Flexiplex: a versatile demultiplexer and search tool for omics data

MOTIVATION

The process of analyzing high throughput sequencing data often requires the identification and extraction of specific target sequences. This could include tasks, such as identifying cellular barcodes and UMIs in single-cell data, and specific genetic variants for genotyping. However, existing tools, which perform these functions are often task-specific, such as only demultiplexing barcodes for a dedicated type of experiment, or are not tolerant to noise in the sequencing data.

RESULTS

To overcome these limitations, we developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell-line-specific sequences in Illumina short-read single-cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single-cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools.

AVAILABILITY AND IMPLEMENTATION

Flexiplex is available at https://davidsongroup.github.io/flexiplex/.

Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects

Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.

JAFFAL: detecting fusion genes with long-read transcriptome sequencing

In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki .

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.

Human yolk sac-like haematopoiesis generates RUNX1-, GFI1- and/or GFI 1B-dependent blood and SOX17-positive endothelium

The genetic regulatory network controlling early fate choices during human blood cell development are not well understood. We used human pluripotent stem cell reporter lines to track the development of endothelial and haematopoietic populations in an in vitro model of human yolk-sac development. We identified SOX17⁻CD34⁺CD43⁻ endothelial cells at day 2 of blast colony development, as a haemangioblast-like branch point from which SOX17⁻CD34⁺CD43⁺ blood cells and SOX17⁺CD34⁺CD43⁻ endothelium subsequently arose. Most human blood cell development was dependent on RUNX1. Deletion of RUNX1 only permitted a single wave of yolk sac-like primitive erythropoiesis, but no yolk sac myelopoiesis or aorta-gonad-mesonephros (AGM)-like haematopoiesis. Blocking GFI1 and/or GFI1B activity with a small molecule inhibitor abrogated all blood cell development, even in cell lines with an intact RUNX1 gene. Together, our data define the hierarchical requirements for RUNX1, GFI1 and/or GFI1B during early human haematopoiesis arising from a yolk sac-like SOX17-negative haemogenic endothelial intermediate.

Highlighted Article: The hierarchical requirements for RUNX1, GFI1 and/or GFI1B during early human haematopoiesis arising from a yolk sac-like haemogenic endothelial intermediate.

Measurement of the fluorescence lifetime of GFP in high refractive index levitated droplets using FLIM

Green fluorescent protein (GFP) is a widely used fluorescent probe in the life sciences and biosciences due to its high quantum yield and extinction coefficient, and its ability to bind to biological systems of interest. This study measures the fluorescence lifetime of GFP in sucrose/water solutions of known molarity in order to determine the refractive index dependent lifetime of GFP. A range of refractive indices from 1.43-1.53 were probed by levitating micron sized droplets composed of water/sucrose/GFP in an optical trap under well-constrained conditions of relative humidity. This setup allows for the first reported measurements of the fluorescence lifetime of GFP at refractive indices greater than 1.46. The results obtained at refractive indices less than 1.46 show good agreement with previous studies. Further experiments that trapped droplets of deionised water containing GFP allowed the hygroscopic properties of GFP to be measured. GFP is found to be mildly hygroscopic by mass, but the high ratio of molecular masses of GFP to water (ca. 1500 : 1) signifies that water uptake is large on a per-mole basis. Hygroscopic properties are verified using brightfield microscope imaging, of GFP droplets at low and high relative humidity, by measuring the humidity dependent droplet size. In addition, this experiment allowed the refractive index of pure GFP to be estimated for the first time (1.72 ± 0.07). This work provides reference data for future experiments involving GFP, especially for those conducted in high refractive index media. The work also demonstrates that GFP can be used as a probe for aerosol studies, which require determination of the refractive index of the aerosol of any shape.

Targeted therapy and disease monitoring in CNTRL-FGFR1-driven leukaemia

We report two patients with leukaemia driven by the rare CNTRL-FGFR1 fusion oncogene. This fusion arises from a t(8;9)(p12;q33) translocation, and is a rare driver of biphenotypic leukaemia in children. We used RNA sequencing to report novel features of expressed CNTRL-FGFR1, including CNTRL-FGFR1 fusion alternative splicing. From this knowledge, we designed and tested a Droplet Digital PCR assay that detects CNTRL-FGFR1 expression to approximately one cell in 100 000 using fusion breakpoint-specific primers and probes. We also utilised cell-line models to show that effective tyrosine kinase inhibitors, which may be included in treatment regimens for this disease, are only those that block FGFR1 phosphorylation.

Using equivalence class counts for fast and accurate testing of differential transcript usage

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differential gene expression is the most widely used application of this technology, RNA-seq data also has the resolution to infer differential transcript usage (DTU), which can elucidate the role of different transcript isoforms between experimental conditions, cell types or tissues. DTU has typically been inferred from exon-count data, which has issues with assigning reads unambiguously to counting bins, and requires alignment of reads to the genome. Recently, approaches have emerged that use transcript quantification estimates directly for DTU. Transcript counts can be inferred from 'pseudo' or lightweight aligners, which are significantly faster than traditional genome alignment. However, recent evaluations show lower sensitivity in DTU analysis compared to exon-level analysis. Transcript abundances are estimated from equivalence classes (ECs), which determine the transcripts that any given read is compatible with. Recent work has proposed performing a variety of RNA-seq analysis directly on equivalence class counts (ECCs). Methods: Here we demonstrate that ECCs can be used effectively with existing count-based methods for detecting DTU. We evaluate this approach on simulated human and drosophila data, as well as on a real dataset through subset testing. Results: We find that ECCs have similar sensitivity and false discovery rates as exon-level counts but can be generated in a fraction of the time through the use of pseudo-aligners. Conclusions: We posit that equivalence class read counts are a natural unit on which to perform differential transcript usage analysis.

Fast and accurate differential transcript usage by testing equivalence class counts

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differential gene expression is the most widely used application of this technology, RNA-seq data also has the resolution to infer differential transcript usage (DTU), which can elucidate the role of different transcript isoforms between experimental conditions, cell types or tissues. DTU has typically been inferred from exon-count data, which has issues with assigning reads unambiguously to counting bins, and requires alignment of reads to the genome. Recently, approaches have emerged that use transcript quantifications estimates directly for DTU. Transcript counts can be inferred from 'pseudo' or lightweight aligners, which are significantly faster than traditional genome alignment. However, recent evaluations show lower sensitivity in DTU analysis. Transcript abundances are estimated from equivalence classes (ECs), which determine the transcripts that any given read is compatible with. Recent work has proposed performing differential expression testing directly on equivalence class read counts (ECs). Methods: Here we demonstrate that ECs can be used effectively with existing count-based methods for detecting DTU. We evaluate this approach on simulated human and drosophila data, as well as on a real dataset through subset testing. Results: We find that ECs counts have similar sensitivity and false discovery rates as exon-level counts but can be generated in a fraction of the time through the use of pseudo-aligners. Conclusions: We posit that equivalence class read counts are a natural unit on which to perform many types of analysis.

Clinker: visualizing fusion genes detected in RNA-seq data

Background

Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging.

Findings

Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia.

Conclusions

Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

Background

RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking.

Findings

Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.

Conclusions

Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms. We further use Lace to combine reference and assembled transcriptomes for chicken and recover hundreds of gaps in the reference genome.

Limb patterning genes and heterochronic development of the emu wing bud

Background

The forelimb of the flightless emu is a vestigial structure, with greatly reduced wing elements and digit loss. To explore the molecular and cellular mechanisms associated with the evolution of vestigial wings and loss of flight in the emu, key limb patterning genes were examined in developing embryos.

Methods

Limb development was compared in emu versus chicken embryos. Immunostaining for cell proliferation markers was used to analyze growth of the emu forelimb and hindlimb buds. Expression patterns of limb patterning genes were studied, using whole-mount in situ hybridization (for mRNA localization) and RNA-seq (for mRNA expression levels).

Results

The forelimb of the emu embryo showed heterochronic development compared to that in the chicken, with the forelimb bud being retarded in its development. Early outgrowth of the emu forelimb bud is characterized by a lower level of cell proliferation compared the hindlimb bud, as assessed by PH3 immunostaining. In contrast, there were no obvious differences in apoptosis in forelimb versus hindlimb buds (cleaved caspase 3 staining). Most key patterning genes were expressed in emu forelimb buds similarly to that observed in the chicken, but with smaller expression domains. However, expression of Sonic Hedgehog (Shh) mRNA, which is central to anterior–posterior axis development, was delayed in the emu forelimb bud relative to other patterning genes. Regulators of Shh expression, Gli3 and HoxD13, also showed altered expression levels in the emu forelimb bud.

Conclusions

These data reveal heterochronic but otherwise normal expression of most patterning genes in the emu vestigial forelimb. Delayed Shh expression may be related to the small and vestigial structure of the emu forelimb bud. However, the genetic mechanism driving retarded emu wing development is likely to rest within the forelimb field of the lateral plate mesoderm, predating the expression of patterning genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-016-0063-5) contains supplementary material, which is available to authorized users.

Cloud condensation nucleation activities of calcium carbonate and its atmospheric ageing products

Aerosol particles can serve as cloud condensation nuclei (CCN) to form cloud droplets, and its composition is a main factor governing whether an aerosol particle is an effective CCN. Pure mineral dust particles are poor CCN; however, changes in chemical composition of mineral dust aerosol particles, due to heterogeneous reactions with reactive trace gases in the troposphere, can modify their CCN properties. In this study we investigated the CCN activities of CaCO3 (as a surrogate for mineral dust) and its six atmospheric ageing products: Ca(NO3)2, CaCl2, CaSO4, Ca(CH3SO3)2, Ca(HCOO)2, and Ca(CH3COO)2. CaCO3 has a very low CCN activity with a hygroscopicity parameter (κ) of 0.001-0.003. The CCN activities of its potential atmospheric ageing products are significantly higher. For example, we determined that Ca(NO3)2, CaCl2 and Ca(HCOO)2 have κ values of ∼0.50, similar to that of (NH4)2SO4. Ca(CH3COO)2 has slightly lower CCN activity with a κ value of ∼0.40, and the κ value of CaSO4 is around 0.02. We further show that exposure of CaCO3 particles to N2O5 at 0% relative humidity (RH) significantly enhances their CCN activity, with κ values increasing to around 0.02-0.04. Within the experimental uncertainties, it appears that the variation in exposure to N2O5 from ∼550 to 15,000 ppbv s does not change the CCN activities of aged CaCO3 particles. This observation indicates that the CaCO3 surface may be already saturated at the shortest exposure. We also discussed the atmospheric implications of our study, and suggested that the rate of change in CCN activities of mineral dust particles in the troposphere is important to determine their roles in cloud formation.

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

BACKGROUND

Despite some advances in recent years, the genetic control of gonadal sex differentiation during embryogenesis is still not completely understood. To identify new candidate genes involved in ovary and testis development, RNA-seq was used to define the transcriptome of embryonic chicken gonads at the onset of sexual differentiation (day 6.0/stage 29).

RESULTS

RNA-seq revealed more than 1000 genes that were transcribed in a sex-biased manner at this early stage of gonadal differentiation. Comparison with undifferentiated gonads revealed that sex biased expression was derived primarily from autosomal rather than sex-linked genes. Gene ontology and pathway analysis indicated that many of these genes encoded proteins involved in extracellular matrix function and cytoskeletal remodelling, as well as tubulogenesis. Several of these genes are novel candidate regulators of gonadal sex differentiation, based on sex-biased expression profiles that are altered following experimental sex reversal. We further characterised three female-biased (ovarian) genes; calpain-5 (CAPN5), G-protein coupled receptor 56 (GPR56), and FGFR3 (fibroblast growth factor receptor 3). Protein expression of these candidates in the developing ovaries suggests that they play an important role in this tissue.

CONCLUSIONS

This study provides insight into the earliest steps of vertebrate gonad sex differentiation, and identifies novel candidate genes for ovarian and testicular development.

JAFFA: High sensitivity transcriptome-focused fusion gene detection

Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimised for short reads. JAFFA (https://github.com/Oshlack/JAFFA/wiki) is a sensitive fusion detection method that outperforms other methods with reads of 100 bp or greater. JAFFA compares a cancer transcriptome to the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or by de novo assembling short reads.

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes

Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a reference genome is circumvented by performing de novo assembly on the RNA-seq data. However, transcriptome assembly produces a multitude of contigs, which must be clustered into genes prior to differential gene expression detection. Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then summarizes read counts to clusters, ready for statistical testing. Using a range of metrics, we demonstrate that Corset out-performs alternative methods. Corset is available from https://code.google.com/p/corset-project/.

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

Oncogenic fusion genes that involve kinases have proven to be effective targets for therapy in a wide range of cancers. Unfortunately, the diagnostic approaches required to identify these events are struggling to keep pace with the diverse array of genetic alterations that occur in cancer. Diagnostic screening in solid tumours is particularly challenging, as many fusion genes occur with a low frequency. To overcome these limitations, we developed a capture enrichment strategy to enable high-throughput transcript sequencing of the human kinome. This approach provides a global overview of kinase fusion events, irrespective of the identity of the fusion partner. To demonstrate the utility of this system, we profiled 100 non-small cell lung cancers and identified numerous genetic alterations impacting fibroblast growth factor receptor 3 (FGFR3) in lung squamous cell carcinoma and a novel ALK fusion partner in lung adenocarcinoma.

RSV-associated hospitalizations in Alaska Native infants

PURPOSE

Retrospective reviews for 1986-1992 suggested that Alaska Native children experience high rates of respiratory syncytial virus (RSV)-associated hospitalization; however, the epidemiology of RSV infections has been poorly characterized.

METHODS

A prospective hospital-based surveillance study was undertaken to determine rates of RSV-associated hospitalization in Alaska Native children < 36 months from the Yukon-Kuskokwim Delta.

RESULTS

During the first study year, October 1993 to September 1994, there were 40 RSV cases (hospitalization rate, 53/1,000 infants < 1 year of age); however, during the second year, October 1994 to September 1995, there were 251 RSV cases (hospitalization rate, 294/1,000 infants). An unusually high proportion, 12%, of RSV cases were < 1 month of age. Disease severity was higher for children with a history of prematurity, heart, or lung disease (p = .001, X2 analysis). Of 255 cell cultures during 1994-1995, 190 were RSV-positive, 11 were positive for influenza, 4 for adenovirus, and 1 for parainfluenza. This study demonstrates wide seasonal variation in a population with an extremely high RSV hospitalization rate; increased disease severity associated with young age and pre-existing medical conditions; and co-circulation of RSV with other viruses.

Kikuchi-Fujimoto disease: a report of two cases and an overview

Kikuchi-Fujimoto disease (KFD) has been widely reported from Japan and sporadically from many parts of the world including Saudi Arabia, since its original description in 1972 but the disease remains poorly known by clinicians. In this paper we report two Saudi patients seen in Tabuk, Saudi Arabia. One was a 36-year-old Saudi man and the other a 16-year-old Saudi girl. Both presented with cervical lymphadenopathy and pyrexia. Histological examination of biopsy material from both showed classical features of KFD. Other laboratory findings were unremarkable except for leucopenia. Following excision biopsy both patients recovered without sequelae. KFD is a self-limiting process of uncertain aetiology that predominantly affects young women aged 20-30 years. We review the pathology, clinical featuers and possible aetiology of this interesting disease, which may well be underdiagnosed. Increased awareness of KFD will minimize the risk of confusing this entity with malignant lymphoma or other serious conditions.

Decline of Haemophilus influenzae type b disease in a region of high risk: impact of passive and active immunization

Haemophilus influenzae type b (Hib) is a major cause of serious childhood bacterial infections. Before 1989 Alaska Native infants in the Yukon Kuskokwim Delta (YKD) had the highest recorded Hib disease rate, 2960:100,000 in children less than 1 year of age with 6 to 35 (mean, 13) cases/year between 1980 and 1988. In July, 1989, Alaska Area Native Health Service initiated a passive immunization project in the YKD using bacterial polysaccharide immunoglobulin (BPIG) administered at 3-month intervals to prevent Hib infections in infants less than 13 months of age. On January 1, 1991, after licensure of Hib conjugate vaccines for infants, the program was modified to a passive-active strategy using BPIG at birth and PedvaxHIB at 2, 4 and 12 months of age. Between July 1, 1989, and December 31, 1990, 80% of YKD children less than 1 year of age received at least 1 dose of BPIG. During this period there were 7 Hib cases in this age group, but only 1 of the cases had received any BPIG. Between January 1, 1991, and December 31, 1992, 4 Hib cases occurred in 2 YKD children. During the combined period, July 1, 1989, to December 31, 1992, the incidence of Hib disease for infants less than 1 year of age was 302:100,000. A dramatic decrease in Hib disease was observed in this high incidence region concurrent with implementation of passive and passive-active immunization strategies.

Peripartum cardiac failure. A ten year follow-up study

A cohort of patients with peripartum cardiac failure (PPCF) was followed for 10 years after the initial illness. The follow up rate was 78%. Fifty two per cent of patients improved without further episodes of heart failure. PPCF recurred in 26 per cent. Heart failure unrelated to pregnancy was seen in 13%, and 9% of the patients progressed to dilated cardiomyopathy. Transient hypertension was seen in 87% of patients on admission, and later hypertension was found in 45%. Late hypertension influenced heart size more when recurrent PPCF or progressive heart failure was present. Anaemia on admission had no effect on subsequent heart size. The electrocardiogram may continue to be abnormal for up to 10 years in normotensive patients who had no heart failure. The abnormal electrocardiogram in patients with persistent cardiomegaly may represent progressive myocardial damage. Mortality rate was highest (11%) in the first year and declined thereafter. Cardiac deaths were common in patients with recurrent PPCF or progressive heart failure.

Possible hepatoxicity of tocainide

A case of a woman on tocainide who developed abnormal liver function. A causal relationship is postulated.

Peripheral blood cell changes in response to acute hypoglycaemia in man

Peripheral white and red blood cell changes were studied in response to acute insulin-induced hypoglycaemia in six normal, six splenectomized and five sympathectomized (tetraplegic) subjects. The normal subjects were restudied during beta (propranolol) and beta 1-selective (metoprolol) adrenergic blockade. In the normal subjects a lymphocytosis immediately followed the acute hypoglycaemic reaction (R) with a neutrophilia 2 h later. The early lymphocytosis was absent in sympathectomized subjects (P less than 0.001) and reduced under beta blockade (P less than 0.02) in normal subjects, indicating mediation via an adrenergic mechanism. The later neutrophilia from R + 60 min was not abolished by adrenergic blockade or preceding sympathectomy; the enhanced response with propranolol was associated with an elevated plasma cortisol. Haemoglobin, packed cell volume and total erythrocyte count rose maximally at R in all groups except the sympathectomized subjects in whom all parameters declined progressively from basal values. These peripheral erythrocytes changes appear to be mediated via an adrenergic mechanism which is unaffected by beta adrenergic blockade and which does not involve splenic contraction.

Dermatomyositis and rapidly progressive fibrosing alveolitis

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Cholinergic manifestations of the acute autonomic reaction to hypoglycaemia in man

1. The effects of insulin-induced hypoglycaemia on pupil size, parotid salivary secretion and sweating were studied in seven normal volunteers. 2. Hypoglycaemia was associated with an acute stimulation of parotid salivary secretion and of sweating, synchronous in onset with the rise in heart rate. There was no clear evidence of concurrent pupillary constriction.

Hormonal and substrate responses during recovery from hypoglycaemia in man during beta 1-selective and non-selective beta-adrenergic blockade

Recovery from acute hypoglycaemia induced by the injection of insulin has been examined in six human subjects under control conditions, under non-selective beta blockade (propranolol) and under selective beta 1 blockade (metoprolol). The normal blood glucose recovery was biphasic with an initial rapid and a slower subsequent phase of recovery. The early recovery mechanism was unaffected by either form of beta blockade, but with propranolol the late phase of recovery was significantly prolonged. Rises in blood lactate and plasma free fatty acids following hypoglycaemia were markedly reduced by propranolol but to a much lesser degree with metoprolol. The counterregulatory hormonal responses of glucagon, cortisol and growth hormone were augmented appropriately for the prolonged hypoglycaemia associated with propranolol. Non-selective beta adrenergic blockade with propranolol is associated with an impairment of the late phase of blood glucose recovery from hypoglycaemia. The possible mechanisms of this impairment are discussed.

Peri-partum cardiac failure

The syndrome of peri-partum cardiac failure (PPCF) has been studied in 224 women seen in three years in Zaria, in northern Nigeria. A very high proportion were rural Hausa patients. There was a seasonal peak in July, and the incidence was about one per cent of deliveries. The risk increased with both age and parity. Symptoms began most commonly in the second week after delivery, and admission was commonest in the fourth. Typical signs of cardiac failure were found, and pulsus alternans, atrio-ventricular valvular incompetence, transient systemic hypertension and splenomegaly were common. The chest radiograph showed marked cardiomegaly, and extrasystoles and inverted T waves were often present in the electrocardiogram (ECG). Hypoalbuminaemia was common. Digoxin and diuretics were rapidly effective, causing a mean weight loss of 29 per cent in 15 days, resolution of hypertension, and a fall in the cardio-thoracic ratio (CTR) from 61 to 53 per cent. During the first year after diagnosis, the CTR became normal in 82 per cent of patients, and the ECG in 60 per cent. PPCF recurred, again with the same seasonal variation, after 19 per cent of subsequent pregnancies. During follow up for two to five years, 22 per cent of the women became hypertensive, and 11 per cent died. The prognosis was worst in those with an arrhythmia, hypertension, sustained cardiomegaly or aged 30 or more. Asymtomatic post-partum hypertension (PPHT) was found in 61 per cent of normal Hausa women, with a seasonal peak in May, especially in those with hypertension during pregnancy or labour, and twin pregnancies. Peri-partum cardiac failure may be due to the combined pressure load of PPHT, the volume load from eating the customary sodium-rich kanwa, and the cardiovascular demands of heat, both climatic and traditionally self-imposed.

Bromocriptine suppression of the thyrotrophin response to thyrotrophin releasing hormone

A single oral dose of 5 mg of bromocriptine significantly lowered the TSH response to 200 microgram TRH intravenously in eight healthy men compared with control experiments in the same subjects. This finding may be relevant in chronic bromocriptine therapy.

Hypothalmic-pituitary adrenal responsiveness to dexamethasone-insulin tolerance test in acromegalic patients before and during treatment with bromocriptine

Insulin tolerance tests were carried out in 10 acromegalic patients after 1 mg dexamethasone had been given the previous evening (DEX-ITT). Nine patients showed a rise in plasma 11-OHCS and four patients showed a rise in plasma growth hormone (GH) levels. These responses were unaltered after treatment with bromocriptine 10 mg daily for two months. Basal plasma GH levels fell in 6 of the patients and the mean plasma GH levels of the 10 patients during an oral glucose tolerance test (OGTT) fell from 63.2 +/- 25.5 ng/ml before treatment to 53.0 +/- 27.1 ng/ml (mean +/- sem; p less than 0.05). These data fail to confirm a previous report of abnormal hypothalmic-pituitary-adrenal suppressibility during a DEX-ITT in acromegalic patients. They also indicate that bromcriptine does not alter the responses of plasma 11-OHCS and plasma GH to the DEX-ITT despite lowering plasma GH levels.

Hazard of chemical sympathectomy

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Seasonal variation of cardiac failure in northern Nigeria

The number of patients with cardiac failure admitted to hospital in Zaria, Nigeria, month by month during 1972-75 differed highly significantly between the cooler dry months and the hot wet months. The reasons are uncertain, but seasonal changes in blood-pressure and the effects of heat on the circulation and of humidity on the efficiency of sweating may be responsible.