Visitor of the Week: Shantanu Shukla

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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: Hayden Huggins

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Meet Hayden Huggins of the East Carolina University Brody School of Medicine. The fourth year Ph.D. Candidate is a member of Dr. Brett Keiper’s lab in the Biochemistry and Molecular Biology Department. He was on campus for the 2018 Germ Cells meeting where he presented a poster entitled, “mRNA cap-binding protein IFE-3 is critical for germ cell sex-determination in C. elegans”.

What are your research interests? What are you working on?
Broadly, my research interests focus on gene regulation by modulating mRNA translation during germline development. Currently, I am working on mRNA cap-binding isoforms (eIF4E) and how they can selectively regulate subsets of mRNAs in C. elegans germline.    

How did you decide to make this the focus of your research?
Two things drew me to what I study: 1) I love watching things grow and change over time so animal development is perfect for me; I’ve always said I’m not happy unless I’m studying a phenotype. 2) How biological information is turned into form and function also greatly interests me, so what better place to study this phenomenon than protein synthesis. 

How did your scientific journey begin? 
I have always known I wanted to be involved in research science, but it wasn’t until late in my undergrad that I determined the capacity. While at the Appalachian State University, I started an undergrad research rotation in a virology lab and got bit by the research-bug pretty hard. I subsequently met my current boss, became very interested in his research direction, and now it’s hard to imagine doing anything else.          

Was there something specific about Germ Cells meeting that drew you to attend?
In a couple years, I will be looking for a postdoc position and since many of the leaders in my field attend the Germ Cells meeting at CSHL, it was the perfect opportunity to introduce myself to them and talk about my and their research interests. 

What is your key takeaway from the meeting?
That there is a really strong germ cell community which spans across many developmental systems, with a lot of really exceptional scientists in each. It makes me happy with my choice to stay in this field.    

What did you pick up or learn from the meeting that you plan to apply to your work?  
In the past year we started CRISPR/Cas9 genome editing in the Keiper lab, with success in tagging our favorite genes with fluorescent proteins. Seeing other researchers’ CRISPR/Cas9 projects has inspired me to do even more genome editing. It is a very powerful tool for developmental biology. I have also learned a little bit about grant writing as a postdoc from Dr. Jordan Ward (UCSC) which I think will prove to be invaluable when I start to secure funding as a postdoc.     

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
I would tell them that CSHL meetings are excellent places to meet like-minded scientists in your field. There is an abundance of networking opportunities, which are important for those interested in pursuing careers in academic research science. 

How many CSHL meetings have you attended?
This is my first one and I will absolutely be attending germ cell meetings – and potentially translation meetings – at CSHL in the future.  

What do you like most about your time at CSHL?
The scenery is quite nice here, and the bar was a great place to hang out after the plenary sessions. I also enjoyed the sense of community that I got from the germ cell field.

Thank you to Hayden 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: Amit Sharma

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Meet Amit Sharma of the Buck Institute. The Indian national is a postdoctoral research fellow in Pankaj Kapahi’s lab which focuses on the influence of diet on lifespan and health span extension, as well as the involvement of DNA damage pathways. Amit was on campus this week to participate in his very first CSHL meeting: Mechanisms of Aging.

What are your research interests? What are you working on?
I am deeply interested in the molecular regulatory pathways involved in cellular senescence and aging, and to leverage these in developing therapies for aging and associated disorders.

How did you decide to make this the focus of your research?
I have always found the process or phenomenon of aging fascinating.

How did your scientific journey begin?
I am originally from India where I earned my PhD. Throughout my career, I have been inspired by several individuals, teachers, and mentors but I credit my dad for setting me on this path. He was the first person to nurture my curiosity and introduce me to scientific methods.

Was there something specific about Mechanisms of Aging meeting that drew you to attend?
I believe the aging meeting at CSHL to be the field’s most important for two reasons: 1) The prestigious array of established scientists speaking at this meeting and discussing their yet-to-be-published, cutting-edge research; and 2) The opportunity to present my research to and get feedback from my peers.

What is your key takeaway from the meeting?
The biggest takeaway for me is that there is an increasing interest in cellular senescence both in understanding basic biology and potential therapy.

What did you pick up or learn from the meeting that you plan to apply to your work?
Every talk was very interesting; however, a few talks regarding the role of long interspersed nuclear elements (LINE) in triggering inflammation and its role in aging was very exciting. The insight I gained from these talks might be useful for my project. In addition to that, I may have a potential collaboration.

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
I would highly recommend this meeting. Keep an eye on the deadline, apply early, and, if possible, present your research. The feedback I got from the attendees were very positive and useful.

How many CSHL meetings have you attended?
I have known about CSHL Meetings & Courses but this is the first time I am attending a CSHL meeting and would love to attend, if possible, every year from now on.

What do you like most about your time at CSHL?
The CSHL campus is beautiful, and the support staff is very helpful and friendly. The level of excitement, sense of cooperation and optimism amongst fellow scientists were the most inspiring this year.

Thank you to Amit 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: Ahlem Assali

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Meet Ahlem Assali of the Medical University of South Carolina. The French-Tunisian national is a postdoctoral scholar in Christopher Cowan’s lab. Ahlem returned to CSHL for her second Molecular Mechanisms in Neuronal Connectivity meeting where she presented a poster titled “Role of EphB1 in axon guidance and fear memory.”

What are your research interests? What are you working on?
I’m interested in the molecular mechanisms that underlie proper brain wiring during development. Using mouse mutants, I currently investigate the role of certain genes in axon guidance, synaptic connectivity and, later on, in behavior as well as the potential involvement of these genes in neurodevelopmental disorders.

How did you decide to make this the focus of your research?
My fascination with brain development began in my PhD years in Patricia Gaspar’s lab during which I used the visual system to study the establishment of neuronal connectivity. I focused on activity-dependent mechanisms involved in synaptic refinement with Alexandra Rebsam and on cAMP signaling involved in the pruning of axonal branches with Xavier Nicol. In line with my PhD and current post-doc work, I would love to pursue my contribution to our understanding of the molecular mechanisms involved in the development of brain connectivity. One phenomenon that particularly amazes me is the neuronal plasticity occurring during critical periods of brain development, when experience interacts with genetics to shape the young brain and predict future personality/behavior.

How did your scientific journey begin?
Since my first experience in a lab, I realized that scientific research fits really well with my curious personality. As scientists, we develop creative hypotheses based on available knowledge and our own preliminary observations, then we design/perform experiments to test our ideas and analyze the data until we come close to some truth. It’s this combination of intellectual and manual work that makes science so personally fulfilling. Science also has a remarkable way to bring people together from all backgrounds/countries to advance our knowledge as a human community.

Nicolas Narboux-Nême introduced me to this fun world of neuroscience: he walked me through my first brain dissection, taught me how to stain for my first proteins, and how to brainstorm on/troubleshoot my first experimental issues. I’m very grateful for the time he granted me during the weeks I followed him around the Gaspar Lab.

Was there something specific about Molecular Mechanisms of Neuronal Connectivity meeting that drew you to attend?
As a mid-term postdoc, I’m in a stage in my career where identifying the focus of my work and heavily networking are important. This meeting is a perfect opportunity to do both: cutting-edge research topics in neurodevelopment are featured through the great talks and poster presentations, and allows me to interact with the more global scientific community.

What is your key takeaway from the meeting?
My key takeaway from this meeting is the discovery of the fascinating roles glial and microglial cells play in brain development, nerve injury, and multiple other brain functions. As neuroscientists, we sometimes tend to focus our work on neurons but should it would be beneficial for us to take into consideration this crucial brain population of glial and microglial cells. I’m glad that the meeting organizers added a beautiful session centered on these cells!

What did you pick up or learn from the meeting that you plan to apply to your work?
While I was presenting my poster, I received a very useful feedback from someone very knowledgeable about the field I work in which I’ll take into account as I design my next experiments.

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
It is a great meeting! It is a small meeting featuring a focused-but-still-diverse topic and experts in the different fields of neurodevelopment who you can interact with and who will provide useful insight and feedback on your project. The most current advances on brain development are discussed it’s a productive way to step away from your very-focused everyday-lab work and gain fresh perspectives on your work and think at a global level.

How many CSHL meetings have you attended? How about courses at CSHL?
This is my second CSHL meeting and I have every plan to come back for future ones. And I’ve never attended any of the courses but I would love to!

What do you like most about your time at CSHL?
I love the fact it is surrounded by nature and that the talks are transmitted to screens placed on the patio. Attending a talk while feeling the breeze and hearing the birds sing in the background is a treat you don’t often experience. Its waterfront, and somewhat isolated location is ideal – and conducive – for focusing on science for a few days. I enjoyed re-connecting with my those I worked with in the past and to catch up with friends. And the food was really great too.

Thank you to Ahlem 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: Mike Tramantano

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Meet Mike Tramantano of Cold Spring Harbor Laboratory (CSHL). Prior to joining CSHL President and Chief Executive Officer Bruce Stillman’s lab in February 2017 as a postdoctoral fellow, Mike earned his Ph.D. in Molecular and Cellular Biology from Stony Brook University (SBU). Since 2012, Mike has participated in six meetings at CSHL plus The Genome Access Course (TGAC) which kicks off later this afternoon.

What are your research interests? What are you working on?
In mammalian cells, stepwise assembly of large multi-protein complexes occurs at specific sites in the genome and is required to initiate DNA replication prior to cell division. My research focuses on understanding the recruitment mechanism that occurs upstream of this assembly and answering the question: How do cells recognize the correct sites in the genome for assembly to begin and what factors are involved in this process?

How did you decide to make this the focus of your research?
How human cells select sites for DNA replication is not well understood. If we can better understand this selection process, it can have broader implications to diseases where normal cell division is disrupted, such as cancer.

How did your scientific journey begin?
My passion for science began in high school Biology when I was first exposed to the topic of genetics. I was struck by the fact that all the information needed to make a human being was encoded in our DNA.

The Genome Access Course is your first CSHL course – was there something about this course in particular that drew you to register for it?
There is an increasing amount of data and tools publicly accessible to scientists online. TGAC appealed to me because it is an intensive instructional course teaching about these resources and how they can be best utilized in your research.

Your course kicks off later today - what do you hope to get out of the two-day course and how will it help with your work?
I hope to learn the fundamentals of analyzing deep sequencing data and the proper way to present this data. My research is beginning to enter a period where genome wide data and analyses will be necessary in order for me to continue my project.

If you can take part in another course or two, which one(s) would you register for and why?
I would like to register for either the Computational Genomics or Chromatin, Epigenetics and Gene Expression course, as the in-depth training in working with next generation sequencing technologies and chromatin biology present in those courses would be helpful in planning future experiments for my project.

Since you’re well-integrated in campus and have participated in a good number of meetings, what tips or insider-knowledge can you share with those attending their first CSHL meeting or course?
Don’t miss the wine and cheese! It is a Cold Spring Harbor tradition where many great ideas are shared and discussed in a casual atmosphere. I also suggest taking a walk up to Hillside (by the Quick building) to get the best views of the Harbor.

What, in your opinion, are the best features of a CSHL meeting that make it unique and worthwhile to participate in?
What I enjoy most about the meetings at CSHL is that they are relatively casual compared to other conferences at which I have participated. The interaction between visiting scientists always seems very constructive and positive. In addition, established faculty are very willing to share their knowledge with younger researchers – especially over a beer at the bar after the talks.

Thank you to Mike 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.