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Guide to the 2020 Journal Clubs

Here's your guide to the in-depth science posts on Bio by the Bay this year.

Are you a student of science? A STEM major considering career opportunities after you graduate? Many of the Journal Club (and Review Paper) posts this year relate to synthetic biology, and that’s a big industry right now. Other fields are represented too, including ecology, stable isotope analysis, physics, and astronomy.

Overall, we’ve got 18 blog posts (some are series) summarizing 18 great peer-reviewed scientific papers. As science gets harder to read, we are practicing to make science more accessible. This is a work in progress, and will hopefully improve in the coming year!

Topics this year are:

  • Synthetic Biology
  • Physics
  • Health
  • Environmental Studies

Synthetic Biology

Synthetic Biology is an exciting new field, replete with job opportunities for fresh-out-of-college bio majors.

How to Build an Industry with Biology
In this paper, we learn a little about how metabolic engineering works. Working in a bio lab nowadays may very well include, say, trying to make E. coli better at producing taxadiene (or some other isoprenoid). What should you be looking for when you optimize this system?

Engineering with Light and Air
Here, we get to learn why more and more scientists are trying to engineer in photosynthetic microbes. We also get to discuss the tools of Synthetic Biology along the way. If you are curious about what a plasmid is, why there are different kinds of promoters, or how transformation differs between the lab protocol and the robots, be sure to check out this series.

How Do I Increase Bioreactor Efficiency?
Another problem you might face in a Syn Bio lab is, how do we optimize this system? In this paper, the researchers use a unique strategy to direct carbon flux into their biofuel product.

Sleuthing Intracellular Communications
A cell is a highly complex system. How do they keep all their genes, enzymes, internal & external signals straight? Any work or study dealing with cells would benefit from an appreciation of the complexity of intracellular cascades, here within the context of a yeast cell’s signaling network.

How Can We Control Proteins with Light?
Another application of Synthetic Biology is developing tools to better understand biological systems, health, and diseases. By engineering proteins (here, protein tyrosine phosphatase) to respond to the flip of a switch, we can learn more about the role they play in human disorders, like obesity, diabetes, and cancer.

Turning Villains into Heroes with Wastewater Clean-Up
A second paper about bioremediation – this time, using E. coli, and to clean up industrial by-products.

Water Safety for the Developing World
In this cell-free synthetic biology case, we look at tool development for checking water for toxins, pollutants, and human health markers.


Dancing Water Droplets and Electro-Elasto-Capillarity
I like this paper because it showcases theories learned in your introductory college physics courses and how they can be applied in interdisciplinary lab projects. Here, gaining insight on how water responds to electric fields has implications for biology & liquid-handling tools.

How Can We Improve Solar Power Technology?
Solar panels are a great renewable energy source, and scientists are actively looking for ways to advance them! In this paper, we get a behind-the-scenes look at exploring new materials to use in solar-powered technology, and use that information to direct improvements. This was the most popular Journal Club post of 2020!

A Universe in Expansion
A classic paper written almost a hundred years ago, but revolutionizing astronomy (the study of the universe) and cosmology (the study of the origins of the universe). What could Hubble’s observations of stars and their redshifting imply?

Exploring Carboxysomes with Imaging Technology
Programming has played a big role in this first year of my PhD, and MatLab is one of those languages. In this paper, we get to explore data collected by microscopes and analyzed by MatLab, which I find pretty inspiring to advancing my expertise in it. There’s so much we can do with a little code!


Always Take Your Vitamins
A little primer on the human immune response.

Covid-19: How Modeling Infection Rates Highlights the Need for Social Distancing
Epidemiology. Mathematical modeling. Current events.

Nanoparticles vs. Superbugs
Introduces the wonderful world of quantum dots, as applied to medicine & fighting superbugs.

Environmental Studies

How Do Plants Battle Biofilms?
Quorum sensing. Cell signaling. Communication across species and even across the kingdom level.

How Do Corals Protect Coastlines?
An example of math, physics, and programming applied to the real world. Another #interdisciplinary paper, exploring a mathematical model put to use for public & environmental health. A bridge connecting economics with coral reefs and climate change.

Can Plants Contribute to TNT Bioremediation?
Working with biosynthetic pathways, bioremediation, and using biology to solve a particular kind of pollution: a kind left by mines and war.

Tracking Turtles with Isotopes
We can use chemistry to save sea turtles. Stable isotopes have many applications; taking samples from sea turtle tissue for environmental monitoring is one of them.

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