Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C

Background Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region. Methods Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis. Results Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B. Conclusions Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.

Partial reconstruction of the trajectories of a discretely observed branching diffusion with immigration and an application to inference

In this treatise we consider finite systems of branching particles where the particles move independently of each other according to d-dimensional diffusions. Particles are killed at a position dependent rate, leaving at their death position a random number of descendants according to a position dependent reproduction law. In addition particles immigrate at constant rate (one immigrant per immigration time). A process with above properties is called a branching diffusion withimmigration (BDI). In the first part we present the model in detail and discuss the properties of the BDI under our basic assumptions. In the second part we consider the problem of reconstruction of the trajectory of a BDI from discrete observations. We observe positions of the particles at discrete times; in particular we assume that we have no information about the pedigree of the particles. A natural question arises if we want to apply statistical procedures on the discrete observations: How can we find couples of particle positions which belong to the same particle? We give an easy to implement 'reconstruction scheme' which allows us to redraw or 'reconstruct' parts of the trajectory of the BDI with high accuracy. Moreover asymptotically the whole path can be reconstructed. Further we present simulations which show that our partial reconstruction rule is tractable in practice. In the third part we study how the partial reconstruction rule fits into statistical applications. As an extensive example we present a nonparametric estimator for the diffusion coefficient of a BDI where the particles move according to one-dimensional diffusions. This estimator is based on the Nadaraya-Watson estimator for the diffusion coefficient of one-dimensional diffusions and it uses the partial reconstruction rule developed in the second part above. We are able to prove a rate of convergence of this estimator and finally we present simulations which show that the estimator works well even if we leave our set of assumptions.

Diffusion boundary layers ameliorate the negative effects of ocean acidification on the temperate coralline macroalga Arthrocardia corymbosa

Anthropogenically-modulated reductions in pH, termed ocean acidification, could pose a major threat to the physiological performance, stocks, and biodiversity of calcifiers and may devalue their ecosystem services. Recent debate has focussed on the need to develop approaches to arrest the potential negative impacts of ocean acidification on ecosystems dominated by calcareous organisms. In this study, we demonstrate the role of a discrete (i.e. diffusion) boundary layer (DBL), formed at the surface of some calcifying species under slow flows, in buffering them from the corrosive effects of low pH seawater. The coralline macroalga Arthrocardia corymbosa was grown in a multifactorial experiment with two mean pH levels (8.05 'ambient' and 7.65 a worst case 'ocean acidification' scenario projected for 2100), each with two levels of seawater flow (fast and slow, i.e. DBL thin or thick). Coralline algae grown under slow flows with thick DBLs (i.e., unstirred with regular replenishment of seawater to their surface) maintained net growth and calcification at pH 7.65 whereas those in higher flows with thin DBLs had net dissolution. Growth under ambient seawater pH (8.05) was not significantly different in thin and thick DBL treatments. No other measured diagnostic (recruit sizes and numbers, photosynthetic metrics, %C, %N, %MgCO3) responded to the effects of reduced seawater pH. Thus, flow conditions that promote the formation of thick DBLs, may enhance the subsistence of calcifiers by creating localised hydrodynamic conditions where metabolic activity ameliorates the negative impacts of ocean acidification.

Seawater carbonate chemistry, cell numbers and growth rate during experiments with dinoflagellates, 2007

The effects of dissolved inorganic carbon (DIC) on the growth of 3 red-tide dinoflagellates (Ceratium lineatum, Heterocapsa triquetra and Prorocentrum minimum) were studied at pH 8.0 and at higher pH levels, depending upon the pH tolerance of the individual species. The higher pH levels chosen for experiments were 8.55 for C. lineatum and 9.2 for the other 2 species. At pH 8.0, which approximates the pH found in the open sea, the maximum growth in all species was maintained until the total DIC concentration was reduced below ~0.4 and 0.2 mM for C. lineatum and the other 2 species, respectively. Growth compensation points (concentration of inorganic carbon needed for maintenance of cells) were reached at ~0.18 and 0.05 mM DIC for C. lineatum and the other 2 species, respectively. At higher pH levels, maximum growth rates were lower compared to growth at pH 8, even at very high DIC concentrations, indicating a direct pH effect on growth. Moreover, the concentration of bio-available inorganic carbon (CO2 + HCO3-) required for maintenance as well as the half-saturation constants were increased considerably at high pH compared to pH 8.0. Experiments with pH-drift were carried out at initial concentrations of 2.4 and 1.2 mM DIC to test whether pH or DIC was the main limiting factor at a natural range of DIC. Independent of the initial DIC concentrations, growth rates were similar in both incubations until pH had increased considerably. The results of this study demonstrated that growth of the 3 species was mainly limited by pH, while inorganic carbon limitation played a minor role only at very high pH levels and low initial DIC concentrations.

Seawater carbonate chemistry and giant kelp Macrocystis pyrifera reproduction processes during experiments, 2011

The worldwide effects of ocean acidification (OA) on marine species are a growing concern. In temperate coastal seas, seaweeds are dominant primary producers that create complex habitats and supply energy to higher trophic levels. Studies on OA and macroalgae have focused on calcifying species and adult stages but, critically, they have overlooked the microscopic stages of the reproductive life cycle, which, for other anthropogenic stress e.g. UV-B radiation, are the most susceptible life-history phase. Also, environmental cues and stressors can cause changes in the sex ratio which has implications for the mating system and recruitment success. Here, we report the effects of pH (7.59-8.50) on meiospore germination and sex determination for the giant kelp, Macrocystis pyrifera (Laminariales), in the presence and absence of additional dissolved inorganic carbon (DIC). Lowered pH (7.59-7.60, using HCl-only) caused a significant reduction in germination, while added DIC had the opposite effect, indicating that increased CO2 at lower pH ameliorates physiological stress. This finding also highlights the importance of appropriate manipulation of seawater carbonate chemistry when testing the effects of ocean acidification on photosynthetic organisms. The proportion of male to female gametophytes did not vary significantly between treatments suggesting that pH was not a primary environmental modulator of sex. Relative to the baseline (pH 8.19), gametophytes were 32% larger under moderate OA (pH 7.86) compared to their size (10% increase) under extreme OA (pH 7.61). This study suggests that metabolically-active cells can compensate for the acidification of seawater. This homeostatic function minimises the negative effects of lower pH (high H+ ions) on cellular activity. The 6-9% reduction in germination success under extreme OA suggests that meiospores of M.pyrifera may be resistant to future ocean acidification.

Seawater carbonate chemistry and growth, reproduction of calcifying and non-calcifying epibionts of a brown macroalga in a laboratory experiment

Seaweeds are key species of the Baltic Sea benthic ecosystems. They are the substratum of numerous fouling epibionts like bryozoans and tubeworms. Several of these epibionts bear calcified structures and could be impacted by the high pCO2 events of the late summer upwellings in the Baltic nearshores. Those events are expected to increase in strength and duration with global change and ocean acidification. If calcifying epibionts are impacted by transient acidification as driven by upwelling events, their increasing prevalence could cause a shift of the fouling communities toward fleshy species. The aim of the present study was to test the sensitivity of selected seaweed macrofoulers to transient elevation of pCO2 in their natural microenvironment, i.e. the boundary layer covering the thallus surface of brown seaweeds. Fragments of the macroalga Fucus serratus bearing an epibiotic community composed of the calcifiers Spirorbis spirorbis (Annelida) and Electra pilosa (Bryozoa) and the non-calcifier Alcyonidium hirsutum (Bryozoa) were maintained for 30 days under three pCO2 conditions: natural 460±59 µatm, present-day upwelling1193±166 µatm and future upwelling 3150±446 µatm. Only the highest pCO2 caused a significant reduction of growth rates and settlement of S. spirorbis individuals. Additionally, S. spirorbis settled juveniles exhibited enhanced calcification of 40% during daylight hours compared to dark hours, possibly reflecting a day-night alternation of an acidification-modulating effect by algal photosynthesis as opposed to an acidification-enhancing effect of algal respiration. E. pilosa colonies showed significantly increased growth rates at intermediate pCO2 (1193 µatm) but no response to higher pCO2. No effect of acidification on A. hirsutum colonies growth rates was observed. The results suggest a remarkable resistance of the algal macro-epibionts to levels of acidification occurring at present day upwellings in the Baltic. Only extreme future upwelling conditions impacted the tubeworm S. spirorbis, but not the bryozoans.

Contrasting effects of ocean acidification on reproduction in reef fishes

Differences in the sensitivity of marine species to ocean acidification will influence the structure of marine communities in the future. Reproduction is critical for individual and population success, yet is energetically expensive and could be adversely affected by rising CO2 levels in the ocean. We investigated the effects of projected future CO2 levels on reproductive output of two species of coral reef damselfish, Amphiprion percula and Acanthochromis polyacanthus. Adult breeding pairs were maintained at current-day control (446 µatm), moderate (652 µatm) or high CO2 (912 µatm) for a 9-month period that included the summer breeding season. The elevated CO2 treatments were consistent with CO2 levels projected by 2100 under moderate (RCP6) and high (RCP8) emission scenarios. Reproductive output increased in A. percula, with 45-75 % more egg clutches produced and a 47-56 % increase in the number of eggs per clutch in the two elevated CO2 treatments. In contrast, reproductive output decreased at high CO2 in Ac. polyacanthus, with approximately one-third as many clutches produced compared with controls. Egg survival was not affected by CO2 for A. percula, but was greater in elevated CO2 for Ac. polyacanthus. Hatching success was also greater for Ac. polyacanthus at elevated CO2, but there was no effect of CO2 treatments on offspring size. Despite the variation in reproductive output, body condition of adults did not differ between control and CO2 treatments in either species. Our results demonstrate different effects of high CO2 on fish reproduction, even among species within the same family. A greater understanding of the variation in effects of ocean acidification on reproductive performance is required to predict the consequences for future populations of marine organisms.

Temperature is the evil twin: Effects of increased temperature and ocean acidification on reproduction in a reef fish

Reproduction in many organisms can be disrupted by changes to the physical environment, such as those predicted to occur during climate change. Marine organisms face the dual climate change threats of increasing temperature and ocean acidification, yet no studies have examined the potential interactive effects of these stressors on reproduction in marine fishes. We used a long-term experiment to test the interactive effects of increased temperature and CO2 on the reproductive performance of the anemonefish, Amphiprion melanopus. Adult breeding pairs were kept for 10 months at three temperatures, 28.5°C (+0.0°C), 30.0°C (+1.5°C) and 31.5°C (+3.0°C), cross-factored with 3 CO2 levels, a current day control (417 µatm) and moderate (644 µatm) and high (1134 µatm) treatments consistent with the range of CO2 projections for the year 2100 under RCP8.5. We recorded each egg clutch produced during the breeding season, the number of eggs laid per clutch, average egg size, fertilization success, survival to hatching, hatchling length and yolk provisioning. Adult body condition, hepatosomatic index, gonadosomatic index, and plasma 17beta-estradiol concentrations were measured at the end of the breeding season to determine the effect of prolonged exposure to increased temperature and elevated CO2 on adults, and to examine potential physiological mechanisms for changes in reproduction. Temperature had by far the stronger influence on reproduction, with clear declines in reproduction occurring in the +1.5°C treatment and ceasing altogether in the +3.0°C treatment. In contrast, CO2 had a minimal effect on the majority of reproductive traits measured, but caused a decline in offspring quality in combination with elevated temperature. We detected no significant effect of temperature or CO2 on adult body condition or hepatosomatic index. Elevated temperature had a significant negative effect on plasma 17beta-estradiol concentrations, suggesting that declines in reproduction with increasing temperature were due to the thermal sensitivity of reproductive hormones rather than a reduction in energy available for reproduction. Our results show that elevated temperature exerts a stronger influence than high CO2 on reproduction in A. melanopus. Understanding how these two environmental variables interact to affect the reproductive performance of marine organisms will be important for predicting the future impacts of climate change.

Tables of [square root sign] 1 - r² and 1 - r² for use in partial correlation and in trigonometry,

Photo-lithoprint reproduction. Ann Arbor, Mich., Edwards Bros., 1947.

An elementary investigation of the theory of numbers, : with its application to the indeterminate and Diophantine analysis, the analytical and geometrical division of the circle, and several other curious algebraical and arithmetical problems. /

Available on demand as hard copy or computer file from Cornell University Library.

Properties of a unique mutant of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus that exhibits a partial many polyhedra and few polyhedra phenotype on extended serial passaging in suspension cell cultures

Serial passaging of wild-type Helicoverpa armigera, single-nucleocapsid (HaSNPV) in H. zea (HzAMI) illsect Cell Cultures results ill rapid selection for the few polyhedra (FP) phenotype. A unique HaSNPV mutant (ppC19) was isolated through plaque purification that exhibited a partial many polyhedra (MP) and FP phenotype. Oil serial passaging in suspension cell cultures, ppC19 produced fivefold more polyhedra than a typical FP mutant (FP8AS) but threefold less polyhedra than the wild-type virus. Most importantly, the polyhedra of ppC19 exhibited MP-like virion occlusion. Furthermore, ppC19 produced the same amount of budded virus (BV) as the FP mutant, which was fivefold higher than that of the wild-type virus. This selective advantage was likely to explain its relative stability in polyhedra production for six passages when compared with the wild-type Virus. However, subsequent passaging of ppC19 resulted in a steel) decline in both BV and polyhedra yields, which was also experienced by FP8AS and the wild-type virus Lit high passage numbers. Genomic deoxyribonueleic Licid profiling of the latter suggested that defective interfering particles (DIPS) were implicated in this phenomenon and represented another Undesirable mutation during serial passaging of HaSNPV Hence, a strategy to isolate HaSNPV Clones that exhibited MP-like polyhedra production but FP-like BV production, coupled with low multiplicities of infection during scale-up to avoid accumulation of DIPS, could prove commerically invaluable.

Roseate spoonbill reproduction as an indicator for restoration of the Everglades and the Everglades estuaries

Ecological monitoring is key to successful ecosystem restoration. Because all components within an ecosystem cannot be monitored, it is important to select indicators that are representative of the system, integrate system responses, clearly respond to system change, can be effectively and efficiently monitored, and are easily communicated. The roseate spoonbill is one ecological indicator species that meets these criteria within the Everglades ecosystem. Monitoring of roseate spoonbills in Florida Bay over the past 70 years has shown that aspects of this species’ reproduction respond to changes in hydrology and corresponding changes in prey abundance and availability. This indicator uses nesting location, nest numbers and nesting success in response to food abundance and availability. In turn, prey abundance is a function of hydrological conditions (especially water depth) and salinity. Metrics and targets for these performance measures were established based on previous findings. Values of each metric were translated into indices and identified as stoplight colors with green indicating that a given target has been met, yellow indicating that conditions are below the target, but within an acceptable range of it, and red indicating the measure is performing poorly in relation to the target.

Seawater carbonate chemistry and reproduction of the two calanoid copepods Centropages typicus and Temora longicornis in a laboratory experiment

Some planktonic groups suffer negative effects from ocean acidification (OA), although copepods might be less sensitive. We investigated the effect of predicted CO2 levels (range 480-750 ppm), on egg production and hatching success of two copepod species, Centropages typicus and Temora longicornis. In these short-term incubations there was no significant effect of high CO2 on these parameters. Additionally a very high CO2 treatment, (CO2 = 9830 ppm), representative of carbon capture and storage scenarios, resulted in a reduction of egg production rate and hatching success of C. typicus, but not T. longicornis. In conclusion, reproduction of C. typicus was more sensitive to acute elevated seawater CO2 than that of T. longicornis, but neither species was affected by exposure to CO2 levels predicted for the year 2100. The duration and seasonal timing of exposures to high pCO2, however, might have a significant effect on the reproduction success of calanoid copepods.

Seawater carbonate chemistry and cell numbers during experiments with dinoflagellates, 2007

The effects of dissolved inorganic carbon (DIC) on the growth of 3 red-tide dinoflagellates (Ceratium lineatum, Heterocapsa triquetra and Prorocentrum minimum) were studied at pH 8.0 and at higher pH levels, depending upon the pH tolerance of the individual species. The higher pH levels chosen for experiments were 8.55 for C. lineatum and 9.2 for the other 2 species. At pH 8.0, which approximates the pH found in the open sea, the maximum growth in all species was maintained until the total DIC concentration was reduced below ~0.4 and 0.2 mM for C. lineatum and the other 2 species, respectively. Growth compensation points (concentration of inorganic carbon needed for maintenance of cells) were reached at ~0.18 and 0.05 mM DIC for C. lineatum and the other 2 species, respectively. At higher pH levels, maximum growth rates were lower compared to growth at pH 8, even at very high DIC concentrations, indicating a direct pH effect on growth. Moreover, the concentration of bio-available inorganic carbon (CO2 + HCO3-) required for maintenance as well as the half-saturation constants were increased considerably at high pH compared to pH 8.0. Experiments with pH-drift were carried out at initial concentrations of 2.4 and 1.2 mM DIC to test whether pH or DIC was the main limiting factor at a natural range of DIC. Independent of the initial DIC concentrations, growth rates were similar in both incubations until pH had increased considerably. The results of this study demonstrated that growth of the 3 species was mainly limited by pH, while inorganic carbon limitation played a minor role only at very high pH levels and low initial DIC concentrations.

Seawater carbonate chemistry and reproduction of a coral reef fish in a laboratory experiment

Ocean acidification is predicted to negatively impact the reproduction of many marine species, either by reducing fertilization success or diverting energy from reproductive effort. While recent studies have demonstrated how ocean acidification will affect larval and juvenile fishes, little is known about how increasing partial pressure of carbon dioxide (pCO2) and decreasing pH might affect reproduction in adult fishes. We investigated the effects of near-future levels of pCO2 on the reproductive performance of the cinnamon anemonefish, Amphiprion melanopus, from the Great Barrier Reef, Australia. Breeding pairs were held under three CO2 treatments [Current-day Control (430 µatm), Moderate (584 µatm) and High (1032 µatm)] for a 9-month period that included the summer breeding season. Unexpectedly, increased CO2 dramatically stimulated breeding activity in this species of fish. Over twice as many pairs bred in the Moderate (67% of pairs) and High (55%) compared to the Control (27%) CO2 treatment. Pairs in the High CO2 group produced double the number of clutches per pair and 67% more eggs per clutch compared to the Moderate and Control groups. As a result, reproductive output in the High group was 82% higher than that in the Control group and 50% higher than that in the Moderate group. Despite the increase in reproductive activity, there was no difference in adult body condition among the three treatment groups. There was no significant difference in hatchling length between the treatment groups, but larvae from the High CO2 group had smaller yolks than Controls. This study provides the first evidence of the potential effects of ocean acidification on key reproductive attributes of marine fishes and, contrary to expectations, demonstrates an initially stimulatory (hormetic) effect in response to increased pCO2. However, any long-term consequences of increased reproductive effort on individuals or populations remain to be determined.