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Quick study notes for Midterm 1 - LIFESCI 2A03

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Life Sciences
Joe Kim

MIDTERM 1 LIFESCI 2A03 Quick-notes October 15, 2013 Lecture 1  Characteristics of Science 1. Science is based on empirical knowledge – based on observations and data 2. Commitment to rationality/natural explanation 3. Repeatability and reliability – subject to confirmation by others; repeat by others and further the study 4. Testability – testable through experimentation; 5. Commitment to use of experimentation – planned intervention into a natural process to observe effects 6. Generality of principles – establishment of principles that operate throughout natural world; understand processes  Scientific Method 1. Define/identify problem 2. Form hypothesis 3. Test hypothesis 4. Organize and analyze data 5. Experiments; do observations support hypothesis? (If no, perform new experiments) 6. Communicate results  Case Study – Human Chromosome Count o Theophilus Painter, 1923 – reported 48 chromosomes in human cell by performing serial sections of testicular cells in metaphase and counting chromosomes  Problems – chromosomes clumped together, curled in and out of focal plane,  Repeatability – other researchers confirmed count using same techniques; many people took result as authoritative  Accepted for 33 years  Incorrect due to – subjective bias (ambiguous data, room for interpretation); samples from single individual from a patient in mental institution (may have had extra chromosome); counted one arm as two o New Technique, 1950s (Hin Tjio, Albert Lecan)– treat cells with colchicine to demolish microtubules, cells stuck in metaphase; treatments to prevent fragmentation and preserve chromosomes; flatten into 2D cell  Can see entire cell at once; spread out metaphase chromosomes  46 chromosomes o Ideograms – used to line up chromosomes (largest to the left) o Karyotyping – now used to line up chromosomes; fluorescently stained based on genes present Lecture 2  Hypothesis – proposal or explanation that makes a prediction about the result of intervention and can account for observations; application of the scientific method allows testing of hypothesis  Inductive Logic – inductive generalizations summarize a set of observations and serve to provide a prediction about unseen events o Singularity  generality; eg/ this ice is cold, therefore all ice is cold  Deductive Logic o Generality  singularity; eg/ if all green apples are sour, then this green apple will be sour o Hypothesis followed by prediction; deductive syllogism = if (generalization)  then (specific instance being tested)  Deductive syllogism leads to prediction – hypothesis can be tested  Testing hypotheses o False prediction  false hypothesis; result inconsistent with prediction  reject hypothesis o True prediction  true or false hypothesis; result consistent with prediction  fail to reject hypothesis o Can never say “hypothesis is true”; can only comment about hypothesis consistent or inconsistent with data  Null Hypothesis – statistical term; no significant difference between two sets of results (control and experimental) o Reject null hypothesis – data consistent with hypothesis; fail to reject hypothesis o Fail to reject null hypothesis – data inconsistent with hypothesis; consider new hypothesis  Case Study 1 – Ice cream evoked headaches (ICE-H) study; randomized trial of accelerated vs. cautious ice cream eating o Hypothesis – if you eat ice cream quickly, there is a higher occurrence of ICE-H than if you eat it slowly o Null Hypothesis – there is no significant difference between eating ice cream quickly and eating it slowly o Experiment – 145 middle school students into two groups; eat slow (green; 100ml in >30 sec),eat fast (red; 100 mL in <5 sec) o Results – 20/73 (27%) ICE-H in red group; 9/72 (9%) ICE-H in green group o Reject null hypothesis – data consistent with hypothesis o Other factors may affect ICE-H – age of participants, coldness of ice cream, amount of ice cream  Case Study 2 – men ear length increasing with age  Case study 3 (tutorial) – women given cup of tea; can distinguish between milk added first or last  Experimental Design – setting up experiment to measure relationship between two variables  Variation in experimental design – differences in factors that affect the experiment; introduces uncertainty, try to reduce variation Lecture 3 – Regeneration  Regeneration – the regrowth of lost or destroyed parts or organs  Plants – commonly show regeneration; can clone entire plant by plant cutting; entire plant can regrow from piece of plant (stem, leaf, root)  Animals – a few invertebrates with simple body plans demonstrate bi-directional regeneration (clonal reproduction); eg/animals with radial symmetry (hydras, sea stars, anemones, planaria) o Eg/ Hydras – cut in half; two new smaller hydra regenerate that can each grow to adult size through cell division  Bidirectional Regeneration – the ability to regenerate whole bodies from small tissue fragments o Eg/ Planaria – non-parasitic flatworm; can cut in many pieces and regrows to full planaria 1 MIDTERM 1 LIFESCI 2A03 o Steps 1) Muscular contraction to limit size of cut surface 2) Thin wound epithelium forms over surface 3) Accumulation of undifferentiated cells (neoblasts) in the blastema 4) Growth and differentiation of blastema o Blastema – mass of undifferentiated cells capable of growth and regeneration into organs or body parts; found in early stages of embryonic development and in regeneration of tissues, organs and bone  Similar to egg fertilized by sperm (embryonic blastema) o Neoblasts – regenerative cells within blastema; small undifferentiated mitotic cells that comprise ~20% of worms body; act as stem cells for growth and regeneration; required for regeneration  Similar to embryonic stem cells  Pluripotent – demonstrate ability to become any different cell type  Single isolated neoblasts, cultured in vitro (cNeoblast) – cells able to differentiate into neuronal, intestinal and other adult cell types; transplanted cNeoblast enables regeneration in those who were unable to regenerate (kill neoblasts cells to prevent regeneration; add single cNeoblast; regeneration restored) o Polarity – information regarding direction of growth (head or tail) is contained within amputated fragment; mechanism unknown  Studies to identify polarity mechanisms – studying errors (missing directional information but capable of; examine grafts from one organism to another (eg/ graft head from another, amputate original head, observe correct direction of growth)  Monodirectional Regeneration – regeneration of appendages that proceeds distally from cut site; eg/ insects and vertebrates(cannot regenerate whole organism, can regenerate appendages) o Eg/ Salamanders (urodele amphibian) – can regenerate throughout entire life  Stages of regeneration  Wound healing  Dedifferentiation – cells losing identity; reforming shape and level of gene and protein expression  Differentiation – cells become specialized  ~40 days to form new limb o Early experiments in regeneration – focused upon investigations of polarity and patterning  Experiment 1 – remove distal region of forelimb and graft to side; remove proximal region of forelimb (forelimb grafted to side of body “upside down”)  2 limbs regenerate; original forelimb and grafted forelimb  Experiment 2 – remove forelimb and hind limb; graft piece of forelimb stump to hind limb stump  3 limbs regenerate; two on hind limb stump and one on original forelimb  Experiment 3 o Blastema – dedifferentiated cells that accumulate at the end of the stump; cells form new limb; contains positional information (grows and dedifferentiates in a proximal to distal fashion, then grows in size to exact original form)  Regenerative cells in blastema act like stem cells  Not neoblasts in planaria  Cells remaining after injury dedifferentiate and migrate to form blastema o Dedifferentiation – loss of differentiated characters of cells after amputation and their concurrent acquisition of an undifferentiated morphology during blastema formation (regeneration liter; the release of living cells from the confines of their previous organization with accompanying active mitosis of these cells(defined in 1961)  Does not imply reversion to pluripotent state (like neoblasts)  May still be a role for reserve stem cells in blastema o Unipotent – the ability to give rise to new cells of a single, specific cell type or lineage o Multipotent – ability to give rise to multiple different cell types (not unlimited) o Dedifferentiated cells can, when they differentiate: 1) Create cells of the tissue they came from – suggesting that regeneration does not require cells to reprogram themselves as dramatically as scientists had assumed  Cells keep memory of tissue origin during axolotl limb regeneration – amputation on salamander limb with fluorescently labeled nerve cells; blastema is heterogeneous collection of restricted progenitor cells 2) Become many or any cell type – multipotent, pluripotent  There is evidence that supports differentiated cells can change functional sta(dedifferentiate and differentiate into different cell type) o Blastema of the urodele (salamander) identity of cells is unclear; unipotent, multipotent or pluripotent o In vivo evidence for dedifferentiation  Inject fluorescent dye into muscle fibers prior to amputation; some multinucleated myofiber can fragment into proliferating mononuclear cells that contribute to blastema  When dedifferentiation occurs, structure of muscle cell is lost; adopted shape structure looks like undifferentiated stem cell  Long term fate of cells still under investigation  Humans – wound healing, generation of new skin, blood, stomach, intestinal and lung linings, liver regeneration o Evolved healing responses to injuries that overrides any possibility for regeneration o Studies to cause adult cells to dedifferentiate into stem cells for human limb regeneration  Induced pluripotent stem cells (iPSCs) – type of pluripotent stem cell artificially der
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