Photosynthesis in Silico: A multimedia CD-ROM combining animations, simulations and self-paced modules for photosynthesis education at all tertiary levels

Photosynthesis is a vital component of any undergraduate biology course. Despite its central importance in providing biochemical energy, fixed carbon and oxygen for all life on Earth, it remains an area which students find uninteresting and difficult to comprehend. This difficulty is compounded by problems with laboratory equipment for practical classes, which tends to be either expensive and complex, or simple and unreliable, making it extremely difficult to provide effective, hands-on teaching of photosynthesis to the large class sizes in undergraduate biology courses. A set of interactive, multimedia modules have been combined on a CD-ROM, which provides a new approach to university teaching of photosynthesis. Features include animations of the photosynthetic electron transport process, serving both as an introduction to experimental exercises and as stand-alone material for use in undergraduate lectures or tutorials, and simulated experimental models of photosynthetic gas exchange and chlorophyll fluorescence which can be used either as stand-alone packages or, where equipment is available, to supplement and enrich a laboratory demonstration/experiment. These provide students with access to the latest experimental techniques and theory, providing an experience and knowledge base that facilitates understanding of the subject in greater depth

Exceptional points in optical systems: A resonant-state expansion study

Exceptional points (EPs) in open optical systems are rigorously studied using the resonant-state expansion (RSE). A spherical resonator, specifically a homogeneous dielectric sphere in a vacuum, perturbed by two point-like defects which break the spherical symmetry and bring the optical modes to EPs, is used as a worked example. The RSE is a non-perturbative approach encoding the information about an open optical system in matrix form in a rigorous way, and thus offering a suitable tool for studying its EPs. These are simultaneous degeneracies of the eigenvalues and corresponding eigenfunctions of the system, which are rigorously described by the RSE and illustrated for perturbed whispering-gallery modes (WGMs). An exceptional arc, which is a line of adjacent EPs, is obtained analytically for perturbed dipolar WGMs. Perturbation of high-quality WGMs with large angular momentum and their EPs are found by reducing the RSE equation to a two-state problem by means of an orthogonal transformation of a large RSE matrix. WGM pairs of opposite chirality away from EPs are shown to have the same chirality at EPs. This chirality can be observed in circular dichroism measurements, as it manifested itself in a squared-Lorentzian part of the optical spectra, which we demonstrate here analytically and numerically in the Purcell enhancement factor for the perturbed dipolar WGMs.Comment: 24 pages. 13 figures (3 in Appendix). To be submitted in Physical Review A. Authors: K S Netherwood (primary author), H Riley (initial concept work), E A Muljarov (theme leader

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed

Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients

Selective digestive microbial decontamination (SDD) is hypothesized to benefit patients in intensive care (ICU) by suppressing Gram-negative potential pathogens from the colon without affecting the anaerobic intestinal microbiota. The purpose of this study was to provide more insight to the effects of digestive tract and oropharyngeal decontamination on the intestinal microbiota by means of a prospective clinical trial in which faecal samples were collected from ICU patients for intestinal microbiota analysis. The faecal samples were collected from ICU patients enrolled in a multicentre trial to study the outcome of SDD and selective oral decontamination (SOD) in comparison with standard care (SC). Fluorescent in situ hybridization (FISH) was used to analyze the faecal microbiota. The numbers of bacteria from different bacterial groups were compared between the three regimens. The total counts of bacteria per gram faeces did not differ between regimens. The F. prausnitzii group of bacteria, representing an important group among intestinal microbiota, was significantly reduced in the SDD regimen compared to the SC and SOD. The Enterobacteriaceae were significantly suppressed during SDD compared to both SOD and SC; enterococci increased in SDD compared to both other regimens. The composition of the intestinal microbiota is importantly affected by SDD. The F. prausnitzii group was significantly suppressed during SDD. This group of microbiota is a predominant producer of butyrate, the main energy source for colonocytes. Reduction of this microbiota is an important trade-off while reducing gram-negative bacteria by SDD

An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats

Background: Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. Results: Plasmid DNA with two resistance genes (nptII and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, where constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. Conclusions: The analyses showed that extensive ingestion of DNA (100 \ub5g plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit <1 transformant per 1.1 x 108 cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed

Photosynthesis In Silico. Overcoming the Challenges of Photosynthesis Education Using a Multimedia CD-ROM

Photosynthesis is a central topic in biology education. It remains one of the most challenging, largely because of a) its conceptual difficulty, leading to lack of interest and misconceptions among students; b) the difficulties students have in visualising the process, or relating it to things they can see, especially when the topic is presented purely as a molecular process; and c) limitations to the practical demonstration of photosynthesis because equipment is either cheap, unreliable and antiquated or prohibitively expensive. In response, we have combined expertise in photosynthesis research and education, and in graphic design, to produce an interactive, multimedia package, available on CD-ROM, containing two practical modules and three theoretical modules, for tertiary level students. Features include an animation of photosynthetic electron transport, suitable for a lecture presentation or for self-paced learning by students, and experimental simulations of photosynthetic gas exchange and chlorophyll fluorescence which can be used either as stand-alone packages or, where equipment is available, to supplement and enrich a laboratory demonstration/experiment. As well as improving learning outcomes through the documented advantages of computer-based learning, this set of modules provides students with access to the latest experimental techniques and theory, improving their understanding, updating their skills and switching them on to the amazing process that brings energy into our biosphere