Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX collaboration

Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (p_T), elliptic flow, two-particle correlations, non-statistical fluctuations, and suppression of particle production at high p_T. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.Comment: 510 authors, 127 pages text, 56 figures, 1 tables, LaTeX. Submitted to Nuclear Physics A as a regular article; v3 has minor changes in response to referee comments. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

The use of airborne laser scanning to develop a pixel-based stratification for a verified carbon offset project

Background The voluntary carbon market is a new and growing market that is increasingly important to consider in managing forestland. Monitoring, reporting, and verifying carbon stocks and fluxes at a project level is the single largest direct cost of a forest carbon offset project. There are now many methods for estimating forest stocks with high accuracy that use both Airborne Laser Scanning (ALS) and high-resolution optical remote sensing data. However, many of these methods are not appropriate for use under existing carbon offset standards and most have not been field tested. Results This paper presents a pixel-based forest stratification method that uses both ALS and optical remote sensing data to optimally partition the variability across an ~10,000 ha forest ownership in Mendocino County, CA, USA. This new stratification approach improved the accuracy of the forest inventory, reduced the cost of field-based inventory, and provides a powerful tool for future management planning. This approach also details a method of determining the optimum pixel size to best partition a forest. Conclusions The use of ALS and optical remote sensing data can help reduce the cost of field inventory and can help to locate areas that need the most intensive inventory effort. This pixel-based stratification method may provide a cost-effective approach to reducing inventory costs over larger areas when the remote sensing data acquisition costs can be kept low on a per acre basis

Development of Sensory, Motor and Behavioral Deficits in the Murine Model of Sanfilippo Syndrome Type B

BACKGROUND: Mucopolysaccharidosis (MPS) IIIB (Sanfilippo Syndrome type B) is caused by a deficiency in the lysosomal enzyme N-acetyl-glucosaminidase (Naglu). Children with MPS IIIB develop disturbances of sleep, activity levels, coordination, vision, hearing, and mental functioning culminating in early death. The murine model of MPS IIIB demonstrates lysosomal distention in multiple tissues, a shortened life span, and behavioral changes. PRINCIPAL FINDINGS: To more thoroughly assess MPS IIIB in mice, alterations in circadian rhythm, activity level, motor function, vision, and hearing were tested. The suprachiasmatic nucleus (SCN) developed pathologic changes and locomotor analysis showed that MPS IIIB mice start their daily activity later and have a lower proportion of activity during the night than wild-type controls. Rotarod assessment of motor function revealed a progressive inability to coordinate movement in a rocking paradigm. Purkinje cell counts were significantly reduced in the MPS IIIB animals compared to age matched controls. By electroretinography (ERG), MPS IIIB mice had a progressive decrease in the amplitude of the dark-adapted b-wave response. Corresponding pathology revealed shortening of the outer segments, thinning of the outer nuclear layer, and inclusions in the retinal pigmented epithelium. Auditory-evoked brainstem responses (ABR) demonstrated progressive hearing deficits consistent with the observed loss of hair cells in the inner ear and histologic abnormalities in the middle ear. CONCLUSIONS/SIGNIFICANCE: The mouse model of MPS IIIB has several quantifiable phenotypic alterations and is similar to the human disease. These physiologic and histologic changes provide insights into the progression of this disease and will serve as important parameters when evaluating various therapies

Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging.

The genome of Mycobacterium tuberculosis (Mtb) encodes nine putative sulfatases, none of which have a known function or substrate. Here, we characterize Mtb's single putative type II sulfatase, Rv3406, as a non-heme iron (II) and α-ketoglutarate-dependent dioxygenase that catalyzes the oxidation and subsequent cleavage of alkyl sulfate esters. Rv3406 was identified based on its homology to the alkyl sulfatase AtsK from Pseudomonas putida. Using an in vitro biochemical assay, we confirmed that Rv3406 is a sulfatase with a preference for alkyl sulfate substrates similar to those processed by AtsK. We determined the crystal structure of the apo Rv3406 sulfatase at 2.5 Å. The active site residues of Rv3406 and AtsK are essentially superimposable, suggesting that the two sulfatases share the same catalytic mechanism. Finally, we generated an Rv3406 mutant (Δrv3406) in Mtb to study the sulfatase's role in sulfate scavenging. The Δrv3406 strain did not replicate in minimal media with 2-ethyl hexyl sulfate as the sole sulfur source, in contrast to wild type Mtb or the complemented strain. We conclude that Rv3406 is an iron and α-ketoglutarate-dependent sulfate ester dioxygenase that has unique substrate specificity that is likely distinct from other Mtb sulfatases

Biochemical characterization of Rv3406.

<p>(A) Rv3406 is an αKG and ascorbate dependent sulfatase. Black squares are the complete assay with Rv3406, 2-EHS, αKG, ascorbate and iron. Red triangles are without 2-EHS. Blue circles are without αKG. (B) Rv3406 is an iron dependent enzyme. (C) The rate of Rv3406 accelerates with the addition of ascorbate up to 1 mM. Rv3406 enzyme concentration was between 0.5 and 0.75 µM for all experiments.</p

The reaction catalyzed by Rv3406.

<p>The alpha carbon of an alkyl sulfate is oxidized by Rv3406 in the presence of α-ketoglutarate and spontaneously collapses to an aldehyde and sulfate, liberating CO₂ and succinate. The product formation was monitored using a coupled assay using LADH to reduce the aldehyde in a NADH dependent manner.</p

Protein alignment of alkyl sulfatase enzymes with taurine dioxygenase enzymes.

<p><b>Enzymes in bold have been biochemically characterized.</b> (A) Alignment of disordered loop 1 where the red boxes are indicating the taurine binding residues in taurine dioxygenases and the analogous amino acids in alkyl sulfatase enzymes. (B) Alignment of disordered loop 2 where the red box is indicating the conserved phenylalanine in taurine dioxygenases and the analogous tyrosine in alkyl sulfate enzymes.</p