Autoregulation of topoisomerase I expression by supercoiling sensitive transcription

The opposing catalytic activities of topoisomerase I (TopoI/relaxase) and DNA gyrase (supercoiling enzyme) ensure homeostatic maintenance of bacterial chromosome supercoiling. Earlier studies in Es-cherichia coli suggested that the alteration in DNA supercoiling affects the DNA gyrase and TopoI expression. Although, the role of DNA elements around the promoters were proposed in regulation of gyrase, the molecular mechanism of supercoiling mediated control of TopoI expression is not yet understood. Here, we describe the regulation of TopoI expression from Mycobacterium tuberculosis and Mycobac-terium smegmatis by a mechanism termed Supercoiling Sensitive Transcription (SST). In both the organisms, topoI promoter(s) exhibited reduced activity in response to chromosome relaxation suggesting that SST is intrinsic to topoI promoter(s). We elucidate the role of promoter architecture and high transcriptional activity of upstream genes in topoI regulation. Analysis of the promoter(s) revealed the presence of suboptimal spacing between the -35 and -10 elements, rendering them supercoiling sensitive. Accordingly, upon chromosome relaxation, RNA polymerase occupancy was decreased on the topoI promoter region implicating the role of DNA topology in SST of topoI. We propose that negative supercoiling induced DNA twisting/writhing align the -35 and -10 elements to facilitate the optimal transcription of topoI.

超声速大攻角旋成体迎风激波数值模拟

旋成弹体在大攻角超声速流动中其迎风面上有时会出现一种迎风激波.采用非定常雷诺平均的Navier-Stokes方程以及两方程kω-sst和代数B-L湍流模型成功地模拟了该现象,验证了该迎风激波是由于流场主旋涡导致超声速流动偏移造成的涡诱导激波的一部分的结论.

Turbulence modeling for flows around convex features giving rapid eddy distortion

Reynolds averaged Navier-Stokes model performances in the stagnation and wake regions for turbulent flows with relatively large Lagrangian length scales (generally larger than the scale of geometrical features) approaching small cylinders (both square and circular) is explored. The effective cylinder (or wire) diameter based Reynolds number, ReW ≤ 2.5 × 103. The following turbulence models are considered: a mixing-length; standard Spalart and Allmaras (SA) and streamline curvature (and rotation) corrected SA (SARC); Secundov's νt-92; Secundov et al.'s two equation νt-L; Wolfshtein's k-l model; the Explicit Algebraic Stress Model (EASM) of Abid et al.; the cubic model of Craft et al.; various linear k-ε models including those with wall distance based damping functions; Menter SST, k-ω and Spalding's LVEL model. The use of differential equation distance functions (Poisson and Hamilton-Jacobi equation based) for palliative turbulence modeling purposes is explored. The performance of SA with these distance functions is also considered in the sharp convex geometry region of an airfoil trailing edge. For the cylinder, with ReW ≈ 2.5 × 103 the mixing length and k-l models give strong turbulence production in the wake region. However, in agreement with eddy viscosity estimates, the LVEL and Secundov νt-92 models show relatively little cylinder influence on turbulence. On the other hand, two equation models (as does the one equation SA) suggest the cylinder gives a strong turbulence deficit in the wake region. Also, for SA, an order or magnitude cylinder diameter decrease from ReW = 2500 to 250 surprisingly strengthens the cylinder's disruptive influence. Importantly, results for ReW ≪ 250 are virtually identical to those for ReW = 250 i.e. no matter how small the cylinder/wire its influence does not, as it should, vanish. Similar tests for the Launder-Sharma k-ε, Menter SST and k-ω show, in accordance with physical reality, the cylinder's influence diminishing albeit slowly with size. Results suggest distance functions palliate the SA model's erroneous trait and improve its predictive performance in wire wake regions. Also, results suggest that, along the stagnation line, such functions improve the SA, mixing length, k-l and LVEL results. For the airfoil, with SA, the larger Poisson distance function increases the wake region turbulence levels by just under 5%. © 2007 Elsevier Inc. All rights reserved.

Protected species aerial survey data collection and analysis in waters underlying the R-5306A airspace: final report submitted to US Marine Corps, MCAS Cherry Point

To be in compliance with the Endangered Species Act and the Marine Mammal Protection Act, the United States Department of the Navy is required to assess the potential environmental impacts of conducting at-sea training operations on sea turtles and marine mammals. Limited recent and area-specific density data of sea turtles and dolphins exist for many of the Navy’s operations areas (OPAREAs), including the Marine Corps Air Station (MCAS) Cherry Point OPAREA, which encompasses portions of Core and Pamlico Sounds, North Carolina. Aerial surveys were conducted to document the seasonal distribution and estimated density of sea turtles and dolphins within Core Sound and portions of Pamlico Sound, and coastal waters extending one mile offshore. Sea Surface Temperature (SST) data for each survey were extracted from 1.4 km/pixel resolution Advanced Very High Resolution Radiometer remote images. A total of 92 turtles and 1,625 dolphins were sighted during 41 aerial surveys, conducted from July 2004 to April 2006. In the spring (March – May; 7.9°C to 21.7°C mean SST), the majority of turtles sighted were along the coast, mainly from the northern Core Banks northward to Cape Hatteras. By the summer (June – Aug.; 25.2°C to 30.8°C mean SST), turtles were fairly evenly dispersed along the entire survey range of the coast and Pamlico Sound, with only a few sightings in Core Sound. In the autumn (Sept. – Nov.; 9.6°C to 29.6°C mean SST), the majority of turtles sighted were along the coast and in eastern Pamlico Sound; however, fewer turtles were observed along the coast than in the summer. No turtles were seen during the winter surveys (Dec. – Feb.; 7.6°C to 11.2°C mean SST). The estimated mean surface density of turtles was highest along the coast in the summer of 2005 (0.615 turtles/km², SE = 0.220). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2005 (0.016 turtles/km², SE = 0.009). The mean seasonal abundance estimates were always highest in the coastal region, except in the winter when turtles were not sighted in either region. For Pamlico Sound, surface densities were always greater in the eastern than western section. The range of mean temperatures at which turtles were sighted was 9.68°C to 30.82°C. The majority of turtles sighted were within water ≥ 11°C. Dolphins were observed within estuarine waters and along the coast year-round; however, there were some general seasonal movements. In particular, during the summer sightings decreased along the coast and dolphins were distributed throughout Core and Pamlico Sounds, while in the winter the majority of dolphins were located along the coast and in southeastern Pamlico Sound. Although relative numbers changed seasonally between these areas, the estimated mean surface density of dolphins was highest along the coast in the spring of 2006 (9.564 dolphins/km², SE = 5.571). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2004 (0.192 dolphins/km², SE = 0.066). The estimated mean surface density of dolphins was lowest along the coast in the summer of 2004 (0.461 dolphins/km², SE = 0.294). The estimated mean surface density of dolphins was lowest in Core and Pamlico Sounds in the summer of 2005 (0.024 dolphins/km², SE = 0.011). In Pamlico Sound, estimated surface densities were greater in the eastern section except in the autumn. Dolphins were sighted throughout the entire range of mean SST (7.60°C to 30.82°C), with a tendency towards fewer dolphins sighted as water temperatures increased. Based on the findings of this study, sea turtles are most likely to be encountered within the OPAREAs when SST is ≥ 11°C. Since sea turtle distributions are generally limited by water temperature, knowing the SST of a given area is a useful predictor of sea turtle presence. Since dolphins were observed within estuarine waters year-round and throughout the entire range of mean SST’s, they likely could be encountered in the OPAREAs any time of the year. Although our findings indicated the greatest number of dolphins to be present in the winter and the least in the summer, their movements also may be related to other factors such as the availability of prey. (PDF contains 28 pages)

Daily scale wintertime sea surface temperature and IPC-Navidad variability in the southern Bay of Biscay from 1981 to 2010

The combination of remotely sensed gappy Sea surface temperature (SST) images with the missing data filling DINEOF (data interpolating empirical orthogonal functions) technique, followed by a principal component analysis of the reconstructed data, has been used to identify the time evolution and the daily scale variability of the wintertime surface signal of the Iberian Poleward Current (IPC), or Navidad, during the 1981-2010 period. An exhaustive comparison with the existing bibliography, and the vertical temperature and salinity profiles related to its extremes over the Bay of Biscay area, show that the obtained time series accurately reflect the IPC-Navidad variability. Once a time series for the evolution of the SST signal of the current over the last decades is well established, this time series is used to propose a physical mechanism in relation to the variability of the IPC-Navidad, involving both atmospheric and oceanic variables. According to the proposed mechanism, an atmospheric circulation anomaly observed in both the 500 hPa and the surface levels generates atmospheric surface level pressure, wind-stress and heat-flux anomalies. In turn, those surface level atmospheric anomalies induce mutually coherent SST and sea level anomalies over the North Atlantic area, and locally, in the Bay of Biscay area. These anomalies, both locally over the Bay of Biscay area and over the North Atlantic, are in agreement with several mechanisms that have separately been related to the variability of the IPC-Navidad, i.e. the south-westerly winds, the joint effect of baroclinicity and relief (JEBAR) effect, the topographic beta effect and a weakened North Atlantic gyre.

The influence of some environmental variables on the apparent abundance of skipjack tuna, Katsuwonus pelamis, in the Eastern Pacific Ocean

ENGLISH: The abundance of skipjack larvae in the central and western Pacific approximately doubled for every 1°C increase in sea-surface temperature (SST) from 23°C to a maximum of about 29°C, and then usually decreased with further increases in SST. Skipjack larvae are scarce in the eastern Pacific Ocean (EPO), so most skipjack recruits and adults in this area are believed to have originated in the central and, possibly, the western Pacific. The catch per unit of effort (CPUE), in short tons per day's fishing, and the catch rate, in number of fish per day's fishing, are estimates of apparent abundance in a fishery. The logarithm of the annual CPUE for skipjack for international baitboats in the EPO for the 1934-1960 period was positively correlated with SST in the spawning area in the central Pacific 18 months earlier (r2 0.31), during the July-June period when most of the recruits in each cohort were presumed to have been spawned. Adequate data for other environmental variables were not available for testing with the baitboat data. The other environmental variables available and selected for testing for correlation with estimates of skipjack abundance for purse seiners for the 1961-1984 period and the reasons for their selection are as follows. 1)Wind-mixing index (WMI). The degree of mixing in the upper layers of the ocean is proportional to the cube of the wind speed, called WMI. The degree of mixing in the spawning areas of the central and the western Pacific may affect the concentration of organisms that skipjack larvae feed upon, thereby influencing their survival, and ultimately determining cohort strength and the number of recruits to the eastern Pacific fishery. 2) SST in the fishing areas at the time of fishing (SST). The CPUE for yellowfin tuna has been shown to be inversely related to SST in the fishing areas, and there are indications that skipjack CPUE is lower during EI Nino events when SST is higher than normal. 3) North-south SST gradient across the thermal front off the Gulf of Guayaquil. This is a measure of the degree of upwelling and nutrient enrichment of the upper waters south of the front and ultimately of the production of food for tunas. 4) Speed of the North Equatorial Countercurrent (NECC). Young skipjack may migrate from the central Pacific to the EPO in the eastward flowing NECC; if so, the number of recruits might be affected by variations in the speed of the current. The logarithm of the annual catch rate of skipjack recruits by international purse seiners in the EPO for the 1961-1984 period was positively correlated with SST in the spawning area of the central Pacific 18 months earlier (r2 = 0.21),and inversely correlated with WMI in the spawning area 18 months earlier (r2 0.46). The logarithm of CPUE for purse seiners in the area off the Gulf of Guayaquil was not correlated with SST in the spawning area 18 months earlier, but was inversely correlated with WMI in the spawning area 18 months earlier (r2 = 0.19), and inversely correlated with the north-south SST gradient in the fishing area at the time of fishing (r2 0.32). Neither of these estimates of apparent abundance from purse seiners were correlated with SST in the fishing areas, or with the speed of the NECC at earlier times. SPANISH: La abundancia de larvas de barrilete en el Pacífico central y occidental se multiplicó por dos, aproximadamente, por cada aumento de 1°Cen la temperatura de la superficie del mar (TSM) entre 23°C y un máximo de unos 29°C, y luego generalmente disminuyó con más aumentos en la TSM. Las larvas de barrilete son escasas en el Océano Pacífico oriental (OPO), y por lo tanto se cree que la mayoría de los reclutas y adultos en esta zona surgieron del Pacífico central, y posiblemente también del Pacífico occidental. La captura por unidad de esfuerzo (CPUE), en toneladas cortas por día de pesca, y la tasa de captura, en número de peces por día de pesca, son estimaciones de la abundancia aparente en una pesquería. El logaritmo de la CPUE anual de barrilete lograda por barcos de carnada en el OPO en el período 1934-1960 se correlacionó positivamente con la TSM en la zona de desove en el Pacífico central de 18 meses antes (r2 = 0.31), durante el período de junio-julio en el cual se cree que nació la mayoría de los reclutas en cada cohorte. No se dispuso de datos suficientes sobre otras variables ambientales para comprobarlos con los datos de los barcos de carnada. Las demás variables ambientales disponibles y seleccionadas para someterlas a pruebas de correlación con las estimaciones de la abundancia del barrilete de barcos cerqueros en el período 1961-1984, y las razones por su selección, son las siguientes: 1) Indice de mezcla por el viento (IMV). El grado de mezcla en las capas superiores del océano es proporcional al cubo de la velocidad del viento, llamado IMV. Es posible que el grado de mezcla en las zonas de desove del Pacífico central y occidental afecte la concentración de los organismos que alimentan a las larvas del barrilete, afectando así la supervivencia de éstas, y finalmente determinando el tamaño de las cohortes y el número de reclutas a la pesquería del OPO. 2) TSM en la zona de pesca al realizarse la pesca (TSM). Se ha mostrado que la relación de la CPUE del atún aleta amarilla a la TSM en la zona de pesca es inversa, y existen indicaciones que la CPUE de barrilete es inferior durante eventos del Niño, cuando las TSM son superiores a lo normal. 3) Gradiente norte-sur de las TSM a través del frente térmico frente al Golfo de Guayaquil. Esto es una medida del grado de afloramiento y enriquecimiento nutritivo del nivel superior de las aguas al sur de dicho frente, y finalmente de la producción de alimento para los atunes. 4) La velocidad de la Contracorriente Ecuatorial del Norte (CCEN). Es posible que los bariletes juveniles migren del Pacífico central al Pacífico oriental en la CCEN, que fluye hacia el este; de ser así, es posible que la cantidad de reclutas se vea afectada por variaciones en la velocidad de la corriente. El logaritmo de la tasa anual de captura de reclutas de barrilete por cerqueros de varias banderas en el OPO en el período 1961-1964 estuvo correlacionado de forma positiva con las TSM en la zona de desove del Pacífico central de 18meses antes (r2 0.21),y de forma inversa con el IMV de la zona de desove de 18 meses antes (r2 0.46). El logaritmo de la CPUE de los cerqueros en la zona frente al Golfo de Guayaquil no estuvo correlacionado con las TSM en la zona de desove de 18 meses antes, pero sí estuvo correlacionado de forma inversa con el IMV en la zona de desove de 18 meses antes (r2 0.19),y con el gradiente norte-sur de las TSM en la zona de pesca al realizarse la pesca (r2 0.32). Ninguna de estas estimaciones de abundancia aparente provenientes de barcos cerqueros estuvo correlacionada con las TSM en las zonas de pesca o con la velocidad de la CCEN en épocas anteriores. (PDF contains 140 pages.)