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: scbailey@jhsph.edu

Sean Prigge, PhD

Email: sprigge@jhsph.edu

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: tshields@jhu.edu

Facility Co-Director

Frank Curriero, PhD Department of Epidemiology

Email: fcurriero@jhu.edu

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: ljacob13@jhu.edu

• Facility Manager: Mr. Christopher Kizito School of Public Health Rm W4008 Tel: 443-287-0789 Email: ckizito1@jhu.edu

http://www.parasitecore.org/

Facility Director: George Dimopoulos, PhD, MBA

gdimopo1@jhu.edu

Facility Co-Manager: Godfree Mlambo, PhD gmlambo1@jhu.edu

Facility Co-Manager: Abhai K. Tripathi, PhD

atripat2@jhu.edu

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: apekosz1@jhu.edu

Facility Manager:

Anne Jedlicka, MS Email: ajedlic1@jhu.edu

Amanda Dziedzic

Email: adziedz1@jhu.edu

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: icoppen1@jhu.edu

For Deconvolution/TIRF Microscope: Anne Hamacher-Brady, PhD

Email: abrady9@jhu.edu

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 lshats1@jhu.edu 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: jbream1@jhu.edu

Joe Margolick, M.D., Ph.D. Email: jmargol1@jhu.edu

Facility Manager: Tricia Nilles

Email: tnilles1@jhu.edu

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: haozhang@jhu.edu

• 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, trish.ward@jhu.edu

Room E5143, 443-287-8745

Seminars, Conferences, Macha/ICEMR items, Website, Listserve:

Genevieve Williams, genevieve.williams@jhu.edu Room E5141, 410-614-4883

Academic questions: Gail O’Connor, gail@jhu.edu

Room E5008, 410-614-4232

Reimbursements, Copier/Printers, Poster Printing:

Thom Hitzelberger, thitzel1@jhu.edu Room E5004, 443-287-5148

Room Access and Lab Equipment Orientation, Training, Maintenance:

Leonid Shats, lshats1@jhu.edu Room E1305 (restricted access), 410-502-0510 Human Resources questions, Badges,

Payroll, Benefits: Lawanda Lewis, llewis36@jhu.edu Room E5003, x 443-287-4775

Public Health Informationist, PubMed and

Research Assistance: Peggy Gross, peggy.gross@jhmi.edu 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 zstolp1@jhmi.edu

(408) 398 6303

MMI/JHMRI Post-doc Organization

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Contacts: mmi.postdoc@gmail.com Sarah Short, Ph.D. Dimopoulos lab Email: sshort7@jhu.edu

Joel Vega-Rodríguez, Ph.D. Jacobs Lorena lab Email: jvegaro1@jhu.edu

Melanie Shears, Ph.D. Sinnis lab Email: mshears2@jhu.edu

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 (dblumen9@jhu.edu)

• 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 (jraifman@jhu.edu) or Alfredo Guerra

(aguerra2@jhu.edu)

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