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\author{Anais (Anais\_Pe)}
\pdfinfo{
  /Title (biology-a-level-manipulating-genomes.pdf)
  /Creator (Cheatography)
  /Author (Anais (Anais\_Pe))
  /Subject (Biology A level - Manipulating genomes Cheat Sheet)
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        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
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    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{Biology A level - Manipulating genomes Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{Anais (Anais\_Pe)} via \textcolor{DarkBackground}{\uline{cheatography.com/151793/cs/43584/}}}
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  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}Anais (Anais\_Pe) \\
  \uline{cheatography.com/anais-pe} \\
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Published 6th June, 2024.\\
   Updated 6th June, 2024.\\
   Page {\thepage} of \pageref{LastPage}.
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  Measure your website readability!\\
  www.readability-score.com
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\begin{multicols*}{3}

\begin{tabularx}{5.377cm}{x{1.4931 cm} x{3.4839 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Human genome - introns}}  \tn
% Row 0
\SetRowColor{LightBackground}
{\emph{Minisatellites}} & 20-50 base pairs (bp) repeated 50-100 times. {\emph{Also called VNTRs (Variable Number Tandem Repeats).}} \tn 
% Row Count 4 (+ 4)
% Row 1
\SetRowColor{white}
{\emph{Microsatellites}} & 2-4 bp repeated 5-15 times. {\emph{Also called STRs (Short Tandem Repeats) or stutters}} \tn 
% Row Count 7 (+ 3)
% Row 2
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\mymulticolumn{2}{x{5.377cm}}{Can repeat a varying amount of times on each homologous chromosome. The number of repeats is inherited from parents.} \tn 
% Row Count 10 (+ 3)
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\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{Satellite DNA is a repeating sequence of DNA found in introns (non-coding DNA).}  \tn 
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\end{tabularx}
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\begin{tabularx}{5.377cm}{x{1.74195 cm} x{3.23505 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Producing a DNA profile}}  \tn
% Row 0
\SetRowColor{LightBackground}
1. Extract DNA & Tissue sample is mixed with phenol solution. PCR can be carried out to multiply sample (more detail later). \tn 
% Row Count 5 (+ 5)
% Row 1
\SetRowColor{white}
2. DNA fragmentation & Restriction endonucleases - cut DNA at specific base sequence (restriction site). \tn 
% Row Count 9 (+ 4)
% Row 2
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3. Gel \seqsplit{electrophoresis} & Used to separate DNA fragments using charge and Mass of DNA fragments (more detail later). \tn 
% Row Count 13 (+ 4)
% Row 3
\SetRowColor{white}
4. Denaturation & Hello soaked with alkali to separate strands. \tn 
% Row Count 15 (+ 2)
% Row 4
\SetRowColor{LightBackground}
5. Southern blotting & Membrane that single strands of DNA are transferred on to. \tn 
% Row Count 18 (+ 3)
% Row 5
\SetRowColor{white}
6. Hybridisation & Complementary radioactive or fluorescent probes are added. Their base sequence is known and so they tag complementary regions so specific genes can be pinpointed. \tn 
% Row Count 25 (+ 7)
% Row 6
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7. Disclosure & X-rays or UV lights are used depending on what type of tag was used. The result will show lines where specific sequences were tagged and a DNA profile is created. \tn 
% Row Count 32 (+ 7)
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\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Gel electrophoresis}}  \tn
\SetRowColor{LightBackground}
\mymulticolumn{1}{p{5.377cm}}{\vspace{1px}\centerline{\includegraphics[width=5.1cm]{/web/www.cheatography.com/public/uploads/anais-pe_1717625226_ec82418c42e1a4176745273dab3c204bf50cc603.png}}} \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}-}
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\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Gel electrophoresis}}  \tn
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{DNA cut up by restriction enzymes and mixed with loading dye is placed in wells in agarose gel. Buffer solution is added to maintain a constant pH and a current is passed through with the anode at the opposite end to the DNA.  \newline % Row Count 5 (+ 5)
Because DNA is negatively charged, the fragments will be pulled towards the anode. Smaller fragments travel faster and further. The loading dye allows us to make sure the DNA doesn't fall off the other end. \newline % Row Count 10 (+ 5)
An alkaline solution is then added to denature the DNA and the other steps of DNA profiling take place (Southern blotting and disclosure).% Row Count 13 (+ 3)
} \tn 
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\end{tabularx}
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\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{PCR}}  \tn
\SetRowColor{LightBackground}
\mymulticolumn{1}{p{5.377cm}}{\vspace{1px}\centerline{\includegraphics[width=5.1cm]{/web/www.cheatography.com/public/uploads/anais-pe_1717625281_PCR.jpeg}}} \tn 
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\begin{tabularx}{5.377cm}{x{2.28942 cm} x{2.68758 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Polymerase chain reaction (PCR)}}  \tn
% Row 0
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\mymulticolumn{2}{x{5.377cm}}{PCRis used when only a small sample of DNA is available, for example at a crime scene. The DNA sample along with excess bases, primers and DNA polymerase are mixed and placed in the PCR machine} \tn 
% Row Count 4 (+ 4)
% Row 1
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1. Separating the strands (90-95C) & 30 seconds, this denatures the DNA - breaks hydrogen bonds between bases. \tn 
% Row Count 8 (+ 4)
% Row 2
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2. Annealing the strands (55-60C) & Primers bind to the ends of the DNA strands. \tn 
% Row Count 11 (+ 3)
% Row 3
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3. DNA synthesis (72-75C) & At least 1 minute, DNA polymerase (Taq polymerase) adds bases to the primer, complementary strand is made. \tn 
% Row Count 17 (+ 6)
% Row 4
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\mymulticolumn{2}{x{5.377cm}}{The cycle is repeated as many times as necessary to produce enough DNA for the necessary usage.} \tn 
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\begin{tabularx}{5.377cm}{X}
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\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{DNA sequencing (Sanger)}}  \tn
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\mymulticolumn{1}{x{5.377cm}}{DNA mixed with primers, DNA polymerase, excess nucleotides and terminator bases (4 separate containers, one for each base).} \tn 
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% Row 1
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\mymulticolumn{1}{x{5.377cm}}{PCR performed to synthesise DNA.} \tn 
% Row Count 4 (+ 1)
% Row 2
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\mymulticolumn{1}{x{5.377cm}}{Terminator nucleotides cause transcription to stop. This therefore produces different lengths of DNA fragments.} \tn 
% Row Count 7 (+ 3)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{Process similar to gel electrophoresis started. Terminator nucleotides contain fluorescent markers, so base which ends sequence can be identified.} \tn 
% Row Count 10 (+ 3)
% Row 4
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\mymulticolumn{1}{x{5.377cm}}{Shortest fragment travels furthest so order of bases can be determined.} \tn 
% Row Count 12 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{5.377cm}}{Next-generation sequencing or massively parallel sequencing is more commonly used than the Sanger method. This is where DNA fragments are put through a plastic slide (flow cell) instead of gel electrophoresis. PCR is then carried out in situ.}  \tn 
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\begin{tabularx}{5.377cm}{x{1.89126 cm} x{3.08574 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Bioinformatics and computational biology}}  \tn
% Row 0
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{\emph{Bioinformatics}} & Stores and organises data. \tn 
% Row Count 2 (+ 2)
% Row 1
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{\emph{Computational biology}} & Uses data to form theoretical models. \tn 
% Row Count 4 (+ 2)
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\begin{tabularx}{5.377cm}{x{1.74195 cm} x{3.23505 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Uses of genome-wide comparisons}}  \tn
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{\emph{Human genome}} & 10,000 Genomes Project UK10K. \tn 
% Row Count 2 (+ 2)
% Row 1
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{\emph{Genomes of pathogens}} & Find source of infection. \tn 
% Row Count 4 (+ 2)
% Row 2
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 & Identify antibiotic-resistant bacteria. \tn 
% Row Count 6 (+ 2)
% Row 3
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 & Track progress of an outbreak. \tn 
% Row Count 8 (+ 2)
% Row 4
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 & Identify target areas of pathogen genome. \tn 
% Row Count 10 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\begin{tabularx}{5.377cm}{x{2.33919 cm} x{2.63781 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Sequencing for classification}}  \tn
% Row 0
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Identifying species (DNA barcoding) & Identify sections of the genome that remain the same within species. Conserved regions in animals are in mtDNA and in plants chloroplast DNA. \tn 
% Row Count 7 (+ 7)
% Row 1
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Evolutionary relationships & Can calculate rate of mutations -{}-\textgreater{} See how long ago two species had same DNA in common ancestor. \tn 
% Row Count 12 (+ 5)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\begin{tabularx}{5.377cm}{x{1.74195 cm} x{3.23505 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Genomics and proteomics}}  \tn
% Row 0
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\mymulticolumn{2}{x{5.377cm}}{{\bf{Genomics}} is the study of genome.} \tn 
% Row Count 1 (+ 1)
% Row 1
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\mymulticolumn{2}{x{5.377cm}}{{\bf{Proteomics}} is the study and amino sequencing of organisms' entire protein complement. More proteins exist than genes.} \tn 
% Row Count 4 (+ 3)
% Row 2
\SetRowColor{LightBackground}
{\emph{Spliceosomes}} & Enzyme complexes which cut out introns and some exons out of pre-mRNA. Exons can be rearranged differently, therefore one section of DNA can code for many proteins. \tn 
% Row Count 11 (+ 7)
% Row 3
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{\emph{Protein modification}} & Proteins modified by other proteins. Can be lengthened or shortened. \tn 
% Row Count 14 (+ 3)
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\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{Spliceosomes and protein modification are some of the reasons why existing proteins do not reflect the genome of an organism.}  \tn 
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\end{tabularx}
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\begin{tabularx}{5.377cm}{X}
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\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Synthetic biology}}  \tn
% Row 0
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\mymulticolumn{1}{x{5.377cm}}{{\emph{Design and construction of novel artificial pathways, organisms...}}} \tn 
% Row Count 2 (+ 2)
% Row 1
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\mymulticolumn{1}{x{5.377cm}}{Genetic engineering.} \tn 
% Row Count 3 (+ 1)
% Row 2
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\mymulticolumn{1}{x{5.377cm}}{Industrial contexts - fixed/immobilised enzymes and drug production.} \tn 
% Row Count 5 (+ 2)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{Synthesis of new genes e.g. treat cystic fibrosis.} \tn 
% Row Count 6 (+ 1)
% Row 4
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{5.377cm}}{Synthesis of new organism. New nucleotides developed (other than ACTG) incorporated in DNA introduced in bacteria.} \tn 
% Row Count 9 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
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\begin{tabularx}{5.377cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Isolating desired gene}}  \tn
\SetRowColor{white}
\mymulticolumn{1}{x{5.377cm}}{mRNA is isolated from target cell using restriction endonucleases and treated with reverse transcriptase to create complementary DNA (cDNA).  \newline % Row Count 3 (+ 3)
Plasmid genetically engineered to have markers, cut by restriction endonucleases (same ones used for DNA for complementary sticky ends).Second marker is added to show plasmid contains recombinant gene. This marker should be corrupted when DNA is added. \newline % Row Count 9 (+ 6)
DNA ligase fuses cDNA and the plasmid by forming phosphodiester bonds. The recombinant plasmid is placed in the host cell. The bacteria multiply in a fermenter.% Row Count 13 (+ 4)
} \tn 
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\SetRowColor{LightBackground}
\mymulticolumn{1}{x{5.377cm}}{Could also use electrofusion: merge two cells + their DNA to form polyploid cells. More used in plants, animal polyploids usually don't survive.}  \tn 
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\begin{tabularx}{5.377cm}{X}
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\mymulticolumn{1}{x{5.377cm}}{\bf\textcolor{white}{Isolating genes}}  \tn
\SetRowColor{LightBackground}
\mymulticolumn{1}{p{5.377cm}}{\vspace{1px}\centerline{\includegraphics[width=5.1cm]{/web/www.cheatography.com/public/uploads/anais-pe_1717670865_Recombinant-DNA-technology.jpg}}} \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
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\begin{tabularx}{5.377cm}{x{1.24425 cm} x{3.73275 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Genetic engineering in different organisms}}  \tn
% Row 0
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{\emph{Prokaryotes}} & Easily genetically modified for hormones, antibiotics... \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
{\emph{Plants}} & {\emph{Agrobaterium tumefaciens}} which usually forms tumours. Desired gene inserted in plasmid, then in plant DNA. Forms a callus of GM plant cells \tn 
% Row Count 7 (+ 5)
% Row 2
\SetRowColor{LightBackground}
 & Can also use {\bf{electrofusion}} - Tiny electric shocks used to fuse the cells and nuclear membranes of two different cells together. Also used for producing monoclonal antibodies. \tn 
% Row Count 13 (+ 6)
% Row 3
\SetRowColor{white}
{\emph{Animals}} & Cell membranes are harder to manipulate than plant cell membranes. Engineering used for medically important proteins and curing human genetic diseases. \tn 
% Row Count 19 (+ 6)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\begin{tabularx}{5.377cm}{x{1.64241 cm} x{3.33459 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Ethics for GM plants}}  \tn
% Row 0
\SetRowColor{LightBackground}
Pest resistance & + Less pesticide spraying \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
 & - Non-pest insects are also affected \tn 
% Row Count 4 (+ 2)
% Row 2
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Disease resistance & + Less crop loss \tn 
% Row Count 6 (+ 2)
% Row 3
\SetRowColor{white}
 & - Superweeds (if genes spread). \tn 
% Row Count 8 (+ 2)
% Row 4
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Herbicide resistance & + Less competition, higher yield \tn 
% Row Count 10 (+ 2)
% Row 5
\SetRowColor{white}
 & - Lower biodiversity, superweeds \tn 
% Row Count 12 (+ 2)
% Row 6
\SetRowColor{LightBackground}
Shelf-life extended & + Less food waste \tn 
% Row Count 14 (+ 2)
% Row 7
\SetRowColor{white}
 & - Lower commercial value and demand \tn 
% Row Count 16 (+ 2)
% Row 8
\SetRowColor{LightBackground}
Growing conditions & + Can grow in a wider range of conditions e.g. flood resistant \tn 
% Row Count 19 (+ 3)
% Row 9
\SetRowColor{white}
 & - N/A \tn 
% Row Count 20 (+ 1)
% Row 10
\SetRowColor{LightBackground}
Nutritional value & + Higher nut. val. \tn 
% Row Count 22 (+ 2)
% Row 11
\SetRowColor{white}
 & - Allergies can develop due to new proteins \tn 
% Row Count 24 (+ 2)
% Row 12
\SetRowColor{LightBackground}
Medical uses & + Medicines and vaccines \tn 
% Row Count 25 (+ 1)
% Row 13
\SetRowColor{white}
 & - N/A \tn 
% Row Count 26 (+ 1)
% Row 14
\SetRowColor{LightBackground}
Patenting & + N/A \tn 
% Row Count 27 (+ 1)
% Row 15
\SetRowColor{white}
 & - Companies charge for seeds, can't harvest seeds, people who may need it the most cannot afford it \tn 
% Row Count 31 (+ 4)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\begin{tabularx}{5.377cm}{x{0.9954 cm} x{3.9816 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Ethics for GM animals}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{5.377cm}}{GM pathogens used for research - modify virus to insert new genes in cells e.g. swine fever-resistant pigs, faster-growing salmon...} \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
{\emph{Pharming}} & Using animals to produce human medicines and research subjects. \tn 
% Row Count 5 (+ 2)
% Row 2
\SetRowColor{LightBackground}
 & Medicine - From GM fertilised animals, human protein collected from milk... \tn 
% Row Count 8 (+ 3)
% Row 3
\SetRowColor{white}
 & Research - Knock-out mice engineered to develop cancer for research. \tn 
% Row Count 11 (+ 3)
% Row 4
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{\emph{Issues}} & - Human genes in animals \tn 
% Row Count 12 (+ 1)
% Row 5
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 & - Reduce animals to commodities \tn 
% Row Count 13 (+ 1)
% Row 6
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 & - Welfare compromised \tn 
% Row Count 14 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
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\begin{tabularx}{5.377cm}{x{2.09034 cm} x{2.88666 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Gene therapy in humans}}  \tn
% Row 0
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{\emph{Germ line cell gene therapy}} & {\bf{Germ cells}} - Sex cells / embryo post-fertilisation. \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
 & Insert healthy gene in germ cell. \tn 
% Row Count 5 (+ 2)
% Row 2
\SetRowColor{LightBackground}
 & Illegal for human embryos - violation of human rights of unborn child, concerns of long term impacts... \tn 
% Row Count 10 (+ 5)
% Row 3
\SetRowColor{white}
{\emph{Somatic cell gene therapy}} & Replace mutant allele with healthy one using viral vector. \tn 
% Row Count 13 (+ 3)
% Row 4
\SetRowColor{LightBackground}
 & Higher rates of success, but still issues to fix e.g. mutant alleles passed on rather than healthy ones. \tn 
% Row Count 18 (+ 5)
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% That's all folks
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