Category Archives: Research

Bacteriophages Enter Bacteria Using an Iron Tipped Spike

Bacteria-Killing Viruses Wield an Iron Spike

Forget needles in haystacks. Try finding the tip of a needle in a virus. Scientists have long known that a group of viruses called bacteriophages have a knack for infiltrating bacteria and that some begin their attack with a protein spike. But the tip of this spike is so small that no one knew what it was made of or exactly how it worked. Now a team of researchers has found a single iron atom at the head of the spike, a discovery that suggests phages enter bacteria in a different way than surmised.

Wherever there are bacteria you will find bacteriophages; digestive tracts, contaminated water, and feces are usually a good start. These viruses begin their dirty work by drilling into the outer membrane of bacteria. Once completely through all of a bug’s defenses, the phages inject their DNA, which essentially turns the bacterium into phage-producing factories. Eventually, the microbes become filled with so many viruses that they burst, releasing a new horde of phages into the environment.

Bacteriophages are amazing. It is so interesting to learn about amazingly creative solutions that have evolved over time. Real-life science is not easy to match with fiction that springs from our imaginations.

How Bee Hives Make Decisions

The Secret Life of Bees by Carl Zimmer

The decision-making power of honeybees is a prime example of what scientists call swarm intelligence. Clouds of locusts, schools of fish, flocks of birds and colonies of termites display it as well. And in the field of swarm intelligence, Seeley is a towering figure. For 40 years he has come up with experiments that have allowed him to decipher the rules honeybees use for their collective decision-making. “No one has reached the level of experimentation and ingenuity of Tom Seeley,” says Edward O. Wilson of Harvard University.
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Enthusiasm translates into attention. An enthusiastic scout will inspire more bees to go check out her site. And when the second-wave scouts return, they persuade more scouts to investigate the better site.

The second principle is flexibility. Once a scout finds a site, she travels back and forth from site to hive. Each time she returns, she dances to win over other scouts. But the number of dance repetitions declines, until she stops dancing altogether. Seeley and his colleagues found that honeybees that visit good sites keep dancing for more trips than honeybees from mediocre ones.

This decaying dance allows a swarm to avoid getting stuck in a bad decision. Even when a mediocre site has attracted a lot of scouts, a single scout returning from a better one can cause the hive to change its collective mind.
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“Bees are to hives as neurons are to brains,” says Jeffrey Schall, a neuroscientist at Vanderbilt University. Neurons use some of the same tricks honeybees use to come to decisions. A single visual neuron is like a single scout. It reports about a tiny patch of what we see, just as a scout dances for a single site. Different neurons may give us conflicting ideas about what we’re actually seeing, but we have to quickly choose between the alternatives. That red blob seen from the corner of your eye may be a stop sign, or it may be a car barreling down the street.

To make the right choice, our neurons hold a competition, and different coalitions recruit more neurons to their interpretation of reality, much as scouts recruit more bees

Very cool stuff.

Milky Way May Have 100,000 Times More Nomad Planets Than Stars

There may be 100,000 times more “nomad planets” in the Milky Way than stars, according to a new study by researchers at the Kavli Institute for Particle Astrophysics and Cosmology (KIPAC), a joint institute of Stanford University and the SLAC National Accelerator Laboratory. How amazing is that. Science is so cool. I had no idea this was the case.

If observations confirm the estimate, this new class of celestial objects will affect current theories of planet formation and could change our understanding of the origin and abundance of life.

“If any of these nomad planets are big enough to have a thick atmosphere, they could have trapped enough heat for bacterial life to exist,” said Louis Strigari, leader of the team that reported the result in a paper: Nomads of the Galaxy. Although nomad planets don’t bask in the warmth of a star, they may generate heat through internal radioactive decay and tectonic activity.

Searches over the past two decades have identified more than 500 planets outside our solar system, almost all of which orbit stars. Last year, researchers detected about a dozen nomad planets, using a technique called gravitational microlensing, which looks for stars whose light is momentarily refocused by the gravity of passing planets.

The research produced evidence that roughly two nomads exist for every typical, so-called main-sequence star in our galaxy. The new study estimates that nomads may be up to 50,000 times more common than that.

To arrive at what Strigari himself called “an astronomical number,” the KIPAC team took into account the known gravitational pull of the Milky Way galaxy, the amount of matter available to make such objects and how that matter might divvy itself up into objects ranging from the size of Pluto to larger than Jupiter. Not an easy task, considering no one is quite sure how these bodies form. According to Strigari, some were probably ejected from solar systems, but research indicates that not all of them could have formed in that fashion.

“To paraphrase Dorothy from The Wizard of Oz, if correct, this extrapolation implies that we are not in Kansas anymore, and in fact we never were in Kansas,” said Alan Boss of the Carnegie Institution for Science, author of The Crowded Universe: The Search for Living Planets, who was not involved in the research. “The universe is riddled with unseen planetary-mass objects that we are just now able to detect.”

A good count, especially of the smaller objects, will have to wait for the next generation of big survey telescopes, especially the space-based Wide-Field Infrared Survey Telescope and the ground-based Large Synoptic Survey Telescope, both set to begin operation in the early 2020s.

A confirmation of the estimate could lend credence to another possibility mentioned in the paper – that as nomad planets roam their starry pastures, collisions could scatter their microbial flocks to seed life elsewhere.

Additional authors included KIPAC member Matteo BarnabÃ¨ and affiliate KIPAC member Philip Marshall of Oxford University. The research was supported by NASA, the National Science Foundation and the Royal Astronomical Society.

Potential Antibiotic Alternative to Treat Infection Without Resistance

Researchers at the University of Michigan have found a potential alternative to conventional antibiotics that could fight infection with a reduced risk of antibiotic resistance. Sadly Michigan is another school that is allowing work of those paid for by the citizens of Michigan to be lock away, only due to the wishes of an outdated journal business model instead of supporting open science. The Big Ten seems much more interested in athletic riches than in promoting science. The Big Ten should be ashamed of such anti knowledge behavior and require open science for their schools if they indeed value knowledge.

By using high-throughput screening of a library of small molecules, the team identified a class of compounds that significantly reduced the spread and severity of group A Streptococcus (GAS) bacteria in mice. Their work suggests that the compounds might have therapeutic value in the treatment of strep and similar infections in humans.

“The widespread occurrence of antibiotic resistance among human pathogens is a major public health problem,” said David Ginsburg, a faculty member at LSI, a professor of internal medicine, human genetics, and pediatrics at the U-M Medical School and a Howard Hughes Medical Institute investigator.

Ginsburg led a team that included Scott Larsen, research professor of medicinal chemistry and co-director of the Vahlteich Medicinal Chemistry Core at U-M’s College of Pharmacy, and Hongmin Sun, assistant professor of medicine at the University of Missouri School of Medicine.

Work on this project is continuing at U-M and the University of Missouri, including the preparation of new compounds with improved potency and the filing of patents, Larsen said. Large research schools are also very interested in patents. That is ok, though seems to cloud the pursuit of knowledge too often when too large a focus is on dollars at many schools. But, it seems to put the schools primary focus on dollars; education seems to start to be a minor activity at some of these large schools.

Current antibiotics interfere with critical biological processes in the pathogen to kill it or stop its growth. But at the same time, stronger strains of the harmful bacteria can sometimes resist the treatment and flourish.

An alternate approach is to suppress the virulence of the infection but still allow the bacteria to grow, which means there is no strong selection for strains that are resistant to antibiotics. In a similar experiment at Harvard University, an anti-virulence strategy was successful in protecting mice from cholera.

About 700 million people have symptomatic group A Streptococcus infections around the world each year, and the infection can be fatal. Most doctors prescribe penicillin. The newly identified compounds could work with conventional antibiotics and result in more effective treatment.

Numeracy: The Educational Gift That Keeps on Giving

I like numbers. I always have. This is just luck, I think. I see, how helpful it is to have a good understanding of numbers. Failing to develop a facility with numbers results in many bad decisions, it seems to me.

A new article published in closed anti-science way, sadly (so no link), examines how people who are numerate (like literate but for number—understand) process information differently so that they ultimately make more informed decisions. Cancer risks. Investment alternatives. Calories. Numbers are everywhere in daily life, and they figure into all sorts of decisions.

People who are numerate are more comfortable thinking about numbers and are less influenced by other information, says Ellen Peters of Ohio State University (sadly Ohio State allows research by staff paid by them to be unavailable to the public – sad), the author of the new paper. For example, in one of Peters’s studies, students were asked to rate undergraduates who received what looked like different test scores. Numerate people were more likely to see a person who got 74% correct and a person who got 26% incorrect as equivalent, while people who were less numerate thought people were doing better if their score was given in terms of a percent correct.

People make decisions based on this sort of information all the time. For example, “A lot of people take medications,” Peters says. Every drug has benefits and potential risks, and those can be presented in different ways. “You can talk about the 10 percent of the population that gets the side effect or the 90 percent that does not.” How you talk about it will influence how dangerous the drug seems to be, particularly among people who are less numerate.

Other research has shown that only less numerate people respond differently to something that has a 1 in 100 chance of happening than something that has a 1 percent chance of happening. The less numerate see more risk in the 1 in 100 chance—even though these numbers are exactly the same.

“In general, people who are numerate are better able to bring consistent meaning to numbers and to make better decisions,” Peters says. “It suggests that courses in math and statistics may be the educational gift that keeps on giving.”

Our Genome Has Adopted Virus Genes Critical to Our Survival

Mammals Made By Viruses by Carl Zimmer

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years. They typically have gotten there by infecting eggs or sperm, inserting their own DNA into ours. There are 100,000 known fragments of viruses in the human genome, making up over 8% of our DNA. Most of this virus DNA has been hit by so many mutations that it’s nothing but baggage our species carries along from one generation to the next. Yet there are some viral genes that still make proteins in our bodies. Syncytin appeared to be a hugely important one to our own biology. Originally, syncytin allowed viruses to fuse host cells together so they could spread from one cell to another. Now the protein allowed babies to fuse to their mothers.
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The big picture that’s now emerging is quite amazing. Viruses have rained down on mammals, and on at least six occasions, they’ve gotten snagged in their hosts and started carrying out the same function: building placentas.
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Some mammals that scientists have yet to investigate, such as pigs and horses, don’t have the open layer of cells in their placenta like we do. Scientists have come up with all sorts of explanations for why that may be, mainly by looking for differences in the biology of each kind of mammals. But the answer may be simpler: the ancestors of pigs and horses might never have gotten sick with the right virus.

More amazing facts from science. This stuff is so interesting. Carl Zimmer is a fantastic science writer and he has written several great science books.

NASA Biocapsules Deliver Medical Interventions Based Upon What They Detect in the Body

Very cool innovation from NASA. The biocapsule monitors the environment (the body it is in) and responds with medical help. Basically it is acting very much like your body, which does exactly that: monitors and then responds based on what is found.

The Miraculous NASA Breakthrough That Could Save Millions of Lives

The Biocapsules aren’t one-shot deals. Each capsule could be capable of delivering many metred doses over a period of years. There is no “shelf-life” to the Biocapsules. They are extremely resilient, and there is currently no known enzyme that can break down their nanostructures. And because the nanostructures are inert, they are extremely well-tolerated by the body. The capsules’ porous natures allow medication to pass through their walls, but the nanostructures are strong enough to keep the cells in one place. Once all of the cells are expended, the Biocapsule stays in the body, stable and unnoticed, until it is eventually removed by a doctor back on Earth.
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Dr. Loftus [NASA] thinks we could realistically see wildspread usage on Earth within 10 to 15 years.
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The cells don’t get released from the capsule. The cells inside the capsule secrete therapeutic molecules (proteins, peptides), and these agents exit the capsule by diffusion across the capsule wall.

NASA plans to use the biocapsules in space, but they also have very promising uses on earth. They can monitor a diabetes patient and if insulin is needed, deliver it. No need for the person to remember, or give themselves a shot of insulin. The biocapsule act just like out bodies do, responding to needs without us consciously having to think about it. They can also be used to provide high dose chemotherapy directly to the tumor site (thus decreasing the side effects and increasing the dosage delivered to the target location. Biocapsules could also respond to severe allergic reaction and deliver epinephrine (which many people know have to carry with them to try and survive an attack).

It would be great if this were to have widespread use 15 years from now. Sadly, these innovations tend to take far longer to get into productive use than we would hope. But not always, so here is hoping this innovation from NASA gets into ourselves soon.

Microbiologist Develops Mouthwash That Targets Only Harmful Cavity Causing Bacteria

A new mouthwash developed by a microbiologist at the UCLA School of Dentistry is highly successful in targeting the harmful Streptococcus mutans bacteria that is the principal cause tooth decay and cavities.

In a recent clinical study, 12 subjects who rinsed just one time with the experimental mouthwash experienced a nearly complete elimination of the S. mutans bacteria over the entire four-day testing period.

Dental caries, commonly known as tooth decay or cavities, is one of the most common and costly infectious diseases in the United States, affecting more than 50 percent of children and the vast majority of adults aged 18 and older. Americans spend more than $70 billion each year on dental services, with the majority of that amount going toward the treatment of dental caries.

This new mouthwash is the product of nearly a decade of research conducted by Wenyuan Shi, chair of the oral biology section at the UCLA School of Dentistry. Shi developed a new antimicrobial technology called STAMP (specifically targeted anti-microbial peptides) with support from Colgate-Palmolive and from C3-Jian Inc., a company he founded around patent rights he developed at UCLA; the patents were exclusively licensed by UCLA to C3-Jian.

The human body is home to millions of different bacteria, some of which cause diseases such as dental caries but many of which are vital for optimum health. Most common broad-spectrum antibiotics, like conventional mouthwash, indiscriminately kill both benign and harmful pathogenic organisms and only do so for a 12-hour time period.

The overuse of broad-spectrum antibiotics can seriously disrupt the body’s normal ecological balance, rendering humans more susceptible to bacterial, yeast and parasitic infections.

Shi’s Sm STAMP C16G2 investigational drug, tested in the clinical study, acts as a sort of “smart bomb,” eliminating only the harmful bacteria and remaining effective for an extended period.

“With this new antimicrobial technology, we have the prospect of actually wiping out tooth decay in our lifetime,” said Shi, who noted that this work may lay the foundation for developing additional target-specific “smart bomb” antimicrobials to combat other diseases.

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Royal Society Journal Embraces Open Access

Royal Society journal archive made permanently free to access

The Royal Society…journal archive – which includes the first ever peer-reviewed scientific journal – has been made permanently free to access online.

Around 60,000 historical scientific papers are accessible via a fully searchable online archive, with papers published more than 70 years ago now becoming freely available.
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reasures in the archive include Isaac Newton’s first published scientific paper, geological work by a young Charles Darwin, and Benjamin Franklin’s celebrated account of his electrical kite experiment.

The move is being made as part of the Royal Society’s ongoing commitment to open access in scientific publishing.

Good for them. Slowly more and more are realizing clinging to old fashion publishing models are contrary to promoting science and scientific literacy.