Grape must profiling and cultivar discrimination based on amino acid composition and general discriminant analysis with best subset

CITATION: Petrovic, G., Aleixandre-Tudo, J. L. & Buica, A. 2019. Grape must profiling and cultivar discrimination based on amino acid composition and general discriminant analysis with best subset. South African Journal of Enology and Viticulture, 40(2):10.21548/40-2-3373, doi:10.21548/40-2-3373.The original publication is available at http://www.journals.ac.za/index.php/sajevThe present study aimed to elucidate the amino acid profile of a number of grapevine cultivars relevant to the South African wine industry using 738 grape must samples obtained during the 2016 and 2017 harvests.  Proline and arginine were found to be the most abundant amino acids, with an average of 697.69 mg/L for proline (range 33.22-3445.43 mg/L) and 388.35 mg/L for arginine (range 13.56-1616.56 mg/L) across all vintages, regions, and cultivars. At the other extreme, ornithine (2.01 mg/L), glycine (3.28 mg/L), methionine (3.64 mg/L) and lysine (3.91 mg/L) were found to have the lowest concentrations, both in terms of the overall average, as well as per cultivar. Furthermore, the data were used to demonstrate how characteristic the amino acid profile is of a particular group (red or white) or cultivar. Cultivars were predicted based on their average amino acid concentrations using general discriminant analysis (GDA) and the best subset principle. For white musts, Chardonnay showed the highest prediction accuracy (100%), and Pinotage (75%) for red cultivars. Overall, the white cultivars included in this study were more accurately distinguished from one another (75.6%) compared to the red (60.1%). This predictive ability was subsequently compared to the accuracy of predicting cultivars based on only the arginine and proline concentrationsas well as the ratio between the two. The use of only these amino acids as well as the addition of the proline/arginine ratio as a predictor variable did not offer satisfactory discriminatory power between either white or red cultivars.https://www.journals.ac.za/index.php/sajev/article/view/3373Publisher's versio

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Cross-reacting antibodies against the pandemic (H1N1) 2009 influenza virus in older Australians

Objective: To assess background pre-pandemic cross-reacting antibodies to the pandemic (H1N1) 2009 virus in older populations in Australia. Design, setting and participants: Data were opportunistically generated from three cross-sectional pre-pandemic studies involving people aged 60 years or older: a 3-year (2006-2008) study of influenza outbreaks in aged care facilities (ACFs) in Sydney; an investigation of a respiratory virus outbreak in an ACF in rural New South Wales in June 2009; and a non-influenza serosurvey undertaken in NSW in 2007 and 2008. Main outcome measure: Prevalence of pandemic (H1N1) 2009 haemagglutination inhibition (HAI) antibody titres ≥1:40 (putative protective level) in pre-pandemic sera. Results: In total, 259 serum samples from individuals aged 60 years or older (range, 60-101 years) were tested. More than half of the individuals tested were women (151/259; 58.3%). About a third of individuals (37.5%) had cross-reacting HAI antibody titres ≥1:40. The prevalence of cross-reacting antibodies was highest in the oldest age groups (≥85 years), with more than 60% of these people having HAI antibody titres ≥1:40. The proportion of subjects with HAI antibody titres ≥1:40 decreased significantly and successively in younger groups to only 12% of those aged 60-64 years. Conclusions: Our study suggests a pre-existing influenza A antibody reserve in most of the oldest group of people that was cross-reactive to the new pandemic (H1N1) 2009 virus; this is likely to be lifelong and to have provided them with clinical protection against the first wave of the pandemic. Pandemic influenza control measures need to focus more on younger adults naive to the pandemic virus and at increased risk of severe disease

Oleoyl coenzyme A regulates interaction of transcriptional regulator RaaS (Rv1219c) with DNA in mycobacteria

We have recently shown that RaaS (regulator of antimicrobial-assisted survival), encoded by Rv1219c in Mycobacterium tuberculosis and by bcg_1279c in Mycobacterium bovis bacillus Calmette-Guérin, plays an important role in mycobacterial survival in prolonged stationary phase and during murine infection. Here, we demonstrate that long chain acyl-CoA derivatives (oleoyl-CoA and, to lesser extent, palmitoyl-CoA) modulate RaaS binding to DNA and expression of the downstream genes that encode ATP-dependent efflux pumps. Moreover, exogenously added oleic acid influences RaaS-mediated mycobacterial improvement of survival and expression of the RaaS regulon. Our data suggest that long chain acyl-CoA derivatives serve as biological indicators of the bacterial metabolic state. Dysregulation of efflux pumps can be used to eliminate non-growing mycobacteria

Tri-, Tetra-, and Hexanuclear Copper(II) Phosphonates Containing N-Donor Chelating Ligands: Synthesis, Structure, Magnetic Properties, and Nuclease Activity

Reaction of Cu(ClO4)2 3 6H2O with cyclopentyl phosphonic acid and 2,20-bipyridine (bpy) in presence of triethylamine afforded a trinuclear compound [Cu3(C5H9PO3)2(bpy)3(MeOH)(H2O)](ClO4)2 (2). The latter dimerizes to a hexanuclear derivative [Cu6(C5H9PO3)4(bpy)6(MeOH)4](ClO4)4 (1) under prolonged reaction conditions. Reaction of CuCl2 with cyclopentyl phosphonic acid and 2,20-bipyridylamine (bpya) affords a tetranuclear derivative [Cu4(C5H9PO3)2( μ-Cl)2(bpya)4](Cl)2, (MeOH)2 (3). Reaction of the latter with NaClO4 also affords a trinuclear compound [Cu3(C5H9PO3)2( μ-Cl)(bpya)3(H2O)](ClO4) (4). Double and single-bridged hexanuclear species, [{Cu3(C5H9PO3)2(bpy)3(bpp)}(MeOH)2(H2O)(CH2Cl2)(ClO4)2]2 (5), [{Cu3(i- PrPO3)2(bpy)3(4.40-bpy)(H2O)}(H2O)2(ClO4)2]2 (6), [{Cu3(C5H9PO3)2(bpya)3(4.40-bpy)(H2O)}(MeOH)(H2O)(ClO4)2]2 (7), and [Cu6(t-BuPO3)4(phen)6(4,40-bpy)(MeOH)4](CH2Cl2)(H2O)(ClO4)4 (8) (phen = 1,10-phenanthroline) were obtained by the reaction of an in situ generated trinuclear complex with appropriate bridging ligands 4,40-bipyridine (4,40-bpy) or 1,3-bis(4- pyridyl)propane (bpp). ESI-MS studies of these complexes reveal that 2-4 retain their structures in solution. Molecular structures of 2-8 were determined by X-ray crystallography. All the compounds reveal a capping coordination mode by tridentate phosphonate [RPO3]2- ligands. Detailed magnetic studies on 2 and 4-8 reveal intramolecular antiferromagnetic interactions between Cu(II) S = 1/2 spins. 2 and 4 are excellent artificial nucleases and can convert supercoiled plasmid DNA (pBR322) into its nicked form without the aid of an external oxidant