Scientists Drawing DNA

I came across a tweet from IDT with a link to DNA drawings made by some pretty formidable scientists while at a meeting at Cold Spring Harbor in 1993.  This list includes Iowa City native and Nobel laureate Tom Cech as well as recognizable names like Brenner, Capecchi, Collins, Greider, Lander (drawing shown here), Paabo, Watson and others.  Here’s the link.

Thesis Seminar: Di Xu

An Old Gene Takes On a New Form:  Expression and Functions of Renin Isoforms:  Di Xu 11.February (Thursday) at 3:00pm in 2117 MERF

Hypertension is a complex disorder that could be a result of genetic defects (for example, interference with the Renin-angiotensin System), or contribution from environmental factors. Reninis the rate-limiting enzyme in the Renin-angiotensin System that modulates blood pressure. The classic renin protein is primarily synthesized and secreted from the kidney. Our lab and others have identified a novel isoform of renin that remains intracellular and mostly expressed in the brain, initially from transgenic animal studies. My thesis project aims to distinguish the difference between the secreted renin (sRen) and the intracellular renin (icRen) with regard to their endogenous expression and functions in vivo using isoform-specific knockout mice. The major findings of this thesis are: 1) sRen and icRen are independently transcribed using different promoters, 2) icRen is the major form of renin in adult mouse brain, 3) there is a developmental shift in utilization of renin isoforms in the mouse brain, 4) peripheral sRen (mostly from the kidney) is crucial for survival and maintenance of normal blood pressure, and 5) depletion of sRen from either neuronal or glial cells in the brain is insufficient to alter blood pressure.

Thesis Seminar: Emily Schindler

“Molecular Genetics of Retinal Degeneration”: Emily Schindler Monday (1.Feburary) at 11:00 in 2117 MERF

Heritable retinal degenerations dramatically affect individuals across the lifespan.  Heritable degenerations with onset in childhood or young adulthood, such as the ABCA4-associated retinopathies (OMIM, ABCA4), generally obey Mendelian segregation and are usually attributable to high penetrance mutations within a single gene.  Heritable retinal degenerations with onset in late adulthood, such as age-related macular degeneration, are usually influenced by a constellation of genetic and environmental factors. This thesis applies several complementary, high-throughput genotyping platforms to identify relationships between specific heritable retinal phenotypes and genetic variation.  The findings of this thesis will help physicians refine their prognoses based on genetic information and determine which patients are best suited for inclusion in clinical trials of novel therapies.



Patricia and Megan to present at Student Seminar Thursday (28.Jan) at noon in 106 BBE

Patricia and Megan will be presenting Student Seminar this week in 2166 MERF at noon. I have asked the speakers to provide a brief overview for their talks. Hope to see you there!

Background for Patricia’s talk

Wnt ligands have pleiotropic effects during development, consequently, multiple negative regulators function to precisely control Wnt activity.  While many genes such as DKK, Axin and Naked are induced by Wnt/β-catenin to negatively regulate β-catenin stabilization, the integration of signals from different arms of the Wnt network, potentially regulated by different classes of Wnt ligands, is emerging as an equally important control mechanism.   I have a special interest in understanding how Wnt signaling controls the formation of the embryonic axis in vertebrates. I use  zebrafish and Xenopus laevis to unravel the mechanisms behind axis formation. In our lab, we utilize gene knockdown as well as transgenic lines to dissect the function of members of this signaling pathway during embryonic stages.

Project 1. Axin is a key player in the degradation complex, as it serves as the scaffold for proteins involved in the phosphorylation of β-catenin. Axin contains four critical domains: a β-catenin binding domain, a GSK3 binding domain, a Regulator of G-protein (RGS) domain and a DIX domain (protein interaction domain shared with Dsh). RGS domains are typical of RGS proteins, which were originally identified as regulators of the active half-life of G-protein signaling. However, it is not known whether the Axin-RGS domain functions in G-protein signaling. My work focuses on the function of the Axin-RGS domain during maternal and zygotic stages.

Project 2. The means by which Wnt/Ca²⁺ signaling negatively regulates the Wnt/β-catenin signaling is unknown, but it likely requires a Ca²⁺ sensor protein. Among candidate mediators, Nkd displays the distinctive property of affecting both β-catenin-dependent and -independent arms of the Wnt signaling network.  Nkd functions as a Wnt/Wg antagonist by binding to the basic/PDZ domain of Dvl.  Vertebrate Nkd overexpression results in convergence and extension (CE) movement defects.

Whereas the precise mechanism underlying Nkd-mediated Wnt antagonism is unresolved, it is well established that Nkd interacts with Dvl and impacts β-catenin-dependent and -independent Wnt signaling networks. My focus on this project is to understand the role of the NKD cuticle during axis formation and how this protein functions in the context of β-catenin stabilization.

Background for Megan’s talk

Otosclerosis has a prevalence of 0.2 – 1% among white adults making it the single most common cause of hearing impairment in persons of northern European ancestry. Histologically, it is characterized by the replacement of discrete areas of endochondral bone in the otic capsule by otosclerotic bone. We have shown that a large number of genes are differentially expressed in otosclerotic stapes footplate samples as compared to normal footplate samples. To identify small molecules that may be potentially useful to treat otosclerosis, we have compared our expression data to the Connectivity Map (cmap) provided by the Broad Institute. This resource allows the user to compare gene expression data in a biological sample/disease with 7,000 expression profiles from 1,309 different small molecules. Negative connectivity of a query profile with cmap data can be used to test specific small molecules that might be therapeutically important based on the disease profile.
Arachidonic acid has the best negative connectivity compared to otosclerosis expression data across all instances (cell lines and doses tested for the cmap project) (p=0.00018). When genes involved in inflammation or interleukin signaling are removed from the otosclerosis expression data and the Connectivity Map is re-queried, arachidonic retains the best negative connectivity (p=0.0002). These findings are noteworthy because arachidonic acid increases osteoclastogenesis by reducing the OPG/RANKL ratio secreted by osteoblasts and is converted to PGE2; PGE2 signaling affects BMP2 expression; and BMP2 is associated with otosclerosis.
In addition to BMP2, TGF-β1 and BMP4 have been shown to be associated with otosclerosis. TGF-β1, BMP2 and BMP4 are present in the otospongiotic phase of otosclerosis as are their receptors.  We have failed to replicate these associations in a German population, however, lack of power and differences in LD may account for lack of replication.  Rather than looking for common variants associated with otosclerosis in this population, we are testing the common disease-rare variant hypothesis, by sequencing TGF-β1, BMP2 and BMP4 in >250 German patients with otosclerosis and in 250 matched controls.  We have found a number of variants that will be used for further functional studies including affects on osteoclast and osteoblast function in the presence of arachidonic acid.

Jan 21: Taste of Nations Food Festival and Call to Service

Jan 21: Taste of Nations Food Festival and Call to Service

Come to the MERF atrium from 12:00-1:00 pm and join your health science colleagues in sampling the diverse fare from around the world available in downtown Iowa City. We will also be holding a volunteer drive at this time: gather your friends and your culinary skills and volunteer to cook a meal for the families at the Ronald McDonald House. We are currently hoping to fill two dates with a limit of ten volunteers per date (Feb 2 and Feb 10) with the possibility of adding more as volunteers and funds allow.

Zen and David to present at Student Seminar Thursday (17.Dec) at noon in 2166 MERF

Zen and David will be presenting Student Seminar this week in 2166 MERF at noon. I have asked the speakers to provide a brief overview for their talks. Hope to see you there!

Background for Zen’s talk

The Role of the Alternative Pathway of the Complement System in the Development of Dense Deposit Disease

Dense Deposit Disease (DDD) causes chronic renal dysfunction which progresses to end-stage renal disease in about half of patients within 10 years of diagnosis.  Deficiency of and mutations in complement Factor H (CFH) are associated with the development of DDD, suggesting that dysregulation of the alternative pathway (AP) of the complement cascade is important in disease pathophysiology.   Patients with DDD are studied to determine whether specific allele variants of the genes of the alternative pathway of the complement system segregate preferentially with the DDD. We have screened coding and intronic regions of genes of the complement system in 71 DDD patients and 268 controls using PCR, restriction digest and bidirectional sequencing.  We are able to identify novel mutations, allele variants and haplotypes in several genes of the complement system which are associated with the DDD phenotype using Chi-square test of independence, Armitage trend test and Haplotype analysis.  The best inheritance model has been determined for each polymorphism.  Our results have shown that the best inheritance pattern for most polymorphisms is a dominant model.  Since we have identified several genes associated with DDD, we have determined possible gene-gene interactions using Multifactorial Dimensionality Reduction, Focused Interaction Testing Framework and Conditional Logistic Regression. We have found a strong synergistic interaction between polymorphisms in CFH and C3.  To ascertain if the associated allele variants have a functional impact in the complement activity of an individual, we have obtained 102 blood samples from a blood bank and measured AP complement activity in these samples.  We then have genotyped CFH and C3 for these samples and determined association using Conditional Logistic Regression, Mann-Whitney Test and Kruskal-Wallis Test.  We have found significant association of main effects and two-way interaction of CFH and C3 with AP complement activity.  Our data imply that DDD is a complex genetic disease and that polymorphisms in the genes of the AP pathway contribute to level of complement activity and the pathogenesis of DDD.

Background for David’s talk

Coming soon!

Colleen and Garrett to present at Student Seminar Thursday (19.Nov) at noon in 2166 MERF

Colleen and Garrett will be presenting Student Seminar this week in 2166 MERF at noon. I have asked the speakers to provide a brief overview for their talks. Hope to see you there!

Background for Garrett’s talk

Since its initial discovery in 1949, lithium continues to be prescribed to patients suffering from bipolar affected disorder (BPD).  However, the underlying mechanisms of how this drug elicits its mood-stabilizing effect remain unknown.  To help identify these lithium-responsive processes, we have used the dominant, X-linked Drosophila mutant Shudderer (Shu). This mutant is characterized by strong jerking and twitching as well as uncoordinated locomotion.  Interestingly, the severity of Shu phenotypes can be significantly reduced upon lithium administration(1). Our behavioral, anatomical and genetic investigations of this mutant have led to the following findings.  Lithium improves Shu mutant climbing and reduces the severity of the jerking phenotypes.  In contrast the same doses of lithium have no significant impact on the same behaviors in wild-type flies.  Shu mutants exhibit down-turned wings and an indentation of the dorsal thorax, a phenotype previously observed in mutants with neuronal excitability. Classic meiotic mapping suggests that the Shu mutation lies near chromosomal region 14D-15F.  Microarray gene expression profiling of the Shu mutant revealed that CanA-14F, which encodes a catalytic subunit of the Ca²⁺/calmodulin-dependent Ser/Thr protein phosphatase calcineurin is up-regulated 2.2-fold compared to wild-type.  To determine if a reduction in CanA-14F levels could improve the mutant phenotypes, hypomorphic mutant alleles of CanA-14F were introduced into the Shu background.  The resultant flies transheterozygous for Shu and the CanA-14F hypomorphic alleles showed a reduction in morphological defects as well as a significant improvement in behavior.  Lastly, expression of the endogenous inhibitor of calcineurin activity, nebula (nla) was sufficient to suppress the morphological phenotypes in Shu when driven in neurons.  Rescue was not observed when expressed in glia, muscle or fat bodies.  These data suggest that overexpression of CanA-14F, and a subsequent increase in calcineurin activity in the nervous system play a role in the manifestation of the Shu phenotypes.

Recent evidence in two human association studies has shown the calcineurin A subunit gene PPP3CC to be a risk factor in both schizophrenia and BPD (2, 3).  Furthermore, several calcineurin mutant mouse models show behavioral deficits reminiscent of those observed in schizophrenia and other mental disorders (4, 5).

1.            R. L. Williamson, Psychopharmacology (Berl) 76, 265 (1982).

2.            F. Mathieu et al., Behav Brain Funct 4, 2 (2008).

3.            D. J. Gerber et al., Proc Natl Acad Sci U S A 100, 8993 (Jul 22, 2003).

4.            T. Miyakawa et al., Proc Natl Acad Sci U S A 100, 8987 (Jul 22, 2003).

5.            C. J. Herzog, S. Miot, I. M. Mansuy, B. Giros, E. T. Tzavara, Eur J Pharmacol 580, 153 (Feb 2, 2008).

Erik Westin to present a Seminar

Our very own Erik Westin will be presenting a Seminar in conjunction with Free Radical and Radiation Biology.

Title:  The Modulation of ROS by Short Telomere Signaling”

When:  Thursday October 22, 2009

Time:  11:30 am

Place:  1117 MERF

Come out and show your support for Erik and learn about telomere signaling!

Special Symposium

A special Symposium will be held on Saturday, September 26, 2009 from 9am-5pm in Kollros Auditorium (101 Biology Building East).  Below is the list adn times for each of the speakers, as well as a link to each of their web pages.  Hope to see you there!

Program Schedule

9:00-9:10 Dr. Susan Gottesman (NIH): “Beyond the Central Dogma:  Regulation by Small RNAs and Protein Turnover”

9:55-10:40 Dr. Peter Moore (Yale):  “The Structural Basis of the Species-Specificity of Anti-Ribosomal Antibiotics”

10:40-11:05 Break

11:05-11:50 Dr. Sankar Adhya (NIH):  “The Puzzle of Lamda Prophage Stability”

11:50-12:35 Dr. David Soll (U of Iowa):  “A Unique View of the Evolution of a New Signal Transduction Pathway in Candida  Albicans“

12:35-2:05 Lunch break (on own)

2:05-2:50 Dr. Louis Reichardt (U of California, San Francisco):  “Straying off the Lambda Trail:  New Findings in the Wilderness of Brain Development”

2:50-3:35  Dr. Jeff Murray (U of Iowa):  “Genome Wide Association Studies, Disclose New Biology”

3:35-4:00 Break

4:00-4:45 Dr. Mario Capecchi (U of Utah):  “Modeling Human Cancers in the Mouse”

Erin and Di to present at Student Seminar Thursday (17.Sept) at noon in 2166 MERF

Erin and Di will be presenting Student Seminar this week in 2166 MERF at noon. I have asked the speakers to provide a brief overview for their talks. Hope to see you there!

Background for Erin’s talk

Integrating vector systems are under current investigation as gene transfer vehicles in treatments for diseases such as cystic fibrosis (OMIM).   Integrating vectors such as retrovirus, lentivirus, and DNA transposons are beneficial in achieving long-term expression of therapeutic genes.  However, vector integration carries the potential for insertional mutagenesis, resulting in aberrant expression of host genes.  Thus, it would be beneficial to develop vectors that target integration to a specific genomic region.  This work aims to direct the DNA transposon vector piggyBAC to a specific locus in the genome.  This strategy attempts to achieve site-directed integration through interaction of the DNA binding domain-modified transposase gene with its target in a human cell line.  We have modified a codon-optimized piggyBAC transposase with the bacterial LacI DNA binding domain in an N-terminal fusion construct.  Transposition assays showed that the modified transposase is active in human cells.  Excision assays indicated that the modified transposase excises precisely.  Moreover, we recovered intact transposase-genomic junctions from cells in which the modified transposase was delivered to catalyze transgene integration.  These data indicate that in addition to precise excision from the transposon plasmid, the modified transposase can carry out correct integration reactions.  Taken together, these results support the hypothesis that a piggyBAC transposase modified with a DNA binding domain can direct integration to a specific site in the genome.  We are currently testing this in a proof-of-principle experiment in which we used a LacI-modified transposase to direct integration in a human cell line containing the target LacO DNA binding sites stably integrated at a single locus.  Site-directed integration is an important step in developing safe and effective integrating vectors for therapeutic gene transfer applications.

Background for Di’s talk

Hypertension is defined as systolic blood pressure (SBP) over 140 mmHg and/or diastolic blood pressure (DBP) over 90 mmHg. It is an established risk factor for a range of diseases including obesity, diabetes, stroke and renal defects. Renin-Angiotensin System (RAS) plays an essential role in blood pressure regulation. Within this system, Renin (OMIM) is the rate-limiting enzyme in generating downstream effector angiotensin peptides. Renin is conventionally recognized as a secreted enzyme from renal JG cells. However, accumulating evidence support the existence and function of a novel Renin isoform that is retained intracellularly. We hypothesis that intracellular renin (icRen) plays a discrete role from its secreted counterpart (sRen), especially in the brain, to fine tune heart rate and blood pressure control via the central nervous system. I have completed a sRen-specific knockout mouse model during my PhD training. They exhibited lower blood pressure and renal atrophy due to the lack of sRen that is abundant in the kidney. This implicates that sRen is a vital isoform in the kidney and preservation of icRen mainly in the brain is not sufficient to rescue lethality.