Eye movements in code reading:relaxing the linear order

Abstract—Code reading is an important skill in programming. Inspired by the linearity that people exhibit while natural lan-guage text reading, we designed local and global gaze-based mea-sures to characterize linearity (left-to-right and top-to-bottom) in reading source code. Unlike natural language text, source code is executable and requires a specific reading approach. To validate these measures, we compared the eye movements of novice and expert programmers who were asked to read and comprehend short snippets of natural language text and Java programs. Our results show that novices read source code less linearly than natural language text. Moreover, experts read code less linearly than novices. These findings indicate that there are specific differences between reading natural language and source code, and suggest that non-linear reading skills increase with expertise. We discuss the implications for practitioners and educators. I

Rapid compensatory evolution promotes the survival of conjugative plasmids

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co-occurring pQBR-family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid-borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus-encoding cluster, and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolise sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by the different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity amongst co-occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction

Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage SBW25φ2 and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that, individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions

The response of microphytobenthos to physical disturbance, herbicide, and titanium dioxide nanoparticles exposure

The research leading to these results received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 730984, ASSEMBLE Plus project. AJW was funded by the John Templeton Grant 60501, “Putting the Extended Evolutionary Synthesis to the Test”. DMP and AJB were supported by the NERC Blue-coast award (NE/N016009/1).The microphytobenthos that form transient biofilms are important primary producers in intertidal, depositional habitats, yet we have only a limited understanding of how they respond to the cumulative impacts of the growing range of anthropogenic stressors to which they are exposed. We know even less about how the temporal alignment of exposure – such as duration and exposure sequence – may affect the response. Estuarine biofilms were cultured in mesocosms and exposed to the herbicide glyphosate and titanium dioxide (TiO2) nanoparticles in different sequences (glyphosate-first or TiO2-first), as well as in the presence and absence of physical disturbance. We found that at environmentally realistic chemical concentrations, the order of exposure was less important than the total stressor scenario in terms of impacts on key functional attributes and diatom community structure. Physical disturbance did not have an impact on functional attributes, regardless of exposure sequence.Publisher PDFPeer reviewe

Dispersed Repetitive DNA Has Spread to New Genomes Since Polyploid Formation in Cotton

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis

The jellification of north temperate lakes.

Calcium (Ca) concentrations are decreasing in softwater lakes across eastern North America and western Europe. Using long-term contemporary and palaeo-environmental field data, we show that this is precipitating a dramatic change in Canadian lakes: the replacement of previously dominant pelagic herbivores (Ca-rich Daphnia species) by Holopedium glacialis, a jelly-clad, Ca-poor competitor. In some lakes, this transformation is being facilitated by increases in macro-invertebrate predation, both from native (Chaoborus spp.) and introduced (Bythotrephes longimanus) zooplanktivores, to which Holopedium, with its jelly coat, is relatively invulnerable. Greater representation by Holopedium within cladoceran zooplankton communities will reduce nutrient transfer through food webs, given their lower phosphorus content relative to daphniids, and greater absolute abundances may pose long-term problems to water users. The dominance of jelly-clad zooplankton will likely persist while lakewater Ca levels remain low.This work was primarily supported by grants from the Natural Sciences and Engineering Research Council of Canada and funding from the Ontario Ministry of the Environment.This is the accepted manuscript. The final version is available at http://rspb.royalsocietypublishing.org/content/282/1798/20142449

Designing dissemination and validation of a framework for teaching cloud fundamentals

Three previous Working Groups (WGs) met at ITiCSE conferences to explore ways to help educators incorporate cloud computing into their courses and curricula by mapping industry job skills to knowledge areas (KAs). These WGs identified, organized, and grouped together student learning objectives (LOs) and developed these KAs and LOs in a repository of learning materials and course exemplars. This WG focused on the sustainability of the work of its predecessors through dissemination, community building and validation of the framework of KAs and LOs and its contribution to curriculum development. Firstly, a case study is presented which analyzed the implementation of a new Masters program which was based on the KAs and LOs. It was found that these provide a useful basis for program development and approval and demonstrate that successful program development of this nature can provide a valuable opportunity to communicate the work of the previous WGs. Thereafter, a plan was formulated for dissemination of the work done in order to drive adoption and to encourage instructors with an interest in teaching cloud computing to participate and grow the community. While the strategy included a range of dissemination methods, the importance of interaction with users was a guiding principle. Initial pilots of webinar and workshop activities have been implemented. Approaches to validating that a cloud computing course designed around the KAs and LOs can meet the needs of industry have been outlined with further iterations being considered. A research plan has been designed for a study to be implemented over the coming year in order to perform this validation

Facilitating Pupil Thinking About Information Literacy

Whilst information literacy is frequently taught through the imposition on learners of an established framework, this paper suggests a different approach by taking a lead from James Herring’s ideas. Specifically, it provides guidance to school-based information professionals who would like to encourage their pupils to devise their own flexible, information literacy models which are unique to them. Drawing on existing material in information science and wider thought, it proposes areas for coverage and considers how information professionals may support the dynamic process of model construction. It is recommended that those who are intent on facilitating the creation of personal information literacy models help pupils to identify the roles they take on in their lives, to reflect on the information needs that result, to ascertain the information they require in particular situations, to explore their information-seeking activities, to consider means by which information can be captured and to give thought as to how the information they have accessed may be used. This framework is, however, by no means rigid and readers are, of course, free to make their own adjustments