BioQuakes

AP Biology class blog for discussing current research in Biology

Are Species We See Everyday Going Extinct Before Our Very Eyes?

A theory has recently surfaced declaring the possibility that there are around 700 species around the world that should be considered threatened species, many of whom who were possibly inaccurately declared non-threatened on the Red List of Threatened Species.

Luca Santini, an ecologist at Radboud University, was quite discouraged by this news and took it upon himself to create a more efficient and precise method when it comes to assessing the extinction risk of a particular animal. On January 17th, Conservation Biology did a segment on Santini’s new approach.

This new approach proved that as much as “20% of 600 species that were impossible to assess before by Red List experts, are likely under threat of extinction, such as the brown-banded rail and Williamson’s mouse-deer.”  In addition, it found that around 600 different species that had been officially declared non-threatened species, were actually likely to be extremely threatened. As Santini, himself, said “This indicates that urgent re-assessment is needed of the current statuses of animal species on the Red List.”

The (IUCN) Red List of Threatened Species is the “world’s most comprehensive information source on the global conservation status of animal, fungi, and plant species.” That being said, every few years, researchers evaluate and record the conservation status of different species, which then gets uploaded into the Red List’s database for the general public to have access to. According to Santini, however, “Often these data are of poor quality because they are outdated or inaccurate because certain species that live in very remote areas have not been properly studied. This might lead to species to be misclassified or not assessed at all.”

Santini’s method provides experts with additional independent information in attempt to help them better assess the species. It uses information gathered from land cover maps, showing how the distribution of different species has changed over time. This then allows said researcher to have more information to be able to more accurately classify species.

Santini describes his goal for this new method in saying “Our vision is that our new method will soon be automated so that data is re-updated every year with new land cover information. Thus, our method really can speed up the process and provide an early warning system by pointing specifically to species that should be re-assessed quickly.” We can only hope that this new method provides better and more accurate information in regards to what and who we will continue to share the planet with, and who we won’t.

 

Video Games: Can They Be Beneficial to a Child’s Learning and Development?

We’re told that video games are the downfall of today’s youth, but is it possible that there are video games that can help advance today’s youth? Well, researchers at the Children’s Hospital of Philadelphia wanted to test exactly that, and thus Project: EVO was born.

They used a fairly new branch of medicine known as “digital medicine.” According to DW Shaffer at the U.S. National Library of Medicine, “…”digital medicine” [is medicine] that is potentially more precise, more effective, more experimental, more widely distributed, and more egalitarian than current medical practice. Critical steps in the creation of digital medicine are careful analysis of the impact of new technologies and coordinated efforts to direct technological development towards creating a new paradigm of medical care.” The researchers set out to prove whether or not digital medicine could be used as an investigational treatment for children with autism spectrum disorder (ASD) and co-occurring attention/deficit-hyperactivity disorder (ADHD).

It is statistically proven that as many as 50 percent of children on the autism spectrum experience symptoms of ADHD, with about 30 percent of said children receiving a secondary diagnosis of ADHD. ADHD medications are far less effective, however, in children with both disorders than in those with only ADHD, which led researchers to conduct a study exploring alternative treatments.

The study included 19 children aged 9-13 who had each been diagnosed on the spectrum and experienced co-occurring ADHD symptoms. The care givers of each child, were asked to submit reports of his/her child’s ADHD symptoms, as well as his/her child’s ability to both plan and carry out specific tasks. Participants in the study were given either the Project: EVO treatment, which is delivered via an action video game experience, or an educational activity involving pattern recognition. The researchers were using the TOVA API score, an FDA-cleared objective, to measure each child’s attention.

“Our study showed that children engaged with the Project: EVO treatment for the recommended amount of time, and that parents and children reported high rates of satisfaction with the treatment,” Benjamin Yerys, Ph.D., a child psychologist at CHOP’s Center for Autism Research (CAR) and first and corresponding author on the study. “Based on the promising study results, we look forward to continuing to evaluate the potential for Project: EVO as a new treatment option for children with ASD and ADHD.”

The overall conclusion of the study, found that children engaged with the treatment for 95% of the recommended treatment sessions. The study also found that upon using Project: EVO, children showed improved attention both quantitatively (on the TOVA API score) and qualitatively, with a noticeable reduction of ADHD symptoms. Both parents and children deemed Project: EVO a worthwhile approach for treatment. Though the sample size of the study was small, the study showed that using Project: EVO was both feasible and acceptable; with potentially therapeutic effects.

CRISPR Gene “Editors” Are Making “Typos” in DNA

Two recently published studies cited two types of CRISPR gene editors that change individual bases in the DNA of mouse embryos and rice plants. While one of these worked as normal, the other introduced unintended mutations, making edits in the wrong places.

If one doesn’t already know what it is, CRISPR is a gene editing tool that can alter DNA sequences and modify gene functions. These “genetic scissors” are easy to use and are more efficient than than the previous genome-editor, TALENS. In particular, the CAS 9 enzyme allows for CRISPR to work the way it does. Recently, scientists demonstrated that CRISPR can be used to fix human genetic defects such as cystic fibrosis and cataracts in animal models.

Back to the topic at the hand, the study created an experiment to test how many accidental edits were made by three different CRISPR editors. After injecting one of the two mouse early-stage embryo cells with a CRISPR editor, the researchers used a genetic trick that made all cells that received the editor glow the color red. They separated the edited cells and the unedited cells before deciphering both of the groups.

Two of the gene editors, the CRISPR CAS9 as well as a base editor that changes adenine to cytosine, didn’t cause any more mutations than unedited cells. For the CRISPR CAS9 editor, this means that that the CAS9 enzyme were making cuts as intended. However, the base editor that changes cytosine to thymine caused 20 times more mutations than that of unedited cells. According to David Liu, a chemical biologist whose team created the two base editors, the cytosine changing enzyme can “grab single-stranded DNA that it gets close and make edits on its own.” The tighter these cytosine base enzymes bind to the DNA, the more likely the editor can introduce mistakes into the DNA.

Obviously, these editors need revising and improvement. “The community needs these worst-case scenario pressure tests so we can make sure there’s a good margin of safety when these agents do enter clinical trials,” says David Liu. He then assures that “newer versions of the cytosine base editors don’t bind to DNA as tightly” and that “more recent versions will produce fewer typos.”

Using CRISPR to Protect the World’s Chocolate

Cacao tree and bean

Around the world, in places 20º North and South of the equator, cacao is grown.  Growing in tropical environments, cacao trees grow pods that contain beans that are the primary ingredient of chocolate.  Unfortunately, fungal infestations have recently had a devastating impact on cacao farms, causing a wide range of diseases in the trees.  The worldwide chocolate business which employs 50 million people, is at serious risk.

Scientists have begun to develop CRISPR technology that can alter the DNA of cacao plants to make them more resistant to both fungal and viral diseases.  CRISPR is a gene-editing technology that works like a molecular pair of scissors, removing sections of DNA and replacing them with new ones.

Candy company Mars Inc. has supported the Innovative Genomics Institute in using CRISPR to engineer better cacao trees.  It will take five to seven years for the genetically engineered cacao trees to grow their pods, so until then, we can’t be certain that the project has been successful.

The lessons learned by the scientists on this project are important as they translate into work that can be done on other, important food plants such as cassava, rice, and wheat.

For the original article on this project, click here.

 

Stem Cells and CRISPR

Many cells can reproduce but there are a few types of cells that are not able to reproduce. One of these types are nerve cells, the cells that cary messages from your brain to your body.  There are many ways nerve cells can be destroyed or damaged, by trauma or drug use.  Millions of people are effected by losing nerve cells and for so long no one could think of a way to recreate them; until the discovery of stem cells.

After fertilization, and when the newly formed zygote is growing, it is made up of a sack of cells.  Some of these cells are stem cells which develop according to their environment. Because of the behavior of stem cells, scientists theorized that if they placed stem cells in the brain or spinal chord, two areas that have an abundance of neurons, the stem cells would turn into a neuron because of the environment it was in.  But, when they tried introducing stem cells into the body, the immune system treated them as an foreign body, as it should. Our immune system has to treat anything that does not come from our body as an enemy or we could get extremely sick.  However, the downside is organ transplants, blood transfusions, etc. are dangerous because they could cause a serious immune rejection.

Someone experiencing a spleen transplant rejection

Cells have a surface protein that displays molecular signals to identify if it is self or foreign.  Removing the protein causes NK (natural killer) cells to target the cell as foreign. Scientist haven’t been able to figure out how to make a foreign cell not seem foreign until Lewis Lanier, chair of UCSF’s Department of Microbiology and Immunology, and his team found a surface protein that, when added to the cell, did not cause any immune response.  The idea would be to use CRISPR/cas9 to edit the DNA of the stem cells, and in doing so would remove the code for the current surface protein and add the code for the new surface protein.

After the scientists had edited the stem cells, to have the correct signal protein, they released them into a mouse and observed that there was no immune rejection. Truly amazing. Maybe brain damage could be helped by this science one day. Tell me your thoughts on Stem Cells in the comments!

For more information, please go check out the primary source of this article.

 

 

New anti-CRISPR Proteins Serving as Impediments to this Miraculous System.

CRISPR-Cas9 systems are bacterial immune systems that specifically target genomic sequences that in turn can enable the bacterium to fight off infecting phages. CRISPR stands for “clusters of regularly interspaced short palindromic repeats” and was  first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco. Cas9 is a protein enzyme that is capable of cutting strands of DNA, associated with the specialized stretches of CRISPR DNA.

Diagram of the CRISPR prokaryotic antiviral defense mechanism.

Recently, a blockage to the systems was found by researchers which are essentially anti-CRISPR proteins. Before, research on these proteins had only showed that they can be used to reduce errors in certain genome editing. But now, according to Ruben Vazquez Uribe, Postdoc at the Novo Nordisk Foundation Center for Biosustainability (DTU), “We used a different approach that focused on anti-CRISPR functional activity rather than DNA sequence similarity. This approach enabled us to find anti-CRISPRs in bacteria that can’t necessarily be cultured or infected with phages. And the results are really exciting.” These genes were able to be discovered by DNA from four human faecal samples, two soil samples, one cow faecal sample and one pig faecal sample into a bacterial sample. In doing so, cells with anti-CRISPR genes would become resistant to an antibiotic while those without it would simply die. Further studies found 11 DNA fragments that stood against Cas9 and through this, researchers were ultimately able to identify 4 new anti-CRIPRS that “are present in bacteria found in multiple environments, for instance in bacteria living in insects’ gut, seawater and food,”  with each having different traits and properties.  “Today, most researchers using CRISPR-Cas9 have difficulties controlling the system and off-target activity. Therefore, anti-CRISPR systems are very important, because you want to be able to turn your system on and off to test the activity. Therefore, these new proteins could become very useful,” says Morten Sommer, Scientific Director and Professor at the Novo Nordisk Foundation Center for Biosustainability (DTU). Only time will tell what new, cool, and exciting discoveries will be made concerning this groundbreaking system! What else have you guys heard? Comment below!

CRISPR and Improving Crops

CRISPR and improving crops

The Article: How scientists are using CRISPR to create non-GMO crops   by Yi Li touches upon how CRISPR can replace the usage of conventional GMO crops today. By using CRISPR to make these new crops we can solve the problems that GMO crops provide because for annual crop plants like corn, tomatoes, and rice can have the CRISPR genes bred out of their gene pool. This would make the effects of these CRISPR crops not undoable and therefore would not pose the same threats that GMO crops do. CRISPR crops could also be created faster and be more precise than GMO crops, making crops with powerful resistances to droughts, pests, and poor soil. Creating new plant technology to increase yields is essential to keeping up with the growing human population so some type of man made crop is needed to serve us. This method seems to be a very viable option to solve this problem. This CRISPR technology also will likely lower the price of crops and help boost the economy and could be used to help third world countries with their famines. Yi Li States that the CRISPR will work to change the plant by being inserted inside the plant cells. From there the CRISPR will locate and rewrite the relevant section of the DNA. Do you want your food to be cheaper? Do you want to boost the economy? Do you wanna help those who are hungry? Want to learn More about how the concept of CRISPR crops will work. This article (What are genome editing and CRISPR-Cas9?) explains what CRISPR is and how it works to change the genome. And the article Bypassing GMO regulations with CRISPR gene editing will show you how CRISPR is better than GMO and is able to be outside of those regulations.

Cocaine Addiction is Curable

University of Chicago researchers have made groundbreaking discoveries in the CRISPR field. Following malaria resistant mosquitoes and heat resistant cows, we are well on our way to creating cocaine-resistant mice. Scientists Xiaoyang Wu and Ming Xu teamed up to create a piece of technology that utilized the human body’s natural ability to break down cocaine, using an enzyme called butyrylcholinesterase, or “BCHE”.

After learning of BCHE, one may wonder, “why do people get addicted to cocaine if the human body makes an enzyme specifically to break it down?” In reality, “its short half-life makes it ineffective in a clinical scenario, since it disappears before it has any long-term impact on the body’s response to cocaine.” Researchers Wu and Xu had to find a way to prolong its life span to allow it time enough to work, as well as increase its potency to combat the severe nature of addiction. The scientists used epidermal stem cells in the mice, and using CRISPR technology, converted them into “BChE-producing factories.” The BCHE is easily distributed into the blood through the skin cells, and resulted in the inhibition of the mice’s withdrawal symptoms, and even preventing death in the case of lethal doses.

Not only did the stem cells work, but the mice responded well- producing high levels of BCHE for over two months without a negative immune system reaction.

“Apparently, the enzyme broke down the drug before much, if any, of it could reach their brains.”

A graph of showing the rapid increase of cocaine-caused deaths in the USA from 2002-2017.

The idea of cocaine-resistant mice may seem oddly specific, but cocaine addiction is a serious problem that we as Americans face. According to Ray Donovan, the special agent in charge of the Drug Enforcement Administration (DEA) New York Division, “cocaine is making a comeback in New York,”. It is a problem that we as Americans, and especially New Yorkers, will likely come into contact with some way or another. It doesn’t have to stop with one drug. While BCHE is unique to cocaine decomposition, there may be other enzymes that can similarly be implemented. The danger is this; if cocaine (or other drug) addiction is easily curable, who is to stop anyone from using it? Hopefully, the general public will have seen the aftereffects of cocaine addiction, and not use this new technology to excuse bad choices because they deem it less dangerous than before.

Monkeys Cloned with CRISPR Technology

Chinese researchers used CRISPR technology to genetically edit macaque monkey embryos in order to create five monkeys with severe sleeping disorders by removing BMAL1, a gene important for circadian regulation. They then chose the monkey of the five with the most severe symptoms to clone as a model to use for future tests on monkeys with these disorders. The idea behind this research was to create a template to create clone monkeys with the disease to run tests on rather than the real monkeys themselves.

A large issue with this experiment was the ethics behind it. While the end result is to reduce the number of monkeys used in research experiments. According to the study, the disorder in the monkeys resulted in not only lack of sleep but also changes in blood hormones, increased anxiety and depression, and even “schizophrenia-like” behavior. Bioethicist Carolyn Neuhaus thinks the study is morally wrong because the monkeys are used as tools, and the research’s success is based on their suffering.

Image result for crispr

Genes

Editing Sickle Cell Disease…

CRISPR gene-editing has recently been involved in the studies of sickle-cell anemia, a gene mutation that causes a decline in children’s health. Sickle cell anemia makes it difficult for oxygen to transport sufficiently throughout the body due to unhealthy blood cells. Some symptoms of the condition are shortness of breath, pale skin, colder body temperatures, headaches, etc…

Photo by SciTechTrend

Looking at sickle-cell anemia from a molecular standpoint, the mutation alters the red-blood cell by producing the wrong form of molecule which is referred to as a subunit. Out of the four subunits in hemoglobin, an “adult-expressed” subunit also known as beta” is produced. In contrast, fetal subunits create “gamma” subunits which are the appropriate molecules in red blood cell development for children. The unfortunate results of a mutated gene are crescent-like and inflexible red blood cells, which can form blockages against the flow of blood and oxygen through blood vessels.

In the past, scientists have been able to increase the gamma production in hemoglobins by “reversing” beta subunits to gamma subunits through a form of therapy, yet in a recent study scientist dove deeper to prevent the mutation as a whole. With gene editing technology, CRISPR has been reported to be useful in putting an end to the hereditary mutation. In that, scientists can identify the mutation and cut the DNA target out by using CRISPR. A specific piece of the DNA, also known as the “control section”, is introduced to gamma subunits during a  process of molecular conversion therapy and the ends of the control section are placed together after the mutated code for the gene is removed. Ultimately, this is said to reduce the adult-expressed subunits and stimulate higher levels of gamma subunits in fetal hemoglobins so that young children affected by sickle cell can avoid invasive treatments in their future.

 

CRISPR used to Control Genetic Inheritance in Mice!

Scientists around the world have been using CRISPR/Cas9 in a variety of plant and animal species to edit genetic information. Although this has been tested recently on insects, it is currently moving towards testing mammals. It happens to be more difficult with mammals due to the longevity between generations. However, It’s been done!!

UC San Diego researchers have developed a new active genetic technology in mice. Graduate student Hannah Grunwald, Assistant Researcher Valentino Gantz and colleagues led by Assistant Professor Kimberly Cooper, layed the groundwork for further advances based on this technology, including biomedical research on human disease.Image result for mice

“To demonstrate feasibility in mice, the researchers engineered an active genetic “CopyCat” DNA element into the Tyrosinase gene that controls fur color. When the CopyCat element disrupts both copies of the gene in a mouse, fur that would have been black is instead white, an obvious readout of the success of their approach. The CopyCat element also was designed so that it cannot spread through a population on its own, in contrast with CRISPR/Cas9 “gene drive” systems in insects that were built on a similar underlying molecular mechanism.”

The project duration was two years, and the researchers used many ways to “determine that the CopyCat element could be copied from one chromosome to the other to repair a break in the DNA targeted by CRISPR”. Some gene that was originally existent on only one of the two chromosomes was copied to the other chromosome. They were able to convert one genotype from heterozygous to homozygous, and they were able to tell in that there were  as many as 86 percent of offspring that inherited the CopyCat element from the female parent instead of the usual 50 percent.

The test was successful for the female mice’s production of eggs, but not for the males production of sperm. The researchers predict this is a possibility to a difference in the timing of male and female meiosis.

As this test was only the beginning, researchers such as those at UC San Diego hope to soon move on to research on human disease. They say that “Future animal models may be possible of complex human genetic diseases, like arthritis and cancer, which are not currently possible.”, and with their hard work, their research can lead to miracles.

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

Planet of the (CRISPR-Edited, Cloned) Apes

Several months ago, scientists in China cloned five gene-edited macaque monkeys. The clones were made through the somatic cell nuclear transfer method (SCNT)—a process in which a viable embryo is created from a body cell and an egg cell—that was used to produce the first primate clones around a year ago. In this instance, however, the monkeys’ genomes were first edited using CRISPR-Cas9—a unique genome editing tool that enables geneticists to edit parts of the genome by removing, adding, or altering sections of the DNA sequence—to show symptoms of sleep disorders by eliminating BMAL1, one of the positive elements in the mammalian auto-regulatory TTFL, which is responsible for generating molecular circadian rhythms. The result? The monkeys exhibited a wide range of circadian disorder phenotypes, including elevated night-time locomotive activities, reduced sleep time, reduced circadian cycling of blood hormones, increased anxiety and depression, and other schizophrenia-like behaviors. 

File:Macaque Monkey (16787053847).jpg

Macaque Monkey

Naturally, the results of the investigation triggered much backlash. According to Carolyn Neuhaus of The Hastings Center, the researchers viewed the suffering of the monkeys as a triumph, and failed to consider the moral implications of their investigation. “It’s very clear that these monkeys are seen as tools,” she told Gizmodo, the latter publication writing in a similar sentiment, “Their experiment is a minefield of ethical quandaries—and makes you wonder whether the potential benefits to science are enough to warrant all of the harm to these monkeys”. 

Nevertheless, the researchers involved in the experiment remain firm in their support of the experiment—the goal of which was to produce genetically identical monkey models of disease for biomedical research—on both moral and scientific grounds. “We believe that this approach of cloning gene-edited monkeys could be used to generate a variety of monkey models for gene-based diseases, including many brain diseases, as well as immune and metabolic disorders and cancer,” stated Qiang Sun, one of the research paper’s authors and director of the Nonhuman Primate Research Facility at the Chinese Academy of Science’s Institute of Neuroscience in Shanghai. Moreover, Reuters reported, “Xinhua [the state news agency] said the program, supervised by the institute’s ethics panel, was in line with international ethical standards for animal research”. Time will tell, ultimately, if the results of their experiment prove consequential on a larger scale. 

Scientist from China creates a baby resistant to HIV

The development of CRISPR technology has drastically progressed in the recent years, and He Jiankui, a scientist from China, took a step that most people judge to be crazy: he used CRISPR technology to create a human who is resistant to the HIV virus.

What is CRISPR? Good question.

CRISPR-Cas9 is a gene editing tool made from an ancient bacterial immune system. In bacteria, this system identifies DNA of invading viruses and send in different enzymes, such as Cas-9 to target and cut out a piece of DNA. Researchers quickly realized that almost any sequence of DNA can be cut out and modified the system to any sequence desired, even one that can prevent HIV. This is what Jianku’s work comprised of.

Jiankui and his team targeted the gene CCR5, a gene that provides the blueprint for the cell surface protein involved in the immune system, in the DNA of human embryos. The cell surface protein is usually involved in relaying information between cells, and HIV can use it to dock onto cells, infecting them with their own genetic material. Jianku eliminated the CCR5 gene to prevent HIV from docking onto any of the baby’s cells. However CRISPR-Cas9 induces mutations that scientist cannot fully control, and Jianku could not replicate the gene to the exact level. So, he instead created a “mixture of disrupted gene products”, which could potentially have a negative effect on human health.

At first glance, Jiankui’s experiment might be seen as beneficial, but Jiankui’s decision to create this human has been considered by other scientist as premature, drastic, and unethical, and has caused a lot of controversy. Although this was not the first time a scientist tampered with a human embryo, many scientists are outraged and believe that his experiment was a violation of human ethics. According to an article written by Allison Eck, the most notable ethical breach was conducting this experiment without the consent of other scientists, ethicists, regulators, or institutional review boards.

Debates over Jianku’s work have been circulating since the announcement of his experiment. Personally, I think that in the future, if we can prevent HIV and other harmful diseases that cause death, CRISPR can be an effective tool. However, as of now, we do not fully understand are aware of all of its effects. Therefore it is dangerous to test it on other humans. In the wrong hands, this powerful technology might be used in the wrong way and can cause huge repercussions. What do you think?

 

Going into the Brain with CRISPR

CRISPR is a relatively new tool that allows the editing of genomes via cutting and editing through the Cas-9 protein. There are unlimited opportunities and potential with this tool, and scientists are seeing the capability of CRISPR on rat brains.

Despite the advances of CRISPR, it is still difficult to work on central nervous system. Yet, scientists are working on the expression of the genes of rats involved in learning and memory, plasticity, and neuronal development. This technique paves the way for researchers to probe genetic influences on brain health and disease in model organisms that more closely resemble human conditions.

CRISPR is important in the field of neuroscience because it helps scientists understand brain development and neurological diseases like Alzheimer’s.   According to Harvard, CRISPR is the perfect technology to figure out if disrupting certain genes causes neurological disorders like OCD and autism.

In my opinion, the first step of understanding CRISPR’s effects on the mind is to test it out on similar, but less developed brains like rat brains. I do believe that CRISPR is the future of medicine and understanding the brain further and I can’t wait to work with this incredible piece of technology.

 

 

 

CRISPER Monkeys Cloned

“CRISPR-Cas9”, also known as CRISPR, is a relatively new technology that allows scientists to alter the human genome and gene function. CRISPR has been popularized for its many potential abilities, namely, to cure human diseases, but a recent experiment by researchers in Shanghai has shown further use for CRISPR. In a study published in the National Science Review on January 24, Scientists in Shanghai cloned 5 gene-edited Macaque monkeys. The scientists used CRISPER to edit the monkey’s genomes and remove BMAL1, which controls circadian regulation, to create sleeps disorders. The scientists then chose the monkey with the “correct gene editing and most severe disease phenotypes” to clone, a feat first done in China January of 2018.

https://commons.wikimedia.org/wiki/File:Rhesus_Macaque_monkey_look.jpg

Their ultimate goal is to be able to produce genetically identical monkeys for gene disease and biomedical research, and reduce the overall amount of monkeys used for scientific research.  “We believe that this approach of cloning gene-edited monkeys could be used to generate a variety of monkey models for gene-based diseases, including many brain diseases, as well as immune and metabolic disorders and cancer,” says Qiang Sun in the statement. “This line of research will help to reduce the amount of macaque monkeys currently used in biomedical research around the world,” says study coauthor Mu-ming Poo. “Because the clones wouldn’t have confounding genetic differences, preclinical drug trials may be able to get by with fewer animals, Poo suggests.”

 

 

 

Microbial Tape Recorders: A new Application to CRISPR

Research in the new gene-editing technology CRISPR has raised many red flags and ethical dilemmas as its full capabilities prove to be more than what was thought previously possible. It is used by bacteria to combat viral infections, but now scientists have repurposed it to keep records of a given bacteria’s environmental conditions, which could have significant applications to accurate chronicling of biological changes. Scientific American’s article, “Bacterial ‘Tape-Recorder’ Could Keep Tabs on Bodily Function” outlines how CRISPR “is a DNA sequence that makes and keeps a genetic record of viruses the bacterium encounters, commanding it to kill any that try to reinfect the bacterium or its descendants”. This natural function of bacteria, though, can be manipulated so that instead of exclusively accounting viral encounters, any environmental abnormality can be captured by CRISPR. More specifically, the bacterial mechanism would sense a special signal from a change in its surroundings and create trigger DNA, which, according to the U.S. National Library of Medicine, is a noticeable sequence of DNA from the invaders, which could be used to identify what exactly caused the change.

Applications of this technology today are far-reaching. This technology can be theoretically used to measure contaminants in fresh water or saltwater, or the nutrient levels in topsoil, but the predicted first application will be in monitoring bodily function in humans, and other animals. Digestion problems seem likely to be the first human system monitored with this new tool. Fructose Malabsorption is a digestive disorder which results in high levels of fructose sugar remaining in the digestive system. This disorder results from damaged intestines, normally from serious infection. Sugar levels in the digestive tract can now be monitored precisely by using this application of CRISPR in Escherichia coli cells (bacteria which are naturally found in the human digestive system). The record of sugar can identify specific problems diseased patients, after the E. coli cells are recovered from a patient’s feces, and cause them no harm in the process.

This tool is not without its drawbacks. It is reported that millions of modified bacteria need to be placed in a given system to have an accurate reading of environmental surroundings, and these bacteria have to be in the region of interest for at least six hours. The magnitude and duration of this prospective tool leave much to be desired as initial costs would be enormous, and other limitations, which can only be found through proper testing, remain unknown. In all, this advanced tool still seems applicable for now on only a small scale, but it is an example of CRISPR as a tool for good, and shows much hope for the future.

https://commons.wikimedia.org/wiki/File:E._coli_Bacteria_(16578744517).jpg

Escherichia coli bacteria which can be modified with CRISPR to become a “tape-recorder” of the human digestive system

A CRISPR Controversy

The Issue:

A recent article published by Grace Tsoi highlights the ongoing controversy regarding CRISPR, a new technology capable of editing DNA sequences, and thus genomes. Among those experimenting with CRISPR is Chinese researcher He Jiankui, notoriously nicknamed “China’s Dr. Frankenstein.” Many are critical of He Jiankui, as they deem his work with CRISPR — such as producing the world’s first gene-edited babies — inhumane and unethical. He Jiankui, however, argues that CRISPR has the potential to help “…millions of families with inherited diseases or exposure to infectious disease.”

Pictured above is He Jiankui, researcher and associate professor of the Southern University of Science and Technology’s Biology Department.

The Study:

In proving CRISPR’s potential, He Jiankui referenced an experiment in which he was able to produce two healthy twin girls by manipulating their genes, specifically making them resistant to HIV. He Jiankui had ultimate success with CRISPR technology, as the twins produced were not HIV positive, unlike their biological father. To learn more about the threat of HIV during contraception, click here. While He Jiankui expressed pride to his audience, stating, “For this specific case, I feel proud actually. I feel proudest because Mark [father of the twins] thought he had lost hope for life,” some audience members did not feel the excitement. Rather, his animated claims were met with intense criticism.

The Risks and Suspicions:

Given CRISPR’s potential, why are people so critical? Is CRISPR’s label “gene scissors” accurate or oversimplified? Regardless of these answers, it is undeniable that utilizing CRISPR for human embryos is a much more complex process. As Kenneth Lee, a biomedical sciences professor at the Chinese University of Hong Kong, explains it, using CRISPR in human embryos is “highly risky,” and could potentially mutate other genes in the process. As a result, the embryo might not survive, or could acquire deformities and/or other genetic disorders. Adding another element to the audience’s suspicion of He Jiankui’s experiment was the secrecy surrounding it, as he failed to answer why he initially hid it from Chinese officials. Failing to consider the opinions of these aforementioned officials has left many questioning the genuine ethics of He Jiankui’s experiment. In defending his work, He Jiankui emphasized that every individual involved consented to his experiment and were well-educated on the study itself. However, the consent form uploaded to his website, explicitly states that He Jiankui would not be held responsible for any unintended gene mutation. Moreover, the University where he conducted his experiment appeared unaware of his lab work, thus rendering an investigation of He Jiankui’s activities. Although China is a more “relaxed” country regarding its gene editing rules (gene editing is banned in the U.S., as well as many other countries), He Jiankui has faced condemnation from many Chinese scientists. Despite this, he plans to expand his studies, focusing next on another gene-edited pregnancy — yet another controversial experiment that will prove to either have potential or deep ramifications. 

Successful Progeria Treatment in Mice Also Bodes Well For Humans

A successful CRISPR-Cas9 treatment of Progeria in mice may be the beginning of anti-aging in humans.

When Juan Carlos Izpisua Belmonte set out to study “the molecular drivers of aging,” he could not have picked a more appropriate disorder than Progeria. Progeria is an accelerated aging disorder “caused by a mutation in the LMNA gene.” In both mice and humans, progeria induces many symptoms of aging, such as “DNA damage, cardiac dysfunction and dramatically shortened life span,” early in life. Molecularly, Progeria “shifts the production of lamin A,” a protein, ” to progerin,” a toxic form of lamin A that builds up with age.

 

 

In order to “to diminish the toxicity from the mutation of the LMNA gene that leads to accumulation of progerin inside the cell,” the Belmonte-led group used CRISPR-Cas9 to disrupt both lamin A and progerin. To do so, RNA first guides Cas9 to a spot on the DNA. Then, it makes a cut that “renders lamin A and progerin nonfunctional.”

As a result, the treated mice enjoyed a 25% longer life span and were stronger and more active. The successful treatment bodes well not only for mice, but for humans. In the future, “efforts will focus on making the therapy more effective” and compatible for humans.

 

 

CRISPRi Antibiotics: Will Pathogens Cease to Exist?

Recently, a researcher at the University of Wisconsin-Madison and his collaborators at the University of California, San Francisco have discovered a way to repurpose CRISPR, a gene-editing tool, to develop new antibiotics.

What does this mean?

It is known that many disease-causing pathogens are resistant to current antibiotics. This new technique, Mobile-CRISPRi, is helping to change that. Mobile-CRISPRi allows scientists to “screen for antibiotic function in a wide range of pathogenic bacteria.” Scientists used of bacterial sex to transfer Mobile-CRISPRi from laboratory strains into any diverse bacteria. This easily transferred technique will now allow scientists to to study any bacteria that cause disease or help one’s health.

To break it down, Mobile-CRISPRi “reduces the production of protein, from targeted genes, allowing researchers to identify how antibiotics inhibit the growth of pathogens.” This will allow researchers to more thoroughly understand different bacterias’ resistance to current antibiotics.

Unlike CRISPR, which can split DNA into two halves, CRISPRi is a defanged form that is unable to cut DNA. Instead, it stays on top of the DNA, blocking other proteins from being able to turn on a specific gene.

Genes (DNA)

Why is this important?

It has been proved that a decrease in the amount of protein targeted by an antibiotic will make bacteria become more sensitive to lower amounts of that same antibiotic. This evidence association between “gene and drug” has allowed scientists to “screen thousands of genes at a time,” as they try to gain more knowledge about the mechanisms of how antibiotics work in organisms to improve those on the market now.

In order to study how antibiotics directly work in pathogens, researchers needed to make this CRISPRi mobile, or easily transferred onto different bacterias. There were two tests done to test CRISPRi’s mobility using conjugation. One involving a transfer of CRISPRi to the pathogens Pseudomonas, Salmonella, Staphylococcus, Listeria, and others, and another involving the bacteria that grows on cheese.

Science Daily describes the “landscapes of microbes cheese creates as it ages.” A bacteria called “Vibrio casei” was found on a French cheese in a lab back in 2010. With bacteria that have been taken out of their environment, it is hard to manipulate and study said pathogen’s genes, like “Vibrio casei.”

However, the mobile-CRISPRi was able to easily transfer onto the strain of  Vibrio casei that was discovered back in 2010. This has given scientists a new way of understanding how bacteria colonizes and ages cheese.

Peters, the head researcher of mobile-CRISPRi is generous enough to offer this system to other scientists who would like to study other germs. With this technology being available to others, scientists could potentially see first-hand how antibiotics work in pathogens, and use that information to improve those that currently exist, hopefully getting rid of these bacterias like pseudomonas, or listeria before they kill the human they are inside of.

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