Metalloprotein Crystallography: More than a Structure

Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25–50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of advanced detectors, and the incorporation of spectroscopic equipment at a number of synchrotron beamlines, have yielded exciting developments in metalloprotein structure determination. Here we will present results on the advantageous uses of metals in metalloprotein crystallography, including using metallocofactors to obtain phasing information, using K-edge X-ray absorption spectroscopy to identify metals coordinated in metalloprotein crystals, and using UV–vis spectroscopy on crystals to probe the enzymatic activity of the crystallized protein.National Institutes of Health (U.S.) (Grant GM069857)National Institutes of Health (U.S.) (Grant F32-GM099257)National Institutes of Health (U.S.) (Grant F32-GM108189

Work in Progress: A meta-literature review of Moral Foundations Theory as applied in game studies

This paper outlines an in-progress systematic review of extant research in game studies that has incorporated Moral Foundations Theory (MFT), or relevant extensions of that theory to media entertainment, such as the Moral Intuition and Media Entertainment/Model of Intuitive Morality and Exemplars (MIME). Due to the interdisciplinary nature of these theoretical perspectives as well as game studies broadly, systematic review is critical to helping us collectively understand and collate the research in this area. The systematic review is done in two parts, one as a deep description of the characteristics of included studies, and one as a statistical analysis (as well as a qualitative assessment) of the quality of those included studies. At this stage, an initial set of 24-26 articles focused on gaming and MFT/MIME have been uncovered via systematic database searching, and both study characteristic and study quality coding sheets in progress (shared, within)

Factors associated with hepatitis B vaccine series completion in a randomized trial for injection drug users reached through syringe exchange programs in three US cities

juillet 19311931/07 (T8,A1931)-1931/12.Appartient à l’ensemble documentaire : PACA

Assessing exhibition swine as potential disseminators of infectious disease through the detection of five respiratory pathogens at agricultural exhibitions

International audienceAbstractWidespread geographic movement and extensive comingling of exhibition swine facilitates the spread and transmission of infectious pathogens. Nasal samples were collected from 2862 pigs at 102 exhibitions and tested for five pathogens. At least one pathogen was molecularly detected in pigs at 63 (61.8%) exhibitions. Influenza A virus was most prevalent and was detected in 498 (17.4%) samples. Influenza D virus was detected in two (0.07%) samples. More than one pathogen was detected in 165 (5.8%) samples. Influenza A virus remains a top threat to animal and human health, but other pathogens may be disseminated through the exhibition swine population

Bisphenol-A Exposure During Adolescence Leads to Enduring Alterations in Cognition and Dendritic Spine Density in Adult Male and Female Rats

We have previously demonstrated that adolescent exposure of rats to bisphenol-A (BPA), an environmental endocrine disrupter, increases anxiety, impairs spatial memory, and decreases dendritic spine density in the CA1 region of the hippocampus (CA1) and medial prefrontal cortex (mPFC) when measured in adolescence in both sexes. The present study examined whether the behavioral and morphological alterations following BPA exposure during adolescent development are maintained into adulthood. Male and female, adolescent rats received BPA, 40 μg/kg/bodyweight, or control treatments for one week. In adulthood, subjects were tested for anxiety and locomotor activity, spatial memory, non-spatial visual memory, and sucrose preference. Additionally, stress-induced serum corticosterone levels and dendritic spine density in the mPFC and CA1 were measured. BPA-treated males, but not females, had decreased arm visits on the elevated plus maze, but there was no effect on anxiety. Non-spatial memory, object recognition, was also decreased in BPA treated males, but not females. BPA exposure did not alter spatial memory, object placement, but decreased exploration during the tasks in both sexes. No significant group differences in sucrose preference or serum corticosterone levels in response to a stress challenge were found. However, BPA exposure, regardless of sex, significantly decreased spine density of both apical and basal dendrites on pyramidal cells in CA1 but had no effect in the mPFC. Current data are discussed in relation to BPA dependent changes, which were present during adolescence and did, or did not, endure into adulthood. Overall, adolescent BPA exposure, below the current reference safe daily limit set by the U.S.E.P.A., leads to alterations in some behaviors and neuronal morphology that endure into adulthood

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

Background: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. Results: We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Conclusions: Application of this method allows whole genome studies from samples where material or yields are limiting

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a ‘stairstep’ pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity. DOI: http://dx.doi.org/10.7554/eLife.02833.00

Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface

The active site of cytochrome c (Cyt c) consists of a heme covalently linked to a pentapeptide segment (Cys-X-X-Cys-His), which provides a link between the heme and the protein surface, where the redox partners of Cyt c bind. To elucidate the vibrational properties of heme c, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c 552, including 13C8-heme-, 13C 515N-Met-, and 13C15N-polypeptide (pp)-labeled samples, revealing heme-based vibrational modes in the 200- to 450-cm-1 spectral region. Simulations of the NRVS spectra of H. thermophilus cytochrome c552 allowed for a complete assignment of the Fe vibrational spectrum of the protein-bound heme, as well as the quantitative determination of the amount of mixing between local heme vibrations and pp modes from the Cys-X-XCys-His motif. These results provide the basis to propose that heme-pp vibrational dynamic couplings play a role in electron transfer (ET) by coupling vibrations of the heme directly to vibrations of the pp at the protein - protein interface. This could allow for the direct transduction of the thermal (vibrational) energy from the protein surface to the heme that is released on protein/protein complex formation, or it could modulate the heme vibrations in the protein/protein complex to minimize reorganization energy. Both mechanisms lower energy barriers for ET. Notably, the conformation of the distal Met side chain is fine-tuned in the protein to localize heme-pp mixed vibrations within the 250-to 400-cm-1 spectral region. These findings point to a particular orientation of the distal Met that maximizes ET

National Climate Change Adaptation Research Plan Terrestrial Biodiversity: update 2017

In 2011, a National Climate Change Adaptation Research Plan (NARP) was developed for the terrestrial ecosystems and biodiversity theme of climate change adaptation (Terrestrial NARP 2011). The Terrestrial NARP aims to identify priority research questions for climate change adaptation issues relevant to Australia's cities, towns and regions, including coastal communities and regions. This NARP was updated in 2013 (Terrestrial NARP 2013). The purpose of this document is to review the Terrestrial NARP 2013 and this was done through a series of workshops with key stakeholders in 2015-16. The most important component of the NARPs is to identify and prioritise adaptation research questions that are important, often urgent, and will provide knowledge needed by adaptation stakeholders across Australia. Based on the stakholder review, a total of 20 priority research questions (Table 1) are presented in this report within four research themes

The Ursinus Weekly, January 12, 1953

Petitions for May queen to start Feb. 2 • Revised final exam schedule • 11 students to graduate this January • Over 200 people hear Earle Spicer sing ballads Wed. • Lucas, Scott join cast of Alpha Psi • Pettit discovers fire in Bomberger chapel • Library has new collection of great books of western world • Campus Chest total is $955.23 • Y commission holds vespers • Frosh class discusses plans; Sets tentative dance date • Chem group to hear speech • Turkish speaker addresses classes Tuesday morning • Frats hold meetings, set date for dances • Movie to be shown in S-12 • 32 girls invited to Rosie dessert • Ruby wants snaps brought to Hobson • New rules regulate use of Alumni office machines • Editorials: New year suggestion • Goodbye H.S.T. • Letters to the editor • Engagements • Weddings • What are ex-student-teachers doing with their free time? • January graduates reveal variety of future plans • Resolutions of eager frosh contrast to humble seniors • F&M routs Bears 90-65 with second half splurge • Grizzlies rally to smother alumni 96-75 for fifth • Belles drub Moravian 75-22; Kuhn scores 21 • Grapplers down Swarthmore team • Herb Knull tabs record 46 as Ursinus routs Fords • French Club gives moviehttps://digitalcommons.ursinus.edu/weekly/1510/thumbnail.jp