Special stains are staining techniques used in addition to hematoxylin and eosin staining to provide additional information. Some common special stains include fat stains like Oil Red O to identify lipids, periodic acid Schiff to identify carbohydrates like glycogen and mucins, amyloid stains like Congo Red to identify amyloid deposits, trichrome stains to identify collagen and connective tissues, elastic stains to identify elastic fibers, and acid fast stains to identify acid fast organisms like mycobacteria. Romanowsky stains are commonly used in hematology to identify cells and parasites in blood and bone marrow samples.
COMPARISON OF CONVENTIONAL PAPANICOLAOU STAIN WITH MODIFIED ULTRAFAST PAPANIC...SURAMYA BABU
• Body fluid cytology is vital in diagnosis of various neoplastic and non neoplastic lesions and conventional Pap stain is the staining method of choice for the same.
• MUFP is a quick and cheap staining technique which gives good interpretation of cytological features with easily available reagents.
• Preservation of cell morphology and nuclear staining are superior with conventional Papanicolaou technique whereas cytoplasmic staining is comparable with conventional pap and MUFP techniques.
• Though background of stained smears was slightly better with conventional Pap staining; MUFP was superior in case of hemorrhagic samples.
COMPARISON OF CONVENTIONAL PAPANICOLAOU STAIN WITH MODIFIED ULTRAFAST PAPANIC...SURAMYA BABU
• Body fluid cytology is vital in diagnosis of various neoplastic and non neoplastic lesions and conventional Pap stain is the staining method of choice for the same.
• MUFP is a quick and cheap staining technique which gives good interpretation of cytological features with easily available reagents.
• Preservation of cell morphology and nuclear staining are superior with conventional Papanicolaou technique whereas cytoplasmic staining is comparable with conventional pap and MUFP techniques.
• Though background of stained smears was slightly better with conventional Pap staining; MUFP was superior in case of hemorrhagic samples.
This presentation deals tissue processing in histopathology, the detailed of presentation given blow:
Histology, study the organization of tissues at all levels, from the whole organ down to the molecular components of cells that are found in most multicellular plants and animals.
Animal tissues are classified as epithelium, with closely spaced cells and very little intercellular space; connective tissue, with large amounts of intercellular material; muscle, specialized for contraction; and nerve, specialized for conduction of electrical impulses. Blood is also sometimes considered a separate tissue type.
Plants are composed of relatively undifferentiated tissue known as meristematic tissue; storage tissue or parenchyma; vascular tissue; photosynthetic tissue or chlorenchyma and support tissue or sclerenchyma and collenchyma.
Human colors. color of normal and pathologic tissueManan Shah
Colors are important to all living organisms
They are crucial for protection, metabolism, sexual behavior, and communication.
Human organs obviously have color, that is, the liver is brown, the heart is red, bones are white, and so on.
by post graduates from Maratha Mandal's NathajiRao Halgekar Institute of Dental Sciences, Belgavi.
A step wise presentation of Amylodosis covering,
INTRODUCTION
DEFINITION
HISTORY
PHYSICAL NATURE
CHEMICAL NATURE
CLASSIFICATION
PATHOGENESIS
STAINING CHARACTERISTICS
DIAGNOSTIC TESTS
MORPHOLOGY
CLINICAL FEATURES
TREATMENT
PROGNOSIS
This presentation deals tissue processing in histopathology, the detailed of presentation given blow:
Histology, study the organization of tissues at all levels, from the whole organ down to the molecular components of cells that are found in most multicellular plants and animals.
Animal tissues are classified as epithelium, with closely spaced cells and very little intercellular space; connective tissue, with large amounts of intercellular material; muscle, specialized for contraction; and nerve, specialized for conduction of electrical impulses. Blood is also sometimes considered a separate tissue type.
Plants are composed of relatively undifferentiated tissue known as meristematic tissue; storage tissue or parenchyma; vascular tissue; photosynthetic tissue or chlorenchyma and support tissue or sclerenchyma and collenchyma.
Human colors. color of normal and pathologic tissueManan Shah
Colors are important to all living organisms
They are crucial for protection, metabolism, sexual behavior, and communication.
Human organs obviously have color, that is, the liver is brown, the heart is red, bones are white, and so on.
by post graduates from Maratha Mandal's NathajiRao Halgekar Institute of Dental Sciences, Belgavi.
A step wise presentation of Amylodosis covering,
INTRODUCTION
DEFINITION
HISTORY
PHYSICAL NATURE
CHEMICAL NATURE
CLASSIFICATION
PATHOGENESIS
STAINING CHARACTERISTICS
DIAGNOSTIC TESTS
MORPHOLOGY
CLINICAL FEATURES
TREATMENT
PROGNOSIS
Intracellular accumulation refers to the abnormal build-up or accumulation of substances within the cells of an organism. This phenomenon occurs when cells are unable to process, utilize, or eliminate certain substances effectively. These accumulated substances can be diverse and include lipids, proteins, carbohydrates, pigments, and other cellular components.
The accumulation may result from various factors such as genetic mutations, impaired enzymatic activity, or exposure to toxins. Intracellular accumulation can lead to cellular dysfunction, impaired organ function, and, in some cases, contribute to the development of diseases.
Examples of intracellular accumulation include lipid accumulation in hepatocytes (fatty liver disease), protein accumulation in neurodegenerative disorders like Alzheimer's disease, and pigment accumulation in conditions such as hemosiderosis or lipofuscinosis. Understanding the underlying causes and consequences of intracellular accumulation is crucial for developing effective strategies for diagnosis and treatment in medical and research contexts.Intracellular accumulation can manifest in different forms, each associated with specific substances and underlying mechanisms. Here are some additional details on notable types of intracellular accumulation:
1. **Lipid Accumulation:**
- Lipid accumulation, often seen in hepatocytes, can lead to conditions like fatty liver disease. Excessive triglycerides accumulate within liver cells, compromising liver function and potentially progressing to more severe liver disorders.
2. **Protein Accumulation:**
- In neurodegenerative diseases such as Alzheimer's and Parkinson's, misfolded proteins accumulate within neurons, forming aggregates that disrupt cellular function. This can contribute to the progressive degeneration of the nervous system.
3. **Glycogen Accumulation:**
- Glycogen storage disorders result from impaired metabolism of glycogen, leading to its abnormal accumulation within cells. This can affect various organs, including the liver, muscles, and heart, causing functional impairments.
4. **Pigment Accumulation:**
- Abnormal accumulation of pigments can occur, such as hemosiderin in conditions like hemochromatosis, leading to iron overload. Additionally, lipofuscin, often referred to as the "wear and tear" pigment, accumulates in cells over time and is associated with aging.
5. **Calcium Accumulation:**
- Dysregulation of cellular calcium levels can result in calcium accumulation within organelles. This can disrupt cellular signaling and contribute to conditions like calcific vasculopathy or dystrophic calcification in tissues.
Understanding the specific type of intracellular accumulation and its implications is crucial for developing targeted therapeutic interventions. Research in this field plays a vital role in unraveling the complexities of various diseases and advancing our knowledge of cellular biology and pathology.
Difference between Apoptosis versus Necrosis and Types of Necrosis.pptxRukhshanda Ramzaan
Apoptosis Versus Nercosis
Apoptosis Necrosis
Predefined cell suicide or programmed cell death. Natural physiological Process. Involve one cell at a time. Cell shrinkage (Dense eosinophilic cytoplasm) Pyknosis (Condensation) and Karyorrhexis (fragmentation) of nuclear material Formation of membrane blebs and apoptotic bodies
Phagocytosis of apoptotic bodies by Macrophages
Caspase dependent pathway
No Inflammation (no immune response) Premature, unprogrammed cell death always pathological. Involve many cells Cell Swelling (Swelling of endoplasmic reticulum and mitochondria) and membrane blebs Pyknosis (condensation), Karyorrhexis (Fragmentation) and Karyolysis (lysis)of the nucleus. Breakdown of the plasma membrane, organelles (enzymatic digestion), leakage of cellular contents
Increased eosinophilia, Accumulation of Myelin figures (whorled precipitated Phospholipids)
Initiate Inflammation (Strong immune response)
Difference between reversible and irreversible cell injury,Mechanism of cell ...Rukhshanda Ramzaan
Cell Injury: Any change resulting in loss of the ability to maintain the normal or adapted homeostatic state.
Agents that cause cell injury
• Hypoxia / Ischemia (loss of blood supply)
• Microbial
• Parasitic
• Chemical
• Physical
• Trauma
• Genetic
• Nutritious
• Environmental
Types of Cell injury
Reversible Cell Injury
Pathologic changes that can be reversed in mild cellular injury when the stimulus is removed. Cell injury is reversible only up to a certain point otherwise it will be irreversible.
Changes in reversible cell injury
Cellular Swelling: Due to accumulation of intracellular water and endoplasmic reticulum & mitochondria.
Clumping of chromatin.
Irreversible Cell injury
Pathologic changes that are permanent and cause cell death, they cannot be reversed to normal state.
Changes in irreversible cell injury
Irreversible injury is marked by severe mitochondrial vacuolization, extensive damage to plasma membranes, detachment of ribosomes from the granular endoplasmic reticulum (ER). Injury to lysosomal bodies leads to leakage of lysosomal enzymes into the cytoplasm and condensation, fragmentation and lysis of nuclei.
Cellular Response to cell Injury and Cellular Adaptations .pptxRukhshanda Ramzaan
Cellular Adaptations
ability of cells to respond to various types of stimuli and adverse environmental changes
Atrophy(decrease in cell size)
Hypertrophy(increase in cell size)
Hyperplasia(increase in cell number)
Metaplasia(change in cell type): Replacement of one differentiated cell type with another mature differentiated cell type that is not normally present in that tissue.
Dysplasia (increase in abnormal cell): Dysplasia is not cancer, but it may sometimes become cancer.
Terminologies used in Disturbances of Cell Growth which are not adaptations
Agenesis refers to the failure of an organ to develop during embryonic growth and development
Hypoplasia is the underdevelopment or incomplete development of a tissue or organ. It is technically not the opposite of hyperplasia (too many cells). Hypoplasia is a congenital condition, while hyperplasia generally refers to excessive cell growth later in life.
Aplasia is a birth defect where an organ or tissue is wholly or largely absent. It is caused by a defect in a developmental process.
Introduction to Pathology and how to describe a LesionRukhshanda Ramzaan
Introduction to general Veterinary Pathology, Gross examination description, How to describe lesion while doing Gross/ macroscopic examination, Postmortem lesion description at basic leve
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
2. The “special stains” refer to a
large number of alternative
staining techniques that are
used when the H&E does
not provide all the
information the pathologist
or researcher needs
3.
4. Fat stain
• Lipids cannot be demonstrated in routine tissue sections, as during processing the
tissue and clearing, lipids will be dissolved
• Lipids are routinely demonstrated in frozen sections or cryostat sections
• Special fat stains used are
• Oil Red O
• Sudan III
• Sudan IV
• Sudan Black
5. Thing to remember
For these lipid stains, frozen
formalin-fixed sections are
used instead of paraffin-
embedded sections
6. Photomicrograph of liver of goat with diffuse hepatic lipidosis showing fat droplets stained
orange yellow (Sudan III).
12. Mucins are a family of high molecular weight, heavily glycosylated proteins
(glycoconjugates) produced by epithelial tissues in most animals
13.
14.
15. Amyloidosis (Protein aggregation
disease)
• Abnormal deposit of insoluble polymeric protein fibrils (amyloid
starch like) in tissues and organa
• Fibrils formed by the aggregation of misfolded proteins,
normally soluble proteins and it is usually extra cellular
• Congo Red andThioflavin S are the two major histological
stains used to detect any form of amyloid.These dyes bind to
the characteristic β-pleated sheet conformation of amyloid
16.
17. Connective tissue
• Collagen is a strong protein and is a main component of ligaments and
tendon. It is also responsible for skin elasticity and is the most visible type
which can be visualized with an H&E.
• Elastic fibers are located in the skin and walls of blood vessels.They are
composed of elastin - a protein that is flexible and allows many tissues in
the body to resume their shape after stretching or contracting and are not
visualized by an H&E
• Reticular fibers are composed of collagen and form a delicate framework
around nerve fibers, fat cells, lymph nodes, and smooth and skeletal muscle
fibers.They are also not visualized by an H&E.
19. Standard applications Of MT stain: Masson's
trichrome staining is widely used to study muscular
pathologies (muscular dystrophy), cardiac pathologies
(infarct), hepatic pathologies (cirrhosis) or kidney
pathologies (glomerular fibrosis). It can also be used to
detect and analyze tumors on hepatic and kidney
biopsies
20.
21.
22. Liver section stained with
a Gomori’s Trichrome that
colors collagen, green rather
than blue
24. Verhoef stain/ Elastic Stain
Elastic Stain is used to identify the
atrophy of elastic tissue as in emphysema,
evidence of vascular diseases
(arteriosclerosis), and the invasion of
tumors into vessels.
Elastic fibers and nuclei being stained
black, collagen stained red and
cytoplasmic elements stained yellow
25. Skin stained with Elastic Stain
Elastin fibers and elastic lamina in
histological specimens are stained
black, while remaining tissue
elements are stained as follows:
nuclei - blue/black, collagen - red,
other tissue elements - yellow.
26. Reticulin fibers support the body
and are common in the liver,
spleen and kidneys.
Characteristic reticulin patterns
can help diagnose cirrhosis of the
liver, early fibrosis in bone marrow
and tumors
Black Stained Reticulin Fibers
Reticulin Fiber Stain
27. A mast cell is a type Of white blood cellsresident cell of connective tissue that contains many
granules rich in histamine and heparin. Important in allergic and parasitic infection
32. Nucleic Acid (Feulgen Stain)
This Feulgen stain demonstrates DNA (magenta) in breast carcinoma tissue.
DNA Magenta
Background Light
green
33.
34.
35.
36. Acid fast stains /Ziehl–Neelsen
staining
Acid fast stains are used to
differentiate acid fast organisms
such as mycobacteria. Acid fast
bacteria have a high content of
mycolic acids in their cell walls
38. Romanowsky Stains
• Romanowsky Stains are the stains (a mixture of
oxidized methylene blue (azure) dyes and Eosin )
that are used in hematology and cytological studies,
to differentiate cells in microscopic examinations of
blood and bone marrow samples.These stains are
also applied to detect the presence of parasites in
the blood such as malaria parasites. For example
• Giemsa stain
• Wright andWright-Giemsa stain
• May-Grunwald stain
• Leishman stain
43. Giemsa-stained section of small
intestinal mucosa showing
clusters of Giardia that stain
purple (arrows) in the crypts.The
background is stained faint pink
by eosin.
44. Grocott methenamine silver (GMS)
stain
GMS is commonly used for the
identification of fungi on cytosmears
and tissue sections. It imparts a black
color to the fungal profiles and a pale
green color to the background. It
stains all pathogenic and
nonpathogenic fungi
45.
46.
47. Von Kossa stain is widely used in histology
to detect the presence of abnormal
calcium deposits in the body. The
principle of this coloration is based on the
transformation of calcium salts into silver
salts: calcium ions, bound to phosphates,
are replaced by silver ions brought by a
solution of silver nitrate. Placed under a
light source, the silver phosphates undergo
a photochemical degradation, leading to the
observation of metallic silver deposits.
