Systems Biology


    Protocols in Current Issue
    Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila
    [Abstract] Advanced mass spectrometry technology has pushed proteomic analyses to the forefront of biological and biomedical research. Limitations of proteomic approaches now often remain with sample preparations rather than with the sensitivity of protein detection. However, deciphering proteomes and their context-dependent dynamics in subgroups of ...
    Character-State Reconstruction to Infer Ancestral Protein-Protein Interaction Patterns
    Authors:  Florian Rümpler, Günter Theißen and Rainer Melzer, date: 08/20/2015, view: 2991, Q&A: 0
    [Abstract] Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal ...
    A Phosphopeptide Purification Protocol for the Moss Physcomitrella paten
    Authors:  Xiaoqin Wang and Yikun He, date: 07/20/2015, view: 2405, Q&A: 0
    [Abstract] Protein phosphorylation is one of the most common post-translational modifications in eukaryotic cells and plays a critical role in a vast array of cellular processes. Efficient methods of protein extraction and phosphopeptide purification are required to ensure the detection of high quality of proteins. In our hands, phenol extraction of proteins ...
    Protocol for Preparation of Nuclear Protein from Mouse Lungs
    Authors:  Zuoxiang Xiao and Qun Jiang, date: 06/05/2014, view: 4844, Q&A: 0
    [Abstract] This protocol describes how to extract nuclear protein from mouse lungs, including tissue preparation, stepwise lysis of cells and centrifugal isolation of nuclear protein fraction. This is an efficient method to get comparable nuclear protein extracts from lung tissues.
    Protein Sample Preparation for Proteomic Analysis in Leishmania donovani
    Authors:  Alexandros Alexandratos and Despina Smirlis, date: 03/05/2014, view: 3805, Q&A: 0
    [Abstract] Leishmania is a genus of trypanosomatid protozoa and is the parasite responsible for the disease leishmaniasis. These protozoa, regulate their gene expression in an atypical way, compared to other higher eukaryotes. The regulation of gene expression is characterized by a predominance of post-transcriptional over pre-transcriptional ...
    Isolation of the Secretome from Bacillus subtilis
    Authors:  Juri Niño Bach and Marc Bramkamp, date: 01/20/2014, view: 3654, Q&A: 0
    [Abstract] Bacteria are commonly known to secret proteins in large amounts into the surrounding environment in high concentrations via various pathways. These proteins can be involved in numerous processes like cell-cell communication, exopolymer formation but also metabolic active enzymes are secreted that are interesting for industrial production of ...
    Analysis of Moraxella catarrhalis Outer Membrane Protein Profiles
    Authors:  Stefan P.W. de Vries and Hester J. Bootsma, date: 11/05/2013, view: 3475, Q&A: 0
    [Abstract] Phenotypes observed for certain Moraxella catarrhalis wild-type strains or mutants may be caused by a variety of factors including alteration of outer membrane protein composition. Examination of the outer membrane protein profiles may be a valuable tool to identify changes in outer membrane compositions of these strains. Here we describe ...
    Nuclear Extraction from Arabidopsis thaliana
    Authors:  Fang Xu and Charles Copeland, date: 12/20/2012, view: 12541, Q&A: 7
    [Abstract] This protocol is to isolate nuclei from Arabidopsis cells. They can be further used for other experiments, such as nuclear protein detection, nuclear protein immunoprecipitation and so on.
    Proteolytic Fragment Isolation and Analysis (ex. N-terminal GST-tagged CLAVATA3 Protein GST-CLV3)
    Author:  Jun Ni, date: 07/20/2012, view: 5207, Q&A: 0
    [Abstract] It has become clear that the post-embryonic growth and development of plants requires properly controlled short distance cell-to-cell communication not only through the historically well-known phytohormones, but also through secreted small peptide signals. This protocol demonstrates an example of how to isolate small peptides (< 10 daltons) ...
    Probing Yeast Protein Microarrays for Protein-protein Interactions Using V5-epitope Tagged Fusion Protein Probes
    Authors:  Joseph Fasolo and Michael Snyder, date: 03/05/2012, view: 6884, Q&A: 0
    [Abstract] Protein microarray is probably the only technique currently available for systematic investigation of protein-protein interactions. This protocol describes an optimized method to probe yeast protein microarrays for protein-protein interactions using purified V5-epitope tagged fusion protein. It should also apply to any other proteins with ...