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Background: Researchers regularly must decide what information is necessary to understand school climate and how to include climate in a study. For example, which factors and/or scales should be used, is using just 1 scale for school climate sufficient, and to what extent does the selection of a single scale influence the research findings? Aims: Understanding what factors to consider and which available scales to review will assist those interested in measuring school climate. Methods: This study explores 8 validated scales related to school climate. Data used are from a previous study (Social and Character Development cooperative agreement funded by IES #R305L030072 and #R305A080253) that looked at Positive Action, a social emotional and character development program for elementary-, middle-, and high-school students. Results and Conclusion: Scale correlations and factor analyses show how these scales work together to measure overall middle school climate.

The distinctiveness of Maputaland Woody Grassland lies within its richness of geoxylic suffrutices and herbaceous flora. Since it is well documented in the literature and easy to distinguish from other grassland types, it was possible to confirm a locality of this unique vegetation unit west of Richards Bay, where it probably forms the southernmost outlier population of this vegetation unit in the Indian Ocean Coastal Belt Biome. Phytosociological data obtained from the study area were analysed to identify plant communities and subsequent mapping units. Floristic gradients obtained through ordination techniques revealed the relationship that exists between the Woody Grassland of the study area and the Maputaland Woody Grassland of Sileza Nature Reserve. This confirms the occurrence of Maputaland Woody Grassland at Richards Bay. Two of the plant communities identified from the Richards Bay site are distinctively different, despite previously being lumped together by different authorities as either Kwambonambi Grassland or Maputaland Woody Grassland.

A vegetation survey was conducted of the Owen Sitole College of Agriculture (OSCA). Phytosociological data were used to identify plant communities and to determine alpha diversity. Five plant communities were recognised and described. One of these was sub-divided into two sub-communities. An ordination scatter diagram of the distribution of the six vegetation units depicted topographically induced gradients, specifically related to soil depth, rock cover, slope and altitude. Floristic composition of the six vegetation units indicates that this coastal thomveld has affinities to the Grassland, Savanna and Forest biomes. In the study area, closed woodland communities have the highest plant richness and grassland communities the highest plant diversity. Diversity and richness per community compares favourable with the Rocky Highveld Grassland, suggesting that phytodiversity at OSCA was maintained despite a history of multiple disturbances. The habitat on OSCA farm serves as an important refuge for plant species and communities of biological and economic significance, especially the remaining grasslands.

An analysis of the vegetation of the Sterkfontein Caves (i.e. the natural area surrounding the caves) is presented. Releves were compiled in 24 stratified random sample plots. A TWINSPAN classification, refined by Braun-Blanquet procedures, revealed six plant communities, also referred to as vegetation units. For each of these vegetation units the species richness was determined. Plant communities of conservation importance were identified and new associations were formally described.

Data from fifteen phytosociological studies were merged and classified to describe and compare the vegetation of geo­ graphically separated and climatically different Mopanev eld types in South Africa. Namibia and Zimbabw e. Seven v egetation types and ten major plant communities were identified using TW INSPAN. Vegetation types were separated according to geo­ graphical regions. There were significant floristic affinities even though there w ere geological and climatic differences between the regions. Plant communities were described according to vegetation structure, habitat and floristic composition. Although environmental data were not adequate for a detailed ordination. DECORANA reflected the distribution of vegetation types and major plant communities along environmental gradients. Limitations of large phytosociological syntheses were also addressed. Species richness (alpha diversity) was calculated for each geographical region. The Musina (Messina) region north of the Soutpansberg. South Africa, has the highest species richness, and Kaokoland. Namibia, the lowest Due to irregular annual rainfall patterns in semi-arid Mopaneveld, it is suggested that variance in species richness is associated with temporal vegeta­ tion states induced by rainfall events. Species richness of Mopaneveld was further compared w ith other sav anna types.

A hierarchical classification, description, and ecological and floristic interpretations are presented on the vegetation types of the ultramafic rock habitats of the Sekhukhuneland Centre of Plant Endemism. Relevés were compiled in 100 stratified random plots. A TWINSPAN classification, refined by Braun-Blanquet procedures, revealed 17 plant communities, which are classified into 13 associations belonging to four proposed alliances. Many new syntaxa are ecologically interpreted and described. For each syntaxon, the species richness, endemism and conservation status was determined. Much of the plant community distribution can be ascribed to specific habitat preference. The floristic and habitat information, proposed classification, general description and vegetation key are provided to aid future identification of conservation areas, land use planning and research. An ordination (DECORANA) based on floristic data confirmed potential relationships that could exist between the plant communities and associated habitats and environmental gradients.

The national conversation about the importance of social emotional competencies, such as prosocial behaviors, re sponsible decision-making, and problem-solving, has increased greatly in the last 2 decades. There is, however, less robust evidence for social and emotional learning programs' impact on social and emotional outcomes when implemented in low-income, minority populations. The purpose of the present study is to evaluate the effectiveness of a school-based, universal program targeting social-emotional skills in late elementary school (grades 3-5) in a low-income, urban, minority population. Data were collected from 930 students over five waves. Growth curve analyses revealed evidence of favorable program effects on positive youth development, emotional health, self-esteem, problem behaviors, health behaviors, environmental climate, and academics. The study provides evidence for universal school-based interventions in low-income, urban, minority contexts in elementary school grades.

This Data in Brief (DiB) article presents the differences in cycling behaviors related to violations, errors, and positive behaviors by region. The study data were collected by means of a structured questionnaire applied to a full sample of 7,001 participants from 19 countries, distributed over 5 continents. This paper proposes descriptive statistics, as well as common statistical tests. The aim is to enable authors to make their own analyses, not to provide precise interpretations. For further information about the macro project supporting the collection of these data, it is advised to refer to the paper titled "Cross-culturally approaching the cycling behavior questionnaire (CBQ): Evidence from 19 countries", published in Transportation Research Part F: Traffic Psychology and Behavior ., (© 2024 The Author(s).)

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems., (© 2024. The Author(s).)

Introduction: Histological examination of tissue specimens obtained during surgical treatment of trigger finger frequently encountered unclassifiable amyloid deposits in the annular ligament. We systematically explored this unknown type by a comprehensive analysis using histology, immunohistochemistry, and quantitative mass spectrometry-based proteomics., Methods: 205 tissue specimens of annular ligaments were obtained from 172 patients. Each specimen was studied by histology and immunohistochemistry. Tissue specimens obtained from ten patients with histology proven amyloid in annular ligament were analysed by label-free quantitative proteomics. Histological and immunohistochemical findings were correlated with patient demographics., Results: Amyloid was present as band like deposits along the surface of annular ligament, dot like or patchy deposits within the matrix. Immunohistochemistry identified ATTR amyloid in 92 specimens (mostly patchy in the matrix), while the band like deposits of 100 specimens remained unclassifiable. Proteomic profiles identified the unknown amyloid as most likely of fibrinogen origin. The complete cohort was re-examined by immunohistochemistry using a custom-made antibody and confirmed the presence of fibrinogen alpha-chain (FGA) in a hitherto unclassifiable type of amyloid in annular ligament., Conclusion: Our study shows that two different types of amyloid affect the annular ligament, ATTR amyloid and AFib amyloid, with distinct demographic patient characteristics and histomorphological deposition patterns.

Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Botha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Amyloidosis is a disease group caused by pathological aggregation and deposition of peptides in diverse tissue sites. Apart from the fibril protein, amyloid deposits frequently enclose non-fibrillar constituents. In this study, carpal tunnel tissue sections with ATTR amyloid were analysed by quantitative mass spectrometry-based proteomics. Following manual dissection, tissue samples of equal size and with heterogeneous amyloid load were dissected and forwarded to bottom-up proteome analysis and label-free protein profiling. The amyloid-associated proteins showed significant correlations of label-free intensity profiles. A comprehensive list of 83 proteins specifically enriched in amyloid deposits was discovered. In addition to well-known signature proteins (e.g. apolipoprotein E, apolipoprotein A-IV, and vitronectin), 22 members of the complement system, including all seven components of the membrane attack complex could be associated to the disease. These data lend support to the hypothesis that the complement system is activated in ATTR amyloidosis.

Privately protected areas (PPAs) are internationally considered to be important policy implementation instruments to augment and strengthen protected area networks. However, there has been limited reflection on the performance of PPAs over time. This paper aims to identify key risks to the performance of PPAs as policy implementation instruments through the application of Theory of Change (ToC). Identifying and understanding these risks are important to allow for the evaluation and monitoring of PPA performance. The ToC method was applied to a specific PPA policy instrument namely, private nature reserves (PNRs) in the South African context. The research results produced 29 key assumptions translated into 29 key risks. These risk are critically discussed against existing South African and international literature. To test and refine the risks further it is recommended that they be applied to PPA case studies in different contexts., (Copyright © 2022. Published by Elsevier Ltd.)

Ethnopharmacological Relevance: Sceletium tortuosum (L.) N.E.Br, the most sought after and widely researched species in the genus Sceletium is a succulent forb endemic to South Africa. Traditionally, this medicinal plant is mainly masticated or smoked and used for the relief of toothache, abdominal pain, and as a mood-elevator, analgesic, hypnotic, anxiolytic, thirst and hunger suppressant, and for its intoxicating/euphoric effects. Sceletium tortuosum is currently of widespread scientific interest due to its clinical potential in treating anxiety and depression, relieving stress in healthy individuals, and enhancing cognitive functions. These pharmacological actions are attributed to its phytochemical constituents referred to as mesembrine-type alkaloids., Aim of the Review: The aim of this review was to comprehensively summarize and critically evaluate recent research advances on the phytochemistry, pharmacokinetics, biological and clinical activities of the medicinal plant S. tortuosum. Additionally, current ongoing research and future perspectives are also discussed., Methods: All relevant scientific articles, books, MSc and Ph.D. dissertations on botany, behavioral pharmacology, traditional uses, and phytochemistry of S. tortuosum were retrieved from different databases (including Science Direct, PubMed, Google Scholar, Scopus and Web of Science). For pharmacokinetics and pharmacological effects of S. tortuosum, the focus fell on relevant publications published between 2009 and 2021., Results: Twenty-five alkaloids belonging to four structural classes viz: mesembrine, Sceletium A4, joubertiamine, and tortuosamine, have been identified from S. tortuosum, of which the mesembrine class is predominant. The crude extracts and commercially available standardized extracts of S. tortuosum have displayed a wide spectrum of biological activities (e.g. antimalarial, anti-oxidant, immunomodulatory, anti-HIV, neuroprotection, enhancement of cognitive function) in in vitro or in vivo studies. This plant has not yet been studied in a clinical population, but has potential for enhancing cognitive function, and managing anxiety and depression., Conclusion: As an important South African medicinal plant, S. tortuosum has garnered many research advances on its phytochemistry and biological activities over the last decade. These scientific studies have shown that S. tortuosum has various bioactivities. The findings have further established the link between the phytochemistry and pharmacological application, and support the traditional use of S. tortuosum in the indigenous medicine of South Africa., (Copyright © 2021. Published by Elsevier B.V.)

Phytochromes switch between a physiologically inactive and active state via a light-induced reaction cascade, which is initiated by isomerization of the tetrapyrrole chromophore and leads to the functionally relevant secondary structure transition of a protein segment (tongue). Although details of the underlying cause-effect relationships are not known, electrostatic fields are likely to play a crucial role in coupling chromophores and protein structural changes. Here, we studied local electric field changes during the photoconversion of the dark state Pfr to the photoactivated state Pr of the bathy phytochrome Agp2. Substituting Tyr165 and Phe192 in the chromophore pocket by para -cyanophenylalanine (pCNF), we monitored the respective nitrile stretching modes in the various states of photoconversion (vibrational Stark effect). Resonance Raman and IR spectroscopic analyses revealed that both pCNF-substituted variants undergo the same photoinduced structural changes as wild-type Agp2. Based on a structural model for the Pfr state of F192pCNF, a molecular mechanical-quantum mechanical approach was employed to calculate the electric field at the nitrile group and the respective stretching frequency, in excellent agreement with the experiment. These calculations serve as a reference for determining the electric field changes in the photoinduced states of F192pCNF. Unlike F192pCNF, the nitrile group in Y165pCNF is strongly hydrogen bonded such that the theoretical approach is not applicable. However, in both variants, the largest changes of the nitrile stretching modes occur in the last step of the photoconversion, supporting the view that the proton-coupled restructuring of the tongue is accompanied by a change of the electric field.

The genus Merremia Dennst. ex Endl. (Convolvulaceae) is a rich source of structurally diverse phytochemicals with therapeutic relevance. This review presents the first comprehensive, up-to-date information and research progression on the nutritional value, ethnomedicinal uses, phytochemistry, pharmacological activities, and toxicity of the genus Merremia . Using the key search term " Merremia ", relevant documents and information were retrieved from electronic databases. Relevant documents were uploaded in RStudio with installed bibliometric software packages and used for data retrieval, tabulation, and network visualization. Bibliometric analysis revealed that ca. 55% of the studies related to Merremia were published in the last decade, which can be grouped into four thematic areas: (i) drug formulation, (ii) taxonomy, (iii) chemical analysis, and (iv) treatment of diseases. Ethnomedicinal uses, phytochemistry, and biological activities studies showed that species in the genus are promising medicinal plants with various pharmaceutical potentials. However, clinical studies to validate the efficacy of the reported bioactivities and the mechanisms underlying the various activities are lacking and should constitute a future research focus. Additionally, reports on the nutritional and antinutritional constituents of Merremia species revealed that the species meet high nutritional quality criteria for animals and are therefore suitable for inclusion in livestock diets. The few available investigations on toxicity indicated that most Merremia species are safe for human and animal use but not with prolonged chronic administration.

Bacterial phytochromes are sensoric photoreceptors that transform light absorbed by the photosensor core module (PCM) to protein structural changes that eventually lead to the activation of the enzymatic output module. The underlying photoinduced reaction cascade in the PCM starts with the isomerization of the tetrapyrrole chromophore, followed by conformational relaxations, proton transfer steps, and a secondary structure transition of a peptide segment (tongue) that is essential for communicating the signal to the output module. In this work, we employed various static and time-resolved IR and resonance Raman spectroscopic techniques to study the structural and reaction dynamics of the Meta-F intermediate of both the PCM and the full-length (PCM and output module) variant of the bathy phytochrome Agp2 from Agrobacterium fabrum. In both cases, this intermediate represents a branching point of the phototransformation, since it opens an unproductive reaction channel back to the initial state and a productive pathway to the final active state, including the functional protein structural changes. It is shown that the functional quantum yield, i.e. the events of tongue refolding per absorbed photons, is lower by a factor of ca. two than the quantum yield of the primary photochemical process. However, the kinetic data derived from the spectroscopic experiments imply an increased formation of the final active state upon increasing photon flux or elevated temperature under photostationary conditions. Accordingly, the branching mechanism does not only account for the phytochrome's function as a light intensity sensor but may also modulate its temperature sensitivity.

Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition and diversity (using 16S and ITS rRNA amplicon sequencing, respectively) in six long-term (18 to 70 years) ecological research sites in South African savanna and grassland ecosystems. We found that fire and herbivory regimes profoundly modified soil physico-chemical properties, plant species richness and standing biomass. In all sites, an increase in woody biomass (ranging from 12 to 50%) was observed when natural disturbances were excluded. The intensity and direction of changes in soil properties were highly dependent on the topo-pedo-climatic context. Overall, fire and herbivory shaped bacterial and fungal communities through distinct driving forces: edaphic properties (including Mg, pH, Ca) for bacteria, and vegetation (herbaceous biomass and woody cover) for fungi. Fire and herbivory explained on average 7.5 and 9.8% of the fungal community variability, respectively, compared to 6.0 and 5.6% for bacteria. The relatively small changes in microbial communities due to natural disturbance is in stark contrast to dramatic vegetation and edaphic changes and suggests that soil microbial communities, having evolved with disturbance, are resistant to change. This represents both a buffer to short-term anthropogenic-induced changes and a restoration challenge in the face of long-term changes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.

Bacteriophytochromes harboring a biliverdin IXα (BV) chromophore undergo photoinduced reaction cascades to switch between physiologically inactive and active states. Employing vibrational spectroscopic and computational methods, we analyzed the role of propionic substituents of BV in the transformations between parent states Pr and Pfr in prototypical (Agp1) and bathy (Agp2) phytochromes from Agrobacterium fabrum . Both proteins form adducts with BV monoesters (BVM), esterified at propionic side chain B (Ps B ) or C (Ps C ), but in each case, only one monoester adduct is reactive. In the reactive Agp2-BVM- B complex (esterified at ring B ), the Pfr dark state displays the structural properties characteristic of bathy phytochromes, including a protonated Ps C . As in native Agp2, Ps C is deprotonated in the final step of the Pfr phototransformation. However, the concomitant α-helix/β-sheet secondary structure change of the tongue is blocked at the stage of unfolding of the coiled loop region. This finding and the shift of the tautomeric equilibrium of BVM toward the enol form are attributed to the drastic changes in the electrostatic potential. The calculations further suggest that deprotonation of Ps C and the protonation state of His278 control the reactivity of the enol tautomer, thereby accounting for the extraordinarily slow thermal reversion. Although strong perturbations of the electrostatic potential are also found for Agp1-BVM, the consequences for the Pr-to-Pfr phototransformation are less severe. Specifically, the structural transition of the tongue is not impaired and thermal reversion is even accelerated. The different response of Agp1 and Agp2 to monoesterification of BV points to different photoconversion mechanisms.

Savannas are commonly described as a vegetation type with a grass layer interspersed with a discontinuous tree or shrub layer. On the contrary, forbs, a plant life form that can include any nongraminoid herbaceous vascular plant, are poorly represented in definitions of savannas worldwide. While forbs have been acknowledged as a diverse component of the herbaceous layer in savanna ecosystems and valued for the ecosystem services and functions they provide, they have not been the primary focus in most savanna vegetation studies. We performed a systematic review of scientific literature to establish the extent to which forbs are implicitly or explicitly considered as a discrete vegetation component in savanna research. The overall aims were to summarize knowledge on forb ecology, identify knowledge gaps, and derive new perspectives for savanna research and management with a special focus on arid and semiarid ecosystems in Africa. We synthesize and discuss our findings in the context of different overarching research themes: (a) functional organization and spatial patterning, (b) land degradation and range management, (c) conservation and reserve management, (d) resource use and forage patterning, and (e) germination and recruitment. Our results revealed biases in published research with respect to study origin (country coverage in Africa), climate (more semiarid than arid systems), spatial scale (more local than landscape scale), the level at which responses or resource potential was analyzed (primarily plant functional groups rather than species), and the focus on interactions between life forms (rather seldom between forbs and grasses and/or trees). We conclude that the understanding of African savanna community responses to drivers of global environmental change requires knowledge beyond interactions between trees and grasses only and beyond the plant functional group level. Despite multifaceted evidence of our current understanding of forbs in dry savannas, there appear to be knowledge gaps, specifically in linking drivers of environmental change to forb community responses. We therefore propose that more attention be given to forbs as an additional ecologically important plant life form in the conventional tree-grass paradigm of savannas., Competing Interests: None declared.

The tiny picoalga, Ostreococcus tauri, originating from the Thau Lagoon is a member of the marine phytoplankton. Because of its highly reduced genome and small cell size, while retaining the fundamental requirements of a eukaryotic photosynthetic cell, it became a popular model organism for studying photosynthesis or circadian clock-related processes. We analyzed the spectroscopic properties of the photoreceptor domain of the histidine kinase rhodopsin Ot-HKR that is suggested to be involved in the light-induced entrainment of the Ostreococcus circadian clock. We found that the rhodopsin, Ot-Rh, dark state absorbs maximally at 505 nm. Exposure to green-orange light led to the accumulation of a blue-shifted M-state-like absorbance form with a deprotonated Schiff base. This Ot-Rh P400 state had an unusually long lifetime of several minutes. A second long-living photoproduct with a red-shifted absorbance, P560, accumulated upon illumination with blue/UVA light. The resulting photochromicity of the rhodopsin is expected to be advantageous to its function as a molecular control element of the signal transducing HKR domains. The light intensity and the ratio of blue vs green light are reflected by the ratio of rhodopsin molecules in the long-living absorbance forms. Furthermore, dark-state absorbance and the photocycle kinetics vary with the salt content of the environment substantially. This observation is attributed to anion binding in the dark state and a transient anion release during the photocycle, indicating that the salinity affects the photoinduced processes.

Herbivores alter plant biodiversity (species richness) in many of the world's ecosystems, but the magnitude and the direction of herbivore effects on biodiversity vary widely within and among ecosystems. One current theory predicts that herbivores enhance plant biodiversity at high productivity but have the opposite effect at low productivity. Yet, empirical support for the importance of site productivity as a mediator of these herbivore impacts is equivocal. Here, we synthesize data from 252 large-herbivore exclusion studies, spanning a 20-fold range in site productivity, to test an alternative hypothesis-that herbivore-induced changes in the competitive environment determine the response of plant biodiversity to herbivory irrespective of productivity. Under this hypothesis, when herbivores reduce the abundance (biomass, cover) of dominant species (for example, because the dominant plant is palatable), additional resources become available to support new species, thereby increasing biodiversity. By contrast, if herbivores promote high dominance by increasing the abundance of herbivory-resistant, unpalatable species, then resource availability for other species decreases reducing biodiversity. We show that herbivore-induced change in dominance, independent of site productivity or precipitation (a proxy for productivity), is the best predictor of herbivore effects on biodiversity in grassland and savannah sites. Given that most herbaceous ecosystems are dominated by one or a few species, altering the competitive environment via herbivores or by other means may be an effective strategy for conserving biodiversity in grasslands and savannahs globally.

Early research on the four microbial rhodopsins discovered in the archaeal Halobacterium salinarum revealed a structural template that served as a scaffold for two different functions: light-driven ion transport and phototaxis. Bacteriorhodopsin and halorhodopsin are proton and chloride pumps, respectively, while sensory rhodopsin I and II are responsible for phototactic behavior of the archaea. Halorhodopsins have been identified in various other species. Besides this group of archaeal halorhodopsins distinct chloride transporting rhodopsins groups have recently been identified in other organism like Flavobacteria or Cyanobacteria. Halorhodopsin from Natronomonas pharaonis is the best-studied homologue because of its facile expression and purification and its advantageous properties, which was the reason to introduce this protein as neural silencer into the new field of optogenetics. Two other major families of genetically encoded silencing proteins, proton pumps and anion channels, extended the repertoire of optogenetic tools. Here, we describe the functional and structural characteristics of halorhodopsins. We will discuss the data in light of common principles underlying the mechanism of ion pumps and sensors and will review biophysical and biochemical aspects of neuronal silencers.

Objectives: We report on a large prospective, multicentre clinical investigation on inter- and intrapatient genetic variability for antimicrobial resistance of Helicobacter pylori., Methods: Therapy-naive patients (n = 2004) who had undergone routine diagnostic gastroscopy were prospectively included from all geographic regions of Austria. Gastric biopsy samples were collected separately from antrum and corpus. Samples were analysed by histopathology and real-time PCR for genotypic resistance to clarithromycin and quinolones. Clinical and demographic information was analysed in relation to resistance patterns., Results: H. pylori infection was detected in 514 (26%) of 2004 patients by histopathology and confirmed in 465 (90%) of 514 patients by real-time PCR. PCR results were discordant for antrum and corpus in 27 (5%) of 514 patients, indicating inhomogeneous infections. Clarithromycin resistance rates were 17% (77/448) and 19% (84/455), and quinolone resistance rates were 12% (37/310) and 10% (32/334) in antrum and corpus samples, respectively. Combination of test results per patient yielded resistance rates of 21% (98/465) and 13% (50/383) for clarithromycin and quinolones, respectively. Overall, infection with both sensitive and resistant H. pylori was detected in 65 (14%) of 465 patients., Conclusions: Anatomically inhomogeneous infection with different, multiple H. pylori strains is common. Prospective clinical study design, collection of samples from multiple sites and microbiologic methods that allow the detection of coinfections are mandatory for collection of reliable data on antimicrobial resistance patterns in representative patient populations. (ClinicalTrials.gov identifier: NCT02925091)., (Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Background: Helicobacter pylori ( H. pylori ) causes a diversity of gastric diseases. Rapid urease tests (RUT) are well established for the point-of-care, invasive diagnosis of H. pylori infection. The study aimed to evaluate the diagnostic performance of a new liquid RUT, the preOx-HUT, within a prospective cohort of treatment-naïve patients., Methods: The multicenter prospective clinical trial was conducted at nine Austrian centers for gastrointestinal endoscopy. Patients referred for a diagnostic upper gastrointestinal endoscopy underwent gastric biopsy sampling for routine histological evaluation, and in parallel, the preOx-HUT. Histology served as reference standard to evaluate the diagnostic performance of the preOx-HUT., Results: From January 2015 to January 2016, a total of 183 consecutive patients (54 males and 129 females, median age 50 years) were included. Endoscopy revealed pathological findings in 149/183 cases (81%), which were mostly gastritis (59%) and gastro-esophageal reflux disease (27%). H. pylori infection was detected by histology in 41/183 (22%) cases. In relation to histology, the preOx-HUT had a sensitivity of 85%, a specificity of 94%, a positive predictive value of 80% and a negative predictive value of 96%. Performance of preOx-HUT was not affected significantly by concomitant PPI-use as present in 15% of cases (P = 0.73)., Conclusions: This was the first study evaluating the preOx-HUT in a prospective, multicenter clinical setting. We found a high diagnostic accuracy for the point-of-care, invasive diagnostic test of H. pylori infection. Hence, this test may be a valuable diagnostic adjunct to the clinical presentation of patients with suspected H. pylori infection. Trial registration number EK 1548/2014, Name of registry: Register der Ethikkommission der Medizinischen Universität Wien, URL of registry: https://ekmeduniwien.at/core/catalog/2012/, Date of registration: 24.09.2014, Date of enrolment of the first participant to the trial: 15.01.2015.

Phytochromes are bimodal photoreceptors which, upon light absorption by the tetrapyrrole chromophore, can be converted between a red-absorbing state (Pr) and far-red-absorbing state (Pfr). In bacterial phytochromes, either Pr or Pfr are the thermally stable states, thereby constituting the classes of prototypical and bathy phytochromes, respectively. In this work, we have employed vibrational spectroscopies to elucidate the origin of the thermal stability of the Pfr states in bathy phytochromes. Here, we present the first detailed spectroscopic analysis of RpBphP6 (Rhodopseudomas palustris), which together with results obtained for Agp2 (Agrobacterium tumefaciens) and PaBphP (Pseudomonas aeruginosa) allows identifying common structural properties of the Pfr state of bathy phytochromes, which are (1) a homogenous chromophore structure, (2) the protonated ring C propionic side chain of the chromophore and (3) a retarded H/D exchange at the ring D nitrogen. These properties are related to the unique strength of the hydrogen bonding interactions between the ring D N-H group with the side chain of the conserved Asp194 (PaBphP numbering). As revealed by a comparative analysis of homology models and available crystal structures of Pfr states, these interactions are strengthened by an Arg residue (Arg453) only in bathy but not in prototypical phytochromes., (© 2017 The American Society of Photobiology.)

Background: Photodynamic therapy (PDT) is a palliative treatment for malignant biliary obstruction., Objective: The objective of this article is to assess the feasibility and safety of this technique., Methods: In this nationwide, retrospective study of prospectively collected clinical data, all patients treated with PDT using polyhematoporphyrin in Austria from March 2004 to May 2013 were included. Feasibility, adverse events, stent patency and mortality rates were investigated., Results: Eighty-eight patients (54 male, 34 female, median age 69 years) underwent 150 PDT procedures at seven Austrian referral centers for biliary endoscopy. The predominant underlying disease was Klatskin tumor (79/88). All PDT procedures were feasible without technical issues. Cholangitis was the most frequent adverse event (21/88). Stent patency was 246 days (95% CI 203-289) median and was significantly longer for metal than for plastic stents (269 vs. 62 days, p  < 0.01). The median survival was 12.4 months (95% CI 9.7-14.9 m) calculated from first PDT and 15.6 months (95% CI 12.3-18.7 m) calculated from initial diagnosis. In patients suffering from biliary tract cancer, Cox regression revealed the number of PDT treatment sessions as the only independent predictor of survival at a multivariate analysis ( p  = 0.048)., Conclusion: PDT using polyhematoporphyrin was feasible and safe in this nationwide analysis. Survival data suggest a benefit of PDT in this unselected real-life patient population. Prospective trials comparing PDT to other palliative treatments will help to define its role in the management of malignant biliary obstruction. The study is registered at ClinicalTrials.gov number: NCT02504957.

D-lactic acidosis is a rare complication that occurs mainly in patients with malabsorption due to a surgically altered gastrointestinal tract anatomy, namely in short bowel syndrome or after bariatric surgery. It is characterized by rapid development of neurological symptoms and severe metabolic acidosis, often with a high serum anion gap. Malabsorbed carbohydrates can be fermented by colonic microbiota capable of producing D-lactic acid. Routine clinical assessment of serum lactate covers only L-lactic acid; when clinical suspicion for D-lactic acidosis is high, special assays for D-lactic acid are called for. A serum level of more than 3 mmol/L of D-lactate confirms the diagnosis. Management includes correction of metabolic acidosis by intravenous bicarbonate, restriction of carbohydrates or fasting, and antibiotics to eliminate intestinal bacteria that produce D-lactic acid. We report a case of D-lactic acidosis in a patient with short bowel syndrome and review the pathophysiology of D-lactic acidosis with its biochemical and clinical features. D-lactic acidosis should be considered when patients with short bowel syndrome or other malabsorption syndromes due to an altered gastrointestinal tract anatomy present with metabolic acidosis and neurological symptoms that cannot be attributed to other causes. With the growing popularity of bariatric surgery, this metabolic derangement may be seen more frequently in the future., (© Georg Thieme Verlag KG Stuttgart · New York.)