Content Slide

Anatomy 3
Physiology 71
Histology 148
Biochemistry 195
Pathology 213
Microbiology 224
Parasitology 232
 Fossa Content
Infratemporal 1. Muscles of mastication: insertion of temporalis, medial and lateral pterygoid
Fossa muscles.
2. Blood vessels
❑ First and second parts of maxillary artery and their corresponding branches.
❑ Pterygoid venous plexus.
3. Nerves: Mandibular nerve and its branches, otic ganglion and chorda tympani.
4. Ligaments : Sphenomandibular ligament
Pterygopalatin a. Maxillary nerve.
e Fossa b. Pterygopalatine (sphenopalatine) ganglion.
c. Third part of maxillary artery.
 Foramen Structures passing through it
Mental foramen ❑ Terminal branches of the inferior alveolar nerve (the mental nerve)
❑ Mental artery,
❑ Mental vein

Submandibular foramen ❑ Inferior alveolar nerve

❑ Inferior alveolar artery
❑ Inferior alveolar vein
 Muscle - Nerve Supply
it is formed of 3 parts: temporal and zygomatic
a. Orbital part (around the orbital margin): branches of facial nerve.
It closes the eye firmly and suddenly in
Orbicularis oculi danger.

b. Palpebral part (in the eye lids): It closes

the eye gently as in sleep.

c. Lacrimal part: It stretches and dilates the

lacrimal sac to help in drainage of tears.
 Muscle Nerve Supply Action
It consists of extrinsic and intrinsic Buccal and mandibular It is responsible for the
parts: branches of facial movements of the lips and
❑ The intrinsic part surrounds the nerve. act as a sphincter for the
mouth in the upper and lower lips. mouth to close it.
❑ The extrinsic part is formed as
Orbicularis extensions from the surrounding
oris muscles as the buccinator muscle
 Muscle Origin Insertion Nerve Supply Action
Masseter a. Superficial fibers: from Both fibers are inserted Anterior division of 1. Protrusion of the
lower border of zygomatic into the lateral surface mandibular nerve mandible by
arch of ramus of mandible superficial fibers
b. Deep fibers: from deep 2. Elevation by deep
surface of zygomatic arch fibers

Sternomastoid Two heads: Lateral surface of 1. Spinal part of 1. When one muscle
1. Sternal head: Rounded, mastoid process and accessory nerve acts alone, it bends
tendinous head which lateral half of superior (motor). the head to the same
arises from the anterior nuchal line side and rotates the
surface of the upper part 2. Ventral rami of C2 face to the opposite
of manubrium of sternum. and C3 (sensory) side.
2. When the two
2. Clavicular head: Broad, muscles act together
fleshy head which arises they produce flexion
from the medial third of of the neck by
the upper surface of the projecting the head
clavicle. forwards.
They also raise the
head from the supine
position.
 Muscle Origin Insertion Nerve Supply Action
Temporalis a. Temporal fossa a. Tip and medial Anterior division of 1. Elevation of
b. Temporal fascia surface of coronoid mandibular nerve mandible by
c. Inferior temporal process anterior fibers
line b. Anterior border
of ramus of 2. Retraction by
mandible posterior fibers
Muscle Origin Insertion Nerve Supply Action
Lateral a. Upper head: The 2 heads of the Anterior division of 1. Both ms.
pterygoid from infra-temporal surface muscle unite together at mandibular nerve Produce depression
and crest of GW of sphenoid a tendon which enters of mandible
TM joint and inserted
b. Lower head: into: 2. Lateral and medial
from lateral surface of lateral 1. Pterygoid fovea pterygoid of one side
pterygoid Plate of neck of mandible protrude mandible to
2. Articular disc the opposite side
3. Capsule of TM Joint
Medial a- Superficial head: small Medial surface of angle Trunk of 1. Both muscles
pterygoid slip from Maxillary tuberosity and ramus of mandible mandibular nerve elevate the mandible
below the mandibular
b- Deep head: from medial foramen 2. As 2 in lateral
surface of lateral pterygoid pterygoid
plate.
 Muscle Origin Insertion Nerve Supply Action

Omohyoid 1. Upper scapular 1. Intermediate branch from ansa it act with

border near the tendon cervicalis (Sternohyoid –
supra-scapular notch Sternothyroid –
and supra scapular Thyrohyoid ) during
ligament swallowing to
depress hyoid bone
2. Intermediate 2. Body of hyoid and thyroid
tendon of omohyoid bone lateral to cartilage.
muscle sternohyoid
muscle
Parotid gland Submandibular gland
❑ Blood vessels: ❑ Arterial supply : Glandular branches of facial artery.
Arteries : from superficial temporal artery. ❑ Nerve supply :
Veins : The retromandibular and external jugular veins. 1. Parasympathetic: From chorda tympani nerve
2. Sympathetic: From sympathetic plexus around facial
❑ Nerve supply of the parotid gland: artery
1. Parasympathetic: The parotid gland receives 3. Sensory: From lingual nerve
parasympathetic secretomotor fibers from the
glossopharyngeal nerve.
2. Sympathetic: From the sympathetic plexus around
the external carotid and middle meningeal arteries.
3. Sensory: From the auriculotemporal nerve
 Muscle Origin Insertion Nerve Supply Action
Digastric ❑ Anterior belly: from Into intermediate a. Anterior belly: a. Depression of the
muscle digastric fossa of tendon which is Nerve to mylohyoid mandible, when the
mandible. connected to hyoid (from mandibular hyoid bone is fixed.
❑ Posterior belly: from bone by a fibrous loop. nerve).
digastric fossa (mastoid b. Posterior belly: b. Elevation of hyoid
notch) on the medial Facial nerve. bone in swallowing,
surface of mastoid when the mandible
process. is fixed.

Mylohyoid The whole length of a. Anterior and middle nerve to mylohyoid a. Elevation of hyoid
muscle mylohyoid line of the fibers inserted into the from inferior alveolar bone and floor of
mandible mylohyoid raphe. nerve (mandibular mouth.
nerve).
b. Posterior fibers b. Depression of
inserted into body of mandible when
hyoid bone. hyoid bone is fixed.
Vision experiments
Layers of the eye
 Miosis d
My riasis
(constriction of
the pupil)
d
( ilatation of
the pupil)
Think of “ micro”
Think of “Letter d”
 The Visual Field
❑ It is the maximal visual area seen by ONE FIXED eye

❑ Represented in area 17 in OPPOSITE MANNER to that of retina

so the temporal half of retina sees the nasal half of the visual field
and vice versa.
• It is measured by the perimeter or confrontation method
• It is irregular (NOT circular) and it extends:
▪ Upwards (50)
▪Downwards (80)
▪Nasally (60)
▪Temporally (> 90)
❑ Importance of visual field determination:

1) Localization of blind spots (scotomas)

2) Localization of visual pathway defects
3) Diagnosis of some retinal diseases
e.g., retinitis pigmentosa (loss peripheral field before central cone)
1) Confrontation method 2) Perimeter
1) Confrontation method
 2) Perimeter
• The subject should stand 1 foot
away from the blackboard and
should cover one eye and fix
the vision of the other eye on a
marked central point on the
blackboard. The demonstrator
will bring a piece of white chalk
(about 1 inch) into the field of
vision and mark the point
where it is seen. This should be
repeated in all directions
• How to differentiate between lesion in optic tract, LGB and optic
radiation?
Light reflex is preserved in the lesions of LGB and optic radiation. WHY??
(Refer to pathway of light reflex)

• How to differentiate between lesion in LGB and occipital lobe?

In occipital lobe lesion the macula is spared. WHY???

• The sparing of macula is due to:

a. The large cortical area of representation.
b. The double blood supply.
c. Association fibers between 2 maculae.
The sparing of macula is due to:
1) Large cortical representation
2) Bilateral cortical representation (association fibers between 2 maculae)
3) Double blood supply (PCA & collaterals from MCA)
1) Light Reflex (pupillary) : (2,3)
Exposure of ONE eye to light
→ constriction of BOTH pupils
• Afferent: Optic nerve
→ Optic chiasma (partial decussation)
→ Optic tract (no relay in LGB)

• Centre: Pretectal nucleus

→ Both Edinger westphal nucleus
→ Both Oculomotor N. (CN 3)
→ciliary ganglion → constriction of pupillae
muscles

• Response: miosis
2) Light Response: (2,7)
Exposure of ONE EYE to intense light or
approaching object results in reflex closure
of BOTH EYE LIDS

• Afferent: Optic nerve (CN 2)

• Center: Superior colliculus
• Efferent: Facial nerve (CN 7)
•Reflex: Closure of both eyes (Orbicularis oculi)
It is composed of 2 components:

Menase reflex:
• Dazzle reflex:
"foreign object" "intense light"
 3) Corneal Reflex: (5, 7)
Touching cornea, conjunctiva, and eye lashes of
ONE EYE
→ Closure of BOTH EYES
Afferent: Trigeminal nerve "ophthalmic division"
• Center: Superior colliculus
• Efferent: Facial nerve (CN 7)
• Reflex: Closure of both eyes (Orbicularis oculi)
Near Response (Near Reflex)

miosis
Accommodation
• The process by which the ant. curvature of the lens is increased and focus is
adjusted on the retina to see near objects clearly.
• Why anterior not posterior??
 4- Testing for
Accommodation : "Purkinje
Sanson's images"

• Have your partner focus his sight on an object at a distance

more than 6 meters. Carefully observe the size
of his pupil as the object is brought closer to his eyes.

• Repeat the same experiment, while you are holding a

candle beside the eye.

• Normally if we put a candle in front of the patient's eye, 3

images will be reflected from his eye:
• Small clear upright image (cornea).
• Large faint upright image (anterior surface of the lens).
• Small clear inverted image (posterior surface of the lens).
 5- Testing for
Accommodation

• Looking to a near object:

• Ask the patient to look to your finger in front of

his eye while you are observing the images
carefully.
• The followings occur:
• The 1st & 3rd images do not change.
• The 2nd image becomes smaller, clearer and
approaches the first image; this means that the
anterior surface of the lens will change its
curvature.
Testing for
Accommodation:

• 1- Ask patient to fix his eyes on a

distant object
• 2- Bring your finger in front of
his eyes and ask him to focus his
eyes on it
• 3- Observe 3 changes which
occur.
Testing for Accommodation
Near Response
Convergence: is to allow falling of the 2 images of the object on the corresponding points of the
retina i.e. point on a nasal retina in one eye and point on the temporal retina in the other eye
which when stimulated it will stimulate one cortical neuron to prevent diplopia (double vision).
Miosis is to decrease the amount of light entering into the eye to prevent chromatic and spherical
aberration.

Accommodation: Increase power of the lens by increasing curvature of the lens by contraction of
the ciliary muscle mainly anterior
 Accommodation
Pathway of Near
miosis
Reflex (2,3) convergence

Short ciliary Motor

nerves fibers

Ciliary ganglion Optic

chiasma

Occulomotor
nerve

Edinger Westphal
Optic tract
nucleus

Lateral Geniculate Body

Superior Colliculus

Optic Radiation

Primary
visual cortex
If 3 types of cones stimulate the same
ganglion cell (dominator), its signals
play no role in color detection.

COLOUR BLINDNESS:
Inability to perceive portion of
spectrum and detect different colors

1- Red: prot
2-Green: deuter
3-Blue: trit

Anomaly = weakness
Anopia = blindness
 Visual Acuity
It is the ability of the eye to detect the separation between 2 adjacent objects
and detect details & contour of objects.

Measured by the minimum separable distance.

Visual angle at ONE MINUTE= 1/60 degree

the nodal point

The rays from the 2 objects fall at 2 separate cones at the retina,
with one unstimulated cone in between (the diameter of the
cone is 3 microns).
 Determination of visual acuity (Landolt Chart)

CC C

The patient is 6 meters far away from the chart due to:
1- No accommodation. 2- The two ends of the letter "C" of the
smallest row makes an angle one minute at a distance 6 meters
which corresponds to 4 microns distance on the retina "2 cones
stimulated and one unstimulated in between. The two ends of the
biggest row make an angle one minute at 60 meters if one person
sees the last row at 6 meters, his visual activity is 6/60
 How to test visual acuity ?

Snellen chart
Landolt broken C
chart
Visual acuity =
distance from chart / reading distance of identified raw.
• Discover the last row the patient sees = D

• Visual acuity is the ratio between one’s acuity and that

of normal person

• The patient’s visual acuity= d/D

• If the patient sees all rows, his visual acuity is 6/6

• What is meant by? 6/9

A normal person is able to resolve details that subtend
one minute in his eye when they were held 9 meter away,
but the distance at which patient is able to resolve this
detail is 6 meters.
Factors affecting visual acuity??
• Errors of refraction (myopia, hypermetropia,
astigmatism)

• Degree of illumination & contrast

• Diseases of the eye (glaucoma, cataract)

• Miosis → +++ visual acuity

• Fovea centralis → Highest visual acuity

If patient failed in seeing the Snellen's chart: Do

1- Finger counting 2- Hand movement 3-PL
3- Astigmatism (No point focus)

The curvatures of the cornea are not the same

in all planes or directions SO rays in one plane
are focused on the retina while those in other
plane do not.

It is corrected by cylindrical lens with its

longitudinal axis perpendicular to the plane to
be corrected.
 Astigmatism Chart

1- Ask the subject to stand about 6 meters away from

an astigmatism chart, and cover one eye.
This chart consists of a number of dark lines radiating
from a central point. If there is astigmatism, some of
the lines will appear sharp and dark, whereas others
will appear blurred and lighter because they come to
a focus either in front of or behind the retina.

2- Repeat this procedure using the other eye

 11- Blind Spot “Cross & circle experiment”

• Optic disc is an area in which

optic nerve fibers of whole
retina are collected & emerge
as an optic nerve; it has no
receptors, so called blind
spot.
• Procedure:
• 1- A paper with the drawing of the circle (O)
and the cross (X).

• 2- Hold the paper 30 cm from your face with

the left eye closed. Focus on the cross
(nasally), Keeping your right eye focused on
the cross, slowly bring the paper closer to
your face until the circle disappears. Continue
to move the paper slowly toward your face
until the circle reappears.

• 3- Repeat this procedure with the left eye

Normally it is 4-6 mm from the fovea on the
nasal part of the retina (temporal field)
 A 6 cm B

Image distance = Image size D 25 cm

Object distance Object size

15-20 mm = ???????
25 cm (250 mm) 6cm (60 mm) F Why blind spot does not
15 mm
appear in binocular vision?

B’
A’
Smell Sensation
 Smell sensation

Close eye
Close one nostril

Smell a non-irritant
familiar odor (ground
coffee) → avoid
stimulation of the
trigeminal nerve which
supplies the nasal mucosa
Causes of loss of smell sensation
“ANOSMIA"

1- Local cause: common cold.

2- Central cause: lesion of
olfactory nerve.
3- Hysterical.
Gustatory (Taste) Sensation
 10% solution of Weak solution of
sodium chloride. quinidine sulphate.
(Salt → dorsum of (Bitter → dorsum
tongue 2/3 of tongue 1/3
anteriorly) posterior)

3% solution of 5% solution of cane

vinegar (Sour- sugar (sweet → tip
edges of tongue) of tongue)
Cotton swabs and mirror
Dry the dorsum of the tongue
with a clean dry tissue Map the areas of
the tongue which
are sensitive to
different tastes
using 4 soaked
swabs moistened
by different
reagents
Dr. Omnia Mohamed
DEAFNESS
 What are causes of conductive and nerve deafness?

Conductive deafness Nerve (sensorineural) deafness

Disturbance in conduction of Lesion of auditory nervous

sound vibrations to basilar pathway

membrane Damage of organ of Corti,

• Ext. and middle ear diseases cochlear nerve, or auditory

• Blockage of Eustachian tube cortex

 Tuning
fork tests

Short arms, High frequency tuning fork

 Tuning
fork tests
Rinne's Test
 Rinne's Test
Cause the tuning fork to vibrate
by striking it against the palm
of your hand.

The vibrating tuning fork is

placed on the mastoid process
until the subject no longer
hears it, then the fork is held in
air next to the ear.
 Rinne's Test
Can you hear the
sound now?
Yes, because air
conduction is better
than bone conduction
(A.C. > B.C)

A normal person hears

vibrations in air after bone
conduction is over.
 Rinne's Test

In conduction deafness,
the person does not
hear the sound in air
after bone conduction
is over in the diseased
ear (B.C.> A.C.)
Rinne's Test

In nerve deafness
sound in air is heard
after bone conduction
is over
(A.C.> B.C.)
Weber’s Test
 Weber's Test
The base of vibrating tuning
fork is placed on the center of
the patient's forehead

From where does the sound seem

to come?
From both ears or center of head

In normal person, the sound is

equally heard in both ears
 Weber's Test
Close one ear.
• Is there any change in
the sound heard? Yes,
it is more in closed ear.
In conductive deafness, the
sound is better heard in the
diseased ear (not masked by
noise from the external world)
 Weber's Test

In nerve deafness,
sound is louder in
normal ear
What do you mean by masking effect of
Environmental noises?
Pure Tone Audiometry Detection of hearing disabilities

Earphones
electronic Electronic
oscillator emit vibrator for
pure tones of testing bone
various conduction
frequencies from the
through mastoid
earphone to the process to the
subject cochlea
Pure Tone Audiometry

zero intensity
(0 dB) level of
sound at each
frequency is
the intensity
that can be
barely heard
by normal
person
Pure Tone Audiometry

“Y” axis →
intensity
of sound
in decibel
(dB)

“X” axis → frequencies of sound in Hertz (Hz)

Pure Tone Audiometry

Test 8 to 10
frequencies covering
auditory spectrum, one
at a time and the
hearing loss is
determined for each of
these frequencies
Pure Tone Audiometry
Apply different frequencies
from 125 Hz to 8000 Hz

Draw air conduction audiogram

Place bone vibrator over the

mastoid process

Draw bone conduction

audiogram.
Air and bone conduction audiograms are
Repeat the same steps to other
ear and draw air and bone plotted for interpretations
conduction audiograms.
Pure Tone Audiometry

Give the patient

sounds with different
frequencies and
different intensities
Compare air
conduction and bone
conduction of each ear
separately
Pure Tone Audiometry

Normally: Air
conduction is better
than bone conduction

Normal Audiogram
Ç= air conduction
X= bone conduction
What is the difference between audiogram of conductive deafness
and nerve deafness?
Nerve Deafness Conductive Deafness
 Nerve Deafness Conductive Deafness

Both curves show elevated threshold Air conduction curve shows elevated threshold
Bone and air conduction are equally affected Bone conduction is better than air conduction
One frequency may be more affected All frequencies are uniformly affected.
 Important Clinical Applications

Clinical Application :
Retinal detachment : it means separation of the neural retina from the retinal pigment epithelium

Clinical Application :
Cataract : it means opacity of the lens. This is due to degeneration of the lens protein crystallin
Thin Skin
Thin Skin
Thin Skin
Thick Skin
Thick Skin
Thick Skin
❑ Bind to each other by
desmosomes.

❑ Bind to basement
membrane by
hemidemosomes.
❑ The cells adhere
to each other by
desmosomes.
❑ Site: Present in stratum basal.
❑ Branched cell with central indented nucleus.
❑ Attached to keratinocytes by desmosomes.
❑ A nerve fiber loses its myelin, approach merkel
❑ cell and form disk like expansion.
Function → touch receptor.
LIP
LIP
LIP
Tongue
Tongue
Tongue
Tongue
Tongue
Filiform papillae Fungiform papillae: Circumvallate papillae Foliate papillae
❑ Most numerous ❑ Few in number ❑ Number 8-16 ❑ Rudimentary in man, well
❑ Present on the anterior ❑ Present on tips & edges ❑ Along V- shaped line developed in rabbits.
2/3 mainly ❑ Large, broad tip & narrow ❑ Present along the edges of
❑ Conical and the apex is ❑ Fungus like "narrow base base posterior 1/3
directed backward – wide apex" ❑ Surrounded by groove ❑ Parallel ridges separated by
❑ Capped with keratinized ❑ Occasional taste bunds on "valley" parallel grooves
epithelium its upper surface. ❑ Numerous taste buds along ❑ Numerous taste buds along
❑ Have no taste buds ❑ Few secondary papillae the lateral wall of the the lateral wall of the
❑ Core may contain ❑ Rich blood supply → red groove groove.
secondary papillae in color ❑ Serous von Ebner's glands ❑ Serous von Ebner's glands
keep the groove clean keep the groove clean

Function: Function : taste sensation Function : taste sensation Function : taste sensation
❑ Touch sensation
❑ Suckling in infants and
licking in animals
Parotid Gland
Parotid Gland Compound tubulo-alveolar gland
Mucous acinus Serous acinus Mixed acinus:
❑ Large diameter ❑ Small diameter ❑ It is mucus acinus with cap of
❑ Wide lumen. ❑ Narrow lumen. serous cells → serous
❑ Pale in colour ❑ Deeply stained. demilune or crescent of
❑ Cells more or less cuboidal ❑ Cells pyramidal Gianuzzi
❑ Distinct cell boundary ❑ Indistinct cell boundary ❑ Serous secretion passes
❑ Cytoplasm pale, foamy, ❑ Cytoplasm: deep basophilic along intercellular canaliculi
basophilic + apical acidophilic between mucous cells to the
❑ Nucleus: flattened granules. lumen.
peripheral ❑ Nuclei: rounded, near to
❑ Secrete mucous center
❑ Basket cells : numerous ❑ Secretion: serous
❑ Basket cell: less numerous
Parotid Gland
Parotid Gland
Submandibular Gland
Submandibular Gland Compound tubulo-alveolar gland
Sublingual Gland Compound tubulo-alveolar gland
Sublingual Gland
Eye
Eye
 Cornea

1) Corneal epithelium
2) Substentia propria
3) Decemet’s endothelium
Corneal epithelium Substantia propria Corneal endothelium
"Descement's endothelium"
❑ Stratified squamous non ❑ 90 % of thickness. ❑ It lines the internal surface of
keratinized "5-6 layers" ❑ Non vascular. the cornea.
❑ Resting on straight basement ❑ Formed of 200 – 300 parallel ❑ Single layer of flat cells with
membrane. lamellae of collagen I pinocytotic vesicles.
❑ Basal layer is cubical ❑ Successive lamellae are ❑ It absorbs fluid from substantia
❑ Middle layers are polygonal perpendicular to each other. propria to keep it transparent.
connected by desmosomes ❑ In between lamellae → corneal
❑ Superficial cells are flat and have corpuscles (flat fibroblast)
microvilli "to keep tear film" ❑ Ground substance is rich in
❑ Highly sensitive with numerous glycoprotein.
free nerve endings.
❑ High regenerative power "basal
layer"
Corneo-Scleral Junction

1) Cornea
2) Sclera
3) Trabecular meshwork
4) Iris Ciliary processes
5) Lens
 Retina

1) Layer Of Rods And Cones

2) Outer Nuclear Layer
3) Inner Nuclear Layer
4) Ganglion Cell Layer
Corneo-Scleral Junction
Cornea
Bowman's membrane Descement's membrane
❑ Homogenous transparent. ❑ Highly refractile
❑ Formed of collagen I & homogenous, non cellular
intercellular substance "No cells". membrane.
❑ It is protective against bacterial ❑ Formed by endothelium.
invasion. ❑ Formed of collagenous fibers.
❑ If injured → not regenerated →
corneal opacity "leucoma"
Eye Lid
Retina
Ear : Organ Of Corti
Ear : Organ Of Corti
Ear : Organ Of Corti
Integrative bioinformatics in myopathy
diagnosis
 Station 1
• Complete the missing items of the following biomarker applications
flowchart:

Biomarker
Applications

Diagnostic Staging

To predict the
Used for early To monitor
efficacy &
detection treatment effect
toxicity of a drug
 Station
• Complete the missing items of the following biomarker applications
flowchart:

Biomarker
Applications

Diagnostic Predictive Prognostic Staging

To predict the To determine the

Used for early To monitor
efficacy & toxicity disease
detection treatment effect
of a drug progression state
 • Define the following terms:
1-Biomarker.
2- Genetic regulatory network.
3- Test panel.
4- Biomarker panels.

Biomarker: is a molecule (gene, genetic variations, difference in mRNA, protein/peptide, non-coding RNA
or hormone) present in a biological system, used to indicate a physiological or pathological state that can
be diagnosed or monitored.

Genetic regulatory network: is a collection of molecular regulators (miRNA,lncRNA) that interact with each
other and with other substances in the cell to regulate the gene (mRNA) expression.

Test panel (multi-biomarker testing) : is a predetermined group of biomarkers performed together to aid
in diagnosis or treatment follow-up.

Biomarker panels(combination of biomarkers= Multiplex biomarkers):

➢Multi-gene biomarker panels identified from gene expression (messenger RNA is the working copy of the
gene) data can be used to diagnose diseases and/or stratify patients into different disease
 Station
Flowchart for retrieval of regulatory genetic epigenetic network related to
certain diseases

1-Retrieve Gene (mRNA)

related to the selected disease

2-Retrieve miRNA related to

the selected gene

3-Retrieve lncRNA related to

the selected miRNA

Lab validation of the selected

genetic regulatory network
 Station
• Compare between single biomarker and test panel testing:

Single biomarker Test panel

Efficiency in low high

diagnosis
Processing manual automated
cost high low
Time slow fast
Results Not comprehensive comprehensive
• Compare between Gene testing and Regulatory genetic network testing:

Gene testing Regulatory genetic

(RNA testing) network testing
(RNA-RNA testing)
Specificity Low High
Sensitivity Low High
Prediction of Less accurate More accurate
treatment
response
Treatment Less accurate More accurate
monitoring
 Station
• Complete the missing uses of the mentioned databases:
Database Uses
Gene expression omnibus (GEO) to search for expression profiles of genes linked to
profiler certain condition or disease
Human Protein Atlas Database Tissue expression, RNA expression, Disease expression

The Universal Protein Resource Protein sequence, post-translational modifications, gene

uniprot database ontology(functions) subcellular location(s), tissue
specificity, developmentally specific expression,
structure, interactions, splice isoform(s), diseases
associated with deficiencies or abnormalities

Gene Cards subcellular localization, genetic interaction, commercial gene

products
mirDB database miRNA-target mRNA interactions
miRBase database microRNA gene sequence
miRWalk database miRNA-target mRNA interactions
lncRNA-target miRNA interactions
lncRNA-target mRNA interactions
lncRNA-miRNA-mRNA expression in different diseases
LNCipedia database long non-coding RNA (lncRNA) sequence and annotation
 Station
• Match each database with the suitable function it can perform:

Database Function
A. LNCipedia database subcellular localization, genetic
interaction, commercial gene
products
B. Genecards database lncRNA-target mRNA interactions

C. mirDB database Tissue expression, RNA expression,

Disease expression
D. miRWalk database long non-coding RNA (lncRNA)
sequence and annotation
E. protein atlas miRNA-target mRNA interactions
database
 Station:

1-The above presented print screen shows 2-In the above presented print screen, which
target miRNAs for BRCA1 gene, done by using: miRNA is the best possible target of BRCA mRNA:
a) mirDB database. a) hsa-miR-944
b) Gene cards database. b) hsa-miR-3169
c) miRBase database. c) hsa-miR-499b-5p
d) Proteinatlas database. d) hsa-miR-125a-3p
 Station

2-As a part of a new study design about breast cancer,

1-The above presented print screen shows miRNA hsa- choose the best targets to be investigated:
mir-944 information, was retrieved by using:
a) TP53 gene.
a) mirDB database. b) TP53 protein.
b) Gene cards database. c) TP53 gene and hsa-mir-944 miRNA.
c) miRBase database. d) TP53 gene, hsa-mir-944 miRNA and ROR lncRNA.
d) Proteinatlas database.
 Station

2-In the above presented printscreen, HCP5

1-The above presented print screen shows HCP5 lncRNA
lncRNA has a transcript size of:
information, retrieved by using:
a) 1500 bp.
a) Proteinatlas database.
b) 2658 bp.
b) LNCipedia database.
c) 3200 bp.
c) mirwalk database.
d) 560 bp.
d) mirDB database.
 Station

1-The above presented print screen shows genes related 2-In the above presented print screen showing
to breast cancer, was retrieved by using: genes related to breast cancer, the organism is:
a) Proteinatlas database. a) Human.
b) LNCipedia database. b) Mice.
c) Gene cards database. c) Guiana pig.
d) GEO database. d) Horses.
 Station

1-The above presented print screen shows AMT gene 2-In the above presented print screen, the highest AMT
expression in tissues, retrieved by using: gene expression is observed in:
a) Proteinatlas database. a) Kidney.
b) LNCipedia database. b) Liver.
c) Gene cards database. c) Testis.
d) Uniprot database. d) Adipose tissue.
 Station

2-As a part of a new study design about Diabetes

1-The above presented print screen shows MATN3 gene mellitus, choose the best targets to be investigated:
ontology, was retrieved by using:
a) CDKAL1 gene.
a) mirDB database. b) CDKAL1 gene and hsa-mir-526-3p miRNA.
b) Lincepedia database. c) CDKAL1 gene, hsa-mir-526-3p miRNA and HCP5:10
c) BLAST program. lncRNA.
d) Uniprot database. d) CDKAL1 gene, IGF2BP2 gene, hsa-mir-526-3p miRNA
and HCP5:10 lncRNA.
 Station

Complete the missing item in the provided regulatory network

 Diagnosis : Basal Cell Carcinoma

Comment :
Microscopic picture :
❑ The dermis is infiltrated by masses
of malignant epithelial cells
❑ The peripheral cells are columnar
basal cells dark blue with palisade
(parallel) arrangement while the
central cells are polyhedral.
Etiology :
High exposure to ultraviolet rays
Types :
1. Pigmented type
2. Adenoid type:
3. Basosquamous:
Prognosis : Good
Spread : Local spread only
 Diagnosis : Basal Cell Carcinoma

Comment :
Microscopic picture :
❑ The dermis is infiltrated by masses
of malignant epithelial cells
❑ The peripheral cells are columnar
basal cells dark blue with palisade
(parallel) arrangement while the
central cells are polyhedral.
Etiology :
High exposure to ultraviolet rays
Types :
1. Pigmented type
2. Adenoid type:
3. Basosquamous:
Prognosis : Good
Spread : Local spread only
 Diagnosis : Gross Picture of Basal Cell Carcinoma (Rodent Ulcer)

Comment :
Rodent Ulcer characteristic gross
picture of Basal Cell Carcinoma with
rolled in beaded edges necrotic
indurated floor
1) near the ear lobule
2) near the inner canthus of the eye
Aetiology:
High exposure to ultraviolet rays
Types :
1. Pigmented type
2. Adenoid type:
3. Basosquamous:
Prognosis : Good
Spread : Local spread only
 Diagnosis : Gross Picture of Basal Cell Carcinoma (Rodent Ulcer)

Comment :
Rodent Ulcer characteristic gross
picture of Basal Cell Carcinoma with
rolled in beaded edges necrotic
indurated floor
1) near the ear lobule
2) near the inner canthus of the eye
Aetiology:
High exposure to ultraviolet rays
Types :
1. Pigmented type
2. Adenoid type:
3. Basosquamous:
Prognosis : Good
Spread : Local spread only
 Diagnosis : Seborrheic Keratosis

Comment :
Microscope picture of seborrheic
keratosis shows a proliferation of
keratinocytes with keratin-filled cysts
and hyperkeratosis.
There are few foci of lymphocytic
infiltration.

Aetiology: The benign proliferation

of immature keratinocytes
 Diagnosis : Epidermal Cyst

Comment :
Microscopic picture revealed opened
cystic mass lined by squamous
epithelium and keratin flakes

Aetiology: Follicular orifice

becomes plugged with bacteria and
keratin, leading to cystic dilatation and
entrapment of keratin debris

Sites :
❑ Face
❑ Neck
❑ Trunk
 Diagnosis : Pleomorphic Adenoma
Comment :
Gross picture of Pleomorphic
Adenoma presents as :
❑ Rounded to oval, mass greyish
white in color, glistening, about
6 cm in greatest dimension .
❑ The mass is well-demarcated
and surrounded by capsule
which is not well developed in
some areas (see arrows)
NB :
❑ The facial nerve is at risk to be
injured during It surgical
excision
❑ A very small proportion (less
than 2 %) undergo malignant
change
 Diagnosis : Melanoma

Comment :
Microscopic picture of melanoma
❑ Revealed anaplastic melanocytes
with cytoplasmic melanin infiltrate
the dermis.
❑ Malignant cells appear polyhedral
forming cohesive groups (nests)
Prognosis:
Prognosis is generally poor due to
rapid spread of tumor
Spread:
a) Local spread.
b) Lymphatic spread to regional lymph
nodes.
c) Blood spread
 Diagnosis : Melanoma

Comment :
Malignant cells appear as spindle non
cohesive cells with atypia and mitosis
and melanin production

Prognosis:
Prognosis is generally poor due to
rapid spread of tumor
Spread:
a) Local spread.
b) Lymphatic spread to regional lymph
nodes.
c) Blood spread
 Comment : Amelanotic melanoma

Comment :
Rarely the cells do not produce
melanin (amelanotic melanoma)
the cells are spindle in shape
with atypia and mitosis
 Mock exam on practical Microbiology -MUS III module
Spot 1:
You are provided with the following articles. answer the following questions:
1a
b

1. Name of the provided articles:

a. ………………………………….. b. ……………………………………………..
2. Example of a specimen collected by these articles in a patient presented by
skin ulcer and abscess:
a.………………………………….. b. ……………………………………………..
3. Methods of sterilization:
…………………………………………………………………………………………………………………..
4. Proper way of disposal after use:
a.………………………………….. b. ……………………………………………..

1
Spot 2:
A 40-years-old diabetic patient presented to clinic with an abscess on the back
of his neck. On examination, the abscess is multiloculated. A pus specimen was
collected and inoculated on the following culture medium and a Gram-stained
film was prepared from the grown colonies, Examine and answer the following
questions.

1. The most likely causative organism is …………………………………………

2. The name of the provided medium is …………………………………………
3. The morphology of the isolated organism in a direct Gram-
stained film is ………………………………………………………………………………….
4. The effect of the isolated organism on blood agar is
………………………………………………………………………………….
5. the effect of the isolated organism on nutrient agar is
……………………………………………………………………..
6. The catalase test result of the most likely causative organism is
…………………………………….
7. The coagulase test result of the most likely causative organism is
………………………………………
8. The gelatinase (gelatin liquefaction) test result of the most likely
causative organism is ……………………………………………………

2
Spot 3:
A 2-year-old boy presented with red papules and pustules with yellowish
adherent golden honey-colored crusts around his mouth and nose. A specimen
collected from the lesions and direct Gram-stained film revealed the provided
morphology.

1. The most likely causative organism is ………………………………………………………..

2.The character of the grown colonies of the isolated organism on blood agar
medium is………………………………………………………………………………………
3. The expected result of catalase test for the isolated organism is
………………………………………
4. The provided test was performed to the isolated organism

a. The name of this test is …………………………………………………………

b. The result of the isolated organism is ……………………………………..
c. What is the importance of this test?
…………………………………………………………………………………………………………….

3
Spot 4
A 25-year-old patient suffering from third-degree burns developed pain,
redness, swelling in the burn wounds with green pus drainage. A swab was
taken from infected burn lesions. Direct Gram-stained film revealed Gram-
negative bacilli.
1.The most likely causative organism of this infection is
…………………………………………………………
2. The character of the grown colonies of the isolated organism on nutrient agar
medium is ………………………………………………………………
3. The character of the grown colonies of the isolated organism on MacConkey’s
agar medium is ………………………………………………………………………….
4. The character of the grown colonies of the isolated organism on blood agar
medium is ……………………………………………………………………..
5. The expected result of oxidase test for the isolated organism is……………………

6. Interpret the Biochemical reactions of the isolated organism

TSI Indole test Urease test

TSI: …………………………………………….
Indole test: ……………………………………..
Urease test:
……………………………………..

4
Spot 5:
A 30-year-old man presented to the emergency room following a motorcycle
accident. On examination, his leg was swollen with dark serous exudate
draining from the wound and crepitus was felt on the lesion. Deep wound
exudate was collected and inoculated on the following culture medium,
Examine and answer the following questions.
1. The most likely causative organism is
………………………………………………………………..
2. The name of the provided medium is
……………………………………………………………….
3. The morphology of the isolated organism in a Gram-
stained film from culture is…………………………………………………..
4. The solid culture medium inoculated with the causative
organism should be incubated in ……………………………………………
5. The effect of the isolated organism on blood agar is
…………………………………………………………………………………..
6. The gelatinase (gelatin liquefaction) test result of the most likely
causative organism is ……………………………………………………….
7. The effect of the isolated organism on TSI medium is
……………………………………………………………………………………………………………
8. You are provided with an important test used in identification of
this organism, examine and answer the following questions:
a. The name of the provided test
is ……………………………………………
b. The principle of the provided
test is
………………………………………………
…………………………………………….

5
Spot 6
A hide porter abattoir presented with cutaneous lesion in his right arm. It began
as a painless papule that enlarged and rapidly progressed to ulcer with black
eschar (crust) and surrounded by marked edema. A swab was taken from the
lesion and a Gram-stained film reveled this morphology.

1. The most likely causative organism of this infection is

………………………………………………………………..
2. The character of the grown colonies of the isolated organism on nutrient
agar medium is …………………………………………………………………
3. The effect of the grown colonies of the isolated organism on blood agar
medium is……………………………………………………………..
4. The effect of the isolated organism on gelatin medium is
……………………………………………………

6
Spot 7
A 5-year-old boy presented with two circular bald areas with broken hair in his
scalp. Scrapings of skin was obtained and placed in 10% KOH on a glass slide
showed septate hypha under microscopy. You are provided with a culture
medium used to isolate the causative organism, Examine and answer the
following questions.

1. The selective medium used to isolate the causative organism of this

infection is ………………………………………………………..
2. The selective substances in this medium are
……………………………………………………..
3. The special stain used to demonstrate the causative organism is
………………………………………………………………………….

7
▪ Subcutaneous nodule
▪ Over bony prominence
▪ Painless
L3 filariform larva

Adult male and female

Microfilaria

▪ Intense pruritis Diagnosis?

Clinical
▪ Skin darkness (Sawda)
Presentation?
▪ Hypo/
Hypepigmentation
(Leopard skin)

Punctate Keratitis
 Biopsy
L3 filariform larva

Adult male and female

Microfilaria

Diagnosis? Clinical
Skin snip Presentation?
 Cutaneous
leishmaniasis
MOI

Clinical Presentation

Muco-cutaneous
leishmaniasis
 Direct
examination

Biopsy from
indurated edge of
the ulcer

AMASTIGOTE
 Direct
examination

Biopsy from
Culture indurated edge of
the ulcer

PROMASTIGOTE
SUMMARY FOR ENTOMOLOGY
CASES
 SKIN AFFECTION
Skin lesion
SEVERE ITCHING IN SEVERE ITCHING IN ❑ Severe itching and scratching, 1.ULCER/ TRAUMA
HEAD ± Presence of PUBIC AREA, UPPER especially at night and after hot Offensive odour
White dots or Presence of THIGH, EYE LASHES ± baths. presence of worm like
Presence of a parasite ❑ A papular eruption. structure
a parasite
❑ Tunnels appear on skin as 2.NODULE
elevated tracks (FURUNCLE) With
❑ Interdigets, under arms, worm like structure
wrist… inside (larva)
1

2
Skin
Scaping
PEDICULOSIS PHTHIRIASIS Dermatobia hominus
(PEDICULUS (PHTHYRUS PUBIS or
HUMANUS CAPITIS or PUBIC LOUSE Scabies Cutaneous
HEAD LOUSE) Sarcoptes Scabiei Myiasis
 MOTOR AFFECTION OTHER ORGANS
ASCENDING PARALYSIS /
AFFECTION
RESPIRATORY AFFECTION + Intestinal EYE EAR
PRESENCE OF PARASITE manifestation Manifestations
manifestation
MAINLY NEAR THE NECK PRESENCE OF LARVA

TICK PARALYSIS MYIASIS

BY (Intestinal / Ocular/ Aural)
HARD TICK You have to identify the causative parasite
EXAMPLE OF PRACTICAL
EXAM QUESTIONS
This patient suffers from severe itching which is
increased at night. Black tortuous tunnels are
present on the wrists and skin between the
fingers. Which of these figures represent the
diagnostic stage of this infestation?
CHOOSE THE FIGURE & MENTION ITS NAME

FIGURE 1 FIGURE 2 FIGURE 3

 OR
This patient suffers from severe itching which is
increased at night. Black tortuous tunnels are
present on the wrists and skin between the fingers.
Skin scrapping was done and showed the
following parasite.

IDENTIFY THIS DISEASE? IDENTIFY THE

CAUSATIVE PARASITE

A CASE OF SCABIES – SARCOPTES SCABIEI

A 5-year-old girl in Ohio came to the emergency room having trouble
breathing and moving. Her family said she seemed fine one day then
suddenly, she started having difficulty maintaining her balance. Her
mother initially thought that her daughter had vertigo. Which of these
figures represent the diagnostic stage of this infestation?
CHOOSE THE FIGURE & MENTION ITS NAME

FIGURE 1 FIGURE 2 FIGURE 3

A 5-year-old girl in Ohio came to the emergency room having trouble
breathing and moving. Her family said she seemed fine one day then
suddenly, she started having difficulty maintaining her balance. Her
mother initially thought that her daughter had vertigo. On
examination this parasite was found near the neck of the patient.

IDENTIFY THIS DISEASE? IDENTIFY THE

CAUSATIVE PARASITE

A CASE OF TICK PARALYSIS – HARD TICK

A 6-year-old girl complained from severe itching of
the head. The mother reported seeing like white dots
attached to her hair. Which of these figures represent
one of the diagnostic stages of this infestation?

CHOOSE THE FIGURE & MENTION ITS NAME

FIGURE 1 FIGURE 2 FIGURE 3

◎ A 35-year-old male patient came presented with the following
clinical sign on his left hand (Figure A). Direct microscopic
examination of a Giemsa-stained biopsy specimen was done and
demonstrated the following parasite (Figure B).

Figure A Figure B
A. Mention the name of the disease?
B. Mention the name of the parasitic stage seen in (Figure B).
A. Cutaneous Leishmaniasis
B. Amastigote form of Leishmania
◎ A 50-year-old-African male patient came
presented with itching over extremities,
photophobia and the following clinical
sign.

A- Identify the clinical sign?

B- Mention the name of the parasite causing this condition?
A- Onchocerca nodule / Onchocercoma
B- Onchocerca volvolus
 Station (1)
A six-year-old boy from USA presented with a non-migratory
furuncle on his scalp. A small incision was made, and a worm-
like organism was removed.

A- IDENTIFY THIS DISEASE?

B- IDENTIFY THE CAUSATIVE PARASITE.
 ANSWER

A. Cutaneous Myiasis
B. Dermatobia hominis
 Station (2)
A 60-year-old woman from Cameroon presented with skin changes and a
rash on the left leg associated with severe pruritus over a period of 8 years.
Her house was situated by a slow-flowing stream. On examination, there
was a papular rash around the left knee associated with excoriation marks
probably due to scratching. There was hypopigmentation around the shin
of her left leg (leopard skin-like changes) with associated hardening of
the skin around this region. A skin snip of the left leg was done
demonstrating the following figure.

A-IDENTIFY THIS DISEASE.

B-IDENTIFY THIS DIAGNOSTIC STAGE.
 ANSWER

A. Onchocerciasis
B. Microfilaria
 Station (3)
An 8-year-old girl who is sent to the nurse's office had a 2-day
history of scratching her head so badly that she complains
that her “head hurts.” you complete a general examination of
her head and notice that she has red, irritated areas with
several scratch marks; a few open sores and yellow parasites
that are adhered to many of her hair shafts.

Figure A Figure B Figure C

A. Choose the figure of the parasite causing this disease.
B.Mention its name.
 ANSWER

A. Figure C
B. Pediculus hominis capitis
 Station (4)
The following were seen in skin scrapings from a young immigrant
male complaining of severe itching especially at night.

Figure A Figure B Figure C

A.Choose the figure of the parasite causing this disease.
B.Mention its name.
 ANSWER

A. Figure A
B. Sarcoptes scabiei
 Station (5)

This parasite was referred to

the parasitology laboratory for
identification ?
 ANSWER

Pubic lice (Phthirus pubis)

 Station (6)
The Red Cross sends a relief team to visit a refugee camp in central Africa.
It is noted that most of the people have not been able to bathe for weeks,
generally appear unkempt, and many complain of dermatitis and bug
bites. In fact, the clothing seems to be infested or “crawling” with bugs
(shown in the image). With respect to the conditions described above,
which of the following diseases is of principal concern for the examining
physicians?
a) Tick paralysis
b) Epidemic typhus
c) Plague
d) Malaria