Journal of Integrated -OMICS
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Human disease biomarkers: challenges, advances, and trends in their validation
Full text linkBiomarkers are important tools in the medical field, once they allow better prediction, characterization, and treatment of diseases. In this scenario, it is essential that biomarkers are highly accurate. Thus, biomarker validation is an essential part of ensuring the effectiveness of a biomarker. Validation of biomarkers is the process by which biomarkers are evaluated for accuracy and consistency, as well as their ability to inform the condition of health or disease. Although, there is no unique measure that can be used to determine the validity for all biomarkers, there are general criteria that all biomarkers must meet to be useful. In this work, we review the definition of biomarkers and discuss the validity components. We then critically discuss the main methods used to validate biomarkers and consider some examples of biomarkers of the diseases which most killer in the world (cardiovascular diseases, cancer, and viral infections), highlighting the potential biochemical pathways of these biomarkers in the biological system. In addition, we also comment on the omic strategies used in the biomarker discovery process and conclude with information about perspectives in biomarker validation through imaging techniques
Essential elements as critical players against SARS-CoV-2 activity
Full text linkBackground: SARS-CoV-2 virus is currently one of the main causes of death worldwide. Several studies have suggested that various trace elements play a vital role in the immune activity during viral infection, being an important tool to understand the SARS-CoV-2 infection and its systemic behavior, which affects different organs.
Purpose: To summarize recent studies that report the effect of trace elements on the immune system and their role in fighting SARS-CoV-2 infection, presenting potential biochemical routes.
Method: The main databases (ScienceDirect®, Scopus®, PubMed®) were consulted to search for works published up to October 2022, focusing on the role of trace elements in the immune activity against viral infection, including SARS-CoV-2.
Conclusion: Many elements can act both in the activation of the host’s immune activity and in the survival of the virus since these processes occur with the participation of essential metals to guarantee the integrity of their functions. However, the relationship between trace elements and viral infection is complex, and requires further studies, mainly, focusing on the systemic behavior of SARS-CoV-2 infection
Comparative analyses of the complete mitochondrial genomes of the two filarial worms Wuchereria bancrofti & Brugia malayi with Caenorhabditis elegans
Full text linkWuchereria bancrofti and Brugia malayi are the filarial worms belonging to phylum Nematoda and cause lymphatic filariasis (LF) disease in humans. W. bancrofti and B. malayi are Wolbachia dependent organisms while C. elegans is free living Wolbachia independent nematode. In order to investigate the conserved regions present in the mitochondrial genome of these organisms, the complete mitochondrial (mt) genomes of W. bancrofti and B. malayi having size 13,636 bp and 13,657 bp in length, respectively are compared with C. elegans (13794 bp). These mt genomes were similar to each other in respect of their size, AT content and encode the same 12 PCGs (nad1–6, nad4L, cytb, cox1–3, and atp6). Complete mt genome alignment identified 13 conserved regions in each of the organisms with some of these regions unique only to one organism. Phylogenetic analysis using the mt genome showed a close relationship between W. bancrofti and B. malayi but showed a common early ancestor with the C. elegans emphasizing an early evolutionary divergence. 
Computational Nanomedicine: Helping Us Get Through COVID-19
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Proteomic analysis of the mitochondria-enriched fraction from diabetic rat skeletal muscle: DOI: 10.5584/jiomics.v1i1.42
No full textMitochondrial dysfunction in muscle has been implicated to play a causative role or being an indirect consequence of insulin resistance in type-2 diabetes. In order to investigate potential diabetes-related alterations in the mitochondrial proteome of muscle, we have carried out a mass spectrometry-based proteomic analysis of the gastrocnemius muscle from normal versus diabetic Goto-Kakizaki rats. A generally perturbed protein expression pattern was observed in the mitochondria-enriched fraction from diabetic muscle. Various mitochondrial markers, including NADH dehydrogenase, cytochrome b-c1 complex and isocitrate dehydrogenase were reduced in diabetic preparations. Isoforms of pyruvate dehydrogenase and ATP synthase exhibited differential changes in their abundance. The altered protein expression levels of these key metabolic enzymes might trigger a diabetes-dependent decrease in mitochondrial oxidative phosphorylation levels. The proteomic findings presented here support the idea that mitochondrial abnormalities are involved in the molecular pathogenesis of type-2 diabetes and may be crucial for the development of insulin resistance
A simulated annealing-based algorithm for iterative class discovery using fuzzy logic for informative gene selection: DOI: 10.5584/jiomics.v1i1.28
No full textWithin a gene expression matrix, there are usually several particular macroscopic phenotypes of samples related to some diseases or drug effects, such as diseased samples, normal samples or drug treated samples. The goal of sample-based clustering is to find the phenotype structures or subsamples. We present a novel method for automatically discovering clusters of samples which are coherent from a genetic point of view. Each possible cluster is characterized by a fuzzy pattern which maintains a fuzzy discretization of relevant gene expression values. Possible clusters are randomly constructed and iteratively refined by following a probabilistic search and an optimization schema. Evaluation of the proposed algorithm on publicly available microarray datasets shows high accuracy in spite of noise and the presence of other clusters. The results obtained support the appropriateness of using fuzzy logic to represent and filter gene expression values following an iterative approach. The proposed method complements our previous GENECBR system and both are freely available under GNU General Public License from http://www.genecbr.org/fpclustering.htm and http://www.genecbr.org/, respectively
The salivary microbiome, assessed by a high-throughput and culture-independent approach: DOI: 10.5584/jiomics.v1i1.43
No full textThe lack of cultivation of a significant fraction of bacteria found in the oral cavity means that culture-independent approaches are needed for the study of the salivary bacterial community composition and diversity. Saliva is easily obtained and could provide an alternative to blood in diagnostics, forensics, epidemiology and population studies. Our goal in this review is to put together the findings from the handful of recent studies of human salivary bacteria derived from culture-independent high-throughput sequencing of the 16S rRNA gene and look for emerging trends in the resulting larger dataset. Differences in phyla and genera abundances between studies of the salivary microbiome may be due to individual (genetic and lifestyle) variations, geographic variations and biases introduced during the experimental steps. Nevertheless, seven major phyla found in all relevant studies may be arbitrarily assigned into three major categories according to their abundance: (i) Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were very abundant; (ii) TM7 and Fusobacteria were moderately abundant and (iii) Spirochaetes had the lowest abundance. The frequency of genera varied among the studies but many had a relatively consistent presence. Genera found in all of the four reported salivary microbiomes were generally present at a high frequency and contributed to 71-80% of all sequences in the corresponding datasets. Conversely, genera identified in only one available salivary microbiome generally showed a low abundance. Improvements in high-throughput sequencing technology will enable random metagenome fragment sequencing to become a powerful tool to study bacterial, archaeal, fungal, phage and human viral components of the salivary microbiome in parallel
Functional phosphoproteomics for current immunology research: DOI: 10.5584/jiomics.v1i1.40
No full textSignaling networks are key elements in all major aspects of cellular life, playing a major role in inter- and intracellular communications. They are involved in diverse processes such as cell-cycle progression, cellular metabolism, cell-cell communication and appropriate response to the cellular environment. The latter comprises a whole range of networks that are involved in regulation of cell development, differentiation, proliferation, apoptosis, and immunologic responses. The key mechanism involves the transduction of extracellular signals across the cell surface to different effectors in the cytosol and the nucleus. Dysregulation of these pathways is often associated with immunology disorders and malignant diseases such as cancer. One of the most common mechanisms of activation and/or inactivation of signaling transduction pathways is phosphorylation and de-phosphorylation at serine, threonine and tyrosine residues. Phosphoproteomics is playing an important role in our understanding of how phosphorylation participates in translating distinct signals into the normal and or abnormal physiological responses, and has shifted research towards screening for potential therapies for diseases and in-depth analysis of phosphoproteomes. Given the importance of phosphoproteomics in translational research we aim at outlining phosphoproteomic approaches based on mass spectrometry (MS).
This review focuses on (1b) the role of phospho signaling in immunology, (2a) current phosphopeptide enrichment methods based on IMAC and titanium dioxide, (2b) phosphopeptide analysis by MS, and (2c) issues concerned with interpretation of phospho spectra by database dependent search. Finally, quantitative methods used in phosphoproteomics such as Stable Isotope labeling with Amino acid in cell Culture (SILAC), isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and Absolute Quantification (AQUA) is discussed in section 3
