Philip Loziuk

Works (13)

Updated: August 18th, 2023 21:18

2021 journal article

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

FRONTIERS IN PLANT SCIENCE, 12.

By: C. Lin n, Y. Sun *, J. Song n, H. Chen n, R. Shi n, C. Yang n, J. Liu  n, S. Tunlaya-Anukit n ...

author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
TL;DR: It is proposed that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: November 8, 2021

2019 journal article

Label-Free Quantitative Proteomics of Enriched Nuclei from Sugarcane (Saccharum ssp) Stems in Response to Drought Stress

PROTEOMICS, 19(14).

By: F. Salvato *, P. Loziuk n, E. Kiyota*, G. Daneluzzi *, P. Araujo *, D. Muddiman n , P. Mazzafera *

author keywords: drought; RNA regulation; Saccharum spp; shotgun proteomics; transcription factors
MeSH headings : Droughts; Gene Expression Regulation, Plant; Plant Proteins / metabolism; Proteomics; Saccharum / metabolism
TL;DR: The integration of nuclei enrichment sample preparation with the shotgun proteomic approach results in great coverage of the sugarcane stem proteome with 5381 protein groups identified, indicating that drought affects negatively the cell wall metabolism. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: July 22, 2019

2019 journal article

Quantitative proteomic analysis of tomato genotypes with differential cadmium tolerance

ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH, 26(25), 26039–26051.

By: K. Reis Borges *, F. Salvato*, P. Loziuk n, D. Muddiman n  & R. Azevedo *

author keywords: Root proteome; Cd stress; Antioxidant; Redox; Cell wall; Metabolism
MeSH headings : Cadmium / chemistry; Cadmium / metabolism; Cell Wall / metabolism; Drug Tolerance; Genotype; Solanum lycopersicum / metabolism; Plant Roots / metabolism; Proteome / chemistry; Proteome / metabolism; Proteomics; Stress, Physiological / drug effects
TL;DR: Findings could shed some light on the molecular basis underlying the Cd stress response in tomato, providing fundamental insights for the development of Cd-safe cultivars. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, ORCID
Added: September 23, 2019

2017 journal article

N-linked glycosite profiling and use of Skyline as a platform for characterization and relative quantification of glycans in differentiating xylem of Populus trichocarpa

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 409(2), 487–497.

By: P. Loziuk n, E. Hecht n & D. Muddiman n 

author keywords: N-linked glycosite; Skyline; Populus trichocarpa; Monolignol; N-linked glycans
MeSH headings : Computational Biology / standards; Computational Biology / trends; Polysaccharides / analysis; Populus / chemistry; Xylem / chemistry
TL;DR: This study presents a novel workflow for identification of glycans using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT™) strategy developed in the lab, and implements Skyline for relative glycan quantification for improved accuracy and precision of quantitative measurements over current processing tools. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 28(4), 729–732.

By: E. Hecht n, P. Loziuk n & D. Muddiman n 

author keywords: Xylose migration; MS/MS; Glycomics; N-linked glycans; Plants
TL;DR: This work reports the second instance of saccharide migration ever to occur for N-glycans, the first empirical observation of this rearrangement, and warrants dissemination so it may be searched in de novo sequencing glycan workflows. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein

ANALYTICAL BIOCHEMISTRY, 512, 114–119.

By: J. Parker  n, Y. Oh n, Y. Moazami n, J. Pierce n , P. Loziuk n, R. Dean n , D. Muddiman n 

author keywords: Ubiquitination; Gly-Gly enrichment; Enrichment efficiency
MeSH headings : Antibodies, Monoclonal, Murine-Derived / chemistry; Epitopes / chemistry; Muramidase / chemistry; Ubiquitinated Proteins / chemistry; Ubiquitination
TL;DR: It is shown that when conjugated to a lysine containing protein, such as lysozyme, it can be applied as a standard protein to examine ubiquitinated peptide enrichment within a complex background. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

TransOmic analysis of forebrain sections in Sp2 conditional knockout embryonic mice using IR-MALDESI imaging of lipids and LC-MS/MS label-free proteomics

Analytical and Bioanalytical Chemistry, 408(13), 3453–3474.

By: P. Loziuk n, F. Meier n, C. Johnson  n, H. Ghashghaei  n & D. Muddiman n 

author keywords: IR-MALDESI; Proteomics; Lipidomics; Mass spectrometry imaging; Embryonic brain
MeSH headings : Animals; Chromatography, Liquid / methods; Lipids / analysis; Mass Spectrometry / methods; Mice; Mice, Knockout; Prosencephalon / embryology; Prosencephalon / metabolism; Sp2 Transcription Factor / genetics; Spectrophotometry, Infrared / methods; Transcriptome
TL;DR: An integrated approach for systematic analysis of the “lipidome” in tissue revealed many specific changes to fundamental cellular processes and biosynthetic pathways in the cerebral cortices of Sp2-cKO embryos. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018

2015 journal article

4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa

MOLECULAR PLANT, 8(1), 176–187.

By: C. Lin n, J. Wang n , Q. Li *, H. Chen n, J. Liu  n, P. Loziuk n, J. Song  n, C. Williams n  ...

Contributors: C. Lin n, J. Wang n , Q. Li *, H. Chen n, J. Liu  n, P. Loziuk n, J. Song  n, C. Williams n  ...

author keywords: monolignol biosynthesis; Populus trichocarpa; metabolic flux; reaction and inhibition kinetics; LC-MS/MS; 4-coumaroyl and caffeoyl shikimic acids
MeSH headings : Acyl Coenzyme A / metabolism; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Hydroxylation / drug effects; Plant Proteins / metabolism; Populus / drug effects; Populus / enzymology; Populus / metabolism; Propionates; Shikimic Acid / pharmacology
TL;DR: 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr 4CL5, which can reduce lignin content in a number of plant species and play significant regulatory roles when these inhibitors accumulate. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa

JOURNAL OF PROTEOME RESEARCH, 14(10), 4158–4168.

By: P. Loziuk n, J. Parker  n, W. Li n, C. Lin n, J. Wang n , Q. Li *, R. Sederoff n, V. Chiang n, D. Muddiman n 

Contributors: P. Loziuk n, J. Parker  n, W. Li n, C. Lin n, J. Wang n , Q. Li *, R. Sederoff n, V. Chiang n, D. Muddiman n 

author keywords: shotgun discovery proteomics; absolute quantification; PC-IDMS; cellulose biosynthesis; transcription factor; targeted mass spectrometiry; SRM
MeSH headings : Carbohydrate Metabolism; Cellulose / biosynthesis; Cellulose / genetics; Chromatography, Liquid; Gene Expression Regulation, Plant; Molecular Sequence Annotation; Plant Proteins / genetics; Plant Proteins / isolation & purification; Plant Proteins / metabolism; Populus / genetics; Populus / metabolism; Proteome / genetics; Proteome / isolation & purification; Proteome / metabolism; Proteomics; Tandem Mass Spectrometry; Transcription Factors / genetics; Transcription Factors / isolation & purification; Transcription Factors / metabolism; Wood / chemistry; Wood / metabolism; Xylem / genetics; Xylem / metabolism
TL;DR: The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. (via Semantic Scholar)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Mechanisms of Egg Yolk Formation and Implications on Early Life History of White Perch (Morone americana)

PLOS ONE, 10(11).

By: J. Schilling n, P. Loziuk n, D. Muddiman n , H. Daniels n & B. Reading n 

MeSH headings : Animals; Bass / metabolism; Blotting, Western; Chromatography, Liquid; Egg Proteins / metabolism; Egg Yolk / metabolism; Female; Immunohistochemistry; Oocytes / cytology; Oocytes / metabolism; Ovary / cytology; Receptors, Cell Surface / metabolism; Sexual Maturation; Staining and Labeling; Tandem Mass Spectrometry; Vitellogenins / metabolism
TL;DR: The three white perch vitellogenins were quantified accurately and precisely in the liver, plasma, and ovary during pre-vitellogenic oocyte growth using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry

ANALYST, 139(21), 5439–5450.

By: P. Loziuk n, R. Sederoff n, V. Chiang n & D. Muddiman n 

MeSH headings : Chromatography, Liquid; Isotopes / chemistry; Proteins / analysis; Tandem Mass Spectrometry / methods
TL;DR: It is suggested that evaluation of the absolute ion abundance for any given transition is necessary in order to effectively implement RA thresholds, and these RA values should be assessed as close as possible to the time at which data is collected for quantification. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Enzyme-Modified Carbon-Fiber Microelectrode for the Quantification of Dynamic Fluctuations of Nonelectroactive Analytes Using Fast-Scan Cyclic Voltammetry

ANALYTICAL CHEMISTRY, 85(18), 8780–8786.

By: L. Lugo-Morales n, P. Loziuk n, A. Corder n, J. Toups n, J. Roberts n, K. McCaffrey n, L. Sombers n 

MeSH headings : Animals; Biosensing Techniques / methods; Carbon / chemistry; Carbon Fiber; Electrochemical Techniques / methods; Enzyme Induction; Male; Microelectrodes; Rats; Rats, Sprague-Dawley; Time Factors
TL;DR: This work has enabled the real-time detection of dynamic glucose fluctuations in live brain tissue using background-subtracted, fast-scan cyclic voltammetry, and quantitatively and selectively monitored pharmacologically evoked glucose fluctuations with unprecedented chemical and spatial resolution. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments

JOURNAL OF PROTEOME RESEARCH, 12(12), 5820–5829.

By: P. Loziuk n, J. Wang n , Q. Li n, R. Sederoff n, V. Chiang n & D. Muddiman n 

Contributors: P. Loziuk n, J. Wang n , Q. Li n, R. Sederoff n, V. Chiang n & D. Muddiman n 

author keywords: design of experiments; proteolytic digestion; LC-MS/MS; Populus trichocarpa
MeSH headings : Amino Acid Sequence; Animals; Cattle; Chromatography, Liquid / standards; Factor Analysis, Statistical; Hydrogen-Ion Concentration; Isotope Labeling; Molecular Sequence Annotation; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Plant Proteins / chemistry; Plant Proteins / isolation & purification; Populus / chemistry; Protein Stability; Proteolysis; Proteomics / methods; Proteomics / standards; Research Design; Swine; Tandem Mass Spectrometry / standards; Trypsin / chemistry; Xylem / chemistry
TL;DR: The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

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