sciency holidays

by Juliane
For the end of the year, I would like to share another science video, this time holiday themed. enjoy and happy holidays!

 

 

Keeping enthusiasm

by Juliane

As a postdoc it is sometimes hard to maintain enthusiasm. When I started in science I was super-enthusiastic, everything was new and interesting and I learned fascinating stuff every day. I sometimes wish I was still like that. Over time I noticed that there is  another side of lab work: failed experiments, hours of incubations, tons of paperwork. This is balanced by the little successes: a cloning step that finally worked, a stable cell line that stays stable, a band on a gel at just the right size. Those little successes help me to reach the bright spots: the exciting results, when cells behave in unexpected yet fascinating ways, when analysis of the mass spec results in exactly the one protein predicted by your pet theory, when everything falls into place and finally makes sense.

As a postdoc such bright spots become less frequent. This is not the postdoc’s fault; this is how it is supposed to be. PhD projects are designed to yield results in time for a thesis. Committees, supervisors and mentors make sure that the projects aren’t too risky or too long. So who therefore is going to undertake the risky, long projects? Postdocs! New postdocs will often get risky projects, including ones that the PI has been sitting on for some time, or projects other people have failed at (often more than one other person). This can lead to fewer positive moments for the postdoc and instead, longer stretches of frustration interspersed with small successes which become less and less valuable over time. Unfortunately this is normal too, the first time I got a positive clone after a ligation was amazing, the 10th time was nice, but after my 63rd successful plasmid, this is no longer a big deal. It is hard to keep up enthusiasm when you only progress in tiny increments and the big goal is so far away that you can’t even see it yet.

One strategy that works for me is to make the project mine. I found the best way to make a project mine is by talking about it a lot, discussing it with potential collaborators and defending it to colleagues in talks and poster presentations. However postdocs often have few possibilities to present. The reason for this is related to the long and risky projects often undertaken by postdocs. Such research will typically not quickly lead to results that can be presented at conferences. In addition conferences are increasingly expensive. To just go and present a poster that doesn’t add much data to the existing scientific knowledge might not be a cause the PI is willing to spend money on. There are few travel grants available to postdocs and we don’t earn enough to pay for such trip ourselves. At home, postdocs, especially early ones, are seldom invited to speak at department seminars or present their work to other groups in a similar field. The best solution might be to take every opportunity to talk about research, even if it is a chalk talk for 1st year PhD students.

But even if the project works brilliantly and the PI sends you to international conferences and is generally supportive of your career, other things can interfere with enthusiasm for work. We are getting older. Graduate students can readily put their life on hold for 3-5 years, but postdocs have already gone through this. Now other things get important; we might want to take our relationships to the next level: get a mortgage, get married, maybe have children. All those life projects need enthusiasm, enthusiasm that is taken away from work-related enthusiasm. However, this is not a bad thing, very few people can just work and not live and the few that do, end up lonely and burned-out having a heart attack in their 40s. It is important, but difficult to find a good work life balance and neither aspect should take too much strength and enthusiasm away from the other one. Despite this, we should always remember why we have followed this path in life. Working in science, discovering fundamental things about the world around us can be a fascinating and at times fun life, which can and should inspire enthusiasm in other aspects of life. All we can to is keep up enthusiasm for our work and make the little lights shine brighter.

postdocPI At some point another enthusiasm killer rises its head (or so I have heard) is the “why am I doing this for this guy, who doesn’t appreciate me” enthusiasm killer. When you have learned everything you can from your PI, write all your own papers and the ones for the PhD students as well (with minor corrections by the PI), basically wrote the last grant even though it is still their name on the grant, he/she is corresponding author and you only get a pat on the back, then it is hard to keep up the enthusiasm, spread cheerfulness in the lab and keep everything afloat. However, this lack of enthusiasm is a good thing: it means that the postdoc is finally ready to move on to new horizons and challenges.

Nemo

by Juliane

In 2003 these two fish swam across the pacific ocean to find Nemo:

nemofish

Five years earlier, S. Yamaoka and colleagues also set out to find Nemo, the NF-kappaB essential modifier. NF-kappaB is a very famous transcription factor, which is present in all eukaryotic cells and can be activated by a large number of signaling pathways in response to external stimuli, such as viral or bacterial infections or interleukin signaling. It is active as a dimer or trimer of several subunits in different combinations, depending on the activation signal. Canonically all NF-kappaB is regulated by I-kappaB, the Inhibitor of NF-kappaB that prevents multimerization and DNA binding, unless it is modified by IKKs, I-kappaB kinases. Nemo is one of these kinases and is responsible for polyubiquitination of I-kappaB, resulting in degradation of the inhibitor and activation of transcription by NF-kappa-B.

In 1998, Yamaoka et al. were unable to find Nemo in cell-lines that are defective in their NF-kappaB response. The unresponsiveness of these cell-lines to NF-kappaB was altered by transfection of plasmids encoding for Nemo.

With ‘Finding Nemo’ only filmed in 2002 it is more likely that the researchers named their new-found modifier after Captain Nemo!!

nemocapt

The enigmatic explorer from 20000 leagues under the sea, written in the same city where Nemo was discovered, Paris.

The search for Nemo continues, only in 2009 S.Rahigi and colleagues actually caught a glimpse of Nemo, most of its structure is still hidden. Finding the NF-kappaB essential modifier may be way harder then finding a clownfish in the South Pacific, but maybe easier then tracking down Captain Nemo and the Nautilus.

nemoprot

References:

Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, Kato R, Kensche T, Uejima T, Bloor S, Komander D, Randow F, Wakatsuki S, Dikic I. (2009) Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell.;136(6):1098-109. doi: 10.1016/j.cell.2009.03.007.

Yamaoka S, Courtois G, Bessia C, Whiteside ST, Weil R, Agou F, Kirk HE, Kay RJ, Israël A. (1998) Complementation cloning of NEMO, a component of the IkappaB kinase complex essential for NF-kappaB activation Cell. 93(7):1231-40.

http://en.wikipedia.org/wiki/Captain_Nemo

http://www.uniprot.org

The Art of Follow-up

by Lauren, CEO of propel careers

this post is reposted from the propel careers blog.

Following up with individuals who you meet at scientific conferences, through networking, and other activities is important to develop relationships with your connections. Over time, these relationships can provide insight into industry, various career paths, and job opportunities. These connections should be actively fostered. Below are tips on how to follow up and cultivate your network. These tips extend beyond sending the initial “nice to meet you at (fill in the blank) scientific conference / networking event” email.

Read industry relevant newsletters and follow up with your contacts Stay current with industry news by reading sources such as Xconomy http://www.xconomy.com/ (for entrepreneurial companies), Fiercebiotech http://www.fiercebiotech.com/, Biospace http://www.biospace.com/ or MassDevice http://www.massdevice.com/ . Various news sources exist for each focus area so identify ones relevant to you. When you see news about a contact’s company, email them to mention it. For example, congratulate them for their firm’s successful commercial approval, fundraise(r), or partnership. Your contacts will appreciate that you are paying attention to their company and keeping in touch.

Stay in touch on LinkedIn

Use LinkedIn to stay in touch with your contacts. Add details to your profile so your connections can see your background and experiences. Use the status update feature on LinkedIn to let your contacts know when you publish papers and speak at conferences.

Get involved in networking groups or industry associations

Take an active role in a networking group like Healthcare Business Women’s Association (http://www.hbanet.org/ ) or an industry association such as the Boston chapter of AACR (http://aacrboston.org/) to build connections with people who share your passions. Hundreds of such organizations exist, so identify those relevant to your background and interests and become involved. Join a committee within the group, such as event programming, and actively attend the group’s events. Your involvement will build connections and allow you to stay in touch with people who are also active in the organization.

Invite your connections to speak on a panel

When your school or networking group is looking for speakers for career panels, industry focused events, or seminars, reach out to your contacts and ask them to participate. Even if your contacts cannot participate due to schedules, they will appreciate that you reached out. This is a wonderful way to keep in touch.

Ask your connections for career/industry advice

Ask your contacts about their career paths, how they chose them, and what guidance they would provide for someone looking to be in a similar career. People enjoy helping others and feel good when they can provide advice, especially career advice.

Let your contacts know when you publish a paper or speak at a conference

Share details about your recent publications, presentations, conference abstracts, or other scientific details with individuals who have expressed interest in your research. Through this, you build thought leadership and become a resource for your contacts.

Numerous opportunities exist to follow up with your connections. Tailor your approach and use multiple avenues of engagement. Through your effort, not only will you build connections, but you will gain a lot of industry knowledge as well.

 

Career advancement for postdocs – five tips

by Juliane

As postdocs we are always striving to advance our careers, foremost through performing brilliant research in the laboratory or in silico and publication of said brilliant research. Unfortunately being great in the lab is simply not enough to successfully transition to a faculty position. Here are some ideas that could help postdocs acquire the skills necessary.

1.     Write a review

Ask your PI if he is planning to write a review and suggest that you help him write the article. If he is not planning to, suggest a topic, ask for his feedback, write the review and submit it with your PI (after he has corrected it).

What do you win? Another publication for your CV together with in depth knowledge of the current literature

2.     Peer-review manuscripts

A lot of postdocs already help their PIs peer-review manuscripts, but the editors of the journals will often only see the PIs name, since she is the official reviewer. Ask your PI if you can review a manuscript under your own name. She might have to email the editor and suggest you as an expert in the field, but once editors know you, they might continue to use you as a referee.

What do you win? At least one editor will know your name and that you have experience reviewing papers

3.     Be social

Maybe your department, corridor, floor or lab uses a common lunch room, where everybody has lunch at approximately the same time. Join them! Have conversations with different people every day or with the whole group. If your department, floor, or a multi-lab group has any form of social gatherings, go! It could be a happy hour or a monthly bowling night. If nothing like it exists suggest it once or twice, maybe it becomes a regular occurrence!  Even though it might be much nicer to go home and not spend time with people that you have just spent all day with, this is a great opportunity to meet peers in a more relaxed environment and maybe hear some gossip about positions in other institutes.

What do you win? Networking skills, a peer network and a nice evening out

4.     Serve on boards/committees

To get the full benefit of joining scientific societies like AAAS, NPA or AWIS, participate actively in their events. Not only read their newsletter, but attend meetings, join one committee or volunteer to help out during events. This is a great opportunity to meet PIs, postdocs and PhD students from other institutes around Boston and increase your professional network, plus it looks great on your CV.

What do you win? Contacts, experience and insights into alternative careers (e.g. scientific management)

5.     Apply for fellowships

Look for postdoc fellowships, even partial ones, and apply. There are quite a lot of small organizations that sponsor postdocs/PhD students, often with strangely specific topics.

What do you win? Even if you don’t get the fellowship, just writing the application and maybe getting feedback from the organization you applied to, helps to identify areas which you need to improve. If you get it, you now have money! This gives you some independence from your PI, since it is your own money, plus it is a great advantage when applying for grants.

Every postdoc and every PI is different; some of these suggestions may not work for you or your PI. However, if you have experience with any of the above or other suggestions then please leave a comment!

SNAP

You can snap your fingers.

You can snap a photo, use it in windows 7 or snap a lock shut.

To snap is a very useful verb.

No wonder that some scientists (G. Oyler and colleagues) decided that SNAP would be a great acronym for synaptosomal-associated protein.

SNAP was discovered in synaptosomes in 1989. Synaptosomes are obtained by gently homogenizing brain tissue and are isolated synaptic terminals which can be used to study synaptic potentials and transmitters more easily than in complete neurons.

SNAP is a regulator of vesicle docking and fusion and therefore in complex with others responsible for passing signals through synapses to other neurons in the mammalian brain.

There are several SNAPs in humans and other animals, which are numbered according to their molecular weight, e.g. SNAP-25 or SNAP-29.

References:

Oyler GA, Higgins GA, Hart RA, Battenberg E, Billingsley M, Bloom FE, Wilson MC. (1989) The identification of a novel synaptosomal-associated protein, SNAP-25, differentially expressed by neuronal subpopulations. J Cell Biol. 109(6 Pt 1):3039-52.
http://en.wikipedia.org/wiki/Synaptosome
http://www.piercenet.com
http://www.uniprot.org

Advice for Listing Research Details on Your Resume

by Lauren, CEO of propel careers

this post is reposted from the propel careers blog

When you apply to a job, the details listed on your resume provide your “future employer” with information about the type of job you are looking for. The key words you include, the way you phrase your accomplishments and experiences, how you order your bullet points, all of this matters. These details build your brand.

I have been asked numerous times for guidance on what should be included in a resume. Below are a few thoughts on this important topic.

RESEARCH ROLES

If you are looking for a “bench research-based” role, make sure you include major research techniques used during each of your roles, as well as a separate section listing all of the research techniques you have ever used and know well. An HR person and hiring manager will want to see both the current techniques and previous ones since this indicates how you have developed over time. Whether you are a post-doc, or an industry professional, listing these details is important to show growth.

Many companies use resume-parsing systems to input a candidate’s resume details into their database. Companies then scan resumes against job descriptions to see which candidates could be a fit. Resumes without details listed won’t come up as matches when scans are done. Therefore, even if you have the relevant experience, companies won’t be able to tell. You will be passed over in favor of candidates who have listed the relevant skills.

Include research techniques on your resume from the job description, when applying to a job only if you have experience with them. Customize the resume for each job. Don’t just list a general term like molecular biology techniques. Elaborate on exactly which technique you have experience with, such as molecular cloning, recombinant DNA methods, PCR, site directed mutagenesis, DNA isolation, purification, and sequencing, Southern blotting, and Northern blotting. Don’t rely on a hiring manager to guess that you have the right experience. Clearly indicate what you do and have done. Don’t be afraid to take too much space when listing skills; you can recover some of the space through clever formatting: by using a smaller font for the list, as well as going from a vertical bullet point list to a horizontal one. The important part is to be thorough and specific in listing your skills.

NON-RESEARCH ROLES

Resumes for non-research roles should not include significant details about research techniques, since these are not typically relevant to these types of roles. Usually, disease and/or therapeutically-relevant experience is important to highlight, especially if you are considering a role in clinical research, or as a medical science liaison. You can include high-level information about techniques you know under each of your experiences, but it is not needed to include an entire research techniques section. Sending a “research-focused” resume to a non-research role will indicate to the potential employer that you are not sufficiently interested in the role that you are applying to because you did not bother to tailor your resume to the job. Non-research based roles prefer to see more transferable skills and experiences such as: leading teams, managing collaborations, working with clients, managing projects, strong communication and writing experience, and mentoring, rather than specific laboratory skills and techniques. For a non-research role, extra-curricular (i.e. blog writer or teaching assistant) and community service activities (i.e. president of a particular charity) should also gain more prominence on your resume. These activities highlight your transferable skills, especially if your previous job/academic experiences are heavy on the laboratory research exposure and not much else.

What you decide to include on your resume is important. The details tell a story and indicate what type of position you are looking for. Be focused and strategic. The effort will pay off!

LAMP

by Juliane

This is a lamp, lamps come in lots of different sizes and shapes. Some of them are even shaped like this:

The lysosome-associated membrane glycoprotein, Lamp to its friends, is part of the lysosome and therefore involved in digestion of foreign materials and autophagy. LAMP1 and 2 were first discovered in 1985, since then they have been widely studied and shown to be involved in quite a few important pathways in human cells.

Immune response: LAMP1 is necessary for delivery of perforin to lytic granules.

Cancer: LAMP 1 is a marker for melanoma metastasis into lymph nodes.

Apoptosis: LAMP1 and 2 promote apoptosis.

General Research: LAMP is a commonly used as a marker for lysosomes.

The scientists, who named this versatile protein, were either very boring (it describes exactly what it is) or very creative (there is beauty in simplicity).

References:

www.ikea.com
http://www.pathologyoutlines.com/topic/cdmarkerscd107.html
Chen JW et a. (1985) Identification of two lysosomal membrane glycoproteins. J Cell Biol. 1(1):85-95.
Krzewski K et al (2013) LAMP1/CD107a is required for efficient perforin delivery to lytic granules and NK-cell cytotoxicity. Blood. 121(23):4672-83.
Sato H. et al (2009) Altered expression of glycoproteins on the cell surface of Jurkat cells during etoposide-induced apoptosis: shedding and intracellular translocation of glycoproteins. Biochim Biophys Acta. 1790(10):1198-205.

Effects of remote, retroactive intercessory prayer

by Juliane

Effects of remote, retroactive intercessory prayer on outcomes in patients with bloodstream infection: randomized controlled trial. Published by Leibovici in the British Medical Journal BMJ in 2001. BMJ currently has an impact factor of 17.215.

The title of this article sounds kind of strange, so let’s see if I have got this right:

Remote prayer: praying to your deity of choice on behalf of a person you don’t know. There are quite a few websites on which you can submit a prayer request to a holy person or a group of people.

Retroactive: backwards through time, in this case praying for the health of people in the past.

Intercessory prayer: praying to your deity of choice on behalf of somebody else’s health, hoping that said deity will intervene in response to the prayer and speed up recovery of the sick person. Intercessory prayer is actually fairly well studied: there are 94 articles listed in Pubmed (8 of which are responses to the Leibovici paper); however most of them are published in fringe low impact journals. A Cochrane review did not recommend further clinical trials.

Bloodstream infections: Bacteria that spread into the blood of a patient

Randomized controlled study: “A study design that randomly assigns participants into an experimental group or a control group”

The author seemed to have studied the effects of remote prayer on blood stream infections backwards through time.

Let’s now have a look at the abstract: Typical for medical abstracts it is divided into objective, study design, results and conclusions. It confirms what the title promises, the author researched the effects of remote prayer backwards through time. The patients were hospitalized between 1990 and 1996, while the praying took place in 2000. The author measured mortality and length of stay in the hospital as his variables and concluded that the intervention group fared better on both counts. He therefore concludes that retrograde remote prayer works and should be considered as a useful tool for medical doctors.

Let’s examine how he reached this conclusion:

Introduction: here the author sets up the bold hypothesis that time might not be linear which he supports with this highly theoretical paper.

Methods: 3393 patients diagnosed with bloodstream infections in an intensive coronary care unit were randomly distributed into two groups. A list with the first names of one group was given to a (holy?) person who said a prayer for them. Then three variables, death, duration of hospital stay and duration of fever were compared. The null hypothesis, prayer works backwards through time was tested using a chi2 test or a Wilcoxon rank-sum test.

And now the most interesting part, the results. They are rather limited, the main findings are summarized in this table.

There is no significant difference in the duration of fever between the treatment groups, however the duration of hospitalization differs significantly between the two groups. The maximum stay in the control group was almost twice as long as the intervention group. While there are very few differences in the lower quartile the upper quartile differs (significantly?) between the two treatment groups. In conclusion, prayer for people backwards through time works.

The author states that the trial design is “flawless”, because of the “perfect blinding to patients and medical staff of allocation of patient allocation to the two groupss and even the existence of the trial”. He did not offer an explanation or hypothesis for this astonishing result.

Of course there are many problems with this paper, not in the least being the lack of informed consent of the participants and permission of an oversight committee at the hospital such as an IRB or ethical review committee. It appears that most of the significance of this study can be ascribed to one outlier in the control group, whose stay in the hospital was extended. However, without access to the raw data it is hard to prove this. The fact that the median does not differ between the two treatment groups is another hint, i.e. that the results might look very different when the outlier is removed.

This paper takes a ridiculous hypothesis and runs with it. It shows that to do good science we should not just discard a hypothesis, because it sounds too far fetched, but do our best to prove or disprove it. Leibovici did not do this. The experiment wasn’t very well designed, no matter what he claims and additional key information, such as what god was chosen to intervene following receipt of prayers are missing from the paper. The statistical tests the author chose to perform are not commonly used to test for differences in treatment groups during clinical trials, perhaps a T-test would have been more appropriate.

A better-designed experiment might have yielded a different result. However, it is important as scientists, to not just say “that’s stupid, so it can’t be true”, but to prove from the data presented that the conclusions reached are incorrect or point out flaws in the experimental design.

Naturally quite a few papers were published in response to this study, e.g. “You cannae break the laws of physics, Captain.”

This paper also sparked an interesting discussion on the BMJ website and is often cited by people, who believe in intercessory prayer and don’t have a scientific background. This shows that even with the best of intentions to write a light hearted scientific paper with a comedic edge can have a very real and sad backlash.

In conclusion, I like this paper, mainly because in the end they show a picture of a reindeer for some reason.

About being a scientist

by Francesca Seta

Francesca used to be a BUMC postdoc, recently she got a position as assistant Professor in the Department of Medicine at BUMC, where she researches the molecular and genetic mechanisms of arterial stiffness and how to cure and prevent it. She also wrote an interesting post for the postdoc blog, enjoy!

About being a scientist

The Danish toy giant LEGO has recently grabbed media attention for the release of a new minifigure:  the “scientist”. The little yellow brick wearing lab coat, glasses and a pen in the pocket looks cute and sharp; definitely not a mad, nerdy or evil scientist, as often portrayed in the collective imaginary (think Shelley’s Dr. Frankeinstein or Doc from the movie “Back to the Future”). Most of all, the “scientist” is female. As I dug deeper, I was surprised to discover that LEGO has been criticized in the past for gender bias and its previous attempts to market to girls found guilty of perpetuating the “pink and pretty” stereotypes of female representation. The new “lady scientist” may be, in part, an attempt to amend such gender bias accusations.

This came just a few months after yet another much debated release: the book “Lean in” from Sheryl Sandberg, Facebook COO, in which the author encourages women to engage more in leadership roles in the workplace and blames them for not embracing their full potential. All the debate about gender disparity in the American workforce and particularly in STEM careers (science, technology, engineering, mathematics) made me think: what does really take to succeed in science, independently if you are a guy or a girl? I asked myself this very question many years ago as a PhD (female) student when I was looking for sources of inspiration and directions about my future and my career. At that time, I came across a great book, “Advice for a young investigator” from the Spanish scientist Santiago Ramon y Cayal. According to the eminent neuroanatomist, hard work, passion for work, family and country, ambition, patience, humility, pursue of original data and master of the techniques are the qualities required to succeed in science. Most importantly, the idea of having to be exceptionally smart or genius, as sometimes scientists are envisioned in the popular perception, was not even mentioned in the book. Although the book was first published in 1897, the principles it promotes are timeless and universal and I reasoned that being successful in science boils down to willpower, self-motivation and perseverance, none of which, are gender-related qualities or restricted to STEM careers (a sport coach would probably have a similar piece of advice for young athletes as Ramon y Cayal had for young investigators).

In a recent trip to my home country, Italy, I went to renew my ID and the office clerk asked me what my profession was. To my surprise, the profession “scientist” was not in the list of choices although they had “academic researcher”, which is pretty close. Despite the profession of “the scientist”  being somehow nebulous and elusive in Italy, growing up I never felt discouraged to pursue a STEM education and career and definitely not because of my gender. Now, as an early stage investigator, I come to appreciate how lucky I was to have teachers, family and mentors that rewarded perseverance and valued resilience as I was growing up. Those are the very qualities that, during my PhD and postdoctoral years, helped me to face failed experiments, long hours in the lab and many years of training at low pay. And probably these are the very same qualities that keep us scientists going these days in face of NIH spending cuts and low grant success rates that threaten to shut down our labs. Sure, STEM careers are tough but after all, the ideal of making an impact against human suffering, advancing knowledge and the satisfaction that comes from successful experiments, new discoveries, published articles and funded grants, make it all worth it. Despite the hardship and the challenges, science is creative, exciting and rewarding if you do not give up. And hopefully the little “scientist” LEGO figure will help to pull more young people into it.