BIOL 3007W: 11/15/10

THis lecture is on the basal fungal groups: Chytrids, zygomycetes, and glomeromycota. None of them make large fruiting bodies.

chytrid: characterized by anchoring structures.
Zygo = yoke. zygospore is formed.
Arbusculus = small tree. (glomeromycota.)

basidio and ascomycota are the higher fungi. Chytrids appear to be polyphyletic, as do zygomycetes.

Chytrids: typically found in aquatic (freshwater) organisms. They occur as parasites on terrestrial organisms. They are the only fugi with motile cells in their life cycle (posterior, whiplash flagella = opisthokonta.) THey are mostly saprobic, and are important biodegraders. Some of them live in guts of herbivores as cellulose degraders (in which case they are obligate anaerobes. SOme are parasites on algae and other fungi (useful in case of feeding on algal blooms.)

Chytrid baits: chitin , cellulose (cellophane, wood), keratin (eg red hair), pollen grains (pine, spruce, oak) , seeds.
Thallus form: Monocentric thallus (one center with rhizoids.) Inside the host  they do not make rhizoids.  They make a sporangium (center of the picutre) anucleate rhizoids that anchor it. Papilla (where the zoospores emerge from.)

Life cycle of allomyces. allo=different. It is a tropical/subtropical fungus.  One of the best studies chytrids. Starting with the sporophyte: Fusion of two different size gametes. Starts growing by dichotomous branching. The branches have two kinds of sporangia on them. Resistant sporangia are brown. Germinate immediately to produce diploid zoospores. The resistant sporangia lie dormant for many months, so they are released under stress. They produce haploid gametophytes. The gametophytes will produce two kinds of gametangia (make and female.) The female gamete produces sirenin, which will cause male gametes to swim to the females. The AoG is isomorphic.

Chitridiomycosis: parasite of amphibians. (frogs) and has caused mass extinction. The cause is not certain. It attacks the skin of the frog, making the skin thick and inhbiting the ability of frogs to respire.

Zygomycetes: not a monophyletic group. Variable life styles: saprobic, arthropod guts, pathogens. fluffy white growth on bread and strawberries is prime example. They have both sexual and sexual reproduction. The mycelium is coenocytic.

Sexual reproduction involves a zygospore, whereas the asexual reproduction involves non-motile sporangiospores. Sporangia sitting on aerial mycelium. Sterile part = columella.

Mature: protogametangia (two cells that grow towards each other and then swell up.) they each cut off a cell at the tip, called suspensores. We see plasmogamy and karyogamy to produce the zygote, and the zygopore is like a yoke between the two cells,

Mucor: Sticky or slimy sporangia. Don’t get blown away. Insects or water disperse the sporangia.
rhizopus: dry spores. The wall breaks and the wind carries them away.
Thamnidium: Sporangium at the tip have sticky spores. The things down at the bottom are smaller sporangia which are dispersed by the wind.
coemansia: Sporangia have one spore. They are desert organisms. A droplet of water develops around it….
Cunninghamella: like thamidium, but also with 1 spore per sporangium.

Spirodactylon aureum. There ar a lot of spiraly things, which prevent the dispersal by air.
Entomophthora. Destroy flies and stuff. They parasitize flies and other insects. They are ballistospores, so they are shot away. They penetrate the exoskeleton
Pilobolus: Hat throw (the sporangia is the cap.) The sporangia can be shot for over 6 feet. They are adapted to be eaten by animals. They move according to the sun, and shoot at about 9 in the morning. Sticky stuff in the ring at the bottom of the spore.  Great video on pilobolus spore dispersal:

Life cycle of rhizopus: Asexual reproduction by sporangiospores. THey have two mating types (+ and -) There are compounds produced which diffiuse through the agar (and then through the air) to form the gametangia. The gametangia fuse to form the zygosporangium. When the zygosporangium germinates, it forms a sporangium (undergoing meiosis.) The mycelium is haploid, unlike in the oomyces.

Mating types: + and -. Takes two different thalli for mating (heterothallic)

Zygomycetes products: tempeh. Rhizopus oligosporus.

Glomeromycota: They make endomycorrhizae. Within a cell of a root, it looksl ike a root (arbuscule.) The fungus collapses without any obvious impact on the plant cell.

AM vs VAM: VAM: vesicle forms between the cells. It is storage structure that contains nutrients.  Herbaceous and woody plants usually make the arbuscular mycorrhizae.

Glomeromycota are obligate symbionts. They are difficult to grow in culture. They push in the plasma membrane, but the membrane remains intact. The arbuscule is short lived. They penetrate the cell wall, though. We don’t understand the life cycle at all.  They make large spores. Extension of the root system, aggregate the soil, glue together fine soil particles. They aid in phosphate and nitrogen uptake. Defense against parasites.

BIOL 3007W: 2010 Nov 8

Lab summary of stuff:

	Chlorophyta	Cryptophyta	Rhodophyta	Euglenophyta	Dinophyta	Haptophyta
Chloroplast	Primary endosymbiosis	Secondary endosymbiosis of red algae	Primary endosymbiosis	Secondary endosymbiosis of green algae	Secondary endo of red algae	Secondary endosymbiosis
Pigments	Chlorophyll a, b and carotenoids	Chlorophylls a, c and carotenoids	Chlorophyll a, phycobilins	Chlorophyll a, b and carotenoids	Chlorophyll a and c	Chlorophyll a and c
Supergroup	Archeplastida	Chromalveolata	Archeplastida	Excavate	Chromalveolata	Chromalveolata
Flagella	–	2 flagella, interior slightly unequal; apical tinseled	—	2: one emergent, one non-emergent	2: 1 extending	0 or 2 flagella
Storage molecule	starch	Pyrenoids ???	Floridean starch	Paramylon: starch like	Starch	chrysolaminarin

/* Humor
Prof: “How do red algae differ from green algae? It’s obvious! Red Algae are red and Green algae are green!”
Class: “LOL.”
*/

/* Not Humor:
Prof: “Final is on Dec 18: 4-6 PM.”
Class: “BOO.”
*/

Unilocular sporangia always pertain to meiosis, multilocular sporangia pertain to mitosis (preservation of ploidy.)

Resumption of lecture:

Kelps: Important economically. Harvested as though it is a lawn being mowed. Apical meristem: keep growing upwards. Extracted for algin. Mucilagenous cell wall material. Protects the thallus from buildup of organisms. Used as an emulsifier in food, paper coatings, paints, etc.

NEED TO KNOW: Kelp life cycle. Alternation of generations.

Starting in spring: fertilization occurs, zygote forms, zygote grows into typical sporophyte (holdfast, stipe, blade.) They grow all summer. They will undergo reproduction (meiosis)  by producing unilocular sporangia. They will produce two motile cells to produce the male and female gametophyte stages. The male gametophyte appears more hairy?

Alternation of generations is obligatory: selection for sexual reproduction. There is no asexual phase of the life cycle.

/* TECHNICAL PROBLEMS. FORGOT TO PLUG IN INTERNET.*/

Video resumed. Some information on kelp and various ecological roles of kelp can be found on this website. I believe this is the video being shown in class. Very well made.

Stramenophiles: Moving on: Oomycetes, then progress to slime molds.

Xanthophyta: mainly freshwater. “Yellow-green algae.” They are stramenophiles that lack green algae. They mimic the green algae. They have chlorophylls a and b, they have typical motile cells, storage products are not starch based (differentiate them from green algae.)

We will be looking at Vaucheria. Similarity to the oomycetes (morphological:) oogonium fertilized by male gametes from the coiled antheridium.  Relatively easy organism to find.

Oomycota: the “egg” give the fungi their name. Resting stage is called the oospore. Oogamy: egg is much larger than the male gamete. THERE IS NO MOTILE MALE GAMETE IN THE OOMYCETES.

Similarities to the true fungi: heterotrophic nutrition, and acquire nutrients by extracellular degradation. secretion of enzymes to digest substrate followed by absorption of substrate.

Why are oomycota not true fungi? Zoopores with whiplash and tinsel, cellulose and beta glucan in cell walls.

Phytophthora: plant destroyer. caused irish potato famine. Originated in South America, crossed over the Atlantic. Late blight of potatoes and tomatoes. Sporangia disperse. The zoospores are the only motile cells in the life cycle and require water. Derives nutrition initially from living plant tiuuse, then from dead tissue.

The Bordeaux mixture: lime and copper sulfate, used as the first fungicide. Last summer, there was a major outbreak of p. infestans. Another species: p. ramorum. Oaks are susceptible. Brown stuff exuding from the bark is evident in infected plants. Nurseries spread it around.

Genomes of phytophthora: 3 have been sequenced. One is from P. infestans. – 2.5-4 times the other two. one of the other organisms is p. ramorum. Problem: It can change very rapidly. Most of the expansion is non-coding. The disease-causing genese are in the expansion region, and are increasing in copy number.  http://www.nature.com/nature/journal/v461/n7262/full/nature08358.html

Oomycota: Water molds: Did stuff in lab today with putting fly in lake water. Need to keep it dilute. Terrestrial group are the plant pathogens.

Watermolds are abundant in freshwater. Theyir nutrition is mostly saprophytic or parasitic. They reproduce sexually and asexually.  The vegetative state is a coenocytic filament. They have sexual and asexual phases. Transition triggered by deterioration in the environment. The antheridia grow to the oogonia.  Life cycle can be found here. NEED TO KNOW LIFE CYCLE.

White rust: Albugo. We get a white powder on the surface. They are obligate parasites. Can’t grow them in culture. They attack species in the cabbage families. Infects the leaves, grows inside the leaves. Makes chains of sporangia (sporangiophore) which pop out on the surface. The spores are distributed by wind. If conditions are good, they’ll make the zoospore to infect host.

11/03/2010 BIOL 3007 Lecture

Short blurb on coral bleaching.

Stramenophiles aka heterokonts (kont = flagellum.) Common theme: two flagella. One is tinseled, the other is whiplashed. Stramenophiles: straw, hairs. Hairs are tripartite.

They include the golden algae, the brown algae, the diatoms, and oomycota (a fungal group.)

/*this prof really loves the etymology of names, eh*/

Golden algae: chrysophyta. They like unpolluted waters. Mostly cold, freshwater dwelling.  Active during the winter. Won’t survive in warm conditions. They can cause toxic blooms. Can also influence the quality of water. They may be unicellular or colonial. Sitting in a cuplike protective structure: Similar to tricholomonas.

All stramenophiles have the same kind of pigments: chlorophylls a and c, as well as fucoxanthin. The fucoxanthin gives them a yellow colour. golden algae produce chrysolaminarin. They may have scales with silica or walls with cellulose.

Tinsel flagellum is longer than the whiplash flagellum. They have 3 types of hair: thin hair at the top, stouter hair in the middle which connects to a thicker hair at the bottom. The scales have silica.

They also produce cysts in the resting state. Cysts can be produced by asexual or sexual reproduction. THey begin to deposit the silica inside the cytoplasm. They make a bottle, and sit in the bottle. They make a plug, and unplug the bottle during germination.

DIATOMS:

Important components of phytoplankton. THey are both marine and freshwater organisms. THey are major contributors to photosynthesis. ~25% of global carbon is fixed  by diatoms. Important food source of many marine organisms. Their walls have silica and pectin (very distinctive.)

Colonial diatoms, can literally be unfolded or aggregate into starlike shapes. Many are single celled. Some are radially symmetric (Centric diatoms: mostly floating and planktonic), and others are bilaterally symmetric (mostly bottom dwelling on vegetation; little groove that runs through the shell to enable gliding motility.) The surfaces have all sorts of ribbing and sieve like components.

FRUSTULE: ONE PIECE BIGGER THAN THE OTHER. Overlapping halves. Asexual reproduction by mitosis. Formation of a membrane that lies between the two nuclei, made of silica. Makes two new BOTTOMS. They’d have to become smaller and smaller if they kept dividing that way…

/* I wonder if that’s gonna be on the test */

Gametic meiosis . Very large zygote called the auxospore is formed. Divides tor produce some very large cells, then goes through a cascade of shrinking down.

Perforation: solid glass wall would make them sink. Perforation helps them be lighter. Also promotes water and nutrient exchange. http://onlinelibrary.wiley.com/doi/10.1002/adfm.200700609/abstract

Diatomaceous earth: used to make filtered liquids, production of antibiotics, insulation, etc. Also yields geological information of  lakes and oceans. Slide on “Rock Snot“

Brown algae: last group. They do not have any unicellular or multicellular forms. They are usually filamentous (morphologically complex thalli.) Diverse life histories. Grow best in cold water.

The storage products are a little different (laminarin instead of chrysolaminarin.) Ectocarpus is a simple brown alga. Alternation of generations (isomorphic.) They have different types of sporangia. Unilocular in which meiosis occurs to make haploid zoospores (germinate to make gametophytes) and plurilocular which has many chambers, and makes diploid asexual zoospores (motile.)

Fucus, conceptacles. diploid life cycle.

BIOL 3007W Lecture

Part 2: Lecture 15

ALgal motile cells. Basic type: cells with two falgella pointing forward.

Looking at cryptophytes, strameophiles, haptophyta, dinophyta, euglenophyta, chlorophyta.

Chloroplasts occur in 4 supergroups: archeplastida: primary endosymbiosis. others: secondary or tertiary or exotic flavours.

Review of primary/secondary symbiosis. Remember to look at membrane arrangement in chloroplasts.

Beginning with Euglenophyta (Euglenoids.) Green or colorless flagellates. Mostly freshwater. They really like pollution (excess nutrients, etc.) Ancestor s were non-photosynthetic, and phagocytosed things.

Chloroplasts arose by secondary endosymbiosis (have chlorophyll a, b) with an extra membrane. There is no sexual reproduction.

They are widely distributed in freshwater habitats, but oftentimes they are found at air-water or water-soil interfaces. They are highly tolerant of extreme environments. Look at soil on euglenoid diversity.

They don’t have true cell walls. Flagella are apical. long flagellum with tinsels emerges out, but the second one does not emerge. There are a set of protein plates beneath the plasma membrane (called the pellicle.) They have eyespots to orient them towards light.

They have pyrenoids, where photosynthetic carbon is metabolized. However, these pyrenoids are negative for iodine stains, since they do not have starch. They store a material called paramylon. Euglena have contractile vacuoles for water modulation. Lots of contractions and expansions to maintain water balance.

moving onto Chromalveolate group.

Chromalveolates’ origins from endosymbiosis of red algae. Typically they have three or four membranes. Interesting uptake of chloroplasts. THey are not very common. They tend to be in deeper and colder waters. Important components of freshwater and marine habitats/

They have two flagella at the apex, which are differently decorated compared to each others. They have chlorophylls a and c, and phycobilins (light harvesting complexes) and carotenoids. Some are photosynthetic, and some are colorless. Remember: phycobilins are only found in red algae, glaucophytes and cryptomonads.

Outer membrane of chloroplasts (4th) is continuous with host’s nuclear membrane. Review Gene transfer slide. (transfer from plastid to secondary host, plastid to nucleomorph, nucleomorph to nucleus, etc.

SIDE NOTE: the professor is pretty boring.

BACK TO SCHEDULED PROGRAMMING.

Haptophyta. Cells can be unicellular or colonial. Mainly marine. Cell structure is pretty unique. They have two whiplash flagella, with a funny thing coming out of the middle, called a haptonema. They have both chlorophyll a, c, and carotenoids (especially fucoxanthin, makes them look brown.) They store chrysolaminarin in vacuole.

They have scales, which are sometimes calcified (then called coccoliths.) They can take up dissolved nutrients or ______. Haptonema have a sticky tip which adheres to microbes or other food particles. Upon attachment to a food source, the haptonema brings the food closer to a membrane, which allows the haptophyta to engulf them.

Often called coccolithophores. Round, calcium bearing organisms. They can have multiple layers of scales. They come in a remarkable set of patterns. http://en.wikipedia.org/wiki/Coccolithophore

They have a big impact on carbon and sulfur cycles. A big CO2 sink, since the calcium carbonate captures it permanently. They drop down to the bottom of the surface. They also make Dimethyl sulfide, which rises up and provides nucleation sites. Less light on oceans. The sulfur comes back down, enhancing acidity.

Acidic oceans: will the coccoliths breakdown? will the organims be able to compensate? http://www.sciencemag.org/cgi/content/abstract/sci;320/5874/336 At higher concentrations, they are able to compensate by building bigger coccoliths. Evidence for increasing size of coccoliths since industrial revolution. They have big impacts worldwide.

Last group: dinoflagellates. Diverse set or chloroplasts. Some have green plastids, though most have green plastids. Dinos  = whirling. When they swim, they spiral. One flagellum goes around the cell and the other flagellum goes back. The one that goes around is a tinsel flagellum, the other is a whiplash flagellum. Some have amoeboid stages, and some others have starch.

They have chromosomes which are condensed, but there are no histones. They always appear as though they are in division… i.e. always condensed. Possess chlorophylls a and c. They also have carotenoids, (predominantly perdinin.) They characteristically have plates, though some can be unarmored (only with vesicles.) They have a filament that emerges from the cell, an arm of cytoplasm comes down and engulfs the substrate. They are mixotrophic organisms.

They make elaborate cysts. They accumulate in sediments, and used in oil exploration (to date the sediments.)

Pigmented dinoflagellates may be symbionts in other protists or in invertibrates. Zooxanthellae: cells of dinoflagellates that get taken up from organisms. If they re-emerge from hosts, they will have the characteristic dinoflagellate shape. They synthesize many compounds used by the corals. In return, they get CO2 from corals.

Increase in temperatures may cause corals to expel zooxanthellae. Coral bleaching. Red tides. They produce toxins which are colorful, but also responsible for major fish kills. They are neurotoxins which accumulate in fish. Bioluminescence during night. Not known why they do it.

Smallpox vaccine and HIV Link?

Smallpox demise link to HIV boom

The worldwide eradication of smallpox may, inadvertently, have helped spread HIV infection, scientists believe.

Experts say the vaccine used to wipe out smallpox offered some protection against the Aids virus and, now it is no longer used, HIV has flourished.

The US investigators said trials indicated the smallpox jab interferes with how well HIV multiplies.

But they say in the journal BMC Immunology it is too early to recommend smallpox vaccine for fighting HIV.

I just looked at this article in BBC News. I’m a little confused by the science mentioned in the article. A later paragraph states:

The researchers believe vaccination may offer some protection against HIV by producing long-term alterations in the immune system, possibly including the expression of a receptor called CCR5 on the surface of white blood cells, which is exploited by the smallpox virus and HIV.

I figured that I’d learn more by actually reading the paper, and it turns out it was a pretty good idea. A “provisional PDF” of the paper is available here.

The authors drew upon the idea that if a cell is already infected with certain viruses, progression of HIV-1 infection into the cell may be significantly slowed. Human Herpesvirus 6 and 7 and the dengue fever virus are some such examples. The CCR5 chemokine receptor (or its ligands) and the CD4 co-receptor. What’s so special about these receptors?

Well, interestingly, HIV-1 (a particular strain of HIV) uses the CD4 receptor to gain entry into T-cells. Binding to the CD4 receptor allows the virus to bind to the CCR5 or CXCR4 co-receptor (depending on the cell expressing the co-receptor), allowing the virus to fuse with the host cell. It is also known that individuals who have a 32 base-pair deletion in the gene coding for CCR5 do not produce the receptor and are resistant to infection by HIV.

The scientists hypothesized that “immunization [with the smallpox vaccinia vaccine] might confer some protection against initial HIV infection and possibly even disease progression.” The subjects for this experiment included 20 individuals, all of whom had received the same set of vaccinations and none of whom were HIV-positive. Furthermore, none of them had been immunized for smallpox. To 10 of the individuals, they gave the smallpox vaccine, while the other 10 were in the control group. About 6 months later, they collected blood samples from the subjects and centrifuged the samples to obtain the Peripheral Blood Mononuclear Cells (PBMCs) so that they could grow cultures of the cells. They then got two different strains of HIV and mixed them with the culture media or the serum from the subjects. The solutions were then inoculated into cell cultures.

They measured the level of viral replication and levels of certain chemokines in culture. The results showed that in the cultures treated with the R5 strain, the levels of viral replication increased exponentially over a 13-day period in the unvaccinated, but increased initially and plateaued in the the vaccinated samples. There was nearly a 4-fold decrease in the replication levels among the vaccinated samples compared to the unvaccinated samples. Similar results were observed both samples treated with serum and those treated without serum. For the cultures treated with the X4 strain, there was a rise in replication activity until day 5, but subsequently decreased; however, the difference in replication levels in the vaccinated and unvaccinated samples was not statistically significant. No significant difference was observed in the samples pre-treated with serum compared to those that weren’t.

The results also suggest that there wasn’t a difference between the replication levels 3 months after treatment and 6 months after treatment. This contrasts with the previous observations of resistance to co-infection. Infection with the dengue fever virus or the GBV-C only inhibits HIV infection so long as the virus is present; once the virus is cleared, HIV replication increases dramatically. An independent study over a longer timeframe gave nearly identical results. The authors also showed that the long-term expression of certain cytokines was also slightly increased in the vaccinated individuals, though the difference was not statistically significant.

Thus, the authors suggest that there might be an interaction between the HIV-1 strain and the vaccinia virus, and vaccination for the virus might confer resistance to HIV infection. Since the decline of the use of smallpox vaccine and the emergence of the HIV-1 pandemic have sort of coincided, there might be a link between the two events.

Cool stuff, no?

–Gautam

EDIT: I should clarify, I have basically summarized the paper. I haven’t bothered to cite all the stuff since the citations are the original paper. The link to the original paper is provided.

Disappointed

It’s truly a terrible feeling to come out of a test feeling: “that could have gone so much better had I remember to look up X.” I mean, I had all this time, and for some reason, I couldn’t find the focus; I couldn’t get myself to stay concentrated for a few hours and go over the few chapters prior to the microbio and genetics test. I didn’t fail them, but I don’t think I put in my absolute best either.

Here are some lessons learned:

• Come to microbio lecture with adequate sleep. Sure, biochem lab early in the day is tiring, but that doesn’t imply Microbio is nap time.
• Work on lab notebooks during weekends. Midnight on Wednesday is not the time to be filling out notebooks.
• Solve some genetics problems everyday.
• Read textbook before attending lecture.

I think these lessons are easy enough to execute. Time to work on them!

–Gautam

Best Links 1/18 edition

Here are some good links that I came across today.

1. From Capital Gains and Games: “Tim Pawlenty Embarrasses himself on the budget.”
2. From Scientific American: “Im-Propaganda: How Effective Are Misinformation Campaigns to Manipulate Public Opinion?” An interesting interview with a sociologists about how misinformation campaigns are typically run and the outcomes.
3. From Discover Magazine Blogs: “Kinkyness beyond Kinky.” Interesting post about the weirdness of duck genitalia.
4. From Joseph Stiglitz via Project Syndicate: “The Harsh Lessons of 2009.” What happened to the economy in 2009 and what we can do in the future. Key lessons: Markets are not self correcting, market failures are always possible, Keynesian policies can have a strong impact and help economies come out of recession better, inflation targeting shouldn’t be the sole focus of the fed and other central banks, and innovation (especially in the financial sector) won’t always make our lives better.
5. From Not Exactly Rocket Science: “Mathematical support for insect colonies as superorganisms.” Apparently the metabolic rate of an organism can be easily calculated from the size; it’s all a simple linear equation. Even in a large colony, where individuals are often assigned specific tasks, considering the colony as a single “superorganism” gives similar results.
6. From Oscillator: “Quotations That Inspire Synthetic Biologists.” An interesting perspective on what inspires synthetic biologists and their work. Hear what Kant, Feynman, Vico, and Von Neumann had to say that motivates them!
7. From VoxEU: “How Green is China?” An interesting analysis of which Chinese cities are green and which aren’t. Studies like this might be a step in the right direction of identifying where in the chain emissions are coming from and where they can be mitigated, etc.
8. From the Official Google Blog: “Go thataway.” Apparently Google India has implemented features in its Google Maps offering that can tell you take a right at the Pan dabba and then take a left at the Irani Hotel and walk 200 feet from the Banyan tree to get to your Hanuman Mandir; well approximately that.

Gautam

Mass Spectrometry

Today in Mass Spectrometry class, Dr. Higgins talked about a 2002 study that was published in The Lancet (warning: UMN Access required. PubMed Link article access here.) The study used proteomics to generate the profiles of serum proteins from healthy individuals and from individuals suffering from ovarian cancer. The findings, from the abstract, state:

The algorithm identified a cluster pattern that, in the training set, completely segregated cancer from non-cancer. The discriminatory pattern correctly identified all 50 ovarian cancer cases in the masked set, including all 18 stage I cases. Of the 66 cases of non-malignant disease, 63 were recognised as not cancer. This result yielded a sensitivity of 100% (95% CI 93–100), specificity of 95% (87–99), and positive predictive value of 94% (84–99).

There was apparently a lot of hullabaloo raised over the publication of this article. Sorace and Zhan (2003) and Baggerly, Coombs, and Morris (2007) do a lot of good work going over the objections to the conclusions of the Lancet study.

Based on the results I have seen in the Mass Spectrometry course, I feel kind of convinced that in the short term, it will be very difficult for proteomics and mass spec profiling to make waves in the diagnostics world. The technologies still seem to be too expensive, and we still need to target the right variables for these tools (i.e. quantifying a protein might not be enough; we might need to look at ratios of different proteins, etc.). We have also been unable to come up with good solutions to address sample contamination by ubiquitous proteins such as albumin and keratins. I will admit, though, that I don’t know how big of an issue keratin and albumin present; I feel like any contamination would be detrimental, but experts might just be happy enough to acknowledge the problem and move on.

So, in one of my first “thinking about the future” posts, I will say this: I think that before 2020, we won’t have the right set of technologies that might help us come up with robust proteomics-based diagnostic techniques. I will also state that biologists who understand statistics and computational sciences will be worth twice their weight in gold. Biologists who understand biology will only be worth their weight in gold.

Best Links of the day 1/12

1. From Marketplace Radio: “US Exports its Mental Illnesses” – I have had latent suspicions along the line of what this guy is saying. Let’s hope it doesn’t come out true. The last thing I want to see is a bunch of Asian (as in, from China, India, Indonesia, etc.) on medications for being “depressed.”
2. From MoneyWatch: “What Caused the Fed’s Record$45 Billion in Earnings For 2009?” – I had only heard about the $45 Bn figure yesterday, but was unable to place it in context. Here’s Dr. Thoma with some good background and with some thoughts on what could be done with the money.
3. From Wikipedia: “List of Countries by GDP (nominal)” – Mitch and I were talking about relative numbers in the evening, and I thought it would be good to look up some numbers. I can try to get some graphs going tomorrow, but I can’t quite figure out how to download data from IMF repositories; perhaps World Bank figures will be easier to work with.
4. From the San Fran Fed: “Global Household Leverage, House Prices, and Consumption” – I didn’t know about how much the Scands were in debt! (other than Iceland, duh.)
5. And lastly, From the PNAS: “Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma” – Yeah, I know, it’s a 2007 paper which, in the grand scheme of things, may not have a big impact. We just decided to read this paper for the Mass Spec class I’m taking, and I thought it was a pretty well written paper. Perhaps, if I’m in the mood for it, I’ll try to explain this paper to see whether or not I understand the study.

In other news, I am now following 100+ people on Twitter. Also, about 57 people are following me, which, interestingly enough, is up more than 25% from yesterday. Thankfully I archive all the twitter related mail. Thankfully.

–Gautam

Some amazing stuff

So I was perusing through random portions of my biochem textbook, and I was amazed by the amount of stuff out there that remains mysterious or not so well characterised. Examples of questions raised by the author: what dictates how large an elephant’s trunk should be? or why is the asymmetry in our body setup such that our heart is on the left side?

This is one of the reasons why a career in bio research sounds so exciting… there’s too much out there that needs elucidation! And any topic will have something interesting to explore.

I recently spoke with Dr. Gralnick from the MICB dept and am hoping to get some kind of a position in his lab in a few weeks or a month.

That is all I have to say. Also I am adding a self portrait pic for no real reason.