Nick Wong

Nick Wong

I am a PhD Candidate at Johns Hopkins University and the Carnegie Institute in the Ludington Lab.

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Posts

Turbidostat: Optical density sensors

2 minute read

Published:

Optical density (OD) measurements are crucial to measuring bacterial growth. OD describes the transmission (\(T\)) of light through a highly blocking optical filter, in this case bacteria, such that \(T\) of light through the medium is very small. OD is mathematically expressed as the negative \(log_{10}(T)\) where transmission is a physical value between 0 and 1. Typically OD is measured by shooting a specific wavelength through the test tube that the bacteria cannot absorb, but refract and scatter resulting in decreased detectable transmission from an optical sensor on the other end of the tube. Naturally there should be a linear relationship between the amount of light blocked by the number of bacteria cells in the medium.

Turbidostat: Building a UI

less than 1 minute read

Published:

It would be nice to be able to see the data of the bioreactor in real time, and it would be useful to use that data and control the machine if necessary. I used customTkinter library for python, which is a wrapper package of tKinter, which itself is a wrap of javascript snippets to make a nice UI. This makes UI design as simple as calling a selection of classes to draw frames, buttons, switches, sliders, and plots. We can even display animated plots to display data in real time.

Congressional Visit Scientific Advocacy

1 minute read

Published:

The CHIPs act promised to increase the NSF budget to $11.2 billion in 2022, but only enacted $9.1 billion 2 years later 2024. The CHIPs act claimed the NSF’s budget could reach $18.9 billion for FY 2027, but at the current funding rate Congress is far off from reaching this goal. I joined the American Institute for Biological Sciences with other PhD students, postdocs and academics from around the country to advocate increasing NSF funding for the 2025 fiscal year to $11.9 billion. I met with Californian and Maryland congressional staffers with my team to discuss our experiences in academia and how essential NSF funding is to our research and training. Environmental science and conservation projects are almost exclusively funded by government institutions such as NSF, NOAA, and USDA. We were modestly successful, with the NSF budget increasing to $10.183B for 2025 fiscal year.

portfolio

AIBS Algal Bloom Handout

Published:

Advocacy to increase NSF funding for environmental research and conservation

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.