A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.

Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.

The phase transition of E-vanillyl oxime {1-[(E)-(hydroxyimino)methyl]-4-hydroxy-3-methoxybenzene, C8H9NO3} has been analysed by single-crystal and powder X-ray diffraction. The high-temperature (HT) phase (P21/a, Z' = 1) transforms into the low-temperature (LT) phase (threefold superstructure, Poverline{1}, Z' = 6) at ca 190 K. The point operations lost on cooling, {m[010], 2[010]}, are retained as twin operations and constitute the twin law. The screw rotations and glide reflections are retained in the LT phase as partial operations acting on a subset of Euclidean space {b E}^3. The full symmetry of the LT phase, including partial operations, is described by a disconnected space groupoid which is built of three connected components.

It is one of the largest and most productive estuaries in the world, yet dramatic changes are in store for the Chesapeake Bay in coming […]

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Dennis W. Kelly has been named director of the Smithsonian’s National Zoo in Washington, D.C., effective Feb. 15, 2010.

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The anemones—both of which are commonly called Tealia red anemones under the species of Urticina—spawned in late April and early May, just days apart. Henley collected the eggs and sperm from the more than 2,000-gallon tank and put them together in smaller tanks to increase the chances of fertilization. After fertilization, the larvae settled and metamorphosed into a polyp.

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The Panoramic Survey Telescope & Rapid Response System (Pan-STARRS) PS1 telescope has discovered an asteroid about 150 feet in diameter that will come within 4 million miles of Earth in mid-October.

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Although the La Loma tree frog, Hyloscirtus colymba, is notoriously difficult to care for in captivity, the Panama Amphibian Rescue and Conservation Project is the first to successfully breed this species.

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A new species of Brazilian leaf beetle named Cachiporra extremaglobosa, (which translated means the “extremely globular billy club leaf beetle,”) was recently discovered by scientists at the Smithsonian’s National Museum of Natural History.

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The words “box jelly” may bring to mind something sweet and tasty, but the banded box jelly of Bonaire is a highly venomous jellyfish with […]

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A new genetic study by a team of Cuban and American researchers confirms that American crocodiles are hybridizing with wild populations of critically endangered Cuban crocodiles, which may cause a population decline of this species found only in the Cuban Archipelago.

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A new study shows that the desert tortoise, thought to be a single species for the last 150 years, is in fact two separate and distinct species, based on DNA evidence and biological and geographical distinctions.

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The far-out planet, named 55 Cancri e, is twice as big as Earth and nearly nine times more massive. It is most likely composed of rocky material, similar to Earth, supplemented with light elements such as water and hydrogen gas. Scientists estimate the planet’s surface is much hotter than ours: close to 2,700 degrees Celsius.

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A box jellyfish from the Caribbean appears to have recently become established in the red mangroves of Florida near Boca Raton.

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What scientists found was that the domestic turkey that ends up on the dinner table exhibits less genetic variation than its ancestral wild counterparts, which were first domesticated in 800 B.C..

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A specimen recently pulled from deep in the southwest Atlantic may represent a new species of squid, say scientist who have studied the animal’s unusual morphology. But then again, it may not…

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Domestic cats in the United States kill some 2.4 billion birds and 12.3 billion mammals each year, most of them native mammals like shrews, chipmunks […]

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Marmosets on track for obesity appeared to be more efficient in their feeding behavior. “Although all animals consumed the same amount of liquid, the ones […]

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Recent spectroscopic analysis of macaroni penguin (Eudyptes chrysolophus) crest feathers and king penguin (Aptenodytes patagonicus) neck feathers have shown they contain a yellow pigment that […]

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Scientists examining the stomach contents of invasive lionfish caught on the inner barrier reef of Belize have discovered that nearly half of the diet of […]

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Keith Gagnon, a 9-year-old fascinated by birds, talks about the importance of bird conservation and why birds really matter. Step outside your house in the […]

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President Jimmy Carter, an avid birder, talks about the importance of bird conservation and why birds really matter. Step outside your house in the morning […]

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For more than 60 years, researchers have tried to successfully cryopreserve (or freeze) the embryo of zebrafish, a species that is an important medical model […]

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The next time you swat a fly ponder this: inside its belly is the DNA of whatever it ate before landing on your picnic dinner—roadkill, […]

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Chances are, if you’ve been stung by a jellyfish along the Chesapeake Bay it was by a sea nettle jellyfish–one of the most common and […]

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Despite the importance of seasonally dry forests, little is known of their ecology. Now, a new book The Ecology and Conservation of Seasonally Dry Forests in Asia, published by Smithsonian Institution Scholarly Press, explores these unique ecosystems, its animals, plants, and the people that inhabit them.

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Images obtained by NASA’s MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft during the low-altitude orbital phase of the mission have revealed previously undetected […]

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Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacene­quinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.

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Keepers at the Smithsonian's National Zoo perform an artificial insemination procedure on a pair of Stanley Cranes. A Stanley Crane chick was successfully hatched on May 23, 2011.

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It takes a Tlingit artist up to 2,000 hours, or 83 days, to weave just one ceremonial robe. Not surprisingly, this art form is practiced by a dedicated few including Tlingit artists Teri Rofkar and Shelly Laws of Alaska. In their presentation for the Smithsonian Spotlight series hosted by the Arctic Studies Center at the Anchorage Museum, Rofkar and Laws discuss the methods and cultural significance of robes, spruce root baskets and more.
For more information, go to http://www.mnh.si.edu/arctic/html/alaska.htm

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Five critically endangered Cuban crocodiles hatched at the National Zoo’s Reptile Discovery Center between July 29 and Aug. 7. The eggs were laid by Dorothy, […]

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U.S. Secretary of the Interior Sally Jewell talks about the importance of bird conservation and why birds really matter. Step outside your house in the […]

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Catherine McKenna, Canada’s Minister of the Environment and Climate Change, talks about the importance of bird conservation and why birds really matter. Step outside your […]

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Smithsonian staff gathered on Thursday, June 1 outside the National Museum of African American History and Culture to show their support and listen to Director […]

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Now that we have a deal between Time Warner Cable and CBS, we can turn our Hollywood focus back on the movie industry.

Steve Julian: Business analyst Mark Lacter, would you agree it's been an up and down summer at the box office?

Mark Lacter: It's been a flaky summer for Hollywood, Steve.  On the plus side, ticket revenue was up more than 10 percent, and attendance increased around six-and-a-half percent compared with last year (this covers the first week of May through Labor Day weekend).  The problem is that the studios and their investors spent huge amounts of money to make a lot of these movies, and they had to compete in a very crowded market - 23 big-budget films came out this summer, which is way higher than normal, and some of them never had a chance.

Julian: Some examples?

Lacter: Probably the biggest clunker was "The Lone Ranger," which could end up losing close to $200 million for Disney.  Another big disappointment was "White House Down," which was distributed by Sony and brought in only $140 million, which for a big-budget action film is really bad.  Even a film like "Pacific Rim," which did well at the box office, might still end up in the red because the production and marketing costs were so high.

Julian: And summer, of course, is the time when studios want to bring out these monster releases -

Lacter: - right, what they call "tent poles" - and in that category, the biggest winner was Disney's "Iron Man," which took in $1.2 billion.  Also having a great summer was "Monsters University" from Pixar, with $700 million.  You also had "Despicable Me 2" and "Fast and Furious 6," which might not be our cup of tea (speak for yourself, it takes me back to my police car days!), but did very well for Universal.  Eight of the top 12 films this summer were sequels - and yet, sequels were no guarantee of success (a number of them really struggled).  And, some non-blockbuster films found considerable success: "Now You See Me" from Lionsgate only cost $75 million to make.

Julian: So, in some ways, Hollywood was its usual unpredictable self.

Lacter: That's right - and don't expect any big changes in strategy when it comes to big-budget films.  The prospect of having huge success with one of these blockbusters is just too great, but perhaps more important is the fact that many of these films are financed by multiple groups of investors, and so the risk is spread around.  It's not like the old days when a studio bankrolled the whole thing.

Julian: Though, sounds like it's bad news for the city of Los Angeles: the "Man of Steel" sequel is going to be shot in Michigan?

Lacter: Mayor Garcetti has actually declared a state of emergency because the city keeps losing business to other states that offer big tax incentives to films - what's known as runaway production.  The truth is that business has been lost over the years, but L.A. is hardly in any danger of losing its spot as the center of entertainment.  And, you can see that with the L.A. County Board of Supervisors signing off on Disney's plan for a TV and movie production facility near Santa Clarita that will add more than a half-million square feet of studio space.

Julian: And, Universal's expanding, too.

Lacter: Earlier this year, Universal was given the approval to build more production facilities, and Paramount is planning an expansion, as well.  Now, these are all very ambitious projects - not the sort of investments that would be made if these studios were looking elsewhere to make movies and TV shows.  And, of course, they mean jobs - actually, employment levels in the entertainment industry have remained fairly steady going back the last decade.

Julian: Are there states that are pulling back their incentives?

Lacter: Yes, the state of North Carolina, which has been especially aggressive in using tax incentives to draw in movies and television going back to the 80s, is phasing out the giveaways because legislators have decided that the economic benefits aren't worth the tax revenues being lost.  And, other states with tax incentive programs are pulling back as well - they're finding that the payback is very difficult to measure.

Mark Lacter writes for Los Angeles Magazine and pens the business blog at LA Observed.com.

This content is from Southern California Public Radio. View the original story at SCPR.org.

It is one of the rarest shrubs in the southeastern United States but for scientists trying to save it, the critically endangered Michaux’s sumac (Rhus michauxii) is not cooperating.

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Mexico is the fourth largest honey producer and fifth largest honey exporter in the world. A Smithsonian researcher and colleagues helped rural farmers in Mexico […]

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What plant species has just been discovered but is almost gone? Bidens meyeri–a just discovered flowering plant from the small South Pacific island of Rapa, […]

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A newly discovered Hawaiian tree recently had the distinction of being added to the International Union for the Conservation of Nature’s Red List of Critically […]

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This work presents a technique for extracting the detailed shape of peaks with extended, overlapping tails in an X-ray powder diffraction pattern. The application discussed here concerns crystallite size broadening, though the technique can be applied to spectra of any origin and without regard to how the profiles are to be subsequently analyzed. Historically, the extraction of profile shapes has been difficult due to the complexity of determining the background under the peak, resulting in an offset of the low-frequency components of the Fourier transform of the peak known as the `hook' problem. The use of a carefully considered statistical weighting function in a non-linear least-squares fit, followed by summing the residuals from such a fit with the fit itself, allows one to extract the full shape of an isolated peak, without contributions from either the background or adjacent peaks. The extracted shape, consisting of the fit function recombined with the residuals, is not dependent on any specific shape model. The application of this to analysis of microstructure is performed independently of global parametric models, which would reduce the number of refined parameters; therefore the technique requires high-quality data to produce results of interest. The effectiveness of the technique is demonstrated by extraction of Fourier transforms of peaks from two sets of size-broadened materials with two differing pieces of equipment.

A method is described for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films comprising various crystal orientations and/or polymorphs by measuring reciprocal-lattice vectors.