Journal of Integrated -OMICS
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Comparison of protein precipitation methods for two-dimensional electrophoresis of dog salivary proteins: DOI: 10.5584/jiomics.v8i1.232
No full textDespite saliva being one fluid with growing interest as a source of biomarkers, both in humans and animal models, few studies have been reported that use proteomic approaches for canine saliva analyses. Two-dimensional electrophoresis (2-DE) is considerably used in biomarkers research and their use for dog saliva study may had relevant knowledge about pathology/physiology. The quality of the results obtained using 2-DE greatly depends on sample preparation. Different protein precipitation methods are frequently used for removing interfering compounds and concentrating samples, but their efficiency varies according to sample characteristics. For dog saliva samples no information was found about the best precipitant and precipitation method for electrophoretic protein profiling.
In this study, six different protein precipitation methods were compared. Precipitation of dog salivary proteins with trichloroacetic acid 20% (w/v) resulted in lower protein recovery rate than other methods tested, but allowed protein profiles highly correlated with the ones from original samples. Moreover, this protocol resulted in good protein separation in 2-DE, with the visualization of spots from salivary proteins not observed when samples were treated using other methods. Based on this, we propose the use of TCA for dog saliva whenever precipitation is needed for protein profile analysis
Multivariate methods aid in pinpointing promising tumor marker candidates from colorectal biopsies: DOI: 10.5584/jiomics.v2i1.79
No full textThe application of proteomic techniques to the search for disease markers is widely reported nowadays. However, the data rendered by these methods is highly complex and requires mining through statistical methods. Since univariate tests are prone to false positives and require post-test correction, multivariate methods seem more suitable for the task. Here we show an example of their utility, applying both principal component analysis (PCA) and linear discriminant analysis (LDA) to the hydrophobic subproteome of the colorectal mucosa. In order to find proteins specifically altered by colorectal cancer, we compared both the tumor and the adjacent healthy mucosa. PCA followed by variable selection, and corroboration by LDA, pointed out the proteins vimentin and prohibitin as promising candidates for the diagnosis of colorectal tumors
Protein thiols as novel biomarkers in ecotoxicology: A case study of oxidative stress in Mytilus edulis sampled near a former industrial site in Cork Harbour, Ireland: DOI: 10.5584/jiomics.v2i2.77
No full textOxidative stress produces reactive oxygen species which can modify proteins and thiols of cysteines are especially susceptible. Mytilus edulis was sampled from three stations in Cork Harbour, Ireland and from an out-harbour control site in Bantry Bay, Ireland. A variety of traditional biomarkers were benchmarked against thiol oxidation. Lysosomal membrane stability diminished in haemocytes from the three Cork harbour sites, although a stronger effect was observed in two in-harbour stations of environmental concern (Douglas and Haulbowline Island). Catalase and glutathione transferase (GST) activities were decreased in digestive gland extracts of animals from in-harbour sites especially the in-harbour control (Ringaskiddy) showed lower GST than Bantry. Mussels collected at Haulbowline Island showed elevated lipid peroxidation (p
Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes: DOI: 10.5584/jiomics.v3i2.139
No full textOver the past decade, metabolomics has emerged as an important technique for systems biology. Measuring all the metabolites in a biological system provides an invaluable source of information to explore various cellular processes, and to investigate the impact of environmental factors and genetic modifications. Nuclear magnetic resonance (NMR) spectroscopy is an important method routinely employed in metabolomics. NMR provides comprehensive structural and quantitative information useful for metabolomics fingerprinting, chemometric analysis, metabolite identification and metabolic pathway construction. A successful metabolomics study relies on proper experimental protocols for the collection, handling, processing and analysis of metabolomics data. Critically, these protocols should eliminate or avoid biologically-irrelevant changes to the metabolome. We provide a comprehensive description of our NMR-based metabolomics procedures optimized for the analysis of bacterial metabolomes. The technical details described within this manuscript should provide a useful guide to reliably apply our NMR-based metabolomics methodology to systems biology studies
Characterization of temperature-sensing and PIP2-regulation of TRPV1 ion channel at the C-terminal domain using NMR spectroscopy and Molecular Dynamics Simulations: DOI: 10.5584/jiomics.v4i2.158
No full text
Transient receptor potential (TRP) channels are receptors of stimulating signals, such as temperature, taste, odor, and chemo- and mechano-stimuli. Temperature sensing TRP channels coincidently function as pain receptors, and are potential targets for substances of abuse, including alcohol and illicit drugs. TRP vanilloid type 1 (TRPV1) channel is activated by heat (>43 °C) and capsaicin under the tight regulation of membrane-associated second messenger, PIP2 (phosphatidylinositol-4,5-bisphosphate), responds to noxious stimuli and inflammatory substances, and could potentially modulate effects of alcohol and drugs of abuse. Despite the crucial roles in mediating signal transductions at both peripheral and central nervous systems, TRP channels are poorly understood in the context of structures and mechanisms. In this letter, we describe our initial structural characterization of the TRPV1 C-terminal domain, the putative temperature sensing and PIP2-regulatory domain, using NMR spectroscopy and molecular dynamics simulations. Both experimental and computational models suggest the C-terminal domain is intrinsically unstructured at room temperature with and without lipid bicelles. Elevated temperature and PIP2-binding can induce substantial conformational changes and formation of considerable secondary structural components in the C-terminal domain, which could be transduced to the transmembrane domain to potentially sensitize the channel
Vol. 6, No. 2 (2016): SPECIAL ISSUE: DOI: 10.5584/jiomics.v6i2.207
No full textDOI: 10.5584/jiomics.v6i2.20
A novel extraction method for the preparation of heparinized chicken (Gallus gallus domesticus) and horse (Equus caballus) whole blood for 1H-NMR metabolomics using Drabkin’s reagent: DOI: 10.5584/jiomics.v7i1.203
No full textDespite the ease of collection, heparinized whole blood (HWB) is underutilized in 1H-NMR-based metabolomics particularly because of the lack of sample homogeneity. Drabkin’s reagent (DR), an aqueous solution of potassium ferricyanide, potassium cyanide, and sodium bicarbonate, causes hemolysis and has been used for quantification of hemoglobin. The objectives of this study were to determine if the use of DR with HWB for metabolomics samples would result in consistent hemolysis, while being invisible to 1H-NMR and quenching metabolic activity. HWB from a chicken (Gallus gallus domesticus) and a horse (Equus caballus) was used. All HWB samples were mixed 1:10 volume:volume HWB:DR. Spectrophotometric evaluation of incubated DR treated samples revealed little change in absorbance after approximately 10-15 min incubation at room temperature (20-21 °C); all following samples were incubated for 10 min, except where noted. Samples subjected to five repeated extractions with DR showed a decrease in absorbance of >95% after the first extraction; all subsequent samples were extracted with a single aliquot of DR. Lyophilized DR rehydrated with a 100% deuterium oxide solution was invisible to 1H-NMR. Standard (10 min incubation, 20 min centrifugal filtration) and delayed (120 min incubation, 20 min centrifugal filtration) samples were prepared for both species and did not appear considerably different upon visual inspection with the exception of minor differences in the major peaks of the metabolites 3-methylhistidine and betaine in the chicken samples. Comparison of standard and delayed samples via two-sample Kolmogorov-Smirnov tests found no significant differences with either species (chicken p = 1, horse p = 0.9887). Use of DR resulted in consistent, complete hemolysis, while being invisible to 1H-NMR and quenching metabolic activity for at least 140 min at room temperature. This protocol should be considered when HWB is the only sample type available and/or if the investigator is interested in questions specific to erythrocyte metabolism
Special Issue: Book of Abstracts FORENSICS 2017: DOI: 10.5584/jiomics.v7i2.234
No full textSPECIAL ISSUE: SELECTED ABSTRACTS OF THE 1ST INTERNATIONAL CAPARICA CONFERENCE ON TRANSLATIONAL FORENSICS (FORENSICS 2017)
FLIPBOOK VERSION - http://books.bioscopegroup.org/books/awgk
Alcohol and drug use in drug-related deaths in Campania (Italy): a snapshot study over the years 2008-2018: DOI: 10.5584/jiomics.v10i2.334
No full textAim: Aim of the study is the evaluation of incidence of mortality, directly or indirectly linked to drug abuse in one of the most populated Italian region (Campania). Trends on psychotropic substances intake and prevalence of drug-related deaths (DRDs) are assessed over an eleven-year observation period from 2008 to 2018. Data from toxicological investigations applied, for forensic purpose, on post-mortem blood sampled from 640 suspected DRDs (267 in the years 2008– 2012 and 373 in the years 2013 – 2018) has been revised.
Methods: A Systematic Toxicology Analysis (STA) by validated GC/MS or LC-MS/MS methods for licit drugs (benzodiazepines, antidepressants/antipsychotics, hypnotics) and illicit drugs (amphetamine and analogous, cocaine, opiate, methadone, barbiturate, buprenorphine, cannabis and new psychoactive substances) was applied. A conventional methodology (GC/HS-FID) was used to test the blood alcohol concentration (BAC).
Results: Toxicological results were positive in 403 cases out of 640 autopsies totally performed: 202 DRDs out of 267 deaths were identified during the years 2008-12 and 201 DRDs out of 373 during the 2013-2018 period. Among the 403 DRDs, more than 90% of cases were males aged between 41-50 years. A remarkable increase in the number of alcohol related deaths (42 cases) was observed in the years from 2013 to 2018 compared with the previous one. Most of these cases showed a BAC in the range 1.5 – 4 g/L, compared to the only 3 cases occurred in 2008-2012 years. During the eleven-year observation period, the poly-drug use has been recognized as responsible for 258 deaths (64%) out of 403 cases in total. The association of cocaine and morphine was predominant in the years 2008-2012 while in the years 2013-2018 pharmaceuticals (benzodiazepines, antidepressants etc.), alcohol and illicit drugs (cocaine and morphine), alone or in combination, were the substances mainly detected. Methadone was detected more frequently in associations with other drugs (mainly pharmaceuticals) or ethyl alcohol but it was also found alone in 3 DRDs only. Surprisingly in few DRDs cannabis metabolites were found neither a single fatal poisoning by amphetamines and new psychoactive substances (NPS) was recorded.
Conclusion: During the eleven-year observation period, an increase in DRDs involving ethyl alcohol intake has been observed. A relevant variability in the prevalence among the licit/illicit drug use has been also found, mainly represented by the poly-drug intake respect to the abuse of a single drug. Data collected demonstrate that it is crucial a continuous updating about the territorial trends of the drug abuse in order to develop a Community Data Bank, for planning strategies of prevention
SPECIAL ISSUE: SELECTED ABSTRACTS OF THE V INTERNATIONAL CAPARICA CONFERENCE ON ULTRASONIC-BASED APPLICATION FROM ANALYSIS TO SYNTHESIS (ULTRASONICS 2021)
Full text linkSPECIAL ISSUE: SELECTED ABSTRACTS OF THE V INTERNATIONAL CAPARICA CONFERENCE ON ULTRASONIC-BASED APPLICATION FROM ANALYSIS TO SYNTHESIS (ULTRASONICS 2021