Author: Christina Nowicki

This article was originally posted on The Bio Girls.

Working in a lab, especially a research lab, is a little chaotic. Keeping experiments uniform can be a challenge when lab managers are always hunting for the best deal on supplies and equipment is constantly malfunctioning. While you can’t quickly solve all these problems, you can make sure that your protocol is as organized as possible to keep you on track.

Many labs use SOPs, or standard operating procedures, to keep work consistent for all members of the lab. Clinical labs tend to have much more in-depth SOPs compared to translational or basic research labs, but having a detailed protocol to come back to can make running experiments much less stressful!

So, what makes a good SOP?

Detail, detail, detail!

Make sure to list every single step of the process so that if someone came in who had never worked there before, they would know exactly what to do. Of course, you want to include major items like incubation times or reagent concentrations. But you may also want to include where reagents are located around the lab, how best to label things, etc. The more detail, the better. Once you’re confident in a protocol, you can always keep a simplified version of it on hand while you’re moving around the lab.

Keep the official manual

If there’s a protocol from the official manual, include that in your files with your own SOP, especially if you’re planning to make changes. For example, suppose you’re writing the protocol for a qPCR and plan on using a commercial kit. In that case, you’d want to include the kit’s manual alongside any changes that you’ve made in the optimization process. These don’t necessarily need to be in the same document, but having the original manual available (without having to hunt for it on the web) can be useful if you need to go back and check something in the middle of an experiment.

Keep a list of all your materials

A materials list makes it much easy to replicate an experiment if your lab suddenly switches universities or if you get a new job. That way, you know exactly what materials you used to produce the same result as before. This should include item reference numbers and even potentially a link to the item on the company’s website or wherever you bought it from (i.e. Fisher or VWR).

Include methods for analysis!

Sometimes you walk away from your data for a while, and when you come back you just can’t remember what the heck you did. This can be easily solved by writing down the steps or equations you used to analyze your data. If you had to use specific software, include basic instructions on how to use it in case you need to come back later.

Even in the most organized lab environment, SOPs help to provide structure and maintain consistent results throughout the course of your experiments. They can make it easier to train new students, and help keep things running smoothly in the lab. Having thorough lab SOPs can make all the difference!

This article was originally posted on The Bio Girls.

Letters of recommendation are pretty much universal in the academic world. We’re asked for them when applying to grad school or looking for a job. Typically, letters of recommendation come from professors, supervisors, or mentors, and are meant to be a testament to your qualifications and character. A strong letter of recommendation can sometimes make all the difference in your application. This can help provide insight into your career goals, motivations, previous experience, and fit for the position.

Who can you ask for a letter of recommendation?

Professors

I see a lot of grad school applicants hoping for a letter of recommendation from a well-known professor or researcher. While name recognition can mean something, the prestige of the person doesn’t matter nearly as much as personal connections. It’s more important to pick someone who really knows you and can speak to your talents. 

Consider whether you’ve spoken personally to the professor or if you just got a good grade in their class. Keep in mind, if you do ask someone who doesn’t know you well, they may ask you for more information or to actually write the letter of recommendation yourself. Professors are busy people, and sometimes just don’t have the time to dedicate to writing a letter for a student who they don’t recognize.

Research Advisors

Research advisors can be a great resource for letters of recommendation since you tend to work with them more closely. They can speak to your work ethic and research abilities, which is paramount when applying to STEM-related graduate school programs. While you work with other people in the lab, such as Ph.D. students and postdocs, having a letter from the professor in charge of the research can be important.

Bosses/Managers

Now, this somewhat depends on your job. If you’re working on the side as a barista, your boss may not be able to speak to the right skill set. On the other hand, if you’ve worked somewhere for a long time, a letter of recommendation from your boss may demonstrate work ethic, responsibility, loyalty, etc.

How do you ask for a letter of recommendation?

First things first, be polite! Whoever you’re asking is probably a busy person with a full e-mail inbox. Sometimes, it can take a while to get a response. I personally follow the “three e-mail rule” (which I also invented). This includes the original e-mail and two follow-up e-mails. If you’re still not getting a response after the third e-mail, it may not be worth your time. This can indicate how that person will communicate with you in the future and may lead to some last-minute stress.

If they ask you for more information about yourself before writing the letter, the professor may not know you well enough to truly attest to your skills. If they ask you to write your own letter of recommendation, this could actually be better, since you’ll have more control over the focus of the letter. This may also happen if you know the professor well and they simply don’t have enough time.

Afterward, make sure to show your appreciation! Not everyone will have the financial means to thank their references with a gift. This is perfectly fine, just make sure to thoroughly thank the person! Otherwise, a small gift, like a $10 coffee shop gift card, can be a good way to show your appreciation.

Finally, try to keep in contact! While you’re already on your way to applying for grad school or your next job, you may need to use them as a reference again in the future. Your reference will also love to hear when you get in or get hired! It’s good to keep these connections, as you never know how they could help you in the future.

This article was originally posted on The Bio Girls.

Trying to stay organized can seem daunting, especially when life can be so hectic. There’s no one fix to the giant stack of papers on the corner of your desk, but there are some ways to make it easier. Most of us start off organized and then descend into disorganized chaos once our schedules fill up, but organizing materials from the beginning can make it a lot easier to get back on track. So where do you start?

Notebooks

For the lab, it can be nice to have a smaller lab notebook to carry around with you for all your experiments. Sometimes your lab will provide a standard size notebook, but these can be a bother if you’re trying to conserve bench space. Otherwise, they’re also great for keeping track of meeting notes. My personal favorite is grid-style notebooks since they allow for more flexibility in your work. Adding a table of contents at the beginning of your notebooks can also help tremendously. Number and date the page when you begin writing, and then add them to your contents table as you go. Of course, it should also be noted that a good digital notepad app can easily meet all these needs. One of my favorites is GoodNotes, which does cost $10, but it’s worth it if you love taking digital notes.

Planners

Having a way to keep track of all your meetings and experiments can be not only useful but necessary. Some online planners can work just as well, if not better, than having a physical one (see those obsessed with notion or obsidian). However, some people prefer being able to bedazzle their planner or play around with the perfect bullet journal format.

Computer files

Keeping these organized can seem next to impossible sometimes. It’s no fun when you know you have a file, but you can’t seem to find it in your messy system of folders. Instead, start by picking big categories (school, work, personal, etc) and then break those down by year. Classes can then be organized by semester, class, and what kinds of materials the class includes (lectures, papers, homework assignments, etc). Research can be broken down into folders based on what kind of data/files you may end up with. This might mean different kinds of data, presentations, publications, etc. Eventually, it’ll turn into a big beautiful web of files that’s super easy to navigate. This can help tremendously if you ever need to share research with a collaborator or go back to an old homework assignment.

Binders

These can be useful for classes (if professors still print things) and jobs where paperwork is necessary. While most work seems to be moving digital, binders still come in handy for organizing papers if you’re the kind of person who occasionally likes to print them out.

While there’s nothing wrong with having a curated collection of sticky notes and haphazard paper mountains, it can make finding things an absolute nightmare. There’s no absolute cure for the chaos, but starting here will help keep you on track to staying organized in the future.

This article was originally posted on The Bio Girls.

Is it just me, or can talking to the dean of your college seem kind of terrifying sometimes?

When I first started to consider switching advisors in the middle of my PhD, I found that talking to the graduate school administration was one of the first steps I needed to take. This can seem overwhelming and daunting at times, but it’s important to understand the process and get as much information as possible.

But even before that, there were a lot of other people I talked to in the course of making this decision. Personally, I found that hearing other opinions, even if they were different than my own, gave me more clarity and helped me make the right choice for me.

So, who can you talk to about switching advisors?

Friends and Family

I started by turning to my friends and family, the people who know me best on a personal level. Talking to the people I trust most gave me a base level of support that I needed to move forward. Sometimes it can be tough to even start voicing out loud that you want to switch advisors, but talking to the people that love you can be a good start.

Classmates and Coworkers

While I kept my decision under wraps at first, I finally began to confide in several coworkers and classmates before moving forward. Depending on the situation, it can be difficult to talk to your peers about something that might seem sensitive. However, they may understand your situation better than people outside of academia and can help give you a fresh perspective on your decision.

Graduate College Administration (i.e. the dean of your college)

While it can seem scary, talking to your dean or another administration party can be one of the best ways to get information on how your graduate school handles the process of switching advisors. For example, my college had a step-by-step procedure that I needed to follow in order to switch. This can be important to understand your decision, how long it will take, and what you will need to do in the future for the transition to move smoothly.

Your advisor

The final (and most terrifying) step is to discuss everything with your advisor. Some graduate schools may recommend that you find a new advisor before telling your current one. In my case, I spoke to my current advisor before moving forward with the official process. Our conversation was open, honest, and respectful. This not only helped maintain my relationship with my old advisor, but also helped make the transition to a new advisor easier.

Conclusion

Switching advisors can seem like a really daunting process, and will elicit all kinds of advice from different people, with different perspectives. This can be helpful, but overall, it’s important to remember that this decision is about what’s best for you and your future!

This article was originally posted on The Bio Girls.

Searching for a supervisor can seem like a really daunting process at the start. Our supervisor often becomes an integral part of daily life, meaning your day-to-day can be strongly influenced by their leadership and the work environment they create. To some, this can be a major make-or-break moment for a PhD student or starting a new job.

Personally, I’ve found that the relationship you develop with your supervisor can be crucial to succeed both in the short term and long term. Knowing yourself and considering all the factors can be key to making these important decisions.

What is their work style?

In my opinion, this can be one of the biggest factors when it comes to your success but also depends on how well you can identify your own work style. For example, I’m happier and produce better work when I have strict deadlines to meet, while some people really thrive when they have the freedom to work on their own time.

Consider asking them about their work style. I’ve had supervisors that constantly micromanage and I’ve had supervisors that only check in once a month – it just depends on the person. And for me, one of these scenarios works better than the other. It’s good to know your own work style and what you personally would need from a supervisor to succeed.

Are they supportive?

Sometimes, things happen that you can’t predict, like health emergencies and family deaths. If something like this happens and your supervisor doesn’t understand or isn’t compassionate towards the situation, things can become very hard. While no one expects these kinds of things to happen, it’s important to remember the possibility and how your supervisor might respond to that.

Support doesn’t always need to be personal or emotional, but also in terms of career goals. If you know that you want to get out of academia and go into industry, make sure your supervisor knows this and is willing to support that goal, even if it’s outside their personal field of interest.

What’s the work environment like?

Part of this is the other people you’ll be working with – you can have the best supervisor in the world, but if the people you’re working alongside drive you crazy then you’re going to have a rough time. Your supervisor and coworkers’ organizational style will also impact the work environment. Even if your supervisor seems organized, their lab reagents and paperwork might be in a state of constant chaos.

What will you actually be doing?

This boils down to what you’ll actually be working on under the guidance of your supervisor. Often, it seems like this can be the most important factor, but in my opinion, it’s not. You’re better off finding somewhere you love to be, and I promise you will learn to love the work.

Are they well-connected?

Sometimes, your supervisor’s connections can end up greatly benefiting you. However, it’s important to also develop your own network, and not solely rely on your supervisor. But if you’re trying to get into industry and they happen to know a lot of people working in that area, they might be able to help out.

Your relationship with your supervisor can have a huge impact on your studies and your career. Despite this, it’s important to remember that no one is perfect, and your supervisor might not be able to meet all your criteria. Difficult situations are bound to arise, but asking the right questions beforehand can prepare you and help you navigate through these conversations.

For me, it took unpleasant experiences to find what I truly needed out of a supervisor, and my hope is that maybe you won’t have to go through the same.

This article was originally posted on LifeApps.

Your Vaginal Microbiome and How to Take Care of It

Your body consists of trillions of microbes, many of which have made themselves at home in your vagina. Your vaginal microbiome can play a critical role in protecting you from disease and maintaining good vaginal health.

New products on the market have turned their attention to the vaginal microbiome, whether through vaginal probiotics that claim to correct microbiome imbalances or at-home testing to help diagnose the cause of recurrent infections. Unfortunately, not all products match up with the research, and some can even cause harm. So, how do you maintain a healthy vaginal microbiome.

First things first – what is your vaginal microbiome?

Your vaginal microbiome is a dynamic ecosystem that consists of all the microbes that reside in your vagina. This includes a variety of different kinds of bacteria, fungi, and even viruses. However, what kinds of microbes and how many of them are there can change greatly over time. These changes can be caused by pregnancy, menstruation, personal hygiene, hormone levels, sexual intercourse, and more. 

How does your vaginal microbiome keep your vagina healthy?

Many vaginal microbiomes are largely dominated by Lactobacillus species, which tend to be associated with good vaginal health. These bacteria are well-known for their ability to ferment sugars to produce lactic acid, therefore lowering the pH in your vagina and preventing infections. However, significant changes to the vaginal microbiome caused by frequent sexual intercourse, multiple sexual partners, and douching can negatively impact the pH and composition of your vaginal microbiome. 

Similarly, it’s been found that some people have vaginal communities that are more associated with sexually transmitted infections (STIs) and poor reproductive outcomes. Normally, your vaginal microbiome community helps to defend you against vaginal infections, either by directly killing the “harmful” microbes or by outcompeting them. This can also protect you from STIs. But when your vaginal microbiome is imbalanced, sometimes it can’t do its job properly.

Do vaginal healthcare products help?

Although statistics vary from study to study, about one in five women ages 15-49 in the United States clean or wash the inside of their vagina. Further, a survey of hygiene practices in Canadian women showed that 95% used at least one product in/around the vaginal area. However, research has shown that feminine hygiene products increase the risk of infections such as UTIs and bacterial vaginosis, a condition characterized by inflammation due to overgrowth of certain bacteria. 

Some feminine hygiene products also claim to be able to regulate the pH of your vagina. However, it’s actually the Lactobacillus community in your vaginal microbiome that helps to maintain your vaginal pH. It’s been shown that these products are not able to change your pH for more than a few hours. If anything, vaginal cleansing products can be harmful to Lactobacillus and other healthy bacteria. This can cause the pH of your vagina to increase, making it less acidic and making your vagina more prone to infection.

Currently, there are some products on the market that claim to help maintain a healthy  vaginal microbiome. Some even include prebiotics and probiotics to promote the growth of “good” microbes. Prebiotics help to feed the good bacteria in your vaginal microbiome to increase their population, while probiotics directly repopulate your vaginal microbiome with good bacteria. Further, some of these products claim to help relieve bacterial vaginosis-related symptoms, such as itching, irritation, or discharge. 

But what does the research say about vaginal products for the vaginal microbiome?

Overall, studies have shown that most vaginal hygiene products end up harming your vaginal microbiome, instead of keeping it healthy. Intravaginal cleaning has been shown to have many negative effects, and has been linked to an increased risk of STIs, pelvic infection, premature delivery, and more. Further, conditions such as bacterial vaginosis can cause symptoms that many vaginal products claim to treat, such as itchiness and odor. In reality, feminine hygiene products can imbalance your vaginal microbiome, actually causing bacterial vaginosis instead of treating it.

Further, there are mixed options amongst the medical and research community on whether or not probiotics can be effective in helping maintain a healthy vaginal microbiome. What a “healthy” vaginal microbiome is can vary greatly. For example, some people that have an “imbalanced” microbiome may experience no symptoms. This makes it more difficult to conclude exactly how probiotics are impacting the vaginal microbiome from person to person. The variety of different species in probiotics, whether consumed orally or applied vaginally, also makes it difficult to distinguish the effects.

There are currently several clinical trials in progress to look at how probiotics affect the vaginal microbiome and associated health conditions, such as bacterial vaginosis, vaginal candidosis, fertility issues, and more. 

How about at-home vaginal microbiome tests?

There are currently kits on the market to test your vaginal microbiome, marketed mainly toward people experiencing chronic vaginal infections or fertility issues. Unfortunately, while some research has been done to determine what changes in the vaginal microbiome are linked to these issues, there are no definitive answers to these questions or targeted vaginal microbiome treatments available. While it could be interesting to see what your vaginal microbiome looks like, the bacterial community in your vagina is quick-changing and dynamic. This means that the test will only capture a snapshot in time, making it difficult to account for variations such as menses, diet, or changes in hygiene routine. 

So, how do you maintain a healthy vaginal microbiome?

The best thing that you can do to take care of your vaginal microbiome is to do nothing at all!

If you’re washing around your vaginal area, the best thing you can use is a mild, unscented soap. Eating a healthy diet and maintaining a good hygiene routine can also help, but this doesn’t need to include any kind of vaginal hygiene products. It’s been shown in studies that orally consumed probiotics are unlikely to alter your vaginal microbiome. Vaginally-inserted probiotic products, while an interesting idea, have not yet shown promising results in clinical studies. If you’re experiencing issues down there, such as recurrent UTIs or bacterial vaginosis, your doctor will have the best recommendation. It can be tempting to try to reach for a product off the drug store shelves, but most of them are based on unproven claims and, in some cases, can make things worse. 

Overall, if you want to take care of yourself down there, don’t bother doing anything at all! Your vaginal microbiome is a complex and self-regulating community of microbes that quietly work together to protect you from disease. The best thing you can do to maintain your vaginal microbiome is to leave it alone, and let it do its magic.

This article was originally posted through LifeApps.

Throughout the human body, there are trillions of microbes that have made themselves at home. Our microbiome consists of bacteria, fungi, and viruses that interact with our cells and help drive our bodies at a cellular level.

However, in recent years, research has begun to focus on how the microbiome might impact different diseases and conditions in human health. Largely, studies have shown the potential to improve clinical outcomes by manipulating the microbiome in various ways. In particular, more research is investigating the relationship between the microbiome and cancer. While there’s still much to learn about this complex relationship, a better understanding of how the microbiome impacts cancer development and treatment could have huge clinical benefits.

What is the microbiome?

A microbiome consists of microorganisms in a specific environment. In this case, that environment would be different parts of your body like your skin, mouth, and especially your gut. Your gut microbiome is home to billions of bacteria, with 100 billion resident bacteria in each gram of stool. Together, these bacteria impact a variety of different processes in your body such as metabolizing hormones, influencing levels of inflammation, and much, much more.

Every person is born with a microbiome that continues to change and develop as they grow. Many different factors can impact your individual microbiome. Some of these are environmental factors such as where you live, if you live around animals, or what you eat. However, lots of other factors including age, genetics, and even some diseases can greatly impact the community of microorganisms in your personal microbiome.

How does the microbiome impact cancer?

Recently, more studies have begun to investigate how the microbiome impacts cancer. 

Some of the earliest studies looking at the microbiome and cancer focused on colon cancer. It’s been shown that having an imbalanced microbiome, or what scientists call “dysbiosis”, can lead to some types of cancer, including colon cancer. This imbalance could be because a person is missing certain types of bacteria or due to changes in the amounts of different bacteria. These variables factor into how researchers measure diversity in the microbiome. Alternatively, this can also work the other way around in some cases, where cancer is what changes the composition of the microbiome. For example, bone tumors with high levels of hydroxyproline (an amino acid found in collagen) change the bone microbiome by increasing the number of bacteria capable of degrading hydroxyproline.

While having more bacterial diversity is good in the gut, greater microbiome diversity in the female productive tract has been associated with human papillomavirus (HPV). One way in which HPV infection, the major cause of cervical cancer, can be prevented is through vaccination. Although vaccines and cervical cancer screening have been largely effective in reducing cervical cancer rates in the US, prevention is dependent on access to these medical services.

Your gut microbiome can also impact other types of cancer that don’t develop in your gut, such as breast cancer. Breast cancer can be heavily impacted by levels of hormones in your body, especially certain hormone-positive types of breast cancer. Studies have shown that your gut microbiome and the bacteria that inhabit it can impact hormone metabolism and, ultimately, the levels of hormones circulating through your body. High levels of circulating hormones, such as estrogen, are associated with an increased risk of developing cancer.

Even further, the gut microbiome can affect a person’s response to immunotherapy treatments for cancer, such as skin cancer. Some research has indicated that having a diverse microbiome could improve the response to immunotherapy.

How do diet, medications, or supplements affect your microbiome?

For a long time, scientists have understood that different diets lead to different communities of bacteria in the gut. It’s been shown that your microbiome can change as quickly as three or four days after drastically changing your diet. For example, the microbiome composition of meat-eaters is significantly different compared to vegetarians/vegans. Some diets designed to treat certain diseases, such as inflammatory bowel disease (IBD), also change the microbiome. This can be important to cancer prevention, as IBD increases the risk of developing colon cancer.

Some medications can also drastically alter your microbiome. One example of this is antibiotics, which can deplete the good bacteria in your gut at the same time as fighting your infection. However, supplements such as prebiotics and probiotics have been investigated to replenish the good bacteria and rebalance your microbiome. Prebiotics can be consumed as pills or in the form of high-fiber foods like fruits and vegetables. These help to feed the good bacteria in your gut and grow their populations. On the other hand, probiotics directly repopulate the good bacteria in your microbiome. Probiotics can also be consumed as pills or in the form of fermented foods like yogurt, kombucha, or kimchi. Prebiotics and probiotics are used primarily to alleviate side effects from other cancer therapies, such as chemotherapy and radiation. However, it should be noted that recent studies have shown that some probiotic treatments may make cancer immunotherapy treatment less effective.

How can studying the microbiome help improve the lives of cancer patients?

Better understanding how the microbiome impacts cancer, and vice versa, can lead to improved treatment methods and positively impact the quality of life of patients.

In recent years, fecal transplants have grown in popularity as a way to treat an imbalanced microbiome in various gastrointestinal diseases, such as Crohn’s, ulcerative colitis, and irritable bowel syndrome. A fecal transplant is a stool sample taken from a healthy donor and then given to the patient. Sometimes this is as easy as swallowing a pill, while other times fecal transplants will be done by infusing stool during a colonoscopy or through your nose. Many cancer treatments, such as radiation and chemotherapy, can negatively impact the composition of your microbiome and diminish the good bacteria you need in your gut. These bacteria can be replenished through fecal transplants. However, research is still being done to understand how fecal transplants can positively affect the microbiome, as well as how to prevent negative impacts from more dangerous bacteria.

A study published in October 2021 showed that changing the microbiome can positively impact prostate cancer therapy. Prostate cancer is frequently treated with androgen-deprivation therapy (ADT), which depletes the androgens needed for prostate tumors to grow. Unfortunately, patients often become resistant to ADT and alternative treatment options are limited. However, this study found that patients resistant to ADT had a microbiome composition capable of making androgens. Resistance to ADT could then be corrected by treating this imbalance in the microbiome, either through treatment with antibiotics, fecal transplant, or Prevotella species (a bacteria that is depleted in resistant patients).

Ultimately, research has only begun to touch on how the microbiome can be manipulated to improve cancer treatment and the lives of patients.