Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performance

Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performances

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantificatio

Chemical Composition and Biological Activities of Prangos ferulacea Essential Oils

Prangos ferulacea (L.) Lindl, which belongs to the Apiaceae family, is a species that mainly grows in the eastern Mediterranean region and in western Asia. It has been largely used in traditional medicine in several countries and it has been shown to possess several interesting biological properties. With the aim to provide new insights into the phytochemistry and pharmacology of this species, the essential oils of flowers and leaves from a local accession that grows in Sicily (Italy) and has not yet been previously studied were investigated. The chemical composition of both oils, obtained by hydrodistillation from the leaves and flowers, was evaluated by GC-MS. This analysis allowed us to identify a new chemotype, characterized by a large amount of (Z)-beta-ocimene. Furthermore, these essential oils have been tested for their possible antimicrobial and antioxidant activity. P. ferulacea essential oils exhibit moderate antimicrobial activity; in particular, the flower essential oil is harmful at low and wide spectrum concentrations. They also exhibit good antioxidant activity in vitro and in particular, it has been shown that the essential oils of the flowers and leaves of P. ferulacea caused a decrease in ROS and an increase in the activity of superoxide dismutase (SOD), catalase (CAT) and glutathione S-transferase (GST) in OZ-stimulated PMNs. Therefore, these essential oils could be considered as promising candidates for pharmaceutical and nutraceutical preparations

The chemical composition of the aerial parts of Stachys spreitzenhoferi (Lamiaceae) growing in Kythira Island (Greece), and their antioxidant, antimicrobial, and antiproliferative properties

The Stachys L. genus has been used in traditional medicine to treat skin inflammations, stomach disorders, and stress. The aim of this study was to investigate the chemical profile and biological activity of the methanolic extract of Stachys spreitzenhoferi Heldr. (Lamiaceae) aerial parts, collected on the island of Kythira, South Greece. The analysis by liquid chromatography coupled with electrospray ionization and high-resolution mass spectrometry [LC-(-)ESI/HRMSn] of the methanol extract revealed the occurrence of thirty-six compounds - flavonoids, phenylethanoid glycosides, iridoids, quinic acid derivatives, aliphatic alcohol glycosides, and oligosaccharides - highlighting the substantial presence, as main peaks, of the iridoid melittoside (2) along with flavonoid compounds such as 4'-O-methylisoscutellarein mono-acetyl-diglycoside/chrysoeriol mono-acetyl-diglycoside (24), trimethoxy- (35) and tetramethoxyflavones (36). This extract was tested for its antimicrobial properties against Gram-positive and negative pathogenic strains. The extract was not active against Gram-negative bacteria tested, but it possessed a good dose-dependent antimicrobial activity towards S. aureus (MIC: 1.0 mg/mL) and L. monocytogenes (MIC: 1.0 mg/mL) Gram-(+) strains. Furthermore, this extract has been tested for its possible antioxidant activity in vitro. In particular, it has been shown that these molecules cause a decrease in DPPH, ABTS, and H2O2 radicals. The extract of S. spreitzenhoferi exhibited anti-DPPH activity (IC50: 0.17 mg/mL), anti-H2O2 activity (IC50: 0.125 mg/mL), and promising antiradical effect with an IC50 value of 0.18 mg/mL for anti-ABTS activity. S. spreitzenhoferi extract caused a decrease in ROS (at the concentration of 200 μg/mL) and an increase in the activity of the antioxidant enzymes SOD, CAT, and GPX in OZ-stimulated PMNs. Furthermore, it exhibited antiproliferative activity against acute myeloid leukemia (U937 cell), causing 50% of cell death at the 0.75 mg/mL

The Antioxidant Properties and Protective Capacity of <i>Prangos trifida</i> and <i>Cachrys cristata</i> Essential Oils against Cd Stress in <i>Lunularia cruciata</i> and <i>Brassica napus</i>

The genera Prangos Lindl. and Cachrys L., for a long time interpreted as a single genus but today distinct and separate, and both belonging to the majestic Apiaceae family, are species with a large distribution and are used in ethnomedicine in various countries, especially in Asian countries. In this context, we investigated the chemical characteristics and biological properties of two essential oils (EOs) obtained from different specimens, namely Cachrys cristata (Cc) and Prangos trifida (Pt). The chemical composition of the two EOs was investigated by GC-MS analysis. From gas-chromatography analyses, while the (Cc) EO was rich in β-myrcene (45.34%), allo-ocimene (10.90%), and 2,4,6-trimethylbenzaldehyde (23.47%), the (Pt) EO was characterized by moderate amounts of α-pinene (8.85%), sylvestrene (11.32%), α-phellandrene (12.14%), (Z)-β-ocimene (18.12%), and finally, p-mentha-1,3,8-triene (9.56%). Furthermore, the protective and antioxidant capacity of (Pt) and (Cc) EOs on Lunularia cruciata and Brassica napus exposed to cadmium (Cd) stress was studied. To study these possible effects, the liverwort and oilseed rape, previously pretreated with both EOs, were subsequently subjected to oxidative stress by treatment with Cd. Then, DNA damage and antioxidant enzyme activity were measured in both EOs-pretreated and untreated samples to examine EOs-induced tolerance to Cd toxicity. The results indicate that (Pt) and (Cc) EOs have antioxidant and protective capacity in modulating the redox state through the antioxidant pathway by reducing oxidative stress induced by Cd. Furthermore, B. napus was found to be a more resistant and tolerant species than L. cruciata.</i

Chemical Composition of Thymus leucotrichus var. creticus Essential Oil and Its Protective Effects on Both Damage and Oxidative Stress in Leptodictyum riparium Hedw. Induced by Cadmium

The chemical profile of the essential oil (EO) of the aerial parts of Thymus leucotrichus var. creticus (Lamiaceae), a taxon not previously studied, was investigated by GC-MS analysis, using a DB-Wax polar column. Oxygenated monoterpenes and monoterpene hydrocarbons dominate the EO, with thymol (46.97%) and p-cymene (28.64%) as the main constituent of these two classes, respectively. The ability of the EO of T. leucotrichus to reduce Cd toxicity was studied in aquatic moss Leptodictyum riparium. To study EO-induced tolerance to Cd toxicity, apex growth, number of dead cells, DNA damage and antioxidant response in gametophytes were examined. The exogenous application of the EO yields a resumption of growth rate and a reduction in the number of dead cells; it also reduces the oxidative stress induced by Cd, as demonstrated by the reduction of the ROS content (with a decrease of 1.52% and 5%) and by the increased activity of antioxidant enzymes such as superoxide dismutase (SOD) (with an increase of 1.44% and 2.29%), CAT catalase (1.46% and 2.91%) and glutathione-S-transferase GST (1.57% and 1.90%). Furthermore, the application of the EO yields a reduction of DNA damage. These results clearly indicate the protective capacity of the EO of T. leucotrichus in modulating the redox state through the antioxidant pathway by reducing the oxidative stress induced by Cd

Antimicrobial, Antibiofilm, and Antioxidant Properties of Essential Oil of Foeniculum vulgare Mill. Leaves

Foeniculum vulgare (Apiaceae) is an aromatic fennel with important practices in medicinal and traditional fields, used in the treatment of digestive complications, and gastrointestinal and respiratory disorders. Its leaves and stems, tender and fresh, are used in the production of pasta dressing and main courses, while its seeds, with a strong smell of anise, are excellent flavoring for baked goods, meat dishes, fish, and alcoholic beverages. The aim of this work is concerning the extraction of essential oil (EO) from the leaves of F. vulgare subsp. vulgare var. vulgare, investigating antimicrobial, antibiofilm, and antioxidant efficacy. In particular, GC-MS analysis showed how the chemical composition of EO was influenced by the massive presence of monoterpene hydrocarbons (alpha-pinene 33.75%) and phenylpropanoids (estragole 25.06%). F. vulgare subsp. vulgare var. vulgare EO shows excellent antimicrobial activity against both Gram-positive and Gram-negative strains. This EO can inhibit biofilm formation at very low concentrations and has a good ability to scavenge oxygen radicals in vitro. F. vulgare subsp. vulgare var. vulgare EO also has an increased activity of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) enzymes and decreased ROS levels in zymosan opsonized PMNs (OZ)