Ripe strawberries are an excellent source for extracting DNA because they are easy to pulverize and contain enzymes called pectinases and cellulases that help to break down cell walls. And most important, strawberries have eight copies of each chromosome (they are octoploid), so there is a lot of DNA to isolate.
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Why would scientists want to study the DNA of fruits or vegetables like strawberries give two reasons?
7. List two reasons why a scientist might want to study the DNA of strawberries. Scientists might want to compare the DNA of a type of strawberry that is more disease or frost resistant than other strawberries Scientists may want to study the evolutionary relatedness of strawberries to other berries.
Why do strawberries have more chromosomes?
In ‘Nature’: The science of a perfect strawberry
Garden-variety genetics: William & Mary Assistant Professor of Biology Josh Puzey (right), undergraduate Scott Teresi (center) and grad student Ron Smith joined a team of researchers to complete the first chromosome-scale assembly of the strawberry genome. Their work, recently published in the journal “Nature Genetics,” identifies a quirk in the genome that could fundamentally change how the fruit is bred. Photo by Adrienne Berard
by Adrienne Berard | February 25, 2019 The old-fashioned strawberry is having a renaissance thanks to new genetic research. “I always hear, ‘Oh these strawberries today aren’t like the ones from my grandma’s garden,'” said William & Mary Assistant Professor of Biology Josh Puzey.
- So we built a tool by sequencing its genome.
- Now we can drill down and understand how flavor is produced, how texture is produced, how size is produced.
- It will help us understand other crops, but one outcome would hopefully be that you could find strawberries in the store that actually taste like your grandmother’s strawberries.” Puzey and two of his students joined a team of researchers to complete the first chromosome-scale assembly of the strawberry genome.
The newly sequenced genome offers a window into global crop development and highlights the lesser-known power of “junk DNA” to influence gene expression. Their work, recently published in the journal, traces the origin of the North American strawberry and identifies a quirk in the genome that could fundamentally change how the fruit is bred.
- The other partner institutions include Michigan State University, University of California – Davis, University of Alabama, University of Arizona and the University of Nebraska.
- } The garden strawberry ( Fragaria × ananassa ) is extremely sensitive to weather and thrives only in certain climate conditions, Puzey explained.
California is currently the world’s top strawberry producer, according to the U.S. Department of Agriculture. The state accounts for a third of the total global strawberry production, meaning the berries have to be bred to withstand world travel. Selectively breeding for jetsetters comes at a cost to flavor and nutrition, Puzey explained.
By sequencing the full strawberry genome, Puzey and the research team are a step closer to identifying the subset of the genome that accounts for other desired attributes like taste and smell. The findings could open the door to new breeding techniques that could select for both durability and flavor.
“Our analyses revealed that certain metabolic pathways, including those that give rise to strawberry flavor, color and aroma, are largely controlled by the dominant subgenome,” the paper states. “Thus, we anticipate that this new reference genome, combined with insights into subgenome dominance, will greatly accelerate molecular breeding efforts in the cultivated garden strawberry.” It may sound simple, but it’s a long road to shortcake.
Reproduction is a complex process for the cultivated garden strawberry. Depending on the individual strawberry, it either has a lot of parents or no parents at all. Some baby strawberries are the product of four different parental lineages, while others are just a clone of the same strawberry. “Imagine if you could stick your arm out, put it in the ground and then chop it off and make another you,”Ron Smith said.
“That’s essentially what it’s doing. The clone just an appendage of the first strawberry plant.” For the strawberries created through breeding, traits are passed down from four parents. Geneticists call this phenomenon octoploid, when an organism has a complete set of homoeologous chromosomes from all four parents residing within a single nucleus.
- The strawberry Book of Genesis would feature not only Adam and Eve, but Barbara and Steve.
- Imagine you have Parent A,B,C and D,” Puzey said.
- They all hybridize to produce an individual.
- Now, within that individual, all these parents each have their unique evolutionary trajectory and that entire history is within a single nucleus inside the larger genome of that one plant.” Each of those parental lineages is called a subgenome, Puzey explained.
Together, the four lineages hybridized to create the full Camarosa strawberry genome that we eat today. Puzey and the research team wanted to understand the individual attributes of each subgenome. Specifically, they were interested in which of the four parents was more dominant.
To solve that problem, they needed a numbers guy. Smith, a graduate student in Applied Science, fit the bill. He has a degree in mathematics from Farmingdale State College and, as part of his graduate work at William & Mary, he developed a statistical test to evaluate subgenome dominance. “Let’s say I’ve got genes from multiple different lineages and I want to know what happens when I hybridize with another individual that has multiple lineages,” Smith said.
“If we want to know what gene is dominant, there is a mathematical method for solving that problem. Any time you have a polyploid question, a question about which gene from which genome will win out, this method applies.” With plants, as with people, certain traits are passed down to offspring through dominant genes.
- A baby born from a brown-eyed father and blue-eyed mother is much more likely to have brown eyes because the brown-eye gene is more dominant.
- The small piece of DNA that codes for brown eyes will more likely be activated, or expressed, in the baby’s genome and odds are the child will have brown eyes.
Strawberries carry the genomes of four different parents, which make up the offspring’s’ subgenomes. Puzey and his team found that one of the four parental genomes is more active and, therefore, more expressed than the other three. If humans had four parents like strawberries, our offspring would be more likely have the eye color of just one mother.
- That mother’s genome, in this hypothetical case, would be the dominant subgenome in the baby.
- The dominant subgenome in the garden strawberry is called the F.
- Vesca subgenome.
- The researchers found F.
- Vesca has about 20 percent more protein-coding genes than the other three subgenomes.
- They also found F.
vesca may control for disease resistance and other vital aspects of strawberry survival. “Once we made this discovery, the question became, how is a single genome more dominant over the other?” Puzey said. “What we find evidence for in this paper is these things called transposable elements, what people often refer to as junk DNA, actually has an impact on subgenome dominance in ways we didn’t previously anticipate.” The researchers found that the F.
- Vesca subgenome has about 20 percent fewer transposable elements – DNA that doesn’t functionally contribute to a gene product like a protein – than the strawberry’s other three subgenomes.
- That lack of transposable elements may be what makes F.
- Vesca so dominant, Puzey explained.
- We found that this so-called ‘junk DNA’ might actually have a regulatory role in gene expression,” he said.
Understanding the real regulatory role of transposable elements requires a staggering amount of data analysis. Undergraduate Scott Teresi has spent much of his junior and senior year doing just that. He’s currently building a dataset detailing the types of transposable elements and their distance relative to every single gene in the strawberry genome.
The code he’s writing to track “junk DNA” can be run on any genome. “A transposable element, or transposon, is a mobile genetic element that can copy and move itself around the genome, for this reason they are sometimes referred to as jumping genes,” Teresi said. “Historically they’ve been thought of as parasitic genes because they were purported to have no function other than their own proliferation.
Consequently, this has led them to contribute to significant portions of genome size. Your genome is riddled with them.” Almost half of the human genome is made up of transposons, Teresi said. Corn’s genome is about 85 percent transposon. In fact, the multi-colored kernels of Indian corn are a direct result of transposons.
- The reason one kernel looks so different from the kernel next to it is because a transposon landed on or near the pigment gene and basically blew it up,” Teresi said.
- Like corn, strawberries are polyploid.
- They contain the genomes of multiple parents, carrying more than two complete sets of chromosomes.
The researchers believe that the connection they found between transposons and gene expression in strawberries may hold true for many other polyploids. The more transposons a subgenome has, the less likely gene expression is, so another subgenome will win out.
“This is the type of finding we can’t really explain through classical genetics,” Teresi said. “We’re now in the realm of epigenetics, when there are changes to the accessibility of the DNA but not to the code itself. It’s exciting because this goes towards developing a new paradigm for the functions and consequences of transposable elements.” If the team’s discovery can be put into practice, we’ll have strawberries that are colorful, durable and taste like they just came out of Grandma’s garden.
: In ‘Nature’: The science of a perfect strawberry
What is the best thing to extract DNA from?
DNA Extraction and Polymerase Chain Reaction Department of Cytology and Gynaecological Pathology, Postgraduate Institute of Medical Education, Chandigarh, India Find articles by : © 2019 Journal of Cytology This is an open access journal, and articles are distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as appropriate credit is given and the new creations are licensed under the identical terms.
DNA extraction and polymerase chain reaction (PCR) are the basic techniques employed in the molecular laboratory. This short overview covers various physical and chemical methods used for DNA extraction so as to obtain a good-quality DNA in sufficient quantity. DNA can be amplified with the help of PCR.
The basic principle and different variants of PCR are discussed. Keywords: DNA extraction, Polymerase chain reaction, real time PCR DNA extraction is a method to purify DNA by using physical and/or chemical methods from a sample separating DNA from cell membranes, proteins, and other cellular components.
- Friedrich Miescher in 1869 did DNA isolation for the first time.
- The use of DNA isolation technique should lead to efficient extraction with good quantity and quality of DNA, which is pure and is devoid of contaminants, such as RNA and proteins.
- Manual methods as well as commercially available kits are used for DNA extraction.
Various tissues including blood, body fluids, direct Fine needle aspiration cytology (FNAC) aspirate, formalin-fixed paraffin-embedded tissues, frozen tissue section, etc., can be used for DNA extraction. DNA extraction involves lysing the cells and solubilizing DNA, which is followed by chemical or enzymatic methods to remove macromolecules, lipids, RNA, or proteins.
DNA extraction techniques include organic extraction (phenol–chloroform method), nonorganic method (salting out and proteinase K treatment), and adsorption method (silica–gel membrane). This method is labor intensive and time consuming. Cell lysis can be done using nonionic detergent (sodium dodecyl sulfate), Tris–Cl, and Ethylene diamine tetraacetic acid (EDTA), and this step is followed by removal of cell debris by centrifugation.
Protease treatment is then used to denature proteins. Organic solvents such as chloroform, phenol, or a mixture of phenol and chloroform (phenol/chloroform/isoamyl alcohol ratio is 25:24:1) are used for denaturation and precipitation of proteins from nucleic acid solution, and denatured proteins are removed by centrifugation and wash steps.
- RNAse treatment is done for the removal of unwanted RNA.
- Precipitation with ice-cold ethanol is performed for concentrating DNA.
- Nucleic acid precipitate is formed, when there is moderate concentration of monovalent cations (salt).
- This precipitate can be recovered by centrifugation and is redissolved in TE buffer or double-distilled water.
Other methods include silica-based technology (DNA absorbs to silica beads/particles at a specific pH in presence of specific salts), magnetic separation (DNA binds reversibly to magnetic beads, which are coated with DNA-binding antibody), anion exchange technology, salting out, and cesium chloride density gradients.
- Assessing the quality and yield of DNA: The quality and yield of DNA are assessed by spectrophotometry or by gel electrophoresis.
- Spectrophotometry involves estimation of the DNA concentration by measuring the amount of light absorbed by the sample at specific wavelengths.
- Absorption peak for nucleic acids is at ~260 nm.
The A 260 /A 280 ratio is ~1.8 for dsDNA. A ration of less than 1.7 indicates protein contamination. Polymerase chain reaction (PCR) is a robust technique to selectively amplify a specific segment of DNA in vitro, PCR is performed on thermocycler and it involves three main steps: (1) denaturation of dsDNA template at 92–95°C, (2) annealing of primers at 50–70°C, and (3) extension of dsDNA molecules at approx.72°C.
These steps are repeated for 30–40 cycles. Various chemical components of PCR include MgCl 2, buffer (pH: 8.3–8.8), Deoxynucleoside triphosphates (dNTPs), PCR primers, target DNA, and thermostable DNA polymerase. Target sequence is the sequence within the DNA template, which will be amplified by PCR.
PCR primers are single-stranded DNA (usually 18–25 nucleotides long), which match the sequences at the ends of or within the target DNA, and these are required to start DNA synthesis in PCR.
Conventional (qualitative) PCR Multiplex PCR Nested PCR Reverse transcriptase PCR and Quantitative Real-time PCR Quantitative PCR Hot-start PCR Touchdown PCR Assembly PCR Colony PCR Methylation-specific PCR LAMP assay.
Multiplex PCR: It is used to amplify multiple targets in a single PCR permitting their simultaneous analysis. Nested PCR: It is a modified PCR intended to decrease nonspecific binding of products because of amplification of unexpected primer-binding sites.
It involves two PCR steps. In the first PCR reaction, one pair of primers is used to produce DNA products, which act as a target for the second PCR reaction. It helps to increase the specificity of DNA amplification. Reverse transcriptase PCR: RT-PCR involved mRNA as the starting material and it uses reverse transcriptase to convert mRNA into the complementary DNA (cDNA).
This cDNA is then amplified with the help of regular PCR. Quantitative PCR: It is used to quantitate the amount of target DNA (or RNA) in a particular sample. Hot-start PCR: The main advantage of hot-start PCR is to decrease nonspecific amplification of DNA at lower temperature steps of PCR.
- Reaction components are manually heated before adding Taq polymerase to the DNA-melting temperature (i.e.95°C).
- Touchdown PCR: Annealing temperature during the first two cycles of amplification is set at approximately 3–10°C above estimated T m and the temperature is slowly decreased in the subsequent cycles.
Higher annealing temperature in two initial cycles leads to more specificity for primer binding, and the lower temperatures allow more efficient amplification later on. Assembly PCR: Assembly PCR helps in synthesis of long DNA segments by doing PCR on a pool of long oligonucleotides having short overlapping segments and in turn assembling more DNA segments into one segment.
Methylation specific PCR: This PCR involves sodium bisulfite treatment and is used to identify patterns of DNA methylation at cytosine guanine islands in genomic DNA. LAMP assay (loop-mediated isothermal amplification): It is another modification of PCR, which uses 3:6 primers sets, one of which is a loop-like primer.
This technique utilizes Bst-polymerase. Real-time PCR: It allows quantitative estimation of PCR product, as the amplification progresses. It uses nonspecific dye such as SYBR ® green I or fluorescence resonance energy transfer. PCR products are then sequenced to determine the order of bases in the DNA segment.
- There are no conflicts of interest.1.
- Lo AC, Feldman SR.
- Polymerase chain reaction: Basic concepts and clinical applications in dermatology.
- J Am Acad Dermatol.1994; 30 :250–60.2.
- Clark DP, Pazdernik NJ.
- Molecular Biology, Polymerase Chain Reaction.2nd ed.
- United States of America (USA): Elsevier BV; 2013.
pp.163–93. Chap.6.3. Niemz A, Ferguson TM, Boyle DS. Point-of-care nucleic acid testing for infectious diseases. Trends Biotech.2011; 29 :240–50.4. Lorenz TC. Polymerase chain reaction: Basic protocol plus troubleshooting and optimizing strategies. J Vis Exp.2012; 63 :e3998.
Why did you use bananas in DNA extraction?
Explain that crushing the bananas separates its cells and exposes them to the soap and salt. The soap helps break down cell membranes and release DNA. The salt helps bring the DNA together, and the cold alcohol helps the DNA precipitate and come out of solution so it can be collected.
Why do strawberries and bananas go together?
Why You’ll Love Strawberry Banana Smoothie –
- It’s quick and easy, This recipe literally takes a minute or two to make. You require just 4 simple ingredients and a blender, You could even prep the ingredients in advance and store them into individual portions in the freezer. Then just take your portioned amount and blend it up in seconds.
- Provides a healthy energy boost, This perfect combination of strawberry and banana will leave you feeling refreshed and sustained with that extra energy boost you need to get through the rest of the day. Plus, it’s packed with vitamins (hello Vitamin C!) and minerals making it pretty good for you.
- No added sugar. This homemade smoothie contains just fruit and milk. It has no added sugar or sweeteners, unlike many store-bought smoothies which typically contains quite a bit of sugar and possibly artificial flavors.
What do strawberries and bananas do?
How Healthy are Strawberry Banana Smoothies? – Strawberry banana smoothies are a refreshing and healthy breakfast or healthy snack made from strawberries, banana, low-fat yogurt, and ice cubes. While bananas and strawberries have a high level of natural sugars; their nutritional values can actually enhance your diet, providing a wide range of nutritional benefits.
- Here’s the breakdown; bananas supply fiber, which helps regulate digestion.
- They also contain potassium, a vital mineral, and electrolyte that your body needs to maintain blood pressure and support healthy nerve and muscle function.
- Strawberries are packed with vitamins, fiber, and high levels of antioxidants.
WebMD says they are among the top 20 fruits in antioxidant capacity as well as a good source of manganese and potassium. Strawberries are just coming into season from California in my markets. And I can’t seem to get enough of them. Thus, this smoothie is making a regular appearance these days.
What is the purpose of pineapple juice in banana DNA extraction?
Outreach activity – Extracting DNA from kiwi fruit – the Node DNA extraction from fruit is an easy experiment that makes a great demonstration for kids’ science fairs. I ran a DNA extraction stall at Oxford’s a few years back. Unfortunately I didn’t take any photos at the time but I had a lot of fun this weekend recreating the experiment in my kitchen! The experiment is hands on and messy, which kids tend to love, and there’s plenty of opportunity to explain why DNA is important in telling the cells in our body what to do.
- Click for a downloadable instruction sheet that can be printed off for children/parents to take home.
- Here’s what to do:
- 1) Prepare your equipment
- You will need:
- – Two kiwis
- – Pineapple juice
- – Table salt
- – Washing up liquid
- – Cold alcohol – put in the freezer before you start the experiment (I used surgical spirit but strong rum also works well)
- – Two small glass beakers (or plastic cups)
- – Sieve
- – Bowl
- – Tall glass/measuring cylinder
- – Kitchen Roll
- – Stirring rod (or chopstick)
- – Knife
- – Fork
- – Chopping board
- 2) Make the extraction solution
The DNA is tightly packaged inside the nucleus of cells. The membranes of the cell and of the nucleus are rich in fats so we can break them down using a detergent. The salt helps to get rid of the proteins that package the DNA tightly inside the nucleus.
- – In one of your beakers measure out about 80mls water
- – Add half a teaspoon of salt and stir until dissolved
- – Add two teaspoons of washing up liquid and stir gently avoiding making too many bubbles
- 3) Prepare your fruit mush
DNA can be extracted from anything living. You could also try this experiment with strawberries or bananas. Make sure you remove the fruit skins as they are mostly dead and don’t contain DNA. The kiwi needs to be broken up so the extraction solution can get to the cells.
- – Peel your kiwis and chop into small pieces
- – Add the chopped up kiwi to the second small beaker and use the fork to mush it up
- 4) Add the extraction solution to the fruit mush
In this step the detergent breaks down the cell membranes so the DNA can be released. The salt removes proteins that are bound to the DNA.
- – Add your extraction solution to the kiwi mush
- – Leave at room temperature for about 20 minutes
- 5) Filter the solution
- This gets rid of the fruit pulp and seeds and should leave a pure solution of DNA
- – Put your sieve over a clean bowl and line the sieve with a few sheets of damp kitchen roll
- – Pour your green mush into the sieve carefully, being careful not to break the kitchen roll
- – Use a fork to gently push the mixture through the sieve.
– The pulp and seeds should be left in the sieve and there should be a greenish liquid in the bowl. Transfer this to a tall glass or measuring cylinder.6) Purifying the DNA 
If you want an even purer solution of DNA then we need to remove proteins that are bound to the DNA. Pineapple juice contains an enzyme that breaks down proteins. If you haven’t got any pineapple juice then contact lens cleaning solution can also be used. 
DNA dissolves in water so will not be visible. However, it does not dissolve in alcohol so if we add surgical spirit then the DNA will collect as a white mass at the top of the tube.
- – Remove the alcohol from the freezer
- – Carefully pour the alcohol down the side of the glass
- – You need about equal volumes of DNA solution to alcohol
- 8) Visualise the DNA sample
After about 10 minutes you should be able to see a mass of white stringy stuff at the top of the tube (see right hand photo). This is the kiwi DNA! You can fish this out using the chopstick and place it onto a piece of card to take home.
- Sources
- This protocol is adapted from the following sources:
This post is part of a series on science outreach. You can read the introduction to the series and read other posts in this series, ( 21 votes) Loading. Tags: Categories:, : Outreach activity – Extracting DNA from kiwi fruit – the Node