Biomedical subjects

Ben Hankamer

Publications and source records attributed to Ben Hankamer.

9 recordsLinked to original sources

PubMed2006

Perspectives and advances of biological H2 production in microorganisms.

The rapid development of clean fuels for the future is a critically important global challenge for two main reasons. First, new fuels are needed to supplement and ultimately replace depleting oil reserves. Second, fuels capable of zero CO2 emissions are needed to slow the impact of global warming. This review summarizes the development of solar powered bio-H2 production processes based on the conversion of photosynthetic products by fermentative bacteria, as well as using photoheterotrophic and photoautrophic organisms. The use of advanced bioreactor systems and their potential and limitations in terms of process design, efficiency, and cost are also briefly reviewed.

Bioreactors↗

PubMed2006

SwarmPS: rapid, semi-automated single particle selection software.

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Algorithms↗

PubMed2006

The discriminative bilateral filter: an enhanced denoising filter for electron microscopy data.

Advances in three-dimensional (3D) electron microscopy (EM) and image processing are providing considerable improvements in the resolution of subcellular volumes, macromolecular assemblies and individual proteins. However, the recovery of high-frequency information from biological samples is hindered by specimen sensitivity to beam damage. Low dose electron cryo-microscopy conditions afford reduced beam damage but typically yield images with reduced contrast and low signal-to-noise ratios (SNRs). Here, we describe the properties of a new discriminative bilateral (DBL) filter that is based upon the bilateral filter implementation of Jiang et al. (Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struc. Biol. 128, 82-97.). In contrast to the latter, the DBL filter can distinguish between object edges and high-frequency noise pixels through the use of an additional photometric exclusion function. As a result, high frequency noise pixels are smoothed, yet object edge detail is preserved. In the present study, we show that the DBL filter effectively reduces noise in low SNR single particle data as well as cellular tomograms of stained plastic sections. The properties of the DBL filter are discussed in terms of its usefulness for single particle analysis and for pre-processing cellular tomograms ahead of image segmentation.

Animals↗

PubMed2006

A method for screening the temperature dependence of three-dimensional crystal formation.

Temperature is an important parameter controlling protein crystal growth. A new temperature-screening system (Thermo-screen) is described consisting of a gradient thermocycler fitted with a special crystallization-plate adapter onto which a 192-well sitting-drop crystallization plate can be mounted (temperature range 277-372 K; maximum temperature gradient 20 K; interval precision 0.3 K). The system allows 16 different conditions to be monitored simultaneously over a range of 12 temperatures and is well suited to conduct wide (approximately 20 K) and fine (approximately 3 K) temperature-optimization screens. It can potentially aid in the determination of temperature phase diagrams and run more complex temperature-cycling experiments for seeding and crystal growth.

Crystallization↗

PubMed2005

Photosynthesis: a blueprint for solar energy capture and biohydrogen production technologies.

Solar energy capture, conversion into chemical energy and biopolymers by photoautotrophic organisms, is the basis for almost all life on Earth. A broad range of organisms have developed complex molecular machinery for the efficient conversion of sunlight to chemical energy over the past 3 billion years, which to the present day has not been matched by any man-made technologies. Chlorophyll photochemistry within photosystem II (PSII) drives the water-splitting reaction efficiently at room temperature, in contrast with the thermal dissociation reaction that requires a temperature of ca. 1550 K. The successful elucidation of the high-resolution structure of PSII, and in particular the structure of its Mn(4)Ca cluster provides an invaluable blueprint for designing solar powered biotechnologies for the future. This knowledge, combined with new molecular genetic tools, fully sequenced genomes, and an ever increasing knowledge base of physiological processes of oxygenic phototrophs has inspired scientists from many countries to develop new biotechnological strategies to produce renewable CO(2)-neutral energy from sunlight. This review focuses particularly on the potential of use of cyanobacteria and microalgae for biohydrogen production. Specifically this article reviews the predicted size of the global energy market and the constraints of global warming upon it, before detailing the complex set of biochemical pathways that underlie the photosynthetic process and how they could be modified for improved biohydrogen production.

Greenhouse Effect↗

PubMed2005

Improved photobiological H2 production in engineered green algal cells.

Oxygenic photosynthetic organisms use solar energy to split water (H2O) into protons (H+), electrons (e-), and oxygen. A select group of photosynthetic microorganisms, including the green alga Chlamydomonas reinhardtii, has evolved the additional ability to redirect the derived H+ and e- to drive hydrogen (H2) production via the chloroplast hydrogenases HydA1 and A2 (H2 ase). This process occurs under anaerobic conditions and provides a biological basis for solar-driven H2 production. However, its relatively poor yield is a major limitation for the economic viability of this process. To improve H2 production in Chlamydomonas, we have developed a new approach to increase H+ and e- supply to the hydrogenases. In a first step, mutants blocked in the state 1 transition were selected. These mutants are inhibited in cyclic e- transfer around photosystem I, eliminating possible competition for e- with H2ase. Selected strains were further screened for increased H2 production rates, leading to the isolation of Stm6. This strain has a modified respiratory metabolism, providing it with two additional important properties as follows: large starch reserves (i.e. enhanced substrate availability), and a low dissolved O2 concentration (40% of the wild type (WT)), resulting in reduced inhibition of H2ase activation. The H2 production rates of Stm6 were 5-13 times that of the control WT strain over a range of conditions (light intensity, culture time, +/- uncoupler). Typically, approximately 540 ml of H2 liter(-1) culture (up to 98% pure) were produced over a 10-14-day period at a maximal rate of 4 ml h(-1) (efficiency = approximately 5 times the WT). Stm6 therefore represents an important step toward the development of future solar-powered H2 production systems.

Animals↗

PubMed2003

Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase.

The vacuole-type ATPases (V-ATPases) exist in various intracellular compartments of eukaryotic cells to regulate physiological processes by controlling the acidic environment. The crystal structure of the subunit C of Thermus thermophilus V-ATPase, homologous to eukaryotic subunit d of V-ATPases, has been determined at 1.95-A resolution and located into the holoenzyme complex structure obtained by single particle analysis as suggested by the results of subunit cross-linking experiments. The result shows that V-ATPase is substantially longer than the related F-type ATPase, due to the insertion of subunit C between the V(1) (soluble) and the V(o) (membrane bound) domains. Subunit C, attached to the V(o) domain, seems to have a socket like function in attaching the central-stalk subunits of the V(1) domain. This architecture seems essential for the reversible association/dissociation of the V(1) and the V(o) domains, unique for V-ATPase activity regulation.

Base Sequence↗

PubMed2003

Membrane-protein crystallization in cubo: temperature-dependent phase behaviour of monoolein-detergent mixtures.

The lipidic cubic phase of monoolein has proved to be a matrix well suited to the production of three-dimensional crystals of membrane proteins. It consists of a single continuous bilayer, which is contorted in three-dimensional space and separates two distinct water channels. It has previously been proposed that on the addition of precipitants, membrane proteins embedded in the cubic phase migrate through the matrix to nucleation sites and that this process is dependent upon the stability of the lipidic cubic phase. Here, the effect of detergent type (C(8)-C(12) glucosides, C(8)-C(12) maltosides and C(7) thioglucoside) and concentration (1-3x the critical micelle concentration; CMC) on cubic phase stability are reported in the form of the temperature-dependent phase behaviour (268-313 K) in 40% aqueous solution. The results are tabulated to show the best monoolein (MO)-detergent mixtures, mixing temperatures and crystallization temperatures identified. Monoolein-detergent mixtures suited for low-temperature in cubo crystallization of temperature-sensitive proteins are also reported for the first time. These mixtures can be prepared at low temperatures (mixed at <or=288 K) and remain stable at 277 K for a period of at least one Month. They include MO-heptyl thioglucoside (1x and 3x CMC), MO-nonyl glucoside (3x CMC), MO-octyl maltoside (3x CMC), MO-nonyl maltoside (1x CMC) and MO-decyl maltoside (1x CMC).

Crystallization↗

PubMed1997

STRUCTURE AND MEMBRANE ORGANIZATION OF PHOTOSYSTEM II IN GREEN PLANTS.

Photosystem II (PSII) is the pigment protein complex embedded in the thylakoid membrane of higher plants, algae, and cyanobacteria that uses solar energy to drive the photosynthetic water-splitting reaction. This chapter reviews the primary, secondary, tertiary, and quaternary structures of PSII as well as the function of its constituent subunits. The understanding of in vivo organization of PSII is based in part on freeze-etched and freeze-fracture images of thylakoid membranes. These images show a resolution of about 40-50 A and so provide information mainly on the localization, heterogeneity, dimensions, and shapes of membrane-embedded PSII complexes. Higher resolution of about 15-40 A has been obtained from single particle images of isolated PSII complexes of defined and differing subunit composition and from electron crystallography of 2-D crystals. Observations are discussed in terms of the oligomeric state and subunit organization of PSII and its antenna components.

Journal Article↗