Visualization of three-way comparisons of omics data

BACKGROUND: Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limit the visualizations to single datasets or pairwise comparisons. RESULTS: We propose a color-coding approach for the representation of three-way comparisons. The approach is based on the HSB (hue, saturation, brightness) color model. The three compared values are assigned specific hue values from the circular hue range (e.g. red, green, and blue). The hue value representing the three-way comparison is calculated according to the distribution of three compared values. If two of the values are identical and one is different, the resulting hue is set to the characteristic hue of the differing value. If all three compared values are different, the resulting hue is selected from a color gradient running between the hues of the two most distant values (as measured by the absolute value of their difference) according to the relative position of the third value between the two. The saturation of the color representing the three-way comparison reflects the amplitude (or extent) of the numerical difference between the two most distant values according to a scale of interest. The brightness is set to a maximum value by default but can be used to encode additional information about the three-way comparison. CONCLUSION: We propose a novel color-coding approach for intuitive visualization of three-way comparisons of omics data

Carbon monoxide: impact on remethylation/transsulfuration metabolism and its pathophysiologic implications

Carbon monoxide (CO) is a gaseous product generated by heme oxygenase (HO), which oxidatively degrades heme. While the stress-inducible HO-1 has well been recognized as an anti-oxidative defense mechanism under stress conditions, recent studies suggest that cancer cells utilize the reaction for their survival. HO-2, the constitutive isozyme, also plays protective roles as a tonic regulator for neurovascular function. Although protective roles of the enzyme reaction and CO have extensively been studied, little information is available on the molecular mechanisms by which the gas exerts its biological actions. Recent studies using metabolomics revealed that CO inhibits cystathionine β-synthase (CBS), which generates H2S, another gaseous mediator. The CO-dependent CBS inhibition may impact on the remethylation cycle and related metabolic pathways including the methionine salvage pathway and polyamine synthesis. This review focuses on the gas-responsive regulation of metabolic systems, particularly the remethylation and transsulfuration pathways, and their putative implications for cancer and ischemic diseases

Emergence of a Euglena bioconvection spot controlled by non-uniform light

Microorganisms possess taxes, which are the behavioral response to stimuli. The interaction between taxis and fluid dynamic instability leads to a macroscopic flow called bioconvection. In this study, we demonstrated that an isolated, single, three-dimensional bioconvection cell can exist within Euglena suspension. The isolated convection cell was named a “bioconvection spot.” To reveal the formation of this bioconvection spot in a cylindrical container, position-control experiments were designed in a non-uniform light environment. Upon exposure of Euglena suspensions to varying light conditions with white and red regions, Euglena was determined to aggregate into the red (darker) region. This was attributed to its phototactic response of Euglena, causing its movement toward a darker environment and away from a strong light. Thus, the bioconvection spot was created by manipulating the local cell density of the suspension and the light environments. Using our experimental setup, we observed the structure of the spot and established that it radiated pulses of local cell densities of Euglena

Hypotaurine is an Energy-Saving Hepatoprotective Compound against Ischemia-Reperfusion Injury of the Rat Liver

Metabolome analyses assisted by capillary electrophoresis-mass spectrometry (CE-MS) have allowed us to systematically grasp changes in small molecular metabolites under disease conditions. We applied CE-MS to mine out biomarkers in hepatic ischemia-reperfusion. Rat livers were exposed to ischemia by clamping of the portal inlet followed by reperfusion. Metabolomic profiling revealed that l contents of taurine in liver and plasma were significantly increased. Of interest is an elevation of hypotaurine, collectively suggesting significance of hypotaurine/taurine in post-ischemic responses. Considering the anti-oxidative capacity of hypotaurine, we examined if supplementation of the compound or its precursor amino acids could affect hepatocellular viability and contents of taurine in liver and plasma. Administration of hypotaurine, N-acetylcysteine or methionine upon reperfusion comparablly attenuated the post-ischemic hepatocellular injury but with different metabolomic profiling among groups: rats treated with methionine or N-acetylcysteine but not those treated with hypotaurine, exhibited significant elevation of hepatic lactate generation without notable recovery of the energy charge. Furthermore, the group treated with hypotaurine exhibited elevation of the plasma taurine, suggesting that the exogenously administered compound was utilized as an antioxidant. These results suggest that taurine serves as a surrogate marker for ischemia-reperfusion indicating effectiveness of hypotaurine as an energy-saving hepatoprotective amino acid

Metabolic Profiling of the Protozoan Parasite Entamoeba invadens Revealed Activation of Unpredicted Pathway during Encystation

Encystation, which is cellular differentiation from the motile, proliferative, labile trophozoite form to the dormant, resistant cyst form, is a crucial process found in parasitic and free-living protozoa such as Entamoeba, Giardia, Acanthamoeba, and Balamuthia. Since encystation is an essential process to deal with the adverse external environmental changes during the life cycle, and often integral to the transmission of the diseases, biochemical understanding of the process potentially provides useful measures against the infections caused by this group of protozoa. In this study, we investigated metabolic and transcriptomic changes that occur during encystation in Entamoeba invadens, the reptilian sibling of mammal-infecting E. histolytica, using capillary electrophoresis-tandem mass spectrometry-based metabolite profiling and DNA microarray-based expression profiling. As the encystation progressed, the levels of majority of metabolites involved in glycolysis and nucleotides drastically decreased, indicating energy generation is ceased. Furthermore, the flux of glycolysis was redirected toward chitin wall biosynthesis. We found remarkable temporal increases in biogenic amines such as isoamylamine, isobutylamine, and cadaverine, during the early period of encystation, when the trophozoites form large multicellular aggregates (precyst). We also found remarkable induction of γ-aminobutyric acid (GABA) during encystation. This study has unveiled for the first time the dynamics of the transcriptional and metabolic regulatory networks during encystation, and should help in better understanding of the process in pathogenic eukaryotes, and further development of measures controlling infections they cause

Bevacizumab terminates homeobox B9-induced tumor proliferation by silencing microenvironmental communication

Background: Homeobox B9 (HOXB9), a transcriptional factor, regulates developmental processes and tumor progression and has recently been recognized as one of important transcriptional factors related to angiogenesis. This study aimed to investigate the role of HOXB9 in tumorigenesis and angiogenesis. Methods: We examined the expression of HOXB9 in colorectal cancer using qPCR and in situ hybridization. We also examined the effect of HOXB9 overexpression in colorectal cancer using a proliferation assay, ELISA, a multiplex assay, and xenograft models. The clinical significance of HOXB9 was statistically evaluated in resected specimens. Results: HOXB9 was expressed in colorectal cancer specimens. HOXB9 induced angiogenesis and tumor proliferation in vitro, which resulted in high tumorigenicity in vivo and poor overall survival. Bevacizumab, an anti-vascular endothelial growth factor (VEGF) antibody, remarkably suppressed tumor proliferation by inhibiting angiogenesis in HOXB9-overexpressing xenografts, and it improved overall survival and provided prolonged progression-free survival in HOXB9-overexpressing patients. A comprehensive multiplex assay of the supernatant of cancer cells co-cultured with human vascular endothelial cells and fibroblasts indicated significantly higher interleukin-6 (IL6) levels than those in the supernatant of monocultured cells. HOXB9 overexpression in clinical specimens was significantly correlated with increased IL6 expression. An IL6-neutralizing antibody inhibited VEGF secretion and tumor proliferation in the co-culture system. Conclusions: HOXB9 promotes the secretion of angiogenic factors, including VEGF, to induce tumor proliferation through microenvironmental production of cytokines including IL6 signaling. Moreover, silencing of VEGF or IL6 terminates cytokine release in tumor microenvironment. Thus, HOXB9 and IL6 may be potential biomarkers for bevacizumab treatment

Biological performance of novel phosphate-based glass microspheres for mesenchymal stem cell therapy in osteoporotic patients

In this study, degradable phosphate-based bulk or porous glass microspheres (BGMS or PGMS), with nominal molar compositions of P45-(45P2O5-16CaO-24MgO-11Na2O-4Fe2O3) and P40-(40P2O5-16CaO-24MgO-20Na2O), were evaluated for cytotoxicity, cytocompatibility and osteogenic potential for Mesenchymal stem cell (MSC)-based therapy in osteoporotic patients. Evaluations were performed using direct-contact and indirect-contact bone marrow derived human MSC (hMSC)-based experiments, in addition to material characterisations such as morphology, elemental composition and degradation behaviour, which were correlated to the hMSC experiments. Degradation of microspheres (MS) was measured using a novel method where Scanning Electron micrographs was used to assess the number of MS with surface damage (cracks and peeling effect), over 42 days of degradation in culture medium. Results showed that after 42 days, 2%, 46% and 29% of P45 BGMS, P40 BGMS and P40 PGMS, respectively, had cracks or peeling off surfaces. The results for direct-contact hMSC-experiments showed that P45 BGMS supported 1.4 times more hMSCs than P40 BGMS over 31 days of culture period. However, P45 BGMS were not osteoinductive, possibly due to hydrophobic nature of this glass and its slower dissolution rate. On the other hand, in comparison to P45 BGMS, hMSCs seeded on P40 BGMS showed up to 1.7 times higher alkaline phosphatase (ALP) activity on Day 7, up to 1.5 times more collagen and at least 6 times more Ca deposited in extracellular matrix, in addition to osteocalcin on Day 21 of culture, which strongly indicated the osteoinductive nature of P40 BGMS. This effect was also confirmed through indirect-contact experiments where there was higher collagen and Ca production by hMSCs was observed after 25 days of culture in P40 BGMS-conditioned medium as compared to control (no MS) or P45-conditioned medium. Elemental analysis using Energy Dispersive X-Ray Spectroscopic (EDS) analysis revealed that the Ca-based porogen used in the manufacturing of PGMS, may have been retained on the edges of the pores in PGMS. Therefore, an acid-washing step was introduced at the end of manufacturing process in order to remove the porogen and limit the possible cytotoxic effect of porogen and excess calcium. Characterisation results indicated that acid washing changed the physicality of these microspheres without changing their chemical composition. For example, mean and mode pore window sizes on the surface of PGMS increased from 2.63 μm to 2.73 μm and from 1.15 μm to 1.53 μm, respectively, and closed porosity decreased by 27%, as a result of acid washing. However, more detailed EDS analysis revealed that the Ca-based porogen was not being completely removed from PGMS even after acid washing and this may need further investigation. Cytotoxicity evaluations over 7 days of elution (indirect-contact hMSC experiments) suggested that there was marked improvement in hMSC membrane integrity and metabolic activity in PGMS neat extracts after acid washing. Moreover, direct-contact hMSC experiments also showed higher DNA content on acid washed (AW) P40 PGMS over 7 days of culture. Therefore, based on these results, it was hypothesised that acid washing may have opened up some of the pores and removed some of the glass fragments from PGMS surface, which may have been responsible for cytotoxicity in non-AW PGMS. Direct-contact experiments also showed that over 42-day culture period, there was up to 1.6 times higher hMSC numbers in AW P40 PGMS as compared to P40 BGMS. However, this increase was much lower than the expected range as there was more than 10-fold increase in surface area after the introduction of porosity. This was probably due to presence of <5 μm and <10 μm pore window sizes and interconnection sizes, respectively, in these microspheres, which allowed limited penetration of hMSCs into the porous structures. There was also evidence of at least 2 times more ALP activity up to day 42 of culture and up to 1.7 times more collagen production by day 21 of culture, in case of AW P40 PGMS as compared to P40 BGMS, which strongly indicated a positive effect of porosity on osteogenesis. Interestingly, there was also lower Ca and P deposited by hMSCs in porous microspheres, which was in line with the observations made through indirect-contact experiments, where there was lower collagen and Ca production by hMSCs in P40 PGMS-conditioned medium as compared to P40 BGMS-conditioned medium. This negative effect of PGMS was hypothesised due to excess release of glass fragments/particulates and calcium ions into the medium, possibly leading to cytotoxicity. Based on the results shown here, there is a potential of P40 BGMS and AW P40 PGMS for hMSC-based bone repair therapy. However, future work needs to be done in order to limit the delamination of glass surfaces and release of glass fragments/particulates from these MS, as a result of degradation

Japanese VLBI Network observations of radio-loud narrow-line Seyfert 1 galaxies

We performed phase-reference very long baseline interferometry (VLBI) observations on five radio-loud narrow-line Seyfert 1 galaxies (NLS1s) at 8.4 GHz with the Japanese VLBI Network (JVN). Each of the five targets (RXS J08066+7248, RXS J16290+4007, RXS J16333+4718, RXS J16446+2619, and B3 1702+457) in milli-Jansky levels were detected and unresolved in milli-arcsecond resolutions, i.e., with brightness temperatures higher than 10^7 K. The nonthermal processes of active galactic nuclei (AGN) activity, rather than starbursts, are predominantly responsible for the radio emissions from these NLS1s. Out of the nine known radio-loud NLS1s, including the ones chosen for this study, we found that the four most radio-loud objects exclusively have inverted spectra. This suggests a possibility that these NLS1s are radio-loud due to Doppler beaming, which can apparently enhance both the radio power and the spectral frequency.Comment: 8 pages, 2 figures, accepted for publication in PAS

Open Access

Bevacizumab terminates homeobox B9-induced tumor proliferation by silencing microenvironmental communicatio