The first find of Permian ceratodontids (Dipnoi, Osteichthyes) in Russia

© 2015, Pleiades Publishing, Ltd. A huge dipnoan, Permoceratodus gentilis Krupina, gen. et sp. nov. (order Ceratodontiformes), from the terminal Permian beds (Zhukovian Regional Stage, Vyatkian Stage, Upper Permian) of the Sokovka locality (Vladimir Region) is described. It is characterized by the evolutionarily advanced high extent of fusion of skull roof bones and conservative well defined structures of the seismosensory system of the head. This combination distinguishes the new taxon from other Ceratodontiformes. A set of conservative and advanced characters is observed in many vertebrates of the Vyazniki faunal assemblage. Large tetrapods and fishes characterize the terminal developmental stage of the Permian fauna of Eastern Europe, which was followed by impoverishment of the taxonomic composition accompanied by a decrease in body size. The dipnoan described here, like some other vertebrates of this assemblage, belong to high-rank taxa, which had just appeared in the Paleozoic, but reached flourishing in the Mesozoic

New insights into the photochemistry of carotenoid spheroidenone in light-harvesting complex 2 from the purple bacterium Rhodobacter sphaeroides

Light-harvesting complex 2 (LH2) from the semi-aerobically grown purple phototrophic bacterium Rhodobacter sphaeroides was studied using optical (static and time-resolved) and resonance Raman spectroscopies. This antenna complex comprises bacteriochlorophyll (BChl) a and the carotenoid spheroidenone, a ketolated derivative of spheroidene. The results indicate that the spheroidenone-LH2 complex contains two spectral forms of the carotenoid: (1) a minor, ‘‘blue’’ form with an S2 (11 Bu ?) spectral origin band at 522 nm, shifted from the position in organic media simply by the high polarizability of the binding site, and (2) the major, ‘‘red’’ form with the origin band at 562 nm that is associated with a pool of pigments that more strongly interact with protein residues, most likely via hydrogen bonding. Application of targeted modeling of excited-state decay pathways after carotenoid excitation suggests that the high (92%) carotenoid-to-BChl energy transfer efficiency in this LH2 system, relative to LH2 complexes binding carotenoids with comparable double-bond conjugation lengths, derives mainly from resonance energy transfer from spheroidenone S2 (11 Bu ?) state to BChl a via the Qx state of the latter, accounting for 60% of the total transfer. The elevated S2 (11 Bu ?) ? Qx transfer efficiency is apparently associated with substantially decreased energy gap (increased spectral overlap) between the virtual S2 (11 Bu ?) ? S0 (11 Ag -) carotenoid emission and Qx absorption of BChl a. This reduced energetic gap is the ultimate consequence of strong carotenoid–protein interactions, including the inferred hydrogen bondin

Engineering of B800 bacteriochlorophyll binding site specificity in the Rhodobacter sphaeroides LH2 antenna.

The light-harvesting 2 complex (LH2) of the purple phototrophic bacterium Rhodobacter sphaeroides is a highly efficient, light-harvesting antenna that allows growth under a wide-range of light intensities. In order to expand the spectral range of this antenna complex, we first used a series of competition assays to measure the capacity of the non-native pigments 3-acetyl chlorophyll (Chl) a, Chl d, Chl f or bacteriochlorophyll (BChl) b to replace native BChl a in the B800 binding site of LH2. We then adjusted the B800 site and systematically assessed the binding of non-native pigments. We find that Arg-10 of the LH2 β polypeptide plays a crucial role in binding specificity, by providing a hydrogen-bond to the 3-acetyl group of native and non-native pigments. Reconstituted LH2 complexes harbouring the series of (B)Chls were examined by transient absorption and steady-state fluorescence spectroscopies. Although slowed 10-fold to ~6 ps, energy transfer from Chl a to B850 BChl a remained highly efficient. We measured faster energy-transfer time constants for Chl d (3.5 ps) and Chl f (2.7 ps), which have red-shifted absorption maxima compared to Chl a. BChl b, red-shifted from the native BChl a, gave extremely rapid (≤0.1 ps) transfer. These results show that modified LH2 complexes, combined with engineered (B)Chl biosynthesis pathways in vivo, have potential for retaining high efficiency whilst acquiring increased spectral range

The nature of singlet exciton fission in carotenoid aggregates.

Singlet exciton fission allows the fast and efficient generation of two spin triplet states from one photoexcited singlet. It has the potential to improve organic photovoltaics, enabling efficient coupling to the blue to ultraviolet region of the solar spectrum to capture the energy generally lost as waste heat. However, many questions remain about the underlying fission mechanism. The relation between intermolecular geometry and singlet fission rate and yield is poorly understood and remains one of the most significant barriers to the design of new singlet fission sensitizers. Here we explore the structure-property relationship and examine the mechanism of singlet fission in aggregates of astaxanthin, a small polyene. We isolate five distinct supramolecular structures of astaxanthin generated through self-assembly in solution. Each is capable of undergoing intermolecular singlet fission, with rates of triplet generation and annihilation that can be correlated with intermolecular coupling strength. In contrast with the conventional model of singlet fission in linear molecules, we demonstrate that no intermediate states are involved in the triplet formation: instead, singlet fission occurs directly from the initial 1B(u) photoexcited state on ultrafast time scales. This result demands a re-evaluation of current theories of polyene photophysics and highlights the robustness of carotenoid singlet fission.This work was supported by the EPSRC (UK) (EP/G060738/ 1), the European Community (LASERLAB-EUROPE, grant agreement no. 284464, EC’s Seventh Framework Programme; and Marie-Curie ITN-SUPERIOR, PITN-GA-2009-238177), and the Winton Programme for the Physics of Sustainability. G.C. acknowledges support by the European Research Council Advanced Grant STRATUS (ERC-2011-AdG No. 291198). J.C. acknowledges support by the Royal Society Dorothy Hodgkin Fellowship and The University of Sheffield’s Vice- Chancellor’s Fellowship scheme.This is the final published version. It was first made available by ACS at http://pubs.acs.org/doi/abs/10.1021/jacs.5b01130

Development and Evolution of the Muscles of the Pelvic Fin

Locomotor strategies in terrestrial tetrapods have evolved from the utilisation of sinusoidal contractions of axial musculature, evident in ancestral fish species, to the reliance on powerful and complex limb muscles to provide propulsive force. Within tetrapods, a hindlimb-dominant locomotor strategy predominates, and its evolution is considered critical for the evident success of the tetrapod transition onto land. Here, we determine the developmental mechanisms of pelvic fin muscle formation in living fish species at critical points within the vertebrate phylogeny and reveal a stepwise modification from a primitive to a more derived mode of pelvic fin muscle formation. A distinct process generates pelvic fin muscle in bony fishes that incorporates both primitive and derived characteristics of vertebrate appendicular muscle formation. We propose that the adoption of the fully derived mode of hindlimb muscle formation from this bimodal character state is an evolutionary innovation that was critical to the success of the tetrapod transition

Rise of the Earliest Tetrapods: An Early Devonian Origin from Marine Environment

Tetrapod fossil tracks are known from the Middle Devonian (Eifelian at ca. 397 million years ago - MYA), and their earliest bony remains from the Upper Devonian (Frasnian at 375–385 MYA). Tetrapods are now generally considered to have colonized land during the Carboniferous (i.e., after 359 MYA), which is considered to be one of the major events in the history of life. Our analysis on tetrapod evolution was performed using molecular data consisting of 13 proteins from 17 species and different paleontological data. The analysis on the molecular data was performed with the program TreeSAAP and the results were analyzed to see if they had implications on the paleontological data collected. The results have shown that tetrapods evolved from marine environments during times of higher oxygen levels. The change in environmental conditions played a major role in their evolution. According to our analysis this evolution occurred at about 397–416 MYA during the Early Devonian unlike previously thought. This idea is supported by various environmental factors such as sea levels and oxygen rate, and biotic factors such as biodiversity of arthropods and coral reefs. The molecular data also strongly supports lungfish as tetrapod's closest living relative

Ultrafast transient absorption spectroscopy: principles and application to photosynthetic systems

The photophysical and photochemical reactions, after light absorption by a photosynthetic pigment–protein complex, are among the fastest events in biology, taking place on timescales ranging from tens of femtoseconds to a few nanoseconds. The advent of ultrafast laser systems that produce pulses with femtosecond duration opened up a new area of research and enabled investigation of these photophysical and photochemical reactions in real time. Here, we provide a basic description of the ultrafast transient absorption technique, the laser and wavelength-conversion equipment, the transient absorption setup, and the collection of transient absorption data. Recent applications of ultrafast transient absorption spectroscopy on systems with increasing degree of complexity, from biomimetic light-harvesting systems to natural light-harvesting antennas, are presented. In particular, we will discuss, in this educational review, how a molecular understanding of the light-harvesting and photoprotective functions of carotenoids in photosynthesis is accomplished through the application of ultrafast transient absorption spectroscopy

Bare Bones Pattern Formation: A Core Regulatory Network in Varying Geometries Reproduces Major Features of Vertebrate Limb Development and Evolution

BACKGROUND: Major unresolved questions regarding vertebrate limb development concern how the numbers of skeletal elements along the proximodistal (P-D) and anteroposterior (A-P) axes are determined and how the shape of a growing limb affects skeletal element formation. There is currently no generally accepted model for these patterning processes, but recent work on cartilage development (chondrogenesis) indicates that precartilage tissue self-organizes into nodular patterns by cell-molecular circuitry with local auto-activating and lateral inhibitory (LALI) properties. This process is played out in the developing limb in the context of a gradient of fibroblast growth factor (FGF) emanating from the apical ectodermal ridge (AER). RESULTS: We have simulated the behavior of the core chondrogenic mechanism of the developing limb in the presence of an FGF gradient using a novel computational environment that permits simulation of LALI systems in domains of varying shape and size. The model predicts the normal proximodistal pattern of skeletogenesis as well as distal truncations resulting from AER removal. Modifications of the model's parameters corresponding to plausible effects of Hox proteins and formins, and of the reshaping of the model limb, bud yielded simulated phenotypes resembling mutational and experimental variants of the limb. Hypothetical developmental scenarios reproduce skeletal morphologies with features of fossil limbs. CONCLUSIONS: The limb chondrogenic regulatory system operating in the presence of a gradient has an inherent, robust propensity to form limb-like skeletal structures. The bare bones framework can accommodate ancillary gene regulatory networks controlling limb bud shaping and establishment of Hox expression domains. This mechanism accounts for major features of the normal limb pattern and, under variant geometries and different parameter values, those of experimentally manipulated, genetically aberrant and evolutionary early forms, with no requirement for an independent system of positional information

Probing the interplay between factors determining reaction rates on silica gel using termolecular systems

This article was published in the journal, Photochemical and Photobiological Sciences [© Royal Society of Chemistry and Owner Societies]. The definitive version is available at: http://dx.doi.org/10.1039/c2pp25171jIn this study we have compared energy and electron transfer reactions in termolecular systems using a nanosecond diffuse reflectance laser flash photolysis technique. We have previously investigated these processes on silica gel surfaces for bimolecular systems and electron transfer in termolecular systems. The latter systems involved electron transfer between three arene molecules with azulene acting as a molecular shuttle. In this study we present an alternative electron transfer system using trans β-carotene as an electron donor in order to effectively immobilise all species except the shuttle, providing the first unambiguous evidence for radical ion mobility. In the energy transfer system we use naphthalene, a structural isomer of azulene, as the shuttle, facilitating energy transfer from a selectively excited benzophenone sensitiser to 9-cyanoanthracene. Bimolecular rate constants for all of these processes have been measured and new insights into the factors determining the rates of these reactions on silica gel have been obtained