Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

Using Different Co-Adjuvant Activating Agents to Improve Activated Carbon Adsorption Capacities

Activated carbon (AC) has proved to be an effective adsorbent for the removal of an assortment of organic and inorganic pollutants from aqueous or gaseous media. However, the pursuit for more effective and cheaper AC is still very active and a diversity of textural and chemical treatments are described as a way to expand their applications. It is well known that the surface area and surface chemistry of AC strongly affect their adsorption capacity [1-3]. In particular, an increase in the nitrogen content has been related to an increase of the basic character and also to the development of the porous structure. In most published work this was achieved through an AC post treatment, including either a reaction with nitrogen containing reagents, such as ammonia, nitric acid, or a diversity of amines. However, the AC prepared directly from a nitrogen rich precursor through a physical or chemical activation is referred to as presenting the best characteristics, namely high nitrogen content, high basic character, low nitrogen leaching and also a good thermal stability [4]. To improve the AC adsorption capacities for acidic pesticide removal from the aqueous phase, we intend to improve the porous structure and introduce nitrogenated groups directly into the AC matrix, using different co-adjuvant activating agents as a nitrogen source, by chemical activation, with potassium hydroxide, of cork or poly(ethyleneterephthalate) (PET) precursors.

Effects of glyphosate and Roundup upon mammalian gametes

The wide use of glyphosate-based herbicides (GBHs) has become a controversial issue due to the potential harmful effects on human health. Commercial formulations, among which Roundup is the most famous one, contain a number of adjuvants inside; most of these are patented and not publicly known, therefore, they can act differently from glyphosate alone and might strengthen its toxic effect. Our study is focused on GBHs reproductive toxicity with a special regard to glyphosate and Roundup impact on male and female mammalian gametes after exposure to concentrations ranging from the one recommended for agricultural use (0.1% Roundup, containing 360 µg/mL glyphosate) to 70-fold lower or more. Sperm quality analysis, either on boar and stallion, showed that Roundup has much more detrimental impact than glyphosate at equivalent concentrations on spermatozoa function and survival. Basing on our results, the toxic effect of these pesticides on spermatozoa may be linked to an impairment in mitochondrial activity and a subsequent decrease in ATP production and/or alterations in the redox balance, which impact cell motility and plasma membrane stability. Moreover, a different species sensitivity to GBHs may exists as high doses of glyphosate affected sperm quality only in boar and not in stallion; furthermore, Roundup had deleterious effects at lower doses in the first compared to the latter. With regard to female gametes, we found that glyphosate and Roundup exposure during IVM detrimentally affect the subsequent developmental ability of swine embryos, providing further evidence of their potential toxic effect on female reproductive system. In addition, Roundup altered steroidogenesis and increased oocyte ROS levels. Therefore, according to our results, we can conclude that GBHs exert a negative impact on both male and female gametes and that Roundup adjuvants enhance glyphosate toxic effects and/or are biologically active in their side-effect.

R-loops and G4-structures: from DNA damage to innate immune response gene activation

Non-B DNA structures like R-loops and G-quadruplexes play a pivotal role in several cellular vital processes like DNA transcription regulation. Misregulation of said non-canonical DNA structures can often lead to genome instability, DNA damage, and, eventually, to the activation of an innate immune response. For such reasons they have been studied as adjuvants in anticancer therapies. Here we studied drugs targeting R-loops (Top1 poisons) and G4s (hydrazone derivatives) in order to observe their effects in terms of DNA damage induction and, subsequently, activation of innate immune response. We studied how non-cytotoxic doses of ampthotecin and LMP-776 impact on genome instability, are capable to induce DNA damage and micronuclei, and, eventually lead to an innate immune gene response via the cGAS/STING pathway. G-quadruplexes are another ubiquitous, non-canonical DNA structure, more abundant in telomeric regions, demonstrating a marked relation with the impairment of telomerase and the regulation of DNA replication and transcription. Furthermore, we investigated the properties of new-synthesized molecules belonging to the highly promising class of hydrazone derivatives, in terms of cytotoxicity, ability to stabilize G4-structures, induce DNA damage, and activate interferon-B production. Both Top1 poisons and G4-stabilizers possess several features that can be very useful in clinical applications, in light of their ability to stimulate innate immune response factors and exert a certain cell-killing power, plus they offer a broad and diverse range of treatment options in order to face a variety of patient treatment needs. It is for these very reasons that it is of uttermost importance that further studies are conducted on these compounds, in order to synthesize new and increasingly powerful and flexible ones, with fewer side effects to customize therapies on specific cancers’ and patients’ features.