Site-specific Mutants of Oncomodulin: 1H NMR and optical stopped-flow studies of the effect on the metal binding properties of an Asp59 → Glu59 substitution in the calcium-specific site

Abstract High resolution 1H nuclear magnetic resonance spectroscopy and optical stopped-flow techniques have been used to study the metal binding properties of a site-specific mutant of bacterial recombinant oncomodulin in which glutamate has replaced a liganding aspartate at position 59 in the CD calcium-binding site. In particular we have followed the replacement of calcium by lutetium in bacterial recombinant oncomodulin and D59E oncomodulin to provide a measure of the protein's preferences for metal ions of different ionic radii. The result of the Asp----Glu substitution is to make the mutant oncomodulin more similar to rat parvalbumin in terms of its relative CD- and EF-domain affinities for lutetium(III), that is to increase its affinity for metal ions with smaller ionic radii. This finding supports the original hypothesis that the presence of Asp at sequence position 59 is an important factor in the reduced preference of the CD site of oncomodulin for smaller metals such as magnesium (Williams, T. C., Corson, D. C., Sykes, B. D., and MacManus, J. P. (1987) J. Biol. Chem. 262, 6248-6256). However, our studies show that both the CD and the EF sites are affected by this single residue substitution suggesting that many factors play a role in the metal binding affinity and interaction between the two sites

Urban Stream Burial Increases Watershed-Scale Nitrate Export

Nitrogen (N) uptake in streams is an important ecosystem service that reduces nutrient loading to downstream ecosystems. Here we synthesize studies that investigated the effects of urban stream burial on N-uptake in two metropolitan areas and use simulation modeling to scale our measurements to the broader watershed scale. We report that nitrate travels on average 18 times farther downstream in buried than in open streams before being removed from the water column, indicating that burial substantially reduces N uptake in streams. Simulation modeling suggests that as burial expands throughout a river network, N uptake rates increase in the remaining open reaches which somewhat offsets reduced N uptake in buried reaches. This is particularly true at low levels of stream burial. At higher levels of stream burial, however, open reaches become rare and cumulative N uptake across all open reaches in the watershed rapidly declines. As a result, watershed-scale N export increases slowly at low levels of stream burial, after which increases in export become more pronounced. Stream burial in the lower, more urbanized portions of the watershed had a greater effect on N export than an equivalent amount of stream burial in the upper watershed. We suggest that stream daylighting (i.e., uncovering buried streams) can increase watershed-scale N retention

Extended Radio AGN at z ∼ 1 in the ORELSE Survey: The Confining Effect of Dense Environments

Recent hydrodynamic simulations and observations of radio jets have shown that the surrounding environment has a large effect on their resulting morphology. To investigate this, we use a sample of 50 Extended Radio Active Galactic Nuclei (ERAGN) detected in the Observations of Redshift Evolution in Large-Scale Environments survey. These sources are all successfully cross-identified to galaxies within a redshift range of 0.55 ≤ z ≤ 1.35, either through spectroscopic redshifts or accurate photometric redshifts. We find that ERAGN are more compact in high-density environments than those in low-density environments at a significance level of 4.5σ. Among a series of internal properties under our scrutiny, only the radio power demonstrates a positive correlation with their spatial extent. After removing the possible radio power effect, the difference of size in low- and high-density environments persists. In the global environment analyses, the majority (86%) of high-density ERAGN reside in the cluster/group environment. In addition, ERAGN in the cluster/group central regions are preferentially compact with a small scatter in size, compared to those in the cluster/group intermediate regions and fields. In conclusion, our data appear to support the interpretation that the dense intracluster gas in the central regions of galaxy clusters plays a major role in confining the spatial extent of radio jets

Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar

Conflict resolution in genomic variant interpretation is a critical step toward improving patient care. Evaluating interpretation discrepancies in copy number variants (CNVs) typically involves assessing overlapping genomic content with focus on genes/regions that may be subject to dosage sensitivity (haploinsufficiency (HI) and/or triplosensitivity (TS)). CNVs containing dosage sensitive genes/regions are generally interpreted as â likely pathogenicâ (LP) or â pathogenicâ (P), and CNVs involving the same known dosage sensitive gene(s) should receive the same clinical interpretation. We compared the Clinical Genome Resource (ClinGen) Dosage Map, a publicly available resource documenting known HI and TS genes/regions, against germline, clinical CNV interpretations within the ClinVar database. We identified 251 CNVs overlapping known dosage sensitive genes/regions but not classified as LP or P; these were sent back to their original submitting laboratories for reâ evaluation. Of 246 CNVs reâ evaluated, an updated clinical classification was warranted in 157 cases (63.8%); no change was made to the current classification in 79 cases (32.1%); and 10 cases (4.1%) resulted in other types of updates to ClinVar records. This effort will add curated interpretation data into the public domain and allow laboratories to focus attention on more complex discrepancies.The ClinGen Dosage Sensitivity (DS) Map provides evidenceâ based assessments of the haploinsufficiency and triplosensitivity of genes/genomic regions. We identified 251 clinical copy number variants (CNVs) in ClinVar that overlapped known DS genes/regions but were not interpreted as â likely pathogenicâ or â pathogenic;â these were sent back to their original laboratories for reâ evaluation. Of the 246 that were reâ evaluated, 63.0% resulted in updated classifications, showing that the ClinGen DS Map can be an effective initial step in CNV classification discrepancy resolution.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146425/1/humu23610_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146425/2/humu23610.pd

Dark Energy Survey Year 6 Results: Intra-Cluster Light from Redshift 0.2 to 0.5

Using the full six years of imaging data from the Dark Energy Survey, we study the surface brightness profiles of galaxy cluster central galaxies and intra-cluster light. We apply a ``stacking'' method to over four thousand galaxy clusters identified by the redMaPPer cluster finding algorithm in the redshift range of 0.2 to 0.5. This yields high signal-to-noise radial profile measurements of the central galaxy and intra-cluster light out to 1 Mpc from the cluster center. Using redMaPPer richness as a cluster mass indicator, we find that the intra-cluster light brightness has a strong mass dependence throughout the 0.2 to 0.5 redshift range, and the dependence grows stronger at a larger radius. In terms of redshift evolution, we find some evidence that the central galaxy, as well as the diffuse light within the transition region between the cluster central galaxy and intra-cluster light within 80 kpc from the center, may be growing over time. At larger radii, more than 80 kpc away from the cluster center, we do not find evidence of additional redshift evolution beyond the cluster mass dependence, which is consistent with the findings from the IllustrisTNG hydrodynamic simulation. We speculate that the major driver of intra-cluster light growth, especially at large radii, is associated with cluster mass growth. Finally, we find that the color of the cluster central galaxy and intra-cluster light displays a radial gradient that becomes bluer at a larger radius, which is consistent with a stellar stripping and disruption origin of intra-cluster light as suggested by simulation studies.Comment: Submitted to MNRA

CVD growth of carbon nanostructures from zirconia: mechanisms and a method for enhancing yield.

By excluding metals from synthesis, growth of carbon nanostructures via unreduced oxide nanoparticle catalysts offers wide technological potential. We report new observations of the mechanisms underlying chemical vapor deposition (CVD) growth of fibrous carbon nanostructures from zirconia nanoparticles. Transmission electron microscope (TEM) observation reveals distinct differences in morphological features of carbon nanotubes and nanofibers (CNTs and CNFs) grown from zirconia nanoparticle catalysts versus typical oxide-supported metal nanoparticle catalysts. Nanofibers borne from zirconia lack an observable graphitic cage consistently found with nanotube-bearing metal nanoparticle catalysts. We observe two distinct growth modalities for zirconia: (1) turbostratic CNTs 2-3 times smaller in diameter than the nanoparticle localized at a nanoparticle corner, and (2) nonhollow CNFs with approximately the same diameter as the nanoparticle. Unlike metal nanoparticle catalysts, zirconia-based growth should proceed via surface-bound kinetics, and we propose a growth model where initiation occurs at nanoparticle corners. Utilizing these mechanistic insights, we further demonstrate that preannealing of zirconia nanoparticles with a solid-state amorphous carbon substrate enhances growth yield.This material is based upon work supported by the National Science Foundation under Grant No. 1007793 and was also supported by Airbus group, Boeing, Embraer, Lockheed Martin, Saab AB, Hexcel, and TohoTenax through MIT’s Nano- Engineered Composite aerospace STructures (NECST) Consortium. This research was supported (in part) by the U.S. Army Research Office under Contract W911NF-13-D-0001. This work was performed in part at the Center for Nanoscale Systems (CNS), a member of the National Nanotechnology Infrastructure Network (NNIN), which is supported by the National Science Foundation under NSF Award No. ECS-0335765. CNS is part of Harvard University. This work was carried out in part through the use of MIT Microsystems Technology Laboratories. Stephan Hofmann acknowledges funding from EPSRC under grant EP/H047565/1. Piran Kidambi acknowledges the Lindemann Trust Fellowship.This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/ja509872y

The Toronto prehospital hypertonic resuscitation-head injury and multi organ dysfunction trial (TOPHR HIT) - Methods and data collection tools

<p>Abstract</p> <p>Background</p> <p>Clinical trials evaluating the use of hypertonic saline in the treatment of hypovolemia and head trauma suggest no survival superiority over normal saline; however subgroup analyses suggest there may be a reduction in the inflammatory response and multiorgan failure which may lead to better survival and enhanced neurocognitive function. We describe a feasibility study of randomizing head injured patients to hypertonic saline and dextran vs. normal saline administration in the out of hospital setting.</p> <p>Methods/Design</p> <p>This feasibility study employs a randomized, placebo-controlled design evaluating normal saline compared with a single dose of 250 ml of 7.5% hypertonic saline in 6% dextran 70 in the management of traumatic brain injuries. The primary feasibility endpoints of the trial were: 1) baseline survival rates for the treatment and control group to aid in the design of a definitive multicentre trial, 2) randomization compliance rate, 3) ease of protocol implementation in the out-of-hospital setting, and 4) adverse event rate of HSD infusion.</p> <p>The secondary objectives include measuring the effect of HSD in modulating the immuno-inflammatory response to severe head injury and its effect on modulating the release of neuro-biomarkers into serum; evaluating the role of serum neuro-biomarkers in predicting patient outcome and clinical response to HSD intervention; evaluating effects of HSD on brain atrophy post-injury and neurocognitive and neuropsychological outcomes.</p> <p>Discussion</p> <p>We anticipate three aspects of the trial will present challenges to trial success; ethical demands associated with a waiver of consent trial, challenging follow up and comprehensive accurate timely data collection of patient identifiers and clinical or laboratory values. In addition all the data collection tools had to be derived de novo as none existed in the literature.</p> <p>Trial registration number</p> <p>NCT00878631</p