Quantum Coherence as a Witness of Vibronically Hot Energy Transfer in Bacterial Reaction Centre

Photosynthetic proteins have evolved over billions of years so as to undergo optimal energy transfer to the sites of charge separation. Based on spectroscopically detected quantum coherences, it has been suggested that this energy transfer is partially wavelike. This conclusion critically depends on assignment of the coherences to the evolution of excitonic superpositions. Here we demonstrate for a bacterial reaction centre protein that long-lived coherent spectroscopic oscillations, which bear canonical signatures of excitonic superpositions, are essentially vibrational excited state coherences shifted to the ground state of the chromophores . We show that appearance of these coherences is brought about by release of electronic energy during the energy transfer. Our results establish how energy migrates on vibrationally hot chromophores in the reaction centre and they call for a re-examination of claims of quantum energy transfer in photosynthesis

Tips and turns of bacteriophytochrome photoactivation

Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.Peer reviewe

Speech Synthesis Evaluation—State-of-the-Art Assessment and Suggestion for a Novel Research Program

Wagner P, Beskow J, Betz S, et al. Speech Synthesis Evaluation—State-of-the-Art Assessment and Suggestion for a Novel Research Program. In: Proceedings of the 10th Speech Synthesis Workshop (SSW10). 2019.Speech synthesis applications have become an ubiquity, in navigation systems, digital assistants or as screen or audio book readers. Despite their impact on the acceptability of the systems in which they are embedded, and despite the fact that different applications probably need different types of TTS voices, TTS evaluation is still largely treated as an isolated problem. Even though there is strong agreement among researchers that the mainstream approaches to Text-to-Speech (TTS) evaluation are often insufficient and may even be misleading, there exist few clear-cut suggestions as to (1) how TTS evaluations may be realistically improved on a large scale, and (2) how such improvements may lead to an informed feedback for system developers and, ultimately, better systems relying on TTS. This paper reviews the current state-of-the-art in TTS evaluation, and suggests a novel user-centered research program for this area

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.Peer reviewe

Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103-14. ©2016 AACR

Structural Features of Bacteriophytochromes. Photoactivated Proteins studied by Serial Femtosecond Crystallography

The key to life on earth is sunlight, which reaches the planet as an energy source. Nature has evolved different types of photoreceptor proteins to detect optimal light conditions for biochemical processes. A type of red light detecting photoreceptor proteins are called phytochromes and are present in plants, fungi and bacteria. A chromophore, converts the light signal into a structural change in the protein that alter its biochemical properties and thereby control developmental processes in the organism. A structural mechanism for signal transduction within the phytochrome protein is herein proposed. The aim of the work presented in this thesis has been to elucidate the structural changes in bacteriophytochromes upon photoactivation. This has been done by the use of X-ray crystallographic methods that can provide a near-atomic resolution of the dynamic events. Crystallization strategies were developed to experimentally obtain novel structural information on bacteriophytochromes from both conventional crystallography and by Serial Femtosecond Crystallography at X-ray Free electron lasers. The method enable time-resolved structural studies with an ultrafast timeresolution due to the X-ray lasers short pulses. Novel crystallization conditions for a bacteriophytochrome fragment yielded nearatomic resolution structures of both the wild type and a muted variant. The conditions could be modified for microcrystallization that provided microcrystals suitable for two different sample delivery systems at the world’s two most prominent X-ray lasers. The obtained resting state structures and a preliminary data set of the excited state paves the way for future time resolved investigation on the early structural events in photoactivation of phytochromes. Furthermore, the microcrystallization strategies might be applicable to other proteins and are thereby contributing to method development within the emerging field. The crystallographic structure of the mutated variant of the protein fragment supports IR-spectroscopy findings on the importance of the hydrogen bonding network around the chromophore. These results are in agreement with the excited state structural findings that waters might be of highest importance for the initial steps in the photoactivation of phytochromes

Structural features of bacteriophytochromes. Photoactivated proteins studied by serial femtosecond crystallography

The key to life on earth is sunlight, which reaches the planet as an energy source. Nature has evolved different types of photoreceptor proteins to detect optimal light conditions for biochemical processes. A type of red light detecting photoreceptor proteins are called phytochromes and are present in plants, fungi and bacteria. A chromophore, converts the light signal into a structural change in the protein that alter its biochemical properties and thereby control developmental processes in the organism. A structural mechanism for signal transduction within the phytochrome protein is herein proposed. The aim of the work presented in this thesis has been to elucidate the structural changes in bacteriophytochromes upon photoactivation. This has been done by the use of X-ray crystallographic methods that can provide a near-atomic resolution of the dynamic events. Crystallization strategies were developed to experimentally obtain novel structural information on bacteriophytochromes from both conventional crystallography and by Serial Femtosecond Crystallography at X-ray Free electron lasers. The method enable time-resolved structural studies with an ultrafast time-resolution due to the X-ray lasers short pulses. Novel crystallization conditions for a bacteriophytochrome fragment yielded near-atomic resolution structures of both the wild type and a muted variant. The conditions could be modified for microcrystallization that provided microcrystals suitable for two different sample delivery systems at the world’s two most prominent X-ray lasers. The obtained resting state structures and a preliminary data set of the excited state paves the way for future time resolved investigation on the early structural events in photoactivation of phytochromes. Furthermore, the microcrystallization strategies might be applicable to other proteins and are thereby contributing to method development within the emerging field. The crystallographic structure of the mutated variant of the protein fragment supports IR-spectroscopy findings on the importance of the hydrogen bonding network around the chromophore. These results are in agreement with the excited state structural findings that waters might be of highest importance for the initial steps in the photoactivation of phytochromes

Ökar ett praktisk arbetssätt eleversengagemang och begreppsförståelse? : En studie i en mindre undervisningsgrupp med elever med neuropsykiatriska funktionsvariationer.

Syftet med denna studie är att se om begreppsförståelse inom biologi och teknik ökar samt omengagemanget hos elever kan förbättras genom ett praktiskt arbetssätt. I studien har en mindregrupp elever med neuropsykiatriska funktionsvariationer som undervisas i en särskildundervisningsgrupp ingått. Inom biologin var arbetsområdet människans immunförsvar och iteknik handlade undervisningen om begrepp som krafter, tyngdpunkt, lodrät och vågrät. I ämnetbiologi fick eleverna göra en teater om immunförsvaret och i ämnet teknik fick eleverna byggaraketer som sedan sköts i väg av luften i PET-flaskor. I vår studie har vi utgått frånpragmatismens ideér samt ett sociokulturellt perspektiv. Andra viktiga aspekter är attupplevelser samt kroppsliga förnimmelser är viktigt för lärandet. Resultatet i vår studie visaratt engagemanget ökade vid ett praktiskt arbetssätt. Gällande begreppsförståelsen blev denhögre för ämnet teknik vid ett praktiskt arbetssätt. I ämnet biologi var det ingen större skillnadi begreppsförståelsen efter teoretisk respektive praktisk lektion. Begreppen inom ämnet biologii denna studie var dock mer komplexa till sin natur än begreppen inom teknik. Eleverna mindesdock mer av den praktiska lektionen i biologi än vad de gjorde från den teoretiska lektionen.Vår studie kan därmed visa att ett praktiskt arbetssätt kan hjälpa inlärningen för elever medneuropsykiatriska funktionsvariationer

Ökar ett praktisk arbetssätt eleversengagemang och begreppsförståelse? : En studie i en mindre undervisningsgrupp med elever med neuropsykiatriska funktionsvariationer.

Syftet med denna studie är att se om begreppsförståelse inom biologi och teknik ökar samt omengagemanget hos elever kan förbättras genom ett praktiskt arbetssätt. I studien har en mindregrupp elever med neuropsykiatriska funktionsvariationer som undervisas i en särskildundervisningsgrupp ingått. Inom biologin var arbetsområdet människans immunförsvar och iteknik handlade undervisningen om begrepp som krafter, tyngdpunkt, lodrät och vågrät. I ämnetbiologi fick eleverna göra en teater om immunförsvaret och i ämnet teknik fick eleverna byggaraketer som sedan sköts i väg av luften i PET-flaskor. I vår studie har vi utgått frånpragmatismens ideér samt ett sociokulturellt perspektiv. Andra viktiga aspekter är attupplevelser samt kroppsliga förnimmelser är viktigt för lärandet. Resultatet i vår studie visaratt engagemanget ökade vid ett praktiskt arbetssätt. Gällande begreppsförståelsen blev denhögre för ämnet teknik vid ett praktiskt arbetssätt. I ämnet biologi var det ingen större skillnadi begreppsförståelsen efter teoretisk respektive praktisk lektion. Begreppen inom ämnet biologii denna studie var dock mer komplexa till sin natur än begreppen inom teknik. Eleverna mindesdock mer av den praktiska lektionen i biologi än vad de gjorde från den teoretiska lektionen.Vår studie kan därmed visa att ett praktiskt arbetssätt kan hjälpa inlärningen för elever medneuropsykiatriska funktionsvariationer