Exploring Biomedicine - Module 3 BIOM10002

Similarities between Bacterial and mt DNA

double membrane, circular supercoiled molecule, undergoes reproduction via fission

mt DNA in humans

37 genes: 2 rRNA, 22 tRNA, 13 protein genes - some subunits of complexes are coded by nuclear genes. Maternally inherited, possessed in multiple copies

heteroplasmy

not every mitochondrial DNA in a given cell is the same - mitochondria typically have a mix of nonuniformly distributed normal and abnormal tissue 

mtDNA protein transport systems

SAM, OXA1

Production of mitochondrial proteins

occurs via translation by ribosomes in the matrix

Eurkaryotic DNA features

protein-bound, linear, contains introns

Eukaryotic organelle features

contain nucleus, membrane bound organelles, 80S ribosome (subunits 40s and 60s, 1:1 rNA to protein)

Roles of the Mitochondria

producing ATP via oxidative phosphorylation, buffering calcium ions, Fe-S cluster biogenesis, regulation of cell dealth, immune signalling

Endosymbiosis

Modern mitochondria arose from oxygen breathing bacteria: large host cell and ingested bacterium become dependent on each other for survival

Faculative endosymbiosis

inclusion of an autonomous partner

Obligate endosymbiosis

central control, nuclear integration, cell-cycle synchronisation

Endosymbiotic Organelle

obligate codependency - cannot live independently

Nuclear DNA in mitochondria

only 13 proteins coded for in mt. all other required proteins come from outside mitochondria due to endosymbiosis transfer of mitochondrial genome

Nuclear encoded precursors

Synthesised on cytosolic ribosomes and delivered to mitochondria due to targeting sequences. Entry to mitochondria mediated by translocase enzymes.

Membrane proteins in Mitochondria

TOM: translocase of the outer membrane
TIM: Translocase of the inner membrane
SAM: sorting and assembling machinery
OXA1: oxidase assembly protein 1

SAM and OXA conserved proteins from bacterial origins

Mitochondrial Proteome

the entire set of proteins that can be expressed by the genome (including the mitochondrial genome) and is targeted to the mitochondria

Cellular Respiration

C6H12O6 + 6O2 = 6CO2 + 6H2O + ATP

Glycolysis

converts the six-carbon glucose to 2 molecules of the three-carbon pyruvate + 2 net ATP, 2 NADH, and 2 H2O. Pyruvate travels to mitochondrial matrix and is converted to 2-carbon acetyl CoA.

Citric Acid Cycle

Oxidation of acetylCoA within 8 steps. End products after 2 rounds = 2 ATP, 6 NADH, 2 FADH2, 4CO2

Oxidative Phosphorylation

redox reactions generate energy (ETC) which is captured in a proton gradient to produce ATP (chemiosmosis). proteins pumped from intermembrane space to inner membrane driving synthase motor (Complex 5). Produces 32-34 ATP, 10 NAD+, 2 FAD, 6 H2O

Mitochondrial Diseases

long-term, genetic, oft-inherited disorders that occur when the mitochondria fail to produce enough energy for the body to function properly.

Heterogeneity of MD

Clinical presentations and genetic causes of MD can be very different - >280 genes linked to MD.

Origins of MD

mutations can be inherited from parents or occur for the first time in a child - de novo

Clinical features of MD

encephalopathy, neuropathy, stroke-like episodes, hemiplegia, myoconic epilepsy, loss of muscle coordination, myopathy, deafness and blindness, lactic acidosis

Areas of MD effect

tissues heavily reliant on oxidative metabolism: central nervous system, peripheral nerves, the eyes, skeletal and cardiac muscle, endocrine organs

Primary MD

genes with a primary link to the function of the ETC, including mtDNA mutation

Secondary MD

genes with an indirect function on the ETC, or another mitochondrial function

Diagnosis of MD

initial biochemical tests - lactate and pyruvatem cerebrospinal fluid, amino/organic acids.

neuroimaging, electromyography, nerve conduction studies

genetic studies - albeit expensive. typically confirmation of well-suspected mitocondrial origin

muscle and tissue biopsies - less tolerated, less comprehensive

Functional Tests in MD

used to differentiate PMD and SMD as cannot be determined with lab tissue testing alone - RNA sequencing, quantitive proteomics, metabolomics

OMICS

analysis of large amounts of data representing an entire set of some kind e.g. genome, proteome, lipids, metabolome - systems perspective

mtDNA mutation

occurs due to random partitioning of mitochondria between dividing cells - daughter cells recieve non-identical copies of mtDNA. Heterogeneity leads to higher mutation rate.

Maternal mtDNA

Mitochondrial DNA is only recieved maternally as the mitochondria in sperm cells is destroyed post fertilisation

MELAS - Mitochondrial Encephalomyopathy, Lactic Acidosis, Stroke-like Episodes

a rare primary MD beginning in childhood, affecting the brain and nervous system, and the muscles. Caused by mutations in mtDNA gene MT-TL1 responsible for making tRNA to transport Leucine (UUR)

Sengers Syndrome

Secondary MD caused by mutation in acylglyerol kinease (lipid kinease) - responsible for import and assembly of mt carrier proteins and the TIM22 complex

Autosomal recessive - alleles must be homozygous

Respiratory Chain Enzymology Assays

identify malfunctioning electron transport chain complexes to support clinical evaluation of a defect in energy production.

Mitochondrial Replacement Therapy

A potential treatment for mitochondrial disease involves three-parent IVF, where a donor is used to supply healthy mitochondria to a parent couple.

Mito Cocktail

mixture of medications to optimise nutrition and general health - preventing deterioration of symptoms. ubiquinone, L-carnitine, B1 & B2, folic acid

Order of gastrointestinal tract

mouth - esophagus - stomach - small intestine (duodenum, jejunum, ileum) - large intestine - rectum - anus

Gastrointestinal tract

An open tube exposed to external environment, part of the digestive system. sections are anatomically quite similar but possess different characteristics, due to their function as specialised sections for uptake of different components

Nutritions and the GI tract

Stomach: water, ethyl alcohol, copper, iodide, fluride
Duodenum: calcium, phosphorus, magnesium ion, folate, some vitamins
Jejenum: many vitamins, iron, zinc, maganese, lipids, monosaccarides, amino acids
Ileum: other vitamins, depending on transit time
Large intestine: water, vitamin K, sodim, chloride, potassium

Composition of the Gut

muscosal tissue and smooth muscle. Protusions of villi allow for increased surface area

Peyer’s patches

specialised structures where immune cells are located in the gut that allow for fine-tuned interaction and monitoring

Microbiota in the gut

many non-damaging and tend to occupy the space without causing damage to the host - can be aerobic or anaerobic. Largest diversity in the large intestine

Functions of gut microbiota

Protective: production of anti-microbial factors, receptor competition, nutrient competition, pathogen displacement

Structural functions: barrier fortification, stimulation of IgA production, apical tightening of tight junctions

Metabolic functions: control epithelial cell differentiation/proliteration, metabolism of dietary carcinogens, synthesise vitamins, ferment non-digestible residue, ion absorption

Harmful Gut Microbes

Bacteria: salmonella enterica, e. coli
Viruses: norovirus, rotovirus
Parasites: giardia intesinalis, entamoeba histolytica

Pathogenic Traits

promoting colonisation in sterile locations, excessive occupation of specific niches, antagonising host defences, facilitating spread of microbes

Mechanism of Infection

Encounter - arrival of microbe to site
Entry - binding to receptor, triggering uptake mechanisms
Replication - utilising host resources for multiplication
Spread - release of new progeny, causing damage

Gastrointeritis

any inflammation of the gastrointestinal tract. Symptoms include diarrhoea, vomiting and abdominal cramping. Typically self-limiting (repairs itself with time). Can be infectious or non-infectious (caused by host response)

Invasive Gastroenteritis 

infection causes inflammation of the gut that results in breaching of the epithelial lining. Leads to vomiting, fever, abdominal pain and bloody diarrhoea due to blood vessel damage

M cells

specialized epithelial cells in the intestine that act as a crucial part of the immune system by sampling antigens and pathogens from the gut and transporting them to underlying immune cells.

Sources of Invasive Gastroenteritis

Food safety risks - faecal-oral transmission and poor food handling

Salmonella

subspecies of bacteria which cause salmonellosis. Causes either enteric fever or non-typhoidal salmonella

Enteric fever

non-self-limiting, more severe than NTS. Incubation period of 7-14 days. Requires antibiotic treatment. Vaccination available in endemic areas

Non-typhoidal salmonella

Natural hosts of food animals, reptiles and insects - zoonotic. Incubation period of 6-12 hours. Typically self-limiting

Salmonella infection

occupy the extracellular niche of gut luminal space. Can breach epithelial layer through multiple routes and drain to lymph nodes,causing systematic infection. Able to replicate intracellularly and in typically sterile sites

Non-invasive gastroenteritis

inflammation of the gut without the breaching of the mucosal layer. caused by bacterial toxins which are released over the course of infection. Typically self-limiting

Clostridiodes Difficile

A hospital pathogen that typically florishes following wide use of antibiotics. Entirely toxin medicated. Toxins A & B are taken up by colonic epithelial cells, causing cell death, damage, inflammation and fluid accumulation.

Bacillus Cereus

Spore forming bacterium commonly found in soil/on vegetables. causes emetic or diarrhoeal foodborne illness dependent on type of bacterual toxins

Bacillus Cereus - Emetic Toxins

cause emetic syndrome involving ingestion of pre-formed toxin that leads to the destruction of the mitochondria within infected cells. heat-stable and pH resistant. Activates receptors that stimulate the major nerve controlling stomach function

Bacillus Cereus - Enterotoxins

Cause diarrhoeal syndrome involving the production of enterotoxins following ingestion. Pore-forming toxins, e.g. Hbl and Nhe, cause holes in host cell membranes, inducing cell death and leading to fluid accumulation in the ileum.

Homeostasis

The maintanence of a stable internal environment involving the regulation of temperature, pH, ions, and solvents (polar molecules), all of which can disrupt hydrogen bonds and cause denaturation.

Feedback loops

require the transmission of an input from a receptor to a control center, which directs to effector to produce a certain output. Negative Feedback is self regulatory and helps to maintain a level, while positive feedback amplifies a response.

Process of homeostasis

1. stimulus produces change in variable

2. change detected by receptor

3. information sent along afferent pathway to control centre

4. information sent along effect pathway to effector

5. response of effect influences magnitude of stimulus

Blood glucose - Negative Feedback

When blood glucose levels are too low, the pancreas is stimulated to release glucagon which allows stored glycogen in the liver to be released into the blood.

When blood glucose levels are too high, the pancreas is stimulated to release insulin which allows glucose to be removed from the blood via the liver storing it as glycogen

Blood Pressure - Negative Feedback

When mean arterial pressure increases, the heart is stimulated to decrease heart rate and force of heart muscle contraction, and blood vessels are stimulated to dialate. This causes a decrease in MAP.

When mean arterial pressure decreases, the heart is stimulated to increase heart rate and force of heart muscle contraction, and blood vessels are stimulated to contract. This causes a increase in MAP.

Visceral information

Sensory or motor information related to internal organs and smooth/cardiac muscle. Information that is subconscious. Includes homeostatic reflexes.

Somatic Information

sensory or motor information related to the body wall and movement of limbs/joints - conscious information and voluntary movement

Ligands

hormones and neurotransmitters - chemical signalling molecules involved in

Neurotransmitters

Ligands released in small packets at the synapse. They are action discrete - restricted to receptors at the synapse.

Noradrenaline

a neurotransmitter released by the sympathetic nervous system to evoke fear, flight or fight responses. Activates adrenergic receptors.

Endocfrine hormones

released into the circulatory system. Action may occur on any cell in the body with a receptor for the particular ligand.

Adrenaline

a hormone secreted by the adrenal gland under sympathetic control. Activates adrenergic receptors.

Thyroid hormone

a hormone secreted by the thyroid gland under hypothalamic regulation. Increases energy expenditure (heat production).

Circadian Rhythm

24-hour cycles that are part of the body’s internal clock that run in the background carrying out essential functions and processes, resulting in changes of levels of arousal and attention

Changes in body temperature

Body temperatures are higher in the day and fall towards the sleep period. When temperature falls below a certain point, sleep is initiated.

Plasma glucose levels and cortisol levels also follow similar patterns.

Methods of heat exchange

• radiation - heat transfer via electromagnetic waves

• evaporation - heat transfer via conversion of water to vapour

• convection - heat exchange with surrounding medium

• conduction - heat exchange with another object

Non-shivering Thermogenesis

sympathetic regulation that occurs by increased use of energy within the body in cold environments. e.g. generation of heat via brown adipose tissue (BAT) where mitochondrial burn fuel to directly produce heat rather than creating ATP

Shivering thermogenesis

somatic regulation that occurs by contractions of muscles within cold environments. i.e. signalling via the hypothalamus for rapid muscle contraction, burning ATP and creating heat

Four Thermoregulatory Strategies

non-shivering thermogenesis, shivering thermogenesis, vasoconstriction/dilation, water evaporation

Fever

an adaptive response to infection that involves the alteration of core body temperature via reflex.

Infection agents activate the immune response, which results in the release of inflammatory mediators.

Prostaglandin is produced and carried by the blood to the hypothalamus.

An alteration in neuronal activity adjusts for the altered set point.

Pyrogens

agents that incite the fever response.

Impact of fever

Fever helps slow viral replication rate by raising the body’s temperature above their optimal operating temperature.

Certain proteins within the immune system operate better at higher temperature than normal, allowing for an adaptive advantage as they are selectively activated during infection.

Sepsis

an uncontrolled inflammatory response, resulting in excess high temperature that can lead to organ damage.

Responses to temperature

Changes in core body temperature are sensed in the hypothalamus and evoke unconscious visceral responses.

Changes in ambient temperature lead to conscious awareness of thermal discomfort, resulting in behavioural responses.

GI Semi-Permeability

Pros: efficient nutrient absorption, controlled permeability, immune surveillance, microbial homestasis, detoxification

Cons: vulnerability to barrier dysfunction - “leaky gut”, entry point for pathogens, allergen exposure, limited defence

Intestinal Epithelial Cells

form the first physical barrier (tight junctions). produce mucins and antimicrobial enzymes (defensins, lysozymes). act as sentinels with pattern-recognition receptors

Globlet cells

Secrete mucus, forming a protective layer on epithelial surfaces to limit microbial contact

Dendritic cells

Sample antigens from the lumen (e.g. via M cells), present antigens to T cells in Peyer’s patches

Macrophages

Phagocytose pathogenic bodies and maintain gut microbiota balance

M cells

specialised epithelial cells found in Peyers patches that assist in antigen sampling and transport to immune cells

The respiratory system

Purposes of the Respiratory System

• transfer oxygen from the environment to red blood cells

• transfer carbon dioxide from blood to the air

• regulate acid-base balance

The Bronchial System

formed from 22 divisions of the trachea. composed of cartilge, connective tissue, and smooth muscle

Asthma

a disease of the conducting system which leads to variable airflow obstruction, characterised by inflammation and thickening of the airway membrane

Triggers of asthma

air pollution - bushfire smoke, allergens - house dust mite, grass pollens, exercise, viral infections, cigarettes

Spirometry

A measurement of lung performance. Inspiration and expiration are measured on a graph of volume vs time. Asthma is characterised by reduced airflow on expiration

FEV1 value

The amount of air blown out in one second - a measure of how quickly air can leave the lungs. Typically 70-80% of forced vital capacity.

FEV1 in asthma is reduced to <80% of what is predicted.

Forced Vital Capacity

Total volume of air that can be forcibly exhaled after a deep inhalation.

Allergic Asthma

Most cases are eosinophilic, with allergic cells appearing in sputum. Blood eosinophil count can be used to approximate sputum eosinophil count.

Allergens are inhaled and make contact with the respiratory epithelium.

They are picked up by dendritic signalling cells and presented to naive T cells, creating a cell-mediated immune response, as well as to B cells to produce antibodies.

Histamine released by mast cells leads to restriction of the airways and recruitment of eosinophils. 

Non-Allergic Asthma

Pollutants such as fungi or cigarette toxins activate innate lymphoid cells which leads to bronchial hyperreactivity and the recruitment of eosinophils.