Starting grad school is exciting and stressful during regular times; it’s even more stressful during a pandemic! Especially when it’s unclear what fall semester will look like. Here are some of my tips on how to prepare for your first semester.

Preparing for classes

I get asked this a lot, and my honest answer is to not worry about classes. Grades do matter, especially if you’re applying to fellowships or awards during graduate school, but no grade or award is worth it if it’s causing a lot of stress (and if that’s the case, reach out to the professor, they are there to help you). It’s important to note that you learn in class may not be directly related to what you need to know for research. With chemistry and biochemistry classes, the grades usually aren’t even based on assignments or homework. There’s a lot less “busy work” in grad classes and most of the grades come from exams and presentations. The exams are also formatted differently and instead of memorization, are focused on the understanding of scientific papers.

My best advice would be to focus on study habits and organization rather than content. Graduate school is a lot different than undergrad because, for the most part, you don’t have strict deadlines and have to do a lot of the learning on your own. If you want, you can start reading literature from your field, but keep in mind that what you read might not always be relevant. Research takes a lot of unexpected twists and turns, so you’ll never know what you’ll need to end up reading. For example, as a first-year, my project was based on quorum sensing in bacteria. However, after my first summer, we got fascinating data that shifted my project focus and now I’m working in a completely different direction. The knowledge is valuable, so I don’t regret spending the time studying it, but what I’m trying to say is don’t stress and feel like you need to be an expert in a field.

Invest in pens and paper. Rocketbook is a great notebook. In the bottom corner, they have a QR code that lets you scan the pages and upload it to different places like OneNote, google drive, email (outlook, google, etc.), Box, and others. The pages are also reusable. You can “reset” them either by washing off or heating in a microwave depending on the model. I use it so I don’t have to carry around multiple notebooks and things are less cluttered.

Time management

Like I said earlier, graduate school is a lot about self-scheduling. There’s no one perfect method! And it’s a skill so if you feel like you’re not great at time management: 1) you’re not alone and 2) you will get there, but like any skill, it requires patience and practice.

My advice would be to experiment with different scheduling techniques. I’ve found for events that I can’t miss, google calendars or outlook helps. I set a 10-minute reminder for virtual meetings, so I don’t miss it. When meetings are in person, I set it for how long it takes me to walk there + 5-10 minutes.

Some other helpful techniques and apps are:

Pomodoro method- using a tomato timer you work for 25 minutes and then break for 5 and repeat

Forest app- you plant a seed and it will grow into a tree based on productivity

Eisenhower Matrix-you schedule things in a quadrant with the following labels urgent/important, not urgent/important, not important/urgent, not urgent/not important.

5-minute rule- If something takes less than five minutes or so to do, just do it. Then it won’t take up space in your mind and you can focus on the more essential tasks.

I enjoy bullet journaling, so what I do is I have a page for each month with important deadlines and meetings. Then for each week, I try to schedule what I’m doing each day. Break things down! Say I’m working on my methods section on Wednesday, it’s more helpful for me to split that up into three bullets as below

• Write method sections- strains and antibiotics section (~20 minutes)
• Write method sections- experimental setup (~1 hour)
• Write methods section- RNA-seq preparation (~30 minutes)

By breaking things down, it makes tasks feel less daunting and more achievable. By putting an estimated time, I can more see where my day is going. I tell myself that I don’t have to stick to my schedule; they are merely a guideline. Maybe after writing the first section, my foot starts hurting or my friend calls me. Life happens; it is crucial that we are lenient and forgiving with ourselves.

How to navigate grad school during COVID

Take a deep breath. Grad school is hard; there is no doubt about that. You’ve made it this far, so pat yourself on the back.

Ask lots of questions; you’re first and foremost a student. It’s faster and easier to learn by asking questions instead of searching for hours on the internet. If someone makes you feel dumb for asking a question, avoid them if you can. Questions keep the research going, and a lot of times, those people hate questions because they don’t have the answers and don’t like acknowledging that.

Take breaks, don’t feel like you need to understand everything immediately. The science will always be there. Prioritize yourself and your mental health. It is so easy to feel like you have to accomplish everything. Academia is severely flawed in this way, we are all piled with way too much work for one person to do feasibly. If you don’t take care of yourself, it is easy to feel burnt out, making it harder to work.

Reach out to people; your cohort is going through some of the same struggles you are. Build a support system. You can initiate Zoom with your cohort once a week to talk about classes, moving, research, or just play games and hang out. Your peers are your colleagues; if you feel comfortable with it, go to them for support, they will understand your program and your concerns better than anyone else.

Seek professional help. Moving is tough. Starting grad school is tough. Living through a pandemic is tough. Nothing about your first year is easy, so don’t pretend like it is. I felt the need to hold a “strong” façade and just bear with the stress, and it was awful. Around my second year, I almost gave myself a stress-induced ulcer, and two years later am still suffering the consequences of that. I was too prideful to meet with a therapist and address my stress and coping mechanisms. I deeply regret it. Now I meet with a therapist about once a week, and she is terrific at helping me cope and talk through life events both inside and out of grad school. She’s helped me realize that I’m not alone in a lot of what I feel, and that’s super validating for me.

You might feel imposter syndrome! Imposter syndrome is the feeling that you don’t fit in or you don’t belong. Maybe you feel like the grad school will email you one day and be like, “Oh, we’re sorry we didn’t mean to send that acceptance to you” and send you packing. But you do belong! Your accomplishments are valid! I’ve talked to lots of people, and this feeling doesn’t go away on it’s own. You have to work at it because there is SO much science in this world and we’ll only ever know a small bubble. It helps me to realize, I am QUEEN of that bubble.

My mantra, is to say, “I know what I know, but I don’t know what I don’t know.” It sounds confusing but what I mean by it is that what I know, I know well, and I won­­­’t let anyone make me feel otherwise. There are somethings that I don’t know, but it’s impossible to know what I don’t know until I encounter it. And then I can decide whether it’s worth knowing or not.

Take time for yourself; I cannot stress this enough. Graduate school is a marathon, not a sprint. It’s cliché, but it’s true. If you keep sprinting, you will burnout. And recovering from burnout is tough. Find a hobby or simple ways to achieve self-care. Some examples of simple things you can do include:

• Trying new recipes or foods
• Taking a new way to work
• Relaxing with a bath
• Going for a long walk
• Listening to music
• Treating yourself with something small

And if things aren’t working out, take a break. The science will always be there.

Picking a research lab

This was a tough one and why I saved this for last. I’ve been trying to adapt my basic strategies for choosing a lab to account for COVID, and this is what I’ve come up with so far. It might not be perfect and might not work in every scenario, but I hope it helps!

Talk to your potential advisor– do not be afraid to ask them how the rotation will go. Is it virtual or in-person? What project will you be working on? How are group meetings structured? What are their expectations (these may change if they are an assistant professor versus associate professor)? Mentoring style? How will you be funded? Even though conferences will likely be virtual for a while, ask them what their thoughts are regarding conferences. Some professors want their students to start networking as soon as possible While others want students to wait until they have presentable research or the paper is published. Get a sense of whether this advisor will stand up for you or treat you like a gear in the cog. An advisor isn’t just a 4-6 year commitment. They will be writing letters of recommendation and can help open many doors for you even years after you graduate.

Talk to your potential lab– Just like with your cohort, talk to your potential new lab. Ask them if they want to get lunch over zoom either one-on-one or as a group. To get through grad school, you need both a supportive PI and lab group. Don’t be afraid to talk to your lab honestly because if you decide that’s the lab you’re joining, they’ll be your peers and colleagues for 4-6 years. My lab has helped me tremendously by helping me prepare for candidacy exams, applying for fellowships, giving me advice, day to day help, and everything in between.

Talk to people outside the lab– This helps you get to know the department better, but it also lets you know broader things about the lab. In some cases, it can be hard to tell which are the toxic labs, but people in the department know.

It’s okay if it’s not the right fit! There are lots of people who later on realize that their lab isn’t the right fit and move to a different lab. That is perfectly fine. Do what is best for yourself and prioritize your mental health. Taking an extra year to graduate will not close many doors and may even open new ones. It is infinitely better to switch to a lab that makes you happy than to stay in a lab where you are miserable regardless of the reason.

Hand washing and why it’s effective against microbes

 

I want to start out by stating I’m not a virologist, I am a chemistry graduate student studying cellular signaling in bacteria. I’m also learning a lot of this as I go, but I’ve noticed that there’s a lot of misinformation out there so I want to keep everyone up to date on the facts. If there’s something I should edit or if there’s more info you’d like to know, just ask!

 

So to tackle why hand washing is effective let’s first start at the basics of what a virus is and how it works.

What is a virus?

A virus is tiny. They are in the nanometer range. To put that in perspective they are smaller than the mitochondria which is a cellular component in some eukaryotic cells.

Because of their small size you need a specialized microscope to view them; the regular microscopes in most teaching labs will not let you see a virus. This microscope is called an electron microscope and uses electrons as the light source. From electron microscopy we can get images similar to the ones pictured below which show what a few different viruses look like.

Why are these images are in black and white? With electron microscopy you lose color, but these images allow us to create 3D renderings of what the virus would look like.

The CDC, as well as other organizations, have some 3D models of the coronavirus. These renderings are useful because they allow scientists to understand how different parts of the virus functions and thus how the virus itself functions.

Background on coronaviruses

Those red spikes or crowns are what the coronavirus is named after. Most coronaviruses are zootonic in nature, meaning that they can spread between animals and people. Coronaviruses cause respiratory tract infections in humans and while most cases are mild, like the common cold, some coronaviruses can be lethal like SARS (Severe Acute Respiratory Syndrome) or MERS (Middle East Respiratory Syndrome). COVID19 is considered novel because a virus with that sequence wasn’t known before December 2019. Currently the cause of COVID-19 is unknown, but it is thought to have originated at a fish market in Wuhan, China. The name for the virus is now SARS-CoV-2 and the disease is COVID-19 or Corona virus disease-19.

What parts make up a virus and how do they replicate?

So not only are viruses tiny, but they’re so simple that they can’t reproduce on their own. A virus is made up of 3 main things, genetic material (either RNA or DNA), proteins, and lipids. The relevant one is lipids, they are fatty molecules that make up the protective envelope of some viruses including SARS-CoV-2.

Viruses replicate by invading a host cell. Once they’ve invaded, they will hijack the host’s cellular machinery and use it to replicate their own genetic material. So now the host is making viral RNA or DNA, viral proteins, and viral lipids. These components will self-assemble in the host and eventually there will be so many viruses that the host cell will explode, allowing the virus to start infecting new cells in the host and repeating the process.

How do viruses spread and how long do they live?

Viruses can spread through many ways such as bites of infected animals, mosquitoes, and bodily fluids such as blood. SARS-CoV-2 is thought to spread through nasal fluids when sneezing and coughing. In an infected individual, these droplets will contain viruses that can potentially invade a new host. If you are sick, health officials recommend you wear a face mask to prevent spread of your nasal fluids. However, if you are a healthy individual a face mask does not help much because you are likely to touch surfaces containing contagions and if you mess with the face mask, you will introduce those contagions to your face and thus increasing your likelihood of falling ill.

Because viruses need a host to survive, their lifespans are typically shorter. For instance, the flu can last on surfaces for about 48 hours while HIV will only survive 1-2 hours outside of bodily fluids.

Right now SARS-CoV-2 is thought to live up to 3 days on surfaces, however this answer may change as more research is completed and peer reviewed. The good news though is that most coronaviruses can be removed by household disinfectants like ethanol, hydrogen peroxide, and bleach. When using these materials you want to make sure you’re using the right amounts.

For ethanol based products, you want 60-70% ethanol. While it seems like 100% ethanol would be more effective, you need water to actually kill the cells. The way ethanol works is by attacking the lipids in the protective outer envelope and poking holes that allow water to come in. Water can then flood the cell, causing the cell to burst and killing them. On the other hand, 100% ethanol doesn’t work for two reasons, it will simply surround the cell and attack the outer envelope, but instead of poking holes, the envelope will bunch up preventing ethanol from getting into the cells and because it’s pure ethanol instead of staying around the ethanol will just evaporate. High concentrations will definitely still inactivate the microbes, but they will not kill them.

Hydrogen peroxide and bleach, on the other hand, work as oxidizing agents. If you remember your general chemistry this means, it’s an electron acceptor. This means that it will eagerly take electrons from the surfaces (or microbes) that you spray it on. However as oxidizing agents, they are not microbe specific: you can use hydrogen peroxide and bleach to disinfect surfaces, but please do not use it on your skin because it will also kill off your own cells.

There’s no hand sanitizer, should I make my own?

While there are many recipes floating around for how to make your own hand sanitizer, I recommend against it because most OTC alcohol isn’t pure alcohol (usually ranges from 91-99%) so you can’t get to the right concentration easily. Like I mentioned earlier, higher ethanol concentration will not increase antimicrobial activity. If you make your own hand sanitizer that is too high in alcohol it will cause your hands to crack or even bleed which will actually make you more susceptible to microbial infections!

So what exactly is soap and why is it so effective?

First let’s talk about soap. How is soap made? There are hundreds if not thousands of recipes on how to make soap at home, but if you look at the ingredients you need two main things. You need some sort of fat and some sort of basic solution (like lye or sodium hydroxide). On its own lye is harmful and can cause chemical burns, be careful when using it. But in the soap making process the fats and lye will begin to saponify aka the lye and fat will make an exothermic solution, releasing heat and creating soap and glycerin. Soaps are often made with extra fats compared to the lye so the finished product will contain no sodium hydroxide and will therefore not be irritating to the skin.

The fats in the soap are what makes it so effective. The fats allow soap to be both hydrophobic (water hating) and hydrophilic (water loving). What does that actually mean? Soap loves both water and fats and will readily mix with either. Don’t believe me? Try this experiment, in a bottle or glass add some water and some vegetable oil. No matter how hard you try to mix or shake them they will always form two distinct layers. Now add a few drops of soap (doesn’t matter what kind) and try mixing again, now instead of two clear layers, you’ll see that both layers are slightly cloudy. This is because the soap is allowing the oil and water to mix together. If you’re having trouble seeing the difference, try adding a few drops of food coloring to the water!

So now that we know how soap works, how does it help clean your hands? Basically, most of the dirt and food on your hands is also made up of fats.  The hydrophobic tails on the soap molecules will bind to the fats on your hands and trap them inside. The hydrophilic head loves the water and allows the fat contained particle to be washed off your hand. Think of when you have a really dirty pan: you usually use soap and hot water and scrub to remove the grime and it doesn’t happen instantly. It takes some time to clean off all the dirt. The same principle applies to your hands; when you use hot water and soap you can remove the dirt on your hands. And you want to scrub like you’re cleaning a pan – your hand is full of many crevices so you want to take your time to make sure you hit every nook and cranny that dirt can be in.

How does this apply to contagions like viruses and bacteria?

So this makes sense it terms of food, but how does soap help remove bacteria and viruses?

Remember how we talked about that lipid bilayer? The lipid bilayer is on the outside of most viruses and bacteria and it protects the cells.  Unfortunately -for them- the same lipids that protect microbes are their weakest links. The soap particles will be attracted to the lipids in the envelope and will compete with them. This will break up the envelope and allow the virus to be washed off.  If you wash your hands properly and for the recommended time (approximately 20 seconds) you will be able to remove most microbes.

While you can’t really grow viruses in petri dishes, you can grow bacteria. I did a quick experiment showing the effectiveness of soap on bacteria. Since soap works on viruses in the same way it works on bacteria (by attacking the lipid bilayer), rest assured that if you are washing your hands properly you are also removing viruses from your hands.

What you see on these plates is that my hands have tons of bacteria before I wash them. To be fair, I hadn’t washed them in a while! The second picture is me washing my hands with just hot water, no soap no scrubbing, most of the bacteria are still there so even though hot water does kill microbes, it’s not enough. Then I washed my hands with scrubbing for 10 seconds with Softsoap: there’s still bacteria but if you look closely, I did manage to remove some. Finally, I washed my hands for 30 seconds with scrubbing and voila! Most of the bacteria are gone!

And remember, you don’t need fancy or even antibacterial soap! The main agent is soap that makes it useful is the fatty acid loving tails. So even if the market is out of antibacterial soap, the cheap old stuff will work just as well.

Follow WHO and CDC recommendations to stay safe during the coronavirus pandemic. This includes, staying home when you’re sick, practice social distancing (stay 6-10 feet away from people), disinfect surfaces, and avoid touching your face before washing your hands.

Before I actually started working with bacteria, I had no clue what an experiment would even look like. I was familiar with chemistry experiments like volcanoes and elephant toothpaste, but I didn’t even know what bacteria looked like! And honestly, I couldn’t see why anyone would want to work with bacteria. The whole reason I was going to graduate school was because I wanted to make a difference in the world, but how could I do that with bacteria? I can’t even see them without a microscope!

Even though I didn’t plan on being where I am today, I’m happy with what I’ve had to go through. It’s definitely been hard. I feel like there’s a lot of things that microbiologists just assume that everyone knows, but for me, it’s been a lot of questioning and googling and questioning what I’ve googled. Here’s a great example: I can determine how many bacteria are in a liquid sample through their optical density, or OD. I can get the optical density by taking a small amount of my liquid bacteria and measuring the absorbance through a UV spectrophotometer. This is a term I now use daily, before each experiment I need to calculate how many bacteria I’m using and the fastest and most reliable way is through the optical density. But 2 years ago, I wrote in my class notes: “google what OD is, I have no clue what they’re talking about.” This is a more trivial example since I was able to google optical density and I’ve been fine since but there are so many things that I’m just like someone needs to write a Microbiologist’s Guide to Surviving the Lab.

I’m not going to try writing a book, I don’t know enough to do that. But I am going to take what I know and try to visualize some of my experiments or my day to day life so other people know what being a graduate student is like.

To start, here’s the experiment I’m currently working on. Silver is toxic to bacterial cells at high dosages. I’m treating my bacteria with silver nitrate (AgNO3) which is a commercially available (and relatively cheap) silver source.

The experiment starts with bacteria kept in the -80˚C freezer for long term storage. We take a small amount of these cells and streak them onto an agar plate. My agar plates are made with Luria Broth (LB) which gives the bacteria the nutrients they need to grow.

On the agar plate, the circles are large clusters of many individual bacteria, collectively they are referred to as colonies. For each experiment, I take 3 independent colonies as biological replicates. The reason I take biological replicates is to ensure that whatever trait I’m testing isn’t due to a random mutation.

To get these biological replicates, I use a sterile pipette tip and add the colony to a culture tube containing the media I will be testing the bacteria in. This step is vital, bacteria will change their gene expression to respond to different environmental changes, so I always grow my bacteria in the culture I will be doing the test in. The media requires 3 basic things so the bacteria can grow: salts, a carbon source, and water. The media I use is called minimal media (M9). The reason why we use M9 is that it is chemically defined and contains the minimum amount of nutrients to support bacterial growth.

These initial growths are referred to as overnights and usually I grow the bacteria for a maximum of ~18 hours. I can tell right off the bat if an overnight grew because instead of being a clear liquid, the liquid is now opaque. Some bacteria will actually require more time for the overnights to grow but E. coli runs the risk of overgrowing. (Random fun fact: actually if bacteria are grown for too long they will use all the nutrients from the media and will start eating each other in a bid for survival.)

 

From this step, I’ll take a small amount of my overnight and dilute it into fresh media. Again, this has to be the same media I grew the overnight in. Because my experiment takes place in a 96 well plate, I am diluting the bacteria in those white reservoirs. By making the dilution in the reservoir I can use the multichannel pipette to add the bacteria individually to each well.

After I’ve set up the plate, I can monitor their growth. A typical growth curve for bacteria starts with the lag phase, in this phase the bacteria are active but not dividing. When they enter log or exponential phase the bacteria are now rapidly dividing and growing. Finally, the bacteria enter stationary phase, this is the point where the number of cells dying equals the number of surviving cells.

To measure the growth of E. coli I can use the plate reader to measure the OD at a wavelength of 600 nm. By looking at how many bacteria there are at each time point, I can see how the silver nitrate is affecting how the bacteria grow compared to what the normal growth curve should look like.

And that’s all there is to it! From this point, I’ll take the data from the plate reader and use excel or other data processing software to create graphs and other figures that will be used in presentations, yearly committee reports, and eventually into a scientific paper.

 

 

So I realized before I start my blog, I need to give a little insight into who I am and what I do. I’m a chemical biologist. What does that actually mean though? I’m someone who uses chemistry to study biological processes. I’m trying to understand how these certain molecules, which haven’t been studied closely before, affect bacterial cell signaling. But words on paper (or your screen) have no meaning to what I actually do. Whenever I’m running a [what I think is] cool experiment. I’m going to try to walk you through my day and take pictures of key moments. Although, fair warning, my days are never consistent. I’m still learning how to budget time for my experiments so a lot of days I’m rushing around like a chicken with it’s head chopped off because I’m trying to make up for the time I forgot to account for.

Also, there are going to be times I use jargon and I apologize. I’m not trying to, but sometimes it’s just easy to fall into old habits (usually the only writing grad students get to do is proposals and papers which are usually more dry and full of field specific terms). If there’s anything confusing, please let me know! The whole concept only works if this is interactive. I can pick a million things to explain, but none of that helps if that’s not what you’re curious about.

A little bit of a disclaimer-I can’t speak for other departments, or for master’s, but I’m going to try my hardest to explain what it’s like getting a PhD in chemistry while studying biological systems. It’s hard for me to make sweeping generalizations about other fields, because I don’t get to interact with people outside of chemistry/biochemistry that often. I’m not saying I’m completely shut off from the world, but with spending ~50-60 hours/week on campus it’s hard to find time to meet new people. In the meantime if you have questions about other programs, I can try to lead you towards other sources, but my area of expertise, at least when it comes to graduate school, ends outside my little chemical bubble.

Outside of grad school I enjoy cooking, crafting, and trying to organize my life. I’m not extroverted, but I like challenging myself to be comfortable in different social situations. I used to be able to pick up insects and hold them close, but ever since I had 2 traumatic bug related incidents (one where a swarm of bees chased me around the grand canyon, the second was a dragonfly corned me into an outdoor shed) I’ve hated any and all bugs but I have a deeper dislike for things with wings.