Exploring the antifungal potential of novel carbazate derivatives as promising drug candidates against emerging superbug, Candida auris.

Candida auris (C. auris) has caused notable outbreaks across the globe in last decade and emerged as a life-threatening human pathogenic fungus. Despite significant advances in antifungal research, the drug resistance mechanisms in C. auris still remain elusive. Under such pressing circumstances, research on identification of new antifungal compounds is of immense interest. Thus, our studies aimed at identifying novel drug candidates and elucidate their biological targets in C. auris. After screening of several series of synthetic and hemisynthetic compounds from JUNIA chemical library, compounds C4 (butyl 2-(4-chlorophenyl)hydrazine-1-carboxylate) and C13 (phenyl 2-(4-chlorophenyl) hydrazine-1-carboxylate), belonging to the carbazate series, were identified to display considerable antifungal activities against C. auris as well as its fluconazole resistant isolates. Elucidation of biological targets revealed that C4 and C13 lead to changes in polysaccharide composition of the cell wall and disrupt vacuole homeostasis. Mechanistic insights further unravelled inhibited efflux pump activities of ATP binding cassette transporters and depleted ergosterol content. Additionally, C4 and C13 cause mitochondrial dysfunction and confer oxidative stress. Furthermore, both C4 and C13 impair biofilm formation in C. auris. The in vivo efficacy of C4 and C13 were demonstrated in Caenorhabditis elegans model after C. auris infection showing reduced mortality of the nematodes. Together, promising antifungal properties were observed for C4 and C13 against C. auris that warrant further investigations. To summarise, collected data pave the way for the design and development of future first-in-class antifungal drugs.

The food-borne carcinogenic 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) disrupts circadian rhythms and ameliorated by pterostilbene (PSB) in Caenorhabditis elegans.

The food-borne 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a potential human carcinogen abundant in cooked meat. While circadian rhythms are crucial biological oscillations, the negative impact of PhIP on circadian systems and the potential of mitigation remain underexplored. We investigated the effects of PhIP on circadian rhythms and the mitigating effects of the phytochemical antioxidant pterostilbene (PSB) in Caenorhabditis elegans. We show that exposure to 10 µM PhIP disrupts the 24-h circadian rhythms of C. elegans, an effect mitigated by co-exposure to 100 µM PSB. In addition, PhIP-induced circadian disruption can be linked to defective oxidative stress resistance, which is associated with the DAF-16/FOXO pathway and is modulated by PSB. Molecular docking suggested that PhIP and PSB bind similarly to DAF-16. Moreover, 10 µM PhIP abolished the rhythmic expression of the core clock gene prdx-2, which is restored by 100 µM PSB. Findings from this study provide novel insight of how food-borne contaminant like PhIP may contribute to the disruption of circadian rhythms and suggest potential for PSB to mitigate these effects in higher organisms.

Transcriptomic analysis of the spatiotemporal axis of oogenesis and fertilization in C. elegans.

Caenorhabditis elegans hermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene region, the diplotene region, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq (scRNA-seq) protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the gonad and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we delineate transcripts that may serve functions in the interactions between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon.

Mechanical force of uterine occupation enables large vesicle extrusion from proteostressed maternal neurons.

Large vesicle extrusion from neurons may contribute to spreading pathogenic protein aggregates and promoting inflammatory responses, two mechanisms leading to neurodegenerative disease. Factors that regulate the extrusion of large vesicles, such as exophers produced by proteostressed C. elegans touch neurons, are poorly understood. Here, we document that mechanical force can significantly potentiate exopher extrusion from proteostressed neurons. Exopher production from the C. elegans ALMR neuron peaks at adult day 2 or 3, coinciding with the C. elegans reproductive peak. Genetic disruption of C. elegans germline, sperm, oocytes, or egg/early embryo production can strongly suppress exopher extrusion from the ALMR neurons during the peak period. Conversely, restoring egg production at the late reproductive phase through mating with males or inducing egg retention via genetic interventions that block egg-laying can strongly increase ALMR exopher production. Overall, genetic interventions that promote ALMR exopher production are associated with expanded uterus lengths and genetic interventions that suppress ALMR exopher production are associated with shorter uterus lengths. In addition to the impact of fertilized eggs, ALMR exopher production can be enhanced by filling the uterus with oocytes, dead eggs, or even fluid, supporting that distention consequences, rather than the presence of fertilized eggs, constitute the exopher-inducing stimulus. We conclude that the mechanical force of uterine occupation potentiates exopher extrusion from proximal proteostressed maternal neurons. Our observations draw attention to the potential importance of mechanical signaling in extracellular vesicle production and in aggregate spreading mechanisms, making a case for enhanced attention to mechanobiology in neurodegenerative disease.

Neurons are specialized cells in the brain and nervous system that transmit signals between the brain and the rest of the body, enabling humans and animals to react to internal and external stimuli. For this communication system to function effectively, neurons must remain healthy. Neurons maintain their function in a variety of ways, including by removing excess or damaged cellular components (such as organelles and protein aggregates) that could compromise neuron function. One way to do this is by extruding organelles and aggregates. During 'extrusion events', the material to be removed is gathered within a budding portion of the plasma membrane, which forms a vesicle that ejects the material from the neuron. However, the factors driving the extrusion process remained unknown. To investigate, Wang, Guasp, Salam et al. conducted experiments in the roundworm Caenorhabditis elegans, finding that the number of extrusion events in a certain type of neuron increases at the peak of reproduction. More specifically, a greater number of extrusion events were associated with the presence of fertilized eggs, which accumulate in the uterus before they are laid. Disrupting eggs, sperm or the fertilization process suppressed the increase in extrusion events, suggesting the presence of fertilized eggs is responsible. To determine how the eggs might trigger extrusion events, Wang et al. stretched the uterus using dead eggs, unfertilized eggs or by injecting fluid, finding that each of these approaches increased the number of extrusion events. Further analysis suggests that this mechanical stretching of the uterus signals to the neurons that reproduction has started, encouraging the neurons to remove old components and optimize their function. Wang et al. hypothesize that this stretch response could support neuronal behaviors that aid in successful reproduction, such as sensing food and selecting where to lay eggs. The findings increase our understanding of the factors that trigger vesicle extrusion in living organisms. These observations could have implications for human neurodegenerative diseases such as Alzheimer's disease, in which protein aggregates accumulate in neurons. It is possible that mechanical signals generated by factors associated with Alzheimer's disease, such as high blood pressure, could influence neuronal extrusion and contribute to some of the mechanisms underlying aggregate transfer in neurodegenerative diseases.

Subcellular context-specific tuning of actomyosin ring contractility within a common cytoplasm.

The non-muscle actomyosin cytoskeleton generates contractile force through the dynamic rearrangement of its constituent parts. Actomyosin rings are a specialization of the non-muscle actomyosin cytoskeleton that drive cell shape changes during division, wound healing, and other events. Contractile rings throughout phylogeny and in a range of cellular contexts are built from conserved components including non-muscle myosin II (NMMII), actin filaments (F-actin), and crosslinking proteins. However, it is unknown whether diverse actomyosin rings close via a single unifying mechanism. To explore how contractile forces are generated by actomyosin rings, we studied three instances of ring closure within the common cytoplasm of the C. elegans oogenic germline: mitotic cytokinesis of germline stem cells (GSCs), apoptosis of meiotic compartments, and cellularization of oocytes. We found that each ring type closed with unique kinetics, protein density and abundance dynamics. These measurements suggested that the mechanism of contractile force generation varied across the subcellular contexts. Next, we formulated a physical model that related the forces generated by filament-filament interactions to the material properties of these rings that dictate the kinetics of their closure. Using this framework, we related the density of conserved cytoskeletal proteins anillin and NMMII to the kinematics of ring closure. We fitted model rings to in situ measurements to estimate parameters that are currently experimentally inaccessible, such as the asymmetric distribution of protein along the length of F-actin, which occurs naturally due to differences in the dimensions of the crosslinker and NMMII filaments. Our work predicted that the role of NMMII varies across these ring types, due in part to its distribution along F-actin and motoring. Our model also predicted that the degree of contractility and the impact of ring material properties on contractility differs among ring types.

WormCNN-Assisted Establishment and Analysis of Glycation Stress Models in C. elegans: Insights into Disease and Healthy Aging.

Glycation Stress (GS), induced by advanced glycation end-products (AGEs), significantly impacts aging processes. This study introduces a new model of GS of Caenorhabditis elegans by feeding them Escherichia coli OP50 cultured in a glucose-enriched medium, which better simulates human dietary glycation compared to previous single protein-glucose cross-linking methods. Utilizing WormCNN, a deep learning model, we assessed the health status and calculated the Healthy Aging Index (HAI) of worms with or without GS. Our results demonstrated accelerated aging in the GS group, evidenced by increased autofluorescence and altered gene expression of key aging regulators, daf-2 and daf-16. Additionally, we observed elevated pharyngeal pumping rates in AGEs-fed worms, suggesting an addictive response similar to human dietary patterns. This study highlights the profound effects of GS on worm aging and underscores the critical role of computer vision in accurately assessing health status and aiding in the establishment of disease models. The findings provide insights into glycation-induced aging and offer a comprehensive approach to studying the effects of dietary glycation on aging processes.

Strengths and limitations of the worm development and activity test (wDAT) as a chemical screening tool for developmental hazards.

The worm Development and Activity Test (wDAT) measures C. elegans developmental milestone acquisition timing and stage-specific spontaneous locomotor activity (SLA). Previously, the wDAT identified developmental delays and SLA level changes in C. elegans with mammalian developmental toxicants arsenic, lead, and mercury. 5-fluorouracil (5FU), cyclophosphamide (CP), hydroxyurea (HU), and ribavirin (RV) are teratogens that also induce growth retardation in developing mammals. In at least some studies on each of these chemicals, fetal weight reductions were seen at mammalian exposures below those that had teratogenic effects, suggesting that screening for developmental delay in a small alternative whole-animal model could act as a general toxicity endpoint to identify chemicals for further testing for more specific adverse developmental outcomes. Consistent with mammalian developmental effects, 5FU, HU, and RV were associated with developmental delays with the wDAT. Exposures associated with developmental delay induced hypoactivity with 5FU and HU, but slight hyperactivity with RV. CP is a prodrug that requires bioactivation by cytochrome P450s for both therapeutic and toxic effects. CP tests as a false negative in several in vitro assays, and it was also a false negative with the wDAT. These results suggest that the wDAT has the potential to identify some developmental toxicants, and that a positive wDAT result with an unknown may warrant further testing in mammals. Further assessment with larger panels of positive and negative controls will help qualify the applicability and utility of this C. elegans wDAT assay within toxicity test batteries or weight of evidence approaches for developmental toxicity assessment.

Treatment with quercetin mitigates polystyrene nanoparticle-induced reduction in neuron capacity by inhibiting dopaminergic neurodegeneration and facilitating dopamine metabolism in Caenorhabditis elegans.

In organisms, long-term nanopolystyrenes (PS-NPs) exposure can cause toxicity, including neurotoxicity. Quercetin, the flavonol with extensive distribution within plants, possesses diverse biological activities. Nevertheless, the possible effect of quercetin to suppress PS-NPs-induced neurotoxicity and its associated mechanism remains unknown. Thus, in the present work, Caenorhabditis elegans was utilized as the model animal to investigate quercetin's pharmacological effect on suppressing PS-NPs-induced neurotoxicity and the underlying mechanism. PS-NPs exposure at 1-100 µg/L remarkably reduced locomotion behavior, while only PS-NPs exposure at 100 µg/L significantly decrease sensory perception behavior. Meanwhile, the increase in the number of worms with dopaminergic neurodegeneration was detected in nematodes exposed to 100 µg/L PS-NPs and the decreased dopamine content was observed within nematodes exposed to 10-100 µg/L PS-NPs, demonstrating the function of dopaminergic neurodegeneration and disruption of dopamine metabolism in inducing PS-NPs toxicity on neuron capacity. After 100 µg/L PS-NPs exposure, the 25-100 µM quercetin treatment effectively increased the locomotion behavior and the sensory perception behavior. Developmentally, quercetin treatment (100 µM) remarkably enhanced fluorescence intensity while decreasing worm number with neurodegeneration within BZ555 transgenic strains exposed to 100 µg/L PS-NPs. Physiologically, quercetin treatment (100 µM) significantly enhanced dopamine content within nematodes exposed to 100 µg/L PS-NPs. Molecularly, quercetin treatment (100 µM) notably decreased the expressions of genes governing neurodegeneration (mec-4, deg-3, unc-68, itr-1, clp-1, and asp-3) while significantly increasing the expression of genes governing dopamine metabolism (cat-2, cat-1, dop-1, dop-2, dop-3). As revealed by molecular docking results, quercetin might bind to excitotoxic-like ion channels receptors (MEC-4 and DEG-3) and dopamine secreted protein (CAT-2). Consequently, findings in this work demonstrated that long-term PS-NPs exposure within the µg/L range (1-100 µg/L) was toxic to neuron capacity, which was associated with the enhancement in dopaminergic neurodegeneration and disruption of dopamine metabolism. Notably, PS-NPs-mediated neurotoxicity to nematodes is probably suppressed through subsequent quercetin treatment.

Anti-infective Properties of Mung Bean (Vigna Radiata (L.)R. Wilczek) Coat Extract on Pseudomonas aeruginosa-Infected Caenorhabditis elegans: Transcriptomics and Pathway Analysis.

ETHNOPHARMACOLOGICAL RELEVANCE: Mung bean coat has long been known for its wide-ranging health benefits, including antibacterial, anti-inflammatory, and immune-modulatory properties. For many years in China, mung beans have been employed in the therapeutic management of inflammation induced by pathogenic bacteria infection, yet the precise underlying protective mechanisms remain to be comprehensively elucidated. AIM OF THE STUDY: Given the growing concern over antibiotic resistance, there is a necessity to explore new anti-infective agents. Here, the anti-infective properties of Mung bean coat extract (MBCE) were investigated using a model of Pseudomonas aeruginosa-infected nematodes. MATERIALS AND METHODS: The protective effects of MBCE on Pseudomonas aeruginosa (PA14) infected nematodes were assessed by lifespan assay, reactive oxygen species (ROS) levels, transcriptomics, and Quantitative real-time PCR (qRT-PCR). RESULTS: MBCE significantly improved the survival rates and reduced ROS levels in infected worms. Transcriptomic profiling disclosed predominant KEGG pathway enrichments in immune responses, energy metabolism processes such as oxidative phosphorylation and the tricarboxylic acid cycle, alongside aging-related neurodegenerative diseases and longevity regulatory pathways like PI3K-AKT, MAPK, mTOR, and FOXO. qRT-PCR validation showed that MBCE upregulated antimicrobial peptides (spp-3, lys-1, lys-7, abf-2, cnc-2, nlp-33, clec-85), gram-negative responses (irg-3, src-2, grd-3, col-179), and mitochondrial function (mev-1) gene expressions, while downregulated insulin signaling-related (age-1, akt-1, akt-2, daf-15) gene expressions. Mutant strains lifespan analysis indicated that the nsy-1, sek-1, pmk-1, daf-2, aak-2, sir-2.1, and skn-1 were necessary for lifespan extension mediated by MBCE under PA14 infection, but not clk-1, isp-1, mev-1, or daf-16. CONCLUSION: Collectively, our findings suggested that MBCE increased the survival rates of PA14-infected worms by activating downstream antimicrobial and antioxidant gene expressions through modulation of MAPK, daf-2, aak-2, sir-2.1, and skn-1 pathways. The research underscored the potential of natural plant compounds to strengthen the body's defenses against infections, potentially mitigating harmful ROS levels and improving survival. Additionally, these findings elucidated the mechanisms by which these plant-derived compounds enhance the immune system, implying their potential utility as dietary supplements or as an alternative to conventional antibiotics.

Activated hedgehog and insulin ligands by decreased transcriptional factor DAF-16 mediate transgenerational nanoplastic toxicity in Caenorhabditis elegans.

In Caenorhabditis elegans, transcriptional factor DAF-16 in insulin signaling pathway played important role in regulating transgenerational nanoplastic toxicity. Activation of insulin signals mediated transgenerational toxicity of polystyrene nanoparticle (PS-NP) by inhibiting DAF-16. Among identified germline ligands, expression of wrt-3 encoding hedgehog ligand was increased by RNAi of daf-16 in PS-NP exposed C. elegans. In PS-NP exposed C. elegans, expressions of 4 other germline hedgehog ligand genes and 10 hedgehog receptor genes were increased by daf-16 RNAi. Among these candidate genes, expressions of hedgehog ligand genes (grl-15, grl-16, qua-1, and wrt-1) and hedgehog receptor genes (ptr-23, scp-1, ptd-2, and ncr-1) could be increased by PS-NP (1-100 µg/L), and their transgenerational expressions were observed after PS-NP exposure. RNAi of grl-15, grl-16, qua-1, wrt-1, ptr-23, scp-1, ptd-2, and ncr-1 caused resistance to transgenerational PS-NP toxicity. In nematodes exposed to PS-NPs, RNAi of wrt-3, grl-15, grl-16, qua-1, and wrt-1 at parental generation (P0-G) inhibited expressions of ptr-23, scp-1, ptd-2, and ncr-1 in their offspring. Moreover, we observed increased expressions of insulin peptides genes (ins-3, ins-39, and daf-28) in PS-NP exposed daf-16(RNAi) nematodes, suggesting formation of feedback loop. We raise the molecular basis for formation of toxicity on multiple generations after nanoplastic exposure at P0-G.

Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis.

Cuprous copper [Cu(I)] is an essential cofactor for enzymes that support many fundamental cellular functions including mitochondrial respiration and suppression of oxidative stress. Neurons are particularly reliant on mitochondrial production of ATP, with many neurodegenerative diseases, including Parkinson's disease, associated with diminished mitochondrial function. The gene MBLAC1 encodes a ribonuclease that targets pre-mRNA of replication-dependent histones, proteins recently found in yeast to reduce Cu(II) to Cu(I), and when mutated disrupt ATP production, elevates oxidative stress, and severely impacts cell growth. Whether this process supports neuronal and/or systemic physiology in higher eukaryotes is unknown. Previously, we identified swip-10, the putative Caenorhabditis elegans ortholog of MBLAC1, establishing a role for glial swip-10 in limiting dopamine (DA) neuron excitability and sustaining DA neuron viability. Here, we provide evidence from computational modeling that SWIP-10 protein structure mirrors that of MBLAC1 and locates a loss of function coding mutation at a site expected to disrupt histone RNA hydrolysis. Moreover, we find through genetic, biochemical, and pharmacological studies that deletion of swip-10 in worms negatively impacts systemic Cu(I) levels, leading to deficits in mitochondrial respiration and ATP production, increased oxidative stress, and neurodegeneration. These phenotypes can be offset in swip-10 mutants by the Cu(I) enhancing molecule elesclomol and through glial expression of wildtype swip-10. Together, these studies reveal a glial-expressed pathway that supports systemic mitochondrial function and neuronal health via regulation of Cu(I) homeostasis, a mechanism that may lend itself to therapeutic strategies to treat devastating neurodegenerative diseases.

A Fluorescence Lifetime-Based Novel Method for Accurate Lipid Quantification of BODIPY Vital-Stained C. elegans.

Lipid droplets (LDs) are organelles associated with lipid storage and energy metabolism, thus their morphology and quantity are of significant research interest. While commercially available BODIPY dye effectively labels LDs in various cell types, it also labels lysosome-related organelles (LROs) in C. elegans, leading to non-specific LD quantification. Here, we report that the fluorescent signals of BODIPY exhibit distinct fluorescence lifetime patterns for LROs and LDs, which can be captured, visualized, and filtered by fluorescence lifetime imaging microscopy. Furthermore, we proposed and validated a method based on fluorescence lifetime that can improve the accuracy of fat storage quantification in BODIPY vital-staining worms, which holds broad applications, including rapid and accurate LD quantification in forward genetic screening. Additionally, our method enables observing dynamic LD-LRO interactions in living worms, a unique capability of BODIPY vital-staining. Our findings highlight distinct BODIPY fluorescence lifetime characteristics of LDs and LROs, providing a valuable tool for future research on LDs, LROs, or their interactions.

UPRER-immunity axis acts as physiological food evaluation system that promotes aversion behavior in sensing low-quality food.

To survive in challenging environments, animals must develop a system to assess food quality and adjust their feeding behavior accordingly. However, the mechanisms that regulate this chronic physiological food evaluation system, which monitors specific nutrients from ingested food and influences food-response behavior, are still not fully understood. Here, we established a low-quality food evaluation assay system and found that heat-killed E. coli (HK-E. coli), a low-sugar food, triggers cellular UPRER and immune response. This encourages animals to avoid low-quality food. The physiological system for evaluating low-quality food depends on the UPRER (IRE-1/XBP-1) - Innate immunity (PMK-1/p38 MAPK) axis, particularly its neuronal function, which subsequently regulates feeding behaviors. Moreover, animals can adapt to a low-quality food environment through sugar supplementation, which inhibits the UPRER -PMK-1 regulated stress response by increasing vitamin C biosynthesis. This study reveals the role of the cellular stress response pathway as physiological food evaluation system for assessing nutritional deficiencies in food, thereby enhancing survival in natural environments.

We quickly learn to steer clear of eating the moldy apple, the foul-smelling piece of chicken or the leftovers that taste a little 'off'. This survival instinct is shared across most animal species ­ even those with extremely simple and limited visual or taste systems, like the tiny worm Caenorhabditis elegans. Indeed, assessing the safety and quality of available food items can also rely on cells activating built-in cascades of molecular reactions. However, it remains unclear how these 'cellular stress response programs' actually help guide feeding behaviors. To better understand this process, Liu et al. conducted a series of experiments using C. elegans worms exposed to heat-killed bacteria, which are devoid of many nutrients essential for growth. After initially consuming these bacteria, the worms quickly started to avoid feeding on this type of low-quality food. This suggests that mechanisms occurring after ingestion allowed the worms to adjust their feeding choices. Further work showed that the consumption of heat-killed bacteria triggered two essential stress response pathways, known as the unfolded protein response and the innate immune response. The activation of these pathways was essential for the animals to be able to change their behavior and avoid the heat-killed bacteria. These biochemical pathways were particularly active in the worms' nerve cells, highlighting the importance of these cells in sensing and reacting to food. Finally, Liu et al. also found that adding sugars like lactose and sucrose to the low-quality food could prevent the activation of the stress response pathways. This result suggests that specific nutrients play a central role in how these worms decide what to eat. These findings shed light on the complex systems that ensure organisms consume the nutritious food they need to survive. Understanding these processes in worms can provide insights into the broader biological mechanisms that help animals avoid harmful food.

6-PPD quinone at environmentally relevant concentrations induced damage on longevity in C. elegans: Mechanistic insight from inhibition in mitochondrial UPR response.

6-PPD quinone (6-PPDQ) exists widely in water environment media, causing acute lethality to some aquatic species. Long-term exposure to 6-PPDQ reduced the lifespan of Caenorhabditis elegans. However, the molecular basis for mitochondrial control of 6-PPDQ toxicity remains largely unclear. Using HSP-6 as marker of mitochondrial unfolded protein response (mt UPR), we observed activation of mt UPR by 0.1 and 1 µg/L 6-PPDQ and inhibition in mt UPR by 10 µg/L 6-PPDQ. Additionally, increased atfs-1, ubl-5, and dve-1 expressions were caused by 0.1 and 1 µg/L 6-PPDQ and decreased expressions of these genes were induced by 10 µg/L 6-PPDQ. Neuronal and intestinal RNA interference (RNAi) of hsp-6 caused susceptibility to 6-PPDQ toxicity on longevity, and atfs-1, ubl-5, and dve-1 acted in neurons and intestine to modulate mt UPR and 6-PPDQ toxicity on longevity. Meanwhile, 6-PPDQ (1 and 10 µg/L) increased expressions of histone methyltransferase genes met-2 and set-6, and decreased expressions of histone demethylase genes jmjd-1.2 and jmjd-3.1. Neuronal RNAi of set-6 and intestinal RNAi of met-2 accelerated hsp-6, atfs-1, ubl-5, and dve-1 expressions and extended lifespan of 6-PPDQ exposed nematodes. In contrast, neuronal RNAi of jmjd-1.2 and jmjd-3.1 and intestinal RNAi of jmjd-1.2 suppressed these 4 gene expressions and reduced lifespan of 6-PPDQ exposed nematodes o. In nematodes, RNAi of hsp-6 could also enhance mitochondrial dysfunction and mitochondrial reactive oxygen species (ROS) induced by 6-PPDQ. Therefore, 6-PPDQ caused damage on longevity was associated with suppression in mt UPR, which was under regulation of certain histone methylation related signals.

vivoBodySeg: Machine learning-based analysis of C. elegans immobilized in vivoChip for automated developmental toxicity testing.

Developmental toxicity (DevTox) tests evaluate the adverse effects of chemical exposures on an organism's development. While large animal tests are currently heavily relied on, the development of new approach methodologies (NAMs) is encouraging industries and regulatory agencies to evaluate these novel assays. Several practical advantages have made C. elegansa useful model for rapid toxicity testing and studying developmental biology. Although the potential to study DevTox is promising, current low-resolution and labor-intensive methodologies prohibit the use of C. elegans for sub-lethal DevTox studies at high throughputs. With the recent availability of a large-scale microfluidic device, vivoChip, we can now rapidly collect 3D high-resolution images of ~ 1,000 C. elegans from 24 different populations. In this paper, we demonstrate DevTox studies using a 2.5D U-Net architecture (vivoBodySeg) that can precisely segment C. elegans in images obtained from vivoChip devices, achieving an average Dice score of 97.80. The fully automated platform can analyze 36 GB data from each device to phenotype multiple body parameters within 35 min on a desktop PC at speeds ~ 140x faster than the manual analysis. Highly reproducible DevTox parameters (4-8% CV) and additional autofluorescence-based phenotypes allow us to assess the toxicity of chemicals with high statistical power.

Projecting phytochemical bacoside A anti-mucorale agent: An in-silico and in-vitro assessment.

Mucormycosis, a life-threatening fungal infection that primarily affects immunocompromised individuals.The protein family commonly observed in the fugus responsible for causing Mucormycosis. The attachment of spores to host cells surface, facilitated by a protein CotH, is a critical step for the invasion and progression of the disease. Therefore, CotH inhibitors have emerged as a promising therapeutic strategy for treating mucormycosis.This study presents a novel therapeutic target and ligand for controlling the growth of Mucorales. First, to identify potential CotH inhibitors, we surveyed a library antifungal compounds elaborated in AYUSearch database. Next, using machine learning-based algorithms we screend 20 potentials ligands, followed by structure-based molecular modelling and molecular trajectory analysis to identify the three most promising chemical constituents. In-vitro tube assays on selected Mucorales determined the minimum inhibitory concentrations (MIC) for screened chemotypes. The MIC assay revealed that Bacoside inhibits the growth and sporulation at 5 mg/ml concentrations, emerging as a probable CotH inhibitor. Further, the compound's toxicity was evaluated by adding it to the feed of C.elegans, and the finding suggests that the bacoside is reasonably safe at the studied concentration. The findings project bacoside A as a potential anti-mucorale lead compound that can be further validated with preclinical and clinical studies.

Exploratory research on the multi-life stages mesh-type model of Caenorhabditis elegans in radiation ecology.

To address the lack of effective dose quantification methods for the model organism Caenorhabditis elegans (C. elegans) in radiation ecology research, this study employs remeshing techniques to develop a comprehensive mesh-type model covering multi-life stages, from embryonic to larval (L1, L2, L3, L4) and adulthood. Using these models, Dose Coefficients (DC) for C. elegans in a soil environment under different exposure conditions (external and internal), material settings, and radioactive nuclides (³H, 6°Co, 9°Sr, 129I, 1³1I, 1³4Cs, 1³7Cs) were calculated with the Monte Carlo toolkit Geant4. The results show that the difference in DC, when C. elegans material is set as either biological material or water, is within 5%. Under external exposure conditions, the impact of life stages on the population's average DC is minimal (with a maximum deviation not exceeding 10%). However, the distribution within the population varied significantly across life stages (under external exposure to 137Cs, the dispersion was 12.02% for adults and a considerably higher 60.30% for larvae). The earlier the life stage, the greater the variability in DC distribution within the C. elegans population. Furthermore, correlation analysis indicates a strong relationship between DC and life stages under internal exposure scenarios. The mesh-type model of C. elegans established in this study provides a valuable tool for radiation ecology research and has potential applications in broader research fields.

Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.

Upcycling Surinam cherry and spine gourd fruit waste: development of anthelmintic jelly candies using fruit extracts.

Under-utilized fruits and vegetables are rich in nutraceuticals and have several medicinal properties. A large group of people widely consumes gummies and jelly candies, which can serve as an excellent vehicle to increase the intake of functional components. In the present study, jelly candies were developed by incorporating fruit extracts from commonly wasted segments of two under-utilized fruits (Surinam cherry and Spine gourd). Jelly candies were evaluated for their anthelmintic efficacy against Caenorhabditis elegans along with various physicochemical, microbial, colour, texture, and sensory parameters immediately after preparation, as well as during 150 days of storage at two conditions (ambient and accelerated). Ready-to-consume jelly candies (5 g) contained 0.21 g of fruit extract in Surinam cherry and 0.35 g of fruit extract in Spine gourd jelly candies. Jelly candies exhibited TSS in the range of 70.40 - 71.37°Brix, pH 2.33 to 2.84, aw 0.70-0.75, moisture 10.57-15.88%, a* value 5.33-1.27, b*value 10.66-1.28, no microbial contamination, and acceptable sensory parameters. Surinam cherry extract candy (4 mg/ml) showed a higher anthelmintic effect than Spine gourd extract candy (6.66 mg/ml) based on egg inhibition, larval death, and average adult worm paralysis time assays. These fruit extract-incorporated candies can be a novel healthier food product with anthelmintic potential, which can be an alternative to commonly used anthelmintic drugs. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-024-05967-5.

Levels of Amyloid Beta (Aß) Expression in the Caenorhabditis elegans Neurons Influence the Onset and Severity of Neuronally Mediated Phenotypes.

A characteristic feature of Alzheimer's disease (AD) is the formation of neuronal extracellular senile plaques composed of aggregates of fibrillar amyloid ß (Aß) peptides, with the Aß1-42 peptide being the most abundant species. These Aß peptides have been proposed to contribute to the pathophysiology of the disease; however, there are few tools available to test this hypothesis directly. In particular, there are no data that establish a dose-response relationship between Aß peptide expression level and disease. We have generated a panel of transgenic Caenorhabditis elegans strains expressing the human Aß1-42 peptide under the control of promoter regions of two pan-neuronal expressed genes, snb-1 and rgef-1. Phenotypic data show strong age-related defects in motility, subtle changes in chemotaxis, reduced median and maximum lifespan, changes in health span indicators, and impaired learning. The Aß1-42 expression level of these strains differed as a function of promoter identity and transgene copy number, and the timing and severity of phenotypes mediated by Aß1-42 were strongly positively correlated with expression level. The pan-neuronal expression of varying levels of human Aß1-42 in a nematode model provides a new tool to investigate the in vivo toxicity of neuronal Aß expression and the molecular and cellular mechanisms underlying AD progression in the absence of endogenous Aß peptides. More importantly, it allows direct quantitative testing of the dose-response relationship between neuronal Aß peptide expression and disease for the first time. These strains may also be used to develop screens for novel therapeutics to treat Alzheimer's disease.