Structural Mechanisms of Histone Recognition by Histone Chaperones

Chromatin is the complex of DNA and proteins that comprises the physiological form of the genome. Non-covalent interactions between DNA and histone proteins are necessary to compact large eukaryotic genomes into relatively small cell nuclei. The nucleosome is the fundamental repeating unit of chromatin, and is composed of 147bp of DNA wrapped around an octamer of histone proteins: 2 copies of each H2A, H2B, H3 and H4.

Assembly of nucleosomes in the cell requires the coordinated effort of many proteins including ATP-dependent chromatin remodeling enzymes and ATP-independent histone chaperone proteins. Histone chaperones are a large class of proteins responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating nuclear import of histones, and finally depositing histones onto DNA to form nucleosomes. Despite performing many overlapping functions, histone chaperone proteins are highly structurally divergent. However, nearly all histone chaperones contain highly charged intrinsically disordered regions (IDRs)1. In many cases truncation of these conserved regions results in loss of histone affinity and deposition functions.

>Read more on the Stanford Synchrotron Radiation Lightsource

Image: (extract) SAXS analysis of Npm Core+A2 truncation (1-145) bound to five H2A/H2B dimers. Left: small angle x-ray scattering curve of the complex (purple dots). Simulated SAXS curve from the best scoring structural model shown as a black line. Right: SAXS envelope of the complex (pink) with the best scoring structural model inside. Positioning of H2A/H2B dimers by NMR and SAXS structural restraints. Full image here.

Questioning the universality of the charge density wave nature…

… in electron-doped cuprates

The first superconductor materials discovered offer no electrical resistance to a current only at extremely low temperatures (less than 30 K or −243.2°C). The discovery of materials that show superconductivity at much higher temperatures (up to 138 K or −135°C) are called high-temperature superconductors (HTSC). For the last 30 years, scientists have researched cuprate materials, which contain copper-oxide planes in their structures, for their high-temperature superconducting abilities. To understand the superconducting behavior in the cuprates, researchers have looked to correlations with the charge density wave (CDW), caused by the ordered quantum field of electrons in the material. It has been assumed that the CDW in a normal (non-superconducting) state is indicative of the electron behavior at the lower temperature superconducting state. A team of scientists from SLAC, Japan, and Michigan compared the traits of superconducting and non-superconducting cuprate materials in the normal state to test if the CDW is correlated to superconductivity.

>Read more on the SSRL website

Picture: explanation in detail to read in the full scientific highlight (SSRL website)

 

 

 

SLAC scientists investigate how metal 3D printing can avoid producing flawed parts

The goal of these X-ray studies is to find ways to improve manufacturing of specialized metal parts for the aerospace, aircraft, automotive and healthcare industries.

Scientists at the Department of Energy’s SLAC National Accelerator Laboratory are using X-ray light to observe and understand how the process of making metal parts using three-dimensional (3-D) printing can leave flaws in the finished product – and discover how those flaws can be prevented. The studies aim to help manufacturers build more reliable parts on the spot – whether in a factory, on a ship or plane, or even remotely in space – and do it more efficiently, without needing to store thousands of extra parts.

The work is taking place at the lab’s Stanford Synchrotron Radiation Lightsource (SSRL) in collaboration with scientists from the DOE’s Lawrence Livermore National Laboratory and Ames Laboratory.

The 3-D printing process, also known as additive manufacturing, builds solid, three-dimensional objects from a computer model by adding material layer by layer. The use of plastics and polymers in 3-D printing has advanced rapidly, but 3-D printing with metals for industrial purposes has been more challenging to sort out.

>Read more on the SSRL website

Picture: SLAC staff scientist Johanna Nelson Weker, front, leads a study on metal 3-D printing at SLAC’s Stanford Synchrotron Radiation Lightsource with researchers Andrew Kiss and Nick Calta, back.
Credit: Dawn Harmer/SLAC

 

How metal 3-D printing can avoid producing flawed parts

The goal of these X-ray studies is to find ways to improve manufacturing of specialized metal parts for the aerospace, aircraft, automotive and healthcare industries.

Scientists at the Department of Energy’s SLAC National Accelerator Laboratory are using X-ray light to observe and understand how the process of making metal parts using three-dimensional (3-D) printing can leave flaws in the finished product – and discover how those flaws can be prevented. The studies aim to help manufacturers build more reliable parts on the spot – whether in a factory, on a ship or plane, or even remotely in space – and do it more efficiently, without needing to store thousands of extra parts.

The work is taking place at the lab’s Stanford Synchrotron Radiation Lightsource (SSRL) in collaboration with scientists from the DOE’s Lawrence Livermore National Laboratory and Ames Laboratory.

The 3-D printing process, also known as additive manufacturing, builds solid, three-dimensional objects from a computer model by adding material layer by layer. The use of plastics and polymers in 3-D printing has advanced rapidly, but 3-D printing with metals for industrial purposes has been more challenging to sort out.

“With 3-D printing, you can make parts with very complex geometries that are not accessible for casting like regular metal parts,” says SLAC staff scientist Johanna Nelson Weker, who is leading the project. “Theoretically, it can be a quick turnaround – simply design, send, print from a remote location. But we’re not there yet. We still need to figure out all of the parameters involved in making solid, strong parts.”

>Read more on the Stanford Synchrotron Radiation Lightsource website

Image: SLAC staff scientist Johanna Nelson Weker, front, leads a study on metal 3-D printing at SLAC’s Stanford Synchrotron Radiation Lightsource with researchers Andrew Kiss and Nick Calta, back.
Credit: Dawn Harmer/SLAC

A path to a game-changing battery electrode

If you add more lithium to the positive electrode of a lithium-ion battery, it can store much more charge in the same amount of space, theoretically powering an electric car 30 to 50 percent farther between charges. But these lithium-rich cathodes quickly lose voltage, and years of research have not been able to pin down why—until now.

>Read more on the Advance Light Source website

Image: Electric car makers are intensely interested in lithium-rich battery cathodes made of layers of lithium sandwiched between layers of transition-metal oxides. Such cathodes could significantly increase driving range.
Credit: Stanford University/3Dgraphic

Researchers Develop a Way to Better Predict Corrosion from Crude Oil

Using X-ray techniques, scientists are developing an analysis tool to predict how sulfur compounds in a batch of crude oil might corrode equipment.

… an important safety issue for the oil industry.

The results of these ongoing experiments at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory will improve industry guidelines. The goal is to characterize the types of sulfur that are most critical to identify in the oil, in order to better anticipate the potential for corrosion rates.

A team of researchers from Chevron and the University of Saskatchewan are performing a series of studies at SSRL to closely examine forms of sulfur in crude oil.

Direct and Efficient Utilization of Solid-phase Iron by Diatoms

A research team indicates that diatoms, can directly uptake iron from insoluble iron sediments, and thereby potentially affect atmospheric carbon dioxide level.

A research team from Columbia University indicates that diatoms, photosynthetic marine organisms responsible for as much as 20% of photosynthesis in the world’s oceans, can directly uptake iron from insoluble iron sediments, and thereby potentially affect atmospheric carbon dioxide level. Although iron is often present in the ocean, usually there is insufficient iron for diatoms and other organisms to grow quickly unless this iron is dissolved and in a form that can be used readily. This research establishes that iron from mineral phases can be quite bioavailable, and that the diatoms can use most forms of iron, but appear to have a preference for a specific form of iron, ferrous iron, in the mineral phases. This research is applicable to a wide variety of questions in earth and ocean sciences, including basic biology of nutrient acquisition, the coupling of physical and geological processes such as glaciers to climate and geoengineering.

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Picture: Glacial striations seen near Upsala Glacier, Argentina, where scientists collected glacial samples. This physical scraping produces sediments and dust that can fertilize plankton when it is delivered to the ocean.
Photo by Michael Kaplan/Lamont-Doherty Earth Observatory

From Community to Molecule – on Track Towards a Zika Vaccine

A potent new weapon against the Zika virus in the blood of people who have been infected by it.

A research team based at The Rockefeller University has identified a potent new weapon against the Zika virus in the blood of people who have been infected by it. This discovery could lead to new ways of fighting the disease. Detailed examination of the interaction between the virus and antibodies derived from human subjects in Brazil and Mexico, including crystallographic studies performed at the Stanford Synchrotron Radiation Lightsourse (SSRL), have revealed a new potential strategy for developing a vaccine towards this virus.

Through collaborators working in Pau da Lima, Brazil, and Santa Maria Mixtequilla, Mexico, the research team obtained blood samples from more than 400 people, collected shortly after Zika was circulating.

In these samples, antibodies that block the virus from initiating an infection were found. Interestingly, the antibodies appeared to have been initially generated in response to an earlier infection by a related virus (DENV1) that causes dengue fever. It appears that, much like a vaccine, the DENV1 virus can prime the immune system to respond to Zika.