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[
International Worm Meeting,
2021]
Interactions with and alterations of the gut microbiome with age can have a dramatic impact on our physiology. Changes in the membership of the gut microbiome can dictate levels of immunity, stress resistance and vitality across systems. Linking changes in the microbiome to microbial factors that may influence them has been a challenge in many systems due to the complexity of the microbiomes and intractability of following these interactions over an individual's lifespan. To address this gap, we leveraged recent advances in characterization of the natural microbiome of C. elegans to examine both the gut microbiome on the aging process in C. elegans and vice versa. First, we utilized a 64-member microbiome (BIGbiome) and asked whether microbiome membership changed as animals age. Compared to E. coli OP50 controls, the BIGbiome community had several significant impacts on three genetically diverse strains (lab N2, plus wild JU1400 and ED3017), including extended lifespan (up to 10%), improved healthspans (e.g., 36% at
d5) and greater reproductive output (23% higher at
d1 adults). In addition, increases in the levels of Ochrobactrum BH3, a dominant colonizer of the C. elegans gut, from 0% to 25% in the BIGbiome community yielded a dose dependent promotion of reproductive rates. This indicates that specific members (such as Ochrobactrum) may promote reproductive rates and healthy aging in C. elegans. Next, we determined how C. elegans age may influence microbiome membership. To do this, we monitored gut microbiomes of single animals for each of the C. elegans strains for the first 10 days of adulthood. Each of the host strains exhibited gut microbiomes distinct from the surrounding lawn in early adulthood, though they differed in (i) dominant microbes at that age, and (ii) the extent of the lifespan with enriched microbes. This suggests that the ability to maintain a specific microbiome community may be driven by changes in host responses in C. elegans. Last, we sought to examine the genes that mediate Ochrobactrum impact on the aging process. We screened a ~1000 microbiome regulators by RNAi for defects in Ochrobactrum colonization with age, then looked for altered reproductive rates in candidates (32 clones). Hits from these studies suggest that Ochrobactrum may be promoting reproduction via germline interactions directly. Together, our results highlight use of C. elegans as a model system for investigating microbiome influence on host aging.
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Vidal, Daniela, Edwards, Hunter, Samuel, Buck, Vanpalli, Siva, Anupom, Taslim, Zhang, Fan
[
International Worm Meeting,
2021]
Dysregulation of the human gut microbiome has been linked to the development of many human diseases, including inflammatory disorders such as irritable bowel syndrome and ulcerative colitis. Moreover, studies have shown that the microorganisms colonizing the GI tract interact extensively with host signaling pathways, including the highly conserved ageing-related Insulin/IGF signaling pathway. The mechanisms by which the gut microbiota influences host gene expression and physiology remains unclear. With a rapid lifespan of less than one month, C. elegans have been used to study the relationship between host phenotypes and gene expression for decades. C. elegans are typically grown on a non-native singular food source, E. coli OP50, selected for its accessibility and ease of growth in the laboratory environment. The versatility of the soil dwelling nematode offers a unique platform to study complex microbial communities in a well-defined gnotobiotic environment, however very little is known about the effects of non-E.coli bacteria on C. elegans health and survival. Here we conduct comprehensive screen of select individual bacteria isolated from natural C. elegans microbiome. Sterile C. elegans can be housed in pillared microfluidic chambers where bacterial membership can be precisely controlled and readily delivered to control quality and quantity of the bacteria. Using this platform, we show that individual members of the natural microbiome colonize the C. elegans gut and exert variable effects on host physiology including delayed development and growth, stress resistance and survival. Specifically, we find that two bacterial isolates, which dominate the guts of C. elegans, Ochrobactrum BH3 and Myroides BIGb0244, extend lifespan and healthspan in our semi-liquid microfluidic environment. Our results lay the foundation for future, high-throughput screens of larger communities and panels of microbes, such as the BIGbiome and CeMbio model microbiomes. This robust system will allow for simultaneous and comprehensive assessment of the effects of both individual isolates and multi-member communities on host gene expression and aging related phenotypes.
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[
Elife,
2018]
A diverse array of species on the planet employ the Earth's magnetic field as a navigational aid. As the majority of these animals are migratory, their utility to interrogate the molecular and cellular basis of the magnetic sense is limited. Vidal-Gadea and colleagues recently argued that the worm <i>Caenorhabditis elegans</i> possesses a magnetic sense that guides their vertical movement in soil. In making this claim, they relied on three different behavioral assays that involved magnetic stimuli. Here, we set out to replicate their results employing blinded protocols and double wrapped coils that control for heat generation. We find no evidence supporting the existence of a magnetic sense in <i>C. elegans</i>. We further show that the Vidal-Gadea hypothesis is problematic as the adoption of a correction angle and a fixed trajectory relative to the Earth's magnetic inclination does not necessarily result in vertical movement.
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[
Science,
2000]
Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.AD - Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.FAU - Walhout, A JAU - Walhout AJFAU - Sordella, RAU - Sordella RFAU - Lu, XAU - Lu XFAU - Hartley, J LAU - Hartley JLFAU - Temple, G FAU - Temple GFFAU - Brasch, M AAU - Brasch MAFAU - Thierry-Mieg, NAU - Thierry-Mieg NFAU - Vidal, MAU - Vidal MLA - engID - 1 R21 CA81658 A 01/CA/NCIID - 1 RO1 HG01715-01/HG/NHGRIPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Genetic Vectors)RN - 0 (Helminth Proteins)RN - 0 (LIN-35 protein)RN - 0 (LIN-53 protein)RN - 0 (Repressor Proteins)RN - 0 (Retinoblastoma Protein)SB - IM
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[
Worm Breeder's Gazette,
1999]
We are interested in investigating the function of nematode homologues of proteins known to be important for innate immunity in other organisms. Genetic studies with the mouse have shown that a single locus is involved in innate resistance against a range of pathogens including Mycobacterium bovis (BCG), M. intracellulare, M. lepraemurium, Salmonella typhirium and Leishmania. The corresponding gene codes for a protein Nramp1 (Natural resistance-associated macrophage protein; Vidal et al., 1993, Cell, 73, 469-485) that is specifically expressed in macrophages. A highly similar protein, Nramp2, is expressed ubiquitously and appears not to have a role in defense against infection. The Nramp proteins are members of a family of metal ion transporters, that includes the yeast Smf proteins.
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[
J Neurophysiol,
2015]
Although the ability to detect humidity (i.e., hygrosensation) represents an important sensory attribute in many animal species (including humans), the neurophysiological and molecular bases of such sensory ability remain largely unknown in many animals. Recently, Russell and colleagues (Russell J, Vidal-Gadea AG, Makay A, Lanam C, Pierce-Shimomura JT. Proc Natl Acad Sci USA 111: 8269-8274, 2014) provided for the first time neuromolecular evidence for the sensory integration of thermal and mechanical sensory cues which underpin the hygrosensation strategy of an animal (i.e., the free-living roundworm Caenorhabditis elegans) that lacks specific sensory organs for humidity detection (i.e., hygroreceptors). Due to the remarkable similarities in the hygrosensation transduction mechanisms used by hygroreceptor-provided (e.g., insects) and hygroreceptor-lacking species (e.g., roundworms and humans), the findings of Russell et al. highlight potentially universal mechanisms for humidity detection that could be shared across a wide range of species, including humans.
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[
International Worm Meeting,
2019]
Animals change their locomotion or gaits in response to environmental condition. In vertebrates, gait transition has been shown to be mediated by monoamines, which is conserved across many species including the nematode Caenorhabditis elegans (Vidal-Gadea et al., 2011). However, molecular mechanisms of gait transition are still unclear. C. elegans exhibits two gaits, swimming in liquids and crawling on dense gels. C. elegans genome contains evolutionarily conserved 28 DEG/ENaC channels, of which functions may be involved in mechanosensory transduction and locomotion (Goodman and Schwarz, 2003). We first hypothesized that mechanosensitive channels could act as a gait transition initiator and examined crawl-to-swim transition phenotype in DEG/ENaC mutants. We found that while
acd-5 mutants show normal crawling, transition from crawling to swimming upon liquid exposure is defective, suggesting roles of ACD-5 in gait transition. We are currently generating
acd-5 rescue lines and examining expression pattern of
acd-5.
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[
East Coast Worm Meeting,
1998]
The complete genome sequence of C. elegans should be available by the end of this year. It is estimated that the sequence will reveal approximately 13,000 ORFs, most of which correspond to predicted gene-products whose functions have yet to be determined. Hence, in addition to the powerful genetic and biochemical approaches used conventionally, it will be important to develop high-throughput strategies to help addressing the biological role of these gene-products. Since many cellular processes depend on protein-protein interactions, one approach used to elucidate functions consists in identifying physical interactions between proteins. Thus, our long-term goal is to generate a comprehensive protein interaction map for C. elegans, as a way to help characterizing regulatory networks and protein complexes in this model organism (see the abstract by Vidal et al.). We have selected the yeast two-hybrid system to identify potential interactions since on the one hand, its effectiveness has been demonstrated widely, and on the other, it is readily automatable. In this system, interaction between X and Y proteins, expressed as fusions with a DNA binding domain (DB) and an activation domain (AD) respectively, reconstitutes a functional transcription factor which in turn leads to a selectable phenotype. Each potential interaction is referred to as an Interaction Sequence Tag (IST), defined as a pair of short sequences obtained from cDNAs encoding interacting proteins in the two-hybrid system. We intend to release ISTs into AceDB in a format similar to the introduction of ESTs. We will describe the following aspects of the project: -the choice of the first subset of DB-X hybrid proteins used as "baits", -the semi-automated method used to generate the DB-X fusions, -the design and construction of an AD-cDNA library, -the semi-automated two-hybrid selections used to identify ISTs, and -the potential significance of the initial ISTs identified. Since ISTs merely represent hypotheses of interactions, we are also developing high throughput strategies to assess the biological significance of the potential interactions directly in worms (see the abstract by Vidal et al.). The combination of both the IST information available in AceDB and the functional assessment in vivo should be helpful in generating a comprehensive interaction map for C. elegans.
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[
Elife,
2018]
Many animals can orient using the earth's magnetic field. In a recent study, we performed three distinct behavioral assays providing evidence that the nematode <i>Caenorhabditis elegans</i> orients to earth-strength magnetic fields (<xref ref-type="bibr" rid="
bib28">Vidal-Gadea et al., 2015</xref>). A new study by Landler et al. suggests that <i>C. elegans</i> does not orient to magnetic fields (<xref ref-type="bibr" rid="
bib10">Landler et al., 2018</xref>). They also raise conceptual issues that cast doubt on our study. Here, we explain how they appear to have missed positive results in part by omitting controls and running assays longer than prescribed, so that worms switched their preferred migratory direction within single tests. We also highlight differences in experimental methods and interpretations that may explain our different results and conclusions. Together, these findings provide guidance on how to achieve robust magnetotaxis and reinforce our original finding that <i>C. elegans</i> is a suitable model system to study magnetoreception.
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Doucette-Stamm L, Lamesch PE, Reboul J, Temple GF, Hartley JL, Brasch MA, Hill DE, Vaglio P, Thierry-Mieg N, Shin-i T, Lee H, Moore T, Vandenhaute J, Kohara Y, Vidal M, Jackson C, Thierry-Mieg J, Tzellas N, Thierry-Mieg D, Hitti J
[
Nat Genet,
2001]
The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.AD - Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.FAU - Reboul, JAU - Reboul JFAU - Vaglio, PAU - Vaglio PFAU - Tzellas, NAU - Tzellas NFAU - Thierry-Mieg, NAU - Thierry-Mieg NFAU - Moore, TAU - Moore TFAU - Jackson, CAU - Jackson CFAU - Shin-i, TAU - Shin-i TFAU - Kohara, YAU - Kohara YFAU - Thierry-Mieg, DAU - Thierry-Mieg DFAU - Thierry-Mieg, JAU - Thierry-Mieg JFAU - Lee, HAU - Lee HFAU - Hitti, JAU - Hitti JFAU - Doucette-Stamm, LAU - Doucette-Stamm LFAU - Hartley, J LAU - Hartley JLFAU - Temple, G FAU - Temple GFFAU - Brasch, M AAU - Brasch MAFAU - Vandenhaute, JAU - Vandenhaute JFAU - Lamesch, P EAU - Lamesch PEFAU - Hill, D EAU - Hill DEFAU - Vidal, MAU - Vidal MLA - engID - R21 CA81658 A 01/CA/NCIID - RO1 HG01715-01/HG/NHGRIPT - Journal ArticleCY - United StatesTA - Nat GenetJID - 9216904SB - IM