2,259 results match your criteria tag profiling


Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon ().

Conserv Physiol 2020 11;8(1):coaa084. Epub 2020 Sep 11.

U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA.

Chinook salmon () declines are widespread and may be attributed, at least in part, to warming river temperatures. Water temperatures in the Yukon River and tributaries often exceed 18°C, a threshold commonly associated with heat stress and elevated mortality in Pacific salmon. Untangling the complex web of direct and indirect physiological effects of heat stress on salmon is difficult in a natural setting with innumerable system challenges but is necessary to increase our understanding of both lethal and sublethal impacts of heat stress on populations. Read More

View Article and Full-Text PDF
September 2020

Development of a widely-targeted volatilomics method for profiling the volatilomes in plants.

Mol Plant 2021 Sep 9. Epub 2021 Sep 9.

College of Tropical Crops, Hainan University, Haikou 570288, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China. Electronic address:

Volatile organic compounds play essential roles in plant-environment interactions as well as determining the fragrance of plants. Although gas chromatography-mass spectrometry based untargeted metabolomics is commonly used to assess plant volatiles, it suffers from high spectral convolution, low detection sensitivity, limited annotated metabolites and relatively poor reproducibility. Herein, we report a widely-targeted volatilomics (WTV) method: using "targeted spectra extraction" algorithm to address spectral convolution; constructing a high coverage MS spectral tag library to expand volatile annotation; adapting a multiple reaction monitoring mode to improve the sensitivity; and using regression models to adjust for signal drift. Read More

View Article and Full-Text PDF
September 2021

Single-cell analysis of regions of interest (SCARI) using a photosensitive tag.

Nat Chem Biol 2021 Sep 9. Epub 2021 Sep 9.

Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.

The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Read More

View Article and Full-Text PDF
September 2021

Distinct lipidomic signatures in persons living with HIV: combined analysis of ACTG 5260s and MACS/WIHS.

J Clin Endocrinol Metab 2021 Sep 8. Epub 2021 Sep 8.

Albert Einstein College of Medicine, Bronx, NY, USA, Stable Isotope and Metabolomics Core Facility, Department of Medicine, Fleischer Institute for Diabetes and Metabolism.

Purpose: We assessed the effect of untreated HIV infection as well as different antiretroviral therapy (ART) on the metabolome/lipidome.

Methods: Widely-targeted plasma metabolomic and lipidomic profiling was performed on HIV-seronegative individuals and persons living with HIV (PLHIV) before and after initiating ART [tenofovir/emtricitabine plus atazanavir/ritonavir (ATV/r) or darunavir/ritonavir (DRV/r) or raltegravir (RAL)]. Orthogonal partial least squares discriminant analysis was used to assess metabolites/lipid subspecies that discriminated between groups. Read More

View Article and Full-Text PDF
September 2021

Enrichment of provitamin A content in durum wheat grain by suppressing β-carotene hydroxylase 1 genes with a TILLING approach.

Theor Appl Genet 2021 Sep 3. Epub 2021 Sep 3.

Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via S. Camillo de Lellis, SNC, 01100, Viterbo, Italy.

Key Message: The suppression of the HYD-1 gene by a TILLING approach increases the amount of β-carotene in durum wheat kernel. Vitamin A deficiency is a major public health problem that affects numerous countries in the world. As humans are not able to synthesize vitamin A, it must be daily assimilated along with other micro- and macronutrients through the diet. Read More

View Article and Full-Text PDF
September 2021

Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag.

STAR Protoc 2021 Sep 19;2(3):100751. Epub 2021 Aug 19.

Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.

Muscle stem cells (MuSCs) are a rare stem cell population that provides myofibers with a remarkable capacity to regenerate after tissue injury. Here, we have adapted the Cleavage Under Target and Tagmentation technology to the mapping of the chromatin landscape and transcription factor binding in 50,000 activated MuSCs isolated from injured mouse hindlimb muscles. We have applied this same approach to human CD34 hematopoietic stem and progenitor cells. Read More

View Article and Full-Text PDF
September 2021

Utilizing thermal proteome profiling to identify the molecular targets of anti-leishmanial compounds.

STAR Protoc 2021 Sep 18;2(3):100704. Epub 2021 Aug 18.

Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Here, we detail our optimized protocol for the identification of drug targets in using thermal proteome profiling. This approach is based on the principle that binding of a drug to its protein target can significantly alter the thermal stability of that protein. By monitoring changes in the thermal stability of proteins within drug-treated and untreated cell lysates, using mass spectrometry combined with tandem mass tag labeling, putative targets of the drug can be identified in an unbiased manner. Read More

View Article and Full-Text PDF
September 2021

Intra-Ramanome Correlation Analysis Unveils Metabolite Conversion Network from an Isogenic Population of Cells.

mBio 2021 Aug 31;12(4):e0147021. Epub 2021 Aug 31.

Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.

To reveal the dynamic features of cellular systems, such as the correlation among phenotypes, a time or condition series set of samples is typically required. Here, we propose intra-ramanome correlation analysis (IRCA) to achieve this goal from just one snapshot of an isogenic population, via pairwise correlation among the cells of the thousands of Raman peaks in single-cell Raman spectra (SCRS), i.e. Read More

View Article and Full-Text PDF

Proteome profiling of formalin-fixed, paraffin-embedded lung adenocarcinoma tissues using a tandem mass tag-based quantitative proteomics approach.

Oncol Lett 2021 Oct 4;22(4):706. Epub 2021 Aug 4.

Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China.

Over the past few decades, increasing efforts have been made to improve the understanding of, and treatment options for, lung adenocarcinoma (LUAD). However, considering the heterogeneity of LUAD, precise proteomics-based characterization at the molecular level is an urgent clinical requirement for effective treatment. Formalin-fixed, paraffin-embedded (FFPE) tissue is a good option as the working tool for proteomics studies. Read More

View Article and Full-Text PDF
October 2021

Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease.

Int J Mol Sci 2021 Aug 16;22(16). Epub 2021 Aug 16.

Dipartimento di Biologia e Biotecnologie "Charles Darwin", Istituto Pasteur Italia, Università Sapienza, 00185 Rome, Italy.

Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. Read More

View Article and Full-Text PDF

Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry.

Methods Mol Biol 2021 ;2365:301-313

Cell Signaling Technology, INC., Danvers, MA, USA.

Protein degradation is a critical component of all facets of cell biology, and recently methods have been developed to make use of targeted protein degradation as both an investigative tool and a potential therapeutic avenue. Mass spectrometry-based proteomic studies have allowed detailed characterization of changes in protein level and the biology underlying growth, development, and disease. Current methods and instrumentation allow identification and quantitative analysis of thousands of proteins in a single assay. Read More

View Article and Full-Text PDF
January 2021

Evolution of the Selection Methods of DNA-Encoded Chemical Libraries.

Acc Chem Res 2021 09 24;54(17):3491-3503. Epub 2021 Aug 24.

Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.

In the past two decades, a DNA-encoded chemical library (DEL or DECL) has emerged and has become a major technology platform for ligand discovery in drug discovery as well as in chemical biology research. Although based on a simple concept, i.e. Read More

View Article and Full-Text PDF
September 2021

Spleen proteome profiling of dairy goats infected with C. pseudotuberculosis by TMT-based quantitative proteomics approach.

J Proteomics 2021 Sep 17;248:104352. Epub 2021 Aug 17.

College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address:

Corynebacterium pseudotuberculosis (C.pseudotuberculosis) is a zoonotic pathogen that can cause cheese lymphadenitis in goats. In order to obtain detailed information about the pathogenesis and host immune response of goats infected with C. Read More

View Article and Full-Text PDF
September 2021

Ligand-induced native G-quadruplex stabilization impairs transcription initiation.

Genome Res 2021 Sep 16;31(9):1546-1560. Epub 2021 Aug 16.

Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.

G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines, and G4s are distributed widely across the genome. G4 participates in multiple biological processes including gene transcription, and G4-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, genome-wide studies of the exact roles of G4s in transcriptional regulation are still lacking. Read More

View Article and Full-Text PDF
September 2021

Molecular modeling, docking and dynamics analysis of lipid droplet associated enzyme Ypr147cp from Saccharomyces cerevisiae.

Bioinformation 2021 31;17(1):132-138. Epub 2021 Jan 31.

Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana-500046, India.

Ypr147cp of Saccharomyces cerevisiae was localized to lipid droplets. The recombinant Ypr147cp showed both triacylglycerol lipase and ester hydrolase activities. Knock out of YPR147C led to accumulation of TAG in ypr147cΔ when compared to wild type (WT). Read More

View Article and Full-Text PDF
January 2021

SCITO-seq: single-cell combinatorial indexed cytometry sequencing.

Nat Methods 2021 08 5;18(8):903-911. Epub 2021 Aug 5.

Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA.

The development of DNA-barcoded antibodies to tag cell surface molecules has enabled the use of droplet-based single-cell sequencing (dsc-seq) to profile protein abundances from thousands of cells simultaneously. As compared to flow and mass cytometry, the high per cell cost of current dsc-seq-based workflows precludes their use in clinical applications and large-scale pooled screens. Here, we introduce SCITO-seq, a workflow that uses splint oligonucleotides (oligos) to enable combinatorially indexed dsc-seq of DNA-barcoded antibodies from over 10 cells per reaction using commercial microfluidics. Read More

View Article and Full-Text PDF

Time-Resolved Proteome Analysis of during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation.

mSystems 2021 Aug 3;6(4):e0021521. Epub 2021 Aug 3.

Max Planck Unit for the Science of Pathogens, Berlin, Germany.

The cellular proteome comprises all proteins expressed at a given time and defines an organism's phenotype under specific growth conditions. The proteome is shaped and remodeled by both protein synthesis and protein degradation. Here, we developed a new method which combines metabolic and chemical isobaric peptide labeling to simultaneously determine the time-resolved protein decay and synthesis in an intracellular human pathogen. Read More

View Article and Full-Text PDF

Proteomic Profiling of Exosomes From Hemorrhagic Moyamoya Disease and Dysfunction of Mitochondria in Endothelial Cells.

Stroke 2021 Aug 2:STROKEAHA120032297. Epub 2021 Aug 2.

Department of Neurosurgery, The Fifth Medical Centre of PLA General Hospital, Beijing, China (C.H., L.D.).

Background And Purpose: Moyamoya disease (MMD) is a rare steno-occlusive and slowly progressing cerebrovascular disorder. The detailed mechanism of the underlying pathogenesis is still blurry.

Methods: Tandem Mass Tag-labeled quantitative proteomics was performed on serum-derived exosomes (SDEs) extracted from adult patients diagnosed with pure ischemic MMD or hemorrhagic MMD and healthy controls. Read More

View Article and Full-Text PDF

Defining candidate mRNA and protein EV biomarkers to discriminate ccRCC and pRCC from non-malignant renal cells in vitro.

Med Oncol 2021 Jul 31;38(9):105. Epub 2021 Jul 31.

The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.

Renal cell carcinoma (RCC) accounts for over 400,000 new cases and 175,000 deaths annually. Diagnostic RCC biomarkers may prevent overtreatment in patients with early disease. Extracellular vesicles (EVs) are a promising source of RCC biomarkers because EVs carry proteins and messenger RNA (mRNA) among other biomolecules. Read More

View Article and Full-Text PDF

Lipid profiling in chilled coral larvae.

Cryobiology 2021 Jul 27. Epub 2021 Jul 27.

National Museum of Marine Biology & Aquarium, Pingtung, Taiwan; Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan. Electronic address:

Coral reefs are disappearing worldwide as a result of several harmful human activities. The establishment of cryobanks can secure a future for these ecosystems. To design effective cryopreservation protocols, basic proprieties such as chilling tolerance and lipid content must be assessed. Read More

View Article and Full-Text PDF

New Structure Mass Tag based on Zr-NMOF for Multiparameter and Sensitive Single-Cell Interrogating in Mass Cytometry.

Adv Mater 2021 Sep 26;33(35):e2008297. Epub 2021 Jul 26.

State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China.

Mass cytometry, also called cytometry by time-of-flight (CyTOF), is an emerging powerful proteomic analysis technique that utilizes metal chelated polymer (MCP) as mass tags for interrogating high-dimensional biomarkers simultaneously on millions of individual cells. However, under the typical polymer-based mass tag system, the sensitivity and multiplexing detection ability has been highly restricted. Herein, a new structure mass tag based on a nanometal organic framework (NMOF) is reported for multiparameter and sensitive single-cell biomarker interrogating in CyTOF. Read More

View Article and Full-Text PDF
September 2021

The H3.3K27M oncohistone antagonizes reprogramming in Drosophila.

PLoS Genet 2021 Jul 19;17(7):e1009225. Epub 2021 Jul 19.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

Development proceeds by the activation of genes by transcription factors and the inactivation of others by chromatin-mediated gene silencing. In certain cases development can be reversed or redirected by mis-expression of master regulator transcription factors. This must involve the activation of previously silenced genes, and such developmental aberrations are thought to underlie a variety of cancers. Read More

View Article and Full-Text PDF

Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer.

Mol Cell Proteomics 2021 Jul 13;20:100121. Epub 2021 Jul 13.

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. Electronic address:

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer. Patients with TNBC have poor overall survival because of limited molecular therapeutic targets. Recently, exosomes have been recognized as key mediators in cancer progression, but the molecular components and function of TNBC-derived exosomes remain unknown. Read More

View Article and Full-Text PDF

Simplified Epigenome Profiling Using Antibody-tethered Tagmentation.

Bio Protoc 2021 Jun 5;11(11):e4043. Epub 2021 Jun 5.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington 98109, USA.

We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps specific chromatin features in small samples and single cells. With CUT&Tag, intact cells or nuclei are permeabilized, followed by successive addition of a primary antibody, a secondary antibody, and a chimeric Protein A-Transposase fusion protein that binds to the antibody. Addition of Mg activates the transposase and inserts sequencing adapters into adjacent DNA . Read More

View Article and Full-Text PDF

Novel insights into the immune regulatory effects of Megalobrama amblycephala intelectin on the phagocytosis and killing activity of macrophages.

Mol Immunol 2021 09 9;137:145-154. Epub 2021 Jul 9.

Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; School of Marine Science and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China. Electronic address:

Previous studies have found that the expression level of Megalobrama amblycephala intelectin (MaINTL) increased significantly post Aeromonas hydrophila infection, and recombinant MaINTL (rMaINTL) protein could activate macrophages and enhance the phagocytosis and killing activity of macrophages. In order to reveal the immune regulatory mechanisms of MaINTL, primary M. amblycephala macrophages were treated with endotoxin-removed rMaINTL and GST-tag proteins, then total RNA were extracted and used for comparative Digital Gene Expression Profiling (DGE). Read More

View Article and Full-Text PDF
September 2021

CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis.

Bioinformatics 2021 Jul 9. Epub 2021 Jul 9.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

Motivation: Genome-wide profiling of transcription factor binding and chromatin states is a widely-used approach for mechanistic understanding of gene regulation. Recent technology development has enabled such profiling at single-cell resolution. However, an end-to-end computational pipeline for analyzing such data is still lacking. Read More

View Article and Full-Text PDF

A phylogeny-aware approach reveals unexpected venom components in divergent lineages of cone snails.

Proc Biol Sci 2021 07 7;288(1954):20211017. Epub 2021 Jul 7.

Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France.

Marine gastropods of the genus are renowned for their remarkable diversity and deadly venoms. While venoms are increasingly well studied for their biomedical applications, we know surprisingly little about venom composition in other lineages of Conidae. We performed comprehensive venom transcriptomic profiling for and , first time for both respective genera. Read More

View Article and Full-Text PDF

The effect of AINTEGUMENTA-LIKE 7 over-expression on seed fatty acid biosynthesis, storage oil accumulation and the transcriptome in Arabidopsis thaliana.

Plant Cell Rep 2021 Sep 2;40(9):1647-1663. Epub 2021 Jul 2.

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.

Key Message: AIL7 over-expression modulates fatty acid biosynthesis and triacylglycerol accumulation in Arabidopsis developing seeds through the transcriptional regulation of associated genes. Seed fatty acids (FAs) and triacylglycerol (TAG) contribute to many functions in plants, and seed lipids have broad food, feed and industrial applications. As a result, an enormous amount of attention has been dedicated towards uncovering the regulatory cascade responsible for the fine-tuning of the lipid biosynthetic pathway in seeds, which is regulated in part through the action of LEAFY COTYLEDON1, ABSCISSIC ACID INSENSITIVE 3, FUSCA3 and LEC2 (LAFL) transcription factors. Read More

View Article and Full-Text PDF
September 2021

Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases.

Commun Biol 2021 07 2;4(1):830. Epub 2021 Jul 2.

Dermatology Hospital, Southern Medical University, Guangzhou, China.

Genome-wide identification of DNA double-strand breaks (DSBs) induced by CRISPR-associated protein (Cas) systems is vital for profiling the off-target events of Cas nucleases. However, current methods for off-target discovery are tedious and costly, restricting their widespread applications. Here we present an easy alternative method for CRISPR off-target detection by tracing the integrated oligonucleotide Tag using next-generation-sequencing (CRISPR-Tag-seq, or Tag-seq). Read More

View Article and Full-Text PDF

Global Proteomic Profiling of Pediatric AML: A Pilot Study.

Cancers (Basel) 2021 Jun 24;13(13). Epub 2021 Jun 24.

Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA.

Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML's heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limited. Furthermore, the majority of biological functions within cells are operated by proteins (i. Read More

View Article and Full-Text PDF