BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: agriculture

CRISPR Gene editing makes disease resistant rice

Have you ever enjoyed a delicious bowl of rice and thought, “I wish more rice crops didn’t die of disease”? Well, if you’ve ever had that thought, I’ve got some good news for you! Scientists have been using CRISPR gene editing to make rice more resistant to diseases.

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Researchers by identifying a special strain of rice that showed resistance to various pathogens. They then used CRISPR-Cas9, to isolate the specific gene responsible for this resistance which was RESISTANCE TO BLAST1 (RBL1), which plays a crucial role in phospholipid biosynthesis. By tweaking this gene, they were able to enhance the rice plants’ natural defense mechanisms, making them resistant to diseases like rice blast, which is a fungal disease.

This connects with what we learn in AP Biology about genes and how they’re involved in protein synthesis.When a cell makes a protein, it starts with transcription, where the information in DNA, which is made up of genes, is copied onto mRNA. Then, the mRNA goes to the Rough Endoplasmic Reticulum, where it’s read by ribosomes. These ribosomes make the protein according to the instructions in the mRNA. In the case of the RBL1 gene, this means making a phospholipid. After the protein is made, it heads to the Golgi apparatus, where it gets some final changes based on the mRNA’s instructions before going to its final destination.

Wow, I really thought this was really interesting research especially to me personally because I love rice and think CRISPR research is really fascinating. Reading about this research also makes me wonder what are the different applications of CRISPR outside of agriculture?

CRISPR: Ethical Dimensions and The Race for the New Agricultural Revolution

Peter Paul Rubens - Adam and Eve, after Titian, between 1628 and 1629

In the book of Genesis, Satan tells Eve that “God knows that when you eat from [the tree of knowledge] your eyes will be opened, and you will be like God.” As molecular biology and genetic science discover and elevate human knowledge, scientists find themselves considering compelling ethical questions. CRISPR, or clustered regularly interspaced short palindromic repeats, is one of these methods that demands ethical scrutiny. Throughout the course of human history, innovation and technological advancements provoke these philosophical investigations. And for inventions of great destructive and creative potential, a fundamental question arises which confront both CRISPR and the atom bomb. Is it just for humanity to wield divine power? 

On June 28, 2012, CRISPR pioneer Jennifer Doudna and her colleagues published a groundbreaking paper titled “A Programmable Dual RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity.” Just as Oppenheimer’s atomic bomb started the nuclear arms race, Dr. Doudna recalls how she “remember[s] thinking very clearly… [publishing this paper is] like firing the starting gun at a race.” Despite the extraordinarily dense title, the paper actually revealed revolutionary systems for editing DNA. CRISPR technology’s access to modifying DNA has led to advancements in crop resilience, medical breakthroughs, and anthropological knowledge. Using an enzyme called Cas9 that temporarily separates the 5’ and 3’ strands of DNA similar to the effects of helicase during transcription, scientists can access the nucleobases and match a guide RNA up to the relevant strand. If the guide RNA is complementary, then Cas9 will cut the DNA strand. At this point, the repair mechanisms inherent to cell regulation pounce on the DNA strand in an attempt to repair it. In the repair process, the cell must use an identical DNA strand as a template strand to repair the broken one. But scientists are clever, so at this point, a specially engineered and previously inserted DNA strand becomes the template strand. In Summary the CRISPR process takes advantage of the cell’s repair system by cutting DNA and presenting the cell with the blueprint for how to reconstruct it.

But how does this insertion end up changing our DNA? After all, how can such a tiny difference in DNA affect any biological processes when a single strand of human DNA is six feet long when uncoiled? The answer lies in DNA transcription and translation. After transcription in which a messenger RNA complementary to the template DNA strand is synthesized and processed, the mRNA leaves the nucleus and travels to the cytoplasm where translation occurs. The mRNA is effectively the blueprint for a corresponding amino acid. The mRNA enters a ribosome, where anticodons on tRNA read for the codons on the mRNA. As tRNA carries amino acids into the ribosome’s A site, the right codon-anticodon match will trigger a transfer of the amino acid from the tRNA in the P site to the one in the A site, which shifts over into the P site as its predecessor exits through the E site. The process chugs along until the polypeptide chain is complete, at which point a growth factor terminates the synthesis. Triplets of codons correspond to specific amino acids. As a result, having the right nucleobases and codons in place is crucial for attaining the desired amino acid. Thanks to CRISPR, scientists can now identify weaknesses in present DNA structures and engineer potential solutions by inserting the right DNA instructions. 

I think that CRISPR will bear the greatest fruit in the agricultural sector (no pun intended). I think that there aren’t many ethical dilemmas when it comes to engineering more resilient and abundant crops, as few would oppose solving world hunger. However, regarding livestock and poultry, CRISPR could reveal some ethical problems, specifically when the well-being of the animal is sacrificed for more short-term agricultural gain. What do you think? Will CRISPR lead the world into a new era of food security, or will it open a Pandora’s box of moral issues just as the atomic bomb did.

 

The Effect of Ethylene Gas on Plant Growth

Researcher Brad Binder, Professor of Biochemistry & Cellular and Molecular Biology, University of Tennessee, and his team, through their study, accidentally discovered that treating seeds with ethylene gas (C2H4) can enhance the plant’s growth and stress tolerance. This discovery can be a potential breakthrough for improving crop yields and improving plant’s resilience to environmental stress. Where in most cases one gets traded for the other, this revealed that by exposing germinating seeds to ethylene in darkness it is possible to increase growth and stress tolerance.

Plants produce ethylene as a hormone to regulate growth and stress responses. The accidental discovery occurred during an experiment where seeds were exposed to ethylene gas during germination in darkness. The plants exposed had larger leaves, longer root systems, and sustained faster growth throughout their lifespan compared to non-ethylene-exposed plants. The researchers extended their investigation to various crop species, such as tomatoes, cucumbers, wheat, and arugula, and all of them increased growth and stress tolerance after their short-term ethylene treatment.

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The observed effects indicated that brief exposure to ethylene during seed germination can lead to long-lasting growth and stress tolerance benefits. The researchers proposed that ethylene priming enhances photosynthesis, particularly carbon fixation, leading to increased CO₂ absorption and higher levels of carbohydrates like starch, sucrose, and glucose. These molecules contribute to both increased growth and improved stress resilience in plants.

In AP Biology we learned all about the Calvin Cycle! The Calvin Cycle is a series of biochemical reactions that occur in the stroma of chloroplasts during photosynthesis. The cycle starts when the enzyme RuBisCO captures carbon dioxide from the atmosphere, which is then attached to RuBP, forming a six-carbon compound. This compound splits into two molecules of 3-PGA, each containing three carbon atoms. Then ATP and NADPH are reduced, which generates light-dependent reactions that are used to convert 3-PGA into G3P, a three-carbon molecule. Some G3P then continues to cycle and is reused to regenerate RuBP, while the rest contributes to glucose production for cellular respiration. The Calvin Cycle is vital in converting carbon dioxide into glucose for plant growth and sustenance.

I chose this topic because I really loved the photosynthesis unit, and my favorite part about it was memorizing the Calvin cycle, and comparing it to the Citric Acid Cycle.

What specifically about the ethylene gas causes an increased efficiency in Carbon Fixation?

Pesticide Homicide

Typically what comes to mind as staples of a healthy diet  for most people is an abundant amount of fruits and vegetables and while I agree with this and there seems to be nothing wrong with them on the surface…there kind of is. In fact the issue is precisely what’s on the surface. Some research done at the University of Queensland in Australia points to pesticide as a lurking contributor to one’s risk of developing chronic kidney disease (referred to in the article as “CKD”).

CKD essentially prevents the kidney’s ability to filter waste and it’s a gradual process. As it gets worse and the person suffering from CKD experiences renal failure, waste builds up to an amount that can simply not be handled by the body, and one can experience a laundry list of complications due to the illness including but not limited to irreversible damage to the kidneys, excessive fluid retention, and damage to the central nervous system.2610 The Kidney

The study was observed among over 41,000 participants (41,847 to be perfectly accurate) and utilized data from the USA National Health and and Nutrition Examination Survey. The results were alarming to say the least. According to the data collected, those exposed to higher amounts of the insecticide Malathion “had 25 percent higher risk of kidney dysfunction”. Dr. Richard Osbourne, an Associate Professor at the School of Public health claims that “Nearly one in 10 people in high income countries show signs of CKD”. As one can imagine, that fraction of the population adds up rather quickly, resulting in millions of people at risk of or suffering from CKD. It seems very plausible that Malathion is the culprit, especially considering that it is quite literally designed to kill other organisms.

Dr. Osbourne also points to “environmental contamination, pesticide residues, and herbal medicines potentially containing heavy metals” as other possible contributors to this correlation between the consumption of Malathion and CKD. It seems as though ultimately the main issue is foreign particles being in our food.

Washing produce has always been important and should be an absolute must if one is to expect to get the best that they possibly can out of their food. If not, they just may have a consequence for an unwanted accessory to their vegetables. Not the most desired dressing, I’d imagine.

E. coli is Beneficial to Plants?

An enzyme is a biological catalyst and is almost always a protein. It speeds up the rate of a specific chemical reaction in the cell. The enzyme is not destroyed during the reaction and is used over and over. A cell contains thousands of different types of enzyme molecules, each specific to a particular chemical reaction. Studies of scientists in the past focused on improving the photosynthesis of plants using the Rubisco, an enzyme that attracts carbon from carbon dioxide to create sucrose. However, Rubisco occasionally catalyzes a reaction with oxygen and CO2 from the air. By doing so, it creates a toxic byproduct and wastes energy, therefore making photosynthesis inefficient/unsafe.

“You would like Rubisco to not interact with oxygen and to also work faster,” said Maureen Hanson, the Liberty Hyde Bailey Professor of Plant Molecular Biology in the College of Agriculture and Life Sciences.

Scientists at Cornell, Maureen Hanson and Myat Lin, wanted to solve this problem. the conclusion they reached was to utilize E.coli. In order to do this, the researchers took Rubisco from tobacco plants and engineered it into E. coli. Their objective was to make mutations to try to improve the enzyme and then test it in E. coli in a quick and efficient way.

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Colorized scanning electron micrograph of Escherichia coli, grown in culture and adhered to a cover slip.

The fact that bacteria reproduces at a quick rate is an important in their experiments. The researchers were abler to test an altered Rubisco in E. coli and get results the next day. This is a huge improvement compared to normal Rubisco, which normally takes a few months for noticeable results.

The work by another group that engineered tobacco Rubisco into E. coli led to very weak expression of the enzyme. In plants, Rubisco is composed of eight large and eight small subunits. A single gene encodes each large subunit, but many genes encode each small subunit. The complex process of enzyme assembly and the presence of multiple versions of the enzyme in plants has made it very hard to experiment with Rubisco. By doing this, they attained expression of the enzyme in E. coli that matched what was found in plants.

With this newfound ability to develop new mutations of Rubisco in E.coli, researchers can pick out the improved mutations and distribute them to a crop plant which could help improve the economy immensely. The Rubisco in E.coli will help the photosynthesis of the plants, allowing them to produce more glucose as well as oxygen gas.  This will lead to an increase in cell respiration. The chemical energy released by respiration can be used by the plant for cellular activities such as protein synthesis or cell division. The plant will ultimately grow to be bigger, healthier, and in the crops case, more tasty.

CRISPR Produce… the future of Food?

For years, people have been getting their food from, primarily, agricultural and cattle sectors; however, with CRISPR, everything is about to change. Or is it? Can CRISPR actually be used to make food in labs and completely change the way that the world receives their nourishment? These are questions that tech, scientists, and investor moguls have been asking for years, and Bill Gates’ new start up may have found the answer!  

Memphis meats, a new tech company that is backed two tech moguls, Bill Gates’ and Richard Branson, believes that they have found a new way to feed the world. The Memphis team have been successful in creating lab grown meat, using the CRISPR method. With their proprietary patented technique, Memphis meats could be changing the world. One may not understand how beneficial lab grown food would be. It would: save animals, lower the amount of water use (while raising the cattle), and be able to be made both healthier and tastier.

 

The company uses a special technique that allows them to manufacture skeletal muscle, that is edible, using cells from the poultry species Gallus gallus, and from the livestock species Bos Taurus. In addition, Memphis meats is also exploiting new and innovative ways to make their products better for the environment and public health, and more affordable, and in turn, scalable – mass produced. With all this great innovation and progress, Memphis Meats says that they are a long way from making a product that is ready for customers and consumers. However, the future of food and agriculture is promising.

What do you think? Could CRISPR and “lab meats” change the way that humans get their food? Only time will tell.

This article is by Jon Christian from Futurism. The research and technology is proprietary and patented and not for the public to see.

article: https://futurism.com/bill-gates-startup-crispr-lab-meat

Click Here to Learn About the Tomato’s Fancy New Makeover

The sun rose on a dimly light Monday morning when Adriano Nunes-Nesi, Lázaro E.P. Peres, Agustin Zsögön, Lucas de Ávila Silva, Ronan Sulpice, and Emmanuel Rezende Naves published their groundbreaking discovery that could revolutionize the cultivation of chili’s forever.   These insanely talented and well established scientists figured out how to use the CRISPR-Cas9 editing tool to turn a tomato into    a chili.

Capsaicinoids are what give peppers their heat and when these scholars of science mapped the tomato’s and chili’s genomes, they saw that the tomato has genes that, when transcribed, produce these spicy and hot capsaicinoids.

The reason why this is important is because the chili’s cultivation process is extremely tedious and requires many specific conditions, not to mention it having a small yield.  Since the yield of tomatoes is 30x that of the chili, using the CRISPR-Cas9 tool, they could change the shape and taste of the tomato to that of a chili. The price of a chili peppers, per kg, compared to tomatoes is roughly 60 cents higher. It may not seem a ton, but in bulk orders, it quickly adds up.

Lázaro E.P. Peres, who is aProfessor of Plant Physiology at the University of São Paulo and one of the scientists on the team, says, “The proof of concept here is that we can transfer the unique thing endemic to a less-produced plant into another plant that is more widely produced”.  The paper states the tomato “is highly amenable to biotechnological manipulation”. This would drive the price of the chili down which would help markets, restaurants, and Gardners worldwide.

The only issue to this is the publics opinion. For years, the already established “organic” companies having been labelling genetically modified food as unhealthy compared to non-GMO foods.  This claim is simply outright false.  “Any plant or animal product is full of DNA that our body readily digests, messing with one or two genes isn’t going to impact human health. The only way GM food could affect human health is if the modification somehow produce a protein product that was actively toxic to humans.”  This quote is from an article by the Genetic Literacy Project, which could be seen as having bias towards GMO foods, however their mission says,”is to aid the public, media and policymakers in understanding the science and societal implications of human and agricultural genetic and biotechnology research and to promote science literacy.”  All they are interested in doing is educating the public because so many people have been lied to by big organic corporations and the media to prevent customers from eating GMO products.  What would they have to gain by saying they are safe when they are not?    If the public can get passed the idea of genetically modifying foods, I believe turning a tomato into a chili pepper would save much money from hundreds of thousands of businesses– big or small.

What do you guys and gals think of GMO products?

For more information, please go check out the primary source of this article and the researchers report

 

 

Pinot Microbiome- The Wine You Won’t Want to Miss

the brat pack

Sauvignon Blanc, Merlot, Pinot Grigio, Chardonnay, Chablis. Wide varieties of wine are caroused every day, all over the world. Wine connoisseurs will tell you that the taste of each type is radically different. For example, while a Chardonnay flawlessly compliments a chicken or fish dish, a Cabernet Sauvignon is the only appropriate pairing for a simple red meat dish. Scientists and wine experts have grappled with understanding what variable gives wines their distinct flavors for decades. In the past, the public hypothesis was that geographic/environmental features such as soil, fertilizers, temperature and other agricultural features give wine its distinct character. However, this understanding was recently proven (at least partially) wrong with the release of a new scientific study.

Biologists from the University of Lincoln and the University of Auckland recently discovered that the reason for the differences in terroir are not due to environmental factors. Instead, these variations are due to the different microbes used during fermentation. Microbes are microscopic, single-cell organisms. Bacteria, protists, fungi, protists, and archaea (and some viruses) are all types of microbes. This study focuses on how the microbes used during fermentation of the grapes affects the terroir. Microbes make up the yeast used for fermentations in the different wine making regions. The yeast most commonly used is called saccharomyces cerevisiae yeast. This study looked at six variations of this yeast. The resulting data showed that different wines produced different chemical compounds (which give wine its character) through fermentation depending on which yeast was used. This result indicates that microbes are an important factor in the wine-making process, and the character of wines.

This study is important for the scientific community because it indicates that environmental conditions may not be the only factors that contribute to the physical characteristics of plants. It may lead to further studies to see if other types of microbes affect regional agriculture. For the general public, this study gives deeper and biological insight into the process of making wines. Wine serves as a foundation for socializing, fine dining, and much more. Wine tasting is an age-old tradition, and I believe that any new information will be valued by many people around the world. In class we have begun to discuss the structures and make up of different types of microbes and other organisms. This new study is an accessible application of their effect in the real world.  What are your thoughts? Does this change how you look at, or should I say sip, your wine? Let me know in the comments below.

Sources:

http://www.nature.com/articles/srep14233#methods

http://www.sciencedaily.com/releases/2015/09/150924104314.htm

http://www.alphagalileo.org/ViewItem.aspx?ItemId=156664&CultureCode=en

Leading photo by Filtran found here.

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