Bacteria

Bacteria have feelings, too

Anonymous — Tue, 15 Aug 2017 21:31:19 +0000

Bacteria have feelings, too Anonymous (not verified) Tue, 08/15/2017 - 15:31

Ula Chrobak

For humans, our sense of touch is relayed to the brain via small electrical pulses. Now, CU Boulder scientists have found that individual bacteria, too, can feel their external environment in a similar way.

In a new study, CU Boulder researchers have demonstrated that E. coli bacteria cells get excited when poked, sending out voltage induced calcium ion signals—the same way a vertebrate’s sensory nervous system works. The results are believed to be the first documented observation of electrical excitability in individual bacteria cells.

The findings, which could advance fundamental bacteria research and may eventually aid drug development for infectious diseases, were published today in the journal Proceedings of the National Academy of Sciences.

“People typically think that [bacteria] are these little things, that all they are doing is trying to divide and create more energy,” said Giancarlo Bruni, a doctoral candidate in CU Boulder’s Department of Molecular, Cellular, and Developmental Biology and the lead author of the new research. “[But] we’re not all that different.”

Scientists have long known that bacteria respond to certain chemical cues. Feed them sugar, and their populations explode. Douse them in antibiotics and their cell walls rip apart. More recently, though, scientists have noticed that physical signals, too, seem to activate these microbes. For example, Salmonella become more efficient at infecting human cells when placed on a stiff surface as opposed to a soft one.

“What we think could be happening is that they’re using these electrical signals to modify their lifestyle,” said Joel Kralj, the senior author of the study and an assistant professor in MCDB and the BioFrontiers Institute.

To study how bacteria feel their surroundings, the team inserted special genes into E. coli bacteria that glow when calcium ions or electricity pulse through them. The cells were placed in a sticky substrate under a microscope. Left alone, the cells remained dim. But when the scientists pushed a pad against them, the bacteria lit up. The sparks of light indicated that proteins, ions and electricity were moving around in the bacteria.

The results indicate that bacteria and other creatures share a common tool for sensing their environment—an electrical pathway with the same functionality as human sensory neurons. From an evolutionary perspective, this signaling trait could be billions of years old and used by some of the oldest organisms on Earth.

The study also sheds new light on bacterial activity with regard to infection. For example, when exposed to antibiotics, a few bacteria cells with unique electric signals usually survive. These survivors then go on to reproduce and share their drug-resistant capabilities with other bacteria, eventually rendering the antibiotic useless.

The CU Boulder researchers now plan to study how bacteria’s electric pulses are used to sense when to infect human cells. In the future, they hope to test for small, masking molecules that can dull these signals when introduced. Such molecules could eventually translate into drugs that help treat bacterial infections and overcome antibiotic resistance.

“If we can block bacterial electrical activity, they may be less likely to infect, because now they don't know that they have landed on your soft delicious gut cell,” said Kralj. “We could cut their hands off so they can no longer feel.”

Additional co-authors of the new study include Andrew Weekley and Benjamin Dodd of MCDB and BioFrontiers. The National Institutes of Health and the Searle Scholars Program provided funding for the research.

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Cracking the code on bacterial voltage

Anonymous — Mon, 13 Apr 2015 06:00:00 +0000

Cracking the code on bacterial voltage Anonymous (not verified) Mon, 04/13/2015 - 00:00

BioFrontiers

Searle Scholars Award winner is cracking the code on bacterial voltage

Electric voltage powers life – Our brains use electrical transients to process every thought; every heartbeat arises from voltage changes in heart cells. Despite its importance, voltage changes in bacteria were never really studied because the cells were just too small to measure. In fact, biologists historically assumed that these voltage changes were only present in plants and animals. BioFrontiers Institute faculty member, Joel Kralj, an Assistant Professor in Molecular, Cellular and Developmental Biology, developed a method to encode a fluorescent protein into bacterial cells that allow it to become visible, revealing how bacteria use electricity to stay alive.

“Voltage really is everywhere, and life has harnessed it for billions of years in order to evolve. That’s what is amazing,” says Kralj. “Finding these electrical transients in bacteria gives us an entirely new perspective on their evolution.”

Kralj recently became a Searle Scholar for his work on voltage in bacteria. The Searle Scholars Program supports the research of scientists who recently started their appointments at the assistant professor level, and who are in their first tenure-track position at one of 153 participating academic or research institutions. Kralj was one of 15 researchers who were named Searle Scholars this year. As part of this award, he will receive $100,000 per year for three years to support his research.

The evolutionary story of bacteria is interesting enough but Kralj is looking at how bacteria use voltage changes to access hosts or signal other bacteria to colonize a host. The equipment he uses is highly specialized with fluorescent monitors developed specifically for use in bacteria, and a laser microscope to measure the tiny changes in voltage. Kralj’s lab is relatively new. He joined BioFrontiers last year and is in the process of staffing for his research. He is looking forward to using the funds from the Searle Scholars program to build more equipment to do bacterial research, including automatic scanning microscopes.

Although his research subjects are small, Kralj’s research has the potential to make a big impact. He is unlocking the secrets around how bacteria are using voltage to survive antibiotic exposure. He’s hoping to discover whether many of the antibiotic resistant “superbugs” are staying alive because they are modulating their voltage to attack hosts, colonize and evade the drugs developed to kill them. If Kralj finds this to be the case, he hopes to understand how voltage could be inhibited in bacterial cells so that antibiotic drugs could be more effective.

“The Searle Scholar grants are going to give me the flexibility to follow a lead in this research,” says Kralj. “Researchers looked for twenty years to find a way to measure this voltage, and now that we can measure it, there is so much to study.”

The �ֲ��ý in Boulder currently has six other Searle Scholars, including Natalie Ahn, Min Han, Arthur Pardi, Roy Parker, Gia Voeltz and Ding Xue.

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CU Boulder Wins Silver at 2014 iGEM

Anonymous — Thu, 29 Jan 2015 07:00:00 +0000

CU Boulder Wins Silver at 2014 iGEM Anonymous (not verified) Thu, 01/29/2015 - 00:00

BioFrontiers

CU-Boulder Student Team Wins Silver at Premiere Biology Competition

The International Genetically Engineered Machine (iGEM) event is the top synthetic biology competition in the world and the CU-Boulder team wanted to make an impact at this year’s competition in Boston. Last year’s 2013 Buffs iGEM team was successful, winning a North American Regional award for best new BioBrick and publishing their research in ACS Synthetic Biology. The 2014 Buffs iGEM team was confident they could compete at the international level. Unlike previous years, this year the iGEM competition (called a Jamboree) had no regional qualifying round, creating formidable competition: 2,500 undergraduate and graduate synthetic biology researchers from 245 universities across 32 countries. In the end, the CU scientists came home with a Silver medal and an interlab study distinction.

“Hard to believe I had never heard of iGEM until earlier this year,” says Leighla Tayefeh, a CU senior with a double major in MCD biology and neuroscience. “But the idea of synthetic biology’s vast potential to benefit society enticed me to join the team. We wanted to stand out and work with new technology, so this led us straight to the endogenous CRISPR-Cas9 system and the clinical need for an alternative to antibiotics.”

The CU iGEM team wanted to tackle the serious problem of antibiotic-resistant bacterial infections, like MRSA and tuberculosis, in a way that didn’t damage the body’s healthful bacteria colonies at the same time. They focused on phage therapy, which is a virus that uses bacteria’s cellular resources to reproduce until the host bacteria’s cell is eventually destroyed. CRISPR-Cas9 is a phage system that is able to more specifically target the DNA of a bacterial infection, resulting in cell death. What made the CU-Boulder team’s efforts even more valuable was their development of a delivery system for the phage therapy. The result is that the CRISPR-Cas9 phage binds to part of the DNA in the cell and cuts the DNA strand, killing the bacteria cell.

iGEM promotes educational outreach as part of their team projects. The CU team used the opportunity over the summer to host a camp from Heritage High School in Littleton, Colo. to teach them DNA basics. The high school students extracted their own DNA from saliva and examined differences between pathogenic and healthy DNA fragments. The CU team also collaborated with Colorado State University’s iGEM team to validate some of their findings during the project.

“The 2014 CU iGEM team was successful at making progress on a difficult scientific problem, namely alternatives to fight antibiotic resistance, but also at impacting the local community. The high school students who came to visit have written raving about their experiences,” says Assistant Professor of Molecular, Cellular and Developmental Biology and BioFrontiers faculty member, Robin Dowell who served as the CU iGEM mentor for the last two years.

iGEM, which began in 2003, provides each team with a kit of biological parts -- like promoters that respond to particular stimuli, genes, or regulators -- at the beginning of each summer. �ֲ��ý then use these parts, or parts of their own design, in their projects. The iGEM Giant Jamboree was held at the Hynes Convention Center in Boston, October 30 through November 3.

CU is heading to Boston for the iGEM Jamboree

Anonymous — Thu, 29 Jan 2015 07:00:00 +0000

CU is heading to Boston for the iGEM Jamboree Anonymous (not verified) Thu, 01/29/2015 - 00:00

BioFrontiers

In just a few days, members from our team will be boarding a plane to Boston. When we arrive, we are participating in an annual synthetic biology competition against both foreign and domestic teams at an international conference, held by the International Genetically Engineered Machines Foundation (iGEM). There we will present our synthetic biology project designed and executed over the summer.

Despite being named a “Jamboree”, the competition is not a free for all. A specific set of criteria must be met in order to participate, including design of a wiki for the project , concept originality, benefit to society, and proof of concept. Each year, teams identify a clinical and/or societal need and synthesize a biological system to address the issue. The iGEM competition is a forum for undergraduates in molecular biology, advised by graduate students and faculty, to gain hands-on experience working in a lab on a synthetic biology project that we (the undergrads) designed.

Hard to believe I had never heard of iGEM until earlier this year. But the idea of synthetic biology’s vast potential to benefit society enticed me to join the team. As intimidated as I was to embark upon something new, I began meeting with several other prospective iGEMers weekly to decide upon this years’ project. We wanted to stand out and work with new technology, so this led us straight to the endogenous CRISPR-Cas9 system. Now, we needed to decide how we would apply this technology. We chose the clinical need for an alternative to antibiotics.

At that point, our project took off like bacteria without antibiotic selection ….

We broke up into teams across three labs, one on main campus and two in JSCBB. This way productivity would be at its peak each and every week. With only a short time to reach our project goals, we needed all the motivation (coffee and late nights) we could get. A few came with experience but most didn’t. Regardless, each of us gained unique, hands on experience and learned to problem solve when something went wrong—which happened quite often. More importantly, we pulled together from different stages of life and completed a project we could call our own.

We have engineered a novel phage therapy utilizing the endogenous CRISPR-Cas9 system from Streptococcus pyogenes packaged into non-replicating phage. CRISPR-Cas9 systems target 20-32 nucleotide DNA sequences within the bacterial genome. Successful CRISPR targeting to the genome leads to a Cas9-mediated DNA double strand break and subsequent cell death. By cloning targeted CRISPR sequences into the endogenous CRISPR-Cas9 system and introducing this system into Escherichia coli by transformation or through phage infection, we have demonstrated sequence specific killing of bacteria in a heterogeneous bacterial population. The broad ranging applications of such an adaptable and cost effective antibiotic therapy range from healthcare to agriculture, and represent the future of antibacterial research.

With research that can change the future of medicine, my team and I are ready to go to Boston. We hope that the judges find our work exciting and we take home a gold medal. Wish us luck on this journey, and I can’t wait to tell you all about our adventure once we return home.

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Lights, Cells, Action!

Anonymous — Wed, 19 Oct 2011 06:00:00 +0000

Lights, Cells, Action! Anonymous (not verified) Wed, 10/19/2011 - 00:00 BioFrontiers

Lights, Cells, Action!

One of the best ways to really see something is to turn on the lights. Amy Palmer, assistant professor in the Department of Chemistry and Biochemistry and Biofrontiers Institute faculty member, is the kind of professor that can shine a light on subjects for her students, and shine a light on the cellular subjects in her lab.

Shining a light was the kernel of the idea behind fluorescent proteins: proteins that absorb energy at a specific wavelength and re-emit the energy at a different wavelength. Osamu Shimomura discovered the first fluorophore, called the green fluorescent protein (GFP), in jellyfish. GFP was then popularized and turned into a useful tool for cell biology by Martin Chalfie and Roger Tsien. Together, the three scientists shared the Nobel Prize in chemistry in 2008 for their contributions. GFP gave scientists the ability to put these glow-in-the-dark molecules in cells and living organisms and watch action within cells that had never been seen.

“Snapshots of a football game won’t tell you how to play the game,” says Palmer, “Fluorescent proteins allow us to watch the game while it is in motion.”

Palmer’s group is developing tools and technologies around these pretty proteins, which now come in a rainbow of colors in addition to the original jellyfish green. She recently attached fluorescent proteins to the Salmonella bacteria to follow it as it invaded a host organism with the hopes of learning how to prevent the bacteria from taking over and wreaking havoc.

Palmer’s next target is not animal, not vegetable…it’s a mineral. Zinc is an essential trace mineral found in all humans, totaling almost two grams in the average adult. Next to iron, zinc is the most common mineral in the body and is found in every cell, and in large concentrations in the brain, retinas, pancreas and prostate.

Imbalances in zinc levels can cause a myriad of troubles, from Alzheimer’s to diabetes to prostate cancer. In addition, zinc plays important roles in growth and reproduction; taste, vision and smell; and even proper insulin and thyroid function. Zinc deficiency is a worldwide challenge causing problems ranging from stunted growth to fatal diseases.

Palmer is developing fluorescent probes that can attach to zinc. Defining the location of zinc and how it fluctuates in an organism is the first step in knowing how cells regulate it, and how we can regulate it in patients that have imbalances. For example, prostate cancer is difficult to diagnose and predict how it will respond to treatment. By measuring zinc levels, scientists may be able to predict the aggressiveness of the tumors and give a more accurate prognosis of the disease.

“We know very little about what zinc is doing at the cellular level,” says Palmer. “Fluorophores allow us to see how this metal is playing a role in some diseases like prostate cancer and diabetes.” She is aiming for a zinc-tracking technique to catch diseases early in their processes, but don’t expect to be injected with glow-in-the-dark proteins at your next doctor’s visit.

“There isn’t a clinical use for fluorescent proteins right now,” says Palmer. “There isn’t a machine for them that a doctor would use to look inside your body. What makes these proteins special is looking at what happens at the cellular level of an organism. We can see into cells and witness what an X-ray or MRI machine cannot. That fundamental level of understanding is going to lead us to bigger solutions.”