I’ve also been able to put together some really fun pieces in the past few months. A few highlights:

Over at BioTechniques, I spoke with the people behind the proteomics papers, the mass spectrometry experts who tailor their instruments to solve otherwise intractable problems (“Pimp my spec!“, PDF). People like Michael Westphall, an astrophysicist-turned-mass spectrometrist, who developed a gas chromatography-coupled Orbitrap mass spec after a short career detour in rocketry, and Phil Compton, a chemist who devised a more efficient instrument architecture for electron transfer dissociation.

Also in Biotechniques, I wrote about new methods for probing the structure of DNA (PDF), techniques like atomic force microscopy and FRET, magnetic tweezers and electron microscopy.

I wrote about the new technologies of epigenomics over at Science, and also at The Scientist, where I focused on data analysis. At Double X Science, I wrote about a potential antibody therapy for hemophilia A and new methods for downsizing x-ray crystallography. And in The Scientist, I penned a short item on the proliferation of new genomics-focused undergraduate courses. 

It’s been a busy year, and I’m looking forward to an even busier 2013. In the meantime, head over to my Publications page for a complete listing of my work.

First off, some exciting news. The brilliant writers over at Double X Science (“Science, I am just that into you”), have given me a platform to talk tech. I’ve written two posts so far, one on a nanotech-based test for MRSA, the other on microbe-made biofuels.  (I also penned a few pieces for the Huffington Post, on 3D imaging of individual nanoparticles and in vitro molecular evolution.)

I’ve been named a contributing writer over at BioTechniques, writing TechNews features for them about once a month. Some of my favorites from the past year have discussed cell motility, single-cell genomics, and top-down proteomics. I also got to write a fun piece on molecular gastronomy, and another on how researchers spend — and don’t spend — their startup funds (Run your lab on dollars a day!).

I wrote about strategies labs can use to get by in tough economic times for NatureJobs, and about animal-free toxicology and protein microarrays for Science.

At The Scientist, I’ve covered about flow cytometry and microbiology lab automation, and penned a fun Notebook item on the technicians who work in Michael Davidson‘s microscopy lab at Florida State University (Microscopy Boot Camp).

There’s more, of course. For a complete list of my clips, click here.

Image: Petra Fromme & Raimund Fromme, ASU/BioTechniques

Hello, and happy Fall! As our internal clocks labor to get back into sync with the annual falling back of our (physical) clocks, I thought I’d update you on some of my newest and most noteworthy articles:

In the online edition of Chemical and Engineering News, I wrote about devices to monitor tissue oxygenation during surgery (Aug. 26) and chemically sniff out sea mines underwater (Oct. 10), as well as a new method to synthesize fluorescent “upconversion nanoparticles” in the microwave (Nov. 3).

In BioTechniques, I wrote about the ongoing problem of cell line misidentification (August) — a problem that could potentially invalidate thousands of studies and millions of dollars worth of research — as well as techniques for monitoring protein conformation in vivo (October) and antibody engineering (November). The latter methods — phage display, yeast display, and related approaches — could ultimately help generate “protein binders” for every protein in the human proteome, an idea that is already moving ahead (viz: this NIH RFA), albeit slowly.

In the August 18 issue of Nature, I wrote about the challenges and opportunities of the physician-scientist career path, while in The Scientist I wrote a how-to guide to reanalyzing publicly available transcriptome data (September). Also in the pages of The Scientist, as part of the magazine’s 25th Anniversary issue, I looked back at a at a quarter-century of genomics technology (October) with genomics luminaries George Church, Leroy Hood, and Mary-Claire King. In that article Dr. King made, I think, the most wonderful observation:

“The fundamental questions of genetics haven’t really changed; what’s changed is our capacity to answer them. We’re now in a position to be able to answer these questions with technology that simply didn’t exist before. But in a way, this technology is wasted on us. This technology should have been in the hands of Darwin and Mendel and much smarter people than any of us. But we’re the ones that have it, and so we can now go back and answer their questions.”

I might debate that point — I can’t imagine a group of researchers much smarter and more creative than King, Hood, and Church — but I do look forward to seeing what they, and the rest of the ‘omics community can do with those technologies over the next 25 years.

Credit: Biotechniques.com/A. Fromann

It’s been a busy few months of late, and I’ve been remiss in updating you on what I’ve written. So, without further ado, here’s a summary of what’s new:

• A neat article published in C&EN online about a bioluminescent method for measuring DNA methyltransferase activity (May 13);
• TechNews articles in BioTechniques on the Human Proteome Project (March), in vivo stem cell imaging (April), mass spec imaging (May), the development and commercialization of STED superresolution microscopy (June), and copy number variant detection technologies (July);
• A Nature Methods feature on using computer skills to code your way out of a problem (July);
• A Science Life Science Technologies article on the technologies of food forensics (June 24);
• And LabTools articles in The Scientist on how to crunch next-gen sequencing data (March) and how to make your lab more environmentally friendly (July).

Enjoy!

Credit: Science magazine

The March 25 issue of Science magazine includes my latest Life Science Technologies feature, “Synthetic genomics: Building a better bacterium.” Driven by J. Craig Venter’s blockbuster announcement of a “synthetic cell,” this article looks at the technologies and challenges inherent in trying to craft a genome from the ground up.

To build Mycoplasma mycoides JCVI-syn1.0, Venter and his team at the J. Craig Venter Institute ordered up 1,078 synthetic 1-kb cassetes from synthetic gene firm Blue Heron. They then assembled those pieces via recombination in yeast, building first 10-kb pieces, then 100-kb, and finally the complete 1,077,947-bp chromosome. Highlighting the importance of accurate DNA synthesis, a single error in the dnaA coding sequence set the team back three months.

The study attracted serious attention. Watchdog groups weighed in, as did US President Barack Obama. Arthur Caplan, writing in Nature, called the work “one of the most important scientific achievements in the history of mankind.” Others were more measured; New York Times science writer Nicholas Wade called the research “a matter of scale rather than a scientific breakthrough.” The U.K.’s Daily Mail, in a bit of nuanced headline writing (and while simultaneously invoking the specter of global pandemic as in the Will Smith movie, I Am Legend), declared: “Scientist accused of playing God after creating artificial life by making designer microbe from scratch—but could it wipe out humanity?“

The answer to that question is unquestionably no. But, before researchers can hope to replicate Venter’s feat (which took 15 years and cost some $40 million), they’ll have to bone up on their biology. Venter’s study, says Raik Grünberg, a postdoctoral fellow in Barcelona who develops synthetic biological circuits, highlights not only a technological development, but also researchers’ biological ignorance. “It shows that we can now write genomes. But at the same moment everyone is realizing … we don’t really know what to write.”

Or, as Venter himself put it to the New Yorker in 2000, ”My view of biology is, ‘We don’t know shit.’ “

http://www.humanconnectomeproject.org

My feature on neural connectivity — known in ‘omics parlance as “connectomics” — appeared this past October in BioScience Technology magazine [5M PDF]. Appearing shortly after the September 2010 launch of the NIH-funded Human Connectome Project, the article looks at the technologies researchers will use to untangle the cerebral spaghetti that is neural connectivity.

It’s a daunting task; by one estimate, “each human brain contains an estimated 100 billion neurons connected through 100 thousand miles of axons and between a hundred trillion to one quadrillion synaptic connections.” Those connections seemingly govern learning, memory, personality, and disease; says MIT computational neuroscientist Sebastian Seung, “I am my connectome.”

Researchers still cannot plumb connectivity with synaptic resolution, at least not at a whole-brain level, but they can get a 30,000-foot overview. The key tool researchers will use to tease out those tangles: functional and diffusional magnetic resonance imaging. Researchers will be collecting a battery of such data, plus behavioral, genetic and neural activity traces, on each of 1200 or so individuals. The trick will be to integrate all those data into a unified online resource that enables researchers to explore and exploit them.

If the past is any guide, results could come soon. Data from the “1000 Functional Connectomes” project, a retrospective analysis of 1,414 fMRI datasets published in 2009, has already been downloaded thousands of times. Publications utilizing the data have already appeared. “There are a lot of papers around the world in preparation or in press or in current analysis that are all building on this initial bolus of data,” says project director Michael Milham. It’s not synaptic level connectivity, but for connectome researchers, it’s a good start.

[Image credit: Human Connectome Project; http://www.humanconnectomeproject.org/overview/]

With an instrument cost of just $50,000 (and a per-run cost of about $500) the Ion PGM, says the Broad Institute’s Chad Nusbaum, could “democratize” DNA sequencing, filling a need for those researchers who have neither the need for, nor the access to the gigabase-spewing behemoths currently dominating the next-gen market. Other physical methods, though still in development, could similarly upend the sequencing industry. But don’t count existing technologies out just yet, says Harvard geneticist George Church; Life Technologies, Illumina, 454, and the like still have some juice left in them, too. Church cites five niches that could help a new technology establish a beachhead: cheaper instruments, lower costs per run, longer reads, faster speed, and portability. “But to really capture the market,” he says, “it’s going to be dollars per base pair.”

The December issue of BioTechniques includes my TechNews feature on single-molecule FRET, “Bright lights, single molecules.” A technique for measuring the relative distance and orientation of two molecules relative to one another, smFRET has been likened to a “molecular ruler.” It has been used to study the folding of proteins of RNAs, the assembly of macromolecular complexes, and even drives an in-development “3rd-generation” sequencing technology called Project Starlight (Life Technologies).

As the name suggests, smFRET is a variant of FRET, a concept first detailed decades ago and as old as time: it is essentially thanks to FRET that light harvesting complexes in plant leaves can funnel their captured energy to photosynthetic centers. Yet traditional FRET describes the average behavior of a bulk population of molecules—the proverbial roar of the molecular crowd, as it were. smFRET focuses on individual molecules, recording energy transfer events as single molecules flex.

Taekjip Ha developed the technique as a graduate student with Shimon Weiss (then at UC Berkeley). The concluding statement in the abstract of his seminal paper, which his graduate research advisors insisted he include, reads: “Monitoring conformational changes, such as rotations and distance changes on a nanometer scale, within single biological macromolecules, may be possible with single-pair FRET.” “I thought that was bullshit,” Ha now recalls, “but it turned out they were right. It turned out to be a general mechanism to study biomolecular interactions.”

Just a quick note to say ScienceWriters 2010 is done, and I’m heading back home after a lovely weekend in New Haven. I posted a complete roundup of links to our session, including slide decks, blog postings, and video, here. Check it out, and keep the productivity conversation going, on Freelancer Hacks.