Detection of damage-recognition proteins from human lymphocytes

Proteins recognizing and binding to damaged DNA (DDB-proteins) were analyzed in human lymphocytes obtained from healthy donors. Using an electrophoretic mobility shift assay several complexes between nuclear extract proteins and damaged DNA were detected: a complex specific for DNA damaged by N-acetoxy-N-acetylaminofluorene, another complex specific for UV-irradiated DNA, and two complexes specific for DNA damaged by cis-dichlorodiammine platinum. All the detected complexes differed in electrophoretic mobility and possibly contained different proteins. Complexes specific for free DNA ends were also detected in protein extracts from lymphocytes.     

Detection of proteins using a colorimetric bio-barcode assay

The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA detection method that allows for a simple and straightforward detection of biomolecules of interest (here we detect interleukin-2, an important biomarker (cytokine) for many immunodeficiency-related diseases and cancers). The protocol is composed of the following steps: (i) conjugation of target capture molecules and barcode DNA strands onto silica microparticles, (ii) target capture with probes, (iii) separation and release of barcode DNA strands from the separated probes, (iv) detection of released barcode DNA using DNA-modified gold nanoparticle probes and (v) red-to-blue color change analysis with a graphic software. Actual target detection and quantification steps with premade probes take approximately 3 h (whole protocol including probe preparations takes approximately 3 days).     

Multiprobe laser reflectometry in imaging and characterization of biological tissues

Laser backscattered radiation from human forearm and foot were measured by multi-probe reflectometer, which consisted of one input probe and three output probes placed at distances of 2, 4 and 6 mm from the input probe. The normalized backscattered intensity (NBI) signals from the tissue surface, measured by the output probes, after digitization, were used to reconstruct the reflectance images of tissues in various layers below the skin surface. From NBI profiles measured at various locations of the tissues on the forearm the corresponding optical parameters, the scattering (mu(s)) and absorption (mu(a)) coefficients and the anisotropy parameter g, by matching these with profiles as simulated by Monte Carlo procedure were determined. From these data the optical parametric images of forearm were reconstructed which show the variation of these parameters at various locations. Similarly, the NBI data were collected from the foot sole region of healthy and diabetes subjects and their images reconstructed. These images showed the variation in the NBI in the diabetic foot sole compared to that of healthy subject, indicating the tissue structural changes. These procedures could be useful for diagnostic and therapeutic applications of lasers.     

Detection of hypothetical proteins in human fetal perireticular nucleus

There is a legion of hypothetical proteins (HP) in prokaryotic and eukaryotic proteomes and the aim of this study was to describe HP in the perireticular nucleus (PN), a key structure in human brain development. Tissue from four PNs was homogenized and extracted proteins were run on two-dimensional gel electrophoresis followed by in-gel digestion and mass spectrometrical identification of proteins. Several databases were used for obtaining bioinformatic information and searching for functional and structural domains. Five spots represented HP: KIAA0423 protein (Q9Y4F4), hypothetical protein KIAA0153 (Q14166), hypothetical protein DKFZp564A2416 (Q9NTW4), hypothetical protein DKFZp564H1122 (Q9H0W9), and hypothetical protein DKFZp564D1378 (Q9H0R4). These structures were predicted to serve in cell cycle, DNA-condensation, neurogenesis, or apoptosis. The existence of formerly HP proteins in the PN of human fetal brain is shown, thus extending knowledge of the brain proteome and proposing the method used as a suitable analytical tool for searching HP.     

Three-color imaging using fluorescent proteins in living zebrafish embryos

The zebrafish embryo is especially valuable for cell biological studies because of its optical clarity. In this system, use of an in vivo fluorescent reporter has been limited to green fluorescent protein (GFP). We have examined other fluorescent proteins alone or in conjunction with GFP to investigate their efficacy as markers for multi-labeling purposes in live zebrafish. By injecting plasmid DNA containing fluorescent protein expression cassettes, we generated single-, double-, or triple-labeled embryos using GFP, blue fluorescent protein (BFP, a color-shifted GFP), and red fluorescent protein (DsRed, a wild-type protein structurally related to GFP). Fluorescent imaging demonstrates that GFP and DsRed are highly stable proteins, exhibiting no detectable photoinstability, and a high signal-to-noise ratio. BFP demonstrated detectable photoinstability and a lower signal-to-noise ratio than either GFP or DsRed. Using appropriate filter sets, these fluorescent proteins can be independently detected even when simultaneously expressed in the same cells. Multiple labels in individual zebrafish cells open the door to a number of biological avenues of investigation, including multiple, independent tags of transgenic fish lines, lineage studies of wild-type proteins expressed using polycistronic messages, and the detection of protein-protein interactions at the subcellular level using fluorescent protein fusions.     

Innovations in the imaging of brain functions using fluorescent proteins

Fluorescence imaging has enabled us to decipher spatiotemporal information coded in complex tissues. Genetically encoded probes that enable fluorescence imaging of excitable cell activity have been constructed by fusing fluorescent proteins to functional proteins that are involved in physiological signaling. The probes are introduced into an intact organism and targeted to specific tissues, cell types, or subcellular compartments, thereby allowing specific signals to be extracted more efficiently than was previously possible. In this primer, I will describe how this approach has met neuroscientists' demands and desires.     

In situ imaging and isolation of proteins using dsDNA oligonucleotides

As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These techniques, however, cannot be applied to the imaging of nuclear antigens as these single-stranded aptamers bind endogenous RNA and DNA with high affinity. To overcome this problem, we have developed a novel method for the in situ detection of proteins using double-stranded DNA oligonucleotides. To demonstrate this system we have utilized the prokaryotic DNA-binding proteins LacI and TetR as peptide tags to image fusion proteins in situ using dsDNA oligonucleotides encoding either the Lac or Tet operator. Using fluorescent and fluorogold dsDNA oligonucleotides, we localized within the nucleus a TetR–PML fusion protein within promyelocytic leukaemia protein (PML) bodies by LM and a LacI–SC35 fusion protein within nuclear speckles by correlative light and electron microscopy (LM/EM). Isolation of LacI–SC35 was also accomplished by using biotinylated dsDNA and streptavidin sepharose. The use of dsDNA oligonucleotides should complement existing aptamer in situ detection techniques by allowing the multiple detection and localization of nuclear proteins in situ and at high resolution.     

Identification of human nasal mucous proteins using proteomics

The determination of possible biomarkers in nasal secretion of healthy subjects can have a role in early diagnosis of diseases such as rhinosinusitis. For this purpose, nasal lavage fluids (NLFs) from ten volunteers, collected before and after they had been submitted to nasal provocations, were investigated. Separation and analysis of proteins present in this complex matrix was performed using a capillary liquid chromatography-electrospray-quadrupole-time of flight mass spectrometry equipment. From among a total of 111 proteins found (89 known and two unknown proteins), 42 of which had never been previously described in this fluid, such as Deleted in Malignant Brain Tumors 1 isoform a precursors, and cytoskeletal proteins were identified with high statistical score. Three proteins of palate lung nasal epithelial clone (PLUNC) family: SPLUNC1, LPLUNC1, and LPLUNC2 were identified. Proteins involved in innate (27%) and acquired immunity (21%) systems were major components of NLF. Cellular (52% of all proteins identified) such as cytoskeletal (33%), functional (15%), and regulatory (4%) proteins, normally present in the nasal cavity, have also been identified. The proteomic approach presented here allowed us to identify the proteins involved in acquired and innate immune response in the nose against microbial infections and unclean inhaled air.     

Identification of human proteins using the linguist's tools

The symbolic sequences of the exons that make human proteins are subjected to methods of statistical linguistics. The ideas developed for the natural languages by G. K. Zipf, when applied to these sequences, show significant promise. In particular, we argue, the Zipf's exponent differentiates, and hence, identifies disparate human sequences.     

Detection of glucocorticoid sensitive secretory proteins from human melanoma cells

Summary NEL-M1 human melanoma cells have been established to grow in Ham's F12 medium in the absence of serum, hormones, and exogenous growth factors. Conditioned medium from NEL-M1 cultures stimulates growth of these same cells whereas glucocorticoids retard growth in the presence and absence of conditioned medium. Because recent reports indicate that glucocorticoids inhibit the synthesis of growth factors from a variety of cell types, we hypothesized that glucocorticoids may be inhibiting growth of NEL-M1 cells by either suppressing the synthesis of the autocrine growth factor or regulating other secretory proteins that may inhibit the activity of the autocrine growth factor. Initial studies were done to clearly show that NEL-M1 cells were growth inhibited, both in vivo and in vitro, when exposed to the synthetic glucocorticoid, triamcinolone acetonide (TA). When NEL-M1 cells were injected into nude mice and treated with TA (100 μg per mouse per week) a 67% reduction in tumor mass was observed compared to the control group over a 5-wk growth period. Additional studies show that in a serum-free defined medium TA (100 nM) inhibited growth of MEL-M1 cells by 56% after 6 d in culture. At this same time TA was shown to affect the expression of several proteins secreted from these cells. TA treatment resulted in the appearance of a 125 000 molecular weight protein, suppression of the synthesis-secretion of three proteins (37 000, 57 000, and 76 000 molecular weight) and enhanced expression of a 60 000-molecular weight protein. However when NEL-M1 cells were cultured in conditioned medium from TA-treated cells, a stimulation in both [³H]thymidine incorporation into DNA and cell proliferation was observed. When the conditioned medium was fractionated by Amicon ultrafiltration, the growth stimulatory activity was found in the <10 000 molecular weight fraction. These results demonstrate that glucocorticoids, as a single agent, inhibit the growth of NEL-M1 human melanoma cells. However, this growth inhibition by glucocorticoids may not be through the regulation of the synthesis-secretion of the autocrine growth factor. Furthermore, the data suggest that the glucocorticoid-sensitive secretory proteins may not be directly involved in the in vitro regulation of NEL-M1 cellular growth.     

Detection and quantification of proteins using self-excited PZT-glass millimeter-sized cantilever

A composite self-excited PZT-glass cantilever (4mm in length and 2mm wide) was fabricated and used to measure the binding and unbinding of model proteins. A key feature of the cantilever is that its resonant frequency is dependent on its mass. The fabricated cantilever has mass change sensitivity in liquid of 7.2 x 10(-11)g/Hz. Resonant frequency change was measured as protein reacted or bound with the sensing glass cantilever surface. Protein concentrations, 0.1 and 1.0mg/mL, which resulted in nanogram mass change were successfully detected. The mass change sensitivity gave a total mass change of 54+/-0.45 ng for the binding of anti-rabbit IgG (biotin conjugated) to rabbit IgG immobilized cantilever and the subsequent binding of captavidin. The unbinding of anti-rabbit IgG and captavidin gave a total mass change of 54+/-1.70 ng. Fluorescence based assays showed the combined mass of both proteins in the released samples was 54+/-2.24 ng. The binding kinetics of the model proteins is modeled as first order. The initial binding rate constant of anti-rabbit IgG to rabbit IgG was 1.36+/-0.02(min(mg/mL))(-1). The initial binding rate constant of captavidin to biotinylated anti-rabbit IgG was (2.57 x 10(-1))+/-0.003(min(mg/mL))(-1). The significance of the results we report here is that millimeter-sized PZT-actuated glass cantilevers have the sensitivity to measure in real-time protein-protein binding, and the binding rate constant.     

High-resolution imaging of proteins in human teeth by scanning probe microscopy

High-resolution studies of dental tissues are of considerable interest for biomedical engineering and clinical applications. In this paper, we demonstrate the application of piezoresponse force microscopy (PFM) to nanoscale imaging of internal structure of human teeth by monitoring the local mechanical response to an electrical bias applied via a conductive tip. It is shown that PFM is capable of detecting dissimilar components of dental tissues, namely, proteins and calcified matrix, which have resembling morphology but different piezoelectric properties. It is demonstrated that collagen fibrils revealed in chemically treated intertubular dentin exhibit high piezoelectric activity and can be visualized in PFM with spatial resolution of 10 nm. Evidence of the presence of protein inclusions of 100-200 nm wide and several micrometers long in tooth enamel has been obtained. Furthermore, it is found that the peritubular dentin and intertubular dentin exhibit different piezoelectric behavior suggesting different concentration of collagen fibrils. The obtained results demonstrate a high potential of PFM in providing an additional insight into the structure of dental tissues. It is suggested that the PFM approach can be used to study the structure of a wide range of biological materials by monitoring their electromechanical behavior at the nanoscale.     

Detection of gender differences in rat lens proteins using 2-D-DIGE

The glass-like transparency of the human eye lens is achieved by the tight packing of abundant crystallin proteins. However, the precise role of the accessory non-crystallin proteins is not well understood. We have carried out 2-DE mapping of these proteins in rat lens. This showed the presence of the high molecular weight filamentous structural proteins spectrin, filensin, tubulin, vimentin, actin and phakinin as well as several forms of potential crystallin oligomers comprised of alphaA, betaB1, betaA1 and betaA4 chains. Other proteins that were present include, heat shock protein 71, WD repeat protein 1, and several enzymes including alpha-enolase, pyruvate kinase, transketolase and aldose reductase. 2-D-DIGE analysis revealed several expression differences between the lens proteomes of male and female rats. Female rat lenses contained lower levels of aldose reductase, increased proteolyic fragments of the structural proteins filensin, vimentin and phakinin and higher levels of potential alphaA, betaB1 and betaA1 crystallin oligomers. Taken together these findings suggest that there are potential differences in oxidative stress regulation between male and female rat lenses, which may have implications on susceptibility to cataract formation. Future studies aimed at elucidating pre-cataractic changes in the non-crystallin proteins described here may facilitate identification of novel markers involved in cataractogenesis.     

Detection of amino-terminal tryptophan in peptides and proteins using dansyl chloride

A sensitive method is described for the detection of amino-terminal tryptophan in peptides and proteins as the dansyl derivative. The use of the method is illustrated with a tetrapeptide and with the enzyme phospholipase C from Bacillus cereus. The method may also be applicable when internal tryptophanyl residues are encountered during dansyl-Edman manual sequencing of peptides and proteins.     

Detection of biotinylated proteins in polyacrylamide gels using an avidin-fluorescein conjugate

Biotinylated proteins are widely used as a molecular tool in biotechnological applications. In this paper, we demonstrated that biotinylated proteins after electrophoresis were detected directly in gels using an avidin-fluorescein conjugate with a fluorescence image analyzer. Upon analysis of the purified and chemically biotinylated protein, the sensitivity of this method was almost equal to that of silver staining. Chemically biotinylated proteins of Escherichia coli cell surfaces could also be specifically detected with our method. Furthermore, recombinant proteins fused with the biotin acceptor domain and biotinylated enzymatically in vivo were also detected in a lysate of E. coli specifically. The sensitivity and specificity of our method are high, and the procedure is simple. Therefore, our method would benefit detection of biotinylated proteins via gel electrophoresis and also various fields of study using avidin-biotin technology.     

The functional study of human proteins using humanized yeast

Journal of Microbiology - The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the...