Three Finnish incontinentia pigmenti (IP) families with recombinations with the IP loci at Xq28 and Xp11

The locus (IP2) for the hereditary form of incontinentia pigmenti (IP) has been mapped to Xq28 by linkage analysis. We studied three IP families with polymorphic markers in the Xq28 region. In two families we observed recombination between the marker loci and IP. In the third family no crossing overs were seen and linkage to the Xq28 region could not be excluded. The other IP locus (IP1) has been mapped to Xp 11.21, because of sporadic cases of IP with X-chromosomal alterations involving Xp11.21. To check whether this locus is linked to IP in these families, we used polymorphic markers in the Xp11 region. In all three families recombinations were observed, thus excluding linkage to this locus in these IP families.     

Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana.

Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.     

Inositol 1,4,5-trisphosphate receptor associated with focal contact cytoskeletal proteins

The linkage between inositol 1,4,5-trisphosphate (IP(3)) receptors (IP(3)Rs) and cytoskeletal proteins is considered to be important in cell function. In the present study, the association of IP(3)R subtypes with cytoskeletal proteins was examined using monoclonal antibodies specific to each IP(3)R subtype. We found that IP(3)R type 2 colocalized with talin, a focal contact cytoskeletal protein. IP(3)R type 2 exhibited a patchy distribution in the peripheral cytoplasm differently from type 1 and type 3 IP(3)R. Furthermore, IP(3)R subtypes co-immunoprecipitated with talin, vinculin and alpha-actin, but not alpha-actinin or paxillin.     

Linkage relationship between incontinentia pigmenti (IP2) and nine terminal X long arm markers

Summary Linkage data for familial incontinentia pigmenti (IP2) and nine X chromosomal markers are reported. Previously found linkage between IP2 and the DXS52 locus is confirmed with the maximum lod score of 6.19 at a recombination fraction of 0.03. Linkage is also established with loci DXS134, DXS15 and DXS33. Multipoint analysis allows us to localize the IP2 locus outside a block of seven linked markers of the Xq28 region.     

Age related impairment in phosphatidylinositol breakdown of polymorphonuclear granulocytes

It is well known that with aging the immune response decreases. Most of the effector functions occur through specific receptors. Thus, we investigated the effects of various stimulants, acting through receptors or directly through the GTP-binding Gi protein, on phosphatidylinositol breakdown in PMNLs of young and elderly subjects and try to modulate it. A marked decrease in inositol phosphate (IP1, IP2, IP3) formation in PMNLs of elderly was found under FMLP stimulation when compared to that of young subjects. Neither GTP gamma S, nor AIF4- could induce an increase of IP3 in PMNLs of elderly comparable to that of young subjects. The results suggest that at least an alteration exists at the GTP-binding Gi protein level, as well as in the mechanism of linkage of the receptor to the G protein.     

Presence of the inositol 1,4,5-triphosphate receptor isoforms in the nucleoplasm

Although the inositol 1,4,5-triphosphate (IP(3))-induced nuclear Ca(2+) release has been shown to play key roles in nuclear functions, the presence of IP(3) receptor (IP(3)R)/Ca(2+) channels in the nucleoplasm has not been found. Recently, the IP(3)R/Ca(2+) channels were reported to exist in the nucleoplasmic reticulum structure, an extension of the nuclear envelope. Here we investigated the potential existence of the IP(3)Rs in the nucleoplasm and found the presence of all three IP(3)R isoforms in neuroendocrine and non-neuroendocrine cells. The IP(3)Rs were widely scattered in the nucleoplasm, localizing in both the heterochromatin and euchromatin regions.     

SSX2IP: an emerging role in cancer

We describe the emerging role of Synovial Sarcoma X breakpoint 2 Interacting Protein (SSX2IP) in cancer and its still largely unknown function in human cells. In rodents, SSX2IP has been shown to play a role in adherens junctions and cell adhesion, while in chickens SSX2IP was identified by virtue of its regulation by the light cycle and circadian rhythms. In humans, SSX2IP was identified through its interaction with the cancer-testis gene SSX2. However SSX2IP is expressed in a range of normal and fetal tissues unlike SSX2. SSX2IP containing constructs indicated that SSX2IP could be expressed in the nucleus and cytoplasm of transfected human cells, however, SSX2IP expression has been subsequently shown to peak on the surface of myeloid leukaemia cells during mitosis. Here we discuss the current knowledge of SSX2IP function in several species and the growing evidence that SSX2IP may be a suitable target for leukaemia immunotherapy.     

Synthesis and characterization of novel isoform-selective IP6K1 inhibitors

Inositol hexakisphosphate kinases (IP6Ks) have been increasingly studied as therapeutically interesting enzymes. IP6K isoform specific knock-outs have been used to successfully explore inositol pyrophosphate physiology and related pathologies. A pan-IP6K inhibitor, N2-(m-trifluorobenzyl)-N6-(p-nitrobenzyl) purine (TNP), has been used to confirm phenotypes observed in genetic knock-out experiments; however, it suffers by having modest potency and poor solubility making it difficult to handle for in vitro applications in the absence of DMSO. Moreover, TNP’s pan-IP6K inhibitory profile does not inform which IP6K isoform is responsible for which phenotypes. In this report we describe a series of purine-based isoform specific IP6K1 inhibitors. The lead compound was identified after multiple rounds of SAR and has been found to selectively inhibit IP6K1 over IP6K2 or IP6K3 using biochemical and biophysical approaches. It also boasts increased solubility and IP6K1 potency over TNP. These new compounds are useful tools for additional assay development and exploration of IP6K1 specific biology.     

Mapping the d1 and d2 dwarfing genes and the purple foliage color locus P in pearl millet

The d(1) and d(2) dwarfing genes and the P purple foliage color gene were placed on the restriction fragment length polymorphism (RFLP)-based molecular marker linkage map of pearl millet [Pennisetum glaucum (L.) R. Br.] using a mapping population based on a cross of inbred lines IP 18293 (D(1)/D(1), d(2)/d(2), P/P) and Tift 238D1 (d(1)/d(1) D(2)/D(2) p/p). A skeleton genetic linkage map of 562 cM (Haldane function) was constructed using 33 RFLP markers and these three morphological markers. The D(1)/d(1) plant height locus mapped to pearl millet linkage group 1, while the D(2)/d(2) plant height locus and the P/p foliage color locus mapped to pearl millet linkage group 4. Loose genetic linkage was observed between the D(2)/d(2) and P/p loci, with 42% repulsion-phase recombination corresponding to 92 cM (Haldane). This loose linkage of morphological marker loci detected on pearl millet LG4 can likely find use in applied pearl millet breeding programs, as host plant resistances to both downy mildew and rust have previously been identified in this genomic region. Such exploitation of these morphological markers in an applied disease resistance breeding program would require development of appropriate genetic stocks, but the relatively loose genetic linkage between d(2) and P suggests that this should not be difficult.     

Inositol 1,4,5-trisphosphate receptor expression in cardiac myocytes

Calcium release from intracellular stores is the signal generated by numerous regulatory pathways including those mediated by hormones, neurotransmitters and electrical activation of muscle. Recently two forms of intracellular calcium release channels (CRCs) have been identified. One, the inositol 1,4,5-trisphosphate receptors (IP3Rs) mediate IP3-induced Ca2+ release and are believed to be present on the ER of most cell types. A second form, the ryanodine receptors (RYRs) of the sarcoplasmic reticulum, have evolved specialized functions relevant to muscle contraction and are the major CRCs found in striated muscles. Though structurally related, IP3Rs and RYRs have distinct physiologic and pharmacologic profiles. In the heart, where the dominant mechanism of intracellular calcium release during excitation-contraction coupling is Ca(2+)-induced Ca2+ release via the RYR, a role for IP3-mediated Ca2+ release has also been proposed. It has been assumed that IP3Rs are expressed in the heart as in most other tissues, however, it has not been possible to state whether cardiac IP3Rs were present in cardiac myocytes (which already express abundant amounts of RYR) or only in non- muscle cells within the heart. This lack of information regarding the expression and structure of an IP3R within cardiac myocytes has hampered the elucidation of the significance of IP3 signaling in the heart. In the present study we have used combined in situ hybridization to IP3R mRNA and immunocytochemistry to demonstrate that, in addition to the RYR, an IP3R is also expressed in rat cardiac myocytes. Immunoreactivity and RNAse protection have shown that the IP3R expressed in cardiac myocytes is structurally similar to the IP3R in brain and vascular smooth muscle. Within cardiac myocytes, IP3R mRNA levels were approximately 50-fold lower than that of the cardiac RYR mRNA. Identification of an IP3R in cardiac myocytes provides the basis for future studies designed to elucidate its functional role both as a mediator of pharmacologic and hormonal influences on the heart, and in terms of its possible interaction with the RYR during excitation- contraction coupling in the heart.     

The interconversion of inositol 1,3,4,5,6-pentakisphosphate and inositol tetrakisphosphates in AR4-2J cells.

Data from several cell types have indicated that activation of hormone receptors promotes the metabolism of inositol 1,3,4,5,6-pentakisphosphate (IP5) to inositol 3,4,5,6-tetrakisphosphate ((3,4,5,6)IP4). However, to date, metabolism of IP5 by cell-free preparations has resulted in the formation of only inositol 1,4,5,6-tetrakisphosphate ((1,4,5,6)IP4). Thus, the metabolic relationships of IP5 with various inositol tetrakisphosphate (IP4) isomers have been investigated in both intact cells and cell homogenates of the rat pancreatoma cell line, AR4-2J. The steady-state concentration of IP5 was estimated to be 65 microM, while the combined concentration of (3,4,5,6)IP4 and (1,4,5,6)IP4 was approximately 1.0 microM. AR4-2J cell homogenates converted (1,3,4,6)IP4, (3,4,5,6)IP4, and (1,4,5,6)IP4 to IP5. (1,4,5,6)IP4 previously has not been demonstrated to be a precursor of IP5. To alter steady-state levels of inositol phosphates that were maintained by phosphorylation-dephosphorylation cycles, intact cells were treated with 10 microM antimycin A which reduced ATP levels by > 90% within 10 min. Following 2 h of treatment with antimycin A, there was a 6-fold increase in both (3,4,5,6)IP4 and (1,4,5,6)IP4, presumably derived from IP5. Experiments with cell-free systems determined that IP5 was dephosphorylated to (1,4,5,6)IP4 by a predominantly particulate Mg(2+)-independent, Li(+)-insensitive IP5 3-phosphatase. However, in the presence of 5 mM MgATP, IP5 also was metabolized to (3,4,5,6)IP4. Therefore, our data demonstrate novel and complex relationships between IP5, (3,4,5,6)IP4, and (1,4,5,6)IP4.     

Calcium signalling mechanisms in endoplasmic reticulum activated by inositol 1,4,5-trisphosphate and GTP

Ca2+ signals are known to mediate an array of cellular functions including secretion, contraction, and conductivity changes. In spite of the obvious role of Ca2+ in signalling, the control of Ca2+ within cells is known to be a complex phenomenon involving a number of distinct active and passive transport systems functioning within different organelles. Inositol 1,4,5-trisphosphate (IP3) is now established as a central mediator of Ca2+ mobilization, and the endoplasmic reticulum (ER) has been considered to be the site of action of IP3. However, this role has been ascribed almost by default to the ER, based on the knowledge that IP3 functions to release Ca2+ from an intracellular, nonmitochondrial, Ca2+-pumping organelle. Our interest has been to ascertain by what mechanism IP3 activates Ca2+ movements, at what intracellular locations it functions, and how the size and replenishment of the IP3-sensitive Ca2+ pool occurs. During the course of such studies, another mechanism inducing profound movements of Ca2+ within cells was identified. This process is activated by a highly sensitive and specific guanine nucleotide regulatory mechanism, which, while inducing fluxes of Ca2+ that resemble the action of IP3 under certain conditions, has now been determined to involve a quite distinct mechanism. The characteristics of this mechanism are described below. Although involving a very different Ca2+ translocation process to that activated by IP3, several important conclusions have been drawn on the relationship between IP3- and GTP-activated Ca2+ movements leading us to believe that the latter may have a regulatory role in controlling the size and/or entry of Ca2+ into the IP3-sensitive Ca2+ pool.     

Comparison of molecular linkage maps and QTLs for morphological traits in two reciprocal backcross populations of rice

Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal BC1F1 populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two BC1F1 populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.     

Molecular characterization of the starfish inositol 1,4,5-trisphosphate receptor and its role during oocyte maturation and fertilization.

The release of calcium ions (Ca(2+)) from their intracellular stores is essential for the fertilization of oocytes of various species. The calcium pools can be induced to release Ca(2+) via two main types of calcium channel receptor: the inositol 1,4,5-trisphosphate receptor (IP(3)R) and the ryanodine receptor. Starfish oocytes have often been used to study intracellular calcium mobilization during oocyte maturation and fertilization, but how the intracellular calcium channels contribute to intracellular calcium mobilization has never been understood fully, because these molecules have not been identified and no specific inhibitors of these channels have ever been found. In this study, we utilized a novel IP(3)R antagonist, the "IP(3) sponge," to investigate the role of IP(3) during fertilization of the starfish oocyte. The IP(3) sponge strongly and specifically competed with endogenous IP(3)R for binding to IP(3). By injecting IP(3) sponge into starfish oocyte, the increase in intracellular calcium and formation of the fertilization envelope were both dramatically blocked, although oocyte maturation was not blocked. To investigate the role of IP(3)R in the starfish oocyte more precisely, we cloned IP(3)R from the ovary of starfish, and the predicted amino acid sequence indicated that the starfish IP(3)R has 58-68% identity to mammalian IP(3)R types 1, 2, and 3. We then raised antibodies that recognize starfish IP(3)R, and use of the antibodies to perform immunoblot analysis revealed that the level of expression of IP(3)R remained unchanged throughout oocyte maturation. An immunocytochemical study, however, revealed that the distribution of starfish IP(3)R changes during oocyte maturation.     

Antibody to estrogen-induced protein (IP) and quantification of the protein in rat uterus by a radioimmunoassay.

Antibodies to a rat uterine estrogen-induced protein (IP) have been prepared in rabbit and characterized by gel diffusion and immunoelectrophoresis. A radioimmunoassay for IP has been developed using this antibody and (¹²⁵I)-labelled IP. Using this assay, significant levels of IP were detected in uteri of both immature and unstimulated castrated adult rats. Within 12 hours after injection of estradiol, the content of IP increased by almost 100 per cent. The amounts of the protein in mature rats varied according to the stage of estrous cycle.     

The inositol 1,4,5-trisphosphate receptor is required for maintenance of olfactory adaptation in Drosophila antennae

A role for inositol 1,4,5-trisphosphate (IP(3)) as a second messenger during olfactory transduction has been postulated in both vertebrates and invertebrates. However, given the absence of either suitable pharmacological reagents or mutant alleles specific for the IP(3) signaling pathway, an unequivocal demonstration of IP(3) function in olfaction has not been possible. Here we have investigated the role of a well-established cellular target of IP(3)-the IP(3) receptor (IP(3)R)-in olfactory transduction in Drosophila. For this purpose we tested existing viable combinations of IP(3)R mutant alleles, as well as a newly generated set of viable itpr alleles, for olfactory function. In all of the viable allelic combinations primary olfactory responses were found to be normal. However, a subset of itpr alleles (including a null allele) exhibit faster recovery after a strong pulse of odor, indicating that the IP(3)R is required for maintenance of olfactory adaptation. Interestingly, this defect in adaptation is dominant for two of the alleles tested, suggesting that the mechanism of adaptation is sensitive to levels of the IP(3)R.     

Analyzing the role of the putative inositol 1,3,4,5-tetrakisphosphate receptor GAP1IP4BP in intracellular Ca2+ homeostasis

Inositol 1,3,4,5-tetrakisphosphate (IP(4)) has been linked to a potential role in the regulation of intracellular free Ca(2+) concentration ([Ca(2+)](i)) following cellular stimulation with agonists that activate phosphoinositide-specific phospholipase C. However, despite many studies, the function of IP(4) remains unclear and indeed there is still some debate over whether it has a function at all. Here we have used various molecular approaches to address whether manipulation of the potential IP(4) receptor, GAP1(IP4BP), affects [Ca(2+)](i) following cellular stimulation. Using single cell imaging, we show that the overexpression of a constitutively active and a potential dominant negative form of GAP1(IP4BP) appear to have no effect on Ca(2+) mobilization or Ca(2+) entry following stimulation of HeLa cells with histamine. In addition, through the use of small interfering RNA duplexes, we have examined the effect of suppressing endogenous GAP1(IP4BP) production on [Ca(2+)](i). In HeLa cells in which the endogenous level of GAP1(IP4BP) has been suppressed by approximately 95%, we failed to observe any effect on Ca(2+) mobilization or Ca(2+) entry following histamine stimulation. Thus, using various approaches to manipulate the function of endogenous GAP1(IP4BP) in intact HeLa cells, we have been unable to observe any detectable effect of GAP1(IP4BP) on [Ca(2+)](i).     

Identification and subcellular distribution of endogenous Ins(1,4,5)P(3) 3-kinase B in mouse tissues

Inositol 1,4,5-trisphosphate 3-kinase (IP(3)-3K) catalyses the phosphorylation of inositol 1,4,5-trisphosphate to inositol 1,3,4,5-tetrakisphosphate. cDNAs encoding three mammalian isoforms have been reported and referred to as IP(3)-3KA, IP(3)-3KB, and IP(3)-3KC. IP(3)-3KB is particularly sensitive to proteolysis at the N-terminus, a mechanism known to generate active fragments of lower molecular mass. Endogenous IP(3)-3KB has therefore not been formally identified in tissues. We have probed a series of murine tissues with an antibody directed against the C-terminus of IP(3)-3KB and used IP(3)-3KB deficient mouse tissues as negative controls. IP(3)-3KB was shown to be particularly well expressed in brain, lung, and thymus with molecular masses of 110-120kDa. The identification of the native IP(3)-3KB by Western blotting for the first time will facilitate further studies of regulation of its activity by specific proteases and/or phosphorylation.     

Models of IP3 and Ca2+ oscillations: frequency encoding and identification of underlying feedbacks

Hormones that act through the calcium-releasing messenger, inositol 1,4,5-trisphosphate (IP3), cause intracellular calcium oscillations, which have been ascribed to calcium feedbacks on the IP3 receptor. Recent studies have shown that IP3 levels oscillate together with the cytoplasmic calcium concentration. To investigate the functional significance of this phenomenon, we have developed mathematical models of the interaction of both second messengers. The models account for both positive and negative feedbacks of calcium on IP3 metabolism, mediated by calcium activation of phospholipase C and IP3 3-kinase, respectively. The coupled IP3 and calcium oscillations have a greatly expanded frequency range compared to calcium fluctuations obtained with clamped IP3. Therefore the feedbacks can be physiologically important in supporting the efficient frequency encoding of hormone concentration observed in many cell types. This action of the feedbacks depends on the turnover rate of IP3. To shape the oscillations, positive feedback requires fast IP3 turnover, whereas negative feedback requires slow IP3 turnover. The ectopic expression of an IP3 binding protein has been used to decrease the rate of IP3 turnover experimentally, resulting in a dose-dependent slowing and eventual quenching of the Ca2+ oscillations. These results are consistent with a model based on positive feedback of Ca2+ on IP3 production.     

Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project

We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42?× Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42?× rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.