Journal of Integrated OMICS最新文献

{"title":"Comparison of protein precipitation methods for two-dimensional electrophoresis of dog salivary proteins","authors":"S. Lucena, M. Carreira, Lénia Rodrigues, F. Capela-Silva, A. Tvarijonaviciute, E. Lamy","doi":"10.5584/JIOMICS.V8I1.232","DOIUrl":"https://doi.org/10.5584/JIOMICS.V8I1.232","url":null,"abstract":"Despite saliva being one fluid with growing interest as a source of biomarkers, both in humans and animal models, f ew 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.","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/JIOMICS.V8I1.232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45534767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"THE USE OF KALASHNIKOV (AK-47) IN ‘NDRANGHETA MURDERS: THE FIREARM OF THE CLAN.","authors":"I. Aquila, G. Chiaravalloti, Roberto Raffaele, Antonio Ottolino, S. Gratteri, P. Ricci","doi":"10.5584/JIOMICS.V8I1.235","DOIUrl":"https://doi.org/10.5584/JIOMICS.V8I1.235","url":null,"abstract":"‘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. Normal 0 14 false false false IT X-NONE X-NONE /* Style Definitions */ \u0000 table.MsoNormalTable \u0000 {mso-style-name:\"Tabella normale\"; \u0000 mso-tstyle-rowband-size:0; \u0000 mso-tstyle-colband-size:0; \u0000 mso-style-noshow:yes; \u0000 mso-style-priority:99; \u0000 mso-style-qformat:yes; \u0000 mso-style-parent:\"\"; \u0000 mso-padding-alt:0cm 5.4pt 0cm 5.4pt; \u0000 mso-para-margin-top:6.0pt; \u0000 mso-para-margin-right:0cm; \u0000 mso-para-margin-bottom:0cm; \u0000 mso-para-margin-left:0cm; \u0000 mso-para-margin-bottom:.0001pt; \u0000 text-align:justify; \u0000 text-indent:8.5pt; \u0000 mso-line-height-alt:10.0pt; \u0000 mso-pagination:widow-orphan; \u0000 font-size:11.0pt; \u0000 font-family:\"Calibri\",\"sans-serif\"; \u0000 mso-ascii-font-family:Calibri; \u0000 mso-ascii-theme-font:minor-latin; \u0000 mso-fareast-font-family:\"Times New Roman\"; \u0000 mso-fareast-theme-font:minor-fareast; \u0000 mso-hansi-font-family:Calibri; \u0000 mso-hansi-theme-font:minor-latin; \u0000 mso-bidi-font-family:\"Times New Roman\"; \u0000 mso-bidi-theme-font:minor-bidi;}","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/JIOMICS.V8I1.235","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43275789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quality Improvement for Criminal Investigations - Lessons from Science?","authors":"H. Ditrich","doi":"10.5584/JIOMICS.V8I1.215","DOIUrl":"https://doi.org/10.5584/JIOMICS.V8I1.215","url":null,"abstract":"Criminal investigations generally aim at discovering previously unknown facts. The same is true for scientific (or academic) research. Both follow a rather tight framework of rules – most importantly, the principles of objectivity, reliability and validity. However, some of the intentions differ. Science generally attempts to discover and/or explain new principles, while criminal inquiries are instead usually bound to past, often singular, events. For example, the methods used in forensic investigations are required to be well established, standardised and undisputed inasmuch as possible. In contrast, the exploration of new methods is an important feature of the advancement of science. Consequently, both tendencies – similarities and opposites – can be discerned when comparing criminal and academic examinations. The ‘Pareto principle’ indicates that the vast majority of all criminal investigations run rather unproblematically. Nevertheless, the highest quality criteria must be guaranteed for these and the remaining, more challenging cases as well – based on the ‘fair trial’ principle. Acknowledging that mistakes are inevitable (Murphy’s law), methodical approaches for error identification, handling, management and reduction are essential. Error correction mechanisms that are typical for forensic statements normally include a second source of expertise and/or an appeals procedure. In academic science, however, the peer review system has long been established as the most important quality control and error correction system. Furthermore, possible mistakes can usually be corrected in later, more detailed studies. However, the central position of forensic experts and criminal investigators in a legal procedure and the severe personal consequences of incorrect statements emphasize the high importance of continuous improvement of both the qualifications of the investigators and the quality of their methods. Nevertheless, error reduction provisions should not be restricted to technical measures such as quality management and accreditations. Furthermore, a systemic/organisational approach towards error management seems promising. This involves, among other measures, a systematic examination of mistakes and the recognition of the human factors that underlie them. Nevertheless, an indispensable component for quality enhancement is intense cooperation from both sides – the criminalistic and forensic practice as well as the scientific (basic) research.","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/JIOMICS.V8I1.215","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42909754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular analysis of oncogene expressions in different grades of gliomas","authors":"L. Vijayachandran, S. Xavier, K. Sundaram, L. Biswas, D. Panikar, B. Rajamma, S. Nair, K. Menon","doi":"10.5584/JIOMICS.V8I1.242","DOIUrl":"https://doi.org/10.5584/JIOMICS.V8I1.242","url":null,"abstract":"The 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 ( P","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/JIOMICS.V8I1.242","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45226654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preface - Shotgun proteomics: where do we stand now?","authors":"José Capelo","doi":"10.5584/jiomics.v8i1.251","DOIUrl":"https://doi.org/10.5584/jiomics.v8i1.251","url":null,"abstract":"","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48533466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome Analysis Implicates Adaptive Changes in Metabolism and Body Wall Musculature of Caenorhabditis elegans Dauer Larva","authors":"A. Zaidi, K. Vukoti, Q. Sheng, Y. Shyr, M. Miyagi","doi":"10.5584/JIOMICS.V8I1.237","DOIUrl":"https://doi.org/10.5584/JIOMICS.V8I1.237","url":null,"abstract":"Dauer larva is an alternative developmental stage of Caenorhabditis elegans ( C. elegans ) that occurs when the environmental condition is unfavorable for growth. Little is known regarding how the proteome of dauer larvae respond to  poor environmental growth conditions. Such knowledge is expected to help understand the survival mechanism(s) of dauer larvae. In order to uncover the proteome differences between dauer larvae and normally developed third stage larvae (L3),  an L2 stage larvae was starved to create the dauer larvae and this proteome was compared with that of the L3 larvae. Results showed that proteins involved in muscle assembly and fatty acid oxidation are increased in dauer larvae, while proteins involved in maintaining regular organismic activity such as reproduction, translation and apoptotic processes are decreased. The protein expression profile also suggested that the glyoxylate cycle is preferentially utilized during dauer arrest over the tricarboxylic acid (TCA) cycle and significant structural rearrangement occurs on the hypodermis, body wall musculature, and pharynx.","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/JIOMICS.V8I1.237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43975121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative mass spectrometry of urinary biomarkers.","authors":"Marina Jerebtsova,&nbsp;Sergei Nekhai","doi":"10.5584/jiomics.v4i2.177","DOIUrl":"https://doi.org/10.5584/jiomics.v4i2.177","url":null,"abstract":"<p><p>The effectiveness of treatment of renal diseases is limited because the lack of diagnostic, prognostic and therapeutic markers. Despite the more than a decade of intensive investigation of urinary biomarkers, no new clinical biomarkers were approved. This is in part because the early expectations toward proteomics in biomarkers discovery were significantly higher than the capability of technology at the time. However, during the last decade, proteomic technology has made dramatic progress in both the hardware and software methods. In this review we are discussing modern quantitative methods of mass-spectrometry and providing several examples of their applications for discovery and validation of renal disease biomarkers. We are optimistic about future prospects for the development of novel of specific clinical urinary biomarkers.</p>","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/jiomics.v4i2.177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33312390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes.","authors":"Steven Halouska, Bo Zhang, Rosmarie Gaupp, Shulei Lei, Emily Snell, Robert J Fenton, Raul G Barletta, Greg A Somerville, Robert Powers","doi":"10.5584/jiomics.v3i2.139","DOIUrl":"10.5584/jiomics.v3i2.139","url":null,"abstract":"<p><p>Over 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.</p>","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465129/pdf/nihms695220.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33391378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes.","authors":"Eric B Haura,&nbsp;Roberto Sacco,&nbsp;Jiannong Li,&nbsp;André C Müller,&nbsp;Florian Grebien,&nbsp;Giulio Superti-Furga,&nbsp;Keiryn L Bennett","doi":"10.5584/jiomics.v2i1.81","DOIUrl":"https://doi.org/10.5584/jiomics.v2i1.81","url":null,"abstract":"<p><p>In this study we show that via stable, retroviral-expression of tagged EGFR del (L747-S752 deletion mutant) in the PC9 lung cancer cell line and stable doxycycline-inducible expression of tagged Grb2 using a Flp-mediated recombination HEK293 cell system, the SH-TAP can be downscaled to 5 to 12.5 mg total protein input (equivalent to 0.5 - 1 × 15 cm culture plate or 4 - 8 × 10⁶ cells). The major constituents of the EGFR del complex (USB3B, GRB2, ERRFI, HSP7C, GRP78, HSP71) and the Grb2 complex (ARHG5, SOS1, ARG35, CBL, CBLB, PTPRA, SOS2, DYN2, WIPF2, IRS4) were identified. Adjustment of the quantity of digested protein injected into the mass spectrometer reveals that optimisation is required as high quantities of material led to a decrease in protein sequence coverage and the loss of some interacting proteins. This investigation should aid other researchers in performing tandem affinity purifications in general, and in particular, from low quantities of input material.</p>","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/jiomics.v2i1.81","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31768153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of Histone Exchange during Chromatin Purification.","authors":"Stephanie Byrum,&nbsp;Samuel G Mackintosh,&nbsp;Ricky D Edmondson,&nbsp;Wang L Cheung,&nbsp;Sean D Taverna,&nbsp;Alan J Tackett","doi":"10.5584/jiomics.v1i1.26","DOIUrl":"https://doi.org/10.5584/jiomics.v1i1.26","url":null,"abstract":"<p><p>Central to the study of chromosome biology are techniques that permit the purification of small chromatin sections for analysis of associated DNA and proteins, including histones. Chromatin purification protocols vary greatly in the extent of chemical cross-linking used to prevent protein dissociation/re-association during isolation. Particularly for genome-wide analyses, chromatin purification requires a balanced level of fixation that captures native protein-protein and protein/DNA interactions, yet leaving chromatin sections soluble and accessible to affinity reagents. We have applied a relative quantification methodology called I-DIRT (isotopic differentiation of interactions as random or targeted) for optimizing levels of chemical cross-linking for affinity purification of cognate chromatin sections. We show that fine-tuning of chemical cross-linking is necessary for isolation of chromatin sections when minimal histone/protein exchange is required.</p>","PeriodicalId":37675,"journal":{"name":"Journal of Integrated OMICS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5584/jiomics.v1i1.26","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29967021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}