synthetic biology – BioQuakes

Cells are the basic units of life, but now scientists found a way to take matters into their own hands and actually create their own Frankenstein of cells. Scientists first created a single-celled organism with only 473 genes five years ago. Unlike the most recent cellular innovation, this simple cell grew and divided into cells of strange and unusual shapes and sizes. In an attempt to fix this, scientists identified 7 genes that when added to the cell, cause them to divide into perfectly uniform shapes. The J. Craig Venter Institute (JCVI), the National Institute of Standards and Technology(NIST), and the Massachusetts Institute of Technology(MIT) Center for Bits and Atoms all together can be accredited with this success.

How Was It Done?

The first cell with a synthetic genome was created in 2010 by the scientists at JCVI. Rather than building a cell from scratch, they started with cells from a simple bacteria called mycoplasma. The DNA already in those cells were destroyed and replaced with computer designed DNA. Thus lead to the first ever organism on Earth to have an entirely synthetic genome. It was named “JCVI-syn1.0”. Since then scientists have been working on stripping it down and reaching its minimum genetic components. Now scientists added 19 genes into this cell(including the 7 genes needed for proper cell division) and call it JCVI-syn3A. This cell variant also has fewer than 500 genes(a human cell has about 30,000). To find those 7 genes the JCVI synthetic biology group, led by John Glass and Lijie Sun, constructed multiple variants by adding and removing genes. NIST had to observe and measure the changes under a microscope. The difficulty here lay in observing the cells while they were alive, which made imaging them harder because of how small and fragile they were. Even the smallest of force could rupture them. Strychalski and MIT co-authors James Pelletier, Andreas Mershin and Neil Gershenfeld designed a microfluidic chemostat to remedy this. The article by NIST best describes this as a “sort of mini-aquarium where the cells could be kept fed and happy under a light microscope”. They discovered two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, were all required together for cell division. As we learned in AP Bio, organelles like mitochondria and chloroplasts are also autonomous. That simply means that they are self replicating similar to this man-made cell.

The ability to create synthetic cells could lead to potential cells that produce drugs, foods and even fuels. Others can detect disease and the drugs to treat it all while being inside your body. It’s amazing to think that humans are capable of creating synthetic life on a molecular level. One can only hope that this power is used for good in the future. Do you believe that what these scientists are doing is ethical or is “playing God” tampering with forces unknown?

Synthesizing More Durable Bulletproof Vests Using Animal Muscle Fibers!

By rayceptor

On October 27, 2021

In Student Post

Wait, why? Are Animals harmed? These two may be the first two questions that arise after reading the title. Rest assured that no animals will be harmed since the organism producing these muscle fibers will be engineered microbes. A group of researchers at Washington University’s Engineering school conducted this research that leads to the production of stronger clothing that is more durable which makes it more sustainable because we are no longer using traditional materials like cotton, silk, and nylon.

First, what are Microbes? The National Center for Biotechnological Information states that Microbes are tiny living things that are found all around us and are too small to be seen by the naked eye. “They live in water, soil, and in the air. The human body is home to millions of these microbes too, also called microorganisms. … the most common types are bacteria, viruses, and fungi.” There are many different types of microbes, and there are some that are prokaryotic cells and others that are Eukaryotic cells. The difference between the two is that prokaryotes don’t have a nucleoid region while Eukaryotic cells contain a nucleus that stores DNA. Interestingly in prokaryotes, their DNA is circular-shaped while eukaryotes have linear DNA. In this particular study, they used bacteria, a prokaryotic single-celled organism.

Picture of Microbes

Challenge

Through synthetic biology, this team modified bacteria so that the microbes were able to synthesize protein to produce muscle fibers. Synthetic biology is where “engineering principles are mixed with biology.” Well, to produce the proteins for muscle fibers, microbes must have ribosomes that synthesize amino acids and combine them to form protein chains. In this particular case, the protein they are synthesizing is titin. “It’s the largest known protein in nature,” said Cameron Sargent, a researcher on the team. It normally consists of 34,350 amino acids.

One of the problems the researchers overcame was controlling how the microbes were able to produce proteins “50 times” the average protein size. They utilized synthetic chemistry on the microbe they engineered to polymerize proteins and form many peptides and other bonds in the process. Peptide bonds, specifically, are covalent chemical bonds linking two consecutive amino acids.

Muscle Fibers

My Take

I think this research is very advanced with regard to synthetic biology. If we further develop this field of science, in the future we might be able to synthesize more complex protein structures with simple microbes. I don’t see any bad implications that this research might have on society. I can’t wait to see what Professor Zhang and his team will produce in the future. Sargent even said, “we can take proteins from different natural contexts, then put them into this platform for polymerization and create larger, longer proteins for various material applications with a greater sustainability.” With applications that are only limited by our imagination, I want to commend Professor Zhang and his team’s effort.

Points to Ponder and Comment:

If clothing were designed out of muscle fibers ethically, would you wear it? Why or why not? What uses do you have envisioned for this field of science if it continues to advance?

Genetically engineering the microbiome

By alanine

On November 19, 2018

In Student Post

Researchers from Harvard University have successfully taken the first steps in creating a synthetic microbiome. Using signaling between Salmonella Typhimurium and E. coli, the team was able to promote a new “genetic signal-transmission system” in mice.

A cluster of E. coli, a common species of gut bacteria.

With the hope of inducing interspecies bacterial communication, the researchers manipulated the bacterial signaling method of quorum sensing where bacteria receive and send signaling molecules in order to gauge their population density, performing a group behavior after reaching a certain threshold. By using the variant acyl-HSL quorum sensing, a version absent in mammals, the researchers were able to assess the feasibility of using a signaling system nonnative to its host.

In order to see if the two bacterial species successfully communicated, the researchers introduced both a signaler circuit and a responder circuit into the mice. The signaler circuit, put into Salmonella Typhimurium, contained a gene called luxI that, when turned on by a molecule called ATC, produced a quorum signaling molecule. This molecule was received by the bacteria with the responder circuit, E. coli, triggering a cro gene. This gene then turned on a LacZ gene, which caused the bacteria to turn blue when plated with special agar, and another cro gene, creating a loop that continuously activated the LacZ gene. This served as an indicator, as a blue glow would illustrate if the interspecies communication and the E.coli’s “memory” of it were successful.

After the mice were given the two edited strains of bacteria and placed in a container with ATC-infused water for two days, the researchers analyzed their fecal samples. They found that all of them turned blue, indicating that the genetically engineered signaling system was successful: the E. coli received and remembered a signal from Salmonella Typhimurium in response to an environmental factor. This effective engineered communication, as the Director of Harvard’s Wyss Institute for Biologically Inspired Engineering puts it, is a major step forward in “engineer[ing] intestinal microbes for the better while appreciating that they function as part of a complex community”.

With the basic principles of a synthetic microbiome a success, the researchers now want to experiment with new bacterial species and signaling molecules, bringing them closer towards their ultimate goal of engineering a gut microbiome that can perform tasks ranging from improving digestion to curing diseases. As the “next frontier in medicine [and] wellness,” the microbiome will no doubt be a key pillar of medicinal research for decades to come.

BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: synthetic biology

ITS ALIVE!!! Scientists bring their creation to life.

Synthesizing More Durable Bulletproof Vests Using Animal Muscle Fibers!

Genetically engineering the microbiome

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