Living in an oxygenated environment has required the evolution of effective cellular strategies to detect and detoxify metabolites of molecular oxygen known as reactive oxygen species. Here we review evidence that the appropriate and inappropriate production of oxidants, together with the ability of organisms to respond to oxidative stress, is intricately connected to ageing and life span.

Oxidants, oxidative stress and the biology of ageing.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Diabetes-specific microvascular disease is a leading cause of blindness, renal failure and nerve damage, and diabetes-accelerated atherosclerosis leads to increased risk of myocardial infarction, stroke and limb amputation. Four main molecular mechanisms have been implicated in glucose-mediated vascular damage. All seem to reflect a single hyperglycaemia-induced process of overproduction of superoxide by the mitochondrial electron-transport chain. This integrating paradigm provides a new conceptual framework for future research and drug discovery.

http://www.chem.uwec.edu/Chem454/BiochemDiabetes.pdf

Biochemistry and molecular cell biology of diabetic complications

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

/pdf/stacks-an-analysis-tool-set-for-population-genomics-3dmvyh33iq.pdf

Stacks: an analysis tool set for population genomics

Botanical insecticides have long been touted as attractive alternatives to synthetic chemical insecticides for pest management because botanicals reputedly pose little threat to the environment or to human health. The body of scientific literature documenting bioactivity of plant derivatives to arthropod pests continues to expand, yet only a handful of botanicals are currently used in agriculture in the industrialized world, and there are few prospects for commercial development of new botanical products. Pyrethrum and neem are well established commercially, pesticides based on plant essential oils have recently entered the marketplace, and the use of rotenone appears to be waning. A number of plant substances have been considered for use as insect antifeedants or repellents, but apart from some natural mosquito repellents, little commercial success has ensued for plant substances that modify arthropod behavior. Several factors appear to limit the success of botanicals, most notably regulatory barriers and the availability of competing products (newer synthetics, fermentation products, microbials) that are cost-effective and relatively safe compared with their predecessors. In the context of agricultural pest management, botanical insecticides are best suited for use in organic food production in industrialized countries but can play a much greater role in the production and postharvest protection of food in developing countries.

/pdf/botanical-insecticides-deterrents-and-repellents-in-modern-5flrsy0hec.pdf

Botanical insecticides, deterrents, and repellents in modern agriculture and an increasingly regulated world

volume 31 NumBeR 12 DeCemBeR 2013 nature biotechnology 7. Marvier, M. et al. Science 316, 1475–1477 (2007). 8. Millstone, E. et al. Risk Assessment Policies: Differences Across Jurisdictions http://ftp.jrc.es/ EURdoc/JRC37719.pdf (Joint Research Centre, European Commission, 2008). 9. Kuntz, M. et al. Nat. Biotechnol. 31, 498–500 (2013). 10. Food and Agriculture organisation of the United Nations and World Health organisation. Food Safety Risk Analysis: A Guide for National Food Safety Authorities ftp://ftp.fao.org/docrep/fao/009/a0822e/ a0822e00.pdf (FAo and WHo, 2006). arena of great public interest (i.e., the future of food production and biodiversity). Given this, the task of defining the criteria for evaluating quality cannot be legitimately nor sufficiently decided by Romeis et al.1 alone, nor even the world of their peers. It is not for an esoteric group of researchers or experts to pronounce what constitutes quality in science for policy and then dismiss as irrelevant and unreliable any other science not corresponding with how their own particular interests and values have defined what is important. This issue also deserves (and in a democratic society, demands) deliberation across a wide range of stakeholders and implicated actors. Such broad-based deliberation on quality criteria is crucial, not because science “is simply a matter of opinion, no better than any other opinion,”9 but because, as Romeis et al.1 correctly highlight, scientific research can be conducted under a range of test protocols and study designs, with the potential for each of these to lead to contrasting results. Which of the range of possible research approaches is best, with the most relevance for risk assessment and the highest quality as fit for purpose, will inherently depend on what questions are deemed most salient and what is most valued by a broad section of society. That is, it is both a scientific and a social matter. What is at stake here is not only the future of GM crops but also the role and scope of scientific inputs to governance processes; thus, it is crucial that we maintain and enhance the credibility and legitimacy of those inputs. This requires, inter alia, impartial and consistent quality evaluation of all scientific studies, no matter what their conclusions.

Reply to Science-based risk assessment requires careful evaluation of all studies.

http://web.entomology.cornell.edu/shelton/publications/pdf/Wang%20et%20al%202007%20Mechanism%20of%20resistance%20to%20Bt%20toxin%20Cry1Ac%20in%20a%20greenhouse%20population%20of%20cabbage%20looper.pdf

Trichoplusia ni Looper, Population of the Cabbage Toxin Cry1Ac in a thuringiensis Bacillus Mechanism of Resistance to

The Diamondback Moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is a global pest that infests vegetable and field crops within the Brassica family. A genetically engineered strain of P. xylostella, OX4319L, carrying a self-limiting gene, has shown potential for managing P. xylostella populations, using sustained releases of OX4319L male moths. In order for such a strain to provide control, the transgenic individuals must exhibit attraction to female P. xylostella sex pheromone and adequate dispersal in the field. In this study, we tested these key traits. First, we compared the responses of the OX4319L male moths to a synthetic female sex pheromone source in wind tunnel trials to those of males from three other strains. We found that OX4319L males responded comparably to strains of non-engineered males, with all males flying upwind towards the pheromone source. Second, we used mark-release-recapture studies of a wildtype P. xylostella strain, from which the OX4319L strain was originally developed, to assess dispersal under field conditions. Released males were recaptured using both pheromone-baited and passive traps within a 2.83 ha circular cabbage field, with a recapture rate of 7.93 percent. Males were recaptured up to the boundary of the field at 95 m from the central release point. The median dispersal of males was 14 m. These results showed the progenitor strain of OX4319L retained its ability to disperse within a host field. The results of these experiments are discussed in relation to the potential for the effective use of engineered male-selecting P. xylostella strains under field conditions.

https://www.biorxiv.org/content/biorxiv/early/2018/12/19/501924.full.pdf

Response to a Synthetic Pheromone Source by OX4319L, a Self-Limiting Diamondback Moth (Lepidoptera: Plutellidae) Strain, and Field Dispersal Characteristics of Its Progenitor Strain

Funds from the NYS IPM program were used to supplement funds from the NYS Onion Research and Development Program for a pest management program for thrips on onions. The primary goals of the overall project were to monitor thrips susceptibility to Warrior, Lannate and Penncap-M in commercial onion fields in upstate NY using TIBS (Thrips Insecticide Bioassay System) and work with extension educators and one private sector company to educate their personnel to use TIBS. TIBS has proven to be an essential tool to monitor for resistance to Warrior, the most widely used insecticide against thrips (Shelton et al. 2003). Using TIBS, growers can have knowledge about the susceptibility of their thrips populations to Warrior prior to treatment, and thus only use this insecticide when appropriate. However, we needed to develop similar information about the other two major insecticide classes used against thrips in onionsorganophosphates and carbamates. We used methyl parathion and methomyl as representatives of each respective class in eight commercial fields. Using the TIBS assay at the field concentration of each insecticide (3200 ppm for methomyl and 2000 ppm for methyl parathion), we had >90% mortality for both insecticides in seven of the eight populations examined (in the last field, mortality using methomyl was 73%). Based on our previous work with TIBS using Warrior, we can infer that field control would still be acceptable with both insecticides.

/pdf/implementation-of-an-insecticide-resistance-management-2s8ydv7072.pdf

Implementation of an Insecticide Resistance Management Strategy for Onion Thrips on Onions

What is environmentally acceptable plant protection

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