Kumar part 3

Biomagnification

the process by which a compound (such as a pollutant or pesticide) increases its concentration in the tissues of organisms as it travels up the food chain From him:Increase in the concentration of chemicals (pollutants) in organisms from lower to higher level of food chain.

What is the mechanism of action of Bt toxin?

1. Insect eats Bt crystals and spores. 2. The toxin binds to specific receptors in the gut and the insects stops eating. 3. The crystals cause the gut wall to break down, allowing spores and normal gut bacteria to enter the body. 4. The insect dies as spores and gut bacteria proliferate in the body.

What were the major steps used when these transgenic crops were developed?

Three different methods have been employed to introduce foreign DNA into plant cells: (1) protoplast electroporation (2) bombardment of plant cells with particles coated with DNA encoding the intended insert, (3) transformation with various "disarmed" and modified Agrobacterium tumefaciens Ti plasmids.

Nodulin proteins

- Developing nodules

The common marker genes used in plant transformation.

- β-Glucuronidase -neomycin (aminoglycoside) phosphotransferase II gene -the most common marker OR nptII

the lack of labeling severely

--------limits the ability of the public, the FDA and/or other state or federal agencies to identify unintended health effects, because prospective and retrospective studies would be limited in their ability to assess exposure to GE foods ---limits the ability of FDA and/or the public to hold industry legally accountable for any damages to specific consumers and to seek changes in the regulations and/or statutes and ------both of the above considerations weaken the incentives for developers to perform thorough safety evaluation before marketing GE foods

Disadvantages of bioremediation(5)

-Bioremediation process is slow. (take day to months) -The conditions should be suitable for growth of microbes -Lab strains may not perform in field conditions -Contaminant solubility may be increased leading to greater environmental damage and the possibility of leaching. -A stronger scientific base is required for rational designing of process and success. Case by case study required -Regulation on GMO may restrict the use of genetically engineered strains for bioremediation.

The anammox process: denitrification

-In the first step, under oxygen-limiting conditions, partial nitrification takes place -In the second step, anammox bacteria conserve the energy produced in the anoxic oxidation of ammonium with nitrite for autotrophic growth -Hydrazine is an intermediate in this sequence -Anammox bacteria are ubiquitous, and are found in fresh water, in marine sediments, in the world's open oceans, and in wastewater treatment plants.

Patentability Requirements

-Novel (35 USC § 102) -Prior art -Acts -Useful (35 USC § 101) -Judicial Exceptions -Non-Obvious (35 USC § 103) -Known elements combined using known methods to produce predictable results are typically obvious

Factors affecting biodegradation:

-Physical, (temp , volatility) -chemical (photo degradation abioitic hydrolysis or oxidation) -biological facts (mixed community of microbes, presence of heavy metals )

Advantages of bioremediation(4)

-Usually do not generate super toxic chemicals (as generated during incineration) -Can be used to remediate large area with low pollutant concentrations -No collateral damage to the terated environment. -Cheaper compared to landfill or chemical treatment

United States now _______________, previously was __________

-first-to-file country first-to-invent

Benefits of GM crop includes (4)

-potential to address production constraints such as drought, salinity and pests -to reduce or eliminate the need for pesticides and other agricultural chemicals -to increase yields and reduce post-harvest losses and production costs in small- and large-scale agriculture -and to improve micronutrient content, bioavailability and other nutritional properties of important staple crops

Patenting Inventions: What are fundamental requirements for a process or product to be patentable?

1) It must be novel -it had not existed before 2) it hasn't been previously pateneted, discoveries don't count 3) it must be useful -it provides some sort of benefit to the public 4) it must be able to be replicable by someone in the field

Patenting Inventions: What are fundamental requirements for a process or product to be patentable? (4)

1) It must be novel -it had not existed before 2) it hasn't been previously pateneted, discoveries don't count 3) it must be useful -it provides some sort of benefit to the public 4) it must be able to be replicable by someone in the field

Why genetically modify food?

1. Extended self life: -Tomatoes 2. Efficient food processing: Renin . -The protein rennin is used to coagulate milk in the production of cheese. -Rennin has traditionally been made in the stomachs of calves (costly process) -Now as recombinant protein made in bacterial cultures. This saves time, money, space and animals. 3. Better nutrient composition -Scientists have engineered "golden rice", which has received genes from a daffodil and a bacterium that enable it to make beta-carotene. -This offers some promise in helping to correct a worldwide Vitamin A deficiency. 4. Efficient drug delivery -Inserting genes into plants/animals to produce essential medicine or vaccines. -Called "Biopharming"

Food Biotech. : Q. List the advantages genetically modified (GM) food/crops offer. (4)

1. Extended shelf life 2. Efficient Food processing 3. Better nutrient composition 4. Efficient Drug Delivery

Food Biotech: Federal Agencies like FDA, EPA play an important role in regulation of food and environment. Describe the advantages and having reg. bodies.

Advantages: -know whats in your food and intended efficacy of products - help to define unintended side effects -helps instill regulations that everyone has to follow

Env. Biotech:Which bacteria is the most commonly used for soil bioremediation? A. Pseudomonas B. Staphylococcus C. Streptococcus D. E. coli E. all of the above

A. Pseudomonas

Patent term:

20 years from initial filing date

Patent Infringement

Anyone who makes, uses, offers to sell, or sells any patented invention, within the United States, or imports into the United States any patented invention during the term of the patent therefor, infringes the patent

Env. Biotech: The famous clean up of Alaska oil spill in 1989 used in situ method of bioremediation. It is defined by ---- A. adding microbes to the contaminated environment B. adding nutrient to stimulate the microbial growth already present in contaminated environment C. collecting contaminated samples to remediate in lab D. all of above can be defined as in situ bioremediation E. none of the above

B. adding nutrient to stimulate the microbial growth already present in contaminated environment

Env. Biotech: Bioremediation could be used to? A. attack only pathogenic bacteria B. clear pollutant form the environment C. prevent development of bacterial resistance D. quarantine people with drug resisntance infections E. treat prion disease such as kuru

B. clear pollutant form the environment

Legume Rhizobium symbiosis-Root nodules

Bacteroids inside cells Peribacteroid membranes Leghemoglobin O2 regulator

Env. Biotech: What is the difference between biotransformation and mineralization? Define biomagnification?

Biotransformation is the alteration of a chemical compound by an organism. When the substrate is converted to carbon dioxide, water, or inorganic compounds the process is known as mineralization. Biomagnification is when a compound becomes more concentrated in each link of the food chain.

Plant Biotech: Which of these serve as sensors on the plasma membrane of Agrobacterium to detect plant tissue damage? A. T-DNA B. NPTII C. VirA D. VirD E. acetosyringone

C. VirA

Plant Biotech: Transgenic organism means: A. an organism with all desirable characters B. an organism with a particular mutated gene C. an organism carrying an engineered foreign gene D. a number of mutated characters

C. an organism carrying an engineered foreign gene

Aerobic degradation of benzene

Catechol is a central metabolite in many of the degradation pathways for benzene derivatives. The ring can be cleaved by ortho or meta cleavage pathways. Dioxygenases enzymes are involved. Details of pathways are not required.

Ti plasmid

Cloning region Left and right borders Selective marker(s) - for bacteria - for plants

What is coal made of ?

Coal is made up of aromatic rings fused into different small polycyclic, hydroxyl, quinone, and methyl substituents ---Also contains a variety of sulfur compounds ----Many organisms utilize carbon compounds in coal as substrates and can metabolize the sulfur compound

Plant Biotech: The Agrobacterium does not naturally infect the monocot plants (that includes common cereal crops). Which of the following modifications allows introduction of cloned genes into these plants? A. creating Protoplast and incubation with DNA B. electroporation in protoplast C. Use of gene gun (micro-projectiles) D. All of the above methods can work.

D. All of the above methods can work.

Plant Biotech: Which organism naturally produces a protein with insecticidal activity? A. Bacillus cereus B. Bacillus subtilis C. Bacillus stearothermophilis D. Bacillus thuringiensis E. Escherichia coli

D. Bacillus thuringiensis

Plant Biotech: Bt cotton is A. a cotton variety obtained by crossing two different cotton plants B. a cotton variety brought to US from a Baltic country C. a cotton crop sprayed with a protective insecticide D. a transgenic cotton variety carrying a bacterial toxin

D. a transgenic cotton variety carrying a bacterial toxin

Env. Biotech:which of the following is a challenge in treatment of sewage and waste water? A. to remove chemical with high biological demand B. to remove pathogenic organism C. to remove xenobiotics D. all of the above E. none of the above

D. all of the above

Env. Biotech:The process------ that can be used to extract metal from ore using microbes is called? A. biomineralization B. chemical extraction C. mining D. bioleaching E. biotransformation

D. bioleaching

Persistence

Does not undergo biodegradation in certain environments

Plant Biotech: Why do scientists have to make modified binary vector plasmids instead of using the naturally occurring plasmids present in Agrobacterium? A. natural plasmids in Agrobacterium carry undesirable genes B. natural plasmids in Agrobacterium are very large and hard to manipulate C. natural plasmids in Agrobacterium do not have left and right borders of T-DNA D. all these are reasons for using modified binary vectors E. only A and B are correct answers

E. only A and B are correct answers

The safety of GE foods involves two distinct questions:

First, does the inserted DNA and/or its intended expression product or intended compositional changes raise concerns for nutritional content, toxicity or allergenicity. Second, does the insertion of DNA cause any unintended changes in nutritional content, toxicity or allegenicity -------- by disrupting or altering the function of non-target genes (insertional mutagenesis) or altering the chemical composition of food via interdependent metabolic pathways (pleiotropy).

Concerns with GM food

Food safety (are they safe?) unintended environmental impacts, biodiversity in agriculture trade and the ownership and control of seeds, intellectual property and global food production

Dynamic Population

In natural environment the microbial communities interact with each and may cross feed. The population is dynamic.

Why do scientists remove the naturally occurring genes from the T-DNA region?

In the Ti plasmid used for the cointegrate method, tumor-producing genes are either inactivated or removed; otherwise, transformed plant cells would become tumors, not healthy "transgenic plants."

Patenting Inventions: USA is currently an "application first" country when it comes to granting patents. Explain this statement?

In the United States, patents are awarded to the first to file, and that may not necessarily be the first person to invent. If two people come up with the same invention around the same time, but the first person to come up with the invention did not file before the second person, they may not receive the patent. Before this, whoever could prove that they invented the idea first would be the one to receive the patent. Even though the Constitution says the right goes to the first inventor, courts have since decided to choose a first to file system. the patent belongs to the applicant who was able to file the patent first(first-to-file)

Legume Rhizobium symbiosis- infection

Infection thread forms Bacteria enter into cortical cells and divide Enclosed in peribacterial membranes inside cell Cell division enhanced

=> How microbes are used in plant genetic engineering

Inserting foreign genes into plant cells Pass cell wall and plasma membrane Integration in to chromosomes Electrophoration Particle gun Agrobacterium

Non-Patentable Subject Matter

Judicial Exceptions: Laws of Nature, Products of Nature, Abstract Ideas, Natural Phenomenon

eutrophication

ecosystem's response to the addition of artificial or natural nutrients, mainly phosphates, through detergents, fertilizers, or sewage, to an aquatic system.

Genetic Engineering of plants

Modify genes their own genes Insert different genes from other plants Insert genes from other organisms Silence genes to stop an activity

Food Biotech. : Should FDA mandate the labelling of GMO food, Yes or No? Support your answer giving reasons why?

No, the fact is that right now there is a "panic" in GMO where there shouldn't be. I do like the paper you showed us in class and right there is no reason for the panic. Some fears getting debunked include the potential for gene transfer (even though the genes will get broken down from preparation, stomach acid, etc.), consumption of foreign genes (even though this is already down with cauliflower), Unexpected alteration in nutritional value (even though many test show no nutritional difference and that we can add certain nutrients, like vitamin A in rice, that were not previously there), and toxicity (overall could not be proven with contradicting results). That being said there are TONS of pros, some including extended shelf life, efficient food processing, better nutrirnt composition, and effeicent drug deleivery. Quite frankly, this is something that is good for the world and I think needs to continue. That being said adding the label will only limit the growth because of UNFOUND dears I would still want people to educate and let them know instead of keeping it under wrap just because a common man do not understand the science behind it. One drawback of not labeling is that you cannot keep track of their long term effects on population.

What are organo-halogens

Organohalogen compound, any of a class of organic compounds that contain at least one halogen (fluorine, chlorine, bromine, or iodine) bonded to carbon

Patenting Inventions: What is a patent and what is the title 35 of United States code ?

Patent: Legal monopoly given in exchange for giving up how its made and used Title 35: Sections of US law that covers all aspects of patents

What is petroleum made of ? (chemical composition not the stricture)

Petroleum is made up of Parrfins(30-50%), cycloparffins (20-65%), aromatics (6-14%) [509] -Parrfins include n-heptane, n-hexane, 2-methylpentane and 2,3-dimethylhexane -Cycloparffins include cyclohexane, mthylyclohexane, and trimethylcyclopentane - Major Aromatic components include toluene and benzene

Legume Rhizobium symbiosis- intital interaction

Plant root damage exudes chemicals into soil i.e. Acetosyringone Receptors on Agrobacterium sense them Attracted towards root hair

Name a few environmental contaminants that are organo-halogens

Polychlorobinphenyls(PCBs), dichlorodiphenyltrichloroethans (DDT)

US patents

Provisional and Utility

Recalcitrance

Resists biodegradtion in a variety of enviornments

What is the general structure of Ti plasmid in Agribacterium?***********

The structure of the Ti plasmid, with its vir region and T-DNA. In addition, the plasmid contains an origin of replication and several genes that assist in the colonization of host plants, such as the genes for the enzymes that degrade octopines and nopalines

Role of vir genes ***************

The vir genes of the disarmed plasmid effect the transfer of the T-DNA from the other plasmid without the formation of a cointegrate intermediate mportant for the virulence of the bacterium. The genes in this region are expressed in the bacteria and have been proposed to play an important role in the excision, transfer and perhaps integration of the T-DNA(4).

What is the major obstacle in bringing foreign DNA into plant cells?********

Unfortunately, the Ti plasmid is too large to be conveniently manipulated in vitro. Therefore, the piece of foreign DNA to be cloned is almost always introduced into a smaller vector plasmid first.

Food Biotech. : FDA treats GE foods (as a class) with the legal presumption of being as safe as conventional foods. What are the drawback of this assumption?

This assumption is problematic because the FDA urges those who develop GE foods to utilize "decision trees" to determine if the food is safe. However, these trees only focus on the intended changes to the crop and the presence of known allergens, but does not consider the possibility of unintended changes or new allergens or poisons. This presumption also plays an important part in deciding if the GM food should be labelled and other regulatory aspects.

What are '"particle bombardment" of cloned genes

This technique is most suitable for those plants which hardly regenerate and do not show sufficient response to gene transfer through Agrobacterium for example, rice, wheat corn, sorghum, chickpea and pigeon-pea. it shoots foreign DNA into plant cells or tissue at a very high speed.

Waste water treatment: Problems with waste water treatment:

To remove: -Compounds with a high biochemical oxygen demand - Pathogenic organisms and viruses -A multitude of human-made chemical

Helper plasmid

Vir genes Host specificity genes

Our environment is under threat , there are 2 challenges

Waste generated by Human accumulation / spill of pollutant. Dilution is the best solution for the pollution.... (not possible because of the huge amount)

Plant Biotech: How does insertion of viral coat proteins make the transgenic plants resistant to viral attacks?

When viral coat protein genes are transcribed, the plant cells recognize these genes as 'foreign' or 'aberrant'- incorrect genes. siRNAs are made to silence the genes, and thus are present upon infection of the virus or similar viruses and able to combat infection by preventing translation and expression of viral genes.

U.S. Patents are often called

a monopoly to make use and sell the invention, but an over-generalization

FDA has legal authority to regulate GE foods either under the

adulteration clause (section 402(a)(1) of the Federal Food, Drug and Cosmetic Act, or FDCA) or the food additives clause (section 409) (OSTP, 1986).

in situ and examples(5)

bioremediation relies on the indigenous microbial fauna of subsurface soils and groundwater. -Bioventing -Biostimulation -Biosparging -Bioaugmentation -Natural Attenuation

biodegradable compound

chemicals that are degradable due to biological activity

Mineralization

complete oxidation of any organic compound (conversion in to CO2 and H2O)

At present, the most widely grown GM crops contain new genes that__________________

confer herbicide tolerance or insect resistance.

Gratuitous biodegradation

describes the situation in which an enzyme is able to transform a compound other than its natural substrate

Microbes evolved with immense variety and diversity of organic compounds that can be used for the source of energy. Usually the man -made compounds

difficult to degrade by these natural scavengers (microbes) and can cause environmental problems including pollutions.

Food Biotech: Federal Agencies like FDA, EPA play an important role in regulation of food and environment. Describe the disadvantages and having reg. bodies.(3)

disadvantage: - takes longer -expensive - warnings can instill fear in drug takers****

Ex situ and examples(4)

is a biological process in which excavated soil is placed in a lined above-ground treatment area and aerated following processing to enhance the degradation of organic contaminants by the indigenous microbial population. Land farming Composting Biopiles Bioreactors

What are bacteroids?

is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are nonendospore-forming bacilli, The bacteroids are usually much larger and sometimes have more complex and irregular shapes (e.g., a Y-shape) than the vegetative cells Above all, bacteroids carry out nitrogen fixation, which the vegetative cells cannot do. The bacteroids also carry out oxidation of energy sources supplied by the plant, thus depleting the free oxygen level and so creating favorable conditions for nitrogen fixation.

What are 'electroporation'

is a microbiology technique in which an electrical field is applied to cells in order to increase the permeability of the cell membrane

bio-transformation

is alteration of chemical structure due to biological activity (enzymes/ cells)

What is symbiotic nitrogen fixation?

is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen

Cometabolism

is the ability of an organism to transform a nongrowth substrate as long as a growth substrate or other transformable compound is also present.

Food biotechnology

is the application of technology to modify genes of animals, plants, and microorganisms to create new species which have desired production, marketing, or nutrition related properties.

Environmental biotechnology

is the solving of environmental problems through the application of biotechnology.

Bioremediation

is the use of microbes or plants to clean up hazardous environmental wastes. Two types In situ, ex situ

FDA normally applies the adulteration clause to

regulate the safety of whole foods and

Nod factors

signaling molecules for symbiosis

GM crops include

soybean, maize, cotton, canola, potatoes, and tomatoes.

xenobiotics

substances that are foreign to the body or to an ecological system.

Biological oxygen demand

the amount of dissolved oxygen needed (i. e., demanded) by aerobic biological organisms to break down organic material present in a given water sample at certain temperature over a specific time period.

U.S. Patents give patent holders

the legal right to exclude others from practicing their invention in the U.S.

.Why markers are needed?

the region to be introduced into plants must contain a good marker so that plant cells that have received and integrated the foreign genes can be recognized easily.

Called genetically engineered (GE) or genetically modified (GM) foods

they are a source of an unresolved controversy over the uncertainty of their long-term effects on humans and food chains.

Look at the list of priority pollutants by EPA: they are______

they are volatile organic compounds, chlorinated pesticides, phenols, PCBs.

FDA normally applies the food additive clause to

to regulate the safety of chemical substances (or processes, such as irradiation) added to food to achieve an intended effect.

chemical oxygen demand

used to indirectly measure the amount of organic compounds in water.

FDA treat GE foods (as a class)

with the legal presumption of being as safe as conventional foods and urged GE developers to use the decision trees to assess safety on a case-by-case basis. The weakness in this approach is that the decision trees focus primarily on intended changes and/or the possible presence of known toxicants or allergens, but do not adequately address the possibility of novel or unintended allergens or toxicants.

Role of T-DNA border regions

• The ability of Agrobacterium tumefaciens to transfer the T-DNA portion of the Ti-plasmid to the nuclear genome of plant cells has been extensively used to engineer desirable genes into plants • The T-DNA is flanked by 25-bp imperfect direct repeat sequences called 'borders' which appear to define the portion of the DNA destined for transfer (1, 2,