Prevalence of endocrine and genetic abnormalities in boys evaluated systematically for a disorder of sex development.

STUDY QUESTION: What is the likelihood of identifying genetic or endocrine abnormalities in a group of boys with 46, XY who present to a specialist clinic with a suspected disorder of sex development (DSD)? SUMMARY ANSWER: An endocrine abnormality of the gonadal axis may be present in a quarter of cases and copy number variants (CNVs) or single gene variants may be present in about half of the cases. WHAT IS KNOWN ALREADY: Evaluation of 46, XY DSD requires a combination of endocrine and genetic tests but the prevalence of these abnormalities in a sufficiently large group of boys presenting to one specialist multidisciplinary service is unclear. STUDY, DESIGN, SIZE, DURATION: This study was a retrospective review of investigations performed on 122 boys. PARTICIPANTS/MATERIALS, SETTING, METHODS: All boys who attended the Glasgow DSD clinic, between 2010 and 2015 were included in the study. The median external masculinization score (EMS) of this group was 9 (range 1-11). Details of phenotype, endocrine and genetic investigations were obtained from case records. MAIN RESULTS AND THE ROLE OF CHANCE: An endocrine abnormality of gonadal function was present in 28 (23%) with a median EMS of 8.3 (1-10.5) whilst the median EMS of boys with normal endocrine investigations was 9 (1.5-11) (P = 0.03). Endocrine abnormalities included a disorder of gonadal development in 19 (16%), LH deficiency in 5 (4%) and a disorder of androgen synthesis in 4 (3%) boys. Of 43 cases who had array-comparative genomic hybridization (array-CGH), CNVs were reported in 13 (30%) with a median EMS of 8.5 (1.5-11). Candidate gene analysis using a limited seven-gene panel in 64 boys identified variants in 9 (14%) with a median EMS of 8 (1-9). Of the 21 boys with a genetic abnormality, 11 (52%) had normal endocrine investigations. LIMITATIONS, REASONS FOR CAUTION: A selection bias for performing array-CGH in cases with multiple congenital malformations may have led to a high yield of CNVs. It is also possible that the yield of single gene variants may have been higher than reported if the investigators had used a more extended gene panel. WIDER IMPLICATIONS OF THE FINDINGS: The lack of a clear association between the extent of under-masculinization and presence of endocrine and genetic abnormalities suggests a role for parallel endocrine and genetic investigations in cases of suspected XY DSD. STUDY FUNDING/COMPETING INTEREST(S): RN was supported by the James Paterson Bursary and the Glasgow Children's Hospital Charity Summer Scholarship. SFA, RM and EST are supported by a Scottish Executive Health Department grant 74250/1 for the Scottish Genomes Partnership. EST is also supported by MRC/EPSRC Molecular Pathology Node and Wellcome Trust ISSF funding. There are no conflicts of interest. TRIAL REGISTRATION NUMBER: None.

Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a--probably untenable--model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.

What factors shape rates of phenotypic evolution? A comparative study of cranial morphology of four mammalian clades.

Understanding why rates of morphological evolution vary is a major goal in evolutionary biology. Classical work suggests that body size, interspecific competition, geographic range size and specialization may all be important, and each may increase or decrease rates of evolution. Here, we investigate correlates of proportional evolutionary rates in phalangeriform possums, phyllostomid bats, platyrrhine monkeys and marmotine squirrels, using phylogenetic comparative methods. We find that the most important correlate is body size. Large species evolve the fastest in all four clades, and there is a nonlinear relationship in platyrrhines and phalangeriformes, with the slowest evolution in species of intermediate size. We also find significant increases in rate with high environmental temperature in phyllostomids, and low mass-specific metabolic rate in marmotine squirrels. The mechanisms underlying these correlations are uncertain and appear to be size specific. We conclude that there is significant variation in rates of evolution, but that its meaning is not yet clear.

The fast-slow continuum in mammalian life history: an empirical reevaluation.

Many life-history traits co-vary across species, even when body size differences are controlled for. This phenomenon has led to the concept of a "fast-slow continuum," which has been influential in both empirical and theoretical studies of life-history evolution. We present a comparative analysis of mammalian life histories showing that, for mammals at least, there is not a single fast-slow continuum. Rather, both across and within mammalian clades, the speed of life varies along at least two largely independent axes when body size effects are removed. One axis reflects how species balance offspring size against offspring number, while the other describes the timing of reproductive bouts.

Sex and congenital diaphragmatic hernia.

BACKGROUND AND PURPOSE: Human studies note sex reversal syndromes and sex difference(s) in the incidence of congenital diaphragmatic hernia (CDH). Epidemiology surveys record a higher incidence of CDH in females, whilst other reports cite a higher frequency in males. Nitrofen, a teratogen, produces experimental CDH. This agent is speculated to interfere with retinoid acid-steroid signalling pathways and may also be linked with sexual differentiation. This study was designed therefore to test the hypothesis that nitrofen may influence sexual phenotype and frequency of CDH. METHODS: Time mated Sprague Dawley rats were dosed with nitrofen at day 9.5 to generate predominantly left sided CDH. Fetuses were delivered by caesarean section on days 20 or 21 of gestation (term=day 22). External genitalia were examined to define external genital phenotype. The abdominal cavity was opened and the genito-urinary system carefully examined. The internal genital organs were assigned a phenotype and findings correlated with external appearances. The diaphragm of each fetus was studied for the absence or presence of CDH and the laterality of defect recorded. Controls (non nitrofen fed) were used for all comparative analysis. RESULTS: Control (n=600) and nitrofen exposed offspring (n=504) had equal frequencies of males and females. CDH occurred with similar incidence in male and female nitrofen treated pups. In all nitrofen exposed fetuses and normal controls, internal and external genitalia concorded without evidence of significant genital tract malformations or intersex states. CONCLUSIONS: Prenatal nitrofen exposure is not associated with significant gender differences (or prenatal loss) in the risk of CDH. Genital tract malformations do not appear to accompany CDH in the nitrofen model.

Nonplanar photolithography with computer-generated holograms.

We outline a method for accomplishing photolithography on grossly nonplanar substrates. First we compute an approximation of the diffraction pattern that will produce the desired light-intensity distribution on the substrate to be patterned. This pattern is then digitized and converted into a format suitable for manufacture by a direct-write method. The resultant computer-generated hologram mask is then used in a custom alignment tool to expose the photoresist-coated substrate. The technique has many potential applications in the packaging of microelectronics and microelectromechanical systems.

Macroevolutionary trends in the Dinosauria: Cope's rule.

Cope's rule is the tendency for body size to increase over time along a lineage. A set of 65 phylogenetically independent comparisons, between earlier and later genera, show that Cope's rule applied in dinosaurs: later genera were on average about 25% longer than the related earlier genera to which they were compared. The tendency for size to increase was not restricted to a particular clade within the group, nor to a particular time within its history. Small lineages were more likely to increase in size, and large lineages more likely to decrease: this pattern may indicate an intermediate optimum body size, but can also be explained as an artefact of data error. The rate of size increase estimated from the phylogenetic comparisons is significantly higher than the rate seen across the fauna as a whole. This difference could indicate that within-lineage selection for larger size was opposed by clade selection favouring smaller size, but data limitations mean that alternative explanations (which we discuss) cannot be excluded. We discuss ways of unlocking the full potential usefulness of phylogenies for studying the dynamics of evolutionary trends.

The life history legacy of evolutionary body size change in carnivores.

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.

Targeted pharmacological depletion of serum amyloid P component for treatment of human amyloidosis.

The normal plasma protein serum amyloid P component (SAP) binds to fibrils in all types of amyloid deposits, and contributes to the pathogenesis of amyloidosis. In order to intervene in this process we have developed a drug, R-1-[6-[R-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid, that is a competitive inhibitor of SAP binding to amyloid fibrils. This palindromic compound also crosslinks and dimerizes SAP molecules, leading to their very rapid clearance by the liver, and thus produces a marked depletion of circulating human SAP. This mechanism of drug action potently removes SAP from human amyloid deposits in the tissues and may provide a new therapeutic approach to both systemic amyloidosis and diseases associated with local amyloid, including Alzheimer's disease and type 2 diabetes.

Changing the landscape: a new strategy for estimating large phylogenies.

In this paper we describe a new heuristic strategy designed to find optimal (parsimonious) trees for data sets with large numbers of taxa and characters. This new strategy uses an iterative searching process of branch swapping with equally weighted characters, followed by swapping with reweighted characters. This process increases the efficiency of the search because, after each round of swapping with reweighted characters, the subsequent swapping with equal weights will start from a different group (island) of trees that are only slightly, if at all, less optimal. In contrast, conventional heuristic searching with constant equal weighting can become trapped on islands of suboptimal trees. We test the new strategy against a conventional strategy and a modified conventional strategy and show that, within a given time, the new strategy finds trees that are markedly more parsimonious. We also compare our new strategy with a recent, independently developed strategy known as the Parsimony Ratchet.

Stress-induced changes in ubiquinone concentration and alternative oxidase in plant mitochondria.

We have investigated the influence of stress conditions such as incubation at 4 degrees C and incubation in hyperoxygen atmosphere, on plant tissues. The ubiquinone (Q) content and respiratory activity of purified mitochondria was studied. The rate of respiration of mitochondria isolated from cold-treated green bell peppers (Capsicum annuum L) exceeds that of controls, but this is not so for mitochondria isolated from cold-treated cauliflower (Brassica oleracea L). Treatment with high oxygen does not alter respiration rates of cauliflower mitochondria. Analysis of kinetic data relating oxygen uptake with Q reduction in mitochondria isolated from tissue incubated at 4 degrees C (bell peppers and cauliflowers) and at high oxygen levels (cauliflowers) reveals an increase in the total amount of Q and in the percentage of inoxidizable QH2. The effects are not invariably accompanied by an induction of the alternative oxidase (AOX). In those mitochondria where the AOX is induced (cold-treated bell pepper and cauliflower treated with high oxygen) superoxide production is lower than in the control. The role of reduced Q accumulation and AOX induction in the defense against oxidative damage is discussed.

Predicting extinction risk in declining species.

What biological attributes predispose species to the risk of extinction? There are many hypotheses but so far there has been no systematic analysis for discriminating between them. Using complete phylogenies of contemporary carnivores and primates, we present, to our knowledge, the first comparative test showing that high trophic level, low population density slow life history and, in particular, small geographical range size are all significantly and independently associated with a high extinction risk in declining species. These traits together explain nearly 50% of the total between-species variation in extinction risk. Much of the remaining variation can be accounted for by external anthropogenic factors that affect species irrespective of their biology.

The effects of phase control materials on hand skin temperature within gloves of soccer goalkeepers.

In soccer, goalkeepers routinely wear gloves that may restrict heat loss from the hands and cause thermal discomfort. In order to alleviate this problem phase control materials (PCMs) have been incorporated into gloves to reduce heat load inside the glove, thereby maintaining a comfortable temperature. The aim of this study was to assess the efficacy of these materials during a simulation of goalkeeping activities. Seven subjects carried out two sessions of goalkeeper-specific exercise on a non-motorized treadmill, one session with a PCM glove and one session with a normal foam material glove (NFM). All sites of skin temperature measurement, except mean whole-body skin temperature, showed uniformly that the PCM glove caused a greater increase in skin temperature of the hand compared to the NFM glove. These results suggest that this particular specification of PCM promotes heat gain rather than heat loss and is therefore inappropriate to enhance thermal comfort in this setting.

Extinction.

In the life of any species, extinction is the final evolutionary process. It is a common one at present, as the world is entering a major extinction crisis. The pattern of extinction and threat is very non-random, with some taxa being more vulnerable than others. Explaining why some taxa are affected and some escape is a major goal of conservation biology. More ambitiously, a predictive model could, in principle, be built by integrating comparable studies of past and present extinctions. We review progress towards both explanatory and predictive frameworks, comparing correlates of extinction in different groups at different times. Progress towards explanatory models for the current crisis is promising, at least in some well-studied taxa, but the development of a truly predictive model is hampered by the formidable difficulties of integrating studies of present and past extinctions.

Getting the measure of biodiversity.

The term 'biodiversity' is a simple contraction of 'biological diversity', and at first sight the concept is simple too: biodiversity is the sum total of all biotic variation from the level of genes to ecosystems. The challenge comes in measuring such a broad concept in ways that are useful. We show that, although biodiversity can never be fully captured by a single number, study of particular facets has led to rapid, exciting and sometimes alarming discoveries. Phylogenetic and temporal analyses are shedding light on the ecological and evolutionary processes that have shaped current biodiversity. There is no doubt that humans are now destroying this diversity at an alarming rate. A vital question now being tackled is how badly this loss affects ecosystem functioning. Although current research efforts are impressive, they are tiny in comparison to the amount of unknown diversity and the urgency and importance of the task.

Molecular chaperone properties of serum amyloid P component.

The selective binding of serum amyloid P component (SAP) to proteins in the pathological amyloid cross-beta fold suggests a possible chaperone role. Here we show that human SAP enhances the refolding yield of denatured lactate dehydrogenase and protects against enzyme inactivation during agitation of dilute solutions. These effects are independent of calcium ions and are not inhibited by compounds that block the amyloid recognition site on the B face of SAP, implicating the A face and/or the edges of the SAP pentamer. We discuss the possibility that the chaperone property of SAP, or its failure, may contribute to the pathogenesis of amyloidosis.

Nonrandom extinction and the loss of evolutionary history.

The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra loss of mammalian evolutionary history alone would be equivalent to losing a monotypic phylum.

Phosphate ion partially relieves the cooperativity of effector binding in D-3-phosphoglycerate dehydrogenase without altering the cooperativity of inhibition.

The binding of L-serine to phosphoglycerate dehydrogenase from E. coli displays elements of both positive and negative cooperativity. In addition, the inhibition of enzymatic activity by L-serine is also cooperative with Hill coefficients greater than 1. However, phosphate buffer significantly reduces the cooperative effects in serine binding without affecting the cooperativity of inhibition of activity. The maximal degree of inhibition and fluorescence quenching in Tris buffer occurs when an average of two serine binding sites out of four are occupied. This value increases to three out of the four sites at maximal levels of inhibition and quenching in phosphate buffer. The increase from two to three sites appears to be due to the ability of phosphate to reduce the site to site cooperative effects and render each ligand binding site less dependent on each other. The correlation between the level of inhibition and the fractional site occupancy indicates that in Tris buffer, one serine is bound to each interface at maximal effect. In the presence of phosphate, the order of binding appears to change so that both sites at one interface fill before the first site at the opposite interface is occupied. In each case, there is a good correlation between serine binding, conformational change at the regulatory site interfaces, and inhibition of enzyme activity. The observation that phosphate does not appear to have a similar effect on the cooperativity of inhibition of enzymatic activity suggests that there are two distinct cooperative pathways at work: one path between the four serine binding sites, and one path between the serine binding sites and the active sites.

Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia).

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter: supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources. Beyond providing a 'consensus' estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Body size and species-richness in carnivores and primates.

We use complete species-level phylogenies of extant Carnivora and Primates to perform the first thorough phylogenetic tests, in mammals, of the hypothesis that small body size is associated with species-richness. Our overall results, based on comparisons between sister clades, indicate a weak tendency for lineages with smaller bodies to contain more species. The tendency is much stronger within caniform carnivores (canids, procyonids, pinnipeds, ursids and mustelids), perhaps relating to the dietary flexibility and hence lower extinction rates in small, meat-eating species. We find significant heterogeneity in the size-diversity relationship within and among carnivore families. There is no significant association between body mass and species-richness in primates or feliform carnivores. Although body size is implicated as a correlate of species-richness in mammals, much of the variation in diversity cannot be attributed to size differences.