Carnegie Mellon University

January 18

Minyan Zheng
"Regenerating the sea star brain"

Claire Cheetham
"The hunted becomes the hunter: brain circuits for predatory behavior"

February 1

Nick Audette
"Thalamo-cortical circuit rearrangements after sensory association training"

Rita Bottino
"A minimized human insulin-receptor-binding motif revealed in a Conus geographus venom insulin"

February 8

Vinitha Ganesan
"Discovering biomarkers for Rheumatoid Arthritis associated Interstitial lung disease"

Yong Fan
"How much to drink from the Fountain of the Youth - reversal of aging with Yamanaka factors?"

February 15

Berquin Feese
"Rapid adaptability of L2/3 PV inhibitory neurons in mouse primary visual cortex"

Emily Simon
"How does the Ebola virus glycoprotein cause hemorrhage?"

February 1

Rotation Reports

3:30- 3:40: Ashley Leslie - "Using LOVTrap to Investigate the Role of EB1 in Actin Cable Assembly"
3:40- 3:50: Tyler Nelson - "Uncovering the Role of Newborn Olfactory Sensory Neurons with in-vivo Calcium Imaging"
3:50- 4:00 Stephanie Myal - "Cholinergic Modulation of Sensory Cortical Microcircuits" 
4:00- 4:10 Alyssa Lawler - "When all else changes: Orthologous gene targets of transcription factor Tbrain in Echinoderms" \
4:10- 4:20: Jennifer Kunselman - "C-terminal Tail of Atlastin: Role in Membrane Fusion"
4:20- 4:30: Bibifatima Kaupbayeva - "Universal method for proteome purification"

March 1

Salini Konikkat
"Seq'ing RNA Ends: Towards Understanding Transcript Diversity and Regulation Mechanisms"

Tina Lee
"Designed proteins induce formation of nano cage-containing extracellular vesicles" (Nature Dec 2016, 540:292-295.)

March 8

Yizhu Lin
"Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions contribute to paraspeckle architecture"

DJ Brasier
"ApoE and the cell biology of Alzheimer's disease"

March 22

Victoria Corbit
"Dissecting corticostriatal microcircuits involved with compulsive-like grooming in a Sapap3-KO OCD mouse model"

Kevin Mastro
"Title TBA"

March 15

Brendan Redler
"Title TBA"

Russell Schwartz
"Going Out with a Bang: A Big Bang Model of Colorectal Tumor Growth"

April 5

Malachi Blundon
"The impact of microbiota on brain and alcohol responses"

David Hackney
"Going with the flow - microtubules and motors alone can drive directed fluid flow"

April 12

Anagha Kadam
"Promiscuous Signaling by a Regulatory System Unique to the Pandemic PMEN1 Pneumococcal Lineage"

April 19

Ceren Tuzmen
"A very important peptide: VIP as a modulator of bone repair during inflammation"

Andreas Pfenning
"A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication"

April 26

Greg Cary
"Labile transitions between attractor kernels in developmental regulatory network evolution"

Kristin Quick
"The problem of reciprocally connected networks: How to prevent runaway activity"

May 3

Swati Venkat
"Sorting of oligomerized proteins: Implications in Shiga toxin trafficking and quality control"

Amanda Willard
"Time-course of basal ganglia network changes in Parkinson's Disease using a gradual dopamine depletion paradigm"

May 10

Rotation Reports

(3:30) Bibifatima Kaupbayeva - "Universal method for proteome purification"
(3:40) Jennifer Kunselman - "Homeostatic Regulation of Mu-Opioid Receptor Recycling"
(3:50) Alyssa Lawler - "Trans environment affects uORF-mediated regulation of protein expression"
(4:00) Ashley Leslie - "Using LOVTrap to Investigate the Role of EB1 in Actin Cable Assembly"
(4:10) Stephanie Myal - "Title TBA"
(4:20) Tyler Nelson - "High-Throughput Mapping of POm Synapses onto Layer 5 Pyramidal Cells"
(4:30) HAPPY HOUR

May 17

Brian Jeon
"Stability of orientation and spatial frequency tuning in mouse primary visual cortex"

Pati Stan
"Beyond Edge Detection: The Role of Neurons in the Primary Visual Cortex"

August 31

Dan Ackerman 
"The Biotattoo: Developing Novel Technologies for Inflammation Monitoring"

Alison Barth 
"Experimental data and machine learning: lessons from the NeuroHackathon"

September 7

Surya Aggarwal 
"Molecular Mechanisms Linking Penicillin Resistance and Virulence Determinants in Pneumococcus"

Sandra Kuhlman
"Building a circuit for plasticity and learning, what can go wrong?"

September 14

Stephanie Biedka
"Ribosomal protein L19 is required for remodeling events preceding 27SB pre-rRNA processing"

Jon Jarvik
"Wouldn't it be nice"

September 21

David Chen
"Development of Novel PfTMK Inhibitors as Anti-Malarial Agents

Chien Ho
"A New Method for Preparing Mesenchymal Stem Cells for Biomedical & Clinical Applications"

September 28

Rolando Cuevas
"The novel protein VP1 is required for virulence in Streptococcus pneumoniae"

Nick Giannoukakis
"Gut microbiota translocation to the pancreatic lymph nodes trigger NOD2 activation and contributes to T1D onset"

October 5

Ian Fucci
"Structural Characterization of Protein-Polymer Conjugates by NMR Spectroscopy"

Fred Lanni
"Yeast make bad decisions, too!"

October 5

Amber Lucas 
"Development and Commercialization of a Universal Proteome Purification Method"

Joel McManus
"Coming to “terms” with antibiotic resistant bacteria"

October 12

Stephanie Biedka
"Ribosomal protein L19 is required for remodeling events preceding 27SB pre-rRNA processing"

Jon Jarvik
"Wouldn't it be nice"

October 19

Jimmy Khor
"Dissecting GRN Architecture: an Analysis of Alx1, a Key Regulatory Gene in the Sea Urchin Skeletogenic GRN"

Andrew Wolff
"A shift from normal to regeneration-specific proliferation in the sea star Patiria miniata"

October 26

Alan Shteyman
"Guess Who?: The Serious Subject of Inferring Missing Values"

Charles Ettensohn
"Transforming somatic cells into gametes: Complete in vitro reconstitution of the mouse female germ line"

November 2

Elena Shuvaeva
"Regulation of β2-adrenergic receptor post-endocytic trafficking"

Aryn Gittis
"Central Control Circuit for Context-Dependent Micturition"

November 9

Rotation Reports 

(3:30) Fatima Kaupbayeva - "Universal method for proteome purification" 
(3:40) Jennifer Kunselman - "Homeostatic Regulation of Mu-Opioid Receptor Recycling"
(3:50) Alyssa Lawler - "Somatostatin-Expressing Interneurons: Implications in Schizophrenia"

(4:00) Ashley Leslie - "At Last! An Acute Method to Evaluate the Role of Atlastin in ER Dynamics"

(4:10) Stephanie Myal - "Title TBA"

(4:20) Tyler Nelson - "The Role of Motor Cortex in Long-Term Motor Recovery In a 
Mouse Model of Parkinson's Disease"

(4:30) HAPPY HOUR

November 16

Brooke McCartney
"The complexities of cancer: how restoration of a single tumor suppressor can turn back the clock on progression"

November 30

Nathaniel Williams
"Repetition Suppression in Macaque Inferotemporal Cortex"

Veronica Hinman
"Coming onto Land: The Fin to Limb transition"

Date

Speaker

Topic

1/13 Brendan Redler TBA
Kevin Mastro (Pitt) Cell-specific pallidal stimulation produces long-lasting recovery of movement in a mouse model of PD
1/20 Lina Song No More Sugar: Identification and Characterization of a Novel Isoform-Specific GalNAc Transferase Inhibitor
Nick Giannoukakis

Speaking on "Neurostimulation of the Cholinergic Anti-Inflammatory Pathway Ameliorates Disease in Rat Collagen-Induced Arthritis"

Levine YA, Koopman FA, Faltys M, Caravaca A, Bendele A, Zitnik R, Vervoordeldonk MJ, Tak PP. Neurostimulation of the Cholinergic Anti-Inflammatory Pathway Ameliorates Disease in Rat Collagen-Induced Arthritis. PLoS One. 2014 Aug 11;9(8):e104530.

1/27 Ceren Tuzmen Heterotopic ossification has some nerve: Crosstalk between sensory neuropeptides and BMP-2 signaling in tendon
David Hackney How to Build a Superhelicase
2/3 Swati Venkat Sorting of oligomerized proteins: Implications in Shiga toxin trafficking and quality control
Rita Bottino
2/10 Amanda Willard Time-course of basal ganglia network changes in Parkinson's Disease using a gradual dopamine depletion paradigm
2/17 Shawn Burton Molecular identification of a novel GABAergic circuit in the olfactory bulb
Joel McManus

TRAP-ping the translatome of developing Drosophila photoreceptor neurons

Zhang KX, Tan L, Pellegrini M, Zipursky SL, McEwen JM. Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals. Cell Rep. 2016 Feb 9;14(5):1258-71

2/24 Rotation Reports

(3:30) Iris Yang - "Codon Bias and uORF Function"
(3:40) Daniel Wilson - "Developing a Model for Targeted Photoablation of Tumors"
(3:50) Teresa Spix - "Know your gnotobiotics: A tool for investigating the microbiota"
(4:00) Amber Laperuta - TBA
(4:10) Scott Keith - "Mapping the Drosophila Gut Microbiota via Fluorescence in situ Hybridization"
(4:20) Manning Huang - "Putative Export Signals in Streptococcus pneumoniae"
(4:30) Stephanie Crilly - "Investigating atlastin dimerization kinetics"
3/2 Natalie McGuier Learning-induced plasticity in visual cortex: A project proposal
Javier Lopez

Cold Play: Searching for missing human heritability with small sample

Fumagalli et al. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349:1343 Sept 18 2015.

3/9 Spring Break

3/16 Beril Tutuncuoglu Late Nuclear Stages of 60S Ribosomal Subunit Assembly Involve Multiple Conformational Changes in Two Distinct Neighborhoods
Brian Jeon Investigating Properties of Neural Circuits via Ca++ Imaging Based Brain Computer Interface in Mice
Yessica Garcia Figueroa
3/30

Christopher Pratt

Stacie Oliver The Wnt signaling and cytoskeletal regulator APC2 controls stem cell niche size and architecture
4/6 Tanvi Shashikant The Genomic Control of Skeletal Morphogenesis in the Sea Urchin Embryo
Alan Waggoner Neural activity monitoring/mapping in brain
4/13 Dan Shiwarski A Golgi export checkpoint limits the efficacy of delta opioid receptor agonists in sensory neurons
Huajin Wang How Do Lipid Droplets Form and Grow? - Implications From The Lipodystrophy Gene BSCL2/Seipin
4/20 Brett Benedetti
4/27 Rotation Reports
5/4

Philip Davidson

The Kinase Awakens: Investigating the Kinases of the Sporulation Initiation Pathway
5/11 Michael Passineau Salivary Gland Gene Therapy: Clinical Impact and Post-Trial Optimization

Pieter Spealman

Comparative translatomics reveal a conserved class of noncanonical uORFs in yeast

Date

Speaker

Topic

9/2

Katie Lagree

Regulation of Candida albicans adherence and biofilm formation

Manoj Puthenveedu

The brain on the clock - a structural correlate to circadian rhythms

9/9

Dylan McCreary

Experience Dependent Changes in mini EPSC Frequency in Sensory Neocortex Validate Hypotheses Driven by High Throughput Electron Microscopy

Aryn Gittis

9/16

Lydia Perkins

Discovery of New Gene Targets for Synergistic Cystic Fibrosis Therapies

Veronica Hinman

Tracing our Origins: Who was Homo naledi

Berger LR, et al. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. Elife. 2015 Sep 10;4.

9/23

Emily Simon

Regulation of the Dynein Adaptor Golgin-160 for Golgi Membrane Transport

Sandra Kuhlman

On the fly: How opposing signals can create a coherent representation

Mauss AS, Pankova K, Arenz A, Nern A, Rubin GM, Borst A. Neural Circuit to Integrate Opposing Motions in the Visual Field. Cell. 2015 Jul 16;162(2):351-62.

9/30

Zach Weinberg

Controlling Signaling Through Controlling Trafficking

Claire Cheetham

The power of positive thinking: can happy memories prevent depression?

Ramirez S, Liu X, MacDonald CJ, Moffa A, Zhou J, Redondo RL, Tonegawa S. Activating positive memory engrams suppresses depression-like behaviour. Nature. 2015 Jun 18;522(7556):335-9.

10/7

James Winsor

Probing the atlastin fusion mechanism using fluorescence

Fred Lanni

Membrane signal transduction mechanisms

10/14

Minyan Zheng

Examination of gene expression changes during larval regeneration in starfish P.miniata

John Woolford

Using yeast and flies to explore yet another pathway dysfunctional in neurodegenerative disorders (FTD/ALS)

10/21

Malachi Blundon

To put “Apep” in APC’s step: Using proteomics to build molecular pathways

Kenneth Miller (Ph.D. ’95)

Biological Sciences Alumnus Speaker

Senior Scientist, MedImmune

Analytical Characterization of Biopharmaceuticals for First-Time In Human (FTiH) Clinical Trials

10/28

Nick Audette

Sensory input engages different circuit structures in deep and superficial layers of the cortex

Marcel Bruchez

Snap, Crack or Pop: Mechanics of S. Aureus Division

11/4

Vinitha Ganesan

Discovery prognosis biomarkers to predict lung disease in Rheumatoid Arthritis

Victoria Corbit (Pitt)

Novel interneuron-selective pallidostriatal projection is crucial for pathological beta oscillations in a computational model

11/11

Berquin Feese

The Role of ErbB4 in Proper Development of Inhibitory Neurons

Adam Linstedt

Touchy Feely Mechanotransduction

11/18

Rotation Reports

Stephanie Crilly - "Anatomical changes in basal ganglia circuitry in response to dopamine depletion"

Manning Huang - "Characterizing Ywp1, an anti-adhesin that regulates biofilm formation in Candida albicans"

Scott Keith - "Investigating a Potential Family of Exported Peptides in Streptococcus pneumoniae"

Amber LaPeruta - "What's my purpose? Exploring the function of rRNA m3U modifications"

Teresa Spix - "To move or not to move: Behavioral effects of external pallidal stimulation"

Daniel Wilson - Title TBA

Iris Yang - Title TBA

11/25

Thanksgiving Break

12/2

Yong Fan

Mitigating oxygen shock to enhance hematopoietic stem cell engraftment

Kevin Zitelli (Pitt)

12/9

Yizhu Lin

Evolutionary comparison of yeast mRNA secondary structure by high-throughput sequencing

Jon Jarvik

Drug-Target Network

Date

Speaker

Topic

1/21

Tanvi Shashikant

From Genome to Morphology: The Dissection of a Developmental Gene Regulatory Network

Zhongling Sun

Regulation of Skeletal Morphogenesis by TGF-β Signaling in the Sea Urchin Embryo

1/28

Daniel Shiwarski

Unlocking the DOR to the surface: Regulated Surface Delivery of the δ-Opioid Receptor (DOR)

David Hackney

Enzymes on the move in ways you probably did not expect

2/4

Ardon Shorr

How does gravity affect gene expression? A proteomic approach

Chien Ho

Accidental Discovery in Research

2/11

Pieter Spealman

N-terminal extensions: Protein Isoforms Revealed Under Stress

Maureen Stolzer

Evolution of the Metazoan Protein Toolkit

2/18

Shanna Bowersox

A Drug Selective Phosphoswitch Regulates mu-Opioid Receptor Recycling

John Woolford

A novel mechanism for translational control in mammalian development....specialized ribosomes?

Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M. RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature. 2015 Jan 1;517(7532):33-8.

2/25

Christopher Pratt

Red Light, Green Light: Two-Color Fluorogen Labeling Unveils BK Channel Trafficking

Brooke McCartney

Making connections: how "interactomics" teaches us about the inner lives of cells

Nicolas Preitner, Jie Quan, Dan W. Nowakowski, Melissa L. Hancock, Jianhua Shi, Joseph Tcherkezian, Tracy L. Young-Pearse, John G. Flanagan. APC Is an RNA-Binding Protein, and Its Interactome Provides a Link to Neural Development and Microtubule Assembly. Cell, Volume 158, Issue 2, 17 July 2014, Pages 368-382.

3/4

Rotation Talks

Dan Ackerman - “Colocalization of β2AR with TGN46, a Marker for the Trans-Golgi Network”

Amber Lucas - "Proteome sample cleanup using biotinylated proteins and polymer caged Avidin"

Surya Aggarwal - "Streptococcus pneumoniae Penicillin Resistance: Genotypes, Phenotypes & Fitness Costs"

Stephanie Biedka - "The Role of Ribosomal Proteins in 5S rRNA Rotation”

David Chen - "Effects of NGF Treatment on Delta-Opioid Receptor – Rab2/6 Interaction"

Hannah Kim - "A Journey to Find Phenotypes Associated to Gene Knockouts in Streptococcus pneumoniae"

Ian Fucci - “Probing dynamics of mutant and wild-type human thymidylate kinase using NMR spectroscopy”

Jian Ming Khor - "Targeting of Dishevelled in Early Embryogenesis"

Rolando Cuevas - "The CORVET Subunit VPS8 regulates recycling of β2 Adrenergic Receptor"

Alan Shteyman - “To Impute or Not To Impute: That is my Rotation Question”

Elena Shuvaeva - "The role of ribosomal protein L28 in late stage large subunit assembly"

Meiqi Wang - "Image-derived generative models of cellular organization"

Nathaniel Williams - "Defining subnetworks within the mouse visual system"

Andrew Wolff - "Atlastin disease mutation alters mitochondrial distribution"

3/11

Spring Break

3/18

Karen Kormuth

A Novel Mode of Homologous PNA Hybridization to G-quadruplex DNA

Marcel Bruchez

Long Ago and Far Away:  Presynaptic Activity Regulates Gene Expression at the Soma

Daniela Ivanova, Anika Dirks, Carolina Montenegro-Venegas, Cornelia Schöne, Wilko D Altrock, Claudia Marini, Renato Frischknecht, Denny Schanze, Martin Zenker, Eckart D Gundelfinger & Anna Fejtova. Synaptic activity controls localization and function of CtBP1 via binding to Bassoon and Piccolo. The Embo Journal, 4 Feb 2015.

3/25

Han Lai

An Eye Catching Tale: How Gene Transfer Allows Colonization of a New Niche

Jonathan Jarvik

Aging and surviving in the tree of life

4/1

Ting Liu

Polymorphism of DNA ejection dynamics - not every virion is ready to infect

Marcel Bruchez

Long Ago and Far Away:  Presynaptic Activity Regulates Gene Expression at the Soma

Daniela Ivanova, Anika Dirks, Carolina Montenegro-Venegas, Cornelia Schöne, Wilko D Altrock, Claudia Marini, Renato Frischknecht, Denny Schanze, Martin Zenker, Eckart D Gundelfinger & Anna Fejtova. Synaptic activity controls localization and function of CtBP1 via binding to Bassoon and Piccolo. The Embo Journal, 4 Feb 2015.

4/8

Salini Konikkat

New Alleles Reveal Later Functions of Erb1 in Ribosome Assembly

Chuck Ettensohn

Regeneration of digits in mice and humans

4/15

John Pettersson

Single Molecule Studies of Glutathione S-Transferase

Luisa Hiller

The Invisible World: A Source of New Chemistry to Target Superbugs

4/22

Sahil Sangani

Dynamics of a Protein-DNA-Metal Complex

Russell Schwartz

Do You Feel Lucky?

4/29

Madhumitha Ramesh

Novel Roles for  Eukaryote-Specific rRNA Expansion Segments in Ribosome Biogenesis

Tina Lee

Myoblasts perform under pressure

Kim JH, Ren Y, Ng WP, Li S, Son S, Kee, YS, Zhang S, Zhang G, Fletcher

DA, Robinson DN and Chen E. Mechanical Tension Drives Cell Membrane Fusion.

Developmental Cell 32, 561-573, Mar 9, 2015.

5/6

Rotation Talks

Dan Ackerman - “Activity of the ER at sites of endosome tubule fission”

Surya Aggarwal - "Why double you P1 inhibits biofilm formation"

Stephanie Biedka - "The C-terminus of ATL1 inhibits ATL1 GTPase activity in vitro”

David Chen - "Improving Cell Permeability of (R)-Diethylene Glycol-Contacting γ-PNA"

Rolando Cuevas - "Assessing Dishevelled Self-Association During Early Embryogenesis of Lytechinus variegatus"

Hannah Kim - TBA

Ian Fucci - “The Nucleotide-Free Refractory State of Kinesin Motor Domains may be a Molten Globule”

Jian Ming Khor - "The Role of Lunapark in Endoplasmic Reticulum Structuring"

Amber Lucas - "Proteomic analysis of early regeneration in Patiria miniata"

Alan Shteyman - “I think I've seen this Pattern before”

Elena Shuvaeva - "Regulation of β2-adrenergic receptor recycling and resensitization"

Meiqi Wang - "In vivo detection of FAP expression in neurons"

Nathaniel Williams - "Exploring the Effect of Familiarity in the

Visual System"

Andrew Wolff - "Characterization of cell proliferation during sea star regeneration"

5/13

Massimo Trucco

Institute of Cellular Therapeutics at Allegheny

General Hospital

Nick Giannoukakis

Institute of Cellular Therapeutics at Allegheny

General Hospital

Date

Speaker

Topic

9/3

A. Javier López

Woof! Genomics and evolution of our best friend

Nicholas Audette

An Evolving View of the Barrel Cortex Circuit

9/10

Manoj Puthenveedu

Why Pittsburgh Winters are Depressing

Fell GL, Robinson KC, Mao J, Woolf CJ, Fisher DE. Skin β-endorphin mediates addiction to UV light. Cell. 2014 Jun 19;157(7):1527-34.

Berquin Feese

The Role of ErbB4 in Developmental Adaptation in the Primary Visual Cortex

9/17

Frederick Lanni

Cells on the lam(ellipod)

Malachi Blundon

Identifying acute APC-dependent proteome changes in Drosophila melanogaster

9/24

Sandra J. Kuhlman

Closing the loop: brain-computer interfaces for mice

Clancy KB, Koralek AC, Costa RM, Feldman DE, Carmena JM. Volitional modulation of optically recorded calcium signals during neuroprosthetic learning. Nat Neurosci. 2014 Jun;17(6):807-9.

Vinitha Ganesan

Proteomic tool for discovering autoantigens

10/1

Anagha Kadam

Characterization of a Novel Genomic Locus in a Pandemic Pneumococcus Lineage

10/8

Philip Davidson

Tracking the evolution of the sporulation initiation pathway

Yizhu Lin

High-throughput probing of human sno-lncRNA secondary structure

10/15

Adam D. Linstedt

Flipping & scrambling to be eaten

Brendan Redler

Mapping required residues for retrograde trafficking of AB5 toxins

10/22

Dr. Hayder Ali Samaka, Visiting Scientist

Regulators of Candida Drug Responses during Infection

Aaron Karako,

Associate Program Manager -

CRDF Global

International Research Partnerships

Lina Song

Divide and Conquer: From Pan- to Isoform-Specific Sensor for GalNAc Transferases

10/29

Stacie Oliver

The Wnt signaling and cytoskeletal regulator APC2 controls stem cell niche size and architecture

Ceren Tuzmen

Nerves and BOOnes: Neuronal and Musculoskeletal Connections in Heterotopic Ossification

11/5

Beril Kumcuoglu

Ribosomal Protein Mediated Conformational Changes during 60S Subunit Assembly

Amanda Willard

A novel 6-OHDA dopamine depletion paradigm

11/12

Joel McManus

Destined to translate: coupling transcriptional and translational responses to glucose starvation

Zid BM, O'Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature 514; 117-121 (02 October 2014).

Shawn Burton

Inhibition of inhibition in olfaction. Part I: Patterning the olfactory bulb outputs

12/3

Veronica F. Hinman

The single cell and whole-organism science

Swati Venkat

Understanding the molecular mechanisms underlying Shiga toxin-receptor interaction

12/12

*1:30 pm - 5 pm

Rotation Talks

Dan Ackerman - “Assembly of 5S rRNA into Pre-ribosomes”

Amber Lucas - “Assembly of 5S rRNA into Pre-ribosomes”

Surya Aggarwal - "Effects of NGF Treatment & PI3K inhibition on Rab2 localization"

Stephanie Biedka - "Molecular mechanisms of cellular reprogramming in the sea urchin embryo”

Mengshen Chen - "Characterization of Kinesin State Transition"

Hannah Kim - “Buffering between transcription and translation in yeast”

Ian Fucci - Transcriptome-wide mRNA structure probing in two species of yeast

Jian Ming Khor - “Evolution of novelty: co-option of the sea star skeletogenic gene regulatory network into a new spatial-temporal context”

Rolando Cuevas - “Elucidating the mechanism involved in Golgi Positioning”

Alan Shteyman - “Analyzing Cancer Phylogenetics Trees Using Consensus Trees”

Elena Shuvaeva - “A Wolf in SHB's Clothing: Investigation of C. albicans genes"

Meiqi Wang - “Visual acuity test using calcium imaging”

Nathaniel Williams - "Investigating the Role of VPS8 in Sequence Dependent Recycling"

Andrew Wolff - "Using Imaging to Identify Specific Brain Regions"

Date

Speaker

Topic

1/15

Ardon Shorr

Gravity

Matt Saunders

Applications of Fluorogen Activating Proteins (FAPs) in Molecular Biology or FAPlications

1/22

Pieter Spealman

Starvation is Not a Piece of Cake

Alison Barth

The Language-related Transcription Factor FoxP2 Regulates Synaptic Density and Vocalization in Mice

2/5

Shanna Bowersox

Cell Autonomous Tuning of Opioid Responses by Substance P

Chien Ho

An Old Drug With New Tricks

2/12

Rotation 2 Presentations

2/19

Gino Gallo

Biosensor Romance: Match-Making and Love at a Molecular Level

Veronica Hinman

Cerebrating Darwin Day: On the Inheritance of Acquired Characteristics

2/26

Salini Konikkat

Dissecting Molecular Interaction Networks in Ribosome Assembly

David Hackney

Deep Fried Crystallography

3/5

Karen Kormuth

Unconventional Guanine Quadruplexes and their Role in Ribosome Biosynthesis

Xiaohong Tan

A 95% off sale for molecular beacon *with a coupon of label-free

3/12

No Journal Club Due to Spring Break

3/19

Han Lai

What makes a Prochlorococcus a Prochlorococcus? A genome content analysis

Wenjie Xu

Pathogen gene expression during infection

3/26

Ting Liu

Pump DNA into Viral Capsid Shell

Tina Lee

The Cost of Moving a Lipid = Moving Another Lipid

4/2

Kaustubh Sinha

Mapping Metal Ion Effects in a Protein-DNA Complex

4/9

John Pettersson

The Secret Life of GST: Enzyme Characterization in Singulo

Robert Murphy

Learning Protein Function From Noise

4/16

Madhumitha Ramesh

Intriguing Exceptions: Roles of rRNA Expansion Segments in Ribosome Biogenesis

Olivia Molinar

Walking the walk, talking the talk: APC proteins speak the language of actin assembly factors in vivo

4/23

Sahil Sangani

Studying Metal-ion Effects in a Protein-DNA Complex

Russell Schwartz

Death is a journey, not a destination: unraveling mutation processes in cancer development and progression

4/30

ROTATION 3 PRESENTATIONS

Katie Lagree “Trafficking Dynamics of the A118G SNP in the μ-opioid Receptor”

Dylan McCreary "Using Zebrafish to Study BK Ion Channel Trafficking In Vivo"

Lydia Perkins “Using Fluorogen Activating Proteins to Study Beta-2-Adrenergic Receptor Trafficking”

Emily Simon "Rab GTPase Control of Delta Opioid Receptor Golgi Retention"

Zach Weinberg "The role of Golgi positioning in neuronal differentiation"

James Winsor "Brachyury Expression Pattern in Strongylocentrotus Purpuratus"

Mia Zheng “A preliminary study of Yap1, a candidate mechanical sensor in sea urchins”

5/7

Yi Wang

A Toolbox for EGFR Trafficking

Jing Wen

Unreliable stimulus-evoked activity in the olfactory bulb of

an autistic mouse model

5/14

Ritika Tewari

Manganese Induces Oligomerization to Promote Downregulation of the Intracellular Trafficking Receptor used by Shiga toxin

Diego Pafundo

Top-down control of visual response in mouse

5/21

Idil Ulengin

Endoplasmic Reticulum Structure in Sickness and in health until graduation do us part…

Charles Ettensohn

The CRISPR Craze: Targeted Genome Editing

5/28

Zhongling Sun

TBA

Simran Saini

TBA

Date

Speaker

Topic

9/4

Manojkumar Puthenveedu, Ph.D.

How to Get Others Ready for Sex

Regev-Rudzki N, Wilson DW, Carvalho TG, Sisquella X, Coleman BM, Rug M, Bursac D, Angrisano F, Gee M, Hill AF, Baum J, Cowman AF. Cell-cell communication between malaria-infected red blood cells via exosome-like vesicles. Cell. 2013 May 23;153(5):1120-33.

Alys Cheatle

Modularity in DNA Binding Preference of a Tbrain Transcription Factor may Allow for more Versatile Transcriptional Responses and Increased Evolvability

9/11

Joel McManus, Ph.D.

RNA Yoga: Sequence Signatures of Folding Flexibility

Ritz, J., Martin, J. S., & Laederach, A. (2013). Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation. (S.-J. Chen, Ed.)PLoS computational biology, 9(7), e1003152. doi:10.1371/journal.pcbi.1003152.s009

Jineta Banerjee

Elimination of Synaptic Inputs Precedes their Strengthening During Early Postnatal Refinement of a GABA/Glycinergic Circuit in the Mouse Auditory Brainstem

9/18

Aaron Mitchell, Ph.D.

Malassezia: head & shoulders® above the rest
Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M; NIH Intramural Sequencing Center Comparative Sequencing Program, Kong HH, Segre JA. Topographic diversity of fungal and bacterial communities in human skin. Nature. 2013 Jun 20;498(7454):367-70. doi: 10.1038/nature12171. Epub 2013 May 22.

Stacie Oliver

Molecular Mechanisms Governing Stem Cell Niche Architecture in the Drosophila Female Germline

9/25

No Journal Club this week due to the Departmental Seminar

10/2

Aryn Gittis, Ph.D.

Neurotransmitter Switching in the Adult Brain Regulates Behavior

Davide Dulcis et al. (2013) Neurotransmetter Switching in the Adult Brain Regulates Behavior. Science, 340:449.

Shawn Burton

Division of Labor in Mammalian Olfaction: Investigating the Physiology of Mitral and Tufted Cells

10/9

John Woolford, Ph.D.

Using Yeast to Study Ribonucleoprotein Dysfunction in Human Neurodegenerative Diseases

Buchan JR, Kolaitis R-M, Taylor JP, Parker R. (2013) Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell 153: 1461-1474.

10/16

Brooke McCartney, Ph.D.

The Good, the Bad, and the Ugly: Commensals, Pathogens, and Next Generation Therapeutics

Philip Davidson

Evolution of the Sporulation Initiation Pathway

10/23

Nathan Urban, Ph.D.

To sleep, perchance to clean 

http://www.sciencemag.org/content/342/6156/373.full

Adam Foote

Investigating the Roles of Micro-RNAS in Development

10/30

Adam Linstedt, Ph.D.

Novel Enzymes in the Sugar Chain to Muscle Health

Beril Kumcuoglu

Tailypo: The Roles of Eukaryote-specific Ribosomal Protein Extensions in Ribosome Assembly

11/6

Marcel Bruchez, Ph.D.

 

Seriously? We don’t know how antibiotics work YET? Or maybe we do... The controversial role of reactive oxygen.

Christopher Pratt

Two-Color Tracking of an Ion Channe

11/13

Rotation 1 Presentations

Katherine Lagree

“Temporal Expression of GPP130 in response to Manganese”

Lydia Perkins

“Transmembrane Length-Dependent Partitioning of Oligomerized GPP130 into

Lipid Rafts as a Sorting Mechanism”

Dylan McCreary

"MOR Arrestin Signaling."

Emily Simon

“The Role of FGF in Directed Migration of Sea Urchin PMCs”

Zachary Weinberg

"Visualizing Gain Control with 2-Photon Calcium Microscopy"

James Winsor

"Combining FAPs and Voltage Sensitive Dyes in Neurons"

Minyan Zheng

"Regeneration of Serotonergic neurons in starfish"

11/20

Sandra Kuhlman, Ph.D.

Harnessing Plant Cryptochromes to Optically Control Gene Expression in Mammals

Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F. Optical control of mammalian endogenous transcription and epigenetic states. Nature. 2013 Aug 22;500(7463):472-6. doi: 10.1038/nature12466. Epub 2013 Aug 23.

Tanvi Shashikant

"Genome-wide Analysis of Effector Genes in the Sea Urchin Skeletogenic Gene Network"

11/27

No Journal Club due to Thanksgiving Break

12/4

Luisa Hiller, Ph.D.

The Human Gut: A Bacterial World.

Daniel Shiwarski

Unlocking the DOR to the surface: Trafficking of the δ-Opioid Receptor (DOR) 

Date

Speaker

Topic

1/16

Ezgi Kunttas-Tatli

To Dimerize or Not to Dimerize, that is the Question: Role of Dimerization in APC Protein

Deborah Makin

RNA Interference Screens of Trans-Acting Factors for Recursive Splicing in Drosophila

1/23

Suchitra Ramachandran

Statistical Learning of Visual Sequences in Monkey Inferotemporal Cortex depends on the Bidirectional Conditional Probability of the Images

Simran Saini

Mechanism of Membrane Fusion by the Atlastin GTPase

1/30

Amanda Soohoo

Tell me MOR, Tell me MOR: Does your Endocytosis Last Really Long

Gregory Smith

Applying Cellular Crowding Models to Simulations of Virus Capsid Assembly in vitro

2/6

Ritika Tewari

Understanding the Mechanism of GPP130 Sensitivity to Manganese

Idil Ulengin

Dissecting the Catalytic Machinery of Atlastin GTPase

2/13

Rotation 2 Presentations

Anagha Kadam

Insight into Strain Adaptability Through the Characterization of a Novel Streptococcal Histidine Kinase

Advisor: Hiller

Ceren Tuzmen

Construction of Lariat Libraries to Identify Alternative Splice Sites in Yeast

Advisor: McManus

Brendan Redler

A Method for Direct Electroelution of Proteins from Two Dimensional Gels

Advisor: Minden

Amanda Willard

A New Way to Study Parkinson's: Induction of Motor Deficits through 6-OHDA Time-course Dopamine Depletion

Advisor: Gittis

Caitlin Winkler

A Tale of Two Cell Types: Mapping Anatomical Projections of the External Globus Pallidus (GPe)

Advisor: Gittis

2/14

(2 - 3:15 p.m., Mellon Institute Social Room)

Rotation 2 Presentations

Nicholas Audette

Advisor: Barth

Berquin Feese

Neuroanatomical Differences between Layer 2 Neurons

Advisor: Barth

Vinitha Ganesan

The Oligomerization State of Cis-Golgi Protein GPP130 in Response to Golgi Manganese Influx

Advisor: Linstedt

Lina Song

Construction of a Sensor for Monitoring the Activity of ppGlaNAc Transferase 3

Advisor: Linstedt

Yizhu Lin

Yeast Co-regulation: Looking Under the Hood

Advisor: Durand

Swati Venkat

Characterizing a New Tethering Compound, DC18, as an Anchor for Sparsely Tethered Bilayer Lipid Membranes

Advisor: Loesche

Malachi Blundon

Advisor: Hiller

2/20

Phu Van

Optimizing 2DE Protein Gels for Detection with the SIGI

Rachel Vistein

Sequence of Events: Adrenergic Receptor Tail Sequences Direct Recycling

2/27

Mingrui Zhang

Far-red and NIR Fluoromodules for Multi-color in vivo Imaging

Shanna Bowersox

A Tail of Two Receptors: A Pain Receptor Increases Recycling of the Mu-opioid Receptor

3/6

Jigarkumar Desai

Regulatory Role of Glycerol in Candida albicans Biofilm Formation

Olivia Molinar

Novel Roles for Adenomatous polyposis coli Proteins in Actin Assembly

3/13

No Journal Club Due to Spring Break

3/20

Gino Gallo

Engineering Fluorogen-Activating-Proteins as Universal Affinity Biosensors

Salini Konikkat

Knitting Together the Ribosome – How Assembly Factors Facilitate Tertiary Interactions during Ribosome Assembly

3/27

Han Lai

Bursts of Horizontal Transfer Activity: Signal or Noise?

4/3

Madhumitha Ramesh

You know a Man by his Friends: Understanding the Roles of the ITS2 Neighborhood in Ribosome Biogenesis

Karen Kormuth

Exploring New Perspectives of Guanine Quadruplex Biology within Ribosomal DNA

4/10

John Pettersson

Substrate Plasticity of GSTA1-1: Single Molecule Characterization of a Disobedient Enzyme

Veronica Hinman

On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-free Gospel of ENCODE

Graur, D., Zheng, Y., Price, N., Azevedo, R.B., Zufall, R.A., and Elhaik, E. (2013). Genome Biol. Evol. , doi:10.1093/gbe/evt028 | in press.

Ward LD, Kellis M. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science. 2012 Sep 28;337(6102):1675-8. Epub 2012 Sep 5.

4/17

Elizabeth Ransey

Comprehensive Mechanistic and Structural Analysis of an RNA-Lariat Debranching Enzyme

Sahil Sangani

From Thermodynamics to NMR Dynamics of Specific Protein-DNA Interactions

4/24

Zhongling Sun

Differential Gene Expression in Primary Mesenchyme Cells Underlies Skeletogenesis in the Sea Urchin Embryo

Tina Lee

Actin in the Nucleus

5/1

Yi Wang

Directed Molecular Evolution to Diversify Malachite Green Activating Peptide

Ting Liu

Probing Viral DNA Structures - What Renders Fluidity to Rigid Viral Genome

5/9

(11 a.m. - 12:15 p.m., Mellon Institute Social Room)

Rotation 3 Presentations

Anagha Kadam

Advisor: Hiller

Nicholas Audette

Characterization of a Putative Lantibiotic Locus in Streptococcus Pneumonia

Advisor: Hiller

Yizhu Lin

Simulation of Tumor Cell Gene Copy Number Progression

Advisor: Schwartz

Swati Venkat

Simulating MultiDomain Evolution

Advisor: Durand

Lina Song

Establishment of Yeast Based Screen System for Ferritin as an MRI Reporter

Advisor: Ahrens

Malachi Blundon

The Role of APC2 Dimerization in Destruction Complex Formation in Drosophila S2 Cells

Advisor: McCartney

5/10

(11 a.m. - 12:15 p.m., Mellon Institute Social Room)

Rotation 3 Presentations

Vinitha Ganesan

Comparing the Co-evolution of Transcription Start Site Usage and Translation Efficiency

Advisor: McManus

Caitlin Winkler

Enterovirus Meningoencephalitis: Distribution of Virus in Two Fatal Cases

Advisor: Wiley

Amanda Willard

Do Layer 2/3 PV Cells in the Visual Cortex Exhibit Contrast Variance?

Advisor: Kuhlman

Brendan Redler

Advisor: Linstedt

Berquin Feese

Utility of Anti-microRNAs for the Regulation of Bone Regeneration Under Inflammatory Conditions

Advisor: Campbell

Ceren Tuzmen

VIP as an Immunomodulator to Control Inflammation During Bone Regeneration

Advisor: Campbell

Date

Speaker

Topic

8/29

Emily Furbee

Phenotypic Analysis of Hsp27 Phosphorylation Mutants in Drosophila

Manoj Puthenveedu

The Key to Eating (and Digesting) Bugs

Thurston TL, Wandel MP, von Muhlinen N, Foeglein A, Randow F. Galectin 8 targets damaged vesicles for autophagy to defend cells

against bacterial invasion. Nature. 2012 Jan 15;482(7385):414-8. doi: 10.1038/nature10744.

9/5

Merissa Remus

Cue-Evoked ERK Activation in the Nucleus Accumbens during Reward Seeking: Role for D1 Dopamine Receptors

Ayshwarya Subramanian

Inferring Robust Phyloegenetic Markers from Tumor Data

9/12

Jason Talkish

Disruption of Ribosome Biosynthesis Results in a Shift from Co- to Post-transcriptional pre-rRNA Processing and Breakdown of the Traditional Assembly Hierarchy

David Whitney

Evoking Neural Plasticity in the Visual Cortex Depends on Local Map Structure

9/19

Shawn Burton

A Selective Filter Controls Differential Trafficking in Neurons

Philip Davidson

Specificity of Interaction in Two Component Systems

9/26

Adam Foote

A Specific Mitochondrial Stress Engages Apoptotic Signaling to Cause Deafness

Beril Kumcuoglu

Policing Proteins Under Stress : Immobilization of Specific Proteins as a Function of Environmental Cues

10/3

Stacie Oliver

Flocking and Migration: The Lung as a Homing Niche in a Model of Multiple Sclerosis

Christopher Pratt

Seeing Yourself: The Role of Protocadherins in Neuronal Self-Avoidance

10/10

Tanvi Shashikant

The Role of miRNAs in Stem Cell Quiescence

Daniel Shiwarski

cAMP/cGMP Regulation: Breaking Symmetry During the Neuronal Polarization Process

10/17

Ardon Shorr

Renal Cilia Detect Flow

Pieter Spealman

Nuclear/Mitochondrial Incompatibility as a Mechanism for Speciation

10/24

Tara Tappen

Ribosome Profiling Sheds Light on the Black Box of miRNA Regulation

Anmol Grover

Single Molecule Measurement of Eukaryotic Translation

10/31

Jineta Banerjee

Synaptic Changes are Heterogeneous Along the Tonotopic Axis of the MNTB-LSO Circuit of Mouse Auditory Brainstem During Early Development

John Woolford

Ghosts and Horseless Headmen from the RNA World: Riboswitches that Regulate Fluoride Toxicity

Baker JL et al. Widespread Genetic Switches and Toxicity Resistence Proteins for Fluoride. Science. 335:233-235, 2012.

Ren et al. Fluoride ion encapsulation by Mg++ ions and phosphates in a fluoride riboswitch. Nature. 486:85-89, 2012.

11/7

Santosh Chandrasekaran

Exploring the Role of Intrinsic Biophysical Diversity in Coding of Information in the Sensory Cortex

Aryn Gittis

GABAergic RIP-Cre Neurons in the Arcuate Nucleus Selectively Regulate Cell Energy Expenditure

Cell Volume 151, Issue 3, 26 October 2012, Pages 645–657

11/14

12:30 - 1:30 p.m.

Rotation 1 Presentations

Ceren Tuzmen (Dahl Lab)

Expression and Purification of Recombinant Lamin Proteins and Quantification of Lamins in Mammalian Cultured Cells

Brendan Redler (Barth Lab)
Evidence for a Multiwhisker Sensory Function in Mus musculus

Amanda Willard (Barth Lab)

Chemical Activation of Cold Circuits in the Spinal Cord

Vinitha Ganesan (Urban Lab)

Looking for Dendrodendritic Synaptic Junctions in the Olfactory Bulb Primary Neuronal Cultures

Caitlin Winkler (Thiels Lab)

A Possible Role for the Auditory Cortex in Reward-seeking Behavior

Swati Venkat (Ahrens Lab)

Yeast-based Screen for Ferritin as a MRI Reporter

11/14

3:30 - 4:45 p.m.

Rotation 1 Presentations

Nicholas Audette (Linstedt Lab)

In Vitro Pull-down of the Trafficking Receptor GPP130 by Shiga Toxin

Berquin Feese (Lindstedt Lab)

Regulation of Dynein Binding to Golgi Membranes by Golgin160

Malachi Blundon (Minden Lab)

Examination of Mutant APC Proteome Changes in Drosophila melanogaster Early Embryos

Lina Song (Minden Lab)

The New Strategy for Identification of Low Abundance Protein in 2D Gel

Patrick Abbott (Lopez Lab)

RNA Interference Screening for Factors that Affect Recursive Splicing

Yizhu Lin (McManus Lab)

Regulation of Alternative Splicing in Yeast TAD3

Anagha Kadam (Hinman Lab)

Wnt Signaling During Endomesoderm Development in Sea Star Embryos

11/21

No Journal Club Due to Thanksgiving Holiday

11/28

Paul Barton

Doing Some Library Research: Lipocalins as FAPs

Alys Cheatle

Modularity in DNA Binding Preference of a Tbrain Transcription Factor may Allow for more Versatile Transcriptional Responses and Increased Evolvability

12/5

Michael Gamalinda

Factory of Protein Factories: Ribosomal Proteins and the Ribosome Assembly Line

Andrew Kehr

Ongoing Structural and Biochemical Characterizations: ADAR2, 3, 2/3?

Date

Speaker

Topic

1/25

Alys Cheatle

Subtle Changes in DNA Binding Preference May Explain Drastic Rewiring of Tbr Target Genes during Echinoderm Evolution

Jineta Banerjee

Different Rules of Circuit Refinement in Different Parts of the Mouse Lateral Superior Olive

2/1

Cas Priddy

Mammalian Golgi Positioning and the Dynein Motor

Fred Lanni, Ph.D.

When Push Comes to Shove

2/8

Paul Barton

Developing a Novel Lipocalin-based FAP

Michael Gamalinda

Ribosomal Proteins: Step-by-step Choreographers of Ribosome Assembly

2/16

12 - 2 p.m.

Rotation 2 Presentations

Philip Davidson

Rewiring the Sporulation Initiation Pathway

Advisor: Durand

Adam Foote

The Role of Argonaute Proteins in S. Purpuratus Embryonic Patterning

Advisor: Hinman

Tara Tappen

Echinoderm Argonaute Expression Throughout Development and Movement Towards the HITS-CLIP Protocol

Advisor: Hinman

Stacie Oliver

Who’s the Boss? Investigating APC2 and Organization of the Germline Stem Cell Niche in Drosophila Ovaries

Advisor: McCartney

Ardon Shorr

Elementary, my Dear Watson (& Crick)

Advisor: Ettensohn

Christopher Pratt

Developing Biosensors for the Visualization of Synaptic Activity

Advisor: Bruchez

Daniel Shiwarski

Billion Fold Concentration Range Detection using Structure Illumination Gel Imager (SIGI) for 2D-DIGE Proteomic Analysis

Advisor: Minden

Tanvi Shashikant

Spatial Control of Stem Cell Differentiation using BMP-2 Printed DermaMatrix

Advisor: Campbell

Pieter Spealman

The Gearbox of Creation: Translational Regulation

Advisor: McManus

Beril Kumcuoglu

Cargo Specific Regulation of Clathrin-Mediated Endocytosis

Advisor: Puthenveedu

2/22

Joel McManus, Ph.D.

Global Analysis of Gene Regulatory Networks with High-throughput Sequencing and Bioinformatics

Ezgi Kunttas-Tatli

The APC2 Compass: Phosphorylation as a Mechanism to Guide APC2

2/29

Andrew Kehr

RNA Editing: Structural and Biochemical Characterization of hADARs

Bob Murphy, Ph.D.

Image-derived Generative Models of Cell Organization

3/7

Joanna Urban-Ciecko, Ph.D.

Suppression of BK Channel Current by the Trafficking Molecule beta 4

Deb Makin

Subcellular mRNA Localization in Drosophila

3/14

Spring Break - No Journal Club

3/21

Santosh Chandrasekaran

Exploring the Role of Intrinsic Biophysical Diversity in Coding of Information in the Cortex

Suchitra Ramachandran

Characterizing Visual Statistical Learning in Macaque Inferotemporal Cortex

3/28

Stephanie Hughes

Identification and Comparison of Early and Late Otx Targets in Sea Urchins and Sea Stars

4/4

Simran Saini

The Mechanism for Atlastin Mediated ER Membrane Fusion

Greg Smith

Translating Bulk Measures of Viral Capsid Assembly Progress into Insights on Fine-scale Kinetics and Pathways

4/11

Amanda Soohoo

How the Mu-Opioid Receptor Regulates its Own Clathrin-Mediated Endocytosis

Ritika Tewari

Insight into the Mechanism of Manganese-Induced Trafficking of Cis-Golgi Protein GPP130

4/18

Idil Ulengin

Does Spastin ATPase have a Role in ER Network Formation

Mark Macbeth, Ph.D.

It Dices! It Slices! The structural basis for RNA Interference

4/25

Phu Van

There's no Free Lunch: High Dynamic Range Protein Detection with SIGI

Rachel Vistein

Beta-2 Adrenergic Receptor Recycling Switches from Constitutive to Actin Dependent with PKA Phosphorylation

5/2

Mingrui Zhang

Development of Fluoromodule-based Reporters of Physiological Parameters

Jon Minden, Ph.D.

Question-omics

5/10 (4 p.m.)

Rotation 3 Presentations

Ardon Shorr

Building Nature's Oldest Machine

Advisor: Woolford

Tara Tappen

The Role of Nop12 in Ribosomal Processing and Assembly

Advisor: Woolford

Beril Kumcuoglu

The Role of TRAMP4 Complex in Turnover of Aberrant Pre-ribosomes

Advisor: Woolford

Christopher Pratt

Dissecting the Destructosome: The Directors of APC2 Incorporation

Advisor: McCartney

Daniel Shiwarski

Advisor: McCartney

Adam Foote

Optimizing 2D Electrophoresis Gels For Increased Protein Detection

Advisor: Minden

Tanvi Shashikant

The Interaction Between Mu-opioid Receptor and Dynamin and its Role in Mediating Receptor Endocytosis

Advisor: Puthenveedu

Pieter Spealman

GPCR and Glut4 Interactions

Advisor: Jarvik

Stacie Oliver

The miRNA Pathway Modulates Anterior/Posterior and Dorsal/Ventral Patterning in the Sea Urchin Embryo

Advisor: Hinman

Philip Davidson

Predicting the Evolution of Interaction

Advisor: Durand

Date

Speaker

Topic

8/31

Ashrifia Adomako-Ankomah

Regulation of Skeletal Morphogenesis by Cell-cell Interactions in the Sea Urchin Embryo

Kaitlyn Dykstra

Yip1A Cycling Between the ER and Golgi is not Required for its ER Structuring Function

9/7

Anmol Grover

Genetically Tagged pH Biosensor for Endosomal Trafficking

Marcel Bruchez, Ph.D.

Using Generative Models to Enhance Superresolution Imaging

9/14

Tim Jarvela

GRASPing Golgi Ribbon Maintenance

Merissa Remus

ERK Activation in the Nucleus Accumbens: Selectivity by Subregion, Type of Motivationally-relevant Stimulus, and Cell Phenotype

9/21

Ayshwarya Subramanian

Understanding Tumor Progression using Phylogenetics

Brooke McCartney, Ph.D.

Stories from the End of the Filament: APC2 Dependent Regulation of the Actin Cytoskeleton

9/28

Shana Bowersox

Connections Between Nicotine and Weight Loss in the Central Nervous System

Jigarkumar Desai

Candida albicans: Why is it Virulent?

10/5

Eugenio Gallo

Dissecting the Complexity of Hematopoiesis by Mass-Cytometry

Salini Konikkat

Much More than Translation: Specialized Functions of Ribosomes

10/12

Karen Kormuth

Much More than a Vegetable: Spinach and the Development of Fluorescently Tagged RNAs

Han Lai

When Metabolite Genes get Together

10/19

Ting Liu

Temperature Induced Phase Transition and Change in Ejection Kinetics of Phage Genome

Olivia Molinar

Head Versus Tail Regeneration in Planaria

10/26

John Pettersson

Diversifying the Sequence Between Neighbouring Domains can Prevent Interdomain Misfolding

Madhumitha Ramesh

You are What You Eat: Why miRNA Might be the Next Sensational Nutritional Supplement

11/2

Elizabeth Ransey

The Structure-based Design of Amyloid Fibril Inhibitors

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature, Vol 475, 7 July 2011.

Sahil Sangani

Understanding the Mechanism of a GPCR-G Protein Complex Formation

11/9

Zhongling Sun

The Mechanism of Gamete Recognition in the Mouse

Gagandeep Gahlay, Lyn Gauthier, Boris Baibakov, Olga Epifano and Jurrien Dean. Gamete Recognition in Mice Depends on the Cleavage Status of an Egg's Zona Pellucida Protein. Science. Vol. 329 no. 5988 pp. 216-219,9 July 2010. DOI: 10.1126/science.1188178

Yi Wang

Rotation of Rotorless F1-ATPaes

11/16 (Mellon Institute Social Room)

Rotation 1 Presentations

12:30 to 2:20 p.m.

Tanvi Shashikant

MAP Kinase Signaling and Skeletogenesis in Sea Urchin Embryo

Advisor: Ettensohn

Philip Davidson

Unmixing Breast Cancer Expression Data

Advisor: Schwartz

Adam Foote

Muscle-Blind Mutations and Muscle Z-Band Alternative Splicing

Advisor: Lopez

Tara Tappen

Tissue-specific Splicing Patterns of the Drosophila Stunted Gene

Advisor: Lopez

Stacie Oliver

Tagging Vesicular Transporters with Fluorogen-Activating Proteins

Advisor: Bruchez

Ardon Shorr

Occupy Small Street: the Gathering of Yeast

Advisor: Lanni

Christopher Pratt

A Tale of Pain and Relief: Heterologous Signal Activation Downstream of the Mu-Opioid Receptor

Advisor: Puthenveedu

Daniel Shiwarski

Live Cell Imaging of cAMP Signaling Dynamics to Evaluate ß2-Adrenergic Receptor Re-sensitization

Advisor: Puthenveedu

Shawn Burton

Highly Active Layer 2/3 Neurons do not Exhibit Hallmarks of Recent Synaptic Plasticity

Advisor: Barth

Pieter Spealman

Three's a Crowd: APC and Dia Interactions

Advisor: McCartney

Beril Kumcuoglu
Wnt Signaling Pathway Regulates Cell Shape
Advisor: McCartney

11/23

No Journal Club due to Thanksgiving Break

11/30

Kiran Rafiq

Linking a Developmental Gene Regulatory Network to Morphogenesis

Jason Talkish

Understanding How Three Proteins Fold rRNA by Chemical Footprinting and Other “Cutting”-Edge Techniques

12/7

David Whitney

Age-Dependent Changes in the Columnar Organization and Plasticity of the Ferret Visual Cortex

Emily Furbee

hsp27 and Programmed Cell Death in Drosophila Development

Date

Speaker

Topic

1/12

Brenna McCauley

Evolution of a Novel Cell Population in Sea Urchin Embryos: Changes in Specification and Cell Fate

1/19

Jeanne Morin-Leisk

Mutational Analysis of a Large GTPase Required for ER Network Formation

Kalin Vasilev

Biosensors for Protein Proximity at the Cell Surface

1/26

Anmol Grover

Understanding Translation at Single Molecule Level

Alan Waggoner, Ph.D.

Optogenetics

2/2

Smita Yadav

At Long Last, a Golgi Receptor Complex for the Dynein Motor!

Qi Yan

Super-resolution Imaging Using Fluorogen Activating Proteins

(FAPs)

2/8

(2-4 p.m.)

Rotation 2 Presentations

Karen Kormuth

Peptide Nucleic Acids (PNAs) as Inhibitors of Nucleolin/rDNA G-quadruplex Binding

Advisor: Armitage

Sahil Sangani

Investigating the Role of Kinesin Head Domain Surface Residues in Tail Domain Binding

Advisor: Hackney

John Pettersson

Translation in a Crowded Environment

Advisor: Bruchez

Jigarkumar Desai

PNAs: Potential Probes for Site-specific Labeling of Eukaryotic Ribosomes

Advisor: Bruchez

Shanna Bowersox

Agonist Stimulated Internalization of a FAP-Tagged µ-Opioid Receptor

Advisor: Jarvik

Eugenio Gallo

Using Biosensors for Detecting Protein Proximity at the Cell Surface

Advisor: Jarvik

Madhumitha Ramesh

Investigating the Role of RhoB in Actin-mediated b2AR Recycling

Advisor: Puthenveedu

2/9

(12:30-2 p.m.)

Rotation 2 Presentations

Ting Liu

Study of hADAR2 Catalytic Domain Mutants – How Substrate Specificity Information is Hidden in the Structure

Advisor: Macbeth

Elizabeth Ransey

Purification, Crystallization and Mechanistic Studies of RNA Lariat De-branching Enzyme,DBR1

Advisor: Macbeth

Salini Konikkat

Cell-cycle Dependent Phosphorylation of APC2 in Drosophila Embryos

Advisor: McCartney

Zhongling Sun

Spatial and Temporal Expression of alx1-like in the Sea Urchin Embryo

Advisor: McCartney

Han Lai

Protein Location and Sorting Pathway: A Hidden Markov Approach

Advisor: Murphy

Yi Wang

Application of Lanthanide Ions on NMR Analysis of EcoRV

Advisor: Rule

Olivia Molinar

Characterization of Axonal Transport Using High Resolution Imaging Methods

Advisor: Yang

2/16

Bradley Yates

Progress Toward Creation of an scFv-based Protein-Protein Interaction Biosensor

Kaitlyn Dykstra

How Does Yip1A Structure the Mammalian Endoplasmic Reticulum?

2/23

Emily Furbee

Designing a Better in vivo Autophagy Reporter

Nathan Urban, Ph.D.

A Dimorphic Pheromone Circuit in Drosophila from Sensory Input to Descending Output

Ruta V, Datta SR, Vasconcelos ML, Freeland J, Looger LL, Axel R. Nature 468, 686–690 (02 December 2010). doi:10.1038/nature09554

3/2

Ashrifia Adomako-Ankomah

Regulation of Skeletal Morphogenesis in the Sea Urchin Embyro

Jing Wen

Input Specific Critical Periods for Experience-dependent Plasticity in Layer 2/3 Pyramidal Neurons

3/9

No Journal Club - Spring Break

3/16

Timothy Jarvela

Understanding the Dynamics of the Golgi Through Acute Inactivation

Veronica Hinman, Ph.D.

Phenotypic Robustness Conferred by Apparently Redundant Transcriptional Enhancers

Frankel N, Davis GK, Vargas D, Wang S, Payre F, Stern DL. Nature. 466(7305):490-3, 2010 Jul 22.

3/23

Merissa Remus

Region-specific ERK Activation in the Nucleus Accumbens in Response to Reward-predictive Cues: Does Behavioral Context Matter?

Javier Lopez, Ph.D.

Is Aging Necessary? Sexual Antagonism, Epistasis and Deleterious Pleiotropy of Lifespan-extending Mutations in Drosophila

Maguire et al. Quantitative and molecular genetic analyses of mutations increasing Drosophila life span. PLoS Genetics 6:e1001037, 2010.

3/30

Ayshwarya Subramanian

Inferring Evolution of Cell Lineages in Breast Cancer

Jesse Sheehan

Impact of Global and Local Attention on Neuronal Activity in Inferotemporal Cortex

Perceptual psychologists have made frequent use of hierarchical displays to analyze global and local visual perception in humans.  Hierarchical displays are well suited to this purpose because they allow measuring responses to the same shape both at the level of the whole object and at the level of its parts.  A key phenomenon discovered by the use of such stimuli is the global advantage effect:  humans report global shape faster then local shape.  Inferotemporal cortex (IT), as the terminus of the ventral stream, a chain of areas dedicated to pattern vision, contains neurons selective for complex images.  Recent work in the laboratory has shown that IT neurons in the macaque monkey exhibit a signal for global information ~30ms sooner than local information while passively viewing hierarchical displays.  

My research aims to expound upon this finding by requiring the active processing of the global and local content of the displays.  Monkeys are cued which level (global or local) of the display to attend to, and must respond with the identity (shape) of the object at that level.  This will attempt to answer two main questions:  Do monkeys exhibit a behavioral global advantage effect while performing such a task?  Is the discriminative signal latency in IT neurons the same during active as during passive processing?

4/6

Mark DeBlois

Continuous Sensory Input is Not Required to Maintain Synaptic Strength after Plasticity Onset in the Mouse Barrel Cortex

Jason Talkish

Structuring the Preribosome One Subcomplex at a Time: in vivo RNA Footprinting Reveals the RNA Binding Function of Nop12

4/13

Santosh Chandrasekaran

Exploring the Role of Diversity in Cortical Neural Circuits

Jineta Banerjee

Knocking out GABAA Receptor in the Mouse Auditory Brainstem in a Tissue Specific Manner

4/20

Kiran Rafiq

Linking a Developmental Gene Regulatory Network to Morphogenesis

Alys Cheatle

Subtle Changes in DNA Binding May Explain Drastic Rewiring of Tbr Target Genes during Echinoderm Evolution

4/27

David Whitney

Evoking Neural Plasticity in the Visual Cortex Depends on Local Map Structure

Cassandra Priddy

The Role of Ykt6 in Golgi Membrane Fusion Events

5/4 (Mellon Institute Social Room, 12:30 - 1:30 p.m.)

Rotation 3 Presentations

Yi Wang

The Role of GMAP210 and G160 Interaction in Golgi Positioning

Advisor: Linstedt

Sahil Sangani

Cloning, Expression and Purification of scDBR1 for Mechanistic and Crystallographic Studies

Advisor: Macbeth

Jigarkumar Desai

Crystal Structure of hADAR2 Catalytic Domain Mutant: Unraveling the Mechanism behind Substrate Specificity

Advisor: Macbeth

Shanna Bowersox

Effects of an Inflammatory Environment on Gene Expression of BMP2-induced Osteoblastic Differentiation of C2C12 Progenitor Cells

Advisor: Campbell

Elizabeth Ransey

The Effects of Inflammation on Muscle-Derived Stem Cell (MDSC) Differentiation: Implications for Stem-Cell Therapy

Advisor: Campbell

5/5 (Mellon Institute Social Room, 10 - 11:10 a.m.)

Rotation 3 Presentations

Ting Liu

Energetic Study of Viral Genome Ejection

Advisor: Evilevitch

Madhumitha Ramesh

The Role of Ribosomal Protein L17 in Ribosome Assembly

Advisor: Woolford

Salini Konikkat

The Role of Ribosomal Protein L17 in Ribosome Assembly

Advisor: Woolford

Han Lai

Inferring Events in Species Trees with Short Branches

Advisor: Durand

Karen Kormuth

Regulation of the Patterning of the Sea Urchin Embryonic Skeleton

Advisor: Ettensohn

Zhongling Sun

Testing the Role of APC2 SAMP Repeats in Wnt Signaling in Drosophila Embryos

Advisor: McCartney

Olivia Molinar

Investigating the Role of Cell Cycle Dependent Phosphorylation in APC2 Activity

Advisor: McCartney

Eugenio Gallo

Understanding the Biology of Aging via Alternative Splicing Differences in Drosophila melanogaster

Advisor: Lopez

Date

Speaker

Topic

8/25

Paul Barton

Interfering with RNAi: Evasion of Antiviral Activity

Michael Gamalinda

HOTAIR Just Got Hotter: lincRNAS Could Actually Link

9/1

Nathan Hsu

Circadian and Social Cues Regulate Ion Channel Trafficking

James Hughes

DNA Zip Codes Control an Ancient Mechanism for Gene Targeting to the Nuclear Periphery

Ahmed, S. et al. DNA Zip Codes Control an Ancient Mechanism for Gene Targeting to the Nuclear Periphery. Nature Cell Biology 2, 111-118, 2010.

9/8

Stephanie Hughes

Evolutionary Mirages: Illusions of Conserved Structures in Enhancers

Lusk RW, Eisen MB. Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. PLoS Genet 6(1): e1000829, 2010.

Andrew Kehr

A Complex(in) Switch Mechanism for SNARE-Mediated Fusion

Giraudo, et. al. Alternative Zippering as an On-Off Switch for SNARE-Mediated Fusion. Science 323: 512-6, 2009.

9/15

Andrew Markham

mRNA Quality Control: Evidence for a Novel De-capping Enzyme

Jiao X, Xiang S, Oh C, Martin C, Tong L, Kiledjian M. Identification of a quality-control mechanism for mRNA 5'-end capping. Nature:1-5, 2010.

Ashita Magal

NADPH: The Gatekeeper for Drosophila Apoptosis

Yang et. al. Metabolic regulation of Drosophila apoptosis through inhibitory phosphorylation of Dronc. The Embo Journal, 2010.

9/22

Deborah Makin

Dissecting the CTD Code of RNA Polymerase II: Phosphorylation of Ser7 Across Protein-coding Genes

Tietjen JR, et al. Chemical-genomic dissection of the CTD code. Nat. Struct. Mol. Biol. 17: 1154-1161, 2010.

Ezgi Kunttas-Tatli

Testing Interactions between APC2 and Armadillo in Wnt Signaling

9/29

Sailatha Ravi

DNA Packaging Role of phi-29 Homomeric Ring ATPase

Moffitt et al., Intersubunit coordination in a homomeric ring ATPase, Nature, 2009.

Suchitra Ramachandran

Information is Wealth: Midbrain Dopamine Neurons Signal Preference for Advance Information about Upcoming Rewards

Bromberg-Martin E and Hikosaka O. Midbrain Dopamine Neurons Signal Preference for Advance Information about Upcoming Rewards. Neuron, 63(1):119-126, 2009 July 16.

10/6

Simran Saini

Staph vs. Staph: A New Way to Attack Staphylococcus aureus

Iwase et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 2010.

Gregory Smith

Codon Pair Bias: A Powerful Tool in Rational Influenza Vaccine Design

Mueller, S. et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nature Biotechnology 28, 723-726, 2010.

10/13

Amanda Soohoo

With Curves like Those, I'll Go Inside: How Membrane Curvature Proteins Nucleate Endocytosis

Henne et. al. FCHo Proteins Are Nucleators of Clathrin-Mediated Endocytosis. Science 328, June 2010.

Ritika Tewari

Early to Late Endosome Transition

Dmitry Poteryaev,Sunando Datta,Karin Ackema, Marino Zerial and Anne Spang.Identification of the Switch in Early-to-Late Endosome Transition. Cell 141, 497–508, 30 Apr 2010.

10/20

Idil Ulengin

To be or not to be Translocated: A Quality Control Pathway that Regulates Translocation during ER Stress Leads to Neurodegeneration

Rane NS et al. Reduced translocation of Nascent Prion protein during Er stress contributes to Neurodegeneration. Developmental Cell, 15:359-370, 2008.

Phu Van

Targeted Proteomics with Selected Reaction Monitoring

Picotti P, Bodenmiller B, Mueller L, Domon B, Aebersold R.Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell, 138(4)795-806, 2009.

10/27

Rachel Vistein

Hanging in the Balance: CDK5 and Calcineurin Regulate the Exocytosis of Presynaptic Vesicles

Kim SH and Ryan TA. CDK5 Serves as a Major Control Point in Neurotransmitter Release. August 2010.

Mingrui Zhang

Rescuing Vision in Retinitis Pigmentosa Patients

Busskamp et al. Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa. Science (329), 413-417, 2010.

11/3

Shantanu Bhattacharyya

NMR Structure of Single Chain Antibody Fragment M8

Russell Schwartz, Ph.D.

How a Few Years of Work Can Save You a Millisecond

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-Level Characterization of the Structural Dynamics of Proteins. Science:341-346, 15 October 2010.

11/10 (12:30 - 1:40 p.m.)

Rotation 1 Presentations

Shanna Bowersox

Effects of Chronic Morphine on Trafficking of the mu Opioid Receptor

Advisor: Puthenveedu

Ting Liu

Two Small GTPases & One Big Question- Recycling Study of β2 Adrenergic Receptors
Advisor: Puthenveedu

Zhongling Sun

Characterizing Neuronal Diversity in the Neocortex

Advisor: Barth

Madhumitha Ramesh

Correlations in Intrinsic Properties between Sister and Non-sister Mitral Cells

Advisor: Urban

John Pettersson

Osmotic Suppression of Giant Genome Phage λ Ejection

Advisor: Evilevitch

Han Lai

Human Papillomavirus (HPV) Capsid Formation

Advisor: Schwartz

Sahil Sangani

NMR Structure of Single-chain Antibody (ScFv) K7

Advisor: Rule

11/11 (12:30 - 1:40 p.m., Mellon Institute Social Room)

Rotation 1 Presentations

Yi Wang

Altering Dye Binding with Directed Mutagenesis of a Fluorogen Activating Peptide

Advisor: Bruchez

Elizabeth Ransey

Progress in Detection of 5HTR2A Internalization in Live Cells Using FAP-based Biosensor Technology

Advisor: Jarvik

Salini Konikkat

The Role of DNA Replication and Cell Division in Re-wiring Developmental Gene Regulatory Networks

Advisor: Ettensohn

Jigarkumar Desai

Adenomatous Polyposis Coli(APC): Understanding the Mode of Regulation of its Activity in a Cell-cycle Dependent Manner in the Drosophila Syncytial Blastoderm

Advisor: McCartney

Eugenio Gallo

A Rapid and Systematic Approach for Detecting Protein-protein Interactions in Candida Albicans

Advisor: Mitchell

Olivia Molinar

RNA Recognition by DNA Nanotags: A New Approach to Fluorescent Labeling of RNA

Advisor: Armitage

Karen Kormuth

Expression and Purification of RNA Debranching Enzyme

Advisor: Macbeth

11/17

Shantanu Ganguly

Quorum Sensing in Candida albicans Biofilms

John Holleran

Cell Surface Detection of Proteins Implicated in Cystic Fibrosis

11/24

No Journal Club - Thanksgiving Week

12/1

Elmer Ker

Toward Spatial Control of Complex Tissues using Growth Factor Patterns and Fiber Alignment

Aaron Mitchell, Ph.D.

Septins Skore