Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol

IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexafluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.

Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol

IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexa-fluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.

Affinity purification of plasmid DNA directly from crude bacterial cell lysates

We have shown previously that a sequence-specific DNA-binding protein based on the Lac repressor protein can isolate pre-purified DNA efficiently from simple buffer solution but our attempts to purify plasmids directly from crude starting materials were disappointing with unpractically low DNA yields. We have optimized tbe procedure and present a simple affinity methodology whereby plasmid DNA is purified directly by mixing two crude cell lysates, one cell lysate containing the plasmid and the other the protein affinity ligand, without the need for treatment by RNaseA. After IMAC chromatography, high purity supercoiled DNA is recovered in good yields of 100-150 μg plasmid per 200 mL shake flask culture. Moreover, the resulting DNA is free from linear or open-circular plasmid DNA, genomic DNA, RNA, and protein, to the limits of our detection. Furthermore, we show that lyophilized affinity ligand can be stored at room temperature and re-hydrated for use when required.

Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry

Since protein phosphorylation is a dominant mechanism of information transfer in cells, there is a great need for methods capable of accurately elucidating sites of phosphorylation. In recent years mass spectrometry has become an increasingly viable alternative to more traditional methods of phosphorylation analysis. The present study used immobilized metal affinity chromatography (IMAC coupled with a linear ion trap mass spectrometer to analyze phosphorylated proteins in mouse liver. A total of 26 peptide sequences defining 26 sites of phosphorylation were determined. Although this number of identified phosphoproteins is not large, the approach is still of interest because a series of conservative criteria were adopted in data analysis. We note that, although the binding of non-phosphorylated peptides to the IMAC column was apparent, the improvements in high-speed scanning and quality of MS/MS spectra provided by the linear ion trap contributed to the phosphoprotein identification. Further analysis demonstrated that MS/MS/MS analysis was necessary to exclude the false-positive matches resulting from the MS/MS experiments, especially for multiphosphorylated peptides. The use of the linear ion trap considerably enabled exploitation of nanoflow-HPLC/MS/MS, and in addition MS/MS/MS has great potential in phosphoproteome research of relatively complex samples. Copyright (C) 2004 John Wiley Sons, Ltd.

Expression, purification of recombinant flounder MRF4 protein in Escherichia coli and analysis of its polyclonal antibodies

MRF4 is one of muscle regulatory factors and plays critical roles during skeletal muscle development. The muscle development is important for the fish growth which is an important economic factor for the fish culture. To analyze the function of MRF4 in fish, the founder MRF4 antibody was prepared. The flounder MRF4 was cloned, ligated into prokaryotic expression vector pET-30b and expressed in strain E. coli BL21 (130). The recombinant flounder MRF4 fusion protein was soluble and purified with cobalt IMAC resins. To prepare MRF4 polyclonal antibodies, rabbits were immunized with the soluble protein and the increasing level of antibodies was determined by Western blot. Also, the endogenous flounder MRF4 was recognized by the anti-serum. The result further proved the existence of the anti-MRF4 antibody in the anti-serum, which will be useful for studies on the function of flounder MRF4.

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

An iminodiacetic acid (IDA)-type adsorbent is prepared at the one end of a capillary by covalently bonding IDA to the monolithic rods of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate). Cu(II) is later introduced to the support via the interaction with IDA. By this means, polymer monolithic immobilized metal affinity chromatography (IMAC) materials are prepared. With such a column, IMAC for on-line concentration and capillary electrophoresis (CE) for the subsequent analysis are hyphenated for the analysis of peptides and proteins. The reproducibility of such a column has been proved good with relative standard deviations (RSDs) of dead time of less than 5% for injection-to-injection and 12% for column-to-column (n = 3). Through application on the analysis of standard peptides and real protein samples, such a technique has shown promising in proteome study.

Herbal Dietary Supplements: Safety, Efficacy, and Use by Breast Cancer Survivors

Gemstone Team IMAC (Integrative Medicine and Cancer)

Eppin: A Novel Protein Possessing Antimicrobial Properties Against Oral Pathogens

Background: Epididymal protease inhibitor (eppin) is a dual motif protein belonging to the whey acidic protein (WAP) family. Although expressed in numerous different tissues, to date, its functional characterisation is limited. It has been shown to exhibit antibacterial activity against Gram-negative bacteria (Escherichia coli) and antiprotease activity against some proteases of the serine protease family. We are interested in determining the role of eppin in innate immune defence. Objectives: This study aims to determine eppin's potential function in the innate immune response in the oral cavity by investigating the antimicrobial activity of eppin against relevant oral pathogens. Methods: Eppin was recombinantly expressed in E. coli cells and purified by immobilised metal affinity chromatography (IMAC). The antimicrobial effects of the protein were then assessed against two oral pathogens, Fusobacterium nucleatum and Candida albicans, using a double layer radial diffusion assay. Results: Eppin displayed antimicrobial activities against both oral pathogens tested and these activities were shown to be comparable to the well characterised antimicrobial peptide, LL-37. The antifungal effects of eppin were shown to be more potent than those of the human cathelicidin, LL-37. Conclusions: Eppin has been shown to possess both antibacterial and antifungal properties against oral pathogens, suggesting an important role for this protein in the innate immune response in the oral cavity. This study furthers our knowledge of the physiological role exerted by eppin and its possible role in the modulation of chronic diseases such as periodontitis and oral candidiasis.

Optimización del sistema de transporte en el colegio The English School

La optimización de sistemas y modelos se ha convertido en uno de los factores más importantes a la hora de buscar la mayor eficiencia de un proceso. Este concepto no es ajeno al transporte escolar, ambiente que cambia constantemente al ritmo de las necesidades de sus clientes, y que responde ante una fuerte responsabilidad frente a sus usuarios, los niños que hacen uso del servicio, en cuanto al cumplimiento de tiempos y seguridad, mientras busca constantemente la reducción de costos. Este proyecto expone las problemáticas presentadas en The English School en esta área y propone un modelo de optimización simple que permitirá notables mejoras en términos de tiempos y costos, de tal forma que genere beneficios para la institución en términos financieros y de satisfacción al cliente. Por medio de la implementación de este modelo será posible identificar errores comunes del proceso, se identificarán soluciones prácticas de fácil aplicación en el manejo del transporte y se presentarán los resultados obtenidos en la muestra utilizada para desarrollar el proyecto.

Desenvolupament de mètodes de preconcentració emprant membranes líquides suportades i extracció en fase sòlida per a la determinació de l'herbicida glifosat i el seu metabòlit AMPA en aigües naturals

El glifosat, N-(fosfonometil) glicina, és un dels herbicides més utilitzats arreu del món a causa de la seva baixa toxicitat i al seu ampli espectre d'aplicació. A conseqüència del gran ús que se'n fa, és necessari monitoritzar aquest compost i el seu principal metabòlit, l'àcid aminometilfosfònic (AMPA), en el medi ambient. S'han descrit diversos mètodes instrumentals basats en cromatografia de gasos (GC) i de líquids (HPLC), sent aquesta darrera l'opció més favorable a causa del caràcter polar dels anàlits. Per assolir nivells de concentració baixos cal, però, la preconcentració dels anàlits. En aquest treball s'estudien diferents alternatives amb aquest objectiu. S'ha avaluat la tècnica de membrana líquida suportada (SLM) on la membrana consisteix en una dissolució orgànica, que conté un transportador (en el nostre cas, un bescanviador d'anions comercial, Aliquat 336), que impregna un suport polimèric microporós que se situa entre dues solucions aquoses: la de càrrega, que conté els anàlits inicialment, i la receptora, on es retenen els anàlits després del seu transport a través de la membrana. Les condicions d'extracció més adequades s'obtenen treballant en medi bàsic amb NaOH on els anàlits estan en forma aniònica i les majors recuperacions s'obtenen amb HCl 0,1 M o NaCl 0,5 M, la qual cosa indica que l'ió clorur és la força impulsora del transport. Un cop dissenyat el sistema, es duen a terme experiments de preconcentració amb dues geometries diferents: un sistema de membrana laminar (LSLM) on recircula la fase receptora i un sistema de fibra buida (HFSLM). Els millors resultats s'obtenen amb el mòdul de fibra buida, amb factors de concentració de 25 i 3 per a glifosat i AMPA, respectivament, fent recircular durant 24 hores 100 ml de solució de càrrega i 4 ml de solució receptora. També s'aplica una tècnica més selectiva, la cromatografia d'afinitat amb ió metàl·lic immobilitzat (IMAC), basada en la interacció entre els anàlits i un metall immobilitzat en una resina a través d'un grup funcional d'aquesta. En aquest estudi s'immobilitza pal·ladi al grup funcional 8-hidroxiquinoleïna de la resina amb matriu acrílica Spheron Oxine 1000 i s'avalua per a l'extracció i preconcentració de glifosat i AMPA. Per a ambdós anàlits l'adsorció és del 100 % i les recuperacions són superiors al 80 % i al 60 % per a glifosat i AMPA, respectivament, utilitzant HCl 0,1 M + NaCl 1 M com a eluent. Aquests resultats es comparen amb els obtinguts amb dues resines més, també carregades amb pal·ladi: Iontosorb Oxin 100, que té el mateix grup funcional però matriu de cel·lulosa, i Spheron Thiol 1000, on el grup funcional és un tiol i la matriu també és acrílica. Per al glifosat els resultats són similars amb totes les resines, però per a l'AMPA la resina Spheron Thiol és la única que proporciona recuperacions superiors al 93 %. Finalment, una altra opció estudiada és l'acoblament de dues columnes de cromatografia líquida (LC-LC). En l'estudi l'objectiu és millorar el mètode existent per a glifosat i AMPA en aigües naturals on el LOD era de 0,25 ug/l. El mètode consisteix en la derivatització precolumna amb el reactiu fluorescent FMOC i l'anàlisi amb l'acoblament LC-LC-fluorescència. Variant lleugerament les condicions de derivatització s'aconsegueix quantificar 0,1 ug/l de glifosat i AMPA. Es fortifiquen aigües naturals amb 0,1, 1 i 10 ug/l dels anàlits per validar el mètode. S'obtenen recuperacions d'entre el 85 % i el 100 %, amb desviacions estàndard relatives inferiors al 8 %. Aplicant una tècnica de preconcentració prèvia a la derivatització i anàlisi utilitzant una resina de bescanvi aniònic, Amberlite IRA-900, es millora la sensibilitat del mètode i s'assoleix un LOD per al glifosat de 0,02 ug/l.

One-step purification and immobilization of his-tagged rhamnosidase for naringin hydrolysis

α-l-Rhamnosidase (EC 3.2.1.40) is an enzyme that catalyzes the cleavage of terminal rhamnoside groups from naringin to prunin and rhamnose. In this study, a His-tag was genetically attached to the rhamnosidase gene ramA from Clostridium stercorarium to facilitate its purification from Escherichia coli BL21 (DE3) cells containing the pET-21d/ramA plasmid. Immobilized metal-chelate affinity chromatography (IMAC) resulted in one-step purification of N-terminally His-tagged recombinant rhamnosidase (N-His-CsRamA) which was immobilized in Ca²⁺ alginate (3%) beads. The optimum pH levels of the free and immobilized recombinant rhamnosidase were found to be 6.0 and 7.5, and the optimum temperature 55 and 60 °C respectively. At 50 °C, the free enzyme was relatively stable and exhibited a less than 50% reduction in residual activity after 180 min of incubation. The free and immobilized enzymes achieved 76% and 67% hydrolysis of the naringin in Kinnow juice respectively. Immobilization of recombinant rhamnosidase enabled its reutilization up to 9 hydrolysis batches without an appreciable loss in activity. This result indicated that the His-tagged thermostable rhamnosidase could be prepared as described and may serve to illustrate an economical and commercially viable process for industrial application.

Molecular characterization and enzymatic hydrolysis of flavanoid extracted from citrus waste

The citrus fruit processing industry generates substantial quantities of waste rich in phenolic substances, which is a valuable natural source of polyphenols (flavonoids) such as naringin and its disposal is becoming a major problem. In the US alone, the juice processing of oranges and grapefruit generates over 5 Mt of citrus waste every year. In the case of India, about 2.15 Mt of citrus peel out of 6.28 Mt of citrus fruits are produced yearly from citrus juice processing. In case of Australia, about 15-40% of citrus peel waste is generated by processing of citrus fruit (0.85 Mt). Thus Isolation of functional compounds (mostly flavanoids) and their further processing can be of interest to the food and pharmaceutical industry. This peel is rich in naringin and may be used for rhamnose production by utilizing α-L-rhamnosidase (EC 3.2.1.40), an enzyme that catalyzes the cleavage of terminal rhamnosyl groups from naringin to yield prunin and rhamnose. We recently purified recombinant α-L-rhamnosidase from E. coli cells using immobilized metal-chelate affinity chromatography (IMAC) and used it for naringin hydrolysis. The purified enzyme established hydrolysis of naringin extracted from citrus peel and thus endorses its industrial applicability for producing rhamnose. Infrared (IR) spectroscopy confirmed molecular characteristics of naringin extracted from citrus peel waste.

Uso da tecnologia de troca iônica no tratamento de águas contaminadas com Nitrato do Aqüífero Dunas-Barreiras, Natal/RN-Brasil

The city of Natal comprises an area of about 170 km² (65,63 squares miles). The Dunas-Barreiras Aquifer is the most important reservoir of the coastal basin of RN. It is being responsible for the water supplying of about 70% of the population, however, due to the sewage disposal system by cesspools and drains, it is presently affected in a great extent by nitrates contamination. Thus, the present work proposes to research the utilization of contaminated water by nitrates of this fountainhead and find cost of the potable water through the ionic exchange technology. This technology consists in the removal of mineral salts by the exchange of cations for one ion of hydrogen (H+), through the passage of water by cationic resin bed and, secondly, by the exchange of the anions for hydroxyl ions (OH-) through a anionic resin bed. The obtained results have showed the waters derived from fountains, big water holes and shallow wells were microbiologically contaminated, while the waters derived from deep wells (above 70 m 76,58 yards) were free of contamination. Thus, only these ones are suitable to the use of ionic technology. The experiments were conducted with the resin IMAC-HP-555 such as kinetic, thermodynamic, and adsorption by fixed bed studies, being obtained several project variables for the experimental column, as follow: work temperature of 25oC; resin maximum capacity maximum e mean of adsorption ==0,01692 g NO3-1/g R e 0,0110 g NO3-1/g R, respectively. On the experimental column were performed breakthrough tests which pointed for an average ideal average speed of work of 13.2 m / h, with an average efficiency of 45% of adsorption, an optimal concentration of NaCl desorption of 8%, and an ideal desorption time of 80 minutes for the equilibrium conditions of water from the Dunas-Barreiras aquifer. Scale projection for ion-exchange column for denitrification, for these variables, using a computer modeling programme, to project the column of ion exchange ROREX-420/2000, obtained a cost for the drinking water denitrified by this system of R$ 0,16 / m3

Structural integrity identification based on smart materials and neural networks

This paper presents a non-model based technique to detect, locate, and characterize structural damage by combining the impedance-based structural health monitoring technique with an artificial neural network. The impedance-based structural health monitoring technique, which utilizes the electromechanical coupling property of piezoelectric materials, has shown engineering feasibility in a variety of practical field applications. Relying on high frequency structural excitations (typically>30 kHz), this technique is very sensitive to minor structural changes in the near field of the piezoelectric sensors. In order to quantitatively assess the state of structures, two sets of artificial neural networks, which utilize measured electrical impedance signals for input patterns, were developed. By employing high frequency ranges and by incorporating neural network features, this technique is able to detect the damage in its early stage and to estimate the nature of damage without prior knowledge of the model of structures. The paper concludes with an experimental example, an investigation on a massive quarter scale model of a steel bridge section, in order to verify the performance of this proposed methodology.

Structural FRF acquisition via electric impedance measurement applied to damage location

Continuing development of new materials makes systems lighter and stronger permitting more complex systems to provide more functionality and flexibility that demands a more effective evaluation of their structural health. Smart material technology has become an area of increasing interest in this field. The combination of smart materials and artificial neural networks can be used as an excellent tool for pattern recognition, turning their application adequate for monitoring and fault classification of equipment and structures. In order to identify the fault, the neural network must be trained using a set of solutions to its corresponding forward Variational problem. After the training process, the net can successfully solve the inverse variational problem in the context of monitoring and fault detection because of their pattern recognition and interpolation capabilities. The use of structural frequency response function is a fundamental portion of structural dynamic analysis, and it can be extracted from measured electric impedance through the electromechanical interaction of a piezoceramic and a structure. In this paper we use the FRF obtained by a mathematical model (FEM) in order to generate the training data for the neural networks, and the identification of damage can be done by measuring electric impedance, since suitable data normalization correlates FRF and electrical impedance.