Intro to ani sci exam 2 Rutgers

Fitness

- An animals ability to pass on more genetic material which

- This requires an animal being good at locating food and shelter and avoiding predators

Forces of evolution on wild animals

- Natural selection

- Random drift

- Mutation

- Gene flow between populations

Forces of evolution on domestic animals

- Selection (natural, artificial, relaxed)

- Random drift

- Mutation

- Gene flow between populations

Changes seen in domestication

- Loss in fitness

- Deterioration of cognitive mechanisms

- Neoteny

- Size and coat color differences

What impacts animal science

- Public perception

- Advancing knowledge about animals (animal biology and management systems)

Animal Rights

- All animals have comparable rights and each individuals desires should be respected equally

Human Dominion

- Animals were put on this earth for us to use in whatever possible way they can benefit us the most and in the least expensive way possible

Animal welfare

- Using animals for the greater human good but we have an obligation to provide for the majority of their physiological and behavioral needs (most countries have regulations about minimum animal welfare with Eroupe being more strict)

Animal welfare is a mix of

- Science and ethics (a use of objective measurements but weigh them using ethical values)

The ways animal welfare is measured

- Health

- Production

- Physiology

- Behavior

- Mental Health

5 freedoms of animal welfare

- Freedom from hunger or thirst

- Freedom from discomfort

- Freedom from pain, injury, or disease

- Freedom to express normal behavior

- Freedom from fear and distress

The basics of Feelings based approach to animal welfare

- Hypothesized by Duncan

- Subjective experiences of animals

- Negative feelings (pain, discomfort, hunger, fear, etc.)

- Positive feelings (comfort, pleasure, etc.)

- May involve preference/motivation testing

The basics of Biological Functioning based approach to animal welfare

- Hypothesized by Broom

- Physiological measures (Health, longevity, Production)

The basics of Nature based approach to animal welfare

- Hypothesized by Fraser

- How well are you accommodating to the animals natural behavior

- How many natural behaviors can it preform

- Is it allowed to preform the behaviors it is strongly motivated to do

Measures of poor welfare

- Reduced life expectancy

- Reduced ability to grow or breed

- Body damage

- Disease

- Immunosuppression

- Coping behaviors

Measures of good welfare

- Variety of normal behaviors shown

- Physiological indicators of pleasure/contentment

- Behavioral indicators of pleasure/contentment

Using behavior to evaluate Welfare

- Requires knowledge of animal behavior

- Is the animal showing agonistic

- Recognize fear behavior

- Is the animal showing frustrated or boredom behaviors

Low stress cattle handling

- Involves an understanding of Flight distance/zone

- Good for cattle because less stress means better welfare

- Make sure to limit noise apply pressure properly and make the first experience a positive one

Figuring out the normal for your animal is important because

- To know the normal means to know when the animal is off

Welfare auditor

- Part of official organizations that inspect animal facilities (IACUC, Quality checkoffs, zoos, SPCA, etc.)

Professional Animal Auditor Certification Organization

- Provides consistent training to auditors

- Evaluates and certifies Audits

- Links procedures/operations with auditors

3 types of auditing measures

- Outcome based measure

- Management based measure

- Resource Based Measure

Outcome based measure

- Information collected directly from the animal (i.e. animal based measures)

Management based measure

- Information collected from records or personnel or directly observing human behavior (i.e. human actions taken to manage animals)

Resource Based Measure

- Information collected from the animals environment (i.e., resources provided to the animal)

Welfare assessment questions

- Housing conditions, is it safe/accommodates animals nature

- Is the animal fed to its physiological/behavioral needs

- If its a social animal is it allowed social interactions

- Are human interactions often and positive

- How often are animals checked and how smart are those caretakers

- What do health indicators show

- How are potentially stressful situations handled by animals and handlers

- Housing: feed bunk access, access to waterers, space to lie down

- What do physiological indicators show (heart rate, etc.)

- What indicators of stress are shown (vocalizations post weaning, etc.)

Animal welfare judging and assessment contest (AWJAC)

- Hypothetical scenario using realistic data to assess animals/groups of animals

- Decide who has better welfare then justify it with science and give suggestions

Live assessment (AWJAC)

- In a team

- Go to a real facility

- One environment and one question about improving environment

- Real place hypothetical data

The central dogma

- Model for how DNA influences biology

- DNA -> RNA -> Protein

Genome

- An organisms complete set of DNA

- Genetic system

- Contains information for proper development and to maintain physiology

- Responds to the environment

- Undergo long term change

Bacteria (in the context of diversity between genomes)

- Most diverse Clade

- Includes important biomedical tools and pathogens

Archaea (in the context of diversity between genomes)

- Extremophiles

- Hard to study

Eukaryota (in the context of diversity between genomes)

- Animals, plants, etc.

- Most limited diversity

Characteristics all genomes share

- Copy and encode information in very similar ways

- Organized into large and small units

- Many of the units are similar enough between species to be shared

- This means learning about one genome can tell you about another

Model Organism

- Well-studied species that geneticists use to learn about other species

Characteristics of model organisms

- Large (but not too large)

- Short generation time

- Amendable to laboratory study

- Relatively inexpensive

- Recent well characterized genome

Lamarckian evolution

- Incorrect theory that states traits acquired by an animal during its lifetime will be passed down

Preformation

- Incorrect theory that states each individual was performed in the parent and simply grew

Pangenesis

- Incorrect theory that states inheritance from the whole body

Darwin

- Theory of evolution

Mendel

- Discovered the principles of heredity

Weismann

- Hypothesized germplasm theory

Transmission genetics

- How traits are passed from one generation to the next

Molecular genetics

- How the molecules of genetics are copied modified and encode information

Population genetics

- How genomes change within and between populations

Diploids

- Organisms that have one copy of a genome from mom and one from dad

Principle of segregation

- Individuals have two copies of every gene, they are inherited by offspring independent of one another

Independent assortment

- Genes encoding different traits are inherited independent of another

Pawnee Farm Arlinda Chief

- Popular sire in the 60s

- Sired 16,000 daughters, 500,000 granddaughters, 2 million great granddaughters

- Accounts for 14% of the holstein genome in the US today

- Contained lethal mutation that causes increased and spontaneous abortions

Macroevolution

- Dramatic biological changes across species or taxa

- Summary of many, many microevolutions

- Occurs over large time scales

- Must be inferred difficult to measure directly

Microevolution

- Heritable change within a population

- Results from genetic variation within individuals

- May lead to the formation of a new species

- Can occur on a short time scale

- Evolution studyable in a lab

Phylogenetic trees

- describe relationship between species

- Relationships are the result of macro evolution

- trees can be built by comparing genetic variation across many species

- points on the tree are species

- Branch points are the last common ancestor

- Branch lengths may or may not indicate time or evolutionary distance

Tortoise shell coat color

- Result of RNA influencing DNA

Modern dogs

- Result of natural and artificial selection

Biotechnology

- Technology that utilizes biological systems, living organisms or parts of these to develop or create different products

Important points of the molecular revolution

- James Watson and Francis Crick (DNA structure)

- Rosalind Franklins X-ray crystallography

- Herb Boyer and Stanley Cohen introduced DNA into e coli (genetically engineered e coli to synthesize human insulin)

History of biotech

- Large scale yeast and penicillin production 1940

- Discovery of DNA structure and synthesis 1953

- Recombinant DNA technology 1973

- Human Genome project Launched 1990

- Dolly the first cloned sheep 1997

- Synthetic Biology Artemisin 2003

- Immune Checkpoint cancer therapy 2011

- Successful CRISPR-Cas9 gene editing 2013

- CAR T cancer therapy 2017

- CAR T cancer therapy 2020

Blue Biotechnology

- Marine and Freshwater

Red Biotechnology

- Medical/Pharmaceutical

White Biotechnology

- Industrial

Green biotechnology

- Agricultural

Biotechnology in healthcare

- New vaccines

- New diagnostic tools

- Therapies to prevent and treat diseases

Biotechnology in agriculture and food security

- Increase crop yields

- Enhance nutritional value

- And create more resistant plants

Biotechnology in environmental sustainability

- Bioremediation

- Produce renewable biofuels

- Mitigate pollution

Biotechnology in Industrial Processes

- Produce chemicals efficiently and sustainably

- Produce materials efficiently and sustainably

Deoxyribonucleic Acid

- (DNA) the molecule that carries genetic information for the development and functioning of an organism

Ribonucleic acid

- (RNA) A nucleic acid in all living cells similar to DNA but single-stranded. Has a ribose sugar and four bases.

Protein

- A chain of amino acids bound to one another via peptide bonds

3 core concepts of biotechnology in research

- Analytical - 'omics analysis

- Synthetic - direct synthesis

- Manipulation - genetic engineering

Analytical Biotechnology examples

- Chromatography

- Electrophoresis

- DNA sequencing (determines order of nucleotides)

- Polymerase Chain Reaction (PCR)

- Enzyme linked Immunosorbent Assay (ELISA)

- Flow cytometry

PCR aka Polymerase Chain Reaction

- A common laboratory technique used to make millions of copies of a specific segment of DNA

- First denature DNA to make two separate strands

- Second molecules called primers can bind to the specific target sequences on the separated strands

- Lastly an enzyme called DNA polymerase synthesizes new strands of DNA, starting from the primers effectively copying the target sequence

Flow Cytometry

- A laser-based technique used to analyze and quantify cells or particles as they flow in a fluid stream through a beam of light

- Measures cell size, granularity, fluorescence intensity

Bioinformatics

- application of computational and analysis tools to capture and interpret biological data, essential for managing data in biology

Human Gut microbiome

- 16S rRNA gene sequencing which identifies bacteria

- Useful for pro filing microbial communities

Omics-based Approaches

- "omics" in a molecular term implies a comprehensive or global assessment of a set of molecules

- the first omics discipline to appear genomics focused on the study of entire genomes as opposed to "genetics" that assessed individual variants or single genes

Synthetic biology

- A field of science that involves redesigning organisms for useful purposes by engineering them to have new abilities

- Synthetic approaches generate new compounds often to improve human health (exp. mRNA vaccines and drought resistant crops)

SARS-CoV-2

- Enveloped RNA virus with a crown of spike proteins on its surface

- Spikes on crown bind to ACE2 receptors allowing viruses to enter and infect cells

- Targets respiratory epithelial cells

mRNA vaccines

- mRNA vaccines deliver genetic instructions wrapped in lipid nanoparticles

-Once in cell it instructs to produce the spike protein

- The immune system then recognizes this protein as foreign and develops antibodies and memory cells against it

Manipulation Biotechnology

- Genetic engineering - s process that uses laboratory based technologies to alter DNA makeup of an organism

- May be just changing a single base pair or deleting/Adding a new segment of DNA

CRISPR-Cas9

- Clustered regularly interspaced short palindromic repeats were first discovered in the sequences of DNA from e coli in 1987

- Allows engineers to introduce precise changes to DNA sequences

How does CRISPR-Cas9 work

- it has a Guide RNA that tells the system where to go in the genome and a Cas9 protein that will cut the DNA once the guide finds the right spot

- First the protein and guide travel together to find the DNA sequence

- When found the protein will cut the DNA

- Once cut the cell will want to repair and you can insert a template to create new genetic information

Synthetic vs manipulation

- In synthetic your stitching new DNA and inserting them as per the term synthesize meaning to make

- Manipulations is editing a preexisting DNA sequence not stitching a new one

Homeostasis

- Walter B. Cannon (1929) coined the term "relatively constant internal environment

- Adaptive significance of functions

- Keeping internal environment stable

- A dynamic balance between the autonomic branches

Homeostasis Controls

- External or internal change

- Loss of homeostasis is sensed by an organism

- Always a Physiological attempt to correct homeostasis with failure meaning death

Pathophysiology

- Is the study of failure to compensate

Mark Sanchez

- Former professional football player who was a quarterback in the National Football League for 10 seasons

Sympathetic nervous system

- Increases heart rate and breathing rate

- Stimulates bronchodilation to allow for more air to reach lungs

- Pupal dilation

- Decreased intestinal motility/slow down digestive processes

- Fight or Flight is when Sympathetic activity dominates

Response to a threat

- Fight or Flight

Autonomic branches (ANS)

- Sympathetic nervous system

- Parasympathetic nervous system

Parasympathetic nervous system

- Decreases heart rate and breathing rate

- Pupil constriction

- Increases intestinal motility/allows down digestive processes

ANS Divisions role in homeostasis

- Preservation of the fitness of the internal environment

- Up/Down regulation by tonic control

- Antagonistic control (two opposing mechanisms work to create balance)

- Chemical signals with differing effects in dissimilar tissue

CNS-mediated Autonomic, Endocrine, and Behavioral Responses

- The coordination of homeostatic responses (autonomic (just ANS btw), endocrine and behavioral)

Autonomic control centers in brain

- Hypothalamus - water balance, temperature and hungar

- Pons - respiration

- Medulla - Respiration, Cardiac, Vomiting, Swallowing

Autonomic Pathways

- Consist of two neurons that synapse in an automatic ganglion

- Full explanation is: central nervous activates a preganglionic neuron in response to stimuli and that single is sent to the autonomic ganglion which is a cluster of nerv cells that then transfer the signal from the preganglionic neuron to the postganglionic neuron which is connect to the tissue or organs that the signals intended for

Sympathetic vs. Parasympathetic

- Sympathetic pathways use acetylcholine and

norepinephrine and exit the central nervous system in the Thoracolumbar region

- Parasympathetic pathways use acetylcholine and exit the central nervous system in the Craniosacral

Dual intervention

- Means most organs are under Antagonistic control

- one branch is excitatory and the other branch is inhibitory (exp. Heart parasympathetic slows hear rate and sympathetic increases rate)

- Excitatory and inhibitory can work together to coordinate a response

Tonic immobility

- Involuntary, freezing-like state of paralysis that occurs in response to intense fear, acting as a defense mechanism in both animals and humans

Opossum tonic immobility (thanatosis)

- Breathing rat decreases

- Heart rate decreases

- Tongue hangs and turns blue

- Secrets death odor from anal glands

Thanatosis

- Comes from Thanatos in Greek mythology

- Imitation of a dead animal as opposed to tonic immobility which is just an a state of immobility

Reoccurring themes in Physiology

- Homeostasis 2/3s of physiology

- Biological energy use

- Structure-function relationships (molecular inteactions, compartmentation, mechanical properties of cells tissues and organs)

- Communication (chemical and electrical signals