The Future of Bio-technology

Hosts of technologies, most notably in electronics, have been on the path of miniaturization for decades and in 2005 they have crossed the threshold of the nano-scale. Crossing the nano-scale threshold is a milestone in miniaturization, setting impressive new standards for component-packing densities. It also brings technology to a scale at which quantum effects and fault tolerance play significant roles and approaches the feasible physical limit form many conventional "top-down" manufacturing methods. I will suggest that the most formidable manufacturing problems in nanotechnology will be overcome and major breakthroughs will occur in a host of technologies, when nanotechnology converges with bio-technology; i.e. I will argue that the future of bio-technology is in nanotechnology. In 2005, methods in molecular biology, microscopy, bioinformatics, biochemistry, and genetic engineering have focused considerable attention on the nano-scale. On this scale, biology is a kind of recursive chemistry in which molecular recognition, self-assembly, self-organization and self-referencing context-control lead to the emergence of the complexity of structures and processes that are fundamental to all life forms. While we are still far from understanding this complexity, we are on the threshold of being able to use at least some of these biological properties for .technology. I will discuss the use of biomolecules, such as DNA, RNA, and proteins as "tools" for the bio-technologist of the future. More specifically, I will present in some detail an example of how we are using a genetically engineered 60-kDa protein (HSP60) from an organism living in near boiling sulfuric acid to build nano-scale templates for arranging metallic nanoparticles. These "extremophile" HSP60s self-assemble into robust double-ring structures called "chaperonins," which further assemble into filaments and arrays with nanometer accuracy. I will discuss our efforts to use chaperonins to organize quantum dots, electronic and magnetic nano-particles for electronic and photonic applications

Is the Future Really in Algae?

Having just emerged from the warmest decade on record and watching as the oceans acidify, global resources peak, the world's population continues to climb, and nearly half of all known species face extinction by the end of the century. We stand on the threshold of one of the most important transition in human history-the transition from hunting-and-gathering our energy to cultivating sustainable, carbon-neutral, environmentally-friendly energy supplies. Can we "cultivate" enerm without competing with agriculture for land, freshwater, or fertilizer? Can we develop an "ecology of technology" that optimizes our use of limited resources? Is human activity compatible with improved conditions in the world's oceans? Will our ingenuity prevail in time to make a difference for our children and the children of all species? With support from NASA ARMD and the California Energy Commission, a group of dedicated scientists and engineers are working on a project called OMEGA (Offshore Membrane Enclosures for Growing Algae), to provide practical answers to these critical questions and to leave a legacy of hope for the oceans and for the future

OMEGA for the Future of Biofuels

OMEGA: Offshore Membrane Enclosure for Growing Algae. To develop a photobioreactor (PBR) for growing algae (Oil, food, fertilizer) that does not compete with agriculture for land (deployed offshore), water or fertilizer (uses/treats wastewater)

OMEGA (Offshore Membrane for Enclosing Algae). NASA-NAVY: A Strategic Planning Discussion

This briefing packet provides a short introduction to OMEGA and a truncated version of our project approach, with an example of the kind of work break down structure (WBS) used to guide our Phase I activities. It is meant to give you an impression of how we are approaching the challenge of creating the world's first marine photobioreactor (PBR) that will scale to address the strategic energy problems confronting the United States and the world. Some of our conceptual PBR designs and plans for logistics are included to communicate the path we have taken. We have also included an aerial photograph of the experimental tanks we are using at the Cal Fish and Game, followed by concluding remarks. The overarching purpose of the strategic planning discussion in Norfolk is to establish the relationship between the NASA OMEGA Team and the Navy, to unite the strengths of both agencies, and to map a mutual way forward along the project's established critical path

In the Beginning...

Having just emerged from the warmest decade on record and watching as the oceans acidify and sea level rises, global resources peak, the world's population continues to climb, and nearly half of all known species face extinction by the end of the century. We stand on the threshold of one of the most important transition in human history-the transition from hunting-and-gathering our energy to cultivating sustainable, carbon-neutral, environmentally-friendly energy supplies. Can we develop an alternative to fossil fuels in time to make a difference for our children and the "children" of all species? NASA puts people into outer space, where all resources (food, water, air, pressure, gravity, energy) are limited and far away and where conditions (temperature, radiation, vacuum) are problematic and dangerous-the life expectancy of an unprotected astronaut (physically exposed to the space environment) is 15 seconds. Therefore, by necessity, NASA has explored and developed "life-support systems" that optimize the use of resources, minimize the use of energy, and recycle, refurbish, re-use everything that on earth would be considered a waste material. Emerging from the legacy of life-support systems, the NASA OMEGA project uses microalgae, municipal wastewater, and the encroaching oceans to address our global needs for a sustainable, carbon-neutral, environmentally friendly energy supply that does not compete with agriculture. The OMEGA project is focused on producing aviation fuel, treating municipal wastewater, and sequestering carbon dioxide. More generally, however, OMEGA is an example of an "ecology of technologies" in which all processes are integrated and inter-dependent and wastes become resources. From a NASA perspective, the OMEGA project is also a reminder that "we are not passengers on Spaceship Earth, we are the crew.

Experience in Implementing Inpatient Clinical Note Capture via a Provider Order Entry System

Care providers' adoption of computer-based health-related documentation ("note capture”) tools has been limited, even though such tools have the potential to facilitate information gathering and to promote efficiency of clinical charting. The authors have developed and deployed a computerized note-capture tool that has been made available to end users through a care provider order entry (CPOE) system already in wide use at Vanderbilt. Overall note-capture tool usage between January 1, 1999, and December 31, 2001, increased substantially, both in the number of users and in their frequency of use. This case report is provided as an example of how an existing care provider order entry environment can facilitate clinical end-user adoption of a computer-assisted documentation tool—a concept that may seem counterintuitive to som

Ordered biological nanostructures formed from chaperonin polypeptides

The following application relates to nanotemplates, nanostructures, nanoarrays and nanodevices formed from wild-type and mutated chaperonin polypeptides, methods of producing such compositions, methods of using such compositions and particular chaperonin polypeptides that can be utilized in producing such compositions

Ordered Nanostructures Made Using Chaperonin Polypeptides

A recently invented method of fabricating periodic or otherwise ordered nanostructures involves the use of chaperonin polypeptides. The method is intended to serve as a potentially superior and less expensive alternative to conventional lithographic methods for use in the patterning steps of the fabrication of diverse objects characterized by features of the order of nanometers. Typical examples of such objects include arrays of quantum dots that would serve as the functional building blocks of future advanced electronic and photonic devices. A chaperonin is a double-ring protein structure having a molecular weight of about 60 plus or minus 5 kilodaltons. In nature, chaperonins are ubiquitous, essential, subcellular structures. Each natural chaperonin molecule comprises 14, 16, or 18 protein subunits, arranged as two stacked rings approximately 16 to 18 nm tall by approximately 15 to 17 nm wide, the exact dimensions depending on the biological species in which it originates. The natural role of chaperonins is unknown, but they are believed to aid in the correct folding of other proteins, by enclosing unfolded proteins and preventing nonspecific aggregation during assembly. What makes chaperonins useful for the purpose of the present method is that under the proper conditions, chaperonin rings assemble themselves into higher-order structures. This method exploits such higher-order structures to define nanoscale devices. The higher-order structures are tailored partly by choice of chemical and physical conditions for assembly and partly by using chaperonins that have been mutated. The mutations are made by established biochemical techniques. The assembly of chaperonin polypeptides into such structures as rings, tubes, filaments, and sheets (two-dimensional crystals) can be regulated chemically. Rings, tubes, and filaments of some chaperonin polypeptides can, for example, function as nano vessels if they are able to absorb, retain, protect, and release gases or chemical reagents, including reagents of medical or pharmaceutical interest. Chemical reagents can be bound in, or released from, such structures under suitable controlled conditions. In an example of a contemplated application, a two-dimensional crystal of chaperonin polypeptides would be formed on a surface of an inorganic substrate and used to form a planar array of nanoparticles or quantum dots. Through genetic engineering of the organisms used to manufacture the chaperonins, specific sites on the chaperonin molecules and, thus, on the two-dimensional crystals can be chemically modified to react in a specific manner so as to favor the deposition of the material of the desired nanoparticles or quantum dots. A mutation that introduces a cysteine residue at the desired sites on a chaperonin of Sulfolobus shibatae was used to form planar arrays of gold nanoparticles (see figure)

Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal

The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5′-AGGG(TTAGGG)(3)] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na(+) solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K(+) revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K(+) solutions. Sedimentation coefficients were determined experimentally in both Na(+) and K(+) solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na(+) solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K(+) solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K(+) yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K(+) solutions, but not in Na(+) solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K(+) quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K(+) solution is not the one determined in the published crystalline state

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)]2. A library containing ∼2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to ‘scaffold hop’ and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies