It reappeared in 2003 when a botany fan was riding their bike in the Cabezos de Pericón mountain area in Murcia and spotted a strange species of flower in a field. It was so strange that it has been nearly 100 years since it was last seen.

Juan José Martínez Sánchez, author of the study and researcher at the Polytechnic University of Cartagena (UPCT) says that “Astragalus nitidiflorus is a species that was picked for the first time in 1909 in Cartagena and described by the botanist Carlos Pau in 1910.” In his description Pau did not document its exact location and this, along with its rareness, meant that it remained easily unseen for almost a century.

Once this elusive species had been ‘revived’, the Murcia Region Department of Agriculture funded basic studies on its biology and ecology which were carried out by the UPCT. Martínez explains that “these types of tests are vital for approving a recovery plan.”

The study published in Flora brings together the most significant aspects of the plants life cycle: the phenology of flowering and fruiting times, the species’ reproductive success and related factors, and the recruitment patterns of new specimens of the population.

According to Martínez Sánchez, “Here we are looking at a small fragmented metapopulation of small groups of individual plants. It is a perennial plant with a short life cycle of four years at most, with three flowering periods which last for at least two or three months.”
The resurrection of Tallante’s chickpea

In order to assess the possibility of restocking, researchers must pay special attention to the weak points that cause this species to be at risk. According to their report, the most critical part of the life cycle is the seedling stage and mortality rates at this point are very high. Furthermore, the reproductive success of the plant is low.

Martínez Sánchez explains that “the small population size is the main factor that threatens the species because changes in the region’s environmental conditions or random demographic variations could cause its disappearance.”

However, the researcher outlines that “managing the land where the species grows affects the plant’s maintenance and means that it may not expand to outside its potential area. This emphasises the urgency of those studies that are geared towards determining the exact influence that soil management techniques (tilling, grazing, etc.) may have on maintaining the current population.”

The Polytechnic University of Cartagena is conducting tests on the reintroduction of individual plants in field with the help of the environmental group ANSE in the hope of drawing up the recovery plans for this species, something that depends on the regional government.

“Knowing every single plant and the role that it plays in the ecosystem shows that any little herb is just as important and relevant as the biggest of trees,” claims Martínez Sánchez. “As chinks appear in the ecosystem, it suffers and does not function properly. In this sense, the importance lies in preserving biodiversity as a whole, not as a collection of isolated components.”

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The Murcian flower has been ‘revived’ after 100 years

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“The essential components can be buried in a complex physiological context,” said Terence Hwa, a professor of physics at the University of California, San Diego, and one of the leaders of the study published October 14 in Science. “Natural systems make all kinds of wonderful patterns, but the problem is you never know what’s really controlling it.”

With genes taken from one species of bacterium and inserted into another, Hwa and colleagues from the University of Hong Kong assembled a genetic loop from two linked modules that senses how crowded a group of cells has become and responds by controlling their movements.

One of the modules secretes a chemical signal called acyl-homoserine lactone (AHL). As the bacterial colony grows, AHL floods the accumulating cells, causing them to tumble in place rather than swim. Stuck in the agar of their dish, they pile up.

Because AHL doesn’t diffuse very far, a few cells escape and swim away to begin the process again.

Left to grow overnight, the cells create a target-like pattern of concentric rings of crowded and dispersed bacterial cells. By tweaking just one gene that limits how fast and far cells can swim, the researchers were able to control the number of rings the bacteria made. They can also manipulate the pattern by modifying how long AHL lasts before it degrades.

Although individual bacteria are single cells, as colonies they can act like a multicellular organism, sending and receiving signals to coordinate the growth and other functions of the colony. That means fundamental rules that govern the development of these patterns could well apply to critical steps in the development of other organisms.

To uncover these fundamental rules, Hwa and colleagues characterized the performance of their synthetic genetic circuit in two ways.

First, they precisely measured both the activity of individual genes in the circuit throughout the tumble-and-swim cycle. Then they derived a mathematical equation that describes the probability of cells flipping between swim and tumble motions.

Additional equations describe other aspects of the system, such as the dynamics of the synthesis, diffusion and deactivation of one of the cell-to-cell chemical signal AHL.

This three-pronged approach of “wet-lab” experiments, precise measurements of the results, and mathematical modeling of the system, characterize the emerging discipline of quantitative biology, Hwa said. “This is a prototype, a model of the kind of biology we want to do.”

Co-authors include Jian-Dong Huang, associate professor of biochemistry at the University of Hong Kong additional researchers at Hong Kong Baptist University, the University of Marburg, and the University of Hong Kong including members of the 2008 iGEM team, which Hwa co-advised as a Distinguished Visiting Professor at UHK.

Hwa is a senior scientist with UC San Diego’s Center for Theoretical Biological Physics.

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The embryo is built one layer at a time

During the development of an embryo, everything happens at a specific moment. In about 48 hours, it will grow from the top to the bottom, one slice at a time — scientists call this the embryo’s segmentation. “We’re made up of thirty-odd horizontal slices,” explains Denis Duboule, a professor at EPFL and Unige. “These slices correspond more or less to the number of vertebrae we have.”

Every hour and a half, a new segment is built. The genes corresponding to the cervical vertebrae, the thoracic vertebrae, the lumbar vertebrae and the tailbone become activated at exactly the right moment one after another. “If the timing is not followed to the letter, you’ll end up with ribs coming off your lumbar vertebrae,” jokes Duboule. How do the genes know how to launch themselves into action in such a perfectly synchronized manner? “We assumed that the DNA played the role of a kind of clock. But we didn’t understand how.”

When DNA acts like a mechanical clock

Very specific genes, known as “Hox,” are involved in this process. Responsible for the formation of limbs and the spinal column, they have a remarkable characteristic. “Hox genes are situated one exactly after the other on the DNA strand, in four groups. First the neck, then the thorax, then the lumbar, and so on,” explains Duboule. “This unique arrangement inevitably had to play a role.”

The process is astonishingly simple. In the embryo’s first moments, the Hox genes are dormant, packaged like a spool of wound yarn on the DNA. When the time is right, the strand begins to unwind. When the embryo begins to form the upper levels, the genes encoding the formation of cervical vertebrae come off the spool and become activated. Then it is the thoracic vertebrae’s turn, and so on down to the tailbone. The DNA strand acts a bit like an old-fashioned computer punchcard, delivering specific instructions as it progressively goes through the machine.

“A new gene comes out of the spool every ninety minutes, which corresponds to the time needed for a new layer of the embryo to be built,” explains Duboule. “It takes two days for the strand to completely unwind; this is the same time that’s needed for all the layers of the embryo to be completed.”

This system is the first “mechanical” clock ever discovered in genetics. And it explains why the system is so remarkably precise.

This discovery is the result of many years of work. Under the direction of Duboule and Daniël Noordermeer, the team analyzed thousands of Hox gene spools. With assistance from the Swiss Institute for Bioinformatics, the scientists were able to compile huge quantities of data and model the structure of the spool and how it unwinds over time.

The snake: a veritable vertebral assembly line

The process discovered at EPFL is shared by numerous living beings, from humans to some kinds of worms, from blue whales to insects. The structure of all these animals — the distribution of their vertebrae, limbs and other appendices along their bodies — is programmed like a sheet of player-piano music by the sequence of Hox genes along the DNA strand.

The sinuous body of the snake is a perfect illustration. A few years ago, Duboule discovered in these animals a defect in the Hox gene that normally stops the vertebrae-making process.

“Now we know what’s happening. The process doesn’t stop, and the snake embryo just keeps on making vertebrae, all identical, until the process just runs out of steam.”

The Hox clock is a demonstration of the extraordinary complexity of evolution. One notable property of the mechanism is its extreme stability, explains Duboule. “Circadian or menstrual clocks involve complex chemistry. They can thus adapt to changing contexts, but in a general sense are fairly imprecise. The mechanism that we have discovered must be infinitely more stable and precise. Even the smallest change would end up leading to the emergence of a new species.”

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The clock, the spool, and the snake

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“It is still surprising to me,” said Marc Veldhoen of The Babraham Institute in Cambridge. “I would have expected cells at the surface would play some role in the interaction with the outside world, but such a clear cut interaction with the diet was unexpected. After feeding otherwise healthy mice a vegetable-poor diet for two to three weeks, I was amazed to see 70 to 80 percent of these protective cells disappeared.”

Those protective IELs exist as a network beneath the barrier of epithelial cells covering inner and outer body surfaces, where they are important as a first line of defense and in wound repair. Veldhoen’s team now finds that the numbers of IELs depend on levels of a cell-surface protein called the aryl hydrocarbon receptor (AhR), which can be regulated by dietary ingredients found primarily in cruciferous vegetables. Mice lacking this receptor lose control over the microbes living on the intestinal surface, both in terms of their numbers and composition.

Earlier studies suggested that breakdown of cruciferous vegetables can yield a compound that can be converted into a molecule that triggers AhRs. The new work finds that mice fed a synthetic diet lacking this key compound experience a significant reduction in AhR activity and lose IELs. With reduced numbers of these key immune cells, animals showed lower levels of antimicrobial proteins, heightened immune activation and greater susceptibility to injury. When the researchers intentionally damaged the intestinal surface in animals that didn’t have normal AhR activity, the mice were not as “quick to repair” that damage.

As an immunologist, Veldhoen says he hopes the findings will generate interest in the medical community, noting that some of the characteristics observed in the mice are consistent with those seen in patients with inflammatory bowel disease.

“It’s tempting to extrapolate to humans,” he said. “But there are many other factors that might play a role.”

For the rest of us, he says, “it’s already a good idea to eat your greens.” Still, the results offer a molecular basis for the importance of cruciferous vegetable-derived phyto-nutrients as part of a healthy diet.

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Eating green veggies improves immune defenses

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“We can now start to think about constructing mimics of these viral structures to use in candidate vaccines,” said co-senior author Ian Wilson, who is Hansen Professor of Structural Biology and member of the Skaggs Institute for Chemical Biology at Scripps Research.

Other institutions in the United States, United Kingdom, Japan, and the Netherlands contributed to the research as part of an ongoing global HIV vaccine development effort.
Getting a Better Grip on HIV

Researchers from the current team recently isolated the new antibody and 16 others from the blood of HIV-infected volunteers, in work they reported online in the journal Nature on August 17, 2011. Since the 1990s, Burton, Wilson, and other researchers have been searching for such “broadly neutralizing” antibodies against HIV — antibodies that work against many of the various strains of the fast-mutating virus — and by now have found more than a dozen. PGT 128, the antibody described in the new report, can neutralize about 70 percent of globally circulating HIV strains by blocking their ability to infect cells. It also can do so much more potently — in other words, in smaller concentrations of antibody molecules — than any previously reported broadly neutralizing anti-HIV antibody.

The new report illuminates why PGT 128 is so effective at neutralizing HIV. Using the Wilson lab’s expertise in X-ray crystallography, Robert Pejchal, a research associate in the Wilson lab, determined the structure of PGT 128 joined to its binding site on molecular mockups of the virus, designed in part by Robyn Stanfield and Pejchal in the Wilson group and Bill Schief, now an IAVI principal scientist and associate professor at Scripps Research, and his group. With these structural data, and by experimentally mutating and altering the viral target site, they could see that PGT 128 works in part by binding to glycans on the viral surface.

Thickets of these sugars normally surround HIV’s envelope protein, gp120, largely shielding it from attack by the immune system. Nevertheless, PGT 128 manages to bind to two closely spaced glycans, and at the same time reaches through the rest of the “glycan shield” to take hold of a small part of structure on gp120 known as the V3 loop. This penetration of the glycan shield by PGT 128 was also visualized by electron microscopy with a trimeric form of the gp120/gp41 envelope protein of HIV-1 by Reza Kayat and Andrew Ward of Scripps Research; this revealed that the PGT 128 epitope appears to be readily accessible on the virus.

“Both of these glycans appear in most HIV strains, which helps explain why PGT 128 is so broadly neutralizing,” said Katie J. Doores, a research associate in the Burton lab who was one of the report’s lead authors. PGT 128 also engages V3 by its backbone structure, which doesn’t vary as much as other parts of the virus because it is required for infection.

PGT 128′s extreme potency is harder to explain. The antibody binds to gp120 in a way that presumably disrupts its ability to lock onto human cells and infect them. Yet it doesn’t bind to gp120 many times more tightly than other anti-HIV antibodies. The team’s analysis hints that PGT 128 may be extraordinarily potent because it also binds two separate gp120 molecules, thus tying up not one but two cell-infecting structures. Other mechanisms may also be at work.
Toward an AIDS Vaccine

Researchers hope to use the knowledge of these antibodies’ binding sites on HIV to develop vaccines that stimulate a long-term — perhaps lifetime — protective antibody response against those same vulnerable sites.

“We’ll probably need multiple targets on the virus for a successful vaccine, but certainly PGT 128 shows us a very good target,” said Burton.

Intriguingly, the basic motif of PGT 128′s target may mark a general vulnerability for HIV. “Other research is also starting to suggest that you can grab onto two glycans and a beta strand and get very potent and broad neutralizing antibodies against HIV,” Wilson said.

In addition to Pejchal, Doores, and Khayat, Laura M. Walker of Scripps Research and Po-Ssu Huang of University of Washington at Seattle were co-first authors of the study, “A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.” Along with Wilson, Burton, and Ward, additional contributors were Sheng-Kai Wang, Chi-Huey Wong, Robyn L. Stanfield, Jean-Philippe Julien, Alejandra Ramos, Ryan McBride, and James C. Paulson of Scripps Research, and Pascal Poignard, and William R. Schief of Scripps Research, IAVI and University of Washington at Seattle; Max Crispin and Christopher N. Scanlan of the University of Oxford; Rafael Depetris and John P. Moore of Weill Medical College of Cornell University; Umesh Katpally, Andre Marozsan, Albert Cupo, and William C. Olson of Progenics Pharmaceuticals; Sebastien Maloveste of the National Institute of Allergy and Infectious Diseases at the National Institutes of Health; Yan Liu and Ten Feizi of Imperial College, London; Yukishige Ito of the RIKEN Advanced Science Institute in Japan; and Cassandra Ogohara of University of Washington at Seattle.

The research was supported by the International AIDS Vaccine Initiative, National Institutes of Health, the U.S. Department of Energy, the Canadian Institutes of Health Research, the UK Research Councils, the Ragon Institute, and other organizations.

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Scripps Research scientists reveal surprising picture of how powerful antibody neutralizes HIV

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