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

Design and development of a gait training system for Parkinson’s disease

Background. Rhythmic Auditory Stimulation (RAS) is an effective technique to improve gait and reduce freezing episodes for Persons with Parkinson’s Disease (PwPD). The BeatHealth system, which comprises a mobile application, gait sensors, and a website, exploits the potential of the RAS technique. This paper describes the tools used for co-designing and evaluating the system and discusses the results and conclusions. Methods. Personas, interviews, use cases, and ethnographic observations were used to define the functional requirements of the system. Low fidelity prototypes were created for iterative and incremental evaluation with end-users. Field trials were also performed with the final system. The process followed a user centered design methodology defined for this project with the aim of building a useful, usable, and easy-to-use system. Results. Functional requirements of the system were produced as a result of the initial exploration phase. Building upon these, mock-ups for the BeatHealth system were created. The mobile application was iterated twice, with the second version of it achieving a rating of 75 when assessed by participants through the System Usability Scale (SUS). After another iteration field trials were performed and the mobile application was rated with an average 78.6 using SUS. Participants rated two website mock-ups, one for health professionals and another for end-users, as good except from minor issues related to visual design (e.g. font size), which were resolved in the final version. Conclusion. The high ratings obtained in the evaluation of the BeatHealth system demonstrate the benefit of applying a user centered design methodology which involves stakeholders from the very beginning. Other important lessons were learned through the process of design and development of the system, such as the importance of motivational aspects, the techniques which work best, and the extra care that has to be taken when evaluating non-functional mock-ups with end users.This work was supported by the BeatHealth project within the 7th Framework Programme of the European Union – Personalised health, active ageing, and independent living, contract Number FP7-610633. See also: http://www.euromov.eu/beathealth/homepage. This work has been also partially supported by the Ministry of Economy and Competitiveness of the Spanish Government and by the European Regional Development Fund (projects TIN2014-52665-C2-1-R and TIN2017-85409-P), and by the Department of Education, Universities and Research of the Basque Government under grant IT980-16

BeatWalk: Personalized Music-Based Gait Rehabilitation in Parkinson’s Disease

Taking regular walks when living with Parkinson’s disease (PD) has beneficial effects on movement and quality of life. Yet, patients usually show reduced physical activity compared to healthy older adults. Using auditory stimulation such as music can facilitate walking but patients vary significantly in their response. An individualized approach adapting musical tempo to patients’ gait cadence, and capitalizing on these individual differences, is likely to provide a rewarding experience, increasing motivation for walk-in PD. We aim to evaluate the observance, safety, tolerance, usability, and enjoyment of a new smartphone application. It was coupled with wearable sensors (BeatWalk) and delivered individualized musical stimulation for gait auto-rehabilitation at home. Forty-five patients with PD underwent a 1-month, outdoor, uncontrolled gait rehabilitation program, using the BeatWalk application (30 min/day, 5 days/week). The music tempo was being aligned in real-time to patients’ gait cadence in a way that could foster an increase up to +10% of their spontaneous cadence. Open-label evaluation was based on BeatWalk use measures, questionnaires, and a six-minute walk test. Patients used the application 78.8% (±28.2) of the prescribed duration and enjoyed it throughout the program. The application was considered “easy to use” by 75% of the patients. Pain, fatigue, and falls did not increase. Fear of falling decreased and quality of life improved. After the program, patients improved their gait parameters in the six-minute walk test without musical stimulation. BeatWalk is an easy to use, safe, and enjoyable musical application for individualized gait rehabilitation in PD. It increases “walk for exercise” duration thanks to high observance.This research was supported by a European grant: BeatHealth: Health and Wellness on the Beat for VC, DD, CL, AGi, VD, RV, EH, ED, ML, BB, and SB (EU FP7-ICT contract #610633)

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

Alteration of Proteins and Pigments Influence the Function of Photosystem I under Iron Deficiency from Chlamydomonas reinhardtii

BACKGROUND: Iron is an essential micronutrient for all organisms because it is a component of enzyme cofactors that catalyze redox reactions in fundamental metabolic processes. Even though iron is abundant on earth, it is often present in the insoluble ferric [Fe (III)] state, leaving many surface environments Fe-limited. The haploid green alga Chlamydomonas reinhardtii is used as a model organism for studying eukaryotic photosynthesis. This study explores structural and functional changes in PSI-LHCI supercomplexes under Fe deficiency as the eukaryotic photosynthetic apparatus adapts to Fe deficiency. RESULTS: 77K emission spectra and sucrose density gradient data show that PSI and LHCI subunits are affected under iron deficiency conditions. The visible circular dichroism (CD) spectra associated with strongly-coupled chlorophyll dimers increases in intensity. The change in CD signals of pigments originates from the modification of interactions between pigment molecules. Evidence from sucrose gradients and non-denaturing (green) gels indicates that PSI-LHCI levels were reduced after cells were grown for 72 h in Fe-deficient medium. Ultrafast fluorescence spectroscopy suggests that red-shifted pigments in the PSI-LHCI antenna were lost during Fe stress. Further, denaturing gel electrophoresis and immunoblot analysis reveals that levels of the PSI subunits PsaC and PsaD decreased, while PsaE was completely absent after Fe stress. The light harvesting complexes were also susceptible to iron deficiency, with Lhca1 and Lhca9 showing the most dramatic decreases. These changes in the number and composition of PSI-LHCI supercomplexes may be caused by reactive oxygen species, which increase under Fe deficiency conditions. CONCLUSIONS: Fe deficiency induces rapid reduction of the levels of photosynthetic pigments due to a decrease in chlorophyll synthesis. Chlorophyll is important not only as a light-harvesting pigment, but also has a structural role, particularly in the pigment-rich LHCI subunits. The reduced level of chlorophyll molecules inhibits the formation of large PSI-LHCI supercomplexes, further decreasing the photosynthetic efficiency

Lack of muscle activity in leg muscles of office workers : effect of a dynamic office chair

Petra Ihalainen. Kevät 2014. Lihasaktiivisuuden puute alaraajojen lihaksissa toimistotyöläisillä – dynaamisen työtuolin vaikutus. Liikuntabiologian laitos, Jyväskylän Yliopisto. Valmennus- ja testausopin Pro Gradu -tutkielma.57 s, 5 liitettä. Maailman terveysjärjestö WHO on nostanut fyysisen inaktiivisuuden lisääntymisen merkittäväksi terveysriskiksi maailmanlaajuisesti. Fyysisen inaktiivisuuden haittavaikutukset terveyteen ovat riippumattomia fyysisen aktiivisuuden terveyttä edistävistä vaikutuksista. Inaktiivisuusaika kertyy hereillä oloaikana muun muassa toistuvista istumisjaksoista. Toimistotyötä tekevillä päivittäinen istuen kulutettu aika voi olla huomattavan suuri. Lihasaktiivisuuden tuottamat paikalliset vasteet ovat avainasemassa fyysisen aktiivisuuden terveyshyötyjä tarkasteltaessa. Inaktiivisuusjakson keskeyttävien aktiivisuusjaksojen lukumäärällä on havaittu olevan terveysvaikutusten kannalta suurempi merkitys, kuin aktiivisuuden intensiteetillä. Tässä tutkimuksessa tutkittiin istumisen aikaista lihasaktiivisuutta jalkojen lihaksissa suomalaisilla toimistotyöläisillä (n=4) työpäivän aikana. Vertasimme kahta dynaamista työtuolia (HG ja HM tuolit) perinteiseen staattiseen toimistotuoliin (SC tuoli) koehenkilöiden istuessa kolmen viikon aikana 5 peräkkäistä työpäivää kullakin tuolilla satunnaisessa järjestyksessä. Lihasaktiivisuutta rekisteröitiin vaatteeseen integroiduilla tekstiilielektrodeilla nelipäisen reisilihaksen, hamstring-, kaksoiskanta- sekä etummaisen säärilihaksen päältä. Elektromyografia (EMG) data keskiarvoistettiin etu- ja takareiden lihaksista (QH) sekä säärten (LL) lihaksista. Tuoleihin kiinnitettiin kiihtyvyysmittarit (ACC) rekisteröimään istuimen liikkeitä istumisen aikana. Koehenkilöt istuivat keskimäärin 5.16 ± 1.04 h työpäivän aikana omalla työpisteellään. LL-lihakset olivat inaktiiviset 82 ± 1.63 % ja QH-lihakset 92 ± 0.66 % ajasta istumisen aikana. Dynaamisilla tuoleilla istuttaessa LL-lihaksissa rekisteröitiin lievästi korkeampi aktiivisuustaso staattiseen tuoliin verrattuna (+10 % ero), kun tarkasteltiin aktiivisuuden keskiarvoa tai aktiivisuusburstien lukumäärää. QH-lihaksissa tuloksissa ei havaittu systemaattisia eroavaisuuksia. Inaktiivisuusjaksot LL-lihaksissa olivat lyhyempiä dynaamisella tuolilla istuttaessa, mutta inaktiivisuusajassa ei havaittu suurta eroa tuolien välillä. Tulokset tukevat oletusta, että dynaamiset työtuolit saattavat lisätä aktiivisuutta alaraajojen lihaksissa staattiseen tuoliin verrattuna. Lisätutkimuksia tarvitaan, jossa kyetään osoittamaan, onko istumisen aikana rekisteröity lihasaktiivisuus intensiteetiltään riittävää terveyshyötyjen saavuttamiseksi.Petra Ihalainen, Fall 2014. Lack of muscle activity in leg muscles of office workers – effect of a dynamic office chair. Department of Biology of Physical Activity, University of Jyväskylä. M.Sc Thesis in the science of sport coaching and fitness testing. 57 pp, 5 appendicies. The World Health Organization has named physical inactivity as a world-wide health risk. Physical inactivity has shown to induce harmful health responses, independently from physical activity. A great deal of daily physical inactivity is accumulated from prolonged sitting periods. Furthermore, daily sitting may accumulate at work. Office work, in particular, has been identified highly passive due to the high rates of sitting during working hours. Recent findings indicate that local muscular activation is the key factor signaling the metabolic responses to activity behavior. When interrupting prolonged inactivity period, the number of activity breaks has shown to be more significant for health parameters, than the intensity of the activity. In the present study, we investigated local muscle activity in lower extremities during occupational sitting in Finnish office workers (n=4). We expected, that replacing a static office chair with a dynamic chair might induce enhanced muscle activity, and, thus, decrease the inactivity time in lower extremities during sitting. We compared two dynamic chairs (HG and HM) to a conventional static chair (SC) that were used by the office workers, each chair being used for one week in randomized order. Electromyographic (EMG) activity was recorded from quadriceps, hamstring, gastrocnemius and tibialis anterior muscles with textile electrodes embedded into clothing and averaged for quadriceps and hamstring muscles (QH) and lower leg muscles (LL). The average sitting time in the office was 5.16 h ± 1.04 h during the 12 days of measurements. The LL muscles were inactive for 82 ± 1.63 % and QH muscles for 90 ± 0.66 % of sitting time, LL muscles being proportionally more active during sitting than QH muscles. No marked difference between dynamic chairs and SC chair was observed in inactivity time. However, a positive trend was seen in LL muscle activity when dynamic chairs were compared to SC chair: greater than 10 % difference in average EMG, mean amplitude and burst rate was detected with dynamic chairs, when compared to SC chair. The results from the present study give slight support for the hypothesis that dynamic chairs would enhance muscle activity during sitting. Dynamic chairs might predispose leg muscles to more “active” sitting, yet further research is needed to determine if the intensity of the muscle activity induced by dynamic chairs is enough for significant health benefits

Boulderoinnin lajianalyysi ja harjoittelu

Boulderointi on kiipeilyn alalaji, jossa kiivettävät reitit ovat matalia ja kiipeily tapahtuu ilman köysivarmistusta. Lajilla on vahva ulko- ja seikkailuliikunnan maine, sillä boulderointia harrastetaan paljon luonnon kivillä; siirtolohkareilla ja kallioilla. Viimeisten 20 vuoden aikana boulderointi on vakiinnuttanut paikkansa kilpalajina kiipeilyn perinteisempien muotojen, lead- ja speed-kiipeilyn rinnalla. Boulderointi käsitetään usein nopeusvoimaa ja räjähtävää voimantuottoa vaativana lajina, verrattuna kestävyysominaisuuksia korostavaan lead-kiipeilyyn. Sormien koukistajalihasten nopea voimantuotto, käsivarren ja ylävartalon lihasten voimakestävyys sekä edullinen suhde ylävartalon voiman ja kehonpainon välillä ovat keskeisiä suorituskykyä määrittäviä ominaisuuksia boulder-kiipeilijällä. Seinäpinnan muoto ja kaltevuus sekä pinnasta löytyvien otteiden koko ja muoto muovaavat jokaisesta kiipeilysuorituksesta omanlaisensa. Siksi kiipeilyssä korostuvat monipuolinen lajitekniikka sekä reitinlukutaito. Suomalainen kilpakiipeily ei toistaiseksi ole yltänyt kansainväliselle huipputasolle MM- tai EM-kilpailuissa, mutta Pohjoismaiden mestaruus heltisi viimeksi miehissä vuonna 2013. Lajiharjoittelua ohjaa kokemusperäinen tieto, sillä urheilukiipeilyn valmennustoiminta on vähäistä. Henkilökohtaiset tavoitteet ja intohimo kiipeilyn ulkolajimuotoihin ohjaavat harjoittelua toisinaan ennemmin kuin menestyminen virallisissa kilpailuissa. Kansallinen lajiliitto, SKIL, pyrkii kuitenkin kehittämään valmennusjärjestelmää ja ohjaamaan suomalaista urheilukiipeilyä kohti kansainvälistä menestystä. Samaan aikaan kansainvälisen lajiliiton tavoitteena on saada kiipeily hyväksytyksi olympialajien joukkoon. Kiipeilysuoritusta on tutkittu fysiologisesta näkökulmasta joitakin vuosikymmeniä, mutta tutkimusala on suhteellisen nuori etenkin boulderointiin keskittyneen tutkimuksen osalta. Kiipeilyn monipuolisuus luo haasteet tarkkojen tutkimusmenetelmien kehittämiselle. Tutkimuksen lisääntyminen ja kokemusperäisen tiedon toteennäyttäminen edistäisi urheilukiipeilyn valmennusta ja edesauttaisi lajin kehittymistä

Coordination of the biliverdin D-ring in bacteriophytochromes

Phytochrome proteins translate light into biochemical signals in plants, fungi and microorganisms. Light cues are absorbed by a bilin chromophore, leading to an isomerization and a rotation of the D-ring. This relays the signal to the protein matrix. A set of amino acids, which is conserved across the phytochrome superfamily, holds the chromophore in the binding pocket. However, the functional role of many of these amino acids is not yet understood. Here, we investigate the hydrogen bonding network which surrounds the D-ring of the chromophore in the resting (Pr) state. We use UV/vis spectroscopy, infrared absorption spectroscopy and X-ray crystallography to compare the photosensory domains from Deinococcus radiodurans, the phytochrome 1 from Stigmatella aurantiaca, and a D. radiodurans H290T mutant. In the latter two, an otherwise conserved histidine next to the D-ring is replaced by a threonine. Our infrared absorption data indicate that the carbonyl of the D-ring is more strongly coordinated by hydrogen bonds when the histidine is missing. This is in apparent contrast with the crystal structure of the PAS–GAF domain of phytochrome 1 from S. aurantiaca (pdb code 4RPW), which did not resolve any obvious binding partners for the D-ring carbonyl. We present a new crystal structure of the H290T mutant of the PAS–GAF from D. radiodurans phytochrome. The 1.4 Å-resolution structure reveals additional water molecules, which fill the void created by the mutation. Two of the waters are significantly disordered, suggesting that flexibility might be important for the photoconversion. Finally, we report a spectral analysis which quantitatively explains why the histidine-less phytochromes do not reach equal Pfr-type absorption in the photoequilibrium compared to the Deinococcus radiodurans wild-type protein. The study highlights the importance of water molecules and the hydrogen bonding network around the chromophore for controlling the isomerization reaction and spectral properties of phytochromes.peerReviewe

The role of interaction and predictability in the spontaneous entrainment of movement

People walking side by side spontaneously synchronize their steps on some occasions but not on others, which poses a challenge to theories of perception-action based on interactive dynamic systems. How can action be spontaneously entrained by some sources of perceptual information while others are selectively ignored? The predictive processing framework suggests that saliency factors such as stimulus predictability, consistent deviation, and interactivity of the stimulus control the coupling between the motor system and perceptual information. To test this, we compared entrainment of gait cadence by two interactive auditory stimuli and two noninteractive but predictable, faster than preferred stimuli that were isochronous or statistically matched to gait. One interactive stimulus had properties that are optimal for mutual entrainment as per a mathematical model of interactive periodic processes, the Kuramoto system. In particular, the stimulus was faster than the participant but also adapted its rate to a limited degree as function of phase mismatch with the participant's steps. The second interactive stimulus fully mirrored the gait cycle hence it did not induce mutual synchronization. Furthermore, healthy participants were compared to ones with impaired gait due to Parkinson's disease, a model disorder that makes movement more dependent on external cueing. The mutually interactive condition produced the strongest entrainment, in patients and healthy participants, without differences between groups. The stimulus adapted to each participant's gait while maintaining a consistent lead in phase. Auditory-motor coupling may be enhanced by stimuli that are not only predictable but also interactive in that they align to self-generated movements

Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome

Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruitingbody formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.Peer reviewe