Distinct methylation patterns in genes that affect mitochondrial function are associated with kidney disease in blood-derived DNA from individuals with Type 1 diabetes

AIMS: Epigenetic modifications, such as DNA methylation, can influence the risk of developing kidney disease. We studied methylation profiles in genes related to mitochondrial function to assess whether differences in these epigenetic features were associated with diabetic kidney disease in people with Type 1 diabetes.

METHODS: A case-control association study was undertaken (n = 196 individuals with diabetic kidney disease vs. n = 246 individuals without renal disease). Participants were White and diagnosed with Type 1 diabetes before 31 years of age. Genes that encode mitochondrial proteins (n = 780) were downloaded from mitoproteome. org. DNA methylation profiles from blood-derived DNA were generated using the Illumina Infinium HumanMethylation450 (262 samples) and Illumina Infinium HumanMethylation27 (192 samples) arrays. Beta values (β) were calculated and quality control was conducted, including evaluating blind duplicate DNA samples.

RESULTS: Fifty-four Cytosine-phosphate-Guanine probes across 51 unique genes were significantly associated (P ≤ 10(-8) ) with diabetic kidney disease across both the 450K and the 27K methylation arrays. A subanalysis, employing the 450K array, identified 755 Cytosine-phosphate-Guanine probes in 374 genes that were significantly associated (P ≤ 10(-8) ) with end-stage renal disease. Forty-six of the top-ranked variants for diabetic kidney disease were also identified as being differentially methylated in individuals with end-stage renal disease. The largest change in methylation (Δβ = 0.2) was observed for cg03169527 in the TAMM41 gene, chromosome 3p25.2. Three genes, PMPCB, TSFM and AUH, were observed with differential methylation at multiple Cytosine-phosphate-Guanine sites each (P < 10(-12) ).

CONCLUSIONS: Differential methylation in genes that influence mitochondrial function are associated with kidney disease in individuals with Type 1 diabetes. 

Toluene Dioxygenase Catalysed synthesis and reactions of cis-diol metabolites derived from 2 and 3-methoxy phenols

Using toluene dioxygenase as biocatalyst, enantiopure cisdihydrodiol and cis-tetrahydrodiol metabolites, isolated as their ketone tautomers, were obtained from meta and ortho methoxyphenols. Although these isomeric phenol substrates are structurally similar, the major bioproducts from each of these biotransformations were found at different oxidation levels. The relatively stable cyclohexenone cis-diol metabolite from meta methoxyphenol was isolated, while the corresponding metabolite from ortho methoxyphenol was rapidly bioreduced to a cyclohexanone cis-diol. The chemistry of the 3-methoxycyclohexenone cis-diol product was investigated and elimination, aromatization, hydrogenation, regioselective O-exchange, Stork−Danheiser transposition and O-methylation reactions were observed. An offshoot of this technology provided a two-step chemoenzymatic synthesis, from meta methoxyphenol, of a recently reported chiral fungal metabolite; this synthesis also established the previously unassigned absolute configuration.

Heme oxygenase-1: a metabolic nike

SIGNIFICANCE: Heme degradation, which was described more than 30 years ago, is still very actively explored with many novel discoveries on its role in various disease models every year.

RECENT ADVANCES: The heme oxygenases (HO) are metabolic enzymes that utilize NADPH and oxygen to break apart the heme moiety liberating biliverdin (BV), carbon monoxide (CO), and iron. Heme that is derived from hemoproteins can be toxic to the cells and if not removed immediately, it causes cell apoptosis and local inflammation. Elimination of heme from the milieu enables generation of three products that influences numerous metabolic changes in the cell.

CRITICAL ISSUES: CO has profound effects on mitochondria and cellular respiration and other hemoproteins to which it can bind and affect their function, while BV and bilirubin (BR), the substrate and product of BV, reductase, respectively, are potent antioxidants. Sequestration of iron into ferritin and its recycling in the tissues is a part of the homeodynamic processes that control oxidation-reduction in cellular metabolism. Further, heme is an important component of a number of metabolic enzymes, and, therefore, HO-1 plays an important role in the modulation of cellular bioenergetics.

FUTURE DIRECTIONS: In this review, we describe the cross-talk between heme oxygenase-1 (HO-1) and its products with other metabolic pathways. HO-1, which we have labeled Nike, the goddess who personified victory, dictates triumph over pathophysiologic conditions, including diabetes, ischemia, and cancer.

Smac-derived Aza-peptide As an Aminopeptidase-resistant XIAP BIR3 Antagonist

The peptidic nature of anti-IAPs N-terminus Smac-derived peptides precludes their utilization as potential therapeutic anticancer agents. Recent advances in the development of novel Smac-derived peptidomimetics and non-peptidic molecules with improved anti-IAPs activity and resistance to proteolytic cleavage have been reported and led to a number of candidates that are currently in clinical trials including LCL-161, SM-406/AT-406, GDC-0512/GDC-0917, and birinapant. As an attempt to improve the proteolytic stability of Smac peptides, we developed the Aza-peptide AzaAla-Val-Pro-Phe-Tyr-NH2 (2). Unlike unmodified peptide Ala-Val-Pro-Phe-Tyr-NH2 (1), analogue (2) exhibited resistance towards proteolytic cleavage by two aminopeptidases; LAP and DPP-IV, while retaining its IAP inhibitory activity. This was due to the altered planar geometry of the P1 residue side chain. Our findings showed that using aza-isosteres of bioactive peptide sequences imbue the residue with imperviousness to proteolysis; underscoring a potential approach for developing a new generation of Smac-derived Aza-peptidomimetics.

Heme oxygenase-1 derived carbon monoxide permits maturation of myeloid cells

Critical functions of the immune system are maintained by the ability of myeloid progenitors to differentiate and mature into macrophages. We hypothesized that the cytoprotective gas molecule carbon monoxide (CO), generated endogenously by heme oxygenases (HO), promotes differentiation of progenitors into functional macrophages. Deletion of HO-1, specifically in the myeloid lineage (Lyz-Cre:Hmox1(flfl)), attenuated the ability of myeloid progenitors to differentiate toward macrophages and decreased the expression of macrophage markers, CD14 and macrophage colony-stimulating factor receptor (MCSFR). We showed that HO-1 and CO induced CD14 expression and efficiently increased expansion and differentiation of myeloid cells into macrophages. Further, CO sensitized myeloid cells to treatment with MCSF at low doses by increasing MCSFR expression, mediated partially through a PI3K-Akt-dependent mechanism. Exposure of mice to CO in a model of marginal bone marrow transplantation significantly improved donor myeloid cell engraftment efficiency, expansion and differentiation, which corresponded to increased serum levels of GM-CSF, IL-1α and MCP-1. Collectively, we conclude that HO-1 and CO in part are critical for myeloid cell differentiation. CO may prove to be a novel therapeutic agent to improve functional recovery of bone marrow cells in patients undergoing irradiation, chemotherapy and/or bone marrow transplantation.

Novel titania sol-gel derived film for luminescence-based oxygen sensing.

A novel method for the preparation of titania sol–gel derived oxygen sensors based on the ruthenium(II) dye, [Ru(bpy)3]2+, is described. A titania sol–gel paste film was cast onto microscope slides, and the dye ion-paired to the deprotonated, hydroxylated groups on the film's surface from an aqueous solution of the dye at pH 11. The resulting sensor film is extremely oxygen sensitive, with a PO2 (S = 1/2) value (i.e. the partial pressure of oxygen required in order to reduce the original, oxygen free, luminescence intensity by 50%) of 0.011 atm. The sensor undergoes 95% response to oxygen in 4 s, and shows 95% recovery of its luminescence in argon within 7 s.

Active site labeling of cysteine cathepsins by a straightforward diazomethylketone probe derived from the N-terminus of human cystatin C

We designed a straightforward biotinylated probe using the N-terminal substrate-like region of the inhibitory site of human cystatin C as a scaffold, linked to the thiol-specific reagent diazomethylketone group as a covalent warhead (i.e. Biot-(PEG)2-Ahx-LeuValGly-DMK). The irreversible activity-based probe bound readily to cysteine cathepsins B, L, S and K. Moreover affinity labeling is sensitive since active cathepsins were detected in the nM range using an ExtrAvidin®-peroxidase conjugate for disclosure. Biot-(PEG)2-Ahx-LeuValGly-DMK allowed a slightly more pronounced labeling for cathepsin S with a compelling second-order rate constant for association (kass = 2,320,000 M−1 s−1). Labeling of the active site is dose-dependent as observed using 6-cyclohexylamine-4-piperazinyl-1,3,5-triazine-2-carbonitrile, as competitive inhibitor of cathepsins. Finally we showed that Biot-(PEG)2-Ahx-LeuValGly-DMK may be a simple and convenient tool to label secreted and intracellular active cathepsins using a myelomonocytic cell line (THP-1 cells) as model.

Marine-derived quorum-sensing inhibitory activities enhance the antibacterial efficacy of tobramycin against Pseudomonas aeruginosa

Bacterial epiphytes isolated from marine eukaryotes were screened for the production of quorum sensing inhibitory compounds (QSIs). Marine isolate KS8, identified as a Pseudoalteromonas sp., was found to display strong quorum sensing inhibitory (QSI) activity against acyl homoserine lactone (AHL)-based reporter strains Chromobacterium violaceum ATCC 12472 and CV026. KS8 supernatant significantly reduced biofilm biomass during biofilm formation (−63%) and in pre-established, mature P. aeruginosa PAO1 biofilms (−33%). KS8 supernatant also caused a 0.97-log reduction (−89%) and a 2-log reduction (−99%) in PAO1 biofilm viable counts in the biofilm formation assay and the biofilm eradication assay respectively. The crude organic extract of KS8 had a minimum inhibitory concentration (MIC) of 2 mg/mL against PAO1 but no minimum bactericidal concentration (MBC) was observed over the concentration range tested (MBC > 16 mg/mL). Sub-MIC concentrations (1 mg/mL) of KS8 crude organic extract significantly reduced the quorum sensing (QS)-dependent production of both pyoverdin and pyocyanin in P. aeruginosa PAO1 without affecting growth. A combinatorial approach using tobramycin and the crude organic extract at 1 mg/mL against planktonic P. aeruginosa PAO1 was found to increase the efficacy of tobramycin ten-fold, decreasing the MIC from 0.75 to 0.075 µg/mL. These data support the validity of approaches combining conventional antibiotic therapy with non-antibiotic compounds to improve the efficacy of current treatments.

Shallow water methane-derived authigenic carbonate mounds at the Codling Fault Zone, western Irish Sea

Methane-derived authigenic carbonate (MDAC) mound features at the Codling Fault Zone (CFZ), located in shallow waters (50-120m) of the western Irish Sea were investigated and provide a comparison to deep sea MDAC settings. Carbonates consisted of aragonite as the major mineral phase, with δ¹³C depletion to -50‰ and δ¹⁸O enrichment to~2‰. These isotope signatures, together with the co-precipitation of framboidal pyrite confirm that anaerobic oxidation of methane (AOM) is an important process mediating methane release to the water column and the atmosphere in this region. ¹⁸O-enrichment could be a result of MDAC precipitation with seawater in colder than present day conditions, or precipitation with ¹⁸O-enriched water transported from deep petroleum sources. The ¹³C depletion of bulk carbonate and sampled gas (-70‰) suggests a biogenic source, but significant mixing of thermogenic gas and depletion of the original isotope signature cannot be ruled out. Active seepage was recorded from one mound and together with extensive areas of reduced sediment, confirms that seepage is ongoing. The mounds appear to be composed of stacked pavements that are largely covered by sand and extensively eroded. The CFZ mounds are colonized by abundant Sabellaria polychaetes and possible Nemertesia hydroids, which benefit indirectly from available hard substrate. In contrast to deep sea MDAC settings where seep-related macrofauna are commonly reported, seep-specialist fauna appear to be lacking at the CFZ. In addition, unlike MDAC in deep waters where organic carbon input from photosynthesis is limited, lipid biomarkers and isotope signatures related to marine planktonic production (e.g. sterols, alkanols) were most abundant. Evidence for microbes involved in AOM was limited from samples taken; possibly due to this dilution effect from organic matter derived from the photic zone, and will require further investigation. 

Solar coronal magnetic fields derived using seismology techniques applied to omnipresent sunspot waves

Sunspots on the surface of the Sun are the observational signatures of intense manifestations of tightly packed magnetic field lines, with near-vertical field strengths exceeding 6,000 G in extreme cases1. It is well accepted that both the plasma density and the magnitude of the magnetic field strength decrease rapidly away from the solar surface, making high-cadence coronal measurements through traditional Zeeman and Hanle effects difficult as the observational signatures are fraught with low-amplitude signals that can become swamped with instrumental noise2, 3. Magneto-hydrodynamic (MHD) techniques have previously been applied to coronal structures, with single and spatially isolated magnetic field strengths estimated as 9–55 G (refs 4,5,6,7). A drawback with previous MHD approaches is that they rely on particular wave modes alongside the detectability of harmonic overtones. Here we show, for the first time, how omnipresent magneto-acoustic waves, originating from within the underlying sunspot and propagating radially outwards, allow the spatial variation of the local coronal magnetic field to be mapped with high precision. We find coronal magnetic field strengths of 32 ± 5 G above the sunspot, which decrease rapidly to values of approximately 1 G over a lateral distance of 7,000 km, consistent with previous isolated and unresolved estimations. Our results demonstrate a new, powerful technique that harnesses the omnipresent nature of sunspot oscillations to provide magnetic field mapping capabilities close to a magnetic source in the solar corona.