Parasites in the Gut Help Develop a Healthy Immune System

Posted on June 24, 2010 4 Comments

It has long been known that microbes in the gut help to develop a healthy immune system, hence the rise in popularity of probiotic yoghurts that encourage ‘friendly’ bacteria. But new research by Professors Richard Grencis and Ian Roberts shows that larger organisms such as parasitic worms are also essential in maintaining our bodily ‘ecosystem’. “The worms have been with us throughout our evolution and their presence, along with bacteria, in the ecosystem of the gut is important in the development of a functional immune system.”

Parasite Rex is a great book, I have written about previously looking at parasites and their affect on human health.

Professor Grencis adds: “If you look at the incidence of parasitic worm infection and compare it to the incidence of auto-immune disease and allergy, where the body’s immune system over-reacts and causes damage, they have little overlap. Clean places in the West, where parasites are eradicated, see problems caused by overactive immune systems. In the developing world, there is more parasitic worm infection but less auto-immune and allergic problems.

“We are not suggesting that people deliberately infect themselves with parasitic worms but we are saying that these larger pathogens make things that help our immune system. We have evolved with both the bugs and the worms and there are consequences of that interaction, so they are important to the development of our immune system.”

Whipworm, also known as Trichuris, is a very common type of parasitic worm and infects many species of animals including millions of humans. It has also been with us and animals throughout evolution. The parasites live in the large intestine, the very site containing the bulk of the intestinal bacteria.

Heavy infections of whipworm can cause bloody diarrhoea, with long-standing blood loss leading to iron-deficiency anaemia, and even rectal prolapse. But light infections have relatively few symptoms.
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Microcosm by Carl Zimmer

Posted on December 26, 2009 No Comments

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on EarthForeign Cells Outnumber Human Cells in Our BodiesAmazing Designs of LifeAmazing Science: RetrovirusesOne Species’ Genome Discovered Inside Another’s

Web Gadget to View Cell Sizes to Scale

Posted on November 19, 2009 No Comments

graphic of red blood cellImage of cell size gadget from University of Utah

The Genetic Science Learning Center, University of Utah has a nice web gadget that lets you zoom in on various cells to see how large they are compared to each other. Above see a red blood cell, x chromosome, baker’s yeast and (small) e-coli bacterium.

A red blood cell is 8 micron (micro-meter 1/1,000,000 of a meter). E coli is 1.8 microns. Influenza virus is 130 nanometers (1/1,000,000,000 a billionth of a meter). Hemoglobin is 6.5 nanometers. A water molecule is 275 picometers (1 trillionth of a meter).

Related: Red Blood Cell’s Amazing FlexibilityHemoglobin as ArtAtomic Force Microscopy Image of a MoleculeNanotechnology Breakthroughs for Computer Chips

Dennis Bray Podcast on Microbes As Computers

Posted on October 13, 2009 1 Comment

Carl Zimmer interviews Dennis Bray in an interesting podcast:

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes–how they “decide” where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

Related: E. Coli IndividualityWetware: A Computer in Every Living Cell by Dennis Bray – Programing BacteriaMicro-robots to ‘swim’ Through Veins

Why People Often Get Sicker When They’re Stressed

Posted on March 21, 2009 5 Comments

Researchers at UT Southwestern Medical Center identified a receptor, known as QseE, which resides in a diarrhea-causing strain of E coli. The receptor senses stress cues from the bacterium’s host and helps the pathogen make the host ill. A receptor is a molecule on the surface of a cell that docks with other molecules, often signaling the cell to carry out a specific function.

Dr. Vanessa Sperandio, associate professor of microbiology at UT Southwestern and the study’’ senior author, said QseE is an important player in disease development because the stress cues it senses from a host, chiefly epinephrine and phosphate, are generally associated with blood poisoning, or sepsis.

“Patients with high levels of phosphate in the intestine have a much higher probability of developing sepsis due to systemic infection by intestinal bacteria,” Dr. Sperandio said. “If we can find out how bacteria sense these cues, then we can try to interfere in the process and prevent infection.”

Millions of potentially harmful bacteria exist in the human body, awaiting a signal from their host that it’s time to release their toxins. Without those signals, the bacteria pass through the digestive tract without infecting cells. What hasn’t been identified is how to prevent the release of those toxins.

“There’s obviously a lot of chemical signaling between host and bacteria going on, and we have very little information about which bacteria receptors recognize the host and vice versa,” Dr. Sperandio said. “We’re scratching at the tip of the iceberg on our knowledge of this.”

“When people are stressed they have more epinephrine and norepinephrine being released. Both of these human hormones activate the receptors QseC and QseE, which in turn trigger virulence. Hence, if you are stressed, you activate bacterial virulence.” Dr. Sperandio said the findings also suggest that there may be more going on at the genetic level in stress-induced illness than previously thought.

“The problem may not only be that the stress signals are weakening your immune system, but that you’re also priming some pathogens at the same time,” she said. “Then it’s a double-edged sword. You have a weakened immune system and pathogens exploiting it.”

Previous research by Dr. Sperandio found that phentolamine, an alpha blocker drug used to treat hypertension, and a new drug called LED209 prevent QseC from expressing its virulence genes in cells. Next she will test whether phentolamine has the same effect on QseE.

Full press release: Researchers probe mechanisms of infection

Related: posts on the scientific method in actionHow Cells AgeWhy ‘Licking Your Wounds’ WorksWaste from Gut Bacteria Helps Host Control Weight

Silk E.coli Sensors

Posted on October 14, 2008 1 Comment

“Edible Optics” Could Make Food Safer

Scientists at Tufts University’s School of Engineering have demonstrated for the first time that it is possible to design such “living” optical elements that could enable an entirely new class of sensors. These sensors would combine sophisticated nanoscale optics with biological readout functions, be biocompatible and biodegradable, and be manufactured and stored at room temperatures without use of toxic chemicals. The Tufts team used fibers from silkworms to develop the platform devices.

The possibility of integrating optical readout and biological function in a single biocompatible device unconstrained by these limitations is tantalizing. Silk optics has captured the interest of the Defense Department, which has funded and been instrumental in enabling rapid progress on the topic. The Defense Advanced Research Projects Agency (DARPA) awarded Tufts a research contract in 2007 and is funding Tufts and others on groundbreaking projects that could someday result in biodegradable optical sensing communications technology.

To form the devices, Tufts scientists boiled cocoons of the Bombyx mori silkworm in a water solution and extracted the glue-like sericin proteins. The purified silk protein solution was ultimately poured onto negative molds of ruled and holographic diffraction gratings with spacing as fine as 3600 grooves/mm.

The Tufts team embedded three very different biological agents in the silk solution: a protein (hemoglobin), an enzyme (horseradish peroxidase) and an organic pH indicator (phenol red). In the hardened silk optical element, all three agents maintained their activity for long periods when simply stored on a shelf. “We have optical devices embedded with enzymes that are still active after almost a year of storage at room temperature.

Related: E. Coli IndividualityScience Fair Project on Bacterial Growth on Packaged SaladsProtecting the Food Supplyposts on food

Bacteria Evolutionary Shift Seen in the Lab

Posted on June 9, 2008 No Comments

Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait. And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

Related: People Have More Bacterial Cells than Human CellsUnderstanding the Evolution of Human Beings by CountryE. Coli Individuality

E. Coli Individuality

Posted on April 22, 2008 2 Comments

Expressing Our Individuality, the Way E. Coli Do by Carl Zimmer

A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones.

A colony of genetically identical E. coli is, in fact, a mob of individuals. Under identical conditions, they will behave in different ways. They have fingerprints of their own.

E. coli appears to follow a universal rule. Other microbes exploit noise, as do flies, worms and humans. Some of the light-sensitive cells in our eyes are tuned to green light, and others to red. The choice is a matter of chance. One protein may randomly switch on the green gene or the red gene, but not both.

In our noses, nerve cells can choose among hundreds of different kinds of odor receptors. Each cell picks only one, and evidence suggests that the choice is controlled by the unpredictable bursts of proteins within each neuron. It’s far more economical to let noise make the decision than to make proteins that can control hundreds of individual odor receptor genes.

Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.

Related: AndrogenesisSick spinach: Meet the killer E coliParasite Rex

Amazing Designs of Life

Posted on April 19, 2008 1 Comment

The More We Know About Genes, the Less We Understand by Carl Zimmer

All living things, ourselves included, turn genes on and off in a similar way, by making switch-like proteins called transcription factors. And as scientists have identified more of these, they’ve discovered something remarkable: They form a chain of command. The job of some transcription factors is to switch others on and off, and they in turn are controlled by other transcription factors. Even a seemingly simple microbe like E. coli has an impressive hierarchy. Just nine genes rule over about half of the 4,000-odd genes in E. coli.

E. coli’s network allows it to respond quickly to the challenges it meets, from starvation to heat to the loss of oxygen. It can rapidly reorganize itself, switching on hundreds of genes and switching off hundreds of others. What makes this network all the more impressive are the feedback loops that keep it from spinning out of control. When one gene switches on, for example, it may make a protein that shuts down the gene that switched it on in the first place.

Yet even as scientists uncover this network, they discover yet another mystery. In the latest issue of Nature, scientists reported an experiment in which they wreaked havoc with E. coli’s network. They randomly added new links between the transcription factors at the top of the microbe’s hierarchy. Now a transcription factor could turn on another one that it never had before. The scientists randomly rewired the network in 598 different ways and then stepped back to see what happened to the bacteria.

You might expect that they all died. After all, if you were to pop open the back of an iPod and start linking its components together in random ways, you’d expect it to crash. But that’s not what happened.

About 95 percent of the rewired bacteria did just fine with their new networks. They went on with their lives, feeding, growing and dividing. Some even performed better than microbes with the original wiring, under some conditions.

Related: Programing BacteriaSick spinach: Meet the killer E coliBacteria Can Transfer Genes to Other BacteriaEvolution is Fundamental to Sciencegenes tagged posts

2006 Posts

Posted on August 25, 2007 No Comments

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Programing Bacteria

Posted on November 4, 2006 2 Comments

Duke Packard Fellow to Examine Processing Speed of “Reprogrammed” Bacteria:

research into the development of synthetic gene circuits, carefully designed combinations of genes that can be “loaded” into bacteria or other cells, directing their activity in much the same way that a basic computer program directs a computer. Such re-programmed bacteria might eventually serve in a wide variety of applications, including biocomputing, medical treatments, and environmental cleanup

The research now, however, is in its very early stages, You said. So far, E. coli bacteria have been programmed to grow in numbers until a certain population size is reached. The bacteria then kill themselves off, growing again only after their numbers dwindle sufficiently.

The relatively simple program takes advantage of bacteria’s ability to communicate with one another, a process known as “quorum sensing,” and essential genetic pathways that control cell death.

Related: 2006 Packard Fellowships in Science and Engineering Awarded to 20 Young ResearchersDr. Lingchong YouDuke Engineer Designing ‘Gene Circuits’ that Control Cell Populations with Killer GenesSick spinach: Meet the killer E coli