Tomkiewicz D et al. (2010) Antimicrob Agents Chemother "Berberine-INF55 (5-nitro-2-phenylindole) hybrid antimicrobials: effects of varying the relative orientation of the berberine and INF55 components."

Garner J, Moy TI, Larkins-Ford J, Bremner JB, Tomkiewicz D, Casadei G, Lewis K, Kelso MJ, Ausubel FM

[Antimicrob Agents Chemother, 2010]

Hybrid antimicrobials containing an antibacterial linked to a multidrug resistance (MDR) pump inhibitor make up a promising new class of agents for countering efflux-mediated bacterial drug resistance. This study explores the effects of varying the relative orientation of the antibacterial and efflux pump inhibitor components in three isomeric hybrids (SS14, SS14-M, and SS14-P) which link the antibacterial alkaloid and known substrate for the NorA MDR pump berberine to different positions on INF55 (5-nitro-2-phenylindole), an inhibitor of NorA. The MICs for all three hybrids against wild-type, NorA-knockout, and NorA-overexpressing Staphylococcus aureus cells were found to be similar (9.4 to 40.2 microM), indicating that these compounds are not effectively effluxed by NorA. The three hybrids were also found to have similar curing effects in a Caenorhabditis elegans live infection model. Each hybrid was shown to accumulate in S. aureus cells to a greater extent than either berberine or berberine in the presence of INF55, and the uptake kinetics of SS14 were found to differ from those of SS14-M and SS14-P. The effects on the uptake and efflux of the NorA substrate ethidium bromide into S. aureus cells in the presence or absence of the hybrids were used to confirm MDR inhibition by the hybrids. MDR-inhibitory activity was confirmed for SS14-M and SS14-P but not for SS14. Molecular dynamics simulations revealed that SS14 prefers to adopt a conformation that is not prevalent in either SS14-M or SS14-P, which may explain why some properties of SS14 diverge from those of its two isomers. In summary, subtle repositioning of the pump-blocking INF55 moiety in berberine-INF55 hybrids was found to have a minimal effect on their antibacterial activities but to significantly alter their effects on MDR pumps.

Gallud A et al. (2019) Sci Rep "Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study."

Ostberg N, Xue D, Gogvadze V, Ytterberg J, Skoog T, Moya S, Gallud A, Ruiz J, Kere J, Fadeel B, Katayama S, Zubarev R, Astruc D, Chen YZ, Kloditz K

[Sci Rep, 2019]

Systems biology is increasingly being applied in nanosafety research for observing and predicting the biological perturbations inflicted by exposure to nanoparticles (NPs). In the present study, we used a combined transcriptomics and proteomics approach to assess the responses of human monocytic cells to Au-NPs of two different sizes with three different surface functional groups, i.e., alkyl ammonium bromide, alkyl sodium carboxylate, or poly(ethylene glycol) (PEG)-terminated Au-NPs. Cytotoxicity screening using THP-1 cells revealed a pronounced cytotoxicity for the ammonium-terminated Au-NPs, while no cell death was seen after exposure to the carboxylated or PEG-modified Au-NPs. Moreover, Au-NR3+ NPs, but not the Au-COOH NPs, were found to trigger dose-dependent lethality in vivo in the model organism, Caenorhabditis elegans. RNA sequencing combined with mass spectrometry-based proteomics predicted that the ammonium-modified Au-NPs elicited mitochondrial dysfunction. The latter results were validated by using an array of assays to monitor mitochondrial function. Au-NR3+ NPs were localized in mitochondria of THP-1 cells. Moreover, the cationic Au-NPs triggered autophagy in macrophage-like RFP-GFP-LC3 reporter cells, and cell death was aggravated upon inhibition of autophagy. Taken together, these studies have disclosed mitochondria-dependent effects of cationic Au-NPs resulting in the rapid demise of the cells.

Hu CC et al. (2018) Sci Rep "Toxic Effects of Size-tunable Gold Nanoparticles on Caenorhabditis elegans Development and Gene Regulation."

Wu GH, Lai SF, Wagner OI, Hwu Y, Yen TJ, Hu CC, Muthaiyan Shanmugam M

[Sci Rep, 2018]

We utilized size-tunable gold nanoparticles (Au NPs) to investigate the toxicogenomic responses of the model organism Caenorhabditis elegans. We demonstrated that the nematode C. elegans can uptake Au NPs coated with or without 11-mercaptoundecanoic acid (MUA), and Au NPs are detectable in worm intestines using X-ray microscopy and confocal optical microscopy. After Au NP exposure, C. elegans neurons grew shorter axons, which may have been related to the impeded worm locomotion behavior detected. Furthermore, we determined that MUA to Au ratios of 0.5, 1 and 3 reduced the worm population by more than 50% within 72 hours. In addition, these MUA to Au ratios reduced the worm body size, thrashing frequency (worm mobility) and brood size. MTT assays were employed to analyze the viability of cultured C. elegans primary neurons exposed to MUA-Au NPs. Increasing the MUA to Au ratios increasingly reduced neuronal survival. To understand how developmental changes (after MUA-Au NP treatment) are related to changes in gene expression, we employed DNA microarray assays and identified changes in gene expression (e.g., clec-174 (involved in cellular defense), cut-3 and fil-1 (both involved in body morphogenesis), dpy-14 (expressed in embryonic neurons), and mtl-1 (functions in metal detoxification and homeostasis)).

Wang M et al. (2023) Int J Nanomedicine "Gold Nanoparticles Reduce Food Sensation in Caenorhabditis elegans via the Voltage-Gated Channel EGL-19."

Yang B, Sun N, Hu J, Wang M, Wang L, Mo J, Wang D, Zhang Z, Su M

[Int J Nanomedicine, 2023]

INTRODUCTION: The increasing use of gold nanoparticles (Au NPs) in the medical field has raised concerns about the potential adverse effect of Au NPs exposure. However, it is difficult to assess the health risks of Au NPs exposure at the individual organ level using current measurement techniques. METHODS: single cell RNA-seq databases. RESULTS: to NaCl, which was consistent with the decrease in calcium transit of ASEL. Further studies confirmed that the reduced calcium transit was dependent on voltage-gated calcium channel EGL-19. The neuropeptide INS-22 was partially involved in Au NPs-induced NaCl sensation defect. Therefore, we proposed that Au NPs reduced the calcium transit in the ASEL neuron through egl-19-dependent calcium channels. It was partially regulated by the DAF-16 targeting neuropeptide INS-22. DISCUSSION: Our results demonstrate that Au NPs affect food sensation by reducing the calcium transit in ASEL neurons, which further leads to reduced pharynx pumping and feeding defects. The toxicology studies of Au NPs from worms have great potential to guide the usage of Au NPs in the medical field such as targeted drug delivery.

Tsyusko O et al. (2012) Environ Sci Technol "Toxicogenomic responses of the model organism Caenorhabditis elegans to gold nanoparticles."

Blalock EM, Bertsch PM, Tsyusko O, Joice G, Tseng MT, Starnes D, Spurgeon DJ, Unrine JM

[Environ Sci Technol, 2012]

We used Au nanoparticles (Au-NPs) as a model for studying particle-specific effects of manufactured nanomaterials (MNMs) by examining the toxicogenomic responses in a model soil organism, Caenorhabditis elegans . Global genome expression for nematodes exposed to 4-nm citrate-coated Au-NPs at the LC(10) level (5.9 mg-L(-1)) revealed significant differential expression of 797 genes. The levels of expression for five genes (apl-1, dyn-1, act-5, abu-11, and hsp-4) were confirmed independently with qRT-PCR. Seven common biological pathways associated with 38 of these genes were identified. Up-regulation of 26 pqn/abu genes from noncanonical unfolded protein response (UPR) pathway and molecular chaperones (hsp-16.1, hsp-70, hsp-3, and hsp-4) were observed and are likely indicative of endoplasmic reticulum stress. Significant increase in sensitivity to Au-NPs in a mutant from noncanonical UPR (pqn-5) suggests possible involvement of the genes from this pathway in a protective mechanism against Au-NPs. Significant responses to Au-NPs in endocytosis mutants (chc-1 and rme-2) provide evidence for endocytosis pathway being induced by Au-NPs. These results demonstrate that Au-NPs are bioavailable and cause adverse effects to C. elegans by activating both general and specific biological pathways. The experiments with mutants further support involvement of several of these pathways in Au-NP toxicity and/or detoxification.

McCullough AJ et al. (1993) Mol Cell Biol "AU-rich intronic elements affect pre-mRNA 5' splice site selection in Drosophila melanogaster."

McCullough AJ, Schuler MA

[Mol Cell Biol, 1993]

cis-spliced nuclear pre-mRNA introns found in a variety of organisms, including Tetrahymena thermophila, Drosophila melanogaster, Caenorhabditis elegans, and plants, are significantly richer in adenosine and uridine residues than their flanking exons are. The functional significance of this intronic AU richness, however, has been demonstrated only in plant nuclei. In these nuclei, 5' and 3' splice sites are selected in part by their positions relative to AU-rich elements spread throughout the length of an intron. Because of this position-dependent selection scheme, a 5' splice site at the normal (+1) exon-intron boundary having only three contiguous consensus nucleotides can compete effectively with an enhanced exonic site (-57E) having nine consensus nucleotides and outcompete an enhanced site (+106E) embedded within the AU-rich intron. To determine whether transitions from AU-poor exonic sequences to AU-rich intronic sequences influence 5' splice site selection in other organisms, alleles of the pea rbcS3A1 intron were expressed in Drosophila Schneider 2 cells, and their splicing patterns were compared with those in tobacco nuclei. We demonstrate that this heterologous transcript can be accurately spliced in transfected Drosophila nuclei and that a +1 G-to-A knockout mutation at the normal splice site activates the same three cryptic 5' splice sites as in tobacco. Enhancement of the exonic (-57) and intronic (+106) sites to consensus splice sites indicates that potential splice sites located in the upstream exon or at the 5' exon-intron boundary are preferred in Drosophila cells over those embedded within AU-rich intronic sequences. In contrast to tobacco, in which the activities of two competing 5' splice sites upstream of the AU-rich intron are modulated by their proximity to the AU transition point, D. melanogaster utilizes the upstream site which has a higher proportion of consensus nucleotides. The enhanced version of the cryptic intronic site is efficiently selected in D. melanogaster when the normal +1 site is weakened or discrete AU-rich elements upstream of the +106E site are disrupted. Selection of this internal site in tobacco requires more drastic disruption of these motifs. We conclude that 5' splice site selection in Drosophila nuclei is influenced by the intrinsic strengths of competing sites and by the presence of AU-rich intronic elements but to a different extent than in tobacco.

Conrad RC et al. (1995) RNA "SL1 trans-splicing specified by AU-rich synthetic RNA inserted at the 5' end of Caenorhabditis elegans pre-mRNA."

Blumenthal TE, Lea K, Conrad RC

[RNA, 1995]

In Caenorhabditis elegans, pre-mRNAs of many genes are trans-spliced to one of two spliced leaders, SL1 or SL2. Some of those that receive exclusively SL1 have been characterized as having at their 5' ends outrons, AU-rich sequences similar to introns followed by conventional 3' splice sites. Comparison of outrons from many different SL1-specific C. elegans genes has not revealed the presence of any consensus sequence that might encode SL1-specificity. In order to determine what parameters influence the splicing of SL1, we performed in vivo experiments with synthetic splice sites. Synthetic AU-rich RNA, 51 nt or longer, placed upstream of a consensus 3' splice site resulted in efficient trans-splicing. With all sequences tested, this trans-splicing was specifically to SL1. Thus, no information beyond the presence of AU-rich RNA at least as long as the minimum-length C. elegans intron, followed by a 3' splice site, is required to specify trans-splicing or for strict SL1 specificity.

Meng-Qiu Dong et al. (2006) Neuronal Development, Synaptic Function, and Behavior Meeting "Identification of Insulin Signaling Components Using Quantitative Mass Spectrometry"

Tao Xu, Jeffrey Johnson, Nora Au, John Venable, Meng-Qiu Dong, Daniel Cociorva, John Yates III, Andrew Dillin

[Neuronal Development, Synaptic Function, and Behavior Meeting, 2006]

Insulin regulates a wide range of processes including metabolism, development, and aging, but only a handful of its downstream targets are known. We have used 15N metabolic labeling and quantitative proteomics to identify a subset of insulin signaling targets in C. elegans that are differentially expressed in WT, daf-2 (an insulin receptor) and daf-16 (a transcription factor negatively regulated by daf-2) mutants. From the soluble fraction, we have identified 104 proteins that are present in higher or lower levels in daf-2 than in WT and daf-16, including known targets SOD-3 and catalases. Gene ontology analysis revealed that the up-regulated proteins in daf-2 were over-represented in reactive oxygen species metabolism, carbohydrate metabolism, and amino acid biosynthesis, while the down-regulated proteins were enriched in translation and lipid transport. We have confirmed by genetics analysis that some of the candidate insulin signaling components identified in this study play a role in lifespan regulation and/or dauer formation, and one of them is a protein phosphatase. Consistent with our mass spec result that this protein was up-regulated in daf-2 mutants, the intensity of its GFP fusion protein increased when transgenic worms expressing it were treated with daf-2 RNAi. In addition, a loss-of-function mutant of this protein exhibited constitutive dauer formation at 27 ºC and had an extended lifespan, both of which were suppressed by a daf-16 null mutation, suggesting that daf-16 acts downstream of, and/or in parallel to it. These results suggest that this protein phosphatase is a component of insulin signaling and that a feedback mechanism exists to increases its expression to compensate for decreased insulin signaling in daf-2. Our results demonstrate the effectiveness of combining quantitative mass spectrometry and C. elegans genetics. This approach can be extended to other studies beyond insulin signaling.

Fallmann J et al. (2016) Nucleic Acids Res "AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements."

Sedlyarov V, Hofacker IL, Kovarik P, Fallmann J, Tanzer A

[Nucleic Acids Res, 2016]

AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3'UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3'UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans. Furthermore, we include data from CLIP-Seq experiments in order to highlight motifs with validated protein interaction. Additionally, we provide a REST interface for experienced users to interact with the database in a semi-automated manner. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite.

Zhang L et al. (2019) Anal Chem "Interaction-Transferable Graphene-Isolated Superstable AuCo Nanocrystal-Enabled Direct Cyanide Capture."

Xu Y, Liao Y, Li Z, Li S, Zheng Z, Tan W, Chen Z, Zhang J, Liu Z, Yi H, Zhang L

[Anal Chem, 2019]

Noble metals with strong plasmons have been widely used as enhancement substrates for molecule identification. However, cyanide, a toxic and important signaling molecule with a corrosive nature to noble metals, makes direct recognition challenging. Herein a novel superstable magnetic graphene-isolated AuCo nanocrystal (MACG) has been designed. Such graphene isolation enables superior stability without corrosion. Moreover, unexpectedly, although graphene isolated direct contact between Au and cyanide, their interaction was transferable and remained, which gifted MACGs direct cyanide capture capability with no specific ligands needed. Density functional theory calculations and natural bond orbital analysis indicated that the graphene isolation only slightly affected the charge transfer and that a relatively strong interaction was maintained between Au and cyanide. MACGs were utilized for efficient cyanide capture and clearance in various hydrologic environments and sensitive in vivo cyanide capture in C. elegans infected with P. aeruginosa, a pathogen with cyanide as the biomarker, indicating promise for various applications.