Vibronic coupling explains the ultrafast carotenoid-to-bacteriochlorophyll energy transfer in natural and artificial light harvesters

The initial energy transfer in photosynthesis occurs between the light-harvesting pigments and on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that F\"orster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which leads to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited state as part of the system's Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid electronic ground state play a central role in the excited state population transfer to bacteriochlorophyll as the resonance between the donor-acceptor energy gap and vibrational ground state energies is the physical basis of the ultrafast energy transfer rates in these systems

Test bed control center design concept for Tank Waste Retrieval Manipulator Systems

This paper describes the design concept for the control center for the Single Shell Tank Waste Retrieval Manipulator System test bed and the design process behind the concept. The design concept supports all phases of the test bed mission, including technology demonstration, comprehensive system testing, and comparative evaluation for further development and refinement of the TWRMS for field operations

Large magnetoresistance and magnetocaloric effect above 70 K in Gd2Co2Al, Gd2Co2Ga and Gd7Rh3

The electrical resistivity, magnetization and heat-capacity behavior of the Gd-based compounds, Gd2Co2Al, Gd2Co2Ga and Gd7Rh3, ordering magnetically at TC= 78 K, TC= 76 K and TN= 140 K have been investigated as a function of temperature and magnetic field. All these compounds are found to show large magnetoresistance (with a negative sign) in the paramagnetic state at rather high temperatures with the magnitude peaking at respective magnetic ordering temperatures. There is a corresponding behavior in the magnetocaloric effect as inferred from the entropy derived from these data.Comment: Phys. Rev. 65 (2005) 49

Ultrafast depolarization of the fluorescence in a conjugated polymer

The effect of the extent of pi electron conjugation on the primary photophysics in semiconducting polymers is reported. A rapid depolarization of photoluminescence and transient absorption, which indicates a reorientation of the transition dipole moment by similar to 30 degrees on a sub-100 fs time scale, is observed in the fully conjugated polymer poly[2-(2'-ethylhexyloxy)-5-methoxy-1,4-phenylenevinylene] (MEH-PPV). In contrast, partially conjugated polymers exhibit a much slower depolarization. The results reveal rapid changes of exciton delocalization in the fully conjugated MEH-PPV driven by structural relaxation

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii

Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the frst Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from fowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species difering greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These fndings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.Cristian Varela, Joanna Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony Bornema

Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies

The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100-200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation.Benjamin J. Binder, Joanna F. Sundstrom, Jennifer M. Gardner, Vladimir Jiranek, Stephen G. Olive

Nutrient-limited growth with non-linear cell diffusion as a mechanism for floral pattern formation in yeast biofilms

Available online 7 April 2018Abstract not availableAlexander Tam, J. Edward F. Green, Sanjeeva Balasuriya, Ee Lin Tek, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Benjamin J. Binde

Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae

BACKGROUND: Wine fermentation is a harsh ecological niche to which wine yeast are well adapted. The initial high osmotic pressure and acidity of grape juice is followed by nutrient depletion and increasing concentrations of ethanol as the fermentation progresses. Yeast's adaptation to these and many other environmental stresses, enables successful completion of high-sugar fermentations. Earlier transcriptomic and growth studies have tentatively identified genes important for high-sugar fermentation. Whilst useful, such studies did not consider extended growth (>5 days) in a temporally dynamic multi-stressor environment such as that found in many industrial fermentation processes. Here, we identify genes whose deletion has minimal or no effect on growth, but results in failure to achieve timely completion of the fermentation of a chemically defined grape juice with 200 g L-1 total sugar. RESULTS: Micro- and laboratory-scale experimental fermentations were conducted to identify 72 clones from ~5,100 homozygous diploid single-gene yeast deletants, which exhibited protracted fermentation in a high-sugar medium. Another 21 clones (related by gene function, but initially eliminated from the screen because of possible growth defects) were also included. Clustering and numerical enrichment of genes annotated to specific Gene Ontology (GO) terms highlighted the vacuole's role in ion homeostasis and pH regulation, through vacuole acidification. CONCLUSION: We have identified 93 genes whose deletion resulted in the duration of fermentation being at least 20% longer than the wild type. An extreme phenotype, 'stuck' fermentation, was also observed when DOA4, NPT1, PLC1, PTK2, SIN3, SSQ1, TPS1, TPS2 or ZAP1 were deleted. These 93 Fermentation Essential Genes (FEG) are required to complete an extended high-sugar (wine-like) fermentation. Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database. The 93-gene set is collectively referred to as the 'Fermentome'. The fact that 10 genes highlighted in this study have not previously been linked to fermentation-related stresses, supports our experimental rationale. These findings, together with investigations of the genetic diversity of industrial strains, are crucial for understanding the mechanisms behind yeast's response and adaptation to stresses imposed during high-sugar fermentations.Michelle E Walker, Trung D Nguyen, Tommaso Liccioli, Frank Schmid, Nicholas Kalatzis, Joanna F Sundstrom, Jennifer M Gardner and Vladimir Jirane

FindFoci: a focus detection algorithm with automated parameter training that closely matches human assignments, reduces human inconsistencies and increases speed of analysis

Accurate and reproducible quantification of the accumulation of proteins into foci in cells is essential for data interpretation and for biological inferences. To improve reproducibility, much emphasis has been placed on the preparation of samples, but less attention has been given to reporting and standardizing the quantification of foci. The current standard to quantitate foci in open-source software is to manually determine a range of parameters based on the outcome of one or a few representative images and then apply the parameter combination to the analysis of a larger dataset. Here, we demonstrate the power and utility of using machine learning to train a new algorithm (FindFoci) to determine optimal parameters. FindFoci closely matches human assignments and allows rapid automated exploration of parameter space. Thus, individuals can train the algorithm to mirror their own assignments and then automate focus counting using the same parameters across a large number of images. Using the training algorithm to match human assignments of foci, we demonstrate that applying an optimal parameter combination from a single image is not broadly applicable to analysis of other images scored by the same experimenter or by other experimenters. Our analysis thus reveals wide variation in human assignment of foci and their quantification. To overcome this, we developed training on multiple images, which reduces the inconsistency of using a single or a few images to set parameters for focus detection. FindFoci is provided as an open-source plugin for ImageJ