Visitor of the Week: Hossein Davarinejad

Meet Hossein Davarinejad of the University of Ottawa. The second-year PhD student is a member of Dr. Dr. Jean-François Couture’s lab within the Department of Biochemistry, Microbiology, and Immunology, and he recently wrapped up his training at the annual three-week course on X-Ray Methods in Structural Biology.

What are your research interests? What are you working on?
I am interested in studying enzymes that modify the interaction of DNA with DNA-packaging proteins as these important processes affect gene expression.

How did you decide to make this the focus of your research?
When I began my undergraduate studies, epigenetics had gained a spotlight in cellular and molecular biology. The field was relatively new and introduced the histone code with many enzymatic modifications with unmapped individual or combinatory effects on gene expression. It was an attractive puzzle with a lot of room for identifying new pieces.

How did your scientific journey begin?
I enrolled in the biology program with an interest in dentistry or medicine at first. I was not performing well during my first year as courses were very broad and I learn better with more depth and needed to have a good understanding of the applications to engage. During my undergrad second year, my biochemistry and cell biology professor really raised my interest in how life works at the molecular level. I was fascinated with the understanding of how mutations cause changes in the structure and function of macromolecules which contribute to disease. That course paved my path in molecular biology leading to epigenetic studies for MSc and eventually to structural biology in my PhD program.

Was there something specific about the X-Ray Methods in Structural Biology course that drew you to apply?
My PhD studies rely substantially on understanding the structure of the protein complexes which I study in order to understand how they assemble and initiate or inhibit their functions. We have an X-ray source at my home lab which is used extensively by our group for solving protein structure using X-ray crystallography. The X-ray course at CSHL is the most extensive program to my knowledge that covers a wide variety of topic related to this technique including biochemical and lab techniques and strategies for obtaining high quality protein crystals, methods in sample preparation and mounting of the instrument, mathematics and physics at play behind the scenes while using an X-ray source to collect crystallographic refraction data, data processing and analysis using variety of popular software, and information for validation of data for publication. All of the topics covered are directly beneficial to structural biologists using X-rays.  

What is your takeaway from the Course?
There is no single key takeaway from this course. The course covers a large volume of material on very related topics. The majority of topics were important, indispensable, and taught us things to consider ranging from chemical reagents and lab work to instrument function and data processing. In this field, there are many pieces that need to fall into place for obtaining a high-resolution structure and the course teaches you how to optimize the work at each step.

What and/or how will you apply what you’ve picked up from the Course to your work?
Before attending the course, I thought I had an idea of what I didn’t know and what I needed to learn. This course introduced me a lot of new material conceptually and technically. Having attended the course, I have filled in many gaps in my knowledge and my list of things to continue to learn has grown substantially. The sections on laboratory work are readily understandable, relatable, and translatable to my own work such as techniques on better understanding the stability of the protein that I work with and ways to re-evaluate whether my preps can negatively impact my sample before data collection stage. We had training on using many software and this course helped me understand what the application parameters really do, and this can enhance my data processing.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would say the volume and the difficulty of the material would make it suitable for a 4-credit university course which would normally be covered in a full semester (at least by Canadian standards). The 15-day period makes this course very intensive and it could be challenging as lectures are back to back. For a junior researcher, with little time to take them in, it can be exhausting. I think the best strategy to keep up is to keep good track of what you don’t understand and use the short coffee breaks, food breaks, Q/A sessions, and any other time you find to go up to the instructors and resolve the ambiguities as soon as you can since the lectures build on each other to a good extent. If allowed, maybe recording the lectures could be useful as you’d definitely need to come back to the material. The great thing about the course is that there are many instructors and experts around at all times. The instructors are fun, approachable, and genuinely like to be “bothered” with your questions. There were many instructors who are major contributors to the field, and some are the actual developers of the computational software used or leading structural biologists so you will be talking to the best sources. Being able to network with the instructors is invaluable.

It is great to come here with structure problems from your own work and consult the instructors on how to improve your data.

What did you like most about your time at CSHL?
This is a beautiful campus and unlike any laboratory campus I had ever seen. The course directors and instructors were really fun, you can talk to them about anything in science or beyond. Being in the same rooms as all the instructors and other students for a long period made it feel warm and friendly as you get to know each other. The stray cat roaming the campus made it even better.

Thank you to Hossein for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Repeat Visitor: Pau Creixell

Photo provided by Pau Creixell

Pau Creixell of the Koch Institute for Integrative Cancer Research at MIT is the next scientist to be featured in the 2018 edition of our Repeat Visitor series. Pau is a postdoctoral fellow in Michael Yaffe’s lab, which is part of the MIT Center Precision Cancer Medicine. In the thirteen months since October 2017, Pau trained in three of our courses: X-Ray Methods in Structural Biology, Workshop on Leadership in Bioscience, and Scientific Writing Retreat. And with the Network Biology meeting and courses on Cryoelectron Microscopy and Synthetic Biology in his sights, we will likely be seeing Pau again. In the meantime, we reached out to Pau to discuss his experiences so far and learn what keeps him coming back to Cold Spring Harbor.

Talk us through your research interests and how you made them the focus of your work.

Using both computational and experimental quantitative approaches, I am interested in understanding how specific cancer mutations perturb protein function and cause disease. The focus of my work is protein kinases, a subset of proteins highly mutated in cancer and targeted by many therapeutic agents. I find cellular signaling and protein kinases fascinating because even though they have been studied for decades, we are still discovering new molecular functions for them and learning how they are perturbed in cancer. The degree of regulation and functional diversification in protein kinases is very interesting to me, and the amount of sequencing and functional information that we have for them now allows for more systematic studies. It’s a field that has repeatedly shown how fundamental discoveries in molecular biology can lead to effective targeted therapies that benefit patients.

How did your scientific journey begin?

When I was young, a family member was diagnosed with cancer and that had a big impact on me. Since then, I decided that by doing research I could try to contribute to our understanding of the disease which, in turn, could result in better therapies. I was also very fortunate to have a supportive home and school environment, where my curiosity was encouraged by my parents, grandparents, and teachers.

As I was finishing my undergraduate studies in biology, the Human Genome Project was being completed and a number of cancer genome projects were starting. I quickly realized that to address fundamental biological questions, we would need to not only generate quantitative data, but also integrate and decode large and diverse sources of data. This inspired me to pursue a PhD in computational systems biology. Since my ultimate goal is to lead an interdisciplinary lab, I wanted to complement my computational training with expertise in cancer biology. Thus for my postdoc, I purposely transitioned into a lab where I could improve my experimental skills in biochemistry and molecular/cellular cancer biology.

Your most recent course at CSHL was last month’s Scientific Writing Retreat. Can you tell us what attracted you to the retreat?

Scientific Writing Retreat Class of 2018

Given the time scientists invest in writing and the number of versions every manuscript, grant, or application goes through, I always felt that the process of writing could be improved and made more enjoyable. I wanted to learn more about scientific writing in general and how the process may change depending on the purpose of each document. A major takeaway from the retreat is to focus on the audience and how it will interpret your writing. The audience is often broader and more diverse than most of us appreciate; keeping this in mind ensures that key information is presented clearly and your writing is easy to understand.

Since part of the retreat is devoted to practicing on your own work, I returned from it with much-improved versions of abstracts for two manuscripts as well as a research statement. I also learned how to give better feedback on the scientific documents of others, and I increased my understanding of how scientific stories are crafted, submitted, and published. I picked up general writing strategies (e.g., given the limited space in titles, abstracts, and summaries, one has to use the most meaningful words and avoid superfluous ones) and became aware of my major writing weakness (referred to as “your kryptonite” in the retreat). Communicating your science effectively is required to become a successful scientist, and I would like to thank the great instructors, coaches, and my fellow participants for their help.

It’s becoming more common for trainees of the Scientific Writing Retreat to also participate in the Workshop on Leadership in Bioscience. In fact, you are among six recent alums who participated in both the retreat and leadership workshop. Was there something specific about the leadership workshop that led you to apply for it?

I think it is no coincidence that several trainees attend both the leadership workshop and writing retreat as these skills are critical for those transitioning to scientific independence.

I have found there to be little leadership training for scientists, who are supposed to run labs without any formal training on how to successfully manage and lead others. Similar to how I looked for both computational and experimental training opportunities during my PhD and postdoc, I attended the leadership workshop because, in my mind, it was important to be as prepared as possible if I want to effectively lead my own interdisciplinary laboratory in the future.

Workshop on Leadership in Bioscience Class of 2018

Generally speaking, any starting junior faculty will want to set up an exciting, fun, and creative lab environment but, as covered in the workshop, this will ultimately depend on hiring the right people and setting the right lab environment and expectations. Another important takeaway from the workshop is to recognize that no one is infallible and everyone makes mistakes when running a lab. You have to be open to feedback from everyone and ready to learn from your own mistakes so you can fix them as soon as they are detected. By establishing consistent and objective parameters during the hiring stage and requesting independent feedback from everyone in the lab, one can aim to counteract intrinsic biases and group-thinking, thereby cultivating a diverse and creative lab.

Though I currently have limited opportunities to manage others, I have already implemented some of the aspects I learned and have been working to overcome some of my weaknesses as a leader. The facilitators of the workshop are incredibly knowledgeable and I plan to stay in touch with them as my leadership skills develop. I, along with the facilitators and other workshop participants, have joined a LinkedIn group where we keep in touch and share our ideas.

Finally, the laboratory short course on X-Ray Methods in Structural Biology: Was there something specific that led you to apply for this course?

For my postdoc, I was interested in learning techniques that would allow me to better characterize the molecular effects of mutations in proteins. During a meeting with my PI, he recommended this course, which he himself attended and enjoyed twenty years prior.

From my participation in the course, I took away an appreciation for the physical principles behind x-ray crystallography. It is extremely exciting to be able to learn the fundamentals from those who pioneered the field and developed the technologies and software that are now commonplace. I crystallized many different proteins and learned how to explore different crystallization conditions. I also emerged from the course clearly understanding how diffraction data are interpreted so that structural models can be derived. Being able to transition from raw data to a model and back to the data is an important skill, so that one doesn’t simply take the structural model as the only solution. As I am working on solving structures for protein kinases in complex with specific substrate peptides, this has allowed me to critically evaluate the different research options moving forward. Coming from a computational background, it is also appealing to consider that a research project can now begin by mining millions of cancer somatic mutations, and finish by resolving the molecular differences between mutant and wild-type proteins at atomic resolution.

The overall format of your three courses are different. What differences or similarities did you pick up, and what advice can you share with future participants?

All three of the courses had a direct impact on the way I now look at scientific problems and the scientific process in general. The training was intense but extremely worthwhile, and I learned something new every day. In all cases it also felt like the more effort you put in, the more knowledge you get out, so I would certainly encourage future attendees to complete any assignments that are suggested by the instructors.

An aspect easily overlooked about these courses is that they offer a great opportunity to build community. The topics, formats, duration, location (Banbury versus CSHL main campus), instructors, and attendees were obviously different in the courses I took, but they all had a similar feeling of being part of a community. My memories include laughing and sharing experiences with participants and instructors of diverse origins and backgrounds, going for morning runs together, and relaxing in the basement of Robertson House and on a sailing trip. When one is an early-stage scientist like I am, often competing with peers, it is important to remember that the vast majority of us are driven by shared interests in addressing thought-provoking scientific questions and contributing positively to society.

Pau received financial support from the Convergence Scholars Program, Helen Hay Whitney Foundation, Helmsley Charitable Trust, National Cancer Institute, and National Institute of General Medical Sciences. On behalf of Pau, we would like to thank these organizations and agencies for continuing to support and enable our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

The three courses Pau took part in - Workshop on Leadership in Bioscience, X-Ray Methods in Structural Biology, and Scientific Writing Retreat - will again be offered at CSHL in 2019. All three courses have already begun to accept applications, and applications for the leadership workshop are due by January 15, 2019 here.

Thank you to Pau for sharing with us his experience, and we look forward to having him back at the Laboratory again. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here and here.

Visitor of the Week: Shantanu Shukla

Meet Shantanu Shukla of the Genome Sciences and Technology Program, a joint initiative between the University of Tennessee, Knoxville (UTK) and Oak Ridge National Laboratory (ORNL). He is a graduate research assistant working towards his Ph.D. under the supervision of Dr. Dean Myles in the Neutron Diffraction Group at the Spallation Neutron Source (SNS) in ORNL. Shantanu is presently training at our annual course on X-Ray Methods in Structural Biology – his first course at CSHL.

What are your research interests? What are you working on?
I am investigating the selective substrate translocation across bacterial membranes facilitated by primary and secondary transporter proteins.

How did you decide to make this the focus of your research? 
In March 2016, I met Dr. Matthew Cuneo, a very talented and dynamic beamline scientist, who first introduced me to the regulation of substrate transport across bacterial inner membrane. I have since been interested in understanding the membrane channels and transporters in bacteria for improving their druggability. Dr. Myles and Dr. Cuneo suggested that I investigate specificity versus affinity profiles of these selective transport systems (especially of their periplasmic binding proteins) which then motivated me to further investigate the role of both structure and dynamics in selective substrate binding and transport across bacterial inner membrane. 

How did your scientific journey begin?
Darwin’s theory of evolution based on natural selection has had a profound impact on me and my scientific career. I was in 8th grade when I first read about the adventures of Charles Darwin onboard HMS Beagle and his postulation of the theory of evolution. That same year, as part of my summer science project, I cataloged different species of birds found around the old colonial-era town of Jamalpur in India and couldn’t help but notice how evolution shaped speciation in birds. I then realized that what is postulated as a hypothesis can be tested and confirmed in science. Since that day, both bird watching and science have become personal passions.

Was there something specific about the X-Ray Methods in Structural Biology course that drew you to apply?
As someone with no or limited knowledge of X-ray diffraction, the fact that this training program encourages students in my situation to apply was the strongest reason for my application. Additionally, the focus on lab training is another strong point of this training program that attracted me. Plus, this course brings in the most experienced instructors -- some of who are pioneers of their fields -- to teach crystallography.

What and/or how will you apply what you've learned from the course to your work?
At SNS, we are focused on determining positions of hydrogens in protein structures, which account for around half of the total atoms in a system. Both X-ray and neutron crystallography require growth of high-quality protein crystals, but the crystals required for neutron analysis are much larger (x1000-fold). The first step to solving any neutron structure is to collect X-ray data on the same system and then jointly refine the X-ray data with the neutron diffraction data to get a complete density of individual atoms. X-ray crystallography is, therefore, the stepping stone to neutron crystallography. To this end, I will use the knowledge gained at this course towards crystallization, diffraction data collection, and data refinement of protein structures in my lab.

What is your key takeaway from the course?
My key takeaway from this course is that even in this era of fast computers and robustly automated algorithms, there is still a need to train good crystallographers. Macromolecular structure determination is not a trivial task and a clear understanding of the theoretical background is often a key determinant of the success or failure of any crystallographic project.

How many CSHL courses have you attended?
This is my first CSHL meeting, but I would definitely look forward to attending more: the Cryo-Electron Microscopy course looks very interesting.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would encourage them to apply for this course – even if they have limited X-ray crystallography experience (as was my case). I would share with them my own experience so that they feel equally motivated to apply for this program. I would also tell them about how the productive interactions I have had with the instructors and fellow course participants has positively changed my approach towards my own research.

What do you like most about your time at CSHL?
It is a privilege for me to attend this course; and it is not just the course itself but also the whole atmosphere -- it is so energizing around here. Also, the sheer beauty of this place is unmistakable and will be difficult to leave at the end of the course.

Shantanu received a scholarship from the National Institute of General Medical Sciences (NIGMS) to cover a portion of his course tuition. On behalf of Shantanu, thank you to the NIGMS for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Shantanu for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Pearl Magala

Meet Pearl Magala of the University of Washington. The postdoctoral fellow is a member of Rachel Klevit's lab. She visits Cold Spring Harbor Laboratory for the first time to attend our X-Ray Methods in Structural Biology course, and will be on campus until the end of October. 

What are your research interests? What are you working on?
I work with a bacterial protein called FimH that is implicated in urinary tract infections. I’m interested in understanding how it functions by examining its structural and dynamical properties. This knowledge will be helpful in the development of alternative treatments against bacterial infections as antibiotic treatments are becoming less effective.  

Was there something specific about the X-Ray Methods in Structural Biology course that drew you to apply?
Knowledge of the structure of biological macromolecules is paramount to understanding macromolecular function. X-ray methods have been the cornerstone of macromolecular structure determination for many decades. As an aspiring structural biologist, these methods are a critical tool to have.

What is your key takeaway from the Course?
The x-ray course is incredibly multidimensional in the knowledge that is required to understand how the method works. Within the last four days (of 15), we have covered topics spanning from the physical sciences to biological sciences as well as good lab techniques. 

If someone curious in attending the X-Ray Methods in Structural Biology course asked you for feedback or advice on it, what would you tell him/her?
I unreservedly recommend this course to anyone interested in learning x-ray crystallography. The class size is small and therefore every student gets hands-on experience in the lab as well as help from the instructors. It also covers very many aspects of x-ray crystallography and so a lot of knowledge is acquired. 

What do you like most about your time at CSHL?
CSHL has the best dining experience of any course or conference I have ever attended. 

Pearl received a scholarship from the National Institute of General Medical Sciences (NIGMS) to cover a portion of her course tuition. On behalf of Pearl, thank you to NIGMS for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Pearl for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course – go here.