New Resources and Opportunities
Seminar Series Kick-Off 9 September 2016
Johns Hopkins Malaria Research Institute Department of Molecular Microbiology and Immunology
Johns Hopkins Bloomberg School of Public Health
History and Goals
Since 2001 Bloomberg Philanthropies has given $125 million to the
Bloomberg School to fund a state-of-the-art research facility that would
mount a broad program of basic-science research to treat and control
malaria, develop a vaccine and find new drug targets to prevent and
cure this deadly disease.
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Diane Griffin, MD, PhD Founding Director
JHMRI Leadership
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Director
Peter Agre, MD Bloomberg
Distinguished Professor
George Dimopoulos, PhD, MBA Professor
Marcelo Jacobs-Lorena, PhD Professor
Photini Sinnis, MD Professor
Fidel Zavala, MD Professor
Deputy Directors
2016 Scientific Advisory Board The external Scientific Advisory Board meets annually to evaluate Malaria Research Institute activity.
• Daniel E. Goldberg, MD, PhD, Professor of Medicine & Molecular Microbiology at Washington University
• Diane Griffin, MD, PhD, Professor and Chair, Department of Molecular Microbiology & Immunology at
JHBSPH and Founding Director of JHMRI
• Thomas Kelly, MD, PhD, Director, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center
• Michael Klag, MD, MPH, Dean, JHBSPH and Chair of the External Advisory Board
• Gregory Lanzaro, PhD, Director, University of California Mosquito Research Program, UC Davis
• Bernard Roizman, ScD, Professor, Departments of Microbiology, and Molecular Genetics & Cell Biology, University of Chicago
• Eric Schoomaker, MD, PhD, LTG USA (Retired) Professor, Office of the President, Uniformed Services University of the Health Sciences
• Alfred Sommer, MD, MHS, Professor and Dean Emeritus, JHBSPH
• Allan Spradling, PhD, Director of the Department of Embryology, Carnegie Institution of Washington
• Kathryn Zoon, PhD, Director, National Institutes of Health Division of Intramural Research
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Malaria Life Cycle
Mosquito
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Malaria Researchers affiliated with the JHMRI
George Dimopoulos Mosquito innate immunity
Marcelo Jacobs-Lorena Mosquito-parasite interactions
Douglas Norris Mosquito biology/ecology
Fidel Zavala Immunology
David Sullivan Heme metabolism
Isabelle Coppens Plasmodium metabolism
Peter Agre Water channel biology
Photini Sinnis Cell Biology
Sean Prigge Drug targets
William Moss Epidemiology
Clive Shiff Passive case detection
Theresa Shapiro Drug development
Jenny Stevenson Entomology
Phil Thuma Clinical malaria
Conor McMeniman Mosquito olfaction
Prakash Srinivasan Host-pathogen interactions
and vaccine development
Chris Potter Sensory/neuronal function
Deborah Andrew Salivary gland biology
Monique Stins Cerebral malaria
Gary Ketner Immunoprophylaxis
Richard Markham Vaccine platform
Sungano Mharakurwa Parasite diagnostics
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Field station in rural Zambia Molecular laboratory Insectary “Mosquito House”
Macha Research Trust Southern Province, Zambia
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Dr. Phil Thuma, MD Senior Scientific Advisor
Dr. Jennifer Stevenson, PhD Lead Entomologist
JHBSPH Faculty Based in Macha
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Core Facilities
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I. JHMRI Cores • Biophysics Core • Environmental Surveillance Core • Insectary Core • Parasitology Core
• Genomic Analysis and Sequencing Facility • Microscopy Facility • Flow Cytometry &Cell Sorting/Becton Dickinson Immune Function Lab
II. JHU & MMI Cores Facilities https://johnshopkins.corefacilities.org
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Biophysics Core
Facility Co-Directors
Scott Bailey, PhD Email: [email protected]
Sean Prigge, PhD
Email: [email protected]
Biophysics Core Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Room W8620 Baltimore, Maryland 21205 Telephone: 443-287-48227 fax: 410-955-0105
Biophysics Core
Isothermal Titration Calorimetry: This technique measures the heat of binding between two molecules, providing a direct measurement of binding affinity. Equipment: MicroCal VP-ITC Location: W8620
The Biophysics Core Facility provides equipment for JHMRI investigators who want to characterize macromolecules or macromolecular complexes using biophysical techniques
Biophysics Core
Dynamic Light Scattering. This technique provides information about the size, shape and oligomerization state of biomolecules. Equipment: Proterion DynaPro with Peltier temperature control Location: W8620
Biophysics Core
Circular Dichroism. This technique measures the overall secondary structure content of proteins and quantifies changes in structure under different conditions. Equipment: Jasco J-810 Spectropolarimeter with Peltier temperature control, automated dual titration system, and scanning emission monochromator Location: W8620
Environmental Surveillance Core
Facility Director Timothy Shields, MA
Department of Epidemiology Email: [email protected]
Facility Co-Director
Frank Curriero, PhD Department of Epidemiology
Email: [email protected]
Environmental Surveillance Core Facility Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Room E3025 Baltimore, Maryland 21205 Telephone: 410-502-9077 fax: 410-955-0105
Overview - Spatial Analysis
Rationale Identified malaria outcomes and measured environmental determinants likely vary spatially. Collect and harness this information to improve
• study design • analysis • prevention, intervention, control and policy efforts
Obtain, Collect, Create Images (Satellite, Google Earth) Spatial Data Accuracy Non-spatial data
Maps Spatial Database/Integration View Patterns Simultaneously Generate/Refine Hypothesis
Quantify Relationships Test Hypothesis Study Design Go Beyond the Map!
Spatial Data GIS* Spatial Statistics
*Geographic Information System
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Spatial Data
- Satellite Imagery
- Geography, Hydrology
- Land Use/Land Cover
- Climate, Census
- GPS’d locations
- Outcome locations
New Analysis Opportunities
Integration, Hypothesis Generation
GIS
Spatial Statistics - Risk map estimation - Identify Env factors - Assess clustering - Trends over space & time - Detect clusters - Movement over space & time Choma Mutasa Nchelenge
Rainy Dry Gambiae Counts
GPS Logged Movement
DESCRIPTION • Location : SPH 4th floor, Room
W4700
• Size: 3000 sq ft. divided into two operational areas – High (Area 2) and Low containment (Areas 1, 3 & 4).
• There are seven procedure rooms and an autoclave.
INSECTARY MAP
The JHMRI Insect Core Facility
• 7 environmentally controlled
walk-in incubators for
mosquito rearing.
• 9 reach-in incubators whose
temperature and humidity can
be custom adjusted.
Walk-in incubator for mosquito rearing
Services • Mosquito rearing : An gambiae and
An. stephensi
• Provide space and assistance for rearing of other mosquito species.
• Training: insectary use, mosquito rearing, handling and identification techniques.
• Mosquito transformation (transgenic mosquitoes
For new insectary users:
• Need orientation training before access to the insectary is granted.
• Need specialized training to work with Plasmodium falciparum-infected mosquitoes.
• Place orders: http://jhmalaria.jhsph.edu/department/insectary/FrameForm.cfm
Contacts
• Facility Director: Dr. Marcelo Jacobs-Lorena School of Public Health Rm E4632 Tel: 443-287-0839 Email: [email protected]
• Facility Manager: Mr. Christopher Kizito School of Public Health Rm W4008 Tel: 443-287-0789 Email: [email protected]
http://www.parasitecore.org/
Facility Director: George Dimopoulos, PhD, MBA
Facility Co-Manager: Godfree Mlambo, PhD [email protected]
Facility Co-Manager: Abhai K. Tripathi, PhD
Parasite Core Facility Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Room W4212 Baltimore, Maryland 21205 Telephone: 410-502-7744 fax: 410-955-0105
Parasite Core Facility
Parasite Core Facility
-TISSUE/CELL/PARASITE CULTURE ROOM W4214 -OFFICE AND MOLECULAR LAB ON 5TH FLOOR, W5315
Location
Major Core Services… P. falciparum Parasite Cultures Asexual Stage (1 week prep time) Gametocyte Stage (3 week prep time)
Mosquito Stage Parasites P. falciparum sporozoites (6 weeks prep time) P. berghei and yoelii sporozoites (4 weeks prep time)
Drug Sensitivity Assays in vitro antimalarial assays (P. falciparum) in vivo antimalarial assays (rodent model)
Training Malaria culture techniques Membrane feeding assay Safe technique for infected mosquito handling
Rings Stage
Trophozoites and Schizonts
Gametocytes
Sporozoites
Parasite Core Facility
Custom Services and Collaboration Opportunities
• Generation of Transgenic parasite lines
• Transmission blocking assays
• IFA (Mosquito stages)
Antimalarial Assays
• Blood schizontocidal assay
• P. falciparum gametocytocidal assays Viaflo Liquid handling system
• In vivo drug efficacy assays
Parasite Core Facility
Genomic Analysis and Sequencing Core Facility
Genomic Analysis and Sequencing Core Facility Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Room E4208 Baltimore, Maryland 21205 Telephone: 443-287-5967 fax: 410-955-0105
Facility Director: Andrew Pekosz, PhD
Email: [email protected]
Facility Manager:
Anne Jedlicka, MS Email: [email protected]
Amanda Dziedzic
Email: [email protected]
Core Services
•Microarray experiments (Affymetrix, Agilent, Custom)
•Next Generation Sequencing (Illumina, Roche 454)
•Genotyping studies (Affymetrix SNP, TaqMan allelic discrimination)
•Real-Time PCR assays (TaqMan, PCRarray)
•DNA and RNA purification and Quality Assessment
•Detailed Data Analysis (microarray and genotyping)
•Consultation on experimental design, implementation, and/or analysis
•Protocol adaptation and development
•Instrument and Applications training (qPCR, imagers, etc)
Next Generation Sequencing • Instruments
– Roche 454 GS FLX+ and GS Junior – Illumina MiSeq (JHMI Biological Chemistry Core) – Illumina HiSeq (JHMI High Throughput Seq Core)
• Applications
– de novo Genome Sequencing (viruses, bacteria, fungi, parasites…) – Targeted Resequencing (amplicon, Sequence Capture) – Metagenomics (microbiome, mycobiome) – Transcriptome Analysis – Gene regulation (CHIP-seq, etc) – miRNA
• Samples
– Genomic DNA – PCR products – RNA, cDNA – Aptamers
Imaging and Microscopy Resource Facility
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http://jhmmi.jhsph.edu/department/microscope1/FrameForm.cfm
Facility Director: Isabelle Coppens, PhD
Email: [email protected]
For Deconvolution/TIRF Microscope: Anne Hamacher-Brady, PhD
Email: [email protected]
Imaging and Microscopy Resource Facility Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Rooms E2214 and E2210 Baltimore, Maryland 21205 Telephone: 443-287-1589 fax: 410-955-0105
Microscopy Facility Services
The Facility contains 5 microscopes (free use):
- Nikon Eclipse E800 - Nikon TE200 - Nikon Eclipse90i - Zeiss AxioImager M2 - DeltaVision Elite New Users must pass a questionnaire before using any microscopes and register each time. Sign up for questionnaire at http://jhmmi.jhsph.edu/department/microscope1/FrameForm.cfm Contact Leonid Shats [email protected] to administer the questionnaire
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Door
Nikon E800 (upright)
NikonTE200 (inverted)
Nikon 90i (upright)
Zeiss AxioImager M2 (upright)
E2214
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slow capture rate of pictures (0.5 frame/sec) that can be replayed as a movie to document moving micro-organisms (1- to 10-second-window)
capable of taking optical sections with multiple color staining but manually
- Inverted microscope (Nikon TE200) observation of live cells
- Upright microscope (Nikon E800) observation of fixed and live specimens
- Upright microscope (Nikon 90i)
.equipped with a video camera capable of documenting dynamic processes at 15 frames/sec and outputting to a computer (cropping areas of interest) .purchased with the software Volocity to explore the captured picture in 3-D and 4-D (confocal quality) .has an automated system with an internal Z-motor and motorized filter turret
observation of fixed specimens
- Upright microscope (Zeiss AxioImager M2) observation of fixed specimens
Same properties as the Nikon90i except 16.2 frames/sec (higher resolution)
E2214
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DeltaVision Elite Deconvolution/TIRF microscope system (Installed: 6/16/2016) Wide-field, fluorescence 3D deconvolution (image restoration) system, with a solid state illumination system and 488nm and 561nm laser lines. Deconvolution is an algorithm uses the point spread function (diffraction pattern) to deblur and remap out-of-focus fluorescent light, improving image resolution and contrast. Long-term live cell imaging experiments possible with incubation system with temperature control and an Ultimate Focus laser that monitors the position of the stage to eliminate z-drift during time-lapse studies. Further, precision stage allows continuous monitoring of multiple fields of view over extended periods of time. Advanced applications : TIRF (total internal reflection microscopy), a technique used to image samples within ~100-200nm of the coverslip surface, useful for cell surface, single molecule imaging (e.g. receptor mediated endocytosis). Photoactivation (PA), Fluorescent Recovery After Photobleaching (FRAP), and Fluorescent Loss in Photobleaching (FLIP), for investigating intracellular dynamics, such as the kinetics of protein diffusion and organelle interactions
E2210
The Becton Dickinson Immune Function Laboratory and Cell Sorting Core
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http://jhmmi.jhsph.edu/FlowCytometry.cfm
Facility Co-Directors: Jay Bream, Ph.D.
Email: [email protected]
Joe Margolick, M.D., Ph.D. Email: [email protected]
Facility Manager: Tricia Nilles
Email: [email protected]
BDIFL and Cell Sorting Core Johns Hopkins Bloomberg School of Public Health 615 N. Wolfe Street, Room E1200 Baltimore, Maryland 21205 Telephone: 410-502-9290
BDIFL Services Basic to advanced training in flow cytometry and related techniques (study
design, fluorochrome selection, instrument setup, data analysis and interpretation).
• New Users must first register (online) • Reserve time on any instrument or workstation (except sorters) • Instruments can be used unassisted or with the help of our friendly staff (assisted)
• Available Equipment:
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BD LSR II BD FACSCalibur amnis imageStream
Flow Cytometers
Cell Sorting Facility Services
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Beckman Coulter MoFlo BD FACSAria Cell Sorter Beckman Coulter XDP
• Contact Dr. Hao Zhang (cell sorting manager) with inquires and to schedule sorting appointments. Email: [email protected]
• Mammalian, non-mammalian, prokaryotic
• Available Equipment
Cell Sorting Flow Cytometers
• Additional Flow Core Equipment/Services
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MSD SECTOR Imager 2400 Luminex MAGPIX
2 Workstations
BioRad QX200
Digital Droplet PCR Soluble Biomarker Analysis
Data Analysis
CTL ImmunoSpot ELISpot
Travel Funds
• Matching PI funds up to $600 per academic year • For JHMRI Pre- and Post-docs to attend a course or a conference
to present a poster or give a talk. • PI approval required before submitting request to Trish Ward.
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MMI Travel Funds • 1st and 2nd year MMI PhD students are eligible for $750 per academic year • Submit requests to Thom Hitzelberger
JHMRI Matching Travel funds
• Global Health Established Field Placement Awards http://www.hopkinsglobalhealth.org/
JH Center for Global Health Travel Funds
JHMRI Pre- and Post-doctoral Fellowships • Maximum two years support for malaria research • Eligibility:
- Currently in JHMRI laboratory - Pre-docs must be PhD candidate, completed all coursework, rotations & departmental/school examinations including oral exam
• Letter of Intent to submit due November 1; Application due December 1
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MMI & JHBSPH Funding Opportunities • Visit http://www.jhsph.edu/offices-and-services/funding-opportunities/
• Contact Gail O’Connor
JHMRI Pilot Grants for Faculty
• Development of new malaria ideas which lead to future external funding
• Maximum support $150,000 over 2 years
• Pre-applications accepted on May 1st
• Full applications will only be accepted by invitation.
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JHMRI Conferences & Seminars • Fall Symposium in Rockville, Maryland
• World Malaria Day Symposium
• Vector Encounter • Malaria Friday Seminars (external speakers and MRI trainees present )
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MMI Events & Seminars • Monday Research Forum
Students present research Sept - May; Post-docs present June - Aug
• Thursday MMI/ID Lecture Series
• Departmental Retreat (Opportunity for trainees to present their research)
Tropical Medicine Dinner Club (meet experts in tropical medicine)
Points of Contact Items related to Dr. Agre, Pilot Grants,
Fellowships, and Travel Funds: Trish Ward, [email protected]
Room E5143, 443-287-8745
Seminars, Conferences, Macha/ICEMR items, Website, Listserve:
Genevieve Williams, [email protected] Room E5141, 410-614-4883
Academic questions: Gail O’Connor, [email protected]
Room E5008, 410-614-4232
Reimbursements, Copier/Printers, Poster Printing:
Thom Hitzelberger, [email protected] Room E5004, 443-287-5148
Room Access and Lab Equipment Orientation, Training, Maintenance:
Leonid Shats, [email protected] Room E1305 (restricted access), 410-502-0510 Human Resources questions, Badges,
Payroll, Benefits: Lawanda Lewis, [email protected] Room E5003, x 443-287-4775
Public Health Informationist, PubMed and
Research Assistance: Peggy Gross, [email protected] Tues & Wed 10:30am - 3pm or by appt
Room E5640, 410-502-7574
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Information Resources MMI Website: http://www.jhsph.edu/departments/w-harry-feinstone-department-of-molecular-microbiology-and-immunology/ MMI Internal Website: http://jhmmi.jhsph.edu New MMI Intranet Portal: https://my.jhsph.edu/sites/MMI/default.aspx (Log-in with JHSPH ID) JHMRI Public Website: http://malaria.jhsph.edu/ Upcoming JHMRI Intranet Portal: https://my.jhsph.edu/sites/MMI/JHMRI/default.aspx Bulletin Board located opposite the MMI Administration Office (E5132)
Student Group
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Contact: Zachary D. Stolp, M.S.
Molecular Microbiology and Immunology Ph.D. Candidate
MMI Student Group President [email protected]
(408) 398 6303
MMI/JHMRI Post-doc Organization
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Contacts: [email protected] Sarah Short, Ph.D. Dimopoulos lab Email: [email protected]
Joel Vega-Rodríguez, Ph.D. Jacobs Lorena lab Email: [email protected]
Melanie Shears, Ph.D. Sinnis lab Email: [email protected]
Post-doc organization
• JHMRI Postdocs from all departments are welcome! • Informal monthly lunch meetings with MMI and MRI post-docs to
promote camaraderie within the department – Able to present results, troubleshoot experiments, discuss events in the
department and plan social gatherings – 3rd Tuesday of every month
• Writing Accountability Group – Weekly meet-up to set and meet writing goals – Contact: Deena Blumenkrantz ([email protected])
• MMI Post-doc Summer Seminar Series – Weekly seminar series for post-docs to present their work
• MMI Post-doc happy hours - Regular happy hours to socialize and meet fellow postdocs. • School of Public Health Postdoc Association
– For all postdocs in SPH – SPH Director of Postdoctoral Training: Val Culotta – Contact: Julia Raifman ([email protected]) or Alfredo Guerra
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