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1. Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria

   https://doi.org/10.1073/pnas.2019715118  

   Grébert, Théophile ; Nguyen, Adam A. ; Pokhrel, Suman ; Joseph, Kes Lynn ; Ratin, Morgane ; Dufour, Louison ; Chen, Bo ; Haney, Allissa M. ; Karty, Jonathan A. ; Trinidad, Jonathan C. ; et al ( February 2021 , Proceedings of the National Academy of Sciences)

   MarineSynechococcuscyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, inSynechococcussp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types ofmore »chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.

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2. Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus

   https://doi.org/10.1073/pnas.1812871115  

   Yang, Yiling ; Lam, Vinson ; Adomako, Marie ; Simkovsky, Ryan ; Jakob, Annik ; Rockwell, Nathan C. ; Cohen, Susan E. ; Taton, Arnaud ; Wang, Jingtong ; Lagarias, J. Clark ; et al ( December 2018 , Proceedings of the National Academy of Sciences)

   Many cyanobacteria, which use light as an energy source via photosynthesis, have evolved the ability to guide their movement toward or away from a light source. This process, termed “phototaxis,” enables organisms to localize in optimal light environments for improved growth and fitness. Mechanisms of phototaxis have been studied in the coccoid cyanobacteriumSynechocystissp. strain PCC 6803, but the rod-shapedSynechococcus elongatusPCC 7942, studied for circadian rhythms and metabolic engineering, has no phototactic motility. In this study we report a recent environmental isolate ofS. elongatus, the strain UTEX 3055, whose genome is 98.5% identical to that of PCC 7942 but which is motile and phototactic. A six-gene operon encoding chemotaxis-like proteins was confirmed to be involved in phototaxis. Environmental light signals are perceived by a cyanobacteriochrome, PixJ_Se(Synpcc7942_0858), which carries five GAF domains that are responsive to blue/green light and resemble those of PixJ fromSynechocystis. Plate-based phototaxis assays indicate that UTEX 3055 uses PixJ_Seto sense blue and green light. Mutation of conserved functional cysteine residues in different GAF domains indicates that PixJ_Secontrols both positive and negative phototaxis, in contrast to the multiple proteins that are employed for implementing bidirectional phototaxis inSynechocystis.
3. The jumping spider Saitis barbipes lacks a red photoreceptor to see its own sexually dimorphic red coloration

   https://doi.org/10.1007/s00114-021-01774-6  

   Glenszczyk, Mateusz ; Outomuro, David ; Gregorič, Matjaž ; Kralj-Fišer, Simona ; Schneider, Jutta M. ; Nilsson, Dan-Eric ; Morehouse, Nathan I. ; Tedore, Cynthia ( December 2021 , The Science of Nature)

   Examining the role of color in mate choice without testing what colors the study animal is capable of seeing can lead to ill-posed hypotheses and erroneous conclusions. Here, we test the seemingly reasonable assumption that the sexually dimorphic red coloration of the male jumping spiderSaitis barbipesis distinguishable, by females, from adjacent black color patches. Using microspectrophotometry, we find clear evidence for photoreceptor classes with maximal sensitivity in the UV (359 nm) and green (526 nm), inconclusive evidence for a photoreceptor maximally sensitive in the blue (451 nm), and no evidence for a red photoreceptor. No colored filters within the lens or retina could be found to shift green sensitivity to red. To quantify and visualize whether females may nevertheless be capable of discriminating red from black color patches, we take multispectral images of males and calculate photoreceptor excitations and color contrasts between color patches. Red patches would be, at best, barely discriminable from black, and not discriminable from a low-luminance green. Some color patches that appear achromatic to human eyes, such as beige and white, strongly absorb UV wavelengths and would appear as brighter “spider-greens” toS. barbipesthan the red color patches. Unexpectedly, we discover an iridescent UV patch that contrasts strongly withmore »the UV-absorbing surfaces dominating the rest of the spider. We propose that red and black coloration may serve identical purposes in sexual signaling, functioning to generate strong achromatic contrast with the visual background. The potential functional significance of red coloration outside of sexual signaling is discussed.

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4. Evaluation of Genomic Sequence-Based Growth Rate Methods for Synchronized Synechococcus Cultures

   https://doi.org/10.1128/AEM.01743-21  

   Carroll, Julia ; Van Oostende, Nicolas ; Ward, Bess B. ( January 2022 , Applied and Environmental Microbiology)

   Glass, Jennifer B. (Ed.)

   ABSTRACT Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus . We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree ofmore »diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate. IMPORTANCE Small but abundant, cyanobacterial strains such as the photosynthetic Synechococcus spp. are important because they contribute significantly to primary productivity in the ocean. These bacteria generate oxygen and provide biologically available carbon, which is essential for organisms at higher trophic levels. The small size and diversity of natural microbial assemblages mean that taxon-specific activities (e.g., growth rate) are difficult to obtain in the field. It has been suggested that sequence-based methods (SBM) may be able to solve this problem. We find, however, that SBM can detect DNA replication and are correlated with phases of the cell cycle but cannot be interpreted in terms of absolute growth rate for Synechococcus cultures growing under a day-night cycle, like that experienced in the ocean.« less
5. Efficiency enhancement of ultrathin CIGS solar cells by optimal bandgap grading. Part II: finite-difference algorithm and double-layer antireflection coatings

   https://doi.org/10.1364/AO.474920  

   Ahmad, Faiz ; Civiletti, Benjamin J. ; Monk, Peter B. ; Lakhtakia, Akhlesh ( November 2022 , Applied Optics)

   In Part I [Appl. Opt.58,6067(2019)APOPAI003-693510.1364/AO.58.006067], we used a coupled optoelectronic model to optimize a thin-film${\mathrm{C}\mathrm{u}\mathrm{I}\mathrm{n}}_{1-<\#comment/>\mathrm{\xi <\#comment/>}}{\mathrm{G}\mathrm{a}}_{\mathrm{\xi <\#comment/>}}{\mathrm{S}\mathrm{e}}_2$(CIGS) solar cell with a graded-bandgap photon-absorbing layer and a periodically corrugated backreflector. The increase in efficiency due to the periodic corrugation was found to be tiny and that, too, only for very thin CIGS layers. Also, it was predicted that linear bandgap-grading enhances the efficiency of the CIGS solar cells. However, a significant improvement in solar cell efficiency was found using a nonlinearly (sinusoidally) graded-bandgap CIGS photon-absorbing layer. The optoelectronic model comprised two submodels: optical and electrical. The electrical submodel applied the hybridizable discontinuous Galerkin (HDG) scheme directly to equations for the drift and diffusion of charge carriers. As our HDG scheme sometimes fails due to negative carrier densities arising during the solution process, we devised a new, to the best of our knowledge, computational scheme using the finite-difference method, which also reduces the overall computational cost of optimization. An unfortunate normalization error in the electrical submodel in Part I came to light. This normalization error did not change the overall conclusions reported in Part I;more »however, some specifics did change. The new algorithm for the electrical submodel is reported here along with updated numerical results. We re-optimized the solar cells containing a CIGS photon-absorbing layer with either (i) a homogeneous bandgap, (ii) a linearly graded bandgap, or (iii) a nonlinearly graded bandgap. Considering the meager increase in efficiency with the periodic corrugation and additional complexity in the fabrication process, we opted for a flat backreflector. The new algorithm is significantly faster than the previous algorithm. Our new results confirm efficiency enhancement of 84% (resp. 63%) when the thickness of the CIGS layer is 600 nm (resp. 2200 nm), similarly to Part I. A hundredfold concentration of sunlight can increase the efficiency by an additional 27%. Finally, the currently used 110-nm-thick layer of${\mathrm{M}\mathrm{g}\mathrm{F}}_2$performs almost as well as optimal single- and double-layer antireflection coatings.

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