Tag: CDB

These graduate students are members of the Cell and Developmental Biology department

Yunshu Song

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Yunshu Song, CDB

Yunshu Song, CDB

History

  • B.S, Biochemistry, University of California San Diego, 2012-2016
  • M.S, Chemistry, University of California San Diego, 2016-2017
  • UIUC Cell and Developmental Biology Ph.D. Program 2018-Present

Current Project

Wbscr17 project

Past Projects

Outside the Lab

Publications

 

Email Yunshu Song

yunshus2@illinois.edu

Soumya Negi

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Graduate Student, CDB

History

  • Anna University, 2013

Current Project

  • Tbox18 Project- I am working on the NIH funded Tbx18 project. I am looking at the postnatal expression of Tbx18 in the prostate.

Past Projects

  • Undergraduate thesis project: I worked on fluorescent imaging of the bacterium Bacillus megaterium. 

Publications

Coming soon.

Outside the Lab

I really like to travel and visit new places. I have been learning a classical Indian dance form called Bharatnatyam for the last 10 years. I also play the guitar.

Email Soumya

snegi2 [at] illinois [dot] edu

Chris Seward

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Chris Seward

Graduate Student, CDB

History

Current Project

Chris is primarily involved in the Simons Project, which is working to identify the molecular and genomic basis of social behavior.  He is focused on using ChIP-Seq to reveal the genetic regulatory mechanisms essential for social behavior in several species.  He is also working on developing bioinformatic pipelines to integrate diverse ChIP-seq and RNASeq data from this project in order to compare cross-species experimental data.

Past Projects

  • Patterns of variation in archaeal genomes from geothermal environments – Whitaker Lab, UIUC
  • Identifying a Role for Vibrio cholerae T3SS Effector VopX – Dziejman Lab, URMC

Outside the Lab

Chris grew up in Boston, MA and went to college in Rochester, NY.  He enjoys travelling, photography, sailing, skiing, weight training, driving, movies, and tinkering with new technology.  Check out his photography on Flickr.

Publications

  1. Shpigler, Hagai; Saul, Michael; Murdoch, Emma; Corona, Frida; Cash-Ahmed, Amy; Seward, Christopher; Chandrasekaran, Sriram; Stubbs, Lisa; Robinson, Gene. Honey bee neurogenomic responses to affiliative and agonistic social interactions, Genes, Brains and Behavior 2018.  doi:10.1111/gbb.12509
  2. Michael Saul*, Charles Blatti, Wei Yang, Syed Abbas Bukhari, Hagai Y. Shpigler, Joseph M. Troy, Chris Seward, Lisa Stubbs, Gene E. Robinson, Sihai Dave Zhao* and Saurabh Sinha*. Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge, Genes, Brains and Behavior 2018. doi:10.1111/gbb.12502
  3. Abbas Bukhari, Michael Saul, Chris Seward, Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell. Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Sticklebacks, PLOS Genetics 2017. doi:10.1371/journal.pgen.1006840
  4. Rika Anderson, Angela Kouris, Chris Seward, Kate Campbell, and Rachel Whitaker. Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements, Genome Biology and Evolution 2017. doi:10.1093/gbe/evx104
  5. Chris Seward*, Michael Saul*, Saurabh Sinha, and Lisa Stubbs, et al. Transcriptional regulatory dynamics set the stage for a coordinated metabolic and neural response to social threat in mice, Genome Research 2017. doi:10.1111/gbb.12379
  6. Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M Troy, Chris Seward, Xiaochen Lu, Lisa Stubbs. ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression, Oncotarget 2017. doi:10.18632/oncotarget.12508
  7. Hagai Shpigler, Michael Saul, Emma Murdoch, Amy Cash‐Ahmed, Chris Seward, Saurabh Sinha, Lisa J Stubbs, Gene E Robinson, et al. Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees, Genes, Brains and Behavior 2017. doi:10.1111/gbb.12379
  8. Chris Seward*, Huimin Zhang*, Zuowei Wu, Huiyan Ye, Youjun Feng. Genomic insights into the ESBL and MCR-1-producing ST648 Escherichia, Science Bulletin 2016. doi:10.1007/s11434-016-1086-y
  9. Kelly Miller, Madeline Sofia, Jacob Weaver, Chris Seward, and Michelle Dziejman.  Regulation by ToxR-like proteins converges on vttRB expression to control T3SS-dependent Caco2-BBE cytotoxicity in V. cholerae, Journal of Bacteriology, 2016. doi:10.1128/JB.00130-16
  10. Christopher H. Seward, Alexander Manzella, Ashfaqul Alam, J. Scott Butler and Michelle Dziejman. Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes, Toxins 2015. doi:10.3390/toxins7104099

Email Chris

seward2 [at] illinois [dot] edu

Li-Hsin Chang

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Graduate Student, CDB

Graduate Student, CDB

History

  • PhD, Cell and Developmental Biology, UIUC 2017
  • MS, Biochemistry and Molecular Biology – National Taiwan University
  • BS, Pharmacy – National Taiwan University

Current Project

Publications

Liu H, Chang LH, Sun Y, Lu X, Stubbs L 2014. Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies. Genome Biol Evol. 2014 Mar;6(3):510-25. doi: 10.1093/gbe/evu030.

Email Li-Hsin

Derek Caetano-Anollés

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Derek Caetano-Anolles

Derek Caetano-Anollés, Ph.D.

Education

Research Interests

  • Recent gene duplication of zinc finger transcription factors – Derek’s PhD research in the Stubbs Lab focused on investigating the role of ZNF286A, a Krüppel-type zinc finger transcription factor with a recently evolved human-specific duplicate, ZNF286B. These transcription factors drive differentiation of neural precursor cells and may play undiscovered key roles in critical neuronal developmental pathways, including pathways that have been implicated in microcephaly, schizophrenia, and other neurological disorders.
  • Molecular roots of the social brain – During his graduate career, Derek also worked on the Simons Project, which investigates the conserved molecular foundations for social behavior in animal brains utilizing mice, stickleback fish, and bees as models. He focused on analyzing the RNA and protein expression profiles of the mouse brain after encountering aggressive or maternal-caring stimuli.
  • Genetic framework for mouse facial structure under selective pressures – Derek has since left the Stubbs Lab to work at the Max Planck Institute for Evolutionary Biology, where his research involves identifying the genes responsible for controlling skull shape and facial structure during mouse development, and how those features are impacted by evolutionary and selection pressures.

Selected Publications

  • Rittschof C, Bukhari S, Sloofman L, Caetano-Anollés D Cash-Ahmed A, Kent M, Lu X, Sanogo O, Weisner PA, Zhang H, Bell A, Ma J, Sinha S, Robinson G, Stubbs L. (2014). Neuromolecular responses to social challenge: Common mechanisms across mice, fish and bees. PNAS, 111(50):17929–17934. [Link]
  • Caetano-Anollés D. (2013). Polymerase Chain Reaction (PCR). In: Maloy S, Hughes K, editors. Brenner’s Encyclopedia of Genetics 2nd Edition. Waltham: Academic Press. Volume 5, pages 392-395. [Link]
  • Nowick K, Fields C, Gernat T, Caetano-Anollés D, Kholina N, Stubbs L. (2011). Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species. PLoS One, 6(6):e21553. [Link]
  • Stubbs L, Sun Y, Caetano-Anollés D. (2011). Function and evolution of C2H2 zinc finger arrays. Subcellular Biochemistry, 52:75-94. [Link]

Full publication list at LinkedIn, ResearchGate, and ORCID.

LinkedIn Profile

Outside the Lab

  • Derek practices art in both traditional and digital media (visit his Bēhance). He is also very well-versed in the art of illeism.

Email Derek

Younguk-Calvin Sun

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Graduate Student

Graduate Student, CDB

History

  • BS Department of Genetic Engineering, SungKyunKwan University, Seoul, South Korea
  • PhD (2016) CDB MCB, University of Illinois at Urbana-Champaign

Current Project

  • Dissecting the role of kruppel-type Zinc finger transcription factor ZSCAN5 and Zim1

Past Projects

Everything is ongoing.

Outside the Lab

Auto aficionado. Computer maniac. Gadget savant. Beer lover. Photography hobbyist. Cuisine hound.

Publications

1.Stubbs L., Sun Y. and, Caetano-Anolles D. Function and Evolution of C2H2 Zinc Finger Arrays. Subcellular Biochemistry 52:75-94, DOI 10.1107/ S1744309110034135. Epub 2010 Nov 16.

Irrelevant Publications


1. Sun Y, Seo MS, Kim JH, Kim YJ, Kim GA, Lee JI, Lee JH, and Kwon ST. Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization.Environmental Microbiology. 2008 Dec;10(12):3212-24. Epub 2008 Jul 16. @PubMed

2. Kim GA, Sun Y, Song JG, Bae H, Kim JH, Kwon ST. Properties of cold-active uracil-DNA glycosylase from Photobacterium aplysiae GMD509, and its PCR application for carryover contamination control.Enzyme and Microbial Technology. 2009 May;44(5)263-68. @ScienceDirect

3. Cho SS, Sun Y, Yu M, Kwon SH, Kwon ST. Characterization and PCR applications of dUTPase from the hyperthermophilic euryarchaeon Thermococcus pacificus.Enzyme and Microbial Technology. 2012 Dec;51(6-7):342-7 @PubMed

4. Supangat S, An YJ, Sun Y, Kwon ST, Cha SS. Purification, crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from Sulfophobococcus zilligii. Acta Crystallography Section F Structural Biology Crystallography Communication. 2010 Dec 1:66(Pt12):1583-5 @PubMed

5. Kim JH, Lee KK, Sun Y, Seo GJ, Cho SS, Kwon SH, Kwon ST. Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles. 2013 May;17(3):515-22 @PubMed

6. Kim GA, Lee MS, Sun Y, Lee BD, Lee JI, Lee JH, Kwon ST. Characterization of cold-active uracil-DNA glycosylase from Bacillus sp. HJ171 and its use for contamination control in PCR. Applied Microbiology and Biotechnology. 2008 Oct;80(5):785-94. @PubMed

7. Song JM, Nam K, Sun Y, Kang MH, Kim CG, Kwon ST, Lee J, Lee YH. Molecular and biochemical characterization of a novel arthropod endo-β-1,3-glucanase from the Antarctic springtail, Cryptopygus antarcticus, horizontally acquired from bacteria. Comparative Biochemistry and Physiology, Part B. 2010;155:403-12. @PubMed

8. Choi JJ, Song JG, Nam KH, Lee JI, Bae H, Kim GA, Sun Y, Kwon ST. Unique substrate spectrum and PCR application of Nanoarchaeum equitans Family B DNA polymerase. Applied and Environmental Microbiology. 2008 Nov;72(24):6563-69. @PubMed

Email Calvin

C. Chase Bolt, Ph.D.

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C. Chase Bolt, Ph.D.

C. Chase Bolt, Ph.D.

Current Position:

Post-doctoral researcher. Laboratory of Denis Duboule.
École Polytechnique Fédérale de Lausanne.

Lausanne, Switzerland.

Current Contact Information

Education

Doctorate of Philosophy, Cell and Developmental Biology
– University of Illinois 2008-2014
Bachelor of Science, Molecular and Cell Biology
– Bradley University 2005-2008

Publications

Tbx18 Regulates the Differentiation of Periductal Smooth Muscle Stroma and the Maintenance of Epithelial Integrity in the Prostate. C. Chase Bolt, Soumya Negi, Guimarães-Camboa N, Zhang H, Troy JM, Lu X, et al PLoS ONE. 2016;11: e0154413–20. PMID 27120339

A distant downstream enhancer directs essential expression of Tbx18 in urogenital tissues.
C. Chase Bolt, Colleen M Elso, Xiaochen Lu, Fuming Pan, Andreas Kispert, and Lisa Stubbs.
Developmental Biology, 2014 pp. 1-11. http://dx.doi.org/10.1016/j.ydbio.2014.05.010

Email Chase