Beer, Madeline et al. (2021) International Worm Meeting "Investigating the Role of sRNA and Argonautes in Intercellular Communication"

Claycomb, Julie M., Beer, Madeline, Lao, Robert X., Seroussi, Uri

[International Worm Meeting, 2021]

The nematode Caenorhabditis elegans uses sRNA and Argonaute proteins (AGOs) to degrade, inhibit the translation of, or upregulate target transcripts in a process called RNA interference (RNAi). Remarkably, the worm is capable of taking up dsRNA from the environment via its intestine and transporting to distant tissues to elicit RNAi systemically. While some of the mechanisms of systemic RNAi are understood, one question that remains is: do AGOs themselves move throughout the animal? There is precedent for mobile AGOs in multiple species. For example, the pathogenic nematode Heligmosomoides bakeri secretes sRNAs and an AGO called exWAGO during infection to manipulate expression of mouse immunity genes. There are three homologs of exWAGO in C. elegans that localize to the apical membrane of the intestine (the intestinal Secondary AGOs, iSAGOs). Their apical intestinal localization places them at an interface with the environment. Our lab used IP/MS to identify protein interactors of iSAGOs and found interactors are involved in membrane and vesicular transport. I hypothesize that the localization of iSAGOs to the intestinal apical membrane allows them to take up dsRNA and sRNA from the environment, and transmit RNAi signals to other tissues in the worm. To test this, I will determine how iSAGOs are localized to the intestinal apical membrane, define the roles of iSAGOs in mediating host-pathogen interactions, and determine whether iSAGOs are necessary for systemic RNAi. This research will illuminate the mechanisms by which the iSAGOs are involved in intercellular communication.

(2022) Development "The people behind the papers - Madeline Cassani and Geraldine Seydoux."

[Development, 2022]

Specification of germ cell fate depends on the asymmetric segregation of germ granules in early embryos. Now, a new paper in Development describes 'germline P-bodies', germ granules in Caenorhabditis elegans embryos, which function cooperatively with another condensate, P granules, in germline specification. To find out more, we caught up with first author Madeline Cassani and corresponding author Geraldine Seydoux, Professor at Johns Hopkins University School of Medicine.

Shin N et al. (2020) Sci Rep "Micelle-stabilized Olfactory Receptors for a Bioelectronic Nose Detecting Butter Flavors in Real Fermented Alcoholic Beverages."

Park TH, Lee SH, Shin N, Pham Ba VA, Hong S

[Sci Rep, 2020]

A bioelectronic nose device based on micelle-stabilized olfactory receptors is developed for the selective discrimination of a butter flavor substance in commercial fermented alcoholic beverages. In this work, we have successfully overexpressed ODR-10, a type of olfactory receptor, from Caenorhabditis elegans using a bacterial expression system at a low cost and high productivity. The highly-purified ODR-10 was stabilized in micelle structures, and it was immobilized on a carbon nanotube field-effect transistor to build a bioelectronic nose for the detection of diacetyl, a butter flavor substance, via the specific interaction between diacetyl and ODR-10. The bioelectronic nose device can sensitively detect diacetyl down to 10 fM, and selectively discriminate it from other substances. In addition, this sensor could directly evaluate diacetyl levels in a variety of real fermented alcoholic beverages such as beer, wine, and makgeolli (fermented Korean wine), while the sensor did not respond to soju (Korean style liquor without diacetyl). In this respect, our sensor should be a powerful tool for versatile food industrial applications such as the quality control of alcoholic beverages and foods.

Palmioli A et al. (2022) ACS Chem Neurosci "Alzheimer's Disease Prevention through Natural Compounds: Cell-Free , In Vitro, and In Vivo Dissection of Hop ( Humulus lupulus L.) Multitarget Activity"

Zoia CP, Bazzini C, Palmioli A, Colombo L, Inserra M, Ferrarese C, Diomede L, Sala G, Bruzzone C, De Luigi A, Mazzoni V, De Noni I, Airoldi C, Salmona M

[ACS Chem Neurosci, 2022]

The relevant social and economic costs associated with aging and neurodegenerative diseases, particularly Alzheimer's disease (AD), entail considerable efforts to develop effective preventive and therapeutic strategies. The search for natural compounds, whose intake through diet can help prevent the main biochemical mechanisms responsible for AD onset, led us to screen hops, one of the main ingredients of beer. To explore the chemical variability of hops, we characterized four hop varieties, i.e., Cascade, Saaz, Tettnang, and Summit. We investigated the potential multitarget hop activity, in particular its ability to hinder Aβ1-42 peptide aggregation and cytotoxicity, its antioxidant properties, and its ability to enhance autophagy, promoting the clearance of misfolded and aggregated proteins in a human neuroblastoma SH-SY5Y cell line. Moreover, we provided evidence of in vivo hop efficacy using the transgenic CL2006 Caenorhabditis elegans strain expressing the Aβ3-42 peptide. By combining cell-free and in vitro assays with nuclear magnetic resonance (NMR) and MS-based metabolomics, NMR molecular recognition studies, and atomic force microscopy, we identified feruloyl and p-coumaroylquinic acids flavan-3-ol glycosides and procyanidins as the main anti-Aβ components of hop.

Zhang SG et al. (2022) Nonlinear Dynamics Psychol Life Sci "Dynamic Markers for Chaotic Motion in C. elegans."

Singhvi A, Hastings HM, Susman KM, Zhang SG, Magnes J

[Nonlinear Dynamics Psychol Life Sci, 2022]

We describe the locomotion of Caenorhabditis elegans (C. elegans) using nonlinear dynamics. C. elegans is a commonly studied model organism based on ease of maintenance and simple neurological structure. In contrast to traditional microscopic techniques, which require constraining motion to a 2D microscope slide, dynamic diffraction allows the observation of locomotion in 3D as a time series of the intensity at a single point in the diffraction pattern. The electric field at any point in the far-field diffraction pattern is the result of a superposition of the electric fields bending around the worm. As a result, key features of the motion can be recovered by analyzing the intensity time series. One can now apply modern nonlinear techniques; embedding and recurrence plots, providing valuable insight for visualizing and comparing data sets. We found significant markers of low-dimensional chaos. Next, we implemented a minimal biomimetic simulation of the central pattern generator of C. elegans with FitzHugh-Nagumo neurons, which exhibits undulatory oscillations similar to those of the real C. elegans. Finally, we briefly describe the construction of a biomimetic version of the Izquierdo and Beer robotic worm using Keener's implementation of the Nagumo et al. circuit.

Li H et al. (2023) Phytother Res "Hordenine improves Parkinsonian-like motor deficits in mice and nematodes by activating dopamine D2 receptor-mediated signaling."

Li W, Chen Z, Li F, Huang C, Gao M, Zhang Y, Wu X, Fan S, Li H, Wang G, Zhu J, Zhou Z, Huang X, Zhang X, Jiang X, Luo L

[Phytother Res, 2023]

Parkinson's disease (PD) is a chronic neurodegenerative disease characterized by selective loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the striatum, leading to dopamine (DA) deficiency in the striatum and typical motor symptoms. A small molecule as a dietary supplement for PD would be ideal for practical reasons. Hordenine (HOR) is a phenolic phytochemical marketed as a dietary supplement found in cereals and germinated barley, as well as in beer, a widely consumed beverage. This study was aimed to identify HOR as a dopamine D2 receptor (DRD2) agonist in living cells, and investigate the alleviative effect and mechanism of HOR on PD-like motor deficits in mice and nematodes. Our results firstly showed that HOR is an agonist of DRD2, but not DRD1, in living cells. Moreover, HOR could improve the locomotor dysfunction, gait, and postural imbalance in MPTP- or 6-OHDA-induced mice or Caenorhabditis elegans, and prevent α-synuclein accumulation via the DRD2 pathway in C. elegans. Our results suggested that HOR could activate DRD2 to attenuate the PD-like motor deficits, and provide scientific evidence for the safety and reliability of HOR as a dietary supplement.

Beer, Katharina et al. (2017) International Worm Meeting "Retromer-associated proteins and PAD-1 control TAT-5 flippase activity to inhibit extracellular vesicle budding."

Nance, Jeremy, Stigloher, Christian, Wehman, Ann, Fazeli, Gholamreza, Beer, Katharina

[International Worm Meeting, 2017]

Cells release extracellular vesicles (EV) that can mediate intercellular communication to influence development and disease (Beer & Wehman, Cell Adh Migr 2017). Despite their pleiotropic functions, the molecular details of EV release are poorly understood, especially for plasma membrane budding (ectocytosis). Previously, we showed that TAT-5 phospholipid flippase activity inhibits ectocytosis and maintains the asymmetric localization of the lipid phosphatidylethanolamine (PE) in the inner leaflet of the plasma membrane (Wehman et al., Curr Biol 2011). In a screen for additional proteins that inhibit EV budding, we identified new TAT-5 regulators related to the retromer recycling pathway (PI3Kinase VPS-34, Beclin1 homolog BEC-1, and RME-8) together with the Dopey domain protein PAD-1. PI3K, RME-8, and sorting nexins are required for the localization of TAT-5 to the plasma membrane, which is important to maintain PE asymmetry. PAD-1 also localizes to the plasma membrane, but is not required for TAT-5 localization. Rather, PAD-1 is required for the lipid flipping activity of TAT-5, further supporting the model that PE asymmetry regulates plasma membrane budding. Our study identifies new proteins that regulate extracellular vesicle release and pinpoints TAT-5 and phosphatidylethanolamine as key regulators of plasma membrane budding. Understanding the mechanisms of EV release will enable us to determine the in vivo roles of EVs during development and homeostasis.

Sinha, Amit et al. (2015) International Worm Meeting "Genome wide analysis of adaptation to acidic environments of the extremophile Turbatrix aceti."

Alkema, Mark, Sinha, Amit, Sarkies, Peter, Pirri, Jennifer

[International Worm Meeting, 2015]

The nematode Turbatrix aceti, commonly known as the vinegar eel, represents one of the rare examples of metazoans that are uniquely adapted to thrive in highly acidic environments. It can grow at a remarkable pH range from 2.5 to 9. To determine the molecular basis of mechanisms of adaptation to extreme environments we initiated a whole genome sequencing of T. aceti. Using Illumina sequencing platform, we have obtained about 11 Gigabases of data, from 55 million paired-end reads at 100 base pair length. We have assembled a first draft version of T. aceti genome to a total size of about 51 Megabases (Mb), indicating an average coverage of about 211-fold over the whole genome. This draft genome is comprised of around 83,000 contigs, with the largest contig at 78kb, and a N50 contig size of 2kb. Using the SNAP gene prediction software on this draft genome, we have identified about 25,000 protein coding genes. To improve the quality and contiguity of the genome assembly, we are currently using very long-read sequencing technology from Pacific Biosciences. T. aceti belongs to Clade IV of nematode phylogeny, which also harbors the beer mat nematode Panagrellus redivivus and many parasitic nematode species including, Strongyloides, and Globodera. We are analyzing the current set of gene predictions to search for novel gene families and protein domains specifically enriched in T. aceti as compared to other sequenced nematode genomes. Furthermore, to specifically identify genes potentially required for acid tolerance, we are using RNAseq to compare the gene expression profiles of T. aceti grown in acidic media versus in neutral media. We will present our analysis which should provide new insights to the physiological and genetic basis of adaptations to extreme environments.

Zucker-Aprison E et al. (1986) Worm Breeder's Gazette "the heptamers in the vitellogenin promoters: an update."

Blumenthal TE, Zucker-Aprison E, Cane J

[Worm Breeder's Gazette, 1986]

There are two heptamers repeated multiple times upstream of the C. enin genes. In order to obtain evidence for or against the functional importance of these heptamers we have investigated their evolutionary stability. We sequenced the homologous promoters from C. briggsae and the only C. enin promoter remaining unsequenced vit-3. This brings the total number of nematode vitellogenin promoters sequenced to eleven. The data are shown schematically in the Figure. Box 1 TGTCAAT, is shown as rectangles; Box 2 CTGATAA is shown as ovals. In general the heptamers have beer very highly conserved while the sequences between them have diverged considerably. In particular there has been strong conservation of the Box 1 heptamers centered at -45 ( just upstream of the TArA box)those at -180 (which we have suggested may be at the 5' border of the promoter regions) and at least one Box 1 between -45 and -180. In each case the locations and sequences of at least these Box 1 heptamers and at least one Box 2 heptamer per promoter have been conserved. This data strongly supports the hypothesis that Box 1 and Box 2 are involved in vit promoter function. We are initiating experiments to determine the relationship between the two heptamers and the three modes of regulation: sex stage and tissue. {Figure 1} We have noted previously the presence of Box 2 in the vertebrate vitellogenin promoters. Klein-Hitpass et al. (Cell 46 1053) have tested the idea that this heptamer plays a role in Xenopus vitellogenin gene induction by estrogen in a transient expression assay using a human mammary cell line. They present evidence that it is a binding site for an activator protein required for estrogen induction but not the site for estrogen receptor itself. They name it the 'elegans box'. Does this mean that the regulatory protein that binds to this sequence in the C. e is also present in human mammary cells?

Michael A Beer (2005) International Worm Meeting "Systematic genome-wide identification of transcriptional cis-regulatory logic in C. elegans."

Michael A Beer

[International Worm Meeting, 2005]

We have developed a systematic approach for inferring cis-regulatory logic from whole-genome microarray expression data.[1] This approach identifies local DNA sequence elements and the combinatorial and positional constraints that determine their context-dependent role in transcriptional regulation. We use a Bayesian probabilistic framework that relates general DNA sequence features to mRNA expression patterns. By breaking the expression data into training and test sets of genes, we are able to evaluate the predictive accuracy of our inferred Bayesian network. Applied to S. cerevisiae, our inferred combinatorial regulatory rules correctly predict expression patterns for most of the genes. Applied to microarray data from C. elegans[2], we identify novel regulatory elements and combinatorial rules that control the phased temporal expression of transcription factors, histones, and germline specific genes during embryonic and larval development. While many of the DNA elements we find in S. cerevisiae are known transcription factor binding sites, the vast majority of the DNA elements we find in C. elegans and the inferred regulatory rules are novel, and provide focused mechanistic hypotheses for experimental validation. Successful DNA element detection is a limiting factor in our ability to infer predictive combinatorial rules, and the larger regulatory regions in C. elegans make this more challenging than in yeast. Here we extend our previous algorithm to explicitly use conservation of regulatory regions in C. briggsae to focus the search for DNA elements. In addition, we expand the range of regulatory programs we identify by applying to more diverse microarray datasets.[3] 1. Beer MA and Tavazoie S. Cell 117, 185-198 (2004). 2. Baugh LR, Hill AA, Slonim DK, Brown EL, and Hunter, CP. Development 130, 889-900 (2003); Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, and Brown EL. Science 290, 809812 (2000). 3. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, and Hunter, CP. Development 132, 1843-1854 (2005); Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, and Kenyon C. Nature 424 277-283 (2003); Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, and Kim SK. Mol Cell 6 605-616 (2000).