Posts tagged as:

molecular biology

Molecular machine animations
in the New York Times

November 16, 2010

The New York Times has an article, “Where Cinema and Biology Meet”, on the recent high-quality animations of biomolecular machines.
The author, Erik Olsen, highlights Drew Barry as the Steven Spielberg of the field:
Mr. Berry’s work is revered for artistry and accuracy within the small community of molecular animators, and has also been shown in museums, [...]

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Trehalose vs. trehalase

September 18, 2010

Update, 3 March 2011: Trehalose reportedly “has good blood–brain barrier penetration”.

My recent post, “Trehalose, autophagy, and brain repair” references a few of the papers that suggest potential advantages to absorbing and circulating some of the wonder-sugar, trehalose. The problem is trehalase.

– Trehalose –

In us animals, trehalase metabolizes trehalose into glucose, but the details differ widely. [...]

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Trehalose, autophagy, and brain repair: Sweet

September 15, 2010

Abstract of recent abstracts:
Trehalose induces autophagy.
Autophagy induces neuronal repair.
Starvation induces autophagy.
Trehalose goes well with coffee and tea.

– Trehalose –Now on sale

Quote: “Macroautophagy (here simply called autophagy) is a cellular housekeeping process that degrades and recycles long-lived proteins, large protein aggregates, and even entire organelles like mitochondria. The term autophagy is of Greek origin and translates [...]

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Autophagy:
Why you should eat yourself

July 24, 2010

I’d like to say a few words about one of the hottest and, in my view, most important areas in biomedicine: autophagy, a process crucial to health, disease, and aging. Autophagy research is expanding rapidly.
In autophagy (“self eating”), cells engulf and digest their own macromolecules and organelles. Autophagy serves two functions: providing critical nutrients in [...]

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Learning Bioinformatics

March 12, 2010

Bioinformatics is huge, growing, fast, and has a surprising range of applications to molecular systems engineering. Here’s a PLoS article: “A Quick Guide for Developing Effective Bioinformatics Programming Skills”. From the abstract:
Successful adoption of these principals will serve both beginner and experienced bioinformaticians alike in career development and pursuit of professional and scientific goals.

[...]

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Molecular Electron Holography:
Progress toward atomic-resolution imaging?

October 20, 2009

Hans-Werner Fink’s group reports a remarkable advance in imaging individual biomolecules, with surprising physics, and (to me, at least) a somewhat mysterious date of publication.
The surprise is that it doesn’t destroy the molecules before imaging them.
The new generation of aberration-corrected electron microscopes achieve atomic resolution, but with a caveat — they succeed with robust, inorganic [...]

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Productive Nanosystems: The Ribosome Videos

July 16, 2009

While browsing the literature on the catalysis of bond formation in protein synthesis by ribosomes*, I came across a wonderful set of videos of the ribosomal protein manufacturing system at work, shown in recent-state-of-the-art molecular detail. These videos were presented in a Chemical & Engineering News article online, but I missed seeing them at the [...]

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Machines Evolving to the Brink of Failure

April 30, 2009

While writing a post on molecular engineering for the Macromolecular Modeling Blog, I came across an EMBO Reports paper that provided new guidelines for protein engineering; It also illustrates a general principle that should be taken to heart by anyone thinking about molecular engineering from a biomolecular perspective:
Molecular machines tend to evolve toward the [...]

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Macromolecular Modeling
for Molecular Systems Engineering

April 16, 2009

Nir London of the Macromolecular Modeling Blog has invited me to offer my perspective on the field. After patiently waiting for me to complete it, he’s posted the resulting essay, which I have cross-posted below.
The Macromolecular Modeling Blog is hosted by the Rosetta Design Group, which offers molecular modeling services based on the Rosetta protein [...]

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A High-Performance Polymer
for Nanosytems Engineering

March 19, 2009

Molecular objects made of a nylon-like, high-performance polymer are among the most intricate and functional nanostructures in existence today, and they’re being used to develop increasingly advanced, atomically precise nanotechnologies. This high-performance polymer is really more of a construction kit: Its monomeric parts can be bonded and folded to build atomically precise structures that self-assemble [...]

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What’s in the Vault?

February 22, 2009

They’re called “vaults”. They‘re in our cells, and in those of every* plant, animal, and fungus. Like ribosomes, they’re atomically precise self-assembled structures made of protein and RNA, but they’re big and hollow, large enough to pack many ribosomes inside. They’re relatively simple and symmetric: A vault consists of two identical halves, each consisting almost [...]

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Productive Nanosystems: The Movies

January 30, 2009

In his comment on Molecular Machine Assembly: The Movie, Drew Whitehouse reminded me of a set of excellent animations of biological productive nanosystems, work done by Drew Berry. These videos are based on scientific data describing molecular structure and function, and from what I’ve seen, Drew Berry’s work is the best of its kind. Below [...]

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