Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish.

The bioluminescent symbiosis involving the urchin cardinalfish, Siphamia tubifer, and Photobacterium mandapamensis, a luminous member of the Vibrionaceae, is highly specific compared to other bioluminescent fish-bacteria associations. Despite this high degree of specificity, patterns of genetic diversity have been observed for the symbionts from hosts sampled over relatively small spatial scales. We characterized and compared sub-species, strain-level symbiont diversity within and between S. tubifer hosts sampled from the Philippines and Japan using PCR fingerprinting. We then carried out whole genome sequencing of the unique symbiont genotypes identified to characterize the genetic diversity of the symbiont community and the symbiont pangenome. We determined that an individual light organ contains six symbiont genotypes on average, but varied between 1-13. Additionally, we found that there were few genotypes shared between hosts from the same location. A phylogenetic analysis of the unique symbiont strains indicated location-specific clades, suggesting some genetic differentiation in the symbionts between host populations. We also identified symbiont genes that were variable between strains, including luxF, a member of the lux operon, which is responsible for light production. We quantified the light emission and growth rate of two strains missing luxF along with the other strains isolated from the same light organs and determined that strains lacking luxF were dimmer but grew faster than most of the other strains, suggesting a potential metabolic trade-off. This study highlights the importance of strain-level diversity in microbial associations and provides new insight into the underlying genetic architecture of intraspecific symbiont communities within a host.

Chromosome-Level Genome Assembly of the Bioluminescent Cardinalfish Siphamia tubifer: An Emerging Model for Symbiosis Research.

The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer-P. mandapamensis association to be used as a model for symbiosis research.

Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands.

Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behaviour on recruitment and dispersal. Population genetic studies can provide insight on the degree to which populations are connected, and the development of restriction site-associated sequencing (RAD-Seq) methods has made such studies of nonmodel organisms more accessible. We applied double-digest RAD-Seq methods to test for population differentiation in the coral reef-dwelling cardinalfish, Siphamia tubifer, which based on behavioural studies, have the potential to use navigational cues to return to natal reefs. Analysis of 11,836 SNPs from fish collected at coral reefs in Okinawa, Japan, from eleven locations over 3 years reveals little genetic differentiation between groups of S. tubifer at spatial scales from 2 to 140 km and between years at one location: pairwise FST values were between 0.0116 and 0.0214. These results suggest that the Kuroshio Current largely influences larval dispersal in the region, and in contrast to expectations based on studies of other cardinalfishes, there is no evidence of population structure for S. tubifer at the spatial scales examined. However, analyses of outlier loci putatively under selection reveal patterns of temporal differentiation that indicate high population turnover and variable larval supply from divergent source populations between years. These findings highlight the need for more studies of fishes across various geographic regions that also examine temporal patterns of genetic differentiation to better understand the potential connections between early life-history traits and connectivity of reef fish populations.

Life history of the symbiotically luminous cardinalfish Siphamia tubifer (Perciformes: Apogonidae).

Characteristics of the life history of the coral reef-dwelling cardinalfish Siphamia tubifer, from Okinawa, Japan, were defined. A paternal mouthbrooder, S. tubifer, is unusual in forming a bioluminescent symbiosis with Photobacterium mandapamensis. The examined S. tubifer (n = 1273) ranged in size from 9·5 to 43·5 mm standard length (LS ), and the minimum size at sexual maturity was 22 mm LS . The number of S. tubifer associated during the day among the spines of host urchins was 22·9 ± 16·1 (mean ± s.d.; Diadema setosum) and 3·6 ± 3·2 (Echinothrix calamaris). Diet consisted primarily of crustacean zooplankton. Batch fecundity (number of eggs; FB ) was related to LS by the equations: males (fertilized eggs) FB = 27·5LS - 189·46; females (eggs) FB = 31·3LS - 392·63. Individual mass (M; g) as a function of LS was described by the equation: M=9·74×10-5LS2·68. Growth, determined from otolith microstructure analysis, was described with the von Bertalanffy growth function with the following coefficients: L∞ = 40·8 mm LS , K = 0·026 day(-1) and t0 = 23·25 days. Planktonic larval duration was estimated to be 30 days. The age of the oldest examined individual was 240 days. The light organ of S. tubifer, which harbours the symbiotic population of P. mandapamensis, increased linearly in diameter as S. tubifer LS increased, and the bacterial population increased logarithmically with S. tubifer LS . These characteristics indicate that once settled, S. tubifer grows quickly, reproduces early and typically survives much less than 1 year in Okinawa. These characteristics are generally similar to other small reef fishes but they indicate that S. tubifer experiences higher mortality.

Segregation effects on the properties of (AuAg)147.

AuAg nanoclusters are promising supported co-catalysts for photocatalytic hydrogen reduction. However, beyond the quantum regime (N > 100) little is known about how the electronic properties of these nanoparticles are affected by chemical ordering. We investigate the effects of chemical ordering on the properties of 147-atom cuboctahedral AuAg nanoclusters, using empirical potentials coupled with an atomic-swap basin-hopping search to optimise the elemental distribution, with the lowest energy arrangements then reminimised using Density Functional Theory (DFT). Force-field calculations show Au atoms preferentially occupy sub-surface positions in the bimetallic structures, which results in the formation of a pseudo-onion structure for Ag-rich compositions. At the DFT-level, however, an Ag core surrounded by an Au shell (Ag@Au) is energetically favoured, as electron density can be drawn more readily when Au atoms are positioned on the nanocluster surface, thus resulting in a partial negative charge. Core@shell configurations are analogous to structures that can be chemically synthesised, and further detailed electronic analysis is discussed in the context of nanocluster applications to co-catalysed photocatalysis.

Symbiosis initiation in the bacterially luminous sea urchin cardinalfish Siphamia versicolor.

To determine how each new generation of the sea urchin cardinalfish Siphamia versicolor acquires the symbiotic luminous bacterium Photobacterium mandapamensis, and when in its development the S. versicolor initiates the symbiosis, procedures were established for rearing S. versicolor larvae in an aposymbiotic state. Under the conditions provided, larvae survived and developed for 28 days after their release from the mouths of males. Notochord flexion began at 8 days post release (dpr). By 28 dpr, squamation was evident and the caudal complex was complete. The light organ remained free of bacteria but increased in size and complexity during development of the larvae. Thus, aposymbiotic larvae of the fish can survive and develop for extended periods, major components of the luminescence system develop in the absence of the bacteria and the bacteria are not acquired directly from a parent, via the egg or during mouth brooding. Presentation of the symbiotic bacteria to aposymbiotic larvae at 8-10 dpr, but not earlier, led to initiation of the symbiosis. Upon colonization of the light organ, the bacterial population increased rapidly and cells forming the light-organ chambers exhibited a differentiated appearance. Therefore, the light organ apparently first becomes receptive to colonization after 1 week post-release development, the symbiosis is initiated by bacteria acquired from the environment and bacterial colonization induces morphological changes in the nascent light organ. The abilities to culture larvae of S. versicolor for extended periods and to initiate the symbiosis in aposymbiotic larvae are key steps in establishing the experimental tractability of this highly specific vertebrate and microbe mutualism.

Baseline differences in A1C explain apparent differences in efficacy of sitagliptin, rosiglitazone and pioglitazone.

AIM: Published studies of patients treated with rosiglitazone or pioglitazone have reported greater reductions in HbA1c (A1C) than studies of patients treated with sitagliptin. However, studies of thiazolidinediones tended to enroll patients with higher baseline A1C levels. This meta-analysis investigates the relationship between baseline A1C and perceived efficacy of treatment. METHODS: This report describes a Bayesian random effects analysis of 23 published studies. We constructed a random effects model including a factor adjusting for between-study differences in baseline A1C levels. RESULTS: The random effects model correctly predicts post-treatment A1C levels from baseline A1C within a 95% confidence interval (CI) for each of the 23 studies included in the meta-analysis. After applying the model to adjust for differences in baseline A1C, we found that the difference in efficacy between rosiglitazone and sitagliptin was not significantly different from zero (0.12; 95% CI -0.09 to 0.34). Similarly, no significant differences are observed between the effects of pioglitazone and sitagliptin (0.01; 95% CI -0.21 to 0.22) or between rosiglitazone and pioglitazone (0.11; 95% CI -0.37 to 0.146). When baseline values are omitted from the Bayesian model, the findings suggest that rosiglitazone is superior to pioglitazone or sitagliptin. CONCLUSIONS: These results illustrate the necessity for careful application of appropriate methodology when comparing results of different studies. When between-study differences in treatment effects are adjusted for baseline differences, then the findings suggest that none of the treatments has an effect that is superior to any of the other treatments.

An evaluation of computer-aided disproportionality analysis for post-marketing signal detection.

To understand the value of computer-aided disproportionality analysis (DA) in relation to current pharmacovigilance signal detection methods, four products were retrospectively evaluated by applying an empirical Bayes method to Merck's post-marketing safety database. Findings were compared with the prior detection of labeled post-marketing adverse events. Disproportionality ratios (empirical Bayes geometric mean lower 95% bounds for the posterior distribution (EBGM05)) were generated for product-event pairs. Overall (1993-2004 data, EBGM05> or =2, individual terms) results of signal detection using DA compared to standard methods were sensitivity, 31.1%; specificity, 95.3%; and positive predictive value, 19.9%. Using groupings of synonymous labeled terms, sensitivity improved (40.9%). More of the adverse events detected by both methods were detected earlier using DA and grouped (versus individual) terms. With 1939-2004 data, diagnostic properties were similar to those from 1993 to 2004. DA methods using Merck's safety database demonstrate sufficient sensitivity and specificity to be considered for use as an adjunct to conventional signal detection methods.

Sample size re-estimation: recent developments and practical considerations.

Interim findings of a clinical trial often will be useful for increasing the sample size if necessary to provide the required power against the null hypothesis when the alternative hypothesis is true. Strategies for carrying out the interim examination that have been described over the past several years include "internal pilot studies", blinded interim sample size adjustment and conditional power. Simulation studies show that the alternative methods generally control the type I error rate satisfactorily, although the power properties are more variable. The important issues associated with sample size re-estimation are strategic, not numeric. Clearly expressed regulatory preferences suggest that methods not requiring unblinding the data before completion of the trial would be most appropriate. Extending a trial has its risks. The investigators/patients enrolled later in the course of a trial are not necessarily the same as those recruited/entered early. Re-activating the enrollment process may be sufficiently complicated and expensive to justify enrolling more investigators/patients at the outset. Since sample size re-estimation adjusts the sample size on the basis of variability while efficacy interim analysis adjusts the sample size based on the basis of estimated effect size, both principles can be used in the same trial. Sample size re-estimation may not be advisable for trials involving extended follow-up of individual patients or, more generally, when the follow-up time is long relative to the recruitment time. In such cases, it may be better to estimate the sample size conservatively and introduce an interim efficacy evaluation.

A practical approach for evaluating population and individual bioequivalence.

Pharmacokinetic measurements provided by subjects to each of two formulations of a drug have a joint distribution that can be characterized by parameters reflecting scale and correlation as well as location. The bioavailability of the formulations can be expressed in terms of the means of the marginal distributions, their means and variances, or the marginal means and variances and the joint correlation. These expressions correspond, respectively, to 'average', 'population', and 'individual' bioequivalence when the joint distribution of the measurements is bivariate normal. Current proposals for assessing the degree of bioequivalence of two formulations are based on statistics that are composites of variance components and squares of expected mean differences from a mixed linear model. There are technical and practical issues associated with these proposals, particularly that they require more complicated designs than the familiar 2x2 cross-over. This paper describes an alternative approach that can be applied with standard 2x2 cross-over designs, and that provides evaluations of population and individual bioequivalence that should be adequate for all practical clinical purposes. The approach is based on easily computed correlation and regression coefficients whose statistical properties under normality are well known and for which non-parametric and robust alternatives exist when normality cannot be assumed. The approach yields conclusions consistent with those obtained by the current proposals when applied to data sets supplied by the FDA. In the cases where the conclusions do not match, the new approach appears to be more consistent with the data.

PhRMA perspective on population and individual bioequivalence.

The Food and Drug Administration (FDA) issued a second-draft guidance in August 1999 on the subject of in vivo bioequivalence, which is based on the concepts of individual and population bioequivalence (IBE and PBE, respectively). The intention of this guidance is to replace the 1992 guidance that requires that in vivo bioequivalence be demonstrated by average bioequivalence (ABE). Although the concepts of population and individual bioequivalence are intuitively reasonable, a detailed review of the literature has not uncovered clinical evidence to justify the additional burden to the innovator and generic companies as well as the consumer that the new guidelines would impose. The criteria for bioequivalence described in the draft guidance employ aggregate statistics that combine information about differences in bioavailability between formulation means and differences in bioavailability variation of formulations between and within subjects. The purely technical aspects of the statistical approach are reasonably sound. However, PhRMA believes that important operational issues remain that need to be resolved before any changes to current practice are implemented. PhRMA believes that the ideals of prescribability and switchability are intuitively reasonable, but it is uncertain of the extent to which the proposed guidance can achieve these goals. It is not clear whether the attainment of such goals is necessary in the evaluation of bioequivalence given the role this plays in drug development, and the lack of clinical evidence argues against a pressing need to change current practice. PhRMA is concerned that the trade-off offered by the aggregate criteria may ultimately represent more harm than good to the public interest. PhRMA recommends more rigorous evaluation of methods based on two-way crossover designs before moving to methods that require more complex designs. One such method is identified herein and contains procedures for estimating prescribability and switchability. The possibility of a phase-in or trial period to collect replicate crossover data to further evaluate IBE and PBE and possibly allow market access based on these criteria as they are being evaluated has been proposed. PhRMA believes this is unprecedented and will offer little additional information beyond that which can be obtained by simulation or has already been collected by the FDA. Simulation studies have the advantage of allowing evaluation of the sensitivity of various procedures to represent the data patterns as created within the simulation. Operating characteristics by which proposed criteria can be adequately judged have not yet been defined. The limitations of ABE for highly variable drugs and narrow therapeutic drugs are well appreciated and may be addressed by means other than a wholesale change in the current criteria.

Serum prostate-specific antigen as a predictor of prostate volume in men with benign prostatic hyperplasia.

OBJECTIVES: To assess the utility of prostate-specific antigen (PSA) as a predictor of prostate volume by characterizing the relationship between prostate volume and serum PSA in men with symptomatic benign prostatic hyperplasia (BPH) and no evidence of prostate cancer, stratified by decade of life. METHODS: Placebo-controlled multicenter trials in patients with BPH and a safety study in normal young men provided baseline measurements of serum PSA and prostate volume. The analyses included patients with a baseline prostate volume measured by either transrectal ultrasound (TRUS) or magnetic resonance imaging and baseline serum PSA. A common central laboratory was used for all but one of the individual studies; both laboratories used the Hybritech method. Patients 80 years of age or older were excluded. Patients with a baseline serum PSA greater than 10 ng/mL were excluded to reduce the likelihood of including occult prostate cancer cases. The patients in the BPH trials were screened at baseline by digital rectal examination (DRE) and serum PSA. Those with suspicious findings underwent TRUS-guided biopsy; only patients with negative biopsies are included in these analyses. RESULTS: The analyses included 4627 patients, 4448 from the BPH trials and 179 from the safety study. The men in the BPH trials were older (mean age+SE, 63.7+0.10 years) than the men in the safety study (mean age + SE, 30.8+/-0.43), had larger prostates (mean volume+/-SE, 43.7+/-0.38 mL versus 26.3+/-0.49 mL in the safety study), and had higher serum PSA values (mean+/-SE, 2.6+/-0.03 ng/mL versus 0.7+/-0.39 ng/mL in the safety study). The relationship between prostate volume and serum PSA was evaluated using only the BPH trial data. Prostate volume and serum PSA have an age-dependent log-linear relationship (ie, their logarithms are linearly related, and the parameters of the relationship depend on age). Older men tend to have a steeper rate of increase in prostate volume with increasing serum PSA (P < 0.00 for differences between slopes), and there was a slight tendency for PSA density to increase with age. Receiver operating characteristic (ROC) curves were constructed to evaluate the ability of serum PSA to predict threshold prostate sizes in men with BPH. The ROC curve analyses revealed that PSA had good predictive value for assessing prostate volume, with areas under the curve ranging from 0.76 to 0.78 for various prostate volume cutoff points (30, 40, and 50 mL). Conclusions. Prostate volume is strongly related to serum PSA in men with BPH and no evidence of prostate cancer, and the relationship depends on age. Since treatment outcome or risk of long-term complications depend on baseline prostate volume, serum PSA can estimate the degree of prostate enlargement sufficiently accurately to be useful for therapeutic decision making. To achieve a specificity of 70% while maintaining a sensitivity between 65% and 70%, approximate age-specific criteria for detecting men with prostate glands exceeding 40 mL are PSA > 1.6 ng/mL, >2.0 ng/mL, and >2.3 ng/mL for men with BPH in their 50s, 60s, and 70s, respectively.

Multi-centre trial analysis revisited.

Analyses of multi-centre trials must consider the effects of the individual centres and the possibility of non-constancy of treatment effect differences among centres. This usually means an ANOVA with terms for centres, treatments, and centre x treatment interactions in practice, at least in the U.S.A. Empirical and conventional Bayes methods provide attractive alternatives to conventional ANOVAs for analysing and reporting the findings from multi-centre trials and do not require more restrictive assumptions than the ANOVA approach. These approaches require regarding the centre effects as random instead of fixed, a view which often will reasonably describe outcomes of clinical trials in spite of the fact that the individual centres certainly do not comprise a random sample of all possible centres. The components of these approaches are well understood and have been employed in related applications such as meta-analysis. Combining them in a way that makes their application to routine multi-centre trial analysis relatively straightforward does not appear to have been described previously, and is what forms the topic of this paper. The empirical Bayes approach leads to useful graphical displays, including one with the data superimposed on probability contours of the joint distribution of the individual centre means and standard deviations, which provides a handy way to identify possible outliers. Covariates can be incorporated without difficulty. The Bayes approach, implemented with Gibbs sampling, provides a convenient way to construct posterior and predictive distributions for a variety of useful statistics. We compare the result of empirical and conventional Bayes analyses with the result of fixed and mixed model ANOVAs applied to data from a multi-centre trial.

Cholesterol reduction yields clinical benefit: impact of statin trials.

BACKGROUND: We determined the effect of incorporating the results of eight recently published trials of Hmg CoA reductase inhibitors ("statins") on the conclusions from our previously published meta-analysis regarding the clinical benefit of cholesterol lowering. METHODS AND RESULTS: We used the same analytic approach as in our previous investigation, separating the specific effects of cholesterol lowering from the effects attributable to the different types of intervention studied. The reductions in coronary heart disease (CHD) and total mortality risk observed for the statins fell near the predictions from our earlier meta-analysis. Including the statin trial findings into the calculations led to a prediction that for every 10 percentage points of cholesterol lowering, CHD mortality risk would be reduced by 15% (P<.001), and total mortality risk would be reduced by 11% (P<.001), as opposed to the values of 13% and 10%, respectively, reported previously. Cholesterol lowering in general and by the statins in particular does not increase non-CHD mortality risk. CONCLUSIONS: Adding the results from the statin trials confirmed our original conclusion that lowering cholesterol is clinically beneficial. The relationships (slope) between cholesterol lowering and reduction in CHD and total mortality risk became stronger, and the standard error of the estimated slopes decreased by about half. Use of statins does not increase non-CHD mortality risk. The effect of the statins on CHD and total mortality risk can be explained by their lipid-lowering ability and appears to be directly proportional to the degree to which they lower lipids.

Modifying the design of ongoing trials without unblinding.

Conventional group sequential designs provide an objective basis for reducing the sample size of a trial if the difference between the treatments is much more or much less than anticipated. The flexibility of group sequential designs can be enhanced by allowing the sample size to increase when the variability turns out greater than expected. This can be accomplished by examining the variability before unblinding the data at the first stage of the trial. Depending on the result of this examination, the trial may continue as planned, or the design may change in various ways, for example, by increasing the sample size or by changing the number of stages or the scheduling of the interim analyses. The effect of this adaptive flexibility on the error rates turns out as one would expect from the findings for fixed-sample designs: no material impact on the type I error rate and an effect on the power that depends on the final total sample size.

Discussion of individual bioequivalence by M.-L. Chen.

We review and discuss some technical statistical issues and practical implementation issues associated with the use of individual as opposed to population average bioequivalence to express the relative bioavailabilities of alternative formulations of a drug. A number of promising methods for addressing individual bioequivalence have been described. Individual bioequivalence calculations can be done using standard crossover designs, although more sophisticated assessments that compare test-reference variability to reference-reference variability require more complex designs. However, more experience about the clinical implications of various degrees of individual bioinequivalence as expressed by various metrics should be accumulated before definitive regulations are set forth mandating the use of individual bioequivalence for expressing relative bioavailabilities.

Prostate volume predicts outcome of treatment of benign prostatic hyperplasia with finasteride: meta-analysis of randomized clinical trials.

OBJECTIVES: Six randomized clinical trials have compared at least 1 year of 5 mg finasteride to placebo in the treatment of clinical benign prostatic hyperplasia (BPH). The findings for the 2601 men in these trials provide an opportunity to investigate the heterogeneity of the effects seen in the individual studies and to identify pretreatment predictors of outcomes as expressed by symptoms or peak urinary flow rates. METHODS: A formal meta-analysis using an Empirical Bayes approach employed data from all finasteride studies which included the Phase III trials in North America and Internationally, the Prospect, Early Intervention, and SCARP trials, and the Veterans Administration Cooperative Study which compared terazosin, finasteride, and the combination of these two drugs. A pooled analysis was also undertaken on the combined dataset. RESULTS: The effect of finasteride treatment on improvements in total symptom severity, frequency score, and peak urinary flow rate was consistent across all six trials and similar among men with similar prostate volumes at baseline. Symptom severity improved by 1.8 points (95% confidence interval [CI], 0.7 to 2.9) in men with prostate volumes less than 20 cc (n = 72), while the improvement was 2.8 points (95% CI, 2.1 to 3.5) for men with volumes greater than 60 cc (n = 272) on the Quasi-IPSS Scale (range 0 to 30). Similarly, improvements in peak urinary flow rate ranged from 0.89 mL/s (95% CI, -0.05 to 1.83) for men with prostate volumes less than 20 cc to 1.84 mL/s (95% CI, 1.37 to 2.30) in men with volumes greater than 60 cc. The difference in the magnitude of improvement between finasteride and placebo becomes significant (that is, no overlap in 95% CI) for men with a baseline prostate volume assessed by either transrectal ultrasonography or magnetic resonance imaging of greater than 40 cc, which encompasses approximately 50% of the entire population. Baseline prostate volume is a key predictor of treatment outcomes: approximately 80% of the variation in the treatment effects noted between studies could be attributed to differences in mean prostate volumes at baseline. Variation in entry criteria results in large differences in baseline symptom severity status, prostate volume, and consequently apparent inconsistencies in the overall outcomes of these trials. CONCLUSIONS: This meta-analysis suggests that finasteride is most effective in men with large prostates. Men with small prostates may not be suitable candidates for finasteride therapy for BPH. The need for a careful reevaluation of the definitions and terminology used when discussing urination problems is apparent.