Classification of Long Noncoding RNAs by k-mer Content

K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack direct evolutionary relationships. In this chapter, we describe methods to compare k-mer content between groups of long noncoding RNAs (lncRNAs), to identify communities of lncRNAs with related k-mer contents, to identify the enrichment of protein-binding motifs in lncRNAs, and to scan for domains of related k-mer contents in lncRNAs. Our step-by-step instructions are complemented by Python code deposited in Github. Though our chapter focuses on lncRNAs, the methods we describe could be applied to any set of nucleic acid sequences.

Gas phase Elemental abundances in Molecular cloudS (GEMS) II. On the quest for the sulphur reservoir in molecular clouds: the H2S case

CONTEXT

Sulphur is one of the most abundant elements in the Universe. Surprisingly, sulphuretted molecules are not as abundant as expected in the interstellar medium and the identity of the main sulphur reservoir is still an open question.

AIMS

Our goal is to investigate the H2S chemistry in dark clouds, as this stable molecule is a potential sulphur reservoir.

METHODS

Using millimeter observations of CS, SO, H2S, and their isotopologues, we determine the physical conditions and H2S abundances along the cores TMC 1-C, TMC 1-CP, and Barnard 1b. The gas-grain model Nautilus is used to model the sulphur chemistry and explore the impact of photo-desorption and chemical desorption on the H2S abundance.

RESULTS

Our modeling shows that chemical desorption is the main source of gas-phase H2S in dark cores. The measured H2S abundance can only be fitted if we assume that the chemical desorption rate decreases by more than a factor of 10 when n H > 2 × 104. This change in the desorption rate is consistent with the formation of thick H2O and CO ice mantles on grain surfaces. The observed SO and H2S abundances are in good agreement with our predictions adopting an undepleted value of the sulphur abundance. However, the CS abundance is overestimated by a factor of 5 - 10. Along the three cores, atomic S is predicted to be the main sulphur reservoir.

CONCLUSIONS

The gaseous H2S abundance is well reproduced, assuming undepleted sulphur abundance and chemical desorption as the main source of H2S. The behavior of the observed H2S abundance suggests a changing desorption efficiency, which would probe the snowline in these cold cores. Our model, however, highly overestimates the observed gas-phase CS abundance. Given the uncertainty in the sulphur chemistry, we can only conclude that our data are consistent with a cosmic elemental S abundance with an uncertainty of a factor of 10.

Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analog of eutherian Xist Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of nonlinear sequence similarity. Xist Repeats B, C, and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.

Functional classification of long non-coding RNAs by k-mer content

The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called kmers. We found that lncRNAs of related function often had similar kmer profiles despite lacking linear homology, and that kmer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. Kmer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.

Thermodynamics of binding by calmodulin correlates with target peptide α-helical propensity

In this work, we have examined contributions to the thermodynamics of calmodulin (CaM) binding from the intrinsic propensity for target peptides to adopt an α-helical conformation. CaM target sequences are thought to commonly reside in disordered regions within proteins. Using the ability of TFE to induce α-helical structure as a proxy, the six peptides studied range from having almost no propensity to adopt α-helical structure through to a very high propensity. This despite all six peptides having similar CaM-binding affinities. Our data indicate there is some correlation between the deduced propensities and the thermodynamics of CaM binding. This finding implies that molecular recognition features, such as CaM target sequences, may possess a broad range of propensities to adopt local structure. Given that these peptides bind to CaM with similar affinities, the data suggest that having a higher propensity to adopt α-helical structure does not necessarily result in tighter binding, and that the mechanism of CaM binding is very dependent on the nature of the substrate sequence.

Idiopathic gonadotrophin deficiency: genetic questions addressed through phenotypic characterization

OBJECTIVE

The association of idiopathic hypogonadotrophic hypogonadism (IHH) with congenital olfactory deficit defines Kallmann's syndrome (KS). Although a small proportion of IHH patients have been found to harbour defined genetic lesions, the genetic basis of most IHH cases remains to be elucidated. Genes currently recognized to be involved comprise KAL (associated with X-linked-KS), the GnRH receptor (associated with resistance to GnRH therapy), DAX 1 (associated with adrenohypoplasia congenita) and three loci also associated with obesity, leptin (OB), leptin receptor (DB) and prohormone convertase (PC1). Because of the rarity of the condition and the observation that patients are almost universally infertile without assistance, familial transmission of IHH is encountered infrequently and pedigrees tend to be small. This has constrained the ability of conventional linkage studies to identify other candidate loci for genetic IHH. We hypothesized that a systematic clinical evaluation of a large patient sample might provide new insights into the genetics of this rare disorder. Specifically, we wished to examine the following propositions. First, whether normosmic (nIHH) and anosmic (KS) forms of IHH were likely to be genetically discrete entities, on the basis of quantitative olfactory testing, analysis of autosomal pedigrees and the prevalence of developmental defects such as cryptorchidism and cleft palate. Second, whether mirror movements and/or unilateral renal agenesis were specific phenotypic markers for X-linked-KS.

DESIGN AND PATIENTS

We conducted a clinical study of 170 male and 45 female IHH patients attending the endocrinology departments of three London University teaching hospitals. Approximately 80% of data were obtained from case records and 20% collected prospectively. Parameters assessed included olfaction, testicular volume, family history of hypogonadism, anosmia or pubertal delay, and history or presence of testicular maldescent, neurological, renal or craniofacial anomalies. Where possible, the clinical information was correlated with published data on genetic analysis of the KAL locus.

RESULTS

Olfactory acuity was bimodally distributed with no evidence for a spectrum of olfactory deficit. Testicular volume, a marker of integrated gonadotrophin secretion, did not differ significantly between anosmic and normosmic patients, at 2.0 ml and 2.2 ml, respectively. Nevertheless, the prevalence of cryptorchidism was nearly three times greater in anosmic (70.3%, of which 75.0% bilateral) than in normosmic (23.2%, of which 43.8% bilateral) patients. Individuals with nIHH, eugonadal isolated anosmia and/or KS were observed to coexist within 6/13 autosomal IHH pedigrees. On three occasions, fertility treatment given to an IHH patient had resulted in the condition being transmitted to the resulting offspring. Mirror movements and unilateral renal agenesis were observed in 24/98 and 9/87 IHH patients, respectively, all of whom were identifiable as X-KS males on the basis of pedigree analysis and/or defective KAL coding sequence. Abnormalities of eye movement and unilateral sensorineural deafness were observed in 10/21 and 6/111 KS patients, respectively, but not in nIHH patients.

DISCUSSION

Patients with IHH are almost invariably either anosmic (KS) or normosmic (nIHH), rather than exhibiting intermediate degrees of olfactory deficit. Moreover, the prevalence of cryptorchidism is nearly three times greater in KS than in nIHH despite comparable testicular volumes, suggesting a primary defect of testicular descent in KS independent of gonadotrophin deficiency. Disorders of eye movement and hearing appear only to occur in association with KS. Taken together, these findings indicate a clear phenotypic separation between KS and nIHH. However, pedigree studies suggest that autosomal KS is an heterogeneous condition, with incomplete phenotypic penetrance within pedigrees, and that some cases of autosomal KS, nIHH and even isolated anosmia are likely to have a common genetic basis. The prevalences of anosmia, mirror movements and unilateral renal agenesis among X-KS men are estimated to be 100, 85 and 31%, respectively. In sporadic IHH, mirror movements and unilateral renal agenesis are 100% specific phenotypic markers of de novo X-KS. By comparison, only 7/10 X-KS families harboured KAL coding defects. Clinical ascertainment, using mirror movements, renal agenesis and ichthyosis as X-KS-specific phenotypic markers, suggested that de novo X-KS was unlikely to comprise more than 11% of sporadic cases. The majority of sporadic KS cases are therefore presumed to have an autosomal basis and, hence, the preponderance of affected KS males over females remains unexplained, though reduced penetrance in women would be a possibility.

Diabetic ketoacidosis in Asian children

Over the 10 year period 1987-1996, 328 children with type 1 diabetes mellitus presented in the city of Birmingham, England, of whom 27% had diabetic ketoacidosis. Asian children under the age of 5 had an eightfold increased risk of presenting in diabetic ketoacidosis compared with non-Asian children of the same age.

Short report: Hyperammonaemia in critically ill septic infants

Three infants with subphrenic abscess, pyonephrosis, and obstructive ureterocoele respectively had grossly increased concentrations of plasma ammonia. This was considered to be a result of infections with urea splitting organisms. All died in spite of intensive care support, including specific measures to reduce plasma ammonia.

Short stature in Noonan syndrome: response to growth hormone therapy

BACKGROUND

Growth hormone (GH) has been used to promote growth in both the short and long term in a number of dysmorphic syndromes, including Turner syndrome. As this condition shares many clinical features with Noonan syndrome, it would seem logical to treat the latter group with GH.

AIMS

To assess the short and long term response to GH therapy in patients with Noonan syndrome.

METHODS

Analysis of patients with Noonan syndrome in the Pharmacia & Upjohn International Growth Study (this post-marketing database contains data on the majority of patients currently treated with GH in the UK). A questionnaire was also sent to participating clinicians.

RESULTS

Data on 66 patients (54 males) were available for study. At the start of GH therapy children were short, compared with both normal and Noonan children. During the first year of GH therapy height velocity increased from a mean of 4.9 to 7.2 cm per year. For patients treated long term with GH, mean height SDS increased from -2.9 pretreatment to -2.6 after one year and -2.3 after five years. Of the 10 patients at near final height, only one had a height above the 3rd centile for normal adults and above the mean for untreated Noonan patients. The mean increment in final height was 3.1 cm (range -1.1 to 6.5 cm).

CONCLUSIONS

GH therapy in patients with Noonan syndrome will improve height velocity in the short term. Longer-term therapy results in a waning of effect; initial indications are that final height is not improved substantially in most patients.

Inconsistencies in sweat testing in UK laboratories

BACKGROUND

Sweat testing procedures are perceived to vary widely.

AIM

To evaluate variability in sweat collection, analysis, and interpretation.

METHODS

Questionnaire responses from 30 self selected centres: 15 paediatric centres, and 15 district general hospitals.

RESULTS

Centres carried out 30-400 tests per year (median 100), with a diagnostic rate of 1:5-152 (median 1:30). Staff performed 5-268 tests per year. Minimum test age varied from 24 hours to four months. All stimulated sweating by pilocarpine iontophoresis using varying currents and times. Twenty six had observed urticaria or skin reddening, and nine blistering or burns. Sweat was collected for 10-60 minutes onto filter paper or into Macroduct coils. Between 2% and 25% of tests were considered insufficient. Twenty eight measured sodium, 24 chloride, and one osmolality and conductivity. Fifteen used literature and five in house reference ranges. Eleven would not test severely eczematous children.

CONCLUSIONS

Local audit is required to improve performance, as well as a national guideline to standardise collection, and external quality assessment to provide analytical feedback.

Glutamine synthetase and protease enzyme activities and growth response of ruminal bacterium Prevotella ruminicola strain B(1)4 to nitrogen source and concentration

The objective of this study was to determine the effects of varying nitrogen sources and concentrations upon glutamine synthetase and protease activities in Prevotella ruminicola strain B(1)4. Based on growth response it appears that ammonium chloride or pepticase limited P. ruminicola becomes nitrogen limited when nitrogen concentration is at 0.5 mM. However, when casein was provided as the sole source of nitrogen P. ruminicola becomes nitrogen limited at 2.5 mM. Glutamine synthetase activity was measured from mid-log phase cells grown in either nitrogen-limited or non-limited conditions. No activity was detectable in the non-limited treatments. However, in the N-limited treatments, pepticase had the highest activity (20.76 units), followed by ammonium chloride (18.72 units) and casein (14.42 units). Protease activity assays indicated that nitrogen-limited cultures had higher proteolytic activity than non-limited cultures. Moreover, these activities appeared to follow the same response pattern as the previously observed glutamine synthetase activities. The results of this study indicate that P. ruminicola strain B(1)4 protease activity may be influenced by nitrogen concentration such that activity increases when nitrogen availability decreases.

Individual differences in the priming effect of ethanol in social drinkers

OBJECTIVE

Alcohol-dependent individuals frequently report increased desire for alcohol and exhibit increased alcohol-seeking behaviors following a single drink. The phenomenon, known as priming, has been demonstrated in the laboratory in alcohol-dependent humans and in nonhumans, but the effect is inconsistently observed in nonproblem social drinkers. The current experiment examined this effect in healthy, nonproblem social drinkers across a range of preload doses.

METHOD

Using a repeated-measures design, 12 social drinkers were given ethanol (0.2, 0.4 or 0.8 g/kg) or placebo preloads. Various subjective effects measures were obtained at regular intervals. In addition, before and after consuming, the preload subjects performed an operant task on which they made repeated choices for either ethanol or money.

RESULTS

Ethanol dose-dependently increased subjective reports of drug liking and desire to take more ethanol. When data from all subjects were examined, ethanol did not affect choices for ethanol on the choice task. However, in subjects who reported the greatest positive mood effects from ethanol (0.8 g/kg), the ethanol preload increased choices for ethanol over money on the choice task.

CONCLUSIONS

These findings provide evidence for a priming effect of ethanol in social drinkers as measured by increased subjective desire for drug. The findings also suggest that the priming effects may be strongest in individuals who experience the greatest subjective positive mood effects from ethanol.

Compound heterozygosity for a Wolman mutation is frequent among patients with cholesteryl ester storage disease

Cholesteryl ester storage disease and Wolman disease are rare autosomal recessive lipoprotein-processing disorders caused by mutations in the gene encoding human lysosomal acid lipase. Thus far we have elucidated the genetic defects in 15 unrelated CESD patients. Seven were homozygotes for the prevalent hLAL exon 8 splice junction mutation which results in incomplete exon skipping, while eight probands were compound heterozygotes for E8SJM and a rare mutation on the second chromosome. In this report, we describe the molecular basis of CESD in three compound heterozygous subjects of Czech and Irish origin. RFLP and DNA sequence analysis revealed that they were heteroallelic for the common G(934)-->A substitution in exon 8 of the hLAL gene and a mutation which, if inherited on both alleles, would be expected to result in complete loss of enzyme activity and to cause Wolman disease. In patients A. M. and J. J., two nucleotide deletions in exons 7 and 10 were detected, involving a T at position 722, 723, or 724 and a G in a stretch of five guanosines at positions 1064;-1068 of the hLAL cDNA. Both mutations result in premature termination of protein translation at residues 219 and 336, respectively, and in the production of truncated, inactive enzymes. Subject D. H., in contrast, is a compound heterozygote for the Arg(44)-->Stop mutation previously described in a French CESD proband. Combined with data in the literature, our results demonstrate that compound heterozygosity for a mutation causing Wolman disease is common among cholesteryl ester storage disease patients.

Quantitative growth hormone secretion and final adult height

OBJECTIVE

The relationship of quantitative GH secretion to height, growth velocity and puberty is complex and has been the subject of extensive study in children. This study was designed to relate quantitative GH secretion to final height.

SUBJECTS

Twenty tall (> 183 cm, 90th centile for adult height) and 20 short (< 166 cm, 10th centile) postpubertal men who had recently completed linear growth (age range 18-27 years).

MEASUREMENTS

GH dynamics were studied on four occasions; insulin (0.15 units/kg, iv)-induced hypoglycaemia and GHRH (100 mg, iv) with and without the anticholinesterase, pyridostigmine (120 mg orally). Spontaneous nocturnal GH secretion was assessed by 20 minute sampling from 2100 h until 0600 h. GH was measured by IRMA. Analysis was by comparison of peak GH response and area under the curve (AUC). GH profiles were further analysed using the 'pulsar' programme.

RESULTS

The mean height in the tall group was 187.7 cm (range 183-197) compared to 163.5 cm (range 160-166) for the short group. No difference existed between groups in the GH response to hypoglycaemia or GHRH with and without pyridostigmine. Area under the curve, pulse number, length and amplitude for spontaneous nocturnal GH secretion showed no significant difference between the tall and short subjects. Serum IGF-I (mean 230.5 +/- 15. 4 vs. 230.6 +/- 18.9 microg/l) did not differ between the groups.

CONCLUSIONS

Quantitative GH secretion does not appear to be an important determinant of final height in healthy individuals.

Pituitary gigantism causing diabetic ketoacidosis

Although growth hormone excess (acromegaly) in association with glucose intolerance and diabetes mellitus is well documented in adult medicine, it is much less common in the paediatric age group. We report the case of a 13 year-old boy who presented with tall stature secondary to a large growth hormone secreting adenoma of the pituitary gland. Random growth hormone was 630 mIU/l and did not suppress during an oral glucose tolerance test. Following debulking of the tumour, he developed diabetic ketoacidosis requiring insulin treatment, but after further surgery glucose handling returned to normal. He has been started on testosterone to arrest further increase in height.

Cushing's syndrome caused by nodular adrenal hyperplasia in children with McCune-Albright syndrome

McCune-Albright syndrome consists of fibrous dysplasia of bone, café-au-lait skin pigmentation, and endocrine dysfunction (usually precocious puberty). Other endocrine abnormalities occur in a minority of patients, and of these, Cushing's syndrome is the least often recognized. We present 5 children (4 girls) with features of McCune-Albright syndrome who had Cushing's syndrome in the infantile period (<6 months). In 2 children spontaneous resolution occurred, but the remaining 3 required bilateral adrenalectomy. In addition, all 4 girls have experienced precocious puberty, and 3 children demonstrated radiologic evidence of nephrocalcinosis. Understanding of the underlying defect causing McCune-Albright syndrome emphasizes the importance of searching for other endocrine dysfunction in these children.

Responses to oral delta9-tetrahydrocannabinol in frequent and infrequent marijuana users

It is known that an individual's drug use history affects the quality of subjective effects experienced following administration of several clinically used psychoactive drugs such as barbiturates, diazepam, and morphine. However, it is not known whether drug use history also affects responses to therapeutic cannabinoids such as delta9-THC. The current experiment compared the subjective and behavioral effects of oral delta9-THC in two groups of volunteers: frequent users (FREQ; n = 11), who reported using marijuana at least 100 times, and infrequent users (INF; n = 10) who reported using marijuana 10 or fewer times. Subjects participated in three sessions during which they received delta9-THC (7.5 and 15 mg) and placebo. They completed subjective effects questionnaires for 5 h following administration. In the FREQ group, the lower dose (7.5 mg) increased ratings of "feel drug," relative to placebo, whereas it had no effect in the INF group. In contrast, at the higher dose (15 mg), ratings of "feel drug" were lower in the FREQ group than in the INF group, suggestive of tolerance. In addition, the INF group reported greater sedative effects than the FREQ group following the higher dose of delta9-THC, again suggesting tolerance to delta9-THC's sedative effects. These findings demonstrate that marijuana use history may affect the subjective effects of oral delta9-THC, but that the influence of drug use history depends on the dose of drug administered. These findings may have implications for the clinical use of delta9-THC and other cannabinoids.

Congenital hypothyroidism, seasonality and consanguinity in the West Midlands, England

Seasonal variation in the incidence of congenital hypothyroidism (CHT) is reported by some centres. Also, the incidence of CHT varies with ethnic origin. We report our experience in the West Midlands, England. The overall incidence of CHT among 1128 632 neonates screened over 16 years in the West Midlands was 1:2924 live births, but was increased (1:2323; p<0.05) between October and December. In the city of Birmingham between 1981 and 1991, the incidence of CHT was 1:781, 1:5540 and 1:2257 in Pakistani, Indian and North-West European children, respectively; no cases were seen in those from other ethnic groups. Consanguinity among those of Pakistani descent could account for the increased incidence within this population. Identification of the cause of seasonal variation may aid development of preventative strategies.

Novel and recurrent tyrosine aminotransferase gene mutations in tyrosinemia type II

Tyrosinemia type II (Richner-Hanhart syndrome, RHS) is a disorder of autosomal recessive inheritance characterized by keratitis, palmoplantar hyperkeratosis, mental retardation, and elevated blood tyrosine levels. The disease results from deficiency in hepatic tyrosine aminotransferase (TAT). We have previously described one deletion and six different point mutations in four RHS patients. We have now analyzed the TAT genes in a further seven unrelated RHS families from Italy, France, the United Kingdom, and the United States. We have established PCR conditions for the amplification of all twelve TAT exons and have screened the products for mutations by direct sequence analysis or by first performing single-strand conformation polymorphism analysis. We have thus identified the presumably pathological mutations in eight RHS alleles, including two nonsense mutations (R57X, E411X) and four amino acid substitutions (R119W, L201R, R433Q, R433W). Only the R57X mutation, which was found in one Scottish and two Italian families, has been previously reported in another Italian family. Haplotype analysis indicates that this mutation, which involves a CpG dinucleotide hot spot, has a common origin in the three Italian families but arose independently in the Scottish family. Two polymorphisms have also been detected, viz., a protein polymorphism, P15S, and a silent substitution S103S (TCG-->TCA). Expression of R433Q and R433W demonstrate reduced activity of the mutant proteins. In all, twelve different TAT gene mutations have now been identified in tyrosinemia type II.

Effects of expectancies on subjective responses to oral delta9-tetrahydrocannabinol

The effects of expectancies on subjective responses to oral delta9-tetrahydrocannabinol (delta9-THC) were examined. Thirty-five regular marijuana users were assigned to one of two groups: one group was told that they may receive a cannabinoid or placebo and a second group was told that they may receive a drug from one of several classes of drugs (e.g., stimulant, sedative, antiemetic) or placebo. Regardless of the group to which they were assigned, subjects received each of two oral doses of delta9-THC (7.5 and 15 mg) and placebo, one dose per session, for a total of three sessions. Measures of subjective effects, including visual analog scales and the Addiction Research Center Inventory (ARCI), were administered at 0.5-h intervals throughout each session. Consistent with previous research using other drugs, subjects in the current experiment who expected to receive a cannabinoid reported greater pleasurable effects than subjects who did not have this expectancy. The results have implications for understanding the effects of cannabinoids when used in both recreational and clinical settings.

P67L: a cystic fibrosis allele with mild effects found at high frequency in the Scottish population

Only three mutant cystic fibrosis (CF) alleles have to date been established as conferring a dominant mild effect on affected subjects who are compound heterozygotes. We now add a fourth, P67L, which occurs on about 1.4% of Scottish CF chromosomes. Among 13 patients (12 unrelated) with this allele, the average age at diagnosis was 22.5 +/- 11.3 years. None of the cases had consistently raised sweat chloride concentrations, the average value being 57 +/- 9 mmol/l; 77% of the patients were pancreatic sufficient. When compared to three other established mild CF alleles, R117H, A455E, and 3849 + 10kb C-T, a compound heterozygote for P67L has minimal disease and clinical suspicions are unlikely to be confirmed other than by DNA typing.

Behavioral responses to ethanol in light and moderate social drinkers following naltrexone pretreatment

The opioid antagonist naltrexone has been shown to be effective in the treatment of alcoholism, possibly by dampening the subjective effects of ethanol. However, naltrexone does not consistently attenuate the effects of ethanol in social drinkers in laboratory-based challenge studies. In the present study, 25 healthy volunteers, who were either light drinkers (mean = 3 drinks per week) or moderate drinkers (mean = 16 drinks per week), participated in six evening sessions. At each session, subjects ingested a capsule containing naltrexone (25 or 50 mg) or placebo, and 1 hr later they consumed a beverage containing ethanol (0.25 g/kg, equivalent to about two standard alcoholic drinks) or placebo. Subjects received all combinations of pretreatments and beverages. They completed self-report mood questionnaires and psychomotor tests at regular intervals. This low dose of ethanol produced modest but significant effects on self-report measures such as ratings of feeling a drug effect and of liking the drug effect. However, naltrexone (25 or 50 mg) pretreatment had no dampening effect on subjects' responses to ethanol. These results indicate that acute doses of naltrexone that are effective when administered chronically to alcoholics do not attenuate the acute effects of a low dose of ethanol in non-problem drinkers.

Effects of deprivation level on humans' self-control for food reinforcers

Deprivation level was manipulated in fourteen food- and water-deprived adult human females to examine its effects on self-control for food (choice of larger, more delayed access to apple juice over smaller, less delayed access to apple juice). Each subject was exposed to two treatments: (1) Consumption of a 500 g tomato soup preload just prior to self-control testing and (2) no soup preload. When subjects had consumed soup, they reported significantly less hunger and showed significantly more self-control as compared to when not having consumed soup. Additionally, when subjects had consumed soup, self-control decreased as a function of session time. Subjects who reported that they were currently dieting drank significantly less juice when they had previously consumed soup than when they do not previously consumed soup. Together, the results indicate that when subjects are more deprived they may be less able to wait for food reinforcers (i.e., show less self-control). Such behaviour may be adaptive in situations in which energy is needed to survive periods of food scarcity.

The neuroradiology of Kallmann's syndrome: a genotypic and phenotypic analysis

A detailed neurological investigation of patients with Kallmann's syndrome (KS) has been performed in an attempt to relate phenotypic characterization with genotype. Twenty-seven subjects with KS were studied (including 12 males with X-linked disease and 3 females). Six male and 2 female normosmics with isolated GnRH deficiency, 1 male with KS variant, and 1 obligate female carrier were also imaged. Evidence for X-linked disease was derived both from analysis of pedigree and by mutation analysis at the KAL locus. The female carrier and all 8 normosmics had normal olfactory bulbs and sulci, as did 3 male KS. The study, therefore, confirms the value of magnetic resonance imaging in the diagnosis of KS, but suggests that the technique is not sufficiently sensitive to differentiate KS from the normosmic form of GnRH deficiency in all cases. Phenotypic characterization of KS was more effectively achieved by accurate estimation of olfactory status. Three new mutations at the KAL locus were identified, 2 single exon deletions and 1 point mutation. In 2 pedigrees with clear X-linked inheritance, no coding sequence mutations were detected; it may be that these harbor mutations of pKAL, the recently characterized 5'-promoter region. No clear relationship could be established between specific phenotypic anomalies and particular KAL mutations. Involuntary, mirror movements of the upper limbs were present in 10 of 12 cases of X-linked KS, but in none of the other subjects. Although this phenomenon has been ascribed to an abnormality of the corpus callosum, in the present study magnetic resonance imaging demonstrated no quantitative or qualitative morphological anomalies of this structure.

Transcutaneous bilirubinometry as a screening tool for neonatal jaundice

Between 25 and 50% of all term newborns develop clinical jaundice, and a serum bilirubin level above 260 microml/l (15 mg/dl) is found in 3% of normal term infants. In the United Kingdom many newborn infants with clinical jaundice have blood samples sent to biochemistry laboratories for assessment of the plasma bilirubin concentration. We planned to assess the cost in terms of finance, medical staff time, numbers of blood samples, and family delay in leaving hospital. We demonstrated that reflectance bilirubinometry is a reliable screening method for identifying which caucasian infants require to have plasma bilirubin concentrations measured in the laboratory. The Minolta Airshields transcutaneous bilirubinometer provided reproducible data, saved time and costs, and often spared infants a capillary or venous blood sample. The transcutaneous bilirubinometer provides a digital assessment of skin pigmentation by xenon reflectance. It has previously been shown to be possible to derive an estimate of plasma bilirubin from the number displayed by the meter and it is suggested as a method for identifying which infants need plasma bilirubin estimations.

Intraluminal bile duct hepatocellular carcinoma

Jaundice is usually a late feature in the course of hepatocellular carcinoma and is only rarely due to obstruction. We present two cases of obstructive jaundice, in which the cause of obstruction in both patients was a massive intraluminal filling defect within the common bile duct which proved to be hepatocellular carcinoma. The radiological features are described.

Identification of olfactory dysfunction in carriers of X-linked Kallmann's syndrome

OBJECTIVE

The aim of the study was to test the hypothesis that clinically unaffected female carriers of X-linked Kallmann's syndrome have an olfactory defect.

DESIGN

Assessment of the olfactory threshold to seven standard odorants, each at a concentration of 1-10(-8) mol/l.

PATIENTS

Five families with X-linked Kallmann's syndrome (KS) were tested, containing 19 males with KS, and 9 female carriers. Related but unaffected males (n = 8) were used as a control group, and in addition seven patients with Turner's syndrome (XO) were assessed.

MEASUREMENTS

The olfactory threshold was taken as the lowest concentration at which each odorant was clearly distinguished from control (liquid paraffin). The threshold for each odorant was compared between the subject groups using the non-parametric Mann-Whitney test.

RESULTS

All patients with KS were anosmic to all odorants. The female carriers had hyposmia, with a significant reduction in the olfactory threshold to putrid, peppermint, floral and pungent odorants compared to control subjects, and to peppermint, floral and pungent odorants compared to subjects with Turner's syndrome. The latter had olfactory thresholds which were statistically identical with the control group.

CONCLUSIONS

Obligate female carriers of X-linked Kallmann's syndrome are hyposmic compared to control subjects. The overlap between the two groups, however, makes olfactory testing unreliable as a diagnostic test.

Treatment with GHRH(1-29)NH2 in children with idiopathic short stature induces a sustained increase in growth velocity

OBJECTIVE

Therapy with GHRH in patients with mild GH insufficiency appears to be more effective than in those with severe insufficiency. We, therefore, studied the clinical response of children with idiopathic short stature to treatment with GHRH(1-29)NH2 (GHRHa) for a period of 12 months.

DESIGN

Eighteen short pre-pubertal children (aged 4.3-11.0 years, 17 male) with idiopathic short stature (height < 3rd centile, peak GH to provocative testing > 20 mU/l) were recruited to receive GHRHa 20 micrograms/kg by twice daily s.c. injection for one year. One patient was non-compliant and was withdrawn prior to 3 months of therapy. Pretreatment height velocity was calculated for 12 months and subjects were measured 3-monthly during therapy. Overnight GH profiles and s.c. GHRH tests (20 micrograms/kg) were performed at 0, 3, 6 and 12 months of therapy. In addition, an i.v. GHRH test (1 microgram/kg) was performed at the start and after 1 month of therapy.

MEASUREMENTS

Overnight GH profiles were analysed using the Pulsar program.

RESULTS

Mean (SD) height velocity (HV) increased from 4.8(0.9)cm/year pre-treatment to 7.2(1.6)cm/year after 12 months of therapy (P = 0.001). The children growing slowly (HV < 25th centile) before treatment had a greater growth response than those growing normally (HV > or = 25th centile) before treatment. Final height prediction increased by a mean (SD) of 3.4(2.6)cm. Overnight GH levels and GH responses to GHRH testing fell during the 12 months of therapy. Fasting blood glucose and insulin levels increased during therapy, as did IGF-I. Cessation of GHRHa was followed by catch-down growth during the first 3 months off therapy: mean (SD) HV 3.89(1.82)cm/year (P < 0.04), although the HV after 6 months (4.9(1.0))cm/year) and 12 months (4.4(1.0)cm/year) was not different from pretreatment values.

CONCLUSIONS

Short-term therapy with twice-daily s.c. injection of GHRHa (20 micrograms/kg) promoted linear growth in short children who were not GH-insufficient. The improved height velocity was sustained throughout the 12 months of treatment, followed by catch-down growth, and returned to pretreatment velocity after cessation of therapy.

Intrathoracic extra-mediastinal cystic hygroma in infancy

An infant with intrathoracic extra-mediastinal cystic hygroma is described. Fluid collection within the fetal chest was noted on routine antenatal ultrasound scan and this was subsequently drained. Postnatally, echocardiogram and thoracic CT scan demonstrated a cystic space between the pericardium and right mediastinal pleura. Thoracotomy performed at six weeks of age showed a multiloculated cystic mass adherent to the right pericardium and to the medial aspect of the diaphragm. Histology revealed the tumour to be a cystic hygroma (lymphangioma). Intrathoracic cystic hygroma occurring outside the mediastinum is extremely rare and has never been diagnosed previously in infancy.

Unilateral renal aplasia in X-linked Kallmann's syndrome

Unilateral renal agenesis is an uncommon association with Kallmann's syndrome (KS) (hypogonadotrophic hypogonadism and olfactory defect). We have investigated affected individuals from six pedigrees: five with X-linked KS, and one with X-linked KS and X-linked ichthyosis (XLI). Seventeen affected individuals have had renal imaging performed, and six scans demonstrated only one kidney. In addition, two pedigrees had males who died in the neonatal period with bilateral renal agenesis. Only two of the four affected individuals in the family with X-linked KS and X-linked ichthyosis (Pedigree 6) showed unilateral renal agenesis, despite all four patients demonstrating an interstitial deletion within the short arm of the X-chromosome. These data indicate that unilateral renal agenesis is much commoner than previously suspected in patients with X-linked Kallmann's syndrome, but that it may have incomplete penetrance within a family.

Gonadal function and response to human chorionic and menopausal gonadotrophin therapy in male patients with idiopathic hypogonadotrophic hypogonadism

OBJECTIVE

This study was designed to determine the response to therapy using human chorionic gonadotrophin (hCG) and human menopausal gonadotrophin (hMG) in males with idiopathic isolated hypogonadotrophic hypogonadism (IHH), and to compare the responses in patients presenting with and without cryptorchidism.

DESIGN

Analysis of male patients with IHH treated with hCG or combined hCG/hMG for a minimum of 6 months at St Bartholomew's Hospital. Clinical and endocrine assessment was performed in all patients prior to commencing therapy.

PATIENTS

A total of 26 males with IHH have been treated with exogenous gonadotrophins. Thirteen patients (Group 1) had cryptorchidism (unilateral in 7, bilateral in 6) at presentation, and 13 (Group 2) did not.

MEASUREMENTS

All patients had basal serum testosterone, LH and FSH determinations. An i.v. GnRH test was performed in 25 patients and an i.m. hCG stimulation test in 19. Testicular volume and serum testosterone were measured during both hCG and combined hCG/hMG therapy. Seminal analysis was performed at the start and monthly during hCG/hMG therapy.

RESULTS

Eighty-five per cent of the 13 patients in Group 1 had an olfactory defect (Kallmann's syndrome), compared with 23% of Group 2. Both groups of patients showed a subnormal response to initial i.v. GnRH and i.m. hCG testing. During hCG therapy only three patients in Group 1 and six in Group 2 achieved normal adult testosterone levels. The non-cryptorchid group achieved a higher mean testicular volume on hCG therapy than the cryptorchid group (mean (SD); 4.7 (1.8) ml vs 3.0 (1.6) ml (P < 0.02)), and for all patients there was a correlation between initial and maximal testicular volume (R = 0.69, P = 0.001). Four patients in Group 1 and five patients in Group 2 were treated with combined hCG/hMG for 6-15 months to induce fertility; only one patient in Group 1 achieved spermatogenesis, compared to all patients in Group 2 (leading to three pregnancies).

CONCLUSIONS

These data indicate that patients with idiopathic hypogonadotrophic hypogonadism (IHH) have a poor response to hCG therapy in terms of testicular growth and normalization of serum testosterone. Final testicular volume is dependent on initial testicular size. In addition, patients with IHH associated with cryptorchidism have a poor fertility potential to combined hCG/hMG therapy.

The implementation of a quality management system in a department of diagnostic radiology

The quality management systems of the Departments of Diagnostic Radiology of St George's Hospital, London, and Bristol Royal Infirmary (BRI) have been certified with the British Standard 5750. These were the first clinical departments in the UK to be certified to this internationally recognized quality assurance (QA) standard. Quality is a much used term; in this context it is defined as 'fitness for purpose', and quality assurance is the mechanism by which quality is achieved. The paper describes the features of the quality system which have been implemented at St George's Hospital, and how a management concept for manufacturing industries has been adapted successfully to a National Health Service Department. The paper also demonstrates how the quality system has led to the setting and achieving of departmental objectives.

Growth in CHARGE association

Growth data is shown from 44 children (aged 0.5-18 years; 27 boys, 17 girls) with CHARGE association. Children had a normal birth weight and length, but in infancy there was a fall in centiles. Children remained small and there was pubertal delay in boys. Close monitoring of growth with early detection and intervention is recommended.

Accuracy of the typical computed tomographic appearances of fibrosing alveolitis

BACKGROUND

Open lung biopsy is often performed to confirm the diagnosis in patients with suspected fibrosing alveolitis. The superior sensitivity and specificity of high resolution computed tomography (CT) over chest radiography in various diffuse lung diseases suggest that the characteristic appearance of fibrosing alveolitis on high resolution CT might render biopsy confirmation unnecessary.

METHODS

The chest radiographs and high resolution CT scans of 86 patients (41 with fibrosing alveolitis and 45 with various other diffuse lung diseases) were examined individually and independently by two observers. No clinical information was given and the observers gave a level of confidence when the diagnosis was thought to be fibrosing alveolitis.

RESULTS

The observers correctly and confidently discriminated between fibrosing alveolitis and other diffuse lung diseases on high resolution CT with an accuracy of 88% and on chest radiography with an accuracy of 76%. The false negative rate for fibrosing alveolitis diminished from 29% on chest radiography to 11% on high resolution CT. The false positive rate on chest radiography was 19% and on high resolution CT 13%; the false positive diagnoses on CT were the result of a few conditions (extrinsic allergic alveolitis, sarcoidosis, cryptogenic organising pneumonia, and pulmonary eosinophilia) which mimicked some of the CT features of fibrosing alveolitis. The superficial similarity of the CT patterns of these conditions are discussed.

CONCLUSIONS

High resolution CT is superior to chest radiography in establishing the diagnosis of fibrosing alveolitis and the typical CT appearances are virtually pathognomonic. The diagnostic advantages of CT over chest radiography should further reduce the need for open lung biopsy in this condition.

Rhizomelic chondrodysplasia punctata with isolated DHAP-AT deficiency

An infant with the characteristic phenotype of classical rhizomelic chondrodysplasia punctata was found to have an isolated deficiency of the peroxisomal enzyme acyl CoA dihydroxyacetone phosphate acyltransferase (DHAP-AT). All other peroxisomal functions measured were found to be normal. Previously described in one other case report, this confirms the existence of another distinct form of peroxisomal disorder characterised biochemically by a deficiency in de novo plasmalogen biosynthesis only.

Acceleration of pubertal development following pituitary radiotherapy for Cushing's disease

A 7-year-old boy with pituitary dependent Cushing's disease was treated with pituitary irradiation following unsuccessful microadenomectomy. This led to normalization of the hypercortisolaemia, but was followed by GH deficiency. Two years after radiotherapy he had the onset of pubertal development with testicular enlargement to 8 ml bilaterally. Pubertal regression was induced using the long-acting GnRH analogue goserelin. Acceleration of skeletal maturation was also arrested, resulting in improvement of final height prediction. Irradiation directly to the hypothalamo-pituitary region, as well as whole brain irradiation, may thus be associated with accelerated pubertal development.

Pyridostigmine partially reverses dexamethasone-induced inhibition of the growth hormone response to growth hormone-releasing hormone

The GH response to insulin-induced hypoglycaemia and growth hormone-releasing hormone (GHRH) has been shown to be impaired in subjects with Cushing's syndrome and in healthy volunteers given oral glucocorticoids. Pyridostigmine is an anticholinesterase that stimulates GH secretion, probably by inhibition of hypothalamic somatostatin secretion. This work was designed to study the site of action of glucocorticoids in inhibiting the secretion of GH. Eight healthy male volunteers were studied on three occasions in random order. They took 2 mg oral dexamethasone or placebo at precisely 6-hourly intervals for 48 h before receiving 120 mg oral pyridostigmine or placebo, followed 60 min later by GHRH (100 micrograms) i.v. Samples for measuring GH were obtained at 15 min intervals for 2 h. The 'area under the curve' (AUC) for each of the treatments was significantly different: dexamethasone-pyridostigmine-GHRH (mean +/- S.E.M., 1938 +/- 631 mU/min per l), dexamethasone-placebo-GHRH (634 +/- 211) and placebo-placebo-GHRH (4267 +/- 1183) (P < 0.02, Wilcoxon test). In conclusion, dexamethasone given for 48 h significantly inhibited the AUC for GH following treatment with GHRH. However, pretreatment with pyridostigmine significantly reversed the inhibition although this was still partial. Our data suggested that this short-term suppressive effect of dexamethasone was independent of GHRH, and most probably relates to stimulation of the release of somatostatin.

Variation of sweat sodium and chloride with age in cystic fibrosis and normal populations: further investigations in equivocal cases

Patients attending cystic fibrosis clinics had sweat sodium and chloride concentrations measured, were reassessed clinically and had DNA studies performed. Sweat test results were compared with a matched control population. In both populations sweat sodium increased with age up to 12 years, and did not change significantly thereafter. The age-related increase was significantly less in the cystic fibrosis group. Sweat chloride increased with age in normal, but not in cystic fibrosis children. After age 12 years there was no age-related change in the normal group, and a fall with age in the cystic fibrosis group. Sweat chloride provided the best discrimination between normal and cystic fibrosis populations and this was particularly important in older subjects. Combining sweat sodium and chloride results did not improve discrimination. Nine patients were identified with equivocal sweat chloride results. DNA studies showed six of these subjects were heterozygous for the delta F508 mutation in the cystic fibrosis gene. Clinical assessment did not always resolve cases with borderline sweat chloride results.

The usefulness of serum thyroglobulin in the follow-up of differentiated thyroid carcinoma in children

Serum thyroglobulin has been measured serially in ten children aged 5-17 years presenting with differentiated thyroid carcinoma. At presentation 4 had intra-thyroidal disease, 3 had lymph node metastases, and 3 had lung metastases. During follow-up for a median of 37.0 months (range 21-108) 3 patients have been disease-free, 4 have had a local relapse, and 3 have had persistent disease. Seventy-seven separate serum thyroglobulin measurements have been performed; 36 on and 41 off thyroid replacement therapy. A level of thyroglobulin of less than 5 ng/ml was taken as indicative of absence of disease, and compared against combined clinical examination and 131I scanning. Overall sensitivity of thyroglobulin measurement was 36/37 (97%), and although specificity was 30/40 (75%), this rose to 30/32 (94%) if raised thyroglobulin levels noted within 3 months of 131I therapy in otherwise asymptomatic patients (n = 4) or in subjects with intact thyroid tissue (n = 4) were excluded. Concordance with clinical status was 30/31 (97%) in measurements taken on, and 31/32 (94%) in those taken off, thyroid replacement. These data indicate that thyroglobulin measurement is a sensitive and specific means of detecting residual, recurrent, and metastatic thyroid carcinoma in children.

Surgical reinforcement of gender identity in adolescent intersex patients

The presentation of phenotypic gender ambiguity at the time of adolescence is uncommon. Surgical reinforcement of gender, or reassignment is often complex and multistage. We present 2 cases of children who developed secondary sexual characteristics contrary to their chromosome status who, because of their late presentation, required significant surgical intervention to reinforce the gender assigned to them. We review some of the surgical techniques involved.

Dental health of young insulin dependent diabetic subjects in Northern Ireland

The present study was undertaken to establish the dental disease and treatment levels in 101 young insulin dependent diabetic patients in Northern Ireland. There was a significantly greater proportion of children from the higher social classes in the diabetic group. Their dental caries experience was lower than that reported for the general population and the restorative indices were high. However, those whose diabetes was diagnosed at a late stage had a higher caries experience. There was significantly more gingivitis detected in older diabetic patients, but oral hygiene status did not significantly differ with age. There was a pattern of regular dental attendance in the majority of diabetic subjects.

A dinucleotide repeat polymorphism at the Kallmann locus (Xp22.3)

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Outcome in tyrosinaemia type II

Tyrosinaemia type II was diagnosed in a boy with failure to thrive and in his sister on neonatal screening. On diet the outcome, at 12 and 10 years respectively, has been excellent in respect of oculocutaneous sequelae, growth, and psychomotor development, contrasting with the generally unfavourable outcome in most reported cases.

Pyridostigmine fails to increase either spontaneous or GHRH-stimulated GH secretion during day or night in growth hormone-insufficient children

OBJECTIVE The aim of the study was to investigate whether pyridostigmine, a cholinesterase inhibitor which is thought to act at the hypothalamus to inhibit somatostatin secretion, would augment spontaneous or GHRH-stimulated serum GH levels in patients with GH-insufficiency. DESIGN Oral pyridostigmine 60 mg or placebo was administered at the start of a 9-h subcutaneous infusion of either GHRH (1-29)NH2 10 micrograms/kg/h or saline control. Studies were performed during the daytime (0900-1800 h) in five patients, and the night-time (2100-0600 h) in a further five. PATIENTS Ten short, pre-pubertal children (aged 6-11 years; eight boys) with growth hormone insufficiency were studied. MEASURES Blood for serum GH was sampled every 20 min, and analysed using the PULSAR program. RESULTS The subcutaneous infusion of GHRH 10 micrograms/kg/h increased mean serum GH levels (+/- SEM): by day 17.7(+/- 6.8) vs placebo 2.2(+/- 0.4) mU/l (P less than 0.01), and by night 26.9(+/- 3.3) vs 5.5(+/- 1.3) mU/l (P less than 0.05). There was a significant rise in mean 'baseline' GH concentration: by day 5.5(+/- 1.7) vs 1.0(+/- 0.0) mU/l (P less than 0.05); and night 8.2(+/- 2.7) vs 1.3(+/- 0.3) mU/l (P less than 0.05). Pyridostigmine failed to produce a significant overall increase in either spontaneous or GHRH-stimulated GH secretion by day or night, although there was a significant rise in mean GH levels during the 3 h following pyridostigmine administration in the morning: 4.4(+/- 1.1) vs 2.4(+/- 0.5) mU/l (P less than 0.001). GHRH or pyridostigmine given singly or in combination had no significant effect on the number of pulses. Side-effects attributable to pyridostigmine occurred in seven children. CONCLUSIONS Pyridostigmine, either on its own or as an adjuvant therapy in combination with GHRH, acts for only a brief time and does not offer any potential benefit in the management of children with short stature.

The effects on anterior pituitary hormone secretion of salmon calcitonin in healthy volunteers

The reports of the effect of calcitonin on pituitary function are confusing and often refer to uncontrolled studies. We have now carried out a double-blind placebo-controlled trial of intravenous and subcutaneous salmon calcitonin on anterior pituitary function in 17 healthy volunteers. Visual analogue scores for the nausea and vomiting seen after salmon calcitonin correlated with the rise in ACTH and, secondarily, cortisol. Calcitonin had no effect on growth hormone, prolactin, thyrotrophin, luteinizing hormone or follicle stimulating hormone. It is concluded that the stimulation of ACTH secretion following a single dose of salmon calcitonin is probably the result of the stress of nausea rather than a direct effect on the pituitary.