Nanobiopsy: the beauty in the very small is a big deal

The ability to study the living without destroying it has been the goal of many scientists for decades. A new article in ACS Nano has paved the road towards noninvasive cellular-level examination. The only true way to study cellular dynamics is to study a single cell over time (temporally). The reason for this is the heterogeneous nature of any cell culture because no two cells are identical spatially and temporally. Each individual cell has its own set of experiences that has generated its current molecular inventory, ie. RNA molecules, metabolites, proteins, sugars, lipids, etc. Studying a community of cells gives rise to noise that makes finding significant differences incredibly difficult.

In the article entitled Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy, the authors used a kind of microscopy called scanning ion conductance microscopy, or SICM, that allows for continuous sampling of a single cell over time. The authors used a nanopipette as part of the SICM and combined this with sensitive sequencing techniques resulting in a high resolution look at what genes are being expressed over time into RNA molecules. Furthermore, this technique was used to study the genomic information of individual mitochondria within a single cell without also studying the nuclear material. In other words, this new technique has resulted in the ability to not only study cellular dynamics, but go beyond that and study subcellular dynamics.

This breakthrough will have impacts across many fields from cancer biology to improving climate models.

Paolo Actis, Michelle M. Maalouf, Hyunsung John Kim, Akshar Lohith, Boaz Vilozny, R. Adam Seger, & Nader Pourmand (2013). Compartmental Genomics in Living Cells Revealed by Single-Cell Nanobiopsy ACS Nano DOI: 10.1021/nn405097u

New Illustration: Yeastie Boys, a powerhouse for synthetic biology

Yeast image, science as art, microbe
An interpretation of the yeast Saccharomyces cerevisiae, a model for synthetic biology
When it comes to synthetic biology, two species of microorganisms should automatically come to mind; E. coli and the yeast Saccharomyces cerevisiae.  Both have been used extensively for proof of principle research. Thanks to these investigations, both are able to synthesize a drop-in biodiesel. 

More Yeastie Boys images available here.


Illustration of the world of synthetic biology: a new phase in science

animated bacteria, bioenergy, synthetic biology graphic
With novel technologies, it is becoming commonplace to manipulate microbes to acquire desired effects. Shown is a bacterium with foreign gene pathways (glowing) that enable this cell to efficiently produce a desired product.

First, there was biology which began in earnest in the 19th century. Then came molecular biology in the 1920s and the foundation of mutagenesis set forth by Herman Muller in 1927. Then, genetic engineering was first applied in 1972 the lab of Paul Berg. Finally, humans had the ability to manipulate living organisms in a specific, directed way. Fast forward 38 years to the announcement by J. Craig Venter that the first synthetic organism was created with a completely synthetic genome. However, Mother Nature is very particular about what exactly humans can do with respect to organismal manipulation. The naive thought that simple addition of genes from one organism into a more suitable organism would lead to theoretical, effective production of desired chemicals was soon the way of the albatros.

This is when scientists had to take a step back and rethink their strategy. They had to consider gene regulation (positive and negative feedback), build-up of secondary metabolites, toxicity of produced end products, etc. It wasn’t enough to add genes coding for enzymes necessary for desired chemical production. Through the advancements of bioinformatics, computation biology, and a nascent field called systems biology, scientists are just now starting to see the fruits of their labor.

Humor me; type in “engineering bacteria” into Google News. Take a look at the headlines that pop up in your browser. Look at the amazing advancements that are happening currently and imagine what is to come…

Molecules generated that can halt metastasis of colon cancer

See on Scoop.itScience Education and Communication

Medical researchers have managed to halt the progress of colon cancer and its metastasis in the liver in an experimental model with mice.

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In Honor of JUICE, a New View of Europa | The Planetary Society

I found out today that my friend does a guest blog for the Planetary Society!

In Honor of JUICE, a New View of Europa | The Planetary Society.

Put #government labs to work on #climatechange – The Washington Post

I want to start by saying I am part of the national labs system. I’m at Oak Ridge National Laboratory and work as a science writer for a small group that publishes for the Office of Biological and Environmental Research within DOE. That being said, I’m still a concerned citizen as well. I want my daughter to experience this planet as I have. This opinion article in the Washington Post by Naomi Oreskes, a professor of history and science studies at the University of California at San Diego, is brilliant and articulate. Straight at the heart of what the Executive Branch can do without going through the cluster f#ck that is Congress. However, as always, it comes down to money and reapportioning funding for the suggested changes in this article would essentially have to go through Congress. Here are the suggestions in the article:

●Alternative energy. The climate problem is fundamentally an energy problem. While strides have been made — by both industry and government — in developing alternative energy sources, renewables still provide only a sliver of the U.S. energy profile. The scale of renewable energy research and development needs to be radically increased.

●Carbon capture and storage. Shale gas development in the United States and Canada is generating jobs and revenue and could substantially decrease our reliance on petroleum. But shale gas is still gas — methane: a fossil fuel that when burned produces carbon dioxide. Large-scale development may exacerbate the climate problem if inexpensive gas undercuts the market for renewables. If, however, shale gas development could be coupled with carbon capture and storage, trapping the carbon dioxide produced, then this resource might be usable without worsening climate change.

●Energy storage. Wind and solar are real sources of energy, but only when the wind blows or the sun shines. Yet many wind and solar projects produce excess capacity that could be used later or elsewhere if it could be stored. Ideas for renewable-energy storage need to be developed and expanded.

●Social obstacles to energy efficiency. Numerous studies show that Americans could cut energy use by 30 percent or more through efficiency measures and save money at the same time. Yet most of us don’t. This is a bit of a mystery for economists; social science research in the laboratory system should be mobilized to figure out why we don’t save energy and money even when we could.

●Climate engineering. Deliberate alteration of the climate to compensate for inadvertent modification is a technically and ethically troubling concept, but it may be one of the only available means to slow climate warming and buy time while other solutions are implemented. Physical scientists should expand their work in this area, and social scientists and humanists should be enlisted to address the ethical dimensions and governance issues.

Curiosity-driven science has not yet provided the solutions to global warming, and universities are not well situated to address a single, overarching problem. Moreover, the president does not have authority over our nation’s universities. But he does have authority over our national laboratory system. The labs have been mobilized before; the time has come to mobilize them again.


The last part (in bold) is a great remark and one I completely agree with. These suggestions should be sent to the White House, perhaps through the petitions website. Are you with me?

Put government labs to work on climate change – The Washington Post.

Climate Change Series: Where Science And Ethics Meet | Cognoscenti #climatechange #science

Climate Change Series: Where Science And Ethics Meet | Cognoscenti.


This is a great, well thought out take on what is happening and what needs to happen. I like the emphasis on the ethical issues involved with changes in climate. I can’t wait to read the rest of the series.