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Science

The Craigslist of Antibiotic Resistance

(Before we get going: this the the 100th post on Byte Size Biology. Happy Birthday to me!) Resistance to antibiotics is a huge clinical problem. In the US, more people die of  methicillin-resistant Staphylococcus aureus (MRSA) infections (nearly 19,000 in 2006) than of AIDS (14,627).  We know that antibiotic resistance is carried on mobile genetic […]

A FLORA of Protein Structure to Protein Function

Proteins are the machinery of life, and they facilitate most of life’s functions. Traffic into and out of the cell? Protein pumps, pores and channels. Respiration? Proteins. Metabolism and catabolism? Proteins. Immune system, signaling, development…  all complex networks of interacting proteins. Understanding a protein’s  structure can tell us a lot about how it performs its […]

Short bioinformatics hacks pt. 3: more FASTA counting

A few one-liners to kick off the workweek: To order a set of fasta files by the number of sequences each one contains. If anyone knows how to put a tab as the output delimiter, please let us know: grep -c “>” fasta-files/*.fna | cut –fields=1,2 -d “:” –output-delimiter=”  ” | sort -k 2 -nr […]

Freeloading pays off, but only up to a point.

Quorum sensing Social behavior is not exactly the first term that comes to mind with relation to microbes. After all, we assume a certain amount of intelligence and an ability to implement a behavioral pattern in response to peer actions. Humans, yes. Apes, yes. Birds of a feather flock together… so birds, yes. Ants and […]

PLoS Currents: Influenza. Because knowledge should travel faster than epidemics

(Full disclosure before I start: I am an academic editor in PLoS ONE. I have no financial stake in PLoS, and as far as I know, they have none in me. They’d better not, if they know what’s good for them). PLoS have come up with yet another cool mechanism for scientific communication: PLoS Currents. […]

Coast to coast (almost) pt. 5: a visit to the Eocene

We drove into Colorado Springs last  night (Friday). In the morning we had a superb breakfast, the best so far, at Smiley’s. Across the street from Smiley’s there is Poor Richard’s Bookstore, a used bookstore large enough to spend whole days in, yet small enough to feel local-neighborhood-y. Definitely a welcome change from the Borders […]

Coast to coast (almost) pt. 4: motel decor, food chains

August 4:  outside motel décor; food chain on a stick. Motel décor The last two motels in which we stayed used discarded agricultural machinery as a decoration outside their parking lots. One in Escalante, Utah has an orange colored tractor. Another in Hanksville had horse-drawn plows. Definitely cheaper than hiring someone to do your outside […]

Coast to coast (almost) pt. 3: big country, small things

We are “going up” the Grand Staircase in Utah now.  After Zion, we hiked in Bryce Canyon, and tomorrow we will explore the area around Escalante and Capitol Reef. While constantly bombarded by the grand geological marvels of these places, it’s probably important to keep track of some small things. Like this leaf -mimicking grasshopper […]

Science 2.0: things that work and things that don’t

Open Notebook What is it? Open Notebook means “no insider information” You lab notebook is on a wiki, out there for everyone to see. Negative results & all.  You share your research process with the world as you go along. There are many shades to this process: you may share some of your data, edit […]

Absolut standards: report from the M3-2009 meeting, part 2: signature genes and big science

Some more presentations from the metagenomics, metadata, and metaanalysis (M3) meeting, Stockholm June 27, 2009 Pathway Signature Genes Lucas A. Brouwers, Martijn A. Huynen and Bas E. Dutilh CMBI / NCMLS, Radboud University Nijmegen Medical Centre, The Netherlands If we take a sample of soil, how can we know whether it is adequate for growing […]

A Flurry of Red and Green

UPDATE: I submitted this post to the National Evolutionary Synthesis Center’s sponsored contest for a travel award to ScienceOnline2010. Let’s see how it goes… #scio10 In a previous post about Hatena we saw what might very well be the beginning of a (beautiful?) [:ttip=”symbiosis where one partner lives inside the cell of the other” id=”10″]endosymbiotic[:/ttip] […]

Swimming lizards and jamming moths

Two interesting stories in Science this week, with some nice movies accompanying each. Swimming lizards The sandfish is a skink that lives in the Sahara desert. Aptly named, it dives into the sand like a fish. After that, it was anybody’s guess how it moves. Until now: researchers in Georgia Tech took high resolution X-ray movies […]

Scientists singing

Somehow, sharing the same problems with Uri Alon makes me feel almost absolved of the sins against my own family in spending Sundays at the lab. Almost: Ron Laskey has a whole collection of songs, published as an audiobook in Cold Spring Harbor Laboratory Press. (I guess CSHL Press does not qualify as an indie […]

Distant homology and being a little pregnant

(Thanks to F.B.  for the inspiration). Sigh… people don’t seem to learn. It’s been almost 22 years (yikes!) since a distinguished group of scientists published a letter in Cell calling for a responsible use of the word “homology”. If you were born when that letter was published, then in the US you can already drink […]