The response of phyllodes tumor of the breast to anticancer therapy: An in vitro and ex vivo study
Alicja Urbaniak, Fariba Jousheghany, Youzhong Yuan, Sergio Piña‑Oviedo, Adam Huczyński, Magdalena Delgado, Thomas Kieber‑Emmons, Behjatolah Monzavi‑Karbassi, Timothy C. Chambers
Oncology Letters
Mukiza TO, Protacio RU, Davidson MK, Steiner WW, Wahls WP.
Genetics.
Histone Modifications as Biomarkers for Immunotherapy.
Taylor EM, Koss B, Davis LE, Tackett AJ.
Methods Mol Biol
The biochemistry department participated in the 18th Annual Village Walk for Cancer Research in Hot Springs Village. The walk is a fundraiser for cancer research at WPRCI. Funds from last years walk are currently funding a project addressing drug resistance in lymphoma in Samantha Kendrick‘s lab. Also walking were Stephanie Byrum, Alicia Byrd, and Tung-chin Chiang.
The Biochemistry and Molecular Biology welcomed new GPIBS students to UAMS with a picnic at Allsopp Park. Thanks to students Katie Bronson and Allie Davis for helping with the organization and set up.
Katie Bronson and Allie Davis
Allie Davis, a graduate student in Dr. Paul Miller’s lab, and Binyam Belachew, a graduate student in Dr. Kevin Raney’s lab received their white coats at the UAMS Graduate School’s annual Research Induction Ceremony celebrating Ph.D. candidates who have successfully passed their qualifying exam in the past year. Congratulations Allie and Binyam!
Allie Davis, a graduate student in Dr. Grover Paul Miller’s lab has recently been elected to two different groups.
Allie was elected to serve on the International Society for the Study of Xenobiotics (ISSX) New Investigator Group. This group comprises promising new investigators (predoctoral, postdoctoral, and new to their careers) that recruit and retain new ISSX members and promote interaction and collaborations between new members and more experienced members to ensure a lively and diverse group for many years to come. Currently, the new investigator group is writing up a conference proceedings paper that covers the ISSX international meeting from this past July.
Allie was also selected to serve on the Drug Metabolism Reviews (DMR) editorial board. Being a predoctoral student, access to many editor friends and colleagues she’s met at conferences and events will help her to learn the editorial process. Allie was selected for this group because she is a promising new investigator who has shown that she is willing and able to communicate and collaborate with scientists across many branches with varying degrees of experience.
Congratulations Allie!
By Amy Widner
Imagine there’s an outbreak of an infectious disease. Could health officials on the ground harness the power of new handheld DNA and RNA sequencers to monitor outbreaks in real-time and quickly contain them?
This question lies at the heart of research published in the journal Infection, Genetics and Evolution by UAMS Biochemistry and Molecular Biology track graduate student Duah Alkam. She and her advisers from the College of Medicine Department of Biomedical Informatics and the Department of Microbiology and Immunology collaborated with the Arkansas Department of Health to look at specimens collected during a 2016 mumps outbreak in Northwest Arkansas.
It took the Human Genome Project 13 years to complete the first sequence of a human genome in 2003. As sequencers became available for purchase, they were large, expensive and slow.
That has changed. Alkam used a device called the Oxford Nanopore Technologies MinION to sequence each sample in a matter of hours. To offload the data, she simply connected the MinION through a USB port to a laptop.
“You see results on your computer in real time,” Alkam said. “It’s fast, affordable and simple. The idea is that something like this might be useful during an outbreak, especially in a rural setting. If you can quickly identify a strain, you’re that much closer to understanding the origin of the outbreak, which may help contain it and protect the at-risk population.”
The new challenge for scientists is how to interpret the massive amount of data produced by these powerful sequencers. That is where the relatively new field of biomedical informatics comes in.
“Biomedical informatics allows us to look at genomes within a matter of hours and compare them, pinpointing connections and what might be important about these datasets,” Alkam said. “In this way, biomedical informatics is sort of the bridge between raw data and relevant information.”
In this case, Alkam was able to determine the unique characteristics of the specific variation of the mumps virus that was behind the 2016 outbreak. They used a computational technique called immunoinformatics to plot a “family tree” of sorts for the virus.
“We found that it was very similar to a strain that started an outbreak in Massachusetts around the same time in 2016, and it was also related to another strain that spread in Washington state, which may suggest that all three outbreaks originated from the same strain.”
While Alkam’s experiment was not conducted during an active outbreak, she and her advisers believe the results demonstrate great promise for the technique to be applied in the real world. Earlier in 2019, other scientists in the Department of Bioinformatics collaborated with researchers around the world for the first demonstration that the MinION could be used for the rapid genetic sequencing of multiple human viruses.
“The possibility of infectious disease outbreaks in health care settings and communities is something that unites us across the globe. We’re all vulnerable,” said Se-Ran Jun, Ph.D., Alkam’s adviser for the project and an assistant professor in biomedical informatics. “So at UAMS, it’s exciting each time we demonstrate how we can harness the power of new sequencing technology, big data science and analytics, and high performance computing in biomedical informatics to offer solutions.”
The project was funded with a grant to Jun from the UAMS for Translational Research Institute.
Alkam is a student in the UAMS Graduate School’s Graduate Program in Interdisciplinary Biomedical Sciences (GPIBS). Her other advisers are David Ussery, Ph.D., a professor in the Department of Biomedical Informatics; and Mark Smeltzer, Ph.D., a professor in the Department of Microbiology and Immunology.
Maroof Zafar, a postdoctoral fellow in Alicia Byrd’s lab, was the featured visitor of the week at Cold Spring Harbor Labs when he attended the CSHL Eukaryotic DNA Replication & Genome Maintenance Meeting. Check out the article about him.
Megan Reed, a graduate student in Robert Eoff’s lab presented a poster entitled “DNA polymerase kappa modulates glioma cell plasticity in response to DNA damage” at the Cold Spring Harbor Labs Eukaryotic DNA Replication & Genome Maintenance Meeting.
Maroof Zafar, a postdoctoral fellow in Alicia Byrd’s lab presented a poster entitled “Human DNA helicase B protects stalled forks from degradation after replication stress” at the Cold Spring Harbor Labs Eukaryotic DNA Replication & Genome Maintenance Meeting.
Davis LE, Shalin SC, Tackett AJ.
Cancer Biol Ther.
PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation.
Ren Z, Ahn JH, Liu H, Tsai YH, Bhanu NV, Koss B, Allison DF, Ma A, Storey AJ, Wang P, Mackintosh SG, Edmondson RD, Groen RWJ, Martens AC, Garcia BA, Tackett AJ, Jin J, Cai L, Zheng D, Wang GG.
Blood.
Glazko G, Zybailov B, Emmert-Streib F, Baranova A, Rahmatallah Y.
PLoS One
Eugene is a Ph.D. Student in his 5th year in the Biochemistry and Molecular Biology Department in the laboratory of Dr. Giulia Baldini.
He has a B.A. in Biochemistry and Molecular Biology from Hendrix College.
The hypothalamus plays a central role in maintaining healthy energy homeostasis. The arcuate nucleus (ARC) of the hypothalamus receives anorexigenic signals from the periphery mediated by increased circulating leptin and insulin, which bind to receptors expressed by proopiomelanocortin (POMC) neurons in the ARC. When activated, POMC neurons release α-Melanocyte stimulating hormone (α-MSH). In the paraventricular nucleus (PVN), α-MSH binds to the melanocortin-4 receptor (MC4R) to signal decreased food intake and increased energy expenditure. Single-minded-1 (Sim1) neurons in the PVN include the population of MC4R neurons. My research uses mice to study the effect of obesity by a high-fat (HF) diet on the PVN neurons expressing Sim1 transcription factor and MC4R. When mice are fed HF diet, they have increased body weight as a result of increased caloric intake. We found that exposure to HF diet induces loss of Sim1 neurons in the PVN and, in male mice, loss of POMC neurons and α-MSH abundance. Because there are no reliable commercial antibodies that can detect MC4R, we generated a knock-in mouse line expressing HA-tagged MC4R (MC4R-HA) by using CRISPR/Cas9 technology to detect MC4R protein. We found that HF diet induces injury to MC4R neurons in the PVN as indicated by loss of MC4R protein, decreased mitochondrial abundance, and mitochondrial network size. The data suggest that HF diet induces loss of MC4R protein rather than of MC4R neurons, suggesting that expression of MC4R could be a target for anti-obesity therapy.
Overall my time in graduate school has been excellent. I would say that I happened to fall into the right group of people. The life lesson I learned is never to translate a joke. The chances are either the joke is not funny, none understands it, or you will offend someone.
I want to do a postdoctoral fellowship for a few years and look for opportunities in biotech and pharmaceutical companies.
I like to do many experiments. I love making DNA constructs. It excites me. If my labmates wanted to subclone anything, I would volunteer to do it.
When I grew up, my mother treated every ailment with a specific type of food (she still does). When I got sick in boarding school, I asked permission to go home. She would cook food for me, and the next day I would feel better and go back to school. Food is still my over-the-counter medicine today. If you see me sick, the first treatment to give me is food (enough of it).
Nyamugenda E, Cox AB, Pierce JB, Banning RC, Huynh ML, May C, Marshall S, Turkal CE, Duina AA. Charged residues on the side of the nucleosome contribute to normal Spt16-gene interactions in budding yeast. Epigenetics. 2018; 13(1):1-7. doi: 10.1080/15592294.2017.1418132. Epub 2018 Feb 8. PMID: 29271283
Nyamugenda E, Trentzsch M, Russell S, Miles T, Boysen G, Phelan KD, Baldini G. Injury to hypothalamic Sim1 neurons is a common feature of obesity by exposure to a high-fat diet in male and female mice. J Neurochem. 2019 Apr; 149(1):73-97. doi: 10.1111/jnc.14662. Epub 2019 Feb 11. PMID: 30615192
Rwanda Presidential Scholarship
