Two potential clinical applications of the alkaline single-cell gel electrophoresis assay .1. Human bladder washings and transitional cell carcinoma of the bladder .2. Human sperm and male infertility

Part 1: The alkaline single-cell gel electrophoresis (comet) assay was used to analyse the integrity and DNA content of exfoliated cells extracted from bladder washing specimens from 9 transitional cell carcinoma patients and 15 control patients. DNA damage, as expressed by % tail DNA and tail moment values, was observed to occur in cells from both control and bladder cancer samples. The extent of the damage was, however, found to be significantly greater in the cancer group than in the control group. Comet optical density values were also recorded for each cell analysed in the comet assay and although differences observed between tumour grades were not found to be statistically significant, the mean comet optical density value was observed to be greater in the cancer group than in the control population studied, These preliminary results suggest that the comet assay may have potential as a diagnostic tool and as a prognostic indicator in transitional cell carcinoma, Part 2: Baseline DNA damage in sperm cells from 13 normozoospermic fertile males, 17 normozoospermic infertile males and 11 asthenozoospermic infertile males were compared using a modified alkaline comet assay technique. No significant difference in the level of baseline DNA damage was observed between the 3 categories of sperm studied; however the untreated sperm cells were observed to display approximately 20% tail DNA. This is notably higher than the background DNA damage observed in somatic cells where the % tail DNA is normally less than 5%. Sperm from the 3 groups of men studied were also compared for sensitivity to DNA breakage, using the modified alkaline comet assay, following X-ray irradiations (5, 10 and 30 Gy) and hydrogen peroxide treatments (40, 100 and 200 mu M). Significant levels of X-ray-induced damage were found relative to untreated control sperm in the two infertile groups following 30 Gy irradiation. Significant damage in hydrogen peroxide-treated sperm was observed in sperm from fertile samples, at 200 mu M and in infertile samples at 100- and 200-mu M doses relative to controls. These results therefore indicate that fertile sperm samples are more resistant to X-ray- and hydrogen peroxide-induced DNA breakage than infertile samples. Further studies involving greater numbers of individuals are currently in progress to confirm these findings.

Activity Enhancement of Tetrahexahedral Pd Nanocrystals by Bi Decoration towards Ethanol Electrooxidation in Alkaline Media

Tetrahexahedral Pd nanocrystals (THH Pd NCs) were prepared on a glassy carbon electrode using a programmed square-wave potential electrodeposition method, and modified by Bi adatoms with a range of coverages via the cyclic voltammetry method. The reactivity of the catalysts prepared towards ethanol electrooxidation reaction (EOR) was studied in alkaline medium at various temperatures and under other conditions that practical fuel cells operate. Significant activity enhancements were observed for the Bi-modified THH Pd NCs with an optimum Bi coverage (θBi) of around 0.68 being obtained. Furthermore, it was found that increasing temperature from 25 ºC to 60 ºC enhances the reactivity significantly. The general kinetics data of EOR on Bi-decorated and bare THH Pd NCs have also been obtained, from the activation energy calculated based on Arrhenius plots, and compared. At the optimum Bi coverage, an enhancement in the activity of almost 3 times was achieved, and the corresponding activation energy was found to be reduced significantly.

Young, Old, and Weathered Carbon—Part 1: Using Radiocarbon and Stable Isotopes to Identify Carbon Sources in an Alkaline, Humic Lake

This article presents a case study of Lower Lough Erne, a humic, alkaline lake in northwest Ireland, and uses the radiocarbon method to determine the source and age of carbon to establish whether terrestrial carbon is utilized by heterotrophic organisms or buried in sediment. Stepped combustion was used to estimate the degree of the burial of terrestrial carbon in surface sediment. ∆14C, δ13C, and δ15N values were measured for phytoplankton, dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), and particulate organic carbon (POC). ∆14C values were used to indicate the presence of different sources of carbon, including bedrock-derived inorganic carbon, “modern,” “recent,” “subsurface,” and “subfossil” terrestrial carbon in the lake. The use of 14C in conjunction with novel methods (e.g. stepped combustion) allows the determination of the pathway of terrestrial carbon in the system, which has implications for regional and global carbon cycling.

Young, Old, and Weathered Carbon—Part 2: Using Radiocarbon and Stable Isotopes to Identify Terrestrial Carbon Support of the Food Web in an Alkaline, Humic Lake

Carbon (C) and nitrogen (N) stable isotope analysis (SIA) has been used to identify the terrestrial subsidy of freshwater food webs. However, SIA fails to differentiate between the contributions of old and recently fixed terrestrial C and consequently cannot fully determine the source, age, and biochemical quality of terrestrial carbon. Natural abundance radiocarbon (∆14C) was used to examine the age and origin of carbon in Lower Lough Erne, Northern Ireland. 14C and stable isotope values were obtained from invertebrate, algae, and fish samples, and the results indicate that terrestrial organic C is evident at all trophic levels. High winter δ15N values in calanoid zooplankton (δ15N = 24‰) relative to phytoplankton and particulate organic matter (δ15N = 6‰ and 12‰, respectively) may reflect several microbial trophic levels between terrestrial C and calanoid invertebrates. Winter and summer calanoid ∆14C values show a seasonal switch between autochthonous and terrestrial carbon sources. Fish ∆14C values indicate terrestrial support at the highest trophic levels in littoral and pelagic food webs. 14C therefore is useful in attributing the source of carbon in freshwater in addition to tracing the pathway of terrestrial carbon through the food web.

Using radiocarbon and stable isotopes to identify sediment carbon sources in an alkaline, humic lake.

We present a pilot study that uses the radiocarbon (∆14C) method to determine the source of carbon buried in the surface sediment of Lough Erne, a humic, alkaline lake in northwest Ireland. ∆14C, δ13C and δ15N values were measured from phytoplankton, dissolved inorganic, dissolved organic and particulate organic carbon. A novel radiocarbon method, Stepped Combustion1 was used to estimate the degree of the burial of terrestrial carbon in surface sediment. The ∆14C values of the low temperature fractions were comparable to algal ∆14C, while the high temperature fractions were 14C-depleted (older than bulk sediment). The ∆14C end-member model indicated that ~64% of carbon in surface sediment was derived from detrital terrestrial carbon. The use of ∆14C in conjunction with stepped combustion allows the quantification of the pathways of terrestrial carbon in the system, which has implications for regional and global carbon burial.
1McGeehin, J., Burr, G.S., Jull, A.J.T., Reines, D., Gosse, J., Davis, P.T., Muhs, D., and Southon, J.R., 2001, Stepped-combustion C-14 dating of sediment: A comparison with established techniques: Radiocarbon, v. 43, p. 255-261.

The prognostic significance of protein tyrosine phosphatase 4A2 in breast cancer

Although PTP4A3 has been shown to be a very important factor in promoting cancer progression, the role of its close family member PTP4A2 is still largely unknown. Recent reports have shown contradicting results on the role of PTP4A2 in breast cancer progression. Considering this, we aimed to investigate the prognostic value of PTP4A2 in five independent breast cancer data sets (minimum 198 patients per cohort, totaling 1,124 patients) in the Gene Expression Omnibus Database. We found that high expression of PTP4A2 was a favorable prognostic marker in all five independent breast cancer data sets, as well as in the combined cohort, with a hazard ratio of 0.68 (95% confidence interval =0.56-0.83; P<0.001). Low PTP4A2 expression was associated with estrogen receptor-negative tumors and tumors with higher histological grading; furthermore, low expression was inversely correlated with the expression of genes involved in proliferation, including MKI67 and the MCM gene family encoding the minichromosome maintenance proteins. These findings suggest that PTP4A2 may play a role in breast cancer progression by dysregulating cell proliferation. PTP4A2 expression was positively correlated with ESR1, the gene encoding estrogen receptor-alpha, and inversely correlated with EGFR expression, suggesting that PTP4A2 may be involved in these two important oncogenic pathways. Together, our results suggest that expression of PTP4A2 is a favorable prognostic marker in breast cancer.

Alkaline-earth aluminosilicate-based glass and glass-ceramic sealants for functional applications

The planar design of solid oxide fuel cell (SOFC) is the most promising one due to its easier fabrication, improved performance and relatively high power density. In planar SOFCs and other solid-electrolyte devices, gas-tight seals must be formed along the edges of each cell and between the stack and gas manifolds. Glass and glass-ceramic (GC), in particular alkaline-earth alumino silicate based glasses and GCs, are becoming the most promising materials for gas-tight sealing applications in SOFCs. Besides the development of new glass-based materials, new additional concepts are required to overcome the challenges being faced by the currently existing sealant technology. The present work deals with the development of glasses- and GCs-based materials to be used as a sealants for SOFCs and other electrochemical functional applications. In this pursuit, various glasses and GCs in the field of diopside crystalline materials have been synthesized and characterized by a wide array of techniques. All the glasses were prepared by melt-quenching technique while GCs were produced by sintering of glass powder compacts at the temperature ranges from 800−900 ºC for 1−1000 h. Furthermore, the influence of various ionic substitutions, especially SrO for CaO, and Ln2O3 (Ln=La, Nd, Gd, and Yb), for MgO + SiO2 in Al-containing diopside on the structure, sintering and crystallization behaviour of glasses and properties of resultant GCs has been investigated, in relevance with final application as sealants in SOFC. From the results obtained in the study of diopside-based glasses, a bilayered concept of GC sealant is proposed to overcome the challenges being faced by (SOFCs). The systems designated as Gd−0.3 (in mol%: 20.62MgO−18.05CaO−7.74SrO−46.40SiO2−1.29Al2O3 − 2.04 B2O3−3.87Gd2O3) and Sr−0.3 (in mol%: 24.54 MgO−14.73 CaO−7.36 SrO−0.55 BaO−47.73 SiO2−1.23 Al2O3−1.23 La2O3−1.79 B2O3−0.84 NiO) have been utilized to realize the bi-layer concept. Both GCs exhibit similar thermal properties, while differing in their amorphous fractions, revealed excellent thermal stability along a period of 1,000 h. They also bonded well to the metallic interconnect (Crofer22APU) and 8 mol% yttrium stabilized zirconium (8YSZ) ceramic electrolyte without forming undesirable interfacial layers at the joints of SOFC components and GC. Two separated layers composed of glasses (Gd−0.3 and Sr−0.3) were prepared and deposited onto interconnect materials using a tape casting approach. The bi-layered GC showed good wetting and bonding ability to Crofer22APU plate, suitable thermal expansion coefficient (9.7–11.1 × 10–6 K−1), mechanical reliability, high electrical resistivity, and strong adhesion to the SOFC componets. All these features confirm the good suitability of the investigated bi-layered sealant system for SOFC applications.

Functional analysis of String/CDC25 phosphatase in post-mitotic neurons

Cell cycle and differentiation are two highly coordinated processes during organ development. Recent studies have demonstrated that core cell cycle regulators also play cell cycle-independent functions in post-mitotic neurons, and are essential for the maintenance of neuronal homeostasis. CDC25 phosphatases are well-established CDK activators and their activity is mainly associated to proliferating tissues. The expression and activity of mammalian CDC25s has been reported in adult brains. However, their physiological relevance and the potential substrates in a non-proliferative context have never been addressed. string (stg) encodes the Drosophila CDC25 homolog. Previous studies from our group showed that stg is expressed in photoreceptors (PRs) and in lamina neurons, which are two differentiated cell types that compose the fly visual system. The aims of this work are to uncover the function of stg and to identify its potential neuronal substrates, using the Drosophila visual system as a model. To gain insight into the function of stg in a non-dividing context we used the GAL4/UAS system to promote downregulation of stg in PR-neurons, through the use of an RNAi transgene. The defects caused by stg loss-of-function were evaluated in the developing eye imaginal disc by immunofluorescence, and during adult stages by scanning electron microscopy. This genetic approach was combined with a specific proteomic method, two-dimensional difference gel electrophoresis (2D-DIGE), to identify the potential substrates in PR-cells. Our results showed that stg downregulation in PRs affects the well-patterned retina organization, inducing the loss of apical maintenance of PR-nuclei on the eye disc, and ommatidia disorganization. We also detected an abnormal accumulation of cytoskeletal proteins and a disruption of the axon structure. As a consequence, the projection of PR-axons into the lamina and medulla neuropils of the optic lobe was impaired. Upon stg downregulation, we also detected that PR-cells accumulate Cyclin B. Although the rough eye phenotype observed upon stg downregulation suggests neurodegeneration, we did not detect neuronal death during larval stages, suggesting that it likely occurs during pupal stages or during adulthood. By 2D-DIGE, we identified seven proteins which were differentially expressed upon stg downregulation, and are potential neuronal substrates of Stg. Altogether, our observations suggest that Stg phosphatase plays an essential role in the Drosophila visual system neurons, regulating several cell components and processes in order to ensure their homeostasis.

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in Biochemistry

A minimal version of a Protein Tyrosine Phosphatase

Phosphatase and tensin homologue (PTEN) protein belongs to the family of protein tyrosine phos-phatase. Mutations on the phosphatase and tensin homologue (PTEN) protein are highly observed in diverse types of human tumors, being mostly identified on the phosphatase domain of the protein. Although PTEN is a modular protein composed by a phosphatase domain and a C2 domain for mem-brane anchoring, this work aimed at developing a minimal version of PTEN´s phosphatase domain. The minimal version (Small Domain) comprises a 28 residue peptide, with the PTEN 8-mer catalytic peptide accommodated between a α-helix and β-turn as observed in PTEN native structure. Firstly, a de novo prediction of the Small Domain´s secondary structure was carried out by molecular modeling tools. The stability of the predicted structures were then evaluated by Molecular Dynamics. Automated molecular docking of PTEN natural substrate PIP3, its analogue (Inositol) and a PTEN inhibitor (L-tar-tare) were performed with the modeled structure, and PTEN used as a positive control. The gene en-coding for Small Domain was designed and cloned into an expression vector at N-terminal of Green Fluorescence Protein (GFP) encoding gene. The fusion protein was then expressed in Escherichia coli cells. Different expression conditions have been explored for the production of the fusion protein to minimize the formation of inclusion bodies.

The protein phosphatase 7 regulates phytochrome signaling in Arabidopsis.

The psi2 mutant of Arabidopsis displays amplification of the responses controlled by the red/far red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) but no apparent defect in blue light perception. We found that loss-of-function alleles of the protein phosphatase 7 (AtPP7) are responsible for the light hypersensitivity in psi2 demonstrating that AtPP7 controls the levels of phytochrome signaling. Plants expressing reduced levels of AtPP7 mRNA display reduced blue-light induced cryptochrome signaling but no noticeable deficiency in phytochrome signaling. Our genetic analysis suggests that phytochrome signaling is enhanced in the AtPP7 loss of function alleles, including in blue light, which masks the reduced cryptochrome signaling. AtPP7 has been found to interact both in yeast and in planta assays with nucleotide-diphosphate kinase 2 (NDPK2), a positive regulator of phytochrome signals. Analysis of ndpk2-psi2 double mutants suggests that NDPK2 plays a critical role in the AtPP7 regulation of the phytochrome pathway and identifies NDPK2 as an upstream element involved in the modulation of the salicylic acid (SA)-dependent defense pathway by light. Thus, cryptochrome- and phytochrome-specific light signals synchronously control their relative contribution to the regulation of plant development. Interestingly, PP7 and NDPK are also components of animal light signaling systems.

Febuxostat, an Inhibitor of Xanthine Oxidase, Suppresses Lipopolysaccharide-Induced MCP-1 Production via MAPK Phosphatase-1-Mediated Inactivation of JNK.

Excess reactive oxygen species (ROS) formation can trigger various pathological conditions such as inflammation, in which xanthine oxidase (XO) is one major enzymatic source of ROS. Although XO has been reported to play essential roles in inflammatory conditions, the molecular mechanisms underlying the involvement of XO in inflammatory pathways remain unclear. Febuxostat, a selective and potent inhibitor of XO, effectively inhibits not only the generation of uric acid but also the formation of ROS. In this study, therefore, we examined the effects of febuxostat on lipopolysaccharide (LPS)-mediated inflammatory responses. Here we show that febuxostat suppresses LPS-induced MCP-1 production and mRNA expression via activating MAPK phosphatase-1 (MKP-1) which, in turn, leads to dephosphorylation and inactivation of JNK in macrophages. Moreover, these effects of febuxostat are mediated by inhibiting XO-mediated intracellular ROS production. Taken together, our data suggest that XO mediates LPS-induced phosphorylation of JNK through ROS production and MKP-1 inactivation, leading to MCP-1 production in macrophages. These studies may bring new insights into the novel role of XO in regulating inflammatory process through MAPK phosphatase, and demonstrate the potential use of XO inhibitor in modulating the inflammatory processes.

Liver-specific loss of lipin-1-mediated phosphatidic acid phosphatase activity does not mitigate intrahepatic TG accumulation in mice.

Lipin proteins (lipin 1, 2, and 3) regulate glycerolipid homeostasis by acting as phosphatidic acid phosphohydrolase (PAP) enzymes in the TG synthesis pathway and by regulating DNA-bound transcription factors to control gene transcription. Hepatic PAP activity could contribute to hepatic fat accumulation in response to physiological and pathophysiological stimuli. To examine the role of lipin 1 in regulating hepatic lipid metabolism, we generated mice that are deficient in lipin-1-encoded PAP activity in a liver-specific manner (Alb-Lpin1(-/-) mice). This allele of lipin 1 was still able to transcriptionally regulate the expression of its target genes encoding fatty acid oxidation enzymes, and the expression of these genes was not affected in Alb-Lpin1(-/-) mouse liver. Hepatic PAP activity was significantly reduced in mice with liver-specific lipin 1 deficiency. However, hepatocytes from Alb-Lpin1(-/-) mice had normal rates of TG synthesis, and steady-state hepatic TG levels were unaffected under fed and fasted conditions. Furthermore, Alb-Lpin1(-/-) mice were not protected from intrahepatic accumulation of diacylglyerol and TG after chronic feeding of a diet rich in fat and fructose. Collectively, these data demonstrate that marked deficits in hepatic PAP activity do not impair TG synthesis and accumulation under acute or chronic conditions of lipid overload.

Single amino acid charge switch defines clinically distinct proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1)-associated inflammatory diseases.

BACKGROUND: Hyperzincemia and hypercalprotectinemia (Hz/Hc) is a distinct autoinflammatory entity involving extremely high serum concentrations of the proinflammatory alarmin myeloid-related protein (MRP) 8/14 (S100A8/S100A9 and calprotectin). OBJECTIVE: We sought to characterize the genetic cause and clinical spectrum of Hz/Hc. METHODS: Proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1) gene sequencing was performed in 14 patients with Hz/Hc, and their clinical phenotype was compared with that of 11 patients with pyogenic arthritis, pyoderma gangrenosum, and acne (PAPA) syndrome. PSTPIP1-pyrin interactions were analyzed by means of immunoprecipitation and Western blotting. A structural model of the PSTPIP1 dimer was generated. Cytokine profiles were analyzed by using the multiplex immunoassay, and MRP8/14 serum concentrations were analyzed by using an ELISA. RESULTS: Thirteen patients were heterozygous for a missense mutation in the PSTPIP1 gene, resulting in a p.E250K mutation, and 1 carried a mutation resulting in p.E257K. Both mutations substantially alter the electrostatic potential of the PSTPIP1 dimer model in a region critical for protein-protein interaction. Patients with Hz/Hc have extremely high MRP8/14 concentrations (2045 ± 1300 μg/mL) compared with those with PAPA syndrome (116 ± 74 μg/mL) and have a distinct clinical phenotype. A specific cytokine profile is associated with Hz/Hc. Hz/Hc mutations altered protein binding of PSTPIP1, increasing interaction with pyrin through phosphorylation of PSTPIP1. CONCLUSION: Mutations resulting in charge reversal in the y-domain of PSTPIP1 (E→K) and increased interaction with pyrin cause a distinct autoinflammatory disorder defined by clinical and biochemical features not found in patients with PAPA syndrome, indicating a unique genotype-phenotype correlation for mutations in the PSTPIP1 gene. This is the first inborn autoinflammatory syndrome in which inflammation is driven by uncontrolled release of members of the alarmin family.

Physical volcanology, sedimentology, stratigraphy and petrochemistry of the Berry Creek metavolcanics: an Archean calc-alkaline complex, Lake of the Woods, Ontario

The steeply dipping, isoclinally folded early Precambrian (Archean) Berry Creek Metavolcanic Complex comprises primary to resedimented pyroclastic, epiclastic and autoclastic deposits. Tephra erupted from central volcanic edifices was dumped by mass flow mechanisms into peripheral volcanosedimentary depressions. Sedimentation has been essentially contemporaneous with eruption and transport of tephra. The monolithic to heterolithic tuffaceous horizons are interpreted as subaerial to subaqueous pumice and ash flows, secondary debris flows, lahars, slump deposits and turbidites. Monolithic debris flows, derived from crumble breccia and dcme talus, formed during downslope collapse and subsequent gravity flowage. Heterolithic tuff, lahars and lava flow morphologies suggest at least temporary emergence of the edifice. Local collapse may have accompanied pyroclastic volcanism. The tephra, produced by hydromagmatic to magmatic eruptions, were rapidly transported, by primary and secondary mechanisms, to a shallow littoral to deep water subaqueous fan developed upon the subjacent mafic metavolcanic platform. Deposition resulted from traction, traction carpet, and suspension sedimentation from laminar to turbulent flows. Facies mapping revealed proximal (channel to overbank) to distal facies epiclastics (greywackes, argillite) intercalated with proximal vent to medial fan facies crystal rich ash flows, debris flows, bedded tuff and shallow water to deep water lava flows. Framework and matrix support debris flows exhibit a variety of subaqueous sedimentary structures, e.g., coarse tail grading, double grading, inverse to normal grading, graded stratified pebbly horizons, erosional channels. Pelitic to psammitic AE turbidites also contain primary stru~tures, e.g., flames, load casts, dewatering pipes. Despite low to intermediate pressure greenschist to amphibolite grade metamorphism and variably penetrative deformation, relicts of pumice fragments and shards were recognized as recrystallized quartzofeldspathic pseudomorphs. The mafic to felsic metavolcanics and metasediments contain blasts of hornblende, actinolite, garnet, pistacitic epidote, staurolite, albitic plagioclase, and rarely andalusite and cordierite. The mafic metavolcanics (Adams River Bay, Black River, Kenu Lake, Lobstick Bay, Snake Bay) display _holeiitic trends with komatiitic affinities. Chemical variations are consistent with high level fractionation of olivine, plagioclase, amphibole, and later magnetite from a parental komatiite. The intermediate to felsic (64-74% Si02) metavolcanics generally exhibit calc-alkaline trends. The compositional discontinuity, defined by major and trace element diversity, can be explained by a mechanism involving two different magma sources. Application of fractionation series models are inconsistent with the observed data. The tholeiitic basalts and basaltic andesites are probably derived by low pressure fractionation of a depleted (high degree of partial melting) mantle source. The depleted (low Y, Zr) calc-alkaline metavolcanics may be produced by partial melting of a geochemically evolved source, e.g., tonalitetrondhjemite, garnet amphibolite or hydrous basalt.