AIBS Algal Bloom Handout
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Advocacy to increase NSF funding for environmental research and conservation
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portfolio
Portfolio item number 2
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Short description of portfolio item number 2 
publications
The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis
Published in IJMS Membrane Proteins: Structure, Function and Motion, 2021
In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis.
Recommended citation: Wong, N. A., & Saier, M. H., Jr (2021). The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. International journal of molecular sciences, 22(3), 1308.
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Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens
Published in ASM Journals mBio, 2021
To investigate the dynamics of ciprofloxacin resistance development, we applied a comparative resistomics workflow for three clinically relevant species of Gram-negative bacteria: Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. We combined experimental evolution in a morbidostat with deep sequencing of evolving bacterial populations in time series to reveal both shared and unique aspects of evolutionary trajectories.
Recommended citation: Zlamal, J. E., Leyn, S. A., Iyer, M., Elane, M. L., Wong, N. A., Wamsley, J. W., Vercruysse, M., Garcia-Alcalde, F., & Osterman, A. L. (2021). Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens. mBio, 12(3), e0098721.
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A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
Published in Nature Scientific Reports, 2022
We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of l-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome.
Recommended citation: Rodionova, I. A., Gao, Y., Monk, J., Hefner, Y., Wong, N., Szubin, R., Lim, H. G., Rodionov, D. A., Zhang, Z., Saier, M. H., Jr, & Palsson, B. O. (2022). A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Scientific reports, 12(1), 7274.
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teaching
BIMM 121 Microbiology Lab Teaching Assistant
Undergraduate lab, University of California San Diego, 2021
Techniques in microbial physiology, microbial genomics, microbial evolution, and microbial ecology will be used to explore the role of microbes in industry, health, and the environment. Inquiry-based experiments will cover the fundamentals of both working with live microscopic organisms at the bench and bioinformatically analyzing their genomes at the computer. Attendance at the first lecture/lab is required. Nonattendance may result in the student being dropped from the course roster. Material lab fees will apply. Prerequisites: BILD 1.
AS.020.153 General Biology Lab Teaching Assistant
Undergraduate Lab, Johns Hopkins University, 2023
This course reinforces the topics covered in AS.020.151. Students participate in a semester-long project, identifying bacteria from Homewood campus soils using molecular biology techniques. Other laboratory exercises cover aspects of evolution, genomics and biochemistry. Cross-listed with Behavioral Biology. Student must have enrolled in AS.020.151 either this term or in past terms. Students who have credit for AP Biology but take General Biology Lab I will lose four credits of AP Biology credit. Cross-listed with Behavioral Biology. This course is offered in fall terms only.
AS.020.315 Biochemistry Project Lab Teaching Assistant
Undergraduate Lab, Johns Hopkins University, 2024
This research project laboratory investigates the flow of energy through biological systems using focused examination of key cellular energy-conversion processes. Students will be introduced to the broad field of biochemistry research through computational structural analysis, directed mutation, recombinant protein production, and enzymatic analysis. Participants will be trained in biochemical laboratory techniques and expected to contribute their findings to the scientific community using formal, academic communications.
AS.020.129.12.IN25 The Microscopic Secret Society Of Bacteria That Rule The World
Intersession Course, Johns Hopkins University, 2025
This course will teach about microbial ecology and evolution with topics ranging from human health to global ecology. Learn about how microbes have evolved to live and shape in their environments and the impacts they have on all orders of life. Gain an understanding of how anthropogenic driven climate change, industrialization and urbanization is changing the microbial environment and its effect on public health. There will be an emphasis on exposure to bacteriology research at Johns Hopkins, greater Maryland area and beyond from a seminar series of guest lectures.