The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Socio-economic drivers of specialist anglers targeting the non-native European catfish (Silurus glanis) in the UK.

Information about the socioeconomic drivers of Silurus glanis anglers in the UK were collected using questionnaires from a cross section of mixed cyprinid fisheries to elucidate human dimensions in angling and non-native fisheries management. Respondents were predominantly male (95%), 30-40 years of age with £500 per annum. The proportion of time spent angling for S. glanis was significantly related to angler motivations; fish size, challenge in catch, tranquil natural surroundings, escape from daily stress and to be alone were considered important drivers of increased time spent angling. Overall, poor awareness of: the risks and adverse ecological impacts associated with introduced S. glanis, non-native fisheries legislation, problems in use of unlimited ground bait and high fish stocking rates in angling lakes were evident, possibly related to inadequate training and information provided by angling organisations to anglers, as many stated that they were insufficiently informed

Coordination of Cell Differentiation and Migration in Mathematical Models of Caudal Embryonic Axis Extension

Vertebrate embryos display a predominant head-to-tail body axis whose formation is associated with the progressive development of post-cranial structures from a pool of caudal undifferentiated cells. This involves the maintenance of active FGF signaling in this caudal region as a consequence of the restricted production of the secreted factor FGF8. FGF8 is transcribed specifically in the caudal precursor region and is down-regulated as cells differentiate and the embryo extends caudally. We are interested in understanding the progressive down-regulation of FGF8 and its coordination with the caudal movement of cells which is also known to be FGF-signaling dependent. Our study is performed using mathematical modeling and computer simulations. We use an individual-based hybrid model as well as a caricature continuous model for the simulation of experimental observations (ours and those known from the literature) in order to examine possible mechanisms that drive differentiation and cell movement during the axis elongation. Using these models we have identified a possible gene regulatory network involving self-repression of a caudal morphogen coupled to directional domain movement that may account for progressive down-regulation of FGF8 and conservation of the FGF8 domain of expression. Furthermore, we have shown that chemotaxis driven by molecules, such as FGF8 secreted in the stem zone, could underlie the migration of the caudal precursor zone and, therefore, embryonic axis extension. These mechanisms may also be at play in other developmental processes displaying a similar mode of axis extension coupled to cell differentiation

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552

Detecting impacts of invasive non-native sharptooth catfish, Clarias gariepinus, within invaded and non-invaded rivers.

In aquatic ecosystems, impacts by invasive introduced fish can be likened to press disturbances that persistently influence communities. This study examined invasion disturbances by determining the relationship between non-native sharptooth catfish Clarias gariepinus and aquatic macroinvertebrates in the Eastern Cape, South Africa. A Multiple Before–After Control–Impact (MBACI) experimental design was used to examine macroinvertebrate communities within two rivers: one with catfish and another one without catfish. Within the invaded river, macroinvertebrates showed little response to catfish presence, whereas predator exclusion appeared to benefit community structure. This suggests that the macroinvertebrate community within the invaded river was adapted to predation impact because of the dominance of resilient taxa, such as Hirudinea, Oligochaeta and Chironomidae that were abundant in the Impact treatment relative to the Control treatment. High macroinvertebrate diversity and richness that was observed in the Control treatment, which excluded the predator, relative to the Impact treatment suggests predator avoidance behaviour within the invaded river. By comparison, within the uninvaded river, catfish introduction into the Impact treatment plots indicated negative effects on macroinvertebrate community that was reflected by decrease in diversity, richness and biomass. A community level impact was also reflected in the multivariate analysis that indicated more variation in macroinvertebrate composition within the Impact treatment relative to the Control in the uninvaded river. Catfish impact within the uninvaded river suggests the dominance of vulnerable taxa, such as odonates that were less abundant in the Impact treatment plots after catfish introduction. From a disturbance perspective, this study revealed different macroinvertebrate responses to catfish impact, and suggests that within invaded habitats, macroinvertebrates were less responsive to catfish presence, whereas catfish introduction within uninvaded habitats demonstrated invasion impact that was shown by a decrease in the abundance of vulnerable taxa. The occurrence of non-native sharptooth catfish within many Eastern Cape rivers is a concern because of its predation impact and potential to influence trophic interrelationships, and efforts should be taken to protect uninvaded rivers, and, where possible, eradicate the invader

Why Should We Preserve Fishless High Mountain Lakes?

High mountain lakes are originally fishless, although many have had introductions of non-native fish species, predominantly trout, and recently also minnows introduced by fishermen that use them as live bait. The extent of these introductions is general and substantial often involving many lakes over mountain ranges. Predation on native fauna by introduced fish involves profound ecological changes since fish occupy a higher trophic level that was previously inexistent. Fish predation produces a drastic reduction or elimination of autochthonous animal groups, such as amphibians and large macroinvertebrates in the littoral, and crustaceans in the plankton. These strong effects raise concerns for the conservation of high mountain lakes. In terms of individual species, those adapted to live in larger lakes have suffered a higher decrease in the size of their metapopulation. This ecological problem is discussed from a European perspective providing examples from two study areas: the Pyrenees and the Western Italian Alps. Species-specific studies are urgently needed to evaluate the conservation status of the more impacted species, together with conservation measures at continental and regional scales, through regulation, and at local scale, through restoration actions, aimed to stop further invasive species expansions and to restore the present situation. At different high mountain areas of the world, there have been restoration projects aiming to return lakes to their native fish-free status. In these areas autochthonous species that disappeared with the introduction of fish are progressively recovering their initial distribution when nearby fish-free lakes and ponds are available

Synonymous but not the same: the causes and consequences of codon bias

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts