AP Biology class blog for discussing current research in Biology

Author: biodevirsity

HIV Resistance to CRISPR/Cas9

A recent study, described in the Science Daily, shows that researches who used the CRISPR/Cas9 to mutate HIV-1 within cellular DNA found that the mutation led to unexpected resistance.

When HIV enters a cell, its RNA genome is converted into DNA and becomes intertwined with the cellular DNA. So the goal for the CRISPR/Cas9 is to target a DNA sequence and cleave viral DNA. The problem is HIV is too good at surviving and thriving despite new mutations, making it more difficult for the CRISPR/CAS9 to target.


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Chen Liang, Senior Investigator at the Lady Davis Institute at the Jewish General Hospital, noted that when they sequenced the viral RNA of escaped HIV, they were surprised to see that majority of the mutations the virus had, instead of resulting from the errors of viral reverse transcriptase, were rather introduced by the cellular non-homologous end joining machinery when repairing the broken DNA.

The mutations to the sequences caused by the HIV were unrecognizable to the Cas9. Thus the resistant viruses just continued to replicate.

This study serves as a cautionary tale for scientists hoping to apply CRISPR/Cas9 as an antiviral. Liang does not believe these efforts are useless, however, as he is hopeful about strategies that could overcome this roadblock. One such strategy would be to target multiple sites with CRISPR/Cas9 or use other enzymes besides Cas9. After the solution is identified, the next step will be figuring out ways to deliver the treatment to patients. Liang is confident that CRISPR/Cas9 will open doors for finding a cure for HIV-1 and many other viruses.

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“Selfish” DNA Defies Mendel’s Laws

R2D2 may be a heroic Star Wars character but in living animals it is a piece of DNA which violates laws of both genetic inheritance and Darwinian evolution. It has swept through mouse populations by mimicking helpful mutations when in fact it damages fertility. These new findings, described in this article by ScienceNews,  propose that even genes that are dangerous to an organism’s evolutionary chances can trick their way to the top. This is a warning for scientists looking for signs that natural selections has picked certain genes because they offer an evolutionary benefit. What looks like survival of the fittest may actually be a “cheater” prospering.


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Geneticist John Didion and colleagues examined DNA samples from wild mice from Europe and North America to determine how widespread R2d2 has become. The proportion of mice with the selfish gene more than tripled in one laboratory population from 18 percent to 62 percent within 13 generations. In another breeding population, R2d2 shot from being in 50 percent of the lab mice to 85 percent in 10 generations. By 15 generations, the selfish element reached “fixation” — all the mice in the population carried it. The rate of spread was much faster than researchers predicted—it was projected it would take 184 generations for the selfish DNA to spread to all of the mice.

R2d2 is a “selfish element,” a piece of DNA that causes itself to be inherited preferentially. It is a stretch of DNA on mouse chromosome 2 that contains multiple copies of the Cwc22 gene. When seven or more copies of that gene build up on the chromosome, R2d2 gets “selfish.” In female mice, it pushes aside the chromosome that doesn’t contain the selfish version of the gene and is preferentially placed into eggs. This violates Gregor Mendel’s laws of inheritance in which each gene or chromosome is supposed to have a fifty-fifty chance of being passed on to the next generation. But there is a cost to R2d2’s selfishness: Female mice that carry one copy of the selfish element have small litter sizes compared with mice that don’t carry the greedy DNA. The loss of fertility should cause natural selection to sift out out R2d2. But the selfish element’s greed is greater than the power of natural selection to combat it, as the lab experiments show.

But based on further lab experiments, researchers may have found that even this successful cheat can get caught. These other results revealed a relatively low proportion of wild mice carrying R2d2. Evolutionary geneticist, Matthew Dean says this could mean that some mice have developed ways to suppress the gene’s selfishness. There is still much more research to conduct on this topic.

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Possible Connections between the Gut Microbiome and the Brain

It is not a new concept that gut bacteria affects a person’s health. But this article published in The Atlantic explains how they may even affect the human brain. Some researchers believe that the microbiome may play a role in regulating how people think and feel. Scientists have found evidence that this community of bacteria (trillions of cells that together weigh between one and three pounds) could play a crucial role in autism, anxiety, depression, and other disorders.


Much of the most intriguing work has been done on autism. For years, it has been noted that about 75 percent of people with autism also have some gastrointestinal abnormality, like digestive issues or food allergies. This has prompted scientists to search for potential connections between the gut microbiome and autism; recent studies find that autistic people’s microbiome differs significantly from those of control groups. Caltech microbiologist Sarkis Mazmanian specifically focuses on a species called Bacteroides fragilis, which is seen in smaller quantities in some children with autism.  Mazmanian and several colleagues fed B. fragilis from humans to mice with symptoms similar to autism. The treatment altered the makeup of the animals’ microbiome, and more importantly, improved their behavior: They became less anxious and communicated more with other mice.

Perhaps the most well-known human study was done by Emeran Mayer, a gastroenterologist at UCLA. He recruited 25 subjects (all healthy women) for four weeks. He had 12 of them eat a cup of commercially available yogurt twice a day, while the rest didn’t. Yogurt is a probiotic, meaning it contains live bacteria. In this case it contained four species: bifidobacterium, streptococcus, lactococcus, and lactobacillus. Before and after the study, subjects were given brain scans to gauge their response to a series of images of facial expressions—happiness, sadness, anger, and so on.

To Mayer’s surprise, the results showed significant differences between the two groups. The yogurt eaters reacted more calmly to the images than the control group. “The contrast was clear,” says Mayer. “This was not what we expected, that eating a yogurt twice a day for a few weeks would do something to your brain.” He thinks the bacteria in the yogurt changed the makeup of the subjects’ gut microbes, and that this led to the production of compounds that modified brain chemistry.

As scientists learn more about how the gut-brain microbial network operates, they think it could be manipulated to treat psychiatric disorders. And because these microbes have eons of experience modifying our brains, they are likely to be more precise and subtle than current pharmacological approaches, which could mean fewer side effects. “I think these microbes will have a real effect on how we treat these disorders,” neuroscientist John Cryan says. “This is a whole new way to modulate brain function.”

New Findings Uncover Clues to Mars’ Watery Past

Mars used to have flowing water, a thick atmosphere, and a magnetic field. But now it is only covered with dusty riverbeds and its air is practically a vacuum. Now how did that happen?! In order to uncover what happened to the planet’s lost features, a spacecraft MAVEN was sent out to search for clues. The probe was able to fight through the red planet’s turbulent lower atmosphere and witness a shimmering aurora and solar storm. The data the probe brings back gives scientists a glimpse into Mars’ past and scientists have now presented the mission’s first findings.


Mars was a different planet in a different solar system billions of years ago. Scientists believe the planet was stripped of its water and atmosphere because the sun was much hotter and radiating then. As Dave Brain, atmospheric physicist at the University of Colorado, said, “Imagine you have a pot of water on the stove and that represents the atmosphere. MAVEN is orbiting Mars at a time when the burner is at a low setting. And by looking at the steam, scientists can extrapolate back to a time when the burner is at a low setting.” The probe is jammed with instruments that count charged ions, measure solar wind, scan for ultraviolet energy, detect magnetic fields, and collect dust.

Thus far, the most impressive findings came from watching the effects of essentially a monster solar storm on the planet’s atmosphere. This was highly significant because, as Brain said, “solar storms are really windows to the past. We got to see what happens when a lot of energy hit all at once.” Solar storms can potentially strip away a ton of atmosphere and they are what most likely happened all the time billions of years ago.

One reason the red planet’s atmosphere is so susceptible to solar activity is due to its lack of a strong magnetosphere. When the sun gets riled up and fires dangerous and energized “blobs” at Earth, our planet’s electromagnetic barrier shields the attack and redirects it towards the poles. While traveling along the magnetic lines towards the poles, the solar particles pick up charge, which they release when encountering particles in Earth’s atmosphere, thus emitting light—an aurora.

Scientists were surprised when MAVEN witnessed an aurora on Mars since the planet does not have a magnetosphere. The aurora lasted five Martian days and potentially even enveloped the whole planet. This is a new kind of aurora for scientists as it doesn’t require a magnetic field. Unfortunately the team doesn’t have any noteworthy pictures of the aurora since the probe only caught it on its ultraviolet imager.

There were other impressive findings as well. “Mars has pretty significant topography,” says Stephen Bougher, an atmospheric scientist at the University of Michigan and MAVEN co-investigator. Surface winds bend over features like Olympus Mons, and those disruptions propagate upward into the atmosphere. “Just like a wave coming onshore would crest and break, atmospheric waves crest and break,” says Bougher. But those winds don’t even explain the presence of heavy dust particles high up in the Martian atmosphere. MAVEN collected dirt from more than 600 miles up that defied the dynamics of Martian gravity. “The puzzle is how did that dust get up so high,” says Brain.

These findings aren’t just flashy—they’re scientifically major. They will help scientists understand more about how and why Earth’s atmosphere is so stable, and give interplanetary scientists a better idea of what to expect in future Martian expeditions. “You can figure out what dosage of radiation astronauts would be getting as they set up shop on the surface,” says Bougher. “You don’t want to send astronauts to certain death without exploring the risks.”

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New Species Related to Humans Uncovered

On September 10th, 2015, the University of Witwatersrand, the National Geographic Society, the Department of Science and the National Research Foundation of South Africa announced the discovery of a new species of human relative, Homo naledi. With more than 1,500 numbered fossil elements, this discovery is the largest fossil hominin find ever made on the continent of Africa. Not only does this finding shed light on the origins and diversity of our genus, but it appears that this new species intentionally deposited the bodies of its dead in a remote cave, an action previously conceived limited to humans.


The species was initially discovered in 2013 in a cave known as Rising Star in the Cradle of Humankind World Heritage Site, some 50 km northwest of Johannesburg, South Africa. The fossils were laid in a chamber about 90 meters from the cave’s entrance, which was accessible only through a narrow chute which required a special team of very skinny individuals to retrieve them. Up and till now the team has recovered parts of at least 15 individuals of the same species. Lee Berger, research professor at Wits University and leader of the expeditions that recovered the fossils said, “With almost every bone in the body represented multiple times, Homo naledi is already practically the best-known fossil member of our lineage.”

Homo naledi has surprisingly human-like features, enough to place it in the genus Homo. It has a tiny brain, about the size of an orange (about 500 cubic centimeters), on top of a very slender body. The research shows that on average H. naledi stood approximately 1.5 meters (about 5 feet) tall and weighed about 45 kilograms (almost 100 pounds). Homo naledi‘s teeth are described as similar to those of the earliest-known members of our genus, such as Homo habilis, as are most features of the skull. The shoulders, however, are more similar to those of apes. The hands also suggest tool-using capabilities. It has extremely curved fingers, more curved than almost any other species of early hominin, which clearly demonstrates possible climbing capabilities.

The most remarkable part of the find is that it has led the researchers to conclude that this primitive-looking hominin may have practiced a form of behavior previously thought to be unique to humanism, intentional body disposal. The space in which the fossils were discovered was so remote that out of more than 1,550 fossil elements recovered, only about a dozen are not hominin, and the few that were not are isolated mouse and bird remains, meaning that the chamber attracted few accidental visitors.

The researchers explored every alternative scenario, including mass death, an unknown carnivore, water transport from another location, or accidental death in a death trap. After examining every other option, they were left to accept intentional body disposal by Homo naledi as the most plausible scenario.

There is still much to be discovered in the Rising Star cave. “This chamber has not given up all of its secrets.” There are potentially hundreds if not thousands of remains of Homo naledi still down there waiting to get uncovered. 

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