Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state

The Src-homology 2 domain containing phosphatase 2 (SHP2) plays a critical role in crucial signaling pathways and is involved in oncogenesis and in developmental disorders. Its structure includes two SH2 domains (N-SH2 and C-SH2), and a protein tyrosine phosphatase (PTP) domain. Under basal conditions, SHP2 is auto-inhibited, with the N-SH2 domain blocking the PTP active site. Activation involves a rearrangement of the domains that makes the catalytic site accessible, coupled to the association between the SH2 domains and cognate proteins containing phosphotyrosines. Several aspects of this transition are debated and competing mechanistic models have been proposed. A crystallographic structure of SHP2 in an active state has been reported (PDB code 6crf), but several lines of evidence suggests that it is not fully representative of the conformations populated in solution. To clarify the structural rearrangements involved in SHP2 activation, enhanced sampling simulations of the autoinhibited and active states have been performed, for wild type SHP2 and its pathogenic E76K variant. Our results demonstrate that the crystallographic conformation of the active state is unstable in solution, and multiple interdomain arrangements are populated, thus allowing association to bisphosphorylated sequences. Contrary to a recent proposal, activation is coupled to the conformational changes of the N-SH2 binding site, which is significantly more accessible in the active sate, rather than to the structure of the central β-sheet of the domain. In this coupling, a previously undescribed role for the N-SH2 BG loop emerged

Initial beam-profiling tests with the NML prototype station at the Fermilab A0 Photoinjector

The beam-profile diagnostics station prototype for the superconducting rf electron linac being constructed at Fermilab at the New Muon Lab has been tested. The station uses intercepting radiation converter screens for the low-power beam mode: either a 100-\mu m thick YAG:Ce single crystal scintillator or a 1-\mu m thin Al optical transition radiation (OTR) foil. The screens are oriented with the surface perpendicular to the beam direction. A downstream mirror with its surface at 45 degrees to the beam direction is used to direct the radiation into the optical transport. The optical system has better than 20 (10) \mu m rms spatial resolution when covering a vertical field of view of 18 (5) mm. The initial tests were performed at the A0 Photoinjector at a beam energy of ~15 MeV and with micropulse charges from 25 to 500 pC for beam sizes of 45 to 250 microns. Example results will be presented.Comment: 3 pp. Particle Accelerator, 24th Conference (PAC'11) 2011. 28 Mar - 1 Apr 2011. New York, US

Chronography of the Milky Way's Halo System with Field Blue Horizontal-Branch Stars

In a pioneering effort, Preston et al. reported that the colors of blue horizontal-branch (BHB) stars in the halo of the Galaxy shift with distance, from regions near the Galactic center to about 12 kpc away, and interpreted this as a correlated variation in the ages of halo stars, from older to younger, spanning a range of a few Gyrs. We have applied this approach to a sample of some 4700 spectroscopically confirmed BHB stars selected from the Sloan Digital Sky Survey to produce the first "chronographic map" of the halo of the Galaxy. We demonstrate that the mean de-reddened g$-$r color, , increases outward in the Galaxy from $-$0.22 to $-$0.08 (over a color window spanning [$-$0.3:0.0]) from regions close to the Galactic center to ~40 kpc, independent of the metallicity of the stars. Models of the expected shift in the color of the field BHB stars based on modern stellar evolutionary codes confirm that this color gradient can be associated with an age difference of roughly 2-2.5 Gyrs, with the oldest stars concentrated in the central ~15 kpc of the Galaxy. Within this central region, the age difference spans a mean color range of about 0.05 mag (~0.8 Gyrs). Furthermore, we show that chronographic maps can be used to identify individual substructures, such as the Sagittarius Stream, and overdensities in the direction of Virgo and Monoceros, based on the observed contrast in their mean BHB colors with respect to the foreground/background field population.Comment: 6 pages, 4 figures, ApJ letter

Structural investigation of Rett-inducing MeCP2 mutations

X-ray structure of methyl-CpG binding domain (MBD) of MeCP2, an intrinsically disordered protein (IDP) involved in Rett syndrome, offers a rational basis for defining the spatial distribution for most of the sites where mutations responsible of Rett syndrome, RTT, occur. We have ascribed pathogenicity for mutations of amino acids bearing positively charged side chains, all located at the protein-DNA interface, as positive charge removal cause reduction of the MeCP2-DNA adduct lifetime. Pathogenicity of the frequent proline replacements, outside the DNA contact moiety of MBD, can be attributed to the role of this amino acid for maintaining both unfolded states for unbound MeCP2 and, at the same time, to favor some higher conformational order for stabilizing structural determinants required by protein activity. These hypotheses can be extended to transcription repressor domain, TRD, the other MeCP2-DNA interaction site and, in general, to all the IDP that interact with nucleic acids

Morphology of two dimensional fracture surface

We consider the morphology of two dimensional cracks observed in experimental results obtained from paper samples and compare these results with the numerical simulations of the random fuse model (RFM). We demonstrate that the data obey multiscaling at small scales but cross over to self-affine scaling at larger scales. Next, we show that the roughness exponent of the random fuse model is recovered by a simpler model that produces a connected crack, while a directed crack yields a different result, close to a random walk. We discuss the multiscaling behavior of all these models.Comment: slightly revise

Nitrogen deprivation induces triacylglycerol accumulation, drug tolerance and hypervirulence in mycobacteria.

Mycobacteria share with other actinomycetes the ability to produce large quantities of triacylglycerol (TAG), which accumulate as intracytoplasmic lipid inclusions (ILI) also known as lipid droplets (LD). Mycobacterium tuberculosis (M. tb), the etiologic agent of tuberculosis, acquires fatty acids from the human host which are utilized to synthesize TAG, subsequently stored in the form of ILI to meet the carbon and nutrient requirements of the bacterium during long periods of persistence. However, environmental factors governing mycobacterial ILI formation and degradation remain poorly understood. Herein, we demonstrated that in the absence of host cells, carbon excess and nitrogen starvation promote TAG accumulation in the form of ILI in M. smegmatis and M. abscessus, used as surrogate species of M. tb. Based on these findings, we developed a simple and reversible in vitro model to regulate ILI biosynthesis and hydrolysis in mycobacteria. We also showed that TAG formation is tgs1 dependent and that lipolytic enzymes mediate TAG breakdown. Moreover, we confirmed that the nitrogen-deprived and ILI-rich phenotype was associated with an increased tolerance towards several drugs used for treating mycobacterial infections. Importantly, we showed that the presence of ILI substantially enhanced the bacterial burden and granuloma abundance in zebrafish embryos infected with lipid-rich M. abscessus as compared to embryos infected with lipid-poor M. abscessus, suggesting that ILI are actively contributing to mycobacterial virulence and pathogenesis

Total- and semi-bare noble metal nanoparticles@silica core@shell catalysts for hydrogen generation by formic acid decomposition

Catalysts are involved in a number of established and emerging chemical processes as well as in environmental remediation and energy conversion. Nanoparticles (NPs) can offer several advantages over some conventional catalysts, such as higher efficiency and selectivity. Nowadays, versatile and scalable nanocatalysts that combine activity and stability are still lacking. Here, we report a comprehensive investigation on the production and characterization of hybrid nano-architectures bringing a partial or total bare surface together with their catalytic efficiency evaluation on, as a proof-of-concept, the formic acid decomposition reaction. In this regard, formic acid (FA) is a convenient and safe hydrogen carrier with appealing features for mobile applications, fuel cells technologies, petrochemical processes and energetic applications. Thus, the design of robust catalysts for FA dehydrogenation is strongly demanded. Due to this, we produced and evaluated nano-architectures with various equilibrium between the size-increase of the active part and the barer catalytic surface. Overall, this work paves the way for the development of new approaches for green energy storage and safe delivery

Field emission from single and few-layer graphene flakes

We report the observation and characterization of field emission current from individual single- and few-layer graphene flakes laid on a flat SiO2/Si substrate. Measurements were performed in a scanning electron microscope chamber equipped with nanoprobes, used as electrodes to realize local measurements of the field emission current. We achieved field emission currents up to 1 {\mu}A from the flat part of graphene flakes at applied fields of few hundred V/{\mu}m. We found that emission process is stable over a period of several hours and that it is well described by a Fowler-Nordheim model for currents over 5 orders of magnitude