11:067:142:01 RUTGERS INTRO TO ANISCI EXAM 2

What shapes the behavior of Wild Animals?

Forces of evolution, natural selection, mutation, gene flow

What shapes the behavior of Domestic Animals

Forces of evolution and Natural, artificial, and/or relaxed selection

Domestication

An evolutionary process where populations of animals change genetically and phenotypically by selection pressure based on human-desired traits

Changes seen in Domestication

Losses in fitness, reduced responsiveness to changes in the environment (cognitive mechanisms), neoteny, size and coat color differences,

T/F: In domestication, we see a lot of change in the types of behaviors

False; you may see a difference in the frequency of certain behaviors, but the actual change in the type of behavior is little.

Tame

conditioned behavioral modification at the individual animal level.

T/F: A domesticated animal can be untamed, and a wild animal can be tame.

True

Feralization

Domestication in reverse. Animals no longer subjected to artificial selection experience stronger natural selection pressure.

T/F: Feralization is not a process

False; Animals that have undergone full feralization are wild, while domestic animals that are experiencing genetic change associated with feralization are feral.

Reasons to domestic Animals

Economic benefits, food and fiber production, hunting/sporting, protection, religious reasons, war, human companions, research

Favorable Characteristics of Domestication

Large social groups like flocks, herds, or packs

Males affiliated with a female group

Males are dominant over females

Sexual signals are provided by movement/posture

Precocial (mature while born)

low reactivity to humans or sudden environmental changes

Omnivorous and limited agility

Unfavorable Characteristics of Domestication

Males in a separate group from females

Males must establish dominance to appease females

Color marking sexual signals

Altricial (immature while born)

Can be easily disturbed by humans or sudden changes in environment

Have dietary habits

Extremely agile

Human Views on Animals

Animal Rights, Animal Welfare, Human Dominion

Animal Rights

Animals have comparable rights, and each individual's desires should be respected equally, similar to those of a human

Animal Welfare

Animals are used for the greater human good, but there is an obligation to provide for the majority of their physiological and behavioral needs.

Human Dominion view on Animals

Animals were put on this planet only to help benefit humans at the most, and in the least expensive way possible

How to measure animal welfare

Health, production, physiology, behavior, mental health

The Five 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

Feeling Based Approach to Animal Welfare

Honored by Duncan

Subjective experiences of animals

Negative (pain, suffering, distress, fear, hunger, thirst)

Positive (comfort, pleasure, etc.)

Not believed by everyone that we have truly proven that animals experience these subjective states.

Biological Functioning Based Approach to Animal Welfare

Honored by Broom

Physiological measures like:

Health, longevity, production (weight gain, conception rates, egg production)

If an animal is physically healthy, does that automatically translate to it having good welfare?

Nature-Based Approach to Animal Welfare

Honored by Fraser

Not all natural behaviors are in the interest of "good" animal welfare for an individual

How well are we accommodating the animal's natural behavior?

Poor Welfare Measurements

Reduced Life Expectancy, reduced ability to grow or breed, body damage, disease, coping behaviors

Good Welfare measurements

Variety of Normal Behaviors shown

Physiological and behavioral indicators of pleasure and contentment

Animal Flight Zone

The personal bubble of an animal is the boundary where, if a predator of an animal steps into it, the animal will move away.

3 Types of Auditing Measures

Outcome-Based Measures(OBM): Information collected directly from the animal

Management-Based Measures (MBM): Information collected from records or personnel or directly observing human behavior (human action taken to manage animals)

Resource-based Measure(RBM): Information collected from the animal's environment

Central Dogma

The Model for how DNA influences biology

Genome/DNA -> RNA -> Protein -> Biology

What is a genome

It is the genetic system of an organism.

Allows the proper individual development, maintains individual physiology, enables individual responses to the environment, and allows the ability for populations to undergo long-term change

Bacteria

The most diverse clade, includes important biomedical tools and pathogens

Archaea

Very hard to study because most species can't be grown or cultured in a standard lab setting

Extremophiles

Eukaryota

Animals, plants, etc

Most limited diversity

Model Organisms

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

Have decently large offspring numbers, short generation times, amendable to lab study, and recently-well-characterized genome. (Fungus, Plants, Mouse, Flies)

Bad human geneticists ideas

Lamarckian evolution: Inheritance of acquired traits

Pangenesis: Inheritance from the whole body

Preformation: Each individual was prefromed in the parent and simply grew.

Very good human geneticists ideas

Darwin: Theory of Evolution

Weismann: Germplasm Theory

Mendel: Principles of Heredity

3 Basic Disciplines of Genetics

Transmission, Molecular, Population

Many areas of genetics research encompass two or all of the basic disciplines

Transmission Genetics

how traits are passed from one generation to the next

Molecular genetics:

how the molecules of genetics (DNA and RNA) are copied, modified, and encode information

Population Genetics

how genomes change within and between populations

What did Gregor Mendel(the father of transmission genetics) do?

Established basic rules of inheritance:

Principles of Segregation: Individuals have two copies of every gene, and they are inherited by ohhspring independent of one another.

Independent Assortment: Genes encoding different traits are inherited independently of one another

BLAD

recessive autosomal disease that causes increased infections and early death

BL - carrier of disease and BLAD allele

TL - free of BLAD allele

Pawnee Farm Arlinda Chief and her importance

An insanely popular sire in the 60's

Sired 2,000,000 great-granddaughters

Accounts for almost 14% of the holstein genome in the US today.

Only problem was that she carried a lethal mutation that causes increased spontaneous abortions.

Worldwide losses: Around 500,000 fetuses and over 400 million dollars

Tortoise-Shell Cats

Almost always, a Tortoise-Shell cat is female because of X-chromosome inactivation within an embryo, allowed by a female's XX chromosomes

What is Xist (X-inactive specific transcript)?

Mostly occuring in females

An RNA that regulates DNA

In each cell, one X chromosome expresses the XIST RNA

The XIST RNA coats the originating chromosome; then the coated chromosome is inactivated

Macroevolution

Dramatic biological changes across species

Sum of MANY microevolutions

Occurs over a VERY large amount of time

Must be inferred because of the time scale; very difficult to measure directly

Microevolution

Heritable change within a population

Results from genetic variation within individuals

May ultimately lead to the formation of a new species

Can occur on a short time scale

Can be studied in a lab

What is Biotechnology?

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

(brewing beer and baking bread for example)

Molecular Revolution

James Watson and Francis Crick (Found DNA structure)

Rosalind Franklin (contributred majorly with findings)

Herb Boyer and Stanley Cohen introduced DNA into E.coli, genetically engineered the synthesis of human insulin.

Color Code of Biotechnology

Blue: Marine and Fresh-Water

Red: Medical/Pharmaceutical

White: Industrial

Green: Agricultural

3 Core Concepts of Biotechnology

Analytical - 'omics analysis

Synthetic - direct synthesis (by the cell)

Manipulation - genetic engineering

Analytical Biotechnologies

Describe or discover biological molecules

Chromatography, Electrophoresis, DNA sequencing, PCR's, ELISA, Flow Cytometry

Flow Cytometry

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

-Measures multiple parameters: cell size, granularity, and fluorescence intensity

-Examples include studying cellular function, analyzing bacteria, and classifying cancer cells based on unique marker expression.

Polymerase Chain Reaction (PCR)

A lab technique that takes a specific, very small sample of a DNA segment and makes a SHIT TON of exact copies of that sample.(millions - billions)

Bioinformatics

Application of computational and analytical tools to capture and interpret biological data

Essential for managing data in biology

'Omics-based Approaches

Omics being added to a molecular term implies a comprehensive or global assessment of a set of molecules.

Synthetic Biotechnology

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

Usually used to improve human health:

-DNA and RNA synthesis underlie all mRNA vaccines, including those for COVID-19

-Enable cells to be programmed to manufacture medicines or fuel

SARS-CoV-2 genome

Type of coronavirus that caused COVID-19

Enveloped RNA virus with a crown of spike proteins on its surfaced

Spikes bind to ACE2 receptors on host cells, allowing virus to enter and infect cells.

Manipulation Biotechnology

Genetic engineering that uses lab-based technologies to alter the DNA makeup of an organism

May involve changing a single base pair, deleting a region of DNA, or adding an entirely new segment of DNA.

CRISPR-Cas9

First discovered in sequences of DNA from E.coli in 1987(Japan)

Allows researchers to introduce precise changes to DNA sequences within cells. Also, as these changes are permanent, they are inherited by the cells offspring

You needed a Guide RNA (A GPS) and a Cas9 protein, the protein is what actually cuts into the DNA once the guide RNA finds the right spot

Transgenic Animals

Organisms whose genome has been intentionally altered by introducing foreign DNA from another species

Transcriptome

Complete set of all RNA molecules produced in a cell, tissue, or entire program

Captures which genes are actively being turned on and off at a specific moment

Proteome

The entire set of proteins expressed by a genome, cell, tissue, or organism at a specific time under defined conditions.

Who are the species supervisors at the farm?

Kelly - Cattle, Emma - Horses, Rebecca - Small Ruminants(sheeps and goats), Ana/Anastasis - Pigs

What terminologies are used for Cattle

Bull(Mature Male), Cow(Mature Female), Heifer (Immature Female), Steer (Castrated Male), Calf(Newborn)

What terminologies are used for swine(pigs)

Boar(Mature Male), Sow(Mature Female), Gilt(immature female), barrow (castrated male), piglet(newborn)

What terminologies are used for Sheep

Ram(Mature male), Ewe(mature female), Lamb (newborn)

What terminologies are used for Goats

Buck (Mature male), Doe(Mature Female), Kid(newborn)

What terminologies are used for horses

Stallion (Mature male), Mare (mature female), Colt (immature male), Gelding (castrated male), foal(newborn)

Parturition

The general physiological act of giving birth

Animal Identification Methods

Ear notching, Tattoos, RFID/EID Tags

Ear Notching

Primarily used in swine production to identify litter number and individual swine number

Tattoos

Applied inside the ear for cattle, goats, and swine, or the upper lip for horses. Stands as a permanent record-keeper

RFID/EID Tags:

Electronic ear tags used for automated tracking of individual animal data, health, and weight updates

Gestation:

Period of pregnancy from conception to birth

Sire and Dam:

The paternal and maternal parents of an animal, respectively

Polled:

An animal that is naturally or genetically born without horns

Freshening:

A dairy-specific term referring to a cow coming into milk production immediately after calving