Automated robotic harvesting of protein crystals—addressing a critical bottleneck or instrumentation overkill?

One of the critical steps in high throughput crystallography that so far has evaded automation is the actual harvesting of the delicate crystals from the mother liquor in which they are growing. The late-stage operation of harvesting is presently a most risky and loss-intensive procedure, compounded by its tight integration with the critical steps of cryo-protection and cryo-quenching. Recent advances in micromanipulation robotics and micro-fabrication have made it possible to seriously consider automation of protein crystal harvesting. Based on the experience gained during the development of an operator-assisted (and now operator-assisting) universal micromanipulation robot (UMR) prototype, we discuss the challenges ahead for the design of a fully autonomous, integrated system capable of the reliable harvesting of protein microcrystals. Experience from participation in NIH structural genomics projects and feedback from bottleneck workshops indicates that genuine demand exists in the high throughput community as well as in pharmaceutical production pipelines, justifying the effort and resources to develop autonomous harvesting robotics.     

Engineering photosynthetic light capture: impacts on improved solar energy to biomass conversion

The main function of the photosynthetic process is to capture solar energy and to store it in the form of chemical 'fuels'. Increasingly, the photosynthetic machinery is being used for the production of biofuels such as bio-ethanol, biodiesel and bio-H₂. Fuel production efficiency is directly dependent on the solar photon capture and conversion efficiency of the system. Green algae (e.g. Chlamydomonas reinhardtii ) have evolved genetic strategies to assemble large light-harvesting antenna complexes (LHC) to maximize light capture under low-light conditions, with the downside that under high solar irradiance, most of the absorbed photons are wasted as fluorescence and heat to protect against photodamage. This limits the production process efficiency of mass culture. We applied RNAi technology to down-regulate the entire LHC gene family simultaneously to reduce energy losses by fluorescence and heat. The mutant Stm3LR3 had significantly reduced levels of LHCI and LHCII mRNAs and proteins while chlorophyll and pigment synthesis was functional. The grana were markedly less tightly stacked, consistent with the role of LHCII. Stm3LR3 also exhibited reduced levels of fluorescence, a higher photosynthetic quantum yield and a reduced sensitivity to photoinhibition, resulting in an increased efficiency of cell cultivation under elevated light conditions. Collectively, these properties offer three advantages in terms of algal bioreactor efficiency under natural high-light levels: (i) reduced fluorescence and LHC-dependent heat losses and thus increased photosynthetic efficiencies under high-light conditions; (ii) improved light penetration properties; and (iii) potentially reduced risk of oxidative photodamage of PSII.     

Influence of different growth conditions on the survival and the efficacy of freeze-dried Pseudomonas fluorescens strain Pf153

High viability, storability and tolerance to variable environmental conditions are key factors in the development of microbial biological control agents (BCAs). The efficacy of microbial BCAs is influenced by the culture conditions and formulation process. Therefore, we investigated the influence of diverse growth conditions on the survival during freeze-drying and on the biocontrol efficacy of Pseudomonas fluorescens strain Pf153. Culture time, temperature and media, mild heat shock and pH change influenced the bacterium viability after freeze-drying. The best survival rate was reached by cultivation in King’s broth for 16 or 20 h. Growth temperatures of 25 and 30°C and a mild heat shock at 35°C for one hour influenced the survival rate positively. In all bioassays against Botrytis cinerea on Vicia faba leaves, Pf153 showed a significant increased efficacy compared to the untreated control. No differences of the efficacy between fresh and freeze-dried cells were observed. Furthermore, a growth temperature of 20°C increased the efficacy of Pf153 against B. cinerea. These results underline that the quality of the formulated product can be improved by manipulating the fermentation process.     

‘Ecologically complex carbon’– linking biodiversity values,carbon storage and habitat structure in some austral temperate forests

Aim We assessed how avian biodiversity and above‐ground carbon storage were related in different forest age‐classes, including mature stands (> 100 years), in a managed, mixed‐species eucalypt forest. Location Gippsland, south‐eastern Australia. Methods In 50 2‐ha stands ranging in age from ≤ 5 years to mature stands > 100 years, we undertook repeated avian surveys, performed detailed habitat measurements and estimated amounts of above‐ground carbon. Extensive wildfire reduced the number of sites to 28 (seven in each of four age classes) upon which analyses and inferences were made. We also analysed data on carbon storage and some bird responses from previously published studies. Results Mature vegetation (> 100 years) had the greatest richness, abundance and biomass of birds. Key ecological resources, such as tree‐hollows for nesting, generally occurred mostly in stands > 60 years. Avian richness per unit of above‐ground carbon storage was relatively low for stands of 20–60 years. While above‐ground carbon storage appeared to increase in a monotonic fashion as stands age and mature, there were quantum increases in all measures of avian biodiversity in mature stands (> 100 years). Main conclusions Our results suggest that carbon is organized in a different way, with substantially greater biodiversity benefits, in very old stands. Mature vegetation simultaneously maximizes both avian biodiversity and above‐ground carbon storage. These results bolster arguments for allocating highest priorities to the preservation of old‐growth forest stands rather than alternative investments (e.g. reafforestation for carbon sequestration).     

Simulated long‐term effects of harvest and biomass residue removal on soil carbon and nitrogen content and productivity for two Upper Great Lakes forest ecosystems

We used the ecosystem process model Biome‐BGC to simulate the effects of harvest and residue removal management scenarios on soil carbon (C), available soil nitrogen (N), net primary production (NPP), and net ecosystem production (NEP) in jack pine (Pinus banksiana Lamb.) and sugar maple (Acer saccharum Marsh) ecosystems in northern Wisconsin, USA. To assess harvest effects, we simulated short (50‐year) and long (100‐year) harvest intervals, high (clear‐cut) and low (selective) harvest intensities, and three levels of residue retention (15%, 25%, and 35%) over a 500‐year period. The model simulation of NPP, soil C accumulation, and NEP agreed reasonably well with biometric and eddy‐covariance measurements of these two ecosystems. The more intensive (50‐year rotation clear‐cuts with low residue retention) harvest scenarios tended to have the greatest NEP (420 and 678 t C ha^?1 for the 500‐year interval for jack pine and sugar maple, respectively). All the harvest scenarios decreased mineral soil C and available mineral soil N content relative to the no‐harvest scenario for jack pine and sugar maple. The rate of change in mineral soil C decreased the greatest in the most intensive biomass removal scenarios (?0.012 and ?0.072 t C ha^?1 yr^?1 relative to no‐harvest for jack pine and sugar maple, respectively) and the smallest decrease was observed in the least intensive biomass removal scenarios (?0.002 and ?0.009 t C ha^?1 yr^?1 relative to no‐harvest for jack pine and sugar maple, respectively). The more intensive biomass removal harvest scenarios in sugar maple significantly decreased peak productivity (NPP) in the simulation period.     

Harvesting of Spirulina platensis by cellular flotation and growth stage determination

AIM: To investigate an effective harvesting method for Spirulina platensis. METHODS AND RESULTS: Eighty per cent of S. platensis cells in the logarithmic growth phase were harvested by flotation when the cells were set in a static condition for 2 h. The optimum harvesting time was about day 6 of cultivation. The flotation activity of S. platensis cells was enhanced by the addition of NaCl. CONCLUSIONS: The harvesting of S. platensis by flotation is a cost-effective and straightforward method that can retain the algal quality. The optimum harvesting time of S. platensis can be predicted by the cellular protein to carbon ratio. SIGNIFICANCE AND IMPACT OF THE STUDY: Flotation harvesting is also applicable to other cyanobacteria with gas vesicles.     

The 8.5A projection structure of the core RC-LH1-PufX dimer of Rhodobacter sphaeroides

Two-dimensional crystals of dimeric photosynthetic reaction centre-LH1-PufX complexes have been analysed by cryoelectron microscopy. The 8.5A resolution projection map extends previous analyses of complexes within native membranes to reveal the alpha-helical structure of two reaction centres and 28 LH1 alphabeta subunits within the dimer. For the first time, we have achieved sufficient resolution to suggest a possible location for the PufX transmembrane helix, the orientation of the RC and the arrangement of helices within the surrounding LH1 complex. Whereas low-resolution projections have shown an apparent break in the LH1, our current map reveals a diffuse density within this region, possibly reflecting high mobility. Within this region the separation between beta14 of one monomer and beta2 of the other monomer is approximately 6A larger than the average beta-beta spacing within LH1; we propose that this is sufficient for exchange of quinol at the RC Q(B) site. We have determined the position and orientation of the RC within the dimer, which places its Q(B) site adjacent to the putative PufX, with access to the point in LH1 that appears most easily breached. PufX appears to occupy a strategic position between the mobile alphabeta14 subunit and the Q(B) site, suggesting how the structure, possibly coupled with a flexible ring, plays a role in optimizing quinone exchange during photosynthesis.     

Band Structure and Local Dynamics of Excitons in Bacterial Light-harvesting Complexes Revealed by Spectrally Selective Spectroscopy

Hole-burned absorption and line-narrowed fluorescence spectra are studied at 5 K in wild type and mutant LH1 and LH2 antenna preparations from the photosynthetic purple bacterium Rhodobacter sphaeroides. Evidence was found in all samples, even in intact membranes, of the presence of a broad distribution of bacteriochlorophyll species that are unable to communicate energy between each other and to the exciton states of functional antenna complexes. The distribution maximum of these localized species determined by zero phonon hole action spectroscopy is at 783.5 nm in purified LH1 complexes and at 786.8 nm in B850-only mutant LH2 complexes. A well-resolved peak at 807 nm in LH1 complexes is assigned to the exciton band structure of functional core antenna complexes. Similar structure in LH2 complexes overlaps with the distribution of localized species. Off-diagonal (structural) disorder may be responsible for this exciton band structure. Our data also imply that pair-wise inter-chlorophyll couplings determine the resonance fluorescence lineshape of excitonic polarons.     

Architecture of the native photosynthetic apparatus of Phaeospirillum molischianum

The ubiquity and importance of photosynthetic organisms in nature has made the molecular mechanisms of photosynthesis a widely studied subject at both structural and functional levels. A current challenge is to understand the supramolecular assembly of the proteins involved in photosynthesis in native membranes. We have used atomic force microscopy to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of Phaeospirillum molischianum. Core complexes are formed by the reaction center enclosed by an elliptical light harvesting complex 1. LH2 are octameric rings, assembled either with cores or in hexagonally packed LH2 antenna domains. The symmetry mismatch caused by octameric LH2 packing in a hexagonal lattice, that could be avoided in a square lattice, suggests lipophobic effects rather than specific inter-molecular interactions drive protein organization. The core and LH2 complexes are organized to form a supramolecular assembly reminiscent to that found in Rhodospirillum photometricum, and very different from that observed in Rhodobacter sphaeroides, Rb. blasticus, and Blastochloris viridis.     

Divergence in behaviour between the European corn borer,Ostrinia nubilalis,and its sibling species Ostrinia scapulalis: adaptation to human harvesting?

Divergent adaptation to host plant species may be the major mechanism driving speciation and adaptive radiations in phytophagous insects. Host plants can differ intrinsically in a number of attributes, but the role of natural enemies in host plant specialization is often underappreciated. Here, we report behavioural divergence between the European corn borer (ECB, Ostrinia nubilalis) and its sibling species Ostrinia scapulalis, in relation to a major enemy: humans. Harvesting maize imposes selective mortality on Ostrinia larvae: those located above the cut-off line of the stalk face almost certain death. We show that ECB larvae diapause closer to the ground than those of O. scapulalis, which is sympatric but feeds mainly on weeds. The difference in diapause height results from genetically determined differences in geotactic behaviour. ECB larvae descend towards the ground specifically at harvest time, increasing their chances of surviving harvesting by about 50 per cent over O. scapulalis larvae. Natural enemies appear as a major driver of host-plant specialization in this example, stressing the need to consider ‘tri-trophic’ ecological niches to understand insect diversification. Our results also strongly suggest that geotaxis evolved as a singular instance of behavioural resistance in a major agricultural pest.