News

Graduate student S Fallacaro' s book chapter on  quantifying protein enrichment at target loci in live embryos using light-sheet imaging is now online in a Methods in Molecular Biology edition on Zygotic Genome Activation. A comprehensive python notebook is available along with the text. Check it out here: 

Appy gave a virtual talk in Light Microscopy Interest Group at the NIH on his work on RNA Polymerase II clusters. 

Mustafa gave a seminar on the labs work at the UW Madison School of Medicine and Public Health in the Department of Biomolecular Chemistry

We had our first lab retreat in the lovely Pochonos. Highlights include science pictionary, activities on lab values, communication, and feedback, crazy idea pitches, chalk talks, and group cooking extravaganza. 

We pre-printed our work on Dorsal hub properties, We show that Dorsal hubs have gene specific biophysical properties that tune target gene expression This project was led by graduate student Samantha Fallacaro. Read it here: https://www.biorxiv.org/content/10.1101/2025.04.07.647578v1

Mustafa gave a seminar on the labs work at the Baylor College of Medicine Department of Molecular and Cellular Biology

We have two new undergraduate researchers who joined the lab this month, Justin Lee, a Freshman majoring in Biochemistry, and Heritage Ayodele, a freshman majoring in Neuroscience. 

The lab attended a 76'ers game where our very own graduate student, Manya Kapoor, performed during the opening ceremony with her dance team. 

The lab celebrated St. Patrick's day with a happy hour including a water pong (beer pong water) tournament. 

Mustafa gave a seminar on the labs work at Northwestern University department of Molecular Biosciences

The lab celebrated Valentines day with a happy hour and notes of appreciation for each other.

We pre-printed our work on RNA Polymerase II clusters during zygotic genome activation. We show that PolII clusters are functionally labile during development and are stably associated with single active genes. This project was led by postdoc Apratim Mukherjee. Read it here: https://doi.org/10.1101/2025.02.10.637507

Our monthly themed happy hour series was initiated for the year with a new years celebration

Cibele who is a  2nd year medical student at Faculdade de Ciências Médicas da Santa Casa de São Paulo – São Paulo, is visiting for 1 month to gain research experience at CHOP

Mustafa gave a seminar at the NIH Bethesda campus hosted by the 
Laboratory of Receptor Biology and Gene Expression

Alex was awarded the NIH F31 Predoctoral Individual National Research Service Award for her project on  "Illuminating the Molecular Mechanisms of Replication and Transcription Coordination"

The lab dressed up as their favorite fluorescent proteins and we had some fun with very interpretative recreations of photophysical processes. Check out more here:

https://x.com/MustafaMir16/status/1852056008006180986

S Fallacaro and Mustafa gave talks and Appy, Santosh, Kaeli, and Ella all presented posters. 

We continued our happy hour series organized by Alexandria Adigun with a Halloween themed happy hour for October.

Alex was awarded the Theo Wilson dissertation fellowship for her research as well as her efforts to improve diversity and inclusion in science and medicine. 

We had an amazing potluck and dinner at Mustafa's house. Good food, drinks, and of course great company!

 S Fallacaro received an honorable mention in the Nikon Small World
In Motion competition for their lovely compilation video of zooming into a fruit fly embryo: https://www.nikonsmallworld.com/galleries/2024-small-world-in-motion-competition/three-views-of-a-fruit-fly

Alex and Sena won 2/3 of the poster awards at the annual retreat for the DSRB graduate group. Way to represent the lab!

Mustafa gave a talk at the EMBL Heidelberg transcription meeting on the labs work on RNA Polymerase II clusters

We had a great time hosting our third annual annual workshop for high schoolers in the Penn OER summer program program with activities on regenerative medicine, optical alignment, light-sheet microscopy, image segmentation, and of course Drosophila!

Congratulations to Raymond to being appointed to the Structural Biology and Molecular Biophysics training program which will provide funding and training oppurtunities.

The 2024 Prelim season was a big one for us with 5 students taking qualifying exams. Big congratulations to Alexandria Adigun, Raymond Carter, Kyle Ferguson, Manya Kapoor, and Sena Sarıkaya.

Dr. Hrabowski delivered the second annual Juneteenth lecture at Penn followed by a book signing. Mustafa had the honor of introducing him. 

For this months happy hour we had a wonderful painting and sipping session. There are a lot of hidden talents in the group!

Mustafa had fun writing this journal club article on Steve McKnight's 1976 paper using Miller spreads to quantify transcription activation in Drosophila embryos & a chance to reflect on the importance of spending time with your raw imaging data! https://rdcu.be/dHNbf

Congratulations to Appy for winning the best postdoc talk award at the Cell and Developmental Biology Departments retreat. 

The lab did an Easter egg hunt  (Mustafa won) and egg spoon race for our monthly themed happy hour!

Graduate student Alexandria Adigun shared her experiences and perspectives as part of a panel discussion that Mustafa helped organize.

The lab put up its first preprint on Zelda hub relocalization. A true team effort lead by Appy, S, Net, and Joe. See twitter thread here: https://x.com/MustafaMir16/status/1780544766175756497

and preprint here: https://www.biorxiv.org/content/10.1101/2024.04.16.589811v1

Mustafa spoke about the labs work at IGMM in Montpellier, France

Mustafa spoke about the labs work at IJM in Paris, France

Mustafa gave a talk in the unconventional imaging session at SPIE Photonics Europe in Strasbourg, France in honor of his PhD Advisor Gabriel Popescu. 

Kareena, an undergraduate researcher, gave a talk on her work on inhibiting transcription in Drosophila embryos. We heard it was the best of the conference.

We celebrated St. Patrick's day for our monthly themed happy hour!

Celebrating the amazing women in our lab!

Kaeli received a nice trophy and a check for her cutting edge work!

We celebrated Valentines day for our monthly themed happy hour!

Mustafa gave a symposium select talk on the labs work on Zelda hub localization

Ella presented a poster on her work on polycomb bodies, people could not get enough of their movies!

Appy gave a fantastic platform talk on his work on RNA Polymerase II kinetics during Zygotic Genome Activation!

S presented a poster on their work on Dorsal hubs, their was a line of people waiting to talk to them!

Manya Kapoor, who is in the Bioengineering Program, decided to join us for her PhD work!

Julia who is a medical student at Faculdade de Ciencias Medicas Santa Casa SP (FCMSCSP) in Sao Paulo Brazil is visiting for 2 months to gain research experience at CHOP

We had a Dim Sum Feast for our Annual Lab Holiday Dinner

Alex decided to join the lab for her PhD after a successful rotation!

We had a great time watching the 76ers demolish the Wizards.

The lab dressed up as their very scary PI. Mustafa was a Banana. 

Derene, a Freshman majoring in Neuroscience at U Penn and a FERBS Scholar has joined us for her first research experience.  Welcome to academic research!

Alex is an MD PHD student in the DSRB graduate group. She has already completed 2 years of medical school and is doing her 3rd rotation with us. Prior to coming to Penn she completed her B.S in Biology at Howard University. 

S Fallacaro and Mustafa attended the lab's first HHMI science meeting at the HHMI Headquarters in Chevy Chase, MD. S presented a poster on a large interactive touch screen and Mustafa gave a talk. 

The lab got together to celebrate labor day and the many accomplishments this year with a feast at Mustafa's house.

S Fallacaro and Ella Hayward-Lara presented their work at the annual DSRB Graduate Group retreat. S was awarded 2nd place in the poster competition.

Manya Kapoor, a bioengineering PhD student joined the lab for her first rotation. Manya recently completed a Masters in Electrical and Computer Engineering at Princeton University. 

Kyle Ferguson, a bioengineering PhD student joined the lab for his thesis work. He just completed his M.S. in Medical Physics from Duke University. 

Kareena Shankta, a sophomore at Penn participated in the IDEAL Research SUIP summer program interning with our lab this year. She presented a poster on her work studying changes in chromatin mobility during development using single-molecule tracking

Welcome Matthew Fischer who joined us for his Postdoc today, Matthew just finished his PhD work in Dr. Leslie Pick's lab at the University of Maryland.

Siani Elliot, a recent high school graduate, who interned with us this summer through the Penn Office of Outreach, Education, & Research (OER) program presented her work on investigating if the fluorescent tags we use for live imaging influence fly lifespan & fecundity.  She concluded that they don't in the lines she quantified. 

We had a great time hosting Penn Office of Outreach, Education, & Research (OER ) summer students. They learned about optics, fly genetics, image segmentation, and regenerative medicine. 

Mustafa gave an invited talk at the Satellite Symposium titled" Outside of Exomes: Enhancers in Development and Congenital Disorders" at the 2023 SDB Annual Meeting in Chicago. There were lots of great discussions on how enhancers work!

Our collaborative work with Mellissa Harrison's group is now published in Developmental Cell (https://doi.org/10.1016/j.devcel.2023.06.010). We show that GAF nuclear foci form through binding to AAGAG satellite repeats in an IDR independent manner. 

We welcomed Yara Haloush a new Research Technician and Siani Elliot a recent highschool graduate who is interning with us for the summer. 

Kaeli was awarded a NIH-National Cancer Institute F31 Predoctoral fellowship to pursue her work on Mechanisms of pathogenic gene activation by aberrant transcriptional hubs formed by mutant ENL. 

Raymond will be co-mentored by Gerd Blobel and will be working on questions related to the dynamics of nuclear organization and genome folding. 

Check out this video about life in our lab made by the very talented 
CHOP Research  Creative Services team as part of their "lab life" series 

https://www.youtube.com/watch?v=_A6Go_PEJjI&t=1s

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Ella and S passed their exams in spectacular manner and are now PhD candidates!

The Stem Cell Niche conference is sponsored by the Novo Nordisk Foundation and hosted in Favrholm, Denmark just outside of Copenhagen

Mustafa was selected as part of the inaugural class of Freeman Hrabowski Scholars, 31 outstanding early career faculty in science who have potential to become leaders in their research fields and to create diverse and inclusive lab environments.

Read more here : https://www.research.chop.edu/cornerstone-blog/new-technologies-lead-to-new-discoveries-qa-with-hhmi-scholar-mustafa-mir-phd

S Fallacaro and Ella Hayward-Lara, 2nd year students in DSRB, were both awarded the prestigious NSF GRFP Award to support their doctoral work.

Raymond Carter (BMB) is doing his third rotation with us. He is interested in applying single molecule tracking to study transcription regulation.

We attended the 63rd Annual Drosophila Research Conference in Chicago. Mustafa gave a plenary talk, Appy, Alan, S, and Net presented posters on their latest and greatest work!

The Keystone Symposium on Biomolecular Condensates was held in Vancouver, Canada this year. There was lots of interesting debate especially on the role of condensates in transcription regulation. 

Mustafa presented a seminar and met with students, postdocs, and faculty in the Center for the Physics of  Biological Function

Kaeli won both the best application and peoples choice awards at the CCGM retreat!

Mustafa visited the department to give a seminar, meet with students, and faculty.

Highlights this year included "Drosop-Leia" and "Polycomb-repressed graduate student"

Mustafa gave a seminar and met with students and faculty in the Center for Computational and Integrative Biology at Rutgers University, Camden Campus

We contribute to work on oncogenic condensates formed by ENL spearheaded by our close collaborators in Liling Wan's lab. Read the paper here. co-authors from our lab are Alan Boka and Kaeli Mathias.

Sena Sarıkaya (DSRB) is doing her 1st rotation with us. She wants to push the limits of in vivo imaging!

We contributed to work led by Melissa Harrison's lab (U. Wisconsin) on understanding how GAF foci are formed: https://www.biorxiv.org/content/10.1101/2022.11.29.518380v1

Santosh Adhikari joins the lab as a postdoc, He just completed his PhD in physics from U. of Minnesota.

Mattisen Dimler joined us a research technician, she will be supporting the labs mission and learning to do research.

Gabriela Hayward-Lara joined the lab after rotating with us last fall. We are very excited to have her on board. 

The talk was a part of the Telluride Science Reearch Center workshop series

Anna Crombie, a student at the University of Leicester has joined us for an internship this summer

Alan Boka was selected to be on the Structural Biology and Molecular Biophysics training grant!

Sapna Krishnakumar, a sophomore in Biological Sciences at IISER Mohali has joined us for an internship this summer

Our team "MS2 good to lose!" (named by S Fallacaro) won the lab Olympics at the CDB Retreat! 

Congratulations Alan Boka on becoming our second PhD Candidate! 

Congratulations Kaeli Mathias on becoming our first PhD Candidate! 

S returned to our lab for their PhD after rotating with us last summer. They will be working on questions related to the mechanotransduction of gene regulation

The ZGA symposium is a virtual series held once a month and hosted by the Giraldez Lab at Yale University. 

Ernesto is a sophomore majoring in Biology at UPenn and has a keen interest in embryonic development!

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Our research was featured in the CHOP cornerstone blog: https://www.research.chop.edu/cornerstone-blog/new-innovator-award-advances-live-imaging-technology-to-see-embryonic-gene-regulation

We received and installed our new Femtojet microinjection system and our new Lecia DMi8 inverted microscope. Lots of poking embryos coming up!

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As our light-sheet microscope is near ready for prime time we had an all hands on deck effort to install a enclosure to protect the optics and shield the instrument form air currents in the room!

Al l the major components of our MOSAIC microscope are finally in place and now its time for fine-tuning!

Sarah is a freshman majoring in Biochemistry at UPenn. She comes to our lab through the Penn Freshmen Exposure to Research in Biological Science (PennFERBS) and we are very happy to have her start her scientific career with us!

We celebrated Halloween with a "meet and treat" with the whole CHOP CCGM! Fun and silly festivities ensued. 

We celebrated getting the NIH New Innovator award with our close collaborators and fellow awardee Liling Wan and her lab. Our co-mentored student Kaeli Mathias is guaranteed/mandated to have a super innovative thesis project! 

The lab was awarded a NIH Directors New Innovator Award (DP2). This $2.4 million award will fund our efforts to develop new approaches to quantify the molecular dynamics of gene expression and nuclear organization during early embryonic development.
NIH Press Release | Awardees | CHOP Press Release | Penn Press Release

We are very happy to have Net on board. Net brings with him tons of experience working with flies and lots of enthusiasm. He has previously worked as a Research Technician with Shawn Little at Penn and Thomas Gregor at Princeton. 

Gabriella Hayward Lara who is in the DSRB program and recently graduated from Princeton joins the lab for her first rotation. Welcome!

We celebrated the end of summer rotations and welcomed some new folks on a beautiful Philly day!

We kicked off our image processing workshop series. We discuss how to write code to analyze imaging data quantitatively while minimizing manual intervention. This workshop is led by Alan Boka and Tomer Lapidot (Ophir Shalem's lab).

Congratulations to Kaeli Mathias for being selected for the Genetics T32 grant. lots of exciting discoveries ahead!

Cody Eskandarian  is an undergraduate in biochemistry and biophysics at UPenn.

We received our second optical table (thanks Melike Lakadamyali's lab), nothing like the feeling of putting the first piece on a blank optical table. We will be using this one for prototyping new optical setups.  

We celebrated the end of Kaeli Mathias's and Adam Jabak's rotations and welcome Guzel and Patrick with libations and games at "The Commons" 

Guzel Naik is joining us for 6 months as a research intern. He has a BSc in Biology and previous research experience in epigenetics at the Lahore University of Management Sciences

Patrick Samaha joins us for the summer. He is currently an undergraduate student in Bioengineering at the University of Toronto.

S Fallacaro joins the lab for their first rotation. They are a student in The Developmental, Stem Cell, and Regenerative Biology division within the Cell and Molecular Biology graduate group. 

I think he may need a ladder soon

Kaeli Mathias decides to be co-mentored by Mustafa and Dr. Liling Wan. She has boundless enthusiasm, energy, and deep curiosity! 

The lab surprised Mustafa with a birthday cake. What a great group of people! :)

Its growing!

Super excited that Alan Boka has decided to join the lab for his PhD work. He is a fantastic young scientist with a fearless attitude. Looking forward to lots of creating and exciting science.

Good progress for one day! After receiving our room we have our optical table, two photon laser, and server rack setup!

The renovation of our microscope room is  complete. After 5 months of anticipation we can finally start on our microscope. Thanks to CHOP for facilitating this large rennovation

Read the feature here: https://cambnewsletter.wixsite.com/blog/single-post/pioneering-pandemic-pis

This is a weekly virtual series. Watch a recording of the talk here: https://www.youtube.com/watch?v=iRTo4HhtttM

Kaeli Mathias and Adam Jabak from the BMB graduate group joined the lab for their third rotations.  The flies still outnumber us significantly.

Weather was warm, vaccines were in arms and our first rotation student Alan Boka's time was up. We had a cookout and some libations to celebrate!

It was fantastic to interact with leading researchers from across the world in this virtual forum

Its so pretty!

Looking forward to lots of photons

We ran a gel and learned something. Science!

And we are off! first group meeting.

Today we welcome our first postdoc Apratim Mukherjee who is a mechanical engineering PhD from Virginia Tech where he studied how cells sense their extracellular matrix using synthetic nanofiber networks. We also welcome Alan Boka a rotation student from BMB Graduate Group. The lab is growing!

Today our environmental chambers to house our flies from Darwin Chambers were installed. Now they have a nice cozy place to grow!

Watch a video of the installation here: https://twitter.com/MustafaMir16/status/1352214822830669826?s=20

We are a "we" now. Our first lab member Nick Gattone has joined us as the labs first Technician! Nick has just finished his Masters working with Nir Yakoby at Rutgers where he worked on the role of tRNA fragments in regulating gene expression. Welcome Nick!

The lab is officially open!