A Lab Notebook

 
A new model?
I just skimmed over a paper by Li et al. [2001]. Offhand, I am curious if I can couple the model of Li et al. [2004] with Jackson's [2001] model? Li predict the slope of the PSD while Jackson predicts the carbon flux. Coupling the models would allow for optical determination of particualte carbon flux? Maybe, but I need to to read the Li paper closely and see if the two models can be brought together.
- posted by alex @ 23:48 0 comments

 
Boats and thoughts
Today, Liz instructed Donglai and I how to deploy a glider (an Autonomous Underwater Vehicle -AUV- buoyancy driven robots used to observe water properties and characteristics along a transect over a period of time ranging from days to weeks) from a boat in moderate seas. We deployed one of the COOL gliders from the RV Arabella off the coast of Tuckerton, NJ. As I am writing this, my desk feels as though it is still rocking back and forth ever so slightly. Both Donglai and I threw up once each. All in all, we were both stoked to finally see a glider launched, in person, after having heard about and studied the robots for a a few weeks. A few thoughts I needed to spit out about the paper I read earlier today (the actual paper notes are the previous post).
I think the last paragraph of the Kiørboe and Hansen [1993] paper gets towards the heart of my thesis. Basically, the coagulation models of Jackson [1990] and others rely on cell-cell stickiness. This however may severely underestimate overall coagulation and subsequent surface export flux if the colloidal or more loosely bound exudates allow for flocculation of materials that do not come into contact with cell. If this is the case, species with higher growth rates may hit more bloom/bust cycles more often than species with slower growth rates. If the the colloidal exudates are more readily released during the stationary phase, then the high growth rate species (although not necessarily as sticky during the growth phase) may actually cause a higher rate of export from the surface when compared to slower growth rate species. One of the goals of my thesis work is to try to decipher a) the origin of stickiness affecting particulates in the ocean and b) the relative importance of the different coagulation/flocculation mechanisms through models/experiments.
- posted by alex @ 17:56 0 comments

 
Ki%F8rboe & Hansen [1993]
Kiørboe and Hansen [1993] did not find any relationship between the age (growth phase) of batch cultures and cell stickiness (5 diatoms and 2 dinoflagellates). Their method of stickiness prameterization utilized a traditional couette device with shear rates near 10/s. They observed S. costatum to have an alpha between 0.036 and 0.049.5. They observed 2 types of sticking; cell-cell (as in S. costatum) and TEP-cell (as in C. affinis). S. costatum also produced an exudate that reduced the apparent stickiness of the culture. They also cleaned S. costatum cells by washig three times by centrifugation and resuspension in filtered seawater. Centrifugation did not have an affect on the cells. T. weissflogii was was not sticky and did not form aggregates in their cultures. This is the resaon I chose T. weissflogii as my non-sticky algal cell in my first flume experiment. Coscinodiscus is a profligate mucus producer.
They also note from this paper and an earlier paper, the apparent relationship between cell concentration and stickiness. This relationship may indicate some sort of repulsive solute or a stickiness inhibitor released by cells at high concentrations. However, they tested for a stickiness inhibtor and could not find strong evidence of the presence of such an exudate.
Additonally, the hypothesis of two different exudates released by plankton is explored. Based on Dechos 1990 review, a capsular mucus is released during exponential growth of diatoms while a colloidal or more loosely bound (to the cell) mucus is released by diatoms during the stationary phase. Kiørboe and Hansen further hypothesized that only the capsular mucus (the one stained by alcian blue - side note: Alcian Blue staining is specific to mucopolysaccharides with carboxyl groups) causes cell-cell aggregation. However the loose exudates may be responsible for flocculation beyond the interaction of cells.
- posted by alex @ 17:55 0 comments

 
Rubisco and photorespiration
Some incoherent thoughts on the potential role of Rubisco in the physiological model of phytoplankton exudation. Rubisco groups and propensity to aggregate? During photorespiration rubisco is used to hydrolize phosphoglycate into Pi and glycate. This may occur in order to generate Pi for consumption (under P limitation). The glycolate is either further consumed for biomass synthesis or is excreted.
- posted by alex @ 18:42 0 comments

 
Alldredge, 1993
Alldredge et al. [1993] provided the first pretty cool pics of TEP stained by Alcian Blue. Additionally, they found 24-68% of the bacteria in the samples to be entrained within TEP which only became evident after staining. Furthermore, only 5% of the bacteria in their samples we free-floating. EDTA used to break flocs apart which identified cation bridging as one of the main adhesive forces of TEP. They cite Gordon[1970] and Emery et al. [1984] as the early pioneers of the TEP explorations. TEP most abundant during Diatom blooms although all plankton secrete polysaccharides. They also cite the following papers as having documented the process of exoplymer/colloid formation in freshwater (Leppard et al. [1977], Massalski and Leppard [1979] ).
- posted by alex @ 18:33 0 comments

 
Ernst, 2000
These notes and thoguhts arose form the reading of Ernst et al. [2000] Carbohydrates in Biochemistry and Biology.
Can polysialic acid (PSA) be used to test S.costatum as a physiological or morphological coagulator? PSA is used to for repulsive carbo-carbo interaction (pp1073). Repulsion is due to either pure ionic repulsion or due to physical hinderance as a result of the large hydration volume of thed polymer. Hyaluronon (HA) may also function in the same capacity as PSA.
Molecular interaction involving carbohydrates tend to be weak. Polyvalence is very important for carbohydrate-carbohydrate interactions. Beyond structural arrangements, carbohydrate-carbohydrate models of cellular interaction can be controlled by various means of polyvalence; surface density of presented structures, ionic strength for modulating attractive and repulsive forces, changes in biosynthesis of carbohydrate sequences.
- posted by alex @ 18:01 0 comments

 
More Testing
Being the scientist that I am. This is another test.
- posted by alex @ 00:34 0 comments

 
New Web Page
In a few days I will hopefully have anew web page up on one of the IMCS servers. More to follow...


dromeas
- posted by alex @ 00:19 0 comments