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Shotgun Metagenomic Approaches
The most recent advancements in the knowledge of sourdough ecologic meta-community come from the uncultured approach based on shotgun metagenomics...
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Two-dimensional gel and shotgun proteomics approaches for the comparative evaluation of genetically modified maize
In the safety risk assessment of genetically modified (GM) crops, it is imperative to evaluate potential unintended effects derived from genetic...
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Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage—Application of Next-Generation Amplicon and Shotgun Metagenome Sequences
“Pakhoi” is an ethnic drink of the Tons valley, Uttarakhand, India produced by fermenting jaggery and barley with the help of a starter culture...
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Shotgun proteomics of extracellular matrix in late senescent human dermal fibroblasts reveals a down-regulated fibronectin-centered network
Extracellular matrix (ECM) proteins play a pivotal role in cell growth and differentiation. To characterize aged ECM proteins, we compared the...
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Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing
COVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an...
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Rodent Lung Tissue Sample Preparation and Processing for Shotgun Proteomics
Mass spectrometry (MS) is a routinely used approach to characterize global protein profile in various biological samples. Here we describe rodent...
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Efficient protein extraction for shotgun proteomics from hydrated and desiccated leaves of resurrection Ramonda serbica plants
Resurrection plant Ramonda serbica is a suitable model to investigate vegetative desiccation tolerance. However, the detailed study of these...
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Shotgun Proteomics and Mass Spectrometry as a Tool for Protein Identification and Profiling of Bio-Carrier-Based Therapeutics on Human Cancer Cells
Shotgun proteomics has been widely applied to study proteins in complex biological samples. Combination of high-performance liquid chromatography...
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From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha
A highly multiplexed liquid chromatography mass spectrometry–multiple reaction monitoring (MRM)-based assay has been developed for evaluating 107...
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Monitoring the microbiome for food safety and quality using deep shotgun sequencing
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To...
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Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19
The upper respiratory tract (URT) is home to a diverse range of microbial species. Respiratory infections disturb the microbial flora in the URT,...
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Food authentication from shotgun sequencing reads with an application on high protein powders
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To...
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Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome
It has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate...
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Nanoliter-Scale Sample Preparation for Single-Cell Proteomic Analysis Using Glass-Oil-Air-Droplet Chip
Single-cell proteomic analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems’ heterogeneous...
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2D-DIGE Analysis of Liver Disease in Mice
Hepatocellular carcinoma (HCC) is the major type of primary liver cancer. In this chapter, we describe our routine two-dimensional difference gel...
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Effects of a prebiotic formulation on the composition of the faecal microbiota of people with functional constipation
PurposePrebiotics are defined as substances which selectively promote beneficial gut microbes leading to a health benefit for the host. Limited...
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Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults
PurposePopulation-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the...
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Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome
The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase...
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Nanofluidic Technologies for Drug Screening and Drug Delivery
Recently, nanofluidics exploiting 10–1000 nm spaces has developed and suggested a potential of novel analytical methods for pharmaceutical studies...
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Robust and high-throughput lipidomic quantitation of human blood samples using flow injection analysis with tandem mass spectrometry for clinical use
Direct infusion of lipid extracts into the ion source of a mass spectrometer is a well-established method for lipid analysis. In most cases,...
