Antiviral Immunity in the Fruit Fly, Drosophila melanogaster

The fruit fly, Drosophila melanogaster, is an extremely useful model to study innate immunity mechanisms. A fundamental understanding of these mechanisms as they relate to various pathogens has come to light over the past 30 years. The discovery of Toll‐like receptors and their recognition of shared molecules (pathogen‐associated molecular patterns or PAMPs) among pathogenic bacteria were the first detailed set of receptors to be described that act in innate immunity. The immune deficiency pathway (Imd) described in D. melanogaster functions in a very similar way to the Toll pathway in recognizing PAMPs primarily from Gram‐negative bacteria. The discovery of small interfering RNAs (RNAi) provided a means by which antiviral immunity was accomplished in invertebrates. Another related pathway, the JAK/STAT pathway, functions in a similar manner to the interferon pathways described in vertebrates, also providing antiviral defense. Recently, autophagy was also shown to function as a protective pathway against virus infection in D. melanogaster. At least three of these pathways (Imd, JAK/STAT, and RNAi) show signal integration in response to viral infection, demonstrating a coordinated immune response against viral infection. The number of pathways and the integration of them reflect the diversity of pathogens to which innate immune mechanisms must be able to respond. The viral pathogens that infect invertebrates have developed countermeasures to some of these pathways, in particular to RNAi. The evolutionary arms race of pathogen vs. host is ever ongoing

Effects of an electric field on white sharks: in situ testing of an electric deterrent

Elasmobranchs can detect minute electromagnetic fields, <1 nVcm -1 , using their ampullae of Lorenzini. Behavioural responses to electric fields have been investigated in various species, sometimes with the aim to develop shark deterrents to improve human safety. The present study tested the effects of the Shark Shield Freedom7™ electric deterrent on (1) the behaviour of 18 white sharks ( Carcharodon carcharias ) near a static bait, and (2) the rates of attacks on a towed seal decoy. In the first experiment, 116 trials using a static bait were performed at the Neptune Islands, South Australia. The proportion of baits taken during static bait trials was not affected by the electric field. The electric field, however, increased the time it took them to consume the bait, the number of interactions per approach, and decreased the proportion of interactions within two metres of the field source. The effect of the electric field was not uniform across all sharks. In the second experiment, 189 tows using a seal decoy were conducted near Seal Island, South Africa. No breaches and only two surface interactions were observed during the tows when the electric field was activated, compared with 16 breaches and 27 surface interactions without the electric field. The present study suggests that the behavioural response of white sharks and the level of risk reduction resulting from the electric field is contextually specific, and depends on the motivational state of sharks

Analysis of immune-related genes during Nora virus infection of <em>Drosophila melanogaster</em> using next generation sequencing

Drosophila melanogaster depends upon the innate immune system to regulate and combat viral infection. This is a complex, yet widely conserved process that involves a number of immune pathways and gene interactions. In addition, expression of genes involved in immunity are differentially regulated as the organism ages. This is particularly true for viruses that demonstrate chronic infection, as is seen with Nora virus. Nora virus is a persistent non-pathogenic virus that replicates in a horizontal manner in D. melanogaster. The genes involved in the regulation of the immune response to Nora virus infection are largely unknown. In addition, the temporal response of immune response genes as a result of infection has not been examined. In this study, D. melanogaster either infected with Nora virus or left uninfected were aged for 2, 10, 20 and 30 days. The RNA from these samples was analyzed by next generation sequencing (NGS) and the resulting immune-related genes evaluated by utilizing both the PANTHER and DAVID databases, as well as comparison to lists of immune related genes and FlyBase. The data demonstrate that Nora virus infected D. melanogaster exhibit an increase in immune related gene expression over time. In addition, at day 30, the data demonstrate that a persistent immune response may occur leading to an upregulation of specific immune response genes. These results demonstrate the utility of NGS in determining the potential immune system genes involved in Nora virus replication, chronic infection and involvement of antiviral pathways

Climate Change and invasibility of the Antarctic benthos

Benthic communities living in shallow-shelf habitats in Antarctica (&lt;100-m depth) are archaic in their structure and function. Modern predators, including fast-moving, durophagous (skeleton-crushing) bony fish, sharks, and crabs, are rare or absent; slow-moving invertebrates are the top predators; and epifaunal suspension feeders dominate many soft substratum communities. Cooling temperatures beginning in the late Eocene excluded durophagous predators, ultimately resulting in the endemic living fauna and its unique food-web structure. Although the Southern Ocean is oceanographically isolated, the barriers to biological invasion are primarily physiological rather than geographic. Cold temperatures impose limits to performance that exclude modern predators. Global warming is now removing those physiological barriers, and crabs are reinvading Antarctica. As sea temperatures continue to rise, the invasion of durophagous predators will modernize the shelf benthos and erode the indigenous character of marine life in Antarctica

Networking - A Statistical Physics Perspective

Efficient networking has a substantial economic and societal impact in a broad range of areas including transportation systems, wired and wireless communications and a range of Internet applications. As transportation and communication networks become increasingly more complex, the ever increasing demand for congestion control, higher traffic capacity, quality of service, robustness and reduced energy consumption require new tools and methods to meet these conflicting requirements. The new methodology should serve for gaining better understanding of the properties of networking systems at the macroscopic level, as well as for the development of new principled optimization and management algorithms at the microscopic level. Methods of statistical physics seem best placed to provide new approaches as they have been developed specifically to deal with non-linear large scale systems. This paper aims at presenting an overview of tools and methods that have been developed within the statistical physics community and that can be readily applied to address the emerging problems in networking. These include diffusion processes, methods from disordered systems and polymer physics, probabilistic inference, which have direct relevance to network routing, file and frequency distribution, the exploration of network structures and vulnerability, and various other practical networking applications.Comment: (Review article) 71 pages, 14 figure

Mainstreaming life cycle thinking through a consistent approach to footprints

Over recent years, footprints have emerged as an important means of reporting environmental performance. Some individual footprints have become quite sophisticated in their calculation procedures. However, as an overallclass of environmental metrics they have been poorly defined, having a variety of conceptual foundations and an unclear relationship to LCA. The variety and sometimes contradictory approaches to quantification have also led to confusing and contradictory messages in the marketplace which have undermined their acceptance by industry and governments.In response, a task force operating under the auspices of the UNEP/SETAC Life Cycle Initiative project on environmental Life Cycle Impact Assessment has been working to develop generic guidance for developers of footprint metrics. The initial work involved forming a consensual position on the difference between footprints and existing LCA impact category indicators. In short, footprints are deemed to have a primary orientation toward society and nontechnical stakeholders and report only on selected topics of concern. On the other hand, LCA impact category indicators have a primary orientation toward technical stakeholders and report in relation to a larger framework designed for comprehensive evaluation of environmental performance and trade-offs. The task force has also developed a universal footprint definition. In parallel to Area of Protection, we introduce Area of Concern. In the same way that LCA uses impact category indicators to assess impacts that follow a common cause-effect pathway toward Areas of rotection, ootprint metrics address Areas of Concern. The critical difference is that Areas of Concern are defined by the interests of stakeholders in society rather than the LCA community. In addition, Areas of Concern are stand-alone and not part of a framework intended for comprehensive environmental performance assessment. Accordingly, footprints are universally defined as metrics used to report life cycle assessment results addressing an Area of Concern

An estimate of the number of tropical tree species

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e. at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group