Johns Hopkins University



Note: This document should be tailored for specific RFA submissionsFACILITIES AND RESOURCES21793205080000Johns Hopkins UniversityJHU is one of the world’s leading academic institutions. Health-related research is a particular strength across the institution with annual research funding of $1.4B from the National Institutes of Health, private foundations, and industry collaborations. Multiple Schools of the University are active in clinical and translational (C&T) health-related research, which provides a dynamic environment that fosters ground-breaking discoveries and unparalleled training for the next generation of C&T investigators. This section first describes each of the six JHU Schools that are most engaged in C&T research, followed by a description of a sampling of the key multidisciplinary Centers and Institutes which play a critical role in the C&T research, drawing on faculty and resources from multiple schools across the university to create a synergistic environment for discovery.The Departments of Medicine and PediatricsLed by Dr. Mark Anderson, the Department of Medicine has over 600 members of full-time faculty and 300 fellows. The department strives to improve the health of the community and the world by setting the standard of excellence in medical education, research, and clinical care. The Department of Pediatrics, led by Dr. George Dover, has 135 full-time faculty, over 70 fellows, and 65 house officers. The Department of Pediatrics is committed to studying the effects of the environment on children’s health and developing prevention opportunities. The mission of the department is to improve the health of children, adolescents, and families in our local community and beyond through leadership in clinical care, scholarship, education and advocacy. Both departments foster the spirit of inter and intra-departmental collaboration. The institution is home to both an adult AIDS Clinical Trials Group (ACTG) and pediatric International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) network. There are several studies and protocols in HIV-infected patients and youth approved by the Institutional Review Board.Division of Infectious Diseases, Department of Medicine The Division of Infectious Diseases, Department of Medicine (Chief - Dr. David Thomas), with more than 50 faculty members, 15 clinical fellows, and greater than 25 postdoctoral trainees and other key personnel, is one of the largest members of the Department of Medicine within the Johns Hopkins University School of Medicine. The division has several research groups that focus on HIV and its complications including viral hepatitis, sexually transmitted infections (STIs), and metabolic complications. Comprehensive and longitudinal multidisciplinary HIV care at Johns Hopkins is centered at the Moore Clinic and the inpatient ward, the Polk Unit. In addition, key partners provide additional on-site subspecialty expertise in psychiatry, neurology, pharmacology, gynecology, chronic hepatitis, endocrinology, oncology and other disciplines where HIV-infected patients have unique needs. Clinicians not only provide outstanding medical care, but also extend their reach through the impact of hundreds of biomedical research publications documenting their best medical practices and research findings. Likewise, the Johns Hopkins Center for Global Health, is a nexus for all of the Institution’s international health efforts and provides special opportunities for training and research. There are several opportunities for collaboration and discussion at the several regular divisional conferences (e.g., grand rounds, research conferences, journal club) and research group specific meetings.Division of Infectious Diseases, Department of Pediatrics The Division of Infectious Diseases, Department of Pediatrics (Chief - Dr. Kwang Sik Kim) is based at the Johns Hopkins Hospital. The divisional faculty have a long tradition of NIH-sponsored research. The Division has a strong history of nurturing young investigators and providing them with the resources necessary to develop into independent investigators of international reputation. In the last 12 months, the Division has generated over $3.9 million in direct cost and Division members have over 100 articles in peer-reviewed journals and book chapters on a variety of infectious diseases issues from both clinical and laboratory investigations. The Division also has 9 associated infectious disease-trained pediatricians who are appointed primarily in the Division of General Pediatrics, the Department of International Health or the Stanley Neurovirology Laboratory. Clinical and basic science research activities of the division include: 1) viral pathogenesis, including HIV; 2) bacterial pathogenesis; 3) vaccine development and evaluation; 4) promotion of the judicious use of antimicrobials; 5) epidemiology of vaccine-preventable diseases; 6) epidemiology and prevention of nosocomial infections; and 7) epidemiology and therapy of pediatric and adolescent HIV infection. The Division provides several forums for scientific communication including monthly journal clubs, monthly research in progress conferences, and weekly clinical conferences. Dr. Allison Agwu regularly attends and presents at these conferences. Johns Hopkins Center for Clinical Global Health Education Research (CCGHE) The Johns Hopkins Center for Clinical Global Health Education (CCGHE) is a center of excellence supporting clinical care, clinical research, and research training in resource-limited settings that complements and builds upon the extensive ongoing international, collaborative research and training programs at the Johns Hopkins School of Medicine and the Johns Hopkins Bloomberg School of Public Health. The Center has a large Indo-US clinical research program where clinical trials and observational cohorts on HIV and TB are conducted in Pune, Chennai, Mumbai and other sites in India. The Center also uses innovative technology including telemedicine and e-learning to bring the expertise of Johns Hopkins faculty, from both laboratory and clinic, to the world’s neediest countries and people. Overseas Faculty, Dr. Mave Dr. Mave has private offices in Lloyd’s chambers, Pune, India. The office space approximately encompasses 600 sq. ft. area and has access to 1500 sq. ft. conference room. The office has photocopier, facsimile machine and scanner (leased) and computers. Dr. Mave has access to internet facility; videoconferencing facility and ISDN back up. Office and Computers, Dr. Gupta Office and Computers: Dr. Gupta has a private office on the 5th floor of the Phipps Building located in the CCGHE. The CCGHE space encompasses approximately 2100 square feet with private offices and shared office space. Dr. Gupta has access to a HP Laser Jet combination photocopier, facsimile machine and scanner in the administrative area. Dr. Gupta has a Pentium processor Dell computer systems with ethernet, 2 monitors, HP Laserjet 2420 printer, and appropriate software. The PC is running Windows 2010 and is connected to the University’s local area network (LAN) and can access the school’s UNIX server by TCP/IP protocol. This provides software compatibility and access to e-mail both internally and externally. In addition, Dr. Gupta has a laptop with a Pentium processor and Windows supported by the JHU SOM’s network service. Conferencing Capabilities: The CCGHE office is equipped with hardware and computer software to conduct GoToMeeting? and Skype? conference calling with international partners to reduce costs while maintaining active and frequent communication. The CCGHE also has a conference service to handle multi-point calls for those partners without internet and Skype? capability. Videoconferencing and Multimedia: They have access to a conference meeting room and a fully-equipped, state-of-the art Polycom video conference studio located on the 5th floor of the Phipps building. These rooms are capable of both videoconferencing and multimedia capture and online streaming of training content and support of clinical trial and research training meetings. Drug Development UnitThe Drug Development Unit (DDU) provides clinical research services and support to the faculty of the School of Medicine and to pharmaceutical sponsors. A wide range of services are available, from protocol design and clinical and laboratory support and data analysis, to administrative services including clinical trial agreement negotiation as well as IND and project management.The DDU provides comprehensive clinical research support services with experienced faculty and staff that include:Faculty with decades-long experience in the design and conduct of clinical research, primarily phase I and phase IIStaff engaged in training and educating clinical research coordinators locally, nationally and internationallyAn experienced research team with wide collaborations among the medical specialties at the Johns Hopkins School of MedicineA history of diverse partnerships including numerous pharmaceutical sponsors, fellow academic medical centers, the National Institutes of Health, the Centers for Disease Control, the Food and Drug Administration, and private foundationsAll studies are coordinated by clinical research nurses or individuals with masters-level degreesThe Drug Development Unit is organized to provide comprehensive clinical research services to the faculty in the School of Medicine and pharmaceutical sponsors. The DDU’s primary expertise is in translational research, Phase I, and Phase II clinical studies, but includes all clinical phases of drug development.Established in 1983, the DDU has conducted over 200 trials and clinical studies and has worked with over 30 sponsors, including commercial and federal entities. It has an established record of productive collaborations with numerous Departments within the School of Medicine.The DDU integrates services with the Clinical Pharmacology Analytical Lab (CPAL) to provide a complete range of services for the support of clinical studies of drugs. Investigators and sponsors may select from a range of support services from development of concept proposals to manuscript preparation.NIH Clinical and Translational Science AwardThis Program supports the Institute for Clinical and Translational Research (ICTR) at Johns Hopkins. Dr. Flexner, PD/PI, is the Chief Scientific Officer of the ICTR. This program supports and integrates many of the existing resources for clinical and translational investigation at Johns Hopkins, including the GTPCI program and the NIH-sponsored Clinical Research Units. It also supports important infrastructure for clinical research. This includes a Drug Development Core that provides: 1) medicinal chemistry expertise for design and synthesis of chemical reagents (small molecules, modified peptides and bioconjugates), for preclinical toxicology and early human studies to identify and optimize lead compounds; 2) Good Manufacturing Practices and near-GMP synthesis; and 3) expertise in pharmacologic/biologic endpoints, and in the design and analysis of preclinical and early clinical studies through proof-of-concept.The Johns Hopkins University School of NursingThe Johns Hopkins Hospital and the nursing training program both opened in 1889. In the ensuing decades, founders M. Adelaide Nutting, Isabel Hampton Robb, and Lavinia Dock established what would become the national model for nursing education. In 1983, after turning out generations of exceptional nurses, the School of Nursing was established as the eighth division of the Johns Hopkins University— and opened its doors to students in 1984. In 1998, the School moved to a new state-of-the-art education and research building on the East Baltimore campus, the Anne M. Pinkard Building.In March 2017, the France-Merrick Foundation of Baltimore, Md. has donated $2 million to the Johns Hopkins University School of Nursing to fund the expansion of the Pinkard building. The expansion will add more than 41,000 sq. ft of new space and five additional stories to be used for collaborative spaces, small group study rooms and expanded PhD and Post- doctorate work and research space. Today, under the leadership of Dean Patricia M. Davidson, PhD, MEd, RN, FAAN, the School of Nursing continues to redefine nursing education through a unique combination of academic rigor, extraordinary nursing scholarship, andunparalleled opportunities for nursing graduates.The Johns Hopkins University School of Nursing (JHSON) has 80 Full-time and 130 Part-time faculty with six endowed chairs and 146 joint appointments. The faculty obtained $35.9 million in total sponsored research project funding in Federal fiscal year 2016 and the school ranked 1st in research funding from NIH nationally. In addition, the JHSON is ranked among the top nursing PhD programs in the U.S. by the National Research Council with a Center of Excellence in Nursing Education designated in 2010 by the National League for Nursing.The School of Nursing structure is currently six levels and 93,290 square feet. It consolidates the School’s teaching, research and administrative activities. Space is provided for faculty, clerical, research staff and data management personnel. The School contains a 90-seat flexible space classroom, two adjoining 63- seat classrooms; two 110-seat lecture halls (one with capability for distance learning); three 12-bed practice laboratories (one with capability for distance learning); research space with state-of-the-art laboratories; one 40-seat computer classroom; one 45-seat classroom (with capability for distance learning); two 18-seat seminar rooms; two 15-seat group study rooms; three 16-seat computer/ interactive video labs; and a 230-seat auditorium. The entire building is equipped with MediaSite webcast technology.The JHSON maintains a local area network consisting of 29 physical and 15 virtual Microsoft (MS) Windows servers and approximately 500 MS Windows XP workstations, five MS Windows Vista systems and four Apple Macintosh systems. Network peripherals and systems include a tape library device, monochrome and color printers, copier / scanning systems, storage area networks and network attached storage devices. In addition to the network systems and peripherals previously described, the school maintains six computer labs. These labs consist of a 40-seat teaching lab, two 13-seat application labs, a 16 seat Doctoral Lab, another 10-seat application lab on the buildings lower level and final 9-seat application lab in the NIRC. The first floor café area, second floor lab area, third and fifth floor provide wireless network access for notebook and other computing devices.The JHSON Office for Science and Innovation (OSI), formerly known as the Center for Nursing Research, has encouraged leadership for nursing research within the School, University, community and profession, and facilitates excellence in nursing research. Research is coordinated between the Office for Science and Innovation, Office of Finance Administration, and Johns Hopkins University Research Administration as well as Johns Hopkins Medical Institutes. The OSI provides both pre- and post-award services to faculty, students, and staff, e.g., information on funding sources and grant application processes; including consultation on research design and conduct including data management and analysis; advice on faculty development and continuing education in research; dissemination of research and funding information; and resources such as texts and conference rooms. In these ways, the OSI facilitates faculty and student research by offering programs and resources to support the development, submission, conduct and publication of research; and by providing the needed information technology to foster research. The OSI works in collaboration with the School of Nursing department chairs and Center faculty to provide a supportive environment for faculty, students, and staff involved in research. Bloomberg School of Public HealthThe Johns Hopkins Bloomberg School of Public Health (also referred to as The Bloomberg School or JHSPH) is the oldest and largest public health training facility in the world, and a leading international authority on the improvement of health and prevention of disease and disability. The school's mission is improvement of health through discovery, dissemination, and translation of knowledge and the education of a diverse global community of research scientists and public health professionals. Overall, the school has ranked first in public health according to U.S. News and World Report since 1994. The Bloomberg School has 670 full-time and 709 part-time faculty, and 2,243 students from 81 nations. It is home to over 60 Research Centers and Institutes with research ongoing in the U.S. and more than 130 countries worldwide. The School ranks #1 in federal research support from the National Institutes of Health (NIH), receiving nearly 25 percent of all funds distributed among the 40 U.S. schools of public health.In the 1990s, the School recognized the need for additional space to accommodate the increase in faculty size and student enrollment, allow growth to continue, and encourage interdisciplinary collaboration by consolidating into one building faculty who were housed in different locations. Construction, from 1996 to 2004, doubled the size of the Wolfe Street Building, from approximately 357,000 to 759,000 square feet.The William H. Welch Medical Library The William H. Welch Medical Library is the largest medical library outside of the National Library of Medicine in Bethesda. It collects medical and scientific literature in all fields of teaching and research represented at the Institution, contains more than 35,000 bound volumes and 2,300 audiovisual programs, and receives over 3,000 biomedical periodicals, now exclusively electronically. There are a wide range of computer services including institution-wide e-mail, access to the World Wide Web and hundreds of medical journals and books through online institution subscriptions. A remote access system allows proxy access to all Welch Internet-based resources from off campus locations. The library has a computer training center offering a full range of courses in word processing, use of database and spreadsheet software, and use of the internet. JHU provides for unrestricted online access to institutional subscriptions for most scientific journals and periodicals.The Center for Public Health and Human Rights (CPHHR), was founded by Professor Chris Beyrer in April 2004, and is now in its twelfth year of engagement in research, teaching, and advocacy on the interface of public health and human rights. The Center has 4 full time Research Coordinators, a part time Administrative Assistant, and office space in the Bloomberg School of Public Health. The Center currently has affiliated faculty in the Schools of Public Health, Medicine, and Nursing, including some 22 faculty, 3 Post-Doctoral Fellows, and a number of student investigators. The Center is home to the Desmond M. Tutu Professorship in Public Health and Human Rights, now held by the inaugural Professor, Chris Beyrer. The Center has three programs, 2 led by CFAR Faculty: The Program on Key Populations led by Dr. Stefan Baral; The Program on Women’s Health and Rights, led by Michele Decker; and the Program on Health in Conflict, led by Dr. Len Rubenstein. The Research Ethics Consulting Service (RECS)The Research Ethics Consulting Service (RECS), was started by Drs. Kass and Taylor for JHSPH and now is a component of JHU Institute for Clinical Translational Research (ICTR), and as such will be available for all JHU HIV/AIDS Researchers. RECS has a web-based portal, facilitating the request of consults by those either on campus or in remote sites. While the majority of consults through the RECS are one-time encounters regarding ethics issues emerging in the planning, conduct, or analysis of studies, the services provided for CFAR investigators can be more sustained, as needed.The Urban Health Institute (UHI) The Urban Health Institute (UHI) is a collaboration and a vital connection with East Baltimore. The UHI is the starting point for forging true University and community partnerships in health care, education and community planning, with all partners working to change the trajectory for the children, youth and families of East Baltimore. The UHI draws on the expertise of neighborhood residents, educators, philanthropic organizations, elected representatives and community leaders, in addition to the wealth of intellectual resources that Hopkins can offer.Animal: N/AJohns Hopkins University Clinical Research SiteFacility Johns Hopkins Universityright3138900John G. Bartlett Specialty PracticeThe mission of the John G. Bartlett Specialty Practice is to provide outstanding, evidence-based, clinical infectious disease care with access for all. This 23 exam room clinic co-locates services for patients with an array of infectious diseases including infections obtained after transplantation or on medical devices, HIV, hepatitis, general infectious diseases (such as fever of unknown origin, bone infections, lung infections or patients on IV antibiotics) and PrEP (HIV Pre-exposure prophylaxis) treatment and care.The clinic site location provides street-level access to an onsite pharmacy, phlebotomy services, HCV and HIV counseling and testing services, and social services and case management alongside the various multidisciplinary sub-specialists within the clinic for patients living with HIV (gynecology, medication adherence support, mental health, nephrology, neurology, nutrition, primary care, substance abuse counseling and buprenorphine treatment). The clinic also offers liver elastography, pentamidine inhalation and sputum induction room, support groups, a treatment room and access to clinical trials. The clinic is staffed with more than 70 providers, nurses, medical assistants, social workers, peer navigators, Pharm D’s and research staff who assist with patient care. An inpatient service, the Polk Unit, coordinates inpatient care closely with the patient and outpatient clinic for admissions and discharges.Within the HIV Neurosciences Program, we have fully equipped space for research testing. In this space, we are able to perform skin biopsies, CASE IV testing, and nerve conduction velocities with a dedicated Nicolet machine. The patients will also be seen in the inpatient wards of the Johns Hopkins Hospital, which includes a specialized AIDS Unit on Osler 8, one of the inpatient medical floors. Major clinical resources available for the clinical research project include: Outpatient Clinical Care FacilityThis clinical outpatient facility occupies 8000 sq. ft. in the Park Building of the Johns Hopkins Hospital. The facility includes 24 examining rooms that are outfitted both for clinical care and for clinical research, an infusion and treatment room, phlebotomy services, an on-site full-service pharmacy and multipurpose conference room. The facility provides care for over 3000 HIV-infected patients who have over 25,000 visits annually. In addition to 21 faculty-level care providers (most of whom are also clinical investigators), there are 9 nurses, 8 medical assistants and 12 social case workers working on-site who support both clinical care and research. The facility has 9 dedicated offices for clinical research staff and investigators and is linked by direct elevator access to the investigator offices and laboratory facilities on the Johns Hopkins Medical campus. Primary HIV clinical care is provided here for most study participants and on-site subspecialty care is provided for viral hepatitis, transplant services, gynecology, neurology, nephrology, and psychiatry. A clinical HIV registry is maintained by a team of research staff that has sociodemographic, diagnosis, procedure and treatment data that is described in the Clinical Core proposal.NIH-sponsored Clinical Research UnitsSupported for over 50 years by the NIH’s National Center for Research Resources and National Center for Accelerating Translational Sciences (NCATS), the Inpatient and Outpatient CRUs provide core facilities and personnel for promoting excellent and rigorous clinical research. HIV-related research takes place in the Johns Hopkins Hospital Adult Outpatient and Inpatient CRUs, the Pediatric CRU, and the CRU located on the Bayview Medical Campus. Clinical protocols (already approved by our IRBs) undergo further scientific and ethical review by the CRU Protocol Committee prior to approval for support. The CRU facilities are extraordinarily valuable for the research efforts of the CFAR-affiliated faculty and trainees. Dr. Flexner, CFAR Developmental Core Co-Director, is the Program Director for Clinical Research Units. Existing Cohorts at Johns Hopkins University As described in background, multiple cohorts of HIV-infected and at-risk populations are available at JHU. These include the Multicenter AIDS Cohort Study (MACS), a natural history study in gay and bisexual men (PI Joseph Margolick, MD, PhD, NIAID-funded), the AIDS Link to Intravenous Experience (ALIVE), a natural history study in injecting drug users (PIs Shruti Mehta, PhD, and Greg Kirk, MD, NIDA-funded), the Women’s Interagency HIV Study data center (WIHS, Stephen Gange, PhD, PI), and the Johns Hopkins HIV Clinic Cohort (Richard Moore, MD, MHS, PI, NIDA and NIAID funded). We also have access to an existingNINDS-funded cohort, the NEAD study, and to banked material from the Nerve Project (NS44807).Nelson 4This is the inpatient service of the AIDS Care Program and it is administratively within the Division of Infectious Diseases. There are 18 beds with an average census of 15-18 with overflow patients housed on other wards within the Johns Hopkins Hospital. Patients admitted for evaluation and management of neurological disorders, and participants in our studies may be recruited from this resource for our proposed studies.Public ClinicsThe Baltimore City Health Department contracts with JHU to provide clinical services in a number of public clinics that also provide a research platform. These include the city HIV Clinic (Kathleen Page, MD, Director), Sexually Transmitted Diseases Clinics (2) (Khalil Ganem, MD, Director), Tuberculosis Clinic (Maunank Shah, MD, PhD, Director), and Hepatitis Clinic (Sean Falude, MD, Director).Johns Hopkins Pediatric, Adolescent and Young Adult HIV Clinical Care SitesJohns Hopkins University is located in Baltimore, a city with a significant burden of HIV infection. Individuals between the ages of 12 and 25, the relevant population, comprise a growing proportion of incident infections and largely receive HIV care from the Pediatric Adolescent HIV/AIDS program (PAHAP) and the Accessing Care Early (ACE) Clinic where Dr. Allison Agwu is an active clinician and leader in both programs. The Pediatric and Adolescent HIV/AIDS Program (PAHAP)Founded in 1985 by Dr. Nancy Hutton, and led by Dr. Allison Agwu since 2016, PAHAP (clinic is called the Intensive Primary Care (IPC) Clinic) provides intensive services and support using the primary health care and case management models of service provision. A private, non-profit, comprehensive, and integrated HIV services program, it is composed of an interdisciplinary health team providing a wide array of on-site clinical services for pediatric, adolescent, and young adult patients, many of whom are from vulnerable and disenfranchised populations. The program is fully funded by Ryan White funding is embedded in the Harriet Lane Clinic (described below). A key part of the program’s mission is access to cutting edge research and clinical trials and indeed PAHAP has supported the research efforts of clinical investigators through its core role in IMPAACT, ATN, and multiple investigator-initiated research endeavors. The program provides primary HIV care, medical and non-medical case management, risk reduction including contraception and STI treatment and prevention through adherence promotion, community outreach, dental care, as well as referral/consultation services for providers in the community. Over the past 6 months 600 patient care contacts were completed in PAHAP! Almost 1000 ambulatory care visits were completed in PAHAP. PAHAP also serves as the site where the health department and multiple partnering agencies refer newly diagnosed youth and young adults, refugee and immigrant, and adopted children. As a result, the clinic continues to experience growth in the numbers of infected primarily YMSM (1-2 per month), many between the ages of 8 and 25. In addition to the medical staff (Drs. Lana Lee, Errol Fields, Renata Arrington-Sanders, David Griffith, and Allison Agwu), care is also provided by a pediatric nurse practitioner (Mary Ann Knott-Grasso), a nurse case managers, two social workers, a part-time psychiatrist and psychiatric nurse practitioner, and a non-medical case manager. PAHAP works closely with the adult HIV program referral system taking advantage of a multitude of specialty clinical programs for HIV patients in neurology, oncology, hepatology, ophthalmology, obstetrics/gynecology, endocrinology, nephrology, psychiatry, and substance abuse—all which are based in the adult JHU HIV clinic, where our ACE clinic (see below) is also located. Access Care Early (ACE) ClinicIn 2012, in response to rising awareness of high rates of attrition among HIV-infected youth during transition from pediatric/adolescent to adult care, the ACE clinic was created within JHU’s Moore Clinic (JHMC) where HIV-infected adults are seen. ACE provides a comprehensive, youth-friendly, integrated team approach to HIV care for the increasingly heterogeneous population of young persons aged 18-30 years who are either transitioning from pediatric to adult care or newly engaging into adult HIV care. The clinical team, led by Dr. Agwu (clinic director), includes internal medicine-pediatrics infectious disease providers (Drs. Agwu and Griffith), adolescent subspecialty-trained providers (Drs. Renata Arrington-Sanders and Lana Lee), nurse practitioner (Michael Sanchez), mental health social worker (Nancy Sybert, MSW), social worker, nurse (Stephanie Thomas, BSN, RN, ACRN), and outreach specialist/patient liaison and navigator. All providers also see patients in PAHAP, providing a continuum of care. ACE patients include youth/young adults transitioning from PAHAP or other pediatric HIV programs, perinatally and non-perinatally acquired HIV youth/young adults newly engaging into care at JHMC, including those that are recently diagnosed, and youth receiving care at the JHMC with nonadherence to appointments or ART are also referred to ACE for management. One hundred sixty patients are currently enrolled, a growth of 50% annually since it began. The clinic receives an average of 3-4 new patient referrals each month. Harriet Lane Clinic (HLC) The HLC of the Johns Hopkins Hospital is the main outpatient clinic for the Department of Pediatrics and serves as a major clinical research site for the faculty and fellows in the Division of General Pediatrics and Adolescent Medicine and their collaborators, and houses the PAHAP program where most IMPAACT study participants have been recruited and seen. HLC has served children and their families in East Baltimore since 1912. HLC serves as the medical home and provides comprehensive health care services for approximately 8,500 patients with about 17,000 annual visits. This provides a large pool of patients from which to recruit HIV-negative patients for studies of other infectious diseases (e.g., vaccine studies). It is the principal Johns Hopkins training site in pediatric and adolescent primary care for physicians, social workers, and other pediatric health professionals. The PAHAP and Adolescent Primary Care clinics are incorporated into the HLC, permitting the integration of HIV specialty care and support services with age-appropriate routine health care to our patients from birth to 24 years. The HLC includes two waiting areas (a child-friendly waiting area and an adolescent waiting area), a medical records room and 36 exam rooms (2/3 of rooms for well care and follow-up visits and 1/3 for acute/sick care). All exam rooms are equipped for gynecologic exams. General pediatric and adolescent specialty care is provided by a team of about 30 faculty and fellow preceptors, 8 pediatric residents (providing continuity and adolescent care), and 3 nurse practitioners and a talented staff that includes LPN/RN nurses, social workers, and 10 administrative and support staff members. HLC patients have a high rate of medical and social problems, including obesity in 40% of children over three and identifiable drug or alcohol problem in 20% of families. Other services provided within HLC include developmental evaluations by a developmental pediatrician, lactations specialist consultations, pediatric nutritionist evaluations, dental services, and sexual risk-reduction counseling. An active community advisory board of parents and adolescent patients provide critical feedback on an ongoing basis to improve the comprehensiveness and quality of care in the HLC.JHU Adolescent Medicine ClinicThe Johns Hopkins University School of Medicine Adolescent Medicine Clinic provides comprehensive primary care to 2500 individuals between the ages of 10 and 21 who make approximately 6000 patient visits per year is embedded in the HLC. This outpatient clinic emphasizes a multi-disciplinary team approach to adolescent health problems. The primarily African American patients who attend this clinic reside predominantly in the surrounding East Baltimore area and are burdened disproportionately by exposure to social and economic factors that put them at a high-risk category for developing substance abuse-related problems and STIs including HIV. Patients who attend this clinic have a high prevalence of associated risk factors: (1) abuse and/or neglect, (2) homelessness or truancy, (3) physical or mental handicaps, (4) pregnancy, (5) school dropout, (6) parental abuse of alcohol and other drugs, (7) latchkey children, and (8) economic disadvantage. Many of the adolescents who attend this clinic have similar backgrounds as our HIV-positive patients and are a pool of potential participants for studies of prevention of HIV and other infectious diseases (e.g., PrEP). Dr. Renata Arrington-Sanders, IMPAACT co-Investigator and co-investigator and lead on the community-based protocols for ATN, is a key link to this clinic. Drs. Errol Fields and Maria Trent are also key providers in this clinic, with Dr. Trent heading the adolescent fellowship.Center for Viral Hepatitis ResearchStudy participants will receive HBV care in the previously mentioned John G. Bartlett Specialty Practice, located on the JHH campus with a street entrance at 1717 East Monument Street. This new 24 million dollar, state-of-the art, 16,000 square-foot clinic opened in May 2017 and co-locates much needed services for patients with a range of infectious diseases, including infections obtained after transplantation or from medical devices, HIV and viral hepatitis. In addition to housing various multidisciplinary subspecialists, the facility features a nutritionist, an on-site pharmacy, phlebotomy services and a full complement of social work and case managers. The Viral Hepatitis practice is headed by Dr. Mark Sulkowski and has approximately 80 patient visits each month for HBV care. His program occupies 1200 square feet of office space and dedicated 500 square feet of clinical research space in the John G. Bartlett Specialty Practice. Dr. Sulkowski is fully equipped for clinical research with facilities for specimen processing including biosafety laminar air flow hood, centrifuges, - 80°C and – 20°C freezers, and specialty pharmacy refrigerator with temperature monitoring, and 10 computer workstations. The Bartlett practice has an in-clinic EchoSens Touch 502 fibroscan machine that is staffed during the full clinic day by experienced fibroscan technicians. The clinical-quality results are interpreted by a staff physician. The Viral Hepatitis Clinical Research team is comprised of 11 experienced research professionals. The 11 faculty and staff members include a research program manager (1); research clinicians (5), clinical nurse research coordinators (3), and research assistants (2). More than 1000 patients with hepatitis C or B infections have been evaluated by the Research team and many have been enrolled onto research protocols. The team has conducted Phase I, II, III, and IV studies, including investigator initiated studies. The team has had multiple independent audits that verify its handling of confidential patient records and high attention to detail in managing trials. The team works closely with both the inpatient and outpatient Johns Hopkins Clinical Research Units, which are funded by the NIH to promote clinical research. This collaboration makes it possible to conduct investigator initiated studies and to carefully monitor patients in sensitive clinical trials. Security and HIPAA compliance The JHPCE (Joint High Performance Computing Exchange) system can only be accessed via the secure shell (ssh) protocol. Either two-factor authentication or public/private key-pair authentication is required. Access logs of user logins are maintained and can be examined retrospectively. Multiple failed login attempts result in having the offending IP address blocked. We have a strict policy of one-person/one-user. No sharing of user accounts is permitted. Violations of this policy can result in a user being banned from the system. Either ACLs or unix user and group permissions are used to enforce data access policies (depending on the storage system). Access permissions are determined by project PIs in consultation with the JHPCE staff. Office All investigators and administrators have their own office space entirely sufficient to accomplish the specific aims of the project. Additionally, all investigators have access to meeting space as needed via centrally scheduled conference rooms.Mobile Medical UnitThe SPOT is a 40 ft. 1999 Freightliner mobile medical unit. The unit includes 2 patient exam rooms, a patient waiting space, a laboratory area, and a bathroom. The unit is equipped with two computers linked to the electronic medical system, a small refrigerator for sample, medication and vaccine storage, secure cabinets, two examination chairs (one in each patient room), a phlebotomy chair, a vital sign monitor, and an automated external defibrillator. The unit is powered by an on-board generator, which was replaced in 2014, and has a new motherboard procured in 2016. It has 40,000 miles and a diesel engine. A commercial driver’s license is not required to operate the vehicle.Pharmacy - Johns Hopkins UniversityThe Investigational Drug Service (IDS) Pharmacy has outstanding, high quality infrastructure, storage capacity, inventory control, security, and temperature monitoring systems. The JHU CRS study medication will be stored and dispensed from the IDS Pharmacy. The IDS Pharmacy is a limited access, designated pharmacy satellite of the Johns Hopkins Hospital Department of Pharmacy and is located in the Johns Hopkins Hospital. The 975 square foot pharmacy includes office space, room temperature drug storage with rolling shelves, a dispensing area, a quarantine drug storage area, a sterile product preparation area with a barrier isolator, and a patient waiting area. Access to the area is limited to the IDS pharmacy staff and pharmacy administrators by card key. Study medication is stored on rolling shelves, separated by study and study product at USP room temperature in the IDS Pharmacy. Study medication with more stringent ambient temperature requirements are stored in a large cooling incubator in the IDS Pharmacy. Ambient storage conditions are monitored with temperature and humidity data loggers, which are downloaded and reviewed weekly. In addition, real time room temperature monitoring is recorded daily during the work week using a min/max thermometer. A Sensaphone? is programmed to call the IDS pharmacist on call in the event the room temperature goes out of range. The IDS has six refrigerators, one -20°C freezer and one -80°C freezer. Cold storage is monitored by a hospital-wide central temperature monitoring system. In addition, the IDS monitors each unit with a data logger that records every 5 minutes and the temperature is recorded daily during the work week using a min/max thermometer. The hospital central monitoring service contacts the IDS pharmacist on call if the temperature goes out of range. Each refrigerator and freezer is equipped with an audible alarm that sounds if the temperature goes out of range. All cold storage units are supported by the hospital back-up generator for emergency power. Studies requiring dosing outside of standard working hours are managed by an inpatient pharmacy satellite, eliminating the need for 24-hour coverage in the IDS. The PoR creates instructions and study product accountability logs for use by the satellite pharmacy and provides an in-service to the satellite pharmacists. In the satellite pharmacies, study products are stored separately from routine pharmacy stock. Drug storage temperature conditions are continuously monitored in all pharmacy areas.21477772039400The JHU CRS Pharmacy has specialized capabilities available. The IDS Pharmacy has an electronic balance and other equipment necessary for preparing specialized formulations. The IDS Pharmacy also has the equipment necessary for preparing unit and multi-dose blister card packaging. Non-hazardous sterile study products are prepared in the IDS Pharmacy barrier isolator. Hazardous sterile study products are prepared in a biological safety cabinet in a clean room located in the hospital that is designated for the preparation of hazardous products and is USP <797> compliant.Renovation of the IDS is anticipated to be completed by July 2020. This new larger space will include a larger temperature-controlled drug storage room, more refrigerators and freezers, USP <797> and <800> compliant cleanrooms and work space, a private participant counseling room, a separate dispensing and preparation area, and more office and file space. Laboratory - Johns Hopkins UniversityClinical Pharmacology Analytical Laboratory (CPAL) ProgramThe CPAL is located on the 5th floor of the Osler Building within the Johns Hopkins Hospital (600 N. Wolfe St., Baltimore, MD) and on the 6th floor of the Mason F. Lord Building Center Tower within the Johns Hopkins Bayview Medical Center (4940 Eastern Ave., Baltimore, MD). The Johns Hopkins Hospital space consists of 2500 sq. ft. across 6 rooms in Osler and Carnegie Buildings (Osler 500, 506, 520, 523 and 529; Carnegie 532). The laboratory is equipped for the processing and analysis of samples obtained for human studies. The Johns Hopkins Bayview Medical Center space consists of approximately 3500 sq. ft. of open space and is equipped for processing biological samples, as well as the analysis of specimens via liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis. Access to the MFL6 suite is limited to authorized personnel, and entry to the floor occurs via personnel badge identification.Equipment at the Johns Hopkins Hospital, Osler Building include 1 centrifuge; 1 -70°C freezer , 1 explosion proof refrigerator/freezer ; 1 standard refrigerator/freezer unit; a Guava Personal Cell Analysis System; Molecular Devices SpectraMax Plus microtiter plate reader.1- Perkin Elmer inline radioisotope detector ; 1- Perkin Elmer scintillation counter; 3 biosafety cabinets,4 incubators, 3 fume hoods; shaking water baths; 1table top autoclave unit, 2 flammable cabinets (1 vented 1 standalone); 56-hand held pipettes; 1 computer; 2 flammable cabinets. At the Johns Hopkins Bayview Medical Center, Mason F. Lord Center Tower, equipment includes 2 centrifuges; 2 savant speed vacs; 4 -80 ultralow temperature freezers ; 2 -20 degree freezers; cold room (shared space); 8 computers; 2 portable notebooks; 6 LCMS mass spec analyzer systems; 1 HPLC/UPLC analyzer system; 1 passive generator system; 3 fume hoods; 1 biosafety cabinet; 2 portable nitrogen generators; 4- vortexers ; 65-hand held pipettes; 10-vaccum manifolds; 1-heat sealer; 2 flammable cabinets.Analytical methodologies include use of: Wizard II gamma counter, Liquid TriCarb2810 scintillation counter, Guilford spectrophotometer, Guava? EasyCyte Plus System flow cytometer, Kinetic Microplate reader, Nikon Labophot-2 microscope, complete Alliance-controlled HPLC systems (2), Alliance-controlled UPLC system (1), inline fluorescence and radioisotope detectors. Applied Biosystems APl4000 UPLC/MS/MS system (2), Applied Biosystems APl5000 UPLC/MS/MS system (1), and Applied Biosystems API 5500 Qtrap UPLC/MS/MS system (1) and their supporting nitrogen generator and computers occupy a dedicated 300 sq. ft. of climate-controlled lab space. The laboratory has a JANUS? Automated Workstation with 96-tip modular dispense technology to automate high volume drug assay sample preparation. The facilities are approved by the Johns Hopkins University Biosafety Office for work involving cells and fluids from HIV-infected subjects, and are also approved for work with live recombinant vaccinia viruses, herpes simplex viruses, adenovirus, human cytomegalovirus, African trypanosomes and malaria parasites.Immunology Laboratory ProgramDr. Margolick’s lab was established in 1986 in the Johns Hopkins Bloomberg School of Public Health (JHSPH) with support from the SHARE study and has since expanded into a 2500 square foot facility. It has been directed since its inception by Dr. Joseph B. Margolick of the Department of Molecular Microbiology and Immunology, who is also the Principal Investigator of the SHARE study. The laboratory is utilized by many studies and is the primary flow cytometry facility at Johns Hopkins Medical Institutions for work on HIV-infected specimens, as well as other specimens requiring BSL-3 precautions. It is staffed by four full-time research technicians and performs flow cytometric analysis and sorting of cells from biological specimens, especially HIV-positive specimens. The laboratory is CLIA-certified for the measurement of T cell subsets. The majority of the work done in the laboratory is related to clinical and basic research of HIV/AIDS, processing approximately 2500 specimens per year for several HIV/AIDS related clinical studies. The laboratory also collaborates in non-HIV/AIDS related clinical studies, such as stem cell research, chromosome research, basic cell biology, and immunology.There are three flow cytometers in the laboratory. Flow cytometric analysis is conducted primarily on a Becton-Dickinson FACS Canto II, 3-laser, 8-color flow cytometer. This flow cytometer is located in a BSL-2 laboratory. Cell sorting is conducted on two cytometers located in a BSL-3 laboratory: a Beckman Coulter MoFlo XDP 4-laser 13-color cell sorter, and a Beckman Coulter MoFlo 3-laser, 6-color high-speed cell sorter (both MoFlos can sort up to 30,000 cells/sec in routine use). The laboratory also contains instruments and equipment needed to process specimens for flow cytometric analysis, including fluorescent and light microscopes, a variety of refrigerated centrifuges and mixers, water baths, incubators, and five Biological Safety Cabinets. All cytometers and workstations are connected with the JHSPH computer facilities for communications and backup of data, which is done at least daily.The Flow Cytometry laboratory is integrated with the Becton-Dickinson (BD) Immune Function Laboratory, located in an adjacent laboratory in JHSPH, which has three additional flow cytometers: a BD LSR II 3-laser, 16-color flow cytometer, a BD FACS ARIA 3-laser, 9-color cell sorter, and a BD FACS Calibur HTS (high throughput screening, for 96 and 360 well formats) 2-laser, 4-color flow cytometer. Recently, an Amnis ImageStream imaging flow cytometer was acquired and is now in use. Additionally, the combined laboratories have a dual-color ELISpot reader, and automated electrochemiluminescence (Meso Scale Discovery) and Luminex readers which are used for multiplex detection of analytes in a microwell format, including cytokines and chemokines in biological samples.Infectious Diseases Laboratory Unit The Persaud Pediatric Infectious Disease laboratory is located at the Johns Hopkins University East Baltimore campus, on the 11th floor of the Ross Building and occupies approximately 1500 sq. ft. It contains a state-of-the art BSL-3 virus facility that occupies 800 sq. ft. of space and maintains negative air pressure with respect to the outside (maintained by outside contractor, Siemens). Certification of all the biosafety cabinets is performed bi-annually by Johns Hopkins Health, Safety and Environment Department. The BSL-2 laboratories is equipped with a Sorvall Biofuge Stratus refrigerated high-speed centrifuge, three refrigerated desk-top centrifuges, two desk-top centrifuges, one refrigerated microcentrifuge, three microcentrifuges, three water baths, three non-CO2 injected incubators, two dry heat blocks, three thermomixers, three large sinks equipped with deionized water supply and eyewash stations, three -80? freezers, two large -20? freezers, two small -20? freezers, four small refrigerators, one microplate plate reader (ELISA), eight Thermal Cyclers, one Fotodyne gel documentation system, four electrophoresis gel stations, one two Biomeriuex MiniMAG semi-automated nucleic acid isolation instruments, Biorad QX-100 digital droplet PCR instrument, Biophotometer, two clean hoods dedicated to PCR preparation, two clean hood dedicated to DNA preparation, one clean hood dedicated to digital droplet PCR preparation, one clean hood dedicated to RNA preparation, one clean hood dedicated to nested PCR preparation. The BSL-3 containment facility occupies approximately 800 sq. ft. and contains a pass-through autoclave, one large sinks equipped with deionized water supply and eyewash station, individual eyewash station, four biosafety cabinets equipped with HEPA-filtered exhaust system, three microscopes, two microcentrifuges, one refrigerated high-speed centrifuge, one Beckman Allegra high-speed centrifuge, one ultracentrifuge, one water bath, Beckman AcT10 Hematology Analyzer, a large refrigerator, one small refrigerator, a -80? C freezer, a liquid-N2 freezer, four tissue culture incubators, and other small lab equipment.Johns Hopkins Biological Repository (JHBR)Directed by Dr. Homay Farzadegan, the JHBR consists of 2,000 square feet of biosafety level 2 laboratories on the 6th floor of the Johns Hopkins Bloomberg School of Public Health (JHSPH), as well as 6,000 square feet in an offsite facility (3 miles from JHSPH) to house 60 liquid nitrogen vapor phase cryogenic units. These units recently replaced biological specimen storage in -80 degree C and -150 degree C mechanical freezers as part of JHSPH’s “Greening the Lab” initiative. JHBR manages more than two million biological specimens using a robust specimen management system, FreezerworksTM, for freezer inventory, specimen labeling and tracking for the large repository. Additionally, JHBR is certified by the Clinical Laboratory Improvement Amendment (CLIA) to perform HIV-1 viral load RT-PCR, HCV and HBV serological tests, and maintains participation in proficiency programs through College of American Pathology (CAP), American Association of Bioanalysts (AAB), and Virology Quality Assurance Program (VQA) for all expert testing services. Currently, a fully automated platform for DNA and RNA isolation and quantification system is now in place to support the growing number of epigenetic studies.The newly expanded JHBR Repository Core is a state-of-the-art cryogenic storage facility located on Shannon Drive in Baltimore, Maryland (3 miles from JHSPH). Biological specimens are stored in high capacity vapor phase liquid nitrogen cryogenic storage tanks. Currently, 70 cryogenic units, by Taylor Wharton, are maintained with 24-hour, 365-day security and daily temperature monitoring. The capacity of these units ranges from 20,000, 80,000 and 94,000 vials (2 inch, 10 X 10 freezer boxes). Cryogenic units not only provide ample storage and temperature security, but have also helped JHBR meet and exceed JHSPH’s goals for energy efficiency.JHBR uses Freezerworks (FW), state-of-the-art sample cataloging software. Each aliquot created in the JHBR laboratories is labeled with a FW label. This label includes information such as sample ID, sample date, sample type and can endure temperatures colder than -190. Every label contains a bar code that is used to scan the aliquot into FW, which allows every aliquot to be tracked and linked to the sample record.Viral Diagnostic Laboratory UnitDr. Homay Farzadegan JHBR Viral Diagnostic Laboratory Unit, located on the 6th floor of JHSPH, offers diagnostic serologic and virologic testing. Since its inception in 2002, JHBR Testing Core has achieved and maintained the highest level of international standards (CAP, VQA, AAB) for test result accuracy and quality assurance compliance. In July of 2010, JHBR Testing Core received certification through the Clinical Laboratory Improvement Amendment (CLIA) in Immunology and Molecular Biology, allowing JHBR to process and test specimens for research and clinical purposes.?JHBR utilizes the most up-to-date automated platform for real time PCR and viral load quantification. The COBAS Ampliprep and COBAS TaqMan by ROCHE are fully automated for sample preparation, amplification (real-time PCR) and quantification (FRET analysis).JHBR has relied on the EVOLIS as a self-contained microplate processor for automated EIA testing, manufactured by Bio-Rad for ten years. It contains a pipettor, incubator, washer, reader and date-management system for enzyme immunoassays. EVOLIS streamlines workflow for moderate to high work load volumes and optimizes productivity, using a scheduler program to simplify instrument operation. The current serological markers of interest include: HIV-1/2, plusO, HBsAg, HBsAb, HBcAb and HCV, but the system is capable of detecting a number of different markers.In addition to the fully automated serological tests performed on the EVOLIS, JHBR offers rapid HIV and Geenius testing for HIV seroconversion performed by highly trained staff. Currently, the OraQuick? rapid HIV test kit from Orasure is used and the Geenius HIV-1/2 kit from Bio-RadViral Eradication Laboratory UnitThe laboratory of Professors Robert and Janet Siliciano laboratory is located on the 8th floor of the Miller Research Building at the Johns Hopkins University School of Medicine. The laboratory includes 2,200 square feet of laboratory space and a 670 sq. foot BSL-3 laboratory (described below), as well as two office suites and in-laboratory cubicles for the faculty, students, post-doctoral fellows, and technicians in the Siliciano group. The main laboratory is equipped with a BSL-2 tissue culture room equipped with 2 cell culture hoods, 2 humidified incubators, centrifuges and microscopes. There is also a dedicated PCR setup room with four laminar flow hoods. The laboratory has a large, walk-in cold room as well as a dark room for film processing. Within the main laboratory are two Real-Time PCR machines, one RainDrop Digital Droplet PCR System, more than 20 thermal cyclers capable of handling tubes and plates, two ELISA plate readers, three -80 freezers, one gel imaging system, floor and tabletop centrifuges, as well as standard molecular biology and tissue culture equipment.The BSL-3 laboratory is equipped with five tissue culture hoods, six humidified incubators, four flow cytometers (BD FACS Calibur, BD FACS Canto II, Millipore Muse, and Intellicyte iQue Plus Screener), four -80 freezers, two ultracentrifuges, 5 low speed centrifuges, a pass-through autoclave, large scale cell separation magnets, automated cell separation workstation, automated RNA isolation workstation, as well as standard molecular biology and tissue culture equipment. The BSL-3 laboratory is equipped to process and isolate peripheral blood mononuclear cells from routine peripheral blood draws and large-scale leukapheresis from both HIV-1 infected and uninfected donors. Glass washing and autoclaving facilities are located within the same building as the laboratory.The Retrovirus LaboratoryThe Retrovirus Laboratory is located on the 8th floor of the Miller Research Building at the Johns Hopkins Medical Campus. The laboratory comprises 8,000 sq ft, designed and equipped for interdisciplinary research. The main working area consists of 12 bays completely equipped for molecular and cell biology, histology and pathology research. Equipment includes three real-time PCR machines, a BioRad QX100 digital droplet PCR system, an automatic liquid dispenser for PCR plates, six thermocyclers, two fume hoods, a downdraft table, a Biogenex Optimax Automated slider stainer for immunohistochemistry and in situ hybridization, two spectrophotometers, a Luminoskan fluorometer/luminometer microplate reader, a colorimetric microplate reader, a Qiacube nucleic acid extraction machine, a Typhoon 9210 image scanner, a scintillation counter, and equipment for gel electrophoresis and bacteriological culture. It contains a 1,000 sq ft BSL-3 virology laboratory, equipped with four 6-foot tissue culture hoods, a pass-through autoclave, one ultracentrifuge, one superspeed and three tabletop centrifuges, a cryostat, a Zeiss sliding microtome, and a Becton Dickinson flow-cytometer capable of 14-color analysis.There is 3,000 sq ft of support space including a BSL-2 tissue culture room with three hoods for cell culture and PCR protocols, two rooms for experiments with radioactive materials, a cold room, a dark room, and a glassware washing room. It also contains an image analysis laboratory dedicated to image acquisition and analysis. It is equipped with four primary microscopes, a Zeiss Axiophot microscope, a QImaging Retiga 2000R Camera-based image-capture system mounted on a Nikon Eclipse E600 microscope, a Q Imaging Retiga Exi Camera mounted on a Nikon TE200 inverted microscope and a Nikon C1 confocal microscope equipped with 3 lasers, mounted on a Nikon TE2000E inverted microscope. Service corridors provide space for -80 and -20 freezers, centrifuges, and storage shelves.Core FacilitiesFurthermore, there are currently 120 core facilities available to all investigators at Johns Hopkins located on different Hopkins campuses.Specifically, the School of Medicine houses the following Core Facilities, which are available to all Hopkins researchers: Oligonucleotide and peptide synthesis. The Synthesis & Sequencing Facility (SSF) offers these services at cost.Microscopy. This Microscope Facility provides training on and use of transmission and scanning electron microscopes and confocal microscopes.JHMI Deep Sequencing & Microarray Core. The aim of this core is to provide cost-effective andtime-efficient access to cutting-edge genomic technologies and expert assistance with experimental design and data analysis.Flow cytometry. The core offers state-of-the-art flow cytometry cell analysis and high-speed cell sorting to Hopkins research community.Institute for Cell Engineering encompasses core research programs in stem cell biology and the McKusick-Nathans Institute of Genetic Medicine dedicated to understanding human heredity and genetic medicine and using this knowledge to treat and prevent disease.High throughput assays The lab of Dr. Liu occupies six rooms (about 2,300 sq ft) located on the fifth floor of the Hunterian Building, which is connected to the rest of the Hopkins Basic Science Complex and to the Johns Hopkins Clinical Research Complex. It has a dark room and a shared cold room. The lab is fully equipped to perform experiments in synthetic organic chemistry, molecular biology, protein biochemistry, cell biology. A separate room is designated for organic synthesis with the capacity of housing three synthetic chemists. The Johns Hopkins Drug Library is housed in a separate room of ca 150 sq ft with five -20 degree C freezers.HIV Neurosciences Program Laboratories HIV Neurosciences Program Laboratories: These laboratories, utilized by Drs. Pardo-Villamizar, Brown, McArthur, and Haughey, consist of 2850 sq. ft. of laboratory space, including a university-approved biosafety level 3 laboratory (P3), six additional laboratories for cell culture and related cell studies, two laboratories for histopathological tissue preparation, laboratory for specimen processing and flow cytometry, two molecular biology laboratories and a dedicated room for bacteriology. Also available in the immediate vicinity are shared heavy equipment rooms, materials preparation facilities, warm and cold rooms, a conference room, and two darkrooms, one with a film processor and a second, smaller one for insitu hybridization and photographic work. We also have dedicated access to a PALM laser microdissection device, and share access to a core facility that contains a state-of-the-art Zeiss LS510 meta confocal microscope and a Hitachi H-600 electron microscope that are available for unrestricted use to the Center investigators and is maintained jointly with the Peripheral Nerve Research group. The P3 laboratory, maintained under negative pressure, has a double-sided autoclave, a dedicated vacuum line system, and a double-door entrance with an anteroom for gowning.The HIV Neuroscience Program laboratories are in immediately contiguous areas on the 6th floors of the Pathology, Carnegie, and Meyer Buildings. These buildings are directly connected so that there is maximal proximity and communication of investigators. Within the HIV Neuroscience Laboratories, the Neuropathological facilities include the Cutaneous Nerve laboratory, directed by Dr. Justin McArthur, and the HIV Autopsy Laboratory, directed by Dr Carlos Pardo. These laboratories are immediately adjacent, and some equipment is shared. Dr. Pardo and the facilities for the autopsy technician are located on the 6th floor of the Pathology Building within the HIV Neurology Program Laboratories with adjacent direct elevator access to the autopsy suite, which is located in the basement of the Pathology Building. A full range of sectioning and staining facilities, as well as slide storage space is available on Pathology 6. The laboratory is equipped to process tissue material, perform histological and immunocytochemical techniques, as well as PCR and immunoblotting experiments. Also available in the immediate vicinity is a cell culture room and area for in-situ hybridization and use of radioactive material for molecular biological techniques. Digital cameras and binocular microscopes, as well as a graphics workstation for preparation of publication quality images. The facilities here contain a complete array of equipment for the embedding, cutting, staining, and storage of pathological specimens. An AIDS histology technician works within the HIV Autopsy laboratory and controls a specified area with her own equipment (eg: microscope, rotary microtome, water baths, pipettes, etc) for exclusive use for tissue related to AIDS. Binocular microscopes, multi-headed microscopes equipped with digital cameras, two sliding microtomes, vibratome, paraffin-embedding equipment, and slide storage facilities are all available. The autopsy room of the Johns Hopkins Hospital is located in the basement of the Pathology Building, with direct elevator access from our laboratories to the autopsy room. Refrigerators and 5 Revco –70C freezers for the storage of autopsy tissue are located on the sixth floor of the Pathology Building. An automated telephone alarm system is installed to prevent freezer loss. These freezers are available for storage of blood and CSF specimens, and autopsy tissue. Dr N. Haughey maintains laboratory space consisting of 1200 sq. ft in the Pathology Building. His laboratory contains a tissue culture facility fully equipped with laminar flow hoods, incubators, water baths and dissecting microscope. All equipment necessary for various types of electrophoresis, Western, Northern and Southern blot analyses are present. A Speedvac evaporator/concentrator for concentrating DNA and RNA samples is also present. One large –80o C freezer, 2 refrigerator/freezers, and a liquid nitrogen storage tank are also in the laboratory for sample reagent storage. A PCR temperature cycler is present, as well as various centrifuges. There are two Zeiss 510 fluorescent microscope systems with high resolution Orca cameras for static and real-time imaging. An ESI 3000 Electrospray Ionization Tandem Mass Spectrometer with an HPLC on the front end and autosampler is present in the lab. Core Electron Microscope Hitachi H-600 electron microscope with supporting equipment, including a carbon coater, image processing and printing equipment. Core Confocal Microscope A Zeiss LSM 510 confocal microscope is located on Pathology 5 adjacent to the peripheral nerve laboratories. The microscope is available to the entire group and is a powerful tool with which to measure quantitative fluorescence inimaging 3-dimensional structures. Additional Equipment: In the JHU HIV Neuroimmunology group there is an ABS Gene Analyzer, a Millipore Cytofluor fluorescence plate reader, a visible plate reader, a Zeiss P.A.L.M. MicroLazer capture dissection microscope, an Olympus BX51 with stereologer, a spectrophotometer, a cryostat, freezing microtome and vibratome.Center for TB ResearchThe mission of?The Center for Tuberculosis Research Laboratory?is to apply medical technology towards basic advances in the understanding of the pathogenesis of TB, host immunity to TB, mechanisms of spread, and animal models which better emulate the pathology of human disease.? With these?basic tools the Center intends to build a translational bridge to more effective drugs, vaccines, and diagnostics for tuberculosis.LaboratoryThe Center for Tuberculosis Research Laboratory comprises 5,500 sq ft of BSL-2 laboratory space equipped for molecular biological and microbiological experiments in the Johns Hopkins School of Medicine (Cancer Research Building 2 (CRB-2), Rm 123 and the adjacent Bond St. Building (BSB), Rooms 122, 123, 124, and 127).? Two 200 sq. ft. tissue culture rooms equipped with 6 biological safety cabinets (BSCs) are available for PCR set up and manipulation of slow-growing mycobacterial cultures as well as for sterile tissue culture work. A dark room, cold room and a media prep room are shared with other members of the Center for TB Research. A shared and fully equipped 1,000 sq ft BSL-3 laboratory for the manipulation of M. tuberculosis is adjacent to this space (Rm 176A-D). It contains 4 BSCs, refrigerators, -80 freezers, reach-in incubators, a centrifuge, and a pass-through autoclave. A second 1,000 sq ft BSL-3 laboratory is located one floor below the main lab, within the ABSL-3 facility in CRB-2 (Rm B-93), adjacent to the mouse and guinea pig holding space. It is used exclusively by members of the Center for TB Research for animal tissue preparation and microbiology work. It is equipped with 4 BSCs, refrigerators, -80 freezers, reach-in incubators, a centrifuge, a dishwasher, a tabletop microscope, and a pass-through autoclave.?? ?EquipmentAutoclaves, air incubators, cold room, ultracentrifuges, scintillation counter, microtome, microscopes, fluorescence microscope with camera, gel equipment with gel photography capabilities, fluorimeter, spectrophotometer, PCR machines, eletroporators, balances, iCycler, FACS machine (in BSL-3) are all available either to Dr. Karakousis directly or as shared equipment. All of the equipment is on the same floor as the main lab or next to the BSL-3. Three –70oC freezers for BSL-3 and three for the main BSL-2 lab are available. ?left000?Becton Dickinson FACScalibur (within BSL-3; at right). A 4-color BD FACScalibur flow cytometer and cell sorter is available and is housed within the BSL-3 laboratory in CRB-2 Rm 176.?? Among numerous uses, this instrument is used for T cell subtyping of animal samples, intracellular cytokine staining analysis, and detecting GFP and RFP-expressing recombinant M. tuberculosis.????Imaging Equipment and Software (below). The JHU CTRL has recently acquired state-of-the-art tri-modality (CT, PET, SPECT) imaging instruments, which are located in Rm B.74 in the basement of CRB-2, adjacent to the ABSL-3 vivarium. These scanners are capable of imaging small animals (mice, rats, guinea 016319500pigs, and rabbits) and include:???????????A.? NanoSPECT/CT capable of high-resolution CT (40 ?m) and multiplexed, multi-pinhole high resolution (<0.5 mm), high sensitivity (>250-400 cps/MBq) SPECT imaging.B.? Philips MOSAIC HP PET with PIXELAR? detector technology, large 18 cm imaging bore with clinical reliability.?left000Nikon E800 Fluorescence and phase contrast microscope with digital photography system (at right). A Nikon E800 microscope equipped with state-of-the-art fluorescence and phase contrast optics plus a digital photography system belongs to the CTRL and is housed in CRB-2, Rm 176.???????left000Glas-Col Aerosol Infection Device (at right). Two Glas-Col inhalation infection instruments are housed in the ABSL-3 laboratory (one in CRB-2 and the other in BRB) and are available for infecting mice and guinea pigs via the aerosol route of infection.? The devices can infect 250 mice or 18 guinea pigs simultaneously.???left000Madison Chamber Aerosol Infection Device (at left). One Madison chamber device is housed in the ABSL-3 laboratory (CRB-2, Rm B.82) and is available for low-dose aerosol infections of mice and guinea pigs.? The devices can infect 210 mice or 36 guinea pigs per run.???left000Germfree Class III Glovebox with Automatic AirlockPurge System (at right). One Germfree glovebox is housed in the ABSL-3 laboratory (CRB-2, Rm B.80) and is used for procedures whereby aerosolized M. tuberculosis may be generated at a high level, such as during mechanical homogenization of guinea pig lungs for bacillary enumeration.? ??????OtherDNA sequencing and oligonucleotide synthesis is available from the Johns Hopkins Genetic Core Resource Facility and the Johns Hopkins Protein, Peptide and DNA facility, respectively. The Johns Hopkins University Malaria Research Institute Gene Array Core Facility provides support for analysis of gene expression profiles from mouse tissues. The Johns Hopkins Histopathology and Immunology Core Facilities are also available to us and have previously done our immunohistochemical staining and RT-PCR in tissue analyses.?Johns Hopkins Division of Medical MicrobiologyNicole Parrish, Ph.D. is Director of Mycobacteriology, Division of Medical Microbiology.? All work with M. tuberculosis, including drug susceptible, MDR- and XDR-TB strains is conducted in a BioSafety Level 3 (BSL-3) microbiology laboratory at JHU.? This laboratory was completely renovated in 2006 and consists of 1200 sq. ft. containing 3 Class II biosafety cabinets, multiple enclosed refrigerated centrifuges, multiple -20?C and -80?C freezers, refrigerators, 2 BACTEC MGIT 960 automated culture detection systems, GeneXpert system, and several CO2 and non-CO2 incubators.? Work is conducted according to specifications as outlined in the current Biosafety in Microbiological and Biomedical Laboratories (BMBL) manual, 5th edition and follows a detailed Standard Operating Procedures manual approved by JHU’s Chief Biosafety Officer.? JHU Biosafety registrations for all work conducted with M. tuberculosis are renewed on an annual basis by the Biosafety office. The BSL-3 laboratory and facility is certified annually by independent experts (World BioHazTech). The laboratory also has restricted card-key access limited to specific technologists and key personnel. Appropriate biohazard signs are placed on the entry doors, as required by the Institutional Biosafety Committee (IBC). All manipulation of cultures is performed in Class II biosafety cabinets. Infectious waste is decontaminated with Cavicide and autoclaved in a pass-through unit prior to being disposed of according to approved protocols. Sharps are discarded in approved sharps containers with biohazard signs and are disposed of according to IBC-approved protocols. Laboratory equipment and work surfaces are routinely decontaminated with Cavicide both before and after work with infectious materials. Specific procedures for small and large spills, splashes and other contamination are detailed in the SOP manual which is provided to, and reviewed with, all new personnel. Each employee is required to complete initial and annual training re: BSL-3 procedures, use of personal protective equipment and the laboratory SOP administered by the JHU Biosafety Officer in order to gain and maintain access to the BSL-3 facilities.Laboratory Testing CapacityCRS#1: JHUChemistryXHistologyXToxicologyNAHematologyXImmunologyXCD4XImmunology/SerologyXVirologyXHIV Viral LoadXHIV DNA or Total Nucleic AcidX HIV Resistance GenotypingXMetabolic testsXMicrobiologyXPharmacologyXCytologyXSpecimen processingXTBXUrinalysisXX: capacity on-site, NA: not applicable? ................
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