Spodoptera eridania: current and emerging crop threats from another invasive, pesticide-resistant moth

Open Access Article; Published online: 29 Jun 2022Spodoptera eridania (Stoll), a polyphagous lepidopteran pest from the Americas, has recently invaded western and central Africa. Like its congeners, S. eridania has developed pesticide resistance. The rapid global spread and impacts of Spodoptera frugiperda (J.E. Smith) has raised concerns about whether S. eridania is set to do the same. Here we fit a CLIMEX niche model for S. eridania and apply a climate change scenario for 2050 to investigate the sensitivity of the pest threat. We find that S. eridania can potentially expand its range throughout the tropics and into the sub-tropics, threatening a range of important commercial and subsistence crops. An important feature of the pest threat posed by S. eridania is the extent of its ephemeral habitat during warmer months. Modelled climatic changes will mostly expand this species potential range poleward by around 200 km by 2050, indicating a moderate sensitivity. These areas of emerging potential expansion are mostly into subtropical climates, supporting diverse cropping systems, including at risk crops beans, groundnut, potato, soybeans, tomato and sweet potato. The potential distribution of S. eridania in the Amazon basin and the southern boundary of the Sahara Desert appear set to contract substantially due to increasing heat stress. While it may not be as invasive as some of its congeners, nor acquire pesticide resistance as readily, S. eridania does have some of these traits, and the current and emerging pest threat posed by this moth deserves closer attention, especially in relation to intercontinental phytosanitary measures to slow its spread

Processing of Polarization Patterns and Visual Self-Motion in the Locust Central Complex for Spatial Orientation

Despite their relatively small brains with comparatively low neuron counts, insects show complex navigation behavior such as seasonal long-range migration, path integration, and precise straight-line movement. Spatial navigation requires a sense of current heading, which must be tethered to prominent external cues and updated by internal cues that result from movement. Global external cues such as the position of the sun may provide a reference frame for orientation. Sunlight is polarized by scattering in the atmosphere, which results in a sky-spanning polarization pattern that directly depends on the current solar position and makes polarization information, like the sun itself, useful as an external reference cue. Internally, moving through the environment generates optic flow---the motion of the viewed scenery on the retina---, which may inform about turning maneuvers, movement speed, and covered distance. Many insects use these external and internal cues for orientation, and the neuronal center for spatial navigation likely is the central complex, a higher-order brain structure where sensory information is integrated to form an internal compass representation of the current heading. This thesis addresses the question how celestial compass cues, specifically the polarization pattern, and optic flow are processed in the central complex of the desert locust, a long-range migratory insect. All chapters except the last one are electrophysiological studies in which single central-complex neurons were intracellularly recorded while presenting visual stimuli. The neurons' anatomy was histologically determined by dye injection in order to infer their role in the neural network. The studies in Chapters 1 and 2 show that the central complex contains a neuronal compass that robustly signals the sun direction based on direct sunlight and the integration of the whole solar polarization pattern. This shows that the locust brain uses all available skylight cues in order to form a unified compass signal, enabling robust navigation under different environmental conditions. The study in Chapter 3 further examines how neurons at the input stage of the central complex process skylight cues. Already at this stage, single neurons integrate visual information from large areas of the sky and have receptive fields suitable to build the skylight compass. Chapter 4 sheds light on the detection sensitivity for the angle of polarization, finding that central-complex neurons are highly sensitive in this regard, adapted to analyze the skylight polarization pattern almost in its entirety and under unfavorable environmental conditions. In Chapter 5 the locust central complex was scanned for neurons that receive optic flow information. Neurons at virtually all network stages are sensitive to optic flow, mainly uncoupled from skylight-cue sensitivity. This highlights that sensory information is flexibly processed in the central complex, presumably depending on the animal's current behavioral demands. Further, the study hypothesizes how horizontal turning motion is processed in order to update the internal heading representation, backed up by a computational model that adheres to brain anatomy and physiological data. Altogether, these studies advance the understanding of how external and internal cues are processed in the central-complex network in order to establish a sense of orientation in the insect brain. Finally, I contributed with data sets and programming code to the development of the InsectBrainDatabase (www.insectbraindb.org), a free online database tool designed to manage, share and publish anatomical and functional research data (Chapter 6)

The effects of urbanization on the avian gut microbiome

The gut microbiome influences and is influenced by the host, and can affect the host organism by contributing to health, development and immunity. Similarly, the host can influence this community; it’s makeup can vary with host species, locality, diet, social stressors, and environmental stressors. Some of these environmental stressors have arisen due to human-induced rapid environmental change, like urbanization. The physiology and behaviors of organisms that are able to persist in urban environments are often different from their non-urban congeners. Nutrition, development, and immunity—all of which are affected by the gut microbiome—are important factors that can determine survival in urban environments. Ecologists are therefore asking new questions about how an urban environment shapes gut microbial communities, and how the numerous services gut fauna provide affect host success in an urban context. My dissertation research demonstrated that urbanization changes the bacterial communities of birds as well as provided correlational and experimental evidence for the biotic and abiotic traits driving these changes. Urban birds differed from rural ones by multiple measures. I also found evidence that noise pollution explains some variation in alpha diversity among urban and rural birds. Building upon this finding, I experimentally showed that the gut microbiome changes with exposure to noise, as does food intake and plasma corticosterone. However, contrary to my hypothesis, food intake and corticosterone were not the mediating factors between noise and the gut microbiome. All of this work was accomplished using noninvasive cloacal swabs to measure the gut microbiome, which my dissertation research found are reflective of the large intestine and capture individual variation in the microbiome. The work that comprised my dissertation will impact methods decisions in future microbiome studies in both free-living and captive birds. It will also contribute to the way we look at the relationships between host environment, host, and the gut microbiome, as well as influence how we think about urban ecology as a whole. Altogether, my dissertation research accomplished my goal to work in an emerging field at the interface of urban and microbial ecology

Scientific methods: an online book

BookThis book was originally intended as ˜How to do science™, or ˜How to be a scientist™, providing guidance for the new scientist, as well as some reminders and tips for experienced researchers. Such a book does not need to be written by the most expert or most famous scientist, but by one who likes to see the rules of play laid out concisely. It does need to be written by a working scientist, not by a philosopher of science. The first half of the book, called ˜Scientist's Toolbox", retains this original focus on what Jerome Brumer called the structure of science -- its methodologies and logic. This objective is still present in the second half of the book, ˜Living Science". In researching that section, however, I was fascinated by the perspectives of fellow scientists on ˜What it is like to be a scientist." Encountering their insights into the humanity of science, I found resonance with my already intense enjoyment of the process of science. Gaither and Cavazon-Gaither [2000] provide many additional scientific quotations on the experience of science

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

MACHINE LEARNING AND BIOINFORMATIC INSIGHTS INTO KEY ENZYMES FOR A BIO-BASED CIRCULAR ECONOMY

The world is presently faced with a sustainability crisis; it is becoming increasingly difficult to meet the energy and material needs of a growing global population without depleting and polluting our planet. Greenhouse gases released from the continuous combustion of fossil fuels engender accelerated climate change, and plastic waste accumulates in the environment. There is need for a circular economy, where energy and materials are renewably derived from waste items, rather than by consuming limited resources. Deconstruction of the recalcitrant linkages in natural and synthetic polymers is crucial for a circular economy, as deconstructed monomers can be used to manufacture new products. In Nature, organisms utilize enzymes for the efficient depolymerization and conversion of macromolecules. Consequently, by employing enzymes industrially, biotechnology holds great promise for energy- and cost-efficient conversion of materials for a circular economy. However, there is need for enhanced molecular-level understanding of enzymes to enable economically viable technologies that can be applied on a global scale. This work is a computational study of key enzymes that catalyze important reactions that can be utilized for a bio-based circular economy. Specifically, bioinformatics and data- mining approaches were employed to study family 7 glycoside hydrolases (GH7s), which are the principal enzymes in Nature for deconstructing cellulose to simple sugars; a cytochrome P450 enzyme (GcoA) that catalyzes the demethylation of lignin subunits; and MHETase, a tannase-family enzyme utilized by the bacterium, Ideonella sakaiensis, in the degradation and assimilation of polyethylene terephthalate (PET). Since enzyme function is fundamentally dependent on the primary amino-acid sequence, we hypothesize that machine-learning algorithms can be trained on an ensemble of functionally related enzymes to reveal functional patterns in the enzyme family, and to map the primary sequence to enzyme function such that functional properties can be predicted for a new enzyme sequence with significant accuracy. We find that supervised machine learning identifies important residues for processivity and accurately predicts functional subtypes and domain architectures in GH7s. Bioinformatic analyses revealed conserved active-site residues in GcoA and informed protein engineering that enabled expanded enzyme specificity and improved activity. Similarly, bioinformatic studies and phylogenetic analysis provided evolutionary context and identified crucial residues for MHET-hydrolase activity in a tannase-family enzyme (MHETase). Lastly, we developed machine-learning models to predict enzyme thermostability, allowing for high-throughput screening of enzymes that can catalyze reactions at elevated temperatures. Altogether, this work provides a solid basis for a computational data-driven approach to understanding, identifying, and engineering enzymes for biotechnological applications towards a more sustainable world

From Assessing to Conserving biodiversity. Conceptual and Practical Challenges

This open access book features essays written by philosophers, biologists, ecologists and conservation scientists facing the current biodiversity crisis. Despite increasing communication, accelerating policy and management responses, and notwithstanding improving ecosystem assessment and endangered species knowledge, conserving biodiversity continues to be more a concern than an accomplished task. Why is it so? The overexploitation of natural resources by our species is a frequently recognised factor, while the short-term economic interests of governments and stakeholders typically clash with the burdens that implementing conservation actions imply. But this is not the whole story. This book develops a different perspective on the problem by exploring the conceptual challenges and practical defiance posed by conserving biodiversity, namely: on the one hand, the difficulties in defining what biodiversity is and characterizing that “thing” to which the word ‘biodiversity’ refers to; on the other hand, the reasons why assessing biodiversity and putting in place effective conservation actions is arduous. ; Features essays that are explicitly critical of the species approach to biodiversity Presents bio-philosophical perspectives on the interaction between biodiversity’s units, levels, and scales Serves as an interdisciplinary contribution to the emergent field of biodiversity studie

2019 GREAT Day Program

SUNY Geneseo’s Thirteenth Annual GREAT Day.https://knightscholar.geneseo.edu/program-2007/1013/thumbnail.jp

The mechanisms underlying seasonal timing of breeding : a multi-level approach using bi-directional genomic selection on timing of egg-laying

With climate change being one of the major threats to current biodiversity, it is essential for species to adapt sufficiently in order to survive. Some species adapt their phenology faster, in reaction to increasing temperatures, compared to others, resulting in mismatched timing. For many seasonal breeding avian species in temperate zones, such as the great tit, the reproductive period is short and coincides with warmer temperatures and increased food supplies required for successful rearing of offspring. Therefore, seasonal breeders time their reproductive cycle to the changing seasons in order to maximize reproductive success and offspring survival. With springs getting warmer earlier in the year, it is of importance for great tit females to start laying earlier to be able to raise their offspring in an optimal period (i.e. sufficient food abundance). However, females show large variation in timing of breeding, which lies in the underlying physiology: different cues are used and translated by a cascade of neuro-endocrine processes along the hypothalamic-pituitary-gonadal-liver (HPGL) axis into a laying date. Natural selection could act on this variation between females, but it is still unclear on which of the compartments (brain, ovary, liver) of the HPGL axis cues act and thus where the variation in timing between females arises. It is of importance to understand how the components of the physiological mechanism contribute to genetic variation in timing before one is able to understand how natural selection can act on timing of reproduction. In this thesis, the main aim was to explore the molecular basis of the physiological mechanisms underlying avian seasonal timing of breeding. A promising way to do this is by comparing (extremely) early and (extremely) late laying females. In Chapter 2, I describe a large-scale selection experiment, where we created selection lines for early and late egg-laying using genomic selection. In this chapter we show that genomic selection on a complex trait such as timing of breeding is possible, because we find that the early and late selection line birds differ genomically and that this difference increases over the generations. In addition, we find that F3 generation birds differ also phenotypically, with a significant average difference in egg-laying dates of ~10 days between selection lines. By housing pairs of the selection lines in climate-controlled aviaries and in outdoor aviaries for two consecutive years and in contrasting environments (either artificial or semi-natural), I was able to determine that temperature has a direct effect on timing of breeding instead of via food phenology and that females laid on average earlier in the warm environment (Chapter 3). Further, because we obtained two laying dates per female, we evaluated whether our selection on laying date also changed the birds’ phenotypic plasticity and found early selection line females to initiated egg laying consistently ~9 days earlier compared to late selection line females in outdoor aviaries, but no difference in the degree of plasticity. This suggests that while natural selection may lead to a change in phenotype in the average environment it is unlikely to result in a correlated response on the degree of plasticity in timing of breeding. I also aimed to determine whether individual differences in timing of breeding in females are reflected in differences in their molecular biology and if so where. In Chapter 4 we generated comprehensive RNA expression data from a set of three tissues important in the neuro-endocrine cascade (HPGL axis) underlying avian seasonal timing of breeding, from three different time points and from two temperature treatments and two selection lines for breeding time. Time was the strongest driver in this study, but we found an interesting interaction between time and temperature in hypothalamus, with several genes involved in circadian rhythms differentially expressed. Even though the hypothalamus has been considered the final integration point of environmental cues and guide top down hormonal regulation and in this way direct ovarian function to time breeding, we find evidence for downstream regulation of timing of breeding in Chapter 5. Differences in key reproductive candidate gene expression between phenotypically early and late laying females were found exclusively in the ovary and liver. This also suggests that adaptation in the HPGL axis to changing environments might be downstream. The effects of the environment need to be translated into gene transcription (Chapter 4 and 5), for which DNA methylation is a likely key regulator. Therefore, in Chapter 6, we investigated in great tits whether methylation changes were tissue-specific or tissue-general and whether such methylation changes were associated with expression changes within and between tissues. Overall, we found a positive correlation between changes in DNA methylation in red blood cells and liver, both genome-wide as well as for the sites within the promoter region or transcription start site (TSS) separately. Within the TSS of genes, hyper-methylation over time in red blood cells was highly correlated with a decrease in the expression of the associated gene in the ovary. Tissue-general changes in DNA methylation could potentially be informative for changes in gene expression in inaccessible tissues. I explored the molecular basis of the physiological mechanism underlying seasonal timing of breeding in an avian model species; the great tit. I looked at the phenotype, investigated candidate gene and genome-wide gene expression. In addition, we looked at DNA methylation (in relation to gene expression). The main conclusions are that (1) genomic selection is possible in wild populations, (2) temperature directly influences timing of breeding and (3) that timing of breeding is regulated downstream in the HPLG axis. However, we are only scratching the surface of this complex trait and further studies (also considering other ‘endo-phenotypes’ and their interactions, see Chapter 7) are necessary in order to make predictions about whether birds in general, and great tits specifically, will adapt to rapidly changing environments. </p

A Polyhedral Study of Mixed 0-1 Set

We consider a variant of the well-known single node fixed charge network flow set with constant capacities. This set arises from the relaxation of more general mixed integer sets such as lot-sizing problems with multiple suppliers. We provide a complete polyhedral characterization of the convex hull of the given set