MEDICAL RESEARCH for M.Phil , MD, MS & PhD Program

1. MEDICAL RESEARCH for M.Phil, MD, MS & PhD Program Dr. GhazalaRubi M.Sc, M.Phil, A.I.B.M.S;(UK) PhD (Human Genetics & Mol-Biology) Director Central Research LAB PGMI / LGH / AMC

2. DESCRIPTION, JUSTIFICATION & TECHNICAL PARAMETERS for PhD Program at PGMI

3. Aims & Objectives of PGMI • Post Graduate Medical Institute Lahore (PGMI) was established in 1974 in KE. • The aims objectives of PGMI to • PG medical education& training • in both clinical and basic disciplines, • new medical colleges were being opened at that time • there was an acute shortage of medical teachers particularly in basic medical disciplines.

4. Disciplines • PGMI is running 60 courses in different disciplines of medical science • It includes 12 diplomas (minor qualification) & • 48 degree courses (major qualification). • It serves PGs from KPK, Baluchistan, Islamabad, FATA Azad Jammu & Kashmir and GilgitBaltistan. • PGMI has provided teaching & training facilities to students from other countries • As Sri lanka, Nepal, Bangladesh, Afghanistan, Iran and Arab countries. • UP till now more than 9384 students enrolled in PGMI &3310 doctors awarded PG diplomas/ degrees

5. Central Research Lab • To facilitate the PG teaching & training • As well as to improve the standards of research, • First state-of-the art Research lab in public sectorestablished at PGMI, PINS building. Therefore establishment of Central Research lab at PGMI, Lahore was an overwhelming need of the time. • This research Lab has the facility for doing research at PhD level in all clinical sciencesresearch.

6. CRL • It will  provide a unique interface between clinical & basic biomedical science, • Aiming to understand the cellular basis of disease. • 40% of our researchers are clinically active, • we should move of translating our basic research into successful clinical applications.

7. Mission to start PhD Program • Our researchers should use cell biology to understand molecular mechanisms of disease • To conversely use genetic disease to reveal crucial mechanisms of cell biology. • Although in our country, research has particular strengths in • key cell processes (membrane trafficking and protein folding) • Also in biological areas (immune system and neuronal function), • an important asset at PGMI is the breadth of disease areas that our research impinges on, • That allows us to reveal fundamental principles of disease and infection. • Crucial to this is the use of multiple approaches, including genetics, cellular & structural biology.

8. Facilities for PhD Research • PGMI fulfill criteria like other institutes where PhD programs are going on successfully in various discipline. • Our Research lab has such latest range of automated equipment • That can meet the criteria of Research up to • Gene & allele level to find any minor or major Gene mutations. • All these equipment have been installed and functioning, • Every kind of Clinical material is available in LGH from 33 different departments. • So PGMI is in a Position to start PhD Program • in basic as well as in clinical sciences. • One fulltime PhD and two visiting faculty having PhDs required to conduct PhD Program in the institute.

9. Criteria • We can welcome applications from graduates to undertake research towards a PhD in any of the labs. • We admit those applicants who meet the academic admissions criteria and whose research interests match • those of an available member of the academic staff who is willing to act as the student's supervisor. • Applicants are encouraged to contact potential supervisors directly in the first instance • Also to discuss their application and funding possibilities (HEC, PSF & etc) from national & international funding agencies.

10. Automated DNA / RNA Extraction Automatically extract DNA and RNA From all body fluids In 90 mins. As Blood, CSF, PUS, Fluids, urine as well as brochial washings & etc. DNA / RNA extracted in 90 mins time with good quantitative loads of virus & bacteria.

11. REAL TIME PCR with 6 Fluorophores

12. Detection by REAL TIME PCR • Any viral or bacterial infection diagnosis within • 90 mins time limit. • All kinds of virus & bacteria can be easily detected not by Qualitative analysis but also by Quantitative estimation. • As only 15 no of virus or bacteria can be analyzed within less than 2hrs time. • All kind of bacteria & viruses as Dengue, kongo, herpes, CMV, HBV, HCV, HIV, MTB, H1N1

15. Disease Diagnosis • The development of molecular hybridization techniques such as fluorescence in situ hybridization (FISH) had a major Impact to detect & characterize the genetic changes that give rise to human tumors. • With probes designed to Identify specific chromosomes and chromosomal regions. • FISH is used routinely by cytogenetic & pathology labs to identify recurring chromosomal abnormalities associated with hematologic malignant diseases. • In many cases FISH analysis provides increased sensitivity, as cytogenetic abnormalities found in samples that appeared to be normal by morphologic & conventional cytogenetic examination. • The combination of cytogenetic, FISH, & molecular analyses provides a powerful approach for diagnosing as sub classifying malignant diseases into clinically &biologically relevant subgroups. • In selecting appropriate therapy, & in monitoring the efficacy of therapeutic regimen

16. Tissue Microarray • Microarray is a technique for organizing minute amounts of biological samples on a solid support. • Tissue microarrays are composite paraffin blocks constructed by extracting cylindrical tissue core “biopsies” from different paraffin donor blocks & re-embedding into a single recipient (microarray) block at defined array coordinates. • At first, the donor blocks (invariably stored paraffin blocks) are retrieved and sectioned to produce standard microscopic slides that are stained with hematoxylin and eosin. • An experienced pathologist examines the slides to mark the area of interest, which is commonly an area of cancer after which the samples can be arrayed

17. Advantages of Tissue Microarray • Tissue microarray facilitates rapid translation of molecular discoveries to clinical applications. • The technique has been applied to tumor research (gliomas, breast tumors, lung cancer among others). • The development of novel biochip technologies has opened up new possibilities for the high-throughput molecular profiling of human tumors. • Novel molecular markers emerging from high-throughput expression surveys & analyzed on tumor tissue microarray

20. Platelet Aggregometer • Platelets play a fundamental role in normal hemostasis, while their inherited or acquired dysfunctions are involved in a variety of bleeding disorders or thrombotic events. • Several laboratory methodologies or point-of-care testing methods are currently available for clinical and experimental settings. • These methods describe different aspects of platelet function based on platelet aggregation, platelet adhesion, the viscoelastic properties during clot formation, the evaluation of thromboxane metabolism or certain flow cytometry techniques. • Platelet aggregometry is applied in different clinical settings as monitoring response to antiplatelet therapies, the assessment of perioperative bleeding risk, the diagnosis of inherited bleeding disorders or in transfusion medicine. • The rationale for platelet function-driven antiplatelet therapy was based on the result of several studies on patients undergoing percutaneous coronary intervention (PCI), where an association between high platelet reactivity despite P2Y12 inhibition and ischemic events as stent thrombosis or cardiovascular death was found. • However, recent large scale randomized, controlled trials have consistently failed to demonstrate a benefit of personalized antiplatelet therapy based on platelet function testing.

21. Platelet aggregation systems (as an aggregometer) can be used to determine how well platelets stick together. Such a test measures platelet aggregation with the use of a platelet antagonist, such as ADP, thrombin, and ristocetin. An aggregometer measures the turbidity in the sample & records how quickly the platelets clump together by measuring the increased light & clarity of the sample. Additionally, a platelet aggregation system can encompass several test modes where the number of channels available in an aggregometer is equivalent to the number of tests that can be run simultaneously & independently. Certain aggregometers can test as well as measure platelet function from a patient & can be used to diagnose patients with von Will brands disease. Platelet aggregation systems and aggregometers are reliable diagnostic tools in a clinical research laboratory.

23. Agarose or polyacrylamide gel electrophoresis is a common technique used to separate nucleic acids (DNA and RNA) according to their molecular weight, which generates images that can be analyzed automatically by a system. The separated DNA fragments of different molecular weights give a series of bands with positions in the gel image corresponding to their molecular weights. Automated image analysis of the gels removes much of the subjectivity of manual interpretation of band positions and sizes. In this paper, an automated system was designed for analyzing DNA bands using image and signal processing techniques. The proposed algorithm consists of four main steps: preprocessing to enhance the image, detecting lanes and bands, identifying band lengths and clustering; in which the similarities of biological samples based on shared bands can be identified. The proposed technique eliminates defects due to noise and double bands in images.

24. DNA Gel Electrophoresis Gel electrophoresis is useful in forensics, biochemistry, genetics, microbiology and other applications requiring analysis of nucleic acid and protein molecule size and characteristics. ypically, a DNA molecule is digested with restriction enzymes, and the agarose gel electrophoresis is used as a diagnostic tool to visualize the fragments. An electric current is used to move the DNA molecules across an agarose gel, which is a polysaccharide matrix that functions  Protein electrophoresis is also a common method for analyzing blood plasma in medical applications. Electrophoresis often occurs as a preparatory technique prior to cloning, DNA sequencing, Southern blotting, restriction fragment length polymorphism (RFLP), and analysis via mass spectrometry.

25. Fragment Analysis

26. Agarose or polyacrylamide gel electrophoresis is a common technique used to separate (DNA &RNA) according to their molecular weight, which generates images that can be analyzed automatically by a system. The separated DNA fragments of different molecular weights give a series of bands with positions in the gel image corresponding to their molecular weights. Automated image analysis of the gels removes much of the subjectivity of manual interpretation of band positions and sizes The proposed technique eliminates defects due to noise and double bands in images. Automation advantageous vs Manual Gel System

27. Chemiluminescence Immunoassay (CLIA) • It detect more than 110 immunoassays • CLIA Kits are designed to detect glow-based chemiluminescent reactions. • The kits provide a broader dynamic assay range, superior low-end sensitivity, & • a faster protocol than the conventional Enzyme-linked immunosorbent assays (ELISA). • It also detect Thyroid function markers, Gonadal hormones, Tumor markers, Diabete marker, Cardiac marker & other markers. • They can be used to replace conventional colorimetric ELISAs that have been widely used in many research and diagnostic applications.

28. Automated Blood Culture SystemAutomated Urine analyzerAutomated Chemistry analyzer