Oh, dear [Pharyngula]

The context of this graph isn’t entirely clear, but it’s from Jeffrey Ross-Ibarra of UC Davis, and it’s from a poll of 800 first year students, so I presume it’s the results of a survey of their incoming class?

Maybe one of the things we need to do as part of popularizing science to the general public is to emphasize the diversity of life, and talk more about the cool things plants and bacteria and fungi and so forth do. I know I started out as a zoologist, am still mostly focused on animal development, but over the years I’ve become increasingly aware that there are amazing contrasts to be studied. We might wish we could study aliens from Mars, but every time I look at plant development, for instance, I feel like I’m examining extraterrestrials already.

This Is How You Have to Ship Bugatti’s $3M Supercar

Spencer Berke/Symbolic Motors San Diego

When you drop $3 million on a special-edition Bugatti Veyron Grand Sport Vitesse, you want everything to be perfect. That’s why, before it leaves the factory, Bugatti wraps the car more carefully than royal nurses swaddle the future King George.

This Vitesse, complete with a custom (and questionable) paint job, was delivered to an unnamed buyer at Symbolic Motor Car Company in San Diego. Spencer Berke, an employee at the dealership, photographed the whole unloading process, which took more than two hours from start to finish.

Nearly the entire car is carefully wrapped for protection against scratches, with holes left open for ventilation at the front and exhaust at the rear, and a more translucent covering over the windshield. Only the driver’s door is left uncovered, so the car can be driven on and off a truck during shipping. Each spoke on the rims is individually wrapped with cloth and zip ties. A special mount to store the car’s removable hard top in a garage is included in a separate box. The cars, built in Molsheim, in eastern France, are generally shipped by boat, but impatient customers can have them air mailed for an extra fee.

With 1,200 horsepower, a top-speed of 255 mph, and a 0-60 time of less than 2.6 seconds, the Veyron Grand Sport Vitesse is fantastic machine, and Bugatti and its dealers do everything they can to keep it that way en route from the factory to the owner’s garage.

Once it’s unwrapped, the dealership spends up to 12 hours inspecting every detail, down to the finish, battery, fluids, and wiring. “If you’re going to ship a $3 million car, you want to make sure that it arrives intact and in a presentable condition,” says Rick Ahumada, sales manager at Symbolic. “Every car is special ordered to the client’s requests and tastes. It’s what you would expect of a $3 million car.”

How to Use OS X Yosemite’s Best New Messages Features

Screenshot: WIRED

Apple’s latest desktop operating system, OS X Yosemite, won’t officially come out until sometime this fall. But now that its public beta is open, both developers and a large number of Mac owners are able to use a preview version of the landmark OS.

For those who’ve just started using the beta, or are just anticipating its launch later this year, we’ve got some tips on how to best take advantage of the redesigned OS and its many new features. In this edition, we take on the new features in Messages. Messages spans both iOS 8 and Yosemite, but we’ll focus on the OS X side.

Messages has some great new features, especially for group chats, which historically have tended to get out of hand. In the upper right of a chat you get a new Details button. You can tap that to give a particular conversation a title, mute notifications for the chat, add participants, or remove yourself from the thread entirely. If everyone uses iOS 8 and Find My Friends, you can also share your locations with each other. Your positions are tacked onto a map. This Details button also houses a reverse chronological collection of the photos sent in the messaging thread, like a dedicated private photo stream for a conversation.

Through this details panel you also have the option to select a specific contact in the conversation to voice call, FaceTime, or share your screen with. When you make a request to share your screen, you can accept, decline, or block a user. A screensharing icon shows up in the upper menu bar of your homescreen which you can tap for additional controls like enabling or disabling audio chatting, pausing or ending the screenshare, or allowing the other person to control your screen. This should be incredibly useful for troubleshooting family iOS or OS X issues.

In the shift from making voice calls to more often texting with friends and family members, I occasionally lament being able to hear their voice—but not so much that I’d want to go back and forth leaving voicemails. Those days are definitely over. But that’s where a new feature called Soundbites come in. This is something other messaging apps like WhatsApp have offered for a while, and while you could always choose to send an audio file over text on iOS, this built-in functionality makes it far quicker and simpler.

Soundbites makes it possible to send audio messages to a friend which they can open and listen to at their leisure, without the urgency of a phone call. On the Mac, and in iOS 8, you tap a microphone button to the side of the message compose field to record one of these audio clips to send over Messages. The message is sent as a blue Message bubble the recipient can tap to download and play, and both you and the recipient can individually choose to keep it, or let it expire into the ether of ephemeral, self-destructing messages after a two-minute time span. In the beta I’m using, the audio is noisy and compressed sounding, more like it’s coming from a CB radio rather than a desktop computer, but I’d expect this quality to improve over time. Also in its current implementation, soundbites exist solely within a messaging thread, they aren’t collected in the Details panel for easy perusal later. It could be handy to have these voice messages collected in a single place, but we’ll see if that’s something Apple decides to change as the product evolves.

The beta of Messages works quite well, and the changes Apple has made to the experience, while some are quite subtle, are all positive improvements should you choose to use them. For me, now that I can mute chatty conversation threads, I think I’ll be using Messages far more on the desktop than I did before.

Home is where the microbes are

A person's home is their castle, and they populate it with their own subjects: millions and millions of bacteria.

A study published tomorrow in Science provides a detailed analysis of the microbes that live in houses and apartments. The study was conducted by researchers from the U.S. Department of Energy's Argonne National Laboratory and the University of Chicago.

The results shed light on the complicated interaction between humans and the microbes that live on and around us. Mounting evidence suggests that these microscopic, teeming communities play a role in human health and disease treatment and transmission.

"We know that certain bacteria can make it easier for mice to put on weight, for example, and that others influence brain development in young mice," said Argonne microbiologist Jack Gilbert, who led the study. "We want to know where these bacteria come from, and as people spend more and more time indoors, we wanted to map out the microbes that live in our homes and the likelihood that they will settle on us.

"They are essential for us to understand our health in the 21^st century," he said.

The Home Microbiome Project followed seven families, which included eighteen people, three dogs and one cat, over the course of six weeks. The participants in the study swabbed their hands, feet and noses daily to collect a sample of the microbial populations living in and on them. They also sampled surfaces in the house, including doorknobs, light switches, floors and countertops.

Then the samples came to Argonne, where researchers performed DNA analysis to characterize the different species of microbes in each sample.

"We wanted to know how much people affected the microbial community on a house's surfaces and on each other," Gilbert said.

They found that people substantially affected the microbial communities in a house -- when three of the families moved, it took less than a day for the new house to look just like the old one, microbially speaking.

Regular physical contact between individuals also mattered -- in one home where two of the three occupants were in a relationship with one another, the couple shared many more microbes. Married couples and their young children also shared most of their microbial community.

Within a household, hands were the most likely to have similar microbes, while noses showed more individual variation.

Adding pets changed the makeup as well, Gilbert said -- they found more plant and soil bacteria in houses with indoor-outdoor dogs or cats.

In at least one case, the researchers tracked a potentially pathogenic strain of bacteria called Enterobacter, which first appeared on one person's hands, then the kitchen counter, and then another person's hands.

"This doesn't mean that the countertop was definitely the mode of transmission between the two humans, but it's certainly a smoking gun," Gilbert said.

"It's also quite possible that we are routinely exposed to harmful bacteria -- living on us and in our environment -- but it only causes disease when our immune systems are otherwise disrupted."

Home microbiome studies also could potentially serve as a forensic tool, Gilbert said. Given an unidentified sample from a floor in this study, he said, "we could easily predict which family it came from."

The research also suggests that when a person (and their microbes) leaves a house, the microbial community shifts noticeably in a matter of days.

"You could theoretically predict whether a person has lived in this location, and how recently, with very good accuracy," he said.

Researchers used Argonne's Magellan cloud computing system to analyze the data; additional support came from the University of Chicago Research Computing Center.

The study was funded by the Alfred P. Sloan Foundation. Additional funding also came from the National Institutes of Health, the Environmental Protection Agency, and the National Science Foundation.

Other Argonne researchers on the study included Argonne computational biologist Peter Larsen, postdoctoral researchers Daniel Smith, Kim Handley, and Nicole Scott, and contractors Sarah Owens and Jarrad Hampton-Marcell. University of Chicago graduate students Sean Gibbons and Simon Lax contributed to the paper, as well as collaborators from Washington University in St. Louis and the University of Colorado at Boulder.

Video: http://ift.tt/1n29aW5

Small molecule acts as on-off switch for nature's antibiotic factory: Tells Streptomyces to either veg out or get busy

Scientists have identified the developmental on-off switch for Streptomyces, a group of soil microbes that produce more than two-thirds of the world's naturally derived antibiotic medicines.

Their hope now would be to see whether it is possible to manipulate this switch to make nature's antibiotic factory more efficient.

The study, appearing August 28 in Cell, found that a unique interaction between a small molecule called cyclic-di-GMP and a larger protein called BldD ultimately controls whether a bacterium spends its time in a vegetative state or gets busy making antibiotics.

Researchers found that the small molecule assembles into a sort of molecular glue, connecting two copies of BldD as a cohesive unit that can regulate development in the Gram-positive bacteria Streptomyces.

"For decades, scientists have been wondering what flips the developmental switch in Streptomyces to turn off normal growth and to begin the unusual process of multicellular differentiation in which it generates antibiotics," said Maria A. Schumacher, Ph.D., an associate professor of biochemistry at the Duke University School of Medicine. "Now we not only know that cyclic-di-GMP is responsible, but we also know exactly how it interacts with the protein BldD to activate its function."

Streptomyces has a complex life cycle with two distinct phases: the dividing, vegetative phase and a distinct phase in which the bacteria form a network of thread-like filaments to chew up organic debris and churn out antibiotics and other metabolites. At the end of this second phase, the bacteria form filamentous branches that extend into the air to create spiraling towers of spores.

In 1998 researchers discovered a gene that kept cultured Streptomyces bacteria from creating these spiraling towers of fuzz on their surface. They found that this gene, which they named BldD to reflect this "bald" appearance, also affected the production of antibiotics.

Subsequent studies have shown that BldD is a special protein called a transcription factor, a type of master regulator that binds DNA and turns on or off more than a hundred genes to control biological processes like sporulation. But in more than a decade of investigation, no one had been able to identify the brains behind the operation, the molecule that ultimately controls this master regulator in Streptomyces.

Then scientists at the John Innes Centre in the United Kingdom -- where much of the research on Streptomyces began -- discovered that the small molecule cyclic-di-GMP is generated by several transcription factors regulated by BldD. The researchers did a quick test to see if this small molecule would itself bind BldD, and were amazed to find that it did. They contacted longtime collaborators Schumacher and Richard G. Brennan Ph.D. at Duke to see if they could take a closer look at this important interaction.

The Duke team used a tool known as x-ray crystallography to create an atomic-level three-dimensional structure of the BldD-(cyclic-di-GMP) complex.

BldD normally exists as a single molecule or monomer, but when it is time to bind DNA and suppress sporulation, it teams up with another copy of itself to do the job. The 3D structure built by the researchers revealed that these two copies of BldD never physically touch, and instead are stuck together by four copies of cyclic-di-GMP.

"We have looked through the protein databank and scoured our memories, but this finding appears to be unique," said Brennan, who is a professor and chair of biochemistry at Duke University School of Medicine. "We have never seen a type of structure before where two monomers become a functional dimer, with no direct interaction between them except a kind of small-molecule glue."

To confirm their findings, Schumacher determined several crystal structures from different flavors of bacteria (S. venezuelae and S. coelicolor) and came up with the same unusual result every time.

Now that the researchers know how cyclic-di-GMP and BldD can become glued together to turn off sporulation and turn on antibiotic production, they would like to know how the complex can become unglued again to flip the switch the other way.

The research was supported by a Long Term EMBO Fellowship (ALTF 693-2012), a Leopoldina Postdoctoral Fellowship, the Biotechnology and Biological Sciences Research Council (BB/H006125/1), the MET Institute Strategic Programme, and the Duke University School of Medicine.

Story Source:

The above story is based on materials provided by Duke University . Note: Materials may be edited for content and length.

Up to 3,000 times the bacterial growth on hollow-head toothbrushes

Solid-head power toothbrushes retain less bacteria compared to hollow-head toothbrushes, according to researchers at The University of Texas Health Science Center at Houston (UTHealth) School of Dentistry.

The results of the study are published in the August issue of the Journal of Dental Hygiene. Lead author and professor at the UTHealth School of Dentistry, Donna Warren Morris, R.D.H., M.Ed., notes that microbial counts were lower in the solid-head toothbrush group than in the two hollow-head toothbrush groups in 9 out of 10 comparisons.

"Toothbrushes can transmit microorganisms that cause disease and infections. A solid-head design allows for less growth of bacteria and bristles should be soft and made of nylon," Morris said. "It is also important to disinfect and to let your toothbrush dry between uses. Some power toothbrushes now include an ultraviolet system or you can soak the head in mouthwash for 20 minutes."

The study was conducted over a three-week period where participants brushed twice daily with one out of three randomly assigned power toothbrushes. Participants used non-antimicrobial toothpaste and continued their flossing routine throughout the study, but refrained from using other dental products like mouthwash.

"The packaging on most power toothbrushes won't distinguish between a hollow-head and a solid-head design," Morris said. "The best way to identify a solid-head design is through the connection to the body of the power toothbrush. Naturally, there will be some space to connect the two parts but a significant portion will be solid, up to the bristles or brush head."

During the study the brush heads were exposed to five categories of oral microorganisms: anaerobes and facultative microorganisms, yeast and mold, oral streptococci and oral enterococci anaerobes, Porphyromonas gingivalis and Fusobacterium species.

The article also states that there is no present or published study that has demonstrated that bacterial growth on toothbrushes can lead to systematic health effects, but as Morris stated, several microorganisms have been associated with systemic diseases.

"We do know and there are studies that have linked Fusobacterium to colorectal cancer. Some of these other bacteria have been linked with cardiovascular disease," Morris said. "There is a high association with gum disease and cardiovascular disease. Researchers have been able to culture the same bacteria around the heart that causes gum disease. "

This study was funded in part by the Advanced Response Corporation. Other researchers include Millicent Goldschmidt, Ph.D., M.S., professor emerita at the UTHealth School of Dentistry; Harris Keene, D.D.S., retired professor from The University of Texas M.D. Anderson Cancer Center; and Stanley Cron, M.S.P.H., research instructor at the UTHealth School of Nursing.

Story Source:

The above story is based on materials provided by University of Texas Health Science Center at Houston . Note: Materials may be edited for content and length.

Synthesis produces new fungus-derived antibiotic

A fortuitous collaboration at Rice University has led to the total synthesis of a recently discovered natural antibiotic. The laboratory recreation of a fungus-derived antibiotic, viridicatumtoxin B, may someday help bolster the fight against bacteria that evolve resistance to treatments in hospitals and clinics around the world.

As part of the process, Rice organic chemist K.C. Nicolaou and structural biologist Yousif Shamoo and their colleagues created and tested a number of variants of viridicatumtoxin B that could lead to the simplified synthesis of a new generation of more effective antibiotics.

The work reported this month in the Journal of the American Chemical Society (JACS) focused on a tetracycline discovered in 2008 by scientists who isolated small amounts from penicillium fungi. The yield wasn't nearly enough for extensive testing, but it provided a basis for the discoverers to analyze its structure through magnetic resonance imaging, Nicolaou said.

"We're inspired by molecules that are biologically active and have the potential to become medicines one day," he said.

The new discovery belongs to a class of antibiotics known as tetracyclines for their distinctive molecular structure. They proved potent in initial tests on Gram-positive bacteria, so named for a staining technique to mark bacteria that are more susceptible to antibiotics than their Gram-negative counterparts.

The first tetracyclines, discovered in the late 1940s, ushered in a new class of powerful antibacterial agents to treat high-mortality diseases, among them anthrax and plague as well as such bacterial infections as chlamydia, syphilis and Lyme disease.

To find new weapons, especially against "superbugs" that resist nearly all antibiotics, synthetic chemists pursue the complex process of mimicking the structures of effective natural molecules as they build drug candidates atom by atom.

"Tetracyclines are widespread antibiotics today, but bacteria are building resistance to a lot of them," Nicolaou said. "This new tetracycline is not plentiful in nature, so the only way we can make it available to study by biologists for its potential in medicine is to synthesize it in the laboratory."

Three years of effort led the chemists working at Rice's BioScience Research Collaborative to find a structure that not only matches that of natural viridicatumtoxin B, but also allows the possibility of synthetic variants that could match or surpass its antibiotic potency.

Nicolaou, who is best known for synthesizing the widely used anticancer drug taxol and the chemotherapy agent calicheamicin, said the complicated new molecule offered a challenge he couldn't resist. "The structure (the discoverers) assigned to this molecule was suspicious to us. We didn't actually believe that it was correct," he said.

"Given this, we initiated a research program to synthesize this compound for three purposes," he said. "One was to develop new synthetic chemistry, which is always the case in these kinds of endeavors. Two was to synthesize the molecule itself and confirm its structure. Three was to use the technology we've developed to make analogs of it in the hope that we could find something simpler and yet better in terms of its biological and pharmacological properties."

Nicolaou's team met all of those goals and did indeed revise the structure of the molecule. The lab turned synthetic samples over to biologist Shamoo and his group for testing against a number of bacterial strains and comparison with natural viridicatumtoxin B.

"This was very exciting for us," said Nicolaou, who moved his lab from the Scripps Research Institute and the University of California at San Diego last year to form these kinds of collaborations. "In order to investigate the biological properties of our synthesized compounds, we turned to the Shamoo laboratory for its expertise in the area of antibiotics and drug-resistant bacteria."

The biologists reported that the synthetic version performed as well as the natural, and analogs lacking a hydroxyl group were even more effective against the same Gram-positive bacteria. The results also suggested the possibility of making variants by modifying certain domains of the molecule to improve its overall pharmacological properties.

"The most important finding was that simpler variations that are easier to make are showing equal if not better activity than the natural substance," Nicolaou said.

"My lab was really excited about working with K.C.'s group," Shamoo said. "Our expertise in antibiotic resistance and his synthesis of viridicatumtoxin B and analogs were a perfect opportunity for us to work together on an important problem."

Nicolaou acknowledged it could be years -- even decades -- before an antibiotic derived from viridicatumtoxin B is available to patients. But, he said, careful research from the start pays dividends in the long term, and the tools developed through the process should prove valuable in the synthesis of other fungal tetracyclines.

"Even though you find something that looks good, you shouldn't take the first substance from the shelf and run to develop it into a drug," he said. "We have to worry about solubility, biodegradation, availability and so many different things before we can get on the path of clinical development, because that part of the process is very expensive. We want to be sure at the research stage that we're doing everything we can to ensure the success of our chosen drug candidate."

The subject is very much on his mind these days. In this month's print edition of the journal Angewandte Chemie, Nicolaou laid out strategies for drug development to make what he called "one of the most challenging and difficult human endeavors" more efficient.

"It's said that for a drug to be discovered, a chemist has to make 10,000 compounds on average," he said. "It also means that it takes 12 to 15 years to develop a drug from the beginning to the end, and costs between $1.5 billion to $2 billion.

"Often, these things are not predictable, so experimentation is usually the final proof of what we're trying to do. That's what makes our collaborations at Rice so welcome and fruitful. The interface between chemistry and biology is the key to success in discovering drugs."

Co-authors of the JACS paper are graduate students Christopher Hale, Lizanne Nilewski and Kathryn Beabout and postdoctoral fellows Christian Nilewski, Heraklidia Ioannidou and Abdelatif El Marrouni, all of Rice, and Tim Wang, a Rice undergraduate student and Rice Century Scholar. Hale, Ioannidou, El Marrouni and Christian and Lizanne Nilewski came to Rice from the Scripps Research Institute, where they initiated the project in Nicolaou's lab; Lizanne Nilewski is now a second-year graduate student in the lab of Rice Professor James Tour. Shamoo is Rice's vice provost for research and a professor of biochemistry and cell biology. Nicolaou is the Harry C. and Olga K. Wiess Professor of Chemistry.