Vibronic resonances facilitate excited state coherence in light harvesting proteins at room temperature

Until recently it was believed that photosynthesis, a fundamental process for life on earth, could be fully understood with semi-classical models. However, puzzling quantum phenomena have been observed in several photosynthetic pigment-protein complexes, prompting questions regarding the nature and role of these effects. Recent attention has focused on discrete vibrational modes that are resonant or quasi-resonant with excitonic energy splittings and strongly coupled to these excitonic states. Here we unambiguously identify excited state coherent superpositions in photosynthetic light-harvesting complexes using a new experimental approach. Decoherence on the timescale of the excited state lifetime allows low energy (56 cm-1) oscillations on the signal intensity to be observed. In conjunction with an appropriate model, these oscillations provide clear and direct experimental evidence that the persistent coherences observed require strong vibronic mixing among excited states

Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Investigating acetamidase gene function

© 2016 The Author(s). No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (∼10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms

Quantitative investigations of quantum coherence for a light-harvesting protein at conditions simulating photosynthesis

Recent measurements using two-dimensional electronic spectroscopy (2D ES) have shown that the initial dynamic response of photosynthetic proteins can involve quantum coherence. We show how electronic coherence can be differentiated from vibrational coherence in 2D ES. On that basis we conclude that both electronic and vibrational coherences are observed in the phycobiliprotein light-harvesting complex PC645 from Chroomonas sp. CCMP270 at ambient temperature. These light-harvesting antenna proteins of the cryptophyte algae are suspended in the lumen, where the pH drops significantly under sustained illumination by sunlight. Here we measured 2D ES of PC645 at increasing levels of acidity to determine if the change in pH affects the quantum coherence; quantitative analysis reveals that the dynamics are insensitive to the pH change.We acknowledge financial support from DARPA under the QuBE program, the United States Air Force Office of Scientific Research under contract number FA9550-10-1-0260, and the Natural Sciences and Engineering Research Council of Canada. We thank Min-Duk Seo and Mitsuhiko Ikura for assistance with the CD measurements and Philip Johnson, Alexei Halpin, and Jurgen Hauer for helpful conversations regarding the 2D ES apparatus

Earthworm communities in organic and conventional coffee cultivation.

The objective of this work was to evaluate the effect of organic and conventional coffee crops on biomass, population density and diversity of earthworms, in Lerroville, district of Londrina County, Paraná state, Brazil. Earthworm communities were sampled in three areas with organic coffee cultivation (CO1, CO2 and CO3), two with conventional coffee (CC1 and CC2), and a native forest fragment (MT). The soil of the areas CO1, CC1, and MT was classifi ed as Nitossolo Vermelho (Rhodic Kandiudox), while CO2, CO3, and CC2 were on Latossolo Vermelho (Rhodic Hapludox). Eight samples were taken in each area on two occasions, winter and summer, using the Tropical Soil Biology and Fertility (TSBF) method in the 0–20 cm soil layer. The earthworms were handsorted and preserved in 4% formaldehyde, and were later weighed, counted and identifi ed. The highest earthworm biomass, both in winter and summer, occurred in the CO3 area. For population density, the higher numbers of individuals were found in CO1 and CO3. The highest number of species was identifi ed in the organic cultivation. The adoption of organic practices in coffee cultivation favored the diversity, density and biomass of earthworm communities

Structure of the Janus Protein Human CLIC2

Chloride intracellular channel (CLIC) proteins possess the remarkable property of being able to convert from a water-soluble state to a membrane channel state. We determined the three-dimensional structure of human CLIC2 in its water-soluble form by X-ray crystallography at 1.8-Å resolution from two crystal forms. In contrast to the previously characterized CLIC1 protein, which forms a possibly functionally important disulfide-induced dimer under oxidizing conditions, we show that CLIC2 possesses an intramolecular disulfide and that the protein remains monomeric irrespective of redox conditions. Site-directed mutagenesis studies show that removal of the intramolecular disulfide or introduction of cysteine residues in CLIC2, equivalent to those that form the intramolecular disulfide in CLIC1, does not cause dimer formation under oxidizing conditions.We also show that CLIC2 forms pH-dependent chloride channels in vitro with higher channel activity at low pH levels and that the channels are subject to redox regulation. In both crystal forms, we observed an extended loop region from the C-terminal domain, called the foot loop, inserting itself into an interdomain crevice of a neighboring molecule. The equivalent region in the structurally related glutathione transferase superfamily corresponds to the active site. This so-called foot-in-mouth interaction suggests that CLIC2 might recognize other proteins such as the ryanodine receptor through a similar interaction

Baseline ecological data collection from the marine area around Filfla (Malta, Central Mediterranean Sea)

Acoustic and limited video sampling were carried out in a 1.1 nautical mile-radius area around Filfla, an islet 4.4 to the south-west of Malta, to characterize the benthos and the habitat type distribution. In addition, identified priority areas were sampled during SCUBA diving surveys. A total of 173 species were recorded during the current survey. Rhodophytes were the most represented (29 species), followed by molluscs (25 species). The biotic assemblages recorded from the marine area around Filfla are generally representative of those found in Maltese inshore waters.peer-reviewe

An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea.

MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins

Global Policy Review on Embodied Flows: Recommendations for Australian Construction Sector

There has been a call for the construction industry to become more energy efficient in its planning and activities, to reduce greenhouse gas emissions to help combat climate change. The Australian Building Codes Board has implemented ‘Energy Efficiency’ standards through the National Construction Codes to direct the industry towards net zero emissions goals. However, the Board has maintained a focus on operational flows considerations despite this only being a part of the total expenditure in a building lifecycle. Embodied flows, the energy output, and emissions from harvesting, manufacturing, transporting, and manufacturing materials for a building have not been included as a part of the current standards despite their growing share in the outputs of construction. A qualitative document analysis using data from academic articles and industry publications was performed to identify the context in embodied policy development. Findings reveal an abundance of different legislations and initiatives globally, recommending techniques that may effectively achieve embodied flow reductions. The results highlighted that Australia needs to capitalize on the potential reductions in overall energy and emissions from construction. Other regions have provided a strategic and legislative basis for the industry to emulate