Classnotes

Introduction Three steps for approval of project involving animals. Each step takes approx. 1 month. graph LR Pre-submission --> ORBEA-->DGAV ORBEA: Animal welfare body DGAV: Portugese government organisation that licences facilities. They have 50 year old preserved embryos. Plant Model organism: Nicotiana benthamiana. Gnotobiology comprises the study of germfree plants and animals, as well as living things in which specific microorganisms, added by experimental methods, are known to be present. Metabolic cage: readout-rate is about 1 Hz. Food, water intake; body weight; $O_2$ intake, $CO_2$ output, etc are tracked. ...

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Cell-to-cell communication in bacteria Karina Xavier Quoum Sensing Sounds like an Input Logical Function mechanism. This is the simplest case. Systems were discovered which regulates the temporal order of events. All these mecsshnisms output a singla that is proportional to the number of emitters. These networks hence need to have mechanisms that conserve the amplitude of the input or else have a steady and stable linear gain across the two ends. ...

Introduction Ernest Haeckel (1866): The study of the home life of organisms. Charles Krebs (1972): The scientific study of interactions that determine the distribution and abundance of organisms. On the inequality of species Jérôme Chave What do we conserve? …the abundant, the pretty, or the rare? Bird Count website: https://birdcount.in/ . We can measure relative trends between the different birds species. But how can we measure a composite trends in abundance? Global Living Planet Index 1979: Index value = 1. By 2016, there has been a 68% reduction in the index value. The LPI quantifies the change in numbers of individuals in a seleted subset of animal populations. The LPI includes 20,811 populations and 4,392 species. Trends: ...

Statistics Should falsify an explatory model, not a null model. Bayesian Statistics It is a framework to build statistical models. It extends proportional logic (true/flase) to continuous plausability. More complex to obtain analytical results: but easy to compute computationally (MCMC technique). Models with more ways to realize the data are more plausable. What is a Random-walk Metropolis ? Outliers: Robust linear regression Instead of discarding outliers, we can do Rank-tests (Mann-Whitney test) For outliers: Use distributions with fatter tails. The outliers are then penalised less, and a better linear regression model is achieved which includes outliers. Robust linear regression is just a linear regression, but with Student T-distribution. Pooling of Data Complete pooling: ignore group structure and estimate global effects. Unpooled data: estimate effect in each group seperately. This has low quality of estimates in smaller groups. Partial pooling: assume each group can be different, but they are all part of some larger group. There could be deviations from the large group but not arbitrary. Poisson Regression Coefficients Link function for probabilities: log-odds to map probabilities to a linear $$ ...

Introduction to Neurobiology and Behaviour | Brain 3.0 Rui Olivera 5 things (recommneded) for discussion: 10% of the brain Creativity is in the right hemisphere Dale’s principle — neurons typically use one neurotransmitter and hence forms a good classifier. Adult neurogenesis Mozart effect — by making children listen to music, thier music skills can be improved. Nervous system [simplex] — unoptimized solution by mermaid: flowchart LR cognitive --> sensory sensory --> cognitive cognitive --voluntary--> motor sensory --> state state --> sensory sensory --reflex--> motor motor --reflex--> sensory state --> motor state --> cognitive input -.-> sensory motor -.-> output Reflexes act like ISRs (Interrupt Service Routines). ...

Basics Plants diverged from animals around 1.5 billion years ago. How many genes does a plant have? : 20-25 thousand. 60% of genes are common among plants and animals. How to transform a plant? Stable transformation with Agrobacterium tumefaciens. Infected plants produce tumors at the infrction site. Transfer-DNA (T-DNA): Genes for biosynthesis of auxin and cytokinins. Dip the flower in the solution containing the agrobacteria and now 1% of the seeds will be transgenic. Stable/transient transformation with the particle gun ...

The role of selection in the genetics of populations Isabel Gordo Describe genetic structure of populations Make theories about the evolutionary forces acting on populations. Concerned mainly with understandiong vsriation within species Typically one focuses on the evolution of one or two loci at a time. Evolutionary Forces Mutations (mistakes are unavoidable) Natural selections (there is extensive variability in fitness within populations) Migration (populations are structured) Genetic Drift (every population is finite, and subject to stochastic events) Note: Evolution involves the interplay with all the forces. ...

What is Evolution-Deco? Johannes Jaeger "Yogi" Fisher’s Geomeric Model: A series of concentric spheres that sets a model for evolution of organisms with the optimal phenotypes at the center and an approach from the exterior. What is a mechanism (in terms of Eco-Devo) ?: ??? “natural selection is an analytic consequence of the lives, deaths and reproduction of individuals” Minimal Conditions for Evolution by Natural Selection: Richard Lewontin Phenotypic variation Fitness difference Inheritance Darwinian General Principle by Elliott Sober: If thgere is heritable variation in fitness, then there will be evolution. ...

Introduction Jorge Carniero Project multidimesntional things in lower dimensions. GeneSim Read: Can a biologist fix a radio? Or, what I learned while studting apoptosis by Yuri Lazebnik Read: The evolution of molecular biology into systems biology: Westerhoff & Palsson Read: D’Arcy Wentworth Thompson, one of the first persons to write a book on mathematical biology. The title is “On Growth and Form”. Lookup: Macy Conferences Andrew Huxley and Alan Hodgkin Made a neuron equivalent circuit that fits beautifully fits the data they aquired. ...