Use of SSR and Retrotransposon-Based Markers to Interpret the Population Structure of Native Grapevines from Southern Italy

Native grapevines are the quintessential elements of Southern Italy winemaking, and genomic characterization plays a role of primary importance for preservation and sustainable use of these unexploited genetic resources. Among the various molecular techniques available, SSR and retrotransposons-based markers result to be the most valuable for cultivars and biotypes distinctiveness. A total of 62 accessions including 38 local grape cultivars were analyzed with 30 SSR, four REMAP and one IRAP markers to assess their genetic diversity and obtain a complete genomic profiling. The use of VrZAG79, VrZAG112, VVS2, VVMD25 and VVMD5 combined with retrotransposon-based markers proved to be the most discriminating and polymorphic markers for the rapid and unambiguous identification of minority grapevines from Campania region, which is considered one of the most appreciated Italian districts for wine production. Results revealed 58 SSR marker-specific alleles, 22 genotype-specific SSR alleles, and four REMAP and IRAP private bands. Cases of synonymy and homonymy were discovered. In conclusion, we provided evidences that the integrating SSR and retrotransposon-based markers is an effective strategy to assess the genetic diversity of autochthonous grapes, allowing their easy identification.     

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295^T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO₂, and requires exogenous vitamin B₁₂. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O₂ concentrations. The abundance of a potentially more efficient CO₂-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb₃-type terminal oxidase increased under O₂ limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O₂-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O₂ conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.Subject terms: Water microbiology, Microbial biooceanography, Marine microbiology, Bacterial genomics, Bacterial physiology     

Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases <Emphasis Type="Italic">in silico</Emphasis> docked to different inhibitors

Background  

Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.     

Magnesium in tumoral tissues, in the muscle and serum of subjects suffering from neoplasia

Mg2+ content is significantly increased in malignant neoplastic mammary tissue compared with normal mammary tissue and benign neoplastic tissue of the breast. Significant variations of the ion were not found in the skeletal muscle tissue (rectus abdominis and pectoral muscle) of subjects suffering from malignant neoplasia with diffused metastasis. It seems that the variation of Mg2+ content in malignant neoplastic mammary tissue is a local factor linked with the biological anomalies of the neoplastic cell.     

Further secondary metabolites produced by the fungus Pyricularia grisea isolated from buffelgrass (Cenchrus ciliaris)

The fungal pathogen Pyricularia grisea has been studied to evaluate its production of phytotoxins for the biocontrol of the buffelgrass (Cenchrus ciliaris L.) weed. A first investigation allowed to isolate several new and known phytotoxic metabolites. However, the further investigation on the organic extract obtained from the fungus liquid culture showed the presence of other metabolites possibly contributing to its phytotoxicity. Thus, four known metabolites were isolated and identified by spectroscopic (nuclear magnetic resonance [NMR] and high-resolution electrospray ionization mass spectrometry [HRESIMS]) methods as dihydropyriculol ( 1 ), epi-dihydropyriculol ( 2 ), 3-methoxy-6,8-dihydroxy-3-methyl-3,4-dihydroisocoumarin ( 3 ), and (R)-mevalonolactone ( 4 ). The absolute configuration of 1 – 3 was determined for the first time by a computational analysis of their electronic circular dichroism (ECD) spectra. When the isolated compounds were bioassayed at a concentration of 5 × 10^–3 M in a buffelgrass coleoptile and radicle elongation test no toxicity was detected. On the contrary, compounds 1 and 3 showed a significant stimulating effect of radical elongation. Furthermore, the difference in growth stimulation between 1 and its epimer 2 highlights the tight relationship between absolute configuration and biological activity of these fungal metabolites.     

Two-dimensional gel electrophoresis of endometrial protein in human uterine fluids: qualitative and quantitative analysis

By combining two-dimensional gel electrophoresis, protein staining and a sensitive computer-assisted gel scanning system, it was possible to examine human uterine fluid (n = 56) qualitatively and quantitatively for the presence of endometrial proteins. The protein concentration of uterine fluids ranged from 0.1 to 12.0 mg/ml with early secretory phase samples (n = 15) having significantly less protein (0.72 +/- 0.2 SEM mg/ml p less than or equal to 0.05) than the proliferative phase (n = 57) samples (1.58 +/- .29 SEM mg/ml). Whole blood contamination of uterine fluid, as measured by hemoglobin content, averaged 6.2 +/- 0.88% throughout the menstrual cycle. Human uterine fluids collected throughout the menstrual cycle were found to contain serum and up to 24 other proteins in addition to those previously described (MacLaughlin and Richardson, 1983). These proteins represent approximately 1% of the total protein in the gels and exhibit isoelectric points from 4.5 to 7.0 and molecular weights in the 26,000 to 60,000 range. These proteins are absent from human serum, which exhibits an identical pattern whether obtained in the proliferative or secretory phase of the menstrual cycle. These secreted endometrial proteins now become the standard against which to compare proteins identified in vitro using organ, gland and cell culture techniques and to characterize proteins that are regulated by steroid hormones in vivo.     

Dual-chambered membrane bioreactor for coculture of stratified cell populations

We have developed a dual-chambered bioreactor (DCB) that incorporates a membrane to study stratified 3D cell populations for skin tissue engineering. The DCB provides adjacent flow lines within a common chamber; the inclusion of the membrane regulates flow layering or mixing, which can be exploited to produce layers or gradients of cell populations in the scaffolds. Computational modeling and experimental assays were used to study the transport phenomena within the bioreactor. Molecular transport across the membrane was defined by a balance of convection and diffusion; the symmetry of the system was proven by its bulk convection stability, while the movement of molecules from one flow line to the other is governed by coupled convection-diffusion. This balance allowed the perfusion of two different fluids, with the membrane defining the mixing degree between the two. The bioreactor sustained two adjacent cell populations for 28 days, and was used to induce indirect adipogenic differentiation of mesenchymal stem cells due to molecular cross-talk between the populations. We successfully developed a platform that can study the dermis–hypodermis complex to address limitations in skin tissue engineering. Furthermore, the DCB can be used for other multilayered tissues or the study of communication pathways between cell populations.