Bio exam 3

biotechnology

aimed at cleaning up pollution in industrial and household settings, the specific approach depends on the conditions of the pollution

metagenomics

studies microbe populations in situ. microbes are increasingly discovered in extreme environments and many are resistant to culture

x% of microbes have been studied

0.1-1%

function dependent

studies environmental mRNA, expression screening, phage biopanning

sequence dependent

studies environmental DNA, DNA microarrays, FISH, integron analysis, phylogenic anchors, PCR

Bioremediation

the use of microbes to clean contaminated water and soil

persistent organic pollutants

difficult to eliminate from environment, do not biodegrade quickly or easily, tendency to concentrate over time

indigenous organisms

present in environment with the natural ability to break down POPs, assumed to have adapted to existing contaminants, population size positively correlated to decomposition rates

modified organisms

inserting metabolic pathway genes to achieve same effect, first GMO patented was an oil degrading microbe, stacked traits introduce multiple genes

biostimulation

adds nutrients to increase organism growth and metabolism

bioventing

adds oxygen to increase organism growth and metabolism

microsomes

stimulated version of polluted site, used to characterize the contaminated site and determine the best method of bioremediation

metal recycling

captures metallic waste produced by industry, prevents release from environment and reduces operation costs

in situ bioremediation

on site cleanup, preferred method as more area can be treated at one time and by using indigenous microbes

ex situ bioremediation

off site cleanup, contaminated soil or water is removed, treated, and returned. more expensive and time consuming, may be necessary for rocky terrains or densely packed earth

aquatic bioremediation

natural and man-made require bioremediation, waste water, municipal sewage, home septic, and ground water

aerobic microbes

surface water and soils

anaerobic microbes

deeper soil layers/POPs

bioaugmentation

adds “seed” microbes to enhance bioremediation, may be GM microbes designed for specific treatment

phytoremediation

uses plants, for surface soil layers and air, plants uptake POPs and become hazardous material

mycoremediation

uses fungi, for deeper soil layers

sources of pollution

organic compounds, heavy metals, radiation

alternative fuel sources

a method of indirect conservation biotechnology to promote sustainable resources

methane

anaerobic decomposition of organic waste produces methane which can be used to produce electricity. is common in industrial facilities

microbial fuel cells

anaerobic microbes with oxidative metabolism are called electrogens, common to sediment beneath open bodies of water. generate electrons which are captured by electrodes to produce energy

biodiesel

harvested oil from algae, soy, sunflower, or canola. GM species increase oil production

ethanol

byproduct of fermentation, is currently added to gasoline. GMO microbes may aid in fermentation

challenges of alternative fuel

not enough biomass at present in US, other alternatives will be used in conjunction to meet US fuel demands

genebanks

storage of genetic information as many species as possible through seedbanks which can store tissues, pollens, frozen depositories, or genomic projects

superfund sites

EPA designated superfund site, clean up contaminated areas, often abandoned industrial sites, potentially redevelop land

targeted clean up sites

landfills, chemical spills, wastewater treatment facilities, industrial and military sites, groundwater contamination, pesticide/other runoff, farming operations, mining sites, radioactive releases

Bacillus Thuringiensis

acts as a natural biological control, produces an insect toxin known as cry protein, non GM BT often used as an insecticide in organic farming

enhanced nutrition

designed to combat nutrition, ex golden rice

biofortification

engineering GM crops for improved vitamin or nutrient content such as iron, protein, zinc, vitamins E and A

challenged of enhanced nutrition

logistics and regulation

transfection

insertion of transgenes into plant or animal species which randomly inserts into the genome

targeted transfection methods

consistently high expression created a need for development of these methods

constitutive promotors

always on

inducible promotors

switched on/off by environmental conditions

transfection requires the insertion of

transgenes, promotor, selectable marker

most common selectable marker

antibiotic resistance gene, often removed after confirmation of transfection success

Cre/lox P

system to remove selectable markers due to concerns over outcrossing of antibiotic resistance genes, a recombinase enzyme specifically recognizes a DNA region known as lox P

biolistics

particle bombardment via gene gun, shoots gold or tungsten particles coated with transgene construct into plant tissues

monoculture

cultivation of a single crop in a given area, favors traits like herbicide and insecticide resistance

herbicide resistance

monoculture uses no-till methods that encourage weeds, herbicides combat weed growth so insertion of herbicide resistance genes allow crop dusting with herbicides without harming GM crops

insecticide resistance

BT success as insecticide led to GM crop varieties, unrealized potential to reduce pesticide application

stress tolerance

bioprospecting of plants in harsh conditions reveals novel genes for survival, genes encoding trehalose sugars confer drought/salinity resistance

pathogen resistance

pathogens can destroy crops and are responsible for millions of dollars in damage, plants transfected with genes for pathogen resistance like RNA interference for viral pathogens

aquaculture

used since 6000 BC, controlled production of seafood and its products for medically valuable bioactive compounds

GM salmon

express growth hormone transgenes, antifreeze gene allows aquaculture in lower temperature

genetically engineered livestock

no approved GM livestock to date, research focused on macromolecule synthesis pathways ex cysteine

forensics

biotechnology of law, DNA has advantage of nearly 100% positive ID

forensic DNA testing methods

genomic and bioinformatics used in DNA databases to link information among agencies, bioethical concern over genetic privacy versus improved efficiency

genetic markers

approx 0.1-1% of genome, PCR amplifies small or degraded DNA samples, focus on RFLPs and STRs

DNA fingerprinting/profiling

identifies DNA polymorphisms unique to each individual, combination of genetic markers in DNA comprise to a genetic profile or fingerprint

southern blot

compares and detects RFLPs, size comparisons provide relative length

multiple locus probing

combines several enzymes, high power of discrimination, technical and interpretational difficulties, DNA fingerprinting

single locus probing

lower power of discrimination, DNA profiling

PCR

used to increase DNA sample size to analyze STRs and SNPs, used with lower quantity samples, replaced RFLP methods

flanking regions of STRs

highly conserved, not variable

PCR primers

complementary to flanking regions, 18-24 bp, 40-60% G/C content, start and end with 1-2 G/C pairs, Tm of 50-60, each pair has a Tm within 5 of each other, pairs should not have complementary regions

multiplex PCR

adds several primers to identify multiple STRs in one reaction

Exclusivity

blood typing and fingerprinting typically rule out individuals as sample contributors, DNA analysis positively identifies, more difficult among related individuals

Probability

places numerical value on certainty, DNA compared to reference databases, determines random match probability

Biodefense

improvement of national security through biotechnology

Mass fatality identification system software

world trade center victim identification, DNA Shoah for holocaust victims, tomb of unknown soldier remains

Biowarfare

biologically active weapons, may attack human population directly or indirectly through food supply, often a fear tactic

prevention

several federal agencies monitor biowarfare threats and use detection through biosensors

biosensors

detect biologically active presence such as viruses or toxins, customizable, use nanoparticles such as metallic magnets that attract targets and results in outward warning display

physicochemical component

identifies unique chemical reactions

biological component

often antibodies