Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice

BACKGROUND

Microarray genome analysis is realising its promise for improving detection of genetic abnormalities in individuals with mental retardation and congenital abnormality. Copy number variations (CNVs) are now readily detectable using a variety of platforms and a major challenge is the distinction of pathogenic from ubiquitous, benign polymorphic CNVs. The aim of this study was to investigate replacement of time consuming, locus specific testing for specific microdeletion and microduplication syndromes with microarray analysis, which theoretically should detect all known syndromes with CNV aetiologies as well as new ones.

METHODS

Genome wide copy number analysis was performed on 117 patients using Affymetrix 250K microarrays.

RESULTS

434 CNVs (195 losses and 239 gains) were found, including 18 pathogenic CNVs and 9 identified as "potentially pathogenic". Almost all pathogenic CNVs were larger than 500 kb, significantly larger than the median size of all CNVs detected. Segmental regions of loss of heterozygosity larger than 5 Mb were found in 5 patients.

CONCLUSIONS

Genome microarray analysis has improved diagnostic success in this group of patients. Several examples of recently discovered "new syndromes" were found suggesting they are more common than previously suspected and collectively are likely to be a major cause of mental retardation. The findings have several implications for clinical practice. The study revealed the potential to make genetic diagnoses that were not evident in the clinical presentation, with implications for pretest counselling and the consent process. The importance of contributing novel CNVs to high quality databases for genotype-phenotype analysis and review of guidelines for selection of individuals for microarray analysis is emphasised.

Powder diffraction from a continuous microjet of submicrometer protein crystals

Atomic-resolution structures from small proteins have recently been determined from high-quality powder diffraction patterns using a combination of stereochemical restraints and Rietveld refinement [Von Dreele (2007), J. Appl. Cryst. 40, 133-143; Margiolaki et al. (2007), J. Am. Chem. Soc. 129, 11865-11871]. While powder diffraction data have been obtained from batch samples of small crystal-suspensions, which are exposed to X-rays for long periods of time and undergo significant radiation damage, the proof-of-concept that protein powder diffraction data from nanocrystals of a membrane protein can be obtained using a continuous microjet is shown. This flow-focusing aerojet has been developed to deliver a solution of hydrated protein nanocrystals to an X-ray beam for diffraction analysis. This method requires neither the crushing of larger polycrystalline samples nor any techniques to avoid radiation damage such as cryocooling. Apparatus to record protein powder diffraction in this manner has been commissioned, and in this paper the first powder diffraction patterns from a membrane protein, photosystem I, with crystallite sizes of less than 500 nm are presented. These preliminary patterns show the lowest-order reflections, which agree quantitatively with theoretical calculations of the powder profile. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in free-electron X-ray laser schemes, and for serial crystallography using a single-file beam of aligned hydrated molecules.

Altered cryptal expression of luminal potassium (BK) channels in ulcerative colitis

Decreased sodium (Na(+)), chloride (Cl(-)), and water absorption, and increased potassium (K(+)) secretion, contribute to the pathogenesis of diarrhoea in ulcerative colitis. The cellular abnormalities underlying decreased Na(+) and Cl(-) absorption are becoming clearer, but the mechanism of increased K(+) secretion is unknown. Human colon is normally a K(+) secretory epithelium, making it likely that K(+) channels are expressed in the luminal (apical) membrane. Based on the assumption that these K(+) channels resembled the high conductance luminal K(+) (BK) channels previously identified in rat colon, we used molecular and patch clamp recording techniques to evaluate BK channel expression in normal and inflamed human colon, and the distribution and characteristics of these channels in normal colon. In normal colon, BK channel alpha-subunit protein was immunolocalized to surface cells and upper crypt cells. By contrast, in ulcerative colitis, although BK channel alpha-subunit protein expression was unchanged in surface cells, it extended along the entire crypt irrespective of whether the disease was active or quiescent. BK channel alpha-subunit protein and mRNA expression (evaluated by western blotting and real-time PCR, respectively) were similar in the normal ascending and sigmoid colon. Of the four possible beta-subunits (beta(1-4)), the beta(1)- and beta(3)-subunits were dominant. Voltage-dependent, barium-inhibitable, luminal K(+) channels with a unitary conductance of 214 pS were identified at low abundance in the luminal membrane of surface cells around the openings of sigmoid colonic crypts. We conclude that increased faecal K(+) losses in ulcerative colitis, and possibly other diseases associated with altered colonic K(+) transport, may reflect wider expression of luminal BK channels along the crypt axis.

Phosphorylation regulates an inwardly rectifying ATP-sensitive K(+)- conductance in proximal tubule cells of frog kidney

K(+) channels in the renal proximal tubule play an important role in salt reabsorption. Cells of the frog proximal tubule demonstrate an inwardly rectifying, ATP-sensitive K(+) conductance that is inhibited by Ba(2+), G(Ba). In this paper we have investigated the importance of phosphorylation state on the activity of G(Ba) in whole-cell patches. In the absence of ATP, G(Ba) decreased over time; this fall in G(Ba) involved phosphorylation, as rundown was inhibited by alkaline phosphatase and was accelerated by the phosphatase inhibitor F(-)(10 mM: ). Activation of PKC using the phorbol ester PMA accelerated rundown via a mechanism that was dependent on phosphorylation. In contrast, the inactive phorbol ester PDC slowed rundown. Inclusion of the PKC inhibitor PKC-ps in the pipette inhibited rundown. These data indicate that PKC-mediated phosphorylation promotes channel rundown. Rundown was prevented by the inclusion of PIP-2 in the pipette. PIP-2 also abrogated the PMA-mediated increase in rundown, suggesting that regulation of G(Ba) by PIP-2 occurred downstream of PKC-mediated phosphorylation. G-protein activation inhibited G(Ba), with initial currents markedly reduced in the presence of GTPgammas. These properties are consistent with G(Ba) being a member of the ATP-sensitive K(+) channel family.

The use of milk progesterone to monitor reproductive function in beef suckler cows

Milk progesterone analysis was used to monitor reproductive function in 134 autumn calving cross-bred suckler cows. Progesterone was measured in milk samples collected three times per week from around 4 week post-calving to around day 60 of pregnancy during 1st and 2nd lactation. The mean day of onset of luteal activity (OLA) was 40.7 +/- 1.1 with the distribution skewed towards a later return. Once cyclicity had been initiated the incidence of reproductive cycle problems (6.5%) was low, though animals with such problems (n = 14) exhibited a delayed interval to first service (P < 0.05), lower conception and calving rates (P < 0.001), increased services per pregnancy (P < 0.001) and a higher (P < 0.10) barren rate (14.3% versus 4.0%) compared to animals with normal cycles (n = 201). In conclusion, using milk progesterone analysis we found a relatively low incidence of reproductive cycle problems in beefxdairy suckler cows. However, while the incidence of cycle problems was low, those animals with problems showed significantly impaired reproductive function.

Mechanisms underlying regulation of a barium-sensitive K+ conductance by ATP in single proximal tubule cells isolated from frog kidney

K(+) channels play an important role in pump-leak coupling and volume regulation in the renal proximal tubule. Previous experiments have identified a barium-sensitive K(+) conductance (G(Ba)) in proximal tubule cells isolated from frog kidneys. In this paper we examine the regulation of G(Ba) by ATP. G(Ba) was measured in single cells isolated from frog kidney using the whole-cell patch-clamp technique. G(Ba) was activated by 2 mM: intracellular ATP. This activation was enhanced by inhibition of protein kinase C and attenuated by inhibition of protein kinase A, indicating reciprocal regulation by these kinases. Activation by ATP was reduced in the presence of a hypertonic bath solution, suggesting that cell swelling was required. However, after activation to steady-state, G(Ba )was not sensitive to cell-volume changes. Hypotonic shock-induced volume regulation was inhibited by barium and quinidine, inhibitors of G(Ba). The effect of maximal inhibitory concentrations of barium and quinidine on volume regulation was similar and addition of both blockers together did not augment the inhibitory response. G(Ba) was also activated by ADP, via a mechanism dependent on the presence of Mg(2+). However, the responses to ADP and ATP were not additive, suggesting that these nucleotides may share a common mechanism of activation. The regulation of G(Ba) by ATP was biphasic, with a half-maximal activating concentration of 0.89 mM and a half maximal inhibitory concentration of 6.71 mM. The sensitivity to nucleotides suggests that G(Ba) may be regulated by the metabolic state of the cell. Furthermore, the sensitivity to solution osmolality, coupled with the blocker profile of inhibition of volume regulation, suggests that G(Ba) could play a role in volume regulation.

Endometrial Oxytocin Receptor Concentration and Activity in Prepubertal Ewe Lambs

We have measured endometrial oxytocin receptor concentrations during prepuberty in ewe lambs, and have investigated the effect of progesterone on the activity of these receptors. In the first study, oxytocin receptor concentrations were undetectable in 2-week prenatal lambs but had increased immediately following birth and were then maintained throughout prepubertal life. Despite the presence of oxytocin receptors animals showed no prostaglandin F(2alpha) (PGF(2alpha)) release in response to exogenous oxytocin challenge at either 3 or 5 months of age. In a second study in 4-month-old ewe lambs treatment with exogenous progesterone resulted in the appearance of PGF(2alpha) release in response to oxytocin after 10 days of treatment. Thus, during the prepubertal life, ewe lambs possess the prerequisites of a luteolytic mechanism in that they have a dormant population of oxytocin receptors in which progesterone can induce oxytocin-stimulated PGF(2alpha) release.

The Australian EEG database

The Australian EEG Database is a web-based de-identified searchable database of 18,500 EEG records recorded at a regional public hospital over an 11-year period. Patients range in age from a premature infant born at 24 weeks gestation, through to people aged over 90 years. This paper will describe the history of the database, the range of patients represented in the database, and the nature of the text-based and digital data contained in the database. Preliminary results of the first two studies undertaken using the database are presented. Plans for sharing data from the Australian EEG database with researchers are discussed. We anticipate that such data will be useful in not only helping to answer clinical questions but also in the field of mathematical modeling of the EEG.

Attenuation of PGF2alpha release in ewes infused with the oxytocin antagonist L-368,899

We have investigated the effects of systemic administration of the oxytocin antagonist (OTA) L-368,899 on luteolytic PGF(2alpha) release in ewes. In the first study, carried out in four ovariectomized ewes primed with progesterone to induce responsiveness to oxytocin, 3-h i.v. infusions of 3, 10 and 30 microg/kg/min OTA, carried out on days 12, 14, 16 and 18 in a Latin Square design, resulted in a significant attenuation of the oxytocin induced increase in PGFM concentration at all doses (OTA 139+/-8.3% of pre-oxytocin baseline; control 206.8+/-18.7%; P<0.005). In a further study, continuous infusion of cyclic ewes (n=6) with 10 microg/kg/min OTA from day 13 to day 17 of the cycle resulted in a reduction in both the frequency (OTA 1.0+/-0.4/ewe; control 2.2+/-0.2/ewe; P<0.05) and amplitude (OTA 31.8+/-11.0 pg/ml; control 68.8+/-10.4 pg/ml; P<0.05) of endogenous PGFM episodes compared to control ewes (n=5) measured during daily 8-h sampling windows on days 14-17. This reduction in PGFM concentrations was accompanied by a modest extension in the day of luteolysis (progesterone <0.5 ng/ml) to day 17.5+/-0.4 in the OTA treated group compared with day 16.4+/-0.5 in the control group (P=0.07). The results demonstrate that treatment with OTA caused a significant reduction in episodes of increased PGFM concentration during the period of luteolysis and may provide an approach by which to reduce early pregnancy failure.

Non-genomic regulation of intermediate conductance potassium channels by aldosterone in human colonic crypt cells

BACKGROUND

Aldosterone has a rapid, non-genomic, inhibitory effect on macroscopic basolateral K(+) conductance in the human colon, reducing its capacity for Cl(-) secretion. The molecular identity of the K(+) channels constituting this aldosterone inhibitable K(+) conductance is unclear.

AIM

To characterise the K(+) channel inhibited by aldosterone present in the basolateral membrane of human colonic crypt cells.

METHODS

Crypts were isolated from biopsies of healthy sigmoid colon obtained during colonoscopy. The effect of aldosterone on basolateral K(+) channels, and the possible involvement of Na(+):H(+) exchange, were studied by patch clamp techniques. Total RNA from isolated crypts was subjected to reverse transcriptase-polymerase chain reaction (RT-PCR) using primers specific to intermediate conductance K(+) channels (KCNN4) previously identified in other human tissues.

RESULTS

In cell attached patches, 1 nmol/l aldosterone significantly decreased the activity of intermediate conductance (27 pS) K(+) channels by 31%, 53%, and 54% after 1, 5 and 10, minutes, respectively. Increasing aldosterone concentration to 10 nmol/l produced a further 56% decrease in channel activity after five minutes. Aldosterone 1-10 nmol/l had no effect on channel activity in the presence of 20 micro mol/l ethylisopropylamiloride, an inhibitor of Na(+):H(+) exchange. RT-PCR identified KCNN4 mRNA, which is likely to encode the 27 pS K(+) channel inhibited by aldosterone.

CONCLUSION

Intermediate conductance K(+) channels (KCNN4) present in the basolateral membranes of human colonic crypt cells are a target for the non-genomic inhibitory effect of aldosterone, which involves stimulation of Na(+):H(+) exchange, thereby reducing the capacity of the colon for Cl(-) secretion.

Involving mental health service users and carers in curriculum development: moving beyond 'classroom' involvement

Recent policy statements that address the future priorities for nurse education have emphasized that service users and carers should be actively engaged in partnerships with education professionals in all aspects of the curriculum. The development of this agenda is well advanced; however, examples of 'how to do it' are sparse. The development of a strategy to involve users and carers in the design and delivery of the Diploma of Higher Education in Nursing at Napier University provided an opportunity to evaluate the process of developing partnerships in this area of nurse education. This paper presents the findings from a process evaluation from the various standpoints of the key interest groups. The overall project and evaluation is outlined, along with methodological and practical issues surrounding this type of 'collaborative' evaluation. The importance and satisfaction of practical aspects of the project are examined. The issues of representativeness, expertise in 'involvement' and the importance of the 'process' of involvement are explored. Finally, the challenges to developing 'meaningful involvement' that goes beyond 'classroom involvement' in nurse education are identified and discussed.