Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past.

Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.

Effects of ritonavir-boosted lopinavir on the pharmacokinetics of quinine.

The centuries-old antimalarial drug, quinine, continues to play a critical role in the treatment of severe falciparum malaria and uncomplicated malaria in pregnant women. It shares cytochrome P450 (CYP )-mediated metabolic pathways with several commonly used antiretroviral drugs, raising the potential for clinically important drug­drug interactions. A phase I pharmacokinetic study was conducted to assess the impact of long-term use of ritonavir-boosted lopinavir (LPV/r) on quinine pharmacokinetics in healthy volunteers. LP V/r significantly decreased the exposure of quinine and its major active metabolite, 3-hydroxyquinine, in both total and free (unbound) forms. These findings highlight the complex nature of the influence exerted by LPV/r on several of the drug-metabolizing enzymes involved in quinine disposition,including CYP 3A4, UDP-glucuronosyltransferase (UG T), and P-glycoprotein (P-gp). A decline in quinine exposure may compromise clinical efficacy. Further studies are warranted to assess changes in quinine pharmacokinetics and treatment outcomes in patients with acute malaria receiving antiretroviral therapy that includes LPV/r.

Accelerator mass spectrometry measurement of intracellular concentrations of active drug metabolites in human target cells in vivo.

Accelerator mass spectrometry (AMS) is an ultrasensitive technique to detect radiolabeled compounds. We administered a microdose (100 µg) of (14)C-labeled zidovudine (ZDV) with or without a standard unlabeled dose (300 mg) to healthy volunteers. Intracellular ZDV-triphosphate (ZDV-TP) concentration was measured using AMS and liquid chromatography-tandem mass spectrometry (LC/MS/MS). AMS analysis yielded excellent concordance with LC/MS/MS and was 30,000-fold more sensitive. The kinetics of intracellular ZDV-TP formation changed several-fold over the dose range studied (100 µg-300 mg). AMS holds promise as a tool for quantifying intracellular drug metabolites and other biomediators in vivo.

Effect of semen sampling frequency on seminal antiretroviral drug concentration.

Study of male genital tract (MGT) pharmacology is relevant to the treatment of prostatitis, prostate cancer, infertility, and seminal human immunodeficiency virus transmission. However, the time course of drug concentrations in the MGT is largely unknown. To determine the feasibility of frequent semen sampling in assessing the pharmacokinetics of the MGT, we administered efavirenz, indinavir, and zidovudine to subjects to achieve steady-state levels and then collected semen samples at sequentially decreasing ejaculation intervals. The volume of seminal plasma decreased from 4.0 (1.2-5.1) ml (median with range) at 48 h after the baseline ejaculation to 0.72 (0.45-1.6) ml 1 h after a previous ejaculation, which was still adequate for drug concentration assessment. The seminal fructose concentration also decreased. However, the concentration of prostate-specific antigen and all three drugs did not decrease, even if the ejaculation intervals decreased to 1 h. Thus, semi-intensive semen sampling can be used to assess MGT pharmacokinetics.

Quantitative imaging and sigmoidoscopy to assess distribution of rectal microbicide surrogates.

Understanding the distribution of microbicide and human immunodeficiency virus (HIV) within the gastrointestinal tract is critical to development of rectal HIV microbicides. A hydroxyethylcellulose-based microbicide surrogate or viscosity-matched semen surrogate, labeled with gadolinium-DTPA (diethylene triamine pentaacetic acid) and 99mTechnetium-sulfur colloid, was administered to three subjects under varying experimental conditions to evaluate effects of enema, coital simulation, and microbicide or semen simulant over 5 h duration. Quantitative assessment used single photon emission computed tomography (SPECT)/computed tomography (CT) and magnetic resonance imaging (MRI) imaging, and sigmoidoscopic sampling. Over 4 h, radiolabel migrated cephalad in all studies by a median (interquartile range) of 50% (29-102%; P<0.001), as far as the splenic flexure (approximately 60 cm) in 12% of studies. There was a correlation in concentration profile between endoscopic sampling and SPECT assessments. HIV-sized particles migrate retrograde, 60 cm in some studies, 4 h after simulated ejaculation in our model. SPECT/CT, MRI, and endoscopy can be used quantitatively to facilitate rational development of microbicides for rectal use.

The effect of an exercise program during hemodialysis on dialysis efficacy, blood pressure and quality of life in end-stage renal disease (ESRD) patients.

AIM: We wished to determine if an 8-week program of exercise during dialysis in end-stage renal disease (ESRD) patients would increase urea removal (enhance dialysis efficacy) with subsequent improvements in work performance and perception of quality of life, and/or alterations in cardiovascular status. METHODS: Self-care hemodialysis patients (EX, n = 6) performed cycle ergometry exercise 3 times per week during their dialysis session at 40-50% maximal work capacity for 15 min during each of the first 3 hours of dialysis and were matched for age, protein catabolism rate, and WLmax with a CON group (n = 7). Dialysis efficacy was measured using serum urea clearance (Kt/V) and dialysate urea clearance (DUC) during the first 2 hours of dialysis. Resting blood pressure was monitored on a sessional basis, pre- and postdialysis and during exercise in the EX group. QOL, measured using the SF-36 questionnaire, and WLmax were determined prior to and at 4 and 8 weeks of the exercise program. RESULTS: DUC was significantly elevated in the EX group at the end of the exercise program, but was of insufficient magnitude to result in an overall increase in Kt/V. DUC decreased in the CON group but Kt/V remained unchanged. No changes in resting blood pressure occurred in either group over the course of the study, however, pulse pressure tended to increase in the CON group but decrease in the EX group, indicating a potential beneficial adaptation of the cardiovascular system in patients undergoing an exercise program. The exercise program had no effect on QOL scores and this was most likely due to the short duration of the exercise program and high-functioning level of the population studied as compared to normative data for this patient population. We also found that 33% of the exercise sessions in the 3rd hour of dialysis were not performed due to hypotensive events. CONCLUSION: Exercise during dialysis enhanced dialysate urea removal but not serum urea clearance. Alterations in the modality and the timing of exercise during dialysis may be required to elicit increases in serum urea clearance. It is also recommended that exercise during dialysis be performed during the first 2 hours of dialysis.

The presence of lead decreases the availability of meso-2, 3-dimercaptosuccinic acid for analysis in the monobromobimane assay.

meso-2,3-Dimercaptosuccinic acid is a suitable chelating agent for routine pharmacotherapy of lead poisoning in children. Administration of meso-2,3-dimercaptosuccinic acid presumably permits complexation of lead in vivo, allowing excretion through urine or feces. Quantification of the lead is achieved independently from the analysis of meso-2,3-dimercaptosuccinic acid and metabolites from the monobromobimane assay. To date, no direct chemical characterization of the Pb species excreted in urine has been successful. Pharmacokinetic correlation of lead excretion with excretion of meso-2,3-dimercaptosuccinic acid and metabolites has been utilized as an indirect method to draw conclusions regarding the identity of the active chelating agent. In this study, we hypothesized that the Pb-coordinated thiols are not reactive with respect to monobromobimane, and thus, the active chelator contained in the lead complex escapes detection. We performed variations of the assay and found that (1) the fluorescence detector response for the meso-2,3-dimercaptosuccinic acid-monobromobimane adduct was clearly attenuated as a function of added Pb, (2) when meso-2, 3-dimercaptosuccinic acid and monobromobimane were mixed prior to the addition of lead, the lead had no effect on detector response, (3) the addition of dithiothreitol does not affect the ability of Pb to react with meso-2,3-dimercaptosuccinic acid and verifies that oxidation of meso-DMSA had not occurred, and (4) the addition of ethylenediaminetetraacetic acid to the assay reverses the result found in point 1, presumably through trans chelation of the Pb-DMSA complex. Indirect quantification of the Pb-DMSA complexes found in urine might be accomplished through modification of the standard monobromobimane assay for analysis of meso-2,3-dimercaptosuccinic acid.