The winning article for November’s 21 PAPER OF THE MONTH goes to former doctoral student Hadeel Khamis from Prof. Ariel Kaplan’s lab

09 January 2022

SPOTLIGHT ON RESEARCH
PAPER OF THE MONTH NOVEMBER 21

 

The Committee for Graduate Studies in the Faculty of Biology selects each month the leading scientific article from all the scientific articles published for that month.
We are pleased to announce that the winner of this November’s article is the former doctoral student Hadeel Khamis from Prof. Ariel Kaplan’s lab, whose article was published in the Nucleic Acids Research journal. On the occasion of the win, we asked Hadeel to provide us with some interesting details about the study, the path that led to the research it and also a bit about her.

Hi, could you introduce yourself in a few words?
My name is Hadeel Khamis-Farran, originally from Reineh Village (outskirts of Nazareth City) and now living in Haifa City. A daughter of Issa and Amal Khamis, a sister to three siblings, and a wife of Amir Farran. I have a bachelor’s degree in physics and a doctorate in Biophysics. I started my studies at the Physics faculty at the Technion in 2011. The first degree in Physics was challenging but interesting, it provided me with various skills that shaped my problem-solving approach, not only in Physics. Following my first degree, while searching for the right path for continuing my studies, I stumbled upon the Biophysics world, which tackles questions from the biology field using physics techniques and ways of thinking. I then decided to pursue my higher education at Prof. Ariel Kaplan Lab in the faculty of Biology. A lab specializing in the Biophysics field.

Could you explain what Prof. Kaplan’s laboratory is about?
Kaplan lab uses sophisticated homemade Optical tweezers set up to manipulate the fine interactions between protein and DNA at the single-molecule level by mechanical force. Briefly, an optical tweezer uses high intense laser beams to trap and control the position of a spherical dielectric particle, then by using chemical means, we attach a single molecule of DNA between two particles, wherein we can stretch and, more interestingly, unzip the bases that hold the DNA intact. So, you can think of it as holding between two very tiny hands a single DNA molecule (Diameter of ~2 nm), and you stretch it exactly like you stretch a rubber between your two hands.

Could you tell us about your current article/research, what was the main purpose of the research and what did you discover?
One of the biggest open questions in the biology field is how one genome (DNA sequence) found in all individual cells encodes for various shapes and functions, and how it can be spatially and dynamically modulated, for example, via environmental stimulates. The process that manages the information flow in each cell is called Gene regulation.
This study focuses on the proteins that initiate transcription (the first step of the gene regulation) known as transcription factors (TFs). The main purpose of the study is to develop a means to characterize the full distribution of the binding and dissociation times of the TF in a well-controlled assay and to study factors to regulate its binding kinetics.
Using our state-of-the-art technique (the optical tweezers), we established a novel assay to follow in real-time the binding dynamics of an individual unlabeled TF on a single molecule of DNA. Our findings show how small variations in sequence and methylation (DNA modification) patterns synergistically extend the spectrum of a protein’s binding properties and demonstrate how the proposed approach can provide new insights into the function of transcription factors.

Can you elaborate on the importance of the discovery? Why will this discovery serve you and what directions does it take? What is the application of the discovery (domains, solutions)?
The developed approach can be used to characterize the binding kinetics of various TFs without the need of chemically labeling them, which renders them less mobile and possibly influence their binding kinetics. In addition, it can be incorporated with additional factors, such as nucleosome (the building blocks of the chromatin), polymerase (the enzyme that transcribes the DNA), other TFs, and more, all of which are currently ongoing research in the lab.

What drew you to the current lab/project?
I can name plenty of reasons, but I will name three. First, the system of optical tweezers amazed me, the fact that we can manipulate a small molecule of DNA (~40000 thinner than a hair!) in such a controllable and precise way was intriguing, and I wanted to learn the technique. Back then, I started in a project with Dr. Omri Malik where we followed the real-time activity of an enzyme found in HIV. Afterward, I joined Dr. Sergei Rudnizky in multiple projects regarding the gene regulation process, and then I continued to research gene regulation.

Second, the vibe in the lab was very friendly and cooperative. And finally, Prof. Ariel Kaplan is a very patient, professional, and great supervisor who helped expand and enrich my knowledge and abilities.

When you are not “doing” science, what do you do?
I like to run, read books, and enjoy board/card games.

When you grow up who do you want to be?
I am not sure, but what is definite, I want to be in a place where you continue to learn and grow constantly.

what are your plans for the future of your career?
Currently, I started a new position as a research scientist and algorithm developer in Gateway Institute for Brain Research. So, this is probably my near future.

A link to the full article: https://academic.oup.com/nar/article/49/19/10975/6381139
A link to Associate Prof. Kaplan lab site: https://kaplan.net.technion.ac.il/
To Prof. Kaplan page: https://biology.technion.ac.il/en/member/kaplan/

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