Roy PJ et al. (2002) Nature "Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans."

Roy PJ, Kim SK, Stuart JM, Lund J

[Nature, 2002]

Chromosomes are divided into domains of open chromatin, where genes have the potential to be expressed, and domains of closed chromatin, where genes are not expressed1. Classic examples of open chromatin domains include puffs on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes2,3. If multiple genes were typically expressed together from a single open chromatin domain, the position of co-expressed genes along the chromosomes would appear clustered. To investigate whether co-expressed genes are clustered, we examined the chromosomal positions of the genes expressed in muscle of Caenorhabditis elegans at the first larval stage. Here we show that co-expressed genes in C. elegans are clustered in groups of 25 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome, in which the order of genes along the chromosome is correlated with their expression in specific tissues.

Roy PJ et al. (2000) Development "mab-20 encodes Semaphorin-2a and is required to prevent ectopic cell contacts during epidermal morphogenesis in Caenorhabditis elegans."

Roy PJ, Zheng H, Culotti JG, Warren CE

[Development, 2000]

The Semaphorins are a family of secreted and transmembrane proteins known to elicit growth cone repulsion and collapse. We made and characterized a putative null mutant of the C. elegans gene semaphorin-2a (Ce-sema-2a). This mutant failed to complement mutants of mab-20 (Baird, S. E., Fitch, D. H., Kassem, I. A. A. and Emmons, S. W. (1991) Development 113, 515-526). In addition to low-frequency axon guidance errors, mab-20 mutants have unexpected defects in epidermal morphogenesis. Errant epidermal cell migrations affect epidermal enclosure of the embryo, body shape and sensory rays of the male tail. These phenotypic traits are explained by the formation of inappropriate contacts between cells of similar type and suggest that Ce-Sema-2a may normally prevent formation or stabilization of ectopic adhesive contacts between these cells.

Prathap N et al. (2023) Sci Rep "Prosopis juliflora hydrothermal synthesis of high fluorescent carbon dots and its antibacterial and bioimaging applications."

Karuppiah P, Prathap N, Venkatesan S, Shivakumar MS, Balla P, Ramasamy K, Periyasami G

[Sci Rep, 2023]

Carbon dots have stimulated the curiosity of biomedical researchers due to their unique properties, such as less toxicity and high biocompatibility. The synthesis of carbon dots for biomedical application is a core area in research. In the current research, an eco-friendly hydrothermal technique was employed to synthesize high fluorescent, plant-derived carbon dots from Prosopis juliflora leaves extract (PJ-CDs). The synthesized PJ-CDs were investigated by physicochemical evaluation instruments such as fluorescence spectroscopy, SEM, HR-TEM, EDX, XRD, FTIR, and UV-Vis. The UV-Vis absorption peaks obtained at 270 nm due to carbonyl functional groups shifts of n→π*. In addition, a quantum yield of 7.88 % is achieved. The synthesized PJ-CDs showing the presence of carious functional groups O-H, C-H, C=O, O-H, C-N and the obtained particles in spherical shape with an average size of 8 nm. The fluorescence PJ-CDs showed stability against various environmental factors such as a broad range of ionic strength and pH gradient. The antimicrobial activity of PJ-CDs was tested against a Staphylococcus aureus, and a Escherichia coli. The results suggest that the PJ-CDs could substantially inhibit the growth of Staphylococcus aureus. The findings also indicate that PJ-CDs are effective materials for bio-imaging in Caenorhabditis elegans and they can be also used for pharmaceutical applications.

Dixon SJ et al. (2005) Development "Muscle arm development in Caenorhabditis elegans."

Roy PJ, Dixon SJ

[Development, 2005]

In several types of animals, muscle cells use membrane extensions to contact motor axons during development. To better understand the process of membrane extension in muscle cells, we investigated the development of Caenorhabditis elegans muscle arms, which extend to motor axons and form the postsynaptic element of the neuromuscular junction. We found that muscle arm development is a highly regulated process: the number of muscle arms extended by each muscle, the shape of the muscle arms and the path taken by the muscle arms to reach the motor axons are largely stereotypical. We also investigated the role of several cytoskeletal components and regulators during arm development, and found that tropomyosin (LEV-11), the actin depolymerizing activity of ADF/cofilin (UNC-60B) and, surprisingly, myosin heavy chain B (UNC-54) are each required for muscle arm extension. This is the first evidence that UNC-54, which is found in thick filaments of sarcomeres, can also play a role in membrane extension. The muscle arm phenotypes produced when these genes are mutated support a ''two-phase'' model that distinguishes passive muscle arm development in embryogenesis from active muscle arm extension during larval development.

Ginzburg VE et al. (2002) Development "Semaphorin 1a and semaphorin 1b are required for correct epidermal cell positioning and adhesion during morphogenesis in C. elegans."

Culotti JG, Ginzburg VE, Roy PJ

[Development, 2002]

The semaphorin family comprises secreted and transmembrane proteins involved in axon guidance and cell migration. We have isolated and characterized deletion mutants of C. elegans semaphorin 1a (Ce-sema-1a or smp-1) and semaphorin 1b (Ce-sema-1b or smp-2) genes. Both mutants exhibit defects in epidermal functions. For example, the R1.a-derived ray precursor cells frequently fail to change anterior/posterior positions completely relative to their sister tail lateral epidermal precursor cell R1.p, causing ray 1 to be formed anterior to its normal position next to ray 2. The ray cells, which normally separate from the lateral tail seam cell (SET) at the end of L4 stage, remains connected to the SET cell even in adult mutant males. The ray 1 defects are partially penetrant in each single Ce-sema-1 mutant at 20degreesC, but are greatly enhanced in Ce-sema-1 double mutants, suggesting that Ce-Sema-1a and Ce-Sema-1b function in parallel to regulate ray 1 position. Both mutants also have defects in other aspects of epidermal functions, including head and tail epidermal morphogenesis and touch cell axon migration, whereas, smp-1 mutants alone have defects in defecation and brood size. A feature of smp-1 mutants that is shared with mutants of mab-20 (which encodes Sema-2a) is the abnormal perdurance of contacts between epidermal cells.

Cunningham KA et al. (2009) Cell Metab "Fat rationing in dauer times."

Ashrafi K, Cunningham KA

[Cell Metab, 2009]

The fundamental task of maintaining energy balance is complex when nutrient levels are plentiful, but it becomes even more challenging when nutrients are dynamic or scarce. A recent Nature report delineates a role of the AMP kinase pathway in rationing energy stores for the long-term survival of Caenorhabditis elegans dauers (Narbonne and Roy, 2009).

Dixon SJ et al. (2008) Dev Biol "Insulin-like signaling negatively regulates muscle arm extension through DAF-12 in Caenorhabditis elegans."

Dixon SJ, Alexander M, Roy PJ, Chan KK

[Dev Biol, 2008]

The body wall muscles (BWMs) of nematodes are connected to motor axons by muscle membrane extensions called muscle arms. To better understand how muscle arm extension is regulated, we screened conserved receptor tyrosine kinases for muscle arm defects in Caenorhabditis elegans. We discovered that mutations in daf-2, which encodes the only insulin-like receptor tyrosine kinase, confer a supernumerary muscle arm (Sna) phenotype. The Sna phenotype of daf-2 mutants is suppressed by loss-of-function in the canonical downstream FOXO-family transcription factor DAF-16 in either the muscles or the intestine, demonstrating that insulin-like signaling can regulate muscle arm extension non-autonomously. Furthermore, supernumerary arm extension requires the B isoform of the down-stream DAF-12 nuclear hormone receptor, which lacks the DNA-binding domain, but retains the ligand-binding domain. daf-2 regulates many processes in C. elegans including entry into dauer, which is a diapause-like state that facilitates survival of harsh environmental conditions. We found that wild-type dauers are also Sna. Unlike other changes associated with dauer, however, the Sna phenotype of dauers persists in recovered adults. Finally, disruption of a TGF-beta pathway that regulates dauer formation in parallel to the insulin-like pathway also confers the Sna phenotype. We conclude that supernumerary muscle arms are a novel dauer-specific modification that may facilitate some aspect of dauer behavior.

Tharmalingam S et al. (2012) Neuropharmacology "Orthosteric and allosteric drug binding sites in the Caenorhabditis elegans mgl-2 metabotropic glutamate receptor."

Hampson DR, Roy PJ, Tharmalingam S, Burns AR

[Neuropharmacology, 2012]

The metabotropic glutamate receptors (mGluRs) are evolutionarily conserved from nematodes to vertebrates. The Caenorhabditis elegans (C. elegans) genome contains three mGluR genes referred to as mgl-1, mgl-2, and mgl-3. The aim of this study was to characterize the pharmacological profiles of orthosteric and allosteric mGluR ligands on mgl-2. A phylogenetic analysis revealed that mgl-2 is closely associated with the mammalian Group 1 mGluRs (mGluR1 and mGluR5) and is distinct from Group 2 and 3 mGluRs. The ligand binding domain of mgl-2 displayed higher homology to the rat Group 1 mGluRs binding domains compared to the level of homology in the heptahelical transmembrane domain regions. We found that, when transiently expressed in human embryonic kidney 293 cells, mgl-2 can be activated by glutamate and couples to human G-proteins to induce the release of intracellular calcium. Dose-response analyses revealed that mgl-2 has approximately a 15-20-fold lower affinity for glutamate and quisqualate compared to rat mGluR5. In contrast to orthosteric agonists, Group 1 negative allosteric modulators that target the transmembrane domain were ineffective at mgl-2. Surprisingly, CDPPB, an mGluR5 positive allosteric modulator, potentiated glutamate mediated activation of mgl-2, although MPEP and fenobam, two mGluR5 antagonists that share similar binding residues with CDPPB were ineffective at mgl-2. These findings indicate that selective pressures on mGluR protein structures have resulted in conservation of the glutamate binding site, whereas the allosteric modulator sites have been subjected to greater divergent evolutionary changes.

Dixon SJ et al. (2006) Development "FGF negatively regulates muscle membrane extension in Caenorhabditis elegans."

Alexander M, Roy PJ, Fernandes R, Ricker N, Dixon SJ

[Development, 2006]

Striated muscles from Drosophila and several vertebrates extend plasma membrane to facilitate the formation of the neuromuscular junction (NMJ) during development. However, the regulation of these membrane extensions is poorly understood. In C. elegans, the body wall muscles (BWMs) also have plasma membrane extensions called muscle arms that are guided to the motor axons where they form the postsynaptic element of the NMJ. To investigate the regulation of muscle membrane extension, we screened 871 genes by RNAi for ectopic muscle membrane extensions (EMEs) in C. elegans. We discovered that an FGF pathway, including let-756(FGF), egl-15(FGF receptor), sem-5(GRB2) and other genes negatively regulates plasma membrane extension from muscles. Although compromised FGF pathway activity results in EMEs, hyperactivity of the pathway disrupts larval muscle arm extension, a phenotype we call muscle arm extension defective or MAD. We show that expression of egl-15 and sem-5 in the BWMs are each necessary and sufficient to prevent EMEs. Furthermore, we demonstrate that let-756 expression from any one of several tissues can rescue the EMEs of let-756 mutants, suggesting that LET-756 does not guide muscle membrane extensions. Our screen also revealed that loss-of-function in laminin and integrin components results in both MADs and EMEs, the latter of which are suppressed by hyperactive FGF signaling. Our data are consistent with a model in which integrins and laminins are needed for directed muscle arm extension to the nerve cords, while FGF signaling provides a general mechanism to regulate muscle membrane extension.

Nash B et al. (2000) Genes Dev "The forkhead transcription factor UNC-130 is required for the graded spatial expression of the UNC-129 TGF-beta guidance factor in C. elegans."

Colavita A, Roy PJ, Culotti JG, Zheng H, Nash B

[Genes Dev, 2000]

Secreted proteins required for cellular movements along the circumference of the body wall in Caenorhabditis elegans include UNC-6/netrin and the novel TGF-beta UNC-129. Expression of these proteins is graded along the dorsoventral (D/V) axis, providing polarity information to guide migrations. Here we show that the graded expression of UNC-129 in dorsal but not ventral body muscles depends on unc-130, which encodes a Forkhead transcription factor. The phenotype of unc-130 mutants closely mimics the reported effects of ectopically expressing unc-129 in both dorsal and ventral body muscles (). This fits our present finding that unc-130 cell autonomously represses unc-129 expression in the ventral body muscles. Thus the cell-specific effects of unc-130 on ventral, but not dorsal, body muscle expression of unc-129 accounts for the D/V polarity information required for UNC-129-mediated guidance. Genetic interactions between unc-130 and other guidance genes show that several molecular pathways function in parallel to guide the ventral to dorsal migration of distal tip cells (DTCs) and axonal growth cones in C. elegans. Genetic interactions confirm that UNC-129 does not require the only known type II TGF-beta receptor in C. elegans (DAF-4) for its guidance functions. Also, unc-130 is partially required for male tail morphogenesis and for embryogenesis.