The triple helix: 50 years later, the outcome

Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us

Mechanistic Insights on the Inhibition of C5 DNA Methyltransferases by Zebularine

In mammals DNA methylation occurs at position 5 of cytosine in a CpG context and regulates gene expression. It plays an important role in diseases and inhibitors of DNA methyltransferases (DNMTs)—the enzymes responsible for DNA methylation—are used in clinics for cancer therapy. The most potent inhibitors are 5-azacytidine and 5-azadeoxycytidine. Zebularine (1-(β-D-ribofuranosyl)-2(1H)- pyrimidinone) is another cytidine analog described as a potent inhibitor that acts by forming a covalent complex with DNMT when incorporated into DNA. Here we bring additional experiments to explain its mechanism of action. First, we observe an increase in the DNA binding when zebularine is incorporated into the DNA, compared to deoxycytidine and 5-fluorodeoxycytidine, together with a strong decrease in the dissociation rate. Second, we show by denaturing gel analysis that the intermediate covalent complex between the enzyme and the DNA is reversible, differing thus from 5-fluorodeoxycytidine. Third, no methylation reaction occurs when zebularine is present in the DNA. We confirm that zebularine exerts its demethylation activity by stabilizing the binding of DNMTs to DNA, hindering the methylation and decreasing the dissociation, thereby trapping the enzyme and preventing turnover even at other sites

Greedy algae that are great for our environment

Vulgarization article about a Marsden project (Marsden Fund MAU1711: focusing on polyphosphate synthesis in microalgae) published on the royal society webpage

Mechanistic Model for the Reclamation of Industrial Wastewaters Using Algal-Bacterial Photobioreactors

A mechanistic model describing the steady-state biodegradation of inhibitory pollutants by algal-bacterial consortia in enclosed chemostat photobioreactors; was developed. The model was then validated against experimental data on salicylate removal by a Chlorella Sorokiniana/Ralstonia basilensis consortium cultivated without external O-2 supplied in an enclosed chemostat photobioreactor under various conditions of photon flux radiation, salicylate inlet concentrations, temperatures, and hydraulic retention times (HRT). A satisfactory fit of experimental data was achieved in both the fitting and validation data sets (11% of average relative error). The model was thus capable of describing satisfactorily the influence of the HRT and the combined increase of light input and temperature on salicylate removal efficiency (RE). The potential inhibitory effect of salicylate was considered into the model structure based on the influence of salicylate concentration on microalgae photosynthetic activity. Only four adjustable parameters were necessary when using this modeling approach,which significantly reduces the number of experimental kinetic and stoichiometric coefficients needed for process description. Variables such as reactor geometry and light absorption characteristics of the biomass were grouped into a single parameter, which highly simplifies photobioreactor modeling. Being based on stoichiometric, thermodynamic, and mass balances analysis, this model can be extended to the removal of any organic pollutant in industrial wastewaters and to any photobioreactor configuration. It therefore provides an important tool to assess the feasibility of pollutant biodegradation under full photosynthetic oxygenation (i.e., no external O-2 supply) and to optimize photobioreactors by establishing the conditions under which complete pollutant removal can be achieved. The model herein developed also provides a tool to better understand the complex relationships between microalgae, bacteria, light, and pollutant concentration, which will promote the development of algal-bacterial processes as a cost-effective alternative for wastewater reclamation and algae production from wastewater

Nitrous Oxide (N₂O) production in axenic <i>Chlorella vulgaris</i> microalgae cultures: evidence, putative pathways, and potential environmental impacts

Using antibiotic assays and genomic analysis, this study demonstrates nitrous oxide (N₂O) is generated from axenic <i>Chlorella vulgaris</i> cultures. In batch assays, this production is magnified under conditions favouring intracellular nitrite accumulation, but repressed when nitrate reductase (NR) activity is inhibited. These observations suggest N₂O formation in <i>C. vulgaris</i> might proceed via NR-mediated nitrite reduction into nitric oxide (NO) acting as N₂O precursor via a pathway similar to N₂O formation in bacterial denitrifiers, although NO reduction to N₂O under oxia remains unproven in plant cells. Alternatively, NR may reduce nitrite to nitroxyl (HNO), the latter being known to dimerize to N₂O under oxia. Regardless of the precursor considered, an NR-mediated nitrite reduction pathway provides a unifying explanation for correlations reported between N₂O emissions from algae-based ecosystems and NR activity, nitrate concentration, nitrite concentration, and photosynthesis repression. Moreover, these results indicate microalgae-mediated N₂O formation might significantly contribute to N₂O emissions in algae-based ecosystems (e.g. 1.38–10.1 kg N₂O-N ha⁻¹ yr⁻¹ in a 0.25 m deep raceway pond operated under Mediterranean climatic conditions). These findings have profound implications for the life cycle analysis of algae biotechnologies and our understanding of the global biogeochemical nitrogen cycle

Flaws in the current method for calculating methane emissions during dairy manure management in New Zealand

New Zealand's Greenhouse Gas Inventory (the NZ Inventory) currently estimates methane (CH4) emissions from anaerobic dairy effluent ponds by: (1) determining the total pond volume across New Zealand; (2) dividing this volume by depth to obtain the total pond surface area; and (3) multiplying this area by an observational average CH4 flux. Unfortunately, a mathematically erroneous determination of pond volume has led to an imbalanced equation and a geometry error was made when scaling-up the observational CH4 flux. Furthermore, even if these errors are corrected, the nationwide estimate still hinges on field data from a study that used a debatable method to measure pond CH4 emissions at a single site, as well as a potentially inaccurate estimation of the amount of organic waste anaerobically treated. The development of a new methodology is therefore critically needed

Degradation of acenaphthene, phenanthrene and pyrene in a packed-bed biofilm reactor

Biofilm reactors are particularly suitable for the treatment of large amounts of diluted effluent, such as groundwater contaminated with scarcely soluble pollutants. A packed-bed column reactor was tested for the degradation of acenaphthene, phenanthrene and pyrene provided at their aqueous solubility concentrations. Acenapthene and phenanthrene were removed to more than 99% efficiency from this reactor whilst pyrene was removed to 90%. Pollutant disappearance was also recorded in the control reactor and was probably caused by the adsorption of pollutants into the reactor. The measurement of oxygen consumption in both reactors confirmed that microbial degradation of the pollutants was indeed occurring in the inoculated reactor. Physical adsorption is not however unwanted, as it could help with the formation of a biofilm at an early stage of the treatment