iNR-2L: A two-level sequence-based predictor developed via Chou's 5-steps rule and general PseAAC for identifying nuclear receptors and their families.

Nuclear receptor proteins (NRPs) perform a vital role in regulating gene expression. With the rapidity growth of NRPs in post-genomic era, it is highly recommendable to identify NRPs and their sub-families accurately from their primary sequences. Several conventional methods have been used for discrimination of NRPs and their sub-families, but did not achieve considerable results. In a sequel, a two-level new computational model "iNR-2 L" is developed. Two discrete methods namely: Dipeptide Composition and Tripeptide Composition were used to formulate NRPs sequences. Further, both the descriptor spaces were merged to construct hybrid space. Furthermore, feature selection technique minimum redundancy and maximum relevance was employed in order to select salient features as well as reduce the noise and redundancy. The experiential outcomes exhibited that the proposed model iNR-2 L achieved outstanding results. It is anticipated that the proposed computational model might be a practical and effective tool for academia and research community.

Breast Cancer Outcomes of Neoadjuvant Versus Adjuvant Chemotherapy by Receptor Subtype: A Scoping Review.

BACKGROUND: Trials demonstrate equivalent survival for breast cancers treated with neoadjuvant chemotherapy (NAC) or adjuvant chemotherapy (AC). However, these were conducted before the recognition of the importance of receptor subtype for survival and chemotherapy response. Therefore, chemotherapy timing may impact survival for certain receptor subtypes. A scoping review of studies assessing outcomes by chemotherapy timing based on receptor subtype was conducted to evaluate gaps in the existing literature. METHODS: Three databases were searched in February 2019 with terms related to breast cancer, NAC/AC, and survival. Inclusion criteria were original peer-reviewed studies published in English after 1989 comparing breast cancer outcomes for females based on chemotherapy timing. Studies/sections of studies lacking outcomes by receptor subtype or including patients missing appropriate targeted therapy were excluded. RESULTS: Of 7354 articles, 262 abstracts and 60 full texts were reviewed. Three studies met criteria. All were single-institution retrospective studies analyzing outcomes for triple negative (TN) patients with one study also examining luminal A patients. Significant differences in clinical characteristics existed between patients selected for NAC versus AC. Two studies demonstrated no survival difference by chemotherapy timing for TN patients, with the third showing improved likelihood of survival after AC for TN patients. No difference was seen for patients with luminal A cancer. CONCLUSIONS: Our scoping review reveals a significant gap in the existing literature regarding optimal timing of chemotherapy for modern-era patients receiving targeted therapy based on receptor subtype. Review of the identified studies identified methodological challenges to answering this question through observational study designs.

An emerging link between LIM domain proteins and nuclear receptors.

Nuclear receptors are ligand-activated transcription factors that partake in several biological processes including development, reproduction and metabolism. Over the last decade, evidence has accumulated that group 2, 3 and 4 LIM domain proteins, primarily known for their roles in actin cytoskeleton organization, also partake in gene transcription regulation. They shuttle between the cytoplasm and the nucleus, amongst other as a consequence of triggering cells with ligands of nuclear receptors. LIM domain proteins act as important coregulators of nuclear receptor-mediated gene transcription, in which they can either function as coactivators or corepressors. In establishing interactions with nuclear receptors, the LIM domains are important, yet pleiotropy of LIM domain proteins and nuclear receptors frequently occurs. LIM domain protein-nuclear receptor complexes function in diverse physiological processes. Their association is, however, often linked to diseases including cancer.

Nuclear receptors in nematode development: Natural experiments made by a phylum.

The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.

Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome.

BACKGROUND: Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups. RESULTS: With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14%. CONCLUSIONS: This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly.

Accurate prediction of nuclear receptors with conjoint triad feature.

BACKGROUND: Nuclear receptors (NRs) form a large family of ligand-inducible transcription factors that regulate gene expressions involved in numerous physiological phenomena, such as embryogenesis, homeostasis, cell growth and death. These nuclear receptors-related pathways are important targets of marketed drugs. Therefore, the design of a reliable computational model for predicting NRs from amino acid sequence has now been a significant biomedical problem. RESULTS: Conjoint triad feature (CTF) mainly considers neighbor relationships in protein sequences by encoding each protein sequence using the triad (continuous three amino acids) frequency distribution extracted from a 7-letter reduced alphabet. In addition, chaos game representation (CGR) can investigate the patterns hidden in protein sequences and visually reveal previously unknown structure. In this paper, three methods, CTF, CGR, amino acid composition (AAC), are applied to formulate the protein samples. By considering different combinations of three methods, we study seven groups of features, and each group is evaluated by the 10-fold cross-validation test. Meanwhile, a new non-redundant dataset containing 474 NR sequences and 500 non-NR sequences is built based on the latest NucleaRDB database. Comparing the results of numerical experiments, the group of combined features with CTF and AAC gets the best result with the accuracy of 96.30% for identifying NRs from non-NRs. Moreover, if it is classified as a NR, it will be further put into the second level, which will classify a NR into one of the eight main subfamilies. At the second level, the group of combined features with CTF and AAC also gets the best accuracy of 94.73%. Subsequently, the proposed predictor is compared with two existing methods, and the comparisons show that the accuracies of two levels significantly increase to 98.79% (NR-2L: 92.56 %; iNR-PhysChem: 98.18%; the first level) and 93.71% (NR-2L: 88.68%; iNR-PhysChem: 92.45%; the second level) with the introduction of our CTF-based method. Finally, each component of CTF features is analyzed via the statistical significant test, and a simplified model only with the resulting top-50 significant features achieves accuracy of 95.28%. CONCLUSIONS: The experimental results demonstrate that our CTF-based method is an effective way for predicting nuclear receptor proteins. Furthermore, the top-50 significant features obtained from the statistical significant test are considered as the "intrinsic features" in predicting NRs based on the analysis of relative importance.

RACK1 regulates mesenchymal cell recruitment during sexual and asexual reproduction of budding tunicates.

A homolog of receptor for activated protein kinase C1 (RACK1) was cloned from the budding tunicate Polyandrocarpa misakiensis. By RT-PCR and in situ hybridization analyses, PmRACK1 showed biphasic gene expression during asexual and sexual reproduction. In developing buds, the signal was exclusively observed in the multipotent atrial epithelium and undifferentiated mesenchymal cells that contributed to morphogenesis by the mesenchymal-epithelial transition (MET). In juvenile zooids, the signal was first observable in germline precursor cells that arose as mesenchymal cell aggregated in the ventral hemocoel. In mature zooids, the germinal epithelium in the ovary and the pharynx were the most heavily stained parts. GFP reporter assay indicated that the ovarian expression of PmRACK1 was constitutive from germline precursor cells to oocytes. To elucidate the in vivo function of PmRACK1, RNA interference was challenged. When growing buds were incubated with 5 nmol/mL siRNA, most mesenchymal cells remained round and appeared to have no interactions with the extracellular matrix (ECM), causing lower activity of MET without any apparent effects on cell proliferation. The resultant zooids became growth-deficient. The dwarf zooids did not form buds or mature gonads. Prior to RNAi, buds were treated with human BMP4 that could induce PmRACK1 expression, which resulted in MET activity. We conclude that in P. misakiensis, PmRACK1 plays roles in mesenchymal cell recruitment during formation of somatic and gonad tissues, which contributes to zooidal growth and sexual and asexual reproduction.

The role of nuclear receptors in embryonic stem cells.

Embryonic stem (ES) cells, isolated from pre-implantation embryos, can grow indefinitely invitro (self-renewal) and have potential to differentiate into all cell types in the body (pluripotency). The nuclear receptor gene family is very important for controlling development, differentiation and homeostasis. Here, we review the new progress in understanding the role of nuclear receptors in ES cells focusing on the structure, expression and function of several nuclear receptors. LRH1, DAX1, Esrrß and TR2 play critical roles in maintaining pluripotency, while, GCNF, COUP-TFs and sumoylated TR2 are critical in regulating the exit from pluripotency. Nuclear receptors hold great potential as targets of manipulation of ES and iPS cells for applications in regenerative medicine, because they are ligand-activated transcription factors that can be regulated by small molecule agonists and antagonists.

Retinoid X receptor (RXR), estrogen receptor (ER) and other nuclear receptors in tissues of the mussel Mytilus galloprovincialis: cloning and transcription pattern.

Bivalve molluscs accumulate chemical compounds from the environment that could cause alterations in lipid homeostasis and endocrine system. In vertebrates such cell processes are modulated by transcription factors belonging to the superfamily of nuclear receptors (NRs). The goal of this study was to clone fragments of mussel Mytilus galloprovincialis NR genes that could mediate cell responses such as peroxisome proliferation and endocrine disruption. PCR-based screening of mussel digestive gland cDNA using degenerate primers provided cDNA fragments or whole ORFs of retinoid X receptor (RXR), estrogen receptor (ER) and 5 proteins belonging to the NR1 subfamily highly similar to the arthropod ecdysone inducible protein E75. NR1G, whose whole ORF was cloned, is related to the nematode and trematode G group of NR1 receptors; NR1DEF is related to the D, E and F groups, and NR1Dv1, NR1Dv2 and NR1DΔ belong to the D group. mRNA transcripts for all these receptors were detected in gill, mantle and digestive gland. In all cases, except ER, transcript levels were lower in June than in January. NR1Dv1 and NR1DΔ did not show identical transcription levels, although both were at their lowest in digestive gland in June. On the contrary, NR1Dv2 and NR1DΔ transcription profiles were similar. Further studies are needed to determine the function(s) of mussel RXR, ER and novel NR1 subfamily receptors and their possible role in the regulation of physiological cell responses and/or adaptive response to xenobiotic exposures.

A second class of nuclear receptors for oxysterols: Regulation of RORalpha and RORgamma activity by 24S-hydroxycholesterol (cerebrosterol).

The retinoic acid receptor-related orphan receptors alpha and gamma (RORalpha [NR1F1] and RORgamma [NR1F3]) are members of the nuclear hormone receptor superfamily. These 2 receptors regulate many physiological processes including development, metabolism and immunity. We recently found that certain oxysterols, namely the 7-substituted oxysterols, bound to the ligand binding domains (LBDs) of RORalpha and RORgamma with high affinity, altered the LBD conformation and reduced coactivator binding resulting in suppression of the constitutive transcriptional activity of these two receptors. Here, we show that another oxysterol, 24S-hydroxycholesterol (24S-OHC), is also a high affinity ligand for RORalpha and RORgamma (K(i) approximately 25 nM). 24S-OHC is also known as cerebrosterol due to its high level in the brain where it plays an essential role as an intermediate in cholesterol elimination from the CNS. 24S-OHC functions as a RORalpha/gamma inverse agonist suppressing the constitutive transcriptional activity of these receptors in cotransfection assays. Additionally, 24S-OHC suppressed the expression of several RORalpha target genes including BMAL1 and REV-ERBalpha in a ROR-dependent manner. We also demonstrate that 24S-OHC decreases the ability of RORalpha to recruit the coactivator SRC-2 when bound to the BMAL1 promoter. We also noted that 24(S), 25-epoxycholesterol selectively suppressed the activity of RORgamma. These data indicate that RORalpha and RORgamma may serve as sensors of oxsterols. Thus, RORalpha and RORgamma display an overlapping ligand preference with another class of oxysterol nuclear receptors, the liver X receptors (LXRalpha [NR1H3] and LXRbeta [NR1H2]).

A tale of tailless.

Drosophila Tailless(Tll) and its vertebrate homologue Tlx are conserved orphan nuclear receptors specifically expressed in the eye and the forebrain. Tll and Tlx act primarily as transcriptional repressors through their interactions with transcriptional corepressors, Atrophin family proteins, and histone-tail/chromatin-modifying factors such as lysine-specific histone demethylase 1 and histone deacetylases. The functional importance of Tll and Tlx is made apparent by the recent discovery that they are expressed in neural stem cells (NSCs) and are required for self-renewal of these cells in both Drosophila and the mouse. This review provides a snapshot of current knowledge about Tll and Tlx and their transcriptional network, which maintains NSCs in developing and adult animals.

Genetic polymorphisms of CYP1A2, CYP3A4, CYP3A5, pregnane/steroid X receptor and constitutive androstane receptor in 207 healthy Spanish volunteers.

BACKGROUND: Variability of cytochrome P450 (CYP) in humans is largely related to the pharmacological and toxicological effects of drugs and chemicals. Identification of single nucleotide polymorphisms (SNPs) could be important for knowing their involvement in many drugs metabolism. The goal of this study was to analyze the genotype frequency of 10 SNPs related to mirtazapine metabolism [CYP3A4*17, CYP3A4*18, CYP3A5*3A, CYP1A2*1F, pregnane/steroid X receptor (PXR) (rs3814055, rs38114057, rs3814058) and constitutive androstane receptor (CAR) (rs4073054, rs2307424, rs2502815)]. METHODS: The study was carried out in 207 healthy Spanish volunteers that had participated in phase I clinical trials. Other studies were performed: Hardy-Weinberg equilibrium, haplotype estimation and linkage disequilibrium. RESULTS: No mutation related to CYP3A4*17 and CYP3A4*18 was found. Therefore, we analyzed data for the other eight SNPs. Allele frequencies were in equilibrium with the Hardy-Weinberg equation. Six haplotypes were determined for three PXR SNPs, and four for CAR SNPs. Tests for linkage disequilibrium showed a high association between PXR (rs38114057) and PXR (rs3814058) (p= 0.001), and between the three CAR SNPs (p=0.001), which could be useful for identification of tag SNPs. CONCLUSIONS: In the present study, the genotype frequencies of some SNPs related to mirtazapine metabolism in Spaniards were analyzed and showed that our study population is representative of HapMap European population. The results obtained could be analyzed with pharmacokinetic parameters of mirtazapine to elucidate the genotype-phenotype relationship, the involvement of these SNPs in metabolic reactions, drug interactions, and prediction of treatment response.

Prediction of nuclear receptors with optimal pseudo amino acid composition.

Nuclear receptors are involved in multiple cellular signaling pathways that affect and regulate processes such as organ development and maintenance, ion transport, homeostasis, and apoptosis. In this article, an optimal pseudo amino acid composition based on physicochemical characters of amino acids is suggested to represent proteins for predicting the subfamilies of nuclear receptors. Six physicochemical characters of amino acids were adopted to generate the protein sequence features via web server PseAAC. The optimal values of the rank of correlation factor and the weighting factor about PseAAC were determined to get the appropriate descriptor of proteins that leads to the best performance. A nonredundant dataset of nuclear receptors in four subfamilies is constructed to evaluate the method using support vector machines. An overall accuracy of 99.6% was achieved in the fivefold cross-validation test as well as the jackknife test, and an overall accuracy of 98.4% was reached in a blind dataset test. The performance is very competitive with that of some previous methods.

Nuclear receptors and lipid physiology: opening the X-files.

Cholesterol, fatty acids, fat-soluble vitamins, and other lipids present in our diets are not only nutritionally important but serve as precursors for ligands that bind to receptors in the nucleus. To become biologically active, these lipids must first be absorbed by the intestine and transformed by metabolic enzymes before they are delivered to their sites of action in the body. Ultimately, the lipids must be eliminated to maintain a normal physiological state. The need to coordinate this entire lipid-based metabolic signaling cascade raises important questions regarding the mechanisms that govern these pathways. Specifically, what is the nature of communication between these bioactive lipids and their receptors, binding proteins, transporters, and metabolizing enzymes that links them physiologically and speaks to a higher level of metabolic control? Some general principles that govern the actions of this class of bioactive lipids and their nuclear receptors are considered here, and the scheme that emerges reveals a complex molecular script at work.

Nuclear receptors: one big family.

It is just over 20 years since the first steroid receptor cDNAs were cloned, a development that led to the birth of a superfamily of ligand activated transcription factors: the nuclear receptors. Natural ligands for nuclear receptors are generally lipophilic in nature and include steroid hormones, bile acids, fatty acids, thyroid hormones, certain vitamins and prostaglandins. These molecules act as sensors of the extracellular and intracellular environment and play crucial roles controlling development, differentiation, metabolic homeostasis, and reproduction. Since the original cloning experiments considerable progress has been made in our understanding of the structure, mechanisms of action and biology of this important family of proteins.

Research resource: nuclear hormone receptor expression in the endocrine pancreas.

The endocrine pancreas comprises the islets of Langerhans, tiny clusters of cells that contribute only about 2% to the total pancreas mass. However, this little endocrine organ plays a critical role in maintaining glucose homeostasis by the regulated secretion of insulin (by beta-cells) and glucagon (by alpha-cells). The rapid increase in the incidence of diabetes worldwide has spurred renewed interest in islet cell biology. Some of the most widely prescribed oral drugs for treating type 2 diabetes include agents that bind and activate the nuclear hormone receptor, peroxisome proliferator-activated receptor-gamma. As a first step in addressing potential roles of peroxisome proliferator-activated receptor-gamma and other nuclear hormone receptors (NHRs) in the biology of the endocrine pancreas, we have used quantitative real-time PCR to profile the expression of all 49 members of the mouse NHR superfamily in primary islets, and cell lines that represent alpha-cells (alphaTC1) and beta-cells (betaTC6 and MIN6). In summary, 19 NHR members were highly expressed in both alpha- and beta-cell lines, 13 receptors showed predominant expression (at least an 8-fold difference) in alpha- vs. beta-cell lines, and 10 NHRs were not expressed in the endocrine pancreas. In addition we evaluated the relative expression of these transcription factors during hyperglycemia and found that 16 NHRs showed significantly altered mRNA levels in mouse islets. A similar survey was conducted in primary human islets to reveal several significant differences in NHR expression between mouse and man. These data identify potential therapeutic targets in the endocrine pancreas for the treatment of diabetes mellitus.

Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of Caenorhabditis elegans is partially mediated via a subclass-specific P-box residue.

BACKGROUND: The nuclear receptors of the NR2E class play important roles in pattern formation and nervous system development. Based on a phylogenetic analysis of DNA-binding domains, we define two conserved groups of orthologous NR2E genes: the NR2E1 subclass, which includes C. elegans nhr-67, Drosophila tailless and dissatisfaction, and vertebrate Tlx (NR2E2, NR2E4, NR2E1), and the NR2E3 subclass, which includes C. elegans fax-1 and vertebrate PNR (NR2E5, NR2E3). PNR and Tll nuclear receptors have been shown to bind the hexamer half-site AAGTCA, instead of the hexamer AGGTCA recognized by most other nuclear receptors, suggesting unique DNA-binding properties for NR2E class members. RESULTS: We show that NR2E3 subclass member FAX-1, unlike NHR-67 and other NR2E1 subclass members, binds to hexamer half-sites with relaxed specificity: it will bind hexamers with the sequence ANGTCA, although it prefers a purine to a pyrimidine at the second position. We use site-directed mutagenesis to demonstrate that the difference between FAX-1 and NHR-67 binding preference is partially mediated by a conserved subclass-specific asparagine or aspartate residue at position 19 of the DNA-binding domain. This amino acid position is part of the "P box" that plays a critical role in defining binding site specificity and has been shown to make hydrogen-bond contacts to the second position of the hexamer in co-crystal structures for other nuclear receptors. The relaxed specificity allows FAX-1 to bind a much larger repertoire of half-sites than NHR-67. While NR2E1 class proteins bind both monomeric and dimeric sites, the NR2E3 class proteins bind only dimeric sites. The presence of a single strong site adjacent to a very weak site allows dimeric FAX-1 binding, further increasing the number of dimeric binding sites to which FAX-1 may bind in vivo. CONCLUSION: These findings identify subclass-specific DNA-binding specificities and dimerization properties for the NR2E1 and NR2E3 subclasses. For the NR2E1 protein NHR-67, Asp-19 permits binding to AAGTCA half-sites, while Asn-19 permits binding to AGGTCA half-sites. The apparent conservation of DNA-binding properties between vertebrate and nematode NR2E receptors allows for the possibility of evolutionarily-conserved regulatory patterns.

DNA-binding profiling of human hormone nuclear receptors via fluorescence correlation spectroscopy in a cell-free system.

The nuclear hormone receptors (NHRs), a family of transcription factors, bind directly to the hormone response elements (HREs) to regulate gene expression. In this study, we describe a comprehensive NHR-HRE profiling analysis with a new high-throughput DNA binding assay system utilizing wheat germ cell-free protein production and fluorescence correlation spectroscopy (FCS). This approach revealed NHR binding to natural response elements and new heterodimeric NHR-HRE bindings. We analyzed 408 possible binding combinations between 34 human NHRs and 12 different HREs, and identified 205 NHR-HRE binding combinations, 124 of which have not been previously reported. Thus, this study provides a novel biochemical classification of the human NHRs, as well as describing a novel approach to the large-scale analysis of DNA-protein interactions.

Interstitial cells of Cajal are innervated by nitrergic nerves and express nitric oxide-sensitive guanylate cyclase in the guinea-pig gastrointestinal tract.

Nitric oxide (NO) is a major signaling molecule in the gastrointestinal tract, and released NO inhibits muscular contraction. The actions of NO are mediated by stimulation of soluble guanylate cyclase (sGC, NO-sensitive GC) and a subsequent increase in cGMP concentration. To elucidate NO targets in the gastrointestinal musculature, we investigated the immunohistochemical localization of the beta1 and alpha1 subunits of sGC and the distribution of neuronal NO synthase (nNOS) -containing nerves in the guinea-pig gastrointestinal tract. Distinct immunoreactivity for sGCbeta1 and sGCalpha1 was observed in the interstitial cells of Cajal (ICC), fibroblast-like cells (FLC) and enteric neurons in the musculature. Double immunohistochemistry using anti-c-Kit antibody and anti-sGCbeta1 antibody revealed sGCbeta1 immunoreactivity in almost all intramuscular ICC throughout the entire gastrointestinal tract. Immunoelectron microscopy revealed that sGCbeta1-immunopositive cells possessed some of the criteria for intramuscular ICC: presence of caveolae; frequently associated with nerve bundles; and close contact with smooth muscle cells. sGCbeta1-immunopositive ICC were closely apposed to nNOS-containing nerve fibers in the muscle layers. Immunohistochemical and immunoelectron microscopical observations revealed that FLC in the musculature also showed sGCbeta1 immunoreactivity. FLC were often associated with nNOS-immunopositive nerve fibers. In the myenteric layer, almost all myenteric ganglia contained nNOS-immunopositive nerve cells and were surrounded by myenteric ICC and FLC. Myenteric ICC in the large intestine and FLC in the entire gastrointestinal tract showed sGCbeta1 immunoreactivity in the myenteric layer. Smooth muscle cells in the stomach and colon showed weak sGCbeta1 immunoreactivity, and those in the muscularis mucosae and vasculature also showed evident immunoreactivity. These data suggest that ICC are primary targets for NO released from nNOS-containing enteric neurons, and that some NO signals are received by FLC and smooth muscle cells in the gastrointestinal tract.

Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relatives.

The Pi-ta gene in rice confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. Pi-ta encodes a predicted cytoplasmic receptor protein with a nucleotide-binding site and a leucine-rich domain. A panel of 51 Oryza accessions of AA genome species Oryza sativa, O. glaberrima, O. rufipogon, O. nivara, and O. barthii, and CC genome species O. officinalis were sequenced to investigate the diversity present in the exon and intron regions of the Pi-ta gene. Two major clades were identified, consisting of 16 different sequences with numerous insertion and deletions. Only one Pi-ta resistance allele was identified despite DNA sequences revealing 16 Pi-ta variants. Most differences were identified in the intron region, and obvious selection of any motif was not observed in the coding region of Pi-ta variants. Reverse-transcription polymerase chain reaction analysis of seedlings revealed that all Pi-ta variants were expressed with or without pathogen inoculation. The 15 Pi-ta variants can be translated into nine proteins highly similar to the Pi-ta protein. Resistance to M. oryzae expressing AVR-Pita correlates with alanine and susceptibility correlates with serine at position 918 of Pi-ta in most accessions examined. These data confirm that a single amino acid controlling resistance specificity underlies the evolution of resistance of Pi-ta genes in rice.