Phylogeny of anoxygenic photosynthesis based on sequences of photosynthetic reaction center proteins and a key enzyme in bacteriochlorophyll biosynthesis, the chlorophyllide reductase

Photosynthesis is a key process for the establishment and maintenance of life on earth, and it is manifested in several major lineages of the prokaryote tree of life. The evolution of photosynthesis in anoxygenic photosynthetic bacteria is of major interest as these have the most ancient roots of photosynthetic systems. The phylogenetic relations between anoxygenic phototrophic bacteria were compared on the basis of sequences of key proteins of the type-II photosynthetic reaction center, including PufLM and PufH (PuhA), and a key enzyme of bacteriochlorophyll biosynthesis, the light-independent chlorophyllide reductase BchXYZ. The latter was common to all anoxygenic phototrophic bacteria, including those with a type-I and those with a type-II photosynthetic reaction center. The phylogenetic considerations included cultured phototrophic bacteria from several phyla, including Proteobacteria (138 species), Chloroflexi (five species), Chlorobi (six species), as well as Heliobacterium modesticaldum (Firmicutes), Chloracidobacterium acidophilum (Acidobacteria), and Gemmatimonas phototrophica (Gemmatimonadetes). Whenever available, type strains were studied. Phylogenetic relationships based on a photosynthesis tree (PS tree, including sequences of PufHLM-BchXYZ) were compared with those of 16S rRNA gene sequences (RNS tree). Despite some significant differences, large parts were congruent between the 16S rRNA phylogeny and photosynthesis proteins. The phylogenetic relations demonstrated that bacteriochlorophyll biosynthesis had evolved in ancestors of phototrophic green bacteria much earlier as compared to phototrophic purple bacteria and that multiple events independently formed different lineages of aerobic phototrophic purple bacteria, many of which have very ancient roots. The Rhodobacterales clearly represented the youngest group, which was separated from other Proteobacteria by a large evolutionary gap

A comparison of laboratory, clinical and self-report measures of prospective memory in healthy adults and individuals with brain injury

Individuals with traumatic brain injury (TBI) have demonstrated deficits in prospective memory (PM) functioning when compared to healthy adults. These deficits have been measured using laboratory measures, clinical measures and self-report questionnaires. However, PM has been shown to involve multiple cognitive processes and have a variety of stages. Thus, it is not known if these measures all assess the same aspects of PM. Thus, this study was designed to measure the convergent validity of the three types of PM measures in both healthy adults and individuals with TBI. We aimed to investigate the convergent validity of the three types of tasks in two ways. First, we sought to investigate if the PM deficits experienced by people with TBI are consistent across tasks. And, second, we sought to examine the relationship between the three types of tasks. Results demonstrated that while all three types of measures were sensitive to PM deficits in TBI, there were differences in the aspects/processes of PM being measured. Data from the laboratory measure suggested a specific difficulty with detecting the correct cue. Data from the clinical measure suggested that TBI has a greater effect on time-based cues than event-based cues and that the primary deficit is a prospective intention retrieval deficit rather than the retrospective memory component. In addition, those with TBI did not differ from healthy adults when the time delay was short enough, suggesting that PM is not universally impaired. Data from the self-report questionnaire suggested that those with TBI are more sensitive to difficulties with basic activities of daily living rather than instrumental activities on daily living. These results are discussed in terms of rehabilitation techniques that could focus first on cue detection and use basic activities of daily living as outcome measures

Effects of b-lactam antibiotics and fluoroquinolones on human gut microbiota in relation to clostridium difficile associated diarrhea

Clostridium difficile infections are an emerging health problem in the modern hospital environment. Severe alterations of the gut microbiome with loss of resistance to colonization against C. difficile are thought to be the major trigger, but there is no clear concept of how C. difficile infection evolves and which microbiological factors are involved. We sequenced 16S rRNA amplicons generated from DNA and RNA/cDNA of fecal samples from three groups of individuals by FLX technology: (i) healthy controls (no antibiotic therapy); (ii) individuals receiving antibiotic therapy (Ampicillin/Sulbactam, cephalosporins, and fluoroquinolones with subsequent development of C. difficile infection or (iii) individuals receiving antibiotic therapy without C. difficile infection. We compared the effects of the three different antibiotic classes on the intestinal microbiome and the effects of alterations of the gut microbiome on C. difficile infection at the DNA (total microbiota) and rRNA (potentially active) levels. A comparison of antibiotic classes showed significant differences at DNA level, but not at RNA level. Among individuals that developed or did not develop a C. difficile infection under antibiotics we found no significant differences. We identified single species that were up- or down regulated in individuals receiving antibiotics who developed the infection compared to non-infected individuals. We found no significant differences in the global composition of the transcriptionally active gut microbiome associated with C. difficile infections. We suggest that up- and down regulation of specific bacterial species may be involved in colonization resistance against C. difficile providing a potential therapeutic approach through specific manipulation of the intestinal microbiome.This work was supported by the ERANET Project PathoGenoMics program grant number 0315441A.Peer Reviewe

Electronic Structure of Halogen Doped CuCr2Se4

We have employed element and chemically sensitive X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD) in order to address a long standing controversy regarding the electronic and magnetic state of CuCr{sub 2}Se{sub 4} via halogen doping of the Se anion site in CuCr{sub 2}Se{sub 4-x}Y{sub x} (Y=Cl and Br). Long range magnetic order is observed above room temperature for all samples. The Cr L{sub 2,3} XAS spectra show a prevalent 3+ valence for the Cr ions independent of doping concentration and doping agent. The Cu L{sub 2,3} XAS spectra show a combination of 1+ and 2+ valence states for all samples. XMCD spectra indicate the presence of a magnetic moment associated with the Cu ions that is aligned antiparallel to the Cr moment

Videogame consumption: The apophatic dimension

This article applies psychological-sociological accounts of the ‘apophatic’, a form of negative thinking, to examples of gaming practices to conceptualise a new theory of videogame consumption. It challenges the prevailing notion that the games consumer is always a ‘cataphatic’ thinker – that is, an activistic, rational-pleasure seeker – and looks to the ‘sorrows’ of gaming to find evidence of its more undesirable nature. The term ‘apophatic’ is characterised as an attempt to de-value the rational value purportedly placed on gaming practices. ‘Griefing’ other players is a good example of this apophatic ethic, where players derive value from the subversion of serious play through the disruption and destruction of other players’ game worlds. The struggle with ‘failure’ is another. As such, the article concludes with a reflection on the almost unsayable nature of videogame consumption, and suggests that consumer value may be derived from its more negative, spiritual-like aspects

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

Despite the importance of deep-sea corals, our current understanding of their ecology and evolutionis limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent reevaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea. As such, our data provides direction for future research and further insight to organismal response of deep sea coral to environmental change and ocean warming.Tis work was supported by King Abdullah University of Science and Technology (KAUST), baseline funds to CRV and Center Competitive Funding (CCF) Program FCC/1/1973-18-01

Freedom in mundane mobilities: caravanning in Denmark

Freedom is a widely discussed and highly elusive concept, and has long been represented in exoticised, masculinised and individualised discourses. Freedom is often exemplified through the image of a solitary male explorer leaving the female space of home and familiarity and going to remote places of the world. Through in-situ interviews with families caravanning in Denmark, the primary aim of this study is to challenge existing dominant discourses surrounding the subject of freedom within leisure and tourism studies. Secondly, we shed further light on an under-researched medium of mobility, that of domestic caravanning. This serves to not only disrupt representations of freedom as occurring through exoticised, masculinised and individualised practices, but to give attention to the domestic, banal contexts where the everyday and tourism intersect, which are often overlooked. This novel repositioning opens up new avenues in tourism studies for critical research into the geographies of freedom in mundane, everyday contexts