Algal community membership of estuarine mudflats from the Savannah River, United States

Algae represent a large and diverse group of photosynthetic organisms inhabiting all aquatic habitats. Although the traditional assessment of algal diversity relies mainly on microscopy-based morphological identification, certain limitations exist. In this study, we present a combined molecular and morphological assessment of algal diversity in mudflats from the Savannah River Estuary, Georgia. High diversity of diatoms was documented, and less than 20% of the algal community was physiologically active at the time of collection. From the total genomic DNA extracted from the field samples and lab isolates, 18S rDNA sequences were PCR amplified, cloned, sequenced, identified, and then compared to the taxa identified via microscopy. Only a few of the DNA sequences matched documented taxa, and the abundance of particular algal species was limited to morphological analysis. Surprisingly, upon examination of the remaining lysis buffer from the mechanical lysis step of algal cells, diatom species were left intact even in the presence of a detergent indicating that the diatom species resistant to lysis could be easily underrepresented. Generation of additional algal sequences data, tied to accurate taxonomic identification, is essential to current environmental sequencing projects and potentially would allow faster acquisition of algal community structure within these unique environments

Volume Fractions of the Kinematic "Near-Critical" Sets of the Quantum Ensemble Control Landscape

An estimate is derived for the volume fraction of a subset $C_{\epsilon}^{P} = \{U : ||grad J(U)|\leq {\epsilon}\}\subset\mathrm{U}(N)$ in the neighborhood of the critical set $C^{P}\simeq\mathrm{U}(\mathbf{n})P\mathrm{U}(\mathbf{m})$ of the kinematic quantum ensemble control landscape J(U) = Tr(U\rho U' O), where $U$ represents the unitary time evolution operator, {\rho} is the initial density matrix of the ensemble, and O is an observable operator. This estimate is based on the Hilbert-Schmidt geometry for the unitary group and a first-order approximation of $||grad J(U)||^2$. An upper bound on these near-critical volumes is conjectured and supported by numerical simulation, leading to an asymptotic analysis as the dimension $N$ of the quantum system rises in which the volume fractions of these "near-critical" sets decrease to zero as $N$ increases. This result helps explain the apparent lack of influence exerted by the many saddles of $J$ over the gradient flow.Comment: 27 pages, 1 figur

Rarefied Hypersonic Flow About A Flat-Ended Circular Cylinder

The rarefied Mach 25 flow about a flat-ended cylinder was calculated using Bird's Direct Simulation Monte Carlo technique. Collisions between diatomic molecules were calculated using three rotational-translational energy exchanges models: (1) Pullin's approximate classical model (2) phenomenological (Borgnakke-Larsen) model with the exchange factor depending on the collision energy (variable phi model) (3) and hybrid classical phenomenological exchange model. Two scattering potentials were used to represent nitrogen: (1) the inverse 13.5 power potential and (2) the Morse potential. Simulation results for each collision model were found to be in good agreement with electron beam density surveys in the stagnating flow ahead of the cylinder. Heat transfer to the blunt front face of the cylinder was found to be sensitive to the collision model used, but all were within the statistical scatter of published data. It was suggested that measurements of temperature profiles in the stagnation region would allow better evaluation of the collision models

Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily

Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function

Accuracy of an acoustic location system for monitoring the position of duetting songbirds in tropical forest

A field test was conducted on the accuracy of an eight-microphone acoustic location system designed to triangulate the position of duetting rufous-and-white wrens (Thryothorus rufalbus) in Costa Rica\u27s humid evergreen forest. Eight microphones were set up in the breeding territories of 20 pairs of wrens, with an average intermicrophone distance of 75.2±2.6 m. The array of microphones was used to record antiphonal duets broadcast through stereo loudspeakers. The positions of the loudspeakers were then estimated by evaluating the delay with which the eight microphones recorded the broadcast sounds. Position estimates were compared to coordinates surveyed with a global-positioning system (GPS). The acoustic location system estimated the position of loudspeakers with an error of 2.82±0.26 m and calculated the distance between the male and female loudspeakers with an error of 2.12±0.42 m. Given the large range of distances between duetting birds, this relatively low level of error demonstrates that the acoustic location system is a useful tool for studying avian duets. Location error was influenced partly by the difficulties inherent in collecting high accuracy GPS coordinates of microphone positions underneath a lush tropical canopy and partly by the complicating influence of irregular topography and thick vegetation on sound transmission. © 2006 Acoustical Society of America

The CH fraction of Carbon stars at high Galactic latitudes

CH stars form a distinct class of objects with characteristic properties like iron deficiency, enrichment of carbon and overabundance in heavy elements. These properties can provide strong observational constraints for theoretical computation of nucleosynthesis at low-metallicity. An important question is the relative surface density of CH stars which can provide valuable inputs to our understanding on the role of low to intermediate-mass stars in the early Galactic chemical evolution. Spectroscopic characterization provides an effective way of identifying CH stars. The present analysis is aimed at a quantitative assessment of the fraction of CH stars in a sample of stars using a set of spectral classification criteria. The sample consists of 92 objects selected from a collection of candidate Faint High Latitude Carbon stars from the Hamburg/ESO survey. Medium resolution (R ~ 1300) spectra for these objects were obtained using OMR at VBO, Kavalur and HFOSC at HCT, IAO, Hanle, during 2007 - 2009 spanning a wavelength range 3800 - 6800 A. Spectral analysis shows 36 of the 92 objects to be potential CH stars; combined with our earlier studies (Goswami 2005, Goswami et al. 2007) this implies ~ 37% (of 243) objects as the CH fraction. We present spectral descriptions of the newly identified CH star candidates. Estimated effective temperatures, 12C/13C isotopic ratios and their locations on the two colour J-H vs H-K plot are used to support their identification.Comment: 18 pages, 8 figures,Accepted for publication in MNRA

Unified analysis of terminal-time control in classical and quantum systems

Many phenomena in physics, chemistry, and biology involve seeking an optimal control to maximize an objective for a classical or quantum system which is open and interacting with its environment. The complexity of finding an optimal control for maximizing an objective is strongly affected by the possible existence of sub-optimal maxima. Within a unified framework under specified conditions, control objectives for maximizing at a terminal time physical observables of open classical and quantum systems are shown to be inherently free of sub-optimal maxima. This attractive feature is of central importance for enabling the discovery of controls in a seamless fashion in a wide range of phenomena transcending the quantum and classical regimes.Comment: 10 page

Qualification of tumour mutational burden by targeted next-generation sequencing as a biomarker in hepatocellular carcinoma

Background & Aims: Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next-generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC). Methods: We sequenced 48 non-paired samples (21 fresh-frozen [FF] and 27 paraffin-embedded [FFPE]), among which 11 FFPE samples were pretreated with uracil-DNA glycosylase (UDG). Thirty samples satisfied post-sequencing quality control. High/low TMB was defined by median number of mutations/Mb (Mut/Mb), across different minimum allele frequency (MAF) thresholds ( 650.05, 650.1 and 650.2). Results: Eligible patients (n\ua0=\ua029) were cirrhotic (84%) with TNM stage I-II HCC (75%). FFPE samples had higher TMB (median 958.39 vs 2.51 Mut/Mb, P\ua0\ua0T transitions at CpG sites (median 60.3% vs 9.1%, P\ua0=.002) compared to FF. UDG-treated samples had lower TMB (median 4019.92 vs 353 Mut/Mb, P\ua0=.041) and deamination counts (median 6393.5 vs 328.5, P\ua0=.041) vs untreated FFPE. At 0.2 MAF threshold with UDG treatment, median TMB was 5.48 (range 1.68-16.07) and did not correlate with salient pathologic features of HCC, including survival. Conclusion: While tNGS on fresh HCC samples appears to be the optimal source of tumour DNA, the low median TMB values observed may limit the role of TMB as a predictor of response to immunotherapy in HCC