Journal of Integrated -OMICS
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Bioradical homeostasis as new complex parameters of different biological systems: DOI: 10.5584/jiomics.v10i2.328
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The current state of free radical biomedicine allows us to formulate a fundamentally new parameter of homeostasis – bioradical homeostasis, understood as a state of free radical processes, reflecting the optimal intensity of the body metabolism of oxygen, nitrogen and halogens reactive species, carbonyls and other radical molecules. This term allows us to formulate another term – "bioradical stress". It is proposed to understand the effective violation of the physiological level of free-radical processes associated with the formation of active forms of oxygen, nitrogen or halogens and/or a decrease in the activity of systems that limit their damaging effect. It combines all known syndromes associated with bioradical level shifts (oxidative, nitrosative, halogenating and carbonyl stress). The introduction of the concept of bioradical stress involves the study of the effectiveness of various options for specific pathogenetic correction of bioradical stress (the administration of antioxidants, directed stimulation of antioxidant capacity by active oxygen forms, the use of regulatory properties of NO, etc.)
Cloud point method applied to the Apolipoprotein A-I extraction from human plasma and its identification by tandem mass spectrometry: DOI: 10.5584/jiomics.v1i1.27
No full textThis work describes the extraction of the apolipoprotein A-I (apoA-I) from human plasma using the cloud point extraction (CPE). The CPE was carried out with a nonionic surfactant (5 % w/v Triton® X-114), and the presence of a salting-out effect (10 % w/v NaCl) promoted biocompatible separation conditions at room temperature and pH 6.8. The apoA-I present in the surfactant-rich phase was identified by tandem mass spectrometry after two-dimensional gel electrophoresis
Enzymatic protein digests do not assist in E. coli discrimination at the strain level using mass spectrometry: DOI: 10.5584/jiomics.v3i1.131
No full textDifferent procedures for matrix assisted laser desorption ionization time of flight mass spectrometry-based E. coli classification at the strain level using the enzymatic digestion of proteins from the cell lysate have been studied. The effects of ultrasonic energy as well as the effects of protein reduction and protein alkylation in the sample treatment and in the subsequent classification were assessed. The final optimal method for classification was then compared with an intact cell-based approach in a different set of samples. Our results show that E. coli classification at the strain level is possible as 12 different strains were correctly classified using intact cell analysis. The classification done using protein digestion does not classify the strains with the same level of confidence than intact cell analysis does. 
Quantitative mass spectrometry of urinary biomarkers: DOI: 10.5584/jiomics.v4i2.177
No full textThe effectiveness of treatment of renal diseases is limited because the lack of diagnostic, prognostic and therapeutic markers. Despite the more than a decade of intensive investigation of urinary biomarkers, no new clinical biomarkers were approved. This is in part because the early expectations toward proteomics in biomarkers discovery were significantly higher than the capability of technology at the time. However, during the last decade, proteomic technology has made dramatic progress in both the hardware and software methods. In this review we are discussing modern quantitative methods of mass-spectrometry and providing several examples of their applications for discovery and validation of renal disease biomarkers. We are optimistic about future prospects for the development of novel of specific clinical urinary biomarkers
The Diplomatic and Digital Forensic Science in Born-Digital Records: The Quest for Authenticity: DOI: 10.5584/jiomics.v8i1.219
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This paper aims at the application of Digital Diplomatic and Digital Forensics Science in digital-born records, in order to guarantee its authenticity in institutional routines and processes, but also as a source of proof in possible legal and juridical scenarios. In view of the vast and fruitful discussions focused on the complexity of the digital records in Archival Science and Information Science (I.S.), there is a gap to manage and preserve the digital records, keeping them reliable, accurate and authentic in systems that have the same conditions. This gap makes it impossible to preserve records in the long term due, firstly, to the fragility of the systems where they are stored and, secondly, to the constant risks of obsolescence of hardware and software that occur on a day by day. Digital Diplomatic Science assists this process by determining the form and content of the record to evidence its legal-diplomatic authenticity and establish its historical value. Digital Forensic Science, in turn, provides support for the chain of custody to remain intact, regardless of the medium on which the digital record is fixed. The following questions is raised: Is it possible to apply the practice of law and the Digital Forensics in the area of the Archival Science and information science, guaranteeing the authenticity of the born-digital record. In addition, in which way does the junction between Digital Diplomatic Science and Digital Forensic Science guarantee the preservation and preservation of the born-digital records. To answer such questions, this research proposes to link five areas of knowledge following the scientific experiences conducted at the University of British Columbia in Canada by the InterPares (International Research on Permanent Authentic Records) group. Areas of knowledge that are offering interesting results for the preservation not only of the record, but also of the social memory: 1.Digital Forensics: discipline that joint Forensics Science with Computer Science to analyze the digital evidence. 2. Diplomatics Science: Science to analyze the form and structure to the records. 3. Archival Science: Science to involves the whole of the principles, policies, strategies, and activities designed to ensure the physical and technological stabilization of records for the purpose of extending indefinitely their life and protecting the accuracy and authenticity of and maintaining the accessibility to their intellectually content [1]. 4. Information Science: Science to analyze the information in different contexts. The research will carried out in a theoretical and qualitative way, taking into account the literature shared in the site Digital Records Forensics Project, coordinated by the author Luciana Duranti of the InterPares group, and the bibliography produced in the country of the areas of knowledge already referenced. The results obtained will contribute to the realization of alternative researches in document conservation within the Archival Science and the Information Science. 
The potential benefits of shRNA-mediated MMP1 silencing for psoriasis: DOI: 10.5584/jiomics.v9i1.269
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Matrix metalloproteinases (MMPs) orchestrate structural remodeling of psoriatic skin and accelerate the development of the inflammatory response.
In this paper, we explore whether knocking MMP1 down in epidermal keratinocytes can be beneficial for psoriasis.
We discovered that MMP1 silencing with specific shRNA reduced the migration of epidermal keratinocytes and made the cells susceptible to apoptosis in the presence of interferon-γ. Furthermore, MMP1-deficiency partially normalized the expression of genes involved in the pathogenesis of psoriasis (MMP9, -12, CCNA2, CCND1 and KRT17) and the terminal differentiation (KRT1, -10, IVL and LOR).
In this respect, MMP1 silencing could be beneficial for psoriasis due to MMP1 expression is limited to psoriatic plaques and correlates with disease severity
Ultrasonic Enhanced Applications in Proteomics Workflows: single probe versus multiprobe: DOI: 10.5584/jiomics.v1i1.55
No full textA 96-well plate-based platform in conjunction with an ultrasonic multiprobe of four tips was assessed to develop various fast proteomics workflows for gel-based proteomics. The use of such protocols reduce sample time and handling, allowing rapid processing whilst reducing the risk of contamination. The procedure reduces the time to indentify proteins separated by gel electrophoresis to just 8 min/each. In addition, the ultrasonic multiprobe was compared with the single probe as a tool to obtain high sample throughput in proteomics workflows entailing identification and/or quantification of proteins using mass-spectrometry based approaches. The 18-O labeling-based method was used to study the type of peptides extracted from the gels when the extraction was done with the aid of ultrasonic energy. The assessment was done in ten standard proteins separated by gel elecrophoresis. Two proteins obtained from D. desulfuricans, and from Cyprinus carpio, Split-Soret cytochrome c, and Vitellogenin respectively, were also indentified as a further proof-of-the concept
Mammalian Mitochondrial Proteome And Its Functions: Current Investigative Techniques And Future Perspectives On Ageing And Diabetes: DOI: 10.5584/jiomics.v1i1.51
No full textMitochondria play important roles in cellular physiology and in various pathologies. Over the last decade, great achievements have been made in study of the whole mitochondrial proteome, subproteome, mitochondrial complexes and their molecular organization, and mitochondrial post-translational modifications in both physiological and pathological conditions. Mitochondrial proteomic technologies will be discussed with regard to their applications to the detection of proteins with a net impact on the capacity of the mitochondria to perform various tasks during ageing and in diabetes