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A method for determining the lines of variation (LOV) in the initial confidence region under strong nonlinearity in the orbit improvement problem is developed, based on finding the maximum modulus of the normal vector to the level surfaces of the objective function using the least-squares method. The method was tested for three asteroids using their observations on a short arc of the orbit, namely, the points of two variation lines corresponding to the directions of the greatest deformation of the initial confidence region were determined. Approximation of variation lines was performed using third-degree polynomials. Using the obtained approximations, new variables were introduced in which the initial confidence region is almost ellipsoidal, i.e., nonlinearity is nearly absent. The modeling of the initial probability dispersion of trajectories is performed in the space of new variables. The resulting dispersion can be further used to identify collision orbits and estimate the probability of asteroid collisions with Earth. [ABSTRACT FROM AUTHOR]

Abstract Bacteria perceive light signals via photoreceptors and modulate many physiological and genetic processes. The impacts played by light, oxygen, or voltage (LOV) and blue light (BL) photosensory proteins on the virulence-related traits of plant bacterial pathogens are diverse and complex. In this study, we identified LOV protein (Pc-LOV1) from Pseudomonas cichorii JBC1 (PcJBC1) and characterized its function using LOV1-deficient mutant (JBC1Δlov1). In the dark state, the recombinant Pc-LOV1 protein showed an absorption band in UV-A region with a double peak at 340 nm and 365 nm, and within the blue-region, it exhibited a main absorption at 448 nm along with two shoulder peaks at 425 nm and 475 nm, which is a typical feature of oxidized flavin within LOV domain. The adduct-state lifetime (τrec) of Pc-LOV1 was 67.03 ± 4.34 min at 25 °C. BL negatively influenced the virulence of PcJBC1 and the virulence of JBC1Δlov1 increased irrespective of BL, indicating that Pc-LOV1 negatively regulates PcJBC1 virulence. Pc-LOV1 and BL positively regulated traits relevant to colonization on plant surface, such as adhesion to the plant tissue and biofilm formation. In contrast, swarming motility, exopolysaccharide production, and siderophore synthesis were negatively controlled. Gene expression supported the modulation of bacterial features by Pc-LOV1. Overall, our results suggest that the LOV photosensory system plays crucial roles in the adaptive responses and virulence of the bacterial pathogen PcJBC1. The roles of other photoreceptors, sensing of other wavelengths, and signal networking require further investigation.

Bacteria perceive light signals via photoreceptors and modulate many physiological and genetic processes. The impacts played by light, oxygen, or voltage (LOV) and blue light (BL) photosensory proteins on the virulence-related traits of plant bacterial pathogens are diverse and complex. In this study, we identified LOV protein (Pc-LOV1) from Pseudomonas cichorii JBC1 (PcJBC1) and characterized its function using LOV1-deficient mutant (JBC1Δlov1). In the dark state, the recombinant Pc-LOV1 protein showed an absorption band in UV-A region with a double peak at 340 nm and 365 nm, and within the blue-region, it exhibited a main absorption at 448 nm along with two shoulder peaks at 425 nm and 475 nm, which is a typical feature of oxidized flavin within LOV domain. The adduct-state lifetime (τrec) of Pc-LOV1 was 67.03 ± 4.34 min at 25 °C. BL negatively influenced the virulence of PcJBC1 and the virulence of JBC1Δlov1 increased irrespective of BL, indicating that Pc-LOV1 negatively regulates PcJBC1 virulence. Pc-LOV1 and BL positively regulated traits relevant to colonization on plant surface, such as adhesion to the plant tissue and biofilm formation. In contrast, swarming motility, exopolysaccharide production, and siderophore synthesis were negatively controlled. Gene expression supported the modulation of bacterial features by Pc-LOV1. Overall, our results suggest that the LOV photosensory system plays crucial roles in the adaptive responses and virulence of the bacterial pathogen PcJBC1. The roles of other photoreceptors, sensing of other wavelengths, and signal networking require further investigation. [ABSTRACT FROM AUTHOR]

Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications. [ABSTRACT FROM AUTHOR]

In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based twohybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA [ABSTRACT FROM AUTHOR]

Cementochronologie zaměřená na analýzu přírůstků acelulárního cementu v zubech lovených savců dovoluje relativně přesně zhodnotit jejich stáří a stanovit období v roce, kdy byli uloveni. Obě informace mohou přiblížit využívání přírodních zdrojů živočišného původu a načasování jejich dostupnosti nebo dovolují pochopit sezónní dynamiku aktivit tehdejších společností spojených s konkrétními místy. Studie nejprve představuje výsledky ověření metody cementochronologie na referenčním materiálu, tj. na zubech recentních jelenů lesních (Cervus elaphus), srnců obecných (Capreolus capreolus) a prasat divokých (Sus scrofa), kteří dlouhodobě patří mezi nejčastěji lovenou zvěř ve střední Evropě. Následně přináší výsledky aplikace metody na vybrané nálezy týchž druhů zvířat z raně středověkého hradiště Na Jánu v jihočeských Netolicích.

In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.

Pseudomonas aeruginosa thrives in the airways of individuals with cystic fibrosis, in part by forming robust biofilms that are resistant to immune clearance or antibiotic treatment. In the cystic fibrosis lung, the thickened mucus layers create an oxygen gradient, often culminating with the formation of anoxic pockets. In this environment, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa are limited to the GFP and related analogs. However, these reporters require oxygen for the maturation of their chromophore, making them unsuitable for the study of anaerobically grown P. aeruginosa. To overcome this limitation, we evaluated seven alternative fluorescent proteins, including iLOV, phiLOV2.1, evoglow-Bs2, LucY, UnaG, Fluorescence-Activating and Absorption-Shifting Tag (FAST), and iRFP670, which have been reported to emit light under oxygen-limiting conditions. We generated a series of plasmids encoding these proteins and validated their fluorescence using plate reader assays and confocal microscopy. Six of these proteins successfully labeled P. aeruginosa in anoxia. In particular, phiLOV2.1 and FAST provided superior fluorescence stability and enabled dual-color imaging of both planktonic and biofilm cultures. This study provides a set of fluorescent reporters for monitoring P. aeruginosa under low-oxygen conditions. These reporters will facilitate studies of P. aeruginosa in biofilms or other contexts relevant to its pathogenesis, such as those found in cystic fibrosis airways. Due to the broad host range of our expression vector, the phiLOV2.1 and FAST-based reporters may be applicable to the study of other Gram-negative bacteria that inhabit similar low-oxygen niches. [ABSTRACT FROM AUTHOR]

Copyright of Archeologické Rozhledy is the property of Academy of Sciences of the Czech Republic, Institute of Archaeology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Pseudomonas aeruginosa thrives in the airways of individuals with cystic fibrosis, in part by forming robust biofilms that are resistant to immune clearance or antibiotic treatment. In the cystic fibrosis lung, the thickened mucus layers create an oxygen gradient, often culminating with the formation of anoxic pockets. In this environment, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa are limited to the GFP and related analogs. However, these reporters require oxygen for the maturation of their chromophore, making them unsuitable for the study of anaerobically grown P. aeruginosa. To overcome this limitation, we evaluated seven alternative fluorescent proteins, including iLOV, phiLOV2.1, evoglow-Bs2, LucY, UnaG, Fluorescence-Activating and Absorption-Shifting Tag (FAST), and iRFP670, which have been reported to emit light under oxygen-limiting conditions. We generated a series of plasmids encoding these proteins and validated their fluorescence using plate reader assays and confocal microscopy. Six of these proteins successfully labeled P. aeruginosa in anoxia. In particular, phiLOV2.1 and FAST provided superior fluorescence stability and enabled dual-color imaging of both planktonic and biofilm cultures. This study provides a set of fluorescent reporters for monitoring P. aeruginosa under low-oxygen conditions. These reporters will facilitate studies of P. aeruginosa in biofilms or other contexts relevant to its pathogenesis, such as those found in cystic fibrosis airways. Due to the broad host range of our expression vector, the phiLOV2.1 and FAST-based reporters may be applicable to the study of other Gram-negative bacteria that inhabit similar low-oxygen niches.

In the short stories Navidades de Madrid (Madrid, 1663), by Mariana de Carvajal y Saavedra, various physical and emotional ailments are mentioned, along with therapeutic remedies, particularly for melancholy caused by romantic problems. Among the remedies, humour plays a fundamental role, in various forms (jokes, poems). I would like to examine these ailments, the methods used to cure them, the narrator's opinion on these issues, and humour as a therapy. [ABSTRACT FROM AUTHOR]

Lånordet sharia, som i dag er i alminnelig bruk i svensk, dansk og norsk, har sitt opphav i det arabiske substantivet sharīʿa, med de beslektede formene substantivet sharʿa og verbet sharaʿa, som alle opptrer i koranteksten. Denne artikkelen tar for seg hvordan disse ordene er oversatt, definert, forklart og brukt i skandinaviske koranoversettelser og faglige fremstillinger, i et historisk perspektiv. I koranoversettelsene er ordene gjengitt semantisk med ulike betydninger knyttet til begreper som vei og retning eller terminologisk med vokabular fra et juridisk domene, og lånordet sharia er her fraværende. Frem til 1970-tallet var heller ikke lånordet særlig utbredt i faglitteraturen, men det ble etter hvert en del av et standardvokabular i fremstillinger av og diskusjoner omkring islam. I faglitteraturen varierer forståelsen mellom en legalistisk og en moralsk oppfatning av islams normative aspekter, og forklares gjennom begreper som lovreligion, etikk og hverdagsjuss.

In the scope of four main parts, the article attempts to capture the relationship between the Czech hunting legislation and nature conservation. The question is whether we can consider the current concept of the Hunting Act (449/2001 Sb.) as one of the tools of environmental protection or what should be changed to become such an instrument. For the elaboration the research was based, among other things, mainly on historical and linguistic legal method of research in the part devoted to the term. Text also deals with critical description, classification, analysis and explanation in the part devoted to the core of the issue and the demonstrative comparison and prediction pro futuro at the final part. Furthermore, the text elaborates interesting cases of judicial and administrative practice and, last but not least, it takes into account the relevant legal norms and appropriate literature or professional texts. In the scope of four main parts, the article attempts to capture the relationship between the Czech hunting legislation and nature conservation. The question is whether we can consider the current concept of the Hunting Act No. 449/2001 Sb. (and other related and subsequent legal norms, including current amendments) as one of the tools of environmental protection and if not, what should be changed to become such an effectively protective instrument. The first part of the paper deals in more detail with the very concept of hunting and hunting management, including various interpretations, and therefore also meanings. In this context, greater emphasis is placed primarily on the first signs of nature protection during the history. For the elaboration the research was based, among other things, mainly on historical and linguistic legal method of research in the part devoted to the term. Next part of the article follows the very essence of the headline, namely the role of hunting in environmental protection. Author pays special attention to the hunting ground and game in this regard. One of the separate subchapters then deals with the state administration of hunting and its main issues in everyday practice. Here, the issue of the officers detached from reality is primarily pointed out as well as undersized offices in combination with actually quite impuissant roles of special hunting managers and guards. Then, some fundamental problems of current legislation and hunting practice are highlighted, especially in relation to other human (mostly free time) activities in nature. It is mentioned, for example, the ever-increasing tourist pressure on the landscape, the rather negative perception of Czech hunters by the general public, generally unsatisfactory forestry and intensive agriculture management, high numbers of some species of ungulates in contrast to the alarming decline of small game, and others. The author looks at the possible future development of hunting legislation, especially in the light of two amendments – the first already valid, but probably never effective, and the second so far only in the form of the parliamentary press. Most of the main changes is critically reviewed, outlining the advantages as same as disadvantages that the changes potentially bring. In the last part of the whole text, the readers’ attention is drawn to author´s own proposal for a new concept of hunting legislation and practice in the Czech Republic, for which a great inspiration was found in the functioning of hunting and the overall management of wildlife in the US state of Florida. Brief conclusion is given by summarizing the essentials, while including a consideration of the possibilities of the direction of Czech hunting in the future. Further critical description, classification, analysis and explanation in the part devoted to the core of the issue and the demonstrative comparison and prediction pro futuro at the final part. Furthermore, the text elaborates interesting cases of judicial and administrative practice and, last but not least, it takes into account the relevant legal norms and appropriate literature or professional texts. [ABSTRACT FROM AUTHOR]

Cells generate a highly diverse microtubule network to carry out different activities. This network is comprised of distinct tubulin isotypes, tubulins with different post-translational modifications, and many microtubule-based structures. Defects in this complex system cause numerous human disorders. However, how different microtubule subtypes in this network regulate cellular architectures and activities remains largely unexplored. Emerging tools such as photosensitive pharmaceuticals, chemogenetics, and optogenetics enable the spatiotemporal manipulation of structures, dynamics, post-translational modifications, and cross-linking with actin filaments in target microtubule subtypes. This review summarizes the design rationale and applications of these new approaches and aims to provide a roadmap for researchers navigating the intricacies of microtubule dynamics and their post-translational modifications in cellular contexts, thereby opening new avenues for therapeutic interventions. [ABSTRACT FROM AUTHOR]

Copyright of Časopis za Zgodovino in Narodopisje is the property of University of Maribor and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The review summarizes available knowledge of management of populations of free-living wild boar with the focus on Central Europe. The wild boar is actually a key species that significantly influences the economy of farming, causes traffic accidents on the roads and other damage, and negatively affects the diversity of plant and animal communities. Therefore, regulation of its numbers is necessary. However, effort to reduce the current populations of wild boar is affected by the favourable environmental conditions, which do not limit population growth. In the Central Europe, wild boar finds enough food throughout the whole year. It can be expected that majority of adult females and significant part of young females will be involved in the reproductive process. Although there are several potential methods for regulation, in reality only shooting by hunters can be effectively used in the conditions of Central Europe. Their activity and hunting strategy significantly affect both the success in regulating the number of wild boar and its distribution, behaviour and reproduction. The importance, impacts and consequent responsibility of hunters in management of wild boar populations are thus significantly greater than simply maintaining the abundance. [ABSTRACT FROM AUTHOR]

Copyright of Prameny & Studie is the property of National Museum of Agriculture / Narodni Zemedelske Muzeum and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Light–oxygen–voltage (LOV) proteins are ubiquitous photoreceptors that can interact with other regulatory proteins and then mediate their activities, which results in cellular adaptation and subsequent physiological changes. Upon blue-light irradiation, a conserved cysteine (Cys) residue in LOV covalently binds to flavin to form a flavin–Cys adduct, which triggers a subsequent cascade of signal transduction and reactions. We found a group of natural Cys-less LOV-like proteins in magnetotactic bacteria (MTB) and investigated its physiological functions by conducting research on one of these unusual LOV-like proteins, Amb2291, in Magnetospirillum magneticum. In-frame deletion of amb2291 or site-directive substitution of alanine-399 for Cys mutants impaired the protective responses against hydrogen peroxide, thereby causing stress and growth impairment. Consequently, gene expression and magnetosome formation were affected, which led to high sensitivity to oxidative damage and defective phototactic behaviour. The purified wild-type and A399C-mutated LOV-like proteins had similar LOV blue-light response spectra, but Amb2291A399C exhibited a faster reaction to blue light. We especially showed that LOV-like protein Amb2291 plays a role in magnetosome synthesis and resistance to oxidative stress of AMB-1 when this bacterium was exposed to red light and hydrogen peroxide. This finding expands our knowledge of the physiological function of this widely distributed group of photoreceptors and deepens our understanding of the photoresponse of MTB. Key Points: • We found a group of Cys-less light–oxygen–voltage (LOV) photoreceptors in magnetotactic bacteria, which prompted us to study the light-response and biological roles of these proteins in these non-photosynthetic bacteria. • The Cys-less LOV-like protein participates in the light-regulated signalling pathway and improves resistance to oxidative damage and magnetic crystal biogenesis in Magnetospirillum magneticum. • This result will contribute to our understanding of the structural and functional diversity of the LOV-like photoreceptor and help us understand the complexity of light-regulated model organisms. [ABSTRACT FROM AUTHOR]

The objective of this study was to compare the morphological and physiological responses of maize ideotypes (Zea mays L.) at double planting density, as well as to identify efficient ideotypes for future breeding programs. It is postulated that higher grain-yielding ideotypes are also more physiologically efficient. The experimental design was random blocks arranged in a split plot design; the large plots corresponded to population densities, and the small plots to ideotypes, with four repetitions. Morphological and physiological variables, as well as yield components, allowed the identification of genotypes with better agronomic performance and greater physiological efficiency. The ideotype factor (A) had a more significant effect on the measured variables than population density (D) and D ´ A interaction factors. The increase in D caused an increment in grain yield (p£0.05) mainly due to the increase in leaf area index, without modifying the photosynthetic rate (p=0.05). The outstanding ideotypes were inbred lines L95 and L145, the Dulce variety, and hybrids LPG133 and HS2, due to their higher values of leaf area index (>3 m2 m-2), levels of photosynthetic radiation interception (>89%), instant photosynthesis rate (>39 mmol CO2 m-2 s-1), prolificacy (>1.4 ears per plant), and grain yield (6 to 18 t ha-1), on average of the two densities. [ABSTRACT FROM AUTHOR]

[Display omitted] • Light-oxygen-voltage (LOV) domains are flavin mononucleotide-binding, blue-light receptors. • They regulate cell responses via naturally attached/engineered effector proteins. • The elucidation of their photoreaction dynamics is a major bottleneck in their study. • LOV-based tools can be designed for light-controlled processes (e.g., optogenetic tools). • Advances in time-resolved crystallography, spectroscopy, and computational science will aid in resolving the photoreaction and developing optogenetic tools. The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies. [ABSTRACT FROM AUTHOR]

The ability to manipulate expression of exogenous genes in particular regions of living organisms has profoundly transformed the way we study biomolecular processes involved in both normal development and disease. Unfortunately, most of the classical inducible systems lack fine spatial and temporal accuracy, thereby limiting the study of molecular events that strongly depend on time, duration of activation, or cellular localization. By exploiting genetically engineered photo sensing proteins that respond to specific wavelengths, we can now provide acute control of numerous molecular activities with unprecedented precision. In this review, we present a comprehensive breakdown of all of the current optogenetic systems adapted to regulate gene expression in both unicellular and multicellular organisms. We focus on the advantages and disadvantages of these different tools and discuss current and future challenges in the successful translation to more complex organisms.

The ability to manipulate expression of exogenous genes in particular regions of living organisms has profoundly transformed the way we study biomolecular processes involved in both normal development and disease. Unfortunately, most of the classical inducible systems lack fine spatial and temporal accuracy, thereby limiting the study of molecular events that strongly depend on time, duration of activation, or cellular localization. By exploiting genetically engineered photo sensing proteins that respond to specific wavelengths, we can now provide acute control of numerous molecular activities with unprecedented precision. In this review, we present a comprehensive breakdown of all of the current optogenetic systems adapted to regulate gene expression in both unicellular and multicellular organisms. We focus on the advantages and disadvantages of these different tools and discuss current and future challenges in the successful translation to more complex organisms. [ABSTRACT FROM AUTHOR]

We report natural light-oxygen-voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ~ 10-7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helix in the linker region between the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure-function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (~1 second). The reversible electrostatic interaction is nonselective among anionic phospholipids, exhibiting binding strengths dependent on the total anionic content of the membrane without preference for a specific headgroup. The in vitro and cellular responses were also observed with a BcLOV4 homolog and thus are likely to be general across the dikarya LOV class, whose members are associated with regulator of G-protein signaling (RGS) domains. Natural photoreceptors are not previously known to directly associate with membrane phospholipids in a light-dependent manner, and thus this work establishes both a photosensory signal transmission mode and a single-component optogenetic tool with rapid membrane localization kinetics that approaches the diffusion limit. [ABSTRACT FROM AUTHOR]

Light is important for algae, as it warrants metabolic independence via photosynthesis. In addition to the absorption of light by the photosystems, algae possess a variety of specific photoreceptors that allow the quantification of the light fluxes as well as the assessment of light qualities. About a decade ago, aureochromes have been described in the xanthophyte alga Vaucheria frigida . These proteins represent a new type of blue light photoreceptor as they possess both a light-oxygen-voltage (LOV) domain for light reception as well as a basic region leucine zipper (bZIP) domain for DNA binding, indicating that they represent light-driven transcription factors. Aureochromes so far have been detected only in a single group of algae, photosynthetic stramenopiles, but not in any other prokaryotic or eukaryotic organisms. Recent biophysical work on aureochromes in the absence and the presence of DNA revealed the mechanism of allosteric communication between the sensor and effector domains despite their unusual inversed arrangement. Different molecular models have been proposed to describe the effect of light on DNA binding. Functional characterization of mutants of the diatom Phaeodactylum tricornutum , in which the aureochrome genes have been silenced or deleted, indicate that different aureochromes may have different functions, being involved in central processes like light acclimation and regulation of the cell cycle. [ABSTRACT FROM AUTHOR]

One of the major barriers to the deployment of Linked Data is the difficulty that data publishers have in determining which vocabularies to use to describe the semantics of data. This systematic report describes Linked Open Vocabularies (LOV), a high-quality catalogue of reusable vocabularies for the description of data on the Web. The LOV initiative gathers and makes visible indicators such as the interconnections between vocabularies and each vocabulary’s version history, along with past and current editor (individual or organization). The report details the various components of the system along with some innovations, such as the introduction of a property-level boost in the vocabulary search scoring that takes into account the property’s type (e.g., dc:comment) associated with a matching literal value. By providing an extensive range of data access methods (full-text search, SPARQL endpoint, API, data dump or UI), the project aims at facilitating the reuse of well-documented vocabularies in the Linked Data ecosystem. The adoption of LOV by many applications and methods shows the importance of such a set of vocabularies and related features for ontology design and the publication of data on the Web. [ABSTRACT FROM AUTHOR]

Copyright of Kronika is the property of Kronika, Casopis za Slovensko Krajevno Zgodovino and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors.This review focuses on the potential of Hydrogen-Deuterium exchange coupled to mass spectrometry (HDX-MS) for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on the conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools.

Light-oxygen-voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor-effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here,we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ~42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor-effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor-effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure-function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics. [ABSTRACT FROM AUTHOR]

The increase of Linked Open Data (LOD) usage has grown in the last few years, and the number of datasets available is considerably higher. Taking this into account, another way to make data available is microdata, whose aim is to make information more understandable for search engines to give better results. The Schema.org vocabulary was created for the enrichment of microdata as a way to give more accurate results for user searches. As Schema.org is a kind of ontology, it has the potential to become a bridge to the Web of Linked Data. In this paper we analyze the potential of mapping Schema.org and the Web of Linked Data. Concretely, we have obtained mappings between Schema.org terms and the terms provided by the Linked Open Vocabularies (LOV) collection. In order to measure the limitations of our mappings we have compared the results of our script with some matching tools. Finally, an analysis of the usability of interlinking Schema.org to vocabularies in LOV has been carried out. For this purpose, two studies in which we have been presented aggregated information. Results show that new information has been added a substantial number of times. [ABSTRACT FROM AUTHOR]