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ANS 2: Final Exam Study Guide

by: Mackenzie Hayes

ANS 2: Final Exam Study Guide ANS 002

Mackenzie Hayes

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This guide combines both of the midterm study guides as well as the notes from class following midterm 2
Introductory Animal Science
Dr. James Murray
Study Guide
animal, Science
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This 37 page Study Guide was uploaded by Mackenzie Hayes on Saturday June 4, 2016. The Study Guide belongs to ANS 002 at University of California - Davis taught by Dr. James Murray in Spring 2016. Since its upload, it has received 121 views. For similar materials see Introductory Animal Science in Animal Science at University of California - Davis.

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Date Created: 06/04/16
ANS 2: Final Exam Study Guide Midterm 1 Study Guide: ● Animal Behaviour: ○ The actions and reactions of an animal ○ Ethology:​study of animal behaviour ○ Timbergen: (One of Founding Fathers of Etholo​questions: ■ Proximate Causation: ● What causes the behaviour? ■ Development: ● How does it change over the animal’s life? ■ Function: ● How does it aid the animal’s survival? ■ Evolution: ● How has it come about over the course of evolution? ○ One Newer Question: ■ Affect: ● What does the behaviour mean to the animal? ○ Assessing observed phenomena: ■ ⅔of birds have keel bone damage ● Measuring Behaviour: ○ Who do you sample? ■ Ad-lib:whoever you happen to see ■ Focal​: select one or few ■ Scan:​group as a whole ○ How often do you sample? ■ Continuous​: throughout set amount of time ■ Instantaneous:divided into exact time intervals (ie every 3 min) ■ One-zero:​if behaviour was done in interval at all (yes / no) ● Immediate ancestors to domestic species abiologically the samanimals ○ Yet considered to be different species ● Bladder: ​always serves as a “landmark” ● REPRODUCTION: ● MALES: ● Sperm = smallest cell in body ● General Anatomy: ■ Vas Deferens / Ductus Deferens: ● Transportation of sperm for ejaculation ■ Seminiferous Tubules: ● Site of ​permatogenesis - production of immature sperm ● Sertoli Cellsnourish sperm + help them mature FSH​ ● Leydig Cells:produce testosterone when stimulated ​H L ■ Epididymis: ● Aids sperm maturation (takes 6 weeks to mature) ● Transport to vas deferens ■ Accessory Glands: ● Add extra components to seminiferous fluid ● Ampullary, Vesicular, Prostate, Bulbourethral ■ Pampiniform Plexus: ● Regulates in and outgoing blood temperature in testes ■ Testes:​ (within Scrotum) ● Produce sperm and testosterone ○ Spermatogenesis: ■ Takes place in seminiferous tubules ■ Spermatogonial Cellsgo through meiosis ● Replicate DNA (2N, 2C → 2N, 4C) ● Becomes 4 haploid sperm (1N, 1C) (or duplicates itself) ■ Spermatids:haploid cells produced from spermatogonial dividing ■ Continuous process (keep producing throughout lifetime) ○ Hormones: *be able to reproduce table* ■ GnRH:​ released by hypothalamus to stimulate FSH + LH release ■ FSH:​stimulates sertoli cells in testes ■ LH:​ stimulates testosterone production by leydig cells ■ Feedback: ● Positive: promotes further production ● Negative: inhibits further production ● FEMALES: ● Egg = biggest cell in body ○ General Anatomy: ■ Ovary: ● Theca Cells: ○ Stimulated by​H​→ produceandrogens ● Granulosa Cells: ○ Stimulated by​SH​→ produceestrogen ○ Eventually antrum forms as follicle matures ● Corpus Luteum:​ (CL) ○ Forms after ovulation → ​rogesterone ○ UNLESS no implantation (not pregnant) ● Luteal Cells: ○ Cells of CL that producprogesterone ● Corpus Albicans:(CA) ○ Regressed form of CL if not pregnant ■ Infundibulum: ● Helps shuttle ovum to oviduct ■ Oviduct: ● Where egg and sperm meet for fertilization ■ Cervix: ● Tight opening before uterus + oviduct to keep larger “things” out ■ Zona Pellucida: ● Outer layer of egg ■ Uterus: ● Site of fetal development ● Shape of uterine horns differs by species ○ Reproduction of Hens: ​*not controlled by hormones; cyclical* ■ Oviduct: ● Magnum:​ puts albumen around yolk ● Isthmus:​puts down membranes ● Uterus (aka Shell Gland)lays down calcified hard shell ● Sperm Storage Tubules:​holds sperm for later fertilization ○ Oogenesis: ■ Cyclical process ■ Estrous types: ● Monoestrous (dog) ● Polyestrous (cattle) ● Seasonally polyestrous (goat) ● Reflex ovulator (cat) ● Anestrous ■ Primordial germ cell differentiates into oogonium ■ Oogonium enters meiosis ■ Primary oocyte = 2N, 4C → has replicated DNA ■ 1st metabolic division is very uneven (at ovulation, 1N, 2C) ■ Arrested development ● Essentially stops at metaphase 1 of meiosis ■ LH activates meiotic “machinery” ■ If fertilized then second division occurs ● Restores diploid state with sperm DNA added ● Why do we “throw away” 3 copies of DNA? (unlike males) ○ Allows for cell to be big and retain almost all cellulose and nutrients, DNA is all that’s wasted ○ Ovulation: ■ Release of LH​ causes enzymatic “digestion” stigma ● Stigma​ - area on follicle not vascularized (less blood loss) ■ Follicle ruptures → release of egg = start of ovulation ■ Smooth muscles in the theca externa contract ■ Granulosa cells remain metabolically active for 24-48 hours ● Producing progesterone and prostaglandins ■ ^​ Diagram WILL BE ON AN EXAM​ (be able to recreate / label it) ● Day 0​ = ovulation occurs (and again at day *label*​ ● Cycle​ = period from ovulation to ovulation ● FSH​ = always steady in the background (levels not cyclical) ● Progesterone: ○ Loss of CL → drop in progesterone (day 0) ○ After ovulation: new CL forming → rise in progesterone ● Estrogen: ○ Follicle grows, then levels drop @ ovulation ○ Cells switch to produce progesterone ● Luteal Phase:​area where progesterone is high (between ovulations) ○ Dog luteal phase lasts 5-7 months ○ Longer than gestation, no need for embryo to send “signal”, progesterone constantly high during phase ○ Fertilization: ■ Homunculus - idea of little man inside sperm ■ Physical union of male and female gametes (sperm and ova) ■ Early Development: ● From conception to death: ● Embryonic: from fertilization until all essential organs are formed ● Fetal:​end of embryonic stage until parturition ■ A = z ygote:​single-celled embryo ■ B = 2 cell ■ C = 4 cell ■ E = morula, still held together by zona pellucida ■ F = 72 hours after fertilization ● Dark clump of cells is what actually becomes fetInner Cell Mas)​ ● Mass eventually “hatches” out of zona pellucida ○ Definitions: ■ Blastocyst:​a hollow sphere of cells composed of two cell layers (the trophoblast) with a clump of cells inside (the ICM or inner cell mass) ■ Blastocoele:​ fluid filled interior of blastocyst ■ Trophoblast:​ cells form the extraembryonic membranes ● Extra-embryonic membranes: ○ Provide protection for embryo - fetus and nutrient / waste exchange ○ Amnion: f ​luid filled sac like airbag around embryo ○ Yolk sac: stores yolk (essentially empty in mammals) ○ Chorion and Allantois:(often fused) ■ Chorion = outer layer contributing to placenta ■ Allantois = outgrowth of bladder for nutrient/waste exchange, respiration, and storage of urine ○ Recognition of Pregnancy: “signal” sent to mom from embryo ■ Primates:​ (aka humans) ● Blastocysts secrete chorionic gonadotropin (CG) ● CG binds to LH receptors in the CL and stimulates continued secretion of progesterone ■ Ruminants: ● Not Pregnant:​ CL regresses at end of cycle ○ Due to endometrial secreting PGF ● Pregnant: ○ (bovine) embryo secretes interferon tau which decrease PGF secretion ○ (sheep) embryo secretes ovine trophoblast protein which inhibits production of PGF ■ Pigs: ● Release estradiol to block PGF ● Minimum 3-4 embryos so signal is strong enough ■ Dogs:​ monoestrous (basically keep secreting progesterone anyway) ○ Stress / Parturition: ■ “Triggered” by release ​ortisofrom fetus ■ → increased release o​strogenby placenta ■ → estrogen causes uterus to start contracting ■ Uterus releases prostaglandins which cause regression of CL ● → drop in progesterone ■ Progesterone​inhibits the contractions of uterus ● → drop in ​rogesterone= stimulates contractions ■ Oxytocin​= posterior pituitary hormone ● Stimulates contraction + mammary production ○ Hormones: ■ GnRH:​ released by hypothalamus, stimulates anterior pituitary production of FSH + LH ■ FSH:​ induces growth of follicles in ovary ■ LH:​stimulates estrogen production in ovary and ovulation ■ Progesterone:​released by CL + is vital for pregnancy ■ FSH → causes Corpus Luteum to develop (CL) ● → releases progesterone ● → regresses to CA when done making progesterone ● Pregnant: ○ Maintains CL and progesterone levels ● Not Pregnant: ○ Release of prostaglandin (by granulosa cells) ○ CL regresses ● Mammary Gland Anatomy ○ Exocrine gland - secretes to outside of body ■ Developmentally like salivary + sudoriferous (sweat) glands ○ Defines the class mammalia ○ Number of glands varies with species ● Stages of Mammary Development: ○ 1 - at puberty ■ Ductal elongation promoted by estrogen + IOF-I ○ 2 - lactogenesis - at pregnancy ■ Ductal and alveolar growth (progesterone) ■ Late pregnancy production of milk + secretion initiated ○ 3 - galactopoiesis = lactation ○ 4 - involution - at end of lactation ■ Regression to pre-pregnancy state ● Composition of milk varies across species ○ Changes based on: ■ Breed, Stage of lactation ● Colostrum vs. milk ● Early vs. mid vs. late pregnancy ■ Parity of dam, Type of feed, Age of young ○ 9 of the 20 amino acids are essential ● Colostrum: ○ First milk produced after parturition ■ High protein content ■ High maternal antibody content ● Important for passive immunity ● Neonatal gastrointestinal tract epithelium is porous to large molecules immediately after birth ● Anatomy: *be able to label* ○ True secretory alveoli develop during pregnancy ■ Increasing estrogen - duct and cistern development ■ High progesterone - alveolar growth ○ Structure’s been modified over time (selective breeding) ■ Conformation to fit milking machine ○ Mammary epithelial cells​- produce + secrete milk ○ Meilol epithelial cel- respond to oxytocin to contract ■ Oxytocin release caused by physical stimulation of hypothalamus ○ Parenchyma​ - glandular tissue (alveolar tissue) makes milk (progesterone) ○ Alveolus ■ Lumen​ holds milk ■ Epithelial cellproduce milk ■ Stroma​ = connective tissue ○ Lobule​ - 200-250 alveoli ■ Lobe​ = multiple lobules ○ Mammogenesis​ - mammary gland development ○ Lactogenesis​ - induction of lactation ○ Galactopoiesis​- maintenance of lactation ● *500 gallons of blood / 1 gallon milk* Midterm 2 Study Guide: Functions of the GI tract: ○ All animals are hollow tubes ○ Receiving: ■ Mouth / Teeth / lips / tongue / jaw ■ Way of getting food in (ingesting food) ● Distinctive for different purposes ○ Dog - jaw moves up and down (shearing) ○ Ruminant - jaw moves side to side (grinding) ○ Conduction, storing: ■ Foregut​ - not a lot of digestion ■ Birds have crop to store food ● Allows it to pick up lots of food fast + digest later ○ Digestion, absorption: ■ Acid digestion ● Hydrochloric Acid + pepsin ● Stomach, abomasum ■ Basic Absorption ● Small intestine​- absorbs amino acids, nucleotides, etc. ● Rumen as well (microbes need more neutral environment) ○ Absorbing water, defecating: ■ Large intestine ■ Some animals have storage for waste (birds do not) ● GI Tract overall same idea for all animals ○ Hagfish = almost just a simple hollow tube ○ Complexity and length will vary depending on diet ■ Obligate carnivore : simpler GI tract ■ Ruminant / herbivore : more complex ● Have to incorporate fermentation Tracts: ○ Fish​ = small compact body to fit GI tract into ■ Small intestine is VERY SMALL ● Pyloric cecum helps to hold food before small intestine ● Allows time to digest and absorb fat ■ **diagram appears on tests** ■ Distal Stomach​ = acid stomach ■ Spiral intestine​= increase surface area ○ Bird​ = need to be light for flight ■ Beaks instead of lips (specialized to diet) ■ Crop​ = storage ■ Proventriculus​= acid stomach ■ Gizzard​ = grinds hard food with little rocks ■ Small intestine: ● Most concentrated area of living organisms on earth ● Duodenum, Jejunum, Ileum​ (3 parts) ● Duodenum = loop t ​hat contains the pancreas (beginning) ○ Pancreas produces enzymes and buffers ■ Exocrine and endocrine organ ○ Where gallbladder drains bile into small intestine ● Ileo-cecal junction - 2 ceca - no function ● Large intestine​= extremely small ○ Water + waste = heavy so expel rather than absorb ○ Pig: ■ Salivary glands ■ Esophagus​ = just for transportation ■ Single acid stomach ● Cardiac sphincter ○ Prevents stomach contents from going up into esophaacid(​ refluxburning of esophageal lining) ● Pyloric sphincter ○ Allows food out of stomach and into small intestine ■ Very big large intestine ○ Horse:​ largececum for hindgut fermentation ■ Cecum = ​appendix in humans ● No known function for us (Vestigial structure) ● For plant eaters = helps them withdraw nutrients ■ Coprophagy​ = eat own feces ● Saliva​= minor component of digestion (more ​uffer) ○ Moisten food ​olusfor swallowing ○ 3 groups of salivary glan​arotid, Submandibular, Sublin)ual​ ● Epiglottis​- closes and blocks the trachea so food forced down esophagus ● Ruminant ***diagram on many tests*** ○ Rumen + reticulum(honeycomb) ■ Open to each other ■ Fermentation ○ Omasum ○ Abomasum ■ True acid stomach ● Ruminant Stomach:​ more evolved with 4 chambers ○ Can flow in/out of all chambers (even back up to mouth) ○ Eruption​ = bring up food to chew again ○ Rumen environment​ must be appropriate for bacteria ■ Saliva adds sodium bicarbonate (buffer) to bolus ■ Brings the pH back up to neutral ○ Reticulum​ - honeycomb structure ○ Omasum ​ - absorbs lots of water ■ Also acts as a “size filter”; doesn’t let big molecules through ○ Abomasum​ - true acid stomach ○ Esophageal Groove​ - bypasses the rumen to omasum ■ Good for young when drinking milk / colostrum ● Feeds them and NOT bacteria this way ○ Pyloric Sphincter​ - controls flow from stomach to small intestine ■ Don’t need one for esophagus bc the rumen isn’t acidic, no risk of burns ● Ruminant Digestion: ○ Bacteria → make volatile fatty acids → source of energy ○ Fate of VFA: ■ Energy ■ Muscle - protein synthesis ■ Adipose - fat synthesis ■ Mammary gland - fat and lactose synthesis ● Fistulated​ - Fistula - hole into stomach ● Monogastric Stomach ○ Esophagus moves food ○ Chemical digestion - HCl + enzyme digestion ○ Cardiac + pyloric sphincter ○ Microstructure: ■ Goblet Cells​- specialized epithelial cells that secrete mucous ■ Parietal Cells- secrete HCl ■ Chief Cells​- secrete various enzymes ● Pepsinogen → pepsin ● Pepsin = active form of pepsinogen, breaks down peptides ○ Secreted in inactive form so doesn’t digest cell ● Oral Cavity ○ Lips​ - pick up food ○ Exocrine​ - salivary glands in mouth ■ Sublingual, submandibular, parotid ○ Teeth ​ - dictated by diet (same with tongue) ○ Saliva​ - moistens + buffers food ■ Has anti-microbial proteins to control mouth bacteria ○ Trachea​ - rigid to allow air flow (esophagus is flaccid) ○ Epiglottis​- switches between trachea and esophagus for air / food ● Gall Bladder ​- on liver ○ Secretes bile to assist with lipid absorption ○ LIVER MAKES BILE → gall bladder stores it ○ Breaks fat down to tiny pieces for lipase to digest ● Pancreas​ - secretes enzymes (exocrine and endocrine) Small Intestine-basic digestion + absorption site ○ Know overall plan* ○ Villi​- increase surface area ○ Intestinal Folds- villi are on folds for even more surface area ○ Outgrowths​ : (technically part of intestinal tract)(evolved over time) ■ Crop, liver, pancreas, cecum ○ Peyer's patch​- lymph node embedded into surface ○ Villi​- moves food between for absorption (+increases surface area) ○ Black dots​ =white blood cells= ​osinophils ■ Push their way out to edge of villi to “sample” what’s going on ○ Enterocyte​ - crucial to health, barrier between outside and inside of body inside intestine (form of epithelial cell) ○ White dots​ = goblet cells= fine layer of cells, secretes mucus ○ Diarrhea​ = villi get shorter and thicker = less surface area ■ Less absorption = more liquid released ● Villus ○ Lymph nodes​ = white blood cells ○ Enterocyte​ = absorptive cell ■ Nuclei form dark ring along edge of villi ○ 2 routes: ■ Transcellular​= across membranes of epithelial cells ● Requires energy ■ Paracellular​= squeezed between epithelial cells ● Really only water does this ○ Epithelium of gut is not all one type of cell ■ Cell function/absorption/junctions differ in different parts of GIT ● Glycocalyx: ○ Provides absorption and enzymes for digestion of protein / sugar ○ Prevents some bacteria from entering body w/ m​ucus layer ○ Component of i​ mmune system​ (recognizes “invaders”) Nutrients: ○ Essentially everything can be a toxin - depends on dosage ○ 20 amino acids, 9 are essential, can make 11 of them ● Six Classes of Nutrients + Functions: ○ Carbohydrates​ = energy ○ Fat​ = structure + energy ○ Protein​= structure + energy + regulatory ○ Minerals​= structure + regulatory ○ Water​ = structure + regulatory ○ Vitamins​= regulatory ● Macrominerals​ : bodies require a lot of ○ Microminerals - bodies only require some small amounts ■ Know example ○ Contain a​ny element except C,H,O,N ● Protein​ : Nitrogen in all amino acids ○ Amino acids joined by peptide bond ○ Essential​- must be ingested ■ Most contain ​ulfur(only source of sulfur is in amino acids) ■ Methionine​ = 1st amino acid in protein synthesis ■ 9-11 essential amino acids (depending on growth stage) ○ Nonessential​- body can produce ○ Rumen smell = hydrogen sulfide ■ Bacteria cut the sulfur off amino acids for themselves ○ Lysine​= essential for nonruminants ○ Taurine​= essential for cats (obligate carnivores) ● Water​ : 1st limiting nutrient ○ (die of thirst before you die of hunger) ○ Water not essential for all mammals ■ Gerbils make enough of their own in metabolic processes ● Fat​ : most “bang for your buck” with energy ○ Glycerol backbone + simple fatty acid units ○ Body can make most but some are essential ● Carbohydrates​ : ○ Sugars ■ Simple​ = easy to metabolize (glucos​)omplex ■ C,H,O​ - provide energy ■ Glucose + glycogen can be stored in tissues ○ Crude fiber (cellulose = can’t digest) ● CANNOT STORE ATP IN BODY Digestion: ● Absorption of Nutrients: ○ Passive Transport:​iffusion across membrane (water) ○ Active:​uses energy + transport across membrane (other nutrients) ■ Also called endocytosis / phagocytosis ■ Other form=use of transporter protei(embedded in membrane) ○ *know flow chart* ● Bodies don’t get all of the energy present in food​(not all available) ○ Gross Energy - Feces = Digestible Energy ○ Digestible Energy - Gas/Urine = Metabolizable Energy ○ Metabolizable Energy - Energy Burned = Net Energy ■ Body maintenance first → leftover used for production/repro ○ Body will metabolize itself if not given enough nutrients ● Gut Microbiota: ○ Terms: ■ Microbiota:​ all microbes living inside the gut ■ Microbiome:​ microbes, their genetic elements, + interactions w/ environment ■ Metagenome:​ genetic content of a microbial population ■ Metatranscriptome:​ functions of a microbial population ○ Functions of GI tract Microbiome: ■ *know chart* Skeletal muscle= muscle cells bound together by connective tissue sheaths that are independent of individual cell membranes ○ Born with all the muscle fibres you will ever have, just make them bigger ● Two types of muscle fibres ○ Striated​ - capable of rapid contractions ■ Red ​ - slow twitch - sustained, continued work, more resistant to fatigue - aerobic ■ White​ - fast twitch - quick movement, fatigues rapidly - anaerobic ○ Smooth ■ Controlled by autonomic nerve system ■ Doesn’t contract rapidly ■ Lines hollow organs ■ Can be excited by stretching as well as nerve impulse ● Skeletal Muscle Terms ○ Epimysium​ - connective tissue ○ Perimysium​ - connective tissue ○ Endomysium​ - connective tissue ○ Fasciculi- bundles of myocytes ○ Myocyte​ - muscle fiber or muscle cell ○ Sarcolemma​ - cell membrane of a muscle cell ○ Myofibrils​- functional unit of a muscle cell ○ Sarcomere​ - building block unit of a myofibril ■ Adds length to myofibril ● Structure of a Striated muscle: ○ Epimysium​ = connective tissue surrounding entire muscle ○ Perimysium​ = surrounds bundles of 10-20 myocytes (bundles = fasciculi) ○ Endomysium​ = connective tissue surrounding individual myocytes ● Myocytes​ : ○ individual muscle fibers = cells ■ *they are multinucleate (have multiple nuclei) ○ Each enclosed by cell membrane - sarcolemma ■ Attaches the muscle fiber to connective tissuendomysium) ■ Key to generation of electric potentials for cell contraction ○ Cytoplasm of muscle cells =​arcoplasm ■ Stores glycogen (for energy) and myoglobin (red, stores oxygen) ● Myofibrils ○ Basic units of contraction inside the myocyte ○ Actin - thin filaments ○ Myosin - thick filaments ● More Muscle = more myofibrils ○ Can grow so much they split ○ Adding sarcomeres also grows muscle ■ Z line defines a sarcomere Growth: ● Why is growth so important? Production ○ Meat, milk, eggs, fiber = most important agricultural sector ○ Fertility has gone down in the selection for production ■ Energy all put toward production, none left for repro ■ Need enough energy ​ stored​for reproduction ■ Sheep Flushing - ​ feed more right before ovulation and insemination = more lambs ● Factors Affecting Growth:​ life stage ○ Prenatal​,​Postnatal - preweani,Postnatal - postweaning: ● Growth: ○ Growth = increase in weight until mature size is reached ○ Growth can be Increasing cell numbers and increasing cell size ● Hypertrophy:​ increase cell size ○ Muscle and fat tissue grows this way ● Hyperplasia:​multiplication of cells ● Nutrition of mother affects oocytes (genetic potential) ● Germ Cell Layers: ○ Ectoderm = outside body (Skin) ○ Endoderm = inside body (gut , liver, lungs) ○ Mesoderm = everything in between (Skeleton, muscle, heart, blood) ● Guest Lecturer: ● 2 General Concepts: ○ Animals are very similar and what makes them different are th​nvironment/diets ○ Nutrition and toxicology are just a continuum ■ From nutrient deficient to excess w/ intolerance somewhere in between ● Definition of Nutrition: ○ Integration of knowledge of biochemistry and physiology into a unifying concept of the relationship between an organism and its nutrient supply ○ A science dealing with the relationship between food and organism ○ Similar essential nutrients for all animals including fish ● Toxicology: ○ Study of relationship between dose and its effects on the organism ○ All things are poison / nothing is without poison ■ Only dose can make it poisonous ● General Concept 1: ○ Animals are very similar and what makes them different are th​nvironment Final Exam: (5/16) ● Definitions: ○ Self​ vs.Non-Self: every individual makes self-identification molecules ■ These train your immune system what to recognize as “self” during fetal development, everything else is “non-self” or foreign ○ Antigen​ : anant​bodygen​erator ■ Induces immune response ○ Epitope​ : a facet of an antigen ■ Each antigen can have several epitopes ■ Each epitope can generate a unique antibody ● Primary and Secondary lymphoid organs ○ Bone marrow: ■ Site of all immune progenitor cells ■ Site of B-cell maturation ○ Thymus: ■ Site of T cell maturation ● Broad functions of immune system: ○ Distinguish self from non-self molecules known as antigens ○ Permit absorption of nutrients ○ Protect sterile environments ○ Mobilize cells to sites of infection/inflammation ○ Contain infection ○ Develop antigen-specific antibodies and long-lasting immunity ■ “Immunological memory” ■ Each B cell is only making one antibody to go against one thing ● Need a whole repertoire of antibodies ● Innate immunity or Nonspecific barriers against pathogens: ○ Nonspecific barriers of the body against invaders ○ Physical barriers: ■ Unbroken skin, mucus, peristalsis, flushing (tears, saliva, urine), cilia ○ Chemicals: ■ Acidic pH (stomach, vagina), sweat, bile salts, digestive enzymes, nonspecific IgA, antimicrobial peptides ● Paneth cells in intestines make defensins, cathelicidins, etc. ● Lysozyme in tears, saliva, milk ○ Microbial: ■ Competition for space for nutrients ● Good bacteria fills the niches that bad microbes would want to take but can’t because it’s occupied ● Passive Immunity: ○ Transfer of maternal antibodies to fetus across placenta ○ Colostrum contains antibodies, only works until young’s immune system develops ■ Antibodies absorbed into bloodstream before gut closure <48 hrs postpartum ● What happens?​ If exposed to a pathogen ○ Fever, redness, swelling, pain, decreased function ○ Lactoferrin​= most abundant protein in human milk ● Innate Immunity: ○ Once contact is made, inflammation begins ■ Pathogens have common cell-surface antigens ● Pathogen associated molecular patterns (PAMPs) ○ Ex: lipopolysaccharides ● PAMPs bind to epithelial cells ● Leukocytes respond to inflammation ○ White blood cells ■ neutrophils, monocytes/macrophages (MO), Dendritic Cells(DC), Natural Killer Cells ■ Increase White blood cells production in bone marrow ■ Migrate to site of inflammation ■ Phagocytosis of dead cells and pathogens ■ MO, DC, and B cells are professional antigen presenting cells (APCs) ● When innate immunity fails: Adaptive immune response ○ MO, DC migrate to Peyer’s patches and lymph nodes ○ T cells bind antigens and are activated ● T cells activate B cells in PP/LN ○ Helper T cells (TH cells) ■ Provide help to B cells that is necessary for antibody production ○ B cells bind antigen through B cell receptor ○ T cell activates B cells to proliferate and differentiate into antibody-secreting cells ○ Antibodies coat pathogen, “targets” them for destruction ● When infection is controlled: ○ Must stop immune response ■ Arthritis - your cells are attacking your own body ○ Regulatory T cells suppress inflammation ○ Memory T and B cells form ○ Lasting immunity against pathogen ■ THIS IS HOW VACCINES WORK ● Failure of immune system: ○ Breakdown of tolerance ■ Autoimmunity​ - identifying self antigens as foreign ● Multiple sclerosis​(attack Central Nervous System) ● Lupus​ (attack various organs) ● Type 1 Diabetes​ (attack beta cells in pancreas) ■ Inappropriate response to non-pathogens: ● Commensal bacteria: Crohn’s and colitis ● Non-infectious antigens: allergies to pollen / food ○ Every surface of your body is colonized by commensal microbes ○ Fine balance between ■ Recognizing antigens from non-threatening sources ■ Distinguishing between commensal bacteria (tolerated) and pathogens ■ speed, strength, and duration of immune response ● Immune cells - ​ originate in bone ● Genetic Revolution ○ Gregor Mendel​ - basic mechanisms of inheritance ○ Charles Darwin​ - genetic makeup over time is plastic (changeable) ■ Every animal differs by thousands of base pairs except clones and twins ● Basics: ○ Cell nucleus contains​hromosomes ■ 3 genomes - mom, dad, mitochondria (from mom) ○ Chromosomes are m ​acro-molecules ○ Genes​ - functional segments on chromosomes ■ Encode specific RNA’s or amino acid sequences (proteins) ○ Genome - ​ Sum of all genetic material in one complete set of chromosomes ■ Sperm and egg are the only one cells that have a full genome ○ Locus​ - site or location on a chromosome ○ Gene - ​functional region at a locus ○ Alleles -​different versions of a gene ■ Can be many different alleles for a locus in a population ■ Only 2 alleles for a locus in an individual ● Compatibility Complex - makes antibodies ○ Clustered around one portion​of the chromosomes (only genes that stick together always) ● Genotype - genetic constitution of an INDIVIDUAL ○ Gametes carry only 1​allele for every given locus ○ Individuals carry alleles for each autosomal locus ○ Combination of all allele pairs of all gene loci = the genotype ● Mammals and birds have diploid genomes (2N) ○ Fish may be 2n, 4n, or other variations (and amphibians) ■ Sturgeon = 2n = 217 +/- 6 ● 2 Types of chromosomes: ○ Autosomes:​ paired, diploid organisms, pair at meiosis ○ Sex Chromosomes:​ different between the sexes ■ ZW birds (female) ZZ male ■ Y/X mammals (male/female) ● Gender is determined by temperature(environment) (not chromosomes) ○ In green sea turtles and alligators ○ In humans:​ female development is the default ■ Y chromosome stops that development ● Mitosis​: duplicated DNA and getting ready for dividing (4C) ● Cell cycle​- replication of DNA and duplication of cells mitotically ○ G - g​ap between phases (only place where the process can “pause”) ■ 0 - same as gap 1 but referred to 0 if it probably will never divide again (neurons) ■ 1 - between division and beginning of replication of DNA ■ 2 - between end of replication of DNA and mitosis ● Mitosis​ - go through cell cycle and chromosomes duplicate ● Phenotype:​ the observable properties of an organism: ○ (P) results from action of the genetic (G) makeup of an organism, its environment (E), and the interaction between the genes and the environment (GXE) ○ P = G + E + (GXE) ● Eukaryotes vs. Prokaryotes: ○ Eukaryotes have ​introns​- breaks up genes = more opportunity for variation ● Meiosis:​ modification of mitosis ○ 1 - elongated prophase - chromosomes pair and crossover (exchange material) ○ 2 - go into divisions with absence of duplicating DNA ○ → Results in haploid cells not diploid ○ Meiosis = key to understanding genetics ○ Creates haplous 1N gametes that contain only 1 allele per gene ○ Mendelian inheritance​ is simply following alleles thru meiosis ○ 2 Processes that cause re-shuffling of genes: ■ Random migration of individual chromosomes into gametes ● Results in mix of paternal/maternal chromosomes in each gamete ■ Crossing over / exchange of gene segments btwn homologous chromosomes in prophase of Meiosis 1 ● Types of Gene Action: ○ Dominant​ : heterozygote has the same phenotype as homozygous dominant (Aa = AA) ■ Action of recessive allele completely masked by dominant ○ Co-dominance:​ Aa =/= AA ■ Effect of both alleles observed ■ Phenotype of heterozygote different from both homozygotes ○ Semi / Incomplete Dominance​ : AA =/= Aa ■ Phenotype of heterozygote is midway btwn that of both homozygotes ○ Epistasis:interaction between genes of different loci ● Coat color in horses: ○ Base Coat Color = Dominant ○ The E​xtension Locus ■ E allele​produces both black (eumelanin) and red (phaeomelanin) ■ e allele​produces only red pigment ■ EE/Ee = horses with both red and black color (blacks and bays) ■ ee = only red horses (chestnut) ■ Having black points is the same gene as the agouti in mice ○ Incomplete Dominance in Horses: ■ Chestnut vs. Palomino ■ C’ = cream dilution allele ■ eeCC = chestnut (dark brown body) ■ eeCC’ = palomino (white points and light brown body) ■ eeC’C’ = cremello horse (all white) ○ Epistasis in Horses: ■ G = Grey vs. Extension ■ G masks all other coat colors except dominant white (which trumps all) ■ ggEE/ggEe = black or bay | ggee = chestnut ■ G_ _ _ (anything) = grey ■ All grey horses get melanomas if they live long enough ● Predicting ratios: Single Gene ○ Genotypic Ratio will differ from Phenotypic ○ No 2 individuals have exact same genotype unless clones or identical twins ■ As the number of pairs increases, the number of genotypes grows ● Gene Frequencies: ○ Count frequency of alleles for a population ■ Corollary​ = allele frequency data is population specific ■ Frequencies change based on: ● Population size ○ If small, one little change in allele can lead to huge change in frequency in population ● Differences in fertility / viability ● Migration and mutation ● Mating system ● Hardy-Weinberg Equilibrium: ○ Assumes: Large population, no effect on fertility, equal viability of all gametes, no migration, no mutation, Panmixis (equal opportunity for all mating possibilities) ○ p​ 2+ 2pq + q​= 1 (p/q each represent an allele) ■ Displays the allele frequency of “next generation” ■ Homozygotes = p​ 2/q​ ■ Heterozygotes = 2pq ● Variance: ○ The amount of variation is measured and expressed as variance ○ Phenotypic variance​ : ■ Result of the effects of genetic predisposition and environmental effects ○ Genotypic Variance​ : ■ Variance between individuals in their genetically determined potential ○ Additive Genetic Variance: ■ Component that can be transmitted to the next generation ■ Breeding value:​ genetic value of an individual for a specific trait (population specific) ○ Non-additive genetic Variance: ■ All genetic variability that is unique to individual ■ From dominance, epistatic, and epigenetic effects that are unique to the genotype of the individual ● Heritability: ○ Proportion of observed variability of a trait that is genetic in nature (btwn 0 and 1) ○ Degree of relationship between genotype and phenotype ■ If “leanness” has a high heritability → more lean offspring due to more lean alleles being passed on (high heritability = higher number) ● *Assume Variation is a Bell Shaped Curve* ● Selection Differential: ○ The difference between selected animals and average of all animals in the herd ● Mendel: ○ Principles of Segregation ■ More than one determinant ■ They would segregate going through reproduction process ○ Principle of Independent Assortment ■ Separated independently of each other ■ Just so happened to be because they’re on different chromosomes ● The further away alleles are, the more likely they will segregate independently ○ Exception to Mendel’s rules: ■ Linked genes - don’t sort independently ● More likely to segregate together ■ Genes on sex chromosomes ■ Mitochondrial genes ■ Meiotic-drive mechanisms ● Allele going to show up in the gametes more frequently than it should according to chromosomes ○ Should show up half and half but ISN’T true for this ○ Meiotic drive = advantage of a certain allele of another ■ If one allele is detrimental (kills gametes) ■ The other allele will be better passed on ○ Imprinted genes (epigenetics) ■ Depends upon the parental origin of the allele ● (may express one parental trait from father but not from mother) ● Inbreeding: ○ Mating of individuals related by descent (IBD = identical by descent) ■ Alleles that are identical copies of an allele present in a common ancestor ■ Ex. blood type ■ Reduction in fitness (survival, reproduction) ○ The higher the inbreeding coefficient, the more detrimental on survival ■ California condors have such a small population that it’s very inbred ○ Consequences of inbreeding: ■ Loss of genetic diversity increase risk of extinction ● Cheetahs - least diversity of any mammal ■ Increases risk of extinction in captive and wild populations ■ Loss of genetic diversity reduces ability of species to evolve with change ● Genetic Drift: ○ 1. A result of binomial sampling in small populations ○ 2. More effective in small populations than large populations ○ 3. Alleles could be either fixed or lost by chance ○ In small populations you can by chance get more or less frequency of a specific allele than you probably should ■ Like flipping a coin 10 times and getting all heads vs 1000 times ■ That’s why hardy-weinberg is based on large population size Biotechnology: ○ Artificial insemination ○ Embryo transfer ○ rDNA produced diagnostics, vaccines, biologics ○ Marker assisted selection - whole genome selection ○ Cloning ○ Genetic engineering + gene editing ● Uses: ○ Cryopreservation of sperm, ova, gonads, and embryos ○ Manipulation of embryos: transfer, cloning, ICSI, genetic engineering, gene editing ○ Stem cells ● PCR = polymerase chain reaction ○ a method of amplifying small amounts of DNA ○ need to know sequence to make specific primers ● rVaccines ○ rabies, parvovirus, kennel cough, lyme disease, salmonella ■ Removed rabies from Belgium by picking out rabies areas with animals ○ Inserted rabies glycoprotein gene (the antigen) into vaccina virus (cow pox) ● Marker Assisted Selection Against diseases ● For production traits ○ cattle: milk production, meat quality ○ pigs: litter size, meat quality ○ horses: coat color ○ goats: α-S1-casein ● Marker or whole genome selection ● Selection for markets for better quality meat- even if don’t have genes, thousands of at a time based on markers ● Cloning ○ the asexual reproduction of a genetically (nuclear) identical individual ● History ○ 1981 - Embryo splitting ○ 1987 - Blastomere fusion to an enucleated oocyte ○ 1997 – Adult somatic cell nuclear transfer ● Take out polar body and add a nucleus into empty egg- 3n would die, could grow into whole animal now ○ Pronucleated cell ○ Use electrodes to fuse membranes of cell to the ovocyte, the egg thinks it has been fertilized and begins development ○ Not efficient> no production, but resurrect elite dead bulls to good cows. ● Genetic Engineering or Transgenics ○ Canary in the coal mine ○ glofish originally developed to monitor water pollution ● The beginning - 1982 - ○ Mice ended up sterile but was a first step ● If you have a gene - you can inject into the pronuclei of mice ○ All genes have to have some switch that turns it off ○ Don’t want everything expressed all over body ● Plasmids:​ circular DNA outside a chromosome in a bacteria ○ Can insert gene and put back into bacteria and clone genes ● transgenic/genetically engineered ○ Animal that contains a new gene (or DNA) introduces into the DNA by means other than normal breeding or viral infection ○ GMO =/= GE/transgenic ■ Genetic engineering is not the same as genetically modified ● For the record: ○ US regulates transgenic animals with the FDA ○ Regulated under the animal drug act ■ Transgene is treated as a drug (injected to change form or function) ○ Constantly eat things with DNA in it ■ FDA says this DNA is a drug and may be bad (contradiction) ● Gene construct: ○ embryo→ transgenic animal → ■ → research ■ → biomedical ● Pharmaceuticals ● Xenotransplantation ○ Transferring organs between species ○ Figuring how to get other animals to accept the foreign organs ■ → industrial ● Spider silk ○ Can’t be cultured, trying to make it on an industrial level ■ → agriculture ● Food security ● Nutriceuticals ● Sustainability ● Methods for Making Transgenic livestock: ○ Microinjection: ■ Pronuclear: mammals ■ Cytoplasmic: fish/birds ○ Retroviral infection: mammals/birds/fish ○ Sperm mediated: birds/fish ○ ES/PG cells: pigs/chickens/trout ○ SCNT based cloning: mammals ■ Transfect DNA into cells prior to cloning ● Pronuclear microinjection ○ Mouse zygote - inject DNA into pronuclei ● Programmable endonucleases ○ Include: TALENs, CRISPRs, ZFNs ○ Introduce targeted, double strand break in DNA ○ Used to: ■ Introduce mutations - not GE ■ Target gene insertion - GE ○ Can create low allergen milk by removing protein ● Livestock GE in the Future: ○ TALENs, ZFNs, or CRISPR-Cas9 enzymes can be used for site directed mutagenesis and for gene targeting ○ Using these enzymes gene targeting should now be possible at reasonable efficiencies in any species in which microinjection is possible ○ GT and site directed mutagenesis is now available in all species ● What can we do now? ○ Add new gene ○ Add extra copies of endogenous gene ○ Delete an endogenous gene ○ Mutate an endogenous gene ○ Replace endogenous gene ○ Down-regulate expression of endogenous gene ● Since 1985 ○ Over 200 types of transgenic large animals produced ○ Over 25 species of fish genetically engineered ○ Multiple constructs transferred into poultry ● Agriculture ○ Currently > 60 constructs ■ Modifications of milk components ● Increased nutrition ● Functional food ■ Modification of wool growth ■ Improved growth ■ Improved digestion/nutrition ● Only approved GE animal in the world = AquAdvantage salmon ○ Worried about the gene and human consumption for most other GE animals ● Why use these GE animals? ○ AquAdvantage Salmon - hits market weight in half the time ○ Enviropig - excrete 70% less phosphorus in urine ■ Environmentally better ○ Bovine a-lactalbumin pigs ■ Produce more milk → babies grow faster


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