Tag Archives: biochemistry

The (Mostly) Untold Story of the Oxygen Revolution

[Cyanobacteria–green, brown, and orange streaks–grow in hot spring at Yellowstone National Park. Photo by Harvey Barrison via Flickr & Creative Commons 2.0] 

The troublemakers were hardly new to the neighborhood. For 300 million years, they had lived in the water column, floating in the sunlight near the surface, sending tiny plumes of toxic gas into the air. That was how they ate: sunlight in, poison out. But it was nothing the ecosystem couldn’t handle. The atmosphere was vast, and the troublemakers were microscopic. The poison diffused. Life went on.  

Until something changed. For some reason, there were more of the green troublemakers. Quadrillions more. So many more that their poison became the air itself. An entire world’s atmosphere transformed. Those that could tolerate the miasma grew and spread. Others survived in pockets of the planet where the new air couldn’t reach them. Uncountable numbers died.

The sunlight-eating oxygen-makers inherited the Earth.

In other words, 2.3 billion years ago, photosynthesis caused a mass extinction.

Continue reading “The (Mostly) Untold Story of the Oxygen Revolution” »

Why DNA is like a phone cable (Recap of a Talk by Prof. Jacqueline Barton)

[Computer rendering of DNA. Via Caroline Davis2010 on Flickr & CC 2.0] 

The Talk:

“DNA-mediated Signaling with Metalloproteins”

In Plain English:

DNA can conduct electricity–like metal wire–and that helps the cell life

The Speaker:

Jacqueline Barton of Caltech

The Sponsor:

MIT Inorganic Chemistry (invited by the grad students)

What It Covered:

When Jacqueline Barton’s lab began publishing papers claiming that DNA can conduct electricity, many of her colleagues didn’t believe them. But in experiment after experiment, they kept finding that they could send small amounts of electricity–much lower than the amount that flows through your charger cord–from an electrode on one end of a DNA strand through to the other.

The exceptions were stretches of DNA with “missense mutations“, hiccups in the genetic code that violated the rule of “G” aligns with “C” and “A” aligns with “T”.

A,T, G, and C are biologists’ shorthand for four small molecular structures– adenine, thymine, guanine, and cytosine– that repeat over and over again along DNA’s backbone. It just so happens that a G-C pair takes up exactly the same amount of space and adds exactly the same amount of twist as an A-T pair.  Anything else–a misplaced guanine, a broken cytosine, or a chemical tag on thymine– throws the DNA’s twist out of whack. And apparently,  the missense mutations also blocked electrical currents’ flow through a tiny gap in the center of the DNA.  Mismatched base pairs or base pairs that were even slightly damaged blocked the electrons’ path. Continue reading “Why DNA is like a phone cable (Recap of a Talk by Prof. Jacqueline Barton)” »

What’s in a Mutant Membrane?

[Photo by Yale Rosen, via Creative Commons]

“Pitch Imperfect” is a series of blog posts where I highlight stories that I pitched but didn’t quite sell and discuss why it was tough to sell them. The goal is to share both interesting research stories and some of the obstacles in getting them into the news cycle.

Proposed Headline:

How an Ordinary Piece of Lab Equipment Might Help Identify Fatty Acids in Cell Membranes

Proposed Dek (aka “the sub-headline” or  “social media blurb”)

The makeup of cell membranes is more diverse than many suspect, but it’s hard to tell the molecules in membranes apart. This study might change that

The Pitch: (as sent on February 23rd)

Yesterday, I spoke with a Purdue biochemist whose lab may have opened up a whole new avenue of research on cell membranes and fatty acids. Their paper debuted on PNAS Early Edition , and Purdue has issued a press release, but so far no news outlets have picked up on its potential for helping biologists make sense of fatty tissues.

Yu Xia and her post-doc XiaoXiao Ma were able to identify 96 distinct fatty acids in a sample of rat brain tissue, using one of the most universal pieces of scientific equipment, a mass spectrometer. Up until now, no one has been able to tell fatty acids in cells apart without resorting to extremely expensive techniques.

Continue reading “What’s in a Mutant Membrane?” »

Splice of Life: 3 Examples of How Nature Edits Its Own Genes

About the “Under the Radar” series: Some scientific concepts come up again and again in interviews with scientists but never find their way into newspaper headlines. Each post in this series follows one of those biology “bogeys” that fly under journalism’s radar through 3 different mini-stories.

Story #1: Scientists splice up a CRISPR chicken…and find an evolutionary shortcut

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Birds’ brains have all of the tools to make mammal-like neurons, according to a study in Science from August And, incredibly, the researchers behind the study only had to tinker with one gene  that changes how chicken cells edit their RNA to unlock several seemingly unrelated mammal neuron traits in chicken neural precursor cells.

It was as if the chicken cells instantly acquired a whole bunch of mutations at once, instead of just one. 

Researchers think that this gene editing process– aka “alternative splicing”–may explain why some traits seem to have evolved at such high speeds.

“This is a process that has diverged very rapidly during evolution to produce different versions of proteins,” University of Toronto geneticist Ben Blencowe explained in a phone interview.

500 million years is a long time to evolve, but it’s still hard to account for all of the diversity in vertebrates based on variation in DNA base pairs alone.

The key to animal diversity lies in an aspect of biology that your high school biology class kinda sorta covered, but lots of people forget all the steps after they’re done cramming for the test.

Continue reading “Splice of Life: 3 Examples of How Nature Edits Its Own Genes” »

Gaia Theory, “Irresponsible Heroes”, & Why We’re Like Cyanobacteria- Recap of talk by Dr. Andrew Knoll & Dr. David Grinspoon

The Talk:

“Planetary Changes from Deep Time to the 4th Kind”

In Plain English:

Life doesn’t just adapt to geochemical features; it transforms them simply by…living.

The Speaker:

Andrew Knoll of Harvard and David Grinspoon of the Planetary Science Institute

The Sponsor:

Planet and Life Series, sponsored by MIT Earth, Atmospheric, and Planetary Sciences dept. (EAPS)

What it covered:

Climate shapes life. This is a fact. But when you get right down to it, life is not a fragile, softly-treading phenomenon; every living cell is an interlocking network of chemical reactions. Nutrients and resources are taken in; other chemicals get spewed out.

It would be rather amazing if all those living organisms didn’t have some effect on the non-living environment. But what kinds of impacts? And how can we, as humans with advanced technology, understand and predict the effects our actions will have on the environment?

These are the questions being addressed by The Planets and Life Series at MIT, and the kick-off event, held back in September (unfortunately, I do not get paid to write this blog) was a doozy. Continue reading “Gaia Theory, “Irresponsible Heroes”, & Why We’re Like Cyanobacteria- Recap of talk by Dr. Andrew Knoll & Dr. David Grinspoon” »

Viruses can shut down our anti-viral proteins – Recap of talk by Dr. Ileana Cristea

The Talk:

Host Defense and Viral Immune Evasion: A Proteomics Perspective

In Plain English:

Human cells and viruses are locked in a protein-based arms race for global domination: Will the cell’s defensive proteins successfully recognize viral DNA and alert the immune system? Or will the virus counter with proteins that stop the defensive proteins in their tracks? The answer is that both of these processes are happening all the time.

The Speaker:

Ileana Cristea of Princeton University’s Molecular Biology Department

The Location:

Harvard Medical School’s Microbiology & Immunobiology department

What it covered:

Full disclosure: I got to the talk about 10 minutes late after being stopped by a security guard (who wasn’t sure how to react to a 22-year-old with a backpack who could speak proteomics-babble but couldn’t produce a student ID). So I missed the first few slides of the talk, but when I arrived, Dr. Cristea was introducing the HMS research crowd to Gamma-Interferon-Inducible Protein 16 (IFI-16) and its role in the innate immune system. Continue reading “Viruses can shut down our anti-viral proteins – Recap of talk by Dr. Ileana Cristea” »