Jeffrey W. Adams

6 May

Epibenthic fauna have been enumerated for the mitigation (study) transect. The control transect remains to be analyzed. Great variability was found between replicates of each intertidal elevation. The number of individuals of certain species also appear to change rapidly with changes in elevation. These observations suggest that averaging single samples from different depths within a tidal range, a method used in previous sampling, will not adequately represent the epibenthic assemblage. Even so, after the reamaining data are collected, attempts will be made to draw comparisons between the 1996 data and data from previous studies.

10 April

A total of 63 samples were successfully collected from Diagonal Way restoration site on April 4 and 5th, 30 samples from the mitigation transect; another 30 from the control transect; and 3 from a recently installed intertidal bench located a few meters south of the control transect. A preliminary examination of one sample revealed numerous Oligochaetes, harpacticoid copepods, and gammerid amphipods.

Jeffrey Lawrence Annis

6 June

All data have been processed and the results presented here.

19 April

All (DGPS) files have been converted from ASPEN format to ASCII. I decided to work with ASCII format instead of ARC_VIEW. Now, all files must be merged into arrays of [time, latitude, longitude, salinity] using time as the index.

17 April

These past weeks have been spent manipulating data files. All wind vector data have been collected. I still need to convert the (DGPS) data into ASCII and merge them with the track salinity data. Several graphics programs are being written using IDL to accept and display the data when it is finished being processed. Also, I am working on plotting Elliott Bay's bathymetry from files stored on compact discs. The profile data have been previewed and are waiting to be merged with (DGPS) files. The (DGPS) files that are so crucial need to be converted from ASPEN format into ARC_VIEW format before I can read them into ASCII files. Once this is accomplished (hopefully soon), I shall match the time indexes from all files and create individual files according to track number. Once all data are in ASCII form, I can begin the data visualization phase of the project.

Sean R. Avent

22 April

After counting a number of paired samples, the difference in between the net tows and the pumping samples is insignificant. The counting of samples is progressing. CTD data are being coverted from the recorded hex formats to binary data for use in spreadsheet and plotting programs.

15 April

Counting has begun on the samples, with the paired net tow/pump samples as a priority for assessing the evasion of the copepods from the pump. If the preliminary results show a constant decreased density in the pump samples, then further pump-evasion experiments will be conducted using known densities of E. americana in large (200+ L) fish boxes.

Pump samples are being fully counted without subsampling, while the net tow samples are being subsampled three times, with each subsample containing 3 percent of the total sample. Preliminary counts in marine-layered, copepod-dense areas are running from 1 to 4 E. americana m. In surface layers densities are very low (<1 E. americana m).

10 April

Over 60 samples were collected with success by means of both pump and net tow. Nine stations, each 1 km apart, were sampled from upstream of the saltwedge (upstream of the Boeing Bridge) to almost a full saltwater column (downstream of the 1st Ave. Bridge). The net tows were completed in order to assess the ability of the pump to numerically collect the copepods without severe evasion. In the Eularian mode, six sampling cycles of three different depths each and a CTD cast were made each half hour for a total of 18 samples.

Aaron Bird Bear

1 May

Initial analysis of CTD and current meter data has been completed using Seasoft 4.216 software. Time series cross-sections of the Duwamish River two-layer system are being formed from the data. The next step will be calculating flow through the cross-section based on the current meter data.

Judith A. Boughner

16 April

There were 21 hand auger cores extracted from the project sight. The samples were documented in detail with special attention being paid to the depth of the boundary between the upper unit of medium-grained sand and the underlying relict estuarine clay deposit. A second-order geodetic survey was conducted of an east-west transect on Terminal 107. First order calculations show that there is a 4.2m displacement between the top of the tidal flat deposit and modern mean lower low water.

Andrew Cookson

6 May

Due to circumstances beyond my control, King County Sheriff's Department helicopter pilots were unable to fly during the period of data collection. During the week of April 1 to 5, and for the month of March as well, they were assigned to another unit and were required to be on standby at their base at all times. Thus they were unable to make any flights or video tapes of images from the helicopter thermal imager.

Metro has shown interest in using this method on a continuing basis to monitor the Duwamish River fresh water plume. I hope there may still be some development of this idea in the future. I have moved on to another project, developing a method to quantify the contribution to mixing in Elliott Bay by ferry traffic. Look for the new project summary on the summary web page.

Holly Dail

22 April

Thanks to Jeff Annis and help from Metro, all location files are now available. Maps of Metro sample locations have also been obtained, along with sediment size and contaminant data, thanks to Craig Homan. The next step is to combine files from the CTD, which also contain transmissometer records, with the location files and velocity data. I shall also be spending time preparing to present a paper at The Pacific Estuarine Research Society 1996 Annual Meeting on May 2-4.

5 April

All data collection complete, and all necessary files ready for processing. Using an equipment package consisting of transmissometer, Seacat CTD, and an Aanderaa current meter, 30 profiles were collected throughout the Diagonal Way region. Profiles were taken from the surface to the river bottom; the equipment package was held for 30 seconds at each 1/2 meter interval to allow a consistent reading from the current meter. A 12-hour time series was collected just outside of the Diagonal Way CSO using a tripod consisting of transmissometer, Seacat CTD, and EG&G current meter. Profiles were collected on April 1 and 3, the tripod data on April 4.

Michael Hutnak

22 April

Analysis of seismic reflection profiling data indicates the presence of turbidity current levee deposits within the sea-valley system of Elliott Bay. Four piston cores are currently being analyzed for magnetic susceptibility, and preliminary data suggest repetitive tubidity flows during the recent past. Preliminary paleobathymetic analysis for the time period 1927 to 1983 suggests a general pattern of erosion on the eastern marginal slopes of the bay, and deposition on the western slopes.

Amanda Worthington Jones

30 April

Approximately 2400 copepods have been sorted and analyzed for trace metals. Preliminary results indicate that these animals do retain some trace metals, e.g., cadmium and copper, and I am in the process of determining if the copepods are transporting the metals out of the estuary.

Elaina M. Jorgensen

2 May

The 1 m^2 screen size did not work; the frame broke under the weight of the sample. Instead I used a 25 cm^2 frame which was much more stable and much easier to handle. The smaller screen size, however, required multiple dippings to fill the sampling bottles.

22 April

I am busy counting bacteria. No data have been analyzed yet. I should be finishing up the bacteria counts today. I shall start my metal analysis tomorrow. The metal analysis is going to take much longer than I had anticipated, so the number of samples to be analyzed has been cut back from six sites in each bay to three sites in each bay. One important note: acid melts Nitex screen. This became a rather embarrassing moment when we were out on the cruise in Elliott Bay, and the sampler melted. However, after a quick trip to Research Nets Inc., the problem was solved.

Jennifer Lenaghan

8 May

Four sediment cores were taken from Elliott Bay. Magnetic susceptibility was determined on all cores. Two cores are being analyzed: one from the west-sloping ridge in central Elliott Bay and one from the north shore of the bay, immediately southeast of the Denny Way CSO. Pb-210 dating analysis has begun on the Denny Way core. The results have not yet been determined. The metal analysis has been taking more time because I am working the methods out myself (with guidance of Dr. Glen Shen). In addition to mercury (Hg), levels of lead (Pb), silver (Ag), and arsenic (As) will be determined. Sediment will be partially digested in concentrated hydrogen peroxide for 2 days to release organically bonded metals. This digestion takes place in an open system to release gas produced by the oxidizing reactions and at room temperature to prevent the release of mercury (a volatile element) into the gaseous phase. The second partial digestion uses nitric acid in a closed system, overnight, to release metals bound in iron (Fe) and manganese (Mn) oxides, as well as those adsorbed onto mineral surfaces. Preliminary results show that mercury is predominantly in the organic phase, while the other metals are bonded to both oxides and organics.

Anna Carina Liljevik

16 April

Approximately 800 copepods have been transferred into glass beakers and are being kept alive at 9 degrees C in 26 ppt salinity water. I am feeding the copepods phytoplankton 3 times per week. Last week I did a protein assay to determine how much protein I could extract from 10 copepods. I was hoping to analyse their protein composition, but the amount of protein extracted proved to be insufficient for protein analysis. I decided to increase the number to 25 copepods and tried a number of methods to increase the protein yield. This time the protein yield was still low, but I decided to run a gel anyway. The proteins were separated into soluble and insoluble proteins. Even though the protein bands turned out very faint, it was possible to detect a unique protein composition in the soluble versus insoluble proteins.

Since time and copepods are limited, I need to move on. This week I plan to start the survival experiment, in which I will be exposing the copepods to different salinities and monitoring their survival for a period of seven days. Protein analysis has not been ruled out entirely. If time permits I will be interested in looking at the protein composition of any survivors.

Eric Maddox

30 April

I'm currently working on producing bathymetry profiles of the study area for comparison to bathymetry data gathered in 1993 and in 1935. Comparison of seismic reflection data from 1993 and 1996 suggests there might be some bathymetry changes since 1993. The difference is probably due to the differences in orientation of the seismic reflection track lines and the differences in speed at which the data were gathered, but I'm going to compare bathymetry data to be sure. The 1996 bathymetry data will be compared to the 1935 data to determine the extent of bathymetry changes due to dumping or slide activity, if any.

22 April

The cores were described and analyzed for magnetic susceptibility and shear strength. These tests and the initial description of sediment characteristics of cores both on the fan and the slope correlated nicely. The tests on the slope cores indicate the presence of dredge spoils (sand and sandy-silt) over the natural sedimentation (silt). The core in the fan showed no evidence of dredge spoils and had similar sediment characteristics and magnetic susceptibility to the lower sections of cores taken on the slope. The core in the disposal site showed graded bedding typical of dredge spoils. In one of the upper-slope cores, below the dredge spoil layers, was a thin layer of shell debris and rounded pebbles characteristic of a shallow-water environment. The presence of shallow- water sediment in a core taken at a depth of 151 m indicates slide activity has occurred in the past

.

17 April

Initial seismic reflection data showed no evidence of slope failure at the disposal site. Five 8 ft. piston cores were collected; one on the disposal site and four along a line perpendicular to the slope contours approximately 500 meters west of the disposal site. The first of the cores outside the disposal site was taken on the lower slope near the base, the second was taken on the Duwamish Fan at the base of the slope, and the last two were taken on the slope northwest of the disposal site. In core 1 of the upper-slope cores, the top 3 centimeters were silty sand over liquid silty clay. This liquid silty clay layer was typical of the top layer of the other four cores. This might indicate small-scale sliding on the upper slope.

Sean Steen

6 May

Analysis of all ICP-MS data is now complete and Kds have been calculated. The raw data obtained from the ICP-MS filled 28,334 spreadsheet lines. Fortunately, macros exist. Nevertheless, the condensation of the raw data into a manageable 12 page / 30 chart summary has taken me three weeks. Programs used: Excel, DeltaGraph Pro, and Mathcad. Due to time limitations, it was decided to narrow the scope of this project yet again: Ag, Cd, and Pb only will be the focal metals. Courtesy of K. Krogslund, laboratory analysis of salinity and nutrient samples (taken concurrently with the trace metal samples) has been completed.

17 April

ICP-MS analysis of particulate samples (15) completed.

9 April

All water samples were analyzed by ICP-MS with profound assistance from graduate student Thomas Chapin. We had difficulties with calibration and finally had to use 3 different calibration curves; high salinity, low salinity, and fresh water. At first glance, manganese concentrations were very high (high micro- to low milli-molar, which usually overloaded the detector), and lead and cadmium concentrations were higher than values reported by the King County WPCD (Metro). The fresh water samples were also analyzed without the preconcentration and salt removal technique used for all brackish and salt water samples. Particulate fraction samples are scheduled to be analyzed by ICP-MS Wednesday, April 17. Now, data analysis and interpretation will commence.

2 April

A series of 5 sample sites (CTD-measured salinities of approx. 2, 4, 8, 14, and 27) were chosen along the river's axis. At each site, a CTD depth salinity profile, 30L of water from an approx. depth of 1 meter, and samples for laboratory salinity and nutrient analysis were obtained. Each 30L water sample was pressure filtered immediately through 0.2 and 1.0 micron nucleopore filters, and these, plus an unfiltered sample, were acidified. The failure of an O-ring forced us to abandon the collection of samples intended for laboratory ultra-filtration, so that my project will NOT include any colloidal fraction partitioning information. . . (sigh).

1 April

Fresh-water end-member samples collected about 1 kilometer above the Turning Basin (definitely past the salt wedge). Acidified but unfiltered water returned to lab and filtered through 0.4 and 1.0 micron nucleopore filters. Samples for laboratory salinity and nutrient analysis obtained.

Crystal Thimsen

6 May

I am starting the metal and carbon analysis. The samples will initially be digested with 30% hydrogen peroxide and that will be followed by a digestion with nitric acid. These sequential digestions will give me some idea about the quantity of metals sorbed to the organics in the sediment. I shall concentrate on three metals: cadmium, silver, and lead; these are the same metals that Sean Steen is concentrating on in the water column. I have decided not to do the surface area analysis.

23 April

Three samples were chosen for analysis. One is past the turning basin, one is half way between Elliott Bay and the turning basin, and one is in the West Waterway. The samples are currently being separated using the SPLITT, and will be analyzed for metals and organic carbon next week.

Suzanne Thomas

7 May

I shall not be able to do the Toxicant study for this class but shall be doing that on my own time. I feel that the project will not be entirely rewritten by the end of the quarter, but I shall submit what I have at that time and complete the rest during the summer on my own time. I have been having a lot of problems lately with allocating variables onto the stacks of memory in the computer. For some reason I am getting stack overflow errors as well as floating point errors, which means my numbers are increasing exponentially to greater than 3.4 x 10^34 or 10^-34. So there is a logic error somewhere, or the memory is grabbing the wrong memory locations and giving me odd numbers. To give you an idea on what this program is doing, the output file alone for only one day of data is 230 pages. The program code is now 16 pages long and a lot is left to add.

19 April

Well, I have got the majority of the program rewritten! There are seven more functions left to do! I have run into some problem with using the C compilers math library. For some reason it is not recognizing the sqrt() and exp() functions. If anybody has any ideas, why please share. I should be starting the toxicant model within the next couple of weeks.

15 April

I have been trying to get the old numerical model running. The problem with this model is that it was written on a punch card system in FORTRAN. Due to my limited knowledge of FORTRAN and the lack of a debugger for FORTRAN I am resigned to the fact that I must rewrite this program in a new language. I have decided to rewrite it in the language of ANSI C. This language is standardized and I have access to all the compilers and debuggers that I will need in finishing this project. I have almost finished rewriting the original program. Within the next week I should be adding my part of the model, which is a toxicant study. Hopefully, everything will be up and running within the next couple of weeks. If so, I hope to add some graphical analysis to the program. I will let you know soon if this will happen or not.

Jamie A. Zyskowski

19 April

Bacterial growth rates appear to be very low throughout the water column. Also, the influence of phytoplankton (based on chlorophyll-a measurements) is more important than first suspected.