DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

Phenolic Profiles and Antioxidant Properties of Young Wines Made from Yan73 (Vitis vinifera L.) and Cabernet Sauvignon (Vitis vinifera L.) Grapes Treated by 24-Epibrassinolide

The grape berries of two varieties, Yan73 (Vitis vinifera L.) and Cabernet Sauvignon (CS) (Vitis vinifera L.) were treated with 0.40 mg/L 24-epibrassinolide (EBR), 1.00 mg/L brassinazole (Brz), and deionized water (control), at the veraison period. The EBR treatment significantly increased total phenolic content (TPC), total tannin content (TTC) and total anthocyanin content (TAC) of Yan73 and CS wines, whereas Brz treatment decreased TPC, total flavonoid content (TFC), TAC in the two wines. Moreover, the content of most of the phenolic compounds identified by HPLC-DAD/ESI-MS in EBR-treated wines was significantly higher than that in control. The antioxidant capacities, which determined using DPPH, ABTS and HRSA methods, of the wines were increased by EBR treatment as well. There was a good correlation between the antioxidant capacity and phenolic content. The results demonstrated that EBR could enhance the phenolic compounds and antioxidant capacity of Yan73 and CS wines, but the effects may vary by different cultivars

Study of Fe deposition onto root 3 x root 3-Al/Si(111) template by scanning tunneling microscopy

The surface dynamics of Fe deposited onto the template surface of root 3 x root 3-Al adatom-layer on Si(1 1 1) has been studied using scanning tunneling microscopy (STM). By imaging at both positive and negative sample bias, we identify the locations of Fe, Al and Si atoms by the susceptibility differences of these sites in receiving electrons and holes from the STM tip. When 0.1 ML of Fe atoms are deposited at room temperature, some Fe atoms incorporate themselves into the adlayer as dispersed atoms or small Fe clusters with 2-10 atoms. A smaller amount of Fe atoms choose to sit on the adlayer, once again as dispersed atoms or small Fe clusters. As the Fe coverage increases beyond 0.1 ML, both Fe clusters in and on the adlayer grow into 3-dimensional islands. Raising the growth temperature to 100 degrees C is enough to enhance the diffusivity of Fe atoms and initiate a small degree of cluster coalescence. However, these clusters still do not show any crystallinity by STM observation until they are annealed. Deposition of Fe atoms at 400 degrees C or post-deposition annealing above this temperature leads to the formation of iron silicide islands with a 2 x 2 surface lattice and a CsCl-type iron silicide structure, which are surrounded by root 3 x root 3-Al/Si(1 1 1) adlayer domains with a depletion of Si atoms near the silicide islands. Most of these islands have a triangular shape, and grow preferentially along the step edges of the Si(1 1 1) surface. The root 3 x root 3-Al adlayer appears to passivate the Si surface and enhances the diffusivity of Fe atoms but the passivation is not thermally stable. (c) 2006 Elsevier B.V. All rights reserved

Changes in cardiac volume determined with repeated enhanced 4DCT during chemoradiotherapy for esophageal cancer

Abstract Background Concurrent chemoradiotherapy is considered curative intent treatment for patients with non-operative esophageal cancer. Radiation-induced heart damage receives much attention. We performed repeated four-dimensional computed tomography (4DCT) to detect changes in cardiac volume during radiotherapy for esophageal cancer patients, and explored potential factors responsible for those changes. Methods Forty-six patients with esophageal cancer underwent enhanced 4DCT and three-dimensional (3D) CT scans before radiotherapy and every 10 fractions during treatment. The heart was contoured on 3DCT images, 4DCT end expiratory (EE) images and 4DCT maximum intensity projection (MIP) images by the same radiation oncologist. Heart volumes and other relative parameters were compared by the SPSS software package, version 19.0. Results Compared with its initial value, heart volume was smaller at the 10th fraction (reduction = 3.27%, 4.45% and 4.52% on 3DCT, EE and MIP images, respectively, p < 0.05) and the 20th fraction (reduction = 6.05%, 5.64% and 4.51% on 3DCT, EE and MIP images, respectively, p < 0.05), but not at the 30th fraction. Systolic and diastolic blood pressures were reduced (by 16.95 ± 16.69 mmHg and 7.14 ± 11.64 mmHg, respectively, both p < 0.05) and the heart rate was elevated by 5.27 ± 6.25 beats/min (p < 0.05) after radiotherapy. None of the potential explanatory variables correlated with heart volume changes. Conclusions Cardiac volume reduced significantly from an early treatment stage and maintained the reduction until the middle stage. The heart volume changes observed on 3DCT and 4DCT were consistent during radiotherapy. The changes in heart volume, blood pressure and heart rate may be valuable indicators of cardiac impairment and target dose changes

Rapid Qualitative and Quantitative Determination of Seven Valuable Taxanes from Various Taxus Species by UFLC-ESI-MS and UFLC-DAD

The distribution and level of yew constituents vary with species and tissues. In this study, a rapid and valid method incorporating ultra-fast liquid chromatography (UFLC) with MS and UV detection was developed for simultaneous determination of paclitaxel and its six semisynthesis precursors in needles and hair roots from various Taxus species. All target analytes could be identified by comparing their retention times as well as UV and MS spectra with authentic standards, while seven valuable taxanes in botanical samples can be rapidly determined by UFLC-DAD with excellent sensitivity. Analysis of more than one hundred yew samples from nine species showed significant variations in distribution and content of seven evaluated taxanes. Thus, different developmental schemes should be used for better utilization of various yew resources

Negative costimulatory molecule B7-H4 mediates protective effect of mesenchymal stem cells on experimental autoimmune encephalomyelitis

Our previous study has shown that the negative co-stimulatory molecule B7-H4 is constitutively expressed on human bone marrow-derived mesenchymal stem cells (MSCs) and mediates their immunomodulatory effect on T cells in vitro. However, whether B7-H4 on MSCs can be responsible for their immunomodulation in vivo has not been clarified. The present study investigated the immunomodulatory role and mechanism of B7-H4 on mouse mesenchymal stem cell (MSCs) in the development of experimental autoimmune encephalomyelitis (EAE). Murine MSC C3H/10T1/2 (C3H10) cells were transfected with B7-H4-specific shRNA to silence B7-H4 expression (C3H10-B7H4). The effects of C3H10-B7H4 cells on splenocyte proliferation and cell cycling as well as cytokine responses were examined.We found that B7-H4 silencing mitigated the immune-inhibitory effect of C3H10 cells on PHA-stimulated splenocyte activation and proliferation as well as IL-2, IL-17 and IFN-γ responses. Female C57BL/6 mice were injected with myelin oligodendrocyte glycoprotein peptide (MOG35-55) to induce EAE, then infused with C3H10-B7H4, C3H10-NC (C3H10 transfected with negative control shRNA) or C3H10 cells. The pathological changes of the injured spinal cord were analyzed by hematoxylin and eosin (HE) staining, Luxol fast blue (LFB) staining and immunofluorescence. Infusion with C3H10 or C3H10-NC, but not C3H10-B7H4 cells, dramatically slowed the development of EAE, and reduced the severity and degree of inflammatory infiltrates, demyelination, and axonal damages. The plasma levels of interleukin-2 (IL-2), IL-17, interferon-gamma (IFN-γ), and IL-4 in the different groups of mice were examined. Infusion with C3H10 or C3H10-NC cells significantly decreased the plasma levels of IL-2, IL-17 and IFN-γ in EAE mice, but infusion with C3H10-B7H4 cells only slightly reduced pro-inflammatory cytokine responses in mice. Taken together, these data indicated that B7-H4 was important for the immune characteristics and immunomodulatory capacity of mouse MSCs. B7-H4 decreased Th1/Th17 responses in EAE mice. This is the first report on the role and possible mechanism of B7-H4 in the protection of MSCs against MOG-induced EAE in mice. These findings may provide a new avenue and target molecule in MSC-based therapy for autoimmune diseases in the central nervous system, such as multiple sclerosis and neuromyelitis optica spectrum disorder