ANIMAL BIOTECH Transgenic animals: have a transgene (foreign gene which is stably present in their chromosomes and sex

cells and can be

passed on to offspring). Applications: disease research, economics/quality of life (increase production/decrease costs, healthier animals, more
nutritious food, disease-resistant animals, wool quality. TRANSGENIC COWS: collect eggs from slaughterhouse, egg maturation in vitro, fertilization
in vitro, centrifugation of eggs to clear yolk & see pronuclei, microinject DNA into pronucleus, develop embryos to blastula stage, screen cells for
foreign gene using PCR, implant embryos into surrogate, birth calves. Benefits: altered milk content (increase protein, remove lactose; +milk
production, disease resistance, economic benefit (faster growth, eat less, less fat/cholesterol). TRANSGENIC PIGS: xenotransplantation: use of animal
organs/cells in human patients; inexpensive and have similar organ size to humans. Achieved by Microinjection: ID foreign gene of interest, insert
foreign gene into appropriate vector, microinject DNA into pronucleus of fertilized egg, implant fert. egg into surrogate mother, develop embryo, see
that gene has been transferred/is heritable, and is expressed correctly in host. Goals: livestock – products in milk (human proteins), increased
growth rate, milk/meat quality, disease resistance, animal clones. PATENTING GEN. ENG. ANIMALS controversy over patenting animals –
environmental implications, welfare of animal, ethics of changing evolution, smaller farms vs. factory farms, who can afford it ANIMAL PROPOGATION
artificial insemination  genetically desirable animals bred more efficiently, used to increase gen. diversity of endangered animals in zoos
EMBRYONIC CLONING prize cow has embryo sired by prize bull/donor cow is source of unfertilized eggs, cells are removed from embryo/nuclei are
removed from donor eggs by microsurgery, cell fusion is used to insert nucleus from embryo into egg, eggs are implanted in surrogate mother and
extras are frozen in liquid N for later use EMBRYONIC CLONING embryo is split to form two half-embryos, embryos transferred to an unrelated
surrogate mother, pregnancy is monitored by ultrasound and sheep has identical twins MARINE BIOTECH tools that use living marine
organisms/their parts to make/modify products, improve plants/animals, or develop microorganisms for specific uses…provides opportunities for
improvement of the health of cultivated aquatic organisms and prevent transfer of diseases from cultivated and wild stocks. New frontier, valuable
gene pool; includes secondary compounds (metabolites) for medical research, pharmaceuticals, therapeutics. Must: control pollution, protect
endangered species, understand links between plankton & other organisms. AQUACULTURE/MARICULTURE cultivating aquatic animals/plants at high
densities in fresh, brackish, or saltwater…growing more rapidly than all other food producing sectors. Is destructive, high densities of animals
increase disease  loss of product. Products include food, pharmaceuticals/meds, jewelry, fish for aquariums. Benefits  early detection of diseases
(diagnostics), understanding susceptibility to disease/pathogens, dev./app of new antibiotics/vaccines and pathogen-free stocks. ALGAL PRODUCTS
diverse group of eukaryotes used throughout the world for various products including food. Types: microalgae and macroalgae (more important, 3
groups – green Chlorophyta, red Rhodophyta, brown Phaeophyta). Alginates are the main structureal components of the cell wall & intercellular
matrix of brown seaweeds, used as food thickeners/stabilizers & to retain moisture in frozen foods. Fuels from algae: alternative to use of
nonrenewable fossil fuels = biodiesel. Medical value: secondary metabolites are excellent source of new compounds (anti-tumor, antiviral, anti-
inflammatory, enzymatic, insecticidal/herbicidal, antibacterial, anti-cancer)…cyclic peptide Didemnin shows promise as cancer suppresser. PROBING
THE ENVIRONMENT barely scratched the surface…finding new organisms, increase knowledge of life cycles, understand relationships of marine
organisms, use DNA probes and monoclonal antibodies to identify pathogens TRANSGENIC FISH done through direct gene transfer; eggs are large
and transparent, microinjection = easy & straightforward…experiments use antifreeze genes to allow fish to extend habitat range, also production of
human proteins in fish CONSIDERATIONS accidental introduction of engineered species into population where it may destroy/damage environment
GENOMICS & BEYOND study of an organism’s complete genome; DNA mapping and sequencing. Genome = housed in nucleus and mitochondria,
each person has 1 (plants have 3; extra in chloroplasts), study began in 1990s. Karyotyping: visual mapping of all the chromosomes HUMAN GENOME
PROJECT international research effort to map out all genes in the human genome…like 200 telephone books with 1000 pages each. Goals of the
project: generate new maps to help locate genes found in diseases, complete genome sequence by 2005 (done in 2000 at lower cost), develop new
methods/tools for DNA sequencing, study of gene expression, field of bioinformatics, establishment and management of informational databases.
Applications: molecular medicine (improved diagnosis/treatment, new research areas), increase understanding of human evolution/development, can
be used in forensic identification. First draft in 2000; it was publicly sponsored by NIH and DOE and privately sponsored by Celera Genomics.
FINDINGS: human genome contains a little over 3 billion base pairs, # of genes found was less than 1/3 the expected number, genes aren’t evenly
distributed across a chromosome but concentrated at random regions, Y chromosome has fewest genes (231) and chromosome 1 has the most
(2968), 200 genes originate from bacteria, nucleotide sequence in all humans is 99.9% identical (differences = result of population not race).
ETHICAL, LEGAL, & SOCIAL ISSUES how to ensure fairness in use of info by insurers, employers, court, schools, adoption agencies & the military
among others? Who should have access and how will it be used? How to enforce privacy? Who owns and controls the information? Should testing be
performed when no treatment is available? COMPARATIVE GENOMICS Human Genome differs from others: genomes of other organisms are more
uniform, humans have 3x as many types of proteins, much greater proportion of repeated sequences (50%), humans have stopped accumulating
repeated DNA FUNCTIONAL GENOMICS study of various genes in the genome and their functions…currently investigating exact location of all genes,
regulation of genes, roles of non-coding DNA, what genes play a role in different multi-gene diseases. Proteomes and proteomics: proteome consists
of all proteins in a cell; proteomics is the study of proteins encoded by the genome and encompasses several aspects (expression and identification
of proteins in a given cell, structure of proteins, protein interactions). OTHER “-OMES” Transcriptome: full complement of expressed genes (RNA) in a
cell. Metabolome: all the metabolites within metabolic pathways of a cell. Interactome: all the molecular interactions in cells, indicates biological
complexity of organism. Phenome: all phenotypes (physical characteristics) expressed by cell, tissue, organ, species. PHARMACOGENOMICS new
discipline that studies how the genome is affected by and interacts with different drugs (personalized medicine, reduction in side effects [more
effective drugs], advanced screening for disease, improvement in drug discovery and speed of approval, decrease in health care costs).
BIOINFORMATICS discipline that deals with biology, computer science, and information technology; computers organize, catalog, and store sequence
data and info, gather and analyze data; databases play a large role in bioinformatics (computerized body of data that allows someone to retrieve
specific information) Goals: develop tools that allows for efficient access and management of databases, analysis and interpretation of generated
DNA and protein sequences, develop new algorithms (mathematical computations) and other tools for utilization and manipulation of data. DNA
PROFILING, FINGERPRINTING, FORENSICS ETC. DNA FINGERPRINTING method used by scientists to distinguish between individuals of the same
species using only samples of their DNA; invented in 1985 by Dr. Alec Jeffreys; identifies individuals by DNA banding patterns. Tests for 13
preselected traits (codons) and try to match them up according to parent traits. It’s useful for paternity disputes, immigration investigations, and
forensics…uses the 1%-.1% of unique DNA to generate a unique fingerprint or ID tag for an individual. Today we use DNA to analyze ancient DNA
samples (Dead Sea scrolls, extinct animals). Satellite DNA: fraction of DNA that banded out at a different place from the rest of the DNA during
ultracentrifugation of genomic DNA, only found in eukaryotic organisms, it is repetitive. Divided into 2 major classes (tandemly repeated sequences
– end to end [10% of genome], and interspersed repetitive DNA [5-20% of the genome]). Gel electrophoresis. MICROSATELLITES: short tandem
repeats with the highest rate of variation in copy number among individuals, used in familial studies. MINISATELLITES: located near the end of
chromosomes and vary due to intra-molecular or inter-allelic recombination, used to detect length polymorphisms scattered throughout a genome,
generating multilocus profiles. MACROSATELLITES: located near the centromeres and telomeres (ends), very large DNA sequences and usually
require a special type of electrophoreses for separation, not used in forensic analysis bc are very subject to breakage. POPULATION GENETICS AND
ALLELES Locus: physical location of a DNA sequence. Allele: alternative forms of a locus. Each human individual has 2 alleles per locus…many
alleles exist in a population, max. is twice the number of people in that population. When the frequency with which a combination of banding
patterns occurs is estimated to exceed the frequency found in the population, the evidence is overwhelming that the pattern is individualistic;
therefore DNA profiling is an important and powerful identification tool. MULTILOCUS MINISATELLITE VNTR (Variable number of tandem
repeates) probes have been useful in producing individualized DNA fingerprints in a wide variety of species; multilocus fingerprints are more
difficult to interpret than single-locus banding patterns because of the large number of bonds usually generated, the incomplete cutting of the DNA,
DNA degradation…despite problems it has been used successfully. SINGLE-LOCUS VNTR FOR STR (short tandem repeats, microsatellites)
generate only 1 or 2 DNA fragments (one band for each allele)…simple banding pattern, easier to compare. But the more loci used, the more useful
the analysis. TECHNICAL CONSIDERATIONS standardization of methods of DNA fingerprinting ensures reproducibility of results. To do this, it is
necessary to be sure to preserve the integrity of the DNA, completely digest it with restriction enzymes, standardize hybridizations, and select the
appropriate probes…errors occur through sample contamination, DNA degradation, difficulties interpreting bands on X-ray film or misinterpretation
of a match. EXAM 2 QUESTIONS 1. Two tools that genetic engineers use to clone DNA are restriction endonucleases and DNA ligase. 2.
Transformation is the transfer of DNA into host cells. 3. An example of a secondary metabolite is an antibiotic. 7. The scientific name of the
bacterium that produces pesticides is Bacillus thuringiensis. 8. Phytoremediation is the use of plants to clean up pollutants. 9. Callus:
undifferentiated cells that can give rise to all plant tissues. Somatic embryoids: used for artificial seeds. Somaclonal variation: a method to generate
different characteristics during plant tissue culture. Agrobacterium tumefaciens: used to transform plant cells by use of tumors. Auxin: one of the
plant growth hormones used in tissue culture. 10. Genetically engineered mice…transforming them using embryonic stem cells: insert donor
embryonic stem cell into blastocyst, implant blastocyst into surrogate mother mouse, grows the mouse. 11. POLYMERASE CHAIN REACTIONS can
only occur with the following in the test tube: template DNA, 2 DNA primers, nucleotides, DNA polymerase, thermocycler to heat it. Applications:
genetic typing (amplifying certain DNA to compare between species); ancient DNA studies/studying evolutionary relationships. 12. Micropropogation
is the culturing of plants in sterile conditions. 17. Protoplasts are plant cells minus the cell wall. 18. WHERE TO INSERT GENE IN PLASMID
VECTOR? 19. The chemical method of cell transformation involves salt and heat shock. 20. A micromanipulator is part of a microscope controlled
by knobs, which holds cells in place so they aren’t shaken during microinjection. 23. THE BIG SIX: virus resistance, altered oil content, pollen
control, delayed ripening, pest resistance, herbicide resistance (genetically engineered plant traits). 24. Bactillus thuringiensis: soil-dwelling
bacterium that produces crystals of Bt insecticide, which form in the midgut of the larvae/bugs that ingest it. Electroporation: transformation method
involving an electrical pulse sent through the cell to destabilize the membrane/open the cell so the DNA goes inside. Preimplantation genetic
diagnosis: screening preimplantation embryos for genetic diseases before the embryo transfers to the uterus. Totipotent: ability of a single cell to
divide and produce all the differentiated cells in an organism. Single cell protein (SCP): protein extracted from a monoculture of organisms grown in
large amounts…they have many essential amino acids which can help people with deficiencies. Biodiesel: fuel made from algae or other natural,
non-fossil fuel sources. 25. Bioreactor: produce enzymes for detergents, & pharmaceuticals.