BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: plants

Sour Science!

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On November 5, 2023

In Student Post

Have you ever enjoyed an orange and wondered what causes its amazing citrus flavor? Well, scientists have recently discovered the origins of citrus’s sour taste. 

Scientists have recently discovered the origins of citrus fruits like oranges and lemons. In their study, they discovered a specific gene, PH4, that influences the fruits’ taste by regulating the fruits’ citric acid levels. Additionally, the researchers traced the fruits’ evolutionary journey from the Indian subcontinent to south-central China over millions of years and discussed influences that environments may have had on the citrus.

There are many reasons why these fruits evolved the way they did. One reason discussed in the article is human interference through selective breeding. Thousands of years ago, humans selectively bred certain types of citrus for food and medicinal purposes. Another reason they might have evolved to have more citric acid is to prevent bacterial infections. Bacteria, generally, prefer neutral environments with a pH of about 7. o.  Citric acid has a pH of about 3.2. Therefore, the more citric acid a fruit has the less likely bacteria can infect the fruit.

This relates to AP Bio through the involvement of genes in protein synthesis. During protein synthesis in a cell, the first thing that happens is transcription where information on the DNA is transcribed onto mRNA. The mRNA then is sent to the Rough Endoplasmic Reticulum where it is received on the cis face. There, on the ribosomes of the rough ER, the protein is synthesized. The type of protein that is synthesized here is determined by the information of the mRNA. Then the protein is sent to the Golgi where, based on the information from the mRNA, molecules are added to determine the final location of the protein. Genes, including PH4, are sections of DNA. Therefore, the PH4 gene, in part, determines what type of proteins are produced by the cell and where they go.

Wow! It is fascinating how a gene can influence an orange’s taste. I found this research so interesting because I love oranges. I wonder how other plants’ genes influence their taste?

Genetically Engineering the Food We Eat to Increase Consumer Desire

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On April 26, 2022

In Student Post

Solanaceae is an order of classification for a group of plants known as nightshades. The Solanaceae are a family of plants that ranges from annual and perennial herbs to vines, shrubs, and trees. Included in this family of variety are also a number of agricultural crops like tomatoes, medicinal plants like jimson weed, spices, weeds, and ornamentals. This group of plants are given the term “nightshade” because some of these plants prefer to grow in shady areas, and some flowers at night.Solanum americanum, fruits

The Solanaceae is one of humankind’s most utilized and important families. It contains some of the world’s most important vegetables as well as some of the most deadly toxic plants. Foods like potato, tomato, peppers, ground cherries, and eggplant all hail from this incredible plant. With the benefits of this plant family also comes the dangerous variety of plants. The belladonna, mandrake, Jimson weed, and tobacco also come from this family. Solanum trilobatum flowersNot only does this family of plants produce important vegetables and deadly plants, various chemicals and drugs can be harvested. Some of these include nicotine, solanine, capsaicin, atropine, scopolamine, and hyoscyamine.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a gene editing tool that can be used to edit DNA in cells. It used a specific enzyme called Cas9, which stands for CRISPR associated nuclease 9, and a specific RNA guide to either disrupt host genes or insert sequences of interest. CRISPR was initially used in bacteria as an adaptive immunity response but is now being used as an alternative in genome engineering.CRISPR illustration gif animation 1

In the agricultural world, plant breeding has always been the way to improve the traits wanted in a plant. With technological improvements, increased production has been vastly upgraded. Recent advances in gene editing have revolutionized the field of plant breeding. The process of genetic engineering has allowed people to target specific genes to improve rather than continuous breeding to produce the desired trait. 

Consumers choose the type of foods they want to eat by the traits of the fruit/vegetable, and in response, it leads the path to ensure that plant breeding will produce that trait again. In the horticulture industry, fruits are an important food that many people buy. Fruits are known to have a crucial source of energy, vitamins, fibers, and mineral components. The larger the fruit, the less sour and more nutrients it tends to store, influencing consumers to buy fruits that are bigger in size and shape. As a plant family with various crops, Solanaceae crops have a variety of fruit sizes and shape features. With advancing gene editing technology, Solanaceae fruit crops have been on the receiving end of being genetically modified to increase desirable traits of fruit size, fruit weight, fruit quality, and plant architecture.Maduración del tomate (Solanum lycopersicum)

Many of the vegetables and fruits we eat today are slowly being improved with CRISPR. For instance, in tomatoes, the ARGONAUTE7 (SlAGO7) gene function in leaf shape development was one of the first edits done with CRISPR Cas9. Tomatoes have been at the forefront of CRISPR Cas9 gene editing on plants because it is a model crop that is able to grow variability. Many more plants of the Solanaceae family, like the goji berry and groundcherry, have been engineered to produce the best product and CRISPR gene editing will continue to enhance the fruit and plant.

This CRISPR gene editing research on the order of Solanaceae plants is relevant to AP Biology because of gene editing. In the first year of biology, we learned about the taxonomy of species and the order of specificity. The order of Solanaceae plants indicates that it isn’t a particular family of plants that includes the different genus and species. Instead, it is a broader classification. We didn’t specifically learn about CRISPR gene editing in class this year, but we learned about DNA and RNA and their replication process. In a way, we learned about CRISPR because it relies on a strand of RNA with the preferred traits that is then transcribed into DNA.

Cancer In Humans VS. Plants

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On February 25, 2022

In Student Post

Cancer is a disease that has ranked 2nd in the deaths of the US only falling behind to heart disease. In our AP Biology class, we learned that cancer in humans is caused by a cell that has a genetic defect that is multiplying too quickly causing clumps and tumors. Whilst this has been devastating to humans and other animals for years, how does it affect plants that are another kind of multi-cellular organism?

An article that highlights the effects of cancer on plants states that cancer in plants acts differently than cancer in humans. Within plants, the cells aren’t moving so it can’t affect many other tissues like in animal cells. Furthermore, plants, specifically trees, don’t have any vital organs whereas with humans if cancer reaches an organ such as the Brain or the Liver we will die, however, if cancer reaches a branch the tree can simply grow a new one. In a New York Times article, C. Claiborne Ray states that “Excess plant cell production in the form of galls sometimes benefits future generations of insects” This relationship is not seen in Animals and can really help the wasps as they lay their eggs in the fast-growing tissue. Cancer in plants can almost be seen as helpful to the environment.

Cancer stem cells model

Cancer in humans is vastly different because there is no upside to having cancer as an animal. Cancer in animals is caused by an old cell not dying but instead rapidly multiplying and thus creating an abundance of defective cells that cause things such as tumors and if it were to reach your vital organs you would most likely die. In humans, the only real way to treat cancer so far is to use Chemotherapy. This method of treatment is very basic as it doesn’t distinguish between what fast-growing cells are which and kills any cell that is growing too fast. It is not 100% effective nor is it side effect free. The patient’s hair falls off as hair is very fast-growing and the therapy believes that it is cancer cells so they kill it off.

In conclusion cancer in Humans and Plants are similar at the beginning with things such as how they contract cancer and what exactly happens. However, the effects for plants are severely less than the effects on humans. While plants cancer gives a nice home for wasps to lay eggs as well as simply give the plant a minor bump. Human cancer is a devastating disease that caused the death of millions. Let me know what you think down below!

 

Plant Therapists: Scientists help plants make the decision to regenerate rather than defend themselves after injury

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On February 25, 2022

In Student Post

Plants are very susceptible to injury in many forms. They can’t hide from a hungry bunny rabbit or invasive fungi. As humans, we have “fight or flight” instincts, but flight is a tall order for plants. Instead, they have “fight or fix” instincts. When damaged plants have two responses, to repair and regenerate or defend. New York University’s Center for Genomics and Systems Biology decided to perform a study on this known quality of plants.

The defense method is the production of specific compounds, but the scientists’ experiment focused on the regeneration response. “Breeding crops that more readily regenerate and can adapt to new environments is critical in the face of climate change and food insecurity” said NYU professor and leader of the study, Kenneth Birnbaum. The study was split into two parts a study, and an experiment.

Early corn crop

The goal of the study was to understand the relationship between regeneration and defense responses. Does one happen or the other? Can they occur simultaneously? Does affecting one response have a subsequent affect on the opposing response?

The Scientists studied two plants; Arabidopsis and corn. Arabidopsis is common used as a model organism by plant biologists, while corn is the America’s largest crop. The answers they found to the previously posed questions are as follows. In most cases, both responses happen simultaneously and neither are at full strength. When the Scientists manually affected one of the responses, the other response did increase in frequency as a result. As Marcela Hernández Coronado of Cinvestav in Mexico put it, “The ‘fight or fix’ responses seem to be connected, like a seesaw or scales — if one goes up, the other goes down. Plants are essentially hedging their bets after an attack,”

The scientists were able to narrow down the cause of varying level of each response to plant glutamate receptor-like (GLRs) proteins. These receptors are related to glutamate receptors found in the human brain; hence the title of “Plant Therapists”. They learned that these receptors are responsible for regulating regeneration response and in turn, increasing defense response.

Competitive inhibitorConsidering the relationship with neural receptors, the scientists used preexisting drugs meant for these relative receptors. They used neural antagonists to inhibit GLRs. The antagonists are competitive inhibitors, that bind to the active site of the receptor blocking reception of signal molecules. The limited activity of the GLRs made the plants decide to heavily favor regeneration as the signals telling it otherwise were blocked.

The scientists also studied “quadruple mutants” in comparison to normal plants. The plants with mutated GLR had an increased rate of regeneration, further proving the effects of GLR on regulating the ratio between the two responses. Overall however, the plants that were given the neural antagonists were more successful in increased regeneration than the quadruple mutants.

 

 

How Do Guard Cells Attain Energy?

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On February 15, 2022

In Student Post

Ever since we were young, we understood that plants utilize photosynthesis for energy, releasing oxygen in the process. But, we did not learn which parts of the plant actually perform photosynthesis. This is highlighted by guard cells, the cell located in the upper epidermis that controls the concentration of Carbon Dioxide in the plant. So how do they contribute to photosynthesis?

Stomata & Guard Cells

The team of Dr. Boon Leong Lim at HKU wanted to observe the real-time production of ATP and NADPH in the mesophyll cell chloroplasts, which was done by using planta protein sensors in a model plant, Arabidopsis thaliana. This plant is specifically used due to its small genome, short life cycle, simple process to mutagenize, and easily identifiable genes. Shockingly, the Guard Cells Chloroplasts have not detected any ATP or NADPH production whatsoever. Looking for answers, the researchers decided to contact Dr. Diana Santelia, an expert in cell metabolism. Throughout a decade of research and collaboration, they finally have an answer.

Unlike mesophyll cells, photosynthesis in the Guard Cells is inadequately regulated. This is because synthesized sugars from the mesophyll cells are imported into the Guard cells, in which is used ATP production for the opening of the stomata. Additionally, Guard Cells chloroplasts take cytosolic ATP through nucleotide transporters on the chloroplast membrane for starch synthesis throughout the day. At night, though, Guard Cells degrade starch into sugars for the opening of the stomata. Mesophyll Cells, on the other hand, synthesize starch and export sucrose at dawn. Thus, the chloroplasts of Guard Cells ultimately serve as starch storage for the opening of the stomata. Their function is closely linked to that of MCs in order to effectively coordinate CO2 absorption through stomata and CO2 fixation in MCs. 

Although the Guard Cells seem redundant, their role in the overall process of photosynthesis is absolutely necessary. As seen in AP Bio, the stomata are essential for gas exchange for photosynthetic reactions. The stomata’s main role is to take in Carbon Dioxide and release Oxygen, both of which are necessities for the reaction to occur. 

Thank you so much for reading this blog, and let me know what you think in the comments below!

How are animal carcasses beneficial?

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On January 23, 2020

In Student Post

Studies prove that carcasses of dead animals are important for plant growth. Researcher, Dr. Roel van Klink, conducted an experiment and concluded that carrion, the decaying flesh of dead animals, is essential for many species. Since, carrion of large animals is an extremely nutrient rich, ephemeral resource. The Oostvaardersplassen Nature Reserve found that the leaving the deceased animals on the ground has had a positive effect on biodiversity. The remains attract more insects and other arthropods and increase plant growth. After five months the plants were significantly larger than usual; the biomass was five times larger and nutritional plant quality was higher than the controlled sites.

Many debates have started from this proposition to keep dead animals in nature reserves. The European legislation requires any dead animal to be removed or destroyed, unless the aim is to provide food for endangered scavengers, like vultures. However, in places like Kenya and Tanzania, the Mara River’s ecosystem relies on rotting carcasses for sustenance. The disposal of wildebeests in the river, not only feeds scavengers, but also releases nutrients (phosphorus and carbon) into the river after their body decomposes and releases algae and bacteria, which also nourishes the fish. Although many nature reserves benefit from this concept, the Oostvaardersplassen nature reserve abused their power in 2017-2018. The reserve starved 3,300 deer, horses and cattle to death. These opposing views cause controversy on whether or not decaying animals are beneficial or detrimental to the economy.

Many ecosystems rely on rotting carcasses for sustenance. In the ocean, over 60 species live off of the “whale-fall” communities. This is when a large whale dies and their body sinks to the seafloor, into a new ecosystem. Scavengers (hagfish, sleeper sharks, amphipods, etc.) in the ocean tear away large pieces of soft tissue from the whale and later, “bone-eating” worms help to digest the whale carcass. These new species, developed from the “whale-fall” communities, can last decades in the deep ocean. Unfortunately, many whales suffer from commercial whaling, which also affects the food chain for animals that eat whales. This time of mass slaughter killed off as many as ninety percent of living whales during the 18th and 19th century. Therefore, some of the first extinctions in the ocean have been from whale-fall communities.

Personally, I believe that animal carcasses are beneficial to nature and should be allowed. Though, some people abuse their power to benefit their own land, by slaughtering animals. For that reason, there should be set regulations to ensure the safety of animals so people won’t just go around killing innocent animals for their own advantage.

Is Photosynthesis the Key to World Hunger?

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On January 12, 2019

In Student Post

With a global human population growth of about 83 million annually, one of the most pressing questions of the 21st century is how we will support our ever expanding population. A central study apart of the RIPE (Realizing Increased Photosynthetic Efficiency) International project may have found a key contributor to the solution.

Photosynthesis functions using an enzyme Rubisco and sunlight to turn carbon dioxide and water into sugars and oxygen. Overtime, Rubisco has created our oxygen rich environment, and now is unable to discern accurately between molecules of oxygen and molecules of carbon dioxide. 20% of the time Rubisco will grab oxygen instead of carbon dioxide, creating a toxic substance which must be recycled through a process known as photorespiration. Scientists from the University of Illinois and the U.S. Department of Agriculture Agricultural Research Service reported that plants engineered with photorespiratory shortcuts are 40% more productive in real life situations.

Currently being tested with genetically modifying tobacco plants, experts hope to apply this technology to food related crops within the next ten years. This represents a massive feat for addressing world hunger, as 200 million people could be fed with the calories lost to photorespiration in the midwest United States alone. RIPE and sponsors such a the Bill and Melinda Gates Foundation have pledged to allow small farmers (especially in sub-saharan Africa and Southeast Asia) free access to any project discoveries.

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

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On January 12, 2019

In Student Post

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

 

 

Did You Know Plants Can Talk?

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On October 14, 2018

In Student Post

 

For thousands of years language has been a crucial part of cultures around the world, and a method unique to humanity of transmitting ideas, thoughts, emotions between us. Language has allowed us to work harmoniously together for our mutual improvement and survival. Recently, however, two researchers, Dr. Kim Valenta and her colleague Omar Nevo, have discovered that plants too, have developed their own unique and intricate method of conveying information to their pollinators; “the easier it is for fruit eaters to identify ripe fruits, the better the chance for both [, the plant and the fruit,] to survive.

The most vivid example of plant communication can be found in Madagascar’s Ranomafana National Park and Uganda’s Kiabale National Park where berry plants have evolved “to match each animal’s sensory capacities, [thus] signal[ing] dinner time in the jungle…” Dr. Valenta and Nevo analyzed the exact colors of each fruit with a spectrometer, and “with a model based on the visual capacities of the seed-dispersing animals, they also determined who was most likely to detect different fruit colors contrasting against an assortment of backgrounds.” The researchers concluded that “the colors of each fruit were optimized against their natural backdrops to meet the demands of the visual systems of their primary seed dispersers,” i.e. pollinators. Thus, red-green color-blind lemurs, in Madagascar were best able to detect the fruit with a blue yellow color scheme and monkeys and apes in Uganda, with tricolor vision like humans, were clearly able to distinguish red berries against a green backdrop.

Also recently discovered was that plants can communicate to their pollinators through scent. Dr. Nevo performed a scent-based study on the lemurs in Madagascar. His team collected various ripe and unripe fruits from all over the jungle of Ranomafana. “He suspected the leumur-eaten fruits would have a greater difference in odor after they ripened than the bird-eaten fruits.” To discover exactly how this scent-based communication worked, Nevo used the “semi-static headspace technique.” From this experiment it was confirmed that “fruits dispersed solely by lemurs produced more chemicals and a greater assortment of compounds upon ripening. It is now known that wild lemurs actually spend quite a lot of time smelling for the vivid difference in odor between ripe and unripe fruits in the jungle.

It is astonishing how plants have evolved over the years to be able to communicate with their pollinators for the betterment and expansion of their species. I would be interested to find out, what other organisms communicate (single cellular, multi-cellular, etc.) and what kind of information they find necessary to convey to others for their survival?

 

 

 

 

Secrets (almost) Revealed about the Evolution of Plants

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On January 11, 2012

In Student Post

Now that we are studying plants in class, and learning about different adaptations and some of the evolution of plants I thought this study would be interesting to look at.

The sequencing of the genome of a plant known as spikemoss, may give scientists a better understanding of how all kinds of plants evolved over the past 500 million years! This is the first sequencing for a non-seed vascular plant. Selaginella has been on this earth for about 200 million years and is a lycophyte

I was surprised that the Selaginella genome has about 22,300 genes and that’s small according professor Jody Banks. Selaginella is the only known plan to not have experienced a polyploidy event and is also missing the genes known in other plants to control flowing and becoming and adult. These genes are unknown in the Selaginella, but the genome would help scientists understand how these plants genes give the plant some unique characteristics and also help understand how Selaginella and other plants are evolutionarily connected.

The genome sequence was compared with others, and researchers identified genes that are present only in vascular and flowering plants. These genes that were identified most likely played important roles in the early evolution of vascular and flowering plants. Many of these genes have unknown functions, but it is likely that those genes that were identified may function in the development of fruits and seeds. Banks said: “[having an idea of what the function of the genes is] gives us ideas. It’s an important piece of the puzzle in understanding how plants evolved.” Also there are metabolic genes that evolved independently in Selaginella and flowering plant, which means Selaginella, could be a huge resource for new pharmaceuticals. The Selaginella is defiantly an interesting and great plant to study.

Photo Credit:http://www.flickr.com/photos/ki/195802378/

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