BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Bioengineering

CRISPR Mini | New Territory Unlocked

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On March 20, 2022

In Student Post

For over a million years, DNA has centered itself as the building block of life. On one hand, DNA (and the genes DNA makes up) shapes organisms with regard to physical appearance or ways one perceives the world through such senses as vision. However, DNA may also prove problematic, causing sickness/disease either through inherited traits or mutations. For many years, scientists have focused on remedies that indirectly target these harmful mutations. For example, a mutation that causes cancer may be treated through chemotherapy or radiation, where both good and bad cells are killed to stop unchecked cell replication. However, a new area of research, CRISPR, approaches such problems with a new perspective.

The treatment CRISPR arose to answer the question: what if scientists could edit DNA? This technology involves two key components – a guide RNA and a CAS9 protein. Scientists design a guide RNA that locates a specific target area on a strand of DNA. This guide RNA is attached to a CAS9 protein, a molecular scissor that removes the desired DNA nucleotides upon locating them. Thus, this method unlocks the door to edit and replace sequences in DNA and, subsequently, the ways such coding physically manifests itself. Moreover, researchers at Stanford University believe they have further broadened CRISPR’s horizon with their discovery of a way to engineer a smaller and more accessible CRISPR technology.

This study aimed to fix one of CRISPR’s major flaws – it is too large to function in smaller cells, tissues, and organisms. Specifically, the focus of the study was finding a smaller Cas protein that was still effective in mammalian cells. The CRISPR system generally uses a Cas9 protein, which is made of 1000-1500 amino acids. However, researchers experimented with a Cas12f protein which contained only 400-700 amino acids. Here, the new CasMINI only had 529 amino acids. Still, the researchers needed to figure out if this simple protein, which had only existed in Archaea, could be effective in mammals that had more complicated DNA.

To determine whether Cas12f could function in mammals, researchers located mutations in the protein that seemed promising for CRISPR. The goal was for a variant to activate a protein in a cell, turning it green, as this signaled a working variant. After heavy bioengineering, almost all the cells turned green under a microscope. Thus, put together with a guide RNA, CasMINI has been found to work in lab experiments with editing human cells. Indeed, the system was effective throughout the vast majority of tests. While there are still pushes to shrink the mini CRISPR further through a focus on creating a smaller guide RNA, this new technology has already opened the door to a variety of opportunities. I am hopeful that this new system will better the general well-being as a widespread cure to sickness and disease. Though CRISPR, and especially its mini version, are new tools in need of much experimentation, their early findings hint at a future where humans can pave a new path forward in science.

What do you think? Does this small CRISPR technology unlock a new realm of possibility or does it merely shed light on scientists’ lack of control over the world around us?

The Environment’s New Clothes: Biodegradable Textiles Grown from Live Organisms

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On October 10, 2018

In Student Post

Research in the field of biodegradable materials shows promise to revolutionize the current fashion world. The dominant practice of immediately turning runway prototypes to intensely manufacture goods is an extreme threat to our environment’s future. The concept, commonly known as “fast fashion“, is one which requires vast quantities of clothing to be made for commercial purchase as quick as possible. This forces overproduction, where large corporations shoot individual purchase prices way down to tempt the consumer to buy clothes based on how little they cost. Making enormous quantities of clothes is necessary to make each trend profitable, but it is very destructive. Overproducing clothes requires huge amounts of energy, which uses fossil fuels and water, and results in a massive increase in land-fill waste, once the cheap clothes are out of style or can no longer serve their use. Today nine percent of the municipal solid waste in our landfills are clothing material according Scientific American. This issue of a rapid influx of new waste to landfills is compounded because the cheap materials used to make the clothes, traditionally plastic-based acrylics, are not biodegradable.

Clothing Production in Japanese Factory

New research has proven that it is possible to bioengineer materials from organisms such as bacteria, yeast, algae animal cells, and fungi, which leads us to believe there is a hopeful solution to the multitude of issues caused by “fast fashion’s” need for rapid overproduction. One professor’s work from the Fashion Institute of Technology,  Theanne Schiros is described in great detailed. She mainly works with algae for the production of her material. Her award-winning team, AlgalKit, has created a yarn-like substance by removing alginate, a polysaccharide in kelp, and making a water based gel, which is then died by non-chemical pigments, and is then dried to produce a colored fibrous material which is then woven into fabric. One of the large benefits from this process, as professor Schiros elaborates, is that these gels can be grown to fit molds, ultimately eliminating the massive amount of unused waste material that results from the hasty overproduction in today’s textile factories. Schiros also explains that her material is strong and flexible, which are two major criteria in choosing material to be mass-produced. In addition Schiros has looked into the possibility of synthesizing dyes for the material from bioengineered bacteria, which could supplant the use of toxic dyes normally tested on animals. Addressing both the issues of wasted resources, like energy, water, and material, and the growing problem of clogged landfills with non-biodegradable materials, algal-based fabrics in clothing shows great promise in changing the fashion industry for the betterment of our environment.

Kelp Forest used for Harvesting Alginate

It’s Time to Re-program the Human Gut

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On January 9, 2016

In Student Post

(Photo of the human gut (licensing information here)

“What kind of water would you like? Tap or bottled?” “Bottled, please.”

It is known that when traveling internationally, it is typically unsafe to drink tap water. This is due to the lack of familiarity with the filtering systems used by other countries. This caution extends to certain foods as well. However, Dr. Pamela Silver, Dr. Jeffrey Way, and Dr. Donald Ingber, investigators at Harvard’s Wyss Institute for Biologically Inspired Engineering, may have found a solution to many acute gastrointestinal illnesses, such as this one, that affect the human gut microbiome.

Their goal is to create a bacteria that can detect and fight microbial invaders. This genetically engineered bacteria will specialize in detecting the chemicals given off by gastrointestinal inflammation. After the bacteria makes the detection, it will begin to attack all microbial invaders and restore normality within the gastrointestinal tract. The bacteria will be created in a probiotic pill form. In order to make sure that this probiotic pill does not have a negative impact on the environment after it exits the gastrointestinal tract, Silver and Way will ensure that it will not work unless it is in a specific environment and is triggered by specific chemical signals, both specific to the environment and signals found in the gastrointestinal tract.

Silver, Way, and Ingber will use the gut-on-a-chip technology to test this probiotic pill. The gut-on-a-chip technology will allow them to mimic gastrointestinal inflammation with living human cells. The team plans to study the response of invaders and pathogens, that are causing the inflammation, to the genetically engineered bacteria.

This research will allow for the treatment of a multitude of gastrointestinal illnesses, as well as the introduction to treating other diseases that negatively impact the human gut microbiome. I would love not having to worry about what I drink or eat on vacation! I am excited to see where this newly found research takes the discussion and the treatment of illnesses related to the human gut micobiome.

Source: Biology News

Bacteria become ‘genomic tape recorders’, recording chemical exposures in their DNA

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On January 8, 2015

In Student Post

EscherichiaColi_NIAID

MIT Engineers have developed a way to create genomic tape recorders out of the Bacteria E. Coli. Timothy Lu, an engineering professor at the university describes the method by which they altered the bacterial DNA in order to allow it to store information. The researchers engineered the cells to produce a recombinase enzyme which can insert a certain sequence of Nucleotides into the genome. However, the trait is useful because the enzyme is activated by specific stimuli. In order to retrieve the information the researchers can either sequence the genome and look for the specific code or look for the trait expressed by the targeted gene by using antibiotics. This process will be useful in the future because of its ability to store long term biological memory. Also, this process transcends previous limitations of genome storage as it is now able to indiscriminately store data as opposed to previous methods that were only able to identify a specific stimulus.

Article Link:

http://www.sciencedaily.com/releases/2014/11/141113142006.htm

Useful Links:

http://en.wikipedia.org/wiki/Escherichia_coli

http://en.wikipedia.org/wiki/Whole_genome_sequencing

Image Link:

http://commons.wikimedia.org/wiki/File:EscherichiaColi_NIAID.jpg

Bioengineered Proteins Are Amphibious Adhesives

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On September 28, 2014

In Student Post

A group of researchers from MIT recently published their groundbreaking findings on specially engineered proteins that are able to stick to substances both in and out of water. Using naturally occurring adhesives secreted by mussels as a model for their research, the team combined those proteins with biofilms from certain bacteria to create an especially strong and sticky hybrid.

These new adhesives are much more complex than previously engineered proteins. While other scientists used the E. coli bacteria as a template to engineer proteins that resembled the mussel’s protein, leading researcher Timothy Lu described those methods as unable to “capture the complexity of the natural adhesives”. Therefore, the MIT research team uses several types of bacteria to separately manufacture components of different mussel proteins and then combines them with bacterial curli fibers into one complex adhesive.

There are numerous applications of this discovery. Once the team is able to concoct a method of generating the protein in great quantities, it can be used to repair holes in ships as well as to seal wounds after an accident or surgery. One of the team’s subsequent goals is to create “living glues” composed of bacteria that would react to a breach of a material and repair it through secretion of a protein adhesive. The potential of this discovery is demonstrated by the acclaim of the group’s sponsors, which include The Office of Naval Research, the National Science Foundation, and the National Institutes of Health.

 

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Directed evolution: Bioengineered decoy protein may stop cancer from spreading

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On September 26, 2014

In Student Post

Biomedical_Engineering_Laboratory

Researchers Jennifer Cochran and Amato Giaccia from Stanford University have recently made a breakthrough in cancer research. The Bioengineers have developed a synthetic form of the protein Axls that binds to the protein Gas6 in our blood. Cancerous cells have Axls proteins lining the cell membrane awaiting connections with Gas6 proteins. Once the two join together, the cancerous cells break away from the central cancer mass and spread through the body during a process known as Metastasis. However, the new synthetic Axls protein binds to Gas6 in the blood and inhibits Metastasis from ever beginning. This stops the original Axls cells on the cancer from receiving the chemical signals to break away and form new cancerous nodules.

The scientists conducted preliminary testing on lab mice with aggressive forms of ovarian and breast cancer. The Bioengineers found that, “Mice in the breast cancer treatment group had 78 percent fewer metastatic nodules than untreated mice. Mice with ovarian cancer had a 90 percent reduction in metastatic nodules when treated with the engineered decoy protein.” Scientists currently treat cancers with chemotherapy and radiation, however these early studies show that the synthetic protein Axls could prove to be a safe and effective alternative.

I believe that this type of Bioengineering, specifically directed evolution, holds the key to discovering cures for many of earth’s deadly diseases. Despite the recent breakthrough researchers have made at Stanford, it will still be years before synthetic Axls is approved for clinical studies and then for use in the medical field.

Original Article: http://www.sciencedaily.com/releases/2014/09/140921145112.htm

Source: http://www.sciencedaily.com/

Photo Credit:

http://commons.wikimedia.org/wiki/File:Biomedical_Engineering_Laboratory.jpg

Useful Links:

http://engineering.stanford.edu/news/stanford-researchers-create-evolved-protein-may-stop-cancer-spreading

http://bioengineering.stanford.edu/

http://www.sciencedirect.com/science/article/pii/S1389034405000055

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