Jessica Ponce’s Abstract
Stephanie Haase’s Abstract
The Social Activities Committee would like to remind you all that the second Genetics Winter Party is THIS FRIDAY, December 11 from 7-10p.m. at the North Ridge Pavilion in Coralville (2250 Holiday Rd.). This will be a BYOB (beer and wine only) and potluck-style event, so we request but do not require that people bring an appetizer or dessert option to share. Additionally, this will be an ugly sweater party, so we would love to see everyone’s most garish, gaudy, and hideous holiday wear. Prizes will be awarded for the ugliest sweaters!
The entrance to the North Ridge Pavilion can be difficult to see in the dark. If you are driving in from the East, you will see a blue street sign on the right side of the road for the pavilion and the turn will be on your left. There is a sign for the pavilion next to a row of pine trees. If you are driving in from the West, you will see a blue street sign on the right side of the road for the pavilion and it will be the next right turn.
Please feel free to contact anyone on the Social Activities Committee with any questions.
We look forward to seeing you there!
The Genetics Social Activities Committee would like to congratulate Dr. Fengxiao Bu on the successful defense of his thesis and completion of his Doctorate!
Bu is from the Smith lab in the Otolaryngology department. His thesis seminar, entitled “Exploring the Genetics of a Complex Disease – Atypical Hemolytic Uremic Syndrome”, was on Friday, December 4th, 2015. Bu has accepted a postdoctoral appointment here at the University of Iowa to continue his research, and we expect that he will continue to excel.
We asked Bu a few questions about his experience in the Genetics program here at Iowa:
Q: What is your favorite thing that you have experienced here at Iowa?
A: The best thing is that I had a great advisors and met so many awesome people here.
Q: What was your favorite class to take?
Q: What was your favorite class to TA?
A: Bioinformatics techniques.
Q: Do you have any advice about preparing for defense?
A: Better to start early. I would say 6 months is a good number for prepare everything.
Again, congratulations Bu and good luck on your future research!
A Targeted Sequencing Study of Glutamatergic Candidate Genes in Attempted Suicide
Suicidal behavior has been shown to have a heritable component that is partly driven by psychiatric disorders. However, there is also an independent factor contributing to the heritability of suicidality. We previously conducted a whole exome sequencing study of bipolar suicide attempters and bipolar non-attempters to assess this independent factor. This whole exome study implicated glutamatergic neurotransmission in attempted suicide, as did our genome-wide association study (GWAS) of the attempted suicide phenotype. In the current study, we have conducted a targeted next-generation sequencing study of the glutamatergic N-methyl-D-aspartate (NMDA) receptor, neurexin, and neuroligin gene families in 476 bipolar suicide attempters and 473 bipolar non-attempters. The goal of this study was to gather sequence information from coding and regulatory regions of these glutamatergic genes to identify variants associated with attempted suicide. We identified 186 coding variants and 4,298 regulatory variants predicted to be functional in these genes. No individual variants were overrepresented in cases or controls to a degree that was statistically significant after correction for multiple testing. Additionally, none of the gene-level results were statistically significant following correction. While this study provides no direct support for a role of the examined glutamatergic candidate genes, further sequencing in expanded gene sets will be required to understand the role of glutamatergic signaling in the risk for suicidal behavior.
Soluble CR1 Gene therapy rescues renal phenotypes in a murine model of C3G
Xue Xiao1,2, Yuzhou Zhang1, Janice Staber3, Sanjeev Sethi5, Paul B. McCray, Jr.2,3,
Carla M. Nester1,3,4, Richard JH Smith1,2,3,4
1Molecular Otolaryngology and Renal Research Laboratories, Caver College of Medicine, University of Iowa, Iowa City, Iowa, USA; 2Interdepartmental PhD Program in Genetics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA; 3, 4Departments of Pediatrics and Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA; 5Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
C3 glomerulopathy (C3G) encompasses two prototypical diseases, dense deposit disease (DDD) and C3 glomerulonephritis (C3GN). Both diseases are characterized by fluid-phase dysregulation of the alternative pathway (AP) of complement that leads to C3 deposition in the renal glomerulus. Unknown disease triggers and lacks of specific treatments lead to end-stage renal failure in 50% of patients. Soluble complement receptor 1 (sCR1) is a soluble form of a membrane bound regulator of complement. Short-term studies show that sCR1 is capable of restoring complement control in a murine model of C3G, the Cfh-/-/huCR1-Tg mouse. However, within days of terminating treatment, complement dysregulation is again evident. In this study, we sought to determine whether continuous presence of sCR1 could provide long-term complement control in the C3G murine model. Using the piggyBac transposon system coupled with hydrodynamic tail vein injection, we delivered a construct of sCR1 (LHR A-C) to the C3G murine model to provide constitutive sCR1 expression in mouse circulation. Animals were followed for 6 months. sCR1 expression was detected by real time PCR and ELISA in mouse liver and circulation respectively in 6 months. C3 levels approximately doubled and clearance of glomerular C3 and C3 fragments deposition was documented by immunofluorescence. Electronic microscopy showed a reduction in dense deposits in injected as compared to control animals. There were no changes by light microscopy. Renal function improvements had been revealed from stabilized 24-hr urine albumin creatinine ratio. In this study, we proved that long-term expression of sCR1 could rescue the renal phenotype in C3G mice and may be a viable treatment for patients with this disease.
THE ROLE OF ENDOGENOUS MICROBIOTA IN SEIZURE-LIKE BEHAVIOR OF SHUDDERER, A DROSOPHILA VOLTAGE-GATED SODIUM CHANNEL MUTANT
It is widely recognized that mutations in genes encoding voltage-gated sodium (Nav) channels contribute to the etiology underlying various seizure disorders. Shudderer (Shu), a gain-of-function mutant for the Drosophila Nav channel gene, exhibits neuronal hyperexcitability and seizure-like behavioral defects, including spontaneous leg jerking, twitching, and heat-induced convulsion. Intriguingly, we have recently discovered that food supplemented with milk whey acts as a nutritional therapy, drastically suppressing these behavioral phenotypes. Microarray analysis revealed high levels of insulin receptor (InR) expression in Shu mutants relative to wild-type (WT) flies, indicating Shu has reduced insulin signaling. Following milk whey treatment, InR expression in Shu mutants returned to wild-type levels, suggesting milk whey increases insulin signaling. Because the endogenous gut microbiota are known to impact metabolic and developmental homeostasis through insulin signaling, we hypothesized that the microbiome plays a role in Shu phenotypes and their diet-dependent modification. Raising Shu mutants and WT flies in either antibiotic-containing or sterile food was sufficient to eliminate the gut microbiota. Further, both treatments were found to significantly suppress Shu behavioral phenotypes while having no obvious effect on WT behavior. Culturing extracts of homogenized flies on LB agar plates revealed drastic differences in the number and possibly the species of bacteria found in Shu and WT flies raised on conventional or milk whey-supplemented food. To confirm these results, we plan to perform high-throughput sequencing of the bacterial 16S ribosomal gene to identify differences in the gut microbiome composition of Shu and WT flies in the context of both conventional and milk whey-containing diets. This and future experiments are expected to provide us with a better understanding of the interplay between dietary therapy and the microbiome in the context of seizure disorders.
Homophilic protocadherin cell-cell interactions drive dendrite complexity
Growth of a properly complex dendrite arbor is a key step in neuronal differentiation and a prerequisite for neural circuit formation. Diverse cell surface molecules, such as the clustered protocadherins (Pcdhs), have long been proposed to regulate circuit formation through specific cell-cell interactions. Here, using transgenic and conditional knockout mice to manipulate g-Pcdh repertoire in the cerebral cortex, we show that the complexity of a neuron’s dendritic arbor is determined by homophilic interactions with other cells. Neurons expressing only one of the 22 g-Pcdhs can exhibit either exuberant, or minimal, dendrite complexity depending only on whether surrounding cells express the same isoform. Furthermore, loss of astrocytic g-Pcdhs, or disruption of astrocyte-neuron homophilic matching, reduces dendrite complexity cell non-autonomously. Our data indicate that g-Pcdhs act locally to promote dendrite arborization via homophilic matching and confirm that connectivity in vivo depends on molecular interactions between neurons, and between neurons and astrocytes.
The Genetics Social Activities Committee would like to congratulate Dr. Emily Petruccelli on the successful defense of her thesis and completion of her Doctorate!
Emily is from the Kitamoto lab in the Anesthesia department. Her thesis seminar, entitled “A Tale of Two Genes Controlling Behavior in Drosophila: Role of DopEcR in Alcohol-Induced Behavior and Effects of Epilepsy Mutations on Sleep”, was on Thursday, October 15th, 2015. Emily has accepted a postdoctoral appointment at Brown University, where we expect she will continue to excel.
We asked Emily a few questions about her experience in the Genetics program here at Iowa:
Q: What is the most valuable thing that you have learned here at Iowa?
A: If I can make it through grad school, I can make it through anything.
Q: What was your favorite class to take?
A: GABS, great way to learn about the breadth of research and be introduced to a variety of faculty.
Q: What was your favorite class to TA?
A: Biology of the Brain, a non-major undergrad course.
Q: Do you have any advice about preparing for defense?
A: Think of everything you could possibly be asked and prepare rational answers.
Again, congratulations Emily and good luck at Brown!
The role of copy number variation in cleft lip and palate.
L. A. Harney1,2,3, B. W. Darbro1,3, A. Long2, J. Standley1, A.M. Hulstrand2,3, H. Liu4, R.A Cornell3,4, D.W. Houston2,3, J. C. Murray1,3, J. R. Manak1,2,3
1) Department of Pediatrics, University of Iowa, Iowa City, IA; 2) Department of Biology, University of Iowa, Iowa City, IA; 3) Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA; 4) Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA
Clefts of the lip and/or palate (CL/P) occur in about 1 in 700 live births. Categorized as non-syndromic (NSCL/P) or syndromic (SCL/P), individuals with NSCL/P have isolated clefts and account for about 70% of clefting cases whereas syndromic occurrences include additional cognitive or structural anomalies. Although genome-wide association, candidate gene, and animal model studies have been used to study CL/P, a largescale analysis to determine the contribution of copy number variation (CNV) to CL/P has yet to be performed. We performed the largest high resolution array-based comparative genomic hybridization study to date to identify copy number variants associated with NSCL/P in a cohort of 868 cases from the Philippines and 212 individuals with SCL/P of mixed ethnicities. A preliminary analysis is underway which prioritizes likely causative CN events for follow-up in zebrafish and frogs. Focusing on rare copy number losses, we identified 196 genes that were deleted in greater than one individual while 735 genes were deleted in a single case; collectively, the majority of genes were not previously implicated in clefting. After comparing the list of deleted genes to OMIM, DECIPHER, NCBI, and MGI databases, four were selected for functional follow-up in zebrafish. These genes, ISM1, PKP2, MYO5C and ULK4, are all novel clefting candidates, are overlapped by a CNV loss in greater than one individual, and appear in less than 1% of the cohort. Six additional genes identified have been previously implicated in clefting through association studies (NTN1, PCYT1A), variant analyses (ZNF750, CDH1, OFD1), or chromosomal microarrays (IMMP2L).Together, these studies will define the contribution of copy number variants to disease incidence of CL/P.
TFAP2A drives melanocyte gene expression in parallel with MITF
H E Seberg1, E Van Otterloo2, S K Loftus3, J P Lambert4, G Bonde2, R Sompallae5, J F Santana1, J R Manak1, A C Gingras4, W J Pavan3, R A Cornell1,2
1 Interdisciplinary Graduate Program in Genetics, University of Iowa
2 Department of Anatomy and Cell Biology, University of Iowa
3 Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
4 Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
5 Bioinformatics Division, Iowa Institute of Human Genetics, University of Iowa
Disruption of the transcription factor network governing melanocyte development contributes to the pathogenesis of pigmentation disorders and melanoma. The activity levels of an important member of this network, MITF, have been proposed to control melanoma phenotype. Mid- to high-level MITF activity drives growth and differentiation, while lower levels confer a stem cell-like, invasive quality. Transcription Factor Activator Protein 2 alpha (TFAP2A) expression is reduced in advanced stage melanoma tumors, and mutations in TFAP2A cause pigmentation phenotypes in humans, mice, and zebrafish. Because TFAP2A is widely expressed in the neural crest and skin, its specific role in melanocytes and relationship to MITF has been unclear. To determine the position of TFAP2A in the melanocyte gene regulatory network, we first used microarray analysis of wildtype and tfap2a null zebrafish to profile genes that are downregulated in the absence of TFAP2A. We then conducted anti-TFAP2A ChIP-seq to create a profile of TFAP2A-bound loci in melanocytes. Genes at the intersection of these profiles are likely direct targets of TFAP2A. These include melanin synthesis genes, such as dct, tyrp1, and trpm1, most of which are also thought to be direct targets of MITF. Comparison with published MITF ChIP-seq showed that TFAP2A peaks overlap MITF peaks more often than expected by chance. In reporter assays, deletion of TFAP2A binding sites in a minimal TRPM1 promoter decreased its activity, similar to published results for deletion of MITF binding sites from this element. Furthermore, we found that tfap2a and mitfa interact both physically in vitro and genetically in zebrafish. These results provide evidence that TFAP2A and MITF work in parallel to promote melanocyte differentiation, and show that widely-expressed TFAP2A can directly regulate expression of lineage-specific melanocyte genes. In addition, TFAP2A expression may be able to influence levels of MITF, driving cells toward differentiation and away from an invasive state.
Eric’s Talk Title
Investigating the Human Exome in Suicidal Behavior
|9/17/2015||Eric Monson||12:00-12:50 PM||ML B111|
|10/15/2015||Lisa Harney||12:00-12:50 PM||ML B111|
|11/12/2015||Michael Molumby||12:00-12:50 PM||ML B111|
|12/10/2015||Sophia Gaynor||12:00-12:50 PM||ML B111|
Thank you to all of the students, faculty, and family members who made it out in the rain to join us for the 2015 Genetics Welcome Picnic!
Program Director Dan Eberl kicked off the festivities with his annual address,
followed by the second annual Newly-Grad game!
Our contenders this year were the First year mentees and their mentors: Karen and Kellie, James and Patrick, Tanner and Nikale (standing in for Wes), Zach and Hannah, Adam and Tyson, Alyssa and Sophie, and finally, Kimberly and Lisa. The competition was intense with our MC Tanner asking the tough questions like Where is your mentee’s hometown? and What is your mentee’s favorite food? In the end, Karen and Kellie were able to blow the competition away with their in sync answers.
After the delicious catering by A Guy and a Grill, we completed the raffle with the grand prize, the board game Pandemic, going to James Mrkvicka!