Herman, Michael A. et al. (2009) International Worm Meeting "Identification of QTL involved in the C. elegans response to soil bacteria."

Kammenga, Jan E., Snoek, Basten, Herman, Michael A., Wang, Ziyi

[International Worm Meeting, 2009]

We are investigating the genetic basis of nematode interactions with soil bacteria. To this end, we have isolated soil bacteria in association with native soil nematodes from grassland soils. We are using C. elegans to model the interactions of native soil nematodes with soil bacteria and have identified C. elegans genes induced when worms are grown on various soil bacteria. We have used available mutants to demonstrate that the functions of many of these genes are important for life history traits, including fitness and lifespan (Coolon et al., submitted). However, these experiments were not designed to identify natural variation in genes that may be able to respond to selection pressures presented by soil bacteria. To discover such genes we have taken a quantitative genetic approach to identify quantitative trait loci (QTL) that underlie C. elegans responses to soil bacteria. For this experiment we chose to investigate C. elegans response to Stenotrophmonas maltophila, a ubiquitous bacterium that we isolated in association with an Oscheius sp. from grassland soils. S. maltophila can cause nosocommial infections in immuno-compromised individuals, thus is also of interest to understanding conserved innate immune responses that could affect human health. We have observed that exposure to S. maltophila shortens lifespan in both wild-type and daf-2 animals (see abstract by Vinod et al.), suggesting the involvement of other, perhaps uncharacterized, genes and innate immunity pathways. We used a set of recombinant inbred lines (RILs) generated by crosses between N2 and CB4856 (Li et al., 2006) to map QTL associated with lifespan in the presence of both E. coli and S. maltophila. We scored survivorship in the RILs and performed three replications of 10 animals each. Heritability of average lifespan was high on both E. coli and S. maltophila; 75 and 73 percent, respectively, indicating a large genetic component in the response. We were able to map QTL on LG I, II, IV and X and are now using near isogenic lines (NILs) to refine the positions of these QTL to identify the genes responsible. We will report our progress on these experiments. Reference: Li et al. 2006, PLoS Gen 2, e222.

Michael A. Herman (2006) WormBook "Hermaphrodite cell-fate specification."

Michael A. Herman

[WormBook, 2006]

There are two sexes in C. elegans, hermaphrodite and male. While there are many sex-specific differences between males and hermaphrodites that affect most tissues, the basic body plan and many of its structures are identical. However, most structures required for mating or reproduction are sexually dimorphic and are generated by sex-specific cell lineages. Thus to understand cell fate specification in hermaphrodites, one must consider how the body plan, which is specified during embryogenesis, influences the fates individual cells. One possible mechanism may involve the asymmetric distribution of POP-1 /Tcf, the sole C. elegans Tcf homolog, to anterior-posterior sister cells. Another mechanism that functions to specify cell fates along the anterior-posterior body axis in both hermaphrodites and males are the Hox genes. Since most of the cell fate specifications that occur in hermaphrodites also occur in males, the focus of this chapter will be on those that only occur in hermaphrodites. This will include the cell fate decisions that affect the HSN neurons, ventral hypodermal P cells, lateral hypodermal cells V5 , V6 , and T ; as well as the mesodermal M, Z1 , and Z4 cells and the intestinal cells. Both cell lineage-based and cell-signaling mechanisms of cell fate specification will be discussed. Only two direct targets of the sex determination pathway that influence cell fate specification to produce hermaphrodite-specific cell fates have been identified. Thus a major challenge will be to learn additional mechanisms by which the sex determination pathway interacts with signaling pathways and other cell fate specification genes to generate hermaphrodite-specific cell fates.

Michael A Herman et al. (2010) Evolutionary Biology of Caenorhabditis and Other Nematodes "BACTERIAL-RESPONSIVE TRANSCRIPTOMES OF RHABDITID SOIL NEMATODES"

David Wheeler, Michael A Herman, Brian Darby

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2010]

Nematodes, the most abundant metazoans on earth, are responsive to both biotic and abiotic environmental stimuli. Soil bacteria are an important part of the biotic environment for bacterial feeding soil nematodes, serving not only as food sources but also as potential pathogens. Interactions between nematodes and bacteria, therefore, are of significant importance to understand the ecological dynamics of the soil community. In order to dissect this complexity, we used C. elegans to model the interactions of native soil nematodes with soil bacteria and identified C. elegans genes responsive to various soil bacteria (Coolon et al, 2009 PLoS Genet 5(6): e1000503). Using mutations that inactivate many of the identified genes in C. elegans, we showed that most contribute to fitness and/or defense in a given bacterial environment. Moreover, we showed that for many genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life history traits in those environments. This observation has important implications for interpreting the results of transcriptional profiling experiments of populations of organisms in their native environments, where in many cases the genetic tools to disrupt gene function have not yet been fully developed or that interfering with gene functions in nature may not be feasible. To test this observation we have isolated four rhabditid nematodes (Oscheius tipulae, Oscheius sp. 2, Rhabditis sp, and Mesorhabditis sp.) from soils collected at Konza Prairie Biological Station and used transcriptome sequencing to investigate their responses to native soil bacteria. Specifically, we grew nematodes on a mix of gram-positive and gram-negative bacteria and sequenced normalized cDNA libraries using a Roche GS-FLX Genome Sequencer. Preliminary analysis detected about 12,000 genes expressed in each taxa with an average 10x sequence coverage. Approximately 60-70 percent of transcripts significantly matched database sequences, while another 30 percent may be lineage specific, some of which might shared among these nematodes. Our short-term goal is to use this information to determine patterns of gene expression in response to soil bacteria in the lab and in the field. In addition, these transcriptome sequences will complement genomic information available within the Rhabditid family and be useful in comparative genome studies. Ultimately, our studies will help us understand the gene functions involved in the formation and maintenance of dynamic soil nematode communities in changing environments.

Colonnello A et al. (2020) Neurotox Res "Correction to: Comparing the Neuroprotective Effects of Caffeic Acid in Rat Cortical Slices and Caenorhabditis elegans: Involvement of Nrf2 and SKN-1 Signaling Pathways."

Tunez I, Rubio-Lopez LC, Aguilera-Portillo G, Silva-Palacios A, Evaristo-Priego Y, Santamaria A, Galvan-Arzate S, Cortez-Nunez S, Aschner M, Rangel-Lopez E, Chen P, Colonnello A, Robles-Banuelos B, Garcia-Contreras R

[Neurotox Res, 2020]

One of the authors has incorrect family name spelling in the original article_. Michael Ashner should read as Michael Aschner.

Michael A Herman et al. (2001) International C. elegans Meeting "C. elegans POP-1/TCF functions in a canonical Wnt pathway that controls cell migration and a noncanonical Wnt pathway that controls cell polarity"

Kelly Greene, Michael A Herman

[International C. elegans Meeting, 2001]

In C. elegans , Wnt signaling pathways are important in controlling cell polarity and cell migrations. In the embryo, a novel Wnt pathway functions through a ß-catenin homolog, WRM-1, to down-regulate the levels of POP-1/Tcf in the posterior daughter of the EMS blastomere. The level of POP-1 is also lower in the posterior daughters of many anteroposterior asymmetric cell divisions during development. I found that this is the case for of a pair of postembryonic blast cells in the tail. In wild-type animals, the level of POP-1 is lower in the posterior daughters of the two T cells, TL and TR. Furthermore, in lin-44/Wnt mutants, in which the polarities of the T cell divisions are frequently reversed, the level of POP-1 is frequently lower in the anterior daughters of the T cells. I used a novel RNA mediated interference technique to interfere specifically with pop-1 zygotic function and determined that pop-1 is required for wild-type T cell polarity. Surprisingly, none of the three C. elegans ß-catenin homologs appeared to function with POP-1 to control T cell polarity. Wnt signaling by EGL-20/Wnt controls the migration of the descendants of the QL neuroblast by regulating the expression the Hox gene mab-5 . Interfering with pop-1 zygotic function caused defects in the migration of the QL descendants that mimicked the defects in egl-20/Wnt mutants and blocked the expression of mab-5 . This suggests that POP-1 functions in the canonical Wnt pathway to control QL descendant migration and in novel Wnt pathways to control EMS and T cell polarities. We are currently using available mutations and zygotic RNAi to determine what role other known Wnt pathway components play in the control of T cell polarity.

Zhou MH et al. (1996) Worm Breeder's Gazette "Liquid Culture of the Worms with a Fermentor"

Zhou MH, Yang H, Walthall WW

[Worm Breeder's Gazette, 1996]

The yield of C. elegans and their food (E.coli) are relatively low in the large liquid cultures growth (Koelle et al.,1994) and the whole growth process is tedious. Here we report the successful growth of C.elegans with a fermentor. The following protocol is based on the protocol by Michael Koelle and Tory Herman (1994) from Internet.

Radeke, Leah et al. (2021) International Worm Meeting "Genomic analysis of natural Stenotrophomonas bacteria and their effects on wild and domesticated C. elegans"

Radeke, Leah, Herr, Joshua, Herman, Michael

[International Worm Meeting, 2021]

Natural isolates of Caenorhabditis elegans are found in rotting vegetation in association with a multitude of bacteria (Dirksen et al., 2016). Interestingly, the microbiomes of nematodes isolated from different substrates appear to harbor a common set of bacterial genera (Zhang et al., 2017). Among these are members of the Stenotrophomonas genus. While not specifically identified yet as a component of the C. elegans microbiome, certain strains of Stenotrophomonas maltophilia have been shown to reduce C. elegans survivorship and evade host defense responses (White et al., 2016, Radeke and Herman, 2020). We have found that S. maltophilia strains are differentially virulent to C. elegans and show both common and strain-specific transcriptomic responses (White et al., 2018, Radeke and Herman, 2020). In addition, comparison of S. maltophilia genomes revealed that most S. maltophiliagenes are strain-specific, suggesting that many potential virulence factors are unique. In order to determine whether these observations reflect natural interactions, we explored the interactions between three natural C. elegans strains and 12 Stenotrophomonas sp. previously isolated from the C. elegans microbiomes of each strain or surrounding environment (obtained from the Felix, Samuel and Schulenberg laboratories). Survivorship analysis and brood counts, used as a measure of fitness, revealed that these natural Stenotrophomonas isolates showed variations in virulence and fecundity to the C. elegans natural strains and N2. Moreover, we found variation in survival and fecundity between each natural nematode strain and N2 in response to certain Stenotrophomonas isolates. This suggests differential adaptation of the C. elegans strains to natural Stenotrophomonas isolates. We determined the genome sequences of all 12 Stenotrophomonas strains to discover whether differences in observed pathogenicity between strains can be explained by differences in genetic features. Our phylogenetic analysis includes these, and 142 genomes that represent all identified lineages of Stenotrophomonas. We are testing for the presence of 48 genes previously characterized as virulence genes in other systems and testing whether our C. elegans life history data can aid in finding others. Further analyses of the bacterial genomic differences coupled with genome comparison of the nematode strains could help to understand effects of local adaptation to organismal-microbiome interactions.

Li WQ et al. (1992) Worm Breeder's Gazette "Characterization of the Axonal Guidance and Outgrowth gene Unc-33"

Shaw JE, Li WQ, Herman RK

[Worm Breeder's Gazette, 1992]

Characterization of the axonal guidance and outgrowth gene unc-33 W. Li, R. K. Herman and J. E. Shaw Department of Genetics and Cell biology, University of Minnesota, St Paul, MN 55108

Foltz, Ashley et al. (2021) International Worm Meeting "Microbiome perturbations moderately modulate Caenorhabditis elegans health and life history traits"

Foltz, Ashley, Herman, Michael

[International Worm Meeting, 2021]

Bacteria are the sole food source of C. elegans and many must be advantageous to their health, but some are detrimental. Stenotrophomonas bacteria are members of the natural C. elegans core microbiome described by Zhang et al. (2017). Surprisingly, we have shown that many Stenotrophomonas isolates are detrimental to C. elegans health, although they are an abundant member of the core microbiome. This has led us to ask several questions about the interactions that individual microbiome members have with other microbes, with the host, and how the entire microbiome community interacts with the host. We are characterizing the role of Stenotrophomonas in the microbial community to better understand these interactions. Our approach is to use an experimental microbiome (CeMbio) consisting of representative bacteria (Dirksen et al., 2020) to determine the effects of perturbing the microbiome with various Stenotrophomonas strains. We will analyze the effects on microbiome community composition and host health and fitness. We have found that individual CeMbio members have varying effects on host survival compared to the whole community, indicating that the effect of the community on survival is likely additive. We used the effects of individual Stenotrophomonas strains on C. elegans health in monoculture and their isolation source (worm or substrate) to select strains for substitution experiments. We found that C. elegans survivorship is not significantly affected by most of the perturbations, although communities with more pathogenic Stenotrophomonas strains resulted in reduced survivorship. This suggests that the CeMbio community is resilient to perturbations at least in terms of the effect on host survival. We also found that development time, used as a measure of host fitness, is mostly unaffected as compared to the intact community. Future work will determine if other measures of fitness, such as brood size, are affected by these microbiome perturbations, and how community composition of the gut microbiome might be altered.

Hengartner MO et al. (1992) Worm Breeder's Gazette "unc-50, a Gene Required for Acetylcholine Receptor Function, Encodes an Unfamiliar Protein"

Horvitz HR, Tsung N, Hengartner MO, Lewis JA

[Worm Breeder's Gazette, 1992]

unc-50, a gene requiired for acetylcholine receptor function, encodes an unfamiliar protein Michael Hengartner, Nancy Tsung, Jim Lewist, and Bob Horvitz HHMI, Dept. Biology, MIT, Cambridge, MA 02139, USA. t Division of Life Sciences, U. of Texas at San Antonio, San Antonio, IX 78249