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Proteins consist of long chains of building blocks known as amino acids that fold up into precise 3D shapes that govern their function. David Baker, a computational biochemist at the University of Washington, Seattle, has spent years deciphering the rules that govern how these amino acid chains fold, and develop software to predict the 3D shape unknown amino acid chains are likely to take. Recent improvements to this software from Baker and others now make it possible to extend such prediction to the majority of proteins in nature. That's likely to lead to novel insights for biochemists working to understand what all these proteins do. It is also allowing Baker and his colleagues to design novel proteins to work as everything from medicines to materials, and catalysts to biochemical sensors.
http://science.sciencemag.org/content/353/6297/338
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A study published online in Science (http://doi.org/bmkx) presents the most detailed view yet of part of the immature form of HIV, and reveals that a new type of HIV drug currently being tested works in an unusual way. Led by John Briggs at EMBL and Hans-Georg Kräusslich at Heidelberg University Hospital, the scientists discovered that when the virus became resistant to early versions of these drugs, it did not do so by blocking or preventing their effects, but rather by circumventing them. 
Study reveals how new HIV drugs prevent virus from maturing, and how the virus becomes resistant to those drugs
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Kam-Yung Soh

• Biology  - 
 
"Researchers employing near infrared still photographs and time-lapse video have peered into the pupa of the living tsetse fly and for the first time have watched its development unfold from its start as a larva to its completion and emergence as an adult. The research is described in the Journal of Insect Science.

The fact that the pupae are transparent to near infrared imaging not only promises improved observation of other pupal insects but, importantly, more effective ways to engineer the release of sterile male adult tsetse flies used to control sleeping sickness and nagana. The tsetse fly is the vector of both diseases, forms of trypanosomiasis that infect people and livestock in many areas of Africa.
[...]
The authors express hopes for wide application of the infrared technique they have used, writing that “It is our hope that this technique will be adapted for many purposes in the field of entomology and beyond.”"

Reference: "Near Infrared Imaging As a Method of Studying Tsetse Fly (Diptera: Glossinidae) Pupal Development" [ http://jinsectscience.oxfordjournals.org/lookup/doi/10.1093/jisesa/iew047 ]
By Ed Ricciuti Researchers employing near infrared still photographs and time-lapse video have peered into the pupa of the living tsetse fly and for the first time have watched its development unfo…
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I would spray RAID on this nasty creature.
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In what is believed to be the largest study of its kind, scientists at PNNL, +Johns Hopkins University and collaborators from institutions across the nation have examined the collections of proteins in the tumors of 169 ovarian cancer patients to identify critical proteins present in their tumors. By integrating their findings about the collection of proteins (the proteome) with information already known about the tumors' genetic data (the genome), the investigators report the potential for new insights into the progress of the most malignant form of the disease. Read more about this research: http://goo.gl/71mIVL; watch our video: https://youtu.be/eLJGepkGLdY.

* * *

The researchers say their achievement illustrates the power of combining genomic and proteomic data — an approach known as proteogenomics — to yield a more complete picture of the biology of a cancer that accounts for three percent of all cancers in women and is the fifth leading cause of cancer deaths among women in the United States.

The work is published June 29, 2016, in the advance online edition of the journal Cell.

"Historically, cancer's been looked at as a disease of the genome," said Karin Rodland, a senior author of the study and chief scientist for biomedical research at PNNL, a +U.S. Department of Energy laboratory. "But that genome has to express itself in functional outcomes, and that's what the proteomic data adds, because proteins do the actual work of the genome."

Daniel W. Chan, the study's other senior author, who led the team at the Johns Hopkins University School of Medicine, said, "Correlating our data with clinical outcomes is the first step toward the eventual ability to predict outcomes that reflect patient survival, with potential applications for precision medicine and new targets for pharmaceutical interventions. But just like anything in medicine, clinical validation will be a long and rigorous process."

The authors say that with the findings, researchers expect to be better able to identify the biological factors defining the 70% of ovarian cancer patients who suffer from the most malignant form of ovarian cancer, called high-grade serous carcinoma. Currently, only one in six such patients lives five or more years beyond diagnosis.

The power of collaboration: The work draws on the efforts of physicians, scientists and patients who have worked together to understand ovarian cancer. The investigators say the effort requires collaboration among physicians as well as patients willing to take part in research to benefit others with the disease or even to prevent others from ever developing cancer.

Under the leadership of the National Cancer Institute, scientists around the nation have worked together to create the Cancer Genome Atlas (TCGA), a collaborative effort to map cancer's genetic mutations. The task for ovarian cancer was completed in 2011. In the current study, the PNNL and JHU teams each studied subsets of 169 high-grade serous carcinoma tissue samples and accompanying genomic and clinical data drawn from that study.

The Johns Hopkins team initially selected 122 of the samples based on those tumors' ability to repair damaged DNA — known as homologous recombination deficiency — and characterized by changes in genes including BRCA1, BRCA2 and PTEN, mutations long linked to increased cancer risk and severity.

"We chose to examine these samples because patients with changes in these genes already are benefiting from a specific drug regimen for breast cancer, so if we could find similar changes in ovarian cancer genomes and proteomes, those patients would likely benefit from the same regimen," said Chan, a professor of pathology and oncology at JHU. Chan is one of the inventors of the OVA1 ovarian cancer detection test, which is licensed to Vermillion Inc. of Austin, Texas.

The PNNL team initially selected 84 samples based on overall patient survival times. "We examined the data for the shortest-surviving patients and the longest-surviving patients hoping to pinpoint biological factors associated with extremely short survival or better-than-average, longer survival," said Rodland.

Then, through their participation in the Clinical Proteomic Tumor Analysis Consortium (CPTAC), another program of the National Cancer Institute which funded both teams, the two groups combined their efforts.

Using protein measurement and identification techniques based on mass spectrometry, the teams identified 9,600 proteins in all the tumors, and pursued study on 3,586 proteins common to all 169 tumor samples.

Beyond the genome: While many people are familiar with the role our genes play in the development of cancer, the genes are often just a starting point, for patients and researchers alike. Genes are transcribed into RNA, the genetic material that makes proteins, which are the workhorses of cells. The activity of the proteins varies dramatically, with many undergoing changes that affect their impact and interactions with other proteins.

A detailed look at the activity of proteins in cancer biology gives researchers insight into specific molecular events that would otherwise remain unknown.

A hallmark of cancer, and particularly high grade serous carcinoma, is when genetic instructions go awry. One form is the appearance of more copies of certain regions of the genome. These so-called copy number alterations can lead to changes in protein abundance. When the researchers compared known regions of copy number alterations, they found that parts of chromosomes 2, 7, 20 and 22 led to changes in abundance of more than 200 proteins. A more careful study of those 200 proteins revealed that many are involved in cell movement and immune system function, both processes implicated in cancer progression, the researchers said.

"Adding the information about the proteome on top of the genome provides an entirely new dimension of information that has enabled the discovery of new biological insights to ovarian cancer, while creating a valuable resource that the scientific community can use to generate new hypotheses about the disease, and how to treat it," said Rodland.

"High grade serous carcinoma is such a challenging disease, requiring complex clinical care to achieve long-term survival. This new knowledge gives us new directions to test in the lab and clinic," said study author Douglas A. Levine, director of gynecologic oncology at the Laura and Isaac Perlmutter Cancer Center of NYU Langone Medical Center. "This proteogenomic analysis will help us improve patient outcomes and quality of life."

In addition to large teams of scientists from PNNL and Johns Hopkins, contributors included colleagues from Stanford University School of Medicine, Vanderbilt University School of Medicine, University of California at San Diego, New York University School of Medicine, Virginia Tech, the National Cancer Institute's Office of Cancer Clinical Proteomics Research, as well as CPTAC investigators.

The proteomic analyses performed by the PNNL team were done at teh +Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility at PNNL.
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Daniel Montesinos

• Biology  - 
 
Two invasive acacia species secure generalist pollinators in invaded communities

Exotic entomophilous plants need to establish effective pollinator interactions in order to succeed after being introduced into a new community, particularly if they are obligatory outbreeders. By establishing these novel interactions in the new non-native range, invasive plants are hypothesized to drive changes in the composition and functioning of the native pollinator community, with potential impacts on the pollination biology of native co-flowering plants.

In this study, we used two different sites in Portugal, each invaded by a different acacia species, to assess whether two native Australian trees, Acacia dealbata and Acacia longifolia, were able to recruit pollinators in Portugal, and whether the pollinator community visiting acacia trees differed from the pollinator communities interacting with native co-flowering plants.

Our results indicate that in the invaded range of Portugal both acacia species were able to establish novel mutualistic interactions, predominantly with generalist pollinators. For each of the two studied sites, only two other co-occurring native plant species presented partially overlapping phenologies. We observed significant differences in pollinator richness and visitation rates among native and non-native plant species, although the study of b diversity indicated that only the native plant Lithodora fruticosa presented a differentiated set of pollinator species. Acacias experienced a large number of visits by numerous pollinator species, but massive acacia flowering resulted in visitation rates frequently lower than those of the native co-flowering species.

The establishment of mutualisms in Portugal contributes to the effective and profuse production of acacia seeds in Portugal. Despite the massive flowering of A. dealbata and A. longifolia, native plant species attained similar visitation rates than acacias.


Link to pdf: http://authors.elsevier.com/a/1TE0O,Q4YJBumi

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Kam-Yung Soh

• Biology  - 
 
Ants are known to interact with butterfly larvae. Here is the first description of an interaction between ants and adult butterflies. Link includes a video. Link to paper (PDF) at [ http://www.thenextgenscientist.com/wp-content/uploads/2016/06/lepi07Pomerantz70-2_Hi.pdf ]. Article by Aaron Pomerantz. "Phil [Torres] and I both have backgrounds in entomology, and yet we had never seen anything like this before. I mean sure, we knew that some butterfly larvae have symbiotic relationships with ants, known as myrmecophily. This is well documented, as many of the caterpillars that associate with ants have special organs that secrete sugars and amino acids. The ants get a sugary nutritious meal from the caterpillars and, in return, the fragile caterpillars get personal ant bodyguards which defend against predators and parasites. But this is not the case for the adult butterflies, which usually have to evade ants, lest they become their next meal.
[...]
The butterfly appears to be a known species, Adelotypa annulifera, but these pictures could be revealing an undocumented observation for this butterfly interacting with ants and a potentially new wing-mimicry pattern. Super cool, I thought, but there was just one problem: we know little about this butterfly beyond some dead pinned specimens. What is its life cycle? Where do the larvae develop? What do the larvae even look like? In other words, next to nothing was known about the life history of this butterfly. So to solve this mystery, Phil and I decided to collaborate. I was making a return trip to this exact field site in the coming months, so I set out to uncover the missing pieces of this puzzle."
It was late 2014 when Phil Torres first showed me the photos from his recent trip to the Peruvian Amazon. Among them were amazing images of the tropical wildlife, from brilliant macaws to elusive pumas. But there were a few critters in that album that stood out to us in particular.
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Although this is more Biomechanics, I have the question of why haven't we used the chemical makeup of skin to alter it and make it a better functioning version of a shear thickening fluid?
I get that STF says fluid in its name, which means it would need to be contained, but I expect that could be done though our blood cells or a mutated combination of our blood and STF. Correct me if they have already done this or this idea is absurd and evidence would be nice, thanks!
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+David Scharf It's cool, I get the same way, but this glove we're planning on making allow for full movement win the hand, wrist areas
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The Steinmetz lab at EMBL and collaborators at +Université de Genève have discovered that, contrary to the prevailing assumption, transcription and translation are not independent of each other. They share a molecule that balances transcription and translation to maintain a steady level of protein production. This molecule, called Not1, controls RNA throughout its lifecycle, fine-tuning how much RNA is produced in the nucleus and how much is translated into protein in the cytoplasm. The finding was published in Cell Reports (http://doi.org/bhqt ). One of the first authors, Ishaan Gupta, recounts how it all started with a shared room at a conference:
PhD student Ishaan Gupta recounts how shared interests at a conference led to a surprising discovery: transcription and translation are not independent
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A closer look at the 3D molecular structure of Death Associated Protein Kinases (DAPK) reveals an unexpected dual-purpose loop in the folded string of amino acids. Work by researchers in the Wilmann’s group at EMBL Hamburg, published in Structure (http://doi.org/bg83), suggests that the small loop is crucial for dimer formation and calmodulin binding. “What started as a small side project, unearthed a complex and important signaling pathway within this group of kinases,” says Matthias Wilmanns, “It goes to show, you can’t always plan science!”
Unexpected results: structure of DAPK enzyme reveals dual-purpose loop
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Deep Look

• Biology  - 
 
Winter Is Coming for These Argentine Ant Invaders

Those garden-variety ants in your kitchen are anything but ordinary.

Most likely, they’re Argentine ants, recognizable by their telltale straight lines and proficiency at capturing food, like that errant drop of honey on your counter, with stunning speed.

For about 200 years, the Argentine ant expansion story has been the slow-moving train wreck of myrmecology, the study of ants. From remote origins in the Paraná River valley in Paraguay and Argentina, this virulent invasive species has moved out to claim much of the world’s most desirable territory, whether you’re an ant or a human.

Wherever they go, Argentine ants eliminate the competition — mostly other ants, but sometimes bees, termites and ladybugs — with a take-no-prisoners approach. Invade, dismember, consume. Repeat. Resistance is futile. The basic wisdom among ant scientists is that if you see Argentines, it’s already too late.

The invasion got personal for Deborah Gordon, a professor of biology who studies ants at Stanford University, 12 years ago when Argentine ants broke into her lab overnight. The invaders destroyed a harvester ant colony she was studying, killing the queen. Harvester queens live deep underground, and acquiring one for study is a back-breaking process. “They’re very precious,” she recalled, “I don’t think I’ll ever recover.”

So you can imagine Gordon’s surprise when researchers in her lab found one common native California ant species thriving behind enemy lines, in Argentine ant territory near Palo Alto. This stubborn survivor is called the winter ant, and its persistence, through a novel defensive strategy, seems to offer hope that invasions on the scale of the Argentine ant can be halted, and even reversed.

Argentine ants first came to the U.S. through New Orleans onboard coffee ships from Brazil in the 1890s. They have since made landfall in California, Japan and the Mediterranean coast, following the many sea and land routes of human commerce. “What we’ve learned is they don’t become established at a certain distance from people,” said Gordon, “They need us.”

As early as the 1970s, scientists began to notice a peculiar fact about the Argentine ant and its unusual success.

In the ant world, colony-mates all carry the same smell, embedded in the waxy stuff that makes their exoskeletons shiny. A single tap of antennae is enough to tell friend from foe.

Usually, when ants from different colonies are put together, even from the same species, they fight. Warfare among colonies is a major factor keeping ant populations in balance. But Argentine worker ants can be combined from colonies in Spain, Japan and California, and they will recognize each other — they won’t fight.

Without this natural check, researchers say, a single colony of ants from Argentina has spread across continents and oceans. “They escaped the war zone,” said Brian Whyte, a Ph.D. student in evolutionary biology at UC Berkeley, “and the colony doesn’t seem to have a limit.”

A 2010 paper called the so-called super-colony “the most populous known animal society.”

Its trillions upon trillions of inhabitants dwarf the human population by a long shot.

Not all Argentine ants get along so well. Scientists, including David Holway from UC San Diego and Neil Tsutsui from UC Berkeley, have mapped out a handful of super-colonies worldwide. “They have very clean, demarcated boundaries,” said Holway.

The picture that seemed to emerge amounted to a battle of empires dividing up the world, yet still fighting bitterly wherever their territories met.

But Jasper Ridge, a 1,200-acre Stanford preserve in the hills west of Palo Alto, is different. In 1993, Gordon’s laboratory began tracking ant populations there. At the time, Jasper Ridge was unconquered territory for the Argentines, but they already had been spotted.

“It’s unusual to be able to monitor an invasion,” Gordon said. She predicted that within one to five years, it would all be over. “I thought they would just move quickly through.”

A series of Ph.D. students conducting the field research, including Nicole Heller, who tracked ants at Jasper for six years, began to notice a different trend. One species of native ant was holding its own inside the boundary of the Argentine advance. “They were coping, increasing their distribution over time,” said Heller, who’s now the director of conservation science at the Peninsula Open Space Trust, an environmental organization in Palo Alto.

The winter ant has several advantages over the Argentine: deeper nests, a different cycle of seasonal activity. But other ant species with similar advantages have fallen before the Argentine onslaught. What, the Stanford researchers wondered, was different here?

In 2008, Gordon was using the ant counts at Jasper Ridge to teach undergraduates about invasion ecology. In their final project, where Argentine and winter ants were observed side-by-side in controlled conditions, one group of students claimed to have made a novel discovery. Winter ants, the students found, showed a distinct behavior when they were put on the defensive.

The students watched the winter ants wave their abdomens at their enemies, known as “gaster-flagging” in ant circles, before a cloudy liquid blob appeared at the tip. Approaching the secretion sent the Argentines reeling away. Touching it could kill them.

Gordon admitted she was skeptical.

“I didn’t completely believe it,” she said, “but by the end of the class I was persuaded there was enough there to explore.”

Over the next two years, the students repeated and studied the winter ant’s apparently novel defensive behavior. They also analyzed the the secretion. (Turns out it comes from the same gland used by the ants’ ancestors, wasps, to sting.)

By the time the students’ data was published, asserting that the winter ant’s defensive secretion “may account for its ability to persist” in Argentine-invaded territory, the ant counts at Jasper Ridge had long surpassed Gordon’s initial expectation of one to five years. The ant population data, now at 20 years and counting, bears out the students’ findings.

In fact, the preserve’s winter ants are not only surviving, they’re now pushing back, opening up space for other native ant populations to rebound.

Whether scientists (and the pest control industry) can take a lesson from the winter ant or will remain on the sidelines of this epic ant battle is still unclear.

“Some invasive species may be successful in the beginning, but in the long term may not do as well,” Gordon said. “It’s about how it plays out over time.”

Link to article: http://ww2.kqed.org/science/2016/05/03/winter-is-coming-for-the-argentine-ant-invaders/

Links to researchers:
Deborah Gordon, a professor of biology, Stanford University: https://web.stanford.edu/~dmgordon/

Brian Whyte, a Ph.D. student in evolutionary biology at UC Berkeley: https://ourenvironment.berkeley.edu/people/brian-whyte

David Holway, Professor and Vice Chair of Ecology, Behavior, Evolution, UC San Diego: http://invasivespecies.ucsd.edu/

Neil Tsutsui, Associate Professor, Vice Chair for Instruction
Department of Environmental Science, Policy & Management, UC Berkeley: http://scheckek.wix.com/tsutsuilab
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Sometimes the biggest surprises come in the smallest packages. PNNL scientists contributed to a recent Nature Microbiology letter on novel metabolic strategies in the ocean bacterium Pelagibacterales (SAR11). To their surprise, scientists discovered that the bacterium’s metabolic circuits stay activated all the time as a “survival mechanism.” Read more at http://goo.gl/qkKPHG.

* * *

At PNNL, scientists applied standard proteomic technology to unlock gene-switching mechanisms in SAR11. A strain of Pelagibacterales called HTCC1062 was grown in artificial sea water, cultured samples were subjected to chemical analysis to measure SAR11 metabolic products, and mass spectrometry was used to identify the proteins involved in the synthesis of SAR11's signature sulfur gases. "A lot of the genes here expressed at very low levels, so the advanced sensitivity of our instruments helped," said Lipton.

Researchers discovered that some of SAR11's metabolic circuits stay activated all the time. "The lights in the house are always on," said corresponding author Stephen Giovannoni, an Oregon State University marine biologist. "We were not expecting this story at all." He noted that most genes switch on and off as they are needed. For the paper's data on SAR11's gene switches, he turned to PNNL proteomics experts Joshua T. Aldrich, Mary S. Lipton, Carrie D. Nicora, Richard D. Smith, and Samuel H. Payne.

SAR11's hardwired metabolic circuitry is a "survival mechanism" for an organism that lives a calorically boom-and-bust existence in nutrient-poor regions of the open ocean, said Lipton. "It's very energetically costly for an organism to start ramping genes up. Being prepared all the time, SAR11 can take advantage of the nutrients as they come along."

The study uncovered other surprises. For one, SAR11 makes methanethiol, a sulfur gas, in amounts far greater than scientists previously knew. SAR11 also makes another sulfur gas, dimethyl sulfide (DMS), a nutrient processing "degradation product" previously unknown in this microbe. Such DMS production is controlled by the gene SAR11_0394.

That function was recognized only now by Giovannoni and his team, despite scientists doing extensive genomic and metagenomic work on SAR11 for years. Lastly, researchers were surprised to find two sulfur gas-making degradation pathways in SAR11 - one for DMS and one for methanethiol. This is a surprise because the organism's genome is among the smallest of any free-living microbe. Its tightly packed genome is barely more than 1,000 genes long.

Its small size, simplicity, and robust survivability in the face of harsh conditions makes SAR11 attractively elegant. "We think these cells evolved this way, with very small, genomes, a very long time ago in the oceans," said Giovannoni, who recalled that Leonardo da Vinci once equated elegant simplicity with sophistication. "It's an ancient trait, but not primitive, because these are the most abundant cells on the planet today. They are very successful with this strategy."

Why is this important?  The atmospheric impacts of SAR11 and bacterioplankton like it are enormous. "These cells oxidize a very large amount of total photosynthesis that occurs on Earth every day," said Giovannoni. Of all the world's organic carbon produced through sunlight, SAR11 converts from 5 to 22 percent of it to CO2. As for the paper itself, he added, "The whole world now works on genome predictions." But studying something as old and small and simple as SAR11 may point to a new direction for biologists studying larger and more complex genetic systems. "We've been mesmerized by genomics," said Giovannoni, "but here we see a really simple form of regulation happening at the biochemical level."

Then there is the impact of understanding how microbes and microbial communities operate in their real-world environments, including metabolic strategies that assure survival, like the ones the SAR11 discoveries illustrate. "There's so much we don't know about microbes in nature," said Lipton, a microbiologist with postdoctoral training in mass spectrometry. "They make up our oceans, soils, and lakes. They make up everything around us. We don't understand how they survive or interact as a community."

What's Next? Giovannoni and his team at Oregon State University's High Throughput Microbial Cultivation Lab will publish a paper soon on dissolved organic carbon cycling by SAR11. And related field research is under way in the North Atlantic on the production of DMS and methanethiol by plankton.

This work was sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research (BER) and the Pan-omics program at PNNL.
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Deep Look

• Biology  - 
 
This Vibrating Bumblebee Unlocks a Flower’s Hidden Treasure

In the summertime, the air is thick with the low humming of bees delivering pollen from one flower to the next. If you listen closely, a louder buzz may catch your ear.

This sound is the key to a secret stash of pollen that some flowers hide deep within their anthers, the male parts of the plant. Only pollinators that buzz in just the right way can vibrate tiny grains out of minuscule holes at the top of the anthers for a protein-rich snack.

A Risky Game
The strategy, called buzz-pollination, is risky. But it’s also critical to human agriculture. Tomatoes, potatoes and eggplants need wild populations of buzz pollinators, such as bumblebees, to produce fruit. Honeybees can’t do it.

Plants need a way to get the pollen — basically sperm — to the female parts of another flower. Most plants lure animal pollinators to spread these male gametes by producing sugary nectar. The bee laps up the sweet reward, is dusted with pollen and passively delivers it to the next bloom.

In contrast, buzz-pollinated flowers encourage bees to eat the pollen directly and hope some grains will make it to another flower. The evolutionary strategy is baffling to scientists.

“The flower is almost like playing hard to get,” says Anne Leonard, a biologist at the University of Nevada, Reno who studies buzz pollination. “It’s intriguing because these buzz-pollinated plants ask for a huge energy investment from the bees, but don’t give much back.”

Buzz Breakdown
Bumblebees forage for two food sources: nectar for a quick sugar rush to power their flights and pollen for protein. Most buzz-pollinated flowers are specialists that only offer pollen and they hide the grains at the bottom of tall, skinny anthers.

The bee bites down at the base of the anther, leaving little marks called bee kisses. She “unhooks” her flying muscles from her wings so she can contract them without taking flight. Then she begins to vibrate violently, a behavior scientists call sonication.

The vibrations travel through her soft body to the flower and shake up the pollen grains trapped inside anthers. When she buzzes hard enough, the pollen shoots out of the top and covers the bee. The bumblebee grooms herself, combing the pollen down and mixing it with saliva. She stores the pollen in sacs stuck to her legs as she makes her rounds.

What’s the Buzz?
Buzz pollination is an unlikely evolutionary strategy because the plants are banking on bees working extra hard for a modest reward. Despite the risk of being ignored, buzz pollination has popped up in 20,000 flowering plants across a smattering of unrelated species. Leonard and her team are investigating what the strategy is all about. What are the evolutionary pressures that led so many buzz-pollinated plants to lose their nectar and to specialize in pollen? How do pollinators forage for pollen?

Leonard and her graduate student Jacob Francis search for answers from the bee’s point of view. They dosed fake flowers with different amounts of sugar water to see if the bee works harder to get pollen and nectar. To measure the bee’s effort, Francis rigged a mini-accelerometer to the base of the flowers with some structural wax, the kind you put on braces as a lip protectant.

“If the plant also offers nectar, for example, are the bees on a sugar high and buzz more vigorously?” asks Francis. Does this extra “buzz-thusiasm,” as he calls it, remove too much pollen and actually harm the plant?

Previous research shows that the harder the bee buzzes, the more pollen it gets. The flower could be selecting for the bigger stronger buzzers that can fly longer distances and spread the flower’s genes farther. The bee may be willing to put in the extra work because the buzz technique reduces competition — even honeybees are barred from access.

Reaping the Rewards
You may never have heard of buzz pollination, but chances are you’ve enjoyed blueberries, cranberries and peppers — just a few of the many crops that require a healthy population of wild bumblebees and other buzz-pollinators to produce fruit. Not only do these bees help buzz-pollinated plants, research shows that the presence of wild bumblebees improves the success of honeybee-managed crops.

Despite their importance to human agriculture, we are just beginning to understand what makes buzz-pollinators tick. Wild bumblebee populations are in wide decline partially because humans are messing with their pollen sources by replacing habitats with gardens or agricultural fields, Leonard says. She hopes her research will help reveal what will keep bee populations healthy.

“They pollinate lots of crops that can’t be pollinated by honeybees,” says Leonard. “People will be shocked about how little we know about the bee’s most important resource.”

Links to researchers:
Anne Leonard's Lab: http://www.anneleonard.com/
Buzz Pollination: http://www.anneleonard.com/buzz-pollination/
Jake Francis: https://jacobsfrancis.wordpress.com/
Wild bumble bees reduce pollination deficits in a crop mostly visited by managed honey bees: http://www.sciencedirect.com/science/article/pii/S0167880914003946
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Fascinating!
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In the first genome-scale experiment of its kind, researchers have gained new insights into how a mouse embryo begins to transform from a ball of unfocussed cells into a small, structured entity. Published in Nature (http://doi.org/bmjm), the single-cell genomics study was led by EMBL-EBI and the Wellcome Trust–MRC Cambridge Stem Cell Institute. The new atlas of gene expression during the earliest stages of life could boost studies of mammalian development.
Researchers have gained new insights into how a mouse embryo first begins to develop from a ball of unfocussed cells into a small, structured entity.
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Deep Look

• Biology  - 
 
These Carnivorous Worms Catch Bugs by Mimicking the Night Sky

In 1887, a Maori chief and an English surveyor on New Zealand’s North Island rode a handmade raft through a cave entrance where a local stream disappeared into the darkness. Locals called the place Waitomo, or “where the water flows into the ground.” At the time, what lay beyond was unknown.

Once in the Waitomo cave, Fred Mace and Tane Tinorau looked up from their candles and were dazzled by the thousands of tiny blue lights coating the rock surfaces, giving the ceiling the appearance of a natural planetarium.

But what looked like galaxies overhead to these first explorers at Waitomo were colonies of glow worms, the larval stage of a flying gnat species that has earned the name Arachnocampa luminosa (“glowing spider-worm”) for its combination of awe-inspiring bioluminescence and clever — if grisly — predatory habits.

Like fireflies, Waitomo’s worms glow by breaking down a light-emitting protein. But unlike the characteristic yellow flashes from fireflies, which attract mates, the glow worm’s steady blue light has a more insidious purpose: it’s bait.

The glow worms’ victims are flying insects that inhabit the caves, sometimes hatching from eggs at the stream’s surface and sometimes drifting in from the outside world by air or water.

The strategy is simple. Many of these insects, including moths, navigate by starlight. They keep the celestial bodies at a constant angle to fly in a straight line. “That works fine when the moon and stars are real,” said Dave Merritt, a biologist at the University of Queensland in Brisbane, Australia, “but when the source is close they end up spiraling into it.”

Bioluminescence serves many purposes in nature, but using light to attract prey is relatively rare, especially on land. The Waitomo glow worm species is endemic to New Zealand, occurring in a number of limestone cave systems throughout the country. Related species occupy similar habitats in Tasmania and on Australia’s east coast.

With their glowing lures in place, the worms drop threadlike snares, thin filaments of silk secreted from their mouths and dotted with balls of mucous, to trap confused flyers. Besides being extra-sticky, those mucous balls lend the strands the appearance of mardi gras beads, which magnify the worms’ spectral light like chandeliers.

Wind can tangle the sticky strings, so the deeper you go into the cave, the longer the threads.

When potential prey touches a snare, the worm hangs back while its next meal struggles, becoming entangled in the gooey threads. Scientists who’ve analyzed the mucous haven’t found any toxins in it, but suspect it may clog the breathing holes of insects fighting to get free.

Once the victim grows still, it’s time to reel in the catch. The worm hangs out of its hammock and pulls up the thread the same way it went down: through its mouth. Those mucous balls also absorb water from the damp air in the cave. The worm is hydrating with every glob it swallows.

The prey is typically still alive when it arrives at the glow worm’s mouth, which has teeth sharp enough to bore through insect exoskeletons. A single catch may serve up several meals before it’s cut loose from the threads.

Glow worms can live a year in this glowing larval stage — a long time compared to the adults, which perish within a week of emerging. The adults retain some bioluminescence, but seem to exist for just one purpose: to mate. Based on their anatomy — they lack mouths — it’s doubtful they even eat in their short lifespan.

The big question for scientists now is what makes the worms’ lights turn on and off.

There can be several colonies of glow worms in a cave, though usually a dominant one occupies the best hunting spot. Some researchers have noticed that the glow worms seem to sync their lights to the other glow worms in their colony, brightening and dimming on a 24-hour cycle. Larger worms remain brighter for more of the cycle than do smaller ones.

Studies also have shown that different colonies are on different cycles. The colonies seem to be taking turns at peak illumination, when they’re most attractive to prey, possibly as a result of their position in the cave relative to those food sources.

“They’re reacting to local conditions,” said Merritt, “The cave structure is complex.”

If conditions are good, a colony near the cave mouth can expand into the vegetation beyond, but even as flying adults most of the glow worms will never see the outside world, including that night sky they so closely resemble.

“They can’t move far from where they were deposited as eggs,” said Merritt, “so larva that hatches deep in the cave would never see the light of day.”

Not surprisingly, the worms glow brighter when they’re hungry.

Link to article: http://ww2.kqed.org/science/2016/06/28/these-carnivorous-worms-catch-bugs-by-mimicking-the-night-sky/

Dr. David Merritt: http://researchers.uq.edu.au/researcher/29
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I can see a sci fi story there, +bowser jr ...
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The buildup of protein deposits in cells is a hallmark of neurodegenerative diseases such as Alzheimer’s and Parkinson’s. “If the process by which the cell removes those proteins can be enhanced, then you might be able to prevent that disease progression,” says Carsten Sachse from EMBL. Before scientists can give the cell’s rubbish collectors a boost, they have to understand how the system works. In a paper published in EMBO Reports – http://doi.org/f3qdj7 – Sachse and his lab drew on expertise from colleagues throughout EMBL to do just that.
How cells eliminate protein deposits that can lead to Alzheimer's, Parkinson's and other neurodegenerative disorders
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Researchers from the Environmental Molecular Sciences Laboratory (EMSL) at PNNL, Washington State University, Duke University Medical Center and Miami University developed a new technique to dramatically reduce data acquisition time and amplify metabolite identification. The research team used a new synthetic biology-based engineering method. Learn more at https://goo.gl/N4zvIW.

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The Science:  More rapid and improved estimates of metabolic fluxes in cells are possible thanks to a new technique that combines 13C-Metabolic Flux Analysis (13C-MFA) with non-uniform sampling nuclear magnetic resonance (NMR) spectroscopy data.

Summary: The use of 13C-MFA can provide key insights into metabolic networks of microbial cells that are used for production of biofuels or valuable chemicals. This technique can be combined with either NMR spectrometry or mass spectrometry to infer metabolic fluxes within cells based on the characteristic rearrangement of 13C tracers through metabolic pathways.

However, position-specific 13C-labeling of metabolites has been particularly difficult to obtain using conventional NMR or mass spectrometry techniques, hindering accurate estimations of metabolic fluxes. To overcome this problem, researchers from EMSL, the Environmental Molecular Sciences Laboratory, Washington State University, Duke University Medical Center and Miami University developed a new technique that combines 13C-MFA with non-uniform sampling (NUS), which dramatically reduces time required to collect high-resolution NMR data.

NUS techniques acquire only a subset of NMR data points and use sophisticated reconstruction methods that ultimately allow extraction of complete sets of chemical shift information. Using 600 MHz and 800 MHz NMR spectrometers at EMSL, a national scientific user facility, the research team demonstrated their approach provides detailed information about position-specific labeling patterns that can be incorporated into metabolic flux models. By enabling more accurate estimations of metabolic fluxes in complex biological systems, the new technique could shed light on environmental nutrient cycling and enhance synthetic biology-based engineering efforts to modify living systems for production of metabolites or other products of interest, such as biofuels or fine chemicals.

Why is this important? Key insights into metabolic networks provided by the new technique could be used for synthetic biology-based efforts to modify living systems for production of metabolites or other products of interest, such as biofuels or fine chemicals.

Notes: This work was supported by the U.S. Department of Energy’s Office of Science, Office of Biological and Environmental Research, including support of EMSL, an Office of Science User Facility; William Wiley Distinguished Postdoctoral Fellowship from EMSL; and an EMSL intramural research project entitled “Development of an Integrated EMSL Mass Spectrometry and Nuclear Magnetic Resonance Metabolic Flux Analysis Capability in Support of Systems Biology: Test Application for Biofuels Production.”
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In nature, DNA exists within a solution rife with electrostatically charged atoms or molecules called ions. A recent study led by PNNL researchers investigated a new model of how B-DNA, the form of DNA that predominates in cells, is influenced by the water-and-ions “atmosphere” around it. Learn more at http://goo.gl/aFyuj8.

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Nucleic acids, large biomolecules essential to life, include the familiar double-stranded deoxyribonucleic acid (DNA), a very stable long molecule that stores genetic information.

In nature, DNA exists within a solution rife with electrostatically charged atoms or molecules called ions. A recent study by researchers at Pacific Northwest National Laboratory (PNNL) proposed a new model of how B-DNA, the form of DNA that predominates in cells, is influenced by the water-and-ions "atmosphere" around it.

Understanding the ionic atmosphere around nucleic acids, and being able to simulate its dynamics, is important. After all, this atmosphere stabilizes DNA's structure; it impacts how DNA is folded and "packed" in cells, which triggers important biological functions; and it strongly influences how proteins and drugs bind to DNA.

The research combines theoretical modeling and experiments in a study of ion distribution around DNA. It was led by PNNL physical scientist Maria Sushko, computational biologist Dennis Thomas, and applied mathematician Nathan Baker, in concert with colleagues from Cornell University and Virginia Tech.

Earlier approaches have been used to simulate the distribution of ions around biomolecules like DNA. But only roughly. The PNNL-led study goes beyond commonplace electrostatics to propose a more refined but still computationally efficient model of what happens in these critical ionic atmospheres.

"The main idea was to dissect the complex interplay of interactions, and to understand the main forces driving ions deep inside the DNA helix and the forces keeping them on its surface," said Sushko, the paper's first author. That interplay includes the correlation of ions within the solution, how they move, how they interact with one another, and how they interact with the DNA.

The new model has two key advantages over older simulations: It allows researchers to turn ion-water and ion-ion interactions on and off at will. "We can calculate important interactions independently," she said, a flexibility not present in previous simulations. And the new model is computationally efficient, allowing researchers to cheaply simulate a large-scale molecular event over a long time scale.

Results: Importantly, both previous and new experiments by the Cornell colleagues identified the number of bound ions around DNA. Previous simplified models were also able to reproduce this number. But the new model "is richer than that," said Sushko, because it gives more details on how ions are distributed along the surface of DNA and within DNA's critical grooves. "DNA interaction will strongly depend on where those ions sit," she said. For one, the presence of ions in the grooves relates to how compact DNA will be. "The more ions within the grooves," said Sushko, "the more compact the structure."

The researchers confirmed that biological "correlation," a measure of ion affinity, allowed DNA to pack more tightly by effectively neutralizing DNA's electrostatic charge. Researchers also observed how ions get distributed through a solution, a water-ion interaction called solvation. The stronger the water-ion interaction, the larger the effective ion size, and therefore the less likely the ion was to settle in the DNA's grooves. More strongly solvated ions, therefore, create a different environment for DNA folding.

Researchers observed results regarding the activity of three types of salts within the simulated ionic environment. Small, single-charge ions did not strongly react with water; about 50 percent of these bond ions could penetrate into DNA grooves. Large ions with triple charges were not strongly hydrated, but their size prevented penetration into the grooves. ("They just decorate the surface," said Sushko.)

Only 15 to 20 percent of ions with double charges, which were strongly hydrated and strongly correlated, settled in DNA grooves. That showed a "very delicate interplay" of ion-to-ion and ion-to-water interactions, according to Sushko.

Why It Matters: These results highlight important aspects of the properties of electrolyte solutions influencing the ionic atmosphere that impacts DNA condensation. This "packing" of DNA, which is otherwise one of the longest molecules in nature, is essential to DNA's role in gene regulation. DNA condensation is also the key to protein binding and drug binding. It therefore points to practical applications in medicine and biotechnology.

This research also highlights the impact of the ionic atmosphere on the interaction between biomolecules and a ligand: that is, the molecule, ion, or protein that binds with a protein or the DNA double helix for some biological purpose.

But it is the "methodology itself," not the designed simulations of DNA, that is most important, said Sushko, in part because it provides a new computational model of how to see into complex molecular systems. "We get a better fundamental understanding of the important forces."

Methods: Researchers employed two coarse-grained models to simulate the DNA macroion, which is a large colloidal ion carrying a charge. The goal was to capture two versions of detail on how ions spread out in a solvent and how they interact with simulations of DNA topology.

One DNA model posited an infinitely long cylinder with a uniform charge density along one axis. Sushko called it "a very crude model used a lot in the past. It explains quite a lot about ion interactions, but it is deficient in some ways." The second, more complex "discrete charge" model posited three types of spheres in a helical array that mimics B-form DNA. It had a 3D-like character that allowed ions to penetrate into DNA grooves.

The DNA simulations were run through four computational models of classical density function theory to assess the energetics of different ion-DNA interactions. Results were also compared to data from what Sushko called "state-of-the-art experiments" that used anomalous small-angle x-ray scattering. This technique, used to investigate the spatial dimensions of structures in the nanometer range, always yields a lot of detail about how ions are distributed around a biomolecule.

The uniformly charged cylinder model was not good at simulating the ionic atmosphere around DNA. "This model is a very common simplification," said Sushko. "You get the same number of ions attached to DNA, but the distribution is completely wrong. In this model, ions will just sit somewhere on the surface."

But their more complex discrete charge model provided a much more naturalistic portrait of ion distribution in an ionic atmosphere. Its simulations showed ions both clinging to the helical DNA surface and also penetrating into the DNA's grooves. "The small details of ion penetration are very important for the way DNA will package the chromosome," she said.

What's Next? Researchers plan to study the role of the ionic atmosphere in mediating interactions between DNA molecules. They also plan to extend their DNA model to include DNA sequence-specific effects, which often influence ion binding, and DNA sequence-dependent structural variations.
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Deep Look

• Biology  - 
 
These Lizards Have Been Playing Rock-Paper-Scissors for 15 Million Years

Every spring, keen-eyed biologists carrying fishing poles search the rolling hills near Los Banos, about two hours southeast of San Francisco. But they’re not looking for fish.

They’re catching lizards.

The research team collects Western side-blotched lizards, which come in different shades of blue, orange and yellow. They’re studying the intricate mating strategies that earned the diminutive reptiles the nickname “rock-paper-scissors lizards.”

The dramas that play out between the lizards of these three colors offer the researchers a window into how how species evolve and diversify.

The lizards look like tiny dinosaurs, but are actually more closely related to iguanas. At about two inches long, they may not appear ferocious, but that won’t stop them from issuing threat displays — which looks like a series of pushups — to lizard and human intruders alike. It’s one of the territorial behaviors that first caught the eye of Barry Sinervo, a professor of ecology and evolutionary biology at UC Santa Cruz. Sinervo leads the team as they unlock an incredibly intricate and ancient game of strategy that steers the love lives of these colorful creatures.

Link to full article: http://ww2.kqed.org/science/2016/05/17/these-lizards-have-been-playing-rock-paper-scissors-for-15-million-years/

Link to research:

Barry Sinervo: http://bio.research.ucsc.edu/~barrylab/lizardland/game.html
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Nice work.. keep it up.
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ULg Reflexions

• Biology  - 
 
The #Feline #ParvoVirus (#FPV) attacks cells in the digestive tract and the precursor cells of bone marrow in cats. It triggers feline panleukopenia, a disease which generally leads to few symptoms in healthy, adult cats but which can lead to developmental problems in the cerebellum of kittens infected just before or just after birth.  However, during the feline parvovirus outbreak in 2013, vets reported very unusual nervous symptoms in adult cats infected by FPV. They asked the autopsy department of the University of Liège to investigate. What were the conclusions(1) of this investigation? It is not impossible that the virus has evolved and become capable of reactivating the cell cycle (at least its initial phases) in the neurons, a mechanism which they need to multiply. This is an observation which could change our perception of the parvoviruses in general and raises questions as to the use of this type of #virus for therapeutic ends, particularly in the fight against #cancer. A research published in BMC Veterinary Research.
http://reflexions.ulg.ac.be/en/FPV
(1) Mutien Garigliany · Gautier Gilliaux · Sandra Jolly · Tomas Casanova · Calixte Bayrou · Kris Gommeren · Thomas Fett · Axel Mauroy · Etienne Lévy · Dominique Cassart · Dominique Peeters · Luc Poncelet · Daniel Desmecht. Feline panleukopenia virus in cerebral neurons of young and adult cats. BMC Veterinary Research. 12/2016; 12(1). DOI: 10.1186/s12917-016-0657-0
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The largest-ever study to sequence the whole genomes of breast cancers has uncovered five new genes associated with the disease and 13 new mutational signatures that influence tumour development. Published in Nature (http://doi.org/bf46) and Nature Communications (http://doi.org/bf47), two studies from the Wellcome Genome Campus pinpoint where genetic variations in breast cancers occur. The findings provide insights into the causes of breast tumours and demonstrate that breast-cancer genomes are highly individual.
Largest-ever study of breast cancer genomes, led by Wellcome Genome Campus researchers, reveals new genes and mutations involved in the disease.
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Yes, we all know about women's cancers. How about a little more talk about men's cancers - you know, the one's had by people less likely to be informed about their bodies and more poorly incentivised to seek health advice - and about just cancer in general. Why is it always "women's this" and "women's that"? Nobody cares about women.






Sorry. That should have read "Nobody cares about men."
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