Global Efforts to Address Severe Acute Malnutrition.

Detailed description on the two formats presented, proBAM (S1A) and proBed (S1B). (XLSX 46 kb

Grand Canonical Adaptive Resolution Simulation for Molecules with Electrons: A Theoretical Framework based on Physical Consistency

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. T he Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.Comment: Computer Physics Communications (2017), in pres

Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability

Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers

Methodology for Determining Disulfide Linkage Patterns of Closely Spaced Cysteine Residues

We report the development and application of a method for determining bonding patterns in disulfide-linked peptides containing closely spaced cysteine residues. Through the utility of classic N-terminal sequencing chemistry coupled with facile liquid chromatography and mass spectrometric analysis of the cleavage products, we report the ability to demonstrate unambiguous assignment of paired cysteine residues, using human insulin as a model protein. The conditions of the technique were selected and optimized to maintain disulfide integrity. In a forthcoming article, we will present the results of this method as applied to the complete elucidation of linkages in disulfide variants of a therapeutic monoclonal antibody of the IgG2 subclass

Methodology for Determining Disulfide Linkage Patterns of Closely Spaced Cysteine Residues

We report the development and application of a method for determining bonding patterns in disulfide-linked peptides containing closely spaced cysteine residues. Through the utility of classic N-terminal sequencing chemistry coupled with facile liquid chromatography and mass spectrometric analysis of the cleavage products, we report the ability to demonstrate unambiguous assignment of paired cysteine residues, using human insulin as a model protein. The conditions of the technique were selected and optimized to maintain disulfide integrity. In a forthcoming article, we will present the results of this method as applied to the complete elucidation of linkages in disulfide variants of a therapeutic monoclonal antibody of the IgG2 subclass

Mass Spectrometric Identification of <em>In Vivo</em> Phosphorylation Sites of Differentially Expressed Proteins in Elongating Cotton Fiber Cells

<div><p>Two-dimensional gel electrophoresis (2-DE)-based proteomics approach was applied to extensively explore the molecular basis of plant development and environmental adaptation. These proteomics analyses revealed thousands of differentially expressed proteins (DEPs) closely related to different biological processes. However, little attention has been paid to how peptide mass fingerprinting (PMF) data generated by the approach can be directly utilized for the determination of protein phosphorylation. Here, we used the software tool FindMod to predict the peptides that might carry the phosphorylation modification by examining their PMF data for mass differences between the empirical and theoretical peptides and then identified phosphorylation sites using MALDI TOF/TOF according to predicted peptide data from these DEP spots in the 2-D gels. As a result, a total of 48 phosphorylation sites of 40 DEPs were successfully identified among 235 known DEPs previously revealed in the 2-D gels of elongating cotton fiber cells. The 40 phosphorylated DEPs, including important enzymes such as enolase, transketolase and UDP-L-rhamnose synthase, are presumed to participate in the functional regulation of numerous metabolic pathways, suggesting the reverse phosphorylation of these proteins might play important roles in elongating cotton fibers. The results also indicated that some different isoforms of the identical DEP revealed in our 2-DE-based proteomics analysis could be annotated by phosphorylation events. Taken together, as the first report of large-scale identification of phosphorylation sites in elongating cotton fiber cells, our study provides not only an excellent example of directly identifying phosphorylation sites from known DEPs on 2-D gels but also provides a valuable resource for future functional studies of phosphorylated proteins in this field.</p> </div

Analysis of the identified phosphorylated differentially expressed proteins in elongating cotton fiber cells.

<p>A) Functional classification and distribution of the 40 identified phosphorylated differentially expressed proteins. The number represents the number of protein spots in each functional catalog of the 40 phosphorylated DEPs and the 195 DEPs not identified as phosphorylated. B) and C) Close-up analysis of the relationship between phosphorylation modification and the possible isoforms detected by 2-DE. 35 DEP spots matched to 15 unique proteins are shown. The identified phosphoproteins are shown in red. Abbreviations: HSP70, Heat shock protein 70, chloroplast; IMP-α: Putative importin alpha protein; SAM: S-adenosylmethionine synthetase 1; GS: Glutamine synthetase; UER: UDP-L-rhamnose synthase; RabGDI: Rab GDP dissociation inhibitor; TK: Transketolase; PPIase: Peptidyl-prolyl cis-trans isomerase; CPN60: Chaperonin CPN60, mitochondrial; Tubβ-19: Beta-tubulin 19; F-ATPase-β: Plasma ATP synthase subunit beta; ENO: Enolase; CAT1: Catalase 1; DHAR1: GSH-dependent dehydroascorbate reductase; MetE: 5-methyltetrahydropteroyltriglutamate–homocysteine methyltransferase.</p

Phosphorylation site prediction of 235 differentially expressed proteins in elongating cotton fiber cells.

<p>The Peakeraser filter could partly eliminate the contamination peaks from the raw MS spectra, and further manual filter of the mistaken assignments of contaminated peptides to possible phosphopeptide largely diminished the prediction false-positive rate.</p

Information of the protein phosphorylation sites identified in this study.

<p>Abbreviations: P, phosphorylation; Cam, carboxyamidomethylation; *, phosphorylation sites already recorded in the P³DB database.</p

Flowchart of the 2-DE-based phosphorylation site identification method.

<p>Mass spectra and accurate amino acid sequence of the selected protein are analyzed by FindMod tool to predict the possible phosphopeptides, which are further confirmed by MS/MS and MASCOT scoring to elucidate the precise phosphorylation sites.</p