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FOLLOW THIS LINK FOR THE FULL ARTICLE FROM UCONN TODAY.
BY LAUREN WOODS

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The Society for Craniofacial Genetics & Developmental Biology (SCGDB) announced that Justin Cotney, Ph.D., associate professor in the UConn School of Medicine’s Department of Genetics and Genome Sciences, will receive its 2023 Marylou Buyse Distinguished Scientist in Craniofacial Research Award.

The award, named after the first female president of the SCGDB, was created to recognize SCGDB members like Cotney who have made important contributions to the craniofacial sciences.

Cotney will be honored on October 10 at the Society’s 46th annual meeting in in Ohio at the Cincinnati Children’s Hospital Medical Center where he will receive a commemorative plaque and deliver a plenary lecture on his functional genomics of craniofacial development research.

In 2015 Cotney joined UConn and launched his research program. He is a member of UConn Health’s Institute for Systems Genomics. He received his B.S. degree in Biology from Birmingham-Southern College and Ph.D. in Genetics and Molecular Biology from Emory University. Prior to joining UConn, Cotney was a postdoctoral fellow in the Department of Genetics at Yale University’s medical school.

His research applies genomic technologies to understand regulatory architecture of mammalian development and disease which has been a hallmark of his independent research program. The Cotney Laboratory at UConn has revealed new insights into the role and evolution of enhancers in controlling craniofacial, heart, limb, and brain development. He has made strong contributions to understating genetic variants associated with normal facial variation in humans and risk for congenital craniofacial anomalies. This work has been published in a number of high-impact journals and led to robust funding from the NIH. Cotney has also made an impact on the field of craniofacial biology through his sharing of genomic datasets to create an epigenomic and transcriptomic atlas of human craniofacial development through Facebase.

In addition to his research, Cotney serves the UConn academic community as director of the Genetics and Developmental Biology Graduate Program, a mentor to dozens of trainees, and an educator across the campus. Beyond his own institution, he serves on grant review panels for the NIH and other national/international grant programs. Cotney and his lab members have contributed to multiple annual SCGDB meetings.

Learn more about the Society founded in 1975 and its goals to improve our understanding of craniofacial development and disease, promote policy and patient advocacy, and translate basic science discoveries into clinical therapies and improved patient care.

Follow this link for the full article from UConn Today.
by Kim Krieger

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Butternuts are soft and oily, with a light walnut flavor that lingers on the tongue. But few Americans have tasted this endangered native. Now, UConn undergraduates have published the first full map of the unusual tree’s DNA in G3 .

The butternut is just the first in an ambitious effort to record the DNA of overlooked endangered species before they’re gone. Pumpkin ash, deep sea zigzag coral, and the red-vented cockatoo are a few of the other organisms whose genes are getting thoroughly sequenced by the Biodiversity and Conservation Genomics team at UConn’s Institute for Systems Genomics. The program provides undergraduates with a full year of training in how to sequence, reconstruct, and describe the full genetic code of a single species. Other members of the team include Oxford Nanopore Technologies, and scientists at the Institute for Systems Genomics (ISG). Students working on specific species also collaborate with people on the ground making restoration and conservation decisions. For the butternut, this includes the US Department of Agriculture Forest Service.

What all the organisms they’re sequencing have in common is that they are endangered species that don’t have a history of major agricultural, medical, or scientific uses.

The butternut Juglans cinerea, for example, is a species of walnut native to North America that looks similar to black walnut but has elongated nuts that are very oily. It was occasionally collected for its oil and harvested for its wood. Butternut trees are now disappearing as a fungus imported from Asia kills them off, with the few survivors tending not to be pure butternut but rather hybrids of Japanese walnut, which interbreeds with butternut easily and has some fungal resistance. Pumpkin ash is one of the 16 species of North American ash being killed off by emerald ash borer insects. The red-vented cockatoo is critically endangered by habitat loss and poaching for pets. And deep-sea corals are threatened by the acidification of the oceans, which threatens their ability to create their skeletons of calcium carbonate.

Many of these organisms are not well studied scientifically. Until recently it was extremely time consuming and costly to sequence an organism’s DNA. Often there are no reference genomes, or full sequences of their genetic code, for entire families of organisms.

“Deep sea coral genomes are incredibly sparse. There are two published out of 5,000 species! This one could be the third,” says Michelle Neitzey, a graduate student in the R. O’Neill Lab.

Deep sea coral genomes are particularly interesting because deep water, much like ocean acidification, makes it difficult for corals to grab calcium carbonate out of the water, and yet deep sea corals manage to do it anyway. Understanding which of the genes make this possible could also help us understand how shallow water corals could survive acidification.

Other organisms might have other secrets. Fungal diseases spread by the horticultural trade are rapidly killing off trees in the great forests of Asia, Europe and the Americas. Sequencing the genomes of related species that evolved with different diseases–such as the butternut and the Japanese walnut—could give valuable insights into which genes provide which type of resistance. It might enable us to save species by replacing a single gene. Even though the Japanese walnut is not endangered, the team is sequencing its genome this year, for this very reason.

“We’re interested in knowing how much of the butternut population is already hybridized with Japanese walnut, and what is contributing to the genetic resistance,” to the fungal infection, says computational biologist Jill Wegrzyn, lead investigator on the team.

And in addition to the practical interest in sequencing these genomes, it’s also interesting simply because they are different from anything else anyone has ever looked at. The ploidy, or number of chromosome copies, can be wildly different than anyone had assumed. Most animals are diploid: they have two copies of each chromosome, one from mom and one from dad. Some plants can be tri- or tetraploid, meaning they have three or four copies of each. But the pumpkin ash tree the team is sequencing this year goes way beyond.

“It’s…maybe…octaploid!” says Emily Strickland ’24 (CLAS). She started work on the pumpkin ash as an independent research project, found it rather more complex than anyone expected, and is now working on it as part of the Biodiversity and Conservation Genomics team.

The program started last year with a grant from the College of Liberal Arts and Sciences Earth and Its Future initiative, and has subsequently been supported by the ISG, with material support from Oxford Nanopore Technologies and ORG.one, of which the Center for Genome Innovation in the ISG is an international partner. Org.one is an Oxford Nanopore project to develop high quality assemblies of the genomes of a number of critically endangered plant and animal species.  Oxford Nanopore’s DNA/RNA sequencing technology offers real-time analysis that can sequence any length of fragment, from short to ultra-long, flexibility that is necessary for assembling reference genomes. If the genome was a book, this would be whole phrases instead of single words, making it much faster to assemble.

The 11 undergraduates on the project are primarily MCB and biology majors. For many of them, this is their first research experience. And several of them chose it because of its practical impact.

“I really liked the idea of using computational techniques to solve problems immediately. On the conservation side, we can do so much,” says Emily Trybulec ’24 (CLAS). She was one of the team members who sequenced the butternut genome last year and wrote the paper they’ve just published, and she’s returned as a mentor this year. Other students point out that doing real research as a part of this project is completely different from a typical classroom experience in which everything is designed to work.

“It forces you to reach out and collaborate, and look for answers yourself, before you ask for help,” Harshita Akella ’24 (CLAS) says.

In addition to providing research experience, the team provides support for students to develop independent research proposals for Summer Undergraduate Research Fund (SURF) awards. All three undergraduate members of the Biodiversity and Conservation Genomics team who applied last year won their SURFs.

The program accepts 8 students a year, and interested undergraduates should inquire in March.

The Biodiversity and Conservation Genomics team’s reference genome of the butternut tree can be found here: https://gitlab.com/PlantGenomicsLab/butternut-genome-assembly It’s annotated with pictures, so scroll down and check it out.

Follow this link for information on the application procedure.

MOST CREATIVE: 

Foxp1 and Foxp2 regulate cerebellar hemisphere formation by controlling the diversification of Purkinje cells
Presenter name: Nagham Khouri-Farah, PhD Candidate
Affiliated Lab: Li and Cotney Labs, Department of Genetics and Genome Sciences, UConn Health
Abstract: Purkinje cells (PC) are the sole output neurons of the cerebellar cortex and play a pivotal role in cerebellum functioning. Furthermore, PC are presumed to orchestrate cerebellar development by regulating the differentiation of other cerebellar cell types. In the mammalian cerebellum, PC display transient molecular heterogeneity during development. However, the underpinnings of PC heterogeneity remain poorly understood due to the lack of entry to assess individual PC subtypes. Through single-cell RNA sequencing, we identified 11 molecularly distinct PC subtypes in the embryonic mouse cerebellum. Using CyCIF, a highly multiplexed immunofluorescence imaging method, and light-sheet fluorescent microscopy (LSFM), we assigned PC subtypes to their positions and resolved their three-dimensional distribution in the cerebellar cortex. Different subtypes of PCs form distinct cell clusters coinciding with the anteroposterior and mediolateral patterning of the developing cerebellum. Remarkably, PC subtypes display distinctive combinatorial expression patterns of Foxp1 and Foxp2, which have been implicated in developmental speech and language disorders and Autism in humans. Through single-cell genomics and quantitative spatial transcriptomic analysis, we showed that cerebellum-specific deletion of Foxp1 and Foxp2 disrupted a subset of PC subtypes and the formation of the cerebellar hemisphere. Together, our findings demonstrate that Foxp1 and Foxp2 act in concert to govern the differentiation of PC subtypes and, subsequently, control the formation and expansion of the cerebellar hemispheres, which is an innovative feature of the mammalian cerebellum and is involved in higher cognitive functions.

BEST OVERALL:

Novel gene evolution and 3D genome organization
Presenter name: Katherine Fleck, PhD Candidate
Affiliated Lab: Erceg Lab, Department of Molecular and Cell Biology, UConn
Abstract: Genome organization may be intricately tied to regulating genes and associated cell fate decisions. Recent technological advances in mapping of chromosomal interactions and single-cell imaging have provided insights into chromatin organization at various levels including domains, loops, and boundaries. However, how the placements of genes of different evolutionary age in the 3D genome landscape relate to their biological role remains unclear. In this study, we examine the positioning and functional associations of human genes, grouped by their evolutionary age, within the 3D genomeorganization. We reveal that genes of different evolutionary origin have variable positioning relationships with both domains and loop anchors, but remarkably consistent associations with boundaries across cell types. The functional associations of each grouping of genes are primarily cell type-specific, however, those with recently evolved genes are sensitive to 3D genome architecture. Moreover, the sensitivity of such recent genes in diseased state is more pronounced in loop anchors compared to domains. We complement these findings with analysis of the expression from genes of differing evolutionary ages across cell types. Altogether, these distinct relationships between gene evolutionary age, their function, and positioning within 3D genomic features may contribute to understanding tissue-specific gene regulation in development and disease.

After a competitive selection process, we are pleased to announce six excellent recipients for this year’s The Kenneth and Paula Munson Family Fund for Student Support in Health Science Fellowship, in the amount of $1,000. Congratulations to:

Yetunde Akinlaja, Department of Physiology and Neurobiology

Kate Denegre, Department of Molecular and Cell Biology

Nadine Lebek, Department of Molecular and Cell Biology

Rachael Massey, Biomedical Science

Weizi Wu, School of Nursing

Yiming Zhang, Department of Computer Science and Engineering

The RNA Society Outstanding Career Researcher Award recognizes the exceptional contributions of career research scientists in advancing the field of RNA. The 2023 award goes to Sara Olson, who has been a key member in the laboratory of Dr. Brenton Graveley at the University of Connecticut for 21 years and has contributed to 38 published papers. During her career, she has spearheaded a number of important discoveries spanning a wide variety of RNA biology, including the alternative splicing mechanism of the Dscam gene, the characterization of recursive splicing and circular RNAs in Drosophila, the processing of CRISPR RNAs from a multi-cistronic precursor, and extensive characterization of the Drosophila and human transcriptomes as part of the modENCODE, ENCODE and ENCORE collaborative projects. In addition to making key scientific contributions in the Graveley lab, Ms. Olson oversees the DNA sequencing and ancillary equipment within the department, and is responsible for training all personnel on the use of the equipment

Follow this link for the full UConn Today article.

Click here to view the job description and application.