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Creators/Authors contains: "Holmes, Christopher J"

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  1. Abstract The assembly of host‐associated microbial communities is influenced by multiple factors, but the effect of microbiomes on host phenotypes is often not well understood. To address questions of food‐web effects on host microbiome assembly, we manipulated the resource environment (grass only [G] vs. grass + nutrients [GN]), competition type (intra‐ vs. inter‐specific) and density (high vs. low) forCulex restuans mosquito larvae. We predicted the microbial communities in fourth‐instar larvae would differ between these environmental treatments and that these treatments would translate into differences in the adult phenotype.Resource environment and density influenced the larval microbiome. In addition, the larval microbiome exhibited notable differences compared to the free‐living microbial communities.Resource‐driven differences in the larval samples can be attributed to Arcobacteraceae being more abundant in larvae reared in the GN treatments relative to those reared in the G treatments and Comamonadaceae being more abundant in the G treatment. Although significant, the difference in community structure between density treatments was difficult to discern. This appears to be driven by Weeksellaceae only being abundant in the high‐density, interspecific, GN treatment.Rearing larvae to adulthood under severe food limitation resulted in low survival (<25%) in both resource environments. Approximately 60% of survivors to adulthood were male. Larvae reared in the intraspecific, G treatment had the shortest development time to adulthood and emerged as the smallest adults.These results demonstrate how environmental variation can significantly alter the alpha and beta diversity of free‐living microbes, which in turn can significantly affect host phenotype and critical life history traits, such as development time, size at adulthood, and survival. These findings highlight the importance of considering environmental influences on microbiome diversity to understand and predict host outcomes, offering valuable insights for diverse applications in fields such as ecology, public health, and agriculture. 
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  2. Diseases that are transmitted by mosquitoes are a tremendous health and socioeconomic burden with hundreds of millions of people being impacted by mosquito-borne illnesses annually. Many factors have been implicated and extensively studied in disease transmission dynamics, but knowledge regarding how dehydration impacts mosquito physiology, behavior, and resulting mosquito-borne disease transmission remain underdeveloped. The lapse in understanding on how mosquitoes respond to dehydration stress likely obscures our ability to effectively study mosquito physiology, behavior, and vectorial capabilities. The goal of this review is to develop a profile of factors underlying mosquito biology that are altered by dehydration and the implications that are related to disease transmission. 
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  3. Scientific knowledge has been under attack recently, especially during and from the Trump administration. This article discusses the value of research in social studies of science in relation to scientific practice and post‐truth attacks on science. This literature analyzes the expert work and social values that enter into the production of evidence, the development and testing of methods, and the construction of theoretical and epistemological frames for connecting evidence, methods, and methodologies. Although researchers in this area argue that there are politics in science, this article demonstrates that their analyses of the processes of adjudicating evidence and epistemologies contribute to science. In contrast, post‐truth attacks on scientific expertise exemplify a particular kind of politics aimed at supporting a particular group's political and economic interests. 
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  4. null (Ed.)
    Abstract The Antarctic midge, Belgica antarctica , is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least 2 years, but adults live only 2 weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source as well as a buffer for thermal and dehydration stress. All of these function are critical to juvenile survival. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may have a significant impact on population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect of this work is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical in determining how climate change will alter their survivability. 
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  5. Abstract BackgroundThe stable fly,Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship ofStomoxysto other blood-feeding (horn flies andGlossina) and non-blood-feeding flies (house flies, medflies,Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha. 
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  6. null (Ed.)
    Abstract Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species. 
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