Genetically Encoded Trensor Circuits Report HeLa Cell Treatment with Polyplexed Plasmid DNA and Small-Molecule Transfection Modulators.

HeLa cell transfection with plasmid DNA (pDNA) is widely used to materialize biologicals and as a preclinical test of nucleic acid-based vaccine efficacy. We sought to genetically encode mammalian transfection sensor (Trensor) circuits and test their utility in HeLa cells for detecting molecules and methods for their propensity to influence transfection. We intended these Trensor circuits to be triggered if their host cell was treated with polyplexed pDNA or certain small-molecule modulators of transfection. We prioritized three promoters, implicated by others in feedback responses as cells import and process foreign material and stably integrated each into the genomes of three different cell lines, each upstream of a green fluorescent protein (GFP) open reading frame within a transgene. All three Trensor circuits showed an increase in their GFP expression when their host HeLa cells were incubated with pDNA and the degraded polyamidoamine dendrimer reagent, SuperFect. We next experimentally demonstrated the modulation of PEI-mediated HeLa cell transient transfection by four different small molecules, with Trichostatin A (TSA) showing the greatest propensity to boost transgene expression. The Trensor circuit based on the TRA2B promoter (Trensor-T) was triggered by incubation with TSA alone and not the other three small molecules. These data suggest that mammalian reporter circuits could enable low-cost, high-throughput screening to identify novel transfection methods and reagents without the need to perform actual transfections requiring costly plasmids or expensive fluorescent labels.

Genomic data provide insights into the classification of extant termites.

The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements analyzed as concatenated matrices or within the multi-species coalescence framework. Our classification is further supported by analyses controlling for rogue loci and taxa, and topological tests. We show that the Neoisoptera are composed of seven family-level monophyletic lineages, including the Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae Holmgren, raised from subfamilial rank. The species-rich Termitidae are composed of 18 subfamily-level monophyletic lineages, including the new subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae, Neocapritermitinae, Protohamitermitinae, and Promirotermitinae; and the revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and Mirocapritermitinae Kemner. Building an updated taxonomic classification on the foundation of unambiguously supported monophyletic lineages makes it highly resilient to potential destabilization caused by the future availability of novel phylogenetic markers and methods. The taxonomic stability is further guaranteed by the modularity of the new termite classification, designed to accommodate as-yet undescribed species with uncertain affinities to the herein delimited monophyletic lineages in the form of new families or subfamilies.

Experimental evidence that dung beetles benefit from reduced ivermectin in targeted treatment of livestock parasites.

Anthelmintic residues in livestock dung can adversely affect beneficial organisms. Targeted selective treatment (TST) of a reduced proportion of livestock with anthelmintics can slow resistance development in gastrointestinal nematodes by providing residue-free dung which could also benefit non-target organisms. We tested effects of TST on survival and reproduction of the dung beetle Onthophagus taurus (Scarabaeidae) in a factorial glasshouse experiment (Experimental treatments: five TST levels, 0.00, 0.25, 0.50, 0.75, 1.00 x four ivermectin concentrations, 125, 250, 375, 500 ppb). Each mesocosm comprised a 60 L bin containing sand, four dung pats and six pairs of adult beetles (F0 generation). No effects of TST level and ivermectin concentration on mortality of F0 adults after one week were observed. F0 adult brood ball production was affected by TST level, particularly at high ivermectin concentrations. Brood ball production increased as more untreated pats became available, with greater increases at higher ivermectin concentrations. We tested for evidence of a reported attraction of dung beetles to ivermectin-treated dung using a novel glitter-marker to trace the origin of dung used in brood balls. Where mesocosms contained both dung types, the proportion of brood balls created from untreated dung showed no statistical difference from the null expectation based on untreated dung availability in the mesocosm. Emergence of F1 adults was affected by the increase in TST, with this effect dependent on concentration. Treatments with concentrations of 250-500 ppb had the lowest emergence rates (ca. 5-20 % in mesocosms where all dung pats were treated) but emergence rates increased with TST level, reaching 68-88 % emergence where no dung pats were treated with ivermectin. Ivermectin-induced mortality occurred predominantly at egg and first instar stages. TST can provide refuges for dung beetles offering a strategy for livestock producers to maintain livestock welfare whilst benefiting from ecosystem services provided by important insects.

Solving the 250-year-old mystery of the origin and global spread of the German cockroach, Blattella germanica.

The origin of the German cockroach, Blattella germanica, is enigmatic, in part because it is ubiquitous worldwide in human-built structures but absent from any natural habitats. The first historical records of this species are from ca. 250 years ago (ya) from central Europe (hence its name). However, recent research suggests that the center of diversity of the genus is Asian, where its closest relatives are found. To solve this paradox, we sampled genome-wide markers of 281 cockroaches from 17 countries across six continents. We confirm that B. germanica evolved from the Asian cockroach Blattella asahinai approximately 2,100 ya, probably by adapting to human settlements in India or Myanmar. Our genomic analyses reconstructed two primary global spread routes, one older, westward route to the Middle East coinciding with various Islamic dynasties (~1,200 ya), and another younger eastward route coinciding with the European colonial period (~390 ya). While Europe was not central to the early domestication and spread of the German cockroach, European advances in long-distance transportation and temperature-controlled housing were likely important for the more recent global spread, increasing chances of successful dispersal to and establishment in new regions. The global genetic structure of German cockroaches further supports our model, as it generally aligns with geopolitical boundaries, suggesting regional bridgehead populations established following the advent of international commerce.

Deliberately introduced dung beetles in Australia: 12 years of occurrence and abundance records from 2001 to 2022.

Since 1968, the Australian Dung Beetle Project has carried out field releases of 43 deliberately introduced dung beetle species for the biological control of livestock dung and dung-breeding pests. Of these, 23 species are known to have become established. For most of these species, sufficient time has elapsed for population expansion to fill the extent of their potential geographic range through both natural and human-assisted dispersal. Consequently, over the last 20 years, extensive efforts have been made to quantify the current distribution of these introduced dung beetles, as well as the seasonal and spatial variation in their activity levels. Much of these data and their associated metadata have remained unpublished, and they have not previously been synthesized into a cohesive dataset. Here, we collate and report data from the three largest dung beetle monitoring projects from 2001 to 2022. Together, these projects encompass data collected from across Australia, and include records for all 23 species of established dung beetles introduced for biocontrol purposes. In total, these data include 22,718 presence records and 213,538 absence records collected during 10,272 sampling events at 546 locations. Most presence records (97%) include abundance data. In total, 1,752,807 dung beetles were identified as part of these data. The distributional occurrence and abundance data can be used to explore questions such as factors influencing dung beetle species distributions, dung beetle biocontrol, and insect-mediated ecosystem services. These data are provided under a CC-BY-NC 4.0 license and users are encouraged to cite this data paper when using the data.

Dung beetles increase plant growth: a meta-analysis.

The ecosystem services provided by dung beetles are well known and valued. Dung beetles bury dung for feeding and breeding, and it is generally thought that the process of burying dung increases nutrient uptake by plant roots, which promotes plant growth. Many studies have tested the effects of dung beetles on plant growth, but there has been no quantitative synthesis of these studies. Here we use a multi-level meta-analysis to estimate the average effect of dung beetles on plant growth and investigate factors that moderate this effect. We identified 28 publications that investigated dung beetle effects on plant growth. Of these, 24 contained the minimum quantitative data necessary to include in a meta-analysis. Overall, we found that dung beetles increased plant growth by 17%; the 95% CI for possible values for the true increase in plant growth that were most compatible with our data, given our statistical model, ranged from 1% to 35%. We found evidence that the dung beetle-plant growth relationship is influenced by the plant measurement type and the number of beetles accessing the dung. However, beetles did not increase plant growth in all quantitative trials, as individual effect sizes ranged from -72% to 806%, suggesting important context-dependence in the provision of ecosystem services.

First Peoples' knowledge leads scientists to reveal 'fairy circles' and termite linyji are linked in Australia.

In the past, when scientists encountered and studied 'new' environmental phenomena, they rarely considered the existing knowledge of First Peoples (also known as Indigenous or Aboriginal people). The scientific debate over the regularly spaced bare patches (so-called fairy circles) in arid grasslands of Australian deserts is a case in point. Previous researchers used remote sensing, numerical modelling, aerial images and field observations to propose that fairy circles arise from plant self-organization. Here we present Australian Aboriginal art and narratives, and soil excavation data, that suggest these regularly spaced, bare and hard circles in grasslands are pavement nests occupied by Drepanotermes harvester termites. These circles, called linyji (Manyjilyjarra language) or mingkirri (Warlpiri language), have been used by Aboriginal people in their food economies and for other domestic and sacred purposes across generations. Knowledge of the linyji has been encoded in demonstration and oral transmission, ritual art and ceremony and other media. While the exact origins of the bare circles are unclear, being buried in deep time and Jukurrpa, termites need to be incorporated as key players in a larger system of interactions between soil, water and grass. Ecologically transformative feedbacks across millennia of land use and manipulation by Aboriginal people must be accounted for. We argue that the co-production of knowledge can both improve the care and management of those systems and support intergenerational learning within and across diverse cultures.

Explainability and causability in digital pathology.

The current move towards digital pathology enables pathologists to use artificial intelligence (AI)-based computer programmes for the advanced analysis of whole slide images. However, currently, the best-performing AI algorithms for image analysis are deemed black boxes since it remains - even to their developers - often unclear why the algorithm delivered a particular result. Especially in medicine, a better understanding of algorithmic decisions is essential to avoid mistakes and adverse effects on patients. This review article aims to provide medical experts with insights on the issue of explainability in digital pathology. A short introduction to the relevant underlying core concepts of machine learning shall nurture the reader's understanding of why explainability is a specific issue in this field. Addressing this issue of explainability, the rapidly evolving research field of explainable AI (XAI) has developed many techniques and methods to make black-box machine-learning systems more transparent. These XAI methods are a first step towards making black-box AI systems understandable by humans. However, we argue that an explanation interface must complement these explainable models to make their results useful to human stakeholders and achieve a high level of causability, i.e. a high level of causal understanding by the user. This is especially relevant in the medical field since explainability and causability play a crucial role also for compliance with regulatory requirements. We conclude by promoting the need for novel user interfaces for AI applications in pathology, which enable contextual understanding and allow the medical expert to ask interactive 'what-if'-questions. In pathology, such user interfaces will not only be important to achieve a high level of causability. They will also be crucial for keeping the human-in-the-loop and bringing medical experts' experience and conceptual knowledge to AI processes.

Pesticides reduce tropical amphibian and reptile diversity in agricultural landscapes in Indonesia.

Pesticide use on tropical crops has increased substantially in recent decades, posing a threat to biodiversity and ecosystem services. Amphibians and reptiles are common in tropical agricultural landscapes, but few field studies measure pesticide impacts on these taxa. Here we combine 1-year of correlative data with an experimental field approach from Indonesia. We show that while pesticide application cannot predict amphibian or reptile diversity patterns in cocoa plantations, our experimental exposure to herbicides and insecticides in vegetable gardens eliminated amphibians, whereas reptiles were less impacted by insecticide and not affected by herbicide exposure. The pesticide-driven loss of a common amphibian species known to be a pest-control agent (mainly invertebrate predation) suggests a strong indirect negative effect of pesticides on this service. We recommend landscape-based Integrated Pest Management and additional ecotoxicological studies on amphibians and reptiles to underpin a regulatory framework and to assure recognition and protection of their ecosystem services.

Gas exchange patterns for a small, stored-grain insect pest, Tribolium castaneum.

Insects breathe using one or a combination of three gas exchange patterns; continuous, cyclic and discontinuous, which vary in their rates of exchange of oxygen, carbon dioxide and water. In general, there is a trade-off between lowering gas exchange using discontinuous exchange that limits water loss at the cost of lower metabolic rate. These patterns and hypotheses for the evolution of discontinuous exchange have been examined for relatively large insects (>20 mg) over relatively short periods (<4 h), but smaller insects and longer time periods have yet to be examined. We measured gas exchange patterns and metabolic rates for adults of a small insect pest of grain, the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae), using flow-through respirometry in dry air for 48 h. All adults survived the desiccating measurement period; initially they used continuous gas exchange, then after 24 h switched to cyclic gas exchange with a 27% decrease in metabolic rate, and then after 48 h switched to discontinuous gas exchange with increased interburst duration and further decrease in metabolic rate. The successful use of the Qubit, a lower cost and so more common gas analyser, to measure respiration in the very small T. castaneum, may prompt more flow-through respirometry studies of small insects. Running such studies over long durations may help to better understand the evolution of respiration physiology and thus suggest new methods of pest management.

Recommendations on compiling test datasets for evaluating artificial intelligence solutions in pathology.

Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological diagnosis. Prior to routine use, it is important to evaluate their predictive performance and obtain regulatory approval. This assessment requires appropriate test datasets. However, compiling such datasets is challenging and specific recommendations are missing. A committee of various stakeholders, including commercial AI developers, pathologists, and researchers, discussed key aspects and conducted extensive literature reviews on test datasets in pathology. Here, we summarize the results and derive general recommendations on compiling test datasets. We address several questions: Which and how many images are needed? How to deal with low-prevalence subsets? How can potential bias be detected? How should datasets be reported? What are the regulatory requirements in different countries? The recommendations are intended to help AI developers demonstrate the utility of their products and to help pathologists and regulatory agencies verify reported performance measures. Further research is needed to formulate criteria for sufficiently representative test datasets so that AI solutions can operate with less user intervention and better support diagnostic workflows in the future.

Low radiodensity µCT scans to reveal detailed morphology of the termite leg and its subgenual organ.

Termites sense tiny substrate-borne vibrations through subgenual organs (SGOs) located within their legs' tibiae. Little is known about the SGOs' structure and physical properties. We applied high-resolution (voxel size 0.45 µm) micro-computed tomography (µCT) to Australian termites, Coptotermes lacteus and Nasutitermes exitiosus (Hill) to test two staining techniques. We compared the effectiveness of a single stain of Lugol's iodine solution (LS) to LS followed by Phosphotungstic acid (PTA) solutions (1% and 2%). We then present results of a soldier of Nasutitermes exitiosus combining µCT with LS + 2%PTS stains and scanning electron microscopy to exemplify the visualisation of their SGOs. The termite's SGO due to its approximately oval shape was shown to have a maximum diameter of 60 µm and a minimum of 48 µm, covering 60 ± 4% of the leg's cross-section and 90.4 ± 5% of the residual haemolymph channel. Additionally, the leg and residual haemolymph channel cross-sectional area decreased around the SGO by 33% and 73%, respectively. We hypothesise that this change in cross-sectional area amplifies the vibrations for the SGO. Since SGOs are directly connected to the cuticle, their mechanical properties and the geometric details identified here may enable new approaches to determine how termites sense micro-vibrations.

Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera, Kalotermitidae).

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75-93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at <50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.

Submillimetre mechanistic designs of termite-built structures.

Termites inhabit complex underground mounds of intricate stigmergic labyrinthine designs with multiple functions as nursery, food storage and refuge, while maintaining a homeostatic microclimate. Past research studied termite building activities rather than the actual material structure. Yet, prior to understanding how multi-functionality shaped termite building, a thorough grasp of submillimetre mechanistic architecture of mounds is required. Here, we identify for Nasutitermes exitiosus via granulometry and Fourier transform infrared spectroscopy analysis, preferential particle sizes related to coarse silts and unknown mixtures of organic/inorganic components. High-resolution micro-computed X-ray tomography and microindentation tests reveal wall patterns of filigree laminated layers and sub-millimetre porosity wrapped around a coarse-grained inner scaffold. The scaffold geometry, which is designed of a lignin-based composite and densely biocementitious stercoral mortar, resembles that of trabecula cancellous bones. Fractal dimension estimates indicate multi-scaled porosity, important for enhanced evaporative cooling and structural stability. The indentation moduli increase from the outer to the inner wall parts to values higher than those found in loose clays and which exceed locally the properties of anthropogenic cementitious materials. Termites engineer intricately layered biocementitious composites of high elasticity. The multiple-scales and porosity of the structure indicate a potential to pioneer bio-architected lightweight and high-strength materials.

Predicting ecological impacts of invasive termites.

There are 28 invasive termite species, most belong to two families, the Kalotermitidae (esp. Cryptotermes spp.) and Rhinotermitidae (esp. Coptotermes spp.). Six invasive termite species are known to have spread into natural habitats, but little direct research has been conducted into their ecological impacts. Predictions based on indirect research (natural durability of commercial wood species) suggest fast-growing, pioneer tree species with low density wood, perhaps notably legumes, are most vulnerable to invasive termites, but even slow growing climax tree species may succumb. Cryptotermes will likely have less ecological impact, due to small colonies attacking dead branch stubs in the canopy. Coptotermes will likely have greater impact, due to large colony sizes and nesting in living trees, which they hollow out and can kill. There are no studies of invasive termites on native termites, other wood-eating insects, or predators, such as ants, showing considerable scope for future research.

Revisiting stigmergy in light of multi-functional, biogenic, termite structures as communication channel.

Termite mounds are fascinating because of their intriguing composition of numerous geometric shapes and materials. However, little is known about these structures, or of their functionalities. Most research has been on the basic composition of mounds compared with surrounding soils. There has been some targeted research on the thermoregulation and ventilation of the mounds of a few species of fungi-growing termites, which has generated considerable interest from human architecture. Otherwise, research on termite mounds has been scattered, with little work on their explicit properties. This review is focused on how termites design and build functional structures as nest, nursery and food storage; for thermoregulation and climatisation; as defence, shelter and refuge; as a foraging tool or building material; and for colony communication, either as in indirect communication (stigmergy) or as an information channel essential for direct communication through vibrations (biotremology). Our analysis shows that systematic research is required to study the properties of these structures such as porosity and material composition. High resolution computer tomography in combination with nonlinear dynamics and methods from computational intelligence may provide breakthroughs in unveiling the secrets of termite behaviour and their mounds. In particular, the examination of dynamic and wave propagation properties of termite-built structures in combination with a detailed signal analysis of termite activities is required to better understand the interplay between termites and their nest as superorganism. How termite structures serve as defence in the form of disguising acoustic and vibration signals from detection by predators, and what role local and global vibration synchronisation plays for building are open questions that need to be addressed to provide insights into how termites utilise materials to thrive in a world of predators and competitors.

Water Costs of Gas Exchange by a Speckled Cockroach and a Darkling Beetle.

Respiratory water loss during metabolic gas exchange is an unavoidable cost of living for terrestrial insects. It has been suggested to depend on several factors, such as the mode of gas exchange (convective vs. diffusive), species habitat (aridity), body size and measurement conditions (temperature). We measured this cost in terms of respiratory water loss relative to metabolic rate (respiratory water cost of gas exchange; RWL/V˙CO2) for adults of two insect species, the speckled cockroach (Nauphoeta cinerea) and the darkling beetle (Zophobas morio), which are similar in their mode of gas exchange (dominantly convective), habitat (mesic), body size and measurement conditions, by measuring gas exchange patterns using flow-through respirometry. The speckled cockroaches showed both continuous and discontinuous gas exchange patterns, which had significantly a different metabolic rate and respiratory water loss but the same respiratory water cost of gas exchange. The darkling beetles showed continuous gas exchange pattern only, and their metabolic rate, respiratory water loss and respiratory cost of gas exchange were equivalent to those cockroaches using continuous gas exchange. This outcome from our study highlights that the respiratory water cost of gas exchange is similar between species, regardless of gas exchange pattern used, when the confounding factors affecting this cost are controlled. However, the total evaporative water cost of gas exchange is much higher than the respiratory cost because cuticular water loss contributes considerably more to the overall evaporative water loss than respiratory water. We suggest that the total water cost of gas exchange is likely to be a more useful index of environmental adaptation (e.g., aridity) than just the respiratory water cost.

Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes.

Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.