Small Things Considered

A blog for sharing appreciation of the width and depth of microbes and microbial activities on this planet.

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Of Terms in Biology: DGGE

DGGE, to keep the title short, stands for de­na­tur­ing gra­dient gel elec­tro­pho­re­sis. You may won­der what an elec­tro­pho­re­sis tech­nique is do­ing in our 'of Terms in Bio­lo­gy' sect­ion, but it was once a nifty way to ex­plore mi­cro­bial di­ver­si­ty in en­vi­ron­men­tal samp­les. And some­times it still is, which struck me... Read more →

Posted on September 19, 2022 at 01:30 AM in Methodology | Permalink | Comments (0)

Heavy-duty Traffic, Microscale

by Christoph  
Men­tion "fla­gel­la" and we mi­cro­bio­lo­gists in­stant­ly think of these in­gen­ious ap­pe­nda­ges that bac­te­ri­al cells use to pro­pel them­selves through fluids of va­ry­ing vis­co­si­ties (ar­chaea do this, too, with their ar­cha­el­la). We ra­re­ly think of them as an ac­ces­sory to trans­port car­go. Yes "car­go," you read cor­rect­ly, but may­be you re­mem­ber... Read more →

Posted on July 18, 2022 at 01:30 AM in Methodology, Physiology & Genetics, Teachers Corner | Permalink | Comments (0)

Of Terms in Biology: The Polony Method

by Christoph  
If there is one venerable la­bo­ra­to­ry tech­nique in vi­ro­lo­gy, it is the plaque assay for the de­tect­ion and quan­ti­fi­ca­tion of bac­te­rio­pha­ges. It was pio­neer­ed by Fe­lix d'He­rel­le al­ready around 1917, and in the ear­ly 1950s, plaque as­says were also es­tab­lish­ed for eu­kar­yot­ic vi­rus­es... Read more →

Posted on January 10, 2022 at 01:30 AM in Methodology, Viruses | Permalink | Comments (0)

Grant's Anatomy

by Christoph  
At an EMBO workshop in Copen­ha­gen in 2006 on 'Cell cycle and cy­to­ske­le­tal ele­ments in bac­te­ria,' I was al­most un­able to stay put in my seat dur­ing one pre­sen­ta­tion: Grant Jen­sen showed the 3D-mon­tage of cryoET ima­ges of mag­ne­to­somes in Mag­ne­to­spi­ril­lum mag­ne­to­tac­ti­cum. It was a vi­su­al jour­ney in­to and through the in­ter­ior of a cell,... Read more →

Posted on December 09, 2021 at 01:30 AM in Methodology, Teachers Corner | Permalink | Comments (0)

Getting to grips with the intangible

by Christoph | Imagine the E. coli nucleoid as a swig but of of a high­ly vis­cous tan­gle of a 2 nm thin and ~1.5 mm long DNA poly­mer, de­co­rat­ed with and high­ly com­pact­ed by a ple­tho­ra of pro­teins, and some­how sus­pend­ed in the cy­to­plasm of a cell with a vol­ume of ~1.3 µm3. It's vir­tu­al­ly im­pos­si­ble to "grip" the nu­cleoid, to mea­sure... Read more →

Posted on September 14, 2020 at 01:26 AM in Methodology, Physiology & Genetics | Permalink | Comments (0)

Of Terms in Biology: Phylogeny, Phylogenetics, Phylogenomics

by Elio | You may remember the solemn proclamation that "ontogeny recapitulates phylogeny," meaning that during our embryological development we (and everybody else) go through the steps in our evolution. This turns out to be quite wrong, but I bring it up because because it illustrates that phylogeny denotes the history... Read more →

Posted on September 03, 2020 at 01:54 AM in Methodology, Teachers Corner | Permalink | Comments (0)

Streptomyces spores taking a ride...

by Christoph | Streptomycetes, these non-mo­tile Ac­ti­no­bac­te­ria that are cap­able of my­cel­ial growth much like fungi, are quite in­vent­ive when it comes to the dis­tri­bu­tion of their spores. They don't just re­ly on en­chant­ing scents like geos­min that they emit to at­tract spring­tails, which trans­port their spores over long dis­tan­ces (see Ro­berto's re­cent post). They also rou­tine­ly em­ploy bac­te­rial trans­port wor­kers. Read more →

Posted on July 16, 2020 at 01:16 AM in Methodology, Physiology & Genetics, Teachers Corner | Permalink | Comments (0)

Mueller-Hinton Medium

by the STC team  
On June 11th, we were addressed in a tweet by microbiologist Joe Harrison (@JoeHarrison1):"This seems like a timely topic for a blog or an article @ASMicrobiology @STCmicrobeblog. Mueller-Hinton agar is used globally and has standardized the study of #AMR. Before today, I'd never read the story of Jane Hinton @citeblackwomen"... Read more →

Posted on June 18, 2020 at 01:13 AM in Methodology, Odds & Ends | Permalink | Comments (0)

Fine Reading: Guts and Glory, Microbiome Edition

by Janie
Research on the microbiome, particularly the gut microbiome, garners ever-increasing attention from both the scientific and public eye (and the press). But as with most other fads, there’s a need to parse out fact from fiction... Read more →

Posted on April 16, 2020 at 01:19 AM in Methodology, Physiology & Genetics | Permalink | Comments (0)

Of Terms in Biology: The Exome

by Elio | An exome is the collection of exons, the sequences within the primary mRNA transcripts of an organism that are eventually used for making proteins. The rest, non-coding sequences, called introns, are removed by RNA splicing. (Note that there is no ‘introme,’ at least not yet.)   Read more →

Posted on January 16, 2020 at 04:00 AM in Methodology, Physiology & Genetics | Permalink | Comments (0)

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