The new lab is open

Starting a lab is an exciting way to make a dream come true. It’s also a turbulent time to be a new principal investigator.
Published in Protocols & Methods
The new lab is open
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 For the Nature Methods column Lab & Life, I wrote about new PIs. You can find the piece here.  And here is some additional material from my reporting.

Ola Sabet : Her new lab is at The Children's Cancer Hospital of Egypt 57357 and she is keeping the lab at  Children’s Hospital of Zurich (KISPI) 

From the moment Ola Sabet left her home country of Egypt, she says, “I knew I would want to come back and start a lab there and help be part of the small pioneering group trying to push the local scientific efforts forward.”

 The return took longer than she had expected, but after a two-year hunt she has found “a place that has both the vision, the understanding and scientific community to support me,” she says. That place is The Children's Cancer Hospital of Egypt 57357 (CCHE 57357), one of the world’s largest pediatric cancer hospitals “and the coolest thing about it is that it was completely built by public donations,” she says.

 At CCHE 57357, she is starting an imaging-based systems biology lab with the vision that it can be the first and central imaging lab in Egypt and the Arab World. There is, she says, no one covering this essential aspect of science for the whole region where imaging is used as an accessory rather than an empowering tool for accessing spatial information. “If you want to be part of this cross-continent ambitious plan and you have interest in computation, imaging, molecular biology or pediatric diseases, reach out and join the adventure,” she says.

“If you want to be part of this cross-continent ambitious plan and you have interest in computation, imaging, molecular biology or pediatric diseases, reach out and join the adventure,” she says.

She faces a mammoth task because CCHE 57357 depends on donations and seeks to now propel its research capabilities to accompany its clinical work. She will begin her big task to start her new imaging-based systems biology lab with grant-writing and fundraising as she continues with her research at Children’s Hospital of Zurich (KISPI) where she is in the middle of starting an imaging platform. Sabet feels fortunate to have this double affiliation.

“I found my love for science through my love for art and patterns,” says Sabet. After graduating with her undergraduate degree in pharmaceutical sciences from Cairo University, she knew she didn’t want to work in a pharmacy; “that’s all.” She didn’t realize how much she had been missing when she began her graduate degree at University of Bath.

She is “eternally grateful” to her mentor Wiliam Wood at the university who “set me on the right path.” When she looks back on that early phase of her career, she thinks of the saying ‘your destiny chooses you’. Wood’s research involved much live cell imaging of Drosophila embryonic blood cells and this meant hours and days sitting at a microscope. “Simply put, I was hooked and I knew at this point that this is what I wanted to do for the rest of my academic career,” says Sabet. Imaging is an art and when you capture a phenomenon in a reproducible and quantitative way it’s the scientific way of ‘believing‘ it.

 Her steps from then on have been about always expanding her imaging skills technically, in all possible scales; meaning the physical scales of time and space. While she doesn’t have one favorite type of microscopy, she has felt that if she did mainly high-content imaging, she would miss live-cell imaging and super-resolution and vice versa. “I guess I like all techniques and I enjoy learning something new all the time,” says Sabet.

“I guess I like all techniques and I enjoy learning something new all the time,” says Sabet.

MIngjie Dai: His new lab is at Rice University

“I am very excited to start my own lab,” says Mingjie Dai, a new PI at Rice University. The Department of Bioengineering is being supportive and he likes his new departmental home’s strong expertise in synthetic biology and molecular engineering.

Dai’s interests and work to date have been interdisciplinary given how he likes to tackle difficult problems from multiple angles. “My dream for the next chapter would be to enable deep and sensitive proteomics,” he says. High-throughput sequencing has brought deep changes to science. Proteomics, in his view, holds more promise but still faces big challenges, such as limited detection depth and lack of sensitivity.

“My dream for the next chapter would be to enable deep and sensitive proteomics,” he says.

 For example he would like to be able to dig into the ‘dark matter’ of the proteome when a biologist says: ‘I can see this protein on my western, why can’t I see in mass spec?’; offer a solution that can sensitively detect functional proteins in small samples, such as transcription factors in single cells to help a biologist looking at cellular heterogeneity of a particular signaling pathway;  help researchers investigate protein modifications in ways that cannot yet be achieved with current technologies, such as for looking at the patterns of post-translational modifications when a biologist asks: ‘how many phosphorylations [that's not phos-sites] are there in this protein domain?’ His goal, he says, is to ultimately translate these new capabilities into better research tools as well as more effective clinical diagnostics.

He will miss many of his friends and colleagues in Boston, but “I am excited about the possibilities ahead – I think of it as a time when many of my ideas can finally take off,” he says.  He knows his work schedule will get ever busier but he feels ready for that and the other challenges of transition, such as remodeling a lab space, recruiting, managing and other tasks.

The lab culture is going to be diverse. “We welcome a variety of cultures – the more the better,” says Dai. To start, the lab languages will be English and Chinese, “and maybe physics, biology, computer science,” he says. “Or maybe coffee, ping pong; music, art? Lab retreat?”

“We welcome a variety of cultures – the more the better,” he says. 

He, too, is looking for postdoctoral fellows and graduate students are welcome to apply to join the lab. He is looking for “highly motivated postdoctoral researchers who like to push the limit of molecular bioengineering and super-resolution microscopy.” They might also be looking into developing ‘next-generation’ proteomic technologies. Even as a new PI, he feels the pressure on academic hiring that comes from industry recruitment. “I feel that we are missing out on so many talented young minds,“ he says. It’s not under his purview, he says, but his sense is that it’s reasonable to ask someone to be paid 20-30% less to pursue his or her dreams. But “if the ratio becomes 50% or more, it is a tough call…”

 Part of setting up a lab is figuring out spaces where people might congregate for conversations of various types, also informal ones. “I have yet to figure out the details and whether we have a shared kitchen area with other labs, but I’d like to have some space, or activity, that lab members congregate and relax between experiments,” says Dai. “It could be a coffee machine, snack bar, or even a ping pong table in the hallway – if space and rules allow.”

His current priorities are setting up lab space, purchasing equipment, and looking for graduate students and postdocs. But that is challenging given the ongoing labor shortage and supply chain delays. This means that the lead time for equipment purchases and renovation both take much longer than previously expected, which is “a big challenge for setting up a new lab at this time.”

Dai’s background and training is in physics, math and computer science and he’s intrigued “by the complex yet organized molecular details of biological systems,” he says. His research interests lie in developing tools for biological and biomedical studies that bridge physical and engineering capabilities at the nanoscale and computer sciences for systems-level integration. “I like to think of myself as more of a biology-driven technologist, as compared to a technology-enabled biologist,” he says.

“I like to think of myself as more of a biology-driven technologist, as compared to a technology-enabled biologist,” he says.

As methods developers, he sees aspects that can be further improved in many methods that he uses. One example is a way to investigate intracellular organization and activity of not just one or a few proteins, but entire signaling or metabolic pathways. This calls for a new level of a --preferably super-resolution--microscopy method that can observe not only four or ten colors, but dozens to hundreds of ‘colors.’ This, he says, is possible in principle with current methods that involve serial imaging but such experiments “would take a really long time” and risk sample degradation.

Another issue he sees are patent barriers. For example, for mass spectrometry-based proteomics ThermoFisher makes state-of-the-art mass spectrometers for quantitative proteomics and, in his view, excels at making high resolution mass analyzers. Then there is, for example, Bruker’s ion mobility separation device, which, in his assessment, has shown superior resolving power and ion efficiency. “In my dream world, one would combine the best from both worlds, which would enable single-cell proteomics at a much higher level of sensitivity,” says Dai. But this seems quite challenging, he says, given the current patent landscape.

Atilgan Yilmaz: His new lab is at KU Leuven

Atilgan Yilmaz, is a new principal investigator (PI) at KU Leuven and is looking forward to running after the scientific questions that excite him the most. “Of course, my dream would be to contribute to the current understanding in these fields in the most extensive way possible,” he says. He plans to combine his experience from different stages of his scientific training both thematically and methodologically and “I hope to have my own unique niche in science.”

“I hope to have my own unique niche in science.”

 As a principal investigator, such a dream cannot be achieved without excellent students and good mentoring skills, he says. It’s why one of his biggest aspirations is to become a good mentor and train young scientists for academia or industry. “It sure is a learning curve but I consider myself lucky,” he says. His advisor during his postdoctoral fellowship, Nissim Benvenisty at Hebrew University, “set an excellent example for me on how to be not only a great scientist but also an outstanding mentor.”

 As he starts his lab, he says he will be looking for highly motivated graduate students and postdocs and a technician to join his group in the next few months. “I would welcome anyone, who is genuinely interested in studying the development, regeneration and diseases of human skeletal muscle by using a wide range of stem cell methodologies and gene editing” he says.

“I would welcome anyone, who is genuinely interested in studying the development, regeneration and diseases of human skeletal muscle by using a wide range of stem cell methodologies and gene editing” he says.

 His sense is that his previous work gives the lab a foundation to build on and complements the way the new department, his new “host”, KU Leuven’s Department of Development and Regeneration. will help set up future interactions with other research groups in developmental biology and stem cell biology. He also values the university’s facilities and its vibrant scientific environment.

Yilmaz works on the factors that underpin cellular plasticity and his research also focuses on ways to capture and track the ‘essentialome.’ the genes that define pluripotency and other cell states. It’s a system he enjoys working with and one that provides a way of studying early human development, “I will certainly keep thinking about the essentialome and how to adapt the system to the new questions I will be focusing on in my laboratory and perhaps also how to combine it with new technologies,” he says.

 His new department at KU Leuven, is, he says, making his transition to his new position smooth in terms of lab space and buying equipment, but there are always some adjustments to be made when people start their own lab and even when all the equipment is ready. “I expect that it will take some time to get the lab up and running,” he says. He feels ready for the challenge and his sense is that “the friendly and welcoming environment in my new department will make things easier.” The first few months will also be all about hiring people to join the lab as he begins this next phase of research at KU Leuven.  

 Becoming a new PI is a shower of many emotions. “I feel super excited and happy for sure,” he says about this milestone and a great undertaking that also comes with many responsibilities. “So, besides giving lots of joy and a feeling of achievement, it can also feel a bit overwhelming and scary at times,” he says. This emotional diversity is true for almost everyone who starts from scratch. “What makes the real difference is choosing the right and nurturing environment and colleagues,” he says. It’s his sense that he has made the right choices also given the warm welcome from is new department colleagues. This is helping him “overcome most of my worries about the challenges of the new beginning.”

 Speaking more generally about methods, he says he is fascinated with new developments in single-cell technologies and organoid systems. “Lineage-tracing methodologies for studying human development will certainly keep changing the way we look at these processes related to early human life and potential regenerative therapies,” he says. 3D culture systems have, in his view, already shifted some paradigms and these in vitro models will keep improving. “In addition, stem cell technologies are nowadays also offering opportunities to save endangered species, which I find very exciting,” he says.

“Lineage-tracing methodologies for studying human development will certainly keep changing the way we look at these processes related to early human life and potential regenerative therapies,” he says. 

Aside from these new methodologies related to developmental biology, other methods he follows with great interest are experimental and computational methods to study ancient DNA samples. “Being a history enthusiast, I am amazed by the fact that this field of biology is revolutionizing our way of understanding human evolution and the history of hominid species,” he says.

 The language of Yilmaz lab will be English for practical reasons, he says. But he would love if the lab could host graduate students and postdocs from a wide range of linguistic backgrounds. “I, myself, am a polyglot and lived in four different countries/cultures and really enjoy an international and inter-cultural environment,” he says. Anyone from any background, community or identity is welcome. “The overarching theme connecting everyone will be the science that we are all enthusiastic about,” he says.

“I, myself, am a polyglot and lived in four different countries/cultures and really enjoy an international and inter-cultural environment,” he says. Anyone from any background, community or identity is welcome. 

Yilmaz’s scientific journey started during his undergraduate studies at Boğaziçi University on the hills of Bosporus in his hometown of Istanbul, Turkey. As an undergraduate there, he started volunteering in a laboratory.

“Even though I admire this beautiful city and its endless romantic inspirations, my curiosity and thirst for knowledge pushed me towards new horizons and I spent two summers abroad during my undergraduate studies,” he says. One stint was ay Georg August University in Göttingen, Germany and the other was at UCLA. After he obtained his bachelor’s degree, he set out to complete his PhD research at Brown University, after which he did a short postdoc at ETH Zurich. It was there he began working on one of the scientific questions that he will continue working on in his new lab. After ETH, he was a postdoctoral fellow at Hebrew University of Jerusalem, where he learned about on human embryonic stem cells and early human development.

 He feels fortunate to have had this training and to have lived in multiple countries. “Having lived in all these different geographies and cultures makes me also one of those people, who call many places home,” he says. “In that sense, I started thinking of myself as the collection of pieces, each of which belongs to a different city and makes up different percentages of me as a whole based on the time I spent in them.”

“In that sense, I started thinking of myself as the collection of pieces, each of which belongs to a different city and makes up different percentages of me as a whole based on the time I spent in them.”

 As for the lab set up and crafting a spot where lab members can chat about their work or have more informal exchanges, the decision of which coffee-machine to buy is not one he will make. “A fun fact about me,” he says, “I do not really drink coffee.” He likes the smell of coffee and has no coffee allergies, and he drinks it once in every blue moon “but, somehow, I never developed a habit of drinking coffee and I managed to go through my PhD without it.” He feels quite ignorant on coffee culture, both in terms of types of coffee and types of machines. “I barely know the Turkish coffee :-),” he says. His plan is to leave the decision which coffee machine to get up to the group.

 As for those informal chats, he knows they are valuable in science. “Those quick chitchats are healthy breaks during the daily lab routine and can sometimes lead to the best experimental ideas,” he says. He plans to actively promote such breaks and participate in them. “They also help the lab members, including myself, to get to know each other better on the personal level and foster friendly interactions.”

an open sign on a door

(Credit: Gibgalich Getty Images/iStockphoto)

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