PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project.

MOTIVATION: The Division of Cancer Epidemiology and Genetics (DCEG) and the Division of Cancer Prevention (DCP) at the National Cancer Institute (NCI) have recently generated genome-wide association study (GWAS) data for multiple traits in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Genomic Atlas project. The GWAS included 110 000 participants. The dissemination of the genetic association data through a data portal called GWAS Explorer, in a manner that addresses the modern expectations of FAIR reusability by data scientists and engineers, is the main motivation for the development of the open-source JavaScript software development kit (SDK) reported here. RESULTS: The PLCO GWAS Explorer resource relies on a public stateless HTTP application programming interface (API) deployed as the sole backend service for both the landing page's web application and third-party analytical workflows. The core PLCOjs SDK is mapped to each of the API methods, and also to each of the reference graphic visualizations in the GWAS Explorer. A few additional visualization methods extend it. As is the norm with web SDKs, no download or installation is needed and modularization supports targeted code injection for web applications, reactive notebooks (Observable) and node-based web services. AVAILABILITY AND IMPLEMENTATION: code at https://github.com/episphere/plco; project page at https://episphere.github.io/plco.

A rapid, sensitive and solvent-less method for determination of malonaldehyde in meat by stir bar sorptive extraction coupled thermal desorption and gas chromatography/mass spectrometry with in situ derivatization.

RATIONALE: The traditional methods for analysis of malonaldehyde (MDA), such as the thiobarbituric acid (TBA) assay, require strong acidity at high temperature for derivatization and lack specificity in analysis. Stir bar sorptive extraction (SBSE) coupled with thermal desorption-gas chromatography/mass spectrometry (TD-GC/MS) with in situ derivatization using pentafluorophenylhydrazine (PFPH) under mild conditions is an emerging technique for MDA analysis. METHODS: MDA in meat was derivatized with PFPH at pH ~4 for 1 h at room temperature, forming a relative stable derivative of MDA-PFPH. The derivative of MDA-PFPH was simultaneously extracted using SBSE. Then, MDA-PFPH was thermally released and quantitatively analyzed by GC/MS in selected ion monitoring (SIM) mode. RESULTS: The method of SBSE-TD-GC/MS for MDA analysis with in situ derivatization was optimized and validated with good linearity, specificity and limit of detection/quantification (LOD/LOQ). The method was successfully applied for analysis of MDA in raw and cooked meat (pork). CONCLUSIONS: The SBSE-TD-GC/MS method was suitable to monitor and analyze MDA in meat samples at trace levels. The simple, sensitive and solvent-less method with moderated in situ derivatization can be applied for analysis of MDA in a wide variety of foods and biological samples.

Characteristics of glycation and glycation sites of lysozyme by matrix-assisted laser desorption/ionization time of flight/time-of-flight mass spectrometry and Liquid chromatography-electrospray ionization tandem mass spectrometry.

Protein glycation with reducing sugars through the Maillard reaction is regarded as one of the most important reactions in food chem- istry. Amadori rearrangement products [ARPs] are produced at the initial stage of the Maillard reaction and then advanced glycation products may be formed. We report here that using matrix-assisted laser desorption/ionization mass spectrometry with time-of-flight detection [MALDI-TOF-MS] and electrospray ionization mass spectrometry (ESI-MSJ to monitor the glycation process in lysozyme and the D-glucose model system. MALDI-TOF-MS displayed a heterogeneous distribution of glycation via a total mass shift in spectra. However electrospray ionization mass spectrometry [ESI-MS] data showed that a total of four molecules of glucose reacted with Lysozyme at an increase in molecular weight by a 162 Da unit. Further, we identified the glycation sites of lysozyme by using MALDI-TOF/TOF-MS and Liquid chromatography [LC]-ESI-MS/MS. Besides the two glycation sites of Lys1 and Lys97 identified by MALDI-TOF/TOF-MS, the other two glycation sites of Lys13 and Lys116 were characterized unambiguously by LC-ESI-MS/MS. Both MALDI-TOF/TOF-MS and LC-ESI-MS/ MS provided confidence in the study of the glycation by restricting the number of possible residues through (un]modified ions. The study is useful to monitor and characterize glycation in protein systems based on both MALDI-TOF-MS and ESI-MS. Comparatively, LC-ESI-MS/MS provides more fragments with better recovery for the identification of glycation than MALDI-TOF/TOF-MS.

Study of fragmentation behavior of amadori rearrangement products in lysine-containing peptide model by tandem mass spectrometry.

Protein and peptide glycation with reducing sugars through Maillard reaction is recognized as one of the most critical and fundamental reactions in food and in the human body. Amadori rearrangement products (ARPs) are formed at the initial stage of Maillard reaction and then may be converted into intermediate and advanced glycation products. We report here that using electrospray ionization-mass spectrometry (ESI-MS) to directly and rapidly characterize fragmentation behavior of ARPs in a Lysine-containing peptide-reducing sugars unambiguously model and identify the modification sites in glycated tri- and tetrapeptides. Tandem mass spectrometry (MS2) results showthat the sugar moiety was preferentially fragmented, whereby the neutral loss of small molecules, such as 18 Da (-H2O), 36 Da (-2 x H2O), 54 Da (-3 x H2O), 84 Da (-H2O-HCOH) and 162 Da from monosaccharide (glucose) moieties and 18 Da, 36 Da, 216 Da, 246 Da and 324 Da from disaccharide moieties. Among the fragmented ions, (M-84+H)+ of monosaccharides and (M-246+H)+ of disaccharides are relatively stable. Further multi-stage mass spectrometry (MS3) of (M-84+H)+ for tri- and longer peptides displays peptide sequence and glycation sites by providing modified y ions (y*), and/or modified b ions (b*) and even a modified a ion (a*). The study is useful to monitor and characterize PMTs of glycation in complex protein systems based on ESI-MS related techniques.

Sub-optimal nutrient regime coupled with Bacillus and Pseudomonas sp. inoculation influences trichome density and cannabinoid profiles in drug-type Cannabis sativa.

Cannabis sativa remains under heavy legal restriction around the globe that prevents extensive investigations into agricultural applications for improving its development. This work investigates the potential of specific plant growth-promoting rhizobacteria (PGPR) to improve Cannabis cannabinoid yield through increased trichome densities on floral organs, and to determine if sub-optimal environmental conditions would affect the outcomes of PGPR presence by altering plant development and cannabinoid profiles. Here, Pseudomonas sp. or Bacillus sp. were applied to the root system either separately or in a consortium to determine the effect of this bacterial treatment on the density of stalked glandular trichomes. Further, a low nutrient regime was applied for the first half of plant development to determine if an environmental stressor interacts with the effects of the microbial treatments on stalked trichome densities. Following 8 weeks of flower development, trichome density on calyces and bracts of inflorescences were determined using microscopy. Our findings unexpectedly indicate that recommended nutrient levels were linked to a decreasing trend in trichome densities with PGPR inoculations, but a low nutrient regime coupled with PGPR treatment increased them. Cannabinoid content is partially consistent with these results, in that a low nutrient regime increased the abundance of key cannabinoids compared to recommended regimes, with Bacillus sp. inoculation linked to the greatest number of significant changes between the two nutrient regimes. Overall, this work provides insight into how PGPR presence affects Cannabis stalked trichome development and cannabinoid profiles, and how environmental stressors can affect, and even enhance, trichome densities and influence major cannabinoid production, thereby pointing towards avenues for reducing the reliance on synthetic fertilizers during plant production without compromising yield.

Non-zwitterionic structures of aliphatic-only peptides mediated the formation and dissociation of gas phase radical cations.

We have investigated how the non-zwitterionic and zwitterionic structures of aliphatic-only tripeptides affect the formation and dissociation of peptide radical cations in the gas phase. The non-zwitterionic forms of the aliphatic-only peptides in their metal complexes play an important role in determining whether the electron transfer pathway predominates. We extended this study by synthesizing permanent non-zwitterionic and zwitterionic forms of aliphatic-only peptide radical cations and exploring their reactivities in the gas phase. Collision-induced dissociation spectra demonstrated the feasibility of generating both non-zwitterionic and zwitterionic forms. Radical cations in zwitterionic forms may indeed mediate the beta and gamma carbon-carbon bond cleavages of leucine and isoleucine side chains from the GlyGlyXle radical peptides; this feature allows leucine and isoleucine residues to be distinguished unambiguously.

Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B.

RNA polymerase II (RNAP II) C-terminal domain (CTD) phosphorylation is important for various transcription-related processes. Here, we identify by affinity purification and mass spectrometry three previously uncharacterized human CTD-interaction domain (CID)-containing proteins, RPRD1A, RPRD1B and RPRD2, which co-purify with RNAP II and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. RPRD1A and RPRD1B can accompany RNAP II from promoter regions to 3'-untranslated regions during transcription in vivo, predominantly interact with phosphorylated RNAP II, and can reduce CTD S5- and S7-phosphorylated RNAP II at target gene promoters. Thus, the RPRD proteins are likely to have multiple important roles in transcription.