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Journal Cover Journal of Integrated OMICS
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  This is an Open Access Journal Open Access journal
   ISSN (Print) 2182-0287 - ISSN (Online) 2182-0287
   Published by Proteomass Homepage  [1 journal]
  • Editorial board Vol6, No1 (2016)

    • PubDate: 2016-06-30
      Issue No: Vol. 6 (2016)
       
  • VOL 6, NO 1 (2016)

    • PubDate: 2016-06-30
      Issue No: Vol. 6 (2016)
       
  • Implementing effective machine learning-based workflows for the analysis
           of mass spectrometry data

    • Abstract: Mass 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.
      PubDate: 2016-06-19
      Issue No: Vol. 6 (2016)
       
  • Vaginal bacterial microbiota of an endangered donkey breed: a comparison
           between Miranda donkey breed (Equus asinus) jennies with and without
           reproductive problems

    • Abstract: This 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.
      PubDate: 2016-04-09
      Issue No: Vol. 6 (2016)
       
  • A DIGE proteomic analysis of wheat flag leaf treated with TERRA-SORBĀ®
           foliar, a free amino acid high content biostimulant

    • Abstract: The 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 p
      PubDate: 2016-03-02
      Issue No: Vol. 6 (2016)
       
  • Myosin light chain and calcium regulating protein differences in chronic
           musculoskeletal neck and shoulder pain

    • Authors: Jenny Hadrevi, Maria V Turkina, Anders Carlsson, Bjorn Gerdle, Britt Larsson, Fredrik Hellstrom, Bijar Ghafouri
      Abstract: Proteomic 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.
      PubDate: 2016-01-21
      Issue No: Vol. 6 (2016)
       
 
 
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