AP Biology class blog for discussing current research in Biology

Author: shallele

Potato, Patato No More? Scientists have cracked the code to diversifying the classical starch

With gene-editing technologies such as CRISPR, the variety in produce has been growing at greater rates than ever. It seems as if it is only a matter of time until we get a talking pepper. However, potatoes have been lagging behind. A potato may look quite simple to the human eye, but it is actually quite complex in the world of genomes. For this reason, the human genome was discovered more than 20 years before the genomes that make up a delicious fast food French fry.French Fries

So what is it that makes the potato genome puzzle so difficult to crack? Human offspring receive one of each chromosome from the mother and father, while potatoes receive two of each chromosome from each parent. This results in 4 total copies of each chromosome and in turn four copies of a given gene. A species such as this is called tetraploid. The increase in genes per trait makes editing a given trait that much more difficult. Another task of great difficulty is recreating the potato genome. A task much more difficult than doing so for humans. 


Haploid, diploid ,triploid and tetraploid

Scientists Korbinian Schneeberger and Hequan Sun found a clever shortcut. They realized that the pollen cells of potatoes, similar to gametes in humans, contain only half the chromosomes of a body cell. Pollen cells are by this logic, diploid cells containing two of each chromosome. Sequencing the DNA of large amounts of pollen cells allowed the scientists to map out the full genome of a potato. The construction of this genome will make identifying and editing diverse variants of potatoes a much easier task. 

This begs the question of why? Why do we need variety in species of potato? Historical events such as the Irish potato famine of  1840 are a prime example of the importance of produce variety. The famine was caused by tuber blight. A potato is a tuber, a storage stem of plats, and blight is a plant disease commonly caused by fungi. Despite being the most important crop and source of food at the time in most of Europe, the incredible lack of variability of a potato meant no species of potato was resistant to the disease. With concerns over climate change, and an increase in potato popularity; “The potato is becoming more and more integral to diets worldwide including even Asian countries like China where rice is the traditional staple food. Building on this work, we can now implement genome-assisted breeding of new potato varieties that will be more productive and also resistant to climate change — this could have a huge impact on delivering food security in the decades to come.” (Max Planck Institute for Plant Breeding Research), make this issue more important than it may appear. 

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

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.



Vampires and COVID-19? They may have something in common; and spoiler, it has nothing to do with bats

Researchers from Trinity College Dublin and the University of Edinburgh think they may have found a new weakness of COVID-19; sunlight! More specifically,  ambient ultraviolet B (UVB) radiation which provides the body with vitamin D. The researchers knew of previous studies of the susceptibility of those with vitamin D deficiency to not only receiving the virus, but also experiencing the entirety of it’s wrath. However, in most cases measures weren’t taken to rule out the possibility of confounding factors (other conditions that can cause both vulnerability to COVID-19 and vitamin D deficiency). In order to jump this hurdle, the researchers used “genetically predicted” vitamin D levels.

Sunny day

With this averaged sample, the researchers used an analytical process called Mendelian Randomization . The process allowed them to test correlations between Vitamin D levels and COVID-19. This process had been attempted in past studies, and the researchers results did not contradict previous conclusions; a link between vitamin D levels and COVID-19 was not evident. However, the researchers of Trinity and Edinburgh wanted to test the effects of UVB radiation. UVB radiation from sunshine is the most important supplier of vitamin D for many, yet it was not included in previous studies.


Studying almost half a million people from the UK, the researchers compared the genetically predicted levels effect versus UVB predicted levels effect on COVID-19 infection. “researchers found that correlation with measured vitamin D concentration in the circulation was three-fold stronger for UVB-predicted vitamin D level, compared to genetically-predicted” (Trinity College Dublin). The researchers found a correlation of high strength in the negative between UVB radiation and hospitalization and death due to COVID-19 as well.

While the researchers admit that the sample size of the study is not quite large enough to be entirely conclusive, especially considering the surprising deviation from the results of the genetically predicted study, they are optimistic that with time their theory will prove significant. The odds are with them as vitamin D has been found to be a benefactor of the immune system in general. A fact demonstrated by the presence of vitamin D receptor on both B and T cells, and the trend of higher susceptibility to infection of those with lesser amounts of vitamin D.


A New Way to “Tangle” with Diseases? British Scientists Think They’ve Stumbled Upon the Future

A team of scientist from the Universities of Bath and Birmingham have made a discovery that is making noise in the world of Biology. Ironically, they had the realization while studying silent mutations in DNA. What they found is a new method of evolution. Well not a new method per say as the scientists predict this method is being used in all forms of life; however, new in the sense that it was only recently realized. What they have discovered is a trend of tangles in DNA strands. This tangling occurs in DNA strands that are not in a double helix as DNA typically is. However The DNA strands are separated during copying. This task is done by DNA polymerase enzymes. During the copying process, the enzymes are often disrupted by the tangles in the strand. The resulting skipping of genes causes specific mutations to the DNA.

DNA replication split horizontal

The scientists then tested their hypothesis by way of experiment. They did so by studying the evolution of soil bacteria called Pseudomonas fluorescens (SBW25 and Pf0-1). They began by removing the gene that give the bacteria the ability to swim. They then observed the re-evolution of the strains to regain the ability swim. Both strains evolved quickly; however, there was a clear differences in predictability. One strain (SBW25) mutated the same part of a particular gene in every trial. The other strain (Pf0-1) varied in which gene and where the mutation occurred in each trial. Upon further observation, this contrast coincided with a hair-pin shaped tangle in the SBW25 strain. As the DNA polymerase enzymes would pass this tangle they would be effected in a predictable manner that would disrupt copying of DNA and result in a mutation that allows for the bacteria to swim. The scientists tested the theory by removing the tangle. They did so using 6 silent mutations so that the DNA sequence would not have a relevant change. The trials after the change showed that both strains showed inconsistent areas being mutated.


DNA are the dictators of protein synthesis in the body. The DNA sequences code for the types of proteins that are created. Proteins perform many of the bodies function. This means that even the slightest change in the sequencing of DNA can have major effects on the functioning of a human body or any organism. The process of evolution was thought to be caused by random errors in DNA sequencing that coincidentally gave an organism a survival advantage. These mutations would then be tested in the concept of survival of the fittest. While this is still thought to be the most prevalent form of evolution, especially with eukaryotic organisms, the tangling of DNA strands proposes a form of evolution that would be easier to study and predict.


The predictability of such a phenomenon is where the intrigue in viruses arises. “If we knew where the potential mutational hotspots in bacteria or viruses were, it might help us to predict how these microbes could mutate under selective pressure.” says Dr. Tiffany Taylor, from the Milner Centre for Evolution. Mutational hotspots have already been found in cancer, and the new information on their significance is getting scientists excited about the opportunities present. The new ways to understand and predict evolution of bacteria and viruses may allow scientists to be a step ahead on vaccines and be able to anticipate and understand new variants. It’s hard not to think this information would’ve been nice before the rise of SARS-CoV-2.

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