Characterization of DRP2, a novel human dystrophin homologue.

The currently recognised dystrophin protein family comprises the archetype, dystrophin, its close relative, utrophin or dystrophin-related protein (DRP), and a distantly related protein known as the 87K tyrosine kinase substrate. During the course of a phylogenetic study of sequences encoding the characteristic C-terminal domains of dystrophin-related proteins, we identified an unexpected novel class of vertebrate dystrophin-related sequences. We term this class dystrophin-related protein 2 (DRP2), and suggest that utrophin/DRP be renamed DRP1 to simplify future nomenclature. DRP2 is a relatively small protein, encoded in man by a 45 kb gene localized to Xq22. It is expressed principally in the brain and spinal cord, and is similar in overall structure to the Dp116 dystrophin isoform. The discovery of a novel relative of dystrophin substantially broadens the scope for study of this interesting group of proteins and their associated glycoprotein complexes.

Laser microdissection expression profiling of marginal edges of colorectal tumours reveals evidence of increased lactate metabolism in the aggressive phenotype.

BACKGROUND: The morphology of the invasive margin in colorectal cancer can be described as either pushing or infiltrative. These phenotypes carry prognostic significance, particularly in node negative disease, and provide an excellent model for the study of invasive behaviour in vivo. METHODS: The marginal edges of 16 stage-matched tumours exhibiting these contrasting growth patterns were microdissected. The extracted mRNA was amplified and hybridised to a 9546 feature oligonucleotide array. Selected differentials were validated using real-time polymerase chain reaction and the protein product was interrogated by using immunohistochemistry. RESULTS: After stringent quality control and filtering of data generated, 39 genes were identified as being significantly differentially expressed between the two types of marginal edge. Several genes involved in cellular metabolism were identified as differentials including lactate dehydrogenase B (LDHB) and modulators of glucose transport. CONCLUSIONS: The LDH expression profile differs between the invasive phenotypes. A hypothesis is proposed in which altered metabolism is a cause of contrasting invasive behaviour independent of the hypoxia-inducible factor mediated hypoxic response, consistent with the Warburg phenomenon.

Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis.

Conventional approaches to target labelling for expression microarray analysis typically require relatively large amounts of total RNA, a serious limitation when the sample available is small. Here we explore the cycle-dependent amplification characteristics of Template-Switching PCR and validate its use for microarray target labelling. TS-PCR identifies up to 80% of the differentially expressed genes identified by direct labelling using 30-fold less input RNA for the amplification, with the equivalent of 1000-fold less starting material being used for each hybridisation. Moreover, the sensitivity of microarray experiments is increased considerably, allowing the identification of differentially expressed transcripts below the level of detection using targets prepared by direct labelling. We have also validated the fidelity of amplification and show that the amplified material faithfully represents the starting mRNA population. This method outperforms conventional labelling strategies, not only in terms of sensitivity and the identification of differentially expressed genes, but it is also faster and less labour intensive than other amplification protocols.

Characterisation of a novel murine intestinal serine protease, DISP.

A putative novel murine serine protease, DISP, was identified by cDNA indexing and shown to be expressed primarily in distal gut. FISH analysis showed it to be localised to mouse chromosome 17A3. A possible human homologue for DISP has been identified. DISP is a novel member of clan SA/family S1 of the serine proteases, at present of unknown function.

The expression of the Na+/glucose cotransporter (SGLT1) gene in lamb small intestine during postnatal development.

We have shown previously that the activity and abundance of the intestinal Na+/glucose cotransporter (SGLT1) declines dramatically during the postnatal development of lambs, and that it can be restored in the intestine of ruminant sheep by intra-luminal infusion of D-glucose. The work presented in this paper has followed the expression of the SGLT1 gene along the vertical and horizontal axes of the ovine small intestine during early development, using quantitative in situ hybridisation histochemistry. Along the vertical axis, SGLT1 mRNA was first detectable just below the crypt-villus junction and rose rapidly to a peak level approx. 150 microns above this point. After reaching a maximum, the amount of message gradually declined towards the villus tip. This pattern of mRNA accumulation along the crypt-villus axis was similar in all intestinal positions and age groups. Along the length of the small intestine (horizontal axis), a decline in the level of SGLT1 mRNA was observed first in the distal intestine. This decrease in SGLT1 mRNA was significant in the intestine (75% of length) of 5-week-old lambs when compared to tissue taken from 25 and 50% of length (P < 0.01 and P < 0.02, respectively). However, the observed fall in the expression of this gene during weaning did not coincide with the fall in activity and amount of SGLT1. In adult animals, where the activity of SGLT1 is very low, the amount of message was greatly reduced. This work supports the finding that the expression of SGLT1 is primarily controlled at the post-transcriptional level during the postnatal development of ovine intestine.

Expression of the dystrophin-related protein 2 (Drp2) transcript in the mouse.

We have recently characterised a new member of the dystrophin gene family, DRP2, and its murine counterpart, Drp2, which encode dystrophin-related protein 2 (DRP2). DRP2 is predicted to resemble certain short C-terminal isoforms of dystrophin and dystrophin-related protein 1 (DRP1 or utrophin). We describe here a comprehensive survey of Drp2 expression in the mouse by RT-PCR, and compare the expression profile of Drp2 with that of the related genes Dmd, Drp1 and Dag1 that encode all the known isoforms of dystrophin, DRP1/utrophin and a component of the dystrophin-associated protein complex, dystroglycan, respectively. Drp2 was shown to be expressed throughout the central nervous system (CNS) and in several peripheral tissues including the eye, kidney, teeth, oesophagus, colon, epididymis and ovary. The expression of Drp2 in the CNS was then further defined by in situ hybridization. Overall, the pattern of Drp2 expression corresponds to a subset of the brain regions known to express Dag1, and shows substantial overlap with regions that express various isoforms of dystrophin (particularly in the cerebral cortex, hippocampus and cerebellum). These data define the distribution of Drp2 expression in the mouse, and raise the possibility that in the CNS it may be an important component in neuronal dystrophin-associated complexes.

Analysis of gene expression in single cells.

A cell's structural and functional characteristics are dependent on the specific complement of genes it expresses. The ability to study and compare gene usage at the cellular level will therefore provide valuable insights into cell physiology. Such analyses are complicated by problems associated with sample collection, sample size and the limited sensitivity of expression assays. Advances have been made in approaches to the collection of cellular material and the performance of single-cell gene expression analysis. Recent development in global amplification of mRNA may soon permit expression analyses of single cells to be performed on DNA microarrays.

Identification of genes regulated by leukemia-inhibitory factor in the mouse uterus at the time of implantation.

The endometrium is prepared for implantation by the actions of estradiol (E2) and progesterone (P4). In mice the luminal epithelium (LE) only becomes fully receptive to the attaching blastocyst in response to the nidatory estrogen surge on d 4 of pregnancy. The cytokine leukemia-inhibitory factor (LIF) is rapidly induced by nidatory estrogen and has been shown to be the primary mediator of its action. Implantation fails in the absence of LIF, and injection of LIF on d 4 of pregnancy can substitute for the nidatory estrogen. In this study, we sought to identify genes regulated by LIF in the uterine epithelium. We used oligonucleotide microarrays to compare the transcript profiles of paired uterine horns from LIF-deficient MF1 mice after intraluminal injection of LIF or PBS on d 4 of pseudopregnancy. IGF-binding protein 3 was identified as a gene up-regulated by LIF; this was confirmed by RT-PCR. In situ hybridization showed that the primary site of IGF-binding protein 3 expression is the luminal epithelium (LE), the known site of LIF action in the uterus. We identified two other genes: amphiregulin and immune response gene-1, the expression of which were also up-regulated by LIF. Immune response gene 1 has recently been shown to be essential for implantation. Expression of all three of these genes in the LE is known to be regulated by P4. The expression of osteoblast-specific factor 2 and leukocyte 12/15 lipoxygenase, which are also expressed in LE under the control of P4, were not increased by LIF. This suggests that one of the actions of LIF on LE may be to enhance the expression of a subset of P4-regulated genes.

Distribution of mRNA encoding the inwardly rectifying K+ channel, BIR1 in rat tissues.

The distribution of mRNA encoding the inwardly rectifying K+ channel, BIR1 [1] was investigated in rat tissues, and a comparison made with the expression of related genes rcKATP and GIRK1 using the reverse transcription-polymerase chain reaction (RT-PCR). This showed BIR1 to be expressed in all areas of the brain examined, in the eye but not in any other peripheral tissue. This pattern was distinct from rcKATP and GIRK1. Additional in situ hybridisation studies of the central expression of BIR1 demonstrated high levels of BIR1 mRNA in the hippocampus, dentate gyrus, taenia tecta and cerebellum and at lower levels in the cortex, habenular nucleus, olfactory bulb, primary olfactory cortex, thalamus, pontine nucleus and amygdaloid nucleus.

Conduction and synaptic transmission in the optic nerve and the superior colliculus during development of the retinocollicular projection in the wallaby (Macropus eugenii).

When do the developing connections between mammalian retinal ganglion cells and the superior colliculus become functional? Evoked potentials elicited by optic nerve stimulation in the pouch young of the wallaby were used to answer the question. Up to 42 days after birth, the evoked potentials in the colliculus appeared to be generated by axon conduction. Synaptic activity was first recorded from the rostral colliculus at 45 days, and was found to be progressively more caudal, spreading to cover the colliculus, by 65 days. From the earliest indication of synaptic activity until eye opening at 140 days, current source density (CSD) analysis consistently showed the same basic pattern: an initial deep sink from synaptic activity of fast (Y type) fibres, and a more superficial longer-latency sink from slower (W type) fibres. All features became more clearly delineated with age. The indirect retinocorticocollicular connection appeared between 134 days and 146 days. The ability of optic nerve fibres to sustain action potentials precedes their formation of functional synapses with collicular neurons, which happens abruptly at three months before eye opening. CSD analysis showed that the relationship between the conduction velocity of optic nerve fibres and their depth of termination is evident from the first signs of synapse formation.

Improved method for detecting differentially expressed genes using cDNA indexing.

In cDNA indexing, differentially expressed genes are identified by the display of specific, corresponding subsets of cDNA. Subdivision of the cDNA population is achieved by the sequence-specific ligation of adapters to the overhangs created by class IIS restriction enzymes. However, inadequate specificity of ligation leads to redundancy between different adapter subsets. We evaluate the incidence of mismatches between adapters and class IIS restriction fragments during ligation and describe a modified set of conditions that improves ligation specificity. The improved protocol reduces redundancy between amplified cDNA subsets, which leads to a lower number of bands per lane of the differential display gel, and therefore simplifies analysis. We confirm the validity of this revised protocol by identifying five differentially expressed genes in mouse duodenum and ileum.

Tissue distribution of adenosine receptor mRNAs in the rat.

1. A degree of ambiguity and uncertainty exists concerning the distribution of mRNAs encoding the four cloned adenosine receptors. In order to consolidate and extent current understanding in this area, the expression of the adenosine receptors has been examined in the rat by use of in situ hybridisation and the reverse transcription-polymerase chain reaction (RT-PCR). 2. In accordance with earlier studies, in situ hybridisation revealed that the adenosine A1 receptor was widely expressed in the brain, whereas A2A receptor mRNA was restricted to the striatum, nucleus accumbens and olfactory tubercle. In addition, A1 receptor mRNA was detected in large striatal cholinergic interneurones, 26% of these neurones were also found to express the A2A receptor gene. Central levels of mRNAs encoding adenosine A2B and A3 receptors were, however, below the detection limits of in situ hybridisation. 3. The more sensitive technique of RT-PCR was then employed to investigate the distribution of adenosine receptor mRNAs in the central nervous system (CNS) and a wide range of peripheral tissues. As a result, many novel sites of adenosine receptor gene expression were identified. A1 receptor expression has now been found in the heart, aorta, liver, kidney, eye and bladder. These observations are largely consistent with previous functional data. A2A receptor mRNA was detected in all brain regions tested, demonstrating that expression of this receptor is not restricted to the basal ganglia. In the periphery A2A receptor mRNA was also found to be more widely distributed than generally recognised. The ubiquitous distribution of the A2B receptor is shown for the first time, A2B mRNA was detected at various levels in all rat tissues studied. Expression of the gene encoding the adenosine A3 receptor was also found to be widespread in the rat, message detected throughout the CNS and in many peripheral tissues. This pattern of expression is similar to that observed in man and sheep, which had previously been perceived to possess distinct patterns of A3 receptor gene expression in comparison to the rat. 4. In summary, this work has comprehensively studied the expression of all the cloned adenosine receptors in the rat, and in so doing, resolves some of the uncertainty over where these receptors might act to control physiological processes mediated by adenosine.

Adenosine receptor expression and function in rat striatal cholinergic interneurons.

Cholinergic neurons were identified in rat striatal slices by their size, membrane properties, sensitivity to the NK(1) receptor agonist (Sar(9), Met(O(2))(11)) Substance P, and expression of choline acetyltransferase mRNA. A(1) receptor mRNA was detected in 60% of the neurons analysed, and A(2A) receptor mRNA in 67% (n=15). The A(1) receptor agonist R-N(6)-(2-phenylisopropyl)adenosine (R-PIA) hyperpolarized cholinergic neurons in a concentration dependent manner sensitive to the A(1) antagonist 8-cyclopentyl-1, 3-dipropylxanthine (DPCPX, 100 nM). In dual stimulus experiments, the A(2A) receptor antagonist 8-(3-chlorostyryl)caffeine (CSC, 500 nM) decreased release of [(3)H]-acetylcholine from striatal slices (S2/S1 0.78+/-0.07 versus 0.95+/-0.05 in control), as did adenosine deaminase (S2/S1 ratio 0.69+/-0.05), whereas the A(1) receptor antagonist DPCPX (100 nM) had no effect (S2/S1 1.05+/-0.14). In the presence of adenosine deaminase the adenosine A(2A) receptor agonist 2-p-((carboxyethyl)phenylethylamino)-5'-N-ethylcarboxamidoadeno sin e (CGS21680, 10 nM) increased release (S2/S1 ratio 1.03+/-0.05 versus 0.88+/-0.05 in control), an effect blocked by the antagonist CSC (500 nM, S2/S1 0.68+/-0.05, versus 0.73+/-0.08 with CSC alone). The combined superfusion of bicuculline (10 microM), saclofen (1 microM) and naloxone (10 microM) had no effect on the stimulation by CGS21680 (S2/S1 ratio 0.99+/-0.04). The A(1) receptor agonist R-PIA (100 nM) inhibited the release of [(3)H]-acetylcholine (S2/S1 ratio 0.70+/-0.03), an effect blocked by DPCPX (S2/S1 ratio 1.06+/-0.07). It is concluded that both A(1) and A(2A) receptors are expressed on striatal cholinergic neurons where they are functionally active.

An analysis using DNA microarray of the time course of gene expression during syncytialization of a human placental cell line (BeWo).

Placental trophoblast syncytialization is a unique biological process. We have studied the time course of this process using DNA microarray in a cell model of syncytialization (the cytotrophoblast cell line BeWo following increased intracellular cAMP by forskolin). Total RNA was extracted from BeWo cells and labelled-cRNA target was then hybridized to a specific oligonucleotide probe set containing probes to over 12?000 human transcripts. Detectable levels of signal were found on average for 44 per cent of the total number of genes assayed. The correlation coefficient for the level of expression of independent replicates was #10878;0.99. The mRNA expression profile of specific genes analysed by microarray correlated quantitatively well with that analysed by reverse transcription-polymerase chain reaction and with protein secretion. In the absence of forskolin there are relatively few changes in gene expression (reaching a threshold of two fold); in the presence of forskolin there are a substantial number of changes. By clustering the patterns of altered gene expression at least ten groups could be extracted. Seven of these clusters involved increased gene expression and three decreased expression. Each cluster has been categorized by gene ontology (confining the analysis to genes with 'known' function). Among the genes with increased expression following forskolin treatment were many required for cellular communication (such as placental specific peptide hormones) and metabolism (such as cholesterol side chain cleavage enzyme). Several genes known to be involved in cell adhesion and fusion have markedly changed expression levels very early following forskolin exposure, thus preceding morphological fusion of BeWo cells. Further analysis of this data and expression profiling in general will be able to contribute to understanding the functional basis for the formation of the placental syncytiotrophoblast.

Interocular suppression in cat striate cortex is not orientation selective.

For the majority of neurones in cat striate cortex, the response to an optimal stimulus presented to one eye is suppressed when a stimulus of substantially different orientation is presented to the other eye. In order to determine the true orientational tuning of the underlying inhibitory interactions in the absence of binocular facilitation for matched stimuli, we tested how the response of such cells to an optimal grating in one eye is affected by gratings in the other eye of spatial frequencies too high or low to elicit an excitatory response through either eye: the vast majority of cells displayed suppression that was essentially independent of orientation. Our results indicate that interocular inhibition derives from cells representing all orientations, but is swamped by interocular facilitation for stimuli matched in orientation and spatial frequency.

Two stages in the development of a mammalian retinocollicular projection.

The retinocollicular projection in the marsupial mammal the wallaby Macropus eugenii, has been investigated anatomically to determine the order in the developing projection and electrophysiologically to determine the time of onset of synaptic transmission by recording evoked potentials in the colliculus in response to stimulation of the optic nerve. There are two clear stages: a protracted period when retinal axons grow into the colliculus in coarse retinotopic order with no recordable electrical activity followed by the formation of terminal zones in retinotopically correct positions, the loss of more widely distributed axons and the onset of evoked potentials. The two stages are not seen in non-mammalian vertebrates where the projection is functional from the beginning.

Do normal plasma neurotensin concentrations increase ileal output?

Infusions of neurotensin increase ileal secretion in experimental animals, and the volume of ileal effluent in patients with ileostomies. The aim of the present study was to determine whether normal postprandial plasma concentrations of neurotensin increase the volume of fluid leaving the ileum. Basal and peak postprandial plasma neurotensin concentrations were 23 (17-36) and 39 (25-43) pmol/l (median and range) respectively in five subjects with ileostomies and 15 (3-27) and 32 (15-82) pmol/l respectively in nine normal subjects. Infusion of neurotensin for 30 min at a rate of 6.3 pmol/kg/min into six patients with ileostomies increased ileostomy output about 10-fold, and produced a significant decrease in the concentration of solid material, but plasma neurotensin concentrations rose to 237 (82-422) pmol/l during infusion at this rate. Infusion of neurotensin at 2.3 pmol/kg/min, producing plasma levels of 60 (16-108), had no significant effect the amount or nature of ileostomy effluent. We conclude that normal postprandial plasma concentrations of neurotensin are unlikely to influence the volume of fluid leaving the ileum.

Interactions of pancreatic secretory trypsin inhibitor in small intestinal juice: its hydrolysis and protection by intraluminal factors.

It has been proposed that modulation of cholecystokinin (CCK) release by proteinases, proteinase inhibitors and protein is mediated by a pancreatic secretory trypsin inhibitor (PSTI), also called monitor peptide, in the rat. When human [125I]-PSTI was incubated with fasting small bowel juice or activated pancreatic juice greater than 88% of tracer eluted from gel chromatography in the characteristic position of hydrolysed PSTI. However, when the small bowel juice had been pre-incubated with soybean trypsin inhibitor 3 g/l, casein 5 g/l or lactalbumin 30 g/l, the hydrolysis of PSTI diminished so that 95%, 32%, and 33% respectively, now eluted in the characteristic position of free (i.e. intact and not bound to an enzyme) PSTI. When [125I]-PSTI was incubated with pure trypsin, chymotrypsin, elastase or enterokinase greater than 95% of tracer eluted in the position of PSTI-enzyme complex. Incubation of PSTI with trypsin plus one other enzyme was required to produce hydrolysis. The degree of protection of PSTI from hydrolysis in duodenal juice produced by these substances correlates with their affects on CCK release. Our findings support the hypothesis that PSTIs mediate the modulation of CCK release by intraluminal proteinases, proteinase inhibitors and proteins.

Transducer models of head-centred motion perception.

By adding retinal and pursuit eye-movement velocity one can determine the motion of an object with respect to the head. It would seem likely that the visual system carries out a similar computation by summing extra-retinal, eye-velocity signals with retinal motion signals. Perceived head-centred motion may therefore be determined by differences in the way these signals encode speed. For example, if extra-retinal signals provide the lower estimate of speed then moving objects will appear slower when pursued (Aubert-Fleischl phenomenon) and stationary objects will move opposite to an eye movement (Filehne illusion). Most previous work proposes that these illusions exist because retinal signals encode retinal motion accurately while extra-retinal signals under-estimate eye speed. A more general model is presented in which both signals could be in error. Two types of input/output speed relationship are examined. The first uses linear speed transducers and the second non-linear speed transducers, the latter based on power laws. It is shown that studies of the Aubert-Fleischl phenomenon and Filehne illusion reveal the gain ratio or power ratio alone. We also consider general velocity-matching and show that in theory matching functions are limited by gain ratio in the linear case. However, in the non-linear case individual transducer shapes are revealed albeit up to an unknown scaling factor. The experiments show that the Aubert-Fleischl phenomenon and Filehne illusion are adequately described by linear speed transducers with a gain ratio less than one. For some observers, this is also the case in general velocity-matching experiments. For other observers, however, behaviour is non-linear and, according to the transducer model, indicates the existence of expansive non-linearities in speed encoding. This surprising result is discussed in relation to other theories of head-centred motion perception and the possible strategies some observers might adopt when judging stimulus motion during an eye movement.

Path perception and Filehne illusion compared: model and data.

Pursuit eye movements introduce retinal motion that complicates the recovery of self-motion from retinal flow. An extra-retinal, eye-velocity signal could be used to aid estimation of the observer's path, perhaps by converting retino-centric into head-centric motion. This conversion is apparently not precise because we often misperceive head-centric object velocity: in the Filehne illusion, for example, a stationary object appears to move in the opposite direction to the eye movement. Similar errors should be expected when extra-retinal, eye-velocity signals are used in self-motion tasks. However, most self-motion studies conclude that path direction is recovered quite accurately. Path perception and the Filehne illusion were therefore compared directly in order to examine the apparent discrepancy. A nulling technique determined the velocity of simulated eye rotation that cancelled the perceived curvature of the path or, in a Filehne condition, the perceived rotation of the ground-plane stimulus. In either case, observers typically set the simulated eye rotation to be a fixed proportion of the actual eye pursuit made. No differences were found between path perception and Filehne illusion. The apparent inaccuracy of path perception during a real eye movement was confirmed in a second experiment, using a standard 'mouse-pointing' technique. The experiments provide support for a model of head-centric motion perception based on extra-retinal and retinal signals that are linearly related to pursuit and retinal speed, respectively.