ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community.

Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors

BACKGROUND

The human mitochondrial genome is transcribed as long strands of RNA containing multiple genes, which require post-transcriptional cleavage and processing to release functional gene products that play vital roles in cellular energy production. Despite knowledge implicating mitochondrial post-transcriptional processes in pathologies such as cancer, cardiovascular disease and diabetes, very little is known about the way their function varies on a human population level and what drives changes in these processes to ultimately influence disease risk. Here, we develop a method to detect and quantify mitochondrial RNA cleavage events from standard RNA sequencing data and apply this approach to human whole blood data from > 1000 samples across independent cohorts.

RESULTS

We detect 54 putative mitochondrial RNA cleavage sites that not only map to known gene boundaries, short RNA ends and RNA modification sites, but also occur at internal gene positions, suggesting novel mitochondrial RNA cleavage junctions. Inferred RNA cleavage rates correlate with mitochondrial-encoded gene expression across individuals, suggesting an impact on downstream processes. Furthermore, by comparing inferred cleavage rates to nuclear genetic variation and gene expression, we implicate multiple genes in modulating mitochondrial RNA cleavage (e.g. MRPP3, TBRG4 and FASTKD5), including a potentially novel role for RPS19 in influencing cleavage rates at a site near to the MTATP6-COX3 junction that we validate using shRNA knock down data.

CONCLUSIONS

We identify novel cleavage junctions associated with mitochondrial RNA processing, as well as genes newly implicated in these processes, and detect the potential impact of variation in cleavage rates on downstream phenotypes and disease processes. These results highlight the complexity of the mitochondrial transcriptome and point to novel mechanisms through which nuclear-encoded genes can potentially influence key mitochondrial processes.

Highly accurate quantification of allelic gene expression for population and disease genetics

Analysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation, particularly when sample sizes are small, such as for rare diseases, or when studying the effects of rare genetic variation. However, detection of ASE events relies on accurate alignment of RNA sequencing reads, where challenges still remain, particularly for reads containing genetic variants or those that align to many different genomic locations. We have developed the Personalised ASE Caller (PAC), a tool that combines multiple steps to improve the quantification of allelic reads, including personalized (i.e., diploid) read alignment with improved allocation of multimapping reads. Using simulated RNA sequencing data, we show that PAC outperforms standard alignment approaches for ASE detection, reducing the number of sites with incorrect biases (>10%) by ∼80% and increasing the number of sites that can be reliably quantified by ∼3%. Applying PAC to real RNA sequencing data from 670 whole-blood samples, we show that genetic regulatory signatures inferred from ASE data more closely match those from population-based methods that are less prone to alignment biases. Finally, we use PAC to characterize cell type-specific ASE events that would be missed by standard alignment approaches, and in doing so identify disease relevant genes that may modulate their effects through the regulation of gene expression. PAC can be applied to the vast quantity of existing RNA sequencing data sets to better understand a wide array of fundamental biological and disease processes.

Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

BACKGROUND

Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed.

RESULTS

Using a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during aging only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with the total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, the rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are < 5%.

CONCLUSIONS

Our work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.

Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease

Mitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases. The mitochondrial genome encodes core respiratory chain proteins, but the vast majority of mitochondrial proteins are nuclear-encoded, making interactions between the two genomes vital for cell function. Here, we examine these relationships by comparing mitochondrial and nuclear gene expression across different regions of the human brain in healthy and disease cohorts. We find strong regional patterns that are modulated by cell-type and reflect functional specialisation. Nuclear genes causally implicated in sporadic Parkinson's and Alzheimer's disease (AD) show much stronger relationships with the mitochondrial genome than expected by chance, and mitochondrial-nuclear relationships are highly perturbed in AD cases, particularly through synaptic and lysosomal pathways, potentially implicating the regulation of energy balance and removal of dysfunction mitochondria in the etiology or progression of the disease. Finally, we present MitoNuclearCOEXPlorer, a tool to interrogate key mitochondria-nuclear relationships in multi-dimensional brain data.

Nuclear genetic regulation of the human mitochondrial transcriptome

Mitochondria play important roles in cellular processes and disease, yet little is known about how the transcriptional regime of the mitochondrial genome varies across individuals and tissues. By analyzing >11,000 RNA-sequencing libraries across 36 tissue/cell types, we find considerable variation in mitochondrial-encoded gene expression along the mitochondrial transcriptome, across tissues and between individuals, highlighting the importance of cell-type specific and post-transcriptional processes in shaping mitochondrial-encoded RNA levels. Using whole-genome genetic data we identify 64 nuclear loci associated with expression levels of 14 genes encoded in the mitochondrial genome, including missense variants within genes involved in mitochondrial function (TBRG4, MTPAP and LONP1), implicating genetic mechanisms that act in trans across the two genomes. We replicate ~21% of associations with independent tissue-matched datasets and find genetic variants linked to these nuclear loci that are associated with cardio-metabolic phenotypes and Vitiligo, supporting a potential role for variable mitochondrial-encoded gene expression in complex disease.

Integrated genomic analysis of mitochondrial RNA processing in human cancers

BACKGROUND

The mitochondrial genome is transcribed as continuous polycistrons of RNA containing multiple genes. As a consequence, post-transcriptional events are critical for the regulation of gene expression and therefore all aspects of mitochondrial function. One particularly important process is the m¹A/m¹G RNA methylation of the ninth position of different mitochondrial tRNAs, which allows efficient processing of mitochondrial mRNAs and protein translation, and de-regulation of genes involved in these processes has been associated with altered mitochondrial function. Although mitochondria play a key role in cancer, the status of mitochondrial RNA processing in tumorigenesis is unknown.

METHODS

We measure and assess mitochondrial RNA processing using integrated genomic analysis of RNA sequencing and genotyping data from 1226 samples across 12 different cancer types. We focus on the levels of m¹A and m¹G RNA methylation in mitochondrial tRNAs in normal and tumor samples and use supervised and unsupervised statistical analysis to compare the levels of these modifications to patient whole genome genotypes, nuclear gene expression, and survival outcomes.

RESULTS

We find significant changes to m¹A and m¹G RNA methylation levels in mitochondrial tRNAs in tumor tissues across all cancers. Pathways of RNA processing are strongly associated with methylation levels in normal tissues (P = 3.27 × 10^-31), yet these associations are lost in tumors. Furthermore, we report 18 gene-by-disease-state interactions where altered RNA methylation levels occur under cancer status conditional on genotype, implicating genes associated with mitochondrial function or cancer (e.g., CACNA2D2, LMO2, and FLT3) and suggesting that nuclear genetic variation can potentially modulate an individual's ability to maintain unaltered rates of mitochondrial RNA processing under cancer status. Finally, we report a significant association between the magnitude of methylation level changes in tumors and patient survival outcomes.

CONCLUSIONS

We report widespread variation of mitochondrial RNA processing between normal and tumor tissues across all cancer types investigated and show that these alterations are likely modulated by patient genotype and may impact patient survival outcomes. These results highlight the potential clinical relevance of altered mitochondrial RNA processing and provide broad new insights into the importance and complexity of these events in cancer.

A haplotype-based normalization technique for the analysis and detection of allele specific expression

Background

Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used to both identify disease loci and consider the penetrance of damaging alleles. The detection of ASE using high throughput technologies relies on aligning short-read sequencing data, a process that has inherent biases, and there is still a need to develop fast and accurate methods to detect ASE given the unprecedented growth of sequencing information in big data projects.

Results

Here, we present a new approach to normalize RNA sequencing data in order to call ASE events with high precision in a short time-frame. Using simulated datasets we find that our approach dramatically improves reference allele quantification at heterozygous sites versus default mapping methods and also performs well compared to existing techniques for ASE detection, such as filtering methods and mapping to parental genomes, without the need for complex and time consuming manipulation. Finally, by sequencing the exomes and transcriptomes of 96 well-phenotyped individuals of the CARTaGENE cohort, we characterise the levels of ASE across individuals and find a significant association between the proportion of sites undergoing ASE within the genome and smoking.

Conclusions

The correct treatment and analysis of RNA sequencing data is vital to control for mapping biases and detect genuine ASE signals. By normalising RNA sequencing information after mapping, we show that this approach can be used to identify biologically relevant signals in personal genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1238-8) contains supplementary material, which is available to authorized users.

Gain-of-function missense variant in SLC12A2, encoding the bumetanide-sensitive NKCC1 cotransporter, identified in human schizophrenia

Perturbations of γ-aminobutyric acid (GABA) neurotransmission in the human prefrontal cortex have been implicated in the pathogenesis of schizophrenia (SCZ), but the mechanisms are unclear. NKCC1 (SLC12A2) is a Cl(-)-importing cation-Cl(-) cotransporter that contributes to the maintenance of depolarizing GABA activity in immature neurons, and variation in SLC12A2 has been shown to increase the risk for schizophrenia via alterations of NKCC1 mRNA expression. However, no disease-causing mutations or functional variants in NKCC1 have been identified in human patients with SCZ. Here, by sequencing three large French-Canadian (FC) patient cohorts of SCZ, autism spectrum disorders (ASD), and intellectual disability (ID), we identified a novel heterozygous NKCC1 missense variant (p.Y199C) in SCZ. This variant is located in an evolutionarily conserved residue in the critical N-terminal regulatory domain and exhibits high predicted pathogenicity. No NKCC1 variants were detected in ASD or ID, and no KCC3 variants were identified in any of the three neurodevelopmental disorder cohorts. Functional experiments show Y199C is a gain-of-function variant, increasing Cl(-)-dependent and bumetanide-sensitive NKCC1 activity even in conditions in which the transporter is normally functionally silent (hypotonicity). These data are the first to describe a functional missense variant in SLC12A2 in human SCZ, and suggest that genetically encoded dysregulation of NKCC1 may be a risk factor for, or contribute to the pathogenesis of, human SCZ.

Investigation on the electron flux to the wall in the VENUS ion source

The long-term operation of high charge state electron cyclotron resonance ion sources fed with high microwave power has caused damage to the plasma chamber wall in several laboratories. Porosity, or a small hole, can be progressively created in the chamber wall which can destroy the plasma chamber over a few year time scale. A burnout of the VENUS plasma chamber is investigated in which the hole formation in relation to the local hot electron power density is studied. First, the results of a simple model assuming that hot electrons are fully magnetized and strictly following magnetic field lines are presented. The model qualitatively reproduces the experimental traces left by the plasma on the wall. However, it is too crude to reproduce the localized electron power density for creating a hole in the chamber wall. Second, the results of a Monte Carlo simulation, following a population of scattering hot electrons, indicate a localized high power deposited to the chamber wall consistent with the hole formation process. Finally, a hypervapotron cooling scheme is proposed to mitigate the hole formation in electron cyclotron resonance plasma chamber wall.

Development status of a next generation ECRIS: MARS-D at LBNL

To demonstrate a Mixed Axial and Radial field System (MARS) as the best magnet scheme for future ECRISs, MARS-D, a demonstrative ECRIS using a NbTi MARS magnet is progressing at Lawrence Berkeley National Laboratory. An optimized MARS design can use either NbTi or Nb3Sn coils with reduced engineering complexities to construct the needed high-field magnets. The optimized magnet design could enhance MARS-D to a next generation ECRIS by producing minimum-B field maxima of 5.6 T axially and 3.2 T radially for operating frequencies up to 45 GHz. In-progress test winding has achieved a milestone demonstrating the fabrication feasibility of a MARS closed-loop coil.

Replication study of MATR3 in familial and sporadic amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterized by an extensive loss of motor neurons in the primary motor cortex, brainstem, and spinal cord. Genetic studies report a high heritability of ALS. Recently, whole-exome sequencing analysis of familial ALS (FALS) patients allowed the identification of missense variations within the MATR3 gene. MATR3 was previously associated to distal myopathy 2 and encodes for a nuclear matrix and DNA/RNA binding protein that has been shown to interact with TDP43 in an RNA-dependent manner. Here, we assessed the MATR3 mutation frequency in French-Canadian ALS and control individuals (nFALS = 83, sporadic ALS [nSALS] = 164, and ncontrols = 162) and showed that MATR3 mutations were found in 0%, 1.8%, and 0% of FALS, SALS, and controls, respectively. Interestingly, among the mutations identified in SALS, the splicing mutation c.48+1G>T was found to result in the insertion of 24 amino acids in MATR3 protein. These findings further support the role of MATR3 in ALS, and more studies are needed to shed more light on MATR3 proteinopathy.

Genetically encoded impairment of neuronal KCC2 cotransporter function in human idiopathic generalized epilepsy

The KCC2 cotransporter establishes the low neuronal Cl(-) levels required for GABAA and glycine (Gly) receptor-mediated inhibition, and KCC2 deficiency in model organisms results in network hyperexcitability. However, no mutations in KCC2 have been documented in human disease. Here, we report two non-synonymous functional variants in human KCC2, R952H and R1049C, exhibiting clear statistical association with idiopathic generalized epilepsy (IGE). These variants reside in conserved residues in the KCC2 cytoplasmic C-terminus, exhibit significantly impaired Cl(-)-extrusion capacities resulting in less hyperpolarized Gly equilibrium potentials (EG ly), and impair KCC2 stimulatory phosphorylation at serine 940, a key regulatory site. These data describe a novel KCC2 variant significantly associated with a human disease and suggest genetically encoded impairment of KCC2 functional regulation may be a risk factor for the development of human IGE.

Production of high intensity 48Ca for the 88-Inch Cyclotron and other updates

Recently the Versatile ECR for NUclear Science (VENUS) ion source was engaged in a 60-day long campaign to deliver high intensity (48)Ca(11+) beam to the 88-Inch Cyclotron. As the first long term use of VENUS for multi-week heavy-element research, new methods were developed to maximize oven to target efficiency. First, the tuning parameters of VENUS for injection into the cyclotron proved to be very different than those used to tune VENUS for maximum beam output of the desired charge state immediately following its bending magnet. Second, helium with no oxygen support gas was used to maximize the efficiency. The performance of VENUS and its low temperature oven used to produce the stable requested 75 eμA of (48)Ca(11+) beam current was impressive. The consumption of (48)Ca in VENUS using the low temperature oven was checked roughly weekly, and was found to be on average 0.27 mg/h with an ionization efficiency into the 11+ charge state of 5.0%. No degradation in performance was noted over time. In addition, with the successful operation of VENUS the 88-Inch cyclotron was able to extract a record 2 pμA of (48)Ca(11+), with a VENUS output beam current of 219 eμA. The paper describes the characteristics of the VENUS tune used for maximum transport efficiency into the cyclotron as well as ongoing efforts to improve the transport efficiency from VENUS into the cyclotron. In addition, we briefly present details regarding the recent successful repair of the cryostat vacuum system.

Development of a new superconducting Electron Cyclotron Resonance Ion Source for operations up to 18 GHz at LBNL

A new superconducting Electron Cyclotron Resonance Ion Source (ECRIS) is under development at LBNL to harness the winding techniques of a closed-loop sextupole coil for the next generation ECRIS and to enhance the capability of the 88-in. cyclotron facility. The proposed ECRIS will use a superconducting closed-loop sextupole coil to produce the radial field and a substantial portion of the axial field. The field strengths of the injection, central and extraction regions are adjusted by a three solenoids outside the closed-loop sextupole coil. In addition to maintaining the typical ECRIS magnetic field configuration, this new source will also be able to produce a dustpan-like minimum-B field to explore possible ECRIS performance enhancement. The dustpan-like minimum-B field configuration has about the same strengths for the maximum axial field at the injection region and the maximum radial pole fields at the plasma chamber walls but it can be substantially lower at the extraction region. The dustpan-like minimum-B will have a field maximum Bmax ≥ 2.6 T for operations up to 18 GHz with a ratio of Bmax/Bres ≥ 4 and higher ratios for lower frequencies. The field maxima of this new source can reach over 3 T both at the injection and the plasma chamber walls which could also support operation at 28 GHz. The source will be built of cryogen-free with the magnets directly cooled by cryo-coolers to simplify the cryostat structure. The source design features will be presented and discussed.

A mode converter to generate a Gaussian-like mode for injection into the VENUS electron cyclotron resonance ion source

A number of superconducting electron cyclotron resonance (ECR) ion sources use gyrotrons at either 24 or 28 GHz for ECR heating. In these systems, the microwave power is launched into the plasma using the TE01 circular waveguide mode. This is fundamentally different and may be less efficient than the typical rectangular, linearly polarized TE10 mode used for launching waves at lower frequencies. To improve the 28 GHz microwave coupling in VENUS, a TE01-HE11 mode conversion system has been built to test launching HE11 microwave power into the plasma chamber. The HE11 mode is a quasi-Gaussian, linearly polarized mode, which should couple strongly to the plasma electrons. The mode conversion is done in two steps. First, a 0.66 m long "snake" converts the TE01 mode to the TE11 mode. Second, a corrugated circular waveguide excites the HE11 mode, which is launched directly into the plasma chamber. The design concept draws on the development of similar devices used in tokamaks and stellerators. The first tests of the new coupling system are described below.

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans

Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk.

Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia

BACKGROUND

Congenital multiple intestinal atresia (MIA) is a severe, fatal neonatal disorder, involving the occurrence of obstructions in the small and large intestines ultimately leading to organ failure. Surgical interventions are palliative but do not provide long-term survival. Severe immunodeficiency may be associated with the phenotype. A genetic basis for MIA is likely. We had previously ascertained a cohort of patients of French-Canadian origin, most of whom were deceased as infants or in utero. The goal of the study was to identify the molecular basis for the disease in the patients of this cohort.

METHODS

We performed whole exome sequencing on samples from five patients of four families. Validation of mutations and familial segregation was performed using standard Sanger sequencing in these and three additional families with deceased cases. Exon skipping was assessed by reverse transcription-PCR and Sanger sequencing.

RESULTS

Five patients from four different families were each homozygous for a four base intronic deletion in the gene TTC7A, immediately adjacent to a consensus GT splice donor site. The deletion was demonstrated to have deleterious effects on splicing causing the skipping of the attendant upstream coding exon, thereby leading to a predicted severe protein truncation. Parents were heterozygous carriers of the deletion in these families and in two additional families segregating affected cases. In a seventh family, an affected case was compound heterozygous for the same 4bp deletion and a second missense mutation p.L823P, also predicted as pathogenic. No other sequenced genes possessed deleterious variants explanatory for all patients in the cohort. Neither mutation was seen in a large set of control chromosomes.

CONCLUSIONS

Based on our genetic results, TTC7A is the likely causal gene for MIA.

Recent progress on the superconducting ion source VENUS

The 28 GHz Ion Source VENUS (versatile ECR for nuclear science) is back in operation after the superconducting sextupole leads were repaired and a fourth cryocooler was added. VENUS serves as an R&D device to explore the limits of electron cyclotron resonance source performance at 28 GHz with its 10 kW gryotron and optimum magnetic fields and as an ion source to increase the capabilities of the 88-Inch Cyclotron both for nuclear physics research and applications. The development and testing of ovens and sputtering techniques cover a wide range of applications. Recent experiments on bismuth demonstrated stable operation at 300 eμA of Bi(31+), which is in the intensity range of interest for high performance heavy-ion drivers such as FRIB (Facility for Rare Isotope Beams). In addition, the space radiation effects testing program at the cyclotron relies on the production of a cocktail beam with many species produced simultaneously in the ion source and this can be done with a combination of gases, sputter probes, and an oven. These capabilities are being developed with VENUS by adding a low temperature oven, sputter probes, as well as studying the RF coupling into the source.

Concept for a fourth generation electron cyclotron resonance ion source

A fourth generation electron cyclotron resonance ion source with an operating frequency between 40 and 56 GHz has the potential to quadruple the heavy-ion beam currents and provide a cost effective upgrade path for heavy ion drivers in use or in the planning stage at radioactive beam facilities. Design studies show it is feasible to produce the required magnetic fields in the plasma chamber, 7 T axially and 4 T in the radial direction with a magnetic structure using commercially available Nb(3)Sn superconducting materials. In this paper we describe the design of such a magnet structure including a 3D analysis of the Lorentz forces generated by the magnetic fields and the necessary clamping structure to stabilize the conductor against these forces.

The large-scale distribution of somatic mutations in cancer genomes

Recently, the genome sequences from several cancers have been published, along with the genome from a noncancer tissue from the same individual, allowing the identification of new somatic mutations in the cancer. We show that there is significant variation in the density of mutations at the 1-Mb scale within three cancer genomes and that the density of mutations is correlated between them. We also demonstrate that the density of mutations is correlated to that in the germline, as measured by the divergence between humans and chimpanzees and humans and macaques. We show that the density of mutations is correlated to the guanine and cytosine (GC) conent, replication time, distance to telomere and centromere, gene density, and nucleosome occupancy in the cancer genomes. However, overall, all factors explain less than 40% of the variance in mutation density and each factor explains very little of the variance. We find that genes associated with cancer occupy regions of the genome with significantly lower mutation rates than the average. Finally, we show that the density of mutations varies at a 10-Mb and a chromosomal scale, but that the variation at these scales is weak.

The genomic distribution and local context of coincident SNPs in human and chimpanzee

We have previously shown that there is an excess of sites that are polymorphic at orthologous positions in humans and chimpanzees and that this is most likely due to cryptic variation in the mutation rate. We showed that this might be a consequence of complex context effects since we found significant heterogeneity in triplet frequencies around coincident single nucleotide polymorphism (SNP) sites. Here, we show that the heterogeneity in triplet frequencies is not specifically associated with coincident SNPs but is instead driven by base composition bias around CpG dinucleotides. As a result, we suggest that cryptic variation in the mutation rate is truly cryptic, in the sense that the mutation rate does not appear to depend on any specific primary sequence context. Furthermore, we propose that the patterns around CpG dinucleotides are driven by the mutability of CpG dinucleotides in different DNA contexts. We also show that the genomic distribution of coincident SNPs is nonuniform and that there are some subtle differences between the distributions of single and coincident SNPs. Furthermore, we identify regions that contain high numbers of coincident SNPs and suggest that one in particular, a region containing the gene PRIM2, may be under balancing selection.

Cryptic variation in the human mutation rate

The mutation rate is known to vary between adjacent sites within the human genome as a consequence of context, the most well-studied example being the influence of CpG dinucelotides. We investigated whether there is additional variation by testing whether there is an excess of sites at which both humans and chimpanzees have a single-nucleotide polymorphism (SNP). We found a highly significant excess of such sites, and we demonstrated that this excess is not due to neighbouring nucleotide effects, ancestral polymorphism, or natural selection. We therefore infer that there is cryptic variation in the mutation rate. However, although this variation in the mutation rate is not associated with the adjacent nucleotides, we show that there are highly nonrandom patterns of nucleotides that extend approximately 80 base pairs on either side of sites with coincident SNPs, suggesting that there are extensive and complex context effects. Finally, we estimate the level of variation needed to produce the excess of coincident SNPs and show that there is a similar, or higher, level of variation in the mutation rate associated with this cryptic process than there is associated with adjacent nucleotides, including the CpG effect. We conclude that there is substantial variation in the mutation that has, until now, been hidden from view.

Immune components of bovine colostrum and milk

Colostrum and milk provide a complete diet for the neonate. In ruminants, colostrum is also the sole source of initial acquired immunity for the offspring. Milk therefore plays an important role in mammalian host defense. In colostrum, the concentration of immunoglobulins is particularly high, with IgG being the major immunoglobulin class present in ruminant milk, in contrast to IgA being the major immunoglobulin present in human milk. Immunoglobulins are transported into mammary secretions via specialized receptors. In addition to immunoglobulins, both colostrum and milk contain viable cells, including neutrophils and macrophages, which secrete a range of immune-related components into milk. These include cytokines and antimicrobial proteins and peptides, such as lactoferrin, defensins, and cathelicidins. Mammary epithelial cells themselves also contribute to the host defense by secreting a range of innate immune effector molecules. A detailed understanding of these proteins and peptides offers great potential to add value to the dairy industry. This is demonstrated by the wide-ranging commercial applications of lactoferrin derived from bovine milk. Knowledge of the immune function of milk, in particular, how the gland responds to pathogens, can be used to boost the concentrations of immune factors in milk through farm management practices and vaccination protocols. The latter approach is currently being used to maximize yields of bovine milk-derived IgA directed at specific antigens for therapeutic and prophylactic use. Increasingly sophisticated proteomics technologies are being applied to identify and characterize the functions of the minor components of milk. An overview is presented of the immune factors in colostrum and milk as well as the results of research aimed at realizing this untapped value in milk.

Social, neuroradiologic, medical, and neuropsychologic correlates of sexually aberrant behavior after traumatic brain injury: a controlled study

OBJECTIVE

To identify social, neuroradiological, medical, and neuropsychological correlates of sexually aberrant behavior (SAB) after traumatic brain injury (TBI).

DESIGN

A controlled study using a retrospective file review.

SETTING

A brain injury unit providing inpatient and outpatient rehabilitation services.

PARTICIPANTS

A sample of males (n = 25) exhibiting SABs and a control group (n = 25) matched for gender, severity of injury, age at injury, and time after injury.

MAIN OUTCOME MEASURES

A protocol that recorded data on demographic, injury, radiological, medical, and neuropsychological variables.

RESULTS

The SAB group had a significantly higher incidence of postinjury psychosocial disturbance in areas of nonsexual crime and failure to return to work than the matched TBI group. There were no significant differences between the two groups in the incidence of premorbid psychosocial disturbance or postinjury radiological, medical, or neuropsychological variables.

CONCLUSIONS

The study results caution against simplistic explanations of SAB as the product of damage to the frontal-lobe systems or premorbid psychosocial disturbance. Furthermore, the results suggest that a wide-ranging assessment of people with TBI who exhibit SABs is required, because results of neuropsychological examination alone cannot be considered conclusive. Future research into the etiology of SABs could examine additional factors such as lack of insight, lack of empathy, and premorbid history of family dysfunction.

Service utilization following traumatic brain injury

OBJECTIVES

To document service utilization by people with a traumatic brain injury at different times postinjury and to identify factors that predict service use.

DESIGN

Cross-sectional study design. Four groups of subjects were randomly selected from a regional database, according to their time postinjury: 6-18 months; 2-4 years; 6-9 years; and 10-17 years.

SUBJECTS

A total of 119 adults with a traumatic brain injury (TBI).

SETTING

Hospital and community-based clients in Sydney, Australia.

OUTCOME MEASURES

Glasgow Outcome Scale, Disability Rating Scale; Functional Independence Measure; Lidcombe Psychosocial Disability Scale; number, type, and frequency of services used in the previous 12 months.

RESULTS

Subjects in all four groups used a variety of services. The mean number of services used was 4.2, and there was only a moderate decline in service use over time. The use of medical and allied health services remained high in all four groups. Severity of injury, physical and cognitive disability, and psychosocial disability were all predictors of service utilization. Psychosocial disability was strongly associated with ongoing service utilization.

CONCLUSION

In this study, people with TBI used services well beyond the early stage of recovery. Psychosocial disability may be a better predictor of service use than physical and cognitive disability alone.

Measuring psychosocial recovery after traumatic brain injury: psychometric properties of a new scale

OBJECTIVES

To determine the psychometric properties of the Sydney Psychosocial Reintegration Scale (SPRS), an instrument developed to quantify disability and handicap in persons with traumatic brain injury (TBI).

DESIGN

Descriptive correlational study.

SETTING

Brain Injury Rehabilitation Unit and Brain Injury Outpatient Clinic.

PARTICIPANTS

Two samples, a "subacute" group (n = 20) and a "long-term" group (n = 40), were studied to examine responsiveness (subacute group), reliability, and validity (long-term group) of the SPRS.

MAIN OUTCOME MEASURE

The SPRS is a 12-item questionnaire measuring three domains of everyday living commonly disrupted after severe TBI: occupational activities, interpersonal relationships, and independent living skills.

PROCEDURE

Patients in the subacute group were rated with the SPRS by a clinician at admission to the rehabilitation unit and again three months later or at discharge from the unit (whichever occurred first). For individuals from the long-term group attending the outpatient clinic, a close relative was interviewed with the SPRS and other validating measures. The SPRS was readministered one month later.

RESULTS

Internal consistency of the SPRS was high (alpha coefficient = .90), as was agreement between raters and stability over a one-month period (r(i) = .95 and .90, respectively). Reliability and stability coefficients for the three domains of the scale were also high, ranging from.86 to.94 for reliability and.77 to.93 for stability. Preliminary evidence for construct validity was established with a number of standard instruments, with evidence of both convergent and discriminant construct validity from the Sickness Impact Profile (SIP). The SPRS was sensitive to group differences on the Glasgow Outcome Scale (GOS) and to changes occurring during the period of active recovery.

CONCLUSIONS

The results suggest that the SPRS has sound psychometric properties, being a reliable, stable, sensitive, and valid instrument. It is potentially useful in both clinical and research settings.

Sex offending as a psychosocial sequela of traumatic brain injury

OBJECTIVE

To describe the nature and extent of sexual offending after traumatic brain injury (TBI).

DESIGN

Retrospective file review.

SETTING

A brain injury unit providing inpatient and outpatient rehabilitation services.

PARTICIPANTS

A review of five years of admissions to the Brain Injury Rehabilitation Unit (N = 477) identified a sample of 29 males who committed 128 incidents of sex offending.

MAIN OUTCOME MEASURES

A protocol to record data on demographic, injury, radiological, and psychosocial variables and offending behaviors.

RESULTS

Of the total population of 445 clients with TBI, 6.5% (n = 29) were identified as having committed some form of sexual offense. Alcohol was a factor in only three (2.3%) of the incidents, and only two clients had a preinjury history of sexual offending. The most common offenses were the "touching" offenses, followed by exhibitionism and overt sexual aggression. Staff members were the most common targets of the offenses, followed by members of the general public, other people with TBI, and family members.

CONCLUSIONS

Sex offending is a significant clinical problem among a small minority of men after TBI. The absence of alcohol and preinjury histories of sexual offending suggest that the brain injury and contingent sequelae were a significant etiological factor underlying the offenses. A number of implications for the clinical management of clients with sexually aberrant behaviors is identified and discussed.

Linking public health education and practice: the Australian experience

The public health workforce in Australia is highly skilled, multifunctional, and drawn from a variety of backgrounds, including clinical practice and non-health areas. A wide range of activities is needed to meet the educational and training requirements of this workforce, including on the job inservice training, context specific continuing education programs and short courses, distance and self-directed learning packages, and postgraduate University level courses. The core components of public health today include: a social and political commitment to health, a shared responsibility between government and the public, and a multidisciplinary field of action. The challenge for those providing education and training for the public health workforce is to ensure graduates have the broad range of knowledge and skills needed in this climate. A system-wide approach to learning, where knowledge and skill development is related to the practices and settings of service and program delivery, will ensure strong links between education and practice.

Prolonged, severe behavioural disturbance following traumatic brain injury: what can be done?

At the end of 1994 the New South Wales Department of Health identified the need for a specialized unit for people with a brain injury who exhibited aggressive and violent behaviour at such a level that they could not be cared for in standard rehabilitation programmes and who were not mentally ill as defined by the Mental Health Act. An interim unit based on the principles of neurobehavioural rehabilitation was opened in the grounds of Lidcombe Hospital, and in January 1995 the first patient (SA) was admitted. Following intervention weekly aggression decreased from a peak of 159 incidents to zero after ten months. Other maladaptive behaviours also decreased markedly. Simultaneous attempts to improve adaptive behaviours were successful. At 11 months follow-up in the community, these gains were all noted to have been maintained. This article discusses the need for specialized units dealing with severe behavioural problems following head injury, presents the case of SA for illustrative purposes, and addresses some of the more common criticisms of such environments.

A non-aversive approach to reducing hospital absconding in a head-injured adolescent boy

Patients who abscond from hospital exclude themselves from therapy, and attempts to stop the person can quickly become confrontational with the inherent risk of aggression. Although information is available on absconding in psychiatric settings little is known about the type of person with a head injury who absconds, why such people do so, or how the problem might best be approached. This paper presents a non-aversive approach to hospital absconding in a head-injured adolescent male, discusses how his case relates to the psychiatric literature, and looks at the feasibility of adopting such interventions in general hospital wards.

Tackling the tobacco challenge: achieving 'healthy public policy' in tobacco control in Guernsey

Scientific evidence identifying smoking as the major cause of poor health and premature death in both industrialised and increasingly in developing countries is now overwhelming. Despite this, for a variety of reasons, there has been reluctance amongst many Governments including that of Britain, to take all logical action necessary to restrict and reduce smoking, especially amongst the young. The States of Guernsey in the Channel Islands has recently agreed to introduce an integrated package of measures designed specifically to make smoking less attractive and less accessible and less affordable to young people in an attempt to reduce the number of addicted adult smokers. These measures include a total ban of all public advertising of tobacco, apart from at point of sale, a substantial price rise followed by further price rises for a minimum period of five years, a raising of the minimum age for the purchase of tobacco from 16 to 18 years, an increase in the size and content of pack health warnings, and increased funding for specific nonsmoking health promotion activities. The various barriers to achieving these reforms are described.

Inpatient quality assurance by local analysis of uniform data set data

We constructed a data base in order to examine the profile of patients admitted to a 24 bed inpatient rehabilitation unit at Fairfield Hospital. Data were collected according to the Uniform Data Set for Medical Rehabilitation, and collated and analysed using the Clinical Reporting System database software and the Statistical Package for Interactive Data Analysis statistical software. Outcome data collected included the patients domicile before and after admission, the duration of stay, medical diagnoses before admission to and during the stay in the Rehabilitation Unit, as well as the Functional Independence Measure item scores at admission and discharge. Analysis of the first 100 patients in the data base indicated a duration of stay of 43 +/- 34 days with a right skew distribution. Scatter plots of age and duration of stay, and age and functional improvement showed no bias in the Unit concerning these parameters. The Wilcoxon rank sum test indicated a highly significant difference (P = 0) between entry and exit Functional Independence Measure scores, indicating that patients improved functionally in the unit. Eighty three patients returned home on discharge and only five required admission to a nursing home. With the data base, the course of patients whose performance lies outside the range of normal for the unit can be examined and factors identified which produce a prolonged stay or failure to progress.

Effects of oral ethinyl oestradiol and norethisterone on plasma copper and zinc complexes in post-menopausal women

Orally administered ethinyl oestradiol increased the plasma total copper concentration and reduced the albumin concentration in post-menopausal women. Approximately 80% of the increase in copper was due to a rise in caeruloplasmin-bound copper and 20% to an increase in the amount of copper bound per gram of albumin. The plasma total zinc concentration was reduced, due partly to the decrease in albumin concentration and partly to a reduction in the amount of zinc bound per gram of albumin. Norethisterone had no significant effect on plasma copper but it reduced plasma zinc and albumin, though to a lesser extent than ethinyl oestradiol. When administered sequentially with ethinyl oestradiol, norethisterone diminished the effects of the former on plasma copper, zinc and albumin.

Hypothesis. Biochemical changes at the menopause: possible role of the central nervous system

Some of the biochemical changes which occur at the menopause can be attributed to an increased rate of loss of bone but others cannot be explained in this way. Data, collected through literature search, are presented which suggest that the rise in plasma phosphate concentration at the menopause is not due primarily to increased breakdown of bone but rather to the following sequence of events: progesterone deficiency----respiratory hypoventilation----mild respiratory acidosis and hypoxia----compensatory metabolic alkalosis----altered carbohydrate metabolism----rise in plasma phosphate concentration. Increases in the concentration of many plasma constituents occur at the menopause, which appear to be due to fluid loss and haemoconcentration. A possible cause of these changes is a reduced secretion of vasopressin by the pituitary gland as a result of oestrogen deficiency. Increases in the fasting urinary excretion of phosphate, sodium and magnesium also occur at the menopause. These changes cannot be attributed to increased bone loss but could be due to the effects of oestrogen deficiency on circadian rhythms in the hypothalamus.

Increase in plasma lactate at the menopause and its relation to the "anion gap"

The mean plasma anion gap (Na + K + Ca + Mg)--(Cl + HCO3(-) + HPO4(2-) + protein), was significantly higher in post-menopausal women compared with pre-menopausal women (8.04 mEq/l compared with 7.03 mEq/l). This change was due, in part, to an increase in the plasma lactate concentration and to smaller increases in citrate and pyruvate concentrations. There were also changes in bicarbonate and chloride concentrations which suggested an increase pH of approximately 0.02 U. Together, these changes accounted for 46% of the increase in the "anion gap", leaving 54% unexplained. It is suggested that the rise in plasma lactate concentration may be due to mild alkalosis and that this change may account for the rise in plasma urate concentration which also occurs at the menopause.

The effect of ethinyl oestradiol on calcium and bone metabolism in peri- and postmenopausal women

The effects of ethinyl oestradiol on plasma and urinary calcium and other indices of bone turnover have been compared in peri- and postmenopausal women. In postmenopausal women ethinyl oestradiol caused significant decreases in the fasting plasma total and ionised calcium and phosphate concentrations, in alkaline phosphatase activity and in the fasting urinary Ca/Cr and OHPr/Cr ratios. Similar, but less marked, effects were observed in peri-menopausal women, with significant decreases in the fasting plasma phosphate and urinary Ca/Cr ratio. Small decreases in the plasma total and ionised calcium concentrations, in alkaline phosphatase activity and in the urinary OHPr/Cr ratio also occurred but were not statistically significant in our sample. Ethinyl oestradiol therefore appears to reduce bone loss in peri- as well as post-menopausal women, at least in the short term, but the effect is less pronounced in the former group.

Changes in plasma sodium concentration in women at the menopause

A significant increase in the mean plasma sodium concentration and in the fasting urinary Na/Cr ratio was observed in healthy women at the menopause. Both of these changes were reversed by administering oestrogens. None of the above effects appeared to be due to alterations in sodium intake or in renal glomerular function. The most likely cause of the increase in plasma sodium concentration at the menopause appeared to be a decrease in plasma volume since there were also significant increases in the mean plasma albumin and total protein concentrations.

Plasma electrolyte concentrations in women and the effects of oestrogen administration

Age-related changes in the concentrations of the main plasma electrolytes and in the urinary excretion of some of these ions have been examined in 436 pre-menopausal and 117 post-menopausal women. The main changes up to the menopause were decreases in the mean plasma potassium, calcium and total protein concentrations, accompanied by increases in the renal excretion of calcium and inorganic phosphate. The decrease in plasma total calcium concentration was completely accounted for by the fall in albumin and globulin concentrations. The main changes observed at the menopause were increases in plasma sodium, total calcium, inorganic phosphate and magnesium concentrations, an increase in the plasma "anion gap" and increases in the renal excretion of sodium, magnesium and inorganic phosphate. All these changes were reversed by treatment with ethinyl oestradiol. The causes and significance of some of these changes are discussed, particularly the menopausal rises in plasma sodium concentration and in the plasma "anion gap".

Measurement of the fasting urinary hydroxyproline: creatinine ratio in normal adults and its variation with age and sex

Conditions for the determination of the fasting urinary hydroxyproline: creatinine ratio (OHPr: Cr ratio) have been examined, using a resin-catalysed hydrolysis and automated colorimetric procedure for the determination of hydroxyproline. Feeding experiments with gelatin showed that hydroxyproline is rapidly absorbed and excreted in the urine and that a 12-hour (overnight) fast is sufficient to ensure correct and reproducible fasting OHPr: Cr ratios. The mean fasting OHPr: Cr ratio decreased slightly with increasing age in both men and premenopausal women but there was no significant difference between the sexes. There was, however, a significant increase in the mean ratio in postmenopausal women. The normal range of fasting OHPr: Cr ratios for men and premenopausal women was found to be 0.003--0.015.