An investigation into nitrogen uptake by Emilania huxleyi during continuous darkness

Experiments were conducted with two strains of the coccolithophorid Emiliania huxleyi. Previous experiments with CCMP1742 and 372 at a light intensity of 60 µEin/m²-s showed that during five-day periods of continuous darkness, strain 1742 was taking up nitrate from the media while strain 372 was not. The nitrate uptake in strain 1742 was concurrent with an increase in particulate nitrogen. This observation, combined with the fact that carbon-rich alkenones decreased during the same dark period, led to the hypothesis that amino acids were being synthesized during the continuous darkness period in E. huxleyi strain 1742. This thesis presents results from three separate continuous darkness experiments with E. huxleyi strains 1742 and 372, run at a light intensity of 165 µEin/m²-s. These experiments were conducted to determine whether 1) amino acids are synthesized in E. huxleyi strain 1742 during continuous darkness, 2) this strain is physiologically unique in this regard, and 3) any amino acid accumulation is compound-specific. Two separate and independent methods for amino acid determination were utilized: gas chromatography paired with a flame ionization detector (GC-FID) and the ninhydrin method. Alkenones, media nutrients, and particulate organic carbon and particulate nitrogen (PN) were also measured. Results showed that no dark-period nutrient uptake or PN accumulation occurred in strain 372, in agreement with previous findings. No accumulation of amino acids was displayed in this strain during the continuous darkness period. CCMP1742 displayed nitrogen uptake, PN accumulation, and amino acid synthesis during the first experiment, but not the second or third experiments. The argument is presented that the increased light intensity of 165 µEin/m²-s inhibited the above dark-period nitrogen dynamics. This inhibition may have been overcome in the first experiment due to a previous nutrient stress experienced by the cells used to inoculate the experiment culture. Future experiments should utilize ¹⁵NO₃ to track the media nitrogen into cells, and also investigate the effects of light intensity and nutrient stress on dark-period protein production

Hydroacoustic Evaluation of Overwintering Summer Steelhead Fallback and Kelt Passage at The Dalles Dam Turbines, Early Spring 2011

This report presents the results of an evaluation of overwintering summer steelhead (Oncorhynchus mykiss) fallback and early out-migrating steelhead kelts downstream passage at The Dalles Dam turbines during early spring 2011. The study was conducted by Pacific Northwest National Laboratory (PNNL) for the U.S. Army Corps of Engineers, Portland District (USACE) to investigate whether adult steelhead are passing through turbines during early spring before annual sluiceway operations typically begin. The sluiceway surface flow outlet is the optimal non-turbine route for adult steelhead, although operating the sluiceway reduces hydropower production. This is a follow-up study to similar studies of adult steelhead passage at the sluiceway and turbines we conducted in the fall/winter 2008, early spring 2009, fall/winter 2009, and early spring 2010. The goal of the 2011 study was to characterize adult steelhead passage rates at the turbines while the sluiceway was closed so fisheries managers would have additional information to use in decision-making relative to sluiceway operations. Sluiceway operations were not scheduled to begin until April 10, 2011. However, based on a management decision in late February, sluiceway operations commenced on March 1, 2011. Therefore, this study provided estimates of fish passage rates through the turbines, and not the sluiceway, while the sluiceway was open. The study period was March 1 through April 10, 2011 (41 days total). The study objective was to estimate the number and distribution of adult steelhead and kelt-sized targets passing into turbine units. We obtained fish passage data using fixed-location hydroacoustics with transducers deployed at all 22 main turbine units at The Dalles Dam. Adult steelhead passage through the turbines occurred on 9 days during the study (March 9, 12, 30, and 31 and April 2, 3, 5, 7, and 9). We estimated a total of 215 {+-} 98 (95% confidence interval) adult steelhead targets passed through the turbines between March 1 and April 10, 2011. Horizontal distribution data indicated Main Unit 18 passed the majority of fish. Fish passage occurred throughout the day. We conclude that adult steelhead passed through turbines during early spring 2011 at The Dalles Dam

Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Detroit Dam, 2011

Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Detroit Dam (DET) on the North Santiam River, Oregon for the U.S. Army Corps of Engineers (USACE) to provide data to support decisions on long-term measures to enhance downstream passage at DET and others dams in USACE’s Willamette Valley Project. This study was conducted in response to regulatory requirements necessitated by the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. The goal of the study was to provide information of juvenile salmonid passage and distribution at DET from February 2011 through February 2012. The results of the hydroacoustic study provide new and, in some cases, first-ever data on passage estimates, run timing, distributions, and relationships between fish passage and environmental variables at the dam. This information will inform management decisions on the design and development of surface passage and collection devices to help restore Chinook salmon populations in the North Santiam River watershed above DET. During the entire study period, an estimated total of 182,526 smolt-size fish (±4,660 fish, 95% CI) passed through turbine penstock intakes. Run timing peaked in winter and early spring months. Passage rates were highest during late fall, winter and early spring months and low during summer. Horizontal distribution for hours when both turbine units were operated simultaneously indicated Unit 2 passed almost twice as much fish as Unit 1. Diel distribution for smolt-size fish during the study period was fairly uniform, indicating fish were passing the turbines at all times of the day. A total of 5,083 smolt-size fish (± 312 fish, 95% CI) were estimated passed via the spillway when it was open between June 23 and September 27, 2011. Daily passage was low at the spillway during the June-August period, and increased somewhat in September 2011. When the spillway was operated simultaneously with the turbines, spillway efficiency (efficiency is estimated as spillway passage divided by total project passage) was 0.72 and effectiveness (fish:flow ratio—proportion fish passage at a route (e.g., spillway) divided by proportion water through that route out of the total project) was 2.69. That is, when the spillway was open, 72% of the fish passing the dam used the spillway and 28% passed into the turbine penstocks. Diel distribution for smolt-size fish at the spillway shows a distinct peak in passage between mid-morning and mid-afternoon and low passage at night. We estimated that 23,339 smolt-size fish (± 572 fish, 95% CI) passed via the Regulating Outlet (RO) when it was open from October 29 through November 12, 2011, January 2-6, and January 20 through February 3, 2012. During the October–November period, RO passage peaked at 1,086 fish on November 5, with a second peak on November 7 (1,075 fish). When the RO was operated simultaneously with the turbines, RO efficiency was 0.33 and effectiveness was 0.89. In multiple regression analyses, a relatively parsimonious model was selected that predicted the observed fish passage data well. The best model included forebay temperature at depth, forebay elevation, total discharge, hours of daylight, and the operation period. The vertical distribution of fish in the forebay near the face of the dam where the transducers sampled showed fish were generally distributed throughout the water column during all four operational periods. During the refill and full pool periods, vertical distribution was bi-modal with surface-layer and mid-water modes. Patterns for day and night distributions were variable. Fish were distributed above and below the thermocline when it was present (full pool and drawdown periods)

Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Detroit Dam, 2011

Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Detroit Dam (DET) on the North Santiam River, Oregon for the U.S. Army Corps of Engineers (USACE) to provide data to support decisions on long-term measures to enhance downstream passage at DET and others dams in USACE’s Willamette Valley Project. This study was conducted in response to regulatory requirements necessitated by the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. The goal of the study was to provide information of juvenile salmonid passage and distribution at DET from February 2011 through February 2012. The results of the hydroacoustic study provide new and, in some cases, first-ever data on passage estimates, run timing, distributions, and relationships between fish passage and environmental variables at the dam. This information will inform management decisions on the design and development of surface passage and collection devices to help restore Chinook salmon populations in the North Santiam River watershed above DET. During the entire study period, an estimated total of 182,526 smolt-size fish (±4,660 fish, 95% CI) passed through turbine penstock intakes. Run timing peaked in winter and early spring months. Passage rates were highest during late fall, winter and early spring months and low during summer. Horizontal distribution for hours when both turbine units were operated simultaneously indicated Unit 2 passed almost twice as much fish as Unit 1. Diel distribution for smolt-size fish during the study period was fairly uniform, indicating fish were passing the turbines at all times of the day. A total of 5,083 smolt-size fish (± 312 fish, 95% CI) were estimated passed via the spillway when it was open between June 23 and September 27, 2011. Daily passage was low at the spillway during the June-August period, and increased somewhat in September 2011. When the spillway was operated simultaneously with the turbines, spillway efficiency (efficiency is estimated as spillway passage divided by total project passage) was 0.72 and effectiveness (fish:flow ratio—proportion fish passage at a route (e.g., spillway) divided by proportion water through that route out of the total project) was 2.69. That is, when the spillway was open, 72% of the fish passing the dam used the spillway and 28% passed into the turbine penstocks. Diel distribution for smolt-size fish at the spillway shows a distinct peak in passage between mid-morning and mid-afternoon and low passage at night. We estimated that 23,339 smolt-size fish (± 572 fish, 95% CI) passed via the Regulating Outlet (RO) when it was open from October 29 through November 12, 2011, January 2-6, and January 20 through February 3, 2012. During the October–November period, RO passage peaked at 1,086 fish on November 5, with a second peak on November 7 (1,075 fish). When the RO was operated simultaneously with the turbines, RO efficiency was 0.33 and effectiveness was 0.89. In multiple regression analyses, a relatively parsimonious model was selected that predicted the observed fish passage data well. The best model included forebay temperature at depth, forebay elevation, total discharge, hours of daylight, and the operation period. The vertical distribution of fish in the forebay near the face of the dam where the transducers sampled showed fish were generally distributed throughout the water column during all four operational periods. During the refill and full pool periods, vertical distribution was bi-modal with surface-layer and mid-water modes. Patterns for day and night distributions were variable. Fish were distributed above and below the thermocline when it was present (full pool and drawdown periods)

Acoustic Imaging Evaluation of Juvenile Salmonid Behavior in the Immediate Forebay of the Water Temperature Control Tower at Cougar Dam, 2010

This report presents the results of an evaluation of juvenile Chinook salmon (Oncorhynchus tshawytscha) behavior at Cougar Dam on the south fork of the McKenzie River in Oregon in 2010. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers (USACE). The overall goal of the study was to characterize juvenile salmonid behavior and movement patterns in the immediate forebay of the Water Temperature Control (WTC) tower of the dam for USACE and fisheries resource managers use in making decisions about bioengineering designs for long-term structures and/or operations to facilitate safe downstream passage for juvenile salmonids. We collected acoustic imaging (Dual-Frequency Identification Sonar; DIDSON) data from March 1, 2010, through January 31, 2011. Juvenile salmonids (hereafter, called 'fish') were present in the immediate forebay of the WTC tower throughout the study. Fish abundance index was low in early spring (<200 fish per sample-day), increased in late April, and peaked on May 19 (6,039 fish). A second peak was observed on June 6 (2904 fish). Fish abundance index decreased in early June and remained low in the summer months (<100 fish per sample-day). During the fall and winter, fish numbers varied with a peak on November 10 (1881 fish) and a minimum on December 7 (12 fish). A second, smaller, peak occurred on December 22 (607 fish). A univariate statistical analysis indicated fish abundance index (log10-transformed) was significantly (P<0.05) positively correlated with forebay elevation, velocity over the WTC tower intake gate weirs, and river flows into the reservoir. A subsequent multiple regression analysis resulted in a model (R2=0.70) predicting fish abundance (log-transformed index values) using two independent variables of mean forebay elevation and the log10 of the forebay elevation range. From the approximate fish length measurements made using the DIDSON imaging software, the average fish length during early spring 2010 was 214 {+-} 86 mm (standard deviation). From May through early November, the average fish length remained relatively consistent (132 {+-} 54 mm), after which average lengths increased to 295 {+-} 148 mm for mid-November though early December. From mid-December through January the average fish length decreased to 151 {+-} 76 mm. Milling in front of the WTC tower was the most common fish behavior observed throughout the study period. Traversing along the front of the tower, east-to-west and west-to-east, was the next common behavior. The percentage of fish events showing movement from the forebay to the tower or from the tower to the forebay was generally low throughout the spring, summer, and early fall (0 to 30% for both directions combined, March through early November). From mid-November 2010 through the end of the study (January 31, 2011), the combined percentages of fish moving into and out of the tower were higher (25 to 70%) than during previous months of the study. Schooling behavior was most distinct in the spring. Schooling events were present in 30 to 96% of the fish events during that period, with a peak on May 19. Schooling events were also present in the summer, but at lower numbers. With the exception of some schooling in mid-December, few to no schooling events were observed in the fall and winter months. Diel distributions for schooling fish during spring and fall months indicate schooling was concentrated during daylight hours and no schooling was observed at night. However, in December, schooling occurred at night, after midnight, and during daylight hours. Predator activity, most likely bull trout or rainbow trout according to a USACE biologist, was observed during late spring, when fish abundance index and schooling were highest for the year, and again in the fall months when fish events increased from a summer low. No predator activity was observed in the summer, and little activity occurred during the winter months

Improving time-efficiency in blocking expanding ring search for mobile ad hoc networks

We propose a new strategy for reducing the amount of latency and energy consumption in Blocking Expanding Ring Search (BERS) and enhanced Blocking Expanding Ring Search (BERS*) for mobile ad hoc networks (MANETs). BERS and BERS* are respectively energy and energy–time efficient route discovery protocols for MANETs as compared to conventional Expanding Ring Search (ERS). In this study, we identify unnecessary waiting time caused by a STOP/END instruction in BERS/BERS* and explore the potential of further improvement of their time efficiency. This leads to tBERS and tBERS*, the improved BERS and BERS* respectively. In tBERS/tBERS*, a route node may also issue the STOP/END instruction to terminate flooding. We implement this idea in algorithms, conduct analysis, and achieve further latency reduction in both tBERS and tBERS* as well as the energy saving in tBERS*

Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Lookout Point Dam, 2010

Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Lookout Point Dam (LOP) on the Middle Fork Willamette River for the U.S. Army Corps of Engineers, Portland District (USACE), to provide data to support decisions on long-term measures to enhance downstream passage at LOP and others dams in USACE's Willamette Valley Project. This study was conducted in response to the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. We conducted a hydroacoustic evaluation of juvenile salmonid passage and distribution at LOP during February 2010 through January 2011. Findings from this 1 year of study should be applied carefully because annual variation can be expected due to variability in adult salmon escapement, egg-to-fry and fry-to-smolt survival rates, reservoir rearing and predation, dam operations, and weather. Fish passage rates for smolt-size fish (> {approx}90 mm and < 300 mm) were highest during December-January and lowest in mid-summer through early fall. Passage peaks were also evident in early spring, early summer, and late fall. During the entire study period, an estimated total of 142,463 fish {+-} 4,444 (95% confidence interval) smolt-size fish passed through turbine penstock intakes. Of this total, 84% passed during December-January. Run timing for small-size fish ({approx}65-90 mm) peaked (702 fish) on December 18. Diel periodicity of smolt-size fish showing crepuscular peaks was evident in fish passage into turbine penstock intakes. Relatively few fish passed into the Regulating Outlets (ROs) when they were open in summer (2 fish/d) and winter (8 fish/d). Overall, when the ROs were open, RO efficiency (RO passage divided by total project passage) was 0.004. In linear regression analyses, daily fish passage (turbines and ROs combined) for smolt-size fish was significantly related to project discharge (P<0.001). This relationship was positive, but there was no relationship between total project passage and forebay elevation (P=0.48) or forebay elevation delta, i.e., day-to-day change in forebay elevation (P=0.16). In multiple regression analyses, a relatively parsimonious model was selected that predicted the observed data well. The multiple regression model indicates a positive trend between expected daily fish passage and each of the three variables in the model-Julian day, log(discharge), and log(abs(forebay delta)); i.e., as any of the environmental variables increase, expected daily fish passage increases. For vertical distribution of fish at the face of the dam, fish were surface-oriented with 62%-80% occurring above 10 m deep. The highest percentage of fish (30%-60%) was found between 5-10-m-deep. During spring and summer, mean target strengths for the analysis periods ranged from -44.2 to -42.1 dB. These values are indicative of yearling-sized juvenile salmon. In contrast, mean target strengths in fall and winter were about -49.0 dB, which are representative of subyearling-sized fish. The high-resolution spatial and temporal data reported herein provide detailed information about vertical, horizontal, diel, daily, and seasonal fish passage rates and distributions at LOP from March 2010 through January 2011. This information will support management decisions on design and development of surface passage and collection devices to help restore Chinook salmon populations in the Middle Fork Willamette River watershed above LOP

Surgically Implanted JSATS Micro-Acoustic Transmitters Effects on Juvenile Chinook Salmon and Steelhead Tag Expulsion and Survival, 2010

The purpose of this study was to evaluate survival model assumptions associated with a concurrent study - Acoustic Telemetry Evaluation of Dam Passage Survival and Associated Metrics at John Day, The Dalles, and Bonneville Dams, 2010 by Thomas Carlson and others in 2010 - in which the Juvenile Salmonid Acoustic Telemetry System (JSATS) was used to estimate the survival of yearling and subyearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) migrating through the Federal Columbia River Power System (FCRPS). The micro-acoustic transmitter used in these studies is the smallest acoustic transmitter model to date (12 mm long x 5 mm wide x 4 mm high, and weighing 0.43 g in air). This study and the 2010 study by Carlson and others were conducted by researchers from the Pacific Northwest National Laboratory and the University of Washington for the U.S. Army Corps of Engineers, Portland District, to meet requirements set forth by the 2008 FCRPS Biological Opinion. In 2010, we compared survival, tag burden, and tag expulsion in five spring groups of yearling Chinook salmon (YCH) and steelhead (STH) and five summer groups of subyearling Chinook salmon (SYC) to evaluate survival model assumptions described in the concurrent study. Each tagging group consisted of approximately 120 fish/species, which were collected and implanted on a weekly basis, yielding approximately 600 fish total/species. YCH and STH were collected and implanted from late April to late May (5 weeks) and SYC were collected and implanted from mid-June to mid-July (5 weeks) at the John Day Dam Smolt Monitoring Facility. The fish were collected once a week, separated by species, and assigned to one of three treatment groups: (1) Control (no surgical treatment), (2) Sham (surgical implantation of only a passive integrated transponder [PIT] tag), and (3) Tagged (surgical implantation of JSATS micro-acoustic transmitter [AT] and PIT tags). The test fish were held for 30 days in indoor circular tanks at the Bonneville Dam Juvenile Monitoring Facility. Overall mortality ranged weekly from 45 to 72% for YCH, 55 to 83% for STH, and 56 to 84% for SYC. The high background mortality in all groups and species made it difficult to discern tag effects. However, for YCH, STH, and SYC, the Tagged treatment groups had the highest overall mean mortality - 62%, 79%, and 76%, respectively. Fungal infections were found on 35% of all fish. Mean tag burden for the Tagged treatment group was relatively low for YCH (1.7%) and moderate for SYC (4.2%), while STH had a very low mean tag burden (0.7%). Tag burden was significantly higher in the Tagged treatment group for all species when compared to the Sham treatment group because of the presence of two tags. Surgeon performance did not contribute to the difference in mortality between the Sham and Tagged treatment groups. Tag expulsion from fish that survived to the end of the 30-day experiment was low but occurred in all species, with only two PIT tags and one AT lost, one tag per species. The high background mortality in this experiment was not limited to a treatment, temperature, or month. The decreased number of surviving fish influenced our experimental results and thus analyses. For future research, we recommend that a more natural exposure to monitor tag effects and other factors, such as swimming ability and predator avoidance, be considered to determine the effects of AT- and PIT- implantation on fishes

Habitable Zones in the Universe

Habitability varies dramatically with location and time in the universe. This was recognized centuries ago, but it was only in the last few decades that astronomers began to systematize the study of habitability. The introduction of the concept of the habitable zone was key to progress in this area. The habitable zone concept was first applied to the space around a star, now called the Circumstellar Habitable Zone. Recently, other, vastly broader, habitable zones have been proposed. We review the historical development of the concept of habitable zones and the present state of the research. We also suggest ways to make progress on each of the habitable zones and to unify them into a single concept encompassing the entire universe.Comment: 71 pages, 3 figures, 1 table; to be published in Origins of Life and Evolution of Biospheres; table slightly revise

Survival and Passage of Juvenile Chinook Salmon and Steelhead Passing through Bonneville Dam, 2010

Pacific Northwest National Laboratory (PNNL) and subcontractors conducted an acoustic-telemetry study of juvenile salmonid fish passage and survival at Bonneville Dam in 2010. The study was conducted to assess the readiness of the monitoring system for official compliance studies under the 2008 Biological Opinion and Fish Accords and to assess performance measures including route-specific fish passage proportions, travel times, and survival based upon a single-release model. This also was the last year of evaluation of effects of a behavioral guidance device installed in the Powerhouse 2 forebay. The study relied on releases of live Juvenile Salmon Acoustic Telemetry System tagged smolts in the Columbia River and used acoustic telemetry to evaluate the approach, passage, and survival of passing juvenile salmon. This study supports the U.S. Army Corps of Engineers continual effort to improve conditions for juvenile anadromous fish passing through Columbia River dams