word of the day: smectic

The word of the day is smectic:

Etymology:  < Latin smēcticus (Pliny), < Greek σμηκτικός , < σμήχειν to wipe, cleanse 

1. Cleansing, abstersive, detergent. rare.

2. Physical Chem. Applied to (the state of) a mesophase (a liquid crystal) in which the molecules all have the same orientation and are arranged in well-defined planes.  (OED)

"From the recent work of de Haas and co-workers, it appeared that the mode of aggregation of lecithins plays an essential role in their interaction with porcine pancreatic lipase A.  This enzyme catalyses the hydrolysis of the 2 fatty acid ester bonds.  It was found to be very weakly active on dispersions of natural or synthetic lecithins, when aggregated in the form of smectic liquid crystals."

 - Tausk et al., "Physical chemical studies of short-chain lecithin homologues.  I.  Influence of the chain length of the fatty acid ester and of electrolytes on the critical micelle concentration", Biophysical Chemistry 1:175 (1973)

molecule of the day: p-chloromercuribenzoic acid

The molecule of the day is p-chloromercuribenzoic acid (PCMB):

(PubChem)

It's a sulfhydryl reagent, which means it reacts with sulfhydryl groups, in proteins, for example, as in this paper.

word of the day: lecithin

The word of the day is lecithin:

Etymology:  < French lécithine (N. T. Gobley 1850, in Jrnl. de Pharm. et de Chim. XVII. 411), < Greek λέκιθος yolk of egg 

Chem. 

a. Any of a group of phospholipids found in plants and animals which are esters of a phosphatidic acid with choline and on hydrolysis yield choline, phosphoric acid, glycerol, and two fatty acids; also used as a generic name for these compounds. 

b. A commercial mixture of lecithin with other phosphatides and often other lipids obtained from natural products and used industrially, esp. that from soya beans. (OED)

i.e., phosphatidylcholine,

(PubChem)
phosphatidylethanolamine,


(PubChem)

etc.


"Physical chemical studies of short-chain lecithin homologues.  I.  Influence of the chain length of the fatty acid ester and of electrolytes on the critical micelle concentration", Tausk et al., Biophysical Chemistry 1:175 (1973)


I guess these days we'd just say "phospholipids"?  Not quite sure what the significance of the choline part of the molecule is that it deserves its own term.

word of the day: nomogram

The word of the day is nomogram:

Etymology:  < nomo- comb. form + -gram comb. form, after French nomogramme (1905). Compare nomograph n. 

 

A diagram representing a relationship between three or more variables by means of a number of straight or curved scales, so arranged that the value of one variable corresponding to given values of the others can be found by a simple geometrical construction (e.g. by means of one or more straight lines drawn to intersect the scales at the appropriate values). Also called alignment chart. (OED)

"McClure has solved Eq. (12) numerically, and the results are presented in Fig. 3 as nomograms showing the time required to reach 99% of Qss for different values of k2 and k3."

 - "Techniques in Coupled Enzyme Assays", Rudolph et al., Methods in Enzymology 63:22 (1979)

molecule of the day: tartaric acid

The molecule of the day is tartaric acid:

(PubChem)

It can be used to model Ins(1,3,4,5)P4

(PubChem)

in crystal structures.

word of the day: hysteresis

The word of the day is hysteresis:

< Greek ὑστέρησις a coming short, deficiency, < ὑστερεῖν to be behind, come late, etc., < ὕστερος late.











A phenomenon observed in some physical systems, by which changes in a property (e.g. magnetization, or length) lag behind changes in an agent on which they depend (e.g. magnetizing force, or stress), so that the value of the former at any moment depends on the manner of the previous variation of the latter (e.g. whether it was increasing or decreasing in value); any dependence of the value of a property on the past history of the system to which it pertains. (OED)


"Lag time will depend on the system being studied.  A lag of 30 sec, or longer, may not be a problem in some assays if a long linear region is then observed.  If the primary enzyme is suspected of being hysteretic, the lag time should be minimal to ensure the actual measurement of the primary enzyme's behavior."

 - "Techniques in Coupled Enzyme Assays", Rudolph et al., Methods in Enzymology, 63:22 (1979)

molecule of the day: diisopropyl fluorophosphate

The molecule of the day is diisopropyl fluorophosphate:

(PubChem)

 Like other organophosphates (the most famous being sarin), it inhibits cholinesterases, but also lipases.  (And if the authors appreciated how dangerous this chemical they were working with was, they don't mention it in the methods.)

molecule of the day: leupeptin

The molecule of the day is leupeptin:

(PubChem)
It's a protease inhibitor produced by actinomycetes (source), which, as far as I can tell, is a polyphyletic group.

word of the day: plasmalemma

The word of the day is plasmalemma:

Etymology:  < plasma n. + lemma n.²  

 

A lipid bilayer surrounding the cytoplasm of a cell; a plasma membrane, a cell membrane; esp. one immediately within the wall of a plant cell. (OED)

"The inner surface of the plasma membrane is rich in phsophatidylserine, making the erythrocyte inside-out vesicle a good model for studying the translocation of diacylglycerol kinase and protein kinase C from cytosol to the inner aspect of the plasmalemma."

 - Besterman et al., "Diacylglycerol-induced translocation of diacylglycerol kinase: Use of affinity-purified enzyme in a reconstitution system", Proceedings of the National Academy of Sciences 83:9378 (1986).


These days I think we use the term "plasma membrane", but, if you are going to use plasmalemma, I do wholeheartedly endorse the use of the plural plasmalemmata.  (Maybe if you're talking about intercellular interactions?)

the importance of quantitative analysis

"In practice, FRET can be detected when the distance between the dyes is < 2 x Ro (27).  The Forster radius for the Alexa dyes used was calculated to be 5.4 nm (see Materials and Methods).  This means that the distance between PLA2 molecules at the end of the lag phase and the burst of activity are, on average, below 11 nm."

 - "Amyloid-Type Fiber Formation in Control of Enzyme Action: Interfacial Activation of Phospholipase A2", Code et al., Biophysical Journal 95:215 (July 2008)


The really great thing about FRET (Forster resonance energy transfer) is its high signal-to-noise ratio: you get a signal when two molecules are close, and you don't when they're far.

So I have no idea how they can conclude, from the fact that they have a FRET signal, that the distance "on average" is below 11 nm: it seems to me they can only conclude that at least some of the molecules are within 11 nm of each other.  Any determination of what proportion of the molecules are within 11 nm would require a more quantitative analysis comparing the amplitude of the signal they detect with the amplitude they would expect if all their molecules were lit up.  And, because you aren't seeing the molecules that are far away from one another, I have no idea how you would determine the average distance.

They go on:

"On the other hand, for a uniform distribution the average distance between PLA2 molecules on the liposome surface would be ~30 nm (Data S1).  Thus, the sole fact that we see FRET demonstrates a non-uniform distribution of PLA2 on the membrane surface."

I guess this statement is true: you would indeed expect zero FRET signal if all the molecules were exactly 30 nm away from one another.  But the statement still seems vacuous to me, because when do you ever expect a uniform distribution in that sense?

Consider: if I drop 100 balls onto a 10 x 10 grid, and if the balls don't interact with one another in any way (imagine the squares are very large compared to the size of the ball, for example), although you do indeed expect to find, on average, one ball per square, I would actually be quite surprised if I found exactly one ball per square.  Instead, I would expect some squares to have more than one ball in them, and some squares to have no balls in them.  Considering from the balls' point of view, I would expect some balls would be close to other balls, and some balls would be far from other balls.

Similarly, if molecules are randomly distributed on the surface of a liposome, I would expect some molecules, by chance, to be close to one another, and some, by chance, to be far away from any other molecules.  If I plotted the distance between molecules as a histogram, I would expect a normal distribution around 30 nm (assuming neither attraction nor repulsion among molecules, our null hypothesis).

So, once again, because FRET will give a signal for close molecules, but no signal for molecules far away from one another, even with this random distribution, I would still expect some nonzero FRET signal.  So once again, in order to determine whether there are additional forces at play here, I would still think that "the sole fact that we see FRET" is not the evidence we need: what is needed here is a quantitative analysis comparing the signal observed to the signal expected.


I once again conclude that the reviewers were not doing their job.  Or am I missing something here?

word of the day: antipode

The word of the day is antipode:

Etymology:  < Latin antipodes, < Greek (οἱ) ἀντίποδες (in sense 1 below), plural of ἀντίπους having the feet opposite, < ἀντί opposite + πούς foot (whence also a singular antipos n.).  

1. Those who dwell directly opposite to each other on the globe, so that the soles of their feet are as it were planted against each other; esp. those who occupy this position in regard to us. Obs.

2. fig. Those who in any way resemble the dwellers on the opposite side of the globe. Obs.

3. Places on the surfaces of the earth directly opposite to each other, or the place which is directly opposite to another; esp. the region directly opposite to one's own. 

4. a. transf. The exact opposite of a person or thing. (In this sense the sing. antipode is still used.) 

b.   at antipodes phr. in direct opposition.

5. As adv. (orig. n. in apposition) in phrases like to walk antipodes to . Obs. 

6. Chem. (with pronunc. /ˈæntɪpəʊdz/ ); sing. antipode. An enantio-morphic compound. (OED)

"Another very clear situation is found in the work of Bonsen et al (86) with the two optical antipodes of dihexanoyl, diheptanoyl, and dioctanoyl lecithin."

 - Verger and de Haas, "Interfacial enzyme kinetics of lipolysis", Annual Review of Biophysics & Bioengineering 5:77 (1976)


Personally, I would use the word "enantiomer".

letter to the Sun: horror vs. terror

Here's a letter I sent to the Sun:

Dear Baltimore Sun,

I was intrigued by your choice to use the word “horror” and not “terror” in your headline for your report on the devastating shooting in Colorado (“Real-life horror”, July 21).  I was then disappointed to not find any meaningful discussion in the story about whether this act of violence should be considered an act of terrorism.  Perhaps there are good reasons not to, but, without a presentation of those reasons, I cannot help but wonder whether if the suspected shooter were Muslim, had brown-colored skin, or had an Arabic-sounding name, your editorial choices would have been different.

The distinction may seem academic to the families of the victims, who are now going through the darkest hours of their lives, but this question actually raises two important issues.  During a time of limited resources and concern about the deficit, questions about how we will allocate those resources get to the very core of our priorities as Americans.  Our nation spends literally billions of dollars fighting terrorism: are we going to spend some of those dollars to prevent violent and, yes, terrifying attacks in our own country, even when the perpetrators are white?

The second issue is continued hostility toward Muslim Americans.  These sorts of editorial choices contribute to the misconception that only Muslims are terrorists, which leads to the further confusion that all Muslims are terrorists, which leads to irrational activities such as the inquiries currently led by U.S. Rep. Bachmann.  Not only are these inquiries a poor use of our aforementioned scant resources, but they also broadcast to the world how hypocritical Americans are: the First Amendment to the U.S. Constitution reflects that this country was first colonized by Europeans primarily in order to escape religious persecution, and, by prohibiting any sort of religious test for public office, our Founding Fathers recognized that someone’s religion is a poor basis on which to judge their character.  And an ugly perception of Americans around the world will, sadly, fuel more violence against Americans.

****

Tone Alert gave me five red bars for this one: but I'm not sure there's a way to talk about terrorism and racism without setting it off.

word of the day: obviate

The word of the day is obviate:

Etymology:  < classical Latin obviāt-, past participial stem (compare -ate suffix³) of obviāre to act contrary to, to go against (late 2nd cent. a.d.), in post-classical Latin also to meet (Vulgate), to withstand, oppose, prevent (5th cent.) 

1. trans.  

a. To meet and dispose of; to circumvent, do away with, remove (a difficulty, need, etc.); to prevent or avoid by anticipatory measures.

b. To anticipate, forestall. Obs. rare.

2. trans. To meet, encounter; to withstand, oppose. Obs. 

3. trans. To lie in the way between. Obs. rare.

"The endotherm asymmetry at 13 mole % GD1a suggests a phase transition which is more complex than a simple first order transition.  (Fig. 6 1B, 1C, also see ref. 34.)  It also obviates the possibility that a new species, such as mixed micelles, is formed in the dispersion (as was suggested for egg PC: GD1a dispersions having more than 10 mole% GD1a."

 - Barenholz et al., "Characterization of micellar and liposomsal dispersions of gangliosides and phospholipids", Advances in experimental medicine and biology 125:105 (1980)


Of course, knowing the meaning of this word is not enough to help me decipher this sentence: it would be nice if this paper actually had a Figure 6 1B and 1C.

Molecule of the day: trinitrobenzenesulfonic acid

The molecule of the day is trinitrobenzenesulfonic acid (TNBS).

It's often used to neutralize peptide terminal amino groups, but will react with any primary amine, and can also be used to measure the bilayer integrity of membranes containing phosphatidylethanolamine:

(Sadly, the "submitted" reference appears to have never made it into print.)

word of the day: lyotropic

The word of the day is lyotropic:

Etymology:  lyotrop- (in lyotrope adj.) + -ic suffix: see -tropic comb. form.
Physical Chem.  1. Associated with the change of internal pressure of a solution from that of the solvent which is caused by the solute. lyotropic series, a series in which ions are arranged in order of their lytropic effects, esp. their ability to cause precipitation of a lyophilic sol.   
2. Of a mesophase: having its phase transitions readily effected by a change of concentration. Also applied to the mesomorphism exhibited by such a mesophase. (OED)

Perhaps this definition from Case Western is a little more helpful:

"Liquid crystals come in two basic classifications: thermotropic and lyotropic . The phase transitions of thermotropic liquid crystals depend on temperature, while those of lyotropic liquid crystals depend on both temperature and concentration."


"The gangliosides, which are part of the lipid bilayer of the membranes differ in their lyotropic behaviour from the phospholipids and cholesterol which constitute the main components of the membrane.  The membrane phospholipids have two long hydrophobic chains, an interface region and a relatively small inogenic head group.  They are classified as 'non-soluble swelling amphipaths, implying that they do not form micelles but disperse spontaneously in water, forming bilyaered multilamellar large liposomes (MLV) or, upon ultrasonic irradiation small unilamellar vesicles (SUV).  In contrast, the gangliosides are 'soluble amphipaths' which form micelles in water.  The fact that, in spite of their two long hydrophobic chains the gangliosides are classified as 'soluble' amphipaths is explained by their large and highly negatively charged polar head group."

 - Barenholz et al., "Characterization of micellar and liposomal dispersions of gangliosides and phospholipids", Advances in Experimental Medicine and Biology 125:105 (1980).


I'm pretty sure they meant "ionogenic" instead of "inogenic".

I also have an irrepressible desire to look up the authors and mail them each a copy of Lynne Truss's Eats, Shoots, & Leaves.

molecules of the day: filipin and amphotericin B

The molecules of the day are filipin:

(PubChem)









and amphotericin B:

 (PubChem)

They're antibiotics that work by associating with cholesterol and thereby altering membrane structure.  (Not clear to me why that would select prokaryotic over eukaryotic cells: any ideas?)

word of the day: monotectic

The word of the day is monotectic:

The reversible transition, on cooling, of a liquid to a mixture of a second
liquid and a solid.  (IUPAC Compendium on Chemical Terminology)


"An equimolar mixture of dilauroyl phosphatidylcholine and distearoyl phosphatidylcholine, which shows a monotectic behaviour, is hydrolysed at all temperatures."

 - J.A.F. Op den Kamp et al., "Action of pancreatic phospholipase A2 on phosphatidylcholinebilayers in different physical states", Biochimica et Biophysica Acta 406:169 (1975).

Word of the day: sessile

The word of the day is sessile:

sessile, adj.




Etymology:  < Latin sessilis sitting down, dwarfed, stunted, < sess- , participial stem of sedēre to sit  

1. Having no footstalk. 
a. Bot. Of leaves, fruits, flowers, or other organs: Immediately attached by the base; not having a peduncle, pedicel, or the like. Hence of a species or variety (e.g. of oak) bearing sessile fruits: opposed to pedunculated. 
b. Zool. Of limbs or organs: Immediately in contact with the structure to which they are attached; having no connecting neck or footstalk. Also of certain animals.c. Pathol. Of morbid growths, warts, etc.: Adhering close to the surface.
2. Of certain animals: Sedentary, fixed to one spot; not ambulatory. Of cells: Immobile. Also in extended use. 
3. Crystallogr. Of a dislocation in a crystal: unable to migrate through the lattice; fixed. (OED)


"This is ridiculous!  Hive queens are supposed to be sessile!"

 - Tarvek, Girl Genius volume 12, page 103, Phil and Kaja Foglio