Journal of Integrated -OMICS
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Iberian Lynx (Lynx pardinus) from the captive breeding program as reservoir of antimicrobial resistant enterococci and Escherichia coli isolates: DOI: 10.5584/jiomics.v3i2.142
No full textA total of 98 faecal samples from captive specimens of Iberian lynx were collected and analysed for enterococci (96 isolates) and Escherichia coli (90 isolates) recovery. These 186 isolates were tested for antimicrobial resistance, molecular mechanisms of resistance, and detection of virulence genes. Among the enterococci, Enterococcus hirae was the most prevalent species (35 isolates), followed by Enterococcus faecalis (30 isolates), Enterococcus faecium (27 isolates), and Enterococcus durans (4 isolates). High rates of resistance to tetracycline, erythromycin and high-level-kanamycin were detected among enterococcal isolates (41%, 26%, and 19%, respectively). The tet(M) and/or tet(L), erm(B), aac(6′)-Ie-aph(2″)-Ia, ant(6)-Ia, or aph(3′)-IIIa genes were detected among resistant enterococci. Likewise, high rates of resistance were detected in E. coli isolates to tetracycline, streptomycin, sulfamethoxazole-trimethoprim (SXT), nalidixic acid, ampicillin, and ciprofloxacin (34%, 28%, 26%, 21%, 17%, and 16%, respectively). Furthermore, the blaTEM or blaSHV, tet(A) and/or tet(B), aadA or strA-strB, aac(3)-II and/or aac(3)-IV, and different combinations of sul genes were detected among most resistant isolates. Fifteen isolates contained class 1 and/or class 2 integrons and 3 different gene cassette arrays were identified (aadA1, dfrA1+aadA1, and estX+psp+aadA2). The E. coli isolates were ascribed to phylo-groups A (12%); B1 (40%); B2 (37%), and D (11%), being fimA the most prevalent virulence gene (n=84), followed by aer (n=13), cnf1 (n=13), papC (n=10) and papG-allele III (n=9). This study showed specimens of Iberian lynx acting as reservoirs of resistance genes, and in future (re)introductions they could spread resistant bacteria throughout the environment
A Novel High Throughput High Content Analysis Assay for Intermediate Filament Perturbing Drugs: DOI: 10.5584/jiomics.v4i1.159
No full textKeratins form the intermediate filament (IF) component of the epithelial cytoskeleton. Depolymerisation of these filaments causes the cell to collapse and become more plastic. We have previously shown that short chain fatty acids may trigger depolymerisation of keratins through altered protein acetylation. Currently, there is no single functional assay for screening of the cytoskeleton. The aim of this study is to develop a high-throughput assay to quantify IF depolymerisation and to apply as a screen for IF-perturbing nutrients and drugs. Three treatments were used in a proof-of-principle study: the anti-fungal drugs griseofulvin and cordycepin (the former a c-mitotic drug known to suppress microtubule growth, the latter inducing abnormal mitosis by suppressing microtubule dynamics) and sodium butyrate, a histone deacetylase inhibitor which disrupts IF formation in cancer cells via post-translational modification of keratins.
Methods were optimised for cell fixation using methanol or formalin, permeabilising agents for Keratin 8 (krt8) antibody (triton-x100, digitonin and saponin) and blocking of non-specific binding prior to cell staining using BSA. High Content Analysis (HCA) was employed to quantify cell staining intensities by comparing co-occurrence of adjacent pixel intensities. Immunocytochemistry was used to identify Krt 8 intermediate filaments. Indicators of depolymerisation include Krt 8 fluorescence intensity, filamentousness or texture intensity, fibre spot count and fibre spot total area. All treatments resulted in significant decreases for texture intensity. Assessment of this assay using a Z prime calculation recorded gace a statistic of 0.95, indicating suitability for high-throughput applications.
In conclusion, a HCA assay for intermediate filament integrity has been demonstrated, establishing proof of principle with griseofulvin, and cross-validating with two further treatments assayable using this method
A Call for Benchmark Data in Mass Spectrometry-Based Proteomics: DOI: 10.5584/jiomics.v2i2.113
No full textProteomics is a quickly developing field. New and better mass spectrometers, the platform of choice in proteomics, are being introduced frequently. New algorithms for the analysis of mass spectrometric data and assignment of amino acid sequence to tandem mass spectra are also presented on a frequent basis. Unfortunately, the best application area for these algorithms cannot be established at the moment. Furthermore, even the accuracy of the algorithms and their relative performance cannot be established. This is due to the lack of proper benchmark data. This letter first introduces the field of mass spectrometry-based proteomics and then defines the expectations of a well-designed benchmark dataset. Thereafter, the current situation is compared to this ideal. A call for the creation of a proper benchmark dataset is then placed and it is explained how measurement should be performed. Finally, the benefits for the research community are highlighted
Values for evaluating the nutritional status of water-soluble vitamins in humans: DOI: 10.5584/jiomics.v3i1.130
No full textPreviously, we clarified that the amount of urinary excretion of water-soluble vitamins closely reflects the surplus amount of water-soluble vitamins in the body stores of rats and humans. We tried to set a tentative amount of urinary excretion of eight water-soluble vitamins of nine water-soluble vitamins (except vitamin B12) for maintaining health based on experiments in healthy young females administered a semi-chemically defined diet according to Japanese Dietary Reference Intakes and related data. We proposed a tentative value for the amount of urinary excretion of water-soluble vitamins for maintaining health. The values were: 200–2000 nmol/d for vitamin B1; 200–2000 nmol/d for vitamin B2; 2–15 µmol/d for 4-pyridoxic acid (a catabolite of vitamin B6); 50–300 µmol/d for the sum of the nicotinamide catabolites N1-methylnicotinamide, N1-methyl-2-pyridone-5-carboxamide, and N1-methyl-4-pyridone-3-carboxamide; 10–30 µmol/d for pantothenic acid; 15–100 nmol/d for folate; 50–200 nmol/d for biotin; and 100–2000 µmol/d for vitamin C. By using these values, we attempted to evaluate the nutritional status of water-soluble vitamins for 709 young Japanese females. The percentage within the tentative value of urinary excretion of water-soluble vitamin for maintaining health was 73.6% for vitamin B1, 63.5% for vitamin B2, 90.0% for vitamin B6, 85.6% for niacin, 58.1% for folate, 85.6% for pantothenic acid, 70.2% for biotin, and 65.4% for vitamin C. The percentage beyond the lower limit of detection was 22.4% for vitamin B1, 31.3% for vitamin B2, 6.2% for vitamin B6, 14.0% for niacin, 40.9% for folate, 12.4% for pantothenic acid, 26.2% for biotin, and 33.0% for vitamin C. The percentage over the upper limit of detection was 4.1% for vitamin B1, 5.2% for vitamin B2, 3.8% for vitamin B6, 0.4% for niacin, 1.0% for folate, 2.0% for pantothenic acid, 3.6% for biotin, and 1.6% for vitamin C. Nutritional assessment using urinary excretion amounts of water-soluble vitamins is persuasive, and leads to the transformation of habitual dietary intakes
Preface - Vol.3 Issue 2 - 2013: DOI: 10.5584/jiomics.v3i2.162
No full textDOI: 10.5584/jiomics.v3i2.16
Proteomic profiling of the HSPB chaperonome: Mass spectrometric identification of small heat shock proteins in stressed skeletal muscles: DOI: 10.5584/jiomics.v5i1.186
No full textThe continuing maintenance of protein homeostasis and the safeguarding of proteomic integrity is essential for the survival of complex cellular systems under stressful conditions. Proteostasis is maintained by a complex system of protective pathways that involve several classes of molecular chaperones, now referred to as the chaperonome. The elaborate interplay of these components averts detrimental protein aggregation and supports proteins in resuming their functional fold. In skeletal muscle tissues, molecular chaperones protect contractile functions throughout fibre adaptations to changed physiological demands and prevent tissue damage during acute phases of protein misfolding or prolonged periods of proteotoxic stress. This results in considerable changes in the expression profile of individual members of the large family of heat shock proteins. Systematic proteomic surveys of skeletal muscle tissues have revealed that the concentration of small heat shock proteins is especially affected following strenuous exercise, in various neuromuscular disorders and during the natural aging process. Of the 10 identified members of the small heat shock protein HSPB family, HSPB1 (Hsp25), HSPB2 (MKBP), HSPB3 (Hsp27), HSPB4 (αA-crystallin), HSPB5 (αB-crystallin), HSPB6 (Hsp20), HSPB7 (cardiovascular cvHsp) and HSPB8 (Hsp22) are clearly present in skeletal muscle tissues. This review outlines the proteomic identification of small heat shock proteins and their muscle-specific expression and induction patterns in health and disease. Since HSPB molecules are of relatively low molecular mass, belong to the markedly soluble type of proteins and represent critical pro-survival proteins that are intrinsically involved in the prevention of stress-induced fibre damage, they present ideal muscle-associated biomarker candidates for the establishment of superior diagnostic and therapy-monitoring approaches to assess stress-related skeletal muscle degeneration
VOL 5, NO 2 (2015) - Special Issue: DOI: 10.5584/jiomics.v5i2.192
No full textDOI: 10.5584/jiomics.v5i2.19
