scholarly journals Front cover: Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level

PROTEOMICS ◽  
2016 ◽  
Vol 16 (3) ◽  
pp. NA-NA
Author(s):  
Dalila Bensaddek ◽  
Vikram Narayan ◽  
Armel Nicolas ◽  
Alejandro Brenes Murillo ◽  
Anton Gartner ◽  
...  
Keyword(s):  
Data Analysis ◽  
Proteome Analysis ◽  
Front Cover ◽  
C Elegans ◽  
Single Worm

scholarly journals Micro-proteomics with iterative data analysis: Proteome analysis inC. elegansat the single worm level

PROTEOMICS ◽  
2016 ◽  
Vol 16 (3) ◽  
pp. 381-392 ◽  
Author(s):  
Dalila Bensaddek ◽  
Vikram Narayan ◽  
Armel Nicolas ◽  
Alejandro Brenes Murillo ◽  
Anton Gartner ◽  
...  
Keyword(s):  
Data Analysis ◽  
Proteome Analysis ◽  
Single Worm

scholarly journals Effects of larval density on gene regulation in C. elegans during routine L1 synchronization

2018 ◽  
Author(s):  
Io Long Chan ◽  
Oliver J. Rando ◽  
Colin C. Conine
Keyword(s):  
Gene Regulation ◽  
Larval Density ◽  
Low Density ◽  
Rna Seq ◽  
C Elegans ◽  
Signalling Molecule ◽  
Gfp Reporter ◽  
Short Period ◽  
Early Developmental ◽  
Single Worm

ABSTRACTBleaching gravid C. elegans followed by a short period of starvation of the L1 larvae is a routine method performed by worm researchers for generating synchronous populations for experiments. During the process of investigating dietary effects on gene regulation in L1 stage worms by single-worm RNA-Seq, we found that the density of resuspended L1 larvae affects expression of many mRNAs. Specifically, a number of genes related to metabolism and signalling are highly expressed in worms arrested at low density, but are repressed at higher arrest densities. We generated a GFP reporter strain based on one of the most density-dependent genes in our dataset – lips-15 – and confirmed that this reporter was expressed specifically in worms arrested at relatively low density. Finally, we show that conditioned media from high density L1 cultures was able to downregulate lips-15 even in L1 animals arrested at low density, and experiments using daf-22 mutant animals demonstrated that this effect is not mediated by the ascaroside family of signalling pheromones. Together, our data implicate a soluble signalling molecule in density sensing by L1 stage C. elegans, and provide guidance for design of experiments focused on early developmental gene regulation.

scholarly journals The TGF-β ligand DBL-1 is a key player in a multifaceted probiotic protection against MRSA in C. elegans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria G. M. Mørch ◽  
Katrine V. Møller ◽  
Marianne O. Hesselager ◽  
Rikke H. Harders ◽  
Caroline L. Kidmose ◽  
...  
Keyword(s):  
Proteome Analysis ◽  
Mechanisms Of Action ◽  
Probiotic Bacteria ◽  
Host Responses ◽  
Resistant Bacteria ◽  
C Elegans ◽  
Beneficial Effects ◽  
Evolutionarily Conserved ◽  
Control Food ◽  
Mechanistic Basis

AbstractWorldwide the increase in multi-resistant bacteria due to misuse of traditional antibiotics is a growing threat for our health. Finding alternatives to traditional antibiotics is thus timely. Probiotic bacteria have numerous beneficial effects and could offer safer alternatives to traditional antibiotics. Here, we use the nematode Caenorhabditis elegans (C. elegans) to screen a library of different lactobacilli to identify potential probiotic bacteria and characterize their mechanisms of action. We show that pretreatment with the Lactobacillus spp. Lb21 increases lifespan of C. elegans and results in resistance towards pathogenic methicillin-resistant Staphylococcus aureus (MRSA). Using genetic analysis, we find that Lb21-mediated MRSA resistance is dependent on the DBL-1 ligand of the TGF-β signaling pathway in C. elegans. This response is evolutionarily conserved as we find that Lb21 also induces the TGF-β pathway in porcine epithelial cells. We further characterize the host responses in an unbiased proteome analysis and identify 474 proteins regulated in worms fed Lb21 compared to control food. These include fatty acid CoA synthetase ACS-22, aspartic protease ASP-6 and vitellogenin VIT-2 which are important for Lb21-mediated MRSA resistance. Thus, Lb21 exerts its probiotic effect on C. elegans in a multifactorial manner. In summary, our study establishes a mechanistic basis for the antimicrobial potential of lactobacilli.

scholarly journals Topological Data Analysis of C. elegans Locomotion and Behavior

2021 ◽  
Vol 4 ◽  
Author(s):  
Ashleigh Thomas ◽  
Kathleen Bates ◽  
Alex Elchesen ◽  
Iryna Hartsock ◽  
Hang Lu ◽  
...  
Keyword(s):  
Data Analysis ◽  
Persistent Homology ◽  
Model Organism ◽  
Topological Data Analysis ◽  
Trade Off ◽  
High Throughput Data ◽  
C Elegans ◽  
Novel Technique ◽  
And Behavior ◽  
Topological Data

We apply topological data analysis to the behavior of C. elegans, a widely studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data. Our methods allow us to distinguish and classify videos from various environmental conditions and we analyze the trade-off between accuracy and interpretability. Furthermore, we present a novel technique for visualizing the outputs of our analysis in terms of the input. Specifically, we use representative cycles of persistent homology to produce synthetic videos of stereotypical behaviors.

scholarly journals Mating-induced Male Death and Pheromone Toxin-regulated Androstasis

2015 ◽  
Author(s):  
Cheng Shi ◽  
Alexi M. Runnels ◽  
Coleen T. Murphy
Keyword(s):  
Ectopic Expression ◽  
Cost Of Reproduction ◽  
Male Pheromone ◽  
Male Population ◽  
Reproduction Mode ◽  
C Elegans ◽  
Evolutionarily Conserved ◽  
Chemical Messenger ◽  
Species Specific ◽  
Single Worm

AbstractHow mating affects male lifespan is poorly understood. Using single worm lifespan assays, we discovered that males live significantly shorter after mating in both androdioecious (male and hermaphroditic) and gonochoristic (male and female) Caenorhabditis. Germline-dependent shrinking, glycogen loss, and ectopic expression of vitellogenins contribute to male post-mating lifespan reduction, which is conserved between the sexes. In addition to mating-induced lifespan decrease, worms are subject to killing by male pheromone-dependent toxicity. C. elegans males are the most sensitive, whereas C. remanei are immune, suggesting that males in androdioecious and gonochoristic species utilize male pheromone differently as a toxin or a chemical messenger. Our study reveals two mechanisms involved in male lifespan regulation: germline-dependent shrinking and death is the result of an unavoidable cost of reproduction and is evolutionarily conserved, whereas male pheromone-mediated killing provides a novel mechanism to cull the male population and ensure a return to the self-reproduction mode in androdioecious species. Our work highlights the importance of understanding the shared vs. sex- and species-specific mechanisms that regulate lifespan.

scholarly journals Improved methods for protein and single-molecule RNA detection in C. elegans embryos

2021 ◽  
Author(s):  
Dylan M Parker ◽  
Lindsay P Winkenbach ◽  
Annemarie Parker ◽  
Sam Boyson ◽  
Erin Osborne Nishimura
Keyword(s):  
Data Analysis ◽  
Single Molecule ◽  
Gene Products ◽  
Biological Functions ◽  
Single Molecule Fluorescence ◽  
Rna Detection ◽  
C Elegans ◽  
Improved Methods ◽  
Data Analysis Methods

Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule Fluorescence In Situ Hybridization (smFISH) and Immunofluorescence (IF) visualize the abundance and localization of mRNAs and proteins, respectively, allowing researchers to elucidate the localization, dynamics, and functions of many genes. Here, we describe several improvements and optimizations to existing IF and smFISH approaches specifically for use in C. elegans embryos. We present 1) optimized fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility, 2) a streamlined, in-tube approach that negates freeze-cracking, 3) the smiFISH (single molecule inexpensive FISH) adaptation that reduces cost, 4) an assessment of optimal anti-fade products, and 5) straightforward quantification and data analysis methods. Most importantly, published IF and smFISH protocols have predominantly been mutually exclusive, preventing exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we present methods to combine IF and smFISH protocols in C. elegans embryos including an efficient method harnessing nanobodies. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol.

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