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Biotechnology

91607Demonstrate understanding of human manipulations of genetic transfer and its biological implications


Introduction to the standard and key words list



A super amazing (it really is) place to start.

This assessment could be run as a research task by your teachers so the content will only be provided to understand the concepts around the standard. The main idea is that you will be looking at two biological manipulations (that's something that us humans have done directly to a genome of an animal or plant) and linking this to multiple implications for THAT organism. Remember this standard is not about the human implications and only how it affects the organism or populations. Make sure you build a good understanding as whatever you do will have to be from your own perspective/ words.  The big idea for 91607 is on how humans are potentially impacting on and changing the rate and direction of the evolution of populations so make sure you focus on this during your research/ classroom learning.

You will need to know about the following topics before doing your assessment. Down the bottom of the page many of these are covered.
  • basic principles of gene expression, gene technology, genetic engineering and genetic modification
  • techniques used in gene technology, e.g. restriction enzymes, ligation, polymerase chain reaction, electrophoresis, tissue culture, DNA sequencing.

As biological knowledge and techniques have developed the actual processes used change. When you are researching you have to try to sort out what techniques have been used in the past and what are being used now. Usually the longer a process has been used the more automated it becomes. Another change, for example, is that when the sequence of a gene becomes known the gene can be produced rather than isolated from the genes in an organism.

When researching on the internet it is important to look at the age of the info you are reading.....one way is to use the dates of any material being referenced and a second is to look at the last date the info was updated. eg look at this site which contains good basic info about how the processes used to be carried out Transgenic crops
Look at the dates of referenced material - 1997, 1998, 1999, and last updated says "March 11, 2004"(from studyit.org ST5)


What is biotechnology?

Click on the picture top right to see all the areas Biotechnology now covers.

Watch this video for a general introduction, the second video goes into more biological detail and is a good watch (compared to some boring classroom videos..).



Starter resources


Also read the following page from the Biotechnology learning hub Link

Yes, its Australian but a good starter site.

An excellent Powerpoint from I think TGHS.

Interactive terms




term

Link to information covering this

annealing

How PCR Works

An animation of the process.

blunt ends

Link (Wikipedia) The overhanging ends created by some restriction enzymes. Useful for Biotech applications.

cloning

Animation

Early experiments

Animation

DNA profiling



DNA Applications Choose "Recovering the Romanovs" from the bottom of this page

Fish http://www.thefishsite.com/articles/336/fish-fingerprints-dna-screening-tracks-and-monitors-offenders

DNA sequencing

Excellent animation/ tutorial To determine the sequence of bases in a segment of DNA (usually a gene).

gel electrophoresis

 Link to interactive gel - awesome, unplug your headphones!


gene cloning

 Animation

genetic engineering

Genetic engineering, also called genetic modification, is the direct manipulation of an organism's genome using biotechnology

GMO

 A good online interactive quiz

ligase enzyme

Wiki link DNA Ligase completes the phosphate-sugar backbone of a piece of DNA. Used to join DNA fragments, created by Restriction enzymes, together. Ligase is a type of enzyme. This Permanently joins two pieces of DNA together (by completing the phosphate-sugar backbone.

microsatellite

 Interesting powerpoint

plasmid

Make one! A circular piece of DNA found in bacteria. A wanted gene is inserted into the plasmid during gene cloning.

PCR


Excellent interactive tutorial

Another one

The purpose of PCR is to amplify a small amount of DNA into a huge amount of DNA so it can be used in techniques such as gel electrophoresis.

primer

Work through this

recognition site

Great activity (animation) The sequence of bases a restriction enzyme recognises and cuts. Unique to each Restriction enzyme.

recombinant DNA

Animation DNA which is from more than one species, e.g. salmon DNA containing a gene from a jellyfish.

restriction enzyme

Interactive tutorial Restriction enzymes cut DNA – breaking chemical bonds.the site that a restriction enzyme cuts DNA is called the Recognition site/recognition sequence.  DNA is much too small to cut using a scalpel and we can’t tell easily the base sequence but a restriction enzyme has the ability to recognize a base sequence and cut there. It means we can cut genes out of a piece of DNA and insert them into other pieces of DNA

extracting DNA

 Workshop

Marker assisted selection

A good website. There is a growing arsenal of molecular markers (polymorphisms) that aid in identifying QTL and selecting them for crop and animal enhancement. The process of using such markers is called marker-assisted selection (MAS), which differs from genetic modification because the genes being selected for crop or animal improvement are not altered in any way.





Implications

Once you have worked out the manipulation your animals go through for your 2 topics you will have to research the effect of these changed on the gene pools and evolution of the organisms. Remember that with natural selection it happens on POPULATIONS and not individuals. Individuals need to reproduce and then survive in their habitat to reproduce or else their alleles will be removed from the population. What implications with this in mind has the genetic manipulation caused? The term 'biological implications' means the biological consequences or changes that are caused or could be caused by the manipulation you are studying. The list of implications you are given is written in broad terms that are often linked together but the terms give you a good starting point for your research. Each different manipulation and species studied has different implications. Remember to look for both positive and negative implications.(From Studyit.org.nz)

All the examples below may not be isolated case but be linked. For example (in brief), Bt cotton has been genetically engineered to include a gene that is toxic to bollworm, a parasite that kills the cotton plant.  This removes the need for chemical sprays on Bt cotton crops.  This modification increases the survival of individuals and the population in relation to bollworm, so crop size increases but, because it is a monoculture, Bt cotton has reduced genetic biodiversity and a limited gene pool.  This means that if the organism is susceptible to another disease or parasite, the whole population is susceptible so affects the survival of the population as a whole where other risks are concerned.  The absence of chemical sprays increases the occurrence of other non-target pests, which in turn not only damage cotton but also other crops, affecting the ecosystem.

ecosystems

(animals, plants and physical environment) - How does the manipulation effect the ecosystem. Think about predator prey relationships, food webs, energy flow and pressures. 
 
Animation looking at the basics of ecosystems

genetic biodiversity

(amount of genes available in a gene pool for an species)

Genetic diversity, the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species. The level of genetic diversity found in a population highly depends on the mating system, the evolutionary history of a species and the population history (the latter is usually unknown). Biotechnology effects the biodiversity both directly and indirectly. Lots to talk about here!

Here you have to look for examples of possible changes to the range of genes in a species or ecosystem. For example in the past selective breeding of crop species such as wheat or potatoes have reduced genetic biodiversity. In a different example selective breeding of individuals with a specific mutation has increased genetic biodiversity eg different breeds of dog. (From Studyit.org.nz)


health or survival of individuals (not humans but individual organisms)

(survival of set of organisms able to breed together e.g horses or cattle...) Survival is both the process of staying alive and breeding.
If you are studying the manipulation 'whole organism cloning' and have researched Dolly the sheep you will be able to explain the negative impact being cloned had on Dolly's health. (From Studyit.org.nz)

survival of populations

(likelihood of individual animal/plant to live/die) If an animal is altered in such a way that breeding is hampered or the group of animals in the population is effected then you should be discussing the survival of the population.
 
Look at the animal and plant topic. These could be both positive and negative implications.

eg plant species with low genetic diversity (eg wheat) are more likely to all suffer from the same disease. eg populations a transgenic plant species such as Bt-corn have increased survival due to resistance to certain pest insects.
(From Studyit.org.nz)

PowerPoint looking at how populations survive.

evolution of populations

(how a population changes over time - at a genetic level as well as physical)

Plant species with low genetic diversity (eg wheat) are less likely to under go evolution because the population has more fixed alleles so when the environment changes the population has less opportunity to change allele frequency.
 
Look at the evolution topic for ideas here.

Some excellent places to start your research

http://www.biotechlearn.org.nz/ The Biotechnology Learning Hub provides teaching resources for primary and secondary schools.

https://blogs.otago.ac.nz/ouassa/category/resources/biology-resources/ Another great website run by the University of Otago.



Human manipulations


Explaining the ‘how’ of the manipulations involves the techniques used in the process. This is important!


For example, recombinant DNA used in transgenesis, genome analysis used in selective breeding.


selective breeding




(could include embryo selection, animal breeding, plant breeding, development of new crops)


PPT - Uni of Otago

Genetic Engineering PPT

New Crops - Nature Link


Interactive tasks

Dog breeding Game

Domestication of animals

Selective breeding



whole organism cloning


Start here

The coning process interactive task

Click and clone game learn.genetics.utah

Dog Cloning

Cloning interactive

cloning online task - Tutorvista



transgenesis


Make a transgenic plant.

A organism containing DNA from another species. The gene of interest is the gene that codes for a protein that the scientists want to be expressed in another species. The gene must be located and a restriction enzyme is used to cut the DNA outside the gene. Sticky ends are needed so the fragment can anneal to the DNA it is being inserted into before ligase completes the phosphate-sugar backbone.

ALWAYS involves the transfer of a gene from one species of organism to a different species of organism. ie Transgenesis = across species.


Create a transgenic animal - Fun task.

Make a Mouse!

Engineer a crop

Recombinant DNA

transgenic plants


Methods of creation of transgenic animals


For practical reasons, i.e., their small size and low cost of housing in comparison to that for larger vertebrates, their short generation time, and their fairly well defined genetics, mice have become the main species used in the field of transgenics.

The three principal methods used for the creation of transgenic animals are DNA microinjection, embryonic stem cell-mediated gene transfer and retrovirus-mediated gene transfer.
a) DNA microinjection.

This method involves the direct microinjection of a chosen gene construct (a single gene or a combination of genes) from another member of the same species or from a different species, into the pronucleus of a fertilized ovum. It is one of the first methods that proved to be effective in mammals (Gordon and Ruddle, 1981). The introduced DNA may lead to the over- or under-expression of certain genes or to the expression of genes entirely new to the animal species. The insertion of DNA is, however, a random process, and there is a high probability that the introduced gene will not insert itself into a site on the host DNA that will permit its expression. The manipulated fertilized ovum is transferred into the oviduct of a recipient female, or foster mother that has been induced to act as a recipient by mating with a vasectomized male.

A major advantage of this method is its applicability to a wide variety of species.
b) Embryonic stem cell-mediated gene transfer.

This method involves prior insertion of the desired DNA sequence by homologous recombination into an in vitro culture of embryonic stem (ES) cells. Stem cells are undifferentiated cells that have the potential to differentiate into any type of cell (somatic and germ cells) and therefore to give rise to a complete organism. These cells are then incorporated into an embryo at the blastocyst stage of development. The result is a chimeric animal. ES cell-mediated gene transfer is the method of choice for gene inactivation, the so-called knock-out method.

This technique is of particular importance for the study of the genetic control of developmental processes. This technique works particularly well in mice. It has the advantage of allowing precise targeting of defined mutations in the gene via homologous recombination.
c) Retrovirus-mediated gene transfer.

To increase the probability of expression, gene transfer is mediated by means of a carrier or vector, generally a virus or a plasmid. Retroviruses are commonly used as vectors to transfer genetic material into the cell, taking advantage of their ability to infect host cells in this way. Offspring derived from this method are chimeric, i.e., not all cells carry the retrovirus. Transmission of the transgene is possible only if the retrovirus integrates into some of the germ cells.

For any of these techniques the success rate in terms of live birth of animals containing the transgene is extremely low. Providing that the genetic manipulation does not lead to abortion, the result is a first generation (F1) of animals that need to be tested for the expression of the transgene. Depending on the technique used, the F1 generation may result in chimeras. When the transgene has integrated into the germ cells, the so-called germ line chimeras are then inbred for 10 to 20 generations until homozygous transgenic animals are obtained and the transgene is present in every cell. At this stage embryos carrying the transgene can be frozen and stored for subsequent implantation.

investigation and modification of the expression of existing genes


This is a good recap on expression of genes Link 

Biological implications may involve the impact on: For this part look at Animal and Plant/ Evolution sections

·         ecosystems

·         genetic biodiversity

·         health or survival of individuals

·         survival of populations

·         evolution of populations.


And finally the PCR SONG!! Should be a number 1 download on itunes... or not.




Exemplars and guidance

Some examples that may be used - there are many more and some have much more usable information than others.

Selective Breeding

Transgenesis

Horses

Golden rice

Corn

Whiffy wheat

Dogs

Daisy’s modified milk

Apples

GLO fish

Sheep

"Fish tomato"


Achievement

Merit

Excellence

Demonstrate understanding by using biological ideas to describe:

·        two human manipulations of genetic transfer

·        two biological implications for each human manipulation of genetic transfer.

As for Achieved and,

Demonstrate in-depth understanding by using biological ideas to explain how or why:

·        genetic transfer is manipulated for each human manipulation context

and

·        explain two biological implications within or between the two human manipulation contexts of genetic transfer.

As for Merit and,

Demonstrate comprehensive understanding by:

·        linking biological ideas within or between human manipulations of genetic transfer

and

·        two biological implications

The linking of ideas may involve justifying, relating, evaluating, comparing and contrasting, and analysing.



it could be linking 'one implication with another'. Forming links means putting ideas together to explain something eg how whole organism cloning, of an animal used for food, could result in a specific problem (eg reduced genetic diversity) for humans in the future and what the implication of this problem could be (eg reduced survival leading to reduced food supply).


For your Biotech project a possible format could be (please note this may or may not be relevant to the way your teacher has run your internal) - please talk to them first..

Intro - Introduction to what genetic manipulation is including a brief description of focus manipulations of manupulation 1 and 2.

P1 - Introduce case study for 1.

P2 - Biological processes of 1 in relation to your case study (e.g. selection, inbreeding and marker assisted selection for selective breeding though your topic may be different)

P3 - Biological implications of selective breeding of your case study (e.g. at least 2 of; ecosystems, genetic biodiversity, health or survival of individuals, survival of populations or evolution of populations)

P4 - Introduce case study for 2.

P5 - Biological processes of 2 in relation to your case study
(e.g. gene cloning using plasmids as vectors with reference to restriction enzymes and ligase, transfection, PCR for transgenesis)

P6 - Biological implications of 2 of your case study (e.g. at least 2 of; ecosystems, genetic biodiversity, health or survival of individuals, survival of populations or evolution of populations)

P7 - Comparison between the two processes 

Conclusion - Summary of main points

References: List of sources used

Links to context readings


General reading

http://www.brown.edu/ce/adult/arise/resources/docs/yw10_1.pdf



salmon

http://erepository.law.shu.edu/cgi/viewcontent.cgi?article=1311&context=student_scholarship&sei-redir=1&referer=http%3A%2F%2Fscholar.google.co.nz%2Fscholar%3Fq%3Dgenetically%2Bmodified%2Bsalmon%26btnG%3D%26hl%3Den%26as_sdt%3D0%252C5#search=%22genetically%20modified%20salmon%22

http://science.kennesaw.edu/~jdirnber/Bio2108/Lecture/LecEvolution/TransgeneSalm.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC438972/



Salt tolerant crops

http://www.thenakedscientists.com/HTML/news/news/1760/



GM crops

http://cib.org.br/wp-content/uploads/2011/10/estudos_alimentares06.pdf

http://jxb.oxfordjournals.org/content/54/386/1317.full

http://ask-force.org/web/Bt/OCallaghan-Effects-Plants-Genetically-2005.pdf

http://www.ask-force.org/web/Benefits/Phipps-Park-Benefits-2002.pdf

http://www.biol.uw.edu.pl/pl/files/docs/st_dokt/SD_SCB_TREE2000.pdf

http://www.ask-force.org/web/biodiversity/Dale-Pot-Imp-nbt0602-567.pdf

http://bmb.oxfordjournals.org/content/56/1/62.full.pdf

http://www.e-library.lt/resursai/ES/Leidiniai/EEA_issue_reports/GMOsforwww.pdf



Protein enhanced rice

http://www.ask-force.org/web/Africa-Harvest-Sorghum-Lit-1/Wu-et-al-Plant-Biotech-J-2003.pdf



Enhanced potato

http://www.gmo-compass.org/eng/grocery_shopping/crops/23.genetically_modified_potato.html



rapeseed

http://www.gmo-compass.org/eng/safety/environmental_safety/185.rapeseed.html

Potato

http://www.gmo-compass.org/eng/safety/environmental_safety/183.potato.html



Transgenic animals

http://www.researchgate.net/publication/6124633_Transgenic_farm_animals_an_update/file/f3df2af1e895ffdb3815a55f4a8a9342.pdf

Glow in the dark rabbits

Goats

http://www.sciencebasedmedicine.org/recombinant-human-antithrombin-milking-nanny-goats-for-big-bucks/

http://www.researchgate.net/publication/12966532_Production_of_goats_by_somatic_cell_nuclear_transfer/file/d912f5098103a9392b.pdf

http://www.managedcaremag.com/archives/0903/0903.biotech.html

Selective breeding

sheep

http://www.oie.int/doc/ged/d8293.pdf

http://www.beeflambnz.com/Documents/Farm/Breeding%20sheep%20with%20bare%20breech%20and%20belly.pdf

http://www.biotechlearn.org.nz/focus_stories/easy_care_sheep/video_clips/selective_breeding_cloning_and_gm


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