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Purification Services at University
Covid-19 Impact on our Facility
Our facility is fully operational. However please note that other than self-service user training, communication is done by email or scheduling a virtal meeting. For full details on how we are maintaining a safe enviroment, please see our Covid-19 Safety Plan.
For customers wishing to submit samples or schedule time on an instrument, please first review our Policies and Procedures Manual then refer to the appropriate section of our website, either the Full Services or Self Services tab, for more detailed information.
As we continue to navigate this current situation, we will be posting updates on our website and twitter account, where we invite you to follow us.
Our Mission
The Proteomics and Metabolomics Facility (PMF) at the Center for Biotechnology was established in 2015 under the leadership of the Director, Dr. Sophie Alvarez and the Assistant Director, Dr. Mike Naldrett to meet ever increasing needs for a range of technical services using mass spectrometry, including identification and relative quantification of proteins and several advanced methods for profiling and quantitation of small molecules.
The primary aim of the PMF is to provide high quality service and collaborative work in the fields of Proteomics and Metabolomics to support scientists and students within our University community and around the world. Through this we strive to advance world-class research, support grant proposals, assist in the education of future scientists and support economic and scientific advancements. We offer both Full-Service and Self-Service options to meet the unique needs, time requirements and budgets of our users. Our outreach and education program includes workshops, seminars and courses.
On this site you will find detailed and up to date information about our offerings.
Full Service User Overview
A virtual consultation with the PMF Director is required prior to submitting samples to check for compatibility of sample type and format with our analytical approaches and to confirm the experimental approach and expectations for the services. Please review the Full Service Users section of our Policies and Procedures Manual for detailed instructions then complete our new Sample Submission Form. For local users, instructions to drop off samples can be found in our Users Covid-19 Safety Plan. For Metabolomics customers, instructions to properly prepare your samples for submission can be found in our Metabolomics Sample Prep document.
If you have any questions, you can find our contact information in the "PERSONNEL" tab. For pricing see the "SERVICE FEES" tab.
Full Service Offering
Proteomics services include:
- Bottom-up Proteomics of whole organisms, organs, organelles, tissues, cell pellets, pulldowns, complex or single protein mixes from solutions or gels.
- Quantification by label-free or multiplexed labeling techniques (eg TMT-10/16plex) with microscale subfractionation to increase coverage.
- Post Translational Modification Characterization especially phosphopeptide enrichment from whole organism digests, but also ubiquitylation, acetylation, etc.
- See "PROTEOMICS PLATFORM" tab for more information on our proteomics instrumentation.
Metabolomics services include:
- Untargeted Quantification of a wide range of small molecules
- Primary metabolism using GC-MS and NIST/Fiehn Libraries
- Secondary metabolism using LC-MS and Progenesis QI, NIST Library, mzCloud
- Targeted Quantification using HPLC or LCMS. See table below for a full list of compounds.
- See "METABOLOMICS PLATFORM" tab for more information on our metabolomics instrumentation.
| Targeted Primary Metabolites | |
| Polyamines | Putrescine, Spermine, Spermidine |
| Pyrimidine Pathway | ATP, GTP, dATP, dGTP, dCTP, UTP, dUTP, Uridine, UMP, UDP, dCDP, CTP, CDP, Cytidine, dUMP, Deoxyuridine, dTDP, Thymidine, dTTP, car-Asp, dTMP |
| Free Sugars | Fructose, Sucrose, Glucose, Raffinose, Arabinose, Mannose, Xylose, Galactose, Lactose, Pinitol, Trehalose |
| Free Amino Acids | Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val, Tau, GABA, Orn, HyPro |
| Hydrolyzed Amino Acids | Arg, Ile, Leu, Val, Phe, Tyr, Asp, Glu, MetS, CyA, Ser, Thr, Arg, His, Lys, Gly, Pro |
| TCA Cycle/ Glycolysis/ Pentose Phosphate Pathway | Pyruvic Acid, Glutamic Acid, Aconitate, Keto-Glutaric Acid, Lactic Acid, Fumaric Acid, Succinic Acid, Malic Acid, Phosphoenolpyruvate, Glyceraldehyde 3-phosphate, Dihydroxyacetone phosphate, L-Glycerol 3-phosphate, D-(-)-3-Phosphoglyceric Acid, D-(+)-2-Phosphoglyceric Acid, Citric Acid, Ribose-5-phosphate, Fructose-6-Phosphate, Glucose-6-Phosphate, Glucose-1-Phosphate, Fructose-1,6-Bisphosphate, Sedoheptulose-7-Phosphate, Succinyl Coenzyme A, Erythrose-4-Phosphate, Ribulose-5-Phosphate |
| Short Chain Fatty Acids | Acetic Acid, Formic Acid, Propionic Acid, Butyric Acid, Isobutyric Acid, 2-Methylbutanoic Acid, Valeric Acid, Isovaleric Acid, Hexanoic Acid |
| Fatty Acid Methyl Esters (FAMEs) | Methyl Octanoate, Methyl Decanoate, Methyl Laurate, Methyl Myristate, Methyl Palmitate, Methyl Palmitoleate, Methyl Stearate, Methyl Oleate, Methyl Linoleate, Methyl Arachidiate, Methyl Linoleate, Methyl Behenate, Methyl Erucate, Methyl Lignocerate |
| Targeted Secondary Metabolites | |
| Non-Mevalonate Pathway | DXP, MEP, CDP-ME, MEcPP, DMAPP, HDMAPP, IPP |
| Phytohormones (inclu. Gibberellins) | ABA, SA, JA, JA-Ile, OPDA, IAA, IAA-Asp, Methyl-IAA, IAA-Ala, IAA-Trp, t-Zeatin, c-Zeatin, t-ZRiboside, c-ZRiboside, Strigol, 5-Deoxystrigol, Orobanchol, DIMBOA, GA1, GA3, GA4, GA8, GA9, GA12, GA19, GA20, GA24, GA29, GA53 |
| Flavonoids and Phenolic Acids | Acacetin, Apigenin, Catechin, Chlorogenic Acid, Delphinidin, Daidzein, Epicatechin, Genistein, Hesperetin, Kaempferol, Luteolin, Naringenin, Phloretin, Proanthocyanidin A2, Procyanidin B2, Protocatechuic Acid, Quercetin-3-Glucoside, Quercetin-3-Galactoside, Chalconaringenin, Quercetin, Rutin, Syringic Acid, Vanillic Acid, Resveratrol, Caffeic Acid, Cinnamic Acid, p-Courmaric Acid, Ferulic Acid, Gallic Acid |
| Carotenoids/ Xantophylls | Zeaxanthin, Lutein, Antheraxanthin, Violaxanthin, Chlorophyll A, Chlorophyll B |
| Bile Acids | Cholic Acid, Chenodeoxycholic Acid, Deoxycholic Acid, Glycocholic Acid, Glycochenodeoxycholic Acid, Glycodeoxycholic Acid, Glycolithocholic Acid, Hyocholic Acid, Lithocholic Acid, Taurocholic Acid, Taurodeoxycholic Acid, Taurochenodeoxycholic Acid, Taurolithocholic Acid, Alpha-muricholic Acid, Beta-muricholic Acid, Omega-muricholic Acid |
| Alpha and Beta Acids | Cohumulone, Humulone, Adhumulone, Colupulone, Lupulone, Adlupulone |
Self Service User Overview
At the Nebraska Center for Biotechnology Proteomics and Metabolomics Facility, we offer our University of Nebraska users the opportunity to access our facility instrumentation for self-service work as a more cost effective alternative to our full-service offerings. It also allows users the chance to gain meaningful training and experience working with state-of-the-art mass spectrometry equipment.
To become a self-service user, a consultation meeting with the PMF Director is required to discuss the scope and feasibility of the intended project. The user will be expected to complete safety training, instrument training or familiarization (based on the user’s technical background), and successfully pass a proficiency test. Users will need to follow the approved method developed and agreed to during training, and get any changes approved by the Director. Users can book time on the instrument by emailing the Director to check on instrument availability.
Please refer to the self service user section of our new Policies and Procedures Manual for additional details and instructions. Changes to user expectations due to COVID-19 can be found in our Users Covid-19 Safety Plan.
If you have any questions, or want to start the process, you can find our contact information in the "PERSONNEL" tab. For pricing, see the "SERVICE FEES" tab.
Self Service Offering
Initial Training:
- Upon completion of their safety training courses, users can schedule a time to have one-on-one training on the instrument they desire to use. Group training is currently suspended due to COVID-19.
- As part of training, users will become proficient in the use of the instrument for their desired outcome, and will have assistance in developing their method.
- During training, users will be required to provide the materials necessary to set up their method, which will be developed as part of their training.
- Users can ask for additional training as needed over the course of their project.
Instruments Available for Self Service:
Sciex QTRAP 6500+ mass spectrometer with SelexION+ ion mobility coupled to Shimadzu Nexera II UHPLC- Targeted quantification of a wide range of small molecules.
- Up to 6 orders of detector dynamic range
- Polarity switching speeds of 5 msec
- Mass range 50-2000 m/z
- Scan speeds of up to 20,000 Da/second
- SelexION+ Differential Ion Mobility Technology for added selectivity
- UHPLC with extended pressure range up to 19,000 psi for the smallest particle columns
- Increased chromatographic reproducibility through use of micro-volume plungers
- Autosampler has multiple rinsing lines enabling low sample carry over
- High-speed injection
- Separation, profiling and quantification of a wide range of small molecules: PEG, dyes, vitamins, organic acids, carbohydrates, triglycerides, phospholipids, FAME, and more….
- Peptide and protein fractionation for proteomics applications.
- Flow rate range: 0.05 to 5 mL/min
- Pressure 1300 bar (18,800 psi)
- Multicolumn thermostat and multisampler
- DAD, ELSD and Fluorescence detector allowing detection of a wide range of compounds (absorbing, fluorescent, non-volatile, and semi-volatile compounds)
- Targeted and untargeted profiling and quantification of volatile compounds for food regulation, environmental analysis, forensic analysis, drug detection, research.
- Headspace sampler for analysis of volatile and semi-volatile compounds in solid, liquid and gas samples (without sample extraction)
- NIST and Fiehn GC-MS compound libraries for identification/confirmation of unknown volatile compounds
- Integrates with Mass Profiler Professional for qualitative and quantitative studies
Service Fees
Please contact us if you have any questions regarding the services offered and costs.
External users can pay their invoices via check, wire transfer or credit card. Wire transfer and credit card payments will incur additional fees.
| University Users | External Academic Users | Industry Users | |
| Full Service | |||
| HPLC Targeted Assay | $50/sample | $65/sample | $100/sample |
| LC-MS Targeted Assay | $65/sample | $120/sample | $180/sample |
| GC-MS Targeted Assay | $55/sample | $80/sample | $120/sample |
| LC-MS Untargeted Assay | $90/sample | $150/sample | $200/sample |
| GC-MS Untargeted Assay | $60/sample | $80/sample | $120/sample |
| Protein Identification-Low Complexity | $100/sample | $150/sample | $200/sample |
| Protein Identification-High Complexity | $180/sample | $220/sample | $280/sample |
| Quantitative Proteomics using Labeling or Label-Free | Contact us for quote | ||
| Phosphoenrichment and Phosphoproteomics | Contact us for quote | ||
| Targeted Metabolomics | Contact us for quote | ||
| Non-targeted metabolomics | Contact us for quote | ||
| Instrument Time UPLC | $25/hour | $50/hour | $100/hour |
| Instrument Time GC-MS | $25/hour | $50/hour | $100/hour |
| Instrument Time QTRAP | $80/hour | $115/hour | $150/hour |
| Instrument Time QE-HF | $80/hour | $115/hour | $150/hour |
| Instrument Time Eclipse | $80/hour | $115/hour | $150/hour |
| Method Development/Sample Preparation | $65/hour | $100/hour | $150/hour |
| Training/Data Analysis | $65/hour | $100/hour | $150/hour |
| Self Service* | |||
| Instrument Time UPLC | $12/hour | $45/hour | $65/hour |
| Instrument Time GC-MS | $15/hour | $45/hour | $65/hour |
| Instrument Time QTRAP | $20/hour | $60/hour | $80/hour |
| Training | $65/hour | $100/hour | $150/hour |
*Self-service instrument time rates only apply to users previously trained and checked off by facility staff.
IMPORTANT Note: Scientists must contact us before submitting samples to check for compatibility of sample type and format with our analytical approaches and to confirm the experimental approach and expectations for the services.
Policies and Procedures
We ask that all users review our facility Policies and Procedures Manual before submitting samples or scheduling self-service instrument time. You can link to the full document below.
Policies and Procedures ManualFull service Metabolomics users should review the document below which outlines how to prepare samples for submission. Samples that are not submitted correctly may require additional handling, which the customer will be charged for.
Metabolomics Sample PrepSelf-Service users wanting to schedule time on an instrument and Full-service users wishing to hand deliver samples should review the following document. It outlines the expectations and precautions we have put in place to keep our users and staff safe as we go forward with our work during this pandemic.
Users Covid-19 Safety PlanAdditionally, Self-Service Users are asked to read the policy for their instrument. Policies are linked below.
HPLC User PolicyQtrap User Policy
GCMS User Policy
Proteomics Platform
- Proteomics of whole organisms, organs, organelles, tissues, cell pellets, pulldowns, complex or single protein mixes from solutions or gels
- Quantification by label-free or multiplexed labeling (e.g., TMT-10/16plex) techniques with microscale sub-fractionation to increase coverage
- High resolution/high mass accuracy data for intact mass protein analysis
- Phosphoproteomics using TiO2 phosphopeptide enrichment
- Technological platforms supported by bioinformatics tools to process data and report results
- Post-translational modification characterization
❖ Thermo Orbitrap Eclipse Tribrid with FAIMS and ETD coupled to a Dionex U3000 RSLCnano
- Resolving power up to 500,000 FWHM
- MS acquisition rate up to 40 Hz
- Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
- Pressure to 800 bar (11,600 psi)
❖ Thermo Q-Exactive – High Field (QE-HF) coupled to Dionex U3000 nanoRSLC
- High Resolution/Accurate Mass (HR/AM) instrument
- Resolving power up to 240,000 at 200 m/z
- Sub ppm mass accuracy
- Scan speed of 18 Hz at 15,000 resolution
- Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
- Pressure to 800 bar (11,600 psi)
❖ Mascot 2.6.1 (Matrix Science Ltd) for protein identification from MS/MS spectra
❖ Proteome Discoverer 2.4 Search Engine (Thermo) for metabolic, isotope labeling and label free quantitative proteomics
❖ Scaffold 4.8.9 (Proteome Software) for protein identification, reporting and label-free quantitative proteomics
❖ PEAKS 8 (Bioinformatics Solutions Inc) for de novo sequencing and PTM characterization
Metabolomics Platform
❖ Sciex QTRAP 6500+ mass spectrometer with SelexION+ ion mobility coupled to Shimadzu Nexera II UHPLC
- Targeted quantification of a wide range of small molecules.
- Up to 6 orders of detector dynamic range
- Polarity switching speeds of 5 msec
- Mass range 50-2000 m/z
- Scan speeds of up to 20,000 Da/second
- SelexION+ Differential Ion Mobility Technology for added selectivity
- UHPLC with extended pressure range up to 19,000 psi for the smallest particle columns
- Increased chromatographic reproducibility through use of micro-volume plungers
- Autosampler has multiple rinsing lines enabling low sample carry over
- High-speed injection
❖ Agilent 1290 Infinity II UPLC
- Separation, profiling and quantification of a wide range of small molecules: PEG, dyes, vitamins, organic acids, carbohydrates, triglycerides, phospholipids, FAME, and more….
- Peptide and protein fractionation for proteomics applications.
- Flow rate range: 0.05 to 5 mL/min
- Pressure 1300 bar (18,800 psi)
- Multicolumn thermostat and multisampler
- DAD, ELSD and Fluorescence detector allowing detection of a wide range of compounds (absorbing, fluorescent, non-volatile, and semi-volatile compounds)
❖ Agilent GC-MS 5977A
- Targeted and untargeted profiling and quantification of volatile compounds for food regulation, environmental analysis, forensic analysis, drug detection, research.
- Headspace sampler for analysis of volatile and semi-volatile compounds in solid, liquid and gas samples (without sample extraction)
- NIST and Fiehn GC-MS compound libraries for identification/confirmation of unknown volatile compounds
- Integrates with Mass Profiler Professional for qualitative and quantitative studies
❖ Thermo Q-Exactive – High Field (QE-HF) coupled to Thermo Vanquish H binary UPLC
- Untargeted profiling and quantification of metabolitc compounds
- High Resolution/Accurate Mass (HR/AM) instrument
- Resolving power up to 240,000 at 200 m/z
- Sub ppm mass accuracy
- Scan speed of 18 Hz at 15,000 resolution
- Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
- Pressure to 800 bar (11,600 psi)
Workshops & Training
Self Service TrainingThe facility offers training for the walk-in equipment, including the Infinity II UPLC and QTRAP 6500+. Refer to the usage and sign-up policy documents here for more information.
Workshops, Seminars and CoursesEducational workshops and seminars are also organized by the facility throughout the year on a broad range of proteomics and metabolomics topics. See list below of educational workshops and seminars currently available.
- Nebraska Center for Biotechnology - Spring Course: Intro to UNL Core Facilities and Research Methods, offered each Spring Semester
- Women in Science
- Nebraska Center for Biotechnology - Summer Workshop, offered each July
See list below of previous educational workshops and seminars.
- Special Topics in Life Sciences: LIFE 491/891, Spring 2022
- Nebraska Center for Biotechnology - Summer Proteomics Workshop, July 15-16, 2019
- Metabolomics Workshop, May 9, 2017
- Waters seminar : Lunch and Learn, Method Development for (U)HPLC, July 26, 2016
- Mass Spectrometry-Based Proteomics Workshop, May 9-10, 2016
Contact Us
Dr. Sophie Alvarez, Director
E154 Beadle Center
Phone: 402-472-4575
Email Dr. Alvarez
Publications for Dr. Alvarez
Dr. Mike Naldrett, Assistant Director
E154 Beadle Center
Phone: 402-472-4575
Email Dr. Naldrett
Publications for Dr. Naldrett
Anne Fischer, Lab Manager
E145 Beadle Center
Email Anne
Rosimeire Barboza Bispo, Graduate Student Worker
Carrigan Hurst, Undergraduate Student Worker
Juliana Gonzalez Ronseria, Undergraduate Student Worker
Shipping Address
Sophie Alvarez
University of Nebraska – Lincoln
E-119 Beadle Center
1901 Vine St
Lincoln, NE 68588
Previous Lab Members
Alivia Bechler (August 2022 - May 2023)
Lori Loucks (August 2019 - September 2022)
Felicia Phares (May 2017 - August 2021)
Danh Vu (October 2018 - December 2019)
Aaron Decker (May 2018 - January 2020)
Chase Kimberling
Bryce Sebada
Publication Acknowledgement
We ask users to include the sentence below in the acknowledgement of their publications when results from our facility are being used. We also strongly recommend contacting us before submitting any publications to request a detailed description of the methodology used to include in the Method section.
We thank the Proteomics & Metabolomics Facility (RRID:SCR_021314), Nebraska Center for Biotechnology at the University of Nebraska-Lincoln for the mass spectrometry analysis. The facility and instrumentation are supported by the Nebraska Research Initiative.
Publication List
Below are the publications which our facility provided collaboration or assistance on through the services that our facility offers. For a full list of publications co-authored by individuals on our team, see the personnel page.
2024
Hayer SS, Conrin M, French JA, Benson AK, Alvarez S, Cooper K, Fischer A, Alsafwani ZW, Gasper W, Suhr Van Haute MJ, Hassenstab HR, Azadmanesh S, Briardy M, Gerbers S, Jabenis A, Thompson JL, Clayton JB. Antibiotic-induced gut dysbiosis elicits gut-brain axis relevant multi-omic signatures and behavioral and neuroendocrine changes in a nonhuman primate model. Gut Microbes. 2024 Jan- Dec;16(1):2305476. PubMed PMID: 38284649.
Nolasco E, Baraka E, Yang J, Ciftci ON, Majumder K. In-vitro bio- accessibility and antioxidant activity of commercial standard and enriched whole egg compounds influenced by production and domestic cooking practices. Food Chem. 2024 Jan 1;430:136948. PubMed PMID: 37542967.
2023
Hao J, Yang Y, Futrell S, Kelly EA, Lorts CM, Nebie B, Runo S, Yang J, Alvarez SA, Lasky JR, Schachtman DP. CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase (CCD) genes in sorghum alters strigolactone biosynthesis and plant biotic interactions. Phytobiomes J. 2023 7:3, 339-351. PubMed PMID: 29614837.
Olanrewaju GO, Haveman NJ, Naldrett MJ, Paul AL, Ferl RJ, Wyatt SE. Integrative transcriptomics and proteomics profiling of Arabidopsis thaliana elucidates novel mechanisms underlying spaceflight adaptation. Front Plant Sci. 2023 Nov 27;14:1260429. PubMed PMID: 38089794.
Ogbu CP, Kapoor S, Vecchio AJ. Structural basis of Clostridium perfringens enterotoxin activation and oligomerization by trypsin. Toxins (Basel). 22023 Oct 31;15(11):637. PubMed PMID: 37999500.
Liu B, Nguyen PL, Yu H, Li X, Wang H, Price J, Niu M, Guda C, Cheng X, Sun X, Moreau R, Ramer-Tait A, Naldrett MJ, Alvarez S, Yu J. Critical contributions of protein cargos to the functions of macrophage-derived extracellular vesicles. Nanobiotechnology. 2023 Sep 28;21(1):352. PubMed PMID: 37770932.
Palmer NA, Alvarez S, Naldrett MJ, Muhle A, Sarath G, Edmé SJ, Tatineni S, Mitchell RB, Yuen G. Dynamic reconfiguration of switchgrass proteomes in response to rust (Puccinia novopanici) infection. Int J Mol Sci. 2023 Sep 27;24(19):14630. PubMed PMID: 37834079.
Can H, Chanumolu SK, Nielsen BD, Alvarez S, Naldrett MJ, Ünlü G, Otu HH. Integration of meta-multi-omics data using probabilistic graphs and external knowledge. Cells. 2023 Aug 4;12(15):1998. PubMed PMID: 37566077.
Hao G, Naumann TA, Chen H, Bai G, McCormick S, Kim H, Tian B, Trick HN, Naldrett MJ, Proctor R. Fusarium graminearum effector FgNls1 targets plant nuclei to induce wheat head blight. Mol Plant Microbe Interact. Aug;36(8):478-488. PubMed PMID: 36853197.
Matthes, M. S., Best, N. B., Robil, J. M., & McSteen, P. Enhancement of developmental defects in the boron-deficient maize mutant tassel-less1 by reduced auxin levels. J Plant Nutr Soil Sci. 2023; 00, 1–10. Link to Article.
Li G, Gong Z, Dulal N, Marroquin-Guzman M, Rocha RO, Richter M, Wilson RA. A protein kinase coordinates cycles of autophagy and glutaminolysis in invasive hyphae of the fungus Magnaporthe oryzae within rice cells. Nat Commun. 2023 Jul 12;14(1):4146. PubMed PMID: 37438395.
Heinis FI, Alvarez S, Andrews MT. Mass spectrometry of the white adipose metabolome in a hibernating mammal reveals seasonal changes in alternate fuels and carnitine derivatives. Front Physiol. 2023 Jun 28;14:1214087. PubMed PMID: 37449012.
Newton A, Majumder K. Germination and simulated gastrointestinal digestion of chickpea (Cicer arietinum L.) in exhibiting in vitro antioxidant activity in gastrointestinal epithelial cells. Antioxidants (Basel). 2023 May 18;12(5):1114. PubMed PMID: 37237980.
Palmer NA, Sarath G, Bowman MJ, Saathoff AJ, Edmé SJ, Mitchell RB, Tobias CM, Madhavan S, Scully ED, Sattler SE. Divergent metabolic changes in rhizomes of lowland and upland switchgrass (Panicum virgatum) from early season through dormancy onset. Plants (Basel). 2023 Apr 21;12(8):1732. PubMed PMID: 37111955.
Dunigan DD, Agarkova IV, Esmael A, Alvarez S, Van Etten JL. Early-phase drive to the precursor pool: Chloroviruses dive into the deep end of nucleotide metabolism. Viruses. 2023 Mar 31;15(4):911. PubMed PMID: 37112891.
Lopes LD, Futrell SL, Bergmeyer E, Hao J, Schachtman DP. Root exudate concentrations of indole-3-acetic acid (IAA) and abscisic acid (ABA) affect maize rhizobacterial communities at specific developmental stages. FEMS Microbiol Ecol. 2023 Feb 28;99(3):fiad019. PubMed PMID: 36861302.
Akey ME, Xu R, Ravindran S, Funkhouser-Jones L, Sibley LD. Apical secretory glycoprotein complex contributes to cell attachment and entry by Cryptosporidium parvum. mBio. 2023 Feb 28;14(1):e0306422. PubMed PMID: 36722968.
2022
Nguyen THD, Vu DC, Alvarez S, Nguyen KD, Nguyen TLT, Tuan NN, Minh-Nguyet NT, Tam LN, Ho TL, Vo XT. Comparative examination of phytonutrients and antioxidant activity of commonly consumed nuts and seeds grown in Vietnam. Horticulturae. 2022; 8(6):521. Link to Abstract.
Zhang B, Lewis JA, Vermerris W, Sattler SE, Kang C. A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids. Plant Physiol. 2022 Dec 28:kiac604. PubMed PMID: 36575825.
Sun G, Wase N, Shu S, Jenkins J, Zhou B, Torres-Rodríguez JV, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Pedersen C, Gottilla T, Foltz A, Yu H, O'Malley R, Zhang C, Devos KM, Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nat Commun. 2022 Dec 13;13(1):7731. PubMed PMID: 36513676.
He X, Gao T, Chen Y, Liu K, Guo J, Niu W. Genetic code expansion in Pseudomonas putida KT2440. ACS Synth Biol. 2022 Nov 18;11(11):3724-3732. PubMed PMID: 36287825.
Ashkarran AA, Gharibi H, Voke E, Landry MP, Saei AA, Mahmoudi M. Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities. Nat Commun. 2022 Nov 3;13(1):6610. PubMed PMID: 36329043.
Grzybowski MW, Zwiener M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC. Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC Plant Biol. 2022 Sep 9;22(1):433. PubMed PMID: 36076172.
Grover S, Cardona JB, Zogli P, Alvarez S, Naldrett MJ, Sattler SE, Louis J. Reprogramming of sorghum proteome in response to sugarcane aphid infestation. Plant Sci. 2022 Jul;320:111289. PubMed PMID: 35643611.
Lou X, Xiong J, Tian H, Yu H, Chen C, Huang J, Yuan H, Hanna M, Yuan L, Xu H. Effect of high-pressure processing on the bioaccessibility of phenolic compounds from cloudy hawthorn berry (Crataegus pinnatifida) juice. J Food Compost Anal. 2022 Jul;110. Link to Article.
Ray S, Chee L, Zhou Y, Schaefer MA, Naldrett MJ, Alvarez S, Woods NT, Hewitt KJ. Functional requirements for a Samd14-capping protein complex in stress erythropoiesis. Elife. 2022 Jun 17;11:e76497. PubMed PMID: 35713400.
Wang P, Lopes LD, Lopez-Guerrero MG, van Dijk K, Alvarez S, Riethoven JJ, Schachtman DP. Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes. J Exp Bot. 2022 May 11;erac202. PubMed PMID: 35552399.
Matthes MS, Darnell Z, Best NB, Guthrie K, Robil JM, Amstutz J, Durbak A, McSteen P. Defects in meristem maintenance, cell division, and cytokinin signaling are early responses in the boron deficient maize mutant tassel-less1. Physiol Plant. 2022 Mar;174(2):e13670. PubMed PMID: 35292977.
Moss WJ, Patterson CE, Jochmans AK, Brown KM. Functional analysis of the expanded phosphodiesterase gene family in Toxoplasma gondii tachyzoites. mSphere. 2022 Feb 23:7(1):e0079321. PubMed PMID: 35107337.
Grover S, Puri H, Xin Z, Sattler S, Louis J. Dichotomous role of jasmonic acid in modulating sorghum defense against aphids. Mol Plant-Microbe Interact. 2022:Online ahead of print. PubMed PMID: 35394339.
Lopez-Guerrero MG, Wang P, Phares F, Schachtman DP, Alvarez S, Van Dijk K. A glass bead semi-hydroponic system for intact maize root exudate analysis and phenotyping. Plant Methods. 2022;18(25). PubMed PMID: 35246193.
Moss WJ, Patterson CE, Jochmans AK, Brown KM. Functional analysis of the expanded phosphodiesterase gene family in Toxoplasma gondii tachyzoites. Mol Cell Biol. 2022;7(1). PubMed PMID: 35107337.
Polyanskaya SA, Moreno RY, Lu B, Feng R, Yao Y, Irani S, Klingbeil O, Yang Z, Wei Y, Demerdash OE, Benjamin LA, Weiss MJ, Zhang YJ, Vokac CR. SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia. Cell Reports. 2022;38(2). PubMed PMID: 35021089.
2021
Nolasco E, Naldrett MJ, Alvarez S, Johnson PE, Majumder K. Bioactivity of cooked standard and enriched whole eggs from White Leghorn and Rhode Island Red in exhibiting in-vitro antioxidant and ACE-inhibitory effects. Nutrients. 2021;13(12):4232. Link to Article.
Bandyopadhyay M, Guha S, Naldrett MJ, Alvarez S, Majumder K. Evaluating the effect of high-pressure processing in contrast to boiling on the antioxidant activity from alcalase hydrolysate of Great Northern Beans (Phaseolus vulgaris). J Food Biochem. 2021 Nov 18:e14004. PubMed PMID: 34792196.
Vu DC, Alvarez S. Phenolic, carotenoid and saccharide compositions of Vietnamese Camellia sinensis teas and herbal teas. Molecules. 2021,26(21):6496. Link to Article.
Liu B, Li X, Yu H, Shi X, Zhou Y, Alvarez S, Naldrett MJ, Kachman SD, Ro SH, Sun X, Chung S, Jing L, Yu J. Therapeutic potential of garlic chive-derived vesicle-like nanoparticles in NLRP3 inflammasome-mediated inflammatory diseases. Theranostics. 2021;11(19):9311-30. PubMed PMID: 34646372.
Vu DC, Vu QT, Huynh L, Lin C-H, Alvarez S, Vo XT, Nguyen THD. Evaluation of fatty acids, phenolics and bioactivities of spent coffee grounds prepared from Vietnamese coffee. Int J Food Prop. 2021,24:1,1548-58. Link to Article.
Rosenberg A, Sibley LD. Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis. Cell Host Microbe. 2021 Jul 14;29(7):1186-1198.e8. PubMed PMID: 34043960.
Wang X, Fu Y, Deatty WL, Ma M, Brown A, Sibley LD, Zhang R. Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins. Nature Comm. 2021 May 24;12:3065. PubMed PMID: 34031406.
Alvarez S, Naldrett MJ. Mass spectrometry based untargeted metabolomics for plant systems biology. Emerg Top Life Sci. 2021 May 21;5(2):189-201. PubMed PMID: 33704399.
Nolasco E, Yang J, Ciftci O, Vu DC, Alvarez S, Purdum S, Majumder K. Evaluating the effect of cooking and gastrointestinal digestion in modulating the bio-accessibility of different bioactive compounds of eggs. Food Chem. 2021 May 15;344:128623. PubMed PMID:33221100.
Guha S, Alvarez S, Majumder K. Transport of Dietary Anti-Inflammatory Peptide, γ-Glutamyl Valine (γ-EV), across the Intestinal Caco-2 Monolayer. Nutrients. 2021 Apr 24;13(5):1448. PubMed PMID: 33923345.
King HM, Rana S, Kubica SP, Mallareddy JR, Kizhake S, Ezell EL, Zahid M, Naldrett MJ, Alvarez S, Law HC, Woods NT, Natarajan A. Aminopyrazole based CDK9 PROTAC sensitizes pancreatic cancer cells to venetoclax. Bioorg Med Chem Lett. 2021 Apr 23;43:128061. PubMed PMID: 33895280.
Liu E, Segato F, Wilkins MR. Fed-batch production of Thermothelomyces thermophilus lignin peroxidase using a recombinant Aspergillus nidulans strain in stirred-tank bioreactor. Bioresour Technol. 2021 Apr;325. PubMed PMID: 33461124.
Casey CA, Donohue TM Jr, Kubik JL, Kumar V, Naldrett MJ, Woods NT, Frisbie CP, McNiven MA, Thomes PG. Lipid droplet membrane proteome remodeling parallels ethanol-induced hepatic steatosis and its resolution. J Lipid Res. 2021 Feb 20;62:100049. PubMed PMID: 33617872.
Chen X, Liu B, Li X, An TT, Zhou Y, Li G, Wu-Smart J, Alvarez S, Naldrett MJ, Eudy J, Kubik G, Wilson RA, Kachman SD, Cui J, Yu J. Identification of anti-inflammatory vesicle-like nanoparticles in honey. J Extracell Vesicles. 2021 Feb;10(4):e12069. PubMed PMID: 33613874.
2020
Rao PS, Nolasco E, Handa A,Naldrett MJ, Alvarez S, Majumder K. Effect of pH and Heat Treatment on the Antioxidant Activity of Egg White Protein-Derived Peptides after Simulated In-Vitro Gastrointestinal Digestion. Antioxidants (Basel). 2020 Nov 11;9(11):1114. PubMed PMID: 33187320.
Liu E, Wilkins MR. Process optimization and scale-up production of fungal aryl alcohol oxidase from genetically modified Aspergillus nidulans in stirred-tank bioreactor. Bioresour Technol. 2020 Nov;315. PubMed PMID: 32659422.
Pingault L, Palmer NA, Koch KG, Heng-Moss T, Bradshaw JD, Seravalli J, Twigg P, Louis J, Sarath G. Differential defense responses of upland and lowland switchgrass cultivars to a cereal aphid pest. Int J Mol Sci. 2020 Oct 27;21(21):7966. PubMed PMID: 33120946.
Grover S, Agpawa E, Sarath G, Sattler SE, Louis J. Interplay of phytohormones facilitate sorghum tolerance to aphids. Plant Mol Biol. 2020 Oct 15. PubMed PMID: 33063221.
Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. J Exp Bot. 2020 Oct 7;71(19):5880-5895. PubMed PMID: 32667993.
Zogli P, Alvarez S, Naldrett MJ, Palmer NA, Koch KG, Pingault L, Bradshaw JD, Twigg P, Heng-Moss TM, Louis J, Sarath G. Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum). Sci Rep. 2020 Sep 9;10(1):14842. PubMed PMID: 32908168.
Lou X, Xu H, Hanna M, Yuan L. Identification and quantification of free, esterified, glycosylated and insoluble-bound phenolic compounds in hawthorn berry fruit (Crataegus pinnatifida) and antioxidant activity evaluation. LWT. 2020 Aug;130:109643. Link to Article.
Guha S, Paul C, Alvarez S, Mine Y, Majumder K. Dietary γ-glutamyl valine ameliorates TNF-α-induced vascular inflammation via endothelial calcium-sensing receptors. J Agric Food Chem. 2020 Aug 26;68(34):9139-9149. PubMed PMID: 32786865.
Naumann TA, Naldrett MJ, Prince NPJ. Kilbournase, a protease-associated domain subtilase secreted by the fungal corn pathogen Stenocarpella maydis. Fungal Genet Biol. 2020 Aug;141:103399. PubMed PMID: 32387407.
Edwards RL, Heueck I, Lee SG, Shah IT, Miller JJ, Jezewski AJ, Mikati MO, Wang X, Brothers RC, Heidel KM, Osbourn DM, Burnham CAD, Alvarez S, Fritz SA, Dowd CS, Jez JM, Odom John AR. Potent, specific MEPicides for treatment of zoonotic staphylococci. PLoS Pathog. 2020 Jun 4;16(6):e1007806. PubMed PMID: 32497104.
Rahman H, Rudrow A, Carneglia J, Joly SP, Nicotera D, Naldrett MJ, Choy J, Ambudkar SV, Golin J. Nonsynonymous Mutations in Linker-2 of the Pdr5 Multidrug Transporter Identify a New RNA Stability Element. G3 (Bethesda). ). 2020 Jan 7;10(1):357-369. PubMed PMID: 31757931.
2019
Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM. Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid. J Biol Chem. 2019 Nov 8;294:16855-16864. PubMed PMID: 31575658.
Obasa K, Adesemoye A, Obasa R, Moraga-Amador D, Shinogle H, Alvarez S, Kelley K. Endohyphal bacteria associated with virulence, increased expression of fumonisin biosynthetic genes, and production of fumonisin and macroconidia in Fusarium fujikuroi W343. Plant Path. 2019 Oct 12: 69(1). Link to Article.
Lagundžin D, Hu WF, Law HCH, Krieger KL, Qiao F, Clement EJ, Drincic AT, Nedić O, Naldrett MJ, Alvarez S, Woods NT. Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome. PLoS One. 2019 Aug 28;14(8):e0220568. PubMed PMID: 31461451.
Hankore ED, Zhang L, Chen Y, Liu K, Niu W, Guo J. Genetic Incorporation of Noncanonical Amino Acids Using Two Mutually Orthogonal Quadruplet Codons. ACS Synth Biol. 2019 May 17;8(5):1168-1174. PubMed PMID: 30995842.
Graham LC, Naldrett MJ, Kohama SG, Smith C, Lamont DJ, McColl BW, Gillingwater TH, Skehel P, Urbanski HF, Wishart TM. Regional Molecular Mapping of Primate Synapses during Normal Healthy Aging. Cell Rep. 2019 Apr 23;27(4):1018-1026.e4. PubMed PMID: 31018120.
Varsani S, Grover S, Zhou S, Koch KG, Huang PC, Kolomiets MV, Williams WP, Heng-Moss T, Sarath G, Luthe DS, Jander G, Louis J. 12-Oxo-Phytodienoic Acid Acts as a Regulator of Maize Defense against Corn Leaf Aphid. Plant Physiol. 2019 Apr;179(4):1402-1415. PubMed PMID: 30643012.
Graybosch r, Bai G, Amand PS, Sarath G. Persistence of rye (Secale cereale L.) chromosone arm 1RS in wheat (Triticum aestivum L.) breeding programs of the Great Plains of North America. Gen Res Crop Evol. 2019 Apr 1;66 (4):941-950. Link to Article.
Kim WS, Krishnan HB. Impact of co-expression of maize 11 and 18 kDa δ-zeins and 27 kDa γ-zein in transgenic soybeans on protein body structure and sulfur amino acid content. Plant Sci. 2019 Mar;280:340-347. PubMed PMID: 30824013.
Shihabudeen Haider Ali MS, Cheng X, Moran M, Haemmig S, Naldrett MJ, Alvarez S, Feinberg MW, Sun X. LncRNA Meg3 protects endothelial function by regulating the DNA damage response. Nucleic Acids Res. 2019 Feb 20;47(3):1505-1522. PubMed PMID: 30476192.
Zapf RL, Wiemels RE, Keogh RA, Holzschu DL, Howell KM, Trzeciak E, Caillet AR, King KA, Selhorst SA, Naldrett MJ, Bose JL, Carroll RK. The Small RNA Teg41 Regulates Expression of the Alpha Phenol-Soluble Modulins and Is Required for Virulence in Staphylococcus aureus. mBio. 2019 Feb 5;10(1). PubMed PMID: 30723124.
Shah SB, Parmiter D, Constantine C, Elizalde P, Naldrett M, Karpova TS, Choy JS. Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics. 2019 Feb;211(2):531-547. PubMed PMID: 30546002.
Pan M, Li M, Li L, Song Y, Hou L, Zhao J, Shen B. Identification of Novel Dense-Granule Proteins in Toxoplasma gondii by Two Proximity-Based Biotinylation Approaches. J Proteome Res. 2019 Jan 4;18(1):319-330. PubMed PMID: 30362762.
Palmer NA, Basu S, Heng-Moss T, Bradshaw JD, Sarath G, Louis J. Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass. PLoS One. 2019;14(6):e0218352. PubMed PMID: 31194847.
2018
Wang X, Edwards RL, Ball H, Johnson C, Haymond A, Girma M, Manikkam M, Brothers RC, McKay KT, Arnett SD, Osbourn DM, Alvarez S, Boshoff HI, Meyers MJ, Couch RD, Odom John AR, Dowd CS. MEPicides: α,β-Unsaturated Fosmidomycin Analogues as DXR Inhibitors against Malaria. J Med Chem. 2018 Oct 11;61(19):8847-8858. PubMed PMID: 30192536.
Chapman KM, Marchi-Werle L, Hunt TE, Heng-Moss TM, Louis J. Abscisic and Jasmonic Acids Contribute to Soybean Tolerance to the Soybean Aphid (Aphis glycines Matsumura). Sci Rep. 2018 Oct 11;8(1):15148. PubMed PMID: 30310120.
Beltrán J, Wamboldt Y, Sanchez R, LaBrant EW, Kundariya H, Virdi KS, Elowsky C, Mackenzie SA. Specialized Plastids Trigger Tissue-Specific Signaling for Systemic Stress Response in Plants. Plant Physiol. 2018 Oct;178(2):672-683. PubMed PMID: 30135097.
Garcia Tavares R, Lakshmanan P, Peiter E, O'Connell A, Caldana C, Vicentini R, Soares JS, Menossi M. ScGAI is a key regulator of culm development in sugarcane. J Exp Bot. 2018 Jul 18;69(16):3823-3837. PubMed PMID: 29767776.
Shang X, Chen Y, Wang N, Niu W, Guo J. Oxidation-induced generation of a mild electrophile for proximity-enhanced protein-protein crosslinking. Chem Commun (Camb). 2018 Apr 19;54(33):4172-4175. PubMed PMID: 29629441.
Long S, Brown KM, Sibley LD. CRISPR-mediated Tagging with BirA Allows Proximity Labeling in Toxoplasma gondii. Bio Protoc. 2018 Mar 20;8(6). PubMed PMID: 29644258.
Kesinger E, Liu J, Jensen A, Chia CP, Demers A, Moriyama H. Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. PLoS One. 2018;13(6):e0199227. PubMed PMID: 29927982.
2017
Long S, Anthony B, Drewry LL, Sibley LD. A conserved ankyrin repeat-containing protein regulates conoid stability, motility and cell invasion in Toxoplasma gondii. Nat Commun. 2017 Dec 21;8(1):2236. PubMed PMID: 29269729.
Shang X, Lai R, Song X, Li H, Niu W, Guo J. An Improved Photoinduced Fluorogenic Alkene-Tetrazole Reaction for Protein Labeling. Bioconjug Chem. 2017 Nov 15;28(11):2859-2864. PubMed PMID: 29022697.
Liu K, Enns B, Evans B, Wang N, Shang X, Sittiwong W, Dussault PH, Guo J. A genetically encoded cyclobutene probe for labelling of live cells. Chem Commun (Camb). 2017 Sep 21;53(76):10604-10607. PubMed PMID: 28902227.
Ross KC, Andrews AJ, Marion CD, Yen TJ, Bhattacharjee V. Identification of the Serine Biosynthesis Pathway as a Critical Component of BRAF Inhibitor Resistance of Melanoma, Pancreatic, and Non-Small Cell Lung Cancer Cells. Mol Cancer Ther. 2017 Aug;16(8):1596-1609. PubMed PMID: 28500236.
Long S, Brown KM, Drewry LL, Anthony B, Phan IQH, Sibley LD. Calmodulin-like proteins localized to the conoid regulate motility and cell invasion by Toxoplasma gondii. PLoS Pathog. 2017 May;13(5):e1006379. PubMed PMID: 28475612.
Belayneh HD, Wehling RL, Reddy AK, Cahoon EB, Ciftci ON. Ethanol-modified supercritical carbon dioxide extraction of the bioactive lipid components of Camelina sativa seed. Seed. J Am Oil Chem Soc. 2017 Apr;94:855-865. Link to Article.
Belayneh HD, Wehling RL, Cahoon EB, Ciftci ON. Lipid composition and emulsifying properties of Camelina sativa seed lecithin. Food Chem. 2017 Aug;242:139-146. Link to Article.
Khasin M. Phytohormone signaling in Chlorella sorokiniana: perspectives on the evolution of plant cell-to-cell signaling Dissertations and Theses in Biological Sciences. 2017 Apr;95. Link to Article.
Gulati P, Li A, Holding D, Santra D, Zhang Y, Rose DJ. Heating Reduces Proso Millet Protein Digestibility via Formation of Hydrophobic Aggregates. J Agric Food Chem. 2017 Mar 8;65(9):1952-1959. PubMed PMID: 28198183.
Belayneh HD, Wehling RL, Cahoon EB, Ciftci ON. Effect of Extraction Method on the Oxidative Stability of Camelina Seed Oil Studied by Differential Scanning Calorimetry. J Food Sci. 2017 Mar;82(3):632-637. PubMed PMID: 28182838.
Shang X, Song X, Faller C, Lai R, Li H, Cerny R, Niu W, Guo J. Fluorogenic protein labeling using a genetically encoded unstrained alkene. Chem Sci. 2017 Feb 1;8(2):1141-1145. PubMed PMID: 28451254.
Deniz Ciftci, PhD Thesis: Subcritical Water-Assisted Fractionation of Lupin Hull for Production of Cellulose Nanofiber Hydrogels and Aerogels. 2017. Link to Article.
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