Trigger for crucial immune system cell identified

Scientists at The Scripps Research Institute (TSRI) have identified the long-sought activating molecules for a rare but crucial subset of immune system cells that help rally other white blood cells to fight infection.



In the process, the team also uncovered a previously unsuspected link between the mammalian immune system and the communication systems of simpler organisms such as bacteria.


The findings, published online ahead of print on October 16 by the journal Immunity, could lead to novel therapeutic approaches for diseases such as type 1 diabetes that are the result of immune system overactivity, as well as new ways to boost the effectiveness of vaccines, according to study leader Luc Teyton, a professor in TSRI's Department of Immunology and Microbial Science.


A Bridge


When a virus, bacteria or foreign substance invades the body, specialized cells known as dendritic cells present in the skin and other organs capture the trespassers and convert them into smaller pieces called antigens that they then display on their cell surfaces. White blood cells known as T and B cells recognize the antigens to launch very specific attacks on the invaders.


Dendritic cells also activate a specialized population of T cells known as type 1 diabetes (NKT) cells. Once activated, NKT cells can commandeer the functions of dendritic cells to make them more effective and also recruit and coordinate the responses of T- and B-type cells.


"Because of their dual functions, NKT cells are a bridge between the body's innate immunity, which is characterized by rapid but less specific responses to pathogens, and adaptive or acquired immunity, which is composed of specialized white blood cells that can remember past invaders," Teyton said.


Previous studies indicated that NKT cells are activated by molecules known as glycolipids that dendritic cells produce and then display on their outer surfaces. It was widely assumed that the activating molecules were a class of glycolipids known as beta-glycosylceramides, an important component of nervous system cells.


However, this hypothesis had not been thoroughly examined, in part because there is no chemical test currently available to distinguish between two forms of the molecule that have slightly different configurations -- beta-glycosylceramide and alpha-glycosylceramide. In addition, when scientists attempt to create either form synthetically for testing, there is always the possibility of small contamination of one by the other.


"When you're making glycolipids, there is no completely faithful way of controlling the form that you're making," Teyton said. "You're favoring the making of one, but you cannot say for sure that you don't have a small amount of the other form."


A Surprising Result


In their new study, Teyton and his colleagues, who included scientists from Brigham Young University, the La Jolla Institute for Allergy & Immunology and the University of Chicago, abandoned the chemical approach altogether. Instead, they combined a series of biochemical and biological assays to create a test that was sensitive enough to distinguish between the two different forms of glycolipids.


"Biological assays are exquisitely sensitive to low amounts of otherwise unmeasurable molecules," said study first author Lisa Kain, a research technician in Teyton's lab.


The scientists used custom antibodies to identify and eliminate alpha-glycosylceramides from their test batches. When the team was confident that their test batch contained only beta forms of the glycolipid, they tested it on NKT cells gathered from mice. To their surprise, however, nothing happened. Contrary to the conventional wisdom, the beta-glycosylceramides failed to activate the NKT cells.


"We were very skeptical about the early results," Teyton said. "We thought we had used the wrong antibody."


Next, the team combined enzymes designed to digest molecular linkages found only on beta-glycosylceramides with mice NKT cells inside test tubes. Surprisingly, the NKT cells were still being activated.


Finally, when the team used antibodies to disable alpha-glycosylceramides inside live mice, not only did the NKT cells fail to activate, they disappeared altogether from organs such as the thymus, where NKT cells are produced.


These multiple lines of evidence strongly indicated that it was the alpha form of the glycolipids that were the triggers for NKT cells. "What we thought was the contaminant turned out to be the activating molecule we were looking for," Teyton said.


New Therapies


The results were surprising for another reason. Until that moment, scientists did not think mammalian cells were capable of producing alpha forms of the glycolipids. The molecules were thought to exist only in bacteria and other simple organisms, which use them primarily as a means of communicating with one another. The findings thus suggest that the roots of a crucial part of the mammalian immune response are even more ancient than previously thought.


"Nobody expected this," Teyton said. "It's like discovering that all languages share a common origin."


Now that scientists know that alpha-glycosylceramides are made by our own body and activate NKT cells, they might be able to exploit it to create new therapies. For example, Teyton said, researchers could use enzymes to reduce alpha-glycosylceramide levels in order to suppress an overactive immune response, which happens with diseases such as type 1 diabetes. Or they could combine the molecules with antigens to create vaccines that elicit a faster and more efficient immune response.


"This opens up an avenue of new therapeutic approaches that we've never even thought about," Teyton said.



Cells' powerhouses were once energy parasites: Study upends current theories of how mitochondria began

Parasitic bacteria were the first cousins of the mitochondria that power cells in animals and plants -- and first acted as energy parasites in those cells before becoming beneficial, according to a new University of Virginia study that used next-generation DNA sequencing technologies to decode the genomes of 18 bacteria that are close relatives of mitochondria.



The study appears this week in the online journal PLoS ONE, published by the Public Library of Science. It provides an alternative theory to two current theories of how simple bacterial cells were swallowed up by host cells and ultimately became mitochondria, the "powerhouse" organelles within virtually all eukaryotic cells -- animal and plant cells that contain a nucleus and other features. Mitochondria power the cells by providing them with adenosine triphosphate, or ATP, considered by biologists to be the energy currency of life.


The origin of mitochondria began about 2 billion years ago and is one of the seminal events in the evolutionary history of life. However, little is known about the circumstances surrounding its origin, and that question is considered an enigma in modern biology.


"We believe this study has the potential to change the way we think about the event that led to mitochondria," said U.Va. biologist Martin Wu, the study's lead author. "We are saying that the current theories -- all claiming that the relationship between the bacteria and the host cell at the very beginning of the symbiosis was mutually beneficial -- are likely wrong.


"Instead, we believe the relationship likely was antagonistic -- that the bacteria were parasitic and only later became beneficial to the host cell by switching the direction of the ATP transport."


The finding, Wu said, is a new insight into an event in the early history of life on Earth that ultimately led to the diverse eukaryotic life we see today. Without mitochondria to provide energy to the rest of a cell, there could not have evolved such amazing biodiversity, he said.


"We reconstructed the gene content of mitochondrial ancestors, by sequencing DNAs of its close relatives, and we predict it to be a parasite that actually stole energy in the form of ATP from its host -- completely opposite to the current role of mitochondria," Wu said.


In his study, Wu also identified many human genes that are derived from mitochondria -- identification of which has the potential to help understand the genetic basis of human mitochondrial dysfunction that may contribute to several diseases, including Alzheimer's disease, Parkinson's disease and diabetes, as well as aging-related diseases.


In addition to the basic essential role of mitochondria in the functioning of cells, the DNA of mitochondria is used by scientists for DNA forensics, genealogy and tracing human evolutionary history.




Story Source:


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



Staph 'gangs' share nutrients during infection

Antibiotic-resistant bacteria can share resources to cause chronic infections, Vanderbilt investigators have discovered. Like the individual members of a gang who might be relatively harmless alone, they turn deadly when they get together with their "friends."



The findings, reported Oct. 8 in Cell Host & Microbe, shed light on a long-standing question in infectious diseases and may inform new treatment strategies, said Eric Skaar, Ph.D., MPH, Ernest W. Goodpasture Professor of Pathology, Microbiology and Immunology.


One way that Staphylococcus aureus and other pathogens can become resistant to antibiotics is by changing the way they generate energy and becoming "small colony variants," which are small and weak, Skaar explained.


The question has been: how do bacteria that are less fit and grow poorly in the laboratory cause such persistent infections in humans?"The question has been: how do bacteria that are less fit and grow poorly in the laboratory cause such persistent infections in humans?"


The current studies support the notion that antibiotic-resistant staph bacteria, including methicillin-resistant (MRSA) strains, can exchange nutrients with each other and even with other bacterial species, including the "normal" microbes of the microbiome, to increase their virulence during an infection.


The findings challenge infectious disease dogma, Skaar said.


"The thinking has been that if an infection becomes resistant to antibiotics, then the resistant organisms appeared clonally, meaning they're all genetically the same."


Skaar and his colleagues wondered if perhaps instead "there are a bunch of organisms that became resistant in different ways and that can exchange the molecules they're each individually missing."


Two fellows in the lab, Neal Hammer, Ph.D., and James Cassat, M.D., Ph.D., now an assistant professor of Pediatrics at Vanderbilt, tested this hypothesis by mixing together two different small colony variant strains of staph -- one that can't produce heme and the other that can't make menaquinone. They found that in culture, these strains exchanged the two metabolites and grew as if they were wild-type staph.


Next, they tested the idea in a mouse model of bone infection (osteomyelitis). Antibiotic-resistant small colony variant S. aureus is the cause of chronic and difficult to treat osteomyelitis and also of lung infections in patients with cystic fibrosis (CF).


The investigators demonstrated that either staph strain alone (heme- or menaquinone-deficient) caused only minimal bone infection, but mixed together, they caused a fully virulent and bone-destroying infection.


"In bone, these bacteria are trading molecules," Skaar said.


In collaboration with C. Buddy Creech, M.D., MPH, associate professor of Pediatrics, the researchers isolated samples of staph small colony variants and normal bacteria from the lungs of CF patients.


When individual CF staph small colony variants were mixed together in culture, they grew like wild-type bacteria. Likewise, co-culture of CF staph small colony variants with normal microbiome bacterial species also enhanced the growth of staph in culture.


"The microbiome of a cystic fibrosis patient's lungs can provide nutrients to these small colony variants and revert them to wild-type behavior," Skaar said.


"Our findings show that these antibiotic-resistant infections are not what we thought they were -- they're not a single strain of bacteria with a single lesion leading to the small colony variant phenotype," he said. "Instead, they're a mixed population of organisms that are sharing nutrients.


"They act like a big group of bullies until you hit them with drugs, then they stop sharing resources and are resistant. When the drugs go away, they start sharing resources again and get even tougher.


"We're now a little bit smarter about how these organisms are behaving in an infection, which I think we can use to inform new treatment approaches."


Preventing the nutrient exchange, for example, may offer a new therapeutic strategy against these antibiotic-resistant organisms, Skaar said.



Jet lag can cause obesity by disrupting the daily rhythms of gut microbes

Organisms ranging from bacteria to humans have circadian clocks to help them synchronize their biological activities to the time of day. A study published by Cell Press October 16th in Cell now reveals that gut microbes in mice and humans have circadian rhythms that are controlled by the biological clock of the host in which they reside. Disruption of the circadian clock in the host alters the rhythms and composition of the microbial community, leading to obesity and metabolic problems.



"These findings provide an explanation for a long-standing and mysterious observation, namely that people with chronically disturbed day-night cycles due to repetitive jet lag or shift work have a tendency to develop obesity and other metabolic complications," says senior study author Eran Elinav of the Weizmann Institute of Science. "These surprising findings may enable us to devise preventive treatments for these people to lower their risk for these complications."


Disruption of the circadian clock in humans is a hallmark of relatively recent lifestyle changes involving chronic shift work or frequent flights across time zones. These widespread behavioral patterns have been linked to a wide range of diseases, including obesity, diabetes, cancer, and cardiovascular disease. But, until now, it has not been clear how changes in circadian rhythms increase the risk for these diseases.


In the new study, Elinav and his team set out to determine whether gut microbes could be the missing link. When they analyzed microbes found in fecal samples collected from mice and humans at different times of day, they discovered rhythmic fluctuations in the abundance of microbes and their biological activities. The host's circadian clock and normal feeding habits were required for the generation of these rhythmic fluctuations in the gut microbes.


When mice were exposed to changing light-dark schedules and abnormal 24 hr feeding habits, the microbial community lost its rhythmic fluctuations and changed in composition. Moreover, a high-fat diet caused these jet-lagged mice to gain weight and develop metabolic problems associated with diabetes. Similarly, jet lag in two humans who had traveled from the United States to Israel changed the composition of gut microbes, favoring the growth of bacteria that have been linked to obesity and metabolic disease.


"Our findings highlight a new therapeutic target that may be exploited in future studies to normalize the microbiota in those people whose lifestyle involves frequent alterations in sleep patterns, such as shift workers and very frequent fliers," Elinav says. "Targeting the harmful changes in the microbiota in these large human populations with probiotic or antimicrobial therapies may reduce or even prevent their risk of developing obesity and its complications."




Story Source:


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



Report Says 72 Percent of Airbnb’s New York Rentals Are Illegal


New York State Attorney General Eric Schneiderman speaks at a news conference in his in New York offices, Tuesday, Nov. 19, 2013.

New York State Attorney General Eric Schneiderman speaks at a news conference in his in New York offices, Tuesday, Nov. 19, 2013. Richard Drew / AP



A whopping 72% of Airbnb’s listings in New York are illegal, according to a new state report, and together with city regulators, the office of New York Attorney General Eric Schneiderman is actively cracking down on the room-rental service.


Covering four years of data provided to the attorney general after a court battle, the report indicates that more than a third of the listings posted on the online marketplace are run by large-scale operators, not permanent residents, and generate more than a third of the revenue. In New York City, laws are in place to prevent people from renting out their residences for less than 30 days, unless the tenants are also home. Schneiderman is looking to shut down these operations, which are essentially run like hotels.


The findings run counter to Airbnb’s previous claims on how people use its service. It prefers to paint its marketplace as a way for individuals to “share” available rooms with others. In September, it proudly announced that 87 percent of Airbnb hosts in New York actually share the home in which they live. But this hardly tells the whole story.


According to the New York report, six percent of Airbnb hosts made 37 percent of the revenue in New York City, amounting to $168 million. Within this pool, hosts posted three to 272 units on the home rental service. The person who had listed 272 units has made as much as $6.8 million in revenue.


Airbnb has not publicly denied the figures. But last week, in San Francisco, the company wholeheartedly embraced new regulations that were put into place to address the risk of hosts renting out properties as if they were full-time hotels. Now, at least officially, only permanent San Francisco residents can offer their homes for rent, entire homes can only be rented out for a maximum of 90 days per year, hotel tax is collected, and each rental must carry $500,000 in liability insurance.


Yes, New York’s report makes Airbnb look rather disingenuous. But it also shows that all cities need regulations along the lines of those in San Francisco. Room sharing is one thing. A hotel business is another. What needed is a way of distinguishing between the two.



Everything Apple Announced at Today’s Event


The iPad Air 2, right, and iPad Mini 3 are photographed side by side at Apple headquarters on Thursday, Oct. 16, 2014 in Cupertino, Calif. Apple unveiled the thinner iPad with a faster processor and a better camera as it tries to drive excitement for tablets amid slowing demand.

The iPad Air 2, right, and iPad Mini 3 are photographed side by side at Apple headquarters on Thursday, Oct. 16, 2014 in Cupertino, Calif. Apple unveiled the thinner iPad with a faster processor and a better camera as it tries to drive excitement for tablets amid slowing demand. Marcio Jose Sanchez / AP



CUPERTINO, CALIFORNIA—Today, Apple introduced new iPads, a new 5K iMac, and detailed two of its latest software offerings: OS X Yosemite and iOS 8.1. Unlike the giant media event the company held last month to show off its new iPhones and Watch, today’s gathering at its headquarters here was more subdued.


First, the software news. OS X Yosemite is available as a free download starting today. The latest update to Apple’s mobile operating system, iOS 8.1, will be available Monday. In addition to a beta of iCloud photo libraries, 8.1 will also include Apple Pay. It will also bring back Camera Roll, for those who missed that feature. On top of that, Apple reworked its iWork suite in an update you can grab today. And for developers looking forward to the Apple Watch, the company announced WatchKit, an SDK for those who want to get their apps ready for the device before it goes on sale.


Thinner, Lighter, More Golden iPads


20141016ipad004

Josh Valcarcel / WIRED



But Apple knew what everyone was really there for: new iPads. Shaving 18 percent of its thickness from the iPad Air (which was already 20 percent thinner than its predecessor), the iPad Air 2 measures in at 6.1mm thick, making it the thinnest tablet on the market. You can stack two on top of one another and they’ll still be thinner than the original iPad.


To make it so thin, Apple eliminated all the micro thin layers of air between the layers of the display, optically bonding them together. The company also reduced internal reflection and added an anti-reflective coating that it claims reduces reflections by 56 percent. Inside, the new iPad Airs have a 64-bit A8x processor that offers 40 percent faster CPU performance and 2.5 percent faster GPU performance. In all, it’s 180 times faster than the original iPad. It gets 10 hours of battery life, too.


Better Camera, and TouchID


20141016ipad003

Josh Valcarcel / WIRED



Apple also updated its camera, which is now 8 megapixels, with f/2.4 aperture. It can shoot 1080p video, and can also do panoramas, burst mode, time-lapse, and slo-mo. The FaceTime HD front camera is also improved with an f/2.2 aperture. Connectivity is faster with more LTE bands and faster 802.11ac Wi-Fi. Oh, and of course, it has TouchID, so it can take advantage of ApplePay and TouchID app extensions.


The new iPad Air 2 can be pre-ordered tomorrow starting at $499 for 16 GB, $599 for 64 GB, and $699 for 128 GB. In addition to Silver and Space Gray, it now comes in Gold.


Mini Gets TouchID Too


20141016ipad005

Josh Valcarcel / WIRED



Apple also upgraded the iPad mini, giving it Touch ID. The iPad Mini 3 starts at $399 for 16 GB, $499 for 64 GB and $599 for 128 GB. Apple dropped the price of the iPad mini 2 and iPad Air by $100, and you can still grab the original iPad mini for $249.


Big Resolution Bump for iMacs


5k

Josh Valcarcel / WIRED



In other news, Apple introduced the iMac with Retina Display. It’s a 27-inch display with 5120 x 2880 pixel resolution (that’s 14.7 million pixels). Apple calls it a “Retina 5K” display. Apple’s introduced a slew of new technologies to control all those pixels, including a new timing chip, oxide TFT materials, and organic passivation, as well as a thinner, more efficient LED backlight. The company says the new machine is 30 percent more energy efficient than its predecessor.


Powering that beautiful display is a 3.5 Ghz i5 processor (upgradable to 4 Ghz), Radeon graphics, 8 GB of memory, and a 1 TB fusion drive. Apple is selling the iMac with Retina display starting today for $2,499. It’s configurable all the way up to roughly $5,000.


Last but not least, Apple updated the Mac Mini with 4th-generation Intel processors, Iris and HD graphics 5000, PCIe based Flash storage, and 802.11ac WiFi. It also has two Thunderbolt 2 ports. The tiny, energy-efficient desktop starts at $499.



Everything Apple Announced at Today’s Event


Apple CEO Tim Cook shows off his company's latest products: Apple Watch, the iPhone 6, the iPad Air 2, the MacBook Pro, and the new 5K iMac.

Apple CEO Tim Cook shows off his company’s latest products: Apple Watch, the iPhone 6, the iPad Air 2, the MacBook Pro, and the new 5K iMac. WIRED screenshot



CUPERTINO, CALIFORNIA—Today, Apple introduced new iPads, a new 5K iMac, and detailed two of its latest software offerings: OS X Yosemite and iOS 8.1. Unlike the giant media event the company held last month to show off its new iPhones and Watch, today’s gathering at its headquarters here was more subdued.


First, the software news. OS X Yosemite is available as a free download starting today. The latest update to Apple’s mobile operating system, iOS 8.1, will be available Monday. In addition to a beta of iCloud photo libraries, 8.1 will also include Apple Pay. It will also bring back Camera Roll, for those who missed that feature. On top of that, Apple reworked its iWork suite in an update you can grab today. And for developers looking forward to the Apple Watch, the company announced WatchKit, an SDK for those who want to get their apps ready for the device before it goes on sale.


Thinner, Lighter, More Golden iPads


But Apple knew what everyone was really there for: new iPads. Shaving 18 percent of its thickness from the iPad Air (which was already 20 percent thinner than its predecessor), the iPad Air 2 measures in at 6.1mm thick, making it the thinnest tablet on the market. You can stack two on top of one another and they’ll still be thinner than the original iPad.


To make it so thin, Apple eliminated all the micro thin layers of air between the layers of the display, optically bonding them together. The company also reduced internal reflection and added an anti-reflective coating that it claims reduces reflections by 56 percent. Inside, the new iPad Airs have a 64-bit A8x processor that offers 40 percent faster CPU performance and 2.5 percent faster GPU performance. In all, it’s 180 times faster than the original iPad. It gets 10 hours of battery life, too.


Better Camera, and TouchID


Apple also updated its camera, which is now 8 megapixels, with f/2.4 aperture. It can shoot 1080p video, and can also do panoramas, burst mode, time-lapse, and slo-mo. The FaceTime HD front camera is also improved with an f/2.2 aperture. Connectivity is faster with more LTE bands and faster 802.11ac Wi-Fi. Oh, and of course, it has TouchID, so it can take advantage of ApplePay and TouchID app extensions.


The new iPad Air 2 can be pre-ordered tomorrow starting at $499 for 16 GB, $599 for 64 GB, and $699 for 128 GB. In addition to Silver and Space Gray, it now comes in Gold.


Mini Gets TouchID Too


Apple also upgraded the iPad mini, giving it Touch ID. The iPad Mini 3 starts at $399 for 16 GB, $499 for 64 GB and $599 for 128 GB. Apple dropped the price of the iPad mini 2 and iPad Air by $100, and you can still grab the original iPad mini for $249.


Big Resolution Bump for iMacs


In other news, Apple introduced the iMac with Retina Display. It’s a 27-inch display with 5120 x 2880 pixel resolution (that’s 14.7 million pixels). Apple calls it a “Retina 5K” display. Apple’s introduced a slew of new technologies to control all those pixels, including a new timing chip, oxide TFT materials, and organic passivation, as well as a thinner, more efficient LED backlight. The company says the new machine is 30 percent more energy efficient than its predecessor.


Powering that beautiful display is a 3.5 Ghz i5 processor (upgradable to 4 Ghz), Radeon graphics, 8 GB of memory, and a 1 TB fusion drive. Apple is selling the iMac with Retina display starting today for $2,499. It’s configurable all the way up to roughly $5,000.


Last but not least, Apple updated the Mac Mini with 4th-generation Intel processors, Iris and HD graphics 5000, PCIe based Flash storage, and 802.11ac WiFi. It also has two Thunderbolt 2 ports. The tiny, energy-efficient desktop starts at $499.