Wind Flow Dynamics over Complex Terrain

Understanding the exchange of energy, moisture, and trace gases between the terrestrial biosphere and the atmosphere over complex terrain is a fundamental goal in achieving a complete model of global or regional climate. Net ecosystem exchange (NEE) of carbon dioxide is often a crucial input into climate models, and is also used as a means of validating regional model outputs. Calculations obtained from eddy flux tower data provide some of the best quality sources of NEE values; however, the standard formulation of the eddy covariance method is incomplete in terrain that includes common features such as hills, forests, cities, or other large obstructions. A field experiment using two towers with eddy covariance instrumentation at multiple heights on a forested hillside was conducted to examine the physical phenomena behind the eddy covariance problems. Specifically, both recirculation and advective flux were measured and analyzed. Recirculation was caused leeward of an obstruction in an unstable atmosphere, characterized by a negative vertical potential temperature gradient. A weak recirculation effect was also seen during conditions when the potential temperature was nearly constant with height (near-neutral). Lee waves appeared under stable conditions, affecting the measured direction of carbon dioxide flux depending on coincidences such as wind speed and air temperature. A full investigation of NEE in complex terrain must include both horizontal and vertical advective flux. Sensors placed at multiple heights on a single tower yielded vertical advection calculations. Vertical advective flux was non-trivial in any atmosphere, and must be measured to fully investigate the NEE at sites in complex terrain. The horizontal advection analysis was incomplete, because the distance between the two towers in this experiment was similar to the size of the hillside, undermining the horizontal gradient measurement. Estimated horizontal advective flux was typically less than vertical advection, though not an order of magnitude less. Any horizontal advective flux measurement over complex terrain must be undertaken using a separate but nearby tower with sensors at multiple heights. The separation distance must be much less than the scale of the obstruction, in order to minimize the chances that complex flow patterns established by the terrain cause mismatches between air parcels measured at the first tower and those at the second

Numerical Study of the Interplay between Thermo-topographic Slope Flow and Synoptic Flow on Canopy Transport Processes

Canopy flow resulting from interaction between thermo-topographic slope flow and large-scale synoptic flow is very complicated and has been poorly understood. We apply a Reynolds-averaged Navier-Stokes (RANS) turbulence model to investigate how the interactions between local flow and synoptic winds affect CO2 movement in the canopy layer at the Renon site in the Italian Alps. Since the RANS simulations are compared to the data measured by multiple-tower experiments conducted during CarboEurope-IP advection campaigns (ADVEX) at Renon, our study can be viewed as a case study of a relatively common wooded slope. The thermal condition in the canopy is directly related to the canopy morphology: the dense canopy at our site causes stronger cooling but limits vertical exchange of heat flux, resulting in weak temperature inversion in the deep canopy. Under conditions with no synoptic wind, local flow leads to CO2 build-up mainly at downslope locations and no recirculation is formed. Recirculation that holds high CO2 mole fraction in the canopy is developed only under the condition that local slope wind is enhanced by northerly synoptic winds. No recirculation forms when southerly synoptic wind direction is opposite to the local wind direction, in which case CO2 is quite well mixed. This numerical study approach brings to light a better understanding of the CO2 closure problem: the measured net ecosystem exchange of CO2 is more likely to be underestimated in local non-synoptic slope flow and local synoptic-enhanced slope flow regimes at Renon. However, small-scale heterogeneity in canopy structure, variability in the CO2 source from soil and higher-resolution and larger-scale topography still challenge the application of this numerical approach in the FLUXNET community

Recirculation over Complex Terrain

This study generated eddy covariance data to investigate atmospheric dynamics leeward of a small, forested hillside in upstate New York. The causes and effects of recirculation eddies were examined to support the larger goal of improving measurement of the exchange of energy, moisture, and trace gases between the terrestrial biosphere and the atmosphere over complex terrain. Sensors operated at five different altitudes on two separate towers—one at the top of the hill and one down the slope to the east—for approximately 8 weeks in the spring of 2013. During the experiment, the vertical potential temperature gradient was found to be the primary factor for determining whether winds interacting with the terrain features caused a recirculating eddy leeward of the hill. The study found evidence that the recirculation influenced carbon dioxide flux and caused the air column to be vertically well mixed

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

T4-Related Bacteriophage LIMEstone Isolates for the Control of Soft Rot on Potato Caused by ‘Dickeya solani’

The bacterium ‘Dickeya solani’, an aggressive biovar 3 variant of Dickeya dianthicola, causes rotting and blackleg in potato. To control this pathogen using bacteriophage therapy, we isolated and characterized two closely related and specific bacteriophages, vB_DsoM_LIMEstone1 and vB_DsoM_LIMEstone2. The LIMEstone phages have a T4-related genome organization and share DNA similarity with Salmonella phage ViI. Microbiological and molecular characterization of the phages deemed them suitable and promising for use in phage therapy. The phages reduced disease incidence and severity on potato tubers in laboratory assays. In addition, in a field trial of potato tubers, when infected with ‘Dickeya solani’, the experimental phage treatment resulted in a higher yield. These results form the basis for the development of a bacteriophage-based biocontrol of potato plants and tubers as an alternative for the use of antibiotics

Cryogenic Orbital Test Bed 3 (CRYOTE3) Overview and Status

CRYOTE3 is a grassroots CFM test effort with contributing government and industry partners focused on developing and testing hardware to produce needed data for model validation and implementation into flight systems

Stably stratified canopy flow in complex terrain

Stably stratified canopy flow in complex terrain has been considered a difficult condition for measuring net ecosystem–atmosphere exchanges of carbon, water vapor, and energy. A long-standing advection error in eddy-flux measurements is caused by stably stratified canopy flow. Such a condition with strong thermal gradient and less turbulent air is also difficult for modeling. To understand the challenging atmospheric condition for eddy-flux measurements, we use the renormalized group (RNG) k–ϵ  turbulence model to investigate the main characteristics of stably stratified canopy flows in complex terrain. In this two-dimensional simulation, we imposed persistent constant heat flux at ground surface and linearly increasing cooling rate in the upper-canopy layer, vertically varying dissipative force from canopy drag elements, buoyancy forcing induced from thermal stratification and the hill terrain. These strong boundary effects keep nonlinearity in the two-dimensional Navier–Stokes equations high enough to generate turbulent behavior. The fundamental characteristics of nighttime canopy flow over complex terrain measured by the small number of available multi-tower advection experiments can be reproduced by this numerical simulation, such as (1) unstable layer in the canopy and super-stable layers associated with flow decoupling in deep canopy and near the top of canopy; (2) sub-canopy drainage flow and drainage flow near the top of canopy in calm night; (3) upward momentum transfer in canopy, downward heat transfer in upper canopy and upward heat transfer in deep canopy; and (4) large buoyancy suppression and weak shear production in strong stability

Bacteriophage T4 Genome

Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the “cell-puncturing device,” combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth

Partial sequencing and expression of genes involved in glucose metabolism in adipose tissues and skeletal muscle of healthy cats

Impaired insulin sensitivity is increasingly recognised in cats, but sequences of genes involved in insulin-signalling are largely undetermined in this species. In this study, extended feline mRNA sequences were determined for the adiponectin, glucose transporter-1 (GLUT1), GLUT4, peroxisome proliferative activated receptor-gamma1 (PPARgamma1), PPARgamma2, plasminogen activator inhibitor-1 (PAI-1), monocyte chemoattractant protein-1 (MCP-1) and insulin receptor genes. Conserved dog-specific primers identified from human-dog mRNA alignments were used to amplify feline cDNA in the polymerase chain reaction (PCR). The feline sequences determined by this method were used to design feline-specific primers suitable for real-time PCR for quantification of gene expression in insulin sensitive tissues of healthy cats. Partial sequences of feline mRNAs had 86-95% identity with dog and human genes. Expression of adiponectin, GLUT1, GLUT4, PPARgamma1, PPARgamma2, PAI-1 and insulin receptor mRNA was detected and quantified in subcutaneous and visceral fat and skeletal muscle, whereas MCP-1 mRNA was detected in adipose tissue but not in skeletal muscle. Further characterisation of genes related to glucose metabolism in cats will provide additional insights into insulin-signalling mechanisms in this species