Ret­ro­spec­tive, June to De­cem­ber 2011

We've pre­pared this quick tour for you, with brief vis­its to all the ma­jor ar­ti­cles we posted since our May, 2011, ret­ro­spec­tive.

In Memo­riam

Lynn   a pre­em­i­nent fig­ure in mod­ern bi­ol­ogy, Lynn Mar­gulis died sud­denly at the age of 73. She was a good and an old friend of mine. When we were both liv­ing in New­ton, Mass­a­chu­setts, our spouses wanted noth­ing bet­ter than for us to take the kids out of the house on…

Mi­cro­bial Be­hav­ior

Are You Me or Am I You?  Pro­teus mirabilis is one sen­tient bug: it can dis­tin­guish it­self from its par­ents and rel­a­tives.

Ring­ing a Mi­cro­bial Din­ner Bell  Bac­te­ria make smelly stuff, some of which pro­vides ap­pe­tiz­ing cues for in­sects. As­so­ciate blog­ger Mark Mar­tin ex­plains.

Struc­ture and Func­tion

Hard Bi­ol­ogy  How do di­atoms make their glass-hard shells? Well, they as­sem­ble sub­units within the cells, then ex­port them and in­sert them into pre­formed struc­tures.

Some Like It Curved  How do bac­te­ria make curves in their cell wall? It turns out that car­di­olipin is a curved and curve-in­duc­ing lipid mol­e­cule found in the curvi­lin­ear cell poles of rod-shaped bac­te­ria.

Raft­ing Through Time  Do bac­te­ria have lipid rafts in their mem­branes, a la eu­kary­otic cells? Pos­si­bly.

Vi­tal or Not Vi­tal: That Is the Ques­tion  Guest Gemma Reguera clar­i­fies the con­fu­sion about what is vi­able and what is vi­tal, in­clud­ing what 'vi­tal dyes' tell us about such states.

Viruses

Virus Hacks In­ter­cel­lu­lar Com­mu­ni­ca­tions Net­work  Cells of our im­mune sys­tem talk to each other when mo­bi­liz­ing a de­fense, but vac­cinia has many clever ways to tam­per with those mes­sages for its own ben­e­fit.

Bac­te­ria Liv­ing With­out Phages?  Are there en­vi­ron­ments where there are abun­dant bac­te­ria and no phages? Sounds like one of our Tal­mu­dic Ques­tions, but this one has a spe­cific an­swer, and that an­swer is Yes. That en­vi­ron­ment was found within a cys­tic fi­bro­sis (CF) lung…

Is a Good Of­fense the Best De­fense?  Yeasts have to choose be­tween hav­ing RNAi to de­fend against in­com­ing viruses and such, or host­ing killer viruses that elim­i­nate the com­pe­ti­tion.

Phage Lambda's Po­lar Ex­pe­di­tion  Are all re­gions on the sur­face of an E. coli equally invit­ing to an ad­sorb­ing lambda phage, or does lambda have a pref­er­ence?

Phage DNA: Go­ing with the Flow  To launch an in­fec­tion, a phage needs to trans­fer its DNA into the host cell, but a phage is not a hy­po­der­mic nee­dle.

And We Thought We Knew What CRISPRs Do!  Here's a new twist. A prophage in Pseudomonas aerug­i­nosa in­hibits biofilm for­ma­tion and the host's CRISPRs are re­quired.  

Now That's Us­ing Your Head!  We thought all tailed phages use their tails to rec­og­nize and at­tach to their host cells, but here's one that uses its head in­stead.

Viruses that In­fect Par­a­sites that In­fect Us: The Ma­tryoshka Dolls of Hu­man Pathogens  Grad­u­ate stu­dent Jamie Schafer takes us, layer by layer, through two sto­ries of viruses that in­fect par­a­sites that in­fect us, both with pos­si­ble clin­i­cal im­pli­ca­tions.

Patho­gen­e­sis

A Pestis from the Past  As­so­ciate blog­ger Mar­vin Fried­man re­counts the his­tory of the Great Plague, as il­lu­mi­nated by re­cent ge­nomic stud­ies of old bones.

The Lyme Dis­ease Spiro­chete Feasts on Tick An­tifreeze  A fel­low blog­ger, Mi­crobe Fan, al­lowed us to use his ar­ti­cle on how bor­re­lias use of an­tifreeze in ticks as a nu­tri­ent. Who would have thought?

The Janus Bug  And you thought that He­li­cobac­ter py­lori  was a bad bug, caus­ing ul­cers and can­cer! Well, it may also stim­u­late the im­mune re­sponse to pro­tect peo­ple from asthma.

Go­ing Next Door With­out Get­ting Your Feet Wet  By us­ing novel tech­niques, Daniel Portnoy's lab can in­tro­duce Burk­holde­ria into a cell, thus by­pass­ing early stages of in­fec­tion and iso­lat­ing later ones. New patho­gen­e­sis mech­a­nisms are now re­vealed.

A Clever Bug That Is Dif­fi­cile to Con­trol  Mar­vin Fried­man dis­cusses howClostrid­ium dif­fi­cile adeny­lates its te­i­choic acids to ward off the ac­tion of host de­fen­sive pep­tides.

How We Tell The Good Bac­te­ria From The Bad  MD/PhD stu­dent Micah Ma­n­ary tells us how the in­flam­ma­some (which some of us need to look up) is in­volved in se­lect­ing mem­bers of the in­testi­nal mi­cro­biome.

Ge­nomics and Evo­lu­tion

The Façade of E. coli K‑12  Noth­ing was thought to be less dan­ger­ous than the K‑12 strain of E. coli. Guess again. It's full of genes en­cod­ing fac­tors that can be turned on in HU pro­tein mu­tants.

Fine Read­ing:  Mi­cro­bial Evo­lu­tion  On the 150^th an­niver­sary of pub­li­ca­tion of On the Ori­gin of Species, 34 mi­cro­bi­ol­o­gists met in the Gala­pa­gos to dis­cuss the role of mi­crobes in evo­lu­tion.

Bac­te­ria Ac­ti­vate Fun­gal Gene Clus­ters  Cross-talk among very dif­fer­ent or­gan­isms are the rage. Mar­vin Fried­man presents an­other ex­cit­ing ex­am­ple.

What's Old is New: Genome Wide Ma­nip­u­la­tion of the Bac­te­r­ial Chro­mo­some in Vivo  Guest Michael Schmidt dis­cusses a novel and clever way of ma­nip­u­lat­ing the bac­te­r­ial chro­mo­some on genome-wide ba­sis.

Ecol­ogy

Ship­wreck Mi­cro­bi­ol­ogy  One ship­wreck can dev­as­tate a coral reef for decades. The cul­prit? Iron leached from the wreck­age.

One Size Some­times Can Fit All  And this is of great con­cern when it is one an­tibi­otic re­sis­tance fac­tor that can counter every an­tibi­otic in our ar­se­nal.

Some Like it Cold  Mar­vin Fried­man ex­plains that the trig­ger fac­tor pro­tein (a chap­er­one in­volved in keep­ing nascent pep­tides from fold­ing pre­ma­turely) is se­lec­tively up­reg­u­lated in the cold.

Tak­ing Bugs Out For a Spin  Grad­u­ate stu­dents Linh Truong and Sha­bana Din de­scribe the un­ex­pected re­sis­tance of bac­te­ria to very high g forces.

A Mi­crobe By Any Other Name Would Smell As Sweet...  Mark Mar­tin waxes elo­quent on the sub­ject of smells em­a­nat­ing form bac­te­ria and their uses.

Sym­bio­sis

A Bug in a Bug in a Bug  Bac­te­ria liv­ing in­side bac­te­ria? As­tound­ing as this sounds, you find them as nested en­dosym­bionts of mealy bugs.

Wol­bachia: The Dif­fer­ence Be­tween a Nui­sance and a Threat?  Grad­u­ate stu­dent Jamie Shafer tells a great story about a phage al­ter­ing how the en­dosym­biont Wol­bachia af­fects its in­sect host.

A Worm­ful of Bugs  Here's an­other ex­am­ple of an an­i­mal that con­sid­ers a gut ob­so­lete. In­stead, it em­ploys a sack of densely packed bac­te­ria that feed it by ox­i­diz­ing sul­fur.

Fungi

The King of the Fungi  Imag­ine a fun­gus half the size of a bowl­ing al­ley grow­ing from a fallen tree. A big tree.

Fungi That Spit Like Base­ball Play­ers  Guest Gemma Reguera re­veals new in­sights on how mush­rooms shed their spores. Fast! Very fast!

How to Es­cape a Deadly Em­brace  There lurk fungi in soils that can trap ne­ma­todes. Aha! The ne­ma­todes have evolved an es­cape tac­tic.

Tal­mu­dic Ques­tions

 #76, #77, #78, #79, #80, #81, #82

A Gath­er­ing of Com­ments on a Tal­mu­dic Ques­tion  Our TQ #81 (Given that most mu­ta­tions are dele­te­ri­ous, why does the mu­ta­tion rate not evolve to zero?) elicited es­pe­cially lu­cid com­ments. Here we sum­marize a few only (and apol­o­gize to those whose com­ments are not men­tioned).

Mis­cel­lanea

Did van Leeuwen­hoek Spend His Youth in France?  by Nanne Nan­ninga — This ti­tle might be un­ex­pected. Yet it is not with­out logic af­ter read­ing a lit­tle book, The Cleere Ob­server: A Bi­og­ra­phy of An­toni van Leeuwen­hoek, by Alma Smith Payne. The book­let is am­ply and skill­fully il­lus­trated by Charles Pickard. Ac­cord­ing to the back…

Why Blog?  Af­ter five years, you'd think Merry would have an an­swer to that ques­tion, a co­her­ent and sat­is­fy­ing an­swer that she could share. Well,...

Our Sixth Year Is Start­ing  Five years and over 500 posts be­hind us, I would like to share with you a bit of the his­tory of this blog. How did it start? I had re­tired of­fi­cially…

Fine Read­ing: Adap­ta­tions to en­ergy stress dic­tate the ecol­ogy and evo­lu­tion of the Ar­chaea, by D. L. Valen­tine  It's been over thirty years since Carl Woese dis­cov­ered the Ar­chaea, yet they still qual­ify as the most puz­zling of the do­mains of life. Many of them are ex­tremophiles, but not all, and…

How to Im­prove Vac­cines (or Not), 1912 Style  An­ti­bod­ies, it turns out, make a toxic vac­cine less toxic. So it was thought 100 years ago, and now we find out that this holds up.

Fine Read­ing: Mi­cro­bial Ge­nomics and In­fec­tious Dis­eases  We call at­ten­tion to a sem­i­nal pa­per by David Rel­man on this topic.

Two New Books (with my name on the spine)  When I'm not blog­ging, I tend to get in­volved in book pub­lish­ing. Twelve, so far. Mostly what I do is edit­ing, al­though I have been an hon­est co-au­thor for a few. My most re­cent ven­ture was a project…

Preach­ing to a Prokary­otic Choir  Mark Mar­tin di­rected some prob­ing ques­tions about the mi­cro­bial world to stu­dents in his un­der­grad­u­ate mi­cro class and shares with us the re­sults.

Of Terms in Bi­ol­ogy: Ri­boswitch  Twenty classes of these tal­ented RNAs are known, and they do in­ter­est­ing and di­verse jobs.

The Mi­cro­bial Weltan­schau­ung  Elio muses on the ef­fect of know­ing that there are so many prokary­otic cells on this planet.

What's the Score on the Mi­cro­biome?  Elio asks if the hu­man in­testi­nal mi­cro­biome is a good thing or a bad one? We kept score for a lit­tle while.

The As­ton­ish­ingly Rich Smörgås­bord of New Meth­ods for Light Mi­croscopy  The two age-old prob­lems of the light mi­cro­scope are res­o­lu­tion and con­trast. Res­o­lu­tion is a func­tion of the wave­length of light, so that in the vis­i­ble it is, at best, about 200 nm. This means that…