PathAct: a novel method for pathway analysis using gene expression profiles

We developed PathAct, a novel method for pathway analysis to investigate the biological and clinical implications of the gene expression profiles. The advantage of PathAct in comparison with the conventional pathway analysis methods is that it can estimate pathway activity levels for individual patient quantitatively in the form of a pathway-by-sample matrix. This matrix can be used for further analysis such as hierarchical clustering and other analysis methods. To evaluate the feasibility of PathAct, comparison with frequently used gene-enrichment analysis methods was conducted using two public microarray datasets. The dataset #1 was that of breast cancer patients, and we investigated pathways associated with triple-negative breast cancer by PathAct, compared with those obtained by gene set enrichment analysis (GSEA). The dataset #2 was another breast cancer dataset with disease-free survival (DFS) of each patient. Contribution by each pathway to prognosis was investigated by our method as well as the Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis. In the dataset #1, four out of the six pathways that satisfied p < 0.05 and FDR < 0.30 by GSEA were also included in those obtained by the PathAct method. For the dataset #2, two pathways (“Cell Cycle” and “DNA replication”) out of four pathways by PathAct were commonly identified by DAVID analysis. Thus, we confirmed a good degree of agreement among PathAct and conventional methods. Moreover, several applications of further statistical analyses such as hierarchical cluster analysis by pathway activity, correlation analysis and survival analysis between pathways were conducted.     

Monitoring growth of Escherichia coli using a two-channel optical sensor

Summary The growth of Escherichia coli strain TG 1 was monitored, measuring simultaneously the culture fluorescence and the 360° reflection at 578 nm with a two-channel optical sensor. It was observed that the culture fluorescence at 366 nm excitation was approximately three times higher than the NADH fluorescence of washed E. coli cells whereas the 360° reflection at 578 nm was comparable. The reason for this effect was found to be the accumulation of riboflavin in the cultivation liquid of the E. coli cells being equal to approximately 0.05 mg/g biomass. In shaken batch cultivations of the same strain the amount of riboflavin in the cell-free cultivation liquid correlated with the biomass being a very sensitive indicator of E. coli growth.Correspondence to: W. S. Kunz     

A novel protein refolding method using a zeolite

We have succeeded in developing a simple and effective protein refolding method using the inorganic catalyst, beta-zeolite. The method involves the adsorption of proteins solubilized with 6M guanidine hydrochloride from inclusion body (IB) preparations onto the zeolite. The denaturant is then removed, and the proteins in the IBs are released from the zeolite with polyoxyethylene detergent and salt. All of the IBs tested (11 different species) were successfully refolded under these conditions. The refolded proteins are biochemically active, and NMR analysis of one of the proteins (replication protein A 8) supports the conclusion that correct refolding does occur. Based on these results, we discuss the refolding mechanism.     

Temperature-induced reversals of rotation in phycomyces

The steady state extension and rotation rates of the Phycomyces sporangiophore were measured as a function of temperature. Maximum growth occurred at 27°C; maximum rotation at 28°C. The rotation to extension ratio, a qualitative parameter of cell wall structure, is affected differently by high and low temperatures. Steady state counterclockwise rotation, as opposed to the normal clockwise rotation, was found at both high and low temperatures. The extensional and rotational responses to step changes in temperature were also measured. The conclusions are drawn that a relative decrease in the lysis rate of wall polymer is responsible for the decrease in growth rate at low temperatures, and that a relative increase in the rate of wall synthesis and cross-linking is responsible for the decrease in growth rate at high temperatures. It is suggested that reversals in rotation result from changes in the handedness of the wall's helical structure.     

Characterization of intestinal phosphate absorption using a novel in vivo method

A new, completely in vivo method of measuring the rate of intestinal phosphate absorption has been developed. As expected from previous in vitro and ex vivo measurements, intestinal phosphate absorption is potently and rapidly stimulated by 1,25-dihydroxyvitamin D3. The response is saturated with as little as 11.3 ng of 1,25-dihydroxyvitamin D3 per day, consistent with a genomic mechanism. The effect of 1,25-dihydroxyvitamin D3 disappears when the dosing solution of phosphate is at 2 M, suggesting that 1,25-dihydroxyvitamin D3 stimulates active transport of phosphate but not diffusion of phosphate. Finally, unlike findings resulting from in vitro or ex vivo experiments, no evidence in vivo was obtained that phosphate absorption requires sodium or is inhibited by potassium.     

Intramolecular masking of nuclear localization signals: analysis of importin binding using a novel AlphaScreen-based method

Active nuclear import of proteins requires the recognition of a nuclear localization sequence (NLS) by members of the importin (IMP) family of proteins. We have developed a modified AlphaScreen-based assay able to estimate the solution binding affinities of such interactions using biotinylated IMPs and His6-tagged NLS-containing proteins. We describe this assay in detail as well as its application in documenting the phenomenon of intramolecular masking of NLSs using recombinant green fluorescent protein (GFP) fusion proteins containing sequences from the SV40 large tumor T antigen (T-ag). We also use it to examine, for the first time, IMP binding to the cancer cell-specific proapoptotic factor viral protein 3 (VP3) from the chicken anemia virus (CAV). High-affinity binding of the IMPalpha/beta heterodimer to the T-ag NLS was observed when the GFP tag was fused to its N terminus but not to its C terminus. Effects of flanking residues were also observed in GFP-T-ag fusion derivatives containing the Thr128 NLS-inactivating mutation, whereby the absence of flanking sequences N terminal to the T-ag NLS appeared to decrease the specificity of the mutation in terms of oblating IMPalpha/beta binding. IMPbeta, but not IMPalpha or the IMPalpha/beta heterodimer, was found to bind to CAV VP3 with high affinity. Interestingly, GFP-VP3(74-121) bound to IMPbeta with threefold higher affinity than the full-length protein, GFP-VP3(1-121), implying that the NLS is masked to a significant extent in the context of full-length protein. This may represent a regulatory mechanism to control nuclear import in a tumor cell-specific fashion.     

A novel method for the estimation of soybean chlorophyll content using a smartphone and image analysis

The development of smartphones, specifically their cameras, and imaging technologies has enabled their use as sensors/measurement tools. Here we aimed to evaluate the applicability of a fast and noninvasive method for the estimation of total chlorophyll (Chl), Chl a, Chl b, and carotenoids (Car) content of soybean plants using a smartphone camera. Single leaf disc images were obtained using a smartphone camera. Subsequently, for the same leaf discs, a Chl meter was used to obtain the relative index of Chl and the photosynthetic pigments were then determined using a classic method. The RGB, HSB and CIELab color models were extracted from the smartphone images and correlated to Chl values obtained using a Chl meter and by a standard laboratory protocol. The smartphone camera was sensitive enough to capture successfully a broad range of Chl and Car contents seen in soybean leaves. Although there was a variation between color models, some of the proposed regressions (e.g., the S and b index from HSB and Lab color models and NRI [RGB model]) were very close to the Chl meter values. Based on our findings, smartphones can be used for rapid and accurate estimation of soybean and Car contents in soybean leaves.     

A novel method for detection of virus-infected cells through moving optical gradient fields using adenovirus as a model system.

BACKGROUND: Most methods for cellular analysis require labeling with specific antibodies or dyes and are often destructive. We have developed a technology called Optophoresis trade mark, which measures cell physiology based on the cell's motion in a near-infrared optical gradient. This technique does not require labels, is nondestructive, and involves minimal sample processing. METHODS: We have used Optophoresis to interrogate nonproductive and productive adenovirus-infected cell lines. Using an adenoviral vector containing green fluorescent protein (GFP) as a secondary assay, we show that viral infection can be monitored with Optophoresis. RESULTS: In HeLa cells, adenovirus infection after 24 h caused a 12% to 17% increase in optophoretic motility of the cells. In 293 cells, adenovirus infection resulted in a 40% increase in the optophoretic motility. The P values obtained were 4.5 x 10(-11) between noninfected and infected HeLa cells, and 2.1 x 10(-13) between noninfected and infected 293 cells. Cells infected with adenovirus lacking the GFP reporter gene gave similar shifts. In a time course, we observed an optophoretic shift after 4 h of infection, well before GFP expression. CONCLUSIONS: Optophoresis provides nondestructive, label-free analysis of viral infection. Detection is independent of reporter gene expression and can be observed early in the infection process.     

Tumor growth inhibition by sonodynamic therapy using a novel sonosensitizer

Sonodynamic therapy (SDT) with low-intensity ultrasound combined with a sonosensitizer may be a promising approach to cancer therapy. Use of ultrasound has the advantage of being noninvasive, with deep-penetration properties, and convenient because of the low or no sensitivity of sonosensitizers to light. In this study, SDT with a novel sonosensitizer (a porphyrin derivative) was evaluated in vitro and in vivo. Ultrasound irradiation with a sonosensitizer elicited potent sonotoxicity in vitro without the danger of phototoxicity. The sonotoxic effect was mediated by reactive oxygen species (ROS) and was reduced by ROS scavengers. Cell membrane lipid peroxidation increased significantly just after ultrasound irradiation with a sonosensitizer, but there was no increase in apoptosis. In an in vivo mouse xenograft model, SDT with a sonosensitizer markedly inhibited tumor cell growth. The skin hypersensitivity after light exposure was not observed in a sonosensitizer-treatment group, consistent with the in vitro findings. These results suggest that ROS generated by SDT with a sensitizer can damage tumor cells, resulting in necrosis and prevention of tumor growth. This noninvasive treatment with no adverse effects such as skin sensitivity is therefore promising for therapy of cancers located deep within patients.     

High-throughput analysis of hexosamine using a colorimetric method

A 96-well plate method was developed for analysis of total hexosamine content in biological samples. Four hexosamine monomer derivatives—glucosamine hydrochloride, glucosamine sulfate, galactosamine hydrochloride, and mannosamine hydrochloride—were examined for the linearity of their spectra in the concentration range specified in the assay. The hexosamine concentration analysis range was linear from 0.1 to 1 mM. The quantification of hexosamines from chitin and chitosan upon acid hydrolysis was also tested. Accurate quantification of glucosamine content in chitin and chitosan with different molecular sizes and degrees of acetylation was demonstrated using the new method.     

Development of a novel optical bionanosensor

We have developed a novel optical bionanosensor platform using a supported bilayer lipid membrane (SBLM), which has generic multi-analyte sensing capabilities. The SBLM is produced using a novel combination of ordered nanostructured thin film i.e. Langmuir-Blodgett (LB) and self-assembly deposition methodologies. A heptamer linear RGD (arginine-glycine-aspartate) containing peptide was covalently attached to a BODIPY (donor) lipid dye and utilised as an optical biosensor for integrin alpha(v)beta(3) loaded HUVEC's (sensitivity = 1000 cells ml(-1)). A second BODIPY (acceptor) lipid dye was integrated into the SBLM thus enabling signal amplification via a Forster resonance energy transfer (FRET) mechanism. The fluidity of the bilayer was confirmed via fluorescence recovery after photobleaching (FRAP) techniques and was performed without the need for fusogens.     

Genetic recombination in sexual crosses of phycomyces

Sexual crosses between strains of Phycomyces blakesleeanus , involving three auxotrophic and one color marker and yielding a high proportion of zygospore germination, are described. Samples of 20–40 germ spores from 311 individual fertile germ sporangia originating from five two-factor and three three-factor crosses were characterized. The results show: (1) absence of any contribution of apogamic nuclei to the progeny, (2) confirmation of Burgeff's conjecture that the germ spores of any germ sporangium in most cases derive from one meiosis. In a cross involving two allelic markers the analysis of 175 pooled germ sporangia suggests an intragenic recombination frequency of 0.6%. All other factor combinations tested are unlinked. The bulk of the germ spores are homokaryotic. However, a small portion (4%) are heterokaryotic with respect to mating type.     

A novel electroporation method using a capillary and wire-type electrode

Electroporation is widely used to achieve gene transfection. A common problem in electroporation is that it has a lower viability than any other transfection method. In this study, we developed a novel electroporation device using a capillary tip and a pipette that was effective on a wide range of mammalian cells, including cell lines, primary cells, and stem cells. The capillary electroporation system considerably reduced cell death during electroporation because of its wire-type electrode, which has a small surface area. The experimental results also indicated that the cell viability was dependent on the change in pH induced by electrolysis during electroporation. Additionally, the use of a long and narrow capillary tube combined with simple pipetting shortened the overall time of the electroporation process by up to 15 min, even under different conditions with 24 samples. These results were supported by comparison with a conventional electroporation system. The transfection rate and the cell viability were enhanced by the use of the capillary system, which had a high transfection rate of more than 80% in general cell lines such as HeLa and COS-7, and more than 50% in hard-to-transfect cells such as stem or primary cells. The viability was approximately 70-80% in all cell types used in this study.     

A novel method for the on-line analysis of fermentation broth using a sampling device,microcentrifuge and HPLC

Summary This paper describes a novel system for on-line sampling and analysis of whole broth from a fermenter. The system comprises a steam sterilisable sampling device, high speed microcentrifuge and HPLC. We present results characterising the separation efficiency of the microcentrifuge under different conditions, and illustrate the system with glucose and acetate data from an Escherichia coli fermentation using the system. The on-line measurements have been confirmed by off-line analysis.