Journal of Integrated -OMICS
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Urinary porphyrin profiles as biomarkers of occupational exposures to multiple metals: DOI: 10.5584/jiomics.v8i1.216
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Chronic occupational exposures to low levels of metal mixtures necessitates biomonitoring of exposed workers. However, a single biomarker is rarely sufficient to ascertain the exposure of an individual to a complex mixture, with multiparameter analysis of the same sample considered recently as a preferred approach. Porphyrins are formed as intermediates of heme biosynthesis and different metals can exert their effects at different points of this metabolic pathway, leading to changed urinary porphyrins excretion profiles. The aim of this work was to develop a model that could serve to identify, on an individual basis, multiple metal exposure resulting from mining work, by using urinary porphyrin profiles. Urine samples of workers were obtained from a Portuguese mining company and a non-occupationally exposed group was used as control. The levels of uro-, hepta-, hexa-, penta-, copro- and protoporphyrins were determined by HPLC. It was observed that only heptaporphyrin levels in miners were significantly (
Molecular analysis of oncogene expressions in different grades of gliomas: DOI: 10.5584/jiomics.v8i1.242
No full textThe aggressiveness of brain tumors is attributed to the expression of multiple oncogenes involved in proliferation, metabolism and therapeutic resistance whose potential correlation with tumor progression has not been well-studied. In this study, we aimed to investigate the relationship of oncotargets involved in pathogenesis with respect to glioma grades. Gliomas (n=40) were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing for the detection of epidermal growth factor receptor (EGFR) mutants. Expressions levels of EGFR, EGFR variant III (EGFRvIII), Lck/Yes novel tyrosine kinase (LYN), Spleen tyrosine kinase (SYK), insulin receptor substrate 1 (IRS1), phosphatidylinositol 3-kinase (PI3K), Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) and glucose transporter 3 (GLUT3) were studied using real-time PCR and compared against glioma grades via statistical methods. Protein expressions were analyzed using immunohistochemistry and western blotting. EGFRvIII was detected in 53% and exon 4 deletion (de4 EGFR) in 20% of gliomas. Importantly, the expressions levels of candidate oncogenes were significantly upregulated (
Linguistic Difficulties for Translators and Interpreters: The Case of Forensic Law and Science Documents: DOI: 10.5584/jiomics.v7i2.218
No full textForensic Science (or Forensics) holds various fields of science (Psychology, Pathology, Odontology, Toxicology, Digital Forensics, to cite a few) involved in solving crimes and offences at any stage in criminal proceedings and researches. On the other hand, Forensic Law is a legal branch that involves issues related to forensic techniques in a justice system (being thus linked to Criminology, Criminal Law, and Civil Law). The intersection of Science and Law contributes to finding out the truth of a case, either criminal or civil, and they both have undergone dramatic progress in recent years. The aforementioned intersection provides specialists with a considerable amount of documents, either electronic or paperback…and they often need to be translated or interpreted into other languages. The high level of technical terms, complex nouns and phraseology, hamper their translation, interpreting, and proofreading services. In this paper, we will provide the reader with the main linguistic features of Forensic Science and Law Discourse, matched with source texts and target texts. By means of the use of original Forensic documents, we will provide translators and interpreters with techniques and strategies for facing their translation and proofreading
Identification of NEK3 interacting proteins and functional characterization of its signaling mechanisms: DOI: 10.5584/jiomics.v7i1.195
No full textNEKs (NIMA-related kinases) are a group of kinases that share high amino acid sequence identity to NIMA (Never in mitosis gene A), which exists as a single member in the fungi Aspergillus nidulans and is functionally involved in the initiation of mitosis. NEK3 is a 506 amino acid serine/threonine kinase, localizes both to the nucleus and cytoplasm, and its gene localizes to 13q14.2 chromosome. It has an N-terminal catalytic domain and a C-terminal regulatory domain, which contains Thr475 in its PEST domain, which gets phosphorylated upon activation. Expression of mutants without Thr475 or PEST domain causes changes in cellular morphology and polarity of neuronal cells. NEK3 is also involved in cell motility and invasiveness of breast cancer tumor cells through interaction with regulators of the Rho GTPases Rac1 and RhoA, mediated by prolactin induced association of NEK3 to the human Prolactin Receptor (PRLR). Using the Matchmaker Gold Yeast Two-Hybrid system, a screening for interaction partners wasperformed and 65 clones were obtained, which cDNAs encode 27 different proteins. The identified candidate interacting proteins are functionally involved in sumoylation, ubiquitinylation, transcriptional regulation, DNA repair, RNA processing, and the regulation of cell proliferation, invasiveness and metastasis.Some interaction partners for NEK3 are located in the nucleus and plasma membrane but most of them localize to the cytoplasm. One of the cytoplasmatic interactors for NEK3, RhoGDI2, is a regulator of RhoGTPases and inhibits Rac1 and RhoA activation levels. In our pull down assay, NEK3 overexpression increases Rac1-GTP while concomittant overexpression of RhoGDI2 reducesit to non-detectable levels. Our data suggests that NEK3 interaction with RhoGDI2 is a important new regulatory elements in Rac1 signaling pathways
Myosin light chain and calcium regulating protein differences in chronic musculoskeletal neck and shoulder pain: DOI: 10.5584/jiomics.v6i1.191
No full textProteomic screening analysis has detected myosin light chain (MLC) as a protein implied to be involved in chronic musculoskeletal neck and shoulder pain. Several analyses of MLC proteins have stated a difference in phosphorylation being the determining factor for protein activation hence altered contrability of the muscle in i.e. senescence. In continuation of a previous publication, this study is an attempt to analyze the different MLC isoforms by mass spectrometry and immune-analyses in myalgic and healthy trapezius muscle. In the present study no differences in phosphorylation level between the corresponding individual proteins were detected using LC-MSMS and immunoblotting; instead we assigned different isoforms of regulatory MLCs. To further elucidate the contrability: calcium (Ca2+) regulatory proteins, sarco(endo)plasmic reticulum Ca2+ ATPase 1 (SERCA-1) and calsequestrine (CSQ) were analyzed by western blot. The analysis revealed a significantly increased abundance of SERCA-1 protein in the myalgic muscle and a significantly increased abundance of CSQ in healthy muscle. Myalgic muscle contraction patterns have in previous studies shown to differ from healthy muscle which may be connected to the Ca2+ availability in the muscle. Here we present the proteomic characterization of differences in Ca2+ regulating proteins and particularly regulatory MLCs in trapezius muscle of women with chronic musculoskeletal neck and shoulder pain
Vaginal bacterial microbiota of an endangered donkey breed: a comparison between Miranda donkey breed (Equus asinus) jennies with and without reproductive problems: DOI: 10.5584/jiomics.v6i1.193
No full textThis study provided an overview of the vaginal bacterial microbiota of Asinina de Miranda jennies with and without reproductive problems. This Portuguese autochthonous donkey bred is in danger of extinction. Bacteria isolated were predominantly Gram-positive and belonging to the genera of Bacillus spp, Corynebacterium spp., Lactobacillus spp., Staphylococcus spp. and Streptococcus spp.. The species found in the vaginal microbiota were diverse and didn’t differ much between the jennies with and without reproductive problems. However the isolates of Streptococcus zooepidemicus of jennies with reproductive problems presented a higher number of the studied genes encoding virulence factors then the isolate without reproductive problems. This is the first study reporting vaginal bacterial microbiota of Asinina de Miranda jennies. Since there are few studies regarding the vaginal microbiota of equines, especially in this donkey breed, these results can be an asset for future studies
A DIGE proteomic analysis of wheat flag leaf treated with TERRA-SORB® foliar, a free amino acid high content biostimulant: DOI: 10.5584/jiomics.v6i1.188
No full textThe flag leaf is the most important source of carbohydrate during wheat kernel filling. Around a 75% of all sugars stored in the kernel come from carbon fixed by this leaf. Terra-Sorb® foliar is an L-α-amino acid-based product from enzymatic hydrolysis for foliar application with a high ratio of free to total amino acids. Previous agronomical studies carried out on grassy, horticultural and tree crops have shown that the application of Terra-Sorb® increases photosynthetic plant activity and chlorophyll content, promotes rapid recovery from stress and improves fruit set.
In this work, we have undertaken a proteomic approach to explore molecular mechanisms potentially involved in the stimulating effect of Terra-Sorb® Foliar on wheat yield when applied in commercial fields. Wheat plants at the flag leaf stage were treated, and a DIGE approach was used to compare the proteomes of treated vs. control plants in four biological replicates.
Thirty-seven protein spots were found to change in abundance (ANOVA
Comparative integrated omics approach sterically understanding hepatic metabolic dynamics in mouse model: DOI: 10.5584/jiomics.v7i1.200
No full textCurrently, the general approach of analysis is using a single omics technique, however the combined analysis of data by employing multiple omics analyses can enable a more fundamental understanding of the biological phenomena. Multi-layered combination of multiple omics technologies involves generation of a large amount of data, which leads to increased complexity and makes comprehension of bio-information more difficult. The objective of this study was to investigate the utility of incorporating multiple omics technologies in a multi-layered fashion. Transcriptomic, proteomic, and metabolomic analyses were carried out using a mouse model of diet-induced obesity. The present study reported the comprehensiveness of three omics analyses and the utility of using multiple omics analyses. Uniform changes were observed among changes at all stages but the majority of these specific to the omics approach. This data supports the fact that various molecules progress through the central dogma at differing speeds. Since the time axis differs for each molecule, combining multiple omics analyses makes it possible to investigate the reactions in organisms three-dimensionally. At first glance, it simply appears that combining a number of very large data sets produces even more complexity but, if multi-layered omics data are treated with an awareness of their meaning, benefits, and limitations, then the combination of multiple omics analyses can be extremely useful for research in molecular biology
Proteomic and lipidomic analysis of primary mouse hepatocytes exposed to metal and metal oxide nanoparticles: DOI: 10.5584/jiomics.v5i1.184
No full textThe global analysis of the cellular lipid and protein content upon exposure to metal and metal oxide nanoparticles (NPs) can provide an overview of the possible impact of exposure. Proteomic analysis has been applied to understand the nanoimpact however the relevance of the alteration on the lipidic profile has been underestimated. In our study, primary mouse hepatocytes were treated with ultra-small (US) TiO2-USNPs as well as ZnO-NPs, CuO-NPs and Ag-NPs. The protein extracts were analysed by 2D-DIGE and quantified by imaging software and the selected differentially expressed proteins were identified by nLC-ESI-MS/MS. In parallel, lipidomic analysis of the samples was performed using thin layer chromatography (TLC) and analyzed by imaging software. Our findings show an overall ranking of the nanoimpact at the cellular and molecular level: TiO2-USNP
Improved reconstitution of Trizol derived protein extracts provides high quality samples for comprehensive proteomic characterization of cell cultures: DOI: 10.5584/jiomics.v5i1.185
No full textBackground: The study of RNA, DNA, and protein from the same sample is a great advantage but can be challenging. Using Trizol, one can simultaneously extract RNA, DNA, and protein, leading to efficient sample use and more comprehensive analysis. Although it is used routinely for RNA extraction, the frequency of use of Trizol extracts for proteomics applications is low. The aim of our study was to evaluate the results of a simple modification to the Trizol protocol in terms of extraction and protein recovery efficacy and compatibility of the extracts with proteomics technologies in comparison to our standard extraction protocol including freeze/thaw cycles in urea/ thiourea.
Method: We used the human airway epithelial cell line S9 and extracted proteins either with a modified Trizol protocol or by freeze/thaw cycles in 8M urea/ 2M thiourea. Extracted proteins were quantified and subjected to 1D- and 2D-gel electrophoresis, Western Blotting and LC-coupled tandem mass spectrometry analysis.
Results: Compared to urea/ thiourea extraction, the Trizol-extracted proteins exhibited a similar protein composition and identification rate in LC-coupled tandem mass spectrometry experiments. 1D- and 2D-PAGE of Trizol-extracted proteins revealed excellent protein resolution with better coverage of proteins in the low MW range than urea/ thiourea extraction.
Conclusion: The modified Trizol-protocol enabled excellent protein extraction from cell culture samples and high compatibility with proteomics technologies, especially with LC-tandem mass spectrometry