Personal Statement Flashcards
1
Q
Define symbiosis
A
any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic.
2
Q
Describe the three types of symbiosis
A
1) mutualism - both species benefit from the relationship
2) commensalism - one species benefits from the relationship whilst the other is neither harmed nor benefitted
3) parasitism - one species benefits whilst the other is harmed
3
Q
How did symbiosis evolve?
A
- interaction led to evolution
- predation
- endosymbiotic theory
X
4
Q
Why do you think symbiosis cannot occur between the same species/ has occurred between different species?
A
- maintains species and diversity
- cat licking vs oxpecker and rhinocerous
X
5
Q
What was the most interesting concept from ‘This is Your Brain on Parasites’?
A
Crickets:
Hairworms produce phototaxis alterations (changes in the
responses to light stimuli) could be a part
of the wider strategy for the completion of their life
cycle
The mechanisms used by hairworms to increase the encounter
rate withwater remaina poorly understood a
- worm tampers with visuals
- releases similar chemicals to communicate with cricket
- cricket dies, worm spills out into pool (exit into aquatic enevironment favourable for reproduction), worms mate in water, females lay eggs, eggs turn to larvae, larvae bump into mosquito larvae and hide in them as cysts, mosquito larvae turn to mosquitos carrying the parasite, cricket eats mosquito, dormant cyst now inside cricket grows to a worm again, worm makes cricket go to large expanse of water, cricket drowns and dies.
- worm produces raft of neurochemicals similar to the cricket’s
- cricket attracted to light (water reflects light) (induce a positive photoaxis response)
- blind infected crickets were not attracted to light
-parasite-induced change in host phototaxis is reversible, that
is, once the nematomorph parasite is released, crickets are no
longer attracted to light.
possible mechanism:
- in the central nervous system of manipulated N.
sylvestris (wood cricket) differential expression of proteins (from the BIR; 2 family) was involved in the inhibition of apoptosis - suggests disturbance of a cellular
process could lead to a modified neural circuitry
enhanced walking
How do they know the crickets aren’t just thirsty?
- uninfected water deprived crickets did not show any positive photoaxis (they still didn’t go to the water reflecting light)
phototactic behaviour - moving towards or away from light (cyanobacteria)
How do we know the parasite causes photophilic behaviour and the photophilic behavour doesn’t cause the parasite?
- because the behaviour isn’t maintained after the parasite exits the cricket in the ater
Would be interesting to determine if polarized light, particular wavelengths, or shapes can induce the observed phototactic response or if direction of light alone is responsible for the water-seeking behavior observed for manipulated crickets.
6
Q
Define parasitic manipulation
A
the alteration by the parasite of a host phenotypic trait in a way that enhances the parasite’s probability of transmission and survival
7
Q
What is interesting about parasitic manipulation from an evolutionary perspective?
A
In an evolutionary context, changes in host behaviour upon parasite infection are examples of an extended phenotype, a concept introduced by Dawkins (1982). He stated that the observed host phenotype is a consequence of a parasite’s gene being expressed.
8
Q
Explain how T. Gondii alters the neural activity in the amygdala of rats?
A
T. Gondii resides in faeces which is then digested by rats. It causes behavoural changes within the rat causing it to no longer fear cats. The rats are eaten by cats and the parasite is transferred to the intestine of the cat - a favourable place for reproduction, ( from here stable oocysts are excreted into the faeces) and the cycle is repeated.
T. Gondii blocks an innate aversion of rats for cat urine, instead producing an attraction to their pheromones, increasing the likelihood of the cat predating on the rat
Neural circuits implicated in innate fear, anxiety and learned fear all overlap which suggests T.Gondii may disrupt all of these non specifically
Sapolsky studied the rats and found T. gondii migrates to the brain, forming cysts within the amygdala, a part of the brain associated with the control of fear.
9
Q
What is the behavioural manipulation hypothesis?
How does Sapolsky’s experiment provide evidence for it?
A
a parasite will specifically manipulate a hosts behaviour essential for enhancing its own transmission
life
Innate fear of cat pheromones share similar neurobiological substrates to with pheromones of learnt fear and anxiety like behaviours and yet infection of T.Gondii still only blocks aversion of predator odours (innate fear) and doesn’t compromise learned fear or anxiety (hence parasite is affecting only the part of the behavioural response that is important for its transmission + completing its lifecycle)
10
Q
What did Sapolsky investigate and what did he find in his experiment with T.Gondii?
A
He investigated the distribution of the parasite in the nervous system and the specificity of T.Gondii on the behaviours affected
He found that in infected brains parasite cysts were randomly distributed over the entire brain but cyst density was particularly high in amygdala structures
He found the effect of T.Gondii on behaviour is remarkably specific; infection didn’t decrease learned fear or anxiety like behaviour but it did decrease innate fear even though all of these behaviours are closely related. The infected mammals even still retain an innate aversion to dog urine (because this mammalian predator is not important for the sexual life cycle of the predator)
11
Q
How did Sapolsky know that the innate aversion of cats is not just a generic side effect of sickness? (I.e. not as aware)
A
Because the response of an infected animal to a non predator (rabbit) urine odour remained unchanged and they still had an innate aversion
12
Q
What do mathematical models of a prey-predator-parasite system demonstrate?
A
A small selective increase in susceptibility of a predator to the infected prey population is sufficient to cause a significant increase in parasitic load within the predator population
(Ie. If infected prey becomes more susceptible to the predator so like the rat running to the cat then this increases parasitic load in the predator)
13
Q
Describe the mechanisms of the behavioural effects of T.Gondii on the rat
A
T.gondii subtle tropism for the amygdala to interrupt specific brain wiring (exact mechanism still unknown)
-internalisation of olfactory receptors important for cat odor protection
14
Q
Rat preservation chemical
A
Carosafe
15
Q
6 anatomical regions of rat
CCPTAP
A
Cranial region - head Cervical region - neck Pectoral region - front legs attached Thoracic region - chest area Abdomen - belly Pelvic region - back legs attached
16
Q
Describe what you saw during the rat dissection
A
Peeled the skin back from the incision point and saw the muscular and skeletal system
Latissimus dorsi muscle - retracting the arm - triangular & covers lower back
Gastrocnemius - leg muscle
Lymph glands - dark, circular, pressed against the jaw muscles
Nicitating membrane
17
Q
Describe something particularly interesting from the rat dissection
A
Nicitating membrane
- transparent third eyelid drawn across eye for protection and to maintain moisture
human plica semilunaris (remenants of human nicitating membrane)
secretes immunoglobulins to act as an immunological barrier
- plica semilunaris is a fold of the conjunctiva in the inner corner of the human eye - Vestigial feature
Reason for loss of function: unclear but changes in habitat/eye physiology may have rendered the tissue unecessary
18
Q
Did you manage to locate the encysted parasite?
A
No the skull was too hard to break through
thinking about skeletal structure later on - found out collapsible skeleton - ribs hinged to spine to fold down when fitting through small spaces (pressure at front causes ribs to give way and effortlessly collapse)
19
Q
What is something else that fascinated you in ‘I Contain Multitudes’?
A
- triple symbiotic relationship between citrus mealybug that has mealybug bacteriocyte with tremblaya in it that has moranella inside it. (All three symbionts necessary for mealybug survival, trem and mor are bacteria)
Complimentary genomes - 9 enzymes required to make amino acid phenylalanine - tremblaya builds 1,2,5,6,7,8. Moranelle builds 3,4,5. Mealybug builds 9
Bizarre thing: tremblaya genome missing class of supposedly oldest genes in existence. There should be 20, some symbionts have fewer but tremblaya has none. It survives because the other two symbionts compensate for the vanished genes.
22 bacterial genes integrated into mealybug DNA but these were NOT from either tremblaya or moranella. They came from three other lineages of bacteria living in mealybug ancestors that transferred their genes into the mealybug genome. (Mealybug genome contains genes form bacteria not presently living in symbiosis with it)
Uses genes from former symbionts.
20
Q
How do you think the triple symbiotic relationship evolved?
A
- similar to the endosymbiotic theory
- moranella and tremblaya survived endocytosis by a citrus mealybug
- as symbiont genomes were transferred to host genome the host became increasingly dependent on symbiont mechanisms, in turn reducing the original host genome
- lost genes because didn’t need them
- but doesn’t fit with idea of Junk DNA - would have thought extra genes = protection ?
- BUT: less DNA to pack has been linked to faster nutrient transport and faster cell signalling
21
Q
What is the endosymbiotic theory?
A
Lynn Margulis - late 1900s
Theory that some of the eukaryotic cell organelles originated from prokaryotic microbes
Mitochondria and chloroplasts may have survived endocytosis by a larger cell, lived in symbiosis with it as mitochondria provided energy and chloroplasts nutrients - prokaryotic cells (mitochondria and chloroplasts) receive protection and stable environment in return = Eukaryotic cell forms
Mitochondria evolved from endosymbiotic proteobacteria (prokaryote microbe that was engulfed)
Chloroplasts evolves from endosymbiotic Cyanobacteria (prokaryote microbe that was engulfed)
Mitochondria and chloroplasts are the same size as prokaryotic cells, divide by binary fission and have circular not linear DNA
22
Q
How do genes become integrated into a host genome?
A
X
23
Q
Did anyone raise any interesting questions when you presented about T.Gondii?
A
X
24
Q
Explain the symbiotic relationship between the Hawaiian bobtail squid and bioluminescent V. Fischeri
A
Bobtail squid light organ full of luminous V.fischeri. Bacteria light matches moonlight shining down from above and cancels out the squid’s shadow.
Squid gains camouflage, bacteria gain hospitable environment
McFall Ngai & Ned Ruby: labelled V.Fischeri cells with glowing proteins and tracked them as they journeyed you the light organ (watched symbiosis in action)
25
How do V.Fischeri enter the Hawaiian bobtail squid?
XXXadd more scientific detail
- Surface of light organ covered in cilia and mucus
- creates current that draws in particles of bacterial size but no larger
- microbes collect in mucus with V.Fischeri among them
- when 5 cells make contact with the squid it causes genes within the squid to turn on, these release antimicrobial chemicals that create an inhospitable environment for the other bacteria but leave V.Fischeri unharmed
- other genes code for enzymes that break down mucus releasing chemicals that attract V.Fischeri
- V.Fischeri dominates mucous layer
- nester squid through bottleneck and reach crypts (pockets) in the light organ
- bacteria accommodate crypt, dusts constrict and fields of cilia waste away, light organ matures
26
How does the LuxI-LuxR Quorum sensing system regulate the light producing genes?
1) LuxI (enzyme) produces autoinducer molecules called homoserine lactone that diffuse out of cell
2) once in high enough concentration the autoinducer binds to LuxR partner protein
3) binding of LuxR and autoinducer causes DNA binding domain on LuxR to be unveiled allowing the complex to sit at the gene promoter of the CDABGE operon
4) (aka. formation of this complex activated transcription of the LuxICDABGE operon)
5)
- causes Lux proteins to be made
- LuxA and LuxB genes code for alpha and beta sub units of luciferase that catalyses a redox reaction that produces blue-green light
- LuxC,D and E code for components of the fatty acid reductase complex requires for the synthesis of the aldehyde substrate for luciferase
- LuxG thought time code for flavin mononucleotide reductase that generates reduced flavin mononucleotide as a substrate for luciferase
*this mechanism is on gram negative bacteria
27
Operon
Functioning unit of DNA containing a cluster of genes under the control of a single promoter
28
What was something interesting from the MOOC ‘An Introduction to Microbiology’?
Photosynthetic bacteria ???
29
Explain how coral symbionts transform from mutualists to opportunists due to excessive DOC
Mutualist - both species gain benefit
Opportunist - non-pathogenic organisms that act as a pathogen in certain circumstances
Algae produce DOC (dissolved sugars and carbohydrates in water) - nourish microbes of coral - microbes grow and consume surrounding oxygen - coral suffocates
Opportunistic
30
How does C.Difficile shift from a mutualistic to pathogenic state in the gut?
mutualism:
C.difficile: gram positive bacteria
- C. difficile gain hospitable environment in gut (warmth, nutrients)
- member of normal gut microbiome but growth is suppressed by other more dominant anaerobes
- part of our normal gut microbiome (which has known benefits ie. promoting innate and adaptive immunity)
Pathogenic process: depends on whether C diff can colonies and the colonization resistance of the gut microbiome.
Infection caused by: commensal microbiota which creates a barrier effect is lost following anti microbial therapies (use of antibiotics). Allows C diff to colonies in intestine.
Interaction of C.diff and intestinal epithelial cells* and begins a cascade of inflammatory processes that contribute to intestinal diseases such as diarrhea and pseudomembranous colitis.
*epithelial cells intoxicated with C. Difficult release proinflammatory mediators including interleukin 8 and macrophage inflammatory protein 2 into the lamina propria (thin layer of connective tissue lining GI tract) that initiates an acute intestinal inflammatory response*
Alterations in normal gut microbiome provides a new niche for C. Diff to colonies in
31
What else did you discuss with Dr Knox that was interesting?
- norovirus respiratory virus outbreaks
- C. Difficile came about after poor use of antibiotics, massive outbreak at end of 1990s
- cytotoxicity - how does C. Difficile actually cause disease ?
IGA mucosal immunity
Childhood colonisation is common but childhood disease is not.
MRSA
selective pressure in the hospital setting
Bacteria - epigenetics ?
Gut microbiome and immunity
Bacterial recognition systems
Hepatitis C looking at cellular responses
BZV
Stafforius
Registra ?
Going through blood cultures that come up positive
Was going to shadow her in the laboratory
Looking at culture plates discussing cases
Do a bench round
Pregnancy and neonatal infections
Shumaila:
Faecal transplants
32
How did you challenge the data on the abundance of C. Difficile in the GI tract?
X
- found some alternative articles that suggested C. difficile increase may be due to ?
33
How did you analyse the data on C.difficile’s abundance in the GI tract?
X
- looked at some graphs of its abundance upon antibiotic use
- clearly abundance increased
- linked that to the deteriorating barrier effect of commensal bacteria
Graphs:
Comparing sample from patient and normal person
Before antibiotic treatment,
Klebseilla bacteria - UTI
colours = species
Telling you how many of each species is there
Ackermamansia predominant before treatment
Succession ?
After they added antibiotics, C. Difficile hasn’t grown
May have used narrow spectrum antibiotics only for gram positive bacteria so didn’t target C. Difficile
C. Difficile negative, C. Difficile positive. Colour coding = different pathogens
C. Difficile = gram positive
Why do 70% people not get affected by C. Difficile? Depends on environment, our community, immune system
Microbial forensics
Microbiomes are different in C. Difficile positive and negative people
Bacterial richness
Read the summary of what the graph is apparently showing, read the bit of the paper, see it as a whole
Tuberculosis - screened different genes wanted to know which are specific to mycobacterium and which were not. Clones genes into vectors and developed new vaccines for TB.
PCG vaccine
Note - ask interviewer what the most interesting thing they have ever discovered or learnt about ?
34
Explain how gut dysbiosis, rather than mutations associated with the SHANK3 gene is a cause of autistic behaviour.
bi directional communication between the gut and brain - connected by the vagus nerve
gut microbiome influences our brain and hence behaviour
- effects of probiotics on autistic symptoms
- substances secreted by microbes can infiltrate blood vesels
- microbes prompt neuropod cells lining the gut to stimulate the vagus nerve that connects to the brain
- microbes activate enteroendocrine cells in gut lining which send hormones throughout the body.
35
What else did you discuss in you essay titled ‘to what extent is human behaviour genetically determined’?
Amino acid tryptophan, which some gut bacteria produce, could be a causal link.
Microbes convert tryptophan into serotonin
(a neurotransmitter implicated in depression and other psychiatric disorders)
Cells also turn tryptophan into a substance called kynurenine, (reacts further to form products that can be toxic to neurons)
Changes in the microbiome might tip the production of kynurenine and tryptophan in a way that impairs mental health
Research has shown: people with depression convert tryptophan into kynurenine more readily than into serotonin. (more K means more toxicity to neurons)
36
What about your essay do you think made it come runner up?
500 words
| X
37
What motivated you to complete the MOOC ‘An Introduction to Cancer biology’?
- uncle
- telomeres ?
- interests din cells so made sense ???
X
38
Explain how cancer evades the immune system via the PD-1/PD-L1 complex
- Immune checkpoints: prevent immune responses from damaging healthy cells
- PD-L1 - protein that in humans is coded for by the CD247 gene - on tumour cell
PD-1 - protein on surface of T-cells
PD1 and PD-L1 = immune checkpoint proteins
Anti-PD-1 and anti-PD-L1 = immune checkpoint inhibitors
binding of PD-1 and PD-L1 results in tumour cell not undergoing apoptosis. Cancer cells upregulate PD-L1 to avoid cell death.
So checkpoint inhibitors administered, anti-PD-1 binds to PD-1 and anti-PD-L1 binds to PD-L1 preventing interaction of PD-1 and PD-L1
Normally : interaction of PD-1 and PD-L1 results in T cell immune suppression
39
Does cancer evade the immune system in any other way?
X
| CTLA-4
40
What was something else that interested you in the MOOC ‘Am Introduction to Cancer Biology’?
(telomeres)
OR
Warburg effect
most cancer cells:
predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol
RATHER THAN
low rate of glycolysis followed by oxidation of pyruvate in mitochondria (as in most normal cells).
Two hit hypothesis ?
10 hall marks ?
41
How did you explore the mechanisms of the PD-1/PD-L1 complex further whilst reading ‘The Immunotherapy Revolution’?
I read about a similar mechanism involving CTLA-4 where when CTLA-4 is bound to a B7 protein it inactivates T cells and prevents them from killing cancer cells.
- TCR binds to MHC and antigens on APC,
CD28 (on T cell) binds to B7-1/B7-2 on the APC,
YES BINDING OF B7-1/B7-2 to CTLA-4
= inactive T cell = NO cancer cell death
- TCR binds to MHC and antigens on APC,
CD28 (on T cell) binds to B7-1/B7-2 on the APC,
NO BINDING OF B7-1/B7-2 to CTLA-4 (blocked with anti-CTLA-4)
= activated T cell = cancer cell death
cancer cells hijack macrophages and expresses B7 protein which CTLA-4 on T cell binds to and makes the T cell inactive
42
What was something else you found interesting in ‘The Immunotherapy Revolution’
X
43
Define CAR T-Cell therapy
Genetic engineering of a T cell to possess an artificial chimeric antigen receptor that can target a specific antigen of a cancer or tumour cell
44
Why do you believe CAR T-Cell therapy is crucial in our fight against cancer?
X
45
What do you think CAR T-Cell therapy holds for the future?
X
46
How can the chimeric antigen receptor be effectively designed to overcome a hostile tumour environment?
X
47
What is the skeletal design of a CAR T-Cell?
1) Single Chain Variable Fragment - makes up the receptor's extracellular antigen recognition domain.
consists of a variable region of heavy and light chains derived from a monoclonal antibody which are connected by a flexible peptide linker
2) Spacer or 'hinge' domain - derived from human immunoglobulin connects the transmembrane domain and antigen binding domain. Provides flexibility for the CAR.
3) Transmembrane domain - connects the ectodomain and endodomain so that the CAR is anchored to the surface of the T-cell
4) Intracellular signalling domains -
in all generations of CARs, a CD3-zeta signalling domain, derived from the intracellular portion of a T cell receptor that controls downstream signalling.
costimulatory domain - commonly used ones are derived from CD28 and 4-1BB
48
What is it like in the hostile tumour micro environment?
X
49
Why do you think your dissertation was specially commended by your school?
X
50
Explain by-specific T-cell engagers.
- Class of artificial bispecific monoclonal antibodies
- Direct a T cells' cytotoxic activity against cancer cells
- BiTEs are constructed of two single-chain variable fragments (scFv) connected in tandem by a flexible linker. One scFv binds to a T-cell-specific molecule, usually CD3, whereas the second scFv binds to a tumor-associated antigen. Retargets T cells to tumour cells, bringing them within closer proximity of one another.
- Allows for effective tumour lysis due to BiTEs ability to target specific tumour antigens
- Useful for heterogenous tumour populations where cells have different tumour antigens
- EG. Blinatumomab: enables T cells to recognise malignant B cells - two binding sites (CD3 for T cell and CD19 for malignant B cell)
51
How did you get in contact with Dr Banerji?
X
Read one of his articles ??
52
What did you explore further about bi-specific T-cell engagers?
X
53
What was the article that you read by Dr Brentjens?
X
- it was about anti-PD-1 secreting single chain variable fragments
- saw his name in loads of articles
54
What did you discuss with Dr Brentjens about the use of anti-PD-1 secreting single chain variable fragments within CAR T-cells?
- how scientists are currently looking at ways to manufacture immune checkpoint inhibitors within the CAR T-Cell construct, rather than using them as a combination therapy.
- synthesis of anti-PD-1 producing ScFvs.
OR POTENTIALLY:
- researchers have also synthesised anti-mesothelin CAR T-Cells which bear a dominant-negative PD-1 receptor
- CRISPR-Cas9 and short hairpin RNAs has also been used to silence genes coding for PD-1 in CAR T-Cells. (requires further research - suggested that PD-1 plays a role in T cell activation - undesirable consequences)
55
What findings did you present at your school science club?
Did anyone raise any interesting questions?
X
56
Explain the role of Xist RNA in X inactivation.
Xist = one of first long non coding RNAs to be identified
Long non coding RNAs: one function is tehy attract histone modifying enzymes into vicinity of selected genes
Xist RNA is critical for swiching off expression of one of the X chromosomes in a female cell.
As Xist spreads along X chromosome it attracts otehr proetisn many of which are epigenetic enzymes that add cheical modifications to eitehr DNA or hsitoen rpotein. These enzymes include major repressor and also enzymes thatadd methyl groups.
Epigenetic modifications they produce strengthen the shut down of genes which leads to hyper comaction of inactive X chromsoome and formation of Barr Body.
After cell division these epigentic modifications are reestablshe don the new X chromosome.
Making egss:
inactivating marks removed from X chrosomes and daughetr cells (eggs fresh)
don't pas son inactivation to offspring
epigentic mechanism has to be applied to th chromosem againd urng earkys tage sof developement to re inactivate the X chromsome.
57
Why is X inactivation important?
prevents the female X chromosome have twice as many gene products as the male
58
What was your favourite part of ‘Junk DNA’?
X
Insulating DNA ?
- genome constantly subject to potentially damaging stimuli from the environment (UV from sunlight, carcinogens in food etc)
59
How did you contemplate the genetic factors behind a bats ability to act as a viral reservoir?
How is a bat able to host so many viruses?
Are the viruses hiding from the immune system?
Is it a symbiosis?
Mutation?
60
Explain the benefits of bats’ mutated STING protein.
Bats act as a reservoir for up to 137 different viruses, 67 of which are zoonotic
the STING dependent interferon gene activation mechanism is dampened due to a mutated STING protein (mutation of serine residue) that came about as a result of the metabolic demands of flight causing a release in self-DNA into the cytoplasm in bats.
This mutation has evolved to dampen STING interferon activation.
Allows them to not have such terrible pro-inflammatory responses because less IFN production
- Flight is an energy intensive process
- to provide energy necessary - many oxidative phosphorylation pathways (drives the synthesis of ATP by the movement of protons down an electrochemical gradient through ATP synthase)
- as a result lots of protons and electrons floating around in the mitochondria
- this mixed with high temperatures during flight = lots of Reactive Oxygen Species are formed.
- These can damage DNA in the bat cells causing it to be released into the cytoplasm.
- Normally DNA in the cytoplasm is a sign of a viral infection and this triggers IFN production and an immune response,
61
Explain the cGAS-STING pathway.
signalling pathway involved in innate immunity that senses non-self extracellular DNA
1) internalisation of non-self extracellular DNA into cell cytoplasm
2) DNA binds to cGAS monomers
3) DNA-cGAS monomer complex dimerises (combines) which leads to the activation of the complex
4) the active complex processes ATP and GTP into a signal molecule called cGAMP
5) cGAMP binds to and activates STING
6) STING activates transcription factors that translocate to the nucleus . This activates the interferon gene. The production of the interferon protein stimulates other parts of the immune system.
* sometimes the cell encounters modified extracellular self-DNA which triggers the process unintentionally causing inappropriate activation of the interferon gene. This is the basis of autoimmune diseases.
Basis of autoimmune treatment:
small molecule inhibitor drugs that bind to the active DNA-cGAS complex preventing cGAMP production. Hence blocks interferon gene activation.
62
What was so captivating about the lecture on bat’s mutated STING protein?
X
63
What motivated you to visit body worlds?
X
64
What else did you see at body worlds?
X
| preserved nervous system
65
What did the preserved bat at body worlds look like?
X
66
What did the preserved octopus at body worlds look like?
X
67
What about seeing the preserved bat and octopus at body worlds inspired your interest in evolution?
X
Seeing both disparate species side by side ?
68
What was something interesting you found out about the preserved bat and octopus?
X
69
What was your favourite part of reading ‘Other Minds’?
-quote ?
- ?
X
70
What made you want to start your school’s biology society?
X
71
What is something you have presented about at your biology society?
Telomeres:
Normal cells - stop dividing when their telomeres become too short (hayflick's limit)
* telomere attrition, as a result of successive cell divisions, results in chromosomal instability
* Telomere - protein complex that protects end of chromosomes (repetitive TTAGGG DNA sequence). They protect them from fusion and being recognised as sites of DNA damage.
* Telomeres are maintained by an enzyme called telomerase
* Normal cells: dysfunctional telomeres occur due to successive cell division which eventually shorten the length of the telomere - this then elicits DNA damage responses that trigger cellular senescence.
* Leads to breakage-fusion-bridge cycles where two sister chromatids without telomeres fuse together. (A dicentric chromosome - one with two centromeres) might be produced. Then during anaphase these are drawn apart and they break leading to genomic instability and extensive cell death.
* Some rare cells escape this and maintain stable but with short telomeres. They activate the normally silent human gene TERT that encodes telomerase - a reverse transcriptase enzyme
* Another DNA recombination mechanism (rarer) = Alternative Lengthening of Telomeres (ALT) also reverses telomere attrition
* hTERT activation - mutation in hTERT promoter (scientists have recently found 2 of these), alterations to alternative splicing of the hTERT pre-MRNA
* Scientists have been investigating the molecular mechanisms which regulate hTERT expression and telomerase assembly
* telomerase inhibition strategies - hTERT inhibition - telomere shortens - cancer cell death
* Anti-telomerase therapeutics
72
What books have you read during your biology reading club and what was interesting about them?
Skin book
Mutation that makes u smell like fish?
73
What have you enjoyed about leading discussions in your biology reading club?
Bouncing off others
| Working together an dudes knowledge to work out an answe
74
What is your summer cake selling business?
- did it to try and get flying lessons for a pilots license
75
Why is determination important for biology?
X
76
How would you use your skills and knowledge of biology to better our world?
X
77
If you could do anything with the field of CAR T-Cell therapy, where would you take it?
X
78
What is something that interests you that isn’t on your personal statement?
Gram positive bacteria mechanisms
Wolbachia
Golden panama frog
Telomeres
Social evolution of microorganisms (Kin selection)
Theory of ageing late acting mutations
X
79
Why Oxford?
Because I want to study biology at the place place DUHHH
I want to be brought to my maximum potential
On the back it says Oxford is what you make of it but it’s what Oxford will make of me !!!! I wanna be brought to my full potential !!
80
Why do you want to study biology?
because biology
81
What makes C.difficile resistant to antibiotics?
- C.difficile difficult resistance not only causes CDI but drives emergence of new strains as well. Global spread of hypervirulent NAP1 strain is thought to correlate with widespread use of fluoroquinolone antibiotics.
Spore structural layers
- spore core contains DNA,RNA and most enzymes
- core surrounded by compressed inner membrane protein that has low permeability and prevents core from DNA damaging molecules
- protein coat surrounding outer membrane
82
Which antibiotics can treat C. Difficile infection and what do they target?
Vanomycin
- inhibits spore formation
Normally: spores germinate to vegetative (reproducing) bacteria, spores highly resistant to antibiotics so cause infection.
Mechanism: taurocholic acid and glycine identified as factors that stimulate germination of spores into virulent vegetative cells that secrete potent toxins
- inhibits cell wall synthesis
- fixadomicin targets RNA polymerase, inhibiting RNA and protein production and production of spores
83
What is an ecological niche?
Match of a species to a specific environmental condition
Describes how an organisms responds to a distribution of resources and competitors and how it in turn alters those same factors
84
Explain how bacteria divide?
Binary fission
Bacterium DNA replicates
Bacterial cell elongates and divides into two daughter cells each with identical DNA to the parent cell
Each daughter cell is a clone of the parent cell
85
Why do bacteria form spores?
It’s a response and adaption to a change in the environment
Bacterium produce a dormant and highly resistant cell to preserve the cell’s genetic material in times of extreme stress
Endospores can survival environmental assaults that would normally kill the bacterium
86
How do C. Difficile regulate sporulation?
Regulated by several orphan histidine kinases that can phosphorylate the master transcriptional regulator Spo0A.
(Phosphate group transferred from kinase to Spo0A)
87
What else did you talk about in your essay on gut dysbiosis?
Gut dysbiosis is also a potential cause of depressive behaviours
Faecal microbiota transplants in microbiome depleted mice resulted in behavioural characteristics of depression and anxiety (jittery, socially isolated)
88
What's another microbial symbiosis that fascinates you?
(triple symbiosis)
OR
leguminous plants and the rhizobial bacteria
- bacteria fix nitrogen within root nodules of host plant which benefits plant supplying nitrogen for photosynthesis and growth
- but nitrogen fixing is energetically costly to the
bacteria, and hence reduces the resources that could be allocated to their own growth and reproduction
-if bacteria do not produce nitrogen, the plant punishes them by decreasing the O2 supply to that nodule, which severely reduces the growth rate of the bacteria
similar processes of cooperation may be occuring between V.Fischeri and the squid because mutants that cannot luminescence are unable to colonise the light organ. (no light = squid doesn't favour them and give suitable environment)
89
What was the human genome project and what did they find?
- 2000
- only 26 000 genes appeared to be directing manufacture of proteins and growth
- 98% DNA classed as 'junk'
90
What would you define as 'junk DNA'?
originally a section of the DNA that contained no genetic information
then previously thought to be non-coding sections of the DNA
now this so called 'junk' may play important roles in regulation of gene activity
91
Describe how SARS-CoV-2 replicates.
X
92
Describe the current updates on vaccines for SARS-CoV-2.
X
93
SARS-CoV-2 general knowledge
- betacoronavirus (genus)
- coronaviridae (family)
S protein: mediates viral entry into host cells
N protein: functions to bind to the RNA genome, making up the nucleocapsid
M protein: membrane glycoprotein - defines shape of viral envelope
E protein: participates in virus assembly, maturation, and budding
94
How do you think the cleanliness associated with safety from SARS-CoV-2 will affect our earth microbiome?
X
95
What are amino acid residues?
X
96
Describe epigenetics
- amend histone proteins or DNA itself by adding methyl groups (don't change sequence of genes so stil codes for same RNA molecule and protein but modifications alter likelihood a specific gene is expressed
modifications act as binding sites for other proteins - build up of large complex of proteins thta ultimately switch gene on or off
epigenetic modifications
epigenetic modifications AND genetics code
C base followed by G. CpG sequence, enzyme sin cell can add a methyl group to the C. If lots of CpG motifs in stretch of DNA then lots of methyl groups added
attracts proteins that repress expression of that gene
loads of CpG motifs in close proximity and DNA methylation can have a very big effect - DNA changed shape and gene completely switche doff in that cell and in all daughter cells (in non dividing cells like enurons it just stays)
realised DNA methylation can switch genes off permannetly
not everything explained by genetics - bc when two things identical phenotype differs eg. caterpillar and butterfly use same genome
us: our cells contain same DNA but use in diff ways depending on tissue they are in. Neurons in brain express receptors for neurotransmitters but switch off genes for haemoglobin. Sm else happening in addition to egnetic code. Neuorn: genes responsible for producing haemoglobin heavily methylated so switched off and stay switched off
cells give rise to red blood cells, these geneds arent methylated but genes cding for neurotransmitters ARE switche doff
stable DNA methylation and difficult to remove mod, good if cells need to keep certain genes switched off for long periods
cells need to respond quickly to short term changes in enviornment (alcohol or stress) so turn to adding modifications go histone proteins adjacent to the genes. Changing this can turn genes off but modifications are easy to remove so cell has option to turn genes back on quickly. Histone modifications can also be use dto modulate gene expression (volume)
Histone modifications act as fine tuning mechanism for gene expression bc so many diff hsitones. Lots of amino acid son histone proteins thta can be modigfied and at least 60 chemical groups can be adde dto the amino acids - creates large degree of complexity - lost of combinations of histone modifications which attract different complexes of proteins that control gene expression and patterns. (diff combinations can be interpreted by cell in diff ways) some drive gene ex up or down
97
Discuss long non coding RNAs and epigenetics
puzzle: enzymes that add modificationsn to hsitone proteins don't bind to DNA and cant distinhuish DNA sequences yet in presence of relevant stimulus enxymes are very precsie in how they modify histones..
Long non coding RNAs attract histone modifying enzymes into vicinity of selected genes
evidence: 1/3 long non coding RNAs tehy examined bound to complexes of proteins that included histone modifying enzymes. Then knocked down expression of histone modifying enzymes in the complexes and found that effect on cell and gene expression was as if they had knocked out long non-coding RNAs suggeste dlong non coding RNA and histone modifying enzyes working tgether in the cell
ink between these focuses on major repressor enzyme that deposits specific histone modification that is stronglya ssociated w switching off genes. Majornrepressor been shown to interact w lots of fifferent long non coding RNAs.
Long non-coding RNA from specific gene targets the major repressor to thatgene the RNA is from and the major repressor enzme reates repressive modifications on histones drivving down gene expression. These modificatiosn attract otehr proteins that bind and repress the gene even more.
Common thingw heere major repressor epigenetic enzyme is use dto control genes thta code for other epigentic enzymes. Major repressor has strong influence on egne expression represse gens directky and indirectky by preventing expression of other epigenetic enzyme sthat normally switch otehr gene son
98
Discuss cancer and epigenetics
if long non coding RNA and epigenetic machiney interaction stop working then problems ocurr,
Major repressor overexpressed in subsets of prostate and breast caner
or mutated and abnormally active
(rememeb - major repressor enzyme that deposits specific histone modification that is stronglya ssociated w switching off genes. Majornrepressor been shown to interact w lots of fifferent long non coding RNAs. )
= wrong genes are repressed
incorrect balance where proteins that drive cell into proliferation outrun thsoe thta break t and thus promtes cancerous state
drugs inhibit activity fo major repressor
long non coding RNA shown to nind to major repreessor and directed to certain genes incuding thsoe that normally hold back cell proliefration. Delicate balance between disturbing long non coding RNAs and epigenetic modifier intercation equilibrium
Major repressor can bidn to all sorts of non coding RNA molecules, complexthat contains this repressr can recgnise diff types of histoen modificatiosn depending on the components of teh compelx and these components vary from cell to cell. As they scan nearby histone sthey sue component in compelxes to rceignsie various histone mdoification patterns then they reinforce tehs epatterns by adding major repressor modifications.
99
Squid women
Fish family with luminous bacterial symbiosis
Couldn’t raise in lab
Squid used for study cephalopod embryogenesis which happens to have symbiotic association with luminous bacteria
Studying barracuda
Ned did his dissertation on the ecology of V. FischerI
Collected squid, brought back to mainland, easy to have in lab, 18 labs in USA, tiny
Bury in sand in day, come out at night,
Lux operon creates substrates and enzymes for the reaction
High enough density =
Have they ever turned pathogenic?
If the bacteria don’t make light the animal doesn’t retain them.
Are you a medical microbiologist?
Way one can determine conversation between host and symbionts along apical surfaces of epithelia good model for biomedicine - bacteria loving along apical surfaces on epithelia but inaccessible and huge number of species so huge noise and hard to tell basic principles underplaying colonization of animal tissue by gram negative bacteria.
Knew bacteria induced development of host - caused loss of ciliated fields specific to juvenile - used to collect bacteria - bacteria in light organ an induce cell death in loss of those appendegas associated with colonization.
What induces this loss = molecules on the surface of bacteria (MAMPs). Lipopolysaccharide and peptodogkycan exported from bacteria into animal cells and cause morphogenesis.
In Paris - have speech - looked up - squid! Guy said they have known presence of gram negative bacteria in gut causes maturation of gut associate dlunphoid tissue in small intestine. Wondering if same molecules that cause squid morphogenesis cause morphogenesis in gut associated lymphoid tissue.
As animals evolved, always in presence of bacteria - highly conserved interaction of bacteria and animals.
V. FischerI drive circadian rhythms of the light organ - presence of luminous ones drive circadian rhymth.
Got to look at daily rhythms of the gut - everything in gut is on a daily rhythm - motility. We found this in the squid so u should look in the humans. Bacteria are essential for setting rhythms. JET LAG!!! Why they tell u to eat at time people are eating to reset time and rhythm.
Always funded by national institutes of health because her basic science is so foundational to the field.
Most common way bacteria associate with animal cells is along the apical surfaces.
Israel - eran elanov - Laura hooper - bacteria influence circadian rhythms
How did the quorum sensing system evolve?
Not well
What drive selection o those genes - v. FischerI is a facultative anaerobe so it can use oxygen as a terminal electron acceptor or it can ferment.
Luminescent reaction pulls oxygen down so maybe an efficient change from anaerobic you aerobic osoration may be mediated by luminescence.
Possibility - selection on it when animals evolved.
Free living in water and saprophitic so when fall on dead fish they grow and in colony begins to luminesce which attracts other things and put it in their gut.
Luminescence in two ways:
Reaction between luciferin and Luciferase if oxidized to oxyluciferin OR symbiosis
What’s the most interesting thing:
2006 next generation sequencing
Enabling to the field
Medical applications:
Opened up national cancer institute meeting
EXCUSE ME I STUDY A SQUID
Every tumor has a microbiome - breast tumor has specific microbiome. Invite her to tell her the story of the conservation of interaction between bacteria and animals.
Cancer microbiome HUGE (last year and a half)
Bacteria are intracellular
Vertebrates typically don’t have intracellular bacteria except mitochondria and pathogens.
So why are those cells now allowing bacteria inside of them?
Animal physiologist
100
4 aspects of the hostile TME that must be taken into account when designing CAR T-Cells against tumours
Physical barrier of the TME
Metabolic barriers of the TME
Immunosuppressive cells, factors and cytokines
Inhibitory checkpoints
101
How can CAR T-cells be designed to overcome the physical barrier of the TME?
Engineered to secrete enzymes that degrade extracellular matrix. Eg. Heparanase. ECM has a sub endothelial basement membrane that mainly includes heparan sulphate proteoglycans that can be broken down by heparanase.
Another potential ECM degrading enzyme - metalloproteinase
102
How can CAR T-cells be designed to overcome the metabolic barrier of the TME?
(Three things - hypoxic, acidic, lack nutrients)
Hypoxic TME - CAR T-cell engineered to express catalase enzyme that breaks hydrogen peroxide into oxygen and water (improves CAR T-cell persistence)
Acidic TME as a result of Warburg effect increasing lactate levels. - proton pump inhibitors stop release of H+ ions. Researchers buffered pH at suitable level using PPIs and T cell function did not decrease. (What about acidity affects T cells??)
Lack of nutrients such as amino acids - cancer cells express indoleamine 3,3 dioxygenase (IDO) which breaks tryptophan into kynyrenine. Administer cyclophosphamide and fludarabine decreased expressed of IDO on cancer cells = improved CAR T-cell efficacy
103
How can CAR T-cells be designed to overcome inhibitory checkpoints such as PD-1/PD-L1?
- anti-PD-1 or anti-PD-L1 checkpoint inhibitor drugs (in combination therapy)
- anti-PD-1 producing ScFvs
- dominant negative PD-1 receptor (on the T cell)
- CRISPR and short hairpin RNAs used to silence genes coding for PD-1 on T-cells (although PD-1 could play a role in T-cell activation so potential issues with this)
104
How can CAR T-cells be designed to overcome antigen heterogeneity?
Decrease in expression of target antigen on cancer cell occurs a lot so use of bispecific CARs:
Bispecific/dual CARs —-> CARs that target multiple antigens (one CAR has two antigen recognition domains)
105
(Three ways) CAR T-cells can be genetically engineered to overcome metabolic barriers (immunosuppressive cells and cytokines) of the TME
CAFs,TGF-beta
CAF’s promote tumorigenic features by secreting cytokines -—-> CARs engineered to target Fibroblast Activation Proteins on surface of CAFs (Cancer Associated Fibroblasts). the anti-FAP CAR T-Cells additionally encouraged endogenous CD8 + T cell (AKA Cytotoxic T cell) anti-tumour responses
Immunosuppressive cells secrete TGF-beta cytokines which is associated with tumour progression and metastasis and downregulating T-cell function. -—-> CAR T-cells désignés to express dominant negative TGF-B receptor.
106
CAR T-Cell therapy
Future perspectives (3 things)
CRISPR enables incorporation of suicide genes into CAR design
Universal CAR
Armoured CARs/TRUCKs - T cells armed with immune stimulators cytokines which improve CAR T-cell expansion whilst rendering them resistant to the immunosuppressive tumour microenvironment
107
X inactivation
Female cells use an epigenetics mechanism to inactivate one of the X chromosomes in each cell
```
Female = XX
Male = XY
```
Active X chromosome
Histone modifying enzymes
108
What did I talk to Banerji about?
Bi specific T cell engagera
109
What did u talk to Brentjens about?
Use of anti PD-1 secreting single chain variable fragments with design of CAR T-cells
110
What is a Protozoa?
Single cell microorganisms from protoctista kingdom
111
Something else you found interesting about the parasite book?
The X chromosome has a higher number of genes coding to microRNAs.
If these genes on the X chromosome escape X inactivation, a female could end up with two active copies of a gene coding for microRNAs.
Some microRNAs are thought to be involved in immunity and cancer development, if ur doing something ‘good’ for example helping to control cell growth on cancer then have two copies of the gene for the microRNA is beneficial.
112
If all cells contain the same genetic code, why are they different?
Gene silencing
How is this done?
Gene silencing
Could be done by using microRNA (able to inactivate mRNA)
Genes coding for microRNAs are contained in the nucleus in the DNA. Gene transcribed by RNA polymerase 2. Produces primary microRNA that forms a hairpin structure.
DGCR8 protein and enzyme DROSHA associates to form micro processor complex to cut microRNA to form a smaller precursor microRNA. Exported to cytoplasm (by exportin 5 transporter molecule) where it will inactivate mRNA of one or multiple genes.
In cytoplasm DICER cleaves stem loop and forms short double stranded microRNA molecule
AGO2 protein interacts with DICER and binds with microRNA. MicroRNA unwound and one strand is released.
Other strand Calle s the guide strand interacts with AGO2 and additional proteins to form the RISK - RNA induced silencing complex. This is guided to its target where it can inactivate one or multiple genes.
The mRNA of a target gene is complimentary to the sequence of the microRNA which enables base pairing.
Then two ways RISK can inactivate mRNA:
1) proteins in complex cut mRNA
2) Inhibition of translation by preventing ribosome subunit from bonding
= mRNA not translated into protein and gene is silenced
