A Lab Notebook

 
TA work and more
I spent much of the day being a TA. I am coordinating 26 undergraduates to go out on a ship spread out over four days. Van rentals, preparing of reagents for ship-board measurements, installing software on crappy, old laptops, renting vans etc. Otherwise, I just have some incoherent thoughts about a paper I read the other day, followed by a summary of my run this morning.
Ackleh et al. [1995] estimated stickiness during the 1993 SIGMA tank expereiments using 1) an inverse, least squares methodology 2) an aggregation model 3) individual phytoplankton growth model. Model underpredicted particle densities for larger aggregates (>0.4mm^3) and predicted the peak of the bloom to occur earlier than was observed. They interpret their data to show that aggregation is relatively insensitive to stickiness and as a result it is difficult to estimate stickiness by fitting aggregation data.
I think "efficiency of sticking" is used to describe the strength of the floc after aggregation, while "sticking efficiency" is alpha?
How do they differentiate stickiness and sticking efficiency.
When he visits, ask G. Jackson if he thinks the flumes are more representative of shear (perhaps precluding differential settling?) due to their design (ie. 40 cm water depth)
**Get Reibesell and Wolf Ref. from 1992 DSR**

I ran for about 45 minutes easy this morning. It was misty and around 45F. I came across a young dear carcass in the forest adjacent to the RU campus. It has been a wintry mix all evening so tomorrow's run may be chilly and icy... but we'll see.
- posted by alex @ 22:53 2 comments

 
New S. costatum culture
I waited too long with the S. costatum from the past few weeks. I checked the size distribution of the culture, and there were far too many small cells (indicative of high abundance bacteria). Since I desire low quantities of bacteria, I am starting the whole process over, with more focus on transferring the 1 liter cultures into 20 liter cultures containers when the Fv/Fm is near 0.60
Today I made the Trace Metal solution which will be used for both the 20 liter cultures and the flume runs which should take place in the next 14 days. When the flume experiment starts up this notebook of mine will be very, very active (Zib, Mutz, Stan and Bryan all know what fun my lab work can be as they helped me with my flume run last summer).
Also, today in the lab placed a 5 month old S. costatum culture under a microscope to see what I could see. I'll put up the picture sometime next wseek, but the results were very cool. I cam away with a 3D-like image of the surface of a phytoplankton mat. The phytoplankton mat is the result of a bunch of marine snow that fell to the bottom of the flask over time.
I took yesterday off from running, and did about 5 miles in Central Park with Zib this morning. We ran about 50 minutes at an easy pace in the cool sunny morning of early spring. Unfortunately, I think we may get some snow tomorrow or the day after, so the next few runs will be pretty chilly.
- posted by alex @ 21:35 1 comments

 
Running only post
Yesterday Elizabeth and I decided to be adventurous and run in van Cortlandt park in the Bronx. This park has a famous x-country series and is where Columbia holds their x-country meets, so I wanted to see what it was like. We took the 4 train (the subway train nearest Elizabeth's house) line to its terminus. All in all, the park has pretty variable terrain with some decent hills that I could see becoming a nightmare in a 5km. We pretty much had the park to ourselves and did a loop that took 1.5 hours. We probably held a 9:30 pace for most of the run, with some mild fartlekking during minutes 45-80. Elizabeth had to fight some running demons about half way through but started kicking ass during the fartlek session.
With Elizabeth off to work, I woke up this morning and decided to go for a long run. I actually wanted to go tomorrow, but a snow storm is expected overnight and for tomorrow, so I had to jump on today's prime weather (mostly sunny with highs approaching 60 by midday). However, I had to run with a pack containing clothing in case the storm or its associated cold front arrived early, plus I had to carry all of my own water and energy bars. Total weight of the pack was probably near 10 pounds at the start of the run, but lost weight due to food and water consumption. I have had this certain run in mind for the past few years and wonder how many folks have done it. I ran from Elizabeth's apartment on E. 96th, over the George Washington Bridge to NJ, and ran in the Palisades Interstate Park (along the Hudson). I wanted to run to the NJ/NY border, but was getting low on bars and water so I turned around at a spot Elizabeth and I normally use as turnaround for our normal 10km run in the park (@ the women's monument about 1.25 miles shy of the border). Total distance = 34.7 miles. Total time = 5:20. Pace = 9:13/mile. The route with distances and terrain: Zib's apartment to RIverside Park (streets and Central Park grass) 1 mile, Riverside Park/West Side Drive to George Washington Bridge (mostly wethered blacktop with some grass) 4.25 miles. GWB to Palisades Park entrance (concrete) 1.55 miles. Park entrance to the Women's Monument along the "Shore Trail" with a 500 foot climb from river bank to the monument (500 foot descent to the river where the terrain is mixed between 30 foot rolling embankments and flat sections of rocks and sand) 10.55 miles. Women's Monument to GWB (gorgeous winding single track through a forest atop a 500 foot cliff overlooking the Hudson River with some pretty significantly steep gullys) 10.55 miles. I ran the rest of the run on the same outgoing route but in the reverse direction.
Coolest part of the run was about 2 blocks from Elizabeth's apartment when an employee from a bakery was outside on a smoking break and yelled, "Yo, you been runing since I saw you go by at 11 this morning?" My stunned reply, "Yeah, it was a nice day, so I figured I would spend some time outdoors." To which he took a drag on his cigarette and said, "Cool, you should come by and get some doughnuts tomorrow." All I could say was "Thanks."
- posted by alex @ 17:31 0 comments

 
Lab Meeting and more
I started my presentation to the lab with what can be considered the equivalent of the kiss of death in our lab. I showed the famous Behrenfeld & Falkowski [1997] image of global oceanic primary production. Primary production is the synthesis of plant material (phytoplankton in this case) from the photosynthetic reactions). What made the presentation of this map of global oceanic primary production so treacherous is that Falkowski can be a bit intimidating, but especially so when the work is his own. Anyways, I survived the meeting, a full hour of standing in front of my closest colleagues answering questions about the data I presented, and graphs I made from compiled datasets published by other scientists in the field. Below are more notes for myself than for other, so much of what is below should make little no sense to anyone else. The bottom of this post contains my running log for yesterday an today.

Exudate is both a sink for organic carbon (not observable by satellites for example), and is a cause of increased export rates (due to aggregation/coagulation) of carbon from the surface ocean
and does contribute to heterotrophic bacterial production. There is positively correlated relationship between photosynthetic rate and extracellular release. Indeed this is the most agreed upon fact of the field of study => fig.4 from Mague et al. [1980], Nalewajko [1976]. However, exudate is not merely a portion of the intact cells' contents based on different %mol (a normalized measure of mass) compositions between extracellular and intracellular material (Mague et al. [1980])
What are considered the main hypotheses for the explanation of exudation? It can best be explained by an imbalance between light intensity and nutrient availability. 1) light saturation + normal nutrient levels 2) sub saturating light + nutrient limitation. Both instances provide too much photosynthate compared to the availability of nutrients for biosynthesis of cellular components. Evidence points to an intracelllular pool of carbohydrates (Henriques Viera & myklstad [1986], Lancelot [1984]) as deduced by the observation of continued exudation for up to 24 hours after no light, and delayed resumption of exudation after the light was turned back on. This also is further evidence of exudation of carbohydrate as a result of active photosynthesis. However, these do not seem to cover all of the observed mechanisms for the induction of exudation (I have this chart from my presentation today) One of the more recently focused upon "triggers" of exudation is atmospheric carbon dioxide concentrations, for obvious global warming implications. The Smith and Wiebe [1976] data contradict that from Engel et al. [2001] where both studies examined the affects of concentration of DIC on exudate production. The quantity of material released by the cell can be quite variable. Original extracellular release rates ranged from 5% - 75% throughout the 1970's (Mague et al. [1980]). The most recent estimates are 20+-1% (Marañon et al [2002]). There are two phases of excretion (Nalewajko et al. [1976), and a Kiørboe 1990's paper] of the photosynthate. The first phase sticks to the cell, while the second phase is released to the medium. Lancelot [1984] found small metabolites (<500d, d = daltons, metabolites are substances produced by metabolism such as sugars are metabolites from carbon fixation) are immediately released and after a lag phase large metabolites are released (>500d). Since larger metabolites are less directly usable by bacteria, and as such, the larger molecules have longer residence times in the medium. This allows them more time to interact with other particles compared to small molecular weight metabolites (Lancelot [1984]). Current hypotheses posit that the large molecular weight material coagulates and aggregates with other similarly sized (and compositionally similar - ie acidic polysaccharides derived from extracellular release) particles. The results of such interactions are not entirely clear but it is assumed that fibrils of size >5kd (Leppard [1995]) are formed. Of the initial molecules to be exuded, galactose is the most prominent monosaccharide. Mannos glucose, xylose and arabinose are all usually but not necessarily present (Henriques Viera and Myklestad [1986]). There is also speculation as to the effect of cellular exudates on reducing settling velocity compared to aggregates or particles without increased extracellular material. This was considered a while ago by Alldredge and Gotschalk [1989] in Santa Barbara who deduced that "differential settling" of diatom chains to be the primary mechanism of aggregate formation. And to throw more shit on any notion of a universal relationship between nutrient stress and exudation, Alldredge and Gotschalk [1989] also observed nitrate replete conditions during floc formation off California coast.

Yesterday, I ran for 40 minutes easy at around 7am. The sun was bright and the air was briskly in the 30s. Perfect shorts and long sleeve shirt weather. I stayed up to the wee hours and rose early on thursday to continue preparations for my presentation. As a result, I ran this evening with Elizabeth in Central Park. Temps were in the 40s and the breeze was light. Zib, felt like ass, and wanted to puke. No puking and a very enjoyable 57 minute jaunt in the park tonight. I can promise a good tale or two will come out of my planned adventures for the next few days.
- posted by alex @ 22:47 2 comments

 
Fv/Fm, S. costatum
Fv/Fm = 0.409
Fm = 1403.0
In addition to measuring the efficiency of photosystem II (Fv/Fm) I also took a pretty picture of my culture. Our lab microscope is equipped with some fancy-pants image acquisition hardware. I used this hardware on the microscope to acquire image below. The first image below shows a chain of three S. costatum cells. The largest of the three cells is probably 10 micrometers in its longest dimension (1000 micrometers = 1 millimeter). The cells are linked together by extracellular structures calleded "processes". The processes are barely visible as slight ripples attaching the corners of each cell to the adjacent cell. The lower two cells are particularly well-focused as one can see the large dark pillow structures within the cell. These large pillows are the chloroplasts. All of the production of the oxygen we breathe occurs within similar structures in all photosynthetic cells of plants.


As mentioned in earlier posts, the frustule, or outermost component of the cell wall of a diatom is made of silicate. Scanning electron microgrpah images of diatoms are pretty spectacular such as this one taken by Dee Breger the manager of the SEM/EDX Facility at Lamont-Doherty Earth Observatory. Dr. Breger super imposed the copyright symbol onto the diatom frustule, otherwise the image is completely real. The barel shaped object with the processes sticking outward is a diatom. The cool looking structure is comprised of silicate (glass). Behind this complex looking glass structure is the more familiar eukaryotic photosynthesizing cell described above This particular image is of an unidenitified tropical species, which resembles our beloved S. costatum to some degree.


As for running, Elizabeth and I went to Montauk this weekend. We explored a dizzying network of trails around some pond for about 50 minutes of easy running on Saturday. On Sunday we decided to run along the beach from our motel towards the Montauk Point lighthouse (approximately 7 miles one way by beach). We made it to within sight of the lighthouse, but the wind started to pick up and we were a bit underdressed. We turned back and jogged/scrambled for 90 minutes into a stiff and brisk headwind along the beach. In all, we jog/scrambled on the beach and rocks for 180 minutes on Sunday. I took Monday off and ran today. My run today had a 20 minute warm up and cool down. The warm up and cool down both occur during the run from my office to a Rutgers owned plot of forest which is about 2.5 miles away. The warm up and cool down are pleasant as most of the time is spent running past livestock and geese (I hate these animals with a passion) residing at some Rutgers operated research farms. I ran 2 loops within the forest at moderate pace. The first loop took 15:33 and the second loop took 14:47. The total run was 63 minutes (the warm up and cool down are actually about 17 minutes in length). The forest is pretty technical and has somewhat variable terrain, which combine to make it one of my favorite places to let loose. The sun was bright, the wind was stiff and brisk on the cool down back to the office, and the temp was a perfect 45.
- posted by alex @ 22:34 1 comments

 
Fv/Fm, S. costatum
Fv/Fm = 0.486
Fm = 1152.8

The culture had a collection of cells resting on the bottom of the flask. Hopefully, I can get an image from the microsope of my S. costatum cells up onto the site before the day is over. Also, I am working on some modeling which I don't feel like recording in the public domain until I gain a bit more progress. Plus Falko asked me to give a presentation at our twice monthly lab meeting next week... we'll see how that goes. Hopefully I can present some of the modeling work I am currently working on.
I checked out the Banff International Film festival last night. Of course this motivated me to run a bit this morning (recieving my new ipod shuffle in the mail last night also helped). I ran the outer loop of Central Park Drive (6.019 miles) plus about 0.3 miles from Zibba's place to the park, this morning. Air temp was 16F when I started with wind chill putting the temp near 5F. Crystal clear andvery few people with some of the orange gates still up in the park. The ipod shuffle worked like a champ. I went moderate on the loop doing an extra bit to round up to 10k distance in 46 minutes. I ran the last half of the loop with an economics prof. (Andrew Atkeson) from UCLA who was in NYC giving talk at Columbia. Apparently he runs on a master's cross country team in LA and ran cross at Yale back in the day. I enjoyed talking while listening to my ipod shuffle in the other ear. The moderate pace of the run seemed to loosen up my muscles and reduce the pain I have been having in my left patella quite a bit.
- posted by alex @ 12:01 2 comments

 
Fv/Fm, S. costatum
Fv/Fm = 0.512
Fm = 1269.8

I put the culture under a microscope to try to see the cells. However, the culture is still not dense enough to make finding the cell very easy. More luck tomorrow I hope.

I didn't run this morning due to a combination of the low teens air temp and some congestion/sore throat problems from the past few days. Perhaps tomorrow.
- posted by alex @ 15:34 1 comments

 
Fv/Fm, S. costatum
Fv/Fm = 0.53
Fm = 438.4



Above is an image of the 1 liter culture of S. costatum on a metal rack with a couple of fluorescent lights in the background. The image was taken a few moments prior to determining the health of the cells (Fv/Fm). As one can see, the culture of happily photosynthesizing cells is not very dense. However, either tomorrow or the day after, the same beaker will be brown/green due to the exponential growth of the culture.
- posted by alex @ 14:13 0 comments

 
Sanford Seminar
Although it was 67 and sunny outside (btw it is now 19 hours after the seminar and it is 32 degrees and snowing heavily here in NJ), I managed to convince myself to attend the Larry Sanford seminar yesterday afternoon. He presented a summary of particle transport dynamics in Chesapeake Bay. He used a LISST (Laser In Situ Scattering and Transmission), ADV (Acoustic Doppler Velocimeter), and a high speed camera to observe settling speeds and measure sediment floc volumes in the Chesapeake. Among the more interesting notes from his lecture was the fact that the sediment load (quantity of sediment suspended in the water) of the Chesapeake has actually declined significantly over the past 100 years. This is due primarily to reforestation in the Chesapeake watershed. Forested lands tend to reduce the amount of sediment runoff into rivers and estuaries while land without vegetation is quite sucseptible to erosion ans subsequent increased river sediment loads. Basically, our forefathers (the founding brothers included) cut down a ton of trees for building/fuel and to clear land for agriculture, during the 18th and 19th centuries. However, as industry moved wetsward, the focus of land use shifted, which in turn allowed for reforestation of the eatsern US forests and clearer waters in the Chesapeake.
Beyond direct environmental issues, Larry expolered the current models used for sediment flocculation. The principle theories are the same for sediment and algal flocculation. However, algal flocs have a much larger unknown quantity in the form of biologic acitvity such as cell division, cellular exudates, microbial degradation among others. Indeed, some of these biologic processes afect sediment flocculation, but for the most part have been ignored by estuarine scientists (the group largely repsonsible for studying inorganic flocs). It was cool though, that Larry mentioned how he thought biology actually played a more significant role in the aggregation/flocculation in estuaries. As he was saying this, I thought, "Bingo", this is what I a studying. He then proceeded to show several equations that have recently been formulated to more accurately model sediment flocculation. The two critical terms he pointed at in the equations were the stickiness coefficient and the floc strength. As regards algal cell aggregation, I am particularly interested in the stickiness coefficient (commonly referred to as "alpha", its greek letter representation used in formulae). After the seminar, he andf I talked a bit with some of the other IMCS faculty. He wasn't quite sure how alpha and floc strength would be different other than due to "age". From what I have read (as related to algal cell aggrgeation dynamics), it has been assumed that the alpha for algae is also used for floc strength. For example, if a bloom of phytoplankton is very sticky and has a high value for alpha, current model equations imply that the resultant flocs will be strong due to the high alpha value. The cool thing about breaking the parameter of alpha into interaction and strength components is that it allows for a more comprehensive model for understanding complex aggregation dynamics where a) batceria can degrade adhesive polymers b) aquatic medium chemistry at the time of formation will be manifest in aggregate properties c) modeling of colloidal or dissolved materials apart from the cell surface can also be included. Dr. Sanford also focuse on the fractal dimensions of aggregates. Aggregates are often described as being fractal because they are often comprised of small units clustered together into larger units. This pattern repeats until some maximum size of aggregation is approached, which can be set by floc strength/stickiness and energy levels (ie turbulence) in the aquatic medium of observation. A completely solid aggregate (without pores or interstitial spaces) would have a theoretical fractal number of 3. A loosely aggregated particle would have a fractal number approaching zero. The fractal number is often invoked in equations that help to determine settling speed. Of course, the principle equation governing the vertical velocity of an object is Stokes Law. Stokes Law is a function of the area of the object (usually expressed as the radius perpendicular to the direction of the object's trajectory), the density of the object, the density of the medium through which the object is passing, and of course gravity. The fractal number can be aplied to a variation of Stokes Law in the exponent that would be used to determine the area of the particle (used as [fractal number]- 1, where a solid aggregate would have an exponent of 2). This ends up working out nicely when one wants model a floc with lots of interstitial space that would permit the free flow of water through a certain portion of the floc. Since lower fractal numbers are indicative of more loosely bound aggregates, a lower fractal number applied to a form of Stokes Law would allow for a slower settling velocity of a more porous aggregate (which would settle much slower than a tightly bound aggregate of the same parent material). From what I have read, most algal cell aggregates have a fractal number somewhere near 1.5 to 2 (closer to 2 than 1.5).
Finally, Sanford left me with a point I should try ot nail down in the nest few weeks; what are the standards for algal cell aggregation. As far as I know, nothing has been established. Everyone is competing to have their method and nomenclature accepted as the standard, but very few folks are listening to each other during this whole process.


also, I ran for 50 minutes in 45F rain at the Livingston Capmpus Ecological Reserve.
- posted by alex @ 11:26 0 comments

 
Fv/Fm, S. costatum
I used the Fast Repitition Rate Fluorometer (FRRF or FRR) to determine the health of my S. costatum culture.
Fv/Fm = 0.286
Fm = 567.6
Where Fv is the variable fluorescence and Fm is the maximum fluorescence. The ratio between the variable and maximum fluorescence is an indicator of the health of a photosynthetic organism. The variable fluorescence is the difference between the initial fluorescence (Fo) and the maximum fluorescence (ie. Fv/Fm = [Fm-Fo]/Fm). Fluorescence is the subsequent emission of lower energy light (longer wavelength) following excitation by higher energy light (shorter wavelngth). In the case of the FRRF, the sample of phytoplankton is bombarded by a very rapidly flashing blue light. Concurrently, the sample is surrounded by a detectors which have been set up to measure red light. The computer controllingthe FRRF knows how much blue light was needed to create the fluorescence (red light) observed. The time lag between exposure to the blue light and fluorescence by the phytoplankton is on the order of picoseconds. The FRR allows us to observe the change in fluorescence. A healthy culture of phytoplankton should have an Fv/Fm > .50 (approximately). As one can see, my S. costatum culture is a bit less than ideal. This is likely due to the low concentration of cells in my relatively young culture. As the culture continues to grow, the cel concentration of the culture should rise, thus increasing the fluorescence of the culture (assuming the plankton don't die too soon). The reason a healthy culture should have a high Fv/Fm is due to the photosynthetic ability of the culture. A healthy photosystem (chlorophylls converting light into cellular energy) can absorb a fair bit of light before it becomes saturated and overflows. In this sense, the overflow of light is manifest as fluorescence. More fluorescence = higher Fv = more healthy photosystem. The reason a healthy photosystem can absorb more light than an unhealthy photosystem is because all of its components within the electron transport chain (the fancy name given to the series of components used to transfer light energy into cellular energy such as ATP or NADPH) are well-nourished and in tip-top shape (highly efficient). If any portion of this electron transport chain is deficient (usually due to some sort of stress such as lack of nutrients or high light) the cell will not be able to transport electrons (energy) at a very high rate, thus hitting its overflow level relatively soon resulting in a low range of fluorescence ( a small difference between Fm and Fo => a small Fv => small Fv/Fm).
But, we can expect the S. costatum to be doing slightly better tomorrow. If experience with past cultures is repeated, S. costatum will bloom and senesce very rapidly.

Above are images of increasing magnification of S. coatatum. Recall S. costatum is a diatom, so the cell is encapsulated by a silicious frustule which is the obvious structure in the obove images. The cell has several long processes that allow it to form a chain with other S. costatum cells. Each individual cell is usually in the size range of 5-8um. With chains sometimes several mm long. The above images were obtained from the website of the department of Marine Ecology, Marine Botany at Göteborg University
- posted by alex @ 13:54 0 comments

 
Larry Sanford Lunch
This post is mostly a reminder to myself to pick up Baja Fresh @ 11:45 am Monday for the grad student lunvh with the guest seminar speaker Larry Sanford. Larry id driving up from Horn Point, Maryland, and has written several papers about flocculation in estuaries which I have found to be pretty keen. In particular, he wrote one paper published in 1997 on turbulence in experimental ecosystems, that has had a significant impact on my approach to research. In particular, there is one graph from this paper that shows the range of turbulence used in most lab experiements, and the natural range of turbulence. Everyone has known for decades that we are principally limited by scaling issues (low turbulence levels in the lab require large volumes of water and oong periods of time), but his graph is a wonderful illustration of the desparity between the two.
Remeber to get Baja fresh @ 11:45am!
- posted by alex @ 23:34 1 comments

 
Engel et al. 2004
Engel et al. [2004] cite Obernosterer & Herndl [1995] as having showed that exopolymers released under phosphate limitation are somewhat resistant to bacterial degradation. Engel et al. [2004] comment that other types of nutrient limitiation induced exudates may be recalcitrant to bacterial degradation.
Maranon et al [2004] found that about 20% (compared to the work of Baines and Pace [1991] which estimated 13%) of photosynthate is released as dissolved organic carbon (DOC). They found a decrease in DOC production at night, and an increase in production by healthy populations at suboptimal irradiances. They feel that the traditional perspective of DOC production as an overflow valve for photosynthesis is incorrect. Indeed they interpret their results to show that passive DOC release is a normal physiological mechanism of healthy cells under suboptimal irradiance levels.
Note: glass fiber filters adsob significant amounts of DOC and should not be used for measurements. Maranon et al.'s proposed mechanism for a low irradiance increase in DOC production is the incorporation of inter-cellular C into small molecular weight metabolites due to an irradiance induced slowdown of macromolecular synthesis. Find Raven (1986) which discusses mechanisms of normal cell leakage or exudation. Maranon et al. [2004] conclude that there is no adaptive benefit to enhanced exudation under sub-optimal irradiances, rather it "reflects the inability of the cells to keep all the recent photosynthate within the intracelllular mechanism."
- posted by alex @ 00:41 0 comments

 
Lab Meeting, Kay Bidle
At today's lab meeting Kay Bidle presented his data from the past few months. The first thing he showed, despite Paul's claims otherwise, was a graph of cell number over time in a batch culture. Although the culture was grown in nutrient replete f/2 media, there was a decline in the number of cells after about 10 days. This decline was subsequently followed by another even more populous bloom, of the same species of E. huxleyii. Kay then hypothesized as to why the first bloom died, with such a small number of cells - only to be followed by a larger bloom of the same species. Of particular interest were electron micrographs Kay had from samples prior to and following the peak of the second bloom. If my memory is correct, the organelles of the post bloom cells appeared to be encephalized compared to the pre-bloom cells. Kay then tied this into cell death. Cell death, which can have two forms, either necrosis or apoptosis, is either externall forced or intrinsically wired (repsectively). I have issues with altruism and by inference - group selection ad kin selection. Apoptosis, or Programmed Cell Death (PCD) occurs in all types of cells ranging from unicellular organisms such as phytoplankon, all the way to our own body's cells. In our bodies, PCD occurs numerous times everyday. In fatc, the lack of PCD is commonly manifest as cancer (when cells continue to multiply and will not respond to cues for PCD). However, in phytoplankton commmunities, PCD is viewed by some as an evolutionary advantage. Of course, this is not an advanatge for the individual who succumbs to PCD but is rather an advantage for the remaining members of the population. A selfish gene however has no desire to succumb to PCD such that other genes (individuals in this case) may persist. However, Kay's data showed evidence of caspase activity following infection of a culture by a virus. Increased caspase activity provides a signal for the cell to begin PCD. As a result, the cell will generally lyse (explode, thus killing itself) which will minimize the propagation of the viral infection. The minimization of viral infection relies on the viral strategy of utilizing the transcription machinery of the cell to replicate the viral genetic code. If the cell continues transcription following a viral infection, the virus will soon overtake its host and lyse the cell thus propogating a great number of viral replicates. Obviously, if a cell can die via PCD shortly after infection, it can minimize the extent of viral propagation. That the cell would succumb to PCD following a viral infection relies on the assumption of some sort of altruistic behavior on the cell's behalf. Of course, evolutionary biologists scoff at the idea of an altruistic gene. And, I must agree. It is not in the interest of a unicellular organism to commit suicide and eliminate , on its own, its ability to produce progeny.
While absorbing the end of Kay's talk I devised a silly explanation for such seemingly altruistic behavior. Rather than acting altruistically on behalf of the other members of a species' population, I think the cells the succumb to PCD may in fact be on the losing side of a constant competition for limited resources among all members of a population. I shall explain.
My research is concerned with the constant exudation, by phytoplankton, of extracellular material. In a basic sense this material is hypothesized to be excess photosynthate that leaks as an overflow valve-like mechanism. Now, taking a step back, prokaryotes are known to use quorum sensing to communicate. Such behavior has not yet, to my knowledge, been observed in phytoplankton. As prokaryotes are generally older species than eukaryotes, I do not think it is unreasonable to assume that eukaryotic phytoplankton may utilize similarly complex chemosensing. It is with this in mind that I feel that the exudates of phytoplankton may contribute to PCD. Perchance the exudate from an individual contained discrete chemical cues that that could only be deciphered by another indiviual (of the same species) following a viral infection. My thoughts then proceed: that the viral infection (according to Kay's data) activates caspases (although for wwhat function, we do not know) that react to to specific cues in the exudate of fellow individuals. More plainly put, cells are always exuding potentially lethal cues for their fellow nutrient competitors (other members of the same species) to detect. However, detection of such chemical cues is not possible until an individual's integrity has been compromised, in this case by a virus. This idea, rather than relying on altruistic gene behavior, functions when each gene (individual) is constatntly looking out for themselves by continually emitting a cue to kill compromised competitors, thus increasing the available nutrient pool for itself once the others have died.
Just and incomplete thought on an area of research I know nothing about.
- posted by alex @ 23:17 0 comments

 
paper review
One of the professors at IMCS asked me to review a paper for a journal of which he is an editor. The paper was complete crap. Of course, one has to be somewhat more eloquent in stating as much. Below are my comments on the paper, which at best, can be described as having observed marine snow in the Irish Sea that may have originated from the bottom, yet the authors attempted publication despite the fact that there is very little evidence to support this mundane observation.

Dear Professor,
Overall, this paper needs numerous improvements prior to publication. Although the relationship between the concentration of arabinose in suspended particulate matter and settling velocity may be useful, the data presented here does not make a significant contribution towards further understanding of particle flux from the sea surface.
The paper appears to have been written by estuarine or sediment flocculation scientists who attempt to apply their research towards "marine snow" or planktonically derived oceanic aggregeates. However, a wide body of literature was seemingly overlooked by the authors in their attempt to publish within the realm of another, albeit similar, discipline. For example, the text under review claims (and erroneously cites Alldredge and Silver [1987] as having coined the phrase "marine snow" - in common usage by the 1970's) that phytodetritus flocs are "more widely reported from the open ocean than from the shelf". The only supporting reference for this claim is a previous paper by the author (which does not explore the spatial distribution of marine flocculation studies). Contrary to the dubiously supported statement of the authors, "marine snow" has in fact been primarily studied in coastal environments. Indeed, the authors cite papers by both Alldredge and Engel wherein each conducted the bulk of their research in coastal regions (Alldredge - Santa Barbara Basin and Gulf of California, Engel - Baltic Sea). Furthermore, this faulty assumption of a paucity of coastal data leads to the undermining of one of the authors final conclusions; namely that they have found coastal flocs to be stronger than those previously observed in the open ocean. Unfortunately, the flocs they assumed were observed in the open ocean were primarily observed in coastal regions. Another ill-use of export flux literature was the repeated citation of Smetacek [1985] to support various characteristics of phytoplankton aggregation. However, Smetacek [1987] was self-described as having the intention "to provoke discussion rather than establish consensus". Smetacek [1987] is a text of conjecture on diatom sinking as an evolved life strategy to enhance competitive ability and does not provide first hand data to support statements related to "cell leakage" or "biologically mediated aggregation". In another erroneous citation, the authors attribute Passow et al. [2001] with the determination of glucose as the primary constituent of floc matrices. As the composition of the matrices is central to the marine snow story, and the story of the paper under review, this is an important fact. However, no such data were presented by Passow et al. [2001]. The above three examples of poor scholarship were selected from a handful of noted occurrences within the text. Such behavior is evidence of a lack of understanding of the scientific study of the export of algal aggregate export from the sea surface. If one considers that each of the above authors (Alldredge, Engel, Smetacek, Passow) are considered experts in particle export studies and have each published numerous inter-related papers over the past 20 plus years, such mistakes in scholarship are inexcusable given the proposed context of this paper's research. Without a solid foundation, it is not entirely clear why the research on settling velocity and arabinose concentrations was conducted or how it will benefit the study oceanic particle flux. Another principle argument of the paper is equally as insufficient as the foundation/context of their research. The results of the paper observed a correlation between arabinose (a proxy for phaeocystis photosynthetic activity) and mean particle size. Although arabinose is noted by the authors as not being the agent of aggregation, it is somehow associated with well-aggregated flocs, presumably due to higher turbulence. Without turbulence data from the study sight, this is an unreasonable conclusion, especially since marine aggregates are generally described as fragile and begin to break apart at relatively low levels of turbulence. The parametric relationship between floc viability and turbulence was explored extensively by Alldredge, Kiørboe and Dam in the 1990s, yet was not cited in this context in this paper. As a result of the deficiencies described above the paper does not bring forth a novel contribution to the study of marine particle aggregation.
- posted by alex @ 21:53 0 comments

 
Skeletonema Culture
I started a one liter batch culture of Skeletonema costatum on wednesday afternoon. The media for the culture is f/2 -Si. A 1ml innoculum from Kay Bidle was used. S. costatum is a renowned "sticky" diatom. However, in the cpmmunity, there seems tobe some confusion as to the source of this stickiness. While some folks find the exudate from S. costatum to the reason for theis species' ability to form long chains, other studies have noted the morphology of the cell as being the primary reaosn for chain formation. The morphology of S. costatum looks something like the large black orb used in to torture Princess Lea in the original trilogy. Where the long needle is used to attach to other similarly scary diatoms of the genus Skeletonema.
- posted by alex @ 20:47 0 comments