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81.
《基因组蛋白质组与生物信息学报(英文版)》2020,18(2):104-119
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. 相似文献
82.
83.
Biogas production has been shown to be inhibited by branched chain fatty acids (isobutyric, isovaleric) produced in the digester
by cellulolytic organisms. Performance of these mixed cellulolytic cultures isolated at 25°C (C25) and at 35° (C35) in a batch digester using cattle manure confirmed that C35, which forms mainly straight chain fatty acids from cellulose was more suitable for use as an inoculum than C25 which formed predominantly branched chain fatty acids. Reconstitution of cellulolytic culture C35 and mixed methanogens M35 almost doubled both the amount and rate of methane production. Cellulolytic culture was useful in pretreatment of water hyacinth
prior to its use as a substrate for methane generation A method for preservation and transportation of mixed cellulolytic
culture for use as an inoculum in the digester is described. 相似文献
84.
Bacterial ammonium transport 总被引:10,自引:0,他引:10
D. Kleiner 《FEMS microbiology letters》1985,32(2):87-100
85.
Hyun I. Park 《Analytical biochemistry》2010,396(2):262-60
Matrix metalloproteinases (MMPs) are a family of hydrolytic enzymes that play significant roles in development, morphogenesis, inflammation, and cancer invasion. Endometase (matrilysin 2 or MMP-26) is a putative early biomarker for human carcinomas. The effects of the ionic and nonionic detergents on catalytic activity of endometase were investigated. The hydrolytic activity of endometase was detergent concentration dependent, exhibiting a bell-shaped curve with its maximum activity near the critical micelle concentration (CMC) of nonionic detergents tested. The effect of Brij-35 on human gelatinase B (MMP-9), matrilysin (MMP-7), and membrane-type 1 MMP (MT1-MMP) was further explored. Their maximum catalysis was observed near the CMC of Brij-35 (∼ 90 μM). Their IC50 values were above the CMC. The inhibition mechanism of MMP-7, MMP-9, and MT1-MMP by Brij-35 was a mixed type as determined by Dixon’s plot; however, the inhibition mechanism of endometase was noncompetitive with a Ki value of 240 μM. The catalytic activities of MMPs are influenced by detergents. Monomer of detergents may activate and stabilize MMPs to enhance catalysis, but micelle of detergents may sequester enzyme and block the substrate binding site to impede catalysis. Under physiological conditions, a lipid or membrane microenvironment may regulate enzymatic activity. 相似文献
86.
Peter J. Carrick 《植被学杂志》2003,14(5):761-772
Abstract. The nearest‐neighbour technique is used to infer competition and facilitation between the three most abundant species in a semi‐arid region of western South Africa. Relationships among the shrubs Leipoldtia schultzei and Ruschia robusta, which are leaf‐succulent members of the Mesembryanthemaceae (‘mesembs’) and Hirpicium alienatum a non‐succulent Asteraceae, were compared on two adjacent sites with different histories of browsing intensity. Competition was more prevalent and more important than facilitation. The only evidence for facilitation was found at the heavily‐browsed site where the palatable Hirpicium was larger under the unpalatable Leipoldtia. Generally the prevalence and importance of competition was reduced at the heavily‐browsed site. Strong evidence was obtained for intraspecific competition in each of the three species; also, competition was evident between the two mesembs, where Leipoldtia was competitively dominant over Ruschia, although neither species inhibited Hirpicium. Minimal competition between the mesembs and the asteraceous shrub was interpreted in terms of differentiation in rooting depth, and competition within the mesembs, in terms of overlap in rooting depth. The mesembs had the bulk of their roots in the top 5 cm of soil, while the asteraceous shrub had the bulk of its roots, and all its fine roots, at greater depths. The shallow‐rooted morphology of the mesembs is well adapted to utilize small rainfall events, which occur frequently in the Succulent Karoo, and do not penetrate the soil deeply. Modifications of existing methods are applied for analysing nearest‐neighbour interactions. 相似文献
87.
Neonatal heart rate variability and its relation to respiration 总被引:3,自引:0,他引:3
The heart rate and respiration signals from nine healthy full term neonates were studied using autoregressive spectral analysis and cross-correlation techniques. The heart rate spectra could be divided into three regions of activity: a very low frequency (VLF) region from 0-0.04 Hz; a low frequency (LF) band from 0.04-0.20 Hz; and a high frequency (HF) region above 0.20 Hz. The newborns exhibited very little respiratory sinus arrhythmia in their heart rate variability in contrast to the situation for adults and older infants. However, variations in heart rate correlated strongly with changes in the breath amplitude, leading to what may be termed a breath amplitude sinus arrhythmia. The neonatal heart rate behaviour under stable conditions of oscillation could be simulated with a nonlinear control model provided the delay time in the baroreceptor loop of the model was taken to be approximately 2 seconds longer than in adults. This is consistent with the immature neurological status of neonates. 相似文献
88.
89.
《Molecular & cellular proteomics : MCP》2020,19(1):142-154
Highlights
- •Flow cytometry analysis is used to isolate ASC speck(+) NPC cells.
- •Proteome analysis of ASC speck(+) NPC cells reveals enriched mitochondrial OxPhos proteins.
- •OxPhos proteins mediate NLRP3 inflammasome activation through mtROS.
- •OxPhos proteins, NDUFB8 and ATP5B are correlated with NPC local recurrence.
90.