Qiu, Tian (Autumn) et al. (2021) International Worm Meeting "Bacterial D-alanine metabolism affects C. elegans lifespan under high glucose conditions"

Qiu, Tian (Autumn), Schroeder, Nathan, Sweedler, Jonathan

[International Worm Meeting, 2021]

Microbiome-derived metabolites are able to impact the host's nervous system through the gut-brain axis. D-amino acids (D-AAs), the D-enantiomers of prevalent L-amino acids, have unique functions such as neuromodulators in animals including mollusks, rodents, and primates, while microbiota is a known contributor to the source of D-AAs in animals. Among all D-AAs, D-Ala is a potent agonist of the glycine binding site of N-methyl-D-aspartate (NMDA) glutamate receptors in vitro. Additionally, D-Ala immunoreactivity in pancreatic beta-cells and adrenocorticotropic hormone (ACTH)-secreting cells suggests its involvement in glucose homeostasis. While several researches showed microbiota as a major source of D-Ala in animals, the effect of bacterial D-Ala synthesis and metabolism on host physiology has not been studied. In this study, we fed wild type Caenorhabditis elegans N2 with Escherichia coli mutants with knockout of genes relevant to D-Ala biosynthesis (dadX, alr) and D-Ala metabolism (ddlA), and then examined changes in C. elegans phenotypes with or without the presence of high glucose. All three bacterial mutants displayed similar growth curves in nutrient-rich liquid media, but decreased D-Ala/total alanine ratio compared to the parental E. coli strain. To prevent the introduction of exogenous D-Ala, we cultured C. elegans on peptone-free NGM media. We found no statistically significant differences in life span when fed on the selected E. coli mutants. However, we observed a slight avoidance to all three bacterial mutants compared to the parental strain. When amended with 40 mM glucose, deltaddlA significantly decreased the life span of N2. No food preference was observed on glucose-amended plates. These results indicate that the combination of deficiency in bacterial DdlA activity and high glucose led to a decreased life span in C. elegans.

Qiu, Tian (Autumn) et al. (2021) International Worm Meeting "Chemical profiling of C. elegans single neurons using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)"

Andersen, Peter, Qiu, Tian (Autumn), Schroeder, Nathan, Sweedler, Jonathan

[International Worm Meeting, 2021]

Characterizing single cell heterogeneity helps reveal the chemical and functional complexity in nervous systems and aids in understanding the neurochemical basis of differential neuronal activity. While the nervous system in Caenorhabditis elegans is anatomically and genetically well-defined, the chemical profiles of their single neurons are less well-known. A non-targeted, single-cell chemical profiling of C. elegans neurons of interest is desirable to link the chemical complexity to neuronal activities. Mass spectrometry (MS) has been used to detect proteins, lipids, peptides, and metabolites in single cells. We adapt an optically guided, single cell MS technique, microMS, to profile dissociated and diffusely dispersed C. elegans single neurons. Dissociated single cells from the pan-neuronal RFP reporter rab-3p::NLS::RFP were spread across glass slides, fluorescently imaged, and coated with a chemical matrix. MicroMS identified and converted single cell locations in the fluorescent image into instrument stage positions. The stage positions enable automated single cell sampling with a matrix-assisted laser desorption/ionization MS (MALDI-MS) instrument. We successfully applied lysis and cell dissociation protocols to C. elegans and located individual cells using fluorescent microscopy. Preliminary results showed lipid and peptide-like signals from single neurons and we are currently optimizing the sample preparation to increase mass spectral quality.

Morgado-Palacin L (2021) J Cell Biol "Ye Tian: Surveilling stress to live longer."

Morgado-Palacin L

[J Cell Biol, 2021]

Ye Tian investigates how mitochondrial stress signaling pathways regulate longevity using C. elegans as a model system.

Sulston JE et al. (1992) Nature "The C. elegans genome sequencing project: a beginning."

Wilson RK, Metzstein MM, Ainscough R, Waterston RH, Coulson AR, Craxton M, Thomas K, Dear S, Qiu L, Staden R, Berks M, Halloran N, Thierry-Mieg J, Hillier L, Sulston JE, Du Z, Durbin RM, Hawkins TL, Green P

[Nature, 1992]

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.AD - MRC Laboratory of Molecular Biology, Cambridge, UK.FAU - Sulston, JAU - Sulston JFAU - Du, ZAU - Du ZFAU - Thomas, KAU - Thomas KFAU - Wilson, RAU - Wilson RFAU - Hillier, LAU - Hillier LFAU - Staden, RAU - Staden RFAU - Halloran, NAU - Halloran NFAU - Green, PAU - Green PFAU - Thierry-Mieg, JAU - Thierry-Mieg JFAU - Qiu, LAU - Qiu LAU - et al.LA - engPT - Journal ArticleCY - ENGLANDTA - NatureJID - 0410462RN - 0 (Cosmids)SB - IM

Tatar M et al. (2016) Cell "Mitochondria: Masters of Epigenetics."

Tatar M, Sedivy JM

[Cell, 2016]

Accumulating evidence argues that aging exerts a profound influence on epigenetics, and vice versa. A pair of studies by Merkwirth etal. and Tian etal. now provide insights on how mitochondrial stress experienced by C.elegans larvae propagates a specific and persistent epigenetic response that protects adult cells and extends lifespan.

McPhee CK et al. (2010) Cell "Autophagy shows its animal side."

McPhee CK, Baehrecke EH

[Cell, 2010]

Most autophagy genes have been discovered in the single-celled yeast Saccharomyces cerevisiae, and little is known about autophagy genes that are specific to multicellular animals. In this issue, Tian et al. (2010) now identify four new autophagy genes: one specific to the nematode Caenorhabditis elegans and three conserved from worms to mammals.

Qiu C et al. (2019) Elife "A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity."

Rajeev S, Tanaka Hall TMT, Zhang C, Lasley AE, Campbell ZT, Bhat VD, Qiu C, Wine RN

[Elife, 2019]

In the <i>Caenorhabditis elegans</i> germline, <i>fem-3</i> Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat, Qiu, et al. 2019). <i>In vitro</i> selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.

Sood P et al. (2017) Traffic "Cargo crowding at actin-rich regions along axons causes local traffic jams."

Kumar TV, Koushika SP, Nonet ML, Murthy K, Menon GI, Sood P

[Traffic, 2017]

Steady axonal cargo flow is central to the functioning of healthy neurons. However, a substantial fraction of cargo in axons remains stationary up to several minutes (Kang, Tian et al. 2008, Tang, Scott et al. 2012, Tang, Scott et al. 2013, Iacobucci, Rahman et al. 2014). We examine the transport of precursors of synaptic vesicles (pre-SVs), endosomes and mitochondria in C. elegans touch receptor neurons (TRNs), showing that stationary cargo are predominantly present at actin-rich regions along the neuronal process. Stationary vesicles at actin-rich regions increase the propensity of moving vesicles to stall at the same location, resulting in traffic jams arising from physical crowding. Such local traffic jams at actin-rich regions are likely to be a general feature of axonal transport since they also occur in Drosophila neurons. Repeated touch stimulation of C. elegans reduces the density of stationary pre-SVs, indicating that these traffic jams can act as both sources and sinks of vesicles. This suggests that vesicles trapped in actin-rich regions are functional reservoirs that may contribute to maintaining robust cargo flow in the neuron.

Petersen, Carola et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "New insights into the natural ecology of C. elegans"

Petersen, Carola, Schulenburg, Hinrich

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Only little is known about the ecology of the model nematode Caenorhabditis elegans - in stark contrast to the enormous database on the nematode's biology under laboratory conditions. T o enhance our understanding of the worm's natural requirements and preferences, we sampled Caenorhabditis strains continuously across 1.5 years from rotting apples and compost heaps in three North German locations. C. elegans and the related nematode species C. remanei were isolated throughout summer and autumn from the same site, but rarely the same substrate sample, possibly suggesting niche separation. The occurrence of C. elegans itself was related to environmental humidity and rain, rather than temperature as previously demonstrated for other natural populations. Genetic differentiation was analysed for populations from two locations using microsatellite markers. Significant genetic structuring was detected between locations and, within single locations, across long time periods (i.e., a 10-year time span), but not throughout the 1.5 years sampling period. Our analysis also revealed significant phenotypic variation in the nematode's interaction with naturally coexisting bacteria and pathogens. Our study emphasizes the importance of field studies of C. elegans in order to fully appreciate the nematode's life history characteristics.

Petersen C et al. (2014) BMC Ecol "The prevalence of Caenorhabditis elegans across 1.5years in selected North German locations: the importance of substrate type, abiotic parameters, and Caenorhabditis competitors."

Dirksen P, Petersen C, Schulenburg H, Strathmann EA, Prahl S

[BMC Ecol, 2014]

BACKGROUND: Although the nematode Caenorhabditis elegans is a major model organism in diverse biological areas and well studied under laboratory conditions, little is known about its ecology. Therefore, characterization of the species' natural habitats should provide a new perspective on its otherwise well-studied biology. The currently best characterized populations are in France, demonstrating that C. elegans prefers nutrient- and microorganism-rich substrates such as rotting fruits and decomposing plant matter. In order to extend these findings, we sampled C. elegans continuously across 1.5years from rotting apples and compost heaps in three North German locations. RESULTS: C. elegans was found throughout summer and autumn in both years. It shares its habitat with the related nematode species C. remanei, which could thus represent an important competitor for a similar ecological niche. The two species were isolated from the same site, but rarely the same substrate sample. In fact, C. elegans was mainly found on compost and C. remanei on rotten apples, possibly suggesting niche separation. The occurrence of C. elegans itself was related to environmental humidity and rain, although the correlation was significant for only one sampling site each. Additional associations between nematode prevalence and abiotic parameters could not be established. CONCLUSIONS: Taken together, our findings vary from the previous results for French C. elegans populations in that the considered German populations always coexisted with the congeneric species C. remanei (rather than C. briggsae as in France) and that C. elegans prevalence can associate with humidity and rain (rather than temperature, as suggested for French populations). Consideration of additional locations and time points is thus essential for full appreciation of the nematode's natural ecology.