Pulsed Direct Current Arc-Induced Nanoelectrospray Ionization Mass Spectrometry

This study explores the innovative field of pulsed direct current arc-induced nanoelectrospray ionization mass spectrometry (DCAI-nano-ESI-MS), which utilizes a low-temperature direct current (DC) arc to induce ESI during MS analyses. By employing a 15 kV output voltage, the DCAI-nano-ESI source effectively identifies various biological molecules, including angiotensin II, bradykinin, cytochrome C, and soybean lecithin, showcasing impressive analyte signals and facilitating multicharge MS in positive- and negative-ion modes. Notably, results show that the oxidation of fatty acids using a DC arc produces [M + O - H]- ions, which aid in identifying the location of C═C bonds in unsaturated fatty acids and distinguishing between isomers based on diagnostic ions observed during collision-induced dissociation tandem MS. This study presents an approach for identifying the sn-1 and sn-2 positions in phosphatidylcholine using phosphatidylcholine and nitrate adduct ions, accurately determining phosphatidylcholine molecular configurations via the Paternò-Büchi reaction. With all the advantages above, DCAI-nano-ESI holds significant promise for future analytical and bioanalytical applications.

Ethanolic extract of Caesalpinia bonduc seeds triggers yeast metacaspase-dependent apoptotic pathway mediated by mitochondrial dysfunction through enhanced production of calcium and reactive oxygen species (ROS) in Candida albicans

Candida albicans is a widespread disease-causing yeast affecting humankind, which leads to urinary tract, cutaneous and various lethal systemic infections. As this infection rate steadily increases, it is becoming a significant public health problem. Recently, Caesalpinia bonduc has received much attention from researchers due to its diverse pharmacological properties, including antimicrobial effects. Accordingly, we first planned to explore the in-vitro anticandidal potential of three extracts obtained from C. bonduc seeds against four Candida species. Initially, the anticandidal activity of the seed extracts was checked by the microdilution technique. Out of three seed extracts tested, ethanolic extract of C. bonduc seed (EECS) recorded the best activity against C. albicans. Hence, we next aimed to find out the anticandidal mechanism of EECS in C. albicans. The liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) analysis showed that the major compounds present in the EECS were tocopherols, fucosterol, linoleic acid, β-amyrin, β-sitosterol, campesterol, cassane furanoditerpene, Norcassane furanoditerpene and other diterpenes. To evaluate the cell death mechanism in C. albicans, a series of parameters related to apoptosis, viz., reactive oxygen species (ROS) production, membrane permeability, mitochondrial membrane potential, release of cytochrome c, DNA fragmentation, nuclear condensation, increased Ca²⁺ level in cytosolic and mitochondrial and activation of metacaspase, were analyzed. The results showed that EECS treatment resulted in the elevation of ROS, which leads to plasma membrane permeability in C. albicans. Annexin V staining further confirms the early stage of apoptosis through phosphatidylserine (PS) externalization. We further inspected the late apoptotic stage using DAPI and TUNEL staining assays. From the results, it can be concluded that EECS triggered mitochondrial dysfunction by releasing high levels of ROS, cytochrome c and Ca²⁺resulting in the activation of metacaspase mediated apoptosis, which is the central mechanism behind the cell death of C. albicans. Finally, a Galleria mellonella-C. albicans infection system was employed to assess the in-vivo potential of EECS. The outcomes displayed that the EECS considerably enhanced the recovery rate of G. mellonella larvae from infection after the treatment. Additionally, EECS also recorded low hemolytic activity. This study thus spotlights the anticandidal potential and mechanism of action of EECS against C. albicans and thus delivers a promising treatment approach to manage C. albicans infection in the future.

Single Polylactic Acid Nanowire for Highly Sensitive and Multifunctional Optical Biosensing

Nanowire-based optical biosensors with high sensitivity are highly desired for the detection of biological microenvironments and analysis of cellular processes. However, the current nanowire biosensors are mostly fabricated with metal and semiconductor materials, which are not suitable for long-term use in biological environments due to their incompatible and nondegradable properties. Biosensors based on biofriendly materials (e.g., spider silk) often do not have high enough sensitivity due to high losses or micron sizes. Here, polylactic acid (PLA), a polymer with high optical transparency, good biocompatibility, biodegradability, and flexibility, is used to fabricate nanowires using a directly drawing method for the first time. Because of the strong evanescent wave and abundant carboxyl groups on the surface of nanowires, an ultralow concentration sensing of cytochrome c is achieved with a limit of detection of 1.38 × 10^-17 M, which is much lower than other detection results using semiconductor/metal-based nanosensors (10^-6 to 10^-12 M). On this basis, a label-free and real-time monitoring of cell apoptosis is realized. In addition, by doping quantum dots, the functionalized PLA nanowires can also sense a change in pH. These results are suggestive of the potential for PLA nanowires applied in multifunctional biosensing and biodetection, pushing forward the photomedicine field.

Investigation of interactions between cytochrome c and ginsenosides by native mass spectrometry and molecular docking simulations

RATIONALE

Ginsenosides are considered to be the main functional components in ginseng and possess various important pharmacological activities. The study of the interactions between ginsenosides and proteins is indispensable for understanding the pharmacological activities of ginsenosides. In this work, the interactions of ginsenosides with cytochrome c (cyt c) were investigated by native mass spectrometry and molecular docking simulations.

METHODS

The interactions of four ginsenosides (Rb₁ , Rb₃ , Rf, Rg₁ ) and cyt c in NH₄ OAc solution were investigated by electrospray ionization linear ion trap mass spectrometry (ESI-LTQ-MS). Molecular docking simulations of cyt c complexes were carried out by AutoDock.

RESULTS

The native mass spectrometry results showed that the four ginsenosides were directly bound to cyt c, with stoichiometric ratios of 1:1 and 2:1 in NH₄ OAc. The order of relative binding abilities of ginsenosides to cyt c obtained by ESI-MS was Rb₁  > Rb₃  > Rf > Rg₁ , which was consistent with the docking results. Moreover, molecular docking simulations also indicated potential binding sites of cyt c and ginsenosides. Hydrogen-bond interaction played a very important role in cyt c binding with ginsenosides.

CONCLUSIONS

It has been demonstrated that native MS is a useful tool to investigate the interactions of ginsenosides with cyt c. Molecular docking is a good complement to ESI analysis, and can provide information on potential binding sites of cyt c-ginsenoside complexess. This strategy will be helpful to further understand the interactions of proteins and small molecules.

Gold-Nanoparticle-Functionalized Cobalt-Nickel Phosphate 3D Nanoice Creams to Fabricate Stable and Sensitive Biosensors for the Cytochrome c Assay

Designing a stable and sensitive luminol-based electrochemiluminescence (ECL) analytical platform in the neutral condition has attracted a lot of attention. Here, gold-nanoparticle-functionalized cobalt-nickel phosphate three-dimensional nanoice creams (Au@Co₃Ni₃(PO₄)₄ NICs) are successfully prepared via electrostatic interaction. Generally, cobalt-nickel phosphate nanoice creams (Co₃Ni₃(PO₄)₄ NICs) are synthesized via a mild hydrothermal method and functionalized via polyethylenimine (PEI). Then, Au NPs are adsorbed on the surface of Co₃Ni₃(PO₄)₄ NICs via Au-N weak interaction to fabricate Au@Co₃Ni₃(PO₄)₄ NICs. Owing to the important roles of Au@Co₃Ni₃(PO₄)₄ in exhibiting excellent electrocatalytic activity, as well as preventing the deposition of negatively charged oxidation product induced electrode passivation, luminol in the nanohybrids (LH-Au@Co₃Ni₃(PO₄)₄) gives strong and stable ECL intensity in the neutral conditions. Moreover, the ECL emission of luminol is obviously quenched based on the resonance energy transfer (RET) between luminol as donor and cytochrome c (Cyt c) as acceptor. Hence, a sensitive ECL biosensor is successfully fabricated for the quantitative determination of Cyt c in cell lysates and exhibits wide linear ranges of 1.0 × 10^-4-0.5 × 10^-5 and 0.5 × 10^-5-1.0 × 10^-8 M as well as a low detection limit of 2.48 nM. This novel sensing strategy will broaden the application of transition metal (Co, Ni) phosphates in bioassays.

Apoptosis in cerebrospinal fluid as outcome predictors in severe traumatic brain injury: An observational study

Traumatic brain injury (TBI), due to its high mortality and morbidity, is an important research topic. Apoptosis plays a pathogenic role in a series of neurological disorders, from neurodegenerative diseases to acute neurological lesions.In this study, we analyzed the association between apoptosis and the Glasgow Outcome Scale (GOS), to examine the potential of apoptosis as a biomarker for a TBI outcome. Patients with severe TBI were recruited at the Department of Neurosurgery, Wujin Hospital Affiliated with Jiangsu University, between January 2018 and December 2019. As a control group, healthy subjects were recruited. The concentrations of caspase-3, cytochrome c, sFas, and caspase-9 in the cerebrospinal fluid (CSF) were analyzed by enzyme-linked immunosorbent assay (ELISA). The association between the GOS and the clinical variables age, sex, initial Glasgow Coma Scale (GCS) score, intracranial pressure (ICP), cerebral perfusion pressure (CPP), initial computed tomography (CT) findings, and apoptotic factors was determined using logistic regression. The area under the receiver operator characteristic (ROC) curve (AUC), and thus the sensitivity and specificity of each risk factor, were obtained.The levels of caspase-3, cytochrome c, sFas, and caspase-9 in the TBI group were significantly higher than those in the control group (P < .05). The logistic regression results showed that ICP and caspase-3 were significant predictors of outcome at 6 months post-TBI (P < .05). The AUC was 0.925 and 0.888 for ICP and caspase-3, respectively. However, the AUC for their combined prediction was 0.978, with a specificity and sensitivity of 96.0% and 95.2%, respectively, showing that the combined prediction was more reliable than that of the 2 separate factors.We demonstrated that caspase-3, cytochrome C, sFas, and caspase-9 were significantly increased in the CSF of patients following severe TBI. Furthermore, we found that ICP and caspase-3 were more reliable for outcome prediction in combination, rather than separately.

Finding Value in Wastewaters from the Cork Industry: Carbon Dots Synthesis and Fluorescence for Hemeprotein Detection

Valorisation of industrial low-value waste residues was preconized. Hence, carbon dots (C-dots) were synthesized from wastewaters of the cork industry-an abundant and affordable, but environmentally-problematic industrial effluent. The carbon nanomaterials were structurally and morphologically characterised, and their photophysical properties were analysed by an ensemble of spectroscopy techniques. Afterwards, they were successfully applied as highly-sensitive fluorescence probes for the direct detection of haemproteins. Haemoglobin, cytochrome c and myoglobin were selected as specific targets owing to their relevant roles in living organisms, wherein their deficiencies or surpluses are associated with several medical conditions. For all of them, remarkable responses were achieved, allowing their detection at nanomolar levels. Steady-state and time-resolved fluorescence, ground-state UV-Vis absorption and electronic circular dichroism techniques were used to investigate the probable mechanisms behind the fluorescence turn-off of C-dots. Extensive experimental evidence points to a static quenching mechanism. Likewise, resonance energy transfer and collisional quenching have been discarded as excited-state deactivating mechanisms. It was additionally found that an oxidative, photoinduced electron transfer occurs for cytochrome c, the most electron-deficient protein. Besides, C-dots prepared from citric acid/ethylenediamine were comparatively assayed for protein detection and the differences between the two types of nanomaterials highlighted.

Delayed Desorption Improves Protein Analysis by Desorption Electrospray Ionization Mass Spectrometry

Protein analysis by desorption electrospray ionization mass spectrometry (DESI-MS) is limited and often accompanied by a mass-dependent loss in sensitivity as protein molecular weight increases. Previously, incomplete dissolution was identified as a potential contributing factor to this limitation for larger proteins. Here, we developed a unique two-step configuration in which a prewetting solvent is applied to the sample surface proximal to DESI analysis by a wetting quill to increase dissolution time and the detection of larger proteins. After optimizing the system with a mixture of proteins containing cytochrome c, myoglobin, and chymotripsinogen, we demonstrate the ability of delayed desorption to improve the analysis of larger proteins such as bovine serum albumin. Albumin and other serum proteins, including even larger ones, were also detected directly from diluted goat serum. An additional feature of this technique is the ability to deliver multiple solvents with potential synergistic or cooperative effects. For example, when using acetonitrile solutions of formic acid and ammonium bicarbonate as the prewetting and DESI spray solvent, respectively, the intensity of chymotrypsinogen improved dramatically compared to controls but less so for smaller proteins such as myoglobin and cytochrome c. Adduct removal was also observed for all proteins. These early results demonstrate the ability of this two-step technique for the use of multiple additives and increased dissolution times compared to standard DESI-MS experiments.

The Addition of Polar Organic Solvent Vapors During the Analysis of Proteins by DESI-MS

Exposure of electrospray droplets to organic vapors was shown to dramatically reduce alkali-metal adduction on protein ions and shift protein charge states. Since DESI-MS is affected by similar adduct species as ESI-MS and shares similar ionization mechanisms, polar organic vapor additives should likewise also improve the DESI-MS analysis of proteins. Here the DESI spray was exposed to a variety of polar organic vapor additives. Head space vapors of polar organic solvents were entrained in nitrogen gas and delivered to the atmosphere inside a semi-enclosed plastic enclosure surrounding the spray plume. The vapors of acetone, acetonitrile, ethyl acetate, methanol, and water were investigated. Vapor dependent effects were observed with respect to changes in protein charge state distributions and signal intensities. With ethyl acetate vapor addition, the signal intensities of all proteins investigated were significantly increased, including proteins larger than 25 kDa such as carbonic anhydrase II and bovine serum albumin.

Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes

Protein structures respond to changes in their chemical and physical environment. However, studying such conformational changes is notoriously difficult, as many structural biology techniques are also affected by these parameters. Here, the use of photo-crosslinking, coupled with quantitative crosslinking mass spectrometry (QCLMS), offers an opportunity, since the reactivity of photo-crosslinkers is unaffected by changes in environmental parameters. In this study, we introduce a workflow combining photo-crosslinking using sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA) with our recently developed data-independent acquisition (DIA)-QCLMS. This novel photo-DIA-QCLMS approach is then used to quantify pH-dependent conformational changes in human serum albumin (HSA) and cytochrome C by monitoring crosslink abundances as a function of pH. Both proteins show pH-dependent conformational changes resulting in acidic and alkaline transitions. 93% and 95% of unique residue pairs (URP) were quantifiable across triplicates for HSA and cytochrome C, respectively. Abundance changes of URPs and hence conformational changes of both proteins were visualized using hierarchical clustering. For HSA we distinguished the N-F and the N-B form from the native conformation. In addition, we observed for cytochrome C acidic and basic conformations. In conclusion, our photo-DIA-QCLMS approach distinguished pH-dependent conformers of both proteins.

Ratiometric Nanoparticle Array-Based Near-Infrared Fluorescent Probes for Quantitative Protein Sensing

Quantitative detection of protein biomarkers is crucial to medical diagnosis. Fluorescent probes have been frequently used for protein detection, but they suffered from various weaknesses such as lack of versatility. In particular, most of the reported probes were not capable of simultaneous qualitative and quantitative detection for various proteins. In this paper, we developed novel nanoparticle array-based near-infrared (NIR) ratiometric probes for potent protein analysis, in which the specific protein was able to be distinguished and quantitated within a group of 11 common proteins. The activity of β-galactosidases (β-gal) was temporarily inhibited by the adsorption to magnetic nanoparticles and restored to certain content by replacement with detected proteins, leading to distinctive readout of the enzyme-activatable NIR probe (DCM-β-gal). The readout of the sensor array against 11 proteins, as verified by isothermal titration calorimetry, was processed and transformed into canonical factors with the help of linear discrimination analysis. Moreover, the ratiometric signals of DCM-β-gal were translated to quantitatively detect proteins within the concentration range of 0-100 μg/mL. Based on clear differentiation within both two-dimensional and three-dimensional plots, different proteins could be detected with 100% accuracy with their concentration simultaneously determined, which endowed the sensing system with great potential in clinical diagnosis.

Addition of Serine Enhances Protein Analysis by DESI-MS

Previous studies have suggested that the loss in sensitivity of DESI-MS for large molecules such as proteins is due to the poor dissolution during the short time scale of desorption and ionization. An investigation into the effect of serine as a solvent additive leads to the interesting observation that there is a concentration-dependent improvement in protein signal intensity when micromolar to low millimolar concentrations of serine is combined with a suitable co-additive in DESI spray. This effect, however, was not observed during similar ESI-MS experiments, where the same solvents and proteins were sprayed directly into the MS inlet. This suggests that the mechanism of signal improvement in DESI is associated with the desorption step of proteins, possibly by facilitating dissolution or improving solubility of proteins on the surface in the solvent micro-layer formed during DESI. Other than poor dissolution, cation adduction such as by sodium ions is also a major contributing factor to the mass-dependent loss in sensitivity in both ESI and DESI, leading to an increase in limits of detection for larger proteins. The adduction becomes a more pressing issue in native-state studies of proteins, as lower charge states are more susceptible to adduction. Previous studies have shown that addition of amino acids to the working spray solution during ESI-MS reduces sodium adduction and can help in stabilization of native-state proteins. Similar to the observed reduction in sodium adducts during native-state ESI-MS, when serine is added to the desorbing spray in DESI-MS, the removal of up to 10 mM NaCl is shown. A selection of proteins with high and low pI and molecular weights was analyzed to investigate the effects of serine on signal intensity by improvements in protein solubility and adduct removal. Graphical Abstract.

Electroluminescent aptasensor based on RuSiO2 nanoparticles for detection cytochrome c using ferrocene as quenching probe

A stable sandwiched electrochemiluminescence (ECL) aptasensor was originally constructed established upon Ru(bpy)₃²⁺-doped silica nanoparticles (RuSiO₂ NPs) with ferrocene carboxylic acid-aptamer (Fc-aptamer) to quantitatively detect cytochrome c (Cyt C). Herein, RuSiO₂ NPs and Fc-aptamer were respectively prepared through the microemulsion method and amide reaction to fabricate the ECL aptasensor. Furthermore, Fc-aptamer was used as quenching probe for quenching the ECL emission of RuSiO₂ NPs. In detail, RuSiO₂ NPs were primarily immobilized onto the electrodes by the film-forming function of chitosan. Subsequently, the aptamer was incubated onto the decorated GCE via crosslinking with glutaraldehyde (GA). After Cyt C was connected to the GCE via immunoreaction, Fc-aptamer was immobilized onto the modified electrodes owing to the specific recognition between antigens and aptamer. Ultimately, ECL signals markedly descended owing to the poor electricity conductivity of proteins and superior quenching effect of Fc-aptamer. Under optimum conditions, the designed ECL aptasensor indicated an accurate analysis for Cyt C in a rang of 0.001-100 nM with a detection limit of 0.48 pM (S/N = 3).

High-Resolution HDX-MS of Cytochrome c Using Pepsin/Fungal Protease Type XIII Mixed Bed Column

A pepsin/FPXIII (protease from Aspergillus saitoi, type XIII) mixed bed column significantly improved the resolution of bottom-up hydrogen/deuterium exchange mass spectrometry (HDX-MS) data compared with a pepsin-only column. The HDX-MS method using the mixed bed column determined 65 amide hydrogen exchange rates out of one hundred cytochrome c backbone amide hydrogens. Different cleavage specificities of the two enzymes generated 138 unique high-quality peptic fragments, which allows fine sub-localization of deuterium. The exchange rates determined in this method are consistent within the current study as well as with the previous HDX-NMR study. High-resolution HDX-MS data can determine the exchange rate of each residue not the deuterium buildup curve of a peptic fragment. The exchange rates provide more precise and quantitative measurements of protein dynamics in a more reproducible manner. Graphical Abstract ᅟ.

Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS

Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A₂ (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database. Graphical Abstract ᅟ.

Probing the Dissociation of Protein Complexes by Means of Gas-Phase H/D Exchange Mass Spectrometry

Gas-phase hydrogen/deuterium exchange measured by mass spectrometry (gas-phase HDX-MS) is a fast method to probe the conformation of protein ions. The use of gas-phase HDX-MS to investigate the structure and interactions of protein complexes is however mostly unharnessed. Ionizing proteins under conditions that maximize preservation of their native structure (native MS) enables the study of solution-like conformation for milliseconds after electrospray ionization (ESI), which enables the use of ND₃-gas inside the mass spectrometer to rapidly deuterate heteroatom-bound non-amide hydrogens. Here, we explored the utility of gas-phase HDX-MS to examine protein-protein complexes and inform on their binding surface and the structural consequences of gas-phase dissociation. Protein complexes ranging from 24 kDa dimers to 395 kDa 24mers were analyzed by gas-phase HDX-MS with subsequent collision-induced dissociation (CID). The number of exchangeable sites involved in complex formation could, therefore, be estimated. For instance, dimers of cytochrome c or α-lactalbumin incorporated less deuterium/subunit than their unbound monomer counterparts, providing a measure of the number of heteroatom-bound side-chain hydrogens involved in complex formation. We furthermore studied if asymmetric charge-partitioning upon dissociation of protein complexes caused intermolecular H/D migration. In larger multimeric protein complexes, the dissociated monomer showed a significant increase in deuterium. This indicates that intermolecular H/D migration occurs as part of the asymmetric partitioning of charge during CID. We discuss several models that may explain this increase deuterium content and find that a model where only deuterium involved in migrating charge can account for most of the deuterium enrichment observed on the ejected monomer. In summary, the deuterium content of the ejected subunit can be used to estimate that of the intact complex with deviations observed for large complexes accounted for by charge migration. Graphical abstract ᅟ.

Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array

We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS₂ were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.

Using ZIF-8 as stationary phase for capillary electrophoresis separation of proteins

Recently, the separation of proteins has received much attention, although many techniques require expensive instrumentation and trained analysts. In this work, a low-cost, effective, and environmental friendship capillary electrophoresis (CE) for proteins separation was first time introduced. The ZIF-8 with outstanding properties of large surface area, and accessible tunnels and cages were coated the inner surface of silica capillary as a separation media by electrostatic interaction. The fast baseline separation of Lys, CC, BSA and RNase A can be obtained within 10 min using the ZIF-8 nanocrystals coated capillary column under the optimum separation conditions. Meanwhile, this system showed good reproducibility and stability. Using L-glutamic acid as the selector ligand, the D- and L-phenylalanine were successfully separated by the ZIF-8 nanocrystals coated capillary column. Furthermore, the method was also applied to separate egg white proteins, and three main proteins were separated in a single run.

Label-free fluorescence imaging of cytochrome c in living systems and anti-cancer drug screening with nitrogen doped carbon quantum dots

As an important biomarker for the early stage of apoptosis, cytochrome c (Cyt c) has been recognized as a key component of the intrinsic apoptotic pathway. Fluorescence imaging tools enabling detection of Cyt c in apoptotic signaling have been rarely explored, though they are critical for cell biology and clinical theranostics. Here, we designed a novel label-free N-doped carbon dot (N-doped CD)-based nanosensor that enables fluorescence activation imaging of Cyt c release in cell apoptosis. The inner filter effect of Cyt c towards N-doped CDs enabled quantitative Cyt c measurement. The nanosensor exhibited high sensitivity and selectivity, rapid response, good cell-membrane permeability and low cytotoxicity. All these features are favorable for in situ visualization of Cyt c for apoptosis research. Notably, the developed nanosensor was successfully applied to monitor intracellular release of Cyt c, and to visualize Cyt c in living zebrafish for the first time. Moreover, it also provided a viable platform for cell-based screening of apoptosis-inducing compounds. In virtue of these advantages and potential, the developed assay not only holds great significance for the better understanding of certain diseases at the cellular level, but also provides an invaluable platform for apoptotic studies and screening of anti-cancer drugs toward drug development.

An Aptamer Bio-barCode (ABC) assay using SPR, RNase H, and probes with RNA and gold-nanorods for anti-cancer drug screening

With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer]). After washing and melting, our aptamers, acting as a DNA bio-barcode, are released from the sandwiches and hybridized with the probes specially designed for RNase H for surface plasmon resonance (SPR) sensing. In an aptamer-probe duplex, RNase H digests the RNA in the probe and releases the intact aptamer for another round of hybridization and digestion. With signal enhancement effects from gold-nanorods (Au-NRs) on probes for SPR sensing, the detection limit was found to be 1 nM for the aptamer and 80 pM for Cyto-c. Without the time-consuming DNA amplification steps by PCR, the detection process of this new ABC assay can be completed within three hours. As a proof-of-concept, phenylarsine oxide was found to be a potent agent to kill liver cancer cells with multi-drug resistance at the nano-molar level. This approach thus provides a fast, sensitive and robust tool for anti-cancer drug screening.

Analysis of Cytochrome c Release by Immunocytochemistry

Cytochrome c is normally localized between the inner and outer membranes of mitochondria in healthy cells. However, during apoptosis, it is released into the cytoplasm, where it binds to apoptotic protease activating factor. Caspase-9 is then recruited and activated by this complex in a process known as the induced proximity model. Release of cytochrome c from mitochondria is therefore a critical event in apoptosis and various protocols are available for its measurement. Cytochrome c in mitochondria has a punctate localization pattern in the cell and its translocation to the cytoplasm results in a diffuse distribution. This is visually striking and easily observed by immunocytochemistry. This protocol describes the use of immunocytochemistry to assay cytochrome c release during apoptosis.

Redox-Induced Apoptosis of Human Oocytes in Resting Follicles In Vitro

BACKGROUND

The age-related depletion of the resting follicle (RF) stock occurs as a result of two processes: atresia and entry in growth phase. Due to difficulties in obtaining sufficient numbers of RFs for study, little is known about the apoptotic mechanisms for RF atresia. The present study was designed to investigate the effects of oxidative stress on the apoptosis of RF oocytes.

METHODS

RFs isolated from human adult ovaries were cultured in vitro, treated with H2O2 at various concentrations (50 microM, 100 microM, 1.0 mM) for 1 hour, and observed for up to 48 hours. The oxidant-induced apoptosis of oocytes were observed by detection of DNA fragments, mitochondria membrane potential (MMP), and cytochrome c release.

RESULTS

Based on nuclear morphology and TUNEL (terminal deoxynucleotidyl transferase-mediated dDTP nick end-labeling), oocyte apoptosis was observed in the RFs treated with 50 microM H2O2 with rates of 35% and 43% at 24 and 48 h after treatment, respectively. But intensive oxidative stress (1 mM H2O2) caused mainly necrosis as measured by quantifying propidium iodide (PI)-positive oocytes (44% within 12 hours), with lower level of apoptosis (17%) being observed at 24 hours after treatment. RFs treated with 100 microM H2O2 showed both apoptosis with the similar rate observed at 50microM and necrosis (13% PI-positive oocytes). Although pre-incubation with cyclosporine A (CsA) could effectively prevent oxidant-induced MMP collapse, but failed to suppress apoptosis of oocytes in RFs.

CONCLUSIONS

Oocytes of RFs in adult ovaries retain their ability to undergo apoptosis under oxidative stress, which is both dose- and time-dependent.

Towards nanometer-spaced silicon contacts to proteins

A vertical nanogap device (VND) structure comprising all-silicon contacts as electrodes for the investigation of electronic transport processes in bioelectronic systems is reported. Devices were fabricated from silicon-on-insulator substrates whose buried oxide (SiO2) layer of a few nanometers in thickness is embedded within two highly doped single crystalline silicon layers. Individual VNDs were fabricated by standard photolithography and a combination of anisotropic and selective wet etching techniques, resulting in p(+) silicon contacts, vertically separated by 4 or 8 nm, depending on the chosen buried oxide thickness. The buried oxide was selectively recess-etched with buffered hydrofluoric acid, exposing a nanogap. For verification of the devices' electrical functionality, gold nanoparticles were successfully trapped onto the nanogap electrodes' edges using AC dielectrophoresis. Subsequently, the suitability of the VND structures for transport measurements on proteins was investigated by functionalizing the devices with cytochrome c protein from solution, thereby providing non-destructive, permanent semiconducting contacts to the proteins. Current-voltage measurements performed after protein deposition exhibited an increase in the junctions' conductance of up to several orders of magnitude relative to that measured prior to cytochrome c immobilization. This increase in conductance was lost upon heating the functionalized device to above the protein's denaturation temperature (80 °C). Thus, the VND junctions allow conductance measurements which reflect the averaged electronic transport through a large number of protein molecules, contacted in parallel with permanent contacts and, for the first time, in a symmetrical Si-protein-Si configuration.

Fatigue Test of Cytochrome C Self-Assembled on a 11-MUA Layer Based on Electrochemical Analysis for Bioelectronic Device

A cytochrome c/11-MUA heterolayer was fabricated to analyze its electrochemical characteristics in harsh conditions for a stable bioelectronic device. Since a cytochrome c/11-MUA heterolayer has been applied to construct the bioelectronics device such as non-volatile biomemory device, an understanding of electrochemical property of the heterolayer in harsh conditions such as variation of temperature and pH, and repetition of usage is necessary to manufacture a stable platform of bioelectronic device. Cytochrome c, a metalloprotein to have a heme group, was self-assembled on the Au surface via the chemical linker 11-mercaptoundecanoic acid (11-MUA). Immobilization of the heterolayer was confirmed by surface-enhanced Raman spectroscopy (SERS) and scanning tunneling microscopy (STM). The fatigue test was done by investigating the redox properties based on cyclic voltammetry (CV) of the heterolayer. The retention time test and pH dependence, thermal test of the fabricated heterolayer were conducted by CV, which showed that the fabricated film retained redox properties for more than 33 days, and from pH 5.0 to pH 9.0, from 15 °C to 55 °C. Taken together, our results show that a cytochrome c/11-MUA heterolayer is very stable, which could be used as a platform of bioelectronic device.

Glutamine treatment attenuates hyperglycemia-induced mitochondrial stress and apoptosis in umbilical vein endothelial cells

OBJECTIVE

The aim of this study was to determine the in vitro effect of glutamine and insulin on apoptosis, mitochondrial membrane potential, cell permeability, and inflammatory cytokines in hyperglycemic umbilical vein endothelial cells.

MATERIALS AND METHODS

Human umbilical vein endothelial cells were grown and subjected to glutamine and insulin to examine the effects of these agents on the hyperglycemic state. Mitochondrial function and the production of inflammatory cytokines were assessed using fluorescence analysis and multiple cytotoxicity assays. Apoptosis was analyzed by the terminal deoxynucleotidyl transferase dUTP nick end-labeling assay.

RESULTS

Glutamine maintains the integrity of the mitochondria by reducing the cell permeability and cytochrome c levels and increasing the mitochondrial membrane potential. The cytochrome c level was significantly (p<0.005) reduced when the cells were treated with glutamine. An apoptosis assay revealed significantly reduced apoptosis (p<0.005) in the glutamine-treated cells. Moreover, glutamine alone or in combination with insulin modulated inflammatory cytokine levels. Interleukin-10, interleukin-6, and vascular endothelial growth factor were up-regulated while tumor necrosis factor-α was down-regulated after treatment with glutamine.

CONCLUSION

Glutamine, either alone or in combination with insulin, can positively modulate the mitochondrial stress and cell permeability in umbilical vein endothelial cells. Glutamine regulates the expression of inflammatory cytokines and maintains the balance of the mitochondria in a cytoprotective manner.

New analytical spiral tube assembly for separation of proteins by counter-current chromatography

A new spiral column assembly for analytical separation by counter-current chromatography is described. The column is made from a plastic spiral tube support which has 12 interwoven spiral grooves. The PTFE tubing of 1.6mm ID was first flattened by extruding through a narrow slit and inserted into the grooves to make 5 spiral layers with about 60ml capacity. The performance of the spiral column assembly was tested with separation of three stable protein samples including cytochrome C, myoglobin and lysozyme in a polymer phase system composed of polyethylene glycol 1000 and dibasic potassium phosphate each at 12.5% (w/w) in water. At 2ml/min, three protein samples were well resolved in 1h. The separation time may be further shortened by application of higher revolution speed and flow rate by improving the strength of the spiral tube support in the future.

In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange

Transition of proteins from the solution to the gas phase during electrospray ionization remains a challenging problem despite the large amount of attention it has received during the past few decades. One of the major questions relates to the extent to which proteins in the gas phase retain their condensed phase structures. We have used in-electrospray source hydrogen/deuterium exchange to determine the number of deuterium incorporations as a function of protein mass, charge state and temperature of the desolvating capillary where the reaction occurs. All experiments were performed on a Thermo LTQ FT Ultra equipped with a 7-T superconducting magnet. Ions were generated by an IonMax Electrospray ion source operated in the positive ESI mode. Deuterium exchange was performed by introducing a droplet of D2 O beneath the ESI capillary. We systematically investigated gas phase hydrogen/deuterium (H/D) exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa. We observed that almost all proteins demonstrate similar exchange rates for all charge states and that these rates increase exponentially with the temperature of the desolvating capillary. We did not observe any clear correlation of the number of H/D exchanges with the value of the cross section for a corresponding charge state. We have demonstrated the possibility of performing in-ESI source H/D exchange of large proteins under atmospheric pressure. The simplicity of the experimental setup makes it a useful experimental technique that can be applied for the investigation of gas phase conformations of proteins.

[Effects of bisphenol A exposure during lactation on testicular mitochondria in male mouse offspring]

OBJECTIVE

To study whether maternal bisphenol A (BPA) exposure during lactation stage will induce oxidative stress and apoptosis in male offspring's testis by mitochondrial pathway.

METHODS

After delivery, maternal mice were randomly divided into four groups, including high dose group (50 mg/kg), medium dose group (5 mg/kg), low dose group (0.01 mg/kg) and solvent control group. BPA were given daily by gavage to maternal mice during lactation stage. The pups were raised and sacrificed at PND 75. The effect of BPA exposure on the activity of testicular mitochondrial succinate dehydrogenase (SDH), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA) in male offspring were detected. The expressions of cytochrome C (Cyt C), caspase 3 and apoptosis-inducing factor (AIF) in testes of male offspring were detected by Western blot. Changes of mitochondrial substructure in testicular cells were observed by transmission electron microscopy.

RESULTS

The exposed mice had a significant decrease in the activities of testicular mitochondrial SDH (P < 0.05) in all groups and with notable decrease in the activities of GSH-Px and SOD in the high and medium-dose groups (P < 0.05). BPA also caused testicular mitochondrial MDA increased markedly (P < 0.05). Western blot showed that the expression levels of Cyt C, caspase 3 and AIF increased significantly in the testes of BPA-treated groups (P < 0.05). Under transmission electron microscopy, mitochondria swell, crests obscure and disappear were founded in the high and medium-dose groups.

CONCLUSION

During lactation stage, maternal exposed to BPA induce oxidative stress and apoptosis of testicular cells by possible mechanisms of mitochondrial pathway,which would cause adverse effects on the early development of testis.

Functional microgels assisted tryptic digestion and quantification of cytochrome c through internal standard mass spectrometry

Quantitation of cytochrome c (Cyt c) in cell lysates through surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) using gold nanoparticles (Au NPs) as the matrix and GR-10 peptide as an internal standard has been demonstrated. To shorten digestion time, temperature sensitive microgels containing trypsin (TR) and Au NPs have been employed. As-prepared functional microgels (TR/Au NPs/MGs) allow digestion of Cyt c within 15 s under microwave irradiation. The internal standard SALDI-MS approach provides linearity (R(2) = 0.98) of MS signal ratio (I 1168.6/I 1067.6) of the tryptic digested peptide (m/z 1168.6) to GR-10 peptide (m/z 1067.6) against the concentration of Cyt c ranging from 25 to 200 nM, with a limit of detection (at a signal-to-noise ratio of 3) of 10 nM. This approach has been validated by the analysis of the lysates of HeLa cells, with an average concentration of 13.7 ± 3.5 μM for cytoplasmic Cyt c. Increased concentrations of Cyt c in the HeLa cells treated with etoposide (a commercial drug) or carbon dots (potential drug) have been revealed through this simple, sensitive, and rapid SALDI-MS approach, supporting the drugs induced Cyt c-mediated apoptosis of the cells. This study has shown that this internal standard SALDI-MS approach holds great potential for cell study.

Calcium concentration response to uterine ischemia: a comparison of uterine fibroid cells and adjacent normal myometrial cells

OBJECTIVE

Uterine artery occlusion by laparoscopy (UAOL) has been used for the treatment of uterine fibroids and beneficial effects to patients have been shown in clinical studies since 2000. Fibroid cells are more susceptible to apoptosis than myometrial cells under hypoxic conditions, but the molecular mechanisms underlying this effect remain unclear. The aim of this study was to investigate the role of intracellular calcium (Ca(2+)) release mediated by Ca(2+) channel inositol 1,4,5 trisphosphate receptor1 (IP3R1)/ryanodine receptor1 (RYR1) in the apoptosis of uterine fibroid cells under hypoxia.

STUDY DESIGN

We compared the expressions of IP3R1 and RYR1 in fibroid and surrounding myometrial tissue from 20 patients before UAOL. After 6h treatment under hypoxia (1% O2) with or without Ca(2+) channel blockers (heparin or/and ruthenium red), the intracellular Ca(2+) concentration, cytochrome c (Cytc) protein and cell apoptosis were determined.

RESULTS

IP3R1 and RYR1 mRNA and protein levels were significantly higher in fibroid than in myometrial tissues. Under hypoxic conditions, Ca(2+) concentration in fibroid cells was significantly higher than in myometrial cells (Ca(2+): 82.69±16.92nmol/L vs 46.14±9.11nmol/L, P<0.05), and Cytc increased similarly in fibroid cells. These increases in Ca(2+) concentration, Cytc and cell apoptosis were significantly reversed by calcium blocker in fibroid cells.

CONCLUSION

This study demonstrated that intracellular calcium release mediated by IP3R1/RYR1 could induce apoptosis in uterine fibroid cells under hypoxic conditions, and was responsible for the susceptibility to apoptosis of fibroid cells under UAOL.

Ambient DESI and LESA-MS analysis of proteins adsorbed to a biomaterial surface using in-situ surface tryptic digestion

The detection and identification of proteins adsorbed onto biomaterial surfaces under ambient conditions has significant experimental advantages but has proven to be difficult to achieve with conventional measuring technologies. In this study, we present an adaptation of desorption electrospray ionization (DESI) and liquid extraction surface analysis (LESA) mass spectrometry (MS) coupled with in-situ surface tryptic digestion to identify protein species from a biomaterial surface. Cytochrome c, myoglobin, and BSA in a combination of single and mixture spots were printed in an array format onto Permanox slides, followed by in-situ surface digestion and detection via MS. Automated tandem MS performed on surface peptides was able to identify the proteins via MASCOT. Limits of detection were determined for DESI-MS and a comparison of DESI and LESA-MS peptide spectra characteristics and sensitivity was made. DESI-MS images of the arrays were produced and analyzed with imaging multivariate analysis to automatically separate peptide peaks for each of the proteins within a mixture into distinct components. This is the first time that DESI and LESA-MS have been used for the in-situ detection of surface digested proteins on biomaterial surfaces and presents a promising proof of concept for the use of ambient MS in the rapid and automated analysis of surface proteins.

An aptamer-based bio-barcode assay with isothermal recombinase polymerase amplification for cytochrome-c detection and anti-cancer drug screening

Based on a recently reported ultra-sensitive bio-barcode (BBC) assay, we have developed an aptamer-based bio-barcode (ABC) alternative to detect a cell death marker cytochrome-c (Cyto-c) and its subsequent application to screen anti-cancer drugs. Aptamer is a short single-stranded DNA selected from a synthetic DNA library by virtue of its high binding affinity and specificity to its target based on its unique 3D structure from the nucleotide sequence after folding. In the BBC assay, an antigen (Ag) in analytes is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Abs). Gold nanoparticles (NPs) with another recognition Ab against the same target and hundreds of identical DNA molecules of known sequence are subsequently added to allow the formation of sandwich structures ([MMP-Ab1]-Ag-[Ab2-NP-DNA]). After isolating the sandwiches by a magnetic field, the DNAs hybridized to their complementary DNAs covalently bound on the NPs are released from the sandwiches after heating. Acting as an Ag identification tag, these bio-barcode DNAs with known DNA sequence are then amplified by polymerase chain reaction (PCR) and detected by fluorescence. In our ABC assay, we employed a Cyto-c-specific aptamer to substitute both the recognition Ab and barcode DNAs on the NPs in the BBC assay; and a novel isothermal recombinase polymerase amplification for the time-consuming PCR. The detection limit of our ABC assay for the Cyto-c was found to be 10 ng/mL and this new assay can be completed within 3h. Several potential anti-cancer drugs have been tested in vitro for their efficacy to kill liver cancer with or without multi-drug resistance.

A multifunctional microfluidic droplet-array chip for analysis by electrospray ionization mass spectrometry

This paper describes a multifunctional semi-closed droplet-array chip coupled with electrospray ionization mass spectrometry (ESI-MS) detection for multiple sample pretreatment and analysis. A novel interfacing method for coupling droplet system with ESI-MS was proposed using a sampling probe-two-dimensional (2D) droplet-array strategy. The 2D droplet-array system was composed of an 8 × 8 microwell array chip for droplet storage and a layer of oil covering the droplets served as a "virtual wall" to avoid droplet evaporation or cross-contamination. An L-shaped capillary was adopted as the interface of the droplet array and ESI-MS, using its inlet end as a sampling probe for droplets and its outlet with a tip size of ~20 μm as an electrospray emitter, without the need for any droplet extraction device. The droplet analysis was performed by moving the droplet-array chip to allow the capillary sampling probe to sequentially enter into the droplets through the oil and introduce the sample solution into the capillary emitter for MS detection. The MS analysis time for each droplet sample was 40 s with a sample consumption of ca. 13 nL. A good repeatability of 5.7% (RSD, n = 9) was obtained for 10(-6) M reserpine droplet analysis. The uses of the semi-closed 2D droplet array and off-line interfacing mode provide the system with the substantial flexibility and controllability in droplet indexing, multi-step manipulating, and on-demand sampling for MS analysis. We applied the present system in multi-step pretreatment and identification of small amounts of proteomic samples of myoglobin and cytochrome C, including in-droplet protein reduction, alkylation, digestion, and purification based on solid-phase extraction, matrix modification, sample droplet introduction under flow injection mode, and ESI-MS detection.

A nano LC-MALDI mass spectrometry droplet interface for the analysis of complex protein samples

The integration of matrix-assisted laser desorption ionization (MALDI) mass spectrometry with an upstream analytical separations (such as liquid chromatography and electrophoresis) has opened up new opportunities for the automated investigation of complex protein and peptide mixtures. The ability to efficiently analyze complex proteomic mixtures in this manner is primarily determined by the ability to preserve spatial discrimination of sample components as they leave the separation column. Current interfacing methods are problematic in this respect since minimum fraction volumes are limited to several microliters. Herein we show for the first time an LC-MALDI interface based on the formation, processing and destruction of a segmented flow. The interface consists of a droplet-generator to fractionate LC effluent into nL-volume droplets and a deposition probe that transfers the sample (and MALDI matrix) onto a conventional MALDI-MS target. The efficacy of the method is demonstrated through the analysis of Trypsin digests of both BSA and Cytochrome C, with a 50% enhancement in analytical performance when compared to conventional interface technology.

Immunoexpression of DIABLO, AIF and cytochrome C in gastric adenocarcinoma assessed by tissue Microarray

The aim of this study was to analyze the immunoexpression of (Smac) DIABLO, AIF, cytochrome c, Ki-67 and cleaved caspase-3 in gastric cancer. A tissue microarray (TMA) paraffin block was constructed using gastric adenocarcinoma tissue and adjacent normal adjacent mucosa from 87 patients who had not previously undergone radiotherapy or chemotherapy. Immunohistochemistry was used to evaluate the protein levels. Samples were positive for (Smac) DIABLO in 37 (45.6%) and 37 (46.8%), for AIF in 31 (36.9%) and 36 (45.6%), for cytochrome c in 60 (68.9%) and 44 (54.4%), for Ki-67 in 63 (72.4%) and 52 (61.9%) and for cleaved caspase-3 in 21 (24.1%) and 3 (3.4%) cases of tumor and adjacent normal tissues, respectively. Our results suggest that increased expression of Ki-67 and cleaved caspase-3 could contribute to carcinogenesis. The expression of these proteins indicates an attempt of cells to maintain tissue homeostasis.

Global optimization of the infrared matrix-assisted laser desorption electrospray ionization (IR MALDESI) source for mass spectrometry using statistical design of experiments

Design of experiments (DOE) is a systematic and cost-effective approach to system optimization by which the effects of multiple parameters and parameter interactions on a given response can be measured in few experiments. Herein, we describe the use of statistical DOE to improve a few of the analytical figures of merit of the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source for mass spectrometry. In a typical experiment, bovine cytochrome c was ionized via electrospray, and equine cytochrome c was desorbed and ionized by IR-MALDESI such that the ratio of equine:bovine was used as a measure of the ionization efficiency of IR-MALDESI. This response was used to rank the importance of seven source parameters including flow rate, laser fluence, laser repetition rate, ESI emitter to mass spectrometer inlet distance, sample stage height, sample plate voltage, and the sample to mass spectrometer inlet distance. A screening fractional factorial DOE was conducted to designate which of the seven parameters induced the greatest amount of change in the response. These important parameters (flow rate, stage height, sample to mass spectrometer inlet distance, and laser fluence) were then studied at higher resolution using a full factorial DOE to obtain the globally optimized combination of parameter settings. The optimum combination of settings was then compared with our previously determined settings to quantify the degree of improvement in detection limit. The limit of detection for the optimized conditions was approximately 10 attomoles compared with 100 femtomoles for the previous settings, which corresponds to a four orders of magnitude improvement in the detection limit of equine cytochrome c.

Disposable biosensor based on Au nanoparticles-modified CdS nanorod arrays for detection cytochrome c

A novel disposable biosensor is developed based on gold nanoparticles modified CdS nanorod arrays. The ordered CdS nanorod arrays firstly have been synthesized by a simple hydrothermal method. Then, the CdS nanorod arrays are modified by gold nanoparticles, which are directly fabricated into an electrode for detection of cytochrome c (Cyc) in solution without any pretreatment. The modified CdS nanorod arrays biosensor with the immense surface area and high electrical conductivity shows a good sensitivity and linear range. This method may be used to construct other electrochemical biosensors using aligned nanorod/nanowire films.

Defining the protein complex proteome of plant mitochondria

A classical approach, protein separation by two-dimensional blue native/sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was combined with tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth. We further developed the novel GelMap software package to annotate and evaluate two-dimensional blue native/sodium dodecyl sulfate gels. The software allows (1) annotation of proteins according to functional and structural correlations (e.g. subunits of a distinct protein complex), (2) assignment of comprehensive protein identification lists to individual gel spots, and thereby (3) selective display of protein complexes of low abundance. In total, 471 distinct proteins were identified by mass spectrometry, several of which form part of at least 35 different mitochondrial protein complexes. To our knowledge, numerous protein complexes were described for the first time (e.g. complexes including pentatricopeptide repeat proteins involved in nucleic acid metabolism). Discovery of further protein complexes within our data set is open to everybody via the public GelMap portal at www.gelmap.de/arabidopsis_mito.

Cytochrome c biosensor--a model for gas sensing

This work is about gas biosensing with a cytochrome c biosensor. Emphasis is put on the analysis of the sensing process and a mathematical model to make predictions about the biosensor response. Reliable predictions about biosensor responses can provide valuable information and facilitate biosensor development, particularly at an early development stage. The sensing process comprises several individual steps, such as phase partition equilibrium, intermediate reactions, mass-transport, and reaction kinetics, which take place in and between the gas and liquid phases. A quantitative description of each step was worked out and finally combined into a mathematical model. The applicability of the model was demonstrated for a particular example of methanethiol gas detection by a cytochrome c biosensor. The model allowed us to predict the optical readout response of the biosensor from tabulated data and data obtained in simple liquid phase experiments. The prediction was experimentally verified with a planar three-electrode electro-optical cytochrome c biosensor in contact with methanethiol gas in a gas tight spectroelectrochemical measurement cell.

Reduction in lipopolysaccharide-induced apoptosis of fibroblasts obtained from a patient with gingival overgrowth during nifedipine-treatment

OBJECTIVE

We have previously demonstrated that the mechanism of nifedipine (NIF)-induced gingival overgrowth is related to the observation that proliferation and cell cycle progression of gingival fibroblasts derived from NIF reactive patient (NIFr) are greater than those from NIF non-reactive patient (NIFn). Gingival overgrowth has also been reported to be a result of inhibited apoptosis of gingival fibroblasts. Apoptosis in fibroblasts is induced by lipopolysaccharide (LPS). Thus, we focused upon evaluating whether there is a difference in LPS-induced apoptosis between NIFn and NIFr.

METHODS

Both NIFn and NIFr were arrested in DMEM containing 0.5% FBS, stimulated by LPS, and assayed for apoptosis, cell cycle analysis, Western blotting, and caspase activity.

RESULTS

Compared to NIFn, the number of apoptotic cells was significantly decreased and the percentage of cells in S and G(2)/M phase was significantly increased in NIFr. The levels of Bax and cytochrome c proteins in NIFr were not up-regulated by LPS compared with NIFn. Both NIFn and NIFr displayed the following changes in protein expression: increased Bad, decreased Bcl-xL, and unchanged Bcl-2 and p53. Caspase-3 and -9 activities were significantly increased by LPS in NIFn but were unchanged in NIFr. Caspase-2 activity remained constant whilst caspase-8 activity significantly increased upon LPS treatment in both NIFn and NIFr.

CONCLUSION

Bad, Bax, cytochrome c, p53, and caspases-2, -3, -8, and -9 are pro-apoptotic proteins. Bcl-2 and Bcl-xL are anti-apoptotic proteins. Thus, the mechanism of NIF-induced gingival overgrowth might be related to decreased apoptosis in NIFr through a reduction of Bax, cytochrome c, and caspase-3 and -9.

Highly active antiretroviral therapy drug combination induces oxidative stress and mitochondrial dysfunction in immortalized human blood-brain barrier endothelial cells

The era of highly active antiretroviral therapy (HAART) has controlled AIDS and its related disorders considerably; however, the prevalence of HIV-1-associated neurocognitive disorders has been on the rise in the post-HAART era. In view of these developments, we investigated whether a HAART drug combination of 3'-azido-2',3'-deoxythymidine (AZT) and indinavir (IDV) can alter the functionality of the blood-brain barrier (BBB) endothelial cells, thereby exacerbating this condition. The viability of hCMEC/D3 cells (in vitro model of BBB) that were exposed to these drugs was significantly reduced after 72h treatment, in a dose-dependent manner. Reactive oxygen species were highly elevated after the exposure, indicating that mechanisms that induce oxidative stress were involved. Measures of oxidative stress parameters, such as glutathione and malondialdehyde, were altered in the treated groups. Loss of mitochondrial membrane potential, as assessed by fluorescence microscopy and decreased levels of ATP, indicated that cytotoxicity was mediated through mitochondrial dysfunction. Furthermore, AZT+IDV treatment caused apoptosis in endothelial cells, as assessed by the expression of cytochrome c and procaspase-3 proteins. Pretreatment with the thiol antioxidant N-acetylcysteine amide reversed some of the pro-oxidant effects of AZT+IDV. Results from our in vitro studies indicate that the AZT+IDV combination may affect the BBB in HIV-infected individuals treated with HAART drugs.

Disruption of the mitochondrial thioredoxin system as a cell death mechanism of cationic triphenylmethanes

Alterations in mitochondrial structure and function are a hallmark of cancer cells compared to normal cells and thus targeting mitochondria has emerged as an novel approach to cancer therapy. The mitochondrial thioredoxin 2 (Trx2) system is critical for cell viability, but its role in cancer biology is not well understood. Recently some cationic triphenylmethanes such as brilliant green (BG) and gentian violet were shown to have antitumor and antiangiogenic activity with unknown mechanisms. Here we demonstrate that BG killed cells at nanomolar concentrations and targeted mitochondrial Trx2, which was oxidized and degraded. HeLa cells were more sensitive to BG than fibroblasts. In HeLa cells, Trx2 down-regulation by siRNA resulted in increased sensitivity to BG, whereas for fibroblasts, the same treatments had no effect. BG was observed to accumulate in mitochondria and cause a rapid and dramatic decrease in mitochondrial Trx2 protein. With a redox Western blot method, we found that treatment with BG caused oxidation of both Trx1 and Trx2, followed by release of cytochrome c and apoptosis-inducing factor from the mitochondria into the cytosol. Moreover, this treatment resulted in an elevation of the mRNA level of Lon protease, a protein quality control enzyme in the mitochondrial matrix, suggesting that the oxidized Trx2 may be degraded by Lon protease.

Nanoparticle-functionalized porous polymer monolith detection elements for surface-enhanced Raman scattering

The use of porous polymer monoliths functionalized with silver nanoparticles is introduced in this work for high-sensitivity surface-enhanced Raman scattering (SERS) detection. Preparation of the SERS detection elements is a simple process comprising the synthesis of a discrete polymer monolith section within a silica capillary, followed by physically trapping silver nanoparticle aggregates within the monolith matrix. A SERS detection limit of 220 fmol for Rhodamine 6G is demonstrated, with excellent signal stability over a 24 h period. The capability of the SERS-active monolith for label-free detection of biomolecules was demonstrated by measurements of bradykinin and cytochrome c. The SERS-active monoliths can be readily integrated into miniaturized micrototal-analysis systems for online and label-free detection for a variety of biosensing, bioanalytical, and biomedical applications.

Potential of poly(styrene-co-divinylbenzene) monolithic columns for the LC-MS analysis of protein digests

Two polystyrene-based capillary monolithic columns of different length (50 and 250 mm) were used to evaluate the effects of column length on gradient separation of protein digests. A tryptic digest of a 9-protein mixture was used as a test sample. Peak capacities were determined from selected extracted ion chromatograms, and tandem mass spectrometry data were used for database matching using the MASCOT search engine. Peak capacities and protein identification scores were higher for the long column with all gradients. Peak capacities appear to approach a plateau for longer gradient times; maximum peak capacity was estimated to be 294 for the short column and 370 for the long column. Analyses with similar gradient slope produced a ratio of the peak capacities of 3.36 for the long and the short column, which is slightly higher than the expected value of the square root of the column length ratio. The use of a longer monolith improves peptide separation, as reflected by higher peak capacity, and also increases protein identification, as observed from higher identification scores and a larger number of identified peptides. Attention has also been paid to the peak production rate (PPR, peak capacity per unit time). For short analysis times, the short column produces a higher PPR, while for analysis times longer than 40 min, the PPR of the 250-mm column is higher.

(E)-1-(3,4-dihydroxyphenethyl)-3-styrylurea inhibits proliferation of MCF-7 cells through G1 cell cycle arrest and mitochondria-mediated apoptosis

Growing interest in the beneficial effects of antioxidants has inspired the synthesis of new phenolic acid phenethyl ureas (PAPUs) with enhanced antioxidant potential. We have previously shown the capacity of one PAPU compound, (E)-1-(3,4-dihydroxyphenethyl)-3-styrylurea (PAPU1), to induce caspase-dependent apoptosis in melanoma cells. In the present study, we examined the anti-proliferative effects of PAPU compounds on MCF-7 human breast cancer cells and determined the molecular mechanisms involved. Treatment with PAPU compounds inhibited predominantly proliferation in these cells, where the PAPU1 was the most efficient form. Flow cytometric analysis showed that PAPU1 blocked cell cycle progression in the G(0)/G(1) phase, and reduced the proportion of cells in G(2)/M phase. This was related to the inhibition of cell cycle regulatory factors, including cyclin D/E and cyclin-dependent kinase (CDK) 2/4, through induction of p21(Cip1). PAPU1 also induced the mitochondrial-mediated and caspase-dependent apoptosis in MCF-7 cells. This was evidenced by cellular changes in the levels of Bcl-2 and Bax, loss of the mitochondrial membrane potential, release of cytochrome c into the cytosol, and caspase-9 activation. Collectively, our results suggest that G(1) cell cycle regulatory proteins and mitochondrial pathways are the crucial targets of PAPU1 in the chemoprevention of breast cancer cells.

24R,25-Dihydroxyvitamin D3, lysophosphatidic acid, and p53: a signaling axis in the inhibition of phosphate-induced chondrocyte apoptosis

Maintenance of the pool of chondrocytes in the resting zone of the growth plate in the presence of the physiological apoptogen inorganic phosphate (Pi) is crucial for skeletal development. Costochondral resting zone chondrocytes are regulated by the vitamin D metabolite 24R,25-dihydroxyvitamin D3 [24R,25(OH)(2)D(3)], with increased production of sulfated glycosaminoglycan-rich extracellular matrix, and reduced matrix metalloproteinase activity. The effects of 24R,25(OH)(2)D(3) are mediated by activation of phospholipase D (PLD), resulting in increased production of lysophosphatidic acid (LPA) and LPA-mediated proliferation, maturation, inhibition of Pi-induced apoptosis, and reduction of p53. However, the exact mechanism by which 24R,25(OH)(2)D(3) and LPA exert their effects is not fully understood. It was found that both 24R,25(OH)(2)D(3) and LPA attenuate Pi-induced caspase-3 activity. The actions of 24R,25(OH)(2)D(3) and LPA were dependent upon G(αi), LPA receptor(s) 1 and/or 3, PLD, phospholipase C (PLC), and intracellular calcium, phosphoinositide 3-kinase (PI(3)K) signaling, and nuclear export. 24R,25(OH)(2)D(3) decreased both p53 abundance and p53-medaited transcription and inhibited Pi-induced cytochrome c translocation. Moreover, LPA induced increased mdm2 phosphorylation, a negative regulator of p53. Taken together, these data show that 24R,25(OH)(2)D(3) inhibits Pi-induced apoptosis through Ca(2+), PLD, and PLC signaling and through LPA-LPA1/3-G(αi)-PI(3)K-mdm2-mediated p53 degradation, resulting in decreased cytochrome c translocation and caspase-3 activity.

Overexpression of ornithine decarboxylase suppresses thapsigargin-induced apoptosis

Ornithine decarboxylase (ODC), the key enzyme of polyamine biosynthesis, has paradoxical roles in apoptosis. Our published papers show overexpression of ODC prevents the apoptosis induced by many cytotoxic drugs. Thapsigargin (TG) is an inhibitor of the sarcoplasmic/endoplasmic reticulum (ER) Ca(2+) ATPase (SERCA) pumps and causes ER stress-induced apoptosis. We used ODC overexpressing cell lines to examine whether overexpression of ODC inhibits TG-induced apoptosis. Our results indicated overexpression of ODC attenuated TG-induced apoptosis. Overexpression of ODC blocked procaspase-4 cleavage and phosphorylation of protein kinase-like ER-resident kinase (PERK), triggered by TG. It also attenuated the increase in CAAT/enhancer binding protein homologous protein (CHOP). Cells with overexpressed ODC had greater Bcl-2 expression. Overexpression of ODC preserved the expression of Bcl-2, inhibited the increase in Bak and stabilized mitochondrial membrane potential without the influences of TG. Cytochrome c release and down-stream caspase activation were blocked. That is, overexpression of ODC inhibits the mitochondria-mediated apoptotic pathway, induced by TG. Finally, overexpression of ODC maintains the protein and mRNA expression of SERCA. In conclusion, overexpression of ODC suppresses TG-induced apoptosis by blocking caspase-4 activation and PERK phosphorylation, attenuating CHOP expression and inhibiting the mitochondria-mediated apoptotic pathway.

Aptamer-based bio-barcode assay for the detection of cytochrome-c released from apoptotic cells

The recently developed bio-barcode (BBC) assay using polymerase chain reaction (PCR) to generate signals has been shown to be an extraordinarily sensitive method to detect protein targets. The BBC assay involves a magnetic microparticle (with antibody to capture the target of interest) and gold nanoparticle (with recognition antibody and thiolated single-stranded barcode DNAs) to form a sandwich around the target. The concentration of target is determined by the amount of barcode DNA released from the nanoparticles. Here we describe a modification using aptamers to substitute the gold nanoparticles for the BBC assay. In this study, we isolated a 76-mer monoclonal aptamer against cytochrome-c (cyto-c) and this single-stranded DNA in defined 3D structure for cyto-c was used in the BBC assay for both recognition and readout reporting. After magnetic separation, the aptamer was amplified by PCR and this aptamer-based barcode (ABC) assay was sensitive enough to detect the cyto-c in culture medium released from the apoptotic cells after drug treatment at the picomolar level. When compared to the conventional cyto-c detection by Western blot analysis, our ABC assay is sensitive, and time for the detection and quantification with ready-made probes was only 3 h.

Direct analysis of reversed-phase high-performance thin layer chromatography separated tryptic protein digests using a liquid microjunction surface sampling probe/electrospray ionization mass spectrometry system

The sampling, ionization and detection of tryptic peptides separated in one-dimension on reversed-phase high-performance thin layer chromatography (HPTLC) plates was performed using liquid microjunction surface sampling probe electrospray ionization mass spectrometry. Tryptic digests of five proteins [cytochrome c, myoglobin, beta-casein, lysozyme and bovine serum albumin (BSA)] were spotted on reversed phase HPTLC RP-8 F254s and HPTLC RP-18 F254s plates. The plates were then developed using 70/30 methanol/water with 0.1M ammonium acetate. A dual purpose extraction/electrospray solution containing 70/30/0.1 water/methanol/formic acid was infused through the sampling probe during analysis of the developed lanes. Both full scan mass spectra and data dependent tandem mass spectra were acquired for each development lane to detect and verify the peptide distributions. Data dependent tandem mass spectra provided both protein identification and sequence coverage information. Highest sequence coverages were achieved for cytochrome c and myoglobin (62.5% and 58.3%, respectively) on reversed phase RP-8 plates. While the tryptic peptides were separated enough for identification, the peptide bands did show some overlap with most peptides located in the lower half of the development lane. Proteins whose peptides were more separated gave higher sequence coverage. Larger proteins such as beta-casein and BSA which were spotted in lower relative amounts gave much lower sequence coverage than the smaller proteins.