Basic science Flashcards
eGFR equation
GFR = ( urine concentration (mmol/l) x urine volume (ml/min) ) / plasma concentration (mmol/l)
MA of RCTs level of evidence
Ia
RCT level of evidence
1b
Control trial, not randomised level of evidence
2a
2b level of evidence
evidence from at least one well designed experimental trial
3 level of evidence
evidence from case, correlation and comparative studies
4 level of evidence
evidence from a panel of experts
what regulates cell cycle
proteins called cyclins which in turn control cyclin-dependent kinase (CDK) enzymes.
phases of cell cycle
G0,G1,S,G2,M
G0
‘resting’ phase
quiescent cells such as hepatocytes and more permanently resting cells such as neurons
G1
Gap 1, cells increase in size
determines length of cell cycle
under influence of p53
regulatory proteins G1
Cyclin D / CDK4, Cyclin D / CDK6 and Cyclin E / CDK2: regulates transition from G1 to S phase
S
Synthesis of DNA, RNA and histone
centrosome duplication
regulatory proteins S
Cyclin A / CDK2: active in S phase
G2
Gap 2, cells continue to increase in size
regulatory preoteins G2
Cyclin B / CDK1: regulates transition from G2 to M phase
M
Mitosis - cell division
the shortest phase of the cell cycle
negative predictive value equation
TN / (TN + FN)
sensitivity equation
TP / (TP + FN )
specificity equation
TN / (TN + FP)
PPV equation
TP / (TP + FP)
likelihood ratio for a positive result
sensitivity / (1 - specificity)
How much the odds of the disease increase when a test is positive
likelihood ratio negative test
(1 - sensitivity) / specificity
How much the odds of the disease decrease when a test is negative
most common congenital infection in the UK
CMV
Sensorineural deafness Congenital cataracts Congenital heart disease (e.g. patent ductus arteriosus) Glaucoma congenital infection
rubella
Cerebral calcification
Chorioretinitis
Hydrocephalus
congenital infection
toxoplasmosis
Growth retardation
Purpuric skin lesions
congenital infection
CMV
audit definition
a quality improvement process that seeks to improve patient care and outcomes through systematic review of care against explicit criteria and the implementation of change
what phase of mitosis does vincristine act on?
metaphase
These drugs bind to tubulin stopping the polymerisation and assembly of microtubules. This, in turn, disrupts spindle formation arresting mitosis at metaphase.
what happens in prophase
Chromatin in the nucleus condenses
prometaphase
Nuclear membrane breaks down allowing the microtubules to attach to the chromosomes
metaphase
Chromosomes aligned at middle of cell
anaphase
The paired chromosomes separate at the kinetochores and move to opposite sides of the cell
telophase
Chromatids arrive at opposite poles of cell
cytokinesis
Actin-myosin complex in the centre of the cell contacts resulting in it being ‘pinched’ into two daughter cells
parametric tests
Student’s t-test - paired or unpaired*
Pearson’s product-moment coefficient - correlation
non-parametric tests
Mann-Whitney U test
compares ordinal, interval, or ratio scales of unpaired data
Wilcoxon signed-rank test
compares two sets of observations on a single sample, e.g. a ‘before’ and ‘after’ test on the same population following an intervention
chi-squared test
used to compare proportions or percentages e.g. compares the percentage of patients who improved following two different interventions
Spearman, Kendall rank - correlation
what are compliment
series of proteins that circulate in plasma and are involved in the inflammatory and immune reaction of the body. Complement proteins are involved in chemotaxis, cell lysis and opsonisation
C1 deficiency
C1 inhibitor (C1-INH) protein deficiency causes hereditary angioedema C1-INH is a multifunctional serine protease inhibitor probable mechanism is uncontrolled release of bradykinin resulting in oedema of tissues
classical pathway compliment and deficiency
C1q, C1rs, C2, C4 deficiency (classical pathway components)
predisposes to immune complex disease
e.g. SLE, Henoch-Schonlein Purpura
c3 deficiency
predisposes to bacterial infections
C5 deficiency
predisposes to Leiner disease
recurrent diarrhoea, wasting and seborrhoeic dermatitis
C5-9 deficiency
encodes the membrane attack complex (MAC)
particularly prone to Neisseria meningitidis infection
IL-1 source and functions
Macrophages Acute inflammation
Induces fever
IL-2 source and functions
Th1 cells Stimulates growth and differentiation of T cell response
IL-3 source and functions
Activated T helper cells Stimulates differentiation and proliferation of myeloid progenitor cells
IL-4 source and functions
Th2 cells Stimulates proliferation and differentiation of B cells
IL-5 source and functions
Th2 cells Stimulate production of eosinophils
IL-6 source and functions
Macrophages, Th2 cells Stimulates differentiation of B cells
Induces fever
IL-8 source and functions
Macrophages Neutrophil chemotaxis
IL-10 source and functions
Th2 cells
Inhibits Th1 cytokine production
Also known as human cytokine synthesis inhibitory factor and is an ‘anti-inflammatory’ cytokine
IL-12 source and functions
Dendritic cells, macrophages, B cells
Activates NK cells and stimulates differentiation of naive T cells into Th1 cells
TNF alpha source and functions
Macrophages Induces fever
Neutrophil chemotaxis
interferon Y source and functions
Th1 cells Activates macrophages
type 1 error
the null hypothesis is rejected when it is true - i.e. Showing a difference between two groups when it doesn’t exist, a false positive. This is determined against a preset significance level (termed alpha). As the significance level is determined in advance the chance of making a type I error is not affected by sample size. It is however increased if the number of end-points are increased. For example if a study has 20 end-points it is likely one of these will be reached, just by chance.
type 2 error
the null hypothesis is accepted when it is false - i.e. Failing to spot a difference when one really exists, a false negative. The probability of making a type II error is termed beta. It is determined by both sample size and alpha
define the power of a study
the probability of (correctly) rejecting the null hypothesis when it is false, i.e. the probability of detecting a statistically significant difference
power = 1 - the probability of a type II error
power can be increased by increasing the sample size
what is atrial nartiuretic peptide?
secreted mainly from myocytes of right atrium and ventricle in response to increased blood volume
secreted by both the right and left atria (right»_space; left)
28 amino acid peptide hormone, which acts via cGMP
degraded by endopeptidases
effects of ANP
natriuretic, i.e. promotes excretion of sodium
lowers BP
antagonises actions of angiotensin II, aldosterone
artherosclerosis stages
initial endothelial dysfunction is triggered by a number of factors such as smoking, hypertension and hyperglycaemia
this results in a number of changes to the endothelium including pro-inflammatory, pro-oxidant, proliferative and reduced nitric oxide bioavailability
fatty infiltration of the subendothelial space by low-density lipoprotein (LDL) particles
monocytes migrate from the blood and differentiate into macrophages. These macrophages then phagocytose oxidized LDL, slowly turning into large ‘foam cells’. As these macrophages die the result can further propagate the inflammatory process.
smooth muscle proliferation and migration from the tunica media into the intima results in formation of a fibrous capsule covering the fatty plaque.
artherosclerosis complications
the plaque forms a physical blockage in the lumen of the coronary artery. This may cause reduced blood flow and hence oxygen to the myocardium, particularly at times of increased demand, resulting clinically in angina
the plaque may rupture, potentially causing a complete occlusion of the coronary artery. This may result in a myocardial infarction
what is p53
p53 is a tumour suppressor gene located on chromosome 17p. It is the most commonly mutated gene in breast, colon and lung cancer.
p53 is thought to play a crucial role in the cell cycle, preventing entry into the S phase until DNA has been checked and repaired. It may also be a key regulator of apoptosis
what is Li-fraumeni syndrome?
rare autosomal dominant disorder characterised by the early onset of a variety of cancers such as sarcoma, breast cancer and leukaemias. It is caused by mutation in the p53 gene.
vitamin D function
increases plasma calcium and plasma phosphate
increases renal tubular reabsorption and gut absorption of calcium
increases osteoclastic activity
increases renal phosphate reabsorption
vitamin d deficiency causes
rickets: seen in children
osteomalacia: seen in adults
cerebral metastasis features
Metastatic brain cancer is the most common form of brain tumours. They are often multiple and not treatable with surgical intervention.
Tumours that most commonly spread to the brain include: lung (most common) breast bowel skin (namely melanoma) kidney
glioblastoma features
Glioblastoma is the most common primary tumour in adults and is associated with a poor prognosis (~ 1yr).
- On imaging they are solid tumours with central necrosis and a rim that enhances with contrast. Disruption of the blood-brain barrier and therefore are associated with vasogenic oedema.
- Histology: Pleomorphic tumour cells border necrotic areas
- Treatment is surgical with postoperative chemotherapy and/or radiotherapy. Dexamethasone is used to treat the oedema.
meningioma features
The second most common primary brain tumour in adults
- Meningiomas are typically benign, extrinsic tumours of the central nervous system. They arise from the dura mater of the meninges and cause symptoms by compression rather than invasion.
- They typically are located at the falx cerebri, superior sagittal sinus, convexity or skull base.
- Histology: Spindle cells in concentric whorls and calcified psammoma bodies
- Investigation is with CT (will show contrast enhancement) and MRI, and treatment will involve either observation, radiotherapy or surgical resection.
schwannoma features
A vestibular schwannoma (previously termed acoustic neuroma) is a benign tumour arising from the eighth cranial nerve (vestibulocochlear nerve). Often seen in the cerebellopontine angle. It presents with hearing loss, facial nerve palsy (due to compression of the nearby facial nerve) and tinnitus.
- Neurofibromatosis type 2 is associated with bilateral vestibular schwannomas.
- Histology: Antoni A or B patterns are seen. Verocay bodies (acellular areas surrounded by nuclear palisades)
- Treatment may involve observation, radiotherapy or surgery.
pilocytic astrocytoma features
The most common primary brain tumour in children
• Histology: Rosenthal fibres (corkscrew eosinophilic bundle)
medulloblastoma features
A medulloblastoma is an aggressive paediatric brain tumour that arises within the infratentorial compartment. It spreads through the CSF system. Treatment is surgical resection and chemotherapy.
• Histology: Small, blue cells. Rosette pattern of cells with many mitotic figures
ependymoma features
- Commonly seen in the 4th ventricle
- May cause hydrocephalus
- Histology: perivascular pseudorosettes
oligodendroma features
Benign, slow-growing tumour common in the frontal lobes
• Histology: Calcifications with ‘fried-egg’ appearance
haemangioblastoma features
- Vascular tumour of the cerebellum
- Associated with von Hippel-Lindau syndrome
- Histology: foam cells and high vascularity
pituitary adenoma features
Pituitary adenomas are benign tumours of the pituitary gland. They are either secretory (producing a hormone in excess) or non-secretory. They may be divided into microadenomas (smaller than 1cm) or macroadenoma (larger than 1cm).
- Patients will present with the consequences of hormone excess (e.g. Cushing’s due to ACTH, or acromegaly due to GH) or depletion. Compression of the optic chiasm will cause a bitemporal hemianopia due to the crossing nasal fibers.
- Investigation requires a pituitary blood profile and MRI. Treatment can either be hormonal or surgical (e.g. transphenoidal resection).
craniopharyngioma features
Most common paediatric supratentorial tumour
- A craniopharyngioma is a solid/cystic tumour of the sellar region that is derived from the remnants of Rathke’s pouch. It is common in children, but can present in adults also. It may present with hormonal disturbance, symptoms of hydrocephalus or bitemporal hemianopia.
- Histology: Derived from remnants of Rathke pouch
- Investigation requires pituitary blood profile and MRI. Treatment is typically surgical with or without postoperative radiotherapy.
vitamin c functions
antioxidant
collagen synthesis: acts as a cofactor for enzymes that are required for the hydroxylation proline and lysine in the synthesis of collagen
facilitates iron absorption
cofactor for norepinephrine synthesis
vitamin c deficiency features
gingivitis, loose teeth
poor wound healing
bleeding from gums, haematuria, epistaxis
general malaise
what is fragile X?
trinucleotide repeat disorder
fragile X features
Features in males learning difficulties large low set ears, long thin face, high arched palate macroorchidism hypotonia autism is more common mitral valve prolapse
Features in females (who have one fragile chromosome and one normal X chromosome) range from normal to mild
equation for standard error mean
SEM = SD / square root (n)
where SD = standard deviation and n = sample size
therefore the SEM gets smaller as the sample size (n) increases
95% confidence interval equation
lower limit = mean - (1.96 * SEM)
upper limit = mean + (1.96 * SEM)
collagen structure
Composed of 3 polypeptide strands that are woven into a helix, usually a combination of glycine with either proline or hydroxyproline plus another amino acid
Numerous hydrogen bonds exist within molecule to provide additional strength
Many subtypes but commonest subtype is I (90% of bodily collagen), tissues with increased levels of flexibility have increased levels of type III collagen
Vitamin C is important in establishing cross-links
Synthesised by fibroblasts
where is type 1 collagen found and what are the associated conditions?
Bone, skin, tendon Osteogenesis imperfecta
where is type 2 collagen found ?
Hyaline cartilage, vitreous humour
where is type 3 collagen found and what are the associated conditions?
Reticular fibre, granulation tissue Vascular variant of Ehlers-Danlos syndrome
where is type 4 collagen found and what are the associated conditions?
Basal lamina, lens, basement membrane Alport syndrome, Goodpasture’s syndrome
where is type 5 collagen found and what are the associated conditions?
Most interstitial tissue, placental tissue Classical variant of Ehlers-Danlos syndrome
dry beriberi
B1 (thiamine deficiency)
peripheral neuropathy
wet beriberi
B1 (thiamine deficiency)
dilated cardiomyopathy
causes of thiamine deficiency
alcohol excess. Thiamine supplements are the only routinely recommend supplement in patients with alcoholism
malnutrition
LVEF equation
Left ventricular ejection fraction = (stroke volume / end diastolic LV volume ) * 100%
stroke volume equation
Stroke volume = end diastolic LV volume - end systolic LV volume
factors which increase pulse pressure
a less compliant aorta (this tends to occur with advancing age)
increased stroke volume
systemic vascular resistance calculation
Systemic vascular resistance = mean arterial pressure / cardiac output
vitamin k dependent clotting factors
II, VII, IX, X
how are oncogenes different from tumor supressor genes?
Tumor suppressor genes - loss of function results in an increased risk of cancer
Oncogenes - gain of function results in an increased risk of cancer
CML associated gene
ABL
Cytoplasmic tyrosine kinase
Burkitt’s lymphoma associated gene
c-MYC Transcription factor
neuroblastoma associated gene
n-MYC Transcription factor
follicular lymphoma associated gene
BCL-2 Apoptosis regulator protein
MEN 2+3 gene
RET Tyrosine kinase receptor
RAS gene conditions
G-protein Many cancers especially pancreatic
erb-B2 associated cancer
erb-B2 (HER2/neu) Tyrosine kinase receptor Breast and ovarian cancer
ADH secreted from?
Synthesized in the supraoptic nuclei of the hypothalamus, released by the posterior pituitary
ADH function
Conserves body water Promotes water reabsorption in the collecting ducts of the kidneys by the insertion of aquaporin-2 channels
ADH regulation
Increases secretion extracellular fluid osmolality increase volume decrease pressure decrease angiotensin II
Decreases secretion
extracellular fluid osmolality decrease
volume increase
temperature decrease
Diabetes insipidus (DI) is a condition characterised by either a deficiency of antidiuretic hormone, ADH, (cranial DI) or an insensitivity to antidiuretic hormone (nephrogenic DI)
Cranial DI can be treated by desmopressin, an analog of ADH
Di George syndrome cause
T-cell deficiency and dysfunction. It is an example of a microdeletion syndrome (deletion of a section of chromosome 22).
Di George syndrome features
C - Cardiac abnormalities A - Abnormal facies T - Thymic aplasia C - Cleft palate H - Hypocalcaemia/ hypoparathyroidism (parathyroid gland hypoplasia) 22 - Caused by chromosome 22 deletion
what infection are patients with t-cell dysfunction at risk of
recurrent viral and fungal infections
e.g. cryptococcus
homocystinuria features
often patients have fine, fair hair
musculoskeletal: may be similar to Marfan’s - arachnodactyly etc
neurological patients may have learning difficulties, seizures
ocular: downwards (inferonasal) dislocation of lens
increased risk of arterial and venous thromboembolism
also malar flush, livedo reticularis
homocystinuria diagnosis
cyanide-nitroprusside test, which is also positive in cystinuria.
homocystinuria cause
rare autosomal recessive disease caused by a deficiency of cystathionine beta synthase. This results in severe elevations in plasma and urine homocysteine concentrations.
homocystinuria treatment
vitamin B6 (pyridoxine)
southern blotting detects
DNA
SNOW DROP
northern blotting detects
RNA
SNOW DROP