Jarrell, T. et al. (2011) International Worm Meeting "Progress Towards a Reconstruction of a C. elegans Male Anterior Nervous System."

Bloniarz, A., Wang, Y., Jarrell, T., Xu, M., Emmons, S. W., Nguyen, K., Hall, D. H. H., Brittin, C.

[International Worm Meeting, 2011]

Having completed the connectivity of the posterior nervous system of a C. elegans male, we are now pursuing reconstruction of the male head. The anterior nervous system of the male contains about 200 neurons common to both sexes and only 4 male-specific CEM neurons as well as the processes of three EF neurons from the tail. This is in stark contrast with the posterior nervous system, which contains 85 male-specific neurons, 55 common neurons whose cell bodies are in the posterior and the processes of 18 common neurons running into the tail from the anterior. Our present connectivity results from the tail demonstrate that some common neurons have sexually dimorphic wiring. Therefore, we anticipate that common neurons in the head may also display different wiring in the male compared to the hermaphrodite. Male-specific EF neuron processes which run into the head will establish further differences. In addition to copulation, male behavior differs from that of the hermaphrodite in several general ways, such as locomotion, chemotaxis, and attraction to food and mates. Coordination of mating behavior with non-mating behavior likely is embedded in the nervous system wiring of the head. In order to compare male connectivity in the head to that of the hermaphrodite, and to complete the male connectome, a reconstruction of the anterior nervous system is necessary. Using traditional fixation, sectioning and staining methods, over 5,000 serial thin sections were obtained from a healthy male and then imaged using two TEMs. A Philips CM10 was used to image the ventral and dorsal nerve cords, and a Philips Tecnai 20 was used to generate montages of over 100 images necessary to cover each section in the nerve ring. Over 110,000 images in all were collected during a 17 month period. Images were digitally aligned using software designed by G. Hood and A. Wetzel at the Pittsburgh Supercomputing Center (see abstract). Aligned images were then entered into the software platform Elegance where reconstruction is under way. A full reconstruction is expected to take six to eight weeks. In addition, work has begun on an Elegance-based reconstruction of the hermaphrodite nerve ring from the Cambridge electron micrographs used for Mind of the Worm. Having the connectivity data in the same format will be necessary in order to make a rigorous comparison of male and hermaphrodite wiring, including relative synaptic strengths.

Samuel ADT et al. (2003) J Neurosci "Synaptic activity of the AFD neuron in Caenorhabditis elegans correlates with thermotactic memory."

Murthy VN, Samuel ADT, Silva RA

[J Neurosci, 2003]

Thermotactic behavior in Caenorhabditis elegans is sensitive to both a worm's ambient temperature (T-amb) and its memory of the temperature of its cultivation (T-cult). The AFD neuron is part of a neural circuit that underlies thermotactic behavior. By monitoring the fluorescence of pH-sensitive green fluorescent protein localized to synaptic vesicles, we measured the rate of the synaptic release of AFD in worms cultivated at temperatures between 15 and 25degreesC, and subjected to fixed, ambient temperatures in the same range. We found that the rate of AFD synaptic release is high if either T-amb > T-cult or T-amb > T-cult, but AFD synaptic release is low if T-amb congruent to T-cult. This suggests that AFD encodes a direct comparison between T-amb and T-cult.

Bommireddy R et al. (2007) Trends Mol Med "TGFbeta1 and Treg cells: alliance for tolerance."

Bommireddy R, Doetschman T

[Trends Mol Med, 2007]

Transforming growth factor beta1 (TGFbeta1), an important pleiotropic, immunoregulatory cytokine, uses distinct signaling mechanisms in lymphocytes to affect T-cell homeostasis, regulatory T (T(reg))-cell and effector-cell function and tumorigenesis. Defects in TGFbeta1 expression or its signaling in T cells correlate with the onset of several autoimmune diseases. TGFbeta1 prevents abnormal T-cell activation through the modulation of Ca(2+)-calcineurin signaling in a Caenorhabditis elegans Sma and Drosophila Mad proteins (SMAD)3 and SMAD4-independent manner; however, in T(reg) cells, its effects are mediated, at least in part, through SMAD signaling. TGFbeta1 also acts as a pro-inflammatory cytokine and induces interleukin (IL)-17-producing pathogenic T-helper cells (T(h) IL-17 cells) synergistically during an inflammatory response in which IL-6 is produced. Here, we will review TGFbeta1 and its signaling in T cells with an emphasis on the regulatory arm of immune tolerance.

Emmons, S et al. (2015) International Worm Meeting "Whole-animal C. elegans connectomes."

Emmons, S, Wang, Y, Nguyen, K, Jarrell, T, Cook, S, Yakovlev, M, Hall, D

[International Worm Meeting, 2015]

We have assembled for the first time complete wiring diagrams of the entire nervous systems of C. elegans adults of both sexes. For the hermaphrodite, we reanalyzed the electron micrographs that served as the basis for the 1986 publication "The Mind of a Worm" (White et al, 1986). For the male, we combined the posterior connectivity we published previously (Jarrell et al, 2012), obtained by analyzing Cambridge electron micrographs (Sulston et al, 1970), with data from our own series through a male head. For the pharynx we reanalyzed the micrographs analyzed previously by Donna Albertson (Albertson and Thomson, 1976). For some neurons, we added data from new electron micrographs of legacy grids. Notably, we added connectivity of SAB motorneurons to body wall muscles in the head (muscles 1-7); these neurons contribute 37% of the total input to these muscles. Finally, significant gaps still remained: to our knowledge, a region posterior of the vulva (posterior of the N2U series, anterior of the male N2Y series) has never been examined by electron microscopy. To fill in these areas, we added connections to complete the chains of motor neurons and muscles by assuming a regular structure. Connectivity matrices, neuron maps, and synapse lists are available on our website: WormWiring.org. Analysis of the complete, quantitative datasets by graph layout algorithms yields biologically meaningful displays. When an algorithm is applied that utilizes the "spring-electric" approach, in which nodes repel each other uniformly and attract according to the strength of their connectivity (Allegro Layout, allegroviva.com), neurons of similar or related function are grouped together. At the next higher level, clear modules are separated. When the arrangement is graphically illustrated using the display tools of Cytoscape, the functional pathways and hierarchical arrangement of the entire worm neuromuscular system are revealed-the layout closely matches the worm's anatomy. The overall arrangement is the same in both sexes, with the addition in the hermaphrodite of the vulva muscles and circuits and to the male "tail" of the enormous copulatory circuits. Along with the sensory pathways for head contact and for odorants and chemicals, pathways leading from pheromone sensing neurons reveal a sexual circuit in the head, elements of which (AVF, PVQ, and RIM interneurons) are shared by both sexes, along with, in the hermaphrodite, the HSN neurons, and in the male, the CEM sensory neurons and the EF and MCM interneurons (for the new MCM interneurons, see the Abstract by Sammut et al).

Agulnik SI et al. (1995) Genomics "Conservation of the T-box gene family from Mus musculus to Caenorhabditis elegans."

Bollag RJ, Silver LM, Agulnik SI

[Genomics, 1995]

Recently, a novel family of genes with a region of homology to the mouse T locus, which is known to play a crucial, and conserved, role in vertebrate development, has been discovered. The region of homology has been named the T-box. The T-box domain of the prototypical T locus product is associated with sequence-specific DNA binding activity. In this report, we have characterized four members of the T-box gene family from the nematode Caenorhabditis elegans. All lie in close proximity to each other in the middle of chromosome III. Homology analysis among all completely sequenced T-box products indicates a larger size for the conserved T-box domain (166 to 203 residues) than previously reported. Phylogenetic analysis suggests that one C. elegans T-box gene may be a direct ortholog of the mouse Tbx2 and Drosophila omb genes. The accumulated data demonstrate the ancient nature of the T-box gene family and suggest the existence of at least three separate T-box-containing genes in a common early metazoan ancestor to nematodes and vertebrates.

Ju T et al. (2006) Glycobiology "Identification of core 1 O-glycan T-synthase from Caenorhabditis elegans."

Ju T, Zheng Q, Cummings RD

[Glycobiology, 2006]

The common O-glycan core structure in animal glycoproteins is the core 1 disaccharide Galbeta1-3GalNAcalpha1-Ser/Thr, which is generated by addition of Gal to GalNAcalpha1-Ser/Thr by core 1 UDP-Gal:GalNAcalpha1-Ser/Thr beta1,3-galactosyltransferase (core 1 beta3-Gal-T or T-synthase, EC2.4.1.122)(2). Although O-glycans play important roles in vertebrates, much remains to be learned from model organisms such as the free-living nematode Caenorhabditis elegans, which offer many advantages in exploring O-glycan structure/function. Here we report the cloning and enzymatic characterization of T-synthase from C. elegans (Ce-T-synthase). A putative C. elegans gene for T-synthase, C38H2.2, was identified in GenBank by a BlastP search using the human T-synthase protein sequence. The full-length cDNA for Ce-T-synthase, which was generated by PCR using a C. elegans cDNA library as the template, contains 1,170 bp including the stop TAA. The cDNA encodes a protein of 389 amino acids with typical type-II membrane topology and a remarkable 42.7% identity to the human T-synthase. Ce-T-synthase has 7 Cys residues in the lumenal domain including 6 conserved Cys residues in all of the orthologs. The Ce-T-synthase has 4 potential N-glycosylation sequons, whereas the mammalian orthologs lack N-glycosylation sequons. Only one gene for Ce-T-synthase was identified in the genome-wide search and it contains 8 exons. Promoter analysis of the Ce-T-synthase using green fluorescent protein constructs show that the gene is expressed at all developmental stages and appears to be in all cells. Unexpectedly, only minimal activity was recovered in the recombinant, soluble Ce-T-synthase secreted from a wide variety of mammalian cell lines, whereas robust enzyme activity was recovered in the soluble Ce-T-synthase expressed in Hi-5 insect cells. Vertebrate T-synthase requires the molecular chaperone Cosmc, but our results show that Ce-T-synthase does not require Cosmc, and might require invertebrate-specific factors for formation of the optimally active enzyme. These results show that the Ce-T-synthase is a functional ortholog to the human T-synthase in generating core 1 O-glycans and opens new avenues to explore O-glycan function in this model organism.

Muir RE et al. (2007) Int J Syst Evol Microbiol "Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens."

Muir RE, Tan MW

[Int J Syst Evol Microbiol, 2007]

A yellow-pigmented, Gram-positive, aerobic, non-motile, non-spore-forming, irregular rod-shaped bacterium (strain TAN 31504(T)) was isolated from the bacteriophagous nematode Caenorhabditis elegans. Based on 16S rRNA gene sequence similarity, DNA G+C content of 69.5 mol%, 2,4-diaminobutyric acid in the cell-wall peptidoglycan, major menaquinone MK-11, abundance of anteiso- and iso-fatty acids, polar lipids diphosphatidylglycerol and phosphatidylglycerol and a number of shared biochemical characteristics, strain TAN 31504(T) was placed in the genus Leucobacter. DNA-DNA hybridization comparisons demonstrated a 91 % DNA-DNA relatedness between strain TAN 31504(T) and Leucobacter chromiireducens LMG 22506(T) indicating that these two strains belong to the same species, when the recommended threshold value of 70 % DNA-DNA relatedness for the definition of a bacterial species by the ad hoc committee on reconciliation of approaches to bacterial systematics is considered. Based on distinct differences in morphology, physiology, chemotaxonomic markers and various biochemical characteristics, it is proposed to split the species L. chromiireducens into two novel subspecies, Leucobacter chromiireducens subsp. chromiireducens subsp. nov. (type strain L-1(T)=CIP 108389(T)=LMG 22506(T)) and Leucobacter chromiireducens subsp. solipictus subsp. nov. (type strain TAN 31504(T)=DSM 18340(T)=ATCC BAA-1336(T)).

Agulnik SI et al. (1997) Genome "Three novel T-box genes in Caenorhabditis elegans."

Ruvinsky I, Agulnik SI, Silver LM

[Genome, 1997]

The T-box gene family consists of members that share a unique DNA binding domain. The best characterized T-box gene, Brachyury or T, encodes a transcription factor that plays an important role in early vertebrate development. Seven other recently described mouse T-box genes are also expressed during development. In the nematode Caenorhabditis elegans, four T-box genes have been characterized to date. In this study, we describe three new C. elegans T-box genes, named Ce-tbx-11, Ce-tbx-12, and Ce-tbx-17. Ce-tbx-11 and Ce-tbx-17 were uncovered through the sequencing efforts of the C. elegans Genome Project. Ce-tbx-12 was uncovered through degenerate PCR analysis of C. elegans genomic DNA. Ce-tbx-11 and Ce-tbx-17 are located in close proximity to the four other previously described T-box genes in the central region of chromosome III. In contrast, Ce-tbx-12 maps alone to chromosome II. Phylogenetic analysis of all known T-box domain sequences provides evidence of an ancient origin for this gene family.

Cook, S. et al. (2013) International Worm Meeting "Two Minds of a Worm: Comparison of the L4 and Adult Hermaphrodite Connectomes."

Hall, D., Jarrell, T., Brittin, C., Emmons, S., Cook, S.

[International Worm Meeting, 2013]

The functional output of a nervous system is governed by the properties and connectivity of its individual neurons and the circuitry they form. How neurons wire together during development remains a fundamentally unanswered neurobiological question. We have improved the description of nervous system connectivity of the C. elegans hermaphrodite by performing a complete reconstruction of four of the five serial section EM series used by White et al., 1986. Our new data (see wormwiring.org), include spatial coordinates for neurons, synapses, and NMJs as well as a measurement of synaptic weights. Our adult data (N2U) include a significantly greater number of chemical synapses (presynaptic densities) and gap junctions than in previous reconstructions. These newly scored synapses create 1199 new chemical edges (connected neuron pairs) for a total of 3287, and 234 new gap junction edges for a total of 1034, mostly small, in the graph of connectivity. Comparison of our newly annotated L4 series (JSH) to N2U (an "old" adult) reveals significant ongoing synaptogenesis between these two time points. The adult animal contains twice as many chemical synapses in the nerve ring region (5939 vs 2784) yet a similar number of gap junctions (766 vs 727). Of the 3155 synapses added between L4 and late adulthood, the majority are small, but half create new edges. Conversely, the L4 harbors 609 chemical edges not present in the adult. These could be inter-worm differences, but may also suggest some synaptic pruning during development. Comparison of L4 and adult connectomes using graph theoretic techniques reveals nearly identical network characteristics, including clustering coefficient, path length, and similarity in connectivity between homologous L/R neurons. Partitioning the graph according to the amount of connectivity between neurons reveals biologically relevant communities associated with known circuits involving pheromone sensation, thermosensation, head mechanosensation and locomotion, touch, and motor neuron output. However, some differences between the L4 and adult affecting the connectivity of AIA, AIB, and command interneurons suggest possibly significant differences in navigation that can be tested.

Sara Maxwell et al. (2002) European Worm Meeting "Functional analysis of the C. elegans T-box gene family"

Alison Woollard, Roger Pocock, Lizzie Clarke, Sara Maxwell

[European Worm Meeting, 2002]

T-box genes are a group of developmentally important transcription factors united by a common DNA binding domain. T-box genes are present in all metazoan species so far analysed but are absent from yeast. There are 20 T-box genes in C. elegans, more than twice the number found in Drosophila. Many of the C. elegans T-box genes are highly diverged from those found in other species while others have clear orthologues present throughout the metazoan kingdom. One highly conserved T-box gene is mab-9, a member of the tbx20 sub-family1. This was the first C. elegans T-box gene to be identified by mutation and is required for cell fate specification during hindgut and male tail development, and aspects of nervous system function. One other conserved T-box gene has recently been reported to be important for a particular muscle cell fate specification2. We have inactivated the remaining C. elegans T-box genes by RNAi and have found obvious phenotypes only in very few cases. These phenotypes include embryonic lethality, L1 lethality, and a Dpy phenotype with weakly penetrant male tail defects, and will be described in detail. The remaining T-box genes give no obvious phenotype by RNAi. Phylogenetic analysis reveals that several pairs of T-box genes are very similar to eachother and are therefore likely to be the result of recent duplications. This might suggest functional redundancy. Double RNAi experiments have revealed this to be the case with at least two of the T-box gene pairs (see also poster by Pocock et al). Study of the expression patterns of the whole T-box family may suggest other potential redundancy relationships which can be explored by RNAi. Comparison of the C. elegans T-box genes with the set of T-box genes now defined for C. briggsae is being used as a tool for defining potentially important regulatory regions present in orthologous genes.