The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature

(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 angstrom resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 angstrom resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.Peer reviewe

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.Peer reviewe

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach

The Sodium Sialic Acid Symporter From Staphylococcus aureus Has Altered Substrate Specificity

Mammalian cell surfaces are decorated with complex glycoconjugates that terminate with negatively charged sialic acids. Commensal and pathogenic bacteria can use host-derived sialic acids for a competitive advantage, but require a functional sialic acid transporter to import the sugar into the cell. This work investigates the sodium sialic acid symporter (SiaT) from Staphylococcus aureus (SaSiaT). We demonstrate that SaSiaT rescues an Escherichia coli strain lacking its endogenous sialic acid transporter when grown on the sialic acids N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc). We then develop an expression, purification and detergent solubilization system for SaSiaT and demonstrate that the protein is largely monodisperse in solution with a stable monomeric oligomeric state. Binding studies reveal that SaSiaT has a higher affinity for Neu5Gc over Neu5Ac, which was unexpected and is not seen in another SiaT homolog. We develop a homology model and use comparative sequence analyses to identify substitutions in the substrate-binding site of SaSiaT that may explain the altered specificity. SaSiaT is shown to be electrogenic, and transport is dependent upon more than one Na+ ion for every sialic acid molecule. A functional sialic acid transporter is essential for the uptake and utilization of sialic acid in a range of pathogenic bacteria, and developing new inhibitors that target these transporters is a valid mechanism for inhibiting bacterial growth. By demonstrating a route to functional recombinant SaSiaT, and developing the in vivo and in vitro assay systems, our work underpins the design of inhibitors to this transporter

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach

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

The Primary Structural Photo-Response of a Bacterial Phytochrome Probed by Serial Femtosecond Crystallography

Species across all kingdoms of life rely on the ability to sense different light conditions. Some organisms convert light into chemical energy via the reactions involved in photosynthesis, whereas others use it to trigger cellular signals. The group of proteins that are responsible for light perception are called photoreceptor proteins. Phytochromes are photoreceptors that control diverse physiological responses in plants, algae, fungi and bacteria, through their ability to sense red and far-red light. These proteins absorb light through a bilin cofactor located in the photosensory part of the protein. Changes in the chromophore induce structural rearrangement in the protein and thereby alter its biological activity. Several structural details of the signalling mechanism remain undetermined and require further investigation. This thesis focuses on revealing the early structural changes upon photoactivation in the bacterial phytochrome from Deinococcus radiodurans (DrBphP). Serial femtosecond crystallography (SFX) has been the main method used for our investigations. The papers presented here describe the crystallization strategies that were used preceding data collection at X-ray free electron lasers (XFELs). Structures of the chromophore-binding domain (PAS-GAF) from DrBphP were solved in the resting state, and at 1 ps following light-activation. Additional time-resolved diffraction data were collected at 0-2.7 ps, probing the earliest structural changes after photon absorption. The findings reveal that the captured photoresponse involves extended structural rearrangements including both the chromophore and the protein. Two conserved tyrosine residues are proposed to be involved in the earliest signalling on femtosecond time scale. Subsequently, a collective response of the chromophore and the surrounding binding pocket evolve on an early picosecond time scale. The discoveries have provided insight into the primary molecular mechanism that phytochromes use to convert light signals into structural changes. Such research not only deepens our understanding of how all vegetation on earth function, but could also have applications in agriculture where growth patterns in various crops could be made more effective

Konceptet ekosystemtjänster och dess möjliga roll i planeringen av stadens grönstruktur - intervjustudie och fallstudie

Grönstrukturen kan spela en betydande roll för människors välbefinnande i staden och den urbana grönstrukturen uppmärksammas alltmer för sina fördelar. Ekosystemtjänstkonceptet erbjuder ett alternativt sätt att planera den urbana grönstrukturen. Begreppet ekosystemtjänster har blivit populärt i samhället under en relativt kort period, trots att det råder ovisshet om vad begreppet betyder, samt osäkerhet om hur ett arbete inkluderat ekosystemtjänstbegreppet kan ske. Det finns också en osäkerhet om vad det har för fördelar och vad det ger för möjligheter gentemot traditionella planeringsformer för grönstruktur. Det finns därför ett behov av att öka kunskapen om ekosystemtjänsters eventuella roll i planeringen av grönstrukturer i städer, undersöka vad användningen av begreppet används till, så planerare kan göra adekvata beslut. Syftet med studien är att undersöka användbarheten med ekosystemtjänster som begrepp och koncept vid planering av urban grönstruktur. Studien har tre frågeställningar. Hur har begreppet ekosystemtjänst hittills hanterats och använts i planeringen av grönstruktur i städer? Vad finns det för möjligheter och begränsningar med att arbeta med ekosystemtjänster som verktyg i planeringen av grönstruktur i staden? Och hur skulle en implementering av ekosystemtjänstbegreppet applicerat på Älvstranden Utveckling AB:s planering av grönstruktur i Göteborg kunna se ut? Empirin består av en intervjustudie med personer med erfarenhet av att arbeta med ekosystemtjänster och en fallstudie som applicerar begreppet på en verksamhet, Älvstranden Utveckling AB, för att undersöka implementerbarheten av ekosystemtjänster i en organisation. Resultatet visade att begreppet användes för sina pedagogiska fördelar, det användes som ett retoriskt argument för bevarande av natur, samt användes retoriskt mer specifikt i arbetet med att planera grönstrukturen i funktioner och nyttor, för att få mångfunktionella ytor. Dessutom användes ekosystemtjänstbegreppet för att koppla ihop betydelsen av grönstruktur med mänskligt välmående. Det finns ett glapp mellan hur praktiker och teoretiker närmar sig ekosystemtjänster. Bland teoretiker finns en debatt om konceptet, framförallt eftersom det idag är otydligt på flera sätt. Den främsta kritiken mot ekosystemtjänstkonceptet är aspekter av de ekonomiska värderingarna. Något som inte problematiseras på samma sätt av de yrkesverksamma respondenterna i intervjustudien. Möjligheter med ekosystemtjänster är att begreppet kan göra att nyttor och funktioner i grönstrukturen uppmärksammas och bättre utnyttjas. Ekosystemtjänster är också ett bra begrepp att använda i argumentation och konflikter med andra intressen. En utmaning är att ekosystemtjänstkonceptet inte behandlar konflikter mellan ekosystemtjänster eller med andra intressen. Att begreppet är nytt och ännu inte helt hittat sin form i grönstrukturplaneringen ses också som en utmaning. En ekonomisk värdering av naturen ses som både en utmaning och en möjlighet. Studien visar att inställningen är positiv till att använda ekosystemtjänstkonceptet. En möjlig implementering av ekosystemtjänster i arbetet med planering av grönstrukturen på Älvstranden Utveckling AB kan ske på flera sätt. Den enklaste implementeringen är troligtvis att vidareutveckla planeringsverktyget GrönNytta, då det redan används inom berörda delar av verksamheten. Ett alternativ är att använda sig av en ny modell. Av de modeller som hanterats i uppsatsen är SNF:s modell den med mest potential

Identifiering och utvärdering av växters bullerreducerande förmåga i urban miljö

Trafikbuller är den miljöstörning som påverkar flest människor i Sverige. Studier visar att buller kan påverka människors hälsa genom att orsaka hörselskador, stress, sömnsvårigheter och i förlängningen hjärt- och kärlsjukdomar. Idag byggs städerna i Sverige allt tätare, vilket gör att antalet bullerstörda personer fortsätter att öka. För att dämpa buller används ofta höga och breda bullerskärmar, vilket inte är att föredra i urban miljö. Ny forskning undersöker därför andra alternativ, bland annat hur växter och gröna områden kan verka bullerreducerande. Forskare menar att växter med hjälp av sina stammar, bladverk och substratet de står i kan reducera ljud genom reflektion, absorption och spridning av ljudenergin. Detta examensarbete syftade till att utvärdera olika växtelement ur bullerreducerande synpunkt. Växters bullerreducerande förmåga är något varken akustiker eller landskapsarkitekter generellt sett tar hänsyn till och därför ansågs en kunskapssammanställning ligga i tiden. För att göra detta har en litteraturstudie, två intervjuer samt mätningar på två växtelement utförts. Mätningarna gjordes på häckar längs Luthagsesplanaden i Uppsala och på en fasad med klätterväxter på Norr Mälarstrand i Stockholm. Litteratur- och intervjustudien visade att växtbeklädda bullerbarriärer hade högst potential att reducera buller längs vägar, gröna tak högst potential att reducera buller in på innergårdar och gröna fasader högst potential att dämpa buller på torg. Växter har också möjlighet att osynliggöra ljudkällor, vilket gör att vi upplever ljudet som lägre. Mätningarna visade att häcken på Luthagsesplanaden hade möjlighet att dämpa ljudet precis bakom häcken med upp till 3 decibel (dBA). Minskningen höll sig inte ända in till fasaden vilket tros bero på att det reflekterade ljudet dominerar i gaturummet samt att den avskärmande effekten minskar med ökat avstånd. Höga frekvenser dämpades bäst av häcken med den högsta dämpningen på 18 dBA för frekvensbandet 16000 Hz. Dämpningen av de höga frekvenserna syns även in vid fasaden med en dämpning kring 4-5 dBA. Häcken efterliknades i modelleringsprogrammet CadnaA med den nordiska beräkningsmodellen för vägtrafikbuller, men inget objekt tycktes kunna representera häcken på ett reproducerbart sätt. På Norr Mälarstrand visades ingen signifikant skillnad i varken ljudtrycksnivå eller frekvensfördelning från fasaden med klätterväxter. En dämpning på upp till 4 dBA för frekvenser över 800 Hz kan dock antydas in vid fasaden. Vid modellering av fasaden visades att varken en reflekterande eller en absorberande fasad kunde representera klätterväxterna.Traffic noise is the environmental problem that affects most people in Sweden. Studies show that noise can affect human health by causing hearing damage, stress, insomnia and cardiovascular disease. Swedish cities today are built increasingly close, increasing the number of people that are affected by noise. Today, the most common way to reduce noise is to use barriers. In towns, this is not preferable and new research brings up other suggestions that can fit into an urban environment. Some studies are investigating how plants can reduce noise. Research has shown that plants by their trunks, foliage and substrate can reduce sound by reflection, absorption and diffusion. This thesis aimed to identify and evaluate various plant elements through a noise abatement perspective. This perspective is something neither acoustician nor landscape architects in general takes into account and was therefore considered useful. To do this, a literature study, two interviews and measurements were made. The measurements were made on hedges along Luthagsesplanaden in Uppsala and on a facade with climbing plants on Norr Mälarstrand in Stockholm. The literature and the interviews showed that vegetated noise barriers had the highest potential to reduce noise along roads, green roofs had the maximum potential to reduce noise in courtyards and green facades had the maximum potential to reduce noise in squares. Plants are also able to hide sound sources, enabling us to perceive the sound as lower. The measurements showed that the hedge were able to lower the sound pressure level up to 3 decibels (dBA). This reduction did not last to the facade, which is believed to be due to reflected sound dominating the street canyon and that the shielding ability decreases with increasing distance. The hedge was able to lower the higher frequencies the most with the maximum attenuation of 18 dBA for the frequency 16000 Hz. The attenuation of high frequencies is also visible close by the facade with attenuation around 4-5 dBA. The hedge were imitated by different elements in the sound modeling program CadnaA with the help of the Nordic calculation model for road traffic noise, but no element seemed to be able to represent the hedge. The measurement at Norr Mälarstrand showed no significant difference in either sound pressure level or frequency distribution by the facade with climbing plants. However, a damping of up to 4 dBA for frequencies above 800 Hz could be hinted from the measurement by the facade. When modeling the same it was shown that neither an absorbing facade nor a reflecting facade could represent the facade with climbing plants