Journal of Integrated -OMICS
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BIOCHEMICAL INDICATORS OF DROUGHT TOLERANCE OF CORN: DOI: 10.5584/jiomics.v10i1.309
No full textThe paper deals with impact of water deficit and heat shock on activity of sucrose-phosphate synthase (SPS) – (UDP-glucose: D-fructose-6-phosphat-2-α-glucosyltransferase, E.C. 2.4.1.14) – an enzyme involved in sucrose synthesis, on activity of lectins, as well as sucrose and abscisic acid (ABA) content in germinating kernels of corn lines with different drought tolerance (Zea mays L.). The paper demonstrates that corn lines, which are positively different in terms of drought tolerance, are characterized by varying activity of lectins, abscisic acid, sucrose-phosphate synthase and sucrose content in tissues of the aboveground part and roots of sprouts under the impact of adverse abiotic factors (water deficit and hyperthermia)
Inorganic mass spectrometry-based metallomics for environmental monitoring of terrestrial ecosystems affected by metal pollution using Mus spretus as bioindicator: DOI: 10.5584/jiomics.v3i2.128
No full textA metallomic approach based on the use of size-exclusion chromatography coupled to inductively coupled plasma-mass spectrometry (SEC-ICP-MS) has been used to characterize the biological response in liver, brain, kidneys, lungs and plasma of the free-living mouse Mus spretus in polluted areas located in Doñana National Park (southwest Spain) and the surroundings, mainly affected by agriculture, mining and industry activities, which are responsible for the presence of metallic contaminants. It is remarkable the high presence of Cu, Zn, Cd, As, Pb and Ni in the cytosolic extracts of different organs and plasma, especially in contaminated areas. In liver extracts, high intensity peaks traced by Cu, Zn, Pb and Cd at 7 kDa (matching with metallothionein I standard) are triggered by the presence of contaminants. In kidney, similar Cu and Cd-peaks at 7 kDa were observed but the equivalent Zn-peak was depleted by the competitive interactions of Cu-Cd-Zn for the active sites of these molecules. In addition, peaks traced by Cu and Zn at about 32 kDa in liver extract match with superoxide dismutase standard (Cu,Zn-SOD), which increase in accordance to contamination. An analogous behavior was observed for a Zn,Cu-peak at about 67 kDa that can be related with the bovine serum albumin standard (Cu,Zn-BSA) or other carrier protein such as transferrin (Cu-Tf) present in liver and plasma. Finally, low molecular mass arsenic metabolites were detected in mice captured in MAT site affected by mine waste
Salivary proteomics in ingestive behaviour research: advances, potentialities and limitations: DOI: 10.5584/jiomics.v8i1.231
No full textHuman saliva proteomics gained interest in the last two decades, mostly due to the non-invasive nature of this fluid collection and its potential for the diagnosis of different oral and systemic pathologies. Curiously, despite saliva being the fluid that first contacts with food, only recently it has been an increased interest in its relationship with ingestive behavior. The relevance of saliva protein composition in food acceptance and preferences is evidenced by the observation that individuals differing in oral food perception present particularities at level of salivary proteome. Individuals with different sensitivities for astringency diverge in the levels of several salivary proteins. The same is true concerning the perception of basic tastes, namely bitter and sweet. Even aroma perception depends on saliva protein composition. Interestingly, some of the proteins observed to differ in function of oral food perception are proteins that present variations with Body Mass Index (BMI). Besides this potential role of saliva in driving food choices, this fluid may have also potential as a source of biomarkers of ingestion. Although less explored, until now, there are evidences of changes in saliva protein composition based on the type of diet: diets rich in polyphenols induce modifications in saliva composition, in animal models and high-fat diets were also observed to change the levels of salivary alpha-amylase in rats. These different points will be reviewed in the present article
THIOCHROME ACTIVATES DNA-POLYMERASE I: DOI: 10.5584/jiomics.v9i1.261
No full textWe studied the effect of this metabolite on the activity of DNA polymerase I isolated from the liver of white rats.Established groups in the molecule of DNA polymerase are involved in the interaction thiochrome and responsible for the activation of this enzyme.This article shows the possibility of the influence of the most important metabolite –thiochrome on DNA polymerase I. Role of carboxyl groups of the enzyme and hydrophobic and hydrogen bonds in it in the realization of the activating action of thiochrome on the given enzyme has been studied. The influence of thiochrome on the activity of DNA polymerase was researched. It was found that thiochrome is capable of activating this enzyme through interaction with two sites of the enzyme containing amino acids with hydrophobic radicals
Bacterial two-hybrid analysis of the Shewanella oneidensis MR-1 multi-component electron transfer pathway: DOI: 10.5584/jiomics.v1i2.68
No full textUnderstanding cellular systems requires profound analysis of the protein interaction networks. Protein interaction mapping is performed mainly by co-purification strategies or two-hybrid systems. Recently, we expanded the tools for analyzing protein-protein interactions in bacteria with a two-hybrid technique based on beta-galactosidase complementation, and demonstrated its potential to explore interactions of membrane systems and to study transient interactions between redox partners (Borloo et al. 2007a). We demonstrate here the functionality of this assay to reveal the interactions within the complex electron transfer chain of the dissimilatory metal reducing bacterium Shewanella oneidensis MR-1. Specifically, we identified the cytoplasmic membrane-bound CymA as a key component, after which the electron transport chain is found to bifurcate towards several periplasmic proteins. It again congregates at the crucial MtrA, which in turn forms an electron transfer complex with the outer membrane localized MtrB and the terminal ferric reductases MtrC and OmcA. These data are complemented by mutant screening and confirm previous kinetic analyses (Borloo et al., 2007b)
Label-free protein quantification on tandem mass spectra acquired in a data-independent mode provides accurate measurements over five orders of concentration magnitude in complex matrices: DOI: 10.5584/jiomics.v1i2.45
No full textLabel free quantification using liquid chromatography and electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) is widely used in quantitative proteomics. However, data-dependent bottom-up proteomics suffers from low reproducibility due to semi-random selection of precursor ions for tandem mass spectrometry. In addition, this acquisition mode is biased towards abundant peptides. To overcome these problems, alternative precursor-ion selection methods were developed, such as data-independent acquisition and pseudo-multiple selected reaction monitoring (p-mSRM). With these methods, several tandem mass spectra are acquired over the chromatographic elution time of precursor ions. In this report, we investigated if the acquired tandem mass spectra can be used for label-free quantification. For this, extracted fragment ion currents were correlated to relative protein concentration. A linear relationship between ion current and proteins concentration was observed over five orders of magnitude. Thus, we conclude that relative label-free peptide and protein quantification can be performed in an ion trap using the data-independent acquisition mode. 
Serological secretome analysis of Corynebacterium pseudotuberculosis: DOI: 10.5584/jiomics.v1i2.54
No full textCaseous lymphadenitis (CLA) is a chronic disease affecting small ruminants caused by Corynebacterium pseudotuberculosis and is responsible for significant economic losses. Previous studies have reported that a set of C. pseudotuberculosis secreted proteins react with sera from infected goats. Mapping of the secretome will shed light on the pathogenesis of CLA. We have hereby identified six immunoreactive secreted proteins of C. pseudotuberculosis by 2D Western blotting using sera from goats with CLA and characterized them by mass spectrometry. The information retrieved will support studies leading to the development of efficient vaccines and diagnostic kits
Starvation of Jurkat T cells causes metabolic switch from glycolysis to lipolysis as revealed by comprehensive GC-qMS: DOI: 10.5584/jiomics.v3i1.129
No full text
T cells play a central role in the cellular part of the immune system and their metabolomic activity is strictly bound to the status of activation. Little is known about the metabolomic resilience of T helper cells in the resting status. Therefore we analyzed the metabolomic profile of non-activated Jurkat T cells under normal and starvation conditions by a two-dimensional GC-MS approach. We detected 52 organic and amino acids in the biological replicates covering the majority of central metabolic pathways. Under starvation conditions 21 analytes representing major metabolic pathways showed a significant down-regulation. For palmitoleic acid a significant up-regulation was detected. The annotation of differentially abundant metabolites to the pathways of TCA-cycle, amino acid metabolism and fatty acid biosynthesis indicating a metabolic switch from glycolytic to lipolytic energy generation upon starvation
Environmental OMICS: Current Status and Future Directions: DOI: 10.5584/jiomics.v3i2.141
No full textObjectives: Applications of OMICS to high throughput studies of changes of genes, RNAs, proteins, metabolites, and their associated functions in cells or organisms exposed to environmental chemicals has led to the emergence of a very active research field: environmental OMICS. This developing field holds an important key for improving the scientific basis for understanding the potential impacts of environmental chemicals on both health and the environment. Here we describe the state of environmental OMICS with an emphasis on its recent accomplishments and its problems and potential solutions to facilitate the incorporation of OMICS into mainstream environmental and health research.
Data sources: We reviewed relevant and recently published studies on the applicability and usefulness of OMICS technologies to the identification of toxicity pathways, mechanisms, and biomarkers of environmental chemicals for environmental and health risk monitoring and assessment, including recent presentations and discussions on these issues at The First International Conference on Environmental OMICS (ICEO), held in Guangzhou, China during November 8-12, 2011. This paper summarizes our review.
Synthesis: Environmental OMICS aims to take advantage of powerful genomics, transcriptomics, proteomics, and metabolomics tools to identify novel toxicity pathways/signatures/biomarkers so as to better understand toxicity mechanisms/modes of action, to identify/categorize/prioritize/screen environmental chemicals, and to monitor and predict the risks associated with exposure to environmental chemicals on human health and the environment. To improve the field, some lessons learned from previous studies need to be summarized, a research agenda and guidelines for future studies need to be established, and a focus for the field needs to be developed.
Conclusions: OMICS technologies for identification of RNA, protein, and metabolic profiles and endpoints have already significantly improved our understanding of how environmental chemicals affect our ecosystem and human health. OMICS breakthroughs are empowering the fields of environmental toxicology, chemical toxicity characterization, and health risk assessment. However, environmental OMICS is still in the data generation and collection stage. Important data gaps in linking and/or integrating toxicity data with OMICS endpoints/profiles need to be filled to enable understanding of the potential impacts of chemicals on human health and the environment. It is expected that future environmental OMICS will focus more on real environmental issues and challenges such as the characterization of chemical mixture toxicity, the identification of environmental and health biomarkers, and the development of innovative environmental OMICS approaches and assays. These innovative approaches and assays will inform chemical toxicity testing and prediction, ecological and health risk monitoring and assessment, and natural resource utilization in ways that maintain human health and protects the environment in a sustainable manner