The 5 Keys to A Great Presentation

Gaia Vasiliver-Shamis

We all attend at least 1-2 seminars on a weekly basis, but let’s admit it – they are often boring, not meeting the expectations set by the title and we probably attended because there was free food involved (pizzzzzzza!) or our boss told us to go or both.

Let’s do a virtual raise of hands – how many of you ever attended a seminar where the science was amazing, but it was given in the most boring and impossible way to follow? Right? I mean if all presentations were that good, we wouldn’t need to bring the seminar bingo to it.

Well, it all depends on the presenter, because even the most interesting, Continue reading “The 5 Keys to A Great Presentation”

A Graduate Student's Browser History

Thalyana Smith-Vikos

We’re all guilty of having 10 internet browser tabs open at once on our laptops, but which websites should you be surfing while waiting for that incubation to finish? For “new” and “old” grad students alike, it’s important to balance researching specific details on your project with staying informed about the world outside of your bench. Take the time to give yourself perspective on how your research can be added to the body of scientific knowledge, as well as what is expected of you and what you should expect of yourself as a graduate student. Here are some tabs you can keep open that will meet these requirements:

Something outside your field of study

Staying up-to-date with the latest scientific publications (especially if they have nothing to do with your research) requires a lot of effort, but if you can put aside some time every day (or at least every week) to read about the latest news, it can be a pleasant experience! Start by taking note of which journals usually publish the most important articles in your field, and then browse the table of contents for these journals to see what other articles were published. Also, visit the homepages of Nature, Science, Cell, and other journals in these publishing groups to see which new research stories are highlighted. Lastly, visit the communications/public affairs website for your university to see which of your colleagues got published! (Obviously, these suggestions are in addition to using Scizzle and following our Scizzle Blog!)

Something outside of academia

As Science magazine is distributed by AAAS, the magazine’s website also contains the latest science policy news updates regarding decisions on federal grants, regulatory procedures, etc. It’s also worth your while to read Scientific American and the science sections of the New York Times, Huffington Post, and any other news sources you subscribe to, just to get a sense of how science research is portrayed to the public. This can also help improve your conservations about science with non-scientist friends and relatives! (Another plus for Scizzle Blog: in addition to highlighting the recent literature, we also have many other posts of interest for any scientist.)

Something career-related

It’s never too early to start thinking about your career, especially if you don’t want to stay in academia. Networking with professionals in other fields may seem intimidating, but never fear, LinkedIn is here! I am always surprised to learn how many PhD students are not on LinkedIn: everyone should be on LinkedIn! It’s the best way for you to display an abridged version of your CV for any potential employer to view. Yes, we are students, but we should also be establishing ourselves as professionals at the same time. Start by connecting with your friends and alumni from your PhD program, and you will quickly learn how large your networking circle actually is through 2nd and 3rd-degree connections. Join discussion groups and post on forums regarding your research interests or general scientific interests, careers outside of academia, alumni organizations, etc. Start following companies where you might be interested in working and make a note of how often they have job postings.

Something fun

Science can be very frustrating, especially after repeating that PCR for the third time and still getting a blank gel. To let off some steam and commiserate with other PhD students, I recommend visiting whatshouldwecallgradschool.tumblr.com. This website contains an extensive list of the many unhappy (and some happy) moments we experience as graduate students, accompanied by hilarious GIFs to illustrate these feelings. I also suggest visiting phdcomics.com, which is a comic strip (started by formed PhD student Jorge Cham) with recurring grad student characters who have to TA classes, write grants, perform experiments, attend happy hours, and anything else you can think of. Being able to laugh about all of these experiences will preserve your sanity throughout grad school!

 

Measure for Measure

Celine Cammarata

What exactly makes “good” science?  To some researchers’ chagrin, a group of universities in the UK believe they have it figured out.

The Snowball project, brainchild of eight premier British universities, seeks to set forth a universally applicable set of measures for determining the quality of research and the success of investigators, focusing on factors such as number of grants and patents and the frequency with which papers are cited.  As described by science policy writer Colin Macilwain, the project is part of a growing trend of “science metrics.”  But what does this mean for science and scientists?

Two main issues arise around the use of such measures.  Continue reading “Measure for Measure”

Domesticated HIV Leads to Gene Therapy Success

Alisa Moskaleva

For as long as biomedical scientists have known that DNA mutations cause disease, they wanted to be able to correct them. Dozens of rare but devastating human diseases are caused by a mutation in a single gene. If a mutant form of the gene causes the disease, then giving the patient the correct form of the gene should cure it. This idea is called gene therapy. Now, two papers in the 23 August 2013 issue of Science by Dr. Luigi Naldini and co-workers report prolongation and improvement of quality of life from gene therapy for six children with rare genetic diseases. These papers are not the first to report health benefit from gene therapy and not the first to use the technique of lentivirus-mediated hematopoietic stem cell gene therapy, which involves domesticated HIV and which I’ll explain shortly. However, the papers address two previously incurable diseases, metachromatic leukodystrophy in one paper and Wiskott-Aldrich syndrome in the other, and add to the evidence that the gene-therapy technique that involves something as scary as HIV is safe.

So, what is lentivirus-mediated hematopoietic stem cell gene therapy and what does it have to do with HIV? Let’s start with “lentivirus-mediated.” Lentivirus is a virus with an RNA genome that infects eukaryotic cells. To persist in cells and reproduce, lentivirus integrates its RNA genome by converting it into DNA and adding this DNA into the genome of the host. HIV is a lentivirus that infects T-cells. By replacing the gene in the HIV genome that targets it to T-cells with a gene that recognizes all mammalian cells and further adding a gene of interest, it’s possible to use HIV to integrate the gene of interest into the genome of any mammalian cell. So, if only HIV could be made to stop replicating uncontrollably, gene therapy could use it to deliver correct forms of disease-causing genes to patients’ cells. Over the past twenty years, scientists have domesticated HIV by removing most of its genes, and constructing versions that can infect but can’t replicate. HIV-based lentivirus is now routinely used in research to introduce DNA into mammalian cells and it can be a method of gene therapy. Hematopoietic stem cell gene therapy means that hematopoietic stem cells, the cells that can give rise to red and white blood cells, are the targets of gene therapy.

Why did Dr. Naldini and colleagues target hematopoietic stem cells? Wiskott-Aldrich syndrome is a disease of white blood cells, so it makes sense to deliver the correct form of the disease-causing gene to their source. Metachromatic leukodystrophy is a disease of the brain and the peripheral nervous system, so at first glance brain cells and nerve cells should have been the targets of gene therapy. However, getting the gene to integrate in enough cells requires literally bathing the cells in a high concentration of lentivirus. It’s impossible to achieve a high enough concentration of lentivirus for cells inside the body. Delivering genes to cells inside the body remains one of the biggest challenges in gene therapy. Hematopoietic stem cells are a much easier target because they can be isolated from the body by drawing blood and sorting it. The isolated cells can then be concentrated and bathed in lentivirus before being re-injected into the patient’s bloodstream. In metachromatic leukodystrophy, the disease-causing form of the gene causes the accumulation of a toxin and the correct form destroys it. The authors hoped that hematopoietic stem cells with the correct form of the gene would give rise to cells of the immune system that would migrate to the brain and the peripheral nervous system and scavenge the toxin. Therefore, hematopoietic stem cells are a good target for gene therapy not only because they are easy to isolate but also because they can migrate and help out other cell types that cannot be targeted directly.

However, hematopoietic stem cells have a dark side. When they are injected into the patient’s bloodstream to exert their beneficial effect, they can transform into cancerous cells and cause leukemia. Leukemia was an unfortunate side effect of gene therapy against the Wiskott-Aldrich syndrome and two other rare diseases using a different method of gene delivery called gamma retrovirus that preceded lentivirus. Gamma retrovirus is also a virus that infects eukaryotic cells and integrates its genome into the host genome. Analysis of the genome of cancerous cells revealed that when the gamma retrovirus integrated, a part of its DNA ended up near a cancer-causing gene and, acting like a switch, turned it on. Mindful of this, Dr. Naldini and colleagues analyzed the genome of hematopoietic stem cells from their patients several times after treatment. Reassuringly, they did not find any cells with inappropriately activated cancer-causing genes 1.5 to 2 years after treatment in patients battling metachromatic leukodystrophy and 1.5 to 2.5 years after treatment in patients with Wiskott-Aldrich syndrome. Dr. Naldini and colleagues hypothesize that HIV-based lentivirus may be safer than gamma retrovirus because it has fewer DNA switches that can turn a gene on, and because lentivirus integrates more randomly in the genome than gamma retrovirus. They will be following their patients for years to come.

Is gene therapy with domesticated HIV safe? Only time and more research will tell. But six children who were predicted to die months ago are walking and running, playing and talking. They got a respite from dreadful symptoms, like eczema, internal bleeding, and inability to walk or even to hold up their own head. One fervently hopes for more gene-therapy good news.

Using Your Spidey-Sense to Network

Neeley Remmers

As I am going through the process of solidifying my first position post-graduation, I am realizing more and more the value of networking. I had always had a general appreciation for networking even during undergraduate school and knew that in the professional world, the success of your career can be influenced by knowing the right people. In fact, I used networking to get my two internships in the pharmaceutical industry while still in undergrad.  Thanks to my undergraduate advisor having ingrained in me the importance of networking, I knew the importance of making an impact when meeting people for the first time at the various conferences I attended throughout my graduate career. I also jumped at the opportunity to take invited speakers to breakfast, dinners, or lunches, even if their research area was outside my interests, Continue reading “Using Your Spidey-Sense to Network”

Lessons Learned from the Science Fair

Thalyana Smith-Vikos

When I first started my PhD at Yale University four years ago, one of the program directors held a meeting for new students to learn about extracurricular activities on campus and around New Haven, CT. At first I was a little confused; how did they expect me to participate in all of these programs while still completing my course work and teaching requirements and working in the lab full-time?

However, once I began my lab rotations and had conversations with older graduate students, I quickly realized that many PhD candidates in our program devote a great deal of their time to volunteering for community-wide science activities outside of the lab, Continue reading “Lessons Learned from the Science Fair”

5 Ways to Make the Most Out of Your Grad School Experience

Welcome to grad school, you are on your way to adding 3 magical letters at the end of your name. As we’d like y’all to start well-informed and be prepared, our brilliant contributors share their wisdom and best advice on making the most our of your grad school (and beyond) experience!

That’s our top 5:

  1. Run while you still can! Just kidding….
  2. Learn new things and learn all the time and it will all come together at the end, we promise!
  3. Take a careful look of the PI personality and lab’s dynamics when choosing a lab.
  4. Keep it balanced, as in stay healthy!
  5. Diversify your experience at the bench and beyond it.

Now read on: Continue reading “5 Ways to Make the Most Out of Your Grad School Experience”

Mapping the Human Brain – the Challenges Faced

Sophia David

The human brain is made up of billions of neurons that communicate with each other via trillions of connections. Together, they make up a network of unimaginable intricacy. Perhaps it is not surprising then, given this complexity, that things frequently go wrong within the brain. Approximately 1 in 4 people suffer from a diagnosable mental health disorder within any given year and as many as five million Americans now live with Alzheimer’s disease.

Unfortunately, drugs to treat brain disorders have been slow to materialize. Many large pharmaceutical companies have withdrawn their research on mental health diseases due to the length of time it takes these drugs to be developed and the high failure associated with them. Essentially, to big pharma, the field is unattractive and economically not viable.

Our inability to Continue reading “Mapping the Human Brain – the Challenges Faced”

Leafing Through The Literature

Thalyana Smith-Vikos

Highlighting recently published articles in molecular biology, genetics, and other hot topics

Battle of the Small RNAs

Sarkies et al. have analyzed gene expression in the nematode C. elegans upon infection with the positive-strand RNA virus Orsay. As RNAi is required for the immune response, the Argonaute protein RDE-1exhibits less repression of its endogenous small RNA targets to focus on its exogenous target. The authors also showed that a wild C. elegans isolate exhibits a reduction in miRNA expression and a consequent increase in miRNA target levels upon viral infection.

Continue reading “Leafing Through The Literature”

How Premature Birth Affects the Brain – and How We Can Help

Celine Cammarata

The world can be a pretty tough place – especially if you’re not ready for it.  Among the possible complications of premature birth is reduced oxygen flow to the brain due to an infant’s underdeveloped respiratory system, which in turn can have lasting effects; indeed according to the Mayo Clinic, preemies are more likely to experience cognitive, psychological, and behavioral problems later in life.  While relatively little is understood about how this early hypoxia damages the brain, new work by Komitova et al. offers both insight and a possible route of therapy.

Using a mouse model of premature birth in which animals were exposed to reduced oxygen as infants, the authors demonstrated that Continue reading “How Premature Birth Affects the Brain – and How We Can Help”