was prepared and screened for binding to three epitopes 280 FRGSAQGIEGS 290 , 368 RRPFNIGINNQQ 379 and 436 FRSGFSNSSVSIIR 449 located in loop α8, loop 2 and loop 3 of domain II of Bt Cry1Ab/Ac proteins. A negatively charged and hydrophilic nanoparticle (NP12) was found to have high affinity to one of the epitopes, 368 RRPFNIGINNQQ 379 . This same NP also had specific binding ability to both Bt Cry1Ab and Bt Cry1Ac, proteins that share the same epitope, but very low affinity to Bt Cry2A, Bt Cry1C and Bt Cry1F closely related proteins that lack epitope homology. To locate possible NP- Bt Cry1Ab/Ac interaction sites, NP12 was used as a competitive inhibitor to block the binding of 865 NITIHITDTNNK 876 , a specific recognition site in insect receptor Bt-R 1 , to 368 RRPFNIGINNQQ 379 . The inhibition by NP12 reached as high as 84%, indicating that NP12 binds to Bt Cry1Ab/Ac proteins mainly via 368 RRPFNIGINNQQ 379 . This epitope region was then utilized as a "target" or "bait" for the separation and concentration of Bt Cry1Ac protein from the extract of transgenic Bt cotton leaves by NP12. This strategy, based on the antigen-receptor recognition mechanism, can be extended to other biotoxins and pathogen proteins when designing biomimic alternatives to natural protein affinity ligands.

Protein Stable Isotope Fingerprinting (P-SIF): Multidimensional Protein Chromatography Coupled to Stable Isotope-Ratio Mass Spectrometry

Science.gov (United States)

Pearson, A.; Bovee, R. J.; Mohr, W.; Tang, T.

2012-12-01

As metagenomics increases our insight into microbial community diversity and metabolic potential, new approaches are required to determine the biogeochemical expression of this potential within ecosystems. Because stable isotopic analysis of the major bioactive elements (C, N) has been used historically to map flows of substrates and energy among macroscopic food webs, similar principles may apply to microbes. To address this challenge, we have developed a new analytical approach called Protein Stable Isotope Fingerprinting (P-SIF). P-SIF generates natural stable isotopic fingerprints of microbial individual or community proteomes. The main advantage of P-SIF is the potential to bridge the gap between diversity and function, thereby providing a window into the "black box" of environmental microbiology and helping to decipher the roles of uncultivated species. Our method implements a three-way, orthogonal scheme to separate mixtures of whole proteins into subfractions dominated by single or closely-related proteins. Protein extracts first are isoelectrically focused in a gel-free technique that yields 12 fractions separated over a gradient of pH 3-10. Each fraction then is separated by size-exclusion chromatography into 20 pools, ranging from >100kD to ~10kD. Finally, each of these pools is subjected to HPLC and collected in 40 time-slices based on protein hydrophobicity. Theoretical calculation reveals that the true chromatographic resolution of the total scheme is 5000, somewhat less than the 9600 resulting fractions. High-yielding fractions are subjected to δ13C analysis by spooling-wire microcombustion irMS (SWiM-irMS) optimized for samples containing 1-5 nmol carbon. Here we will present the method, results for a variety of pure cultures, and preliminary data for a sample of mixed environmental proteins. The data show the promise of this method for unraveling the metabolic complexity hidden within microbial communities.

Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling

Energy Technology Data Exchange (ETDEWEB)

Smith, Jordan N.; Tyrrell, Kimberly J.; Hansen, Joshua R.; Thomas, Dennis G.; Murphree, Taylor A.; Shukla, Anil K.; Luders, Teresa; Madden, James M.; Li, Yunying; Wright, Aaron T.; Piehowski, Paul D.

2017-12-06

Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine (“heavy”) feed for 23 days to label proteins. During the chase, feed was changed to an unlabeled equivalent feed (“light”), and blood was repeatedly sampled from rats over 10 time points for 28 days. Plasma samples were digested with trypsin, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used to identify peptides and proteins, and quantify heavy:light lysine ratios. A system of ordinary differential equations was used to calculate protein turnover rates. Using this approach, 273 proteins were identified, and turnover rates were quantified for 157 plasma proteins with half-lives ranging 0.3-103 days. For the ~70 most abundant proteins, variability in turnover rates among rats was low (median coefficient of variation: 0.09). Activity-based protein profiling was applied to pooled plasma samples to enrich serine hydrolases using a fluorophosphonate (FP2) activity-based probe. This enrichment resulted in turnover rates for an additional 17 proteins. This study is the first to measure global plasma protein turnover rates in rats in vivo, measure variability of protein turnover rates in any animal model, and utilize activity-based protein profiling for enhancing measurements of targeted, low-abundant proteins, such as those commonly used as biomarkers. Measured protein turnover rates will be important for understanding of the role of protein turnover in cellular and organism health as well as increasing the utility of protein

[PHEMA/PEI]–Cu(II) based immobilized metal affinity chromatography cryogels: Application on the separation of IgG from human plasma

Energy Technology Data Exchange (ETDEWEB)

Bakhshpour, Monireh; Derazshamshir, Ali; Bereli, Nilay [Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara (Turkey); Elkak, Assem [Laboratory of “Valorisation des Ressources Naturelles et Produits de Santé (VRNPS)”, Doctoral School of Sciences and Technology, Lebanese University, Rafic Hariri University Campus, Hadath (Lebanon); Denizli, Adil, E-mail: denizli@hacettepe.edu [Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara (Turkey)

2016-04-01

The immobilized metal-affinity chromatography (IMAC) has gained significant interest as a widespread separation and purification tool for therapeutic proteins, nucleic acids and other biological molecules. The enormous potential of IMAC for proteins with natural surface exposed-histidine residues and for recombinant proteins with histidine clusters. Cryogels as monolithic materials have recently been proposed as promising chromatographic adsorbents for the separation of biomolecules in downstream processing. In the present study, IMAC cryogels have been synthesized and utilized for the adsorption and separation of immunoglobulin G (IgG) from IgG solution and whole human plasma. For this purpose, Cu(II)-ions were coupled to poly(hydroxyethyl methacrylate) PHEMA using poly(ethylene imine) (PEI) as the chelating ligand. In this study the cryogels formation optimized by the varied proportion of PEI from 1% to 15% along with different amounts of Cu (II) as chelating metal. The prepared cryogels were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and thermogravimetric analysis. The [PHEMA/PEI]–Cu(II) cryogels were assayed for their capability to bind the human IgG from aqueous solutions. The IMAC cryogels were found to have high affinity toward human IgG. The adsorption of human IgG was investigated onto the PHEMA/PEI cryogels with (10% PEI) and the concentration of Cu (II) varied as 10, 50, 100 and 150 mg/L. The separation of human IgG was achieved in one purification step at pH 7.4. The maximum adsorption capacity was observed at the [PHEMA/PEI]–Cu(II) (10% PEI) with 72.28 mg/g of human IgG. The purification efficiency and human IgG purity were investigated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). - Highlights: • Cu(II)-ions were coupled to PHEMA using PEI as the chelating ligand. • Cu(II) chelated [PHEMA/PEI] cryogels for IgG separation were produced. • Maximum IgG adsorption capacity

[PHEMA/PEI]–Cu(II) based immobilized metal affinity chromatography cryogels: Application on the separation of IgG from human plasma

International Nuclear Information System (INIS)

Bakhshpour, Monireh; Derazshamshir, Ali; Bereli, Nilay; Elkak, Assem; Denizli, Adil

2016-01-01

The immobilized metal-affinity chromatography (IMAC) has gained significant interest as a widespread separation and purification tool for therapeutic proteins, nucleic acids and other biological molecules. The enormous potential of IMAC for proteins with natural surface exposed-histidine residues and for recombinant proteins with histidine clusters. Cryogels as monolithic materials have recently been proposed as promising chromatographic adsorbents for the separation of biomolecules in downstream processing. In the present study, IMAC cryogels have been synthesized and utilized for the adsorption and separation of immunoglobulin G (IgG) from IgG solution and whole human plasma. For this purpose, Cu(II)-ions were coupled to poly(hydroxyethyl methacrylate) PHEMA using poly(ethylene imine) (PEI) as the chelating ligand. In this study the cryogels formation optimized by the varied proportion of PEI from 1% to 15% along with different amounts of Cu (II) as chelating metal. The prepared cryogels were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and thermogravimetric analysis. The [PHEMA/PEI]–Cu(II) cryogels were assayed for their capability to bind the human IgG from aqueous solutions. The IMAC cryogels were found to have high affinity toward human IgG. The adsorption of human IgG was investigated onto the PHEMA/PEI cryogels with (10% PEI) and the concentration of Cu (II) varied as 10, 50, 100 and 150 mg/L. The separation of human IgG was achieved in one purification step at pH 7.4. The maximum adsorption capacity was observed at the [PHEMA/PEI]–Cu(II) (10% PEI) with 72.28 mg/g of human IgG. The purification efficiency and human IgG purity were investigated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). - Highlights: • Cu(II)-ions were coupled to PHEMA using PEI as the chelating ligand. • Cu(II) chelated [PHEMA/PEI] cryogels for IgG separation were produced. • Maximum IgG adsorption capacity

Automation of column-based radiochemical separations. A comparison of fluidic, robotic, and hybrid architectures

Energy Technology Data Exchange (ETDEWEB)

Grate, J.W.; O' Hara, M.J.; Farawila, A.F.; Ozanich, R.M.; Owsley, S.L. [Pacific Northwest National Laboratory, Richland, WA (United States)

2011-07-01

Two automated systems have been developed to perform column-based radiochemical separation procedures. These new systems are compared with past fluidic column separation architectures, with emphasis on using disposable components so that no sample contacts any surface that any other sample has contacted, and setting up samples and columns in parallel for subsequent automated processing. In the first new approach, a general purpose liquid handling robot has been modified and programmed to perform anion exchange separations using 2 mL bed columns in 6 mL plastic disposable column bodies. In the second new approach, a fluidic system has been developed to deliver clean reagents through disposable manual valves to six disposable columns, with a mechanized fraction collector that positions one of four rows of six vials below the columns. The samples are delivered to each column via a manual 3-port disposable valve from disposable syringes. This second approach, a hybrid of fluidic and mechanized components, is a simpler more efficient approach for performing anion exchange procedures for the recovery and purification of plutonium from samples. The automation architectures described can also be adapted to column-based extraction chromatography separations. (orig.)

Fluorescent sensors based on bacterial fusion proteins

International Nuclear Information System (INIS)

Mateu, Batirtze Prats; Pum, Dietmar; Sleytr, Uwe B; Toca-Herrera, José L; Kainz, Birgit

2014-01-01

Fluorescence proteins are widely used as markers for biomedical and technological purposes. Therefore, the aim of this project was to create a fluorescent sensor, based in the green and cyan fluorescent protein, using bacterial S-layers proteins as scaffold for the fluorescent tag. We report the cloning, expression and purification of three S-layer fluorescent proteins: SgsE-EGFP, SgsE-ECFP and SgsE-13aa-ECFP, this last containing a 13-amino acid rigid linker. The pH dependence of the fluorescence intensity of the S-layer fusion proteins, monitored by fluorescence spectroscopy, showed that the ECFP tag was more stable than EGFP. Furthermore, the fluorescent fusion proteins were reassembled on silica particles modified with cationic and anionic polyelectrolytes. Zeta potential measurements confirmed the particle coatings and indicated their colloidal stability. Flow cytometry and fluorescence microscopy showed that the fluorescence of the fusion proteins was pH dependent and sensitive to the underlying polyelectrolyte coating. This might suggest that the fluorescent tag is not completely exposed to the bulk media as an independent moiety. Finally, it was found out that viscosity enhanced the fluorescence intensity of the three fluorescent S-layer proteins. (paper)

Meals based on vegetable protein sources (beans and peas) are more satiating than meals based on animal protein sources (veal and pork) - a randomized cross-over meal test study

DEFF Research Database (Denmark)

Kristensen, Marlene Dahlwad; Bendsen, Nathalie Tommerup; Christensen, Sheena M

2016-01-01

BACKGROUND: Recent nutrition recommendations advocate a reduction in protein from animal sources (pork, beef) because of environmental concerns. Instead, protein from vegetable sources (beans, peas) should be increased. However, little is known about the effect of these vegetable protein sources...... on appetite regulation. OBJECTIVE: To examine whether meals based on vegetable protein sources (beans/peas) are comparable to meals based on animal protein sources (veal/pork) regarding meal-induced appetite sensations. DESIGN: In total, 43 healthy, normal-weight, young men completed this randomized, double......-Legume compared to HP-Meat or LP-Legume (pVegetable-based meals (beans/peas) influenced appetite sensations favorably compared to animal-based meals (pork/veal) with similar energy and protein content, but lower fiber content. Interestingly, a vegetable-based meal with low protein content...

DNA & Protein detection based on microbead agglutination

KAUST Repository

Kodzius, Rimantas; Castro, David; Foulds, Ian G.; Parameswaran, Ash M.; Sumanpreet, K. Chhina

2012-01-01

the macroscopic observation. Agglutination-based tests are most often used to explore the antibody-antigen reactions. Agglutination has been used for mode protein assays using a biotin/streptavidin two-component system, as well as a hybridization based two

Nitrogen Trifluoride-Based Fluoride- Volatility Separations Process: Initial Studies

Energy Technology Data Exchange (ETDEWEB)

McNamara, Bruce K.; Scheele, Randall D.; Casella, Andrew M.; Kozelisky, Anne E.

2011-09-28

This document describes the results of our investigations on the potential use of nitrogen trifluoride as the fluorinating and oxidizing agent in fluoride volatility-based used nuclear fuel reprocessing. The conceptual process uses differences in reaction temperatures between nitrogen trifluoride and fuel constituents that produce volatile fluorides to achieve separations and recover valuable constituents. We provide results from our thermodynamic evaluations, thermo-analytical experiments, kinetic models, and provide a preliminary process flowsheet. The evaluations found that nitrogen trifluoride can effectively produce volatile fluorides at different temperatures dependent on the fuel constituent.

Cellulose acetate-based molecularly imprinted polymeric membrane for separation of vanillin and o-vanillin

OpenAIRE

Zhang,Chunjing; Zhong,Shian; Yang,Zhengpeng

2008-01-01

Cellulose acetate-based molecularly imprinted polymeric membranes were prepared using vanillin as template molecule. The microscopic structure of the resultant polymeric membranes was characterized by SEM and FTIR spectroscopy, and the selective binding properties and separation capacity of the membranes for vanillin and o-vanillin were tested with binding experiments and separate experiments, respectively. The results showed that the vanillin-imprinted polymeric membranes displayed higher bi...

Clinical applications of MS-based protein quantification.

Science.gov (United States)

Sabbagh, Bassel; Mindt, Sonani; Neumaier, Michael; Findeisen, Peter

2016-04-01

Mass spectrometry-based assays are increasingly important in clinical laboratory medicine and nowadays are already commonly used in several areas of routine diagnostics. These include therapeutic drug monitoring, toxicology, endocrinology, pediatrics, and microbiology. Accordingly, some of the most common analyses are therapeutic drug monitoring of immunosuppressants, vitamin D, steroids, newborn screening, and bacterial identification. However, MS-based quantification of peptides and proteins for routine diagnostic use is rather rare up to now despite excellent analytical specificity and good sensitivity. Here, we want to give an overview over current fit-for-purpose assays for MS-based protein quantification. Advantages as well as challenges of this approach will be discussed with focus on feasibility for routine diagnostic use. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

Science.gov (United States)

Zhou, Hufeng; Rezaei, Javad; Hugo, Willy; Gao, Shangzhi; Jin, Jingjing; Fan, Mengyuan; Yong, Chern-Han; Wozniak, Michal; Wong, Limsoon

2013-01-01

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some

Blind Separation of Two Users Based on User Delays and Optimal Pulse-Shape Design

Directory of Open Access Journals (Sweden)

Poor HVincent

2010-01-01

Full Text Available A wireless network is considered, in which two spatially distributed users transmit narrow-band signals simultaneously over the same channel using the same power. User separation is achieved by oversampling the received signal and formulating a virtual multiple-input multiple-output (MIMO system based on the resulting polyphase components. Because of oversampling, high correlations can occur between the columns of the virtual MIMO system matrix which can be detrimental to user separation. A novel pulse-shape waveform design is proposed that results in low correlation between the columns of the system matrix, while it exploits all available bandwidth as dictated by a spectral mask. It is also shown that the use of successive interference cancelation in combination with blind source separation further improves the separation performance.

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy.

Science.gov (United States)

Shashilov, Victor A; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K

2010-09-01

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Electrospun fish protein fibers as a biopolymer-based carrier – implications for oral protein delivery

DEFF Research Database (Denmark)

Boutrup Stephansen, Karen; García-Díaz, María; Jessen, Flemming

2014-01-01

Purpose: Protein-based electrospun fibers have emerged as novel nanostructured materials for tissue engineering and drug delivery due to their unique structural characteristics, biocompatibility and biodegradability. The aim of this study was to explore the use of electrospun fibers based on fish...... sarcoplasmic proteins as an oral delivery platform for biopharmaceuticals, using insulin as a model protein. Methods: Fish sarcoplasmic proteins (FSP) were isolated from fresh cod and electrospun into nanomicrofibers using insulin as a model payload. The morphology of FSP fibers was characterized using...... differentiated Caco-2 cell monolayers was followed by RP-HPLC and ELISA, and the transepithelial electrical resistance (TEER) was measured before and after the experiment. Cell viability was assessed by the MTS/PMS assay. Results: Insulin was encapsulated in the electrospun FSP fibers with high efficiency, high...

Separation of replication and transcription domains in nucleoli.

Science.gov (United States)

Smirnov, E; Borkovec, J; Kováčik, L; Svidenská, S; Schröfel, A; Skalníková, M; Švindrych, Z; Křížek, P; Ovesný, M; Hagen, G M; Juda, P; Michalová, K; Cardoso, M C; Cmarko, D; Raška, I

2014-12-01

In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation. Copyright © 2014 Elsevier Inc. All rights reserved.

Meals based on vegetable protein sources (beans and peas) are more satiating than meals based on animal protein sources (veal and pork) – a randomized cross-over meal test study

Science.gov (United States)

Kristensen, Marlene D.; Bendsen, Nathalie T.; Christensen, Sheena M.; Astrup, Arne; Raben, Anne

2016-01-01

Background Recent nutrition recommendations advocate a reduction in protein from animal sources (pork, beef) because of environmental concerns. Instead, protein from vegetable sources (beans, peas) should be increased. However, little is known about the effect of these vegetable protein sources on appetite regulation. Objective To examine whether meals based on vegetable protein sources (beans/peas) are comparable to meals based on animal protein sources (veal/pork) regarding meal-induced appetite sensations. Design In total, 43 healthy, normal-weight, young men completed this randomized, double-blind, placebo-controlled, three-way, cross-over meal test. The meals (all 3.5 MJ, 28 energy-% (E%) fat) were either high protein based on veal and pork meat, HP-Meat (19 E% protein, 53 E% carbohydrate, 6 g fiber/100 g); high protein based on legumes (beans and peas), HP-Legume (19 E% protein, 53 E% carbohydrate, 25 g fiber/100 g); or low-protein based on legumes, LP-Legume (9 E% protein, 62 E% carbohydrate, 10 g fiber/100 g). Subjective appetite sensations were recorded at baseline and every half hour using visual analog scales until the ad libitum meal 3 h after the test meal. Repeated measurements analyses and summary analyses were performed using ANCOVA (SAS). Results HP-Legume induced lower composite appetite score, hunger, prospective food consumption, and higher fullness compared to HP-Meat and LP-Legume (ppeas) influenced appetite sensations favorably compared to animal-based meals (pork/veal) with similar energy and protein content, but lower fiber content. Interestingly, a vegetable-based meal with low protein content was as satiating and palatable as an animal-based meal with high protein content. PMID:27765144

ZifBASE: a database of zinc finger proteins and associated resources

Directory of Open Access Journals (Sweden)

Punetha Ankita

2009-09-01

Full Text Available Abstract Background Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence. Description ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones, the number of finger units in each of the zinc finger proteins (with multiple fingers, the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

Science.gov (United States)

Zeke, András; Misheva, Mariya

2016-01-01

SUMMARY The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states. PMID:27466283

Gene ontology based transfer learning for protein subcellular localization

Directory of Open Access Journals (Sweden)

Zhou Shuigeng

2011-02-01

Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

Phylogeny-dominant classification of J-proteins in Arabidopsis thaliana and Brassica oleracea.

Science.gov (United States)

Zhang, Bin; Qiu, Han-Lin; Qu, Dong-Hai; Ruan, Ying; Chen, Dong-Hong

2018-04-05

Hsp40s or DnaJ/J-proteins are evolutionarily conserved in all organisms as co-chaperones of molecular chaperone HSP70s that mainly participate in maintaining cellular protein homeostasis, such as protein folding, assembly, stabilization, and translocation under normal conditions as well as refolding and degradation under environmental stresses. It has been reported that Arabidopsis J-proteins are classified into four classes (types A-D) according to domain organization, but their phylogenetic relationships are unknown. Here, we identified 129 J-proteins in the world-wide popular vegetable Brassica oleracea, a close relative of the model plant Arabidopsis, and also revised the information of Arabidopsis J-proteins based on the latest online bioresources. According to phylogenetic analysis with domain organization and gene structure as references, the J-proteins from Arabidopsis and B. oleracea were classified into 15 main clades (I-XV) separated by a number of undefined small branches with remote relationship. Based on the number of members, they respectively belong to multigene clades, oligo-gene clades, and mono-gene clades. The J-protein genes from different clades may function together or separately to constitute a complicated regulatory network. This study provides a constructive viewpoint for J-protein classification and an informative platform for further functional dissection and resistant genes discovery related to genetic improvement of crop plants.

PROTEOTRONICS: The emerging science of protein-based electronic devices

International Nuclear Information System (INIS)

Alfinito, Eleonora; Pousset, Jeremy; Reggiani, Lino

2015-01-01

Protein-mediated charge transport is of relevant importance in the design of protein based electronics and in attaining an adequate level of understanding of protein functioning. This is particularly true for the case of transmembrane proteins, like those pertaining to the G protein coupled receptors (GPCRs). These proteins are involved in a broad range of biological processes like catalysis, substance transport, etc., thus being the target of a large number of clinically used drugs. This paper briefly reviews a variety of experiments devoted to investigate charge transport in proteins and present a unified theoretical model able to relate macroscopic experimental results with the conformations of the amino acids backbone of the single protein. (paper)

Polyether based block copolymer membranes for CO2 separation

NARCIS (Netherlands)

Reijerkerk, Sander

2010-01-01

The work described in this thesis is dedicated to the development of polymeric membrane materials for the separation of CO2 from light gases, and in particular to the separation of CO2 from nitrogen as required in a post-combustion capture conguration for the separation of CO2 from flue gases. An

Pseudo-stationary separation materials for highly parallel separations.

Energy Technology Data Exchange (ETDEWEB)

Singh, Anup K.; Palmer, Christopher (University of Montana, Missoula, MT)

2005-05-01

Goal of this study was to develop and characterize novel polymeric materials as pseudostationary phases in electrokinetic chromatography. Fundamental studies have characterized the chromatographic selectivity of the materials as a function of chemical structure and molecular conformation. The selectivities of the polymers has been studied extensively, resulting in a large body of fundamental knowledge regarding the performance and selectivity of polymeric pseudostationary phases. Two polymers have also been used for amino acid and peptide separations, and with laser induced fluorescence detection. The polymers performed well for the separation of derivatized amino acids, and provided some significant differences in selectivity relative to a commonly used micellar pseudostationary phase. The polymers did not perform well for peptide separations. The polymers were compatible with laser induced fluorescence detection, indicating that they should also be compatible with chip-based separations.

Stable Isotope Quantitative N-Glycan Analysis by Liquid Separation Techniques and Mass Spectrometry.

Science.gov (United States)

Mittermayr, Stefan; Albrecht, Simone; Váradi, Csaba; Millán-Martín, Silvia; Bones, Jonathan

2017-01-01

Liquid phase separation analysis and subsequent quantitation remains a challenging task for protein-derived oligosaccharides due to their inherent structural complexity and diversity. Incomplete resolution or co-detection of multiple glycan species complicates peak area-based quantitation and associated statistical analysis when optical detection methods are used. The approach outlined herein describes the utilization of stable isotope variants of commonly used fluorescent tags that allow for mass-based glycan identification and relative quantitation following separation by liquid chromatography (LC) or capillary electrophoresis (CE). Comparability assessment of glycoprotein-derived oligosaccharides is performed by derivatization with commercially available isotope variants of 2-aminobenzoic acid or aniline and analysis by LC- and CE-mass spectrometry. Quantitative information is attained from the extracted ion chromatogram/electropherogram ratios generated from the light and heavy isotope clusters.

Magnetic graphene oxide modified with choline chloride-based deep eutectic solvent for the solid-phase extraction of protein

Energy Technology Data Exchange (ETDEWEB)

Huang, Yanhua; Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn; Pan, Qi; Wang, Ying; Ding, Xueqin; Xu, Kaijia; Li, Na; Wen, Qian

2015-06-02

Highlights: • A strategy for extraction of protein based on DES-coated magnetic graphene oxide. • The deep eutectic solvents were based on choline chloride. • Bovine serum albumin was used as the analyte. • The material prepared works for the acidic but not the basic or the neutral proteins. - Abstract: Four kinds of green deep eutectic solvents (DESs) based on choline chloride (ChCl) have been synthesized and coated on the surface of magnetic graphene oxide (Fe{sub 3}O{sub 4}@GO) to form Fe{sub 3}O{sub 4}@GO-DES for the magnetic solid-phase extraction of protein. X-ray diffraction (XRD), vibrating sample magnetometer (VSM), Fourier transform infrared spectrometry (FTIR), field emission scanning electron microscopy (FESEM) and thermal gravimetric analysis (TGA) were employed to characterize Fe{sub 3}O{sub 4}@GO-DES, and the results indicated the successful preparation of Fe{sub 3}O{sub 4}@GO-DES. The UV–vis spectrophotometer was used to measure the concentration of protein after extraction. Single factor experiments proved that the extraction amount was influenced by the types of DESs, solution temperature, solution ionic strength, extraction time, protein concentration and the amount of Fe{sub 3}O{sub 4}@GO-DES. Comparison of Fe{sub 3}O{sub 4}@GO and Fe{sub 3}O{sub 4}@GO-DES was carried out by extracting bovine serum albumin, ovalbumin, bovine hemoglobin and lysozyme. The experimental results showed that the proposed Fe{sub 3}O{sub 4}@GO-DES performs better than Fe{sub 3}O{sub 4}@GO in the extraction of acidic protein. Desorption of protein was carried out by eluting the solid extractant with 0.005 mol L{sup −1} Na{sub 2}HPO{sub 4} contained 1 mol L{sup −1} NaCl. The obtained elution efficiency was about 90.9%. Attributed to the convenient magnetic separation, the solid extractant could be easily recycled.

Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation?

Directory of Open Access Journals (Sweden)

Iborra Francisco J

2007-04-01

Full Text Available Abstract Background The cell nucleus is highly compartmentalized with well-defined domains, it is not well understood how this nuclear order is maintained. Many scientists are fascinated by the different set of structures observed in the nucleus to attribute functions to them. In order to distinguish functional compartments from non-functional aggregates, I believe is important to investigate the biophysical nature of nuclear organisation. Results The various nuclear compartments can be divided broadly as chromatin or protein and/or RNA based, and they have very different dynamic properties. The chromatin compartment displays a slow, constrained diffusional motion. On the other hand, the protein/RNA compartment is very dynamic. Physical systems with dynamical asymmetry go to viscoelastic phase separation. This phase separation phenomenon leads to the formation of a long-lived interaction network of slow components (chromatin scattered within domains rich in fast components (protein/RNA. Moreover, the nucleus is packed with macromolecules in the order of 300 mg/ml. This high concentration of macromolecules produces volume exclusion effects that enhance attractive interactions between macromolecules, known as macromolecular crowding, which favours the formation of compartments. In this paper I hypothesise that nuclear compartmentalization can be explained by viscoelastic phase separation of the dynamically different nuclear components, in combination with macromolecular crowding and the properties of colloidal particles. Conclusion I demonstrate that nuclear structure can satisfy the predictions of this hypothesis. I discuss the functional implications of this phenomenon.

A hybrid approach to protein differential expression in mass spectrometry-based proteomics

KAUST Repository

Wang, X.

2012-04-19

MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein\\'s associated spectral peaks. However, typical MS-based proteomics datasets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. RESULTS: We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of \\'presence/absence,\\' we enable the selection of proteins not typically amenable to quantitative analysis; e.g. \\'one-state\\' proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence/absence analysis of a given dataset in a principled way, resulting in a single list of selected proteins with a single-associated false discovery rate. AVAILABILITY: All R code available here: http://www.stat.tamu.edu/~adabney/share/xuan_code.zip.

Development of a relatively cheap and simple automated separation system for a routine separation procedure based on extraction chromatography

International Nuclear Information System (INIS)

Petro Zoriy; Reinhold Flucht; Mechthild Burow; Peter Ostapczuk; Reinhard Lennartz; Myroslav Zoriy

2010-01-01

A robust analytical method has been developed in our laboratory for the separation of radionuclides by means of extraction chromatography using an automated separation system. The proposed method is both cheap and simple and provides the advantageous, rapid and accurate separation of the element of interest. The automated separation system enables a shorter separation time by maintaining a constant flow rate of solution and by avoiding clogging or bubbling in the chromatographic column. The present separation method was tested with two types of samples (water and urine) using UTEVA-, TRU- and Sr-specific resins for the separation of U, Th, Am, Pu and Sr. The total separation time for one radionuclide ranged from 60 to 100 min with the separation yield ranging from 68 to 98% depending on the elements separated. We used ICP-QMS, multi-low-level counter and alpha spectroscopy to measure the corresponding elements. (author)

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.

Science.gov (United States)

Finn, Robert D; Miller, Benjamin L; Clements, Jody; Bateman, Alex

2014-01-01

The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

Science.gov (United States)

Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Effect of temperature on acid–base equilibria in separation techniques. A review

International Nuclear Information System (INIS)

Gagliardi, Leonardo G.; Tascon, Marcos; Castells, Cecilia B.

2015-01-01

Studies on the theoretical principles of acid–base equilibria are reviewed and the influence of temperature on secondary chemical equilibria within the context of separation techniques, in water and also in aqueous-organic solvent mixtures, is discussed. In order to define the relationships between the retention in liquid chromatography or the migration velocity in capillary electrophoresis and temperature, the main properties of acid–base equilibria have to be taken into account for both, the analytes and the conjugate pairs chosen to control the solution pH. The focus of this review is based on liquid–liquid extraction (LLE), liquid chromatography (LC) and capillary electrophoresis (CE), with emphasis on the use of temperature as a useful variable to modify selectivity on a predictable basis. Simplified models were evaluated to achieve practical optimizations involving pH and temperature (in LLE and CE) as well as solvent composition in reversed-phase LC. - Highlights: • The study of theoretical principles of acid–base equilibrium has been reviewed. • The proton transfer process is often present in the analytical separation practice. • The influence of temperature on secondary chemical equilibria is examined. • The focus is laid on liquid chromatography and capillary electrophoresis. • Temperature can be a useful variable to modify selectivity under predictable basis

Highly accurate and fast optical penetration-based silkworm gender separation system

Science.gov (United States)

Kamtongdee, Chakkrit; Sumriddetchkajorn, Sarun; Chanhorm, Sataporn

2015-07-01

Based on our research work in the last five years, this paper highlights our innovative optical sensing system that can identify and separate silkworm gender highly suitable for sericulture industry. The key idea relies on our proposed optical penetration concepts and once combined with simple image processing operations leads to high accuracy in identifying of silkworm gender. Inside the system, there are electronic and mechanical parts that assist in controlling the overall system operation, processing the optical signal, and separating the female from male silkworm pupae. With current system performance, we achieve a very highly accurate more than 95% in identifying gender of silkworm pupae with an average system operational speed of 30 silkworm pupae/minute. Three of our systems are already in operation at Thailand's Queen Sirikit Sericulture Centers.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

Science.gov (United States)

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on

5 CFR 837.802 - Benefits under another retirement system for Federal employees based on the most recent separation.

Science.gov (United States)

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Benefits under another retirement system for Federal employees based on the most recent separation. 837.802 Section 837.802 Administrative... system for Federal employees based on the most recent separation. (a) Generally. An annuitant who has...

The potential of pathological protein fragmentation in blood-based biomarker development for dementia – with emphasis on Alzheimer’s disease

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Dilek eInekci

2015-05-01

Full Text Available The diagnosis of dementia is challenging and early stages are rarely detected limiting the possibilities for early interven-tion. Another challenge is the overlap in the clinical features across the different dementia types leading to difficulties in the differential diagnosis. Identifying biomarkers that can detect the pre-dementia stage and allow differential diagnosis could provide an opportunity for timely and optimal intervention strategies. Also, such biomarkers could help in selection and inclusion of the right patients in clinical trials of both Alzheimer’s disease and other dementia treatment candidates.The cerebrospinal fluid (CSF has been the most investigated source of biomarkers and several candidate proteins have been identified. However, looking solely at protein levels is too simplistic to provide enough detailed information to differentiate between dementias, as there is a significant crossover between the proteins involved in the different types of dementia. Additionally, CSF sampling makes these biomarkers challenging for presymptomatic identification. We need to focus on disease-specific protein fragmentation to find a fragment pattern unique for each separate dementia type – a form of protein fragmentology. Targeting protein fragments generated by disease-specific combinations of proteins and proteases opposed to detecting the intact protein could reduce the overlap between diagnostic groups as the extent of processing as well as which proteins and proteases constitute the major hallmark of each dementia type differ. In addition, the fragments could be detectable in blood as they may be able to cross the blood-brain-barrier due to their smaller size. In this review, the potential of the fragment-based biomarker discovery for dementia diagnosis and prognosis is discussed, especially highlighting how the knowledge from CSF protein biomarkers can be used to guide blood-based biomarker development.

Blind Test of Physics-Based Prediction of Protein Structures

Science.gov (United States)

Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

2009-01-01

We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

Increase in local protein concentration by field-inversion gel electrophoresis

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Paulus Aran

2007-09-01

Full Text Available Abstract Background Proteins that migrate through cross-linked polyacrylamide gels (PAGs under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE. Results Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS, which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. Conclusion The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein

Increase in local protein concentration by field-inversion gel electrophoresis.

Science.gov (United States)

Tsai, Henghang; Low, Teck Yew; Freeby, Steve; Paulus, Aran; Ramnarayanan, Kalpana; Cheng, Chung-Pui Paul; Leung, Hon-Chiu Eastwood

2007-09-26

Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE). Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE) in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE) showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS), which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein separation tool.

Essential protein discovery based on a combination of modularity and conservatism.

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Zhao, Bihai; Wang, Jianxin; Li, Xueyong; Wu, Fang-Xiang

2016-11-01

Essential proteins are indispensable for the survival of a living organism and play important roles in the emerging field of synthetic biology. Many computational methods have been proposed to identify essential proteins by using the topological features of interactome networks. However, most of these methods ignored intrinsic biological meaning of proteins. Researches show that essentiality is tied not only to the protein or gene itself, but also to the molecular modules to which that protein belongs. The results of this study reveal the modularity of essential proteins. On the other hand, essential proteins are more evolutionarily conserved than nonessential proteins and frequently bind each other. That is to say, conservatism is another important feature of essential proteins. Multiple networks are constructed by integrating protein-protein interaction (PPI) networks, time course gene expression data and protein domain information. Based on these networks, a new essential protein identification method is proposed based on a combination of modularity and conservatism of proteins. Experimental results show that the proposed method outperforms other essential protein identification methods in terms of a number essential protein out of top ranked candidates. Copyright © 2016. Published by Elsevier Inc.

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...... will continue to be valuable discovery tools, the most exciting developments in the field involve cell-based assays for GPCR function. Some cell-based discovery strategies, such as the use of beta-arrestin as a surrogate marker for GPCR function, have already been reduced to practice, and have been used...... 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...

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

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Jun Ren

2014-01-01

Full Text Available Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.

NAPS: Network Analysis of Protein Structures

Science.gov (United States)

Chakrabarty, Broto; Parekh, Nita

2016-01-01

Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

Acoustofluidic bacteria separation

International Nuclear Information System (INIS)

Li, Sixing; Huang, Tony Jun; Ma, Fen; Zeng, Xiangqun; Bachman, Hunter; Cameron, Craig E

2017-01-01

Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate Escherichia coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care sepsis diagnostic device. (paper)

Acoustofluidic bacteria separation

Science.gov (United States)

Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E.; Zeng, Xiangqun; Huang, Tony Jun

2017-01-01

Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate Escherichia coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care sepsis diagnostic device.

Effects of Hydrolysed Whey Proteins on the Techno-Functional Characteristics of Whey Protein-Based Films

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Klaus Noller

2013-03-01

Full Text Available Pure whey protein isolate (WPI-based cast films are very brittle due to its strong formation of protein cross-linking of disulphide bonding, hydrogen bonding as well as hydrophobic and electrostatic interactions. However, this strong cross-linking is the reason for its final barrier performance. To overcome film brittleness of whey protein layers, plasticisers like glycerol are used. It reduces intermolecular interactions, increases the mobility of polymer chains and thus film flexibility can be achieved. The objective of this study was to investigate the influence of hydrolysed whey protein isolate (WPI in whey protein isolate-based cast films on their techno-functional properties. Due to the fact, that the addition of glycerol is necessary but at the same time increases the free volume in the film leading to higher oxygen and water vapour permeability, the glycerol concentration was kept constant. Cast films with different ratios of hydrolysed and not hydrolysed WPI were produced. They were characterised in order to determine the influence of the lower molecular weight caused by the addition of hydrolysed WPI on the techno-functional properties. This study showed that increasing hydrolysed WPI concentrations significantly change the mechanical properties while maintaining the oxygen and water vapour permeability. The tensile and elastic film properties decreased significantly by reducing the average molecular weight whereas the yellowish coloration and the surface tension considerably increased. This study provided new data which put researchers and material developers in a position to tailor the characteristics of whey protein based films according to their intended application and further processing.

Application of gamma irradiation on forming protein-based edible films

International Nuclear Information System (INIS)

Sabato, Susy Frey

2000-01-01

In the last decade considerable interest has been addressed to the development of protein-based edible films due to their application in the food industry, as a substitute to traditional plastic films. The use of soy and whey proteins to form those films has been investigated, using heat, chemical and enzymatic processes. Gamma irradiation was recently reported to form caseinate-based edible films, due to the increase of the cohesive strength of the proteins by the formation of cross-links. This work aimed to verify the role of the gamma irradiation in the process of forming edible films from soy protein isolate (SPI) alone and in complex mixtures, that is, mixed with whey protein isolate (WPI), with carbethoxymethyl cellulose (CMC) and with poly(vinyl)alcohol (PVA). Gamma irradiation treatment improved significantly the mechanical properties for all films. The mechanical behavior is strongly related to the formulation, showing synergy between the gamma irradiation and the CMC, mainly for SPI-based films. SPI-based films presented a trend to decrease the water vapor permeability values when irradiated. The CMC addition showed significant improvements on the permeability for films from SPI and from the mixture of SPI with WPI. (author)

vProtein: identifying optimal amino acid complements from plant-based foods.

Directory of Open Access Journals (Sweden)

Peter J Woolf