The DAF-7/TGF-β signaling pathway regulates abundance of the Caenorhabditis elegans glutamate receptor GLR-1

A Fiji protocol for analyzing puncta is a robust tool for measuring GLR-1::GFP accumulation in the ventral nerve cord of C. elegans

In C. elegans, DAF-7/TGF-beta signaling regulates development, metabolism, and behavior. In addition loss of daf-7 leads to an increase of the glutamate receptor GLR-1. In daf-7(e1372) mutants, GLR-1 tagged with GFP (GLR-1::GFP) accumulates in wide puncta along the ventral nerve cord of the animal. Previous automated analyses of GLR-1::GFP accumulation relied on the proprietary software, IgorPro, for measurement of GLR-1::GFP puncta size, intensity, and density. We did a side-by-side comparison of analyses by IgorPro and an open source macro written for Fiji to analyze images from animals expressing GLR-1::GFP in wild type and daf-7(e1372) backgrounds. Analyses by the two programs were in strong agreement and are in accordance with previously published data on the effects of daf-7(e1372) on GLR-1::GFP accumulation. Based on these data, we conclude that the Fiji platform is a robust method for analyzing the accumulation of a fluorescently-tagged neurotransmitter receptor and that the Fiji puncta plugin will be applicable for image analysis for other neural markers.

A Fiji process for quantifying fluorescent puncta in linear cellular structures

Understanding the cell biology of protein trafficking and homeostasis requires reproducible methods for identifying and quantifying proteins within cells or cellular structures. Imaging protocols for measuring punctate protein accumulation in linear structures, for example the neurites of C. elegans, have relied on proprietary software for a full range of analysis capabilities. Here we describe a set of macros written for the NIH-supported imaging software ImageJ or Fiji (Fiji is Just ImageJ) that reliably identify protein puncta so that they can be analyzed with respect to intensity, density, and width at half-maximum intensity (Full-Width, Half-Maximum, FWHM). We provide an explanation of the workflow, data outputs, and limitations of the Fiji macro. As part of this integration, we also provide two independent data sets with side-by-side analyses using the proprietary IgorPro software and the Fiji macro (Hulsey-Vincent, et al. A, B., 2023 submitted). The Fiji macro is an important new tool because it provides robust, reproducible data analysis in a free, open-source format.

Foodomics Reveals Anti-Obesity Properties of Cannabinoids from Hemp Oil

SCOPE

Molecular networking (MN) analysis intends to provide chemical insight of untargeted mass spectrometry (MS) data to the user's underlying biological questions. Foodomics is the study of chemical compounds in food using advanced omics methods. In this study, an MS-MN-based foodomics approach is developed to investigate the composition and anti-obesity activity of cannabinoids in hemp oil.

METHODS AND RESULTS

A total of 16 cannabinoids are determined in optimized microwave pretreatment of hemp oil using the developed approach. Untargeted metabolomics analysis reveals that cannabinoid extract (CE) and its major constituent (cannabidiol, CBD), can alleviate high glucose-induced increases in lipids and carbohydrates, and decreases in amino acid and nucleic acid. Moreover, CE and CBD are also found to suppress the expression levels of mdt-15, sbp-1, fat-5, fat-6, fat-7, daf-2, and elevate the expression level of daf-1, daf-7, daf-16, sod-3, gst-4, lipl-4, resulting in the decrease of lipid synthesis and the enhance of kinetism. Canonical correspondence analysis (CCA) uncovers strong associations between specific metabolic alterations and gene expression levels.

CONCLUSION

These findings from this exploratory study offer a new insight into the roles of cannabinoids in the treatment of obesity and related complications.

The transforming growth factor beta ligand TIG-2 modulates the function of neuromuscular junction and muscle energy metabolism in Caenorhabditis elegans

Deciphering the physiological function of TGF-β (the transforming growth factor beta) family ligands is import for understanding the role of TGF-β in animals' development and aging. Here, we investigate the function of TIG-2, one of the ligands in Caenorhabditis elegans TGF-β family, in animals' behavioral modulation. Our results show that a loss-of-function mutation in tig-2 gene result in slower locomotion speed in the early adulthood and an increased density of cholinergic synapses, but a decreased neurotransmitter release at neuromuscular junctions (NMJs). Further tissue-specific rescue results reveal that neuronal and intestinal TIG-2 are essential for the formation of cholinergic synapses at NMJs. Interestingly, tig-2(ok3416) mutant is characterized with reduced muscle mitochondria content and adenosine triphosphate (ATP) production, although the function of muscle acetylcholine receptors and the morphology muscle fibers in the mutant are comparable to that in wild-type animals. Our result suggests that TIG-2 from different neuron and intestine regulates worm locomotion by modulating synaptogenesis and neurotransmission at NMJs, as well as energy metabolism in postsynaptic muscle cells.

Identify differential genes and cell subclusters from time-series scRNA-seq data using scTITANS

Time-series single-cell RNA sequencing (scRNA-seq) provides a breakthrough in modern biology by enabling researchers to profile and study the dynamics of genes and cells based on samples obtained from multiple time points at an individual cell resolution. However, cell asynchrony and an additional dimension of multiple time points raises challenges in the effective use of time-series scRNA-seq data for identifying genes and cell subclusters that vary over time. However, no effective tools are available. Here, we propose scTITANS (https://github.com/ZJUFanLab/scTITANS), a method that takes full advantage of individual cells from all time points at the same time by correcting cell asynchrony using pseudotime from trajectory inference analysis. By introducing a time-dependent covariate based on time-series analysis method, scTITANS performed well in identifying differentially expressed genes and cell subclusters from time-series scRNA-seq data based on several example datasets. Compared to current attempts, scTITANS is more accurate, quantitative, and capable of dealing with heterogeneity among cells and making full use of the timing information hidden in biological processes. When extended to broader research areas, scTITANS will bring new breakthroughs in studies with time-series single cell RNA sequencing data.

The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses

The Doublesex/Mab-3 Domain transcription factor DMD-10 is expressed in several cell types in C. elegans, including in the nervous system. We sought to investigate whether DMD-10 is required for normal neuronal function using behavioral assays. We found that mutation of dmd-10 did not broadly affect behavior. dmd-10 mutants were normal in several behavioral assays including a body bends assay for locomotion, egg laying, chemotaxis and response to gentle touch to the body. dmd-10 mutants did have defects in nose-touch responsiveness, which requires the glutamate receptor GLR-1. However, using quantitative fluorescence microscopy to measure levels of a GLR-1::GFP fusion protein in the ventral nerve cord, we found no evidence supporting a difference in the number of GLR-1 synapses or in the amount of GLR-1 present in dmd-10 mutants. dmd-10 mutants did have decreased responsiveness to high osmolarity, which, along with nose-touch, is sensed by the polymodal sensory neuron ASH. Furthermore, mutation of dmd-10 impaired behavioral response to optogenetic activation of ASH, suggesting that dmd-10 promotes neuronal signaling in ASH downstream of sensory receptor activation. Together our results suggest that DMD-10 is important in regulating the frequency of multiple ASH-dependent behavioral responses.

Intergenerational toxicity of nonylphenol ethoxylate (NP-9) in Caenorhabditis elegans

The ethoxylated isomers of nonylphenol (NPEs, NP-9) are one of the main active ingredients present in nonionic surfactants employed as herbicides, cosmetics, paints, plastics, disinfectants and detergents. These chemicals and their metabolites are commonly found in environmental matrices. The aim of this work was to evaluate the intergenerational toxicity of NP-9 in Caenorhabditis elegans. The lethality, length, width, locomotion and lifespan were investigated in the larval stage L4 of the wild strain N2. Transgenic green fluorescent protein (GFP) strains were employed to estimate changes in relative gene expression. RT-qPCR was utilized to measure mRNA expression for neurotoxicity-related genes (unc-30, unc-25, dop-3, dat-1, mgl-1, and eat-4). Data were obtained from parent worms (P0) and the first generation (F1). Lethality of the nematode was concentration-dependent, with 48 h-LC₅₀ values of 3215 and 1983 μM in P0 and F1, respectively. Non-lethal concentrations of NP-9 reduced locomotion. Lifespan was also decreased by the xenobiotic, but the negative effect was greater in P0 than in F1. Non-monotonic concentration-response curves were observed for body length and width in both generations. The gene expression profile in P0 was different from that registered in F1, although the expression of sod-4, hsp-70, gpx-6 and mtl-2 increased with the surfactant concentration in both generations. None of the tested genes followed a classical concentration-neurotoxicity relationship. In P0, dopamine presented an inverted-U curve, while GABA and glutamate displayed a bimodal type. However, in F1, inverted U-shaped curves were revealed for these genes. In summary, NP-9 induced intergenerational responses in C. elegans through mechanisms involving ROS, and alterations of the GABA, glutamate, and dopamine pathways.

Transcriptomic Profiling of DAF-7/TGFβ Pathway Mutants in C. elegans

The transforming growth factor beta superfamily encompasses a large family of ligands that are well conserved across many organisms. They are regulators of a number of physiological and pathological processes. The model nematode Caenorhabditis elegans has been instrumental in identifying key components of the transforming growth factor beta (TGFβ) pathway. In C. elegans, the TGFβ homolog DAF-7 signals through the DAF-1 Type I and DAF-4 Type II receptors to phosphorylate downstream R-SMADs DAF-8 and DAF-14. These R-SMADs translocate into the nucleus to inhibit Co-SMAD DAF-3. Many of the roles of the canonical DAF-7 pathway, involving both DAF-1 and DAF-3, have been identified using targeted genetic studies. Few have assessed the global transcriptomic changes in response to these genes, especially in adult animals. In this study, we performed RNA sequencing on wild type, daf-1, and daf-1; daf-3 adult hermaphrodites. To assess the overall trends of the data, we identified differentially expressed genes (DEGs) and performed gene ontology analysis to identify the types of downstream genes that are differentially expressed. Hierarchical clustering showed that the daf-1; daf-3 double mutants are transcriptionally more similar to wild type than daf-1 mutants. Analysis of the DEGs showed a disproportionally high number of genes whose expression is increased in daf-1 mutants, suggesting that DAF-1 acts as a general repressor of gene expression in wild type animals. Gene ontology analysis of the DEGs produced many significantly enriched terms, including Molting Cycle, Response to Topologically Incorrect Protein, and Response to Biotic Stimulus. Understanding the direct and indirect targets of the DAF-7 TGFβ pathway through this RNA-seq dataset can provide insight into novel roles of the multifunctional signaling pathway, as well as identify novel genes that may participate in previously reported functions of TGFβ signaling.

Expression of BMP-4 and Smad1 in patients with Hirschsprung disease and its clinical significance

Expression and clinical significance of bone morphogenetic protein (BMP)-4 and Smad1 in patients with Hirschsprung disease (HD) were investigated. A retrospective analysis of 96 HD patients (experimental group) admitted to Xuzhou Children's Hospital, Xuzhou Medical University from June 2015 to June 2017 was performed. According to the samples, the experimental group was divided into the stenosis group, the transition group and the expansion group. Forty-seven children with colostomy due to intestinal obstruction were selected as the control group. The expression levels of BMP-4 and Smad1 proteins were detected by immunohistochemical staining. The expression levels of BMP-4 and Smad mRNA were detected by real-time quantitative PCR (RT-qPCR), and were quantified and compared. Via immunohistochemistry, BMP-4 and Smad1 proteins were detected in the samples of different parts of HD patients and children with intestinal obstruction. The positive expression levels of BMP-4 and Smad1 proteins in the transition group were decreased compared with those in the expansion and control groups (P<0.05), and the positive expression levels of BMP-4 and Smad1 proteins in the stenosis group were decreased compared with those in the transition, expansion, and control groups (P<0.05). Also, the gene expression levels of BMP-4 and Smad1 in the transition and stenosis groups were successively decreased, and the differences were statistically significant (P<0.05). In conclusion, the expression of BMP-4 and Smad1 in the intestinal plexus of HD lesions was significantly reduced, indicating that BMP-4 and Smad1 are closely related to the occurrence of HD, and it is suspected that they have a certain influence on the intestinal development of congenital digestive tract malformations.

Gene structure and expression patterns of Acdaf-1, a TGF-β type I receptor in Ancylostoma caninum

The components of the transforming growth factor β (TGF-β) signaling pathway in parasitic nematodes remain unknown. In this research, a type I receptor for TGF-β was isolated from the hookworm Ancylostoma caninum. The new gene was designated as Acdaf-1, a Caenorhabditis elegans daf-1 homolog. The full-length cDNA of Acdaf-1 encodes a 595-amino-acid protein with an NH₂-terminal signal peptide. This protein has a cytoplasm tail (209-595aa region) which corresponds to the type 1a membrane topology. Between amino acid position 295-500, the protein contains the ATP binding site, substrate binding sites, and PKC-kinase-like domain. Real-time RT-PCR showed that the transcript was expressed in three main stages of A. caninum. It reached the maximal level in the female adult worm stage with lower transcript level in the first and second larvae (L1/L2) and intermediate level in L3 stages as well as in the male worms. After serum activation, the activity of Acdaf-1 was decreased in L3 larvae. These data implied that Acdaf-1 might relate to the infection ability of the larvae. Immunolocalization revealed that AcDAF-1 was present in eggs, intestine, and epidermis cells of larvae (L1, L2, and L3 stages) with strong signal in primordium of the gonads in L3 and was abundant in epidermis, intestine, and ovary of adult worm. These results suggested that Acdaf-1 might be involved in the interaction of the parasite and host relationship and provide a potential target for parasite control.

Effect of Transforming Growth Factor-β upon Taenia solium and Taenia crassiceps Cysticerci

Taeniids exhibit a great adaptive plasticity, which facilitates their establishment, growth, and reproduction in a hostile inflammatory microenvironment. Transforming Growth Factor-β (TGFβ), a highly pleiotropic cytokine, plays a critical role in vertebrate morphogenesis, cell differentiation, reproduction, and immune suppression. TGFβ is secreted by host cells in sites lodging parasites. The role of TGFβ in the outcome of T. solium and T. crassiceps cysticercosis is herein explored. Homologues of the TGFβ family receptors (TsRI and TsRII) and several members of the TGFβ downstream signal transduction pathway were found in T. solium genome, and the expression of Type-I and -II TGFβ receptors was confirmed by RT-PCR. Antibodies against TGFβ family receptors recognized cysticercal proteins of the expected molecular weight as determined by Western blot, and different structures in the parasite external tegument. In vitro, TGFβ promoted the growth and reproduction of T. crassiceps cysticerci and the survival of T. solium cysticerci. High TGFβ levels were found in cerebrospinal fluid from untreated neurocysticercotic patients who eventually failed to respond to the treatment (P = 0.03) pointing to the involvement of TGFβ in parasite survival. These results indicate the relevance of TGFβ in the infection outcome by promoting cysticercus growth and treatment resistance.

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Environmental stress during early development can impact adult phenotypes via programmed changes in gene expression. C. elegans larvae respond to environmental stress by entering the stress-resistant dauer diapause pathway and resume development once conditions improve (postdauers). Here we show that the osm-9 TRPV channel gene is a target of developmental programming and is down-regulated specifically in the ADL chemosensory neurons of postdauer adults, resulting in a corresponding altered olfactory behavior that is mediated by ADL in an OSM-9-dependent manner. We identify a cis-acting motif bound by the DAF-3 SMAD and ZFP-1 (AF10) proteins that is necessary for the differential regulation of osm-9, and demonstrate that both chromatin remodeling and endo-siRNA pathways are major contributors to the transcriptional silencing of the osm-9 locus. This work describes an elegant mechanism by which developmental experience influences adult phenotypes by establishing and maintaining transcriptional changes via RNAi and chromatin remodeling pathways.

DOI:http://dx.doi.org/10.7554/eLife.11642.001

Increasing evidence suggests that experiencing stressful environments early on in life can have profound effects on the health and behavior of adults. For example, stressful conditions in the womb have been linked to adult depression and metabolic disorders. These effects are thought to be the result of changes in the way that genes in specific tissues are regulated in the individuals that have experienced the stress. However, it is not clear how a particular stress can cause long-term changes in gene activity in specific tissues.

A microscopic worm called Caenorhabditis elegans is often used as a simple animal model to study how animals develop and behave. Previous studies have shown that adult worms that experienced stress early in life show differences in behavior and gene activity compared to genetically identical worms that did not experience the stress. Here, Sims, Ow et al. asked what signals are required for these changes to happen.

The experiments show that a gene called osm-9 – which plays a role in the nervous system – is less active in sensory nerve cells in worms that experienced stress early on in life. This loss of activity resulted in the worms being unable to respond to a particular odor. Two proteins called DAF-3 and ZFP-1 are able to bind to a section of DNA in the osm-9 gene to decrease its activity in response to stress. These proteins are similar to human proteins that are important for development and are associated with some types of leukemia. Further experiments show that small molecules of ribonucleic acid in the “RNA interference” pathway also help to decrease the activity of osm-9 after stress.

Together, Sims, Ow et al.’s findings suggest that environmental conditions in early life regulate the osm-9 gene through the coordinated effort of DAF-3, ZFP-1 and the RNA interference pathway. The next steps are to investigate how these molecules are able to target osm-9 and to identify other proteins that regulate gene activity in response to stress in early life.

DOI:http://dx.doi.org/10.7554/eLife.11642.002