The genome sequence of Drosophila melanogaster

Exploring the versatility of Drosophila melanogaster as a model organism in biomedical research: a comprehensive review

Drosophila melanogaster is a highly versatile model organism that has profoundly advanced our understanding of human diseases. With more than 60% of its genes having human homologs, Drosophila provides an invaluable system for modelling a wide range of pathologies, including neurodegenerative disorders, cancer, metabolic diseases, as well as cardiac and muscular conditions. This review highlights key developments in utilizing Drosophila for disease modelling, emphasizing the genetic tools that have transformed research in this field. Technologies such as the GAL4/UAS system, RNA interference (RNAi) and CRISPR-Cas9 have enabled precise genetic manipulation, with CRISPR-Cas9 allowing for the introduction of human disease mutations into orthologous Drosophila genes. These approaches have yielded critical insights into disease mechanisms, identified novel therapeutic targets and facilitated both drug screening and toxicological studies. Articles were selected based on their relevance, impact and contribution to the field, with a particular focus on studies offering innovative perspectives on disease mechanisms or therapeutic strategies. Our findings emphasize the central role of Drosophila in studying complex human diseases, underscoring its genetic similarities to humans and its effectiveness in modelling conditions such as Alzheimer's disease, Parkinson's disease and cancer. This review reaffirms Drosophila's critical role as a model organism, highlighting its potential to drive future research and therapeutic advancements.

25 years of Drosophila "Sleep genes"

The field of Drosophila sleep research, which began 25 years ago, has identified more than 200 genes influencing sleep. In this review, I summarize the foundation of the field and the growing list of genes implicated in sleep regulation. I compare the genetic methods used to identify genes governing sleep and circadian rhythms and the distinct outcomes of screens for genes regulating these two highly related processes. Finally, I discuss the ~ 200 sleep-regulating genes of Drosophila in the context of recent developments in the field and voice reasons for scepticism regarding the relevance of these genes to the homoeostatic regulation of sleep. Finally, I speculate on the future promise of the fly model system for revealing conserved molecular mechanisms of sleep homoeostasis.

Identification, expression profiling and potential functional roles of nuclear receptors in the social aphid Pseudoregma bambucicola

BACKGROUND

Nuclear receptors (NRs) constitute a superfamily of transcription factors that regulate diverse biological processes. In insects, NRs not only govern essential physiological functions including metabolism, development, and reproduction, but also play pivotal roles in regulating caste differentiation and division of labor within social insect colonies. Pseudoregma bambucicola is a species of social aphid in which adults exhibit a specialized reproductive division of labor. This unique system produces first-instar nymphs and soldiers, which share an identical genetic background yet exhibit distinct morphological and behavioral traits. Although NRs exhibit pleiotropic regulatory capacities, their roles in the unique developmental patterns of P. bambucicola remain unclear.

RESULTS

This study identified 21 NR genes based on the genomic data of P. bambucicola and analyzed the duplication and loss events of these genes through phylogenetic analysis. Additionally, differential expression of NR genes was analyzed using transcriptomic data. The TLL exhibited significant differential expression in adults with distinct reproductive behaviors, suggesting its involvement in the regulation of reproductive division of labor. E75 and HNF4 were found to be important for the post-embryonic development of soldiers. Furthermore, quantitative real-time PCR confirmed caste-specific expression patterns of HR4 and HR39, indicating their potential involvement in morphological differentiation and developmental regulation among castes.

CONCLUSIONS

This study conducted bioinformatic identification of NR genes in the social aphid P. bambucicola, and investigated their potential roles in morphological differentiation and behavioral division through analysis of differential gene expression. The findings provide preliminary evidence for the functional significance of NR genes in social aphids, while offering novel insights for subsequent research exploration.

Taking flight, the use of Drosophila melanogaster for neuroscience research in Uruguay

The Sociedad de Neurociencias del Uruguay is celebrating its 30th anniversary, sustained by more than a century of neuroscience research in the country. During this time, different approaches and experimental organisms have been incorporated to study diverse aspects of neurobiology. One of these experimental animals, successfully used in a variety of biological fields, is the fruit fly Drosophila melanogaster. Although Drosophila has been a model organism for neuroscience research worldwide for many decades, its use in Uruguay for that purpose is relatively new and just taking flight. In this special issue article, we will describe some of the research lines that are currently using Drosophila for neuroscience studies, questioning a wide range of issues including thermoreception, neurodegenerative diseases such as Parkinson's, screening of bioactive compounds with a neuroprotective effect, and gene/protein function during development of the nervous system. The consolidation of these research lines has been achieved due to unique features of D. melanogaster as an experimental model. We will review the advantages of using Drosophila to study neurobiology and describe some of its useful genetic tools. Advantages such as having powerful genetics, highly conserved disease pathways, a complete connectome, very low comparative costs, easy maintenance, and the support of a collaborative community allowing access to a vast toolkit, all make D. melanogaster an ideal model organism for neuroscientists in countries with low levels of investment in research and development. This review focuses on the strengths and description of useful techniques to study neurobiology using Drosophila, from the perspective of a Latin-American experience.

Building better genome annotations across the tree of life

Recent technological advances in long-read DNA sequencing accompanied by reduction in costs have made the production of genome assemblies financially achievable and computationally feasible, such that genome assembly no longer represents the major hurdle to evolutionary analysis for most nonmodel organisms. Now, the more difficult challenge is to properly annotate a draft genome assembly once it has been constructed. The primary challenge to annotations is how to select from the myriad gene prediction tools that are currently available, determine what kinds of data are necessary to generate high-quality annotations, and evaluate the quality of the annotation. To determine which methods perform the best and to determine whether the inclusion of RNA-seq data is necessary to obtain a high-quality annotation, we generated annotations with 12 different methods for 21 different species spanning vertebrates, plants, and insects. We found that the annotation transfer method TOGA, BRAKER3, and the RNA-seq assembler StringTie were consistently top performers across a variety of metrics including BUSCO recovery, CDS length, and false-positive rate, with the exception that TOGA performed less well in some monocots with respect to BUSCO recovery. The choice of which of the top-performing methods will depend upon the feasibility of whole-genome alignment, availability of RNA-seq data, importance of capturing noncoding parts of the transcriptome, and, when whole-genome alignment is not feasible, the relative performance in BUSCO recovery between BRAKER3 and StringTie. When whole-genome alignment is not feasible, inclusion of RNA-seq data will lead to substantial improvements to genome annotations.

Estrogen-Related Receptor Potential Target Genes in Silkworm (Bombyx mori): Insights into Metabolic Regulation

Estrogen-related receptors (ERRs) are important transcription factors within the nuclear receptor family that regulate cellular energy storage and consumption by binding to estrogen-related receptor response elements (ERREs) on gene promoters. While ERRs' role in vertebrates is well-studied, their molecular mechanisms in insect metabolism and development remain unclear. This study systematically summarizes the functions of ERRs in insects, focusing on silkworms by analyzing gene functions and comparing databases. ERRE-like elements were identified in the 2000 bp upstream promoter regions of 69 metabolism-related silkworm genes. Furthermore, electrophoretic mobility shift assays (EMSAs) revealed that ERREs within the promoters of 15 genes related to sugar, fat, and protein metabolism specifically bind to ERR. Notably, an ERRE in the promoter of the trehalose transporter 1 gene (BmTret1), crucial for trehalose homeostasis in insect hemolymph, exhibited significantly enhanced activity in ERR-overexpressing cells. These findings suggest that ERR is a potential regulatory factor in silkworm metabolism and refine its metabolic regulatory network. This study highlights the broader and more critical role of ERR in insects than that previously recognized, contributing to a deeper understanding of insect metabolism and its potential applications in related fields.

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

Suppression of meiotic crossovers in pericentromeric heterochromatin requires synaptonemal complex and meiotic recombination factors in Drosophila melanogaster

The centromere effect (CE) is a meiotic phenomenon that ensures meiotic crossover suppression in pericentromeric regions. Despite being a critical safeguard against nondisjunction, the mechanisms behind the CE remain unknown. Previous studies found that different regions of the Drosophila pericentromere, encompassing proximal euchromatin, beta, and alpha heterochromatin, undergo varying levels of crossover suppression, raising the question of whether distinct mechanisms establish the CE in different regions. We asked whether different pericentromeric regions respond differently to mutations that impair features that may play a role in the CE. In flies with a mutation that affects the synaptonemal complex (SC), a structure that is hypothesized to have roles in recombination and crossover patterning, we observed a redistribution of pericentromeric crossovers from proximal euchromatin towards beta heterochromatin but not alpha heterochromatin, indicating a role for the SC in suppressing crossovers in beta heterochromatin. In flies mutant for mei-218 or rec, which encode components of a critical pro-crossover complex, there was a more extreme redistribution of pericentromeric crossovers towards both beta and alpha heterochromatin, suggesting an important role for these meiotic recombination factors in suppressing heterochromatic crossovers. We mapped crossovers in flies mutant for Su(var)3-9, which encodes histone H3-lysine-9 methyltransferase. Although we expected strong alleviation of crossover suppression in heterochromatin, no changes in pericentromeric crossover distribution were observed in this mutant, indicating that this vital heterochromatin factor is dispensable for preventing crossovers in heterochromatin. Thus, in Drosophila. melanogaster the meiotic machinery seems to play a more significant role in suppressing centromere-proximal crossovers than chromatin state.

GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data

Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multispecies focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38 K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single-nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3 K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications. Database URL: https://oryza.gramene.org.

Genome editing in the green alga Chlamydomonas: past, present practice and future prospects

The green alga Chlamydomonas is an important and versatile model organism for research topics ranging from photosynthesis and metabolism, cilia, and basal bodies to cellular communication and the cellular cycle and is of significant interest for green bioengineering processes. The genome in this unicellular green alga is contained in 17 haploid chromosomes and codes for 16 883 protein coding genes. Functional genomics, as well as biotechnological applications, rely on the ability to remove, add, and change these genes in a controlled and efficient manner. In this review, the history of gene editing in Chlamydomonas is put in the context of the wider developments in genetics to demonstrate how many of the key developments to engineer these algae follow the global trends and the availability of technology. Building on this background, an overview of the state of the art in Chlamydomonas engineering is given, focusing primarily on the practical aspects while giving examples of recent applications. Commonly encountered Chlamydomonas-specific challenges, recent developments, and community resources are presented, and finally, a comprehensive discussion on the emergence and evolution of CRISPR/Cas-based precision gene editing is given. An outline of possible future paths for gene editing based on current global trends in genetic engineering and tools for gene editing is presented.

The Never Given 2022 Pittendrigh/Aschoff Lecture: The Clock Network in the Brain-Insights From Insects

My journey into chronobiology began in 1977 with lectures and internships with Wolfgang Engelmann and Hans Erkert at the University of Tübingen in Germany. At that time, the only known animal clock gene was Period, and the location and organization of the master circadian clock in the brain was completely unknown for the model insect Drosophila melanogaster. I was thus privileged to witness and participate in the research that led us from discovering the first clock gene to identifying the clock network in the fly brain and the putative pathways linking it to behavior and physiology. This article highlights my role in these developments and also shows how the successful use of D. melanogaster for studies of circadian rhythms has contributed to the understanding of clock networks in other animals. I also report on my experiences in the German scientific system and hope that my story will be of interest to some of you.

Systematic revelation and meditation on the significance of long exons using representative eukaryotic genomes

BACKGROUND

Long exons/introns are not evenly distributed in the genome, but the biological significance of this phenomenon remains elusive.

MATERIALS AND METHODS

Exon properties were analyzed in seven well-annotated reference genomes, including human and other representative model organisms: mouse, fruitfly, worm, mouse-ear cress, corn, and rice.

RESULTS

In all species, last exons in genes tend to be the longest. Additionally, we found that (1) canonical splicing motifs are strongly underrepresented in 3'UTR; (2) Last exons tend to have low GC content; (3) Comparing with other species, first exons in D. melanogaster genes demonstrate lower GC content than internal exons.

CONCLUSIONS

It cannot be excluded that last exons of genes exert essential regulatory roles and is subjected to natural selection, exhibiting differential splicing tendency, and GC content compared to other parts of the gene body.

A chromosomal-level genome assembly of Trichogramma chilonis Ishii, 1941 (Hymenoptera: Trichogrammatidae)

Trichogramma spp. is a genus of minute egg parasitoids frequently used in agricultural pest management that can feed on the eggs of various lepidopteran pests. Currently, there is a scarcity of high-quality genomic resources for this category of tiny parasitoids, which impedes our comprehension of the population evolution and parasitic ecology of this collective. In this case, a chromosome-level genome of Trichogramma chilonis was produced by integrating PacBio HiFi, Illumina, and Hi-C data. The genome size totals 202.48 Mb, with a scaffold N50 length of 40.00 Mb. A total of 98.59% (199.63 Mb) of contigs were effectively mapped onto five chromosomes. The BUSCO assessment revealed that the genome assembly achieved 98.1% (n = 1,367) completeness, with 95% representing single-copy BUSCOs and 3.1% duplicated BUSCOs. Also, the genome comprises 24.16% (48.91 Mb) repeat elements and 12,163 predicted protein-coding genes. The high-quality genome of T. chilonis presented in this study offers an invaluable asset for elucidating its evolutionary path and ecological interactions.

Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats

BACKGROUND

The Drosophila genus is ideal for studying genome evolution due to its relatively simple chromosome structure and small genome size, with rearrangements mainly restricted to within chromosome arms, such as Muller elements. However, work on the rapidly evolving repetitive genomic regions, composed of transposons and tandem repeats, have been hampered by the lack of genus-wide chromosome-level assemblies.

RESULTS

Integrating long-read genomic sequencing and chromosome capture technology, here we produce and annotate 30 chromosome-level genome assemblies within the Drosophila genus. Based on this dataset, we reveal the evolutionary dynamics of genome rearrangements across the Drosophila phylogeny, including the identification of genomic regions that show comparatively high structural stability throughout evolution. Moreover, within the ananassae subgroup, we uncover the emergence of new chromosome conformations and the rapid expansion of novel satellite DNA sequence families, which form large and continuous pericentromeric domains with higher-order repeat structures that are reminiscent of those observed in the human and Arabidopsis genomes.

CONCLUSIONS

These chromosome-level genome assemblies present a valuable resource for future research, the power of which is demonstrated by our analysis of genome rearrangements and chromosome evolution. In addition, based on our findings, we propose the ananassae subgroup as an ideal model system for studying the evolution of centromere structure.

In vitro and in vivo assessment of nanoceria biocompatibility for their safe use in nervous system applications

Nanoceria, or cerium dioxide nanoparticles (CeO2 NP), are increasingly employed in a number of industrial and commercial applications. Hence, the environmental presence of these nanoparticles is growing progressively, enhancing the global concern on their potential health effects. Recent studies suggest that nanoceria may also have promising biomedical applications particularly in neurodegenerative and brain-related pathologies, but studies addressing their toxicity, and specifically on the nervous system, are still scarce, and their potential adverse effects and action mechanism are not totally understood yet. The objective of this work was to assess the biological behaviour of CeO2 NP in vitro in human nervous systems cells, and in vivo in Drosophila melanogaster to characterize their safety for exposed individuals and verify their suitability to be further employed in diagnosis and treatment of nervous system disorders. Cell cycle alterations, late apoptosis rate and DNA damage (comet and γH2AX assays), were determined in neuronal SH-SY5Y and glial A172 cells treated with nanoceria. Moreover, the survival rate, morphological changes and behavioural alterations were analysed in D. melanogaster individuals chronically exposed to CeO2 NP. The results obtained from the in vitro assessment showed that the nanoceria generally presented a good biocompatibility with scarce cyto- or genotoxic effects, essentially depending the exposure time and cell type, and being restricted to the longer exposure periods. Nevertheless, decrease in adult size and alterations observed in the larval crawling in the in vivo assays highlight the need of further investigations before establishing clinical uses of nanoceria.

Neuroprotective Role of Cyclic AMP Signaling in Dopaminergic Degeneration Induced by a Parkinson's Disease Toxin, Rotenone

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by the selective loss of dopaminergic (DA) neurons in the midbrain. While dopamine precursor levodopa and D2 receptor agonists are commonly used to alleviate PD symptoms, these treatments do not halt or reverse disease progression. Thus, developing effective neuroprotective strategies remains a critical goal. In this study, we explored neuroprotective mechanisms in a Drosophila primary neuronal culture model of PD, created by administering the environmental toxin rotenone. Using the chemogenetic DREADD (designer receptors exclusively activated by designer drugs) system, we selectively activated cAMP signaling in DA neurons within the rotenone-induced model. Our results demonstrate that increasing cAMP signaling via Gs-coupled DREADD (rM3Ds) is protective against DA neurodegeneration. Furthermore, overexpression of the catalytic PKA-C1 subunit fully rescued DA neurons from rotenone-induced degeneration, with this effect restricted to DA neurons where PKA-C1 was specifically overexpressed. These findings reveal that cAMP-PKA signaling activation is neuroprotective in DA neurons against rotenone-induced degeneration, offering promising insights for developing targeted therapeutic strategies to slow or prevent PD pathology progression.

CrisprBuildr: an open-source application for CRISPR-mediated genome engineering in Drosophila melanogaster

CRISPR/Cas9 is a powerful tool for targeted genome engineering experiments. With CRISPR/Cas9, genes can be deleted or modified by inserting small peptides, fluorescent proteins or other tags for protein labelling experiments. Such experiments are important for detailed protein characterization in vivo. However, designing and cloning the corresponding constructs can be repetitive, time consuming and laborious. To aid users in CRISPR/Cas9-based genome engineering experiments, we built CrisprBuildr, a web-based application that allows users to delete genes or insert fluorescent proteins at the N- or C-terminus of their gene of choice. The application is built on the Drosophila melanogaster genome but can be used as a template for other available genomes. We have also generated new tagging vectors, using EGFP and mCherry combined with the small peptide SspB-Q73R for use in iLID-based optogenetic experiments. CrisprBuildr guides users through the process of designing guide RNAs and repair template vectors. CrisprBuildr is an open-source application and future releases could incorporate additional tagging or deletion vectors, genomes or CRISPR applications.

The Biphasic Effect of Lipopolysaccharide on Membrane Potential

Lipopolysaccharide (LPS) from certain strains of Gram-negative bacteria can induce a rapid (<1 s) hyperpolarization of membrane potential, followed by a gradual depolarization exceeding the initial resting membrane potential. Through overexpression of a Drosophila ORK1 two-pore-domain K+ channel (K2P) in larval muscles and altering the external concentrations of K+ and Na+ ions, it is clear that the hyperpolarization is due to activating K2P channels and the depolarization is due to promoting an inward Na+ leak. When the external Na+ concentration is negligible, the LPS-delayed depolarization is dampened. The hyperpolarization induced by LPS can exceed -100 mV when external K+ and Na+ concentrations are lowered. These results indicate direct action by LPS on ion channels independently of immune responses. Such direct actions may need to be considered when developing clinical treatments for certain forms of bacterial septicemia.

Zebrafish and Drosophila as Model Systems for Studying the Impact of Microplastics and Nanoplastics ‐ A Systematic Review

Microplastics and nanoplastics (MNPs) are byproducts of plastics created to benefit humanity, but improper disposal and inadequate recycling have turned them into a global menace that we can no longer conceal. As they interact with all living organisms, including humans, their mechanism of interaction and their perilous impact must be meticulously investigated. To uncover the secrets of MNPs, there must be model systems that exist to interlink the two major scenarios: they must represent the environmental impact and be relevant to humans. Therefore, zebrafish and Drosophila are perfect to describe these two cases, as they are well studied and relatable to humans. In this review, 39% zebrafish studies reported higher mortality and hatching rates at greater MNP concentrations, severe oxidative stress as seen by raised malondialdehyde (MDA) levels, and reduced superoxide dismutase (SOD) activity. About 50% of studies showed severe neurotoxic behavior with drop of locomotor activity, suggesting neurotoxicity. MNPs have a significant impact on fertility rate of Drosophila. More than half of the studies revealed genotoxicity in Drosophila as observed by wing spot assays and modified genomic expressions associated with stress and detoxification processes. These findings emphasize the potential of MNPs to bioaccumulate, impair physiological systems, and cause oxidative and neurobehavioral damage. This study underscores the importance for thorough risk evaluations of MNPs and their environmental and health consequences.

Molecular profiling of invertebrate glia

Caenorhabditis elegans and Drosophila melanogaster are powerful experimental models for uncovering fundamental tenets of nervous system organization and function. Findings over the last two decades show that molecular and cellular features are broadly conserved between invertebrates and vertebrates, indicating that insights derived from invertebrate models can broadly inform our understanding of glial operating principles across diverse species. In recent years, these model systems have led to exciting discoveries in glial biology and mechanisms of glia-neuron interactions. Here, we summarize studies that have applied current state-of-the-art "-omics" techniques to C. elegans and D. melanogaster glia. Coupled with the remarkable acceleration in the pace of mechanistic studies of glia biology in recent years, these indicate that invertebrate glia also exhibit striking molecular complexity, specificity, and heterogeneity. We provide an overview of these studies and discuss their implications as well as emerging questions where C. elegans and D. melanogaster are well-poised to fill critical knowledge gaps in our understanding of glial biology.

Role of the human cytochrome b561 family in iron metabolism and tumors (Review)

The human cytochrome b561 (hCytb561) family consists of electron transfer transmembrane proteins characterized by six conserved α-helical transmembrane domains and two β-type heme cofactors. These proteins contribute to the regulation of iron metabolism and numerous different physiological and pathological processes by recycling ascorbic acid and maintaining iron reductase activity. Key members of this family include cytochrome b561 (CYB561), duodenal CYB561 (Dcytb), lysosomal CYB561 (LCytb), stromal cell-derived receptor 2 (SDR2) and 101F6, which are widely expressed in human tissues and participate in the pathogenesis of several diseases and tumors. They are associated with the promotion or inhibition of tumor growth and progression in various malignancies and are potential therapeutic targets for malignant tumors. The present review summarizes the existing literature regarding the structure of the Cytb561 family, the basic functional characteristics of hCytb561 family members, and the roles of the CYB561, Dcytb, LCytb, SDR2 and 101F6 in various diseases and tumors.

Advances in Detection Methods for A-to-I RNA Editing

Adenosine-to-inosine (A-to-I) RNA editing is a key post-transcriptional modification that influences gene expression and various cellular processes. Advances in sequencing technologies have greatly contributed to the identification of A-to-I editing sites, providing insights into their distribution across coding and non-coding regions. These developments have facilitated the discovery of functionally relevant editing events and have advanced the understanding of their biological roles. This review presents the evolution of methodologies for RNA editing detection and examines recent advances, including chemically-assisted, enzyme-assisted, and quantitative approaches. By evaluating these techniques, we aim to help researchers select the most effective tools for investigating RNA editing and its broader implications in health and disease.

Nrf2 signaling pathway studies in Drosophila melanogaster: parallel roles in human health and insect environmental responses

The Nrf2 signalling pathway is crucial for cellular defense against oxidative stress and xenobiotic toxicity, highlighting its importance in both human health and environmental responses.This review focuses on the dual role of Drosophila melanogaster in Nrf2 research: we utilised the PubMed database to collect and summarised research articles on fruit fly Nrf2 studies published in the past decade, using keywords such as 'Nrf2', 'CncC', and 'Drosophila'.We found that Drosophila melanogaster, as a classical model organism for studying human diseases such as neurodegenerative disorders, cancers, and diabetes, and as an insect model for investigating xenobiotic responses and pesticide resistance, is particularly well-suited for exploring the diverse and complex functions of Nrf2 pathway.Additionally, Natural products such as curcumin and quercetin can modulate Nrf2 activity for cytoprotection. Utilising D. melanogaster's genetic tools and short life cycles, researchers can discover new therapeutics and study their mechanisms.This twofold exploration not only advances our understanding of Nrf2 in human health but also provides insights into pest control strategies through enhanced insect resistance mechanisms. Continued research in this area is essential for developing innovative treatments and effective pest management approaches.

Alternative Splicing as a Modulator of the Interferon-Gamma Pathway

Interferon-gamma (IFN-γ) is a critical cytokine that plays a pivotal role in immune system regulation. It is a key mediator of both cellular defense mechanisms and antitumor immunity. As the sole member of the type II interferon family, IFN-γ modulates immune responses by activating macrophages, enhancing natural killer cell function, and regulating gene expression across multiple cellular processes. Alternative splicing is a post-transcriptional gene expression regulatory mechanism that generates multiple mature messenger RNAs from a single gene, dramatically increasing proteome diversity without the need of a proportional genome expansion. This process occurs in 90-95% of human genes, with alternative splicing events allowing for the production of diverse protein isoforms that can have distinct-or even opposing-functional properties. Alternative splicing plays a crucial role in cancer immunology, potentially generating tumor neoepitopes and modulating immune responses. However, how alternative splicing affects IFN-γ's activity is still poorly understood. This review explores how alternative splicing regulates the expression and function of both upstream regulators and downstream effectors of IFN-γ, revealing complex mechanisms of gene expression and immune response modulation. Key transcription factors and signaling molecules of the IFN-γ pathway are alternatively spliced, and alternative splicing can dramatically alter IFN-γ signaling, immune cell function, and response to environmental cues. Specific splice variants can enhance or inhibit IFN-γ-mediated immune responses, potentially influencing cancer immunotherapy, autoimmune conditions, and infectious disease outcomes. The emerging understanding of these splicing events offers promising therapeutic strategies for manipulating immune responses through targeted molecular interventions.

Organismal complexity strongly correlates with the number of protein families and domains

In the pregenomic era, scientists were puzzled by the observation that haploid genome size (the C-value) did not correlate well with organismal complexity. This phenomenon, called the "C-value paradox," is mostly explained by the fact that protein-coding genes occupy only a small fraction of eukaryotic genomes. When the first genome sequences became available, scientists were even more surprised by the fact that the number of genes (G-value) was also a poor predictor of complexity, which gave rise to the "G-value paradox." The proposed explanations usually invoke mechanisms that increase the information content of each individual gene (protein-protein interactions, intrinsic disorder, posttranslational modifications, alternative splicing, etc.). Less attention has been paid to mechanisms that increase the amount of genetic material but do not increase (or not to the same extent) the amount of information encoded in the genome, such as gene duplication and domain shuffling. Proteins belonging to the same family and/or sharing the same domains often carry out similar or even redundant functions. We thus hypothesized that an organism's number of different protein families and domains should be suitable predictors of organismal complexity. In agreement with our hypothesis, we observed that the number of protein families, clans, domains, and motifs increases from simple to progressively more complex organisms. In addition, these metrics correlate with the number of cell types better than and independently of the number of protein-coding genes and several previously proposed predictors of organismal complexity. Our observations have the potential to represent a resolution to the G-value paradox.

High-throughput sequencing reveals the existence of a novel fucose binding lectin gene from the whole gut and fat body tissues of the grub of darkling beetle, Zophobas morio

Fucose binding lectins are a taxonomically, evolutionarily, and ecologically relevant class of lectins that have been identified among a wide range of taxa. These lectins possess a distinctive ability to identify and bind fucose-containing glycans, thereby lending them the ability to function as immune cell mitogens, diagnostic markers and anti-cancer agents. Our preliminary analysis revealed the existence of a single D-fucose binding lectin from the grub serum of the darkling beetle, Z. morio. Here, whole transcriptome analysis using entire gut and fat body tissues of grub of Z. morio with Illumina NovaSeq6000 sequencing platform revealed the existence of a novel fucose binding lectin (ZmFBL) displaying significant similarity to Diaphorina citri fucolectin-3 and possessing fucolectin-tachylectin4-pentraxin domain. Molecular docking between the structure of the predicted FBL transcript from Z. morio and D-fucose demonstrated the lowest binding energy of -5.4 kcal/mol. The MD simulation and MM/PBSA analysis furnished insights into the binding stability of D-fucose and the ZmFBL. A similar transcript was also identified from the fat body transcriptome. A 2.49-fold increase in the ZmFBL expression was observed in the fat body than the whole gut as evidenced from the relative quantitation using RT-PCR.

Review of Fish Neuropeptides: A Novel Perspective on Animal Welfare

Neuropeptides are highly variable but widely conserved molecules, the main functions of which are the regulation and coordination of physiological processes and behaviors. They are synthesized in the nervous system and generally act on other neuronal and non-neuronal tissues or organs. In recent years, diverse neuropeptide isoforms and their receptors have been identified in different fish species, regulating functions in the neuroendocrine (e.g., corticotropin-releasing hormone and arginine vasotocin), immune (e.g., vasoactive intestinal polypeptide and somatostatin), digestive (e.g., neuropeptide Y), and reproductive (e.g., isotocin) systems, as well as in the commensal microbiota. Interestingly, all these processes carried out by neuropeptides are integrated into the nervous system and are manifested externally in the behavior and affective states of fish, thus having an impact on the modulation of these actions. In this sense, the monitoring of neuropeptides may represent a new approach to assess animal welfare, targeting both physiological and affective aspects in fish. Therefore, although there are many studies investigating the action of neuropeptides in a wide range of paradigms, especially in mammals, their study within a fish welfare framework is scarce. To the best of our knowledge, this is the first review that gathers and integrates up-to-date information on neuropeptides from an animal welfare perspective. In this review, we summarize current findings on neuropeptides in fish and discuss their possible implication in the physiological and emotional state of fish, and therefore in their welfare.

A brief history of insect neuropeptide and peptide hormone research

This review briefly summarizes 50 years of research on insect neuropeptide and peptide hormone (collectively abbreviated NPH) signaling, starting with the sequencing of proctolin in 1975. The first 25 years, before the sequencing of the Drosophila genome, were characterized by efforts to identify novel NPHs by biochemical means, mapping of their distribution in neurons, neurosecretory cells, and endocrine cells of the intestine. Functional studies of NPHs were predominantly dealing with hormonal aspects of peptides and many employed ex vivo assays. With the annotation of the Drosophila genome, and more specifically of the NPHs and their receptors in Drosophila and other insects, a new era followed. This started with matching of NPH ligands to orphan receptors, and studies to localize NPHs with improved detection methods. Important advances were made with introduction of a rich repertoire of innovative molecular genetic approaches to localize and interfere with expression or function of NPHs and their receptors. These methods enabled cell- or circuit-specific interference with NPH signaling for in vivo assays to determine roles in behavior and physiology, imaging of neuronal activity, and analysis of connectivity in peptidergic circuits. Recent years have seen a dramatic increase in reports on the multiple functions of NPHs in development, physiology and behavior. Importantly, we can now appreciate the pleiotropic functions of NPHs, as well as the functional peptidergic "networks" where state dependent NPH signaling ensures behavioral plasticity and systemic homeostasis.

Lipophorin receptor knockdown reduces hatchability of kissing bug Rhodnius prolixus eggs

Lipophorin is the primary lipoprotein present in the hemolymph of insects, responsible for the lipids' transport between organs. It interacts with specific sites on cell membranes in an essential process for transferring lipids. The lipophorin receptor is the protein responsible for the interaction between lipophorin and cell membranes. In the kissing bug Rhodnius prolixus, much information on the interaction of lipophorin with organs is available. However, molecular data on the lipophorin receptor and its functions is still needed. Here, we explored lipophorin receptor gene expression and functions using a functional genomics approach. The R. prolixus genome encodes seven genes from the low-density lipoprotein receptor family, including a single ortholog of the lipophorin receptor. All organs analyzed (anterior and posterior midguts, fat body, ovaries, and flight muscle) expressed this gene. In the fat body, blood-feeding strongly reduced lipophorin receptor gene expression. Lipophorin receptor knockdown by RNA interference delayed egg laying and reduced the triacylglycerol in laid eggs without altering lipid stores in the fat body or lipid levels in the hemolymph. In the ovaries, lipophorin receptor knockdown reduces the expression of acetyl-CoA carboxylase and a fatty acid synthase while altered the gene expression profile in the fat body, causing an increase in the expression of carnitine palmitoyltransferase 1 and a reduction in Brummer lipase and vitellogenin 2. RNA interference treatment reduced the hatching of the eggs, causing the collapse and darkening of the laid eggs, in addition to the hatching of deformed first-stage nymphs. Furthermore, the structure of the chorion showed distortions in patterns and cracks and reduced hydrocarbon levels. These results show that the lipophorin receptor alone is not essential for lipid physiology in R. prolixus. However, this protein plays a fundamental role in the viability of eggs and, consequently, in insect reproduction.

Trithorax regulates long-term memory in Drosophila through epigenetic maintenance of mushroom body metabolic state and translation capacity

The role of epigenetics and chromatin in the maintenance of postmitotic neuronal cell identities is not well understood. Here, we show that the histone methyltransferase Trithorax (Trx) is required in postmitotic memory neurons of the Drosophila mushroom body (MB) to enable their capacity for long-term memory (LTM), but not short-term memory (STM). Using MB-specific RNA-, ChIP-, and ATAC-sequencing, we find that Trx maintains homeostatic expression of several non-canonical MB-enriched transcripts, including the orphan nuclear receptor Hr51, and the metabolic enzyme lactate dehydrogenase (Ldh). Through these key targets, Trx facilitates a metabolic state characterized by high lactate levels in MBγ neurons. This metabolic state supports a high capacity for protein translation, a process that is essential for LTM, but not STM. These data suggest that Trx, a classic regulator of cell type specification during development, has additional functions in maintaining underappreciated aspects of postmitotic neuron identity, such as metabolic state. Our work supports a body of evidence suggesting that a high capacity for energy metabolism is an essential cell identity characteristic for neurons that mediate LTM.

The Genomics Revolution Drives a New Era in Entomology

Thanks to the fast development of sequencing techniques and bioinformatics tools, sequencing the genome of an insect species for specific research purposes has become an increasingly popular practice. Insect genomes not only provide sets of gene sequences but also represent a change in focus from reductionism to systemic biology in the field of entomology. Using insect genomes, researchers are able to identify and study the functions of all members of a gene family, pathway, or gene network associated with a trait of interest. Comparative genomics studies provide new insights into insect evolution, addressing long-lasting controversies in taxonomy. It is also now feasible to uncover the genetic basis of important traits by identifying variants using genome resequencing data of individual insects, followed by genome-wide association analysis. Here, we review the current progress in insect genome sequencing projects and the application of insect genomes in uncovering the phylogenetic relationships between insects and unraveling the mechanisms of important life-history traits. We also summarize the challenges in genome data sharing and possible solutions. Finally, we provide guidance for fully and deeply mining insect genome data.

Exploiting fly models to investigate rare human neurological disorders

Rare neurological diseases, while individually are rare, collectively impact millions globally, leading to diverse and often severe neurological symptoms. Often attributed to genetic mutations that disrupt protein function or structure, understanding their genetic basis is crucial for accurate diagnosis and targeted therapies. To investigate the underlying pathogenesis of these conditions, researchers often use non-mammalian model organisms, such as Drosophila (fruit flies), which is valued for their genetic manipulability, cost-efficiency, and preservation of genes and biological functions across evolutionary time. Genetic tools available in Drosophila, including CRISPR-Cas9, offer a means to manipulate gene expression, allowing for a deep exploration of the genetic underpinnings of rare neurological diseases. Drosophila boasts a versatile genetic toolkit, rapid generation turnover, and ease of large-scale experimentation, making it an invaluable resource for identifying potential drug candidates. Researchers can expose flies carrying disease-associated mutations to various compounds, rapidly pinpointing promising therapeutic agents for further investigation in mammalian models and, ultimately, clinical trials. In this comprehensive review, we explore rare neurological diseases where fly research has significantly contributed to our understanding of their genetic basis, pathophysiology, and potential therapeutic implications. We discuss rare diseases associated with both neuron-expressed and glial-expressed genes. Specific cases include mutations in CDK19 resulting in epilepsy and developmental delay, mutations in TIAM1 leading to a neurodevelopmental disorder with seizures and language delay, and mutations in IRF2BPL causing seizures, a neurodevelopmental disorder with regression, loss of speech, and abnormal movements. And we explore mutations in EMC1 related to cerebellar atrophy, visual impairment, psychomotor retardation, and gain-of-function mutations in ACOX1 causing Mitchell syndrome. Loss-of-function mutations in ACOX1 result in ACOX1 deficiency, characterized by very-long-chain fatty acid accumulation and glial degeneration. Notably, this review highlights how modeling these diseases in Drosophila has provided valuable insights into their pathophysiology, offering a platform for the rapid identification of potential therapeutic interventions. Rare neurological diseases involve a wide range of expression systems, and sometimes common phenotypes can be found among different genes that cause abnormalities in neurons or glia. Furthermore, mutations within the same gene may result in varying functional outcomes, such as complete loss of function, partial loss of function, or gain-of-function mutations. The phenotypes observed in patients can differ significantly, underscoring the complexity of these conditions. In conclusion, Drosophila represents an indispensable and cost-effective tool for investigating rare neurological diseases. By facilitating the modeling of these conditions, Drosophila contributes to a deeper understanding of their genetic basis, pathophysiology, and potential therapies. This approach accelerates the discovery of promising drug candidates, ultimately benefiting patients affected by these complex and understudied diseases.

Studying Cellular Senescence Using the Model Organism Drosophila melanogaster

Cellular senescence, a complex biological process characterized by irreversible cell cycle arrest, contributes significantly to the development and progression of aging and of age-related diseases. Studying cellular senescence in vivo can be challenging due to the high heterogeneity and dynamic nature of senescent cells. Recently, Drosophila melanogaster has emerged as a powerful model organism for studying aging and cellular senescence due to its tractability and short lifespan, as well as due to the conservation of age-related genes and of key age-related pathways with mammals. Consequently, several research studies have utilized Drosophila to investigate the cellular mechanisms and pathways implicated in cellular senescence. Herein, we provide an overview of the assays that can be applied to study the different features of senescent cells in D. melanogaster tissues, highlighting the benefits of this model in aging research. We also emphasize the importance of selecting appropriate biomarkers for the identification of senescent cells, and the need for further understanding of the aging process including a more accurate identification and detection of senescent cells at the organismal level; a far more complex process as compared to single cells.

Animal-based approaches to understanding neuroglia physiology in vitro and in vivo

This chapter describes the pivotal role of animal models for unraveling the physiology of neuroglial cells in the central nervous system (CNS). The two rodent species Mus musculus (mice) and Rattus norvegicus (rats) have been indispensable in scientific research due to their remarkable resemblance to humans anatomically, physiologically, and genetically. Their ease of maintenance, short gestation times, and rapid development make them ideal candidates for studying the physiology of astrocytes, oligodendrocyte-lineage cells, and microglia. Moreover, their genetic similarity to humans facilitates the investigation of molecular mechanisms governing neural physiology. Mice are largely the predominant model of neuroglial research, owing to advanced genetic manipulation techniques, whereas rats remain invaluable for applications requiring larger CNS structures for surgical manipulations. Next to rodents, other animal models, namely, Danio rerio (zebrafish) and Drosophila melanogaster (fruit fly), will be discussed to emphasize their critical role in advancing our understanding of glial physiology. Each animal model provides distinct advantages and disadvantages. By combining the strengths of each of them, researchers can gain comprehensive insights into glial function across species, ultimately promoting the understanding of glial physiology in the human CNS and driving the development of novel therapeutic interventions for CNS disorders.

Suppression of meiotic crossovers in pericentromeric heterochromatin requires synaptonemal complex and meiotic recombination factors in Drosophila melanogaster

The centromere effect (CE) is a meiotic phenomenon that ensures meiotic crossover suppression in pericentromeric regions. Despite being a critical safeguard against nondisjunction, the mechanisms behind the CE remain unknown. Previous studies have shown that various regions of the Drosophila pericentromere, encompassing proximal euchromatin, beta and alpha heterochromatin, undergo varying levels of crossover suppression, raising the question of whether distinct mechanisms establish the CE in these different regions. To address this question, we asked whether different pericentromeric regions respond differently to mutations that impair various features that may play a role in the CE. In flies with a mutation that affects the synaptonemal complex (SC), a structure is hypothesized to have important roles in recombination and crossover patterning, we observed a significant redistribution of pericentromeric crossovers from proximal euchromatin towards beta heterochromatin but not alpha heterochromatin, indicating a role for the SC in suppressing crossovers in beta heterochromatin. In flies mutant for mei-218 or rec, which encode components of a critical pro-crossover complex, there was a more extreme redistribution of pericentromeric crossovers towards both beta and alpha heterochromatin, suggesting an important role for these meiotic recombination factors in suppressing heterochromatic crossovers. Lastly, we mapped crossovers in flies mutant for Su(var)3-9. Although we expected a strong alleviation of crossover suppression in heterochromatic regions, no changes in pericentromeric crossover distribution were observed in this mutant, indicating that this vital heterochromatin factor is dispensable to prevent crossovers in heterochromatin. Our results indicate that the meiotic machinery plays a bigger role in suppressing crossovers than the chromatin state.

Primate Phenotypes: A Multi-Institution Collection of 3D Morphological Data Housed in MorphoSource

The field of phenomics is experiencing unprecedented advances thanks to the rapid growth of morphological quantification based on three-dimensional (3D) imaging, online data repositories, team-oriented collaborations, and open data-sharing policies. In line with these progressions, we present an extensive primate phenotypic dataset comprising >6,000 3D scans (media) representing skeletal morphologies of 386 individual specimens covering all hominoid genera (except humans) and other selected primates. The digitized specimens are housed in physical collections at the American Museum of Natural History, the National Museum of Natural History, the Royal Museum for Central Africa (Belgium), the Cleveland Museum of Natural History, and Stony Brook University. Our technical validation indicates that despite the diverse digitizing devices used to produce the scans, the final 3D models (meshes) can be safely combined to collect comparable morphometric data. The entire dataset (and detailed associated metadata) is freely available through MorphoSource. Hence, these data contribute to empowering the future of primate phenomics and providing a roadmap for future digitization and archiving of digital data from other collections.

Genome-wide phylogenetic analysis and expansion of gene families involved in detoxification in Smittia aterrima (Meigen)and Smittia pratorum (Goetghebuer) (Diptera, Chironomidae)

Smittia aterrima (Meigen, 1818) and Smittia pratorum (Goetghebuer, 1927) are important indicator insects for aquatic environments, showing extensive tolerance to the environment. However, the genome-wide phylogenetic relationships and characteristics of the detoxification mechanisms in S. aterrima and S. pratorum remain unclear. Based on the genomes of the two species obtained in our preliminary studies and nine genomes from the NCBI database, we found that chironomids diverged from other mosquitoes approximately 200 million years ago (MYA), and S. aterrima and S. pratorum diverged about 30 MYA according to phylogenetic analysis. Gene family evolution analysis showed significant expansion of 43 and 15 gene families in S. aterrima and S. pratorum, respectively, particularly those related to detoxification pathways. Positive selection analysis reveals that genes under positive selection are crucial for promoting environmental adaptation. Additionally, the detoxification-associated gene families including Cytochrome P450 (CYP), Glutathione S-transferases (GST), ATP-binding cassette (ABC), carboxylesterase (CCE), and UDP-glucuronosyltransferase (UGT) were annotated. Our analysis results show that these five detoxification gene families have significantly expanded in the chironomid genomes. This study highlights the genome evolution of chironomids and their responses to mechanisms of tolerance to environmental challenges.

Caspar specifies primordial germ cell count and identity in Drosophila melanogaster

Repurposing of pleiotropic factors during execution of diverse cellular processes has emerged as a regulatory paradigm. Embryonic development in metazoans is controlled by maternal factors deposited in the egg during oogenesis. Here, we explore maternal role(s) of Caspar (Casp), the Drosophila orthologue of human Fas-associated factor-1 (FAF1) originally implicated in host-defense as a negative regulator of NF-κB signaling. Maternal loss of either Casp or it's protein partner, transitional endoplasmic reticulum 94 (TER94) leads to partial embryonic lethality correlated with aberrant centrosome behavior, cytoskeletal abnormalities, and defective gastrulation. Although ubiquitously distributed, both proteins are enriched in the primordial germ cells (PGCs), and in keeping with the centrosome problems, mutant embryos display a significant reduction in the PGC count. Moreover, the total number of pole buds is directly proportional to the level of Casp. Consistently, it's 'loss' and 'gain' results in respective reduction and increase in the Oskar protein levels, the master determinant of PGC fate. To elucidate this regulatory loop, we analyzed several known components of mid-blastula transition and identify the translational repressor Smaug, a zygotic regulator of germ cell specification, as a potential critical target. We present a detailed structure-function analysis of Casp aimed at understanding its novel involvement during PGC development.

The fruit fly Drosophila melanogaster as a screening model for antiseizure medications

Objective

Resistance to antiseizure medications (ASMs) is a major challenge in the treatment of patients with epilepsy. Despite numerous newly marketed ASMs, the proportion of drug-resistant people with epilepsy has not significantly decreased over the years. Therefore, novel and innovative seizure models for preclinical drug screening are highly desirable. Here, we explore the efficacy of a broad spectrum of ASMs in suppressing seizure activity in two established Drosophila melanogaster bang-sensitive mutants. These mutants respond with seizures to mechanical stimulation, providing a promising platform for screening novel ASMs.

Methods

Seven frequently used ASMs (brivaracetam, cenobamate, lacosamide, lamotrigine, levetiracetam, phenytoin, and valproate) were administered to the bang-sensitive mutants easily shocked 2F (eas 2F ) and paralytic bss1 (para bss1 ). After 48 h of treatment, the flies were vortexed to induce mechanical stimulation. The seizure probability (i.e., ratio of seizing and non-seizing flies) as well as the seizure duration were analyzed.

Results

In case of eas 2F mutants, treatment with the sodium channel blockers phenytoin and lamotrigine resulted in a robust reduction of seizure probability, whereas flies treated with lacosamide showed a decrease in seizure duration. Treatment with valproate resulted in both a reduction in seizure probability and in seizure duration. In contrast, levetiracetam, brivaracetam and cenobamate had no effect on the bang-sensitive phenotype of eas 2F flies. In case of para bss1 flies, none of the tested medications significantly reduced seizure activity, supporting its role as a model of intractable epilepsy.

Significance

Our results show that particularly sodium channel blockers as well as valproate are effective in suppressing seizure activity in the bang-sensitive mutant eas 2F . These findings demonstrate the usability of Drosophila for screening drugs with antiseizure properties. Due to fewer ethical concerns, the short life cycle, and low maintenance costs, Drosophila might provide an attractive and innovative high-throughput model for the discovery of novel antiseizure compounds.

The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration

Distinctive molecular approaches and tools, particularly high-throughput SNP genotyping, have been applied to determine and discover SNPs, potential genes of interest, indicators of evolutionary selection, genetic abnormalities, molecular indicators, and loci associated with quantitative traits (QTLs) in various livestock species. These methods have also been used to obtain whole-genome sequencing (WGS) data, enabling the implementation of genomic selection. Genomic selection allows for selection decisions based on genomic-estimated breeding values (GEBV). The estimation of GEBV relies on the calculation of SNP effects using prediction equations derived from a subset of individuals in the reference population who possess both SNP genotypes and phenotypes for target traits. Compared to traditional methods, modern genomic selection methods offer advantages for sex-limited traits, low heritability traits, late-measured traits, and the potential to increase genetic gain by reducing generation intervals. The current availability of high-density genotyping and next-generation sequencing data allow for genome-wide scans for selection. This investigation provides an overview of the essential role of advanced molecular tools in studying genetic diversity and implementing genomic selection. It also highlights the significance of adaptive selection in light of new high-throughput genomic technologies and the establishment of selective comparisons between different genomes. Moreover, this investigation presents candidate genes and QTLs associated with various traits in different livestock species, such as body conformation, meat production and quality, carcass characteristics and composition, milk yield and composition, fertility, fiber production and characteristics, and disease resistance.

Functional Roles of Five Cytochrome P450 Transcripts in the Susceptibility of the Yellow Fever Mosquito to Pyrethroids Revealed by RNAi Coupled With Insecticide Bioassay

We evaluated the possible roles of five cytochrome P450 transcripts in the susceptibility of both adults and larvae of Aedes aegypti to three pyrethroids using RNA interference (RNAi) coupled with insecticide bioassays. RNAi by feeding larvae with chitosan/dsRNA nanoparticles led to reductions of CYP6AA5, CYP6AL1, CYP9J32, CYP4J16A, and CYP4J16B transcripts by 38.7%, 46.0%, 46.52%, 44.0%, and 41.0%, respectively, and increased larval mortality by 46.0% to permethrin when CYP9J32 was silenced and by 41.2% to cypermethrin when CYP6AA5 was silenced. RNAi by injecting dsRNA in adults led to reductions of CYP6AA5, CYP6AL1, and CY4J16A transcripts by 77.9%, 80.0%, and 87.1% (p < 0.05), respectively, at 96 h and reduction of CYP9J32 transcript by 46.5% at 24 h after injection. In contrast, CYP4J16B was repressed by 78.2% at 72 h after injection. Exposure of the adults injected with CYP6AA5 dsRNA resulted in 1.5- to 2.0-fold increased susceptibility to cypermethrin as compared with the control. Homology modeling of CYP6AA5 followed by ligand docking showed that distances between the heme iron and the putative aromatic hydroxylation site were 9.2, 7.2, and 9.1 Å for permethrin, cypermethrin, and deltamethrin, respectively. For the aliphatic hydroxylation site, these distances were 5.3, 4.9, and 3.1 Å. These results supported that CYP6AA5 may be able to metabolize cypermethrin preferentially by aliphatic hydroxylation as indicated by the close interaction with the heme iron. Our study also suggests that the detoxification roles of cytochrome P450 genes in A. aegypti may vary according to the mosquito developmental stages, cytochrome P450 genes, and insecticides.

Harnessing Simple Animal Models to Decode Sleep Mysteries

Whether it involves human subjects or non-human animals, basic, translational, or clinical sleep research poses significant ethical challenges for researchers and ethical committees alike. Sleep research greatly benefits from using diverse animal models, each offering unique insights into sleep control mechanisms. The fruit fly (Drosophila melanogaster) is a superior genetic model due to its quick generation period, large progenies, and rich genetic tools. Its well-characterized genome and ability to respond to hypnotics and stimulants make it an effective tool for studying sleep genetics and physiological foundations. The nematode (Caenorhabditis elegans) has a simpler neural organization and transparent body, allowing researchers to explore molecular underpinnings of sleep control. Vertebrate models, like zebrafish (Danio rerio), provide insights into circadian rhythm regulation, memory consolidation, and drug effects on sleep. Invertebrate models, like California sea hare (Aplysia californica) and Upside-down jellyfish (Cassiopea xamachana), have simpler nervous systems and behave similarly to humans, allowing for the examination of sleep principles without logistical and ethical challenges. Combining vertebrate and invertebrate animal models offers a comprehensive approach to studying sleep, improving our understanding of sleep regulation and potentially leading to new drug discovery processes for sleep disorders and related illnesses.

Ozone induced multigenerational glucose and lipid metabolism disorders in Drosophila

Ozone (O3), a persistent pollutant, poses a significant health threat. However, research on its multigenerational toxicity remains limited. Leveraging the Drosophila model with its short lifespan and advanced genetic tools, we explored the effects of O3 exposure across three generations of fruit flies. The findings revealed that O3 disrupted motility, body weight, stress resistance, and oxidative stress in three generations of flies, with varying effects observed among them. Transcriptome analysis highlighted the disruption of glucose metabolism-related pathways, encompassing gluconeogenesis/glycolysis, galactose metabolism, and carbon metabolism. Hub genes were identified, and RT-qPCR results indicated that O3 decreased their transcription levels. Comparative analysis of their human orthologs was conducted using Comparative Toxicogenomics Database (CTD) and DisGeNET databases. These genes are linked to various metabolic diseases, including diabetes, hypoglycemia, and obesity. The trehalose content was reduced in F0 generation flies but increased in F1-F2 generations after O3 exposure. While the trehalase and glucose levels were decreased across F0-F2 generations. TAG synthesis-related genes were significantly upregulated in F0 generation flies but downregulated in F1-F2 generations. The expression patterns of lipolysis-related genes varied among the three generations of flies. Food intake was increased in F0 generation flies but decreased in F1-F2 generations. Moreover, TAG content was significantly elevated in F0 generation flies by O3 exposure, while it was reduced in F2 generation flies. These differential effects of O3 across three generations of flies suggest a metabolic reprogramming aimed at mitigating the damage caused by O3 to flies. The study affirms the viability of employing the Drosophila model to investigate the mechanisms underlying O3-induced glucose and lipid metabolism disorders while emphasizing the importance of studying the long-term health effects of O3 exposure. Moreover, this research highlights the Drosophila model as a viable tool for investigating the multigenerational effects of pollutants, particularly atmospheric pollutants.

The chromosome folding problem and how cells solve it

Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.

Aging impaired locomotor and biochemical activities in Drosophila melanogaster Oregon R (fruit fly) model

Despite advancements in healthcare and increased lifespan, aging populations face numerous challenges, including declining cognitive function, increased susceptibility to chronic diseases, and reduced quality of life. This study investigated Aging impaired Locomotors and Biochemical Activities in Drosophila melanogaster Oregon R (Fruit Fly) Model with the aim to elucidate the mechanism involved. Adult wild-type Drosophila melanogaster Oregon R was used for this study. Survival assay, antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), reduced glutathione (GSH) and malondialdehyde (MDA)) and total protein (TP) concentration were investigated. Data obtained were analyzed using R studio and GraphPad Prism. The result indicated low survival in male flies compared to female flies and the highest survival rate was observed with both flies reared together in the same vial. There was impaired locomotor activity in the flies with age. There was a significant decrease in the level of SOD, CAT, GSH and TP with age with a corresponding significant increase in the level of MDA. This finding demonstrated that locomotor activity decreased with aging with decrease performance index and also established the involvement of oxidation through the activities of antioxidant enzymes in aging; decreased (p < 0.05) concentration of antioxidant enzymes and increased (p < 0.05) lipid peroxidation. Also, it demonstrated that female species had longer lifespan compared to males while co-habiting of male and female species extended lifespan.

Acute lipopolysaccharide (LPS)-induced cell membrane hyperpolarization is independent of voltage gated and calcium activated potassium channels

The gram-negative toxin lipopolysaccharides (LPS) are known to trigger inflammatory cytokines in mammals, which can result in pathological responses. Upon treatment of bacterial sepsis with antibiotics, the lysing bacteria can present a surge in LPS, inducing a cytokine storm. However, LPS can also have direct cellular effects, including transient rapid hyperpolarizing of the membrane potential, blocking glutamate receptors and even promoting release of glutamate. The detailed mechanism of action for these immediate responses is still unresolved. In addressing the membrane hyperpolarization, voltage gated K+ channel blockers 4-aminopyridine (4-AP, 3 mM), quinidine hydrochloride monohydrate (0.1 mM) and tetraethylammonium (TEA, 20 mM) were examined along with RNAi knockdowns of potential calcium activated K+ channels. The immediate responses of LPS were not blocked. Even in the presence of glutamate, the membrane still hyperpolarizes with LPS. When the driving gradient for the ionotropic glutamate receptors is enhanced during hyperpolarization, spontaneous quantal responses are dampened in amplitude. Thus, glutamate receptors are blocked, and the mechanism of hyperpolarization remains unresolved. The larval Drosophila glutamatergic neuromuscular junction is used as a model synaptic preparation to address the direct rapid actions by LPS.

Chronic trans fatty acid consumption shortens lifespan in male Drosophila melanogaster on a high-sugar and high-fat diet

Aging entails the progressive decline in the body's self-regulation and functionality over time. Notably, obesity and aging exhibit parallel phenotypes, with obesity further accelerating the aging process across multiple dimensions and diminishing lifespan. In this study, we explored the impact of trans fatty acid (TFA) consumption on the overall health and lifespan of male Drosophila melanogaster under an isocaloric high-sugar and high-fat diet. Our results indicate that TFA intake results in a shortened lifespan, elevated body weight, and increased triglyceride levels in flies fed a high-sugar and high-fat diet with equivalent caloric intake. Additionally, TFA exposure induces oxidative stress, locomotor deficits, and damage to the intestinal barrier in flies. Collectively, chronic TFA consumption expedites the aging process and reduces the lifespan of male Drosophila melanogaster. These results contribute supplementary evidence regarding the adverse health effects associated with TFAs.

The effects of doxapram and its potential interactions with K2P channels in experimental model preparations

The channels commonly responsible for maintaining cell resting membrane potentials are referred to as K2P (two-P-domain K+ subunit) channels. These K+ ion channels generally remain open but can be modulated by their local environment. These channels are classified based on pharmacology, pH sensitivity, mechanical stretch, and ionic permeability. Little is known about the physiological nature of these K2P channels in invertebrates. Acidic conditions depolarize neurons and muscle fibers, which may be caused by K2P channels given that one subtype can be blocked by acidic conditions. Doxapram is used clinically as a respiratory aid known to block acid-sensitive K2P channels; thus, the effects of doxapram on the muscle fibers and synaptic transmission in larval Drosophila and crawfish were monitored. A dose-dependent response was observed via depolarization of the larval Drosophila muscle and an increase in evoked synaptic transmission, but doxapram blocked the production of action potentials in the crawfish motor neuron and had a minor effect on the resting membrane potential of the crawfish muscle. This indicates that the nerve and muscle tissues in larval Drosophila and crawfish likely express different K2P channel subtypes. Since these organisms serve as physiological models for neurobiology and physiology, it would be of interest to further investigate what types of K2P channel are expressed in these tissues. (212 words).

Differential regulation of sleep by blue, green, and red light in Drosophila melanogaster

Introduction

Exposure to blue-enriched light from electronic devices is an emergent disruptor of human sleep, especially at particular times of day. Further dissection of this phenomenon necessitates modeling in a tractable model organism.

Methods

Thus, we investigated the effects of light color on sleep in Drosophila melanogaster. We measured sleep in red-eyed Canton-S (CS) and white-eyed w 1118 flies in baseline 12:12 light/dark conditions and experimental conditions with light-color (blue, red, or green) exposure for all 12 h of daylight or 3 h in the morning or evening.

Results

Blue light reduced daytime and nighttime sleep in CS but not in w 1118, potentially indicating a role for the compound eye in blue light's effects on fruit fly sleep. Red light, especially in the evening, reduced sleep during exposure in both strains. Green light had minimal effects on sleep in CS flies, but evening exposure reduced sleep in w 1118 flies, mimicking red light's effects.

Discussion

In conclusion, light's effects on sleep in D. melanogaster are dependent on wavelength and time-of-day. Future studies will aim to dissect these mechanisms genetically.

Chromosome-level genome assembly of Cyamophila willieti (Hemiptera: Psyllidae)

Cyamophila willieti (Hemiptera: Psyllidae) is a significant pest that adversely affects the growth of Styphnolobium japonicum and its variant, Styphnolobium japonicum f. pendula. Despite its impact, research on this species remains limited. In this study, we successfully assembled a chromosome-level genome for Cyamophila willieti using a comprehensive approach that integrated Illumina sequencing, PacBio sequencing, and Hi-C technology. The genome size was determined to be 361.61 Mb, with a scaffold N50 length of 28.90 Mb. Additionally, the genome was mapped to 13 chromosomes (N = 12 A + X), and a total of 15,841 genes were predicted, with 90.38% of them functionally annotated. In summary, the high-quality genome of Cyamophila willieti provides valuable data to support further research, including pest management strategies.