Lab Blab #8
Our rainbow of Fumigation extraction samples rested overnight in their little Erlenmeyer flasks under the exhaust hood. The next day came the arduous task of pipetting 10 ml of clear solution from each one, to be read in the spectrophotometer at 600 nanometers. This is not an easy task! Forest soils are filled with debris and ‘floaters’, like little bits of humus. Jay wanted to do the pipettework, so I read the spectrophotometer and recorded the data. Dr. Bill was so interested in the results - intently studying the data sheets, comparing weights and spectral assessments. He encouraged Jay to be patient, and praised his work. At last Jay finished the tough stuff in record time, and off we flew to study for our final exams. Did I say that Jay tutors calculus? On Monday, Dr. Bill had already looked into the idea of filtering samples and had worked on correlations in the data. Thank goodness he knows what he is doing. It is one thing to work hands on, but analysis and statistics are so complex. Oh, well – that will be Spring Quarter. Thanks for listening. Now that we’re starting a new quarter, Dr. Bill will be researching DNA cloning in soil microbes. That will be most interesting. I can’t wait.
Monday, December 10, 2007
Lab Blab #7
Lab Blab #7
The next day Jay and I came in to find that Dr. Bill had repeatedly exhausted the Fumigation box with fresh air to draw all the chloroform gas from the samples and the exhaust hood. We lifted the glass, arranged all in complete order for weighing. Now we would incorporate our control group into the picture. One-half of the 68 samples had been fumigated, and one-half was held for comparison without the lysing of the cells to release the organic Carbon. Everything we did from now on must be performed exactly the same, on both sets of samples. We weighed out small amounts of each sample, arranged them in the hood, and began adding reagents that turned our samples a spectrum of colors from aquamarine, to deep green, and brilliant shades of orange. A series of glucose-based standards were prepared, ranging from 0, 100 and up to 800 ul/g of glucose in solution. The colors and optical density would be indicators of the presence and concentration of organic Carbon. Now we have to perform careful extractions from our samples. Stay tuned for more…
The next day Jay and I came in to find that Dr. Bill had repeatedly exhausted the Fumigation box with fresh air to draw all the chloroform gas from the samples and the exhaust hood. We lifted the glass, arranged all in complete order for weighing. Now we would incorporate our control group into the picture. One-half of the 68 samples had been fumigated, and one-half was held for comparison without the lysing of the cells to release the organic Carbon. Everything we did from now on must be performed exactly the same, on both sets of samples. We weighed out small amounts of each sample, arranged them in the hood, and began adding reagents that turned our samples a spectrum of colors from aquamarine, to deep green, and brilliant shades of orange. A series of glucose-based standards were prepared, ranging from 0, 100 and up to 800 ul/g of glucose in solution. The colors and optical density would be indicators of the presence and concentration of organic Carbon. Now we have to perform careful extractions from our samples. Stay tuned for more…
Great Lab Partner
Lab Blab #4
When Jay and I first reported for our REU – Research Experience for Undergrads: I just thanked my Lucky Stars. I have grown sons and appreciate truly interested young people. Jay has a quiet exuberance about him. What a great sense of cooperation and willingness to tend carefully to our work! He is so much fun! We bailed all the soil samples out of the deep freeze, sorted them into groups by ecosystem and then by numbers identifying survey transect points along the Elwha River. Our hands were tired by the time we had 68 containers and lids perfectly labeled. We started all over the next day, weighing out samples, checking and rechecking labels, numbers, and weights. We really wanted to get it right; recording everything on each container and the data sheets.
Now we were ready to follow Dr. Bill’s advise on the FE Method for Carbon Assessment! Stay tuned! The excitement has just begun!
When Jay and I first reported for our REU – Research Experience for Undergrads: I just thanked my Lucky Stars. I have grown sons and appreciate truly interested young people. Jay has a quiet exuberance about him. What a great sense of cooperation and willingness to tend carefully to our work! He is so much fun! We bailed all the soil samples out of the deep freeze, sorted them into groups by ecosystem and then by numbers identifying survey transect points along the Elwha River. Our hands were tired by the time we had 68 containers and lids perfectly labeled. We started all over the next day, weighing out samples, checking and rechecking labels, numbers, and weights. We really wanted to get it right; recording everything on each container and the data sheets.
Now we were ready to follow Dr. Bill’s advise on the FE Method for Carbon Assessment! Stay tuned! The excitement has just begun!
Lab Blab #3
Lab Blab #3
TOC – Total Organic Carbon is just one index used to assess how healthful a microbial community may be. The focus of Dr. Bill’s research is on soil microbial activity. In delving through pertinent journals – I learned that global warming has an impact on all ecosystems on our Earth – even those underground. As per Moscatelli, (2005) bioindicators measure metabolic responses of microbial communities to alterations in climate. And any disturbance or stressor will be reflected in the metabolic activities of the community. An effective way to study this problem is through the use of several methods of measuring Carbon. TOC compares the relation of C(microbial biomass) to C(soil organic). qCO2 compares community basal respiration to C(microbial biomass). Combined with pH, water availability , exposure to the FACE Method-(Free Atmospheric CO2 Exposure)-(Anderson, 1997), qM (organic carbon in humus), and available Nitrogen, one may gain an accurate assessment of microbial activity. Has the ecosystem been affected by disturbance? Is it in a state of recovery, or basking in Homeostatic balance? Stay tuned for an interesting lab experience!!
TOC – Total Organic Carbon is just one index used to assess how healthful a microbial community may be. The focus of Dr. Bill’s research is on soil microbial activity. In delving through pertinent journals – I learned that global warming has an impact on all ecosystems on our Earth – even those underground. As per Moscatelli, (2005) bioindicators measure metabolic responses of microbial communities to alterations in climate. And any disturbance or stressor will be reflected in the metabolic activities of the community. An effective way to study this problem is through the use of several methods of measuring Carbon. TOC compares the relation of C(microbial biomass) to C(soil organic). qCO2 compares community basal respiration to C(microbial biomass). Combined with pH, water availability , exposure to the FACE Method-(Free Atmospheric CO2 Exposure)-(Anderson, 1997), qM (organic carbon in humus), and available Nitrogen, one may gain an accurate assessment of microbial activity. Has the ecosystem been affected by disturbance? Is it in a state of recovery, or basking in Homeostatic balance? Stay tuned for an interesting lab experience!!
TOC: Totally Outrageous Carbon
Lab Blab #2
Total Organic Carbon may sound like a foreign concept, but it is based on filling the basic needs of microorganisms. Just as all primary, secondary and tertiary consumers need food as a source of nutrients and energy, so do microbes. As our primary producers, microbes utilize organic molecules in their processes of respiration, reproduction and growth. Carbon, Hydrogen and Oxygen are their primary sources of fuel. These molecules are broken up into free molecules, through the process of catalyzation. A process that releases energy with the breaking of molecular bonds, and provides these basic elements in a form usable at the cellular level. Inorganic Carbon is an end product released as atmospheric CO2, while organic Carbon is used to build cell wall structure (i.e. growth). A healthy community of microbes will have high levels of Total Organic Carbon within its population of (consuming, growing, reproducing and expiring) members. Communities under duress from disturbances of their environment, or a new colony will use more organic Carbon as an energy source, just to maintain and stay alive. There is less organic C sequestered in their cell growth and reproduction of new generations of microbes. This is reflected in a much lower index of Total Organic Carbon (TOC). Stay tuned for the ways that we measure TOC!!
http://answers.yahoo.com/question/index?qid=20061202112639AAFnzGj
Total Organic Carbon may sound like a foreign concept, but it is based on filling the basic needs of microorganisms. Just as all primary, secondary and tertiary consumers need food as a source of nutrients and energy, so do microbes. As our primary producers, microbes utilize organic molecules in their processes of respiration, reproduction and growth. Carbon, Hydrogen and Oxygen are their primary sources of fuel. These molecules are broken up into free molecules, through the process of catalyzation. A process that releases energy with the breaking of molecular bonds, and provides these basic elements in a form usable at the cellular level. Inorganic Carbon is an end product released as atmospheric CO2, while organic Carbon is used to build cell wall structure (i.e. growth). A healthy community of microbes will have high levels of Total Organic Carbon within its population of (consuming, growing, reproducing and expiring) members. Communities under duress from disturbances of their environment, or a new colony will use more organic Carbon as an energy source, just to maintain and stay alive. There is less organic C sequestered in their cell growth and reproduction of new generations of microbes. This is reflected in a much lower index of Total Organic Carbon (TOC). Stay tuned for the ways that we measure TOC!!
http://answers.yahoo.com/question/index?qid=20061202112639AAFnzGj
Insightful Lab Blabs
#1 Insightful Lab Blabs:
It has taken weeks to comprehend the depth of my new REU assignment. This Summer '07 was spent on the Nearshore Project - a most interesting experience surveying fish populations in wilderness rivers and adjoining coastal waters, while working with students whom added so much fun and commitment.
Now the focus of my REU experience is in the laboratory, preparing soil samples with Jay, for Dr. Bill Eaton. Starting the work was pretty straightforward, after working at the NOAA/NMFS Lab in Saunderstown, Rhode Island, but the theory behind the work seemed too complex to grasp. Dr. Bill gave us an extended lecture on the use of Organic Carbon by soil microbials, and how different methods of assessment measure the amont of stress, and functioning abilities of these microbes, as they strive for growth and homeostatic balance. Organic Carbon may be used as an energy source (which requires ATP) for respiration in response to ecosystem disturbance (stress), or be sequestered into microbial biomass in the form of tissue growth in more steady-state enviornments. It is the way Carbon is utilized in these assessments in relation to additional parameters, which show if the microbial community is in Recovery from stressors of flooding, sediment starvation, avalance, fire, drought, exposure to toxic waste, etc. Dr, Bill is looking at soil communities on the Elwha River - specifically above, between and below the Upper and Lower Elwha River Dams. Samples also reflect various ecosystems existing as one moves away from the river's edge. Now that my annotated bibliography assignment is complete (which was met with great trepidation!) the theory behind Dr. Bill's madness seems sensible and straightforward. Thank you, Dwight Barry! Working on this new experience has opened a new and interesting world for me. Stay tuned for more!!
It has taken weeks to comprehend the depth of my new REU assignment. This Summer '07 was spent on the Nearshore Project - a most interesting experience surveying fish populations in wilderness rivers and adjoining coastal waters, while working with students whom added so much fun and commitment.
Now the focus of my REU experience is in the laboratory, preparing soil samples with Jay, for Dr. Bill Eaton. Starting the work was pretty straightforward, after working at the NOAA/NMFS Lab in Saunderstown, Rhode Island, but the theory behind the work seemed too complex to grasp. Dr. Bill gave us an extended lecture on the use of Organic Carbon by soil microbials, and how different methods of assessment measure the amont of stress, and functioning abilities of these microbes, as they strive for growth and homeostatic balance. Organic Carbon may be used as an energy source (which requires ATP) for respiration in response to ecosystem disturbance (stress), or be sequestered into microbial biomass in the form of tissue growth in more steady-state enviornments. It is the way Carbon is utilized in these assessments in relation to additional parameters, which show if the microbial community is in Recovery from stressors of flooding, sediment starvation, avalance, fire, drought, exposure to toxic waste, etc. Dr, Bill is looking at soil communities on the Elwha River - specifically above, between and below the Upper and Lower Elwha River Dams. Samples also reflect various ecosystems existing as one moves away from the river's edge. Now that my annotated bibliography assignment is complete (which was met with great trepidation!) the theory behind Dr. Bill's madness seems sensible and straightforward. Thank you, Dwight Barry! Working on this new experience has opened a new and interesting world for me. Stay tuned for more!!
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