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Ischemic heart disease (IHD) is the leading cause of mortality worldwide. Metalloproteins have been linked to human health and diseases. The molecular functions of metalloproteins in IHD is not well understood and require further exploration. The objective of this study was to find out the role of metalloproteins in the pericardial fluid of IHD patients having normal (EF > 45) and impaired (EF < 45) left ventricular ejection fraction (LVEF). IHD patients were grouped into two categories: LVEF<45 (n = 12) and LVEF >45 (n = 33). Pooled samples of pericardial fluid were fractionated by using ZOOM-isoelectric focusing (IEF) followed by further processing using one-dimensional gel electrophoresis (1D SDS-PAGE) and filter-aided sample preparation (FASP). Tryptic peptides of each fraction and differential bands were then analyzed by nano-LC-ESI-MS/MS. Protein identification was performed through a Mascot search engine using NCBI-Prot and SwissProt databases. A total of 1082 proteins including 154 metalloproteins were identified. In the differential bands, 60 metalloproteins were identified, while 115 metalloproteins were identified in all ZOOM-IEF fractions. Twelve differentially expressed metalloproteins were selected in the intense bands according to their molecular weight (MW) and isoelectric point (pI). The 12 differentially expressed metalloprotein includes ceruloplasmin, Prothrombin, Vitamin K-dependent protein, Fibulin-1, Ribosomal protein S6 kinase alpha-6, nidogen, partial, Serum albumin, Hemopexin, C-reactive protein, Serum amyloid P-component, and Intelectin-1 protein which were all up-regulated while serotransferrin is the only metalloprotein that was down-regulated in impaired (LVEF<45) group. Among the metalloproteins, Zn-binding proteins are 36.5 % followed by Ca-binging 32.2 %, and Fe-binging 12.2 %. KEGG, pathway analysis revealed the association of ceruloplasmin and serotransferrin with the ferroptosis pathway. In conclusion, 154 metallopro

Proteoforms, highly related proteins, play critical roles in disease processes such as cancer. However, studying proteoforms is challenging due to their high homology and low abundance. Electrophoretic assays are capable of elucidating proteoforms, which are often indistinguishable with canonical antibody-based protein assays and mass spectrometry. This dissertation presents advancements in microfluidic, material, and mass spectrometry imaging approaches towards improved multiplexing, proteoform specificity, and sensitivity of electrophoretic assays.First, the integration of mass spectrometry imaging and proteoform separation tools paves the way for highly multiplexed single-cell proteomics. Single-cell immunoblotting (scIB) offers proteoform detection specificity but often relies on fluorescence-based readout, limiting its multiplexing capability. Among the rising multiplexed imaging methods is multiplexed ion beam imaging by time-of-flight (MIBI-TOF), a mass spectrometry imaging technology. MIBI-TOF employs metal-tagged antibodies that do not suffer from spectral overlap to the same degree as fluorophore-tagged antibodies. We report for the first time MIBI-TOF of single-cell immunoblotting (scIB-MIBI-TOF). The scIB assay subjects single-cell lysate to protein immunoblotting on a microscale device consisting of a 50- to 75-µm thick hydrated polyacrylamide (PA) gel matrix for protein immobilization before in-gel immunoprobing. We confirm antibody-protein binding in the PA gel with indirect fluorescence readout of metal-tagged antibodies. Since MIBI-TOF is a layer-by-layer imaging technique, and our protein target is immobilized within a 3D PA gel layer, we characterize the protein distribution throughout the PA gel depth by fluorescence confocal microscopy and confirm that the highest signal-to-noise ratio is achieved by imaging the entirety of the PA gel depth. Accordingly, we report the required MIBI-TOF ion dose strength needed to image varying PA gel depths. Las

We demonstrated the fractionation of two amino acids, glutamic acid and histidine, separated via isoelectric focusing (IEF) on filter paper folded and stacked in an origami fashion. Channels for electrophoresis were fabricated as circular zones acquired via wax printing onto the filter paper. An ampholyte solution with amphiphilic samples was deposited on all the circle zones, which was followed by folding to form the electrophoresis channels. IEF was achieved by applying an electrical potential between the anodic and cathodic chambers filled with phosphoric acid and sodium hydroxide solutions, respectively. A pH gradient was formed using either a wide-range ampholyte with a pH of 3 to 10 or a narrow-range version with a pH of 5 to 8, which was confirmed by adding pH indicators to each layer. The origami IEF was used to separate the amino acids, glutamic acid and histidine, by mixing with the ampholytes, which were deposited on the layers. The components in each layer were extracted with water and measured by high-performance liquid chromatography using pre-column derivatization with dansyl chloride. The results indicated that the focus for glutamic acid and that for histidine were at different layers, according to their isoelectric points. The origami isoelectric focusing achieved the fractionation of amino acids in less than 3 min using voltage as low as 30 V.

En förhöjd produktion av fria kappakedjor (KFLC) i serum observeras vanligen vid inflammatoriska processer och vid autoimmuna sjukdomar. En överproduktion av fri kappakedja utgör en markör för intratekal immunglobulinproduktion i centrala nervsystemet (CNS) vilket kan ofta ses vid multipel skleros och andra inflammatoriska nervsjukdomar. Detta kan mätas både kvantitativt genom IgG index med nefelometri och kvalitativt genom att påvisa oligoklonala band i cerebrospinalvätska (CSV) med isoelektrisk fokusering. Syftet med studien är att sätta upp analys för bestämning av fri kappa-kedja i likvor på en nefelometer och utvärdera olika kvantitativa mått för intratekal Ig-syntes där fri kappakedja ingår genom att jämföra de mot isoelektrisk fokusering, vilket är dagens standardmetod för att påvisa intratekal Ig syntes. Studien erhöll goda resultat för olika KFLC parametrar jämfört med oligoklonalaband, där KFLC IF påvisade högst sensitivitet och specificitet (72% och 93%) jämfört med oligoklonala band., An increased production of free coat chains in (KFLC) serum is commonly observed in inflammatory processes and in autoimmune diseases. An overproduction of free kappa chain is a marker for intrathecal immunoglobulinproduction in the central nervous system (CNS), which can often be seen in multiple sclerosis and other inflammatory nerve diseases. This can be measured both quantitatively by IgG index with nephelometry and qualitatively by detecting oligoclonal bands in cerebrospinal fluid (CSF) with isoelectric focusing. The purpose of the studies is to set up analysis for determination of free kappa chain in liquids on a nephelometer and evaluate different quantitative measures for intrathecal Ig synthesis where free kappa chain is included by comparing them against isoelectric focusing, which is the current standard method for detecting intrathecal Ig synthesis. The study obtained good results for different KFLC parameters compared to oligoclonal bands, where KFLC IF has the highest sensitivity and specificity (72%and 93%) compared to oligoclonal bands.

En förhöjd produktion av fria kappakedjor (KFLC) i serum observeras vanligen vid inflammatoriska processer och vid autoimmuna sjukdomar. En överproduktion av fri kappakedja utgör en markör för intratekal immunglobulinproduktion i centrala nervsystemet (CNS) vilket kan ofta ses vid multipel skleros och andra inflammatoriska nervsjukdomar. Detta kan mätas både kvantitativt genom IgG index med nefelometri och kvalitativt genom att påvisa oligoklonala band i cerebrospinalvätska (CSV) med isoelektrisk fokusering. Syftet med studien är att sätta upp analys för bestämning av fri kappa-kedja i likvor på en nefelometer och utvärdera olika kvantitativa mått för intratekal Ig-syntes där fri kappakedja ingår genom att jämföra de mot isoelektrisk fokusering, vilket är dagens standardmetod för att påvisa intratekal Ig syntes. Studien erhöll goda resultat för olika KFLC parametrar jämfört med oligoklonalaband, där KFLC IF påvisade högst sensitivitet och specificitet (72% och 93%) jämfört med oligoklonala band., An increased production of free coat chains in (KFLC) serum is commonly observed in inflammatory processes and in autoimmune diseases. An overproduction of free kappa chain is a marker for intrathecal immunoglobulinproduction in the central nervous system (CNS), which can often be seen in multiple sclerosis and other inflammatory nerve diseases. This can be measured both quantitatively by IgG index with nephelometry and qualitatively by detecting oligoclonal bands in cerebrospinal fluid (CSF) with isoelectric focusing. The purpose of the studies is to set up analysis for determination of free kappa chain in liquids on a nephelometer and evaluate different quantitative measures for intrathecal Ig synthesis where free kappa chain is included by comparing them against isoelectric focusing, which is the current standard method for detecting intrathecal Ig synthesis. The study obtained good results for different KFLC parameters compared to oligoclonal bands, where KFLC IF has the highest sensitivity and specificity (72%and 93%) compared to oligoclonal bands.

Antibodies are Y-shaped proteins. In the human body, antibodies areproduced by plasma cells, mainly T and B cells which are included inthe adaptive immune system. The production of antibodies is stimulatedby antigens. The binding between an antigen-specific antibody and itsantigen can be like the interconnect between a lock and a key.Therefore, antibodies are widely used as diagnostic tools for avariety of diseases but most importantly cancer. Some rapid diagnostictests are completely dependent on the specificity and reactivity ofantibodies such as UBC® Rapid produced by IDL Biotech AB. Therefore,the quality of these antibodies is important. This master thesis at IDL Biotech aimed to validate six anticytokeratinantibodies that are currently used in several rapid cancerdiagnostic tests produced by IDL. Antibody validation is a processwhere specificity, selectivity and reproductivity of an antibody isdemonstrated through specific laboratory investigations. During thisthesis, two laboratory methods were used to validate antibodies,namely, isoelectric focusing electrophoresis and the Attana QuartzCrystal Microbalance based biosensor. Isoelectric focusing electrophoresis (IEF) is a method that determinesproteins pI-values which can then reveal information about posttranslationalmodifications and protein sustainability during storage.IEF revealed changes in pI-values in two antibodies: AB2 and AB4. Attana biosensor analysis on AB1-5 showed that all antibodies havehigh specificity, reactivity and relatively high affinity to theircytokeratin targets. It also revealed that 4 antibodies (AB1 and AB3-5) have lower cross-reactivity with other cytokeratins than theirtarget cytokeratins compared to AB2. Keywords: Antibody validation, Isoelectric focusing, QCM, Attanabiosensor, biosensors, rapid diagnostics, epithelial carcinomas.

Antibodies are Y-shaped proteins. In the human body, antibodies areproduced by plasma cells, mainly T and B cells which are included inthe adaptive immune system. The production of antibodies is stimulatedby antigens. The binding between an antigen-specific antibody and itsantigen can be like the interconnect between a lock and a key.Therefore, antibodies are widely used as diagnostic tools for avariety of diseases but most importantly cancer. Some rapid diagnostictests are completely dependent on the specificity and reactivity ofantibodies such as UBC® Rapid produced by IDL Biotech AB. Therefore,the quality of these antibodies is important. This master thesis at IDL Biotech aimed to validate six anticytokeratinantibodies that are currently used in several rapid cancerdiagnostic tests produced by IDL. Antibody validation is a processwhere specificity, selectivity and reproductivity of an antibody isdemonstrated through specific laboratory investigations. During thisthesis, two laboratory methods were used to validate antibodies,namely, isoelectric focusing electrophoresis and the Attana QuartzCrystal Microbalance based biosensor. Isoelectric focusing electrophoresis (IEF) is a method that determinesproteins pI-values which can then reveal information about posttranslationalmodifications and protein sustainability during storage.IEF revealed changes in pI-values in two antibodies: AB2 and AB4. Attana biosensor analysis on AB1-5 showed that all antibodies havehigh specificity, reactivity and relatively high affinity to theircytokeratin targets. It also revealed that 4 antibodies (AB1 and AB3-5) have lower cross-reactivity with other cytokeratins than theirtarget cytokeratins compared to AB2. Keywords: Antibody validation, Isoelectric focusing, QCM, Attanabiosensor, biosensors, rapid diagnostics, epithelial carcinomas.

Rationale: The role of PI (protease inhibitor) type Z heterozygotes and additional rare variant genotypes in the gene encoding alpha-1 antitrypsin, SERPINA1 (serpin peptidase inhibitor, clade A, member 1), in determining chronic obstructive pulmonary disease risk and severity is controversial.Objectives: To comprehensively evaluate the effects of rare SERPINA1 variants on lung function and emphysema phenotypes in subjects with significant tobacco smoke exposure using deep gene resequencing and alpha-1 antitrypsin concentrations.Methods: DNA samples from 1,693 non-Hispanic white individuals, 385 African Americans, and 90 Hispanics with ≥20 pack-years smoking were resequenced for the identification of rare variants (allele frequency < 0.05) in 16.9 kB of SERPINA1.Measurements and Main Results: White PI Z heterozygotes confirmed by sequencing (MZ; n = 74) had lower post-bronchodilator FEV1 (P = 0.007), FEV1/FVC (P = 0.003), and greater computed tomography-based emphysema (P = 0.02) compared with 1,411 white individuals without PI Z, S, or additional rare variants denoted as VR. PI Z-containing compound heterozygotes (ZS/ZVR; n = 7) had lower FEV1/FVC (P = 0.02) and forced expiratory flow, midexpiratory phase (P = 0.009). Nineteen white heterozygotes for five non-S/Z coding variants associated with lower alpha-1 antitrypsin had greater computed tomography-based emphysema compared with those without rare variants. In African Americans, a 5' untranslated region insertion (rs568223361) was associated with lower alpha-1 antitrypsin and functional small airway disease (P = 0.007).Conclusions: In this integrative deep sequencing study of SERPINA1 with alpha-1 antitrypsin concentrations in a heavy smoker and chronic obstructive pulmonary disease cohort, we confirmed the effects of PI Z heterozygote and compound heterozygote genotypes. We demonstrate the cumulative effects of multiple SERPINA1 variants on alpha-1 antitrypsin deficiency, lung function, and emphysema, thus sig

To understand the function and dysfunction of cells in biological organisms, it is important to characterize one of the key functional actors of the cell, proteins. With indications of poor correlation between mRNA expression and proteomic expression at the single cell level, in vitro assays directly quantifying protein expression, in both the spatial and temporal context, are needed. To span the extensive cellular heterogeneity in gene and protein expression and activity observed in cells and tissues, proteomic assays should interrogate single- and low-cell resolution with sufficiently high throughput to identify cellular sub-populations. These proteomic assays would also require sufficiently high selectivity and analytical sensitivity with which to interrogate protein isoforms and post-translational modifications. To address this measurement gap, we introduce and further develop proteomic assays towards these specifications.We enhanced the analytical sensitivity of the ultrathin isoelectric focusing assay (IEF) with subsequent immunoblot, by developing a highly-porous hydrogel matrix as a new substrate for the assay. We characterized the effect of this 10-fold increase in gel porosity on the IEF separation performance, paired with a reagent modification that directly impacts separation performance. Additionally, we assessed the benefits of the increased porosity on the in-gel immunoblot. Furthermore, we investigated the compartmentalization of protein lysate from single cells within the microwells embedded in the hydrogel substrate in our proteomic assays. We characterized the height of the fluid film between multi-material interfaces. We used numerical modeling and experimental validation to assess the contribution of the fluid film to the diffusive losses that reduce analytical sensitivity in our assays.We then re-imagined the ultrathin IEF assay for a 100-fold increase in throughput by developing 3D projection electrophoresis. We interrogated the IEF separation

To understand the function and dysfunction of cells in biological organisms, it is important to characterize one of the key functional actors of the cell, proteins. With indications of poor correlation between mRNA expression and proteomic expression at the single cell level, in vitro assays directly quantifying protein expression, in both the spatial and temporal context, are needed. To span the extensive cellular heterogeneity in gene and protein expression and activity observed in cells and tissues, proteomic assays should interrogate single- and low-cell resolution with sufficiently high throughput to identify cellular sub-populations. These proteomic assays would also require sufficiently high selectivity and analytical sensitivity with which to interrogate protein isoforms and post-translational modifications. To address this measurement gap, we introduce and further develop proteomic assays towards these specifications.We enhanced the analytical sensitivity of the ultrathin isoelectric focusing assay (IEF) with subsequent immunoblot, by developing a highly-porous hydrogel matrix as a new substrate for the assay. We characterized the effect of this 10-fold increase in gel porosity on the IEF separation performance, paired with a reagent modification that directly impacts separation performance. Additionally, we assessed the benefits of the increased porosity on the in-gel immunoblot. Furthermore, we investigated the compartmentalization of protein lysate from single cells within the microwells embedded in the hydrogel substrate in our proteomic assays. We characterized the height of the fluid film between multi-material interfaces. We used numerical modeling and experimental validation to assess the contribution of the fluid film to the diffusive losses that reduce analytical sensitivity in our assays.We then re-imagined the ultrathin IEF assay for a 100-fold increase in throughput by developing 3D projection electrophoresis. We interrogated the IEF separation

The modeling and simulation software COMSOL Multiphysics (R) was recently extended with an electrophoretic transport interface. Its performance was investigated by comparison to results obtained using the 1D dynamic electrophoresis simulators GENTRANS and SIMUL5. Simulations of zone electrophoresis, isotachophoresis, isoelectric focusing and of an oscillating electrolyte system were performed. Smooth profiles were essentially identical indicating that the COMSOL electrophoretic transport interface is able to reproduce results of the 1D simulators. Differences in the way the respective numerical schemes handle steep concentration gradients and associated instabilities were observed. The COMSOL electrophoretic transport interface is expected to be useful as a general model for simulations in 1D, 2D or 3D geometries, as well as for simulations combining electrophoresis with other physical phenomena., QC 20180219

The influence of growth regulator prohexadione-Ca (ProCa) concurrently with young canes removal on the modification of photosynthetic pigments content and antioxidant enzymes (peroxidase, POD; catalase, CAT; polyphenol oxidase, PPO; superoxide dismutase, SOD) activities in leaves and fruits of raspberry (Rubus idaeus L.) cultivar 'Willamette' was studied. ProCa increased while canes removal decreased chlorophylls and carotenoids content compared to control. POD, CAT, and PPO activities in leaves after removal of young canes were higher compared to control (2-4 times) which was visually confirmed for POD by isoelectrofocusing. Removal of young canes slithly increased, while ProCa significantly enhanced SOD activity in leaves compared to control (475.10 and 218.38 nkat mg(-1) prot, respectively). Pattern of SOD activity in fruit was similar as in leaf with substantial increase compared to control (about 15 times). Combination of implemented measures increased activity of all enzymes in the leaves and fruits. Our study could provide a better knowledge of the ProCa and canes removal influences on the action of enzymes in order to regulate their activities in fruit products.

Tomato spotted wilt virus (TSWV) is mainly vectored by Frankliniella occidentalis Pergande, and it potentially activates the vector's immune response. However, molecular background of the altered immune response is not clearly understood. Therefore, using a proteomic approach, we investigated the immune pathways that are activated in F. occidentalis larvae after 24 h exposure to TSWV. Two-dimensional isoelectric focusing/sodium dodecyl sulfate polyacrylamide gel electrophoresis (2D-IEF/SDS/PAGE) combined with mass spectrometry (MS), were used to identify proteins that were differentially expressed upon viral infection. High numbers of proteins were abundantly expressed in F. occidentalis exposed to TSWV (73%) compared to the non-exposed (27%), with the majority functionally linked to the innate immune system such as: signaling, stress response, defense response, translation, cellular lipids and nucleotide metabolism. Key proteins included: 70 kDa heat shock proteins, Ubiquitin and Dermcidin, among others, indicative of a responsive pattern of the vector's innate immune system to viral infection. © 2016 Elsevier Ltd

The influence of growth regulator prohexadione-Ca (ProCa) concurrently with young canes removal on the modification of photosynthetic pigments content and antioxidant enzymes (peroxidase, POD; catalase, CAT; polyphenol oxidase, PPO; superoxide dismutase, SOD) activities in leaves and fruits of raspberry (Rubus idaeus L.) cultivar 'Willamette' was studied. ProCa increased while canes removal decreased chlorophylls and carotenoids content compared to control. POD, CAT, and PPO activities in leaves after removal of young canes were higher compared to control (2-4 times) which was visually confirmed for POD by isoelectrofocusing. Removal of young canes slithly increased, while ProCa significantly enhanced SOD activity in leaves compared to control (475.10 and 218.38 nkat mg(-1) prot, respectively). Pattern of SOD activity in fruit was similar as in leaf with substantial increase compared to control (about 15 times). Combination of implemented measures increased activity of all enzymes in the leaves and fruits. Our study could provide a better knowledge of the ProCa and canes removal influences on the action of enzymes in order to regulate their activities in fruit products.

The influence of growth regulator prohexadione-Ca (ProCa) concurrently with young canes removal on the modification of photosynthetic pigments content and antioxidant enzymes (peroxidase, POD; catalase, CAT; polyphenol oxidase, PPO; superoxide dismutase, SOD) activities in leaves and fruits of raspberry (Rubus idaeus L.) cultivar 'Willamette' was studied. ProCa increased while canes removal decreased chlorophylls and carotenoids content compared to control. POD, CAT, and PPO activities in leaves after removal of young canes were higher compared to control (2-4 times) which was visually confirmed for POD by isoelectrofocusing. Removal of young canes slithly increased, while ProCa significantly enhanced SOD activity in leaves compared to control (475.10 and 218.38 nkat mg(-1) prot, respectively). Pattern of SOD activity in fruit was similar as in leaf with substantial increase compared to control (about 15 times). Combination of implemented measures increased activity of all enzymes in the leaves and fruits. Our study could provide a better knowledge of the ProCa and canes removal influences on the action of enzymes in order to regulate their activities in fruit products.

Background: The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. Methods: We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase C gamma 1 (PLC gamma 1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. Results: Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLC gamma 1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "com

Background: The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. Methods: We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase C gamma 1 (PLC gamma 1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. Results: Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLC gamma 1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "com

Background: The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. Methods: We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase C gamma 1 (PLC gamma 1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. Results: Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLC gamma 1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "com

Analysis of low-abundance components in small samples remains a challenge within bioanalytical chemistry, and new techniques for sample pretreatments followed by sensitive and informative detection are required. In this thesis, procedures for preconcentration and separation of proteins and peptides in open microchannels fabricated on silicon microchips are presented. Analyte electromigration was induced by applying a voltage along the channel length, and detection was performed either by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) within the open channel, or by sampling a nL fraction containing the preconcentrated analytes from the channel for subsequent nano-electrospray ionization- (nESI-) or MALDI-MS. Utilizing solvent evaporation from the open system during sample supply, sample volumes exceeding the 25-75 nL channel volume could be analyzed. For preconcentration/separation of components in the discrete channel volume a lid of inert fluorocarbon liquid was used for evaporation control. In Papers I and II, aqueous, carrier-free solutions of proteins and peptides were analyzed, and the method was successfully applied for fast and simple preconcentration of amyloid beta (Aβ) peptides, related to Alzheimer’s disease. The impact of possible impurities in the analysis of carrier-free solutions was investigated in Paper III with the 1D simulation software GENTRANS, and a method for open-channel isoelectric focusing in a tailor-made pH gradient was developed. The latter approach was used in Paper IV for preconcentration and purification of Aβ peptides after immunoprecipitation from cerebrospinal fluid and blood plasma, followed by MALDI-MS from a micropillar chip. Paper V includes simulations of an isotachophoretic strategy for selective enrichment of Aβ peptides. GENTRANS simulations were used to select the electrolyte composition, and 2D simulations in a geometry suitable for on-chip implementation were performed using COMSOL Multiphysics., QC 20160930

Analysis of low-abundance components in small samples remains a challenge within bioanalytical chemistry, and new techniques for sample pretreatments followed by sensitive and informative detection are required. In this thesis, procedures for preconcentration and separation of proteins and peptides in open microchannels fabricated on silicon microchips are presented. Analyte electromigration was induced by applying a voltage along the channel length, and detection was performed either by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) within the open channel, or by sampling a nL fraction containing the preconcentrated analytes from the channel for subsequent nano-electrospray ionization- (nESI-) or MALDI-MS. Utilizing solvent evaporation from the open system during sample supply, sample volumes exceeding the 25-75 nL channel volume could be analyzed. For preconcentration/separation of components in the discrete channel volume a lid of inert fluorocarbon liquid was used for evaporation control. In Papers I and II, aqueous, carrier-free solutions of proteins and peptides were analyzed, and the method was successfully applied for fast and simple preconcentration of amyloid beta (Aβ) peptides, related to Alzheimer’s disease. The impact of possible impurities in the analysis of carrier-free solutions was investigated in Paper III with the 1D simulation software GENTRANS, and a method for open-channel isoelectric focusing in a tailor-made pH gradient was developed. The latter approach was used in Paper IV for preconcentration and purification of Aβ peptides after immunoprecipitation from cerebrospinal fluid and blood plasma, followed by MALDI-MS from a micropillar chip. Paper V includes simulations of an isotachophoretic strategy for selective enrichment of Aβ peptides. GENTRANS simulations were used to select the electrolyte composition, and 2D simulations in a geometry suitable for on-chip implementation were performed using COMSOL Multiphysics., QC 20160930

Analysis of low-abundance components in small samples remains a challenge within bioanalytical chemistry, and new techniques for sample pretreatments followed by sensitive and informative detection are required. In this thesis, procedures for preconcentration and separation of proteins and peptides in open microchannels fabricated on silicon microchips are presented. Analyte electromigration was induced by applying a voltage along the channel length, and detection was performed either by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) within the open channel, or by sampling a nL fraction containing the preconcentrated analytes from the channel for subsequent nano-electrospray ionization- (nESI-) or MALDI-MS. Utilizing solvent evaporation from the open system during sample supply, sample volumes exceeding the 25-75 nL channel volume could be analyzed. For preconcentration/separation of components in the discrete channel volume a lid of inert fluorocarbon liquid was used for evaporation control. In Papers I and II, aqueous, carrier-free solutions of proteins and peptides were analyzed, and the method was successfully applied for fast and simple preconcentration of amyloid beta (Aβ) peptides, related to Alzheimer’s disease. The impact of possible impurities in the analysis of carrier-free solutions was investigated in Paper III with the 1D simulation software GENTRANS, and a method for open-channel isoelectric focusing in a tailor-made pH gradient was developed. The latter approach was used in Paper IV for preconcentration and purification of Aβ peptides after immunoprecipitation from cerebrospinal fluid and blood plasma, followed by MALDI-MS from a micropillar chip. Paper V includes simulations of an isotachophoretic strategy for selective enrichment of Aβ peptides. GENTRANS simulations were used to select the electrolyte composition, and 2D simulations in a geometry suitable for on-chip implementation were performed using COMSOL Multiphysics., QC 20160930

Ein Signalweg während der neuronalen Entwicklung im adulten Gehirn ist der PI3K-PTEN-Akt Signalweg. Akt ist eine Kinase die drei verschiedene Isoformen besitzt, welche durch die Phosphorylierung von S473 und T308 aktiviert werden. KO Modelle der Isoformen haben gezeigt, dass nicht alle Funktionen von anderen Isoformen kompensiert werden können. Die genaue Rolle der einzelnen Isoformen in einem neuronalen Zusammenhang ist nur wenig untersucht. Ziel dieser Arbeit war, eine detaillierte Analyse der einzelnen Akt Isoformen nach der Aktivierung des PI3K-PTEN Signalweges. Dazu wurde im Labor eine neue Methode zur isoelektrischen Fokussierung etabliert., welche Proteine nach ihrer Ladung trennt und somit eine Analyse der Dynamik von Akt Phosphorylierungen in neuronalen Zellen erlaubt. Im Zuge dieser Arbeit konnten wir bisher unerkannte Merkmale der Akt Aktivierung und Phosphorylierung identifizieren. Wir konnten zeigen, dass die S473 und T308 Phosphorylierung in Neuroblastomazellen unabhängig voneinander auftreten kann und, dass verschiedene Akt1 Moleküle unterschiedlich auf die Inhibition von PI3K reagieren. Außerdem konnten wir Verschiebungen in der Aktivierung und in der Expression der unterschiedlichen Isoformen während der postnatalen Gehirnentwicklung der Ratte feststellen. Des Weiteren konnten wir zeigen, dass die Aktivierung von Akt von dem Signal und dem Alter der Neurone abhängig ist. Noch nicht vollständig differenzierte Neurone reagieren vor allem auf BDNF Stimulation, wohingegen adulte, differenzierte Neurone hauptsächlich auf EGF reagieren und dort explizit Akt2 über EGFR und PI3K-p110α Signale aktiviert wird. Im Gegensatz dazu führt der Verlust von PTEN zu einer Aktivierung von hauptsächlich Akt1. Zusammenfassend zeigt diese Arbeit einen komplexen Zusammenhang der Phosphorylierung von Akt auf, welcher Signal- und Entwicklungsabhängig ist bei dem unterschiedliche Akt Populationen auf Wachstumsfaktoren und auf PTEN Verlust reagieren., A major pathway involved in neuronal development is the PI3K-PTEN-Akt pathway. Akt comprises three isoforms, which are activated by phosphorylation of the residues S473 and T308. KO animals for the isoforms have shown differential as well as redundant functions of the three isoforms. However, their individual role in neuronal signaling pathways has not yet been studied in great detail. The aim of this study was to obtain further insight into differential Akt isoform signaling in response to changes in the activity of PI3K and PTEN pathway. A new isoelectric focusing method was established, which allowed us to separate Akt proteins according to their charge, therefore, providing a refined read-out to study dynamics of Akt phosphorylation in a neuronal background. In the course of this project we were able to identify previously undescribed features of Akt phosphorylation and activation. First, we could provide evidence for an uncoupling of the two activating phosphorylation events at S473 and T308 in neuroblastoma cells and differential sensitivities of Akt1 forms towards PI3K inhibition. Secondly, we found a transient shift in Akt isoform activation and abundance during postnatal rat brain development. Thirdly, we were able to show that the activation of different Akt isoforms is dependent of the upstream signal as well as the age of the neuron. Immature neurons were found to be highly responsive to BDNF treatment, whereas mature neurons were most responsive to EGF stimulation leading exclusively to activation of Akt2 in an EGFR- and PI3K/p110α-dependent manner. Stimulation of Akt phosphorylation by the loss of PTEN led to an activation of mainly Akt1 forms, which suggests inherent differences in the Akt pools that are accessible to growth factors dependent PI3Ks as compared to the pools that are controlled by PTEN. In summary, this thesis demonstrates the presence of complex phosphorylation events of Akt in a developmental- and signal-dependent manner in neurons.

The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics.

To measure protein isoforms in individual mammalian cells, we report single-cell resolution isoelectric focusing (scIEF) and high-selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17-pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single-charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.

type:Original Article, identifier:http://igakkai.kms-igakkai.com/wp/wp-content/uploads/1983en/9(4)219-228.1983.pdf

Background: The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. Methods: We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase C gamma 1 (PLC gamma 1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. Results: Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLC gamma 1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "com

Background: The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. Methods: We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase C gamma 1 (PLC gamma 1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. Results: Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLC gamma 1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "com

In this work, electrophoretic preconcentration of protein and peptide samples in microchannels was studied theoretically using the 1D dynamic simulator GENTRANS, and experimentally combined with MS. In all configurations studied, the sample was uniformly distributed throughout the channel before power application, and driving electrodes were used as microchannel ends. In the first part, previously obtained experimental results from carrier-free systems are compared to simulation results, and the effects of atmospheric carbon dioxide and impurities in the sample solution are examined. Simulation provided insight into the dynamics of the transport of all components under the applied electric field and revealed the formation of a pure water zone in the channel center. In the second part, the use of an IEF procedure with simple well defined amphoteric carrier components, i.e. amino acids, for concentration and fractionation of peptides was investigated. By performing simulations a qualitative description of the analyte behavior in this system was obtained. Neurotensin and [Glu1]-Fibrinopeptide B were separated by IEF in microchannels featuring a liquid lid for simple sample handling and placement of the driving electrodes. Component distributions in the channel were detected using MALDI- and nano-ESI-MS and data were in agreement with those obtained by simulation. Dynamic simulations are demonstrated to represent an effective tool to investigate the electrophoretic behavior of all components in the microchannel., QC 20151104

With the ever accumulating understanding of the complexity of biological systems, the design of novel research tools is becoming increasingly important for critical advances in biological and medical technology. Innovation is required not only in the development of better alternatives to existing assays, which are plagued by issues such as low throughput and low reproducibility, but also for the creating of completely new tools that can lead to biological inquiry not previously accessible. Theoretical understanding of mass transport and analytical chemistry not only guides the optimal design of highly efficient devices, but also enables insight of the fundamental processes underlying the system being studied. Accordingly, we have paired a strong understanding of theory with the precise material transport afforded by microfluidics to address technological gaps in a wide range of topics relevant to biological research. Utilizing rational device design and simulations for precise electric field control and polyacrylamide photopatterning to control local chemical conditions, we developed a microfluidic version of the traditional two-dimensional electrophoresis (2DE) assay. 2DE yields the isoelectric point and molecular weight of the components in a sample and is therefore an extremely powerful analytical tool for the study of proteins, yet it is underutilized due to its lack of reproducibility, long run times (up to a day), and the high expertise required perform the assay. Prior attempts to develop microfluidic alternatives have had difficulties integrating the two distinct separations that constitute the assay: isoelectric focusing (IEF) for charge-based separations and molecular sizing. By employing a microchamber geometry and using polyacrylamide gels to localize the chemical conditions required for IEF and molecular sizing, we were able to perform 2DE separations under one hour.One of the challenges about IEF separations is that once proteins reach their isoelectri

With the ever accumulating understanding of the complexity of biological systems, the design of novel research tools is becoming increasingly important for critical advances in biological and medical technology. Innovation is required not only in the development of better alternatives to existing assays, which are plagued by issues such as low throughput and low reproducibility, but also for the creating of completely new tools that can lead to biological inquiry not previously accessible. Theoretical understanding of mass transport and analytical chemistry not only guides the optimal design of highly efficient devices, but also enables insight of the fundamental processes underlying the system being studied. Accordingly, we have paired a strong understanding of theory with the precise material transport afforded by microfluidics to address technological gaps in a wide range of topics relevant to biological research. Utilizing rational device design and simulations for precise electric field control and polyacrylamide photopatterning to control local chemical conditions, we developed a microfluidic version of the traditional two-dimensional electrophoresis (2DE) assay. 2DE yields the isoelectric point and molecular weight of the components in a sample and is therefore an extremely powerful analytical tool for the study of proteins, yet it is underutilized due to its lack of reproducibility, long run times (up to a day), and the high expertise required perform the assay. Prior attempts to develop microfluidic alternatives have had difficulties integrating the two distinct separations that constitute the assay: isoelectric focusing (IEF) for charge-based separations and molecular sizing. By employing a microchamber geometry and using polyacrylamide gels to localize the chemical conditions required for IEF and molecular sizing, we were able to perform 2DE separations under one hour.One of the challenges about IEF separations is that once proteins reach their isoelectri

ObjectiveTo determine to what extent oligoclonal band (OCB) specificities are clonally interrelated and to what degree they are associated with corresponding B-cell responses in the peripheral blood (PB) of multiple sclerosis (MS) patients.MethodsMass-spectrometric proteomic analysis of isoelectric focused (IEF) cerebrospinal fluid (CSF) immunoglobulin G (IgG) was used in combination with next-generation deep-immune repertoire sequencing of PB and CSF IgG heavy chain variable regions from MS patients.ResultsWe find evidence for ongoing stimulation and maturation to antibody-expressing B cells to occur primarily inside the central nervous system (CNS) compartment. B cells participating in OCB production can also be identified in PB; these cells appear to migrate across the blood-brain barrier and may also undergo further antigen stimulation in the periphery. In individual patients, different bands comprising OCBs are clonally related.InterpretationOur data provide a high-resolution molecular analysis of OCBs and strongly support the concept that OCBs are not merely the terminal result of a targeted immune response in MS but represent a component of active B cell immunity that is dynamically supported on both sides of the blood-brain barrier.

Chemical mobilization following IEF enables single-point detection of an ideally stationary equilibrium electrophoresis mode. Despite prior studies exploring optimization of chemical mobilization conditions and recent insight from numerical simulations, understanding of both chemical mobilization mechanisms and the implications of mobilization on IEF analytical performance remains limited. In this study, we utilize full-field imaging of microchannel IEF to assess the performance of a range of canonical chemical mobilization schemes. We empirically demonstrate and characterize key areas where limited understanding of performance implications exists, including: the effects of mobilization solution pH and ion concentration, differences between ionic and zwitterionic mobilization, and diffusion as a source of zone broadening. We utilize Simul5 simulations to gain insight into the sources of the measured performance differences. Measurements of the location, linearity, and slope of the IEF pH gradient (via fluorescent pH markers imaged before and during mobilization) as well as mobilization-associated broadening of focused analytes were performed to quantify performance and determine the dominant sources of variability. Our results suggest that nonuniform broadening of the pH gradient and changes in the pH gradient linearity stem from conductivity nonuniformities in the separation channel and not diffusion-associated band broadening during mobilization.

ObjectiveTo determine to what extent oligoclonal band (OCB) specificities are clonally interrelated and to what degree they are associated with corresponding B-cell responses in the peripheral blood (PB) of multiple sclerosis (MS) patients.MethodsMass-spectrometric proteomic analysis of isoelectric focused (IEF) cerebrospinal fluid (CSF) immunoglobulin G (IgG) was used in combination with next-generation deep-immune repertoire sequencing of PB and CSF IgG heavy chain variable regions from MS patients.ResultsWe find evidence for ongoing stimulation and maturation to antibody-expressing B cells to occur primarily inside the central nervous system (CNS) compartment. B cells participating in OCB production can also be identified in PB; these cells appear to migrate across the blood-brain barrier and may also undergo further antigen stimulation in the periphery. In individual patients, different bands comprising OCBs are clonally related.InterpretationOur data provide a high-resolution molecular analysis of OCBs and strongly support the concept that OCBs are not merely the terminal result of a targeted immune response in MS but represent a component of active B cell immunity that is dynamically supported on both sides of the blood-brain barrier.

Chemical mobilization following IEF enables single-point detection of an ideally stationary equilibrium electrophoresis mode. Despite prior studies exploring optimization of chemical mobilization conditions and recent insight from numerical simulations, understanding of both chemical mobilization mechanisms and the implications of mobilization on IEF analytical performance remains limited. In this study, we utilize full-field imaging of microchannel IEF to assess the performance of a range of canonical chemical mobilization schemes. We empirically demonstrate and characterize key areas where limited understanding of performance implications exists, including: the effects of mobilization solution pH and ion concentration, differences between ionic and zwitterionic mobilization, and diffusion as a source of zone broadening. We utilize Simul5 simulations to gain insight into the sources of the measured performance differences. Measurements of the location, linearity, and slope of the IEF pH gradient (via fluorescent pH markers imaged before and during mobilization) as well as mobilization-associated broadening of focused analytes were performed to quantify performance and determine the dominant sources of variability. Our results suggest that nonuniform broadening of the pH gradient and changes in the pH gradient linearity stem from conductivity nonuniformities in the separation channel and not diffusion-associated band broadening during mobilization.

ObjectiveTo determine to what extent oligoclonal band (OCB) specificities are clonally interrelated and to what degree they are associated with corresponding B-cell responses in the peripheral blood (PB) of multiple sclerosis (MS) patients.MethodsMass-spectrometric proteomic analysis of isoelectric focused (IEF) cerebrospinal fluid (CSF) immunoglobulin G (IgG) was used in combination with next-generation deep-immune repertoire sequencing of PB and CSF IgG heavy chain variable regions from MS patients.ResultsWe find evidence for ongoing stimulation and maturation to antibody-expressing B cells to occur primarily inside the central nervous system (CNS) compartment. B cells participating in OCB production can also be identified in PB; these cells appear to migrate across the blood-brain barrier and may also undergo further antigen stimulation in the periphery. In individual patients, different bands comprising OCBs are clonally related.InterpretationOur data provide a high-resolution molecular analysis of OCBs and strongly support the concept that OCBs are not merely the terminal result of a targeted immune response in MS but represent a component of active B cell immunity that is dynamically supported on both sides of the blood-brain barrier.

The goal of the two-dimensional (2D) electrophoresis protocol described here is to show how to analyse the phenotype of human cultured macrophages. The key role of macrophages has been shown in various pathological disorders such as inflammatory, immunological, and infectious diseases. In this protocol, we use primary cultures of human monocyte-derived macrophages that can be differentiated into the M1 (pro-inflammatory) or the M2 (anti-inflammatory) phenotype. This in vitro model is reliable for studying the biological activities of M1 and M2 macrophages and also for a proteomic approach. Proteomic techniques are useful for comparing the phenotype and behaviour of M1 and M2 macrophages during host pathogenicity. 2D gel electrophoresis is a powerful proteomic technique for mapping large numbers of proteins or polypeptides simultaneously. We describe the protocol of 2D electrophoresis using fluorescent dyes, named 2D Differential Gel Electrophoresis (DIGE). The M1 and M2 macrophages proteins are labelled with cyanine dyes before separation by isoelectric focusing, according to their isoelectric point in the first dimension, and their molecular mass, in the second dimension. Separated protein or polypeptidic spots are then used to detect differences in protein or polypeptide expression levels. The proteomic approaches described here allows the investigation of the macrophage protein changes associated with various disorders like host pathogenicity or microbial toxins.

Apoplastic fluid was extracted from maize (Zea mays L) roots using two procedures: collection from the surface of intact plant roots by filter paper strips (AF) or vacuum infiltration and/or centrifugation from excised root segments (AWF). The content of cytoplasmic marker (glucose-6-phosphate, G-6-P) and antioxidative components (enzymes, organic acids, phenolics, sugars, ROS) were compared in the extracts. The results obtained demonstrate that AF was completely free of G-6-P, as opposed to AWF where the cytoplasmic constituent was detected even at mildest centrifugation (200 x g). Isoelectric focusing of POD and SOD shows the presence of cytoplasmic isoforms in AWF, and HPLC of sugars and phenolics a much more complex composition of AWF, due to cytoplasmic contamination. Organic acid composition differed in the two extracts, much higher concentrations of malic acid being registered in AF, while oxalic acid due to intracellular contamination being present only in AWF. EPR spectroscopy of DEPMPO spin trap in the extracts showed persistent generation of hydroxyl radical adduct in AF. The results obtained argue in favor of the filter strip method for the root apoplastic fluid extraction, avoiding the problems of cytoplasmic contamination and dilution and enabling concentration measurements in minute regions of the root.

Fruit extracts of two raspberry (Rubus idaeus L) cultivars (Autumn Bliss and Polka) were analysed for total phenolic (TPC) and anthocyanin (TACY) content. Correlation of TPC with total antioxidant capacity (TAC) showed higher free-radical scavenging properties of Autumn Bliss (r(2) = 0.9999) compared to Polka (r(2) = 0.8972). Correlation coefficient between TACY and TAC were higher in Autumn Bliss (r(2) = 0.9939) compared to Polka fruits (r(2) = 0.8419). Although total protein concentrations were similar in both cultivars (similar to 0.35 mg mL(-1)), activities of peroxidases and polyphenol oxidases were much higher in Polka, which were confirmed with isoelectric focusing in cationic (pl 9.3) and anionic (pl 3.6) range. HPLC detection showed that among detected flavonoids (catechin, epicatechin, epicatechin gallate, rutin, myricetin, resveratrol, quercetin and kaempferol) epicatechin appears to be the most abundant compound. Chlorogenic, caffeic and p-coumaric acid were also detected. The results indicate that the changes in enzymes activities related to content of substrates play an important role in nutrient quality definition of raspberry fruits.

The miniaturization of biological assays for basic science and clinical diagnostics is a strong focus of the microfluidics field. Substantial impacts on assay time, throughput, and sample requirement, for example, can be achieved through integrating process workflows for the detection of protein analytes. Yet to permeate the broader scientific community, a strong focus on simplified device architectures, modularity, and adaptability should be at the forefront of endeavors in the microfluidics field.Here, I describe thesis contributions covering a number of embodiments of a microfluidic immunoblotting toolbox. Central to the themes of each facet of the toolbox are the integration of assay stages from separations to quantitative protein analyte detection using microfabricated polymer structures. These structures immobilize proteins after weight or charge-based separations from complex clinical samples or cell lysates, preserving separation resolution for often protracted immunoprobing or activity-based detection stages.After describing methods to separate, immobilize, and assay for enzyme activity within polyacrylamide gradient gels, I describe the development of photoactive polyacrylamide matrices that yield rapid, highly efficient capture of separated protein bands upon the application of UV light with performance that is robust to a wide range of assay conditions.These materials form the basis of microfluidic immunoblotting methods based on charge and size separations, culminating in microfluidic western blotting architectures that support analysis of low-zeptomole quantities of target proteins from cell lysates, blood sera, and single cells in integrated, automated assay workflows complete in tens of minutes.Among specific contributions of this thesis are, firstly, the discovery and characterization of an isoelectric point photoswitching phenomenon in green fluorescent protein variants from the jellyfish Aequorea victoria in response to different wavelengths of li

The miniaturization of biological assays for basic science and clinical diagnostics is a strong focus of the microfluidics field. Substantial impacts on assay time, throughput, and sample requirement, for example, can be achieved through integrating process workflows for the detection of protein analytes. Yet to permeate the broader scientific community, a strong focus on simplified device architectures, modularity, and adaptability should be at the forefront of endeavors in the microfluidics field.Here, I describe thesis contributions covering a number of embodiments of a microfluidic immunoblotting toolbox. Central to the themes of each facet of the toolbox are the integration of assay stages from separations to quantitative protein analyte detection using microfabricated polymer structures. These structures immobilize proteins after weight or charge-based separations from complex clinical samples or cell lysates, preserving separation resolution for often protracted immunoprobing or activity-based detection stages.After describing methods to separate, immobilize, and assay for enzyme activity within polyacrylamide gradient gels, I describe the development of photoactive polyacrylamide matrices that yield rapid, highly efficient capture of separated protein bands upon the application of UV light with performance that is robust to a wide range of assay conditions.These materials form the basis of microfluidic immunoblotting methods based on charge and size separations, culminating in microfluidic western blotting architectures that support analysis of low-zeptomole quantities of target proteins from cell lysates, blood sera, and single cells in integrated, automated assay workflows complete in tens of minutes.Among specific contributions of this thesis are, firstly, the discovery and characterization of an isoelectric point photoswitching phenomenon in green fluorescent protein variants from the jellyfish Aequorea victoria in response to different wavelengths of li

Fruit extracts of two raspberry (Rubus idaeus L) cultivars (Autumn Bliss and Polka) were analysed for total phenolic (TPC) and anthocyanin (TACY) content. Correlation of TPC with total antioxidant capacity (TAC) showed higher free-radical scavenging properties of Autumn Bliss (r(2) = 0.9999) compared to Polka (r(2) = 0.8972). Correlation coefficient between TACY and TAC were higher in Autumn Bliss (r(2) = 0.9939) compared to Polka fruits (r(2) = 0.8419). Although total protein concentrations were similar in both cultivars (similar to 0.35 mg mL(-1)), activities of peroxidases and polyphenol oxidases were much higher in Polka, which were confirmed with isoelectric focusing in cationic (pl 9.3) and anionic (pl 3.6) range. HPLC detection showed that among detected flavonoids (catechin, epicatechin, epicatechin gallate, rutin, myricetin, resveratrol, quercetin and kaempferol) epicatechin appears to be the most abundant compound. Chlorogenic, caffeic and p-coumaric acid were also detected. The results indicate that the changes in enzymes activities related to content of substrates play an important role in nutrient quality definition of raspberry fruits.

Fruit extracts of two raspberry (Rubus idaeus L) cultivars (Autumn Bliss and Polka) were analysed for total phenolic (TPC) and anthocyanin (TACY) content. Correlation of TPC with total antioxidant capacity (TAC) showed higher free-radical scavenging properties of Autumn Bliss (r(2) = 0.9999) compared to Polka (r(2) = 0.8972). Correlation coefficient between TACY and TAC were higher in Autumn Bliss (r(2) = 0.9939) compared to Polka fruits (r(2) = 0.8419). Although total protein concentrations were similar in both cultivars (similar to 0.35 mg mL(-1)), activities of peroxidases and polyphenol oxidases were much higher in Polka, which were confirmed with isoelectric focusing in cationic (pl 9.3) and anionic (pl 3.6) range. HPLC detection showed that among detected flavonoids (catechin, epicatechin, epicatechin gallate, rutin, myricetin, resveratrol, quercetin and kaempferol) epicatechin appears to be the most abundant compound. Chlorogenic, caffeic and p-coumaric acid were also detected. The results indicate that the changes in enzymes activities related to content of substrates play an important role in nutrient quality definition of raspberry fruits.

Comparison between protein profiles of soybean obtained by commonly used methods of extraction (Tris buffer and Tris-urea buffer) with methods used for extraction of plant proteins for 2D PAGE analysis (direct solubilization in IEF buffer, acetone extraction, phenol extraction, extraction with urea solubilization buffer and thiourea-urea extraction) was investigated. 2D profiles of samples extracted directly in IEF buffer, in urea solubilization buffer and in acetone were characterized with low number of spots. Analysis of 2D PAGE profiles of Tris buffer and Tris-urea buffer extracts showed high degree of horizontal and vertical streaking. Thiourea-urea extraction gave a higher number of less intense protein spots than phenol extraction. The method of choice, due to a large number of intense spots, would be phenol extraction., Upoređeni su profili proteina semena soje dobijeni tradicionalnim metodama ekstrakcije (Tris-HCl puffer i Tris-urea pufer) sa profilima proteina soje ekstrahovanim metodama koje se obično koriste za ekstrakciju biljnih proteina za 2D PAGE analizu (direktno rastvaranje u IEF puferu, acetonska ekstrakcija, fenolna ekstrakcija, ekstrakcija puferom sa ureom i tiourea/urea ekstrakcija). Cilj rada je bio utvrditi primenljivost ekstrakcije Tris-HCl i Tris-urea puferom u 2D PAGE analizi. Raširena primena ove dve metode ekstrakcije zasnovana je na dobijanju visoke koncentracije proteina koji se karakterišu dobrom rastvorljivošću, kao i na već dobro poznatim Rf vrednostima pojedinih proteinskih podjedinica na SDS PAGE elektroforegramima visoke rezolucije. Tako bi njihova eventualna primena u proteomiks analizama, omogućila kako brzu analizu uzoraka, tako i prikupljanje većeg broja podataka, jer bi se izbegla potreba za resolubilizacijom i gubitak proteina. Poređenje ekstrakcionih metoda vršeno je na osnovu broja rastvornih proteina u ekstraktu, kao i denzitometrijskih merenja broja, intenziteta i oštrine tačaka na 2D profilima u okviru dva različita pH opsega. Premda ekstrakcije sa Tris-HCl i Tris-urea puferom daju najveću koncentraciju proteina u ekstraktu, ove metode daju manji broj tačaka u poredjenju sa ostalim ispitivanim metodama. Takođe, izraženo vertikalno i horizontalno 'razvlačenje' onemogućavaju preciznu denzitometrijsku analizu. Dodatni nedostatak ovih metoda (pogotovu ekstrakcije sa Tris-HCl puferom) jeste produženo vreme potrebno za korak izoelektričnog fokusiranja u poredjenju sa ostalim metodama. Direktna ekstrakcija u IEF puferu i ekstrakcija puferom sa ureom daju slične rezultate i karakterišu se malim brojem difuznih tačaka. Acetonskom ekstrakcijom dobija se mala koncentracija rastvorljivih proteina, a na 2D PAGE profilima uočava se visok stepen horizontalnog razvlačenja. Tiourea- urea ekstrakcija daje veći broj manje intenzivnih tačaka u poređenju sa fenol

Immunoassays are workhorse laboratory tools for detecting protein targets based on highly specific antibody-antigen binding interactions. Greater confidence can be ascribed to an immunoassay when the specific binding interaction is coupled with a separation process based upon some characteristic physicochemical property of the analyte. This dissertation describes the maturation and optimization of microfluidic immunoassay technology to enable the simultaneous detection of multiple targets. A multi-analytical immunoblotting technique is reported which integrates electrophoretic protein separation with antibody-mediated target capture in a two dimensional microgel. This immunoassay overcomes challenges to traditional multi-analytical protein blotting, which involves repeated cycles of antibody stripping and reprobing, exacerbating the laborious nature of conventional Western Blots. In contrast, an automated and integrated blotting workflow is made possible through a novel multi-stage photolithography process to pattern antigen capture gels at adjacent regions with zero dead volume. The blotting assay completes within 5 minutes, and exhibits a linear dynamic range from 8-800 nM. A label free detection strategy is also introduced to enable simultaneous and quantitative multiplexed measurements without the need for sample prelabeling.The challenge of separating a post-translationally modified protein target from its unmodified counterpart motivated the development of an immunoprobed isoelectric focusing (IEF) separation within a polyacrylamide gel. Charge separated proteins are immobilized via covalent attachment to polyacrylamide gel, followed by multispectral antibody-based detection, allowing for correlation of probed post-translational modifications to matching protein targets as well as characteristic pI shifts. Device performance was characterized through analysis of phosphorylated and acetylated proteins forms of heat shock protein 27 and superoxide dismutase 2, r

Immunoassays are workhorse laboratory tools for detecting protein targets based on highly specific antibody-antigen binding interactions. Greater confidence can be ascribed to an immunoassay when the specific binding interaction is coupled with a separation process based upon some characteristic physicochemical property of the analyte. This dissertation describes the maturation and optimization of microfluidic immunoassay technology to enable the simultaneous detection of multiple targets. A multi-analytical immunoblotting technique is reported which integrates electrophoretic protein separation with antibody-mediated target capture in a two dimensional microgel. This immunoassay overcomes challenges to traditional multi-analytical protein blotting, which involves repeated cycles of antibody stripping and reprobing, exacerbating the laborious nature of conventional Western Blots. In contrast, an automated and integrated blotting workflow is made possible through a novel multi-stage photolithography process to pattern antigen capture gels at adjacent regions with zero dead volume. The blotting assay completes within 5 minutes, and exhibits a linear dynamic range from 8-800 nM. A label free detection strategy is also introduced to enable simultaneous and quantitative multiplexed measurements without the need for sample prelabeling.The challenge of separating a post-translationally modified protein target from its unmodified counterpart motivated the development of an immunoprobed isoelectric focusing (IEF) separation within a polyacrylamide gel. Charge separated proteins are immobilized via covalent attachment to polyacrylamide gel, followed by multispectral antibody-based detection, allowing for correlation of probed post-translational modifications to matching protein targets as well as characteristic pI shifts. Device performance was characterized through analysis of phosphorylated and acetylated proteins forms of heat shock protein 27 and superoxide dismutase 2, r

QC 20110615

QC 20110615

Isolated cell walls from maize (Zea mays L) roots exhibited ionically and covalently bound NAD-specific malate dehydrogenase activity. The enzyme catalyses a rapid reduction of oxaloacetate and much slower oxidation of malate. The kinetic and regulatory properties of the cell wall enzyme solubilized with 1 M NaCl were different from those published for soluble, mitochondrial or plasma membrane malate dehydrogenase with respect to their ATP, Pi, and pH dependence. Isoelectric focusing of ionically-bound proteins and specific staining for malate dehydrogenase revealed characteristic isoforms present in cell wall isolate, different from those present in plasma membranes and crude homogenate. Much greater activity of cell wall-associated malate dehydrogenase was detected in the intensively growing lateral roots compared to primary root with decreased growth rates. Presence of Zn2+ and Cu2+ in the assay medium inhibited the activity of the wall-associated malate dehydrogenase. Exposure of maize plants to excess concentrations of Zn2+ and Cu2+ in the hydroponic solution inhibited lateral root growth, decreased malate dehydrogenase activity and changed isoform profiles. The results presented show that cell wall malate dehydrogenase is truly a wall-bound enzyme, and not an artefact of cytoplasmic contamination, involved in the developmental processes, and detoxification of heavy metals.