Journal of Integrated -OMICS
Not a member yet
215 research outputs found
Sort by
A novel phosphate-affinity bead with immobilized Phos-tag for separation and enrichment of phosphopeptides and phosphoproteins: DOI: 10.5584/jiomics.v1i1.46
No full textA simple and efficient method was developed for separating and enriching phosphoproteins from crude biological samples containing solubilized cellular proteins by immobilized zinc(II) affinity chromatography. The phosphate-binding site of the affinity gel is an alkoxide-bridged dinuclear zinc(II) complex, Phos-tag, which is linked to a hydrophilic vinylic polymer bead. A novel phosphate-affinity bead (Phos-tag Toyopearl) was prepared by reaction of N-hydroxysuccinimide-activated Toyopearl AF-Carboxy-650M gel with a 2-aminoethylcarbamoyl derivative of Phos-tag. Phosphopeptides were retrieved quantitatively and selectively on a µL-scale column at room temperature. The column was stable for long-term storage and could be reused many times. The technique was used to separate and enrich phosphoproteins from an epidermal growth factor-stimulated human epidermoid carcinoma A431 cell lysate. The operations necessary for 1-mL-scale open-column chromatography were conducted at a physiological pH during 1 h. The strong enrichment of the phosphoproteins into the eluted fraction was evaluated by gel electrophoresis, followed by Western blotting with Phos-tag Biotin and several antibodies, Pro-Q Diamond phosphoprotein gel staining, and mass spectrometry
Where no journal has gone before: DOI: 10.5584/jiomics.v1i1.62
No full textJournal of Integrated OMICS – Where no journal has gone befor
Development of an in-house protocol for the OFFGEL fractionation of plant proteins: DOI: 10.5584/jiomics.v1i2.59
No full textProtein sample prefractionation using off-gel technology coupled to mass spectrometry-based proteomics has proven very efficient in identifying novel proteins of low abundance in various biological systems with the exception of plant tissues. In this study, we have prefractionated protein samples from wheat leaves and apoplastic fluid using the Agilent 3100 OFFGEL fractionator along 3-10 pH range into 24 fractions. Two methods were compared: 1/ the Agilent method based on the use of a proprietary starter kit which comprises all the necessary consumables, and 2/ an in-house method in which focusing solutions were made using electrophoresis grade chemicals, and immobilised pH gradient (IPG) strips and electrode pads were acquired elsewhere. Method comparisons and quality of focusing were assessed using pH distributions, one- and two-dimensional patterns. Both methods produced excellent electrophoretic patterns, with generally more better-resolved bands/spots observed with the in-house method. This study will allow other laboratories using OFFGEL device to consider in-house solutions
Implementing effective machine learning-based workflows for the analysis of mass spectrometry data: DOI: 10.5584/jiomics.v6i1.196
No full textMass spectrometry using matrix assisted laser desorption ionization coupled to time of flight analyzers (MALDI-TOF MS) has become very popular during the last decade due to its high speed, sensitivity and robustness for accurately detecting proteins and peptides. This allows quickly analyzing large sets of samples in one single batch and doing high-throughput proteomics. In this scenario, bioinformatics methods and computational tools play a key role in MALDI-TOF MS data analysis, as they are able to correctly handle the large amount of raw data generated with the goal of discovering new knowledge and extracting useful conclusions.
A typical MALDI-TOF MS data analysis workflow consists of three main stages: data acquisition, preprocessing and analysis. Although the most popular use of this technology is to identify proteins through their peptides, analyses that make use of artificial intelligence (AI), machine learning (ML), and statistical methods are of particular interest to conduct biomarker discovery, automatic diagnosis, and knowledge discovery.
In this introductory work, the potential of these techniques are explored and novel solutions based on the application of AI, ML, and statistical methods are reviewed. In addition, an integrated software platform that supports full MALDI-TOF MS data analysis is presented with the goal of facilitating the work of proteomics researchers without advanced bioinformatics skills
THE USE OF KALASHNIKOV (AK-47) IN ‘NDRANGHETA MURDERS: THE FIREARM OF THE CLAN.: DOI: 10.5584/jiomics.v8i1.235
No full text‘Ndrangheta is a mafia criminal organization, hailing from Calabria, Italy. This organization is able to use any kind of weapon and the choise depends on the type of murder to commit. So, even bazooka have been used when the victims, judges or rival mafia clan boss, travelled by armored cars. Kalashnikov is not only used “normally” to commit mafia ambushes, but often it has been found carbonized with the car used by killers. This act confirm that mafia clan have available vast arsenals of weapons and it is a demonstration of what this organization is able to do. Gunshot wounds cause significant mortality and morbidity. The analysis of the features of injuries makes it possible to establish which kind of weapon has been used. The AK-47 is a selective-fire, gas-operated assault rifle and it uses a long stroke gas system. In order to shoot, who uses a AK-47, inserts a loaded magazine, pulls back and releases the charging handle, and then pulls the trigger. It can be semi-automatic, when the firearm fires only once, or full-automatic, if the rifle continues to fire automatically and cyclically fresh rounds into the chamber. AK-47 rifle bullet injuries present with uncharacteristically large entry wounds and cause complex structural injuries. The consequent trajectory is difficult to predict making regional examination and radiological investigations. Bullets may be retained, leaving no exit wound. We report a case of an AK-47 murder. An autopsy was performed and documented the external lesions. Terminal ballistic reconstructions were carried out. The results of the forensic investigations revealed a mafia matrix in the genesis of the homicide. Kalashnikov is not a frequent weapon, so the wounds are not so common to see in the forensic practice. But, in ‘ndrangheta homicides, this firearm is preferred for its high harmful power that ensure a murder “without mistakes” and with devastating consequences on the shot body
Recovering Damaged Documents to Improve Information Retrieval Processes: DOI: 10.5584/jiomics.v8i3.230
No full textAlthough computer forensics is frequently related to the investigation of computer crimes, it can also be used in civil procedures. An example of case of use is information retrieval from damaged documents, where words have undergone alterations, either accidentally or intentionally. In this paper, we present a new tool able to retrieve information from large volumes of documents whose contents have been damaged. We have designed a new approach to recover the original words, composed of two stages: a text cleaning filter, able to remove non relevant information, and a text correction unit, which gather a general purpose spell checker with a N-gram based spell checker built specifically for the domain of the documents. The benefits of using this combined approach are two-fold: on the one hand, the general spell checker allows us to leverage all the general purpose techniques that are usually used to perform the corrections; on the other hand, the use of an N-gram based model allows us to adapt them to the particular domain we are tackling exploiting text regularities detected in successfully processed domain documents. The result of the correction allows us to improve automatic information retrieval tasks of from the texts. We have tested it using a real data set by using an information extraction tool based on semantic technologies in collaboration with the Spanish company InSynergy Consulting
