WormMine: AnatomyTerm WBbt:0005047

• Definition: Neuron class of one ring interneuron.
• Name: RIR
• Primary Identifier: WBbt:0005047
• Synonym: lineage name: ABprpapppaa

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree ABprpapppaa	ABprpapppaa nucleus		WBbt:0002717

4 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Single-cell RNA-Seq cell group 142_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:142_0
	Transcripts enriched in RIR according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:RIR_enriched
	Single-cell RNA-Seq cell group 88 expressed in: RIH_RIR.	CellRanger, DecontX, Monocle3, Louvain algorithm.	WBPaper00065623:88
	Single-cell RNA-Seq cell group 89 expressed in: AIA.	CellRanger, DecontX, Monocle3, Louvain algorithm.	WBPaper00065623:89

31 Expression Patterns

• Primary Identifier: Expr15649

• Primary Identifier: Expr15385

• Primary Identifier: Expr3681
• Remark: The differences in the expression patterns of Pmbr-1::gfp and mbr-1::gfp might be due to the following reasons: first, additional regulatory elements might exist in introns and 3$(B!l(B-UTR regions, which are not included in the former construct; and second, as the product of Pmbr-1::gfp diffuses throughout the cytoplasm, it might be difficult to detect low levels of GFP expression.
• Pattern: In strains that carry Pmbr-1::gfp, GFP expression was observed in restricted sets of interneurons in the head ganglia: AIM, RIC, RIH (or RIR), RIF (or RIG), and a pair of interneurons tentatively identified as AIN. Expression was also observed in three interneurons of the tail ganglia: PVP and an interneuron tentatively identified as DVA or DVC. In contrast, mbr-1::gfp was expressed in several more neurons compared to Pmbr-1::gfp, including sensory neurons. Expression of mbr-1::gfp was also detected in some intestinal cells at the late embryonic stages as well as in vulval cells and some somatic gonadal cells at the L4 stage. mbr-1::gfp expression becomes detectable first around the early comma stage, which corresponds to the time just after the birth of most neurons.
• Subcellular Localization: The MBR-1::GFP fusion protein was localized to the nuclei, consistent with the idea that MBR-1 functions as a transcription factor.

• Primary Identifier: Expr15571

• Primary Identifier: Expr15572

• Primary Identifier: Expr15573

• Primary Identifier: Expr15579

• Primary Identifier: Expr15586

• Primary Identifier: Expr15651

• Primary Identifier: Expr15652

• Primary Identifier: Expr15589

• Primary Identifier: Expr15591

• Primary Identifier: Expr15598

• Primary Identifier: Expr15604

• Primary Identifier: Expr15608

• Primary Identifier: Expr15611

• Primary Identifier: Expr733
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Staining is seen in a set of 47 nuclei in fixed newly hatched first larval stage (L1). All stained cells are neurons. Hermaphrodite express in cells. RIH, RIR, PVR, IL2L/R, URYVL/R, RIPL/R, AIZL/R, FLPL/R, ADAL/R, RMGL/R, BPUL/R, PLML/R, ALML/R, ALNL/R, HSNL/R, URBL/R, NSML/R, URADL/R, IL2DL/R, I2L/R, IL2VL/R, URAVL/R, URXL/R, AIML/R, URYDL/R, PQR, PVM, SDQL/R, PVDL/R, PHCL/R, PLNL/R. Male cells express as in hermaphrodite except for HSNL/R which die, and show expression in CEMDL/R, CEMVL/R which die in hermaphrodites. Expression pattern is first determined in the Q lineage. Once expression has been initiated in a cell, it is maintained by that cell and all of its descendants in all cases except for SDQ.

• Primary Identifier: Expr15443

• Primary Identifier: Expr15648

• Primary Identifier: Expr15657

• Primary Identifier: Expr8786
• Remark: Picture: Fig 6.
• Pattern: Apart from cells in the neuroblast lineage that generate ASE, nhr-67::mCherry was expressed in multiple other neuroblast lineages in the developing embryo. Expression was usually observed in the grandmother or mother of a neuron, but not earlier. Within the ASEL and ASER-generating lineage branches, nhr-67 was expressed in neuroblasts that generate closely or distantly related cousins of ASEL and ASER. For example, the sister neuroblast of the ASE-generating neuroblast creates the AUA and ASJ neurons and it expressed nhr-67. The cousin of the ASE-mother cell generates the AWB and ADF sensory neurons. nhr-67 was expressed in these cells. In late stage embryos, a few other, postmitotic neurons started to express nhr-67. Embryonic nhr-67 expression was not restricted to the nervous system, but was observed in a small subset of mesodermal and hypodermal cells. No expression was detected in endodermal cells or the germ line. nhr-67 was expressed in the excretory canal cell. Postembryonically, nhr-67 expression persisted only in a few neurons in the head ganglia until the first larval stage and faded shortly thereafter in most, but not all, of these neurons, with expression persisting through adulthood only in the CEPD/V, RMED/V, AVL and RIS neurons. During mid-larval development, nhr-67 was transiently and dynamically expressed in the AC cells of the vulva. Expression was also found in the VU cells and somatic gonad, but not in vulA, vulB or vulC. Within the ASEL/R generating lineages, nhr-67::mCherry was first observed in the grandmother cells of ASEL and ASER. Transgenic animals that co-express a functional nhr-67::mCherry reporter and a functional che-1::yfp reporter revealed that nhr-67 precedes che-1 expression. nhr-67 expression was maintained in the ASEL and ASER neurons until the first larval stage after which it became undetectable, whereas che-1 expression was maintained throughout the life of the animal. In spite of its genetically deduced role in asymmetric gene expression in ASEL and ASER, nhr-67 expression is bilaterally symmetric in ASEL and ASER.

• Primary Identifier: Expr12716

• Primary Identifier: Expr12717

• Primary Identifier: Expr15327
• Remark: 3.7 kb

• Primary Identifier: Expr11224
• Remark: At 335 minutes post fertilization.
• Pattern: efn-2 expression showed widespread left-right asymmetry inembryos, both in amphid neurons and in other cells.

• Primary Identifier: Expr15633

• Primary Identifier: Expr817
• Remark: B0280.12 = glr-2
• Pattern: AVA, AVD, AVE, PVC, RMDV, RMDD, AIA, AIB, AVG, RIG, RIA, M1 pharynx, RIR(?)

• Primary Identifier: Expr3046
• Remark: Reporter gene fusion type not specified.
• Pattern: Transgenic expression of either GFP::GLR-2(Q) or GFP::GLR-2(R) in both the wild-type laboratory strain N2 and in a glr-2 deletion strain resulted in GFP signal in 25 neurons, as reported previously (see Expr817), with one additional cell pair (the DVA neurons) consistently seen in the tail.

• Primary Identifier: Expr8164
• Pattern: Expressed in intestine: Exxx (20 intestine cells). Onset time: <200 cells. Expressed in pharynx: ABalpaxxx, ABaraaxxx, ABarapaxxx (57 pharyngeal cells, 4 neurons, 4 hypodermal cells). MSaaxxx, MSpaxxx (37 pharyngeal cells, 2 neurons, 10 muscle cells). Onset time: <200 cells. Expressed in rectal precursors: ABprpapppxx, ABprpppppax, ABplpppppax, ABplpapppxx (7 rectal and digestive muscle cells, 2 neurons, 1 muscle cell.) Onset time: >350 cells.

• Primary Identifier: Expr8534
• Remark: Picture: Fig 1.
• Pattern: There was also prominent staining of a single cell in the ventral ganglion. This unpaired cell sends a process to the ventral midline of the nerve ring, where it gives rise to two fine branches, one in each side of the ring. This cell resembles the RIR cell of C. elegans. Six sensory neurons, one in each of the subdorsal and subventral and anterior lateral ganglia, stained consistently although weakly.
• Subcellular Localization: P20-6D showed prominent staining of the cell bodies and processes of the two largest cells in the retrovesicular ganglion. These cells are the AVF-like cells, so called because they resemble the AVF neurons of C. elegans; their cell bodies have a characteristic knobbly appearance due to membrane invaginations. In the ventral cord both cells have processes that project both anteriorly and posteriorly and run together as a pair of fibers in the cord. The anterior processes extend to the nerve ring, where they both enter the ring to the left, traverse the ring, reenter the ventral nerve cord, and terminate in the ventral ganglion, often branching into a varicose plexus. As each neurite passes the lateral lines, it sends fine processes into the lateral ganglia and down each lateral line, giving rise to a pair of very small fibers. The posterior AVF processes run the length of the ventral cord, terminating in a plexus in the preanal ganglion.

11 Life Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	The whole period of embryogenesis in the nematode Caenorhabditis elegans, from the formation of an egg until hatching.		embryo Ce	WBls:0000003
	The C. elegans life stage spanning 620-800min(hatch) after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. A stage after elongation is over. The last stage of embryogenesis. Also called pre-hatched embryo, late embryo or morphogenetic embryo.		fully-elongated embryo Ce	WBls:0000021
	The C. elegans life stage spanning 350-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The stage that embryo starts elongation until elongation is over.		elongating embryo Ce	WBls:0000015
	The C. elegans life stage spanning 290-350min after first cleavage at 20 Centigrade. Proliferate from 421 cells to 560 cells. The stage when embryo just finished gastrulation and is enclosing.		enclosing embryo Ce	WBls:0000013
	The C. elegans life stage spanning 0-350min after first cleavage at 20 Centigrade. Proliferate from 1 cell to 560 cells. From start of first cleavage until cleavage is over.		proliferating embryo Ce	WBls:0000004
	The C. elegans life stage spanning 420-460min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and fold back 50%. A stage between comma embryo and 2-fold embryo.		1.5-fold embryo Ce	WBls:0000018
	The C. elegans life stage spanning 390-420min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo looks like a comma. A stage between bean embryo and 1.5-fold embryo.		comma embryo Ce	WBls:0000017
	The C. elegans life stage spanning 460-520min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and double fold. A stage between 1.5-fold embryo and 3-fold embryo.		2-fold embryo Ce	WBls:0000019
	The C. elegans life stage spanning 520-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and tripple fold. A stage between 2-fold embryo and fully-elongated embryo. Also called pretzel embryo or pretzel stage.		3-fold embryo Ce	WBls:0000020
	The C. elegans life stage spanning 350-390min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. Emrbyo elongation started but have not formed comma shape yet. The shape of embryo looks like a lima bean. A stage right before comma embryo. Also called lima embryo or lima bean stage.		bean embryo Ce	WBls:0000016
	The C. elegans life stage spanning 210-350min after first cleavage at 20 Centigrade. Proliferate from 421 cells to 560 cells. The stage before the fast cleavage of cells finishes.		late cleavage stage embryo Ce	WBls:0000014

6 Parents

Definition	Name	Synonym	Primary Identifier
neuron with its cell body situated in the head, excluding the pharynx.	head neuron		WBbt:0006751
	interneuron		WBbt:0005113
embryonic cell	ABprpapppa		WBbt:0005972
ventral ganglion, anterior part.	ventral ganglion (ant)		WBbt:0005266
cell that exists in and is part of an embryo.	embryonic cell		WBbt:0007028
neuron that has neural processes in the nerve ring.	nerve ring neuron		WBbt:0006974