INTRODUCTION TO PATHOLOGY: 1.

Definition of Pathology : The wordPathology is derived from two Greek word: y y pathos means suffering or disease logos means study

Pathology is scientific study of structure and function of the body in disease. It deals with causes, effects, mechanisms and nature of disease. The knowledge and understanding of pathology is essential for all would-be doctors as well as general practitioners and specialists since unless they know the causes and mechanisms of diseaseand understand the language spoken by the pathologistin the form of laboratory reports, they would not be able to institute appropriate treatment or suggest preventive measures to the patient. For the medical student, the discipline of pathology forms a vital bridge between initial learning phase of preclinical science and the final phase of clinical subjects. 2.Evolution of Pathology: From religious beliefs to rational approach (Antiquity to AD 1500) Era of gross pathology (AD 1500 to 1800) Era of technology development and cellular pathology (AD 1800 to 1950s) Modern pathology (1950s to dawn of 21st century)  2.1.From religious beliefs to rational approach (Antiquity to AD 1500) : Hippocrates (Greece) 460-377 BC : Permanently dissociated medicine from religious mysticism. Started study of patients symptoms as method of diagnosis.

Hippocrates (Greece) 460-377 BC Cornelius Celsus (Rome) 53 BC-7 AD : Described 4 cardinal signs of inflammation (redness, heat, swelling, pain)

Giovanni B Morgagni (Italy) 1682-1771 : Introduced clinicopathologic correlation (CPC) in the study of disease John Hunter (Scotland) 1728-1793 : Introduced pathology museum in the study of disease.

John Hunter (Scotland) 1728-1793 R.T.H. Laennec (France) 1781-1826 : Described several lung diseases such as various tuberculouslesions of lungs, bronchiectasis. Described cirrhosis of liver (later called Laennecs cirrhosis). Invented stethoscope.

R.T.H. Laennec (France) 1781-1826

 2.2Era of technology development and cellular : pathology (AD 1800 to 1950s) : Rudolf Virchow (Germany) 1821-1905 : Father of cellular pathology Introduced histopathology as a diagnostic branch by his cellular theory

Rudolf Virchow (Germany) 1821-1905 George N. Papanicolaou (USA) 1883-1962 : Father of exfoliative cytology Developed Pap smear for detection of cervical cancer in 1930s

George N. Papanicolaou (USA) 1883-1962  2.3Modern pathology (1950s to dawn of 21st century) Watsonand Crick1953 : Described the structure of DNA Nowell and Hagerford1960 : Philadelphia chromosome in CML i.e. t(9;22) Galland Pardue1969 : invented In SituHybridi zation Kary Mullis1983 : Introduced polymerase chain reaction (PCR)  3. Division of Pathology : General Pathology --- It deals with general principles of disease Systemic Pathology ---It includes study of diseases pertaining to the specific organs and body systems  3.1.Subdivision of Pathology : 3.1.1Histo-Pathology: it deals with study of tissues in diseased state. 3.1.2Experimental Pathology: Experimental pathology, also known as investigative pathology is the scientific study of disease processes through the microscopic or

molecular examination of organs, tissues, cells, or body fluids from diseased organisms. It is closely related, both historically and in modern academic settings, to the medical field of pathology. 3.1.3Molecular Pathology: Molecular pathology is an emerging discipline within pathology which is focused in the study and diagnosis of disease through the examination of molecules within organs, tissues or bodily fluids 3.1.4.Chemical Pathology: chemical pathology, medical biochemistry or pure blood chemistry) is the area of pathology that is generally concerned with analysis of bodily fluids. The discipline originated in the late 19th century with the use of simple chemical tests for various components of blood and urine. 3.1.5Geographic Pathology: a field of medicine that studies the pathology of humans, animals, and plants in relation to geographic factors, and, in the case of humans, social and economic factors as well. 3.1.6.Immunology: It is a branch of medicine that studies the response of organisms to foreign substances, e.g., viruses, bacteria, and bacterial toxins (see immunity). 3.1.7.Haematology: It is the branch of medical science concerned with diseases of the blood and blood-forming tissues 3.1.8.Medical Genetics: a branch of human genetics that studies hereditary diseases and methods of preventing, diagnosing, and treating them. 4.Methods for the study of Pathology : Autopsy: Autopsy means "see for yourself". It is a special surgical operation, performed by specially-trained physicians, on a dead body. Its purpose is to learn the truth about the person's health during life, and how the person really died Biopsy: A biopsy is the removal of a sample of tissue from the body for examination. The tissue will be examined under a microscope to assist in diagnosis. Therefore, only very small samples are needed. Cytology: Cytology can also refer to cytopathology, which analyzes cell structure to diagnose disease.  5.TECHNIQUES TO STUDY PATHOLOGY:  5.1Autopsy pathology:It also known as a post-mortem examination, necropsy (particularly as to non-human bodies), autopsia cadaverum, or obductionis a highly specialized surgical procedure that consists of a thorough examination of a corpse to determine the cause and manner of death and to evaluate any disease or injury that may be present. It is usually performed by a specialized medical doctor called a pathologist.

5.1.1Prevalence: Autopsies are either performed for legal or medical purposes. In 2004 in England and Wales, there were 514,000 deaths of which 225,500 were referred to the coroner. Of those, 115,800 (22.5%) resulted in post-mortem examinations and there were 28,300 inquests, 570 with a jury. In the United States, autopsy rates fell from 17% in 1980 to 14% in 1985 and 11.5% in 1989, although the figures vary notably from county to county. 5.1.2.Types: There are three main types of autopsies: y Medico-Legal Autopsy or Forensic or coroner's autopsies seek to find the cause and manner of death and to identify the decedent. They are generally performed, as prescribed by applicable law, in cases of violent, suspicious or sudden deaths, deaths without medical assistance or during surgical procedures. Clinical or Pathological autopsies are performed to diagnose a particular disease or for research purposes. They aim to determine, clarify, or confirm medical diagnoses that remained unknown or unclear prior to the patient's death. Anatomical or academic autopsies are performed by students of anatomy for study purpose only.

5.1.3.Purpose: y The principal aim of an autopsy is to determine the cause of death, the state of health of the person before he or she died, and whether any medical diagnosis and treatment before death was appropriate. When a person has given permission in advance of their death, autopsies may also be carried out for the purposes of teaching or medical research. An autopsy is frequently performed in cases of sudden death, where a doctor is not able to write a death certificate, or when death is believed to result from an unnatural cause. These examinations are performed under a legal authority (Medical Examiner or Coroner or Procurator Fiscal) and do not require the consent of relatives of the deceased.

y y

5.1.4Process: There are two parts to the physical examination of the body: the external and internal examination: a. External examination: At many institutions the person responsible for handling, cleaning, and moving the body is often called a diener, the German word for servant. In the UK this role is performed by an Anatomical Pathology Technologist who will also assist the pathologist in eviscerating the deceased and reconstruction after the autopsy. After the body is received, it is first photographed. The examiner then notes the kind of clothes and their position on the body before they are removed. Next, any evidence such as residue, flakes of paint or other material is collected from the external surfaces of the body. Ultraviolet light may also be used to search body surfaces for any evidence not

b.

easily visible to the naked eye. Samples of hair, nails and the like are taken, and the body may also be radiographically imaged. Internal examination: The internal examination consists of inspecting the internal organs of the body for evidence of trauma or other indications of the cause of death. For the internal examination there are a number of different approaches available: a large and deep Y-shaped incision can be made starting at the top of each shoulder and running down the front of the chest, meeting at the lower point of the sternum. This is the approach most often used. a T-shaped incision made from the tips of both shoulder, in a horizontal line across the region of the collar bones to meet at the sternum (breastbone) in the middle. a single vertical cut is made from the middle of the neck (in the region of the 'adam's apple' on a male body)

A brain autopsy demonstrating signs of meningitis. Underneath the dura mater are the leptomeninges, which appear to be edematous and have multiple small hemorrhagic foci. 5.2.Surgical pathology: Surgical pathology is the most significant and timeconsuming area of practice for most anatomical pathologists. Surgical pathology involves the gross and microscopic examination of surgical specimens, as well as biopsies submitted by non-surgeons such as general internists, medical subspecialists, dermatologists, and interventional radiologists. The practice of surgical pathology allows for definitive diagnosis of disease (or lack thereof) in any case where tissue is surgically removed from a patient. This is usually performed by a combination of gross (ie. macroscopic) and histologic (ie. microscopic) examination of the tissue, and may involve evaluations of molecular properties of the tissue by immunohistochemistry or other laboratory tests. 5.2.1Surgical pathology workflow:

Gross examination: Gross examination or "grossing" is the process by which pathology specimens are inspected with the bare eye to obtain diagnostic information, while being processed for further microscopic examination. Histopathologic examination: it refers to the microscopic examination of tissue in order to study the manifestations of disease. Specifically, in clinical medicine, histopathology refers to the examination of a biopsy or surgical specimen by a pathologist, after the specimen has been processed and histological sections have been placed onto glass slides. In contrast, cytopathology examines free cells or tissue fragments. Frozen section: The second method of histology processing is called frozen section processing. In this method, the tissue is frozen and sliced thinly using a microtome mounted in a below-freezing refrigeration device called the cryostat. The thin frozen sections are mounted on a glass slide, fixed immediately & briefly in liquid fixative, and stained using the similar staining techniques as traditional wax embedded sections. It is used in intra-operative pathology for determinations that might help in choosing the next step in surgery during that surgical session (for example, to preliminarily determine clearness of the resection margin of a tumor during surgery). Fixation & Embedding: In chemical fixation, the samples are transferred to a cassette, a container designed to allow reagents to freely act on the tissue inside. This cassette is immersed in multiple baths of progressively more concentrated ethanol, to dehydrate the tissue, followed by toluene or xylene, and finally extremely hot liquid (usually paraffin). During this 12 to 16 hr.

Microtome

process, paraffin will replace the water in the tissue, turning soft, moist tissues into a sample miscible with paraffin, a type of wax. This process is known as tissue processing.

The processed tissue is then taken out of the cassette and set in a mold. Through this process of embedding, additional paraffin is added to create a paraffin block which is attached to the outside of the cassette. The process of embedding then allows the sectioning of tissues into very thin (2 - 7 micrometer) sections using a microtome. The microtome slices the tissue ready for microscopic examination. The slices are thinner than the average cell, and are layered on a glass slide for staining.

automatic tissue processor

tissue embeding centre

Ancillary testing: In a clinical trial, a medical test on a patient that is not a part of the original study design. 5.2.2 The surgical pathology report: the final and most important step is to show accurate and brief significant report regarding: y y y y Gross examination Frozen section Fixation & Embedding Histopathologic examination

Commonly recognized subspecialties of surgical pathology include the following:

y y y y y y

Bone pathology, Cardiac pathology Cytopathology , Dermatopathology ,Endocrine pathology Gastrointestinal pathology, Genitourinary pathology, Gynecologic pathology Head and Neck Pathology,Hematopathology Neuropathology , Ophthalmic pathology Pediatric pathology ,Pulmonary pathology, Renal pathology

 5.3Enzyme histochemistry: A novel technique combining the freeze drying and embedding in glycol methacrylate at low temperature of tissue permitted the histochemical demonstration of a variety of enzymes, showing maintenance of enzyme activity, accurate enzyme localisation without apparent diffusion, and excellent morphological detail. The results obtained with this new approach were superior to standard techniques used for both enzyme histochemical and morphological studies. Moreover, blocks of the embedded tissue were stored for at least one year at room temperature without loss of enzyme activity. This method should find a wide range of applications in histopathology.  5.4 SPECIAL STAINS: The substances ,usually dyes that are used to impart colour to diseased tissue which are helpful in studying pathological conditions are called special stains SPECIAL STAINS PERFORMED IN THE LABORATORY:ELEMENTS STAINED AND NAME OF STAIN: 5.4.1Microorganisms: y y Acid-Fast Organism: Fite stain Bacteria, blood elements: May - Grunwald Giemsa Stain

5.4.2Bacteria: Gram stain y y y Bacteria/Protozoa : Lillie's Azure A Eosin B Stain Helicobacter pylori: Toluidine Method Helicobacter pylori: Alcian yellow, automated

5.4.3Fungi y y Fungi : PAS green, both manual and automated Fungi/Cyptococci: Mucicarmine

5.4.4Spirochetes:Steiner, automated. y Spirochetes Warthin -: Starry microwave method

5.4.5Connective tissue and lipids y y Collagen: Gomori's One-Step Trichrome Stain manual, Trichrome automated Elastic fibers : Verhoeff - Van Gieson stain

y y

Reticulin: Wilder's method, both manual and automated Fat and Oil: red O stain for frozen section

Carbohydrates y y y y Mucopolysaccharid-acid: Modified Mowry's Colloidal iron stain Mucopolysaccharid-acid: Alcian Blue pH 2.5 or pH 1.0 Acid and neutral mucopolysaccharides: Alcian blue 2.5 and PAS Sialomucin: Mayer's mucicarmine stain

Amyloid y y Alkaline Congo Red stain Lieb's crystal violet method

Minerals, pigments and miscellaneous y y y y y y Calcium: Kossa's method Iron:Gomori's method Melanin: Fontana Masson Silver stain Melanin removal: Permanganate method Charcott Leyden crystals:Luna stain Muscle striations: Mallory's PTAH stain

Immunofluorescence: is a technique used for light microscopy with a fluorescence microscope and is used primarily on biological samples. This technique uses the specificity of antibodies to their antigen to target fluorescent dyes to specific biomolecule targets within a cell, and therefore allows visualisation of the distribution of the target molecule through the sample. Immunofluorescence is a widely used example of immunostaining and is a specific example of immunohistochemistry that makes use of fluorophores to visualise the location of the antibodies. Types of immunofluorescence:There are two classes of immunofluorescence techniques, primary (or direct) and secondary (or indirect). Primary (direct): Primary, or direct, immunofluorescence uses a single antibody that is chemically linked to a fluorophore. The antibody recognizes the target molecule and binds to it, and the fluorophore it carries can be detected via microscope. This technique has several advantages over the secondary (or indirect) protocol below because of the direct conjugation of the antibody to the fluorophore. This reduces the number of steps in the staining procedure, is therefore faster, and can avoid some issues with antibody cross-reactivity or non-specificity, which can lead to increased background signal. Secondary (indirect): Secondary, or indirect, immunofluorescence uses two antibodies; the first (the primary antibody) recognises the target molecule and binds to it, and the second (the secondary antibody), which carries the fluorophore, recognises

the primary antibody and binds to it. This protocol is more complex than the primary (or direct) protocol above and takes more time but allows more flexibility.

Immunofluorescence microscope Immunohistochemistry or IHC : Itrefers to the process of detecting antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues.[1] IHC takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Uses: y Diagnosis of neoplasia. Often, the tissue origin of a tumor cannot be determined with routine histology. Using specific antibodies for different tissues or cells (e.g., cytokeratin for epithelium, vimentin for mesenchymal cells, lymphoid markers, etc); the origin of many tumors can be determined with IHC. Detection of micrometastases. Early metastasis can be difficult to detect using conventional histology. IHC highlights the presence of single or small groups of neoplastic cells in metastatic sites. Early detection of micrometastases increases the chances of survival with surgical removal of affected nodes or by modification of the treatment protocol. Prognostic markers. Some proteins are expressed in neoplastic, but not in normal mature cells (e.g. embryonal proteins), expressed in neoplastic cells in larger amounts than in normal cells (e.g. cycle-related proteins), or structurally modified in neoplastic cells (mutant p53 protein). These changes may have prognostic significance in specific tumor types. It has been reported recently that the immuno-histochemical detection of KIT protein in mast cell tumors of dogs has prognostic significance Diagnosis of infectious diseases. Detection of antigens of an infectious agent with IHC has etiologic significance. The advantage of IHC over microbiologic techniques is that antigen detection can be correlated with histopathologic

changes and thus can confirm the significance of a particular bacterial or viral isolate obtained by other methods. Submitting samples for immunohistochemical testing:. Test samples that have been fixed in formalin, so you do not have to do anything special. Just submit the sample as you would for routine histopathology. Please, do not hold fixed samples in your office longer than 2 days as prolonged fixation may destroy antigens. Interpretation of results: Immunohistochemistry facilitates diagnosis of infections and determining the histogenesis and prognosis of neoplasms. A colored reaction (provided that it is specific according to the controls used), indicates the presence of components of the antigen (infectious agent, neoplasm, prognostic marker) sought. Whether this result is significant must be interpreted in the context of the case, as is true for other diagnostic techniques. A careful assessment of the clinical history, lesions and all test results should be made before formulating a definitive diagnosis. Conversely, a negative result by immunohistochemistry does not eliminate the possibility of a particular infectious agent or its potential significance to the case. Due to mutations or other mechanisms, neoplastic cells may modify (upregulate/ downregulate) the expression of proteins resulting in unexpected results. It is important to re-emphasize that immunohistochemistry results, like those obtained by other diagnostic methods, must be supported by clinicopathologic data. Immunohistochemical results should be interpreted by the diagnostician provided that he/she has all the information pertaining to the case.  Cytogenetics: It is a branch of genetics that is concerned with the study of the structure and function of the cell, especially the chromosomes.[1] It includes routine analysis of G-Banded chromosomes, other cytogenetic banding techniques, as well as molecular cytogenetics such as fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH). Techniques: Karyotyping:Routine chromosome analysis (Karyotyping) refers to analysis of metaphase chromosomes which have been banded using trypsin followed by Giemsa, Leishmanns, or a mixture of the two. This creates unique banding patterns on the chromosomes. The molecular mechanism and reason for these patterns is unknown, although it likely related to replication timing and chromatin packing. It involves : y y Cell selection:cells capable of growth and division are selected for cytogenetic analysis Slide preparation/cell culture: Cells from bone marrow, blood, amniotic fluid, cord blood, tumor, and tissues (including skin, umbilical cord, liver, and many other organs) can be cultured using standard cell culture techniques in order to increase their number. A mitotic inhibitor (colchicine, colcemid) is then added

to the culture. This stops cell division at mitosis which allows an increased yield of mitotic cells for analysis. The cells are then centrifuged and media and mitotic inhibitor is removed, and replaced with a hypotonic solution. This causes the cells to swell so that the chromosomes will spread when added to a slide. After the cells have been allowed to sit in hypotonic, Carnoy's fixative (3:1 methanol to glacial acetic acid) is added. This kills the cells, lyses the red blood cells, and hardens the nuclei of the remaining white blood cells. The cells are generally fixed repeatedly to remove any debris or remaining red blood cells. The cell suspension is then dropped onto specimen slides. After aging the slides in an oven or waiting a few days they are ready for banding and analysis. STAINING/Advent of banding techniques:Human male karyotype: In the late 1960s, Caspersson developed banding techniques which differentially stain chromosomes. This allows chromosomes of otherwise equal size to be differentiated as well as to elucidate the breakpoints and constituent chromosomes involved in chromosome translocations. Deletions within one chromosome could also now be more specifically named and understood Microscopic Analysis: Analysis of banded chromosomes is done at a microscope by a clinical laboratory specialist in cytogenetics (CLSp(CG)). Generally 20 cells are analyzed which is enough to rule out mosaicism to an acceptable level. The results are summarized and given to a board-certified cytogeneticist for review, and to write an interpretation taking into account the patients previous history and other clinical findings. The results are then given out reported in an International System for Human Cytogenetic Nomenclature 2009 (ISCN2009).

Applications: Human abnormalities and medical applications: In the event of procedures which allowed easy enumeration of chromosomes, discoveries were quickly made related to aberrant chromosomes or chromosome number. In some congenital disorders, such as Down's syndrome, cytogenetics revealed the nature of the chromosomal defect: a "simple" trisomy. Abnormalities arising from nondisjunction events can cause cells with aneuploidy (additions or deletions of entire chromosomes) in one of the parents or in the fetus. In 1959, Lejeune[16] discovered patients with Down syndrome had an extra copy of chromosome . Down syndrome is also referred to as trisomy .  An electron microscope :Itis a type of microscope that uses a particle beam of electrons to illuminate the specimen and produce a magnified image. Electron microscopes (EM) have a greater resolving power than a light-powered optical microscope, because electrons have wavelengths about 100,000 times shorter than visible light (photons), and can achieve better than 50 pm resolution and magnifications of up to about 10,000,000x, whereas ordinary, non-confocal light microscopes are limited by diffraction to about 200 nm resolution and useful magnifications below 2000x. Typical Applications

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Ultrastructural pathology Quantification of peroxisomes Viral particle identification, characterization and tabulation Cell culture contamination identification Evaluation of tissue/medical device interface Characterization of red blood cell morphology Sectioning of peripheral nerves for neurotoxicology

Transmission Electron Microscopy This imaging technique gives investigators precise data on mitochondria, peroxisomes, smooth and rough endoplasmic reticulum, cytoplasmic granules and inclusion bodies, which assist in determining a compounds mode of action, understanding the pathogenesis of toxicologically related lesions and establishing no observable effect levels. Our investigators perform a variety of ultrastructural analyses, ranging from simple qualitative evaluations to enumeration of lysosomes and peroxisomes, as well as morphometric studies measuring collagen and amyloid fibrils. Subtle lesions not visible in standard H&E slides can be observed and likely pathogenic mechanisms may be identified. Scanning Electron Microscopy: SEM enables the investigator to examine the surface topography and morphology of cells, tissues or medical devices by scanning a beam of electrons across a sample. This imaging technique may be employed in studies in which exterior damage or integrity is of concern. Tissue samples can be mounted such that alterations in cellular growth can be monitored. Samples can be photographed on an SEM and reviewed by our veterinary pathologists.  Flow cytometry (abbreviated: FCM) :It is a technique for counting and examining microscopic particles, such as cells and chromosomes, by suspending them in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of up to thousands of particles per second. Flow cytometry is routinely used in the diagnosis of health disorders, especially blood cancers, but has many other applications in both research and clinical practice. A common variation is to physically sort particles based on their properties, so as to purify populations of interest. Applications: The technology has applications in a number of fields, including molecular biology, pathology, immunology, plant biology and marine biology. It has broad application in medicine (especially in transplantation, hematology, tumor immunology and chemotherapy, genetics and sperm sorting for sex preselection). In marine biology, the auto-fluorescent properties of photosynthetic plankton can be exploited by flow cytometry in order to characterise abundance and community structure. In protein engineering, flow cytometry is used in conjunction with yeast display and bacterial display to identify cell surface-displayed protein variants with desired properties. It is also used to determine ploidy of grass carp fry.

 Molecular pathology: It is an emerging discipline within pathology which is focused in the study and diagnosis of disease through the examination of molecules within organs, tissues or bodily fluids. Molecular pathology shares some aspects of practice with both anatomic pathology and clinical pathology, molecular biology, biochemistry, proteomics and genetics, and is sometimes considered a "crossover" discipline. It is multi-disciplinary in nature and focuses mainly on the sub-microscopic aspects of disease. MOLECULAR METHODS: y Polemerase chain reaction : PCR:It is the most frequently used molecular technique in a molecular pathology laboratory. Using a pair of priming complementary sequences (oligonucleotide primers) flanking a location of interest, together with unique heat-resistant polymerases (DNA copying enzymes), multiple copies of a targeted chimeric gene can be obtained (Figure (Figure22). Each PCR cycle involves 3 basic steps: denaturing, annealing, and polymerization. During denaturing, the 2 strands of the helix of the target genetic material are unwound and separated by heating at 90 to 95C. During annealing, or hybridization, oligonucleotide primers bind to their complementary bases on the single-stranded DNA. This step requires a much cooler temperature, 55C. Finally, during polymerization (at 75C), the polymerase reads the template strand and quickly matches it with the appropriate nucleotides, resulting in 2 new helixes consisting of part of the original strand and the complementary strand that was just assembled. The process is repeated 30 to 40 times, each cycle doubling the amount of the targeted genetic material. At the end of the PCR procedure, millions of identical copies of the original specific DNA sequence have been generated. Fluorescent in situ hybridization: FISH is based on the use of fluorescencelabeled oligonucleotide probes that specifically attach to their complementary DNA sequence target on the genome and label that region with fluorescence color (e.g., Texas red, FITCI green, acridine orange). The labeled region can then be easily visualized under a fluorescence microscope. Currently, 3 types of probes are in wide use: Centromeric probes that identify the centromeric region of a specific chromosome and thus help in enumerating the number of copies of that chromosome even in a nondividing cell interphase state) DNA microarrays: Gene expression profiling using DNA microarrays holds great promise for the future of molecular diagnostics. This technology allows, in one assay, for simultaneous assessment of the expression rate of thousands of genes in a particular sample. The 2 types of DNA microarrays that are widely used are cDNA microarrays and oligonucleotide/DNA chips.

Computers in pathology laboratory: Computer is defined as an electronic instrument which converts raw data into useful information . Computational activities of any Pathology Department can be divided into two broad areas: 1. Administrative

2.

Academic

ADMINISTRATIVE ACTIVITIES:Every Pathology Department whether small or big has substantial amount of administrative work as volume of data is large. The administrative applications include inventory control attendance, and correspondence. One of the most important applications is Records.ie patient reports{Histopathology, Cytology etc and routine correspondence for which a computer is ideally suited. ACADEMIC: The academic applications are those which help the Pathologist in his or her professional practice. Softwares are often tailored to meet the requirements of each application.T here may be some overlap between the administrative and academic applications. y y y y y y y y y y Patient reports and records Inventory control Professional writings and presentations Expert Systems and Knowledge bases CDs and ebooks in Pathology for teaching students MCQ Banks Checking answer sheets of students. Statistics Continuing Medical Education E-mail and Internet access

Research. Anybody who is involved in research knows that a very large part of research work is tedious tabulations, data analysis and painstaking interpretation of experiments. All this can be greatly facilitated using a computer leaving valuable time for the researcher to spend on actual scientific working.. Internet based conferences can be organized Reporting Softwares: They are commercially available usually using a database management system. If billing is not the need of Pathology department an easy way of making reporting software is to make a directory in MS-word named Pathology Reports. Make Sub Directories named Histopathology, Cytology and and Hematology.In each of these make further sub directories for each organ. While reporting make each report with the file name containing the name on number of the report for easy detection.  CELL PROLIFERATION ANALYSIS : it is widely useful to assess the degree of cell proliferation in tumour cells and involves following : y Mitotic count: This method is used to count number of cells in mitosis in carcinoma y Radioautography: This technique may be used to determine the tissue localization of a radioactive substance, either introduced into a metabolic pathway, bound to a receptor or enzyme, or hybridized to a nucleic acid. The film or emulsion is apposed to the labeled tissue section to obtain the

autoradiograph (also called an autoradiogram). The auto- prefix indicates that the radioactive substance is within the sample, as distinguished from the case of historadiography or microradiography, in which the sample is X-rayed using an external source. The use of radiolabeled ligands to determine the tissue distributions of receptors is termed either in vivo or in vitro receptor autoradiography if the ligand is administered into the circulation (with subsequent tissue removal and sectioning) or applied to the tissue sections, respectively. The nucleolus organizer region (NOR): It is a chromosomal region around which the nucleolus forms. This region is the particular part of a chromosome that is associated with a nucleolus after the nucleus divides. The region contains several tandem copies of ribosomal RNA genes.In karyotype analysis, a silver stain can be used to identify the NOR. Silver nitrate inserts into the NORassociated protein in the stalks and satellites, staining the proteins dark black. The amount of stain deposited and the number of NORs differs among the population, although the cell should normally have a maximum of 10 NORs per cell. Immunohistochemistry (IHC) is used to diagnose the type of cancer and to help determine the patient's prognosis. In cases such as metastases or carcinoma of unknown primary origin, where it may be difficult to determine the type of cell from which the tumor originated, immunohistochemistry can identify cells by the characteristic markers on the cell surface. IHC can also help distinguish between benign and malignant tumours.