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Molecular Biology 1: Mutations powerpoint slides for this lecture hereAims: Outline the nature of mutations; Outline the basis for and rate of spontaneous mutation; Outline, with examples, why most mutations are silent or recessive; Explain the different evolutionary histories of recessive and domin...

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Molecular Biology 1: Mutations powerpoint slides for this lecture here Aims: - Outline the nature of mutations; - Outline the basis for and rate of spontaneous mutation; - Outline, with examples, why most mutations are silent or recessive; - Explain the different evolutionary histories of recessive and dominant mutations. Genetics traditionally focuses on heritable mutations in genes, whereas molecular biology can examine ALL mutations. Natural selection requires genetic differences, generated by sex (recombination) and by spontaneous mutation. Very low rate of spontaneous mutation for example in human germline cells. There are approx. 3 new mutations per 108 base pairs per generation and there are approx. 200 new mutations in each human child. The origins of new mutations: - Replication/repair errors - By-product of being alive/metabolism itself (ROS) - Mutagens in food - Ionizing radiation DNA damage – repair = net mutation

- Repair is working to lower net mutation

Can increase net mutation rate by: - Increasing rate of DNA damage > Sunbathing > Being present in a highly radioactive area Can decrease net mutation rate by: - Reducing repair efficiency > In bright sunlight each skin cell suffers 50-100 T-T dimers every second > Xeroderma pigmentosa patients are unable to repair T-T dimers resulting in all T-T dimers becoming mutations making them highly susceptible to sun induced cancers Mutation rate is higher in somatic cells compared to germline cells, somatic cells are not passed on to the offspring and can have 10x to 1000x faster mutation rate compared to germline cells. Most random mutations affect unimportant regions such as between genes or between exons. Most mutations do not change phenotypes unless they affect important parts such as key functional residues or regulatory regions.

Frameshift mutations include insertion or deletion mutations. Most mutations are recessive and hence can only affect phenotype when homozygous, recessive mutations require inbreeding, if two people with the same recessive allele are to have a child ¼ will be r/r. Recessive mutations need inbreeding to enable the phenotype to be shown and on average each person carried 1 or 2 recessive lethal mutations.

Molecular Biology 2: Mutations II powerpoint slides for this lecture here

Aims: - Outline, with examples, why some mutations are dominant; - Outline the main features of the human genome; - Explain the origin, nature, and scientific importance of homologs and orthologs. Four biochemically related conditions: > Albinism > Alkaptonuria > Cretinism > Phenylketonuria (PKU) Albinism: The gene encodes for Tyrosinease: Tyrosine ----Tyrosinease----> Melanin The mutant version of the gene causes less or no activity of the enzyme, the phenotype of albinism is caused by less/none of the product. PKU: Is caused by high levels of phenylpyruvic acid and causes progressive brain dysfunction. The mutation is on the phenylalanine hydroxylase gene and is recessive, it can be treated by getting placed on a low phenylalanine diet. Phenylalanine ----Prehyroxylase----> Tyrosine [If Phe is high and not converted into Tyr it is converted into phenylpyruvic acid] The mutant version has less, or no activity of the enzyme and the phenotype is as a result of having to my substrate. In all cases there is less or no activity of the enzyme in recessive mutations, however, the phenotype can be caused by ether too much substrate or too little product. PKU and alkaptonuria are caused by too much substrate, whereas albinism and cretinism are resultants of too little product.

Most dominant mutations are gain of function rather than loss, however, they are rarely fully dominant and instead are described as being incomplete dominant. It can gain: - More of a normal function, for example, a more active enzyme that produces more protein - New function unrelated to what the normal gene does, however, this is less common Achondroplasia is the most common form of dwarfism and is an autosomal dominant condition. 99% of cases have one of two missense mutations in FGFR3, fibroblast growth factor receptor 3. FGFR3 normally acts to inhibit/slow limb growth- turned on by FGF binding, the mutant receptor is locked in a more active state whether FGF is bound or not hence more ‘normal’ activity which is to inhibit growth. Huntington’s is a progressive neurodegenerative disease and is autosomal dominant, its rare effecting around 1/10,000 people and the symptoms start around 30 to 50yrs old and death normally occurs 10-15yrs from diagnosis. CAG triplets encode for glutamine, the WT allele has a CAG repeat near the start of the open reading frame and repeats up to 35 units. The mutant allele repeats a far longer chain and this longer polyglutamine repeat is neuro toxic. Recessive wingless mutation means the mutant gene has affected the fly’s ability to make a wing and you have a loss of function. Dominant wingless mutation means the mutant gene has gained more function by inhibiting wing growth prematurely. Treatment for recessive and dominant mutations require opposites. Regarding gene therapy a recessive mutation requires the introduction of a WT allele and the dominant needs the mutant allele to be inactivated. In pharmacology recessive would need an agonist drug and dominant an antagonistic drug. Most mutations are recessive (>95%) as changes are much more likely to cause damage and thus make it work worse than normal than they are to make something work better or more efficiently.

Molecular Biology 3: Genomes powerpoint slides for this lecture here. Aims: - Summarise how the human genome sequence varies between people; - Provide a molecular biological definition of “evolution”; - Outline the nature of SNPs; - Summarise the nature and assumptions behind the Hardy-Weinberg equilibrium; - Perform and interpret Hardy-Weinberg calculations.

Species share homologous genes and if an ancestral gene is functional and is playing an important role, it doesn’t get mutated into nothing- it stays. That said gene will have a version in all those descended sequences. Paralogs are duplicated genes probably with a diverged function or role, evolution will ether keep one of those copies and one will mutate away because you don’t need two of the same gene or they’ll start to diverge and shift in function from one another. Orthologs are by common descent, probably the same function/role and there is a version of that gene in everything that is relevant. INDELS > insertion or deletion frameshift mutations > fairly small > can affect: the protein product of a gene, function of ncRNA and regulatory regions > most are silent VNTR’s > Variable Number of Tandem Repeats > microsatellites – 1bp to 9bp repeating = short tandem repeat > minisatellites – 10bp to 100bp > both types are relatively stable but highly variable in length CNV’s > Copy Number Variants > entire segment of a chromosome is ether duplicated or deleted > can affect 500bp to 1millionbp Point mutations range from: Private- the 200 new mutations an individual has Variants- allele frequency of 1% very common SNP’s > Single Nucleotide Polymorphisms > most don’t cause a phenotype > a common SNP occurs approx. every 1000bp Hardy-Weinberg Equilibrium predicts that the allele and genotype frequency in a population will remain constant from one generation to the next. The HWE equation predicts the genotype frequencies. p= allele frequency of A q= allele frequency of a p2 + 2pq + q2 = 1 p2 = frequency of AA homozygotes if no evolution 2pq = frequency of Aa heterozygotes if no evolution q2 = frequency of aa homozygotes if no evolution

HWE fails to take into account: - non-random mating - population is not homozygous - population is or recently was small - mutation happening at high frequency - natural selection is occurring

Genomes to Ecosystems 1: Theme Introduction powerpoint slides for the lecture here.

Aims: - To illustrate how multiple perspectives from genomics to ecology can converge of a single system – we discuss coral bleaching Corals live in shallow, warm and nutrient poor waters. They are colonial cnidarians and feed on zooplankton, they have evolved facultative endosymbiosis with zooxanthellae dinoflagellate algae to provide vital additional nutrients. 90% of algal nutrients are used by coral, including two essential amino acids, the algae get a nutrient rich stable refuge and the coral gets food. Under stressful conditions, algae produce clouds of reactive oxygen species, these ROS cause oxidative damage, DNA mutations and cell death. Stresses include rising sea surface temperature caused by CO2 emissions and climate change, increased solar irradiance as a result of ozone depletion, slit deposition due to deforestation and overabundance of prey because of overfishing. We should protect coral as they provide a habitat for fisheries, biodiversity in the oceans, possible drug discovery’s and economic benefits like tourism. Marine protected areas provide conservation status and prevent physical damage to reefs. The principle driver of coral bleaching is more of an intangible and much harder to address.

Genomes to Ecosystems 2: Evolution and Natural Selection point slides here Aims: - Discuss pattern and process in understanding evolution and natural selection - Discuss principles of natural selection - Describe natural selection and the modern synthesis - Consider how selection can act on phenotypes - Understand quantitative genetics and heritability - Discuss special cases: sexual selection Pattern is the change we see in the fossil record through time, we can infer evolutionary relationships between different fossil organisms and their living descendants. The assumption is made that all extinct or living organisms are in someway related. The process in which evolution is happening, we broadly accept natural selection as the model that best fits the evidence of evolution 1, within our genes 2, within the homologies between living organisms or 3, within the fossil record.

Individuals less suited to the environment are less likely to reproduce and therefore, less likely to produce offspring and pass on their genes. Individuals more suited to the environment are more likely to reproduce and therefore, more likely to produce offspring and pass on their genes to future generations. This creates the process of natural selection, this slowly effects populations allowing them to adapt to their environment and eventually turning into a new species entirely. Selection acting on phenotypes comes in three types: stabilising, directional and disruptive. Type 1 stabilising selects against the extreme trait values, phenotypic variation is lost from the population as the frequency of one trait goes up greatly and the mean trait value stays the same. Type 2 directional selects against extreme trait values and the mean trait value moves in response to the intensity and direction of the selection. Type 3 disruptive is selection against the mean trait and the result is a multimodal trait distribution. Intrasexual selection- competition between members of the same sex for access to mates Intersexual selection- where members from one sex choose members of the opposite sex

Genomes to Ecosystems 3: Evolutionary Genetics powerpoint slides for this lecture here

Genomes to Ecosystems 4: Speciation, Adaptive Radiation and Extinction powerpoint slides for this lecture can be found here

Aims: - Discuss the concept of species and explore modes of speciation -Understand what radiation events are, how to recognise them, and possible causes (environmental, developmental, ecological) - Consider the frequency of occurrence of mass extinctions - Discuss how humans have influenced ecosystems, including concepts such as the Anthropocene and de-extinction. Allopatric speciation- external barrier separates populations and they diverge genetically Allopatric founder event- small isolated population becomes isolated, rapid evolution due to non-random sample of genes, different environments etc. Sympatric speciation- no geographic barrier, populations may differ in habitat, behaviour, assortative mating may lead to genetic divergence within a population Possible causes for adaptive radiations include key innovations, environmental changes such as new habitats and ecological changes such as new opportunities. An example is the bong fish compared to gars and bowfins etc. bong fish have a third whole genome duplication and a swim bladder that gives them buoyancy as well as innovations in jaw structure- protruding upper jaws and secondary jaws. Sharks lack swim bladders and as a result needs to keep swimming constantly and therefore, its body needs to be streamlined. As a bong fish has a swim bladder and can float in the water it has the ability to be many more shapes than the shark, this allows for more variation in fish with a swim bladder.

When a large animal such as an elephant moves to a smaller land mass (island) from the mainland, over generations it will become an insular dwarf. This is reversed regarding smaller animals. Nearly all major animal phyla appear in Cambrian rocks, many creatures appear suddenly in the fossil record, there are three possibilities that could have caused this explosion: -Environmental changes > increased oxygen levels, levels may have finally reached high enough to support large animals -Developmental changes > HOX genes, the regulate developmental segmentation in animals, insects have one whereas we have four -Evolution of eyes > this led to predication this then ignites the arms race between predators and prey There have been 5 major extinction events: -Ordovician-Silurian -Lute Devonian -Permian -Triassic-Jurassic -Cretaceous-Tertiary (wiped out the dinosaurs) One is going on currently, the Anthropocene, this has wiped out megafauna.

Genomes to Ecosystems 5: How to Measure Species Diversity powerpoint slides for this for this lecture can be find here

Aims: - Discuss species diversity and its global distribution. - Discuss the biases in our knowledge of biodiversity. - Discuss the role of citizen science in measuring biodiversity - Explore the huge, mostly undiscovered biodiversity of both microbes and bigger organisms and discuss advances in measuring it (DNA barcoding) If we look where we see the ‘most’ biodiversity, we see that wealthy countries report the highest levels of biodiversity compared to poorer countries, money=biodiversity. So, what seems to be happening is that we aren’t accurately measuring biodiversity just what places have the money to do so. We also hold bias to what diversity is out there, if you go to a museum the majority of things displayed are large animals such as elephants or bears, however, bugs and spiders etc have a far larger biomass on the planet compared with the large animals. - iNaturalist - DNA barcoding

Genomes to Ecosystems 6: Individuals, Communities and Populations Powerpoint slides

Aims: - Define and apply the three levels of ecosystem organisation - Explain what factors influence population growth - Compare competition against coexistence and explain why different organisms might favour one strategy or another - Contrast fundamental and realised niches Primary succession- new bare surface, for example, an earthquake unveils a new path of land Secondary succession- destruction of existing vegetation, for example, a forest fire

Succession- the sequence of development of vegetation from a sterile substance 1. Initiation 2. Colonisation 3. Development 4. Mature

5. Climax

Key biological processes that organisms need to carry out are growth, metabolism, activity, thermoregulation and reproduction. There are two types of population controls density independent and dependent. Density independent stressors are ones that affect all individuals regardless of how large a population is such as light, wind, salt, water, temperature and pH. These can be combatted using dispersal tactics, this means departing, traveling then settling. This is beneficial as it allows finding better resources, conditions and it reduces competition as well as avoiding inbreeding. On the other hand, there are energy costs, possible risk of predation and settlement. Density dependent stressors are in place to keep a population in check via the carrying capacity of the population these checks include parasitism, predation, disease and competition. There are two possible outcomes of competition: coexistence or elimination. Fundamental- where they could survive Realised- where they actually survive Temporal variation- changes throughout time Assemblage- collections interacting populations in the same geographic area

Genomes to Ecosystems 7: Migrations Powerpoint slides

Aims: - Outline the advantages and disadvantages of migrations - Explain some of the physiological and biomechanical adaptations that enable animals to complete migrations - Relate cellular processes that have influenced the ecology of these animals - Describe the challenges present in studying long-distance migrations Migration types include breeding, tracking, resource availability and refuge. Migrating allows animals to exploit new resources seasonally, protect young, avoid inbreeding depression and reduce competition. However, some risks are bad weather, lack of ‘emergency stops’, disorientation, lack of final stop and predation. To track migrating animals, we can take point counts, use radar, satellite tracking and natural markings. Biomechanics can assist during migrations. In insects the larger the surface area of the wing the further the insect will fly. In birds, comparing wing shape and size tells us if they migrate or not. The albatross lacks wing slots and has long narrow wings to glide long distances with ease, whereas the hawk has broad wings with slots. When a bird migrates its muscle, lung fat and heart fat all increase, its liver, kidney and stomach meanwhile decrease. The semipalmated sandpiper doubles its body mass by eating burrowing amphids for 2 weeks. The fatty acids in them activate membrane bound enzymes to increase metabolism and activates genes regulating lipid metabolism.

Genomes to Ecosystems 8: Environmental Conservation & Protection powerpoint slides

Aims: - Discuss the legislation involved in establishing protected spaces - Relate the concerns of different stakeholder groups to the challenges in environmental conservation - Discuss the requirements of designating protected areas Species-based management- protects one type, bias towards ‘loved’ animals e.g. pandas Community-based management- species specific, one community takes control of protection, community benefit but hard to set up Ecosystem-based management- protects whole ecosystems

Designing a Marine Protected Area (MPA): - identification based on the presence of key features - prioritisation based on the qualities of features - assessment of the scale needed to maintain integrity - assessment of the ability to effectively manage features - prioritisation according to their contribution to the MPA network

Genomes to Ecosystems 9: Issues in Aquatic Conservation powerpoint slides Aims: - Discuss the biological effects of plastics in the marine environment - Compare the effects of plastics with those from other human effects - Explore the role of humans in maintaining Good Environmental Status in different habitats - Discuss the solutions to reduce and mitigate human impacts Macroplastics: -ingestion -entanglement -invasive species Microplastics: -false satiation -suffocation -physical blockage -weakened condition/hormonal disruption -accumulate up the food chain Solutions: -plant based plastics -better washing machines -high efficiency waste-water filtration To reduce the number: -education -legislation

Genomes to Ecosystems 10: Ecosystem Goods and Services Powerpoint slides Aims: - Describe what an ecosystem is - Understand the four basic functions carried out by ecosystems - Understand the concept of ecosystem processes

- Understand how the conc...