Direct Electron Microscopy Study on the Morphological Diversity of Bacteriophage Populations in Lake Plußsee

Direct electron microscopy of bacteriophages adsorbed to a carbon film without prior enrichment by specific host strains or concentration by physical or chemical methods was used to study the morphological diversity of natural bacteriophage assemblages in a North German lake. All samples contained a mixture of morphologically different tailed viruses, which were regarded as bacteriophages. Most of them had isometric heads and long noncontractile tails, belonging to morphotype B1 (Siphoviridae). In addition, members of morphotypes A1 (Myoviridae), B2 (Siphoviridae with elongated heads), and C1 (Podoviridae) were present in lower numbers. Only one cubic virus was detected, while no filamentous or pleomorphic phages were found. Up to 11 different phages per sample, and a total of 39 phages when all samples were considered together, could be distinguished by morphological criteria. The total number of phages was estimated to be on the order of 108/ml

Not all adversarial examples require a complex defense : identifying over-optimized adversarial examples with IQR-based logit thresholding

Detecting adversarial examples currently stands as one of the biggest challenges in the field of deep learning. Adversarial attacks, which produce adversarial examples, increase the prediction likelihood of a target class for a particular data point. During this process, the adversarial example can be further optimized, even when it has already been wrongly classified with 100% confidence, thus making the adversarial example even more difficult to detect. For this kind of adversarial examples, which we refer to as over-optimized adversarial examples, we discovered that the logits of the model provide solid clues on whether the data point at hand is adversarial or genuine. In this context, we first discuss the masking effect of the softmax function for the prediction made and explain why the logits of the model are more useful in detecting over-optimized adversarial examples. To identify this type of adversarial examples in practice, we propose a non-parametric and computationally efficient method which relies on interquartile range, with this method becoming more effective as the image resolution increases. We support our observations throughout the paper with detailed experiments for different datasets (MNIST, CIFAR-10, and ImageNet) and several architectures

Evidence for an ecological cost of enhanced herbicide metabolism in Lolium rigidum

1. In some cases, evaluation of resource competitive interactions between herbicide resistant vs. susceptible weed ecotypes provides evidence for the expression of fitness costs associated with evolved herbicide-resistant gene traits. Such fitness costs impact in the ecology and evolutionary trajectory of resistant populations. 2. Neighbourhood experiments were performed to quantify competitive effects and responses between herbicide-susceptible (S) and resistant (R) Lolium rigidum individuals in which resistance is due to enhanced herbicide metabolism mediated by cytochrome P450. 3. In two-way competitive interactions between the S and R phenotypes, individuals of the S phenotype were the stronger effect competitors on both a per capita and per unit-size basis. The S phenotype also exhibited a stronger competitive response to wheat plants than did the R phenotype, displaying significantly greater (30%) above-ground biomass at the vegetative stage. When subjected to competition from wheat, R individuals produced significantly fewer reproductive tillers and allocated fewer resources to reproductive traits than individuals of the S phenotype. 4. The role of potential mechanisms underlying this resistance cost driven by traits such as plant size and tolerance to low resource availability, as well as the evolutionary implications of the results are discussed. 5. Synthesis. Evolved herbicide resistance due to enhanced-herbicide metabolism mediated by cytochrome-P450 in L. rigidum has been shown to be accompanied with an impaired ability to compete for resources. These results are consistent with the resource-based theory that predicts a negative trade-off between growth and plant defence

Fitness costs associated with evolved herbicide resistance alleles in plants

Predictions based on evolutionary theory suggest that the adaptive value of evolved herbicide resistance alleles may be compromised by the existence of fitness costs. There have been many studies quantifying the fitness costs associated with novel herbicide resistance alleles, reflecting the importance of fitness costs in determining the evolutionary dynamics of resistance. However, many of these studies have incorrectly defined resistance or used inappropriate plant material and methods to measure fitness. This review has two major objectives. First, to propose a methodological framework that establishes experimental criteria to unequivocally evaluate fitness costs. Second, to present a comprehensive analysis of the literature on fitness costs associated with herbicide resistance alleles. This analysis reveals unquestionable evidence that some herbicide resistance alleles are associated with pleiotropic effects that result in plant fitness costs. Observed costs are evident from herbicide resistance-endowing amino acid substitutions in proteins involved in amino acid, fatty acid, auxin and cellulose biosynthesis, as well as enzymes involved in herbicide metabolism. However, these resistance fitness costs are not universal and their expression depends on particular plant alleles and mutations. The findings of this review are discussed within the context of the plant defence trade-off theory and herbicide resistance evolution

Quantifying the contribution of free-living nematodes to nitrogen mineralization

Soil fauna are estimated to contribute to approximately 30 % of nitrogen mineralization (Verhoef ∧ Brussaard, 1990). Soil nematodes are important contributors to this process through their key trophic positions as microbial grazers. Quantification of this contribution has mostly relied on theoretical food web analyses (Hunt et al., 1987) or laboratory incubations with simplified and artificially constructed ecosystems (Ferris et al., 1998). Incubations are often performed on homogenized soil, though soil biota is known to be responsive to physical disturbance. Furthermore, sterilization typically relies on methods disruptive of soil structure (e.g. autoclaving, freezing). The aim of this experiment was to quantify the contribution of nematodes to nitrogen mineralization during incubation. Intact cores with a representative pore structure and entire nematode populations instead of single species were used. Gamma irradiation was selected as a sterilization method to remove only soil fauna, leaving the microflora and soil structure largely intact (McNamara et al., 2003)