Effects of thawing,refreezing and storage conditions of tissue samples and protein extracts on 2‐DE spot intensity

We report that reliable quantitative proteome analyses can be performed with tissue samples stored at ?80°C for up to 10 years. However, storing protein extracts at 4°C for 24 h and freezing protein extracts at ?80°C and thawing them significantly altered 41.6 and 17.5% of all spot intensities on 2‐DE gels, respectively. Fortunately, these storing effects did not impair the reliability of quantifying 2‐DE experiments. Nonetheless, the results show that freezing and storage conditions should be carefully controlled in proteomic experiments.     

Chemometric methods for simultaneous quantification of lactic,malic and fumaric acids

Lactic, fumaric and malic acids are commonly used in food and pharmaceutical industries. During microbial production of these compounds, it is important to determine their concentrations in the fermentation broth with a rapid and sensitive method. Spectrophotometry is commonly used. However, UV‐spectral overlap between these organic acids makes it difficult to determine each of them individually from the mixture. In order to overcome this problem, statistical methods, namely principal component regression (PCR) and partial least squares‐1 methods, were tested and compared with conventional HPLC techniques. The absorbance data matrix was obtained by measuring the absorbances of 21 ternary mixtures of lactic, fumaric and malic acids in a wavelength range of 210–260 nm. Calibration and validation were performed by using the data obtained in a mixture of these organic acids. The prediction abilities of the methods were tested by applying them to fermentation broths. The precision of the PCR method was better than that of the partial least squares‐1 method. In the PCR method, the correlation coefficients between actual and predicted concentrations of the organic acids were calculated as 0.970 for lactic acid and 0.996 for fumaric acid in fermentation broths. The concentration of malic acid was not detected due to its low concentration in samples. These results show that the PCR method can be applied for simultaneous determination of lactic, fumaric and malic acids in fermentation broths.     

Diffusion delays and unstirred layer effects at monolayer cultures of Chinese hamster ovary cells

Cells grown in monolayer culture offer a convenient system for binding and other experiments under conditions that preserve the complexity of the living state. Kinetics experiments, however, may be distorted by the time course of drug penetration into even so simple a “tissue” as the monolayer. The impediments include unstirred layers both above and between the cells, the congregation of receptors within the confined space between cells, and nonspecific binding to membrane components. The contributions of these factors were investigated in cultures of Chinese hamster ovary (CHO) cells either nontransfected or stably transfected with μ opioid receptors. The dissociation of [³H]naloxone was four times faster under displacement than under infinite dilution conditions, clearly demonstrating the “retention effect” of receptors confined in space. Even the penetration of this ligand between nontransfected cells showed salient delays with respect to diffusion into a slab, indicating that nonspecific, low-affinity binding to membrane components was arresting its progress. The optical sectioning capabilities of confocal microscopy demonstrated that the kinetics of two fluorescent antagonists depended on the vertical plane, providing direct evidence for slowed diffusion down a single cell depth. Modeling shows that kinetic errors increase with receptor density, forward rate constant, and the thickness of the unstirred layer.     

Phenotypic variation among local populations of phlebotomine sand flies (Diptera: Psychodidae) in southern Turkey.

The wing-shape morphology of local populations of the medically important phlebotomine sand flies, Phlebotomus sergenti, P. papatasi, P. tobbi, and P. similis, were examined in both sexes by using geometric morphometrics. There are three major mountain ranges that may serve as geographical barriers for species distribution in the study area and four main gaps were recognized among these barriers. We found no statistically important differences in wing morphology in all examined species in both sexes for all local populations. These results show that the barriers are not sufficient to stop gene flow among local populations of sand flies. The graphical depiction of PCA, CVA, and F-test confirmed our morphometric study suggesting that the difference in wing morphology between P. similis and P. sergenti indicates that these are clearly different species. These two show sympatric distribution in the Konya Plain of Anatolia.     

DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli

The DcuS-DcuR system of Escherichia coli is a two-component sensor-regulator that controls gene expression in response to external C(4)-dicarboxylates and citrate. The DcuS protein is particularly interesting since it contains two PAS domains, namely a periplasmic C(4)-dicarboxylate-sensing PAS domain (PASp) and a cytosolic PAS domain (PASc) of uncertain function. For a study of the role of the PASc domain, three different fragments of DcuS were overproduced and examined: they were PASc-kinase, PASc, and kinase. The two kinase-domain-containing fragments were autophosphorylated by [gamma-(32)P]ATP. The rate was not affected by fumarate or succinate, supporting the role of the PASp domain in C(4)-dicarboxylate sensing. Both of the phosphorylated DcuS constructs were able to rapidly pass their phosphoryl groups to DcuR, and after phosphorylation, DcuR dephosphorylated rapidly. No prosthetic group or significant quantity of metal was found associated with either of the PASc-containing proteins. The DNA-binding specificity of DcuR was studied by use of the pure protein. It was found to be converted from a monomer to a dimer upon acetylphosphate treatment, and native polyacrylamide gel electrophoresis suggested that it can oligomerize. DcuR specifically bound to the promoters of the three known DcuSR-regulated genes (dctA, dcuB, and frdA), with apparent K(D)s of 6 to 32 micro M for untreated DcuR and < or =1 to 2 microM for the acetylphosphate-treated form. The binding sites were located by DNase I footprinting, allowing a putative DcuR-binding motif [tandemly repeated (T/A)(A/T)(T/C)(A/T)AA sequences] to be identified. The DcuR-binding sites of the dcuB, dctA, and frdA genes were located 27, 94, and 86 bp, respectively, upstream of the corresponding +1 sites, and a new promoter was identified for dcuB that responds to DcuR.     

Col IV and Fn distribution in prostatic adenocarcinoma and correlation of 67LR, MMP-9 and TIMP-1 expression with Gleason score

OBJECTIVE: To assess the immunoreactivity of 5 proteins related to basement membrane (BM) and extracellular matrix in order to investigate whether any of them correlates with differentiation of prostatic adenocarcinoma (PAc). Two of these markers are collagen type IV (Col IV), the collagenous component of basement membrane, and fibronectin (Fn), an adhesion protein in extracellular matrix. Others are matrix metalloproteinase-9 (MMP-9), a type IV collagenase, tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), which has a high affinity for MMP-9, and 67-kd laminin receptor (67LR), which belongs to the non-integrin laminin binding receptor family. STUDY DESIGN: Forty-three PAc cases with Gleason scores ranging between 5 and 10 and 10 benign prostatic hyperplasia (BPH) cases, the control group, were included in the study. Formalin-fixed and paraffin-embedded tissue slides from each case were immunostained with the avidin-biotin-peroxidase method. Immunoreactivity was determined by means of a scoring system similar to the Gleason scoring system. RESULTS: Overexpression of Col IV, Fn, 67LR and MMP-9 was detected in PAc as compared with BPH, whereas no difference was determined in TIMP-1 expression. Among these, only 67LR correlated statistically with Gleason score. CONCLUSION: Expression of 67LR in tumor cells was significantly increased in parallel to tumor grade. This may be useful in microscopic evaluation of PAc.     

Effects of lossy image compression on quantitative image analysis of cell nuclei

OBJECTIVE: To investigate whether statistically significant changes occur in quantitative image analysis of cell nuclei when lossy image compression techniques are used. STUDY DESIGN: Thirty-five stoichiometric, Feulgen-stained samples of rat hepatocytes, human thyroid and ovarian cancer cell nuclei were used. Image analysis was performed by a computerized system that used AutoCyte LINK V1.1.1.56 software (Burlington, North Carolina, U.S.A.) for image acquisition and Zeiss Vision KS 400 V3.0 software (Oberkochen, Germany) for quantitative image analysis. After lossy JPEG compression of acquired images at different quality levels, some densitometric features were selected and measurements performed. RESULTS: We observed that nearly all the standard densitometric features showed statistically significant changes when images were compressed with the lossy JPEG algorithm. However, most invariant densitometric moment features remained free of statistically significant changes. CONCLUSION: The standard densitometric measurements that we used do not tolerate lossy compression. However, analyses using invariant densitometric features may be performed on images compressed with lossy JPEG, resulting in simpler, less expensive systems demanding less network bandwidth.     

Novel metal-chelate affinity adsorbent for purification of immunoglobulin-G from human plasma

Metal-chelating ligand and/or comonomer 2-methacrylolyamidohistidine (MAH) was synthesized by using methacryloyl chloride and L-histidine methyl ester. MAH was characterized by NMR and FTIR. Spherical beads with an average diameter of 75-125 microm were produced by suspension polymerization of methylmethacrylate (MMA) and MAH carried out in an aqueous dispersion medium. Poly(MMA-MAH) beads had a specific surface area of 37.5 m(2)/g. Poly(MMA-MAH) beads were characterized by water uptake studies, FTIR, SEM and elemental analysis. Elemental analysis of MAH for nitrogen was estimated as 34.7 microM/g of polymer. Then, Cu(2+) ions were chelated on the beads. Cu(2+)-chelated beads with a swelling ratio of 38% were used in the adsorption of human-immunoglobulin G (HIgG) from both aqueous solutions and human plasma. The maximum adsorption capacities of the Cu(2+)-chelated beads were found to be 12.2 mg/g at pH 6.5 in phosphate buffer and 15.7 mg/g at pH 7.0 in MOPS. Higher adsorption value was obtained from human plasma (up to 54.3 mg/g) with a purity of 90.7%. The metal-chelate affinity beads allowed one-step separation of HIgG from human plasma. The adsorption-desorption cycle was repeated 10 times using the same beads without noticeable loss in their HIgG adsorption capacity.