Aristilde group members: ***postdoc; **graduate student; *undergraduate student
Corresponding author(s) in bold.


33. **Solhtalab M., **Flannelly D.F., Aristilde L. 2019.
Substrate binding versus escape dynamics in a pH-affected fungal beta-glucosidase revealed by molecular dynamics simulations.
Carbohydrate Research, in press.

32. **Wilkes R.A., **Mendonca C.M., Aristilde L. 2019.
A cyclic metabolic network in Pseudomonas protegens Pf-5 prioritizes the Entner-Doudoroff pathway and exhibits substrate hierarchy during carbohydrate co-utilization.
Applied and Environmental Microbiology, in press.
doi: 10.1128/AEM.02084-18. (e-pub 2018 Oct 26) [Link to Open Access Article]

Preprint posted on bioRxiv, 402073. doi: (e-pub 2018 Aug 28) [Link]


31. **Wushensky J.A., **Youngster T., **Mendonca C.M., Aristilde L. 2018.
Flux Connections between Gluconate Pathway, Glycolysis, and Pentose-Phosphate Pathway during Carbohydrate Metabolism in Bacillus Megaterium QMB1551.
Frontiers in Microbiology, 9:2789.
doi: 10.3389/fmicb.2018.02789. (e-pub 2018 Oct 30) [Link to Open Access Article]
30. ***Barzen-Hanson K.A.#, **Wilkes R.A.#, Aristilde L. 2018.
Quantitation of carbohydrate monomers and dimers by liquid chromatography coupled with high-resolution mass spectrometry.
Carbohydrate Research, 468, 30-35.
# Co-first authors
doi: 10.1016/j.carres.2018.08.007. (e-pub 2018 Aug 12) [Link to Article]
29. Richards B.K., Pacenka S., Meyer M.T., Dietze J.E., Schatz A.L., Teuffer K., Aristilde L., Steenhuis T.S. 2018.
Antecedent and post-application rain events trigger glyphosate transport from runoff-prone soils.
Environmental Science and Technology Letters, 5, 249-254.
doi: 10.1021/acs.estlett.8b00085. (e-pub 2018 Apr 23) [Link to Article]
28. **Okaikue-Woodi F.E.K., **Kelch S.E., Schmidt M.P., Martinez C.E., Youngman R.E., Aristilde L.. 2018.
Structures and mechanisms in clay nanopore trapping of structurally-different fluoroquinolone antimicrobials.
Journal of Colloid and Interface Science, 513, 367-378.
doi: (e-pub 2017 Nov 8) [Link to Article]


27. **Youngster T., **Wushensky J.A., Aristilde L.. 2017.
Profiling glucose-induced selective inhibition of disaccharide catabolism in Bacillus megaterium QM B1551 by stable isotope labeling.
Microbiology, 163, 1509-1514.
doi: 10.1099/mic.0.000540. (e-pub 2017 Sept 28) [Link to Article]
26. Aristilde L.,*Guzman J.F., ***Klein A.R., *Balkind R.J.. 2017.
Compound-specific short-chain carboxylic acids identified in a peat dissolved organic matter using high-resolution liquid chromatography-mass spectrometry.
Organic Geochemistry, 111, 9-12.
doi:10.1016/j.orggeochem.2017.06.006.(e-pub 2017 Jun 21) [Link to Article]
25. Aristilde L., *Reed M.L., **Wilkes R.A., **Youngster T., **Kukurugya M.A., *Katz V., *Sasaki C.R.S. 2017.
Glyphosate-induced specific and widespread perturbations in the metabolome of soil Pseudomonas species.
Frontiers in Environmental Science 5:34.
doi: 10.3389/fenvs.2017.00034. (e-pub 2017 Jun 20) [Open Access Link to Article]

—-Highlighted by American Agriculturist: Weed War may Wound Beneficial Soil Bacteria.
—-Featured by the Cornell Chronicle: Beneficial soil bacteria face a weed-killing threat from above.

24. **Pochodylo A.L, ***Klein A.R., Aristilde L. 2017.
Metal-binding selectivity and coordination dynamics for cyanobacterial microcystins with Zn, Cu, Fe, Mg, and Ca.
Environmental Chemistry Letters, 15, 695-701.
doi: 10.1007/s10311-017-0639-x. (e-pub 2017 May 24) [Link to Article]

23. **Wilkes R.A., Aristilde L.. 2017.
Degradation and metabolism of synthetic plastics and associated products by Pseudomonas spp.: Capabilities and challenges.
Journal of Applied Microbiology, 123, 582-593.
doi:10.1111/jam.13472. (e-pub 2017 Apr 17) [Free Access Link to Article]

22. Aristilde L., *Galdi S.M., **Kelch S.E., *Aoki T.G. 2017.
Sugar-influenced water diffusion, interaction, and retention in clay interlayer nanopores probed by theoretical simulations and experimental spectroscopies.
Advances in Water Resources, 106, 24-38.
doi: 10.1016/j.advwatres.2017.03.014. (e-pub 2017 Mar 18) [Link to Article]

—-Featured in Cornell Chronicle, “Sweet Compounds Aid Water Retention in Dry Soil”.

21. **Pochodylo A.L., Aristilde L.. 2017.
Molecular dynamics of stability and structures in phytochelatin complexes with Zn, Cu, Fe, Mg and Ca: Implications for metal detoxification.
Environmental Chemistry Letters, 15, 495-500.
doi: 10.1007/s10311-017-0609-3. (e-pub 2017 Feb 27) [Link to Article]

20. Aristilde L. 2017.
Metabolite labelling reveals hierarchies in Clostridium acetobutylicum that selectively channel carbons from sugar mixtures towards biofuel precursors.
Microbial Biotechnology, 10, 162-174.
doi: 10.1111/1751-7915.12459. (e-pub 2016 Nov 22) [Open Access Link to Article]

—-Featured as “Highlight Article” in Microbial Biotechnology, “Metabolite labelling as a tool to define hierarchies in Clostridium acetobutylicum sugar usage and its relevance for biofuel production”.
—-Featured in Cornell Daily Sun, “Why Certain Bacteria Are Not So Efficient at Producing Biofuel”.
—-Featured in Cornell Chronicle, “Decoded Microbial Metabolism Explains Biofuel Yield”.

19. McBride M.B., Frenchmeyer, M., **Kelch, S.E., Aristilde L. 2017.
Solubility, structure, and morphology in the co-precipitation of cadmium and zinc with calcium-oxalate.
Journal of Colloid and Interface Science, 486, 309-315.
doi: 10.1016/j.jcis.2016.09.079. (e-pub 2016 Sep 30) [Link to Article]


18. Charlet L., Baham J., Giraldez J., Lo W., Aristilde L., Baveye P.C. 2016.
Éloge de la méthode: A tribute to Garrison Sposito on the occasion of his retirement.
Frontiers in Environmental Science, 4:73.
doi:10.3389/fenvs.2016.00073. (e-pub 2016 Oct 28) [Open Access Link to Article]

17. **Pochodylo A.L., *Aoki, T.G., Aristilde L. 2016.
Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.
Journal of Colloid and Interface Science, 480, 166-174.
doi: 10.1016/j.jcis.2016.07.016. (e-pub 2016 Jul 9) [Link to Article]

—-Featured in The Cornell Daily Sun, Researchers Uncover Sediment Interactions That Filter Toxins in Freshwater.
—-Featured in Cornell Chronicle, “Sedimental journey: Scientists tackle toxin particle capture”.

16. Richter H.#, Molitor B.#, ***Wei H., Chen W., Aristilde L., Angenent L.T., 2016.
Ethanol production in syngas-fermenting Clostridium ljungdahlii is controlled by thermodynamics rather than by enzyme expression.
Energy and Environmental Science, 9, 2392-2399.
# Co-first authors
doi: 10.1039/C6EE01108J. (e-pub 2016 May 20) [Link to Article].

—-Featured in Tech Beat, Biofuel Production Using Syngas Fermentation
—-Featured in Cornell Chronicle, “Biological wizardry ferments carbon monoxide into biofuel”.
—-This story was highlighted on Azo CleanTech Sustainability and Energy News and GlobalSpec Energy and Natural Resources News.

15. Aristilde L., Lanson B., Miéhé-Brendlé J., Marichal C., Charlet L. 2016.
Enhanced interlayer trapping of a tetracycline antibiotic within montmorillonite layers in the presence of Ca and Mg.
Journal of Colloid and Interface Science, 464, 153-159.
doi: 10.1016/j.jcis.2015.11.027. (e-pub 2015 Nov 14) [Link to Article]

—-Featured in Cornell Chronicle, Study: Antibiotics hide within mineral layers”.
—-This story was highlighted on Physics.Org Materials Science News and Technology.Org Science and Technology News.

14. **Sasnow S.S., ***Wei H., Aristilde L. 2016.
Bypasses in intracellular glucose metabolism in iron-limited Pseudomonas putida.
MicrobiologyOpen, 5, 3-20.
doi: 10.1002/mbo3.287. (e-pub 2015 Sept 16) [Open Access Link to Article]


Technical Report
13. Rabinowitz J.D., Aristilde L., Amador-Noguez D. 2015.
Metabolomics of clostridial biofuel production.
Technical Report, SC0006839. United States Department of Energy, doi:10.2172/1213974. (e-pub 2015 Sept 8) [Link].
12. **Flannelly D.F., *Aoki T.G., Aristilde L.. 2015.
Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study.
Journal of Structural Biology, 191, 352-364.
doi: 10.1016/j.jsb.2015.07.002. (e-pub 2015 July 6) [Link to Article]

—-Highlighted by the Cornell Center for Advanced Computing (CAC): Simulating Carbon-Cycling Enzymes. Also see CAC homepage.

11. ***Wei H., Aristilde L.. 2015.
Structural characterization of multiple pyoverdines secreted by two Pseudomonas strains using liquid chromatography-high resolution tandem mass spectrometry with varying dissociation energies.
Analytical and Bioanalytical Chemistry, 407, 4629-4638.
doi: 10.1007/s00216-015-8659-5. (e-pub 2015 Apr 21) [Link to Article]

10. Aristilde L., Lewis I. A., Park J.O., Rabinowitz, J.D. 2015.
Hierarchy in pentose sugar metabolism in Clostridium acetobutylicum.
Applied and Environmental Microbiology, 81, 1452-1462.
doi: 10.1128/AEM.03199-14. (e-pub 2014 Dec 19) [Free Access Link to Article]


9. Aristilde L., Lanson B., Charlet L. 2013.
Interstratified layers from the pH-dependent intercalation of a tetracycline antibiotic within smectite clay layers.
Langmuir , 29, 4492-4501.
doi: 10.1021/la400598x. (e-pub 2013 Mar 25) [Link to Article]

8. Aristilde L., Sposito G. 2013.
Complexes of the antimicrobial ciprofloxacin with soil, peat, and aquatic humic substances.
Environmental Toxicology and Chemistry, 29, 1467-1478.
doi: 10.1002/etc.2214. (e-pub 2013 Mar 1) [Link to Article]


7. Aristilde L., Xu Y., Morel F.M.M. 2012.
Weak organic ligands enhance Zn uptake in marine phytoplankton.
Environmental Science and Technology, 46, 5438-5445. (e-pub 2012 Apr 12) [Link to Article]
6. Xu Y.., Shi D., Aristilde L., Morel F.M.M. 2012.
The effect of pH on the uptake of zinc and cadmium in marine phytoplankton: Possible role of weak complexes.
Limnology and Oceanography, 57, 293-304.
doi: 10.4319/lo.2012.57.1.0293. (e-pub 2012 Jan 16) [Link to Article]
5. Aristilde L., Marichal C., Miéhé-Brendlé J., Lanson B., and Charlet L. 2010.
Interactions of oxytetracycline with a smectite clay: A spectroscopic study with molecular simulations.
Environmental Science and Technology, 44, 7839-7845.
doi: 10.1021/es102136y. (e-pub 2010 Sep 24) [Link to Article]

4. Aristilde L., Melis A., Sposito G. 2010.
Inhibition of photosynthesis by a fluoroquinolone antibiotic.
Environmental Science and Technology, 44, 1451-1457.
doi: 10.1021/es902665n. (e-pub 2010 Jan 13) [Link to Article]

—-Featured in Environ. Sci. Technol., Environmental News: New mode of action for pharmaceuticals in the environment.
—-Featured in Discovery News Online, Earth News: Antibiotics inhibit plant growth.

3. Aristilde L., Sposito G. 2010.
Binding of ciprofloxacin by humic substances: A molecular dynamics study.
Environmental Toxicology and Chemistry 29, 90-98.
doi: 10.1002/etc.19. (e-pub 2009 Sep 25) [Link to Article]

Doctoral Thesis
2. Aristilde L.. 2008.
A mechanistic investigation of the environmental chemodynamics of fluoroquinolone antibiotics.
Ph.D. Thesis, University of California at Berkeley, 266 pp. (2008) [Link to Dissertation]
1. Aristilde L., Sposito G. 2008.
Molecular modeling of metal complexation by a fluoroquinolone antibiotic.
Environmental Toxicology and Chemistry, 27, 103-109.
doi: 10.1897/08-059.1. (e-pub 2008 Jun 11) [Link to Article]