Drosophila melanogaster has one of the deepest research bases within the life sciences, with a wealth of high-quality tissue- and cell type-specific transcriptomic data available. However, integrating large datasets derived from disparate sources is not trivial. We have designed a broadly applicable solution to this problem in the form of the Drosophila Interesting Genes in Individual Tissues-tally (DIGITtally) system. It is freely available online at www.digittally.org. DIGITtally is customizable and hypothesis-free, allowing meta-analysis across the Drosophila research space along with analysis of conservation in other species, querying 10 data sources for seven indicators of tissue-specific activity. We have applied DIGITtally to a pertinent question within entomology—that is, whether a specific pattern of gene expression underlies the transporting activity of epithelial tissues (an ‘epitheliome’). By using DIGITtally to survey gene expression throughout the tissues comprising the D. melanogaster alimentary canal (salivary gland, midgut, Malpighian tubules, and hindgut), we have verified the existence of a specific ‘epithelial’ vacuolar-type ATPase configuration.

MOTIVATION:Basic biological processes are shared across animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell-type gene expression between species reveals conserved and divergent cellular functions. However, as phylogenetic distance increases, gene-based comparisons become less informative. The gene ontology (GO) knowledgebase offers a solution by serving as the most comprehensive resource of gene functions across a vast diversity of species, providing a bridge for distant species comparisons. RESULTS:Here, we present scGOclust, a computational tool that constructs de novo cellular functional profiles using GO terms, facilitating systematic and robust comparisons within and across species. We applied scGOclust to analyse and compare the heart, gut, and kidney between mouse and fly, and whole-body data from Caenorhabditis elegans and Hydra vulgaris. We show that scGOclust effectively recapitulates the function spectrum of different cell types, characterizes functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Additionally, we identified subpopulations within the fly crop that show circadian rhythm-regulated secretory properties and hypothesize an analogy between fly principal cells from different segments and distinct mouse kidney tubules. We envision scGOclust as an effective tool for uncovering functionally analogous cell types or organs across distant species, offering fresh perspectives on evolutionary and functional biology. AVAILABILITY AND IMPLEMENTATION:ScGOclust is publicly available on CRAN: https://cran.r-project.org/web/packages/scGOclust/index.html and development versions are available on GitHub: github.com/Papatheodorou-Group/scGOclust/.

JEB has broadened its scope to include non-hypothesis-led research. In this Perspective, based on our lab's lived experience, I argue that this is excellent news, because truly novel insights can occur from 'blue skies' idea-led experiments. Hypothesis-led and rather, the latter can provide a short-cut to an unbiased view of organism function, and is intrinsically hypothesis generating. Insights derived from hypothesis-free research are commonly obtained by the generation and analysis of big datasets - for example, by genetic screens - or from omics-led approaches (notably transcriptomics). Furthermore, meta-analyses of existing datasets can also provide a lower-cost means to formulating new hypotheses, specifically if researchers take advantage of the FAIR principles (findability, accessibility, interoperability and reusability) to access relevant, publicly available datasets. The broadened scope will thus bring new, original work and novel insights to our journal, by expanding the range of fundamental questions that can be asked.

An anoctamin 4 (ANO4) mutation was identified in dogs with calcium oxalate (CaOx) stones via GWAS, and the content of ANO4 is decreased in urinary extracellular vesicles of human CaOx stone formers. ANO proteins are Ca2+-activated Clchannels and/or Ca2+-activated phospholipid scramblases. In addition to these functions, the homolog of ANO4 in Drosophila, subdued, has been shown to play a role in host defense against gram-negative bacteria. Uropathogenic E. coli (UPEC) increases intrarenal CaOx crystallization in mammals.

Key Points Drosophila can be a model for Dent Disease type 1. Drosophila Clc-C mutations function similar to human CLC-5 Dent 1 mutations. Background Drosophila serve as exceptional alternative models for in vivo and ex vivo research and may provide an avenue for in-depth investigation for human ClC-5 and Dent disease type 1 (DD1). The Drosophila ClC-c (CG5284) has sequence homology with human ClC-5 and is hypothesized to encompass similar functional and phenotypical roles with ClC-5 and variants that cause DD1. Methods Ion transport function and activity of Drosophila ClC-c and homologous DD1 variants were assessed by voltage clamp electrophysiology. Membrane localization was demonstrated in Drosophila expressing a GFP-labeled construct of ClC-c. Genetic expression of an RNAi against ClC-c mRNA was used to generate a knockdown fly that serves as a DD1 disease model. Tubule secretion of cations and protein were assessed, as well as the crystal formation in the Malpighian tubules. Results Voltage clamp experiments demonstrate that ClC-c is voltage-gated with Cl − -dependent and pH-sensitive currents. Inclusion of homologous DD1 mutations pathogenic variants (S393L, R494W, and Q777X) impairs ClC-c ion transport activity. In vivo expression of ClC-c-eGFP in Malpighian tubules reveals that the membrane transporter localizes to the apical membrane and nearby cytosolic regions. RNAi knockdown of ClC-c (48% decreased mRNA expression) causes increased secretion of both urinary protein and Ca 2+ and increased occurrence of spontaneous tubule crystals. Conclusions Drosophila ClC-c shows orthologous function and localization to human ClC-5. Thus, Drosophila and ClC-c regulation may be useful for future investigations of Cl − transport, Ca 2+ homeostasis, and urinary protein loss in DD1.

Basic biological processes are shared among animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell type expression profiles across species reveals the conservation and divergence of cellular functions. With the increase of phylogenetic distance between species of interest, a gene-based comparison becomes limited. The Gene Ontology (GO) knowledgebase is the most comprehensive resource of gene functions, providing a bridge for comparing cell types between remote species. Here, we present scGOclust, a computational tool to construct cellular functional profiles using GO terms and facilitates systematic, robust comparisons within and across species. We use scGOclust to analyse and compare the heart, gut and kidney between mouse and fly. We show that scGOclust recapitulates the function spectrum of different cell types, characterises functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Furthermore, we identify subpopulations in the fly crop by cross-species comparison of GO profiles. Finally, scGOclust resolved the analogy between Malpighian tubule and kidney segments.### Competing Interest StatementThe authors have declared no competing interest.

The Neotropical brown stink bug, Euschistus heros, is a major pest of soybean in South America. The importance of E. heros as a pest has grown significantly in recent times due to increases in its abundance and range, and the evolution of insecticide resistance. Recent work has begun to examine the genetic diversity, population structure, and genetic mechanisms of insecticide resistance in E. heros. However, to date, investigation of these topics has been hampered by a lack of genomic resources for this species. Here we address this need by assembling a high-quality draft genome for E. heros. We used a combination of short and long read sequencing to assemble an E. heros genome of 1.4 Gb comprising 906 contigs with a contig N50 of 3.5 MB. We leveraged this new genomic resource, in combination with genotyping by sequencing, to explore genetic diversity in populations of this species in Brazil and identify genetic loci in the genome which are under selection. Our genome-wide analyses, confirm that there are two populations of E. heros co-occurring in different geographical regions in Brazil, and that, in certain regions of the country these populations are hybridizing. We identify several regions of the genome as under selection, including markers associated with putative insecticide resistance genes. Taken together, the new genomic resources generated in this study will accelerate research into fundamental aspects of stinkbug biology and applied aspects relating to the sustainable control of a highly damaging crop pest.

Introduction: Dent Disease type 1 (DD1) results from X-linked, mutations in CLC-5 (2Cl - /H + exchanger) and results in progressive renal failure by 20-40. DD1 is characterized by kidney Ca 2+ mishandling, and subsequent hypercalcuria, calcium oxalate (CaOx) kidney stones, and kidney calcification as well as proteinuria. We identified Drosophila Clc-c as the CLC-5 homolog with conserved amino acids at DD1 mutation sites. We hypothesize that Clc-c shares functional similarities in Cl - transport, Ca 2+ homeostasis and protein processing. Methods and Results: By voltage clamping Xenopus oocytes expressing Clc‑c and CLC-5, we find that both are electrogenic and have the same outward-rectifying current in Cl - solutions. Cl - transport (current at +80mV) was lowered by acidity (2.37±0.55 μA, pH 6.0, P=0.06), but not by alkaline solution (4.45±0.96 μA, pH 8.5, P= 0.7) when compared to the standard solution of pH 7.5 (4.97±1.12 μA). Similarly, Cl - transport was lowered by homologous DD1 mutations S393L (0.67±0.098 μA, P<0.0001), R494W (2.9±0.46 μA, P =0.006), and Q777x (1.13±0.28 μA, P =0.0001) vs. WT (7.4±1.2 μA) as observed previously for CLC-5 DD1 mutations: S244L, R345W, and Q629x (Tang et al, Physiol Rep 4[8], 2016). To determine cell membrane and possible intracellular localization of DD1 mutations, HA-tagged Clcc and mutations (identical placement as in CLC-5-HA, Tang 2016) were made. Likewise, transgenic Drosophila expressing Clc-c-GFP were made to localize Clc-c in cell and intracellular membranes of renal tubules (Malpighian tubules, MT) in vivo (Judd-Mole, U Monash, Dissertation, 2016). RNAi MT knockdowns of Clc-c (Clc-c-KD) were made and resulted in 50% decrease in Clc-c mRNA expression. CaOx crystals in anterior MT (7 days after eclosure) were present in all Clc-c-KD and were more abundant (15±4 crystals/fly) than w 1118 controls (5±2 crystals/fly, P= 0.02). MT secretions showed that Clc-c KD flies contained higher [Ca 2+ ] while all other cations (Na + , NH4 + , K + , Mg2 + ), and volume were the same as w 1118 . Similarly, urinary protein concentration (4-6 pooled flies per n) appears elevated in DD1 flies (1.41 ± 0.14 mg/mL, n=3) vs w 1118 (1.16 ± 0.08 mg/mL, n=5). Conclusion: Drosophila Clc-c has similarities to human CLC-5 including impaired function of voltage-gated Cl - transport, homologous DD1 mutations, increased CaOx crystal formation, and elevated urinary [Ca 2+ ] and protein. Our results indicate that the Drosophila Clc-c avatar may help to provide more direct insights to the cellular and organismal pathophysiology for future investigations of Cl - transport, Ca 2+ homeostasis and urinary protein loss in DD1. F32 DK128987, T32 DK007013 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

ABSTRACT Transporting epithelia provide a protective barrier against pathogenic insults while allowing the controlled exchange of ions, solutes and water with the external environment. In invertebrates, these functions depend on formation and maintenance of ‘tight’ septate junctions (SJs). However, the mechanism by which SJs affect transport competence and tissue homeostasis, and how these are modulated by ageing, remain incompletely understood. Here, we demonstrate that the Drosophila renal (Malpighian) tubules undergo an age-dependent decline in secretory capacity, which correlates with mislocalisation of SJ proteins and progressive degeneration in cellular morphology and tissue homeostasis. Acute loss of the SJ protein Snakeskin in adult tubules induced progressive changes in cellular and tissue architecture, including altered expression and localisation of junctional proteins with concomitant loss of cell polarity and barrier integrity, demonstrating that compromised junctional integrity is sufficient to replicate these ageing-related phenotypes. Taken together, our work demonstrates a crucial link between epithelial barrier integrity, tubule transport competence, renal homeostasis and organismal viability, as well as providing novel insights into the mechanisms underpinning ageing and renal disease.

Anoctamins (ANO) are activated by intracellular Ca 2+ and function as phospholipid scramblases and/or Cl - channels. ANO4 is mutated in miniature schnauzers with calcium oxalate stones (CaOx), and ANO4 protein in urinary extracellular vesicles is decreased in human CaOx stone formers. In Drosophila Malpighian tubules (MT), subdued (ANO4-homolog) functions as Ca 2+ -activated Cl - channel, scramblase, and plays a role in host defense against gram-negative bacteria. Increasing evidence shows the participation of bacteria in urinary stone formation in humans. We used a Drosophila avatar to investigate whether subdued changes CaOx crystallization and if crystallization increases with bacterial infection.Uro:Gal4 flies were crossed with UAS:subdued-RNAi flies to knockdown (KD) subdued in MT principal cells (PC) or with w 1118 flies to generate normal controls (WT). F1 generation underwent CaOx crystallization in association or not with uropathogenic E. coli (UPEC) infection. In vivo, flies were fed on diet supplemented with 20mM sodium Ox (NaOx) + UPEC:eGFP for 4 days. For ex vivo assays, dissected MTs were submerged in solution containing 10mM NaOx+ UPEC:eGFP for 90 minutes. subdued-KD in PC reduced subdued mRNA by 56% in MT. Neither crystal number nor size were changed by subdued-KD after prolonged NaOx feeding. However, when UPEC is introduced with the NaOx diet, subdued-KD flies exhibited a large bacterial presence in MT lumen and produced enlarged CaOx crystals compared to WT flies. Similar augmented presence of UPEC in subdued-KD MTs was observed during ex vivo assays. Short-term exposure to NaOx+UPEC resulted in increased number of crystals in subdued-KD MTs compared to WT MTs, but no difference was observed in crystal size.Fly cell atlas ( flycellatlas.org ) revealed that subdued is also found in MT stellate cells (SC; water and Cl - secretion). C724:Gal4>UAS:subdued-RNAi flies were used to assess the effect of subdued-KD in SC. This s ubdued-KD slightly increased bacterial infection but did change CaOx crystallization in MTs after 4 days of NaOx+UPEC feeding.The presence of subdued in PC limits CaOx crystals formation and aggregation through reducing bacterial invasion in the MT lumen. These Drosophila results suggest a role for ANO4 in bacterial-related human and dog kidney stone formation. Future experiments will determine whether other functional aspects of subdued affect CaOx crystallization. U54-DK100227, R01-DK092408, FAPESP (2022/01226-1), Mayo Foundation. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Since the transition from water to land, maintaining water balance has been a key challenge for terrestrial arthropods. We explore factors that allow terrestrial arthropods to survive within a variably dry world and how they shape ecological interactions. Detection of water and hydration is critical for maintaining water content. Efficient regulation of internal water content is accomplished by excretory and osmoregulatory systems that balance water intake and loss. Biochemical and physiological responses are necessary as water content declines to prevent and repair the damage that occurs during dehydration. Desiccation avoidance can occur seasonally or daily via a move to more favorable areas. Dehydration and its avoidance have ecological impacts that extend beyond a single species to alter trophic interactions. As climate changes, evolutionary and ecological processes will be critical to species survival during drought.

Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult Drosophila renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified fruitless ( fru ) as playing a role in stem cell regeneration and Hepatocyte nuclear factor 4 ( Hnf4 ) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including Rho guanine nucleotide exchange factor at 64C ( RhoGEF64c ), Frequenin 2 ( Frq2 ), Prip , and CG1093 that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus dataset allows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney.

Insect CAPA neuropeptidesare considered to affect water and ion balance by mediating the physiological metabolism activities of the Malpighian tubules. In previous studies, the CAPA-PK analogue 1895 (2Abf-Suc-FGPRLamide) was reported to decrease aphid fitness when administered through microinjection or via topical application. However, a further statistically significant decrease in the fitness of aphids and an increased mortality could not be established with pairwise combinations of 1895 with other CAPA analogue. In this study, we assessed the topical application of new combinations of 1895 with five CAPA-PVK analogues on the fitness of aphids. We found that 1895 and CAPA-PVK analogue 2315 (ASG-[β3 L]-VAFPRVamide) was statistically the most effective combination to control the peach potato aphid Myzus persicae nymphs via topical application, leading to 72% mortality. Additionally, the combination (1895+2315) was evaluated against a selection of beneficial insects, that is, a pollinator (Bombus terrestris) and three natural enemies (Chrysoperla carnea, Nasonia vitripennis, and Adalia bipunctata). We found no significant influence on food intake, weight increase, and survival for the pollinator and the three representative natural enemies. These results could facilitate to further establish and generate CAPA analogues as alternatives to broad spectrum and less friendly insecticides.

FlyAtlas 2 (flyatlas2.org) is a database and web application for studying the expression of the genes of Drosophila melanogaster in different tissues of adults and larvae. It is based on RNA-Seq data, and incorporates both genes encoding proteins and microRNAs. We have now completed the population of the database with 13 tissues from both male and female adults, five sex-specific tissues, and eight larval tissues. Larval garland cell nephrocytes have also been included. Major enhancements have been made to the application. First, a facility has been added for a ‘Profile’ search for genes with a similar pattern of tissue expression as a query gene. This may help establish the function of genes for which this is currently unknown. Second, a facility has been added dedicated to the larval midgut, where the difference in gene expression in the five regions of different pH can be explored. A variety of further improvements to the interface are described.

Mutations in the 2Cl /H transporter CLC-5 cause Dent Disease Type 1 (DD1) and lead to progressive renal failure by age 20-40. A major characteristic of DD1 is the renal mishandling of Ca that increases urinary Ca excretion, calcium oxalate (CaOx) kidney stones, and kidney calcification. Interestingly, none of the DD1 symptoms include or relate to Cl homeostasis despite impaired transport function. Thus, how does a Cl transporter cause Ca dysregulation? Our laboratory has identified Drosophila Clc-c to be the homolog of CLC-5 with conserved amino acids at DD1 mutation sites. We hypothesize that Clc-c shares functional similarities in Cl transport and Ca homeostasis. To test our hypothesis, we used electrophysiology to measure ion transport, and then assessed CaOx crystal formation in adult fly renal tubules (Malpighian tubules, MTs) of Drosophila. Voltage clamp experiments with Xenopus oocytes show that Clc-c is electrogenic with the same outward-rectifying current in Cl solutions as observed with human CLC-5. Next, knockdown flies (Clc-c-KD) were generated by crossing Uro-Gal4 (MT driver) with UAS-Clc-c-RNAi flies, resulting in 50% Clc-c mRNA expression in the MTs. Crystals in adult MT (7 days after eclosure) were present in 100% of Clc-c-KD compared to 71% of control flies. The average number of crystals in adult tubule pairs was significantly greater in Clc-c-KD flies (15±4 crystals per pair) than control flies (5±2 crystals, P= 0.02). When fed a diet with 2mM NaOx ClcC-KD for 4 days, Clc-c-KD flies had a significantly greater number of crystals in each tubule (24±5 crystals) than controls (4±2 crystals, P=0.005). However, the KD flies did not produce more crystals than control flies when fed a supraphysiological concentration of sodium oxalate (20 mM NaOx diet) for 1 or 4 days and in ex vivo assays of dissected MTs submerged in solution containing 10 mM NaOx for 1 hour. In conclusion, Drosophila Clc-c has both identical sequences at DD1 mutation sites and similar biophysical functions to human CLC-5. Furthermore, Clc-c-KD increases incidence of CaOx crystals which corresponds to the increased risks for kidney stones in DD1 patients. With this fly-DD1 model, we will be able to assess the relationship of Clc-c Cl transport to renal Ca deposits. Future experiments will evaluate renal pathophysiology of DD1 mutations and their relationship to Ca transport in Clc-c transgenic flies.

Simon Maddrell transformed our understanding of how insects regulate their internal environments, a major determinant of their extraordinary success. Raised during wartime on his family's farm, Simon was a grammar school scholar at St Catharine's College, Cambridge, where he obtained the top first of his year in zoology. A keen sportsman, he combined his studies with half-Blues in table tennis and athletics. After a PhD under the supervision of Sir Vincent Wigglesworth FRS, he took a fellowship at Dalhousie University in Canada. He returned to Cambridge as a fellow of Gonville and Caius College, and took up a post in the AFRC Unit housed in the Department of Zoology. His academic work focused on the insect kidney, or Malpighian tubule. He unravelled details both of the mechanisms of secretion of fluids, ions and toxins, and of their control by the nervous system. His favoured organism was the blood-sucking ‘kissing bug’, Rhodnius prolixus, which demonstrated remarkable adaptations to handle massive (but irregular) blood meals. Later he also studied the classic genetic model insect Drosophila melanogaster, helping to lay the framework for combined physiological and genetic approaches in the same organism. Outside the lab, his massive energy and financial skills were potent influences on the Company of Biologists, a charity publishing scientific journals. Living increasingly in the family seat on the Isle of Man, he also brought his perfectionism to bear on daffodil shows and woodland tree planting. He is survived by his wife and four children.

The common green lacewing Chrysoperla carnea (Neuroptera), also called the aphid lion, is an important predator of pest species, especially aphids that cause serious damage in many crops in agriculture. Neuropeptides are involved in regulating various physiological processes in insects. However, there have not been many studies on the neuropeptides found in C. carnea . This study aimed to assemble and define a whole body- and head-specific transcriptome of C. carnea . Interestingly, we found 41 candidate neuropeptide genes to encode precursors, but 10 neuropeptide genes were not found, including kinin. Based on this original hypothesis that this important neuropeptide was lost during evolution in this important natural enemy, it will lose its effect when we expose C. carnea to kinin neuropeptide analogue. Therefore, we tested three kinin analogues 1728, 2460 and 2139, and assessed their effect on the survival of the important green-peach aphid ( Myzus persicae ) via topical application. We found that the 2460 analogue [HCA-R(Aib)WGa] effectively controlled aphids, leading to 46% mortality within 5 days post-exposure. In contrast, 2460 showed no significant lethal or sublethal effects on survival, food intake and weight increase, in the beneficial insect C. carnea . In conclusion, this work suggests that kinin analogues may offer biosafe insecticide compounds, and in turn promote the development of more biosafe and sustainable integrated pest management (IPM) pest control strategies that are based on the combination of peptide analogues and natural enemy insects.