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Physiology
The study of the functions and the control of these functions of the human body.
Pathology
The study of the structural and functional changes in cells, tissues, and organs of the body that are associated with diseases.
Pathophysiology
The study of the physiology of altered health (disease) state.  Mechanisms of the underlying disease.  How does the body change when a disease develops?  Pathophysiology is the basis for preventative and therapeutic health care measures, interventions, and practices.
Disease
The disruption of one or more body systems or organ structures with physiologic consequences.  Diseases are characterized by causative agents, physiological and/or anatomic alterations, and clinical manifestations.
Disease and Homeostasis
Homeostasis is the maintenance of a stable internal environment inside the body to prevent extreme fluctuations.  Use of positive feedback mechanisms which enhance the biologic effects after a stimulus and negative feedback mechanisms which inhibit the biologic effects after a stimulus.  Diseases are homeostatic imbalances or disruptions, such as disruptions with positive or negative feedback mechanisms.  A "new" homeostasis may occur under the diseased condition, even though it may not be favorable for the body.
Etiology
Causative agent(s) of a disease.
-Biologic agents (e.g. bacteria,virus)
-Physical forces (e.g. trauma,burns)
-Radiation (e.g.radioactivity, UV rays)
-Chemical agents (e.g. drugs, poisons, etc all physical states gas, liquid, solid)
-Nutritional imbalances (excess or deficit)
-Genetic causes (e.g. alteration in genetic material like DNA)
-Iatrogenic causes- disease develops as a result of medical interventions such as a blood clot after surgery
-Idiopathic causes- cause is unknown

Etiology is often non-specific; single/multi-organ

*Different patients with the same disease may have different etiology and therefore different treatments. Ex- UTI from E.Coli (gram +) in one person and by another gram - in the second so the treatment could be different.
Pathogenesis
How the disease develops in the body after the initial interaction with the etiologic agent, such as the molecular and cellular events, tissue/organ characteristics and physiologic functions as well as morphologic changes (changes of characteristic anatomy of cells and tissues).
Clinical manifestations/ Clinical Presentations
How the disease becomes notable and detectable
-Signs- A manifestation that is noted by an observer (e.g. fever, breathing difficulty, vomiting)
-Symptoms- Subjective complaint that is noted by the person with the disease (e.g. pain, nausea)

-Often grouped together, however some diseases can be asymptomatic (NO symptoms)
Diagnosis
Designation as to the cause or nature of a health problem.
-Involvment: thorough medical history with careful evaluation, risk factors of the patients for the disease, physical examination, sampling of body fluids or tissues, imaging techniques, and testing procedures.  By medical staff only.
Clinical Course
-Exacerbations
-Remissions
-"wax and wane"
-Progressive- worsens with time
-Self-terminating
Exacerbations
Aggrevation of symptoms and severity of the disease that has been under control; usually for chronic, episodic disease
Remissions
A reduction in severity and symptoms; patient may be asymptomatic during remission (but still has the disease); disease under control
wax and wane
disease course varies over time
Complication
Unfavorable development of a disease, either naturally or related to medical interventions.
-worsening severity or frequency
-become more widespread throughout the body
-new signs and symptoms

A new disease may occur as a complication to a previously existing disease.
Disease Outcomes
-Cure through successful therapy or due to self-limiting disease
-death
-disease progression-worsening manifestations
-progression-free disease (manifestations)
-physical limitation
-complications

-alteration of previous physiologic function; change or loss of previously normal cells/tissues.
Syndrome
A group of signs and symptoms (e.g. chronic fatigue syndrome, heart failure) that are characteristic of a specific disease state and are often related to the underlying physiologic changes.
Epidemiology
The study of a disease occurrence and factors contributing to diseases in human populations
Incidence
The measure of NEW cases arising of a disease in a population at risk during a specified time.
Prevalence
The measure of EXISTING cases of a disease in a population at a given point in time.
Morbidity
"how sick the disease makes the patient"  The functional effects associated with a disease.
Mortality
Death attributed to the disease
Risk factors
Conditions and behaviors that can contribute to the development of a disease.
Prognosis
The likely outcome of an illness in a patient case
Treatment
-medical interventions attempting to terminate the disease (cure), prevent death, delay or stop the disease progression, sign/symptom improvement, or improve or maintain quality of life.
-Modalities (options): lifestyle modification, drug therapy, nutritional therapy, physical therapy, surgery, radiation, organ replacement, or artificial replacement (prosthetics).
Gene
A gene is the basic functional unit of heredity.  It is a part of a chromosome which determines a certain trait, and it is a "stretch" of DNA sequence.
Genome
The complete set of genetic information of an organism, including all of its genes.
Genotype
The genetic makeup of the organism with reference to the trait under consideration.
Phenotype
Physical manifestation of the genotype, however not all of the genotype is manifested.
Alleles
Different forms of the same gene
Polymorphism
Multiple alleles of a given gene within a population, often with different phenotypes.
Genetics
The study of a single gene and what it does (traditional approach)
Genomics
The study of the functions and interactions of all the genes in the genome
Aneuploidy
Extra copy or missing copy of specific chromosomes- Often associated with diseases.  Aneuploidy occurs during meiosis (2N to N); most daughter cells cannot survive aneuploidy issues.
Aneuploidy resulting in excess is most commonly survived with chromosomes 13, 18, and 21.  Trisomy is three copies of the chromosome instead of the normal two.  Down's syndrome is trisomy 21 and Klinefelter's syndrome results in 3 sex chromosomes in males (XXY). 
Deficits result in only one copy of the chromosome instead of the normal 2, example is some cases of Turner Syndrome (only 1 X in females).
Genes and cells
Almost all cells in the body has DNA/ genes, with notable exceptions being RBCs and platelets.
Almost all the cells in the body have the same DNA (and same genes), with notable exception being germ cells.
Alteration of gene activities
Genes can be activated and inactivated by different processes in different cells.  Gene activities can also be affected by epigenetics/epigenomics and RNA interference (RNAi).  Epigenetics leads to changes of phenotype not attributed to changes of DNA sequence.  Mechanisms include: Changes of proteins associated with chromatins (e.g. histone), methylation of DNA bases, and others.  RNA interference (RNAi)- additional small RNA that can enhance/inactivate the transcribed mRNA (i.e. the activated genes).
Mutations
Changes in the nucleotide sequence of genes (ex: environmental damage to DNA, DNA replication errors, and errors in DNA repair)
Single Nucleotide Polymorphisms
aka SNPs
Point mutation (i.e. single nucleotide change) in genome where 2 or more alternative alleles are found in >1% of population.  93% genes have SNPs; ~40% will change the peptide sequence.  SNPs may have important consequences dor disease and drug therapy (alleles, drug response, drug side effects, drug interactions, ex-warfarin or coumadin)
Impact of gene mutations
-No phenotype change
Change in the proteins of the mutated gene; (e.g. alleles, loss of function of the proteins, loss of regulation of the protein activities, others)
-Change the regulation of the genes
-Passing the mutations/ diseases onto the next generation (if not corrected)
-Diseases (genetics diseases (CF, sickle cell), cancer, autoimmune diseases and many others)
Cystic Fibrosis
A chronic genetic disease that causes thick, sticky mucus build up; most commonly in the lungs and digestive tract.  Salty sweat on skin.  One of the common chronic lung diseases in children and young adults (especially caucasian).  It is fatal, but is manageable (life expectancy used to be less than 10 yrs but now with treatment can live to about 4th decade).
Epidemiology of cystic fibrosis
Affects both males and females roughly equally, but it is still a rare disease.  Caucasians are most common, about 10 million u.s. caucasians are carriers of the cf gene with mutations.
Etiology of cystic fibrosis
Mutations of a gene on chromosome 7 that encodes the Cystic Fibrosis Transmembrane conductance Regulator protein (CFTR), which is a chloride channel protein.  CF is an autosomal recessive disease.  Risk factors include family history and having Northern European ancestry.
Diagnosis of Cystic Fibrosis
-Family history
-Genetic testing (parents (carriers,etc), newborn, siblings)
-Patient's clinical presentations
-Sweat test- measures the amount of sodium and chloride in the patient's sweat on arm or leg (consistently high levels are strongly suggestive of CF)
-Median age at diagnosis is about 7 months and most patients are diagnosed by 12 years of age.
Cystic Fibrosis Disease Course
-Early onset (childhood)
-Chronic disease
-Progressive over time
-Prognosis: life expectancy in U.S. about 4th decade with adequate medical and drug management, the median predicted age of survival is about 38 years; however some patients still die early in life but it is often due to the secondary pulmonary complications.
GI complications of CF
-intestinal obstruction
-Steatorrhea (fat/oil drops in the stool)
-flatulence
-Gastroesophageal reflux
-bleeding
-liver cirrhosis & jaundice
-deficiency in digestive enzymes from the pancreas

CF pathophysiology
-Pancreas: Retention of digestive enzymes and destruction of pancreatic tissue
-Intestine: small and large bowel obstruction
-Hepatobillary system: thickened billary secretions; cirrhosis
-malnutrition and fat-soluble vitamin deficiency
Pulmonary complications of CF
-thick sputum
-Dyspnea (shortness of breath) on exertion
-Recurrent wheezing
-Chronic or recurrent cough (with or without sputum)
-Recurrent respiratory tract infections (sinusitis, ottis media, bronchitis, and pneumonia; most common cause of death in CF patients)
-Enlargment or rounding (clubbing) of the fingertips and toes

CF pathophysiology
-Airways
-thickening of mucus
-reduce the volume of liquid on airway surfaces
-adhesion of mucus to the airway surface
-chronic infections by bacteria such as staphylococcus aureus and pseudomonas aeruginosa and others
Skin complications of CF
Sweat with high chloride and sodium concentrations

CF pathophysiology
-secrete nearly normal volume of sweat, but it is concentrated
-unable to absorb Na and Cl from sweat
Endocrine complications of CF
Diabetes (insulin deficiency and insulin insensitivity)

CF pathophysiology
-Damage to pancreas; insulin secretion
Malnutrition complications of CF
-malabsorption of fats, proteins, and some carbohydrates
-fat-soluble vitamin deficiency
-failure to thrive (often in children, poor weight gain and physical groth failure despite an adequate appetite and nutrition intake)
Reproduction complications of CF
-infertility in both men and women (common)
-Amenorrhea (lack of menstrual bleeding; nutritional)
-Azoospermia (insufficient sperms in semen)

CF pathophysiology
-Impaired fertility very common
-vas deferens is often missing
-thickening of mucus in reproductive tract and malnutrition in women
Normal physiology of CFTR
CFTR is a cell surface chloride channel (protein) involved in the balancing the appropriate composition of sweat, digestive secretions, and mucus.  Located on the epithelial cells of sweat ducts (skin), airways, pancreatic ducts, intestinal tract, saliva glands, and hepatobillary tract.

The chloride channel is responsible for: 1. Active transport of chloride transport across cell membrane; in sweat glands- movement of chloride from sweat into the epithelial cell cytoplasm.  In other tissues- Movement of chloride from inside of the epithelial cells to the lumen (outside of the cell) and mucus.
2.  Indirect regulation of sodium transport across cell membrane (this in turn affects water movement leading to changes in tonicity and volume of mucus.  3.  Regulation of bicarbonate ions transport across cell membrane.
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