Tryptophan hydroxylase (TRH) loss of function mutations in Daphnia deregulated growth, energetic, serotoninergic and arachidonic acid metabolic signalling pathways

Activation of RHO-GTPase gene pattern correlates with adverse clinical outcome and immune microenvironment in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC), the most prevalent renal cancer subtype, is frequently associated with poor prognosis. RHO-GTPase signaling genes have been implicated in tumor aggressiveness and unfavorable survival, but their potential in risk stratification and therapeutic guidance for ccRCC patients remains unexplored. Univariate regression identified prognostically relevant RHO-GTPase signaling genes, followed by consensus clustering for ccRCC subtype classification. LASSO regression selected key genes to construct a six-gene risk model. The model was evaluated for prognostic stratification, immune status, immunotherapy response, and chemotherapy sensitivity. Key genes were analyzed at the genomic, single-cell, and protein levels to explore underlying mechanisms. Among 62 prognostically relevant RHO-GTPase signaling genes, six (ARHGAP11B, NUF2, PLK1, CYFIP2, IQGAP2, and VAV3) were identified to form a robust prognostic signature. This model stratified patients into high- and low-risk groups, with high-risk patients demonstrating significantly worse outcomes. The model exhibited excellent predictive accuracy (AUC > 0.7 in training and validation cohorts). High-risk patients were characterized by an immunosuppressive microenvironment and reduced sensitivity to immunotherapy. Drug sensitivity analysis revealed 107 agents correlated with the risk score, underscoring therapeutic relevance. Mechanistically, the six key genes showed distinct expression patterns, cellular distribution, and positive correlation with VHL mutations, highlighting their potential as actionable drug targets. This study established a novel six-gene RHO-GTPase signaling model for predicting prognosis, immune status, and therapeutic responses in ccRCC, which offers potential for improving patient stratification and guiding personalized treatment strategies.

Comparison of behavioral responses, respiratory metabolism-related enzyme activities, and metabolomics of the juvenile Chinese mitten crab Eriocheir sinensis with different tolerance to air exposure

Air exposure is a common stressor for Chinese mitten crab (Eriocheir sinensis) during rearing and transport, and air exposure tolerance can serve as a crucial indicator for assessing the quality of juvenile E. sinensis. In this study, juvenile E. sinensis were divided into two groups based on their behavioral responses: Group S, which exhibited strong tolerance to air exposure, and Group W, which exhibited weak tolerance. Immersed crabs, not exposed to air, served as a control group (Group C). Whole body morphological characteristics and enzyme activities related to respiratory metabolism in the hemolymph and anterior gills were compared among the three groups. Non-targeted LC-MS metabolomic analysis was conducted on anterior gills. The results showed that, independent of developmental stage, crabs that were larger and had higher condition factor were more tolerant to air exposure. Additionally, compared to Group W, air exposure had a relatively small effect on glycolysis and anaerobic respiratory metabolic processes in the hemolymph and anterior gills of Group S. In response to air exposure, E. sinensis experienced increased energy demand, and switched from aerobic to anaerobic respiration to increase energy supply. Simultaneously, air exposure induced oxidative stress in the hemolymph and anterior gills. This study enhances our understanding of the response mechanism of E. sinensis to air exposure and provides a theoretical reference for the identification of high-quality juvenile E. sinensis.

The role of serotonergic signaling on phototactic and locomotor behavior in Daphnia magna

The role of serotonin in Daphnia magna phototactic and locomotor behavior was assessed using reverse genetics and pharmacological treatments with serotonin and fluoxetine. The study was conducted with four clones: the wild type clone and three CRISPR D. magna ones with mutations in the tryptophan hydrolase gene (TRH) that is involved in serotonin synthesis. These included clones TRHA- and TRHB- with mutations in both alleles that lack serotonin and the mono-allelic mutant TRH+, that has serotonin. Obtained results indicated that animals lacking serotonin showed an increased negative phototactism and locomotor activity upon light stimuli and a reduced response to fish kairomones relative to the wild type and TRH+ individuals. Exposure to exogenous serotonin re-established the phototactism and locomotor activity of TRH- individuals to those of the wild type but did not affect phototactic responses to fish kairomones. Unexpectedly, fluoxetine was able to modify locomotor activity and phototactic behavior against fish kairomones in TRH- individuals lacking serotonin, and also it increased the concentrations of acethylcholine and GABA in exposed animals, which support the argument that fluoxetine may also affect other neurological pathways.

The freshwater water flea Daphnia magna NIES strain genome as a resource for CRISPR/Cas9 gene targeting: The glutathione S-transferase omega 2 gene

The water flea Daphnia magna is a small freshwater planktonic animal in the Cladocera. In this study, we assembled the genome of the D. magna NIES strain, which is widely used for gene targeting but has no reported genome. We used the long-read sequenced data of the Oxford nanopore sequencing tool for assembly. Using 3,231 genetic markers, the draft genome of the D. magna NIES strain was built into ten linkage groups (LGs) with 483 unanchored contigs, comprising a genome size of 173.47 Mb. The N50 value of the genome was 12.54 Mb and the benchmarking universal single-copy ortholog value was 98.8%. Repeat elements in the D. magna NIES genome were 40.8%, which was larger than other Daphnia spp. In the D. magna NIES genome, 15,684 genes were functionally annotated. To assess the genome of the D. magna NIES strain for CRISPR/Cas9 gene targeting, we selected glutathione S-transferase omega 2 (GST-O2), which is an important gene for the biotransformation of arsenic in aquatic organisms, and targeted it with an efficient make-up (25.0%) of mutant lines. In addition, we measured reactive oxygen species and antioxidant enzymatic activity between wild type and a mutant of the GST-O2 targeted D. magna NIES strain in response to arsenic. In this study, we present the genome of the D. magna NIES strain using GST-O2 as an example of gene targeting, which will contribute to the construction of deletion mutants by CRISPR/Cas9 technology.

Microbiota-Dependent and -Independent Production of l-Dopa in the Gut of Daphnia magna

Host-microbiome interactions are essential for the physiological and ecological performance of the host, yet these interactions are challenging to identify. Neurotransmitters are commonly implicated in these interactions, but we know very little about the mechanisms of their involvement, especially in invertebrates. Here, we report a peripheral catecholamine (CA) pathway involving the gut microbiome of the model species Daphnia magna. We demonstrate the following: (i) tyrosine hydroxylase and Dopa (3,4-dihydroxyphenylalanine) decarboxylase enzymes are present in the gut wall; (ii) Dopa decarboxylase gene is expressed in the gut by the host, and its expression follows the molt cycle peaking after ecdysis; (iii) biologically active l-Dopa, but not dopamine, is present in the gut lumen; (iv) gut bacteria produce l-Dopa in a concentration-dependent manner when provided l-tyrosine as a substrate. Impinging on gut bacteria involvement in host physiology and ecologically relevant traits, we suggest l-Dopa as a communication agent in the host-microbiome interactions in daphnids and, possibly, other crustaceans.

IMPORTANCE Neurotransmitters are commonly implicated in host-microbiome communication, yet the molecular mechanisms of this communication remain largely elusive. We present novel evidence linking the gut microbiome to host development and growth via neurotransmitter l-Dopa in Daphnia, the established model species in ecology and evolution. We found that both Daphnia and its gut microbiome contribute to the synthesis of the l-Dopa in the gut. We also identified a peripheral pathway in the gut wall, with a molt stage-dependent dopamine synthesis, linking the gut microbiome to the daphnid development and growth. These findings suggest a central role of l-Dopa in the bidirectional communication between the animal host and its gut bacteria and translating into the ecologically important host traits suitable for subsequent testing of causality by experimental studies.

Pharmacological modulation of fish-induced depth selection in D. magna: the role of cholinergic and GABAergic signalling

Animal behaviour is closely related to individual fitness, which allows animals to choose suitable mates or avoid predation. The central nervous system regulates many aspects of animal behaviour responses. Therefore, behavioural responses can be especially sensitive to compounds with a neurodevelopmental or neurofunctional mode of action. Phototactic behavioural changes against fish in the freshwater crustacean Daphnia magna have been the subject of many ecological investigations. The aim of this study was to identify which neurotransmitter systems modulate phototactic behaviour to fish kairomones. We used a positive phototactic D. magna clone (P₁32,85) that shows marked negative phototactism after exposure to fish kairomones. Treatments included up to 16 known agonists and antagonists of the serotonergic, cholinergic, dopaminergic, histaminergic, glutamatergic and GABAergic systems. It was hypothesized that many neurological signalling pathways may modulate D. magna phototactic behaviour to fish kairomones. A new custom-designed device with vertically oriented chambers was used, and changes in the preferred areas (bottom, middle, and upper areas) were analysed using groups of animals after 24 h of exposure to the selected substance(s). The results indicated that agonists of the muscarinic acetylcholine and GABA_A receptors and their equi-effective mixture ameliorated the negative phototactic response to fish kairomones, whereas antagonists and their mixtures increased the negative phototactism to fish kairomones. Interestingly, inhibition of the muscarinic acetylcholine receptor abolished positive phototaxis, thus inducing the phototactic response to fish kairomones. Analysis of the profile of neurotransmitters and their related metabolites showed that the D. magna behavioural responses induced by fish depend on changes in the levels of acetylcholine, dopamine and GABA.

Omega-3 PUFA profoundly affect neural, physiological, and behavioural competences - implications for systemic changes in trophic interactions

In recent decades, much conceptual thinking in trophic ecology has been guided by theories of nutrient limitation and the flow of elements, such as carbon and nitrogen, within and among ecosystems. More recently, ecologists have also turned their attention to examining the value of specific dietary nutrients, in particular polyunsaturated fatty acids (PUFA), among which the omega-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play a central role as essential components of neuronal cell membranes in many organisms. This review focuses on a new neuro-ecological approach stemming from the biochemical (mechanistic) and physiological (functional) role of DHA in neuronal cell membranes, in particular in conjunction with G-protein coupled receptors (GPCRs). We link the co-evolution of these neurological functions to metabolic dependency on dietary omega-3 PUFA. We outline ways in which deficiencies in dietary DHA supply may affect, cognition, vision, and behaviour, and ultimately, the biological fitness of consumers. We then review emerging evidence that changes in access to dietary omega-3 PUFA may ultimately have profound impacts on trophic interactions leading to potential changes in community structure and ecosystem functioning that, in turn, may affect the supply of DHA within and across ecosystems, including the supply for human consumption.

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Simple Summary

Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In the past few years, studies on the gene expression changes of dairy cow mammary glands were only based on transcriptome comparisons between two lactation stages. Few studies focused on the relationships between gene expression of the dairy mammary gland and lactation stage or milk composition in a lactation cycle. In this study, we detected milk yield and composition in a lactation cycle. For the first time, we constructed a gene coexpression network using WGCNA on the basis of 18 gene expression profiles during six stages of a lactation cycle by transcriptome sequencing, generating 10 specific modules. Genes in each module were performed with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Module–trait relationship analysis showed a series of potential candidates related to milk yield and composition. The current study provides an important theoretical basis for the further molecular breeding of dairy cows.

Abstract

Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In this study, the milk yield, lactose, fat, and protein of Holstein dairy cows were detected in a lactation cycle. Meanwhile, a total of 18 gene expression profiles were detected using mammary glands from six lactation stages (day 7 to calving, −7 d; day 30 post-calving, 30 d; day 90 post-calving, 90 d; day 180 post-calving, 180 d; day 270 post-calving, 270 d; day 315 post-calving, 315 d). On the basis of the 18 profiles, WGCNA identified for the first time 10 significant modules that may be related to lactation stage, milk yield, and the main milk composition content. Genes in the 10 significant modules were examined with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results revealed that the galactose metabolism pathway was a potential candidate for milk yield and milk lactose synthesis. In −7 d, ion transportation was more frequent and cell proliferation related terms became active. In late lactation, the suppressor of cytokine signaling 3 (SOCS3) might play a role in apoptosis. The sphingolipid signaling pathway was a potential candidate for milk fat synthesis. Dairy cows at 315 d were in a period of cell proliferation. Another notable phenomenon was that nonlactating dairy cows had a more regular circadian rhythm after a cycle of lactation. The results provide an important theoretical basis for the further molecular breeding of dairy cows.

Characterization of neurotransmitters and related metabolites in Daphnia magna juveniles deficient in serotonin and exposed to neuroactive chemicals that affect its behavior: A targeted LC-MS/MS method

Neurotransmitters are endogenous metabolites that play a crucial role within an organism, at the chemical synapses. There is a growing interest in their analytical determination for understanding the neurotoxic effect of contaminants. Daphnia magna represents an excellent aquatic model for these environmental studies, due to its similarities with vertebrates in several neurotransmitters and related gene pathways and because of its wide application in ecotoxicological studies. Within this study, an accurate and sensible method of analysis of 17 neurotransmitters and related precursors and metabolites was developed. The method was validated in terms of sensitivity, reproducibility, precision, and accuracy, and also matrix effect was evaluated. As an independent probe of method validation and applicability, the method was applied to two different scenarios. First, it was used for the study of neurotransmitter levels in genetically mutated tryptophan hydrolase D. magna clones, confirming the absence of serotonin and its metabolite 5-HIAA. Additionally, the method was applied for determining the effects of chemical compounds known to affect different neurotransmitter systems and to alter Daphnia behavior. Significant changes were observed in 13 of the analyzed neurotransmitters across treatments, which were related to the neurotransmitter systems described as being affected by these neurochemicals. These two studies, which provide results on the ways in which the neurotransmitter systems in D. magna are affected, have corroborated the applicability of the presented method, of great importance due to the suitability of this organism for environmental neurotoxicity studies.

Changes in lipid profiles in Daphnia magna individuals exposed to low environmental levels of neuroactive pharmaceuticals

Disruptive effects of chemicals on lipids in aquatic species are mostly limited to obesogens and vertebrates. Recent studies reported that antidepressants, anxiolytic, antiepileptic and β-adrenergic pharmaceuticals, with putative distinct mechanisms of action at low environmental relevant concentrations, up-regulated common neurological and lipid metabolic pathways and enhanced similarly reproduction in the crustacean Daphnia magna. Conversely CRISPR mutants for the tryptophan hydrolase enzyme gene (TRH) that lack serotonin had the opposed phenotype: the lipid metabolism down-regulated and impaired reproduction. Lipid metabolism is strongly linked to reproduction in D. magna. The aim of this study is to test if the above mentioned neuro-active chemicals disrupted common lipid groups and showed also the opposed lipidomic effects as those individuals lacking serotonin. This study used ultra-high performance liquid chromatography/time-of-flight mass spectrometry (UHPLC/TOFMS) to study how neuro-active chemicals (carbamazepine, diazepam, fluoxetine and propranolol) at low (0.1 μg/L) and higher concentrations (1 μg/L) and three CRISPR TRH mutant clones disrupt the dynamics of glycerophospholipids and glycerolipids in Daphnia adults. Lipidomic analysis identified 267 individual lipids corresponding to three classes of glycerolipids, eleven of glycerophospholipids, one of sterols and one of sphingolipids, of which 132 and 125 changed according to the chemical treatments or across clones, respectively. Most pharmaceutical treatments enhanced reproduction whereas mutated clones lacking serotonin reproduced to a lesser extent. Except for carbamazepine, most of the tested pharmaceuticals increased some triacylglycerol species and decreased monoacylglycerols, lysophospholipids, sphingomyelins and cholesterol esters in exposed females. Opposed lipidomic pattern was observed in mutated clones lacking serotonin. Lipidomic data, thus, indicate a close link between reported transcriptomic and lipidomic changes, which are likely related to serotonin and other neurological signalling pathways.

Analysis of the pharmacological mechanism of Banxia Xiexin decoction in treating depression and ulcerative colitis based on a biological network module

BACKGROUND

The network pharmacology method was used to predict the active components of Banxia Xiexin decoction, its targets and the key signalling pathways that are activated in the treatment of depression and ulcerative colitis to explore the common mechanism.

METHODS

The active components and targets of Banxia Xiexin decoction were obtained by searching the ETCM,TCMSP and TCMIP database. The disease targets of depression and ulcerative colitis were obtained by combining the following the DisGeNET, OMIM,Drugbank,CTD and PharmGKB disease databases. The drug and disease target genes were obtained from the intersection of the herbal medicine targets and the disease targets and were imported into the STRING platform for the analysis of PPI network. The network modules were constructed using Cytoscape software. An analysis of the functional annotations of GO terms and KEGG signalling pathways was performed for each network module. Then, the tissue distribution, sub-cellular distribution and protein attributes of the key targets in the pathway were analysed by the BioGPS, Genecards and DisGeNET databases.

RESULTS

The mechanism of Banxia Xiexin Decoction in the treatment of depression and ulcerative colitis is related to drug reaction, steroid metabolism, lipid metabolism, inflammatory response, oxidative stress response, cell response to lipopolysaccharide, insulin secretion regulation, estradiol response and other biological functions, mainly through the regulation of 5-hydroxytryptamine synaptic, arachidonic acid metabolism, HIF-1 signaling pathway and NF-kappa B signaling pathway can achieve the effect of same treatment for different diseases.

CONCLUSIONS

The mechanism of Banxia Xiexin Decoction in treating different diseases involves direct or indirect correlation of multiple signal pathways, mainly involved in drug metabolism and lipid metabolism, but also through comprehensive intervention of the body's nervous system, immune system, digestive system and other systems. The effective components of Banxia Xiexin Decoction are mainly act on eight key target proteins (such as ALB, IL6, VEGFA, TNF, PTGS2, MAPK1, STAT3, EGFR) to carry out multi-target effect mechanism, biological mechanism of treating different diseases with the same treatment, and related mechanism of overall treatment, which provide theoretical reference for further research on the material basis and mechanism of Banxiaxiexin decoction on antidepressant and prevention and treatment of ulcerative colitis.

Effects of Single and Combined Low Concentrations of Neuroactive Drugs on Daphnia magna Reproduction and Transcriptomic Responses

Assessing the risk of neuroactive pharmaceuticals in the environment requires an understanding of their joint effects at low concentrations across species. Here, we assessed reproductive and transcriptional effects of single and ternary equi-effective mixture exposure to propranolol, diazepam, and carbamazepine on the crustacean Daphnia magna at environmentally relevant concentrations. The three compounds enhanced reproduction in adults and induced specific transcriptome changes in preadolescent individuals. Comparison of the results from single exposures to a ternary equi-effective mixture of the three compounds showed additive action. Transcriptomic analyses identified 3248 genes affected by at least one of the treatments, which were grouped into four clusters. Two clusters (1897 gene transcripts in total) behaved similarly, appearing either over- or under-represented relative to control, in all single and mixture treatments. The third and fourth clusters grouped genes differently transcribed upon exposure to diazepam and propranolol, respectively. Functional transcriptomics analysis indicated that the four clusters shared major deregulated signaling pathways implicated on energy, growth, reproduction, and neurologically related processes, which may be responsible for the observed reproductive effects. Thus, our study showed additive effects at the transcriptional and physiological level and provides a novel approach to the analysis of environmentally relevant mixtures of neuroactive compounds.