Research News, The Klein Omics Lab

Research

The Klein Omics Lab’s current research deals with a range of topics, involving metabolomics and machine learning, most namely the detection and identification of food microbes, studies on metabolic effects of functional foods, metabolic aspects of gut microbiota dysbiosis, metabolomics analyses on maternal health, and metabolism studies of mosquito diapause.

News

I am happy to share that our paper on markers of milk storage was selected as one of 8 Hot Topic Papers Published in 2021 in the “Food Metabolomics” Section: https://www.mdpi.com/journal/metabolites/announcements/5546
Congratulations especially to Kara and Aishwarya, who planned and performed these thought-out experiments!

I feel honored to be awarded an ECM Lightning Talk Award for my presentation on pathogen detection using metabolomics and deep learning at MANA21, the annual conference of the Metabolomics Association of North America: https://twitter.com/MetabolomicsANA/status/1451620203125620737

Journal Articles

Wang, D.; Greenwood, P.; Klein, M.S., “Feature Impact Assessment: A New Score to Identify Relevant Metabolomics Features in Artificial Neural Networks Using Validated Labels” Metabolomics 19 (2023) 22, https://doi.org/10.1007/s11306-023-01996-x

Wang, D.; Greenwood, P.; Klein, M.S., “Deep Learning for Rapid Identification of Microbes Using Metabolomics Profiles” Metabolites 11 (2021) 863, https://doi.org/10.3390/metabo11120863

Edwards, K.M.; Badiger, A.; Heldman, D.R.; Klein, M.S., “Metabolomic Markers of Storage Temperature and Time in Pasteurized Milk” Metabolites 11 (2021) 419, https://doi.org/10.3390/metabo11070419

Shearer, J.; Klein, M.S.; Vogel, H.J.; Mohammad, S.; Bainbridge, S.; Adamo, K.B., “Maternal and Cord Blood Metabolite Associations with Gestational Weight Gain and Pregnancy Health Outcomes” Journal of Proteome Research 20 (2021) 1630-1638, https://doi.org/10.1021/acs.jproteome.0c00854

Wang, D.; Greenwood, P.; Klein, M.S., “A Protein-free Chemically Defined Medium for the Cultivation of Various Microorganisms with Food Safety Significance” Journal of Applied Microbiology 131 (2021) 44-854, https://doi.org/10.1111/jam.15005

Huck, D.T.; Klein, M.S.; Meuti, M.E., “Determining the Effects of Nutrition on the Reproductive Physiology of Male Mosquitoes” Journal of Insect Physiology 129 (2021) 104191,

https://doi.org/10.1016/j.jinsphys.2021.104191

Klein, M.S., “Affine Transformation of Negative Values for NMR Metabolomics Using the mrbin R Package” Journal of Proteome Research 20 (2021) 1397-1404, https://doi.org/10.1021/acs.jproteome.0c00684

Shearer, J.; Reimer, R.A.; Hittel, D.S.; Gault, M.A.; Vogel, H.J.; Klein M.S., “Caffeine-Containing Energy Shots Cause Acute Impaired Glucoregulation in Adolescents” Nutrients 12 (2020) 3850, https://doi.org/10.3390/nu12123850

Lee, A.H.; Dhingra, S.K.; Lewis, I.A.; Singh, M.K.; Siriwardana, A.; Dalal, S.; Rubiano, K.; Klein, M.S.; Baska, K.S.; Krishna, S.; Klemba, M. et al., “Evidence for Regulation of Hemoglobin Metabolism and Intracellular Ionic Flux by the Plasmodium falciparum Chloroquine Resistance Transporter” Scientific Reports 8 1 (2018) 13578, https://doi.org/10.1038/s41598-018-31715-9

Newell, C.; Sabouny, R.; Hittel, D.S.; Shutt, T.E.; Khan, A.; Klein, M.S.; Shearer, J., “Mesenchymal stem cells shift mitochondrial dynamics and enhance oxidative phosphorylation in recipient cells” Frontiers in Physiology 9 (2018) 1572, https://doi.org/10.3389/fphys.2018.01572

Schober, D.; Jacob, D.; Wilson, M.; Cruz, J.A.; Marcu, A.; Grant, J.R.; Moing, A.; Deborde, C.; de Figueiredo, L.F.; Haug K.; Rocca-Serra, P.; Easton, J.; Ebbels, T.M.D.; Hao, J.; Ludwig, C. et al., “nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.” Anal Chem 90 1 (2018) 649-656, https://doi.org/10.1021/acs.analchem.7b02795

Newell, C.; Johnsen, V.L.; Yee, N.C.; Xu, W.J.; Klein, M.S.; Khan, A.; Rho, J.M.; Shearer, J., “Ketogenic diet leads to O-GlcNAc modification in the BTBRT+tf/j mouse model of autism.” Biochim Biophys Acta Mol Basis Dis 1863 9 (2017) 2274-2281, https://doi.org/10.1016/j.bbadis.2017.05.013

Lu, W.; Su, X.; Klein, M.S.; Lewis, I.A. et al., “Metabolite measurement: Pitfalls to avoid and practices to follow” Annual Review of Biochemistry 86 (2017) 277-304, https://doi.org/10.1146/annurev-biochem-061516-044952

Beatty, P.H.; Klein, M.S.; Fischer, J.J.; Lewis, I.A. et al., “Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches.” Plants (Basel) 5 4 (2016), https://doi.org/10.3390/plants5040039

Klein, M.S.; Shearer, J., “Metabolomics and Type 2 Diabetes: Translating Basic Research into Clinical Application.” J Diabetes Res 2016 (2016) 3898502, https://doi.org/10.1155/2016/3898502

Klein, M.S.; Newell, C.; Bomhof, M.R.; Reimer, R.A.; Hittel, D.S.; Rho, J.M.; Vogel, H.J.; Shearer, J., “Metabolomic Modelling to Monitor Host Responsiveness to Gut Microbiota Manipulation in the BTBR T+tf /j Mouse” Journal of Proteome Research 15 (2016) 1143-1150, https://doi.org/10.1021/acs.jproteome.5b01025

Tetens, J.; Heuer, C.; Heyer, I.; Klein, M.S.; Gronwald, W.; Junge, W.; Oefner, P.J.; Thaller, G.; Krattenmacher, N., “Polymorphisms within the APOBR gene are highly associated with milk levels of prognostic ketosis biomarkers in dairy cows.” Physiol Genomics 47 4 (2015) 129-137, https://doi.org/10.1152/physiolgenomics.00126.2014

Ehret, A.; Hochstuhl, D.; Krattenmacher, N.; Tetens, J. et al., “Use of genomic and metabolic information as well as milk performance records for prediction of subclinical ketosis risk via artificial neural networks.” J Dairy Sci 98 1 (2015) 322-329, https://doi.org/10.3168/jds.2014-8602

Deschamps, C.L.; Connors, K.E.; Klein, M.S.; Johnsen, V.L.; Shearer, J.; Vogel, H.J.; Devaney, J.M.; Gordish-Dressman, H.; Many, G.M.; Barfield, W. et al., “The ACTN3 R577X Polymorphism Is Associated with Cardiometabolic Fitness in Healthy Young Adults.” PLoS One 10 6 (2015) e0130644, https://doi.org/10.1371/journal.pone.0130644

Klein, M.S.; Connors, K.E.; Shearer, J.; Vogel, H.J. et al., “Metabolomics reveals the sex-specific effects of the SORT1 low-density lipoprotein cholesterol locus in healthy young adults.” J Proteome Res 13 11 (2014) 5063-5070, https://doi.org/10.1021/pr500659r

Klein, M.S.; Almstetter, M.F.; Nürnberger, N.; Sigl, G.; Gronwald, W.; Wiedemann, S.; Dettmer, K.; Oefner, P.J., “Correlations between milk and plasma levels of amino and carboxylic acids in dairy cows.” J Proteome Res 12 11 (2013) 5223-5232, https://doi.org/10.1021/pr4006537

Zacharias, H.U.; Schley, G.; Hochrein, J.; Klein, M.S.; Köberle, C.; Eckardt, K.U.; Willam, C.; Oefner, P.J.; Gronwald, W., “Analysis of human urine reveals metabolic changes related to the development of acute kidney injury following cardiac surgery” Metabolomics 9 3 (2013) 697-707, https://doi.org/10.1007/s11306-012-0479-4

Klein, M.S.; Oefner, P.J.; Gronwald, W., “MetaboQuant: a tool combining individual peak calibration and outlier detection for accurate metabolite quantification in 1D (1)H and (1)H-(13)C HSQC NMR spectra.” Biotechniques 54 5 (2013) 251-256, https://doi.org/10.2144/000114026

Thomas, A.; Klein, M.S.; Stevens, A.P.; Reinders, Y.; Hellerbrand, C.; Dett, K.; Gronwald, W.; Oefner, P.J.; Reinders, J., “Changes in the hepatic mitochondrial and membrane proteome in mice fed a non-alcoholic steatohepatitis inducing diet.” J Proteomics 80 (2013) 107-122, https://doi.org/10.1016/j.jprot.2012.12.027

Hochrein, J.; Klein, M.S.; Zacharias, H.U.; Li, J.; Wijffels, G.; Schirra, H. R.; Oefner, P.J.; Gronwald, W., “Performance evaluation of algorithms for the classification of metabolic 1H NMR fingerprints.” J Proteome Res 11 12 (2012) 6242-6251, https://doi.org/10.1021/pr3009034

Kohl, S.M.; Klein, M.S.; Hochrein, J.; Oefner, P.J. et al., “State-of-the art data normalization methods improve NMR-based metabolomic analysis.” Metabolomics 8 Suppl 1 (2012) 146-160, https://doi.org/10.1007/s11306-011-0350-z

Thomas, A.; Stevens, A.P.; Klein, M.S.; Hellerbrand, C.; Dettmer, K.; Gronwald, W.; Oefner, P.J.; Reinders, J., “Early changes in the liver-soluble proteome from mice fed a nonalcoholic steatohepatitis inducing diet.” Proteomics 12 9 (2012) 1437-1451, https://doi.org/10.1002/pmic.201100628

Klein, M.S.; Buttchereit, N.; Miemczyk, S.P.; Immervoll, A-K.; Louis, C.; Wiedemann, S.; Junge, W.; Thaller, G.; Oefner, P.J.; Gronwald, W., “NMR metabolomic analysis of dairy cows reveals milk glycerophosphocholine to phosphocholine ratio as prognostic biomarker for risk of ketosis.” J Proteome Res 11 2 (2012) 1373-1381, https://doi.org/10.1021/pr201017n

Klein, M.S.; Dorn, C.; Saugspier, M.; Hellerbrand, C. et al., “Discrimination of steatosis and NASH in mice using nuclear magnetic resonance spectroscopy” Metabolomics 7 2 (2011) 237-246, https://doi.org/10.1007/s11306-010-0243-6

Gronwald, W.; Klein, M.S.; Zeltner, R.; Schulze, B-D.; Reinhold, S.W.; Deutschmann, M.; Immervoll, A.-K.; Böger, C.A. et al., “Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine.” Kidney Int 79 (2011) 1244-1253, https://doi.org/10.1038/ki.2011.30

Klein, M.S.; Almstetter, M.F.; Schlamberger, G.; Nürnberger, N.; Dettmer, K.; Oefner, P.J.; Meyer, H.H.D.; Wiedeman, S.; Gronwald, W., “Nuclear magnetic resonance and mass spectrometry-based milk metabolomics in dairy cows during early and late lactation.” J Dairy Sci 93 4 (2010) 1539-1550, https://doi.org/10.3168/jds.2009-2563

Gronwald, W.; Klein, M.S.; Kaspar, H.; Fagerer, S.R.; Nürnberger, N.; Dettmer, K.; Bertsch, T.; Oefner, P.J., “Urinary metabolite quantification employing 2D NMR spectroscopy.” Anal Chem 80 23 (2008) 9288-9297, https://doi.org/10.1021/ac801627c