BIO-214 #6 Artificial Selection & Agriculture

1. What is biotechnology?

2. What were the first uses of biotechnology?

3. How is biotechnology used in modern times?

1. The use of biological agents for technological advancement

2. Used for breeding livestock & crops

3. Modern times

   1. Vaccine & antibiotic production

   2. Agriculture

      • crop genetic modification to increase yeilds

   3. Industrial Applications

      1. Ferminatation

      2. Treating oil spills

      3. Promoting biofuels

1. What are the techniques of manipulating genetic material?

2. what is a lysis buffer? How is it used?

3. What enzymes are used

1. Isolate or extract DNA or RNA from the cells

2. Gel Electrophoresis

3. Nucleic Acid Fragment Amplification by Polymerase Chain Reaction

4. Hybridization, Southern Blotting, & Northern Blotting

1. What is DNA & RNA Extraction

2. What buffer is used for extraction?

3. What enzymes or substances are used? What are their functions?

1. Isolate or extract DNA/RNA from cells to study or manipulate nucleic acids

2. Lysis Buffer: breaks cells apart

   • Breaks apart lipid molecules in the cell & nuclear membranes

3. Enzymes & Subtances

   1. Proteases: break down proteins & inactivates macromolecules

   2. Ribonucleases: break down RNA

   3. Alcohol: precipitates DNA

1. What is Gel Electrophoresis?

2. What does gel electrophoresis separate?

1. Technique used to separate molecules on the basis of size, using their charge

   • Smaller fragments move toward the positive electrode through the gel faster than larger fragments

   • Uses a dye to observe the fragments

2. Separates the nucleic acids as whole chromosomes or fragments

1. What is the Polymerase Chain Reaction (PCR)?

2. What is it used for?

3. What are the steps for PCR?

4. What is reverse transcriptase PCR?

1. PCR is a technique used to amplify specific DNA regionsfor further analysis

2. Uses

   1. Cloning gene fragments to analyze genetic diseases

   2. Identifying contaminant foreign DNA

   3. Amplifying DNA for sequencing

   4. Determining paternity & detecting genetic diseases

3. Steps

   1. Denaturation of DNA at high temp

   2. Annealing (letting DNA cool slowly)

   3. DNA synthesis

4. Reverse Transcriptase PCR

   • PCR technique that involves converting RNA to DNA by reverse transcriptase

   • also called reverse transcriptase

1. What is the blotting technique?

2. What are hybridization, southern blotting, and northern blotting?

   • How are they used?

1. Blotting: transfer fragmented DNA from a cell onto a nylon membrane

2. Definitions

   • Hybridization: identification of a specific DNA segment within a genomic DNA

   • Southern Blotting: DNA transfer from a gel to a nylon membrane

     • Used to detect the presence of certain DNA sequences in a given genome

   • Northern Blotting: transfer RNA to a nylon membrane

     • used to detect gene expression

1. What does reproductive cloning mean in biology?

2. What is molecular cloning?

3. How does cloning genome fragments help researchers?

1. The recreation of a whole organism

2. Molecular Cloning: Reproduce desired regions/fragments of the genome

3. Cloning Applications

   • Allows researchers to manipulate & study:

     1. Specific genes

     2. Their protein producuts

     3. noncoding regions

1. What is a plasmid/vector?

2. How are plasmids used in cloning?

3. What plasmid vector structure is essential for cloning?

4. What is a restriction endonuclease?

5. What does DNA ligase do?

1. Plasmid: small circular DNA molecule that replicates independently of the chromosomal DNA

2. Plasmids are used to transfer foreign DNA into a cell

   • Used for the large-scale production of important reagents: insulin & human growth hormone

3. Special plasmid feature: Multiple cloning site (MCS)

   • short DNA sequence containing multiple sites that different restriction enzymes can cut

4. Restriction endonuclease: enzyme that can recognize and cleave specific DNA sequences

   • naturally produced as a defense mechanism against foreign DNA

   • “sticky ends: complementary overhangs

5. DNA ligase: permanently joins the DNA fragments

What is antibiotic resistance?

The ability of an organism to be unaffected by an antibiotic’s actions

1. What are recombinant DNA molecules?

2. What’s another name for recombinant DNA?

3. What are recombinant proteins?

1. Recombinant DNA molecules: artificially created plasmids with foreign DNA

2. Chimeric molecules: Recombinant DNA

   • The origin of different molecule parts come from different species

3. Recombinant proteins: proteins that are expressed from recombinant DNA

What is cellular cloning?

• Production of identical cell populations by binary fission (asexual reproduction)

• Used by uncellular organisms (bacteria & yeast)

• Occurs via mitosis (identical daughter cells)

1. What is parthenogenesis?

2. Give examples

1. an asexual reproduction in which a female can produce an embryo without fertilizing an egg with sperm

2. Examples

   • A female lays an egg

     • Fertilized egg: Diploid → develops into a female

     • Unfertilized egg: remains a haploid egg → develops into a male

       • virgin egg

   • sea stars, fish, snakes

1. What is an enucleated egg?

2. What is somatic cell nuclear transfer? What is it used for?

3. How does somatic cell nuclear transfer work?

• Enucleated egg: egg cell that had its nucleus removed

• Somatic cell nuclear transfer:

  • Technique of transferring a diploid nucleus into an enucleated egg

  • Application

    • Therapeutic cloning

    • Reproductive cloning

• Process: diagram

1. What is Genetic Engineering?

2. What technique is used for genetic engineering?

3. What is a genetically modified organism?

4. What is a transgenic organism?

1. Genetic Engineering

   • The alteration of an organism’s genotype using recombinant technology to modify an organism’s DNA to achieve desirable traits

2. Technique: molecular cloning

   • adding foreign DNA in the form of recombinant DNA vectors/plasmids

3. GMO: receives the recombinant DNA

4. Transgenic organism: an organism with foreign DNA

1. What is reverse genetics?

2. What is the classical genetic method?

3. How does mutating/deleting genes help researchers?

4. What is gene targeting?

1. Reverse Genetics: find out what phenotypes are controlled by particular genetic sequences

   • Similar to damaging a body part to determine its function

     

2. Classical Genetic Method: find the genetic basis of a phenotype/trait

3. Mutations

   • Provides with clues about the mutated/deleted gene function

4. Gene Targeting

   • Use of recombinant DNA vectors to alter a particular gene’s expression

     1. Introducing mutations in a gene

     2. Eliminating a gene’s expression (deleting a part/all of the gene sequence from an organism’s genome)

What are the applications of biotechnology in agriculture?

1. Disease resistance

2. Insect resistance

3. Herbecide resistance

4. Environmental stress

   1. Drought tolerance

   2. Hardiness (cold tolerant)

5. Improve crop yield & quality

6. Better nutritional value

1. What is genetic diagnosis?

2. What is genetic testing?

3. What is gene therapy?

4. How does gene therapy work?

1. Genetic diagnosis

   • Diagnosis of the potential for disease development by analyzing disease-causing genes

2. Genetic Testing

   • Process of testing for the presence of disease-causing genes

3. Gene therapy

   • Genetic engineering technique used to cure inheritable diseases by replacing mutant genes with good genes

4. Gene therapy process

   • good gene is introduced to diseased cells as part of a vector transmitted by a virus that can infect the host cell & deliver the foreign DNA

   • Tries to correct the mutation at the original site in the genome

What are the traditional vaccination strategies?

• Use weaked or inactive forms of microorganisms to mount the initial immune response

• Genes of microorganisms are cloned into vectors to mass-produce the desired antigen

1. What are antibiotics?

2. Which organisms produce them?

• Biotechnological product to fight bacterial infections

• Micoorganisms

  • Fungi: Naturally produce them to attain an advantage over bacterial populations

  • cultivating & manipulating fungal cells produce antibodies

1. How was insulin first produced?

2. How was human growth hormone (HGH) created?

1. Insulin production: using reecombinant DNA tech

2. HGH: cloned from a cDNA libray & inserted into E.coli by cloning it into a bacterial vector

1. What are transgenetic animals?

2. How does the government monitor transgenetic plants?

1. Animals that have been modified to express recombinant DNA

2. Government regulation

   1. Fit for human consumption

   2. Don’t endanger other plant & animal life

   3. Extensive testing for ecological stability (foreign genes can spread to other species in the environment)

1. How do plants use Agrobacterium tumefaciens to transform?

2. How does the bacterium affect the plant?

3. Is artificially introducing DNA into plant cells more or less challenging than in animal cells?

• The bacterium Agrobacterium tumefaciens causes tumors by DNA transfer (from bacterium to plant)

• Tumors student the plants → plants become more susceptible to harsh environmental conditions

• More challenging to introduce DNA into plant cells

  • Thick plant cell wal

1. What are Ti plasmids?

2. What do these plasmids carry?

• Ti plasmids: Tumor-inducing plasmids that are derived from Agrobacterium tumefaciens & used to introduce foreign DNA into plant cells

• Carry antibiotic resistance genes to aid selection

1. What was the organic insecticide called?

2. How does the insecticide work?

• Bacillus thuriengsis

• Produces protein crystals during sporulation that are toxic to many insect species that affect plants

  • insects need to ingest Bt toxin to DIE

1. What is a proteome?

2. What is proteomics?

3. Even though all multicellular organisms’ cells have the same set of genes, the set of ________ produced in different tissues is different and dependent on ________ expression.

4. If the genome is constant, is the proteome the same?

1. Proteome: the entire set of proteins that a cell type produces

2. Proteomics: study of proteome’s function

   • Identify/compare the proteins expressed from a given genome under specific conditions→ study those interactions between proteins & use that info to predict cell behavior/develop drug targets

3. Fill in blank:

   • proteins, gene

4. No, the proteome is NOT the same, it varies

   • RNA can be alternately spliced & many proteins modify themselves after translation

     

1. What is metabolmics?

2. What is a metabolome?

1. Metabolomics: study of small molecule metabolites in an organism

   

   • Compares genetic makeup & physical characteristics

   • Compares genetic makeup & environmental factors

2. Metabolome: a complete set of metabolites that are related to an organism’s genetic makeup

   • Identify, quantify, & catalogue all the metabolites in living organisms’ tissues & fluids

1. What is the basic technique for protein analysis?

2. What technique allows scientists to determine a protein’s 3D structure?

3. What is nuclear magnetic resonance?

• Mass spectrometry

  • Identifies and determines a molecule’s characteristics

• X-ray crystallography

• Nuclear Magnetic Resonance (NMR)

  • uses atom's’ magnetic properties to determine a protein’s 3D structure in aq solns

1. What is systems biology?

2. How are proteomes used in systems biology?

3. What do pharmaceutical drug trials target?

• study of whole biological systems (genomes & proteomes) based on interactions within the system

• Proteomes

  • used to compare the protein profiles of different cells to identify proteins & genes involved in disease processes because proteins are direct products of genes & reflect activity at the genomic level

• They target proteins

  • info from proteomics → identify novel drugs → understand protein mechanism of function

1. How do researchers use proteins when detecting cancer?

2. What is a biomarker?

3. What is a protein signature?

4. How much can biomarker/protein signatures be detected?

5. How are biomarkers/protein signatures inaccurate?

• They identify proteins (a biomarker) whose expression indicates the disease process

• Biomarker: individual protein that is uniquely produced in a diseased state

• Protein signature: set of proteins with altered expression (in the diseased state)

• Biomarker/protein signature must be secreted in body fluids (sweat, blood, or urine) (of non-invasive screening)

• They produce a high rate of false negatives (cancer goes undetected)

  • Test should’ve been positive

Why is implementing proteomic analysis difficult?

Difficult to detect small protein quantities

What is artificial selection?

• Intentional human modification of species over many generations by selecing & breeding individuals that posses desirable traits

What traits do humans modify in animals?

1. Muscle Mass

2. Milk production

3. Growth rate

4. Intelligence

5. Number of eggs

6. Amount of feathers

7. Behavioral conditions

8. Health Conditions

What traits do humans breed in plants and animals?

1. Hardiness

   • Tolerates extreme weather

2. Temperament

   • behavior (cattle)

3. Aesthetics

   • Gardening

4. Shape

5. Size

6. Harvest yield

   1. Producing more fruit

   2. Larger grains

7. Flavor

   • spiciness

   • Sweetness

8. Health

   • tolerance to dieases & molds

Examples of artifiical selection on livestock

1. Sheep

2. Horses

3. Goat

4. Cows

5. Chickens

1. What traits are pets bred for?

2. What are the consequences of breeding pets?

• Traits

  1. Behavior

     • Protection

     • Muscle Mass

  2. Eye color

  3. Claws

  4. Hunting

  5. Farming: guarding, herding

  6. Companionship

• Consequences

  1. Health outcomes

  2. Recessive mutations are being expressed

     • Some genes are linked and, when expressed, cause detrimental health outcomes

Artifiical selected traits for gardening plants

1. Shape

2. Size

3. Hardiness

4. Leaf strips

5. Color

6. Size of flower cluster

7. Thorns

8. Stems

   • longer, straighter, stronger

• Flower perfume/smell isn’t potent

Difference between GMOs and trangenetic organisms

• GMOS

  • faster results than artificial selection (application of both genetics and technology

  • contains genes from a naturally occurring gene pool selected by genesis for specific traits

• Transgenic organisms

  • artificially added foreign genes from a different species in a lab

  • “trans”: across (genes are travelling across species)

  • Ex: adding biolumeniscience gene to mice & rabbits

    

Chimeric vs trangenic organisms

Concerns about GMOS

1. Are they safe?

   1. For humans?

      • Increasing essential nutrients (K⁺, minerals, protein, etc)

        • golden rice for

      • Safe for people, the environment, and getting plentiful nutrients

   2. For the environment?

      • RoundUp Ready pesticides & herbicides

2. Are there GMOS in this product?

   • labeling/ingredient list

3. What about human GMOs?

   • Gene therapy

What’s the big deal about RoundUp Ready?

• Created a genetic strain that secreted pesticides & herbicides into their tissues & soils

• The wind dispersed GMO seeds & their pollen ended up to wild habitats

  • Ecological damage

  • Farming damage

How is gene therapy used in humans/application of GMOs in humans?

• Aims to fix a faulty gene or replace it with a healthy gene to cure a disease

  • Turn off genes that cause Alzheimer’s, Parkinson’s disease, cancers, etc

• Create essential neurotransmitters & hormones

  1. Testestorone

  2. Serotonin

  3. Insulin

  4. Oxytocin

  5. Esterogen

1. How much do Californian farms produce?

2. What agricultural products are produced only in California?

3. How is California ranked among dairy production?

1. Californian farms produce nearly half of vegetables, fruits, & nuts grown in the USA

2. Almonds, artichokes, olives, walnuts, & figs

3. Ranked first in dairy production

1. What is Land Conversion?

2. What factors drive land conversion?

1. Land Conversion

   • development & conversion of farmland to urban use

2. Land conversion factors

   • Rising populations

   • Higher land prices (places pressure on farmland)

What challenges do farmers face?

1. Increased willingness to sell off family farms

   • Children want to pursue other careers

   • Farming is less profitable

2. Significant losses in prime farmland (1982-2007) but has since stabilized

   1. Planners advocating for higher density residential areas

   2. Agricultural conservation easements

   3. Novel financing arrangements to help farmers keep their land

Water Use

1. How much water does agriculture use?

2. Where are Californian farms located?

3. How do these farms access water?

4. How are farms being supported?

1. 50-90% of California’s fresh water

2. Farms & ranch land located in the drier Southern hlaf of the state

3. A high percentage of water used in these southern farms is conveyed via aqueducts & dams from the north

4. Support via:

   • Federal government

   • Water subsidies that benefit large industrial growers

1. What are the ecological concerns about agricultural water use?

   • What effect does water use have during the dry season?

2. How does agricultural water contaminate neighboring ecosystems?

1. Coastal summer agricultural water needs are met by tapping riparian and groundwater resources

   • Decreases stream flow during dry season

2. Surface water by surface runoff of fertilizer & pesticides contaminate aquatic life

   • Can also enter ground water & degrades sources of drinking water

How can we practice sustainable agriculture?

• Supply & maintain open space

• Refuge for wildlife

  • letting the land rest from heavy agricultural usage

  • Soil can recupriate nutrients

  • Wildlife will return nutrients to farms

• Possibility of locally based food systems

• Buy local to reduce our carbon footprint

How does sustainable agriculture integrate three main goals from traditional agriculture?

1. Environmental health

2. Economic profitability

3. Social/economic equity

What approaches does sustainable agriculture use?

1. Selection of species & varieties well suited to the site

   • Climate & crop hardiness

   • Seasonal crop rotation

   • Native pollinators & nutrient turnover

2. Diversification of crops (including livestock)

3. Management of the soil to protect & enhance its quality

4. Efficient & humane use of animals

5. Consideration of farmers’ goals & lifestyle choices