sciencenote:

RNA studies under fire

High-throughput RNA sequencing has yielded some unexpected results in the past few years — including some that seem to rewrite conventional wisdom in genetics. But a few of those findings are now being challenged, as computational biologists warn of the statistical pitfalls that can lurk in data-intensive studies.

….

For their study, Dulac and Gregg used high-throughput RNA sequencing to search mouse RNA for single nucleotide polymorphisms (SNPs) — one-letter variations in genetic sequence. The researchers then asked whether the SNPs they found for each gene could be traced to one or to both parents. If the SNPs were encoded mainly by one parent’s copy of the gene, the team concluded that the gene was imprinted (see ‘The silence of the genes’).

…The debate has implications for any sequencing-based study that requires statisticians to identify rare genetic phenomena using relatively new methods. “If you don’t deal with the analytical details very carefully, you’re going to get into trouble because of the low signal-to-noise ratio” in these types of experiments, says Jin Billy Li, a genomicist at Stanford University who was one of the critics of Cheung’s RNA-editing paper.

(via freshphotons)

ucsdhealthsciences:

Bacillus subtilis

A big step writ small

Microbial colonies are tiny cities of life. Understanding how they work – their integrated chemistry, genomics and phenotypes – has long been a sort of “holy grail” among microbiologists.

A step in that direction is reported this week by Pieter C. Dorrestein, PhD, associate professor at the UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences, and colleagues in a paper published in the Proceedings of the National Academy of Sciences.

The scientists describe a new, highly sensitive, broadly applicable and cost-effective technique using mass spectrometry to profile the metabolic activity of live microbes directly from a Petri dish without any sample preparation.

Though most people will never see it at work, the new visualization platform is a significant advance in understanding the space and time dynamics of interacting microbial colonies and communities. It’s a big step writ small, akin perhaps to the qualitative difference between studying a dinosaur fossil and watching a whole herd of frolicking sauropods.

(via n-e-o-n--t-i-g-e-r)

heythereuniverse:

Scanning electron micrograph of Apple iPod earbud filter. Skin is in green.

(via freshphotons)

father-damien:

Knee and Ankle Joints

(via scientificillustration)

doctorswithoutborders:

Lead Poisoning Crisis in Zamfara State, Northern Nigeria

In March 2010, MSF was alerted to a high number of child fatalities in Zamfara state, northern Nigeria—an estimated 400 children died. Laboratory testing later confirmed high levels of lead in the blood of the surviving children.

MSF is a central player in treating lead poisoning in Zamfara state, and is responding to the acute phase of this emergency. MSF has for the moment controlled mortality, but patients with lead poisoning will require significant long-term treatment and follow-up.

The root cause of the lead poisoning crisis is unsafe mining and ore processing. People who engage in mining and ore processing must be given access to facilities and programs to allow them to safely mine and process ore without exposing themselves or others to toxic lead.

There are three pillars that must be implemented for an effective response to the crisis:

▲ Medical care including chelation therapy and health education
▲ Environmental remediation
▲ Safer mining practices

Photo: A worker holds up a piece of mercury-gold amalgam at the Bagega processing site. The gold extraction process produces dangerous lead as a byproduct.
Nigeria 2012 © Olga Overbeek/MSF

isomorphismes:

Brains sound like a wicked-hard space to think about.

• It’s a tightly connected (but not totally connected) network (graph theory)
• Each of the nodes’ 3-D location may be important as well (voxels)
• The signals propagate through time (dynamical)

jtotheizzoe:

Phineas Gage’s Connectome

In 1848, railroad worker Phineas Gage had a 3.5-foot, 13 pound tamping iron blown through the front of his skull in a construction accident. Hell of a way to start your Wednesday (yes, I checked). He survived.

The story of Phineas Gage is now the stuff of legend, taught to first-year neuroscience students around the world. How did this man survive a rod through the frontal lobe? Doctors that wrote of him later spoke of extreme behavioral changes, a man who was “. . . fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows”.

Unfortunately, the legend of Phineas Gage’s post-injury brain is largely exaggerated, or at least based on rather thin evidence. But still, he was still a changed man, even if not in the extreme ways his legend suggests.

UCLA’s Jack Van Horn has reconstructed a model of Phineas Gage’s connectome. In the image above, the lower left image shows the “connectogram” of 110 healthy right-handed males, the major highways and byways between brain regions (the brain stem is at 6 o’clock, left and right hemispheres at 9 and 3 o’clock). The lower right image shows the connections that were likely disrupted by the iron spike through Gage’s frontal lobe.

Mo Costandi has a great write-up that you should check out. We now have a map of the damage to Gage’s brain. But do we really know any more about his supposed behavioral changes? Thanks to the exaggerations and sideshow mentality of those who studied hm while alive, likely not.

BONUS: Be sure to check out Robert Krulwich and Carl Zimmer moderating this debate on how much stock we should put in the connectome.

(via Neurophilosophy blog)

aureliomadrid:

ricin structure

(via scientificillustration)

(via scientificillustration)