Emily Baltz

Emily Baltz

History

  • UIUC Class of 2015: Molecular and Cellular Biology & Psychology
  • Stubbs lab member:  January 2012 – present

Current Project

Emily works with graduate student Annie Weisner. She’s helping to investigate the role of the neurodevelopmental gene, Auts2. Mutations in the Auts2 locus cause autism, epilepsy, and mental retardation in humans, but little is known about the function of this gene or its role during neurodevelopment. In the past, Emily  designed primers to investigate the expression of various isoforms at different stages of murine brain development.  Currently, she’s using immunohistochemistry to examine the differences of expression of  AUTS2 in our translocation mutant 16Gso as compared to its wildtype littermates. 16Gso displays epilepsy and autistic-like behaviors resulting from a reduction in AUTS2 expression.

Outside the Lab

Emily acted as an executive board member for the Undergrad Neuroscience Society for the past 2 years. Outside of neuroscience, Emily still enjoys experiments, including writing with the C-U Experimental Writing Lab. You can find Emily buried in a book, running, swimming, making not very technically-skilled art, and exploring the weird nooks and crannies of Chambana.

LinkedIn Profile

Veena Chatti

Graduate Student, CDB

Graduate Student, CDB

I hold a Bachelor of Science degree in Biomedical Sciences from Rochester Institute of Technology, and a minor degree in French (2011).

My previous research mentors have been Henk Roelink (University of California, Berkeley) and Aurnab Ghose (Indian Institute of Science Education & Research, Pune).

My project at the Roelink lab involved developing the cell-lines and expression constructs to test if calcium ions were acting second messengers upon activation of the Sonic hedgehog signaling pathway. Under Aurnab Ghose’s mentorship, I worked on oxidative stress on the neuronal cytoskeleton.

As a masters student in the Stubbs lab, I worked towards characterizing certain zinc finger protein encoding genes during mouse embryonic and postnatal development, and primarily used in situ hybridization to study their gene expression patterns.

From the Stubbs lab, I moved on to join Scott Holley‘s lab as a Postgraduate Associate in the Department of Molecular, Cellular and Developmental Biology at Yale University.

Soumya Negi

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

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

Joe Troy

Joe Troy, Bioinformatics

Education

  • UIUC Informatics Ph.D. program 2012-Present
  • North Central College, Naperville Computer Science M.S., 2000-2005
  • UIUC Finance B.S., 1977-1981

Work Experience

  • Web Applications Developer and Architect, UIUC Library 2018 to Present
  • Graduate Research Assistant, UIUC 2013 to Present
  • Data Transformation and Database Specialist, UIUC 2017-2018
  • Teaching Assistant, UIUC 2017
  • Visiting Program Manager, UIUC Library 2012-2014
  • Senior Software Development Analyst, The Joint Commission 2005-2013
  • Distribution Systems Team Leader, NAVTEQ 2004-2005
  • Software Engineer, NAVTEQ 1999-2004
  • Adjunct Lecturer, EECS department, University of Illinois at Chicago 1999-1999
  • Software Development Analyst, The Joint Commission 1992-1999
  • Programmer Analyst, Richardson Electronics, LTD. 1985-1992
  • Computer Coordinator, Commercial Law League of America 1984-1985
  • Computer Programmer, Law Data Centre 1983-1984

Projects

As a graduate student pursuing a PhD in informatics I am working in the lab of Dr. Lisa Stubbs, Professor of Cell and Developmental Biology. Presently I am exploring computation methods to identify enhancer / promoter interactions during transcription.  Other projects include searching for new genes by scanning genomes for motifs or by analyzing gene expression data.

Previously I worked on a bioinformatics project to identify interactions between Zinc Finger Protein 558 (ZNF558) and Long Terminal Repeat (LTR) elements in human DNA.  Zinc Finger Protein 558 belongs to the Zinc Finger family of Transcription Factors that bind to DNA thus regulating the expression of DNA.  Through out history many LTRs have been introduced into the human genome via retroviruses.  Of interest is the evolutionary history of Zinc Finger Proteins compared to the evolutionary history of the LTRs they bind to.

Links

Email Joe

Stubbs Lab Bioinformatics Presentations:

 

Li-Hsin Chang

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

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

Annie Weisner

Annie Weisner, Neuroscience

Annie Weisner, Neuroscience

History Annie is a native Nashvillian who started her research career at Vanderbilt University, where she earned her Bachelors of Arts in Neuroscience and Theatre. During her time as an undergraduate, she worked in the Center for Human Genetics, where she investigated the role of heavy-metal processing in autism by screening patients and families for polymorphisms in heavy-metal transport genes. Additionally, she worked on projects investigating the role of glutathione during oxidative injury through site-directed mutagenesis of the gamma-glutamylcysteine gene, and performed large-scale screening of patient populations for polymorphisms in urea cycle genes.

She joined the UIUC Neuroscience Program and Medical Scholars program in 2009, and is working toward her M.D. and Ph.D. Upon completion of her degrees in 2018, she plans to pursue a career as a physician-scientist specializing in Pediatric Neurology, and she intends to continue her research in developmental neuroscience.

Current Project Annie is investigating the role of newly discovered neurodevelopmental gene, Auts2, in abnormal neurodevelopment. Mutations in the Auts2 locus cause autism, epilepsy, and mental retardation in humans, but little is known about the function of this gene or its role during neurodevelopment. She is analyzing the role of AUTS2 in differentiation of neurons in culture to ask what the function of AUTS2 is in normal neurodevelopment. As well, Annie utilizes a unique translocation mutant called 16Gso which displays epilepsy and autistic-like behaviors resulting from a reduction in AUTS2 expression to how AUTS2 disruption can lead to abnormal neurodevelopment.

Annie also works on the Simons Project, investigating the genetic pathways underlying evolutionarily conserved social behaviors, such as aggression and maternal caring, through RNA-sequencing and protein expression analysis of mouse brain after acute social stimuli.

Past Projects Annie began her work in the Stubbs lab studying the role of Pax6 alternative transcripts in development of the eye through histological analysis of the 1Gso translocation mutant.

Publications

Elso, C; Lu, X; Weisner, PA; Thompson, HL; Skinner, A; Carver, E; Stubbs, L (2013). A reciprocal translocation dissects roles of Pax6 alternative promoters and upstream regulatory elements in the development of pancreas, brain, and eye. Genesis, 51:9, 630-646.

Le, TM; Magarik, JA; Cunningham, GR, Weisner, A et al (2008).  gamma-Glutamylcysteine co-migrates at the peak typically assigned to L-aspartate in ion-exchange chromatography-based amino acid analysis.  Molecular Genetics and Metabolism, 93:3, 255-255.

Outside the Lab Annie is the Grants Director of Champaign-Urbana’s only free charitable clinic, Avicenna Community Health Center, and manages a team of 12 graduate, medical, undergraduate student, and faculty volunteers to secure funding for the clinic. She also has twice organized the Illinois Summer Neuroscience Institute, a weeklong research program for undergraduates from underrepresented groups who are interested in pursuing a career in Neuroscience research. She has taught the Medical College’s Cell and Tissue Biology laboratory course since Fall of 2012, and last year ranked in the top 10% of all University instructors, as rated by her students.

In her free time, Annie is an avid powerlifter, cyclist, and climber. She loves to garden and to cook, and teaches healthy cooking classes at the Common Ground Food Co-op. She also volunteers with several organizations for special needs children in town, including taking students on the Swann School’s nature walks, volunteering for the Challenger softball league, and teaching at the CIRCLE Academy.

Email Annie