Impact of virus preparation quality on parvovirus filter performance

Virus‐removal filtration technology is commonly used in the manufacturing process for biologics to remove potential viral contaminants. Virus‐removal filters designed for retaining parvovirus, one of the smallest mammalian viruses, are considered an industry standard as they can effectively remove broad ranges of viruses. It has long been observed that the performance of virus filters can be influenced by virus preparations used in the laboratory scale studies (PDA, 2010 ). However, it remains unclear exactly what quality attributes of virus preparations are critical or indicative of virus filter performance as measured by effectiveness of virus removal and filter capacity consistency. In an attempt to better understand the relationship between virus preparation and virus filter performance, we have systematically prepared and analyzed different grades of parvovirus with different purity levels and compared their performance profiles on Viresolve® Pro parvovirus filters using four different molecules. Virus preparations used in the studies were characterized using various methods to measure DNA and protein content as well as the hydrodynamic diameter of virus particles. Our results indicate that the performance of Viresolve® Pro filters can be significantly impacted depending on the purity of the virus preparations used in the spike and recovery studies. More importantly, we have demonstrated that the purity of virus preparations is directly correlated to the measurable biochemical and biophysical properties of the virus preparations such as DNA and protein content and monodispersal status, thus making it possible to significantly improve the consistency and predictability of the virus filter performance during process step validations. Biotechnol. Bioeng. 2013; 110: 229–239. © 2012 Wiley Periodicals, Inc.     

An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution

A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models.     

Impacts of logging and conversion of rainforest to oil palm on the functional diversity of birds in Sundaland

Commercial selective logging and the conversion of primary and degraded forests to agriculture are the biggest threats to tropical biodiversity. Our understanding of the impacts of these disturbances and the resulting local extinctions on the functional roles performed by the remaining species is limited. We address this issue by examining functional diversity (FD), which quantifies a range of traits that affect a species' ecological role in a community as a single continuous metric. We calculated FD for birds across a gradient of disturbance from primary forest through intensively logged forest to oil palm plantations on previously forested land in Borneo, Southeast Asia, a hotspot of imperilled biodiversity. Logged rainforest retained similar levels of FD to unlogged rainforest, even after two logging rotations, but the conversion of logged forest to oil palm resulted in dramatic reductions in FD. The few remaining species in oil palm filled a disproportionately wide range of functional roles but showed very little clustering in terms of functional traits, suggesting that any further extinctions from oil palm would reduce FD even further. Determining the extent to which the changes we recorded were due to under‐utilization of resources within oil palm or a reduction in the resources present is an important next step. Nonetheless our study improves our understanding of the stability and resilience of functional diversity in these ecosystems and of the implications of land‐use changes for ecosystem functioning.     

Practical considerations in the study of spectral analysis of discrete processes

Abstract

Clock hour independent groups of young female rats received a series of 3 alternate day intra‐articular injections of methylprednisolone acetate. All rats lost body weight, but the change was minimal when the injections were given in the late afternoon (‐30.8 g) vs the night (‐42.4 g, P < .02). The data imply that methylprednisolone acetate, which is designed to be locally active in joint spaces, can be absorbed into the circulation and that the rate of absorption is subject to circadian control.     

Phytotoxicity induced by Phragmites australis: an assessment of phenotypic and physiological parameters involved in germination process and growth of receptor plant

This study investigated the possible phytotoxicity induced by Phargmites australis on phenotypic and physiological parameters of recipient plants with identification of major inhibitors in the donor plant. This was achieved using aqueous extracts of different organs and root exudates of P. australis in laboratory and greenhouse experiments with Lactuca sativa as the model test plant. The observed reduced liquid imbibition and altered resource mobilization in seeds of L. sativa, in particular an insufficient carbohydrate supply, demonstrated that the onset of germination might be negatively affected by phytotoxicity. Dose-response studies pointed out that oxidative stress through reactive oxygen species production could potentially cause the observed germination and seedling growth reductions. The osmotic effects by mannitol solution on germination as well as growth and physiology at a level of ?0.57 and ?0.45 bar, respectively, demonstrated that the results from aqueous plant extracts were partially induced by the osmotic potential on and above those levels. Overall, the relative strength of inhibition on measured parameters was the highest in leaf extract, followed by rhizome, root, stem, and inflorescence. Root exudates of P. australis also had negative impacts by reducing germination and growth of plant. High-performance liquid chromatography (HPLC) analysis revealed gallic acid, a potent phytotoxin, as a major compound with an order of leaf >inflorescence>rhizome>root>stem.     

Potential impacts on ecosystem services of land use transitions to second‐generation bioenergy crops in GB

We present the first assessment of the impact of land use change (LUC) to second‐generation (2G) bioenergy crops on ecosystem services (ES) resolved spatially for Great Britain (GB). A systematic approach was used to assess available evidence on the impacts of LUC from arable, semi‐improved grassland or woodland/forest, to 2G bioenergy crops, for which a quantitative ‘threat matrix’ was developed. The threat matrix was used to estimate potential impacts of transitions to either Miscanthus, short‐rotation coppice (SRC, willow and poplar) or short‐rotation forestry (SRF). The ES effects were found to be largely dependent on previous land uses rather than the choice of 2G crop when assessing the technical potential of available biomass with a transition from arable crops resulting in the most positive effect on ES. Combining these data with constraint masks and available land for SRC and Miscanthus (SRF omitted from this stage due to lack of data), south‐west and north‐west England were identified as areas where Miscanthus and SRC could be grown, respectively, with favourable combinations of economic viability, carbon sequestration, high yield and positive ES benefits. This study also suggests that not all prospective planting of Miscanthus and SRC can be allocated to agricultural land class (ALC) ALC 3 and ALC 4 and suitable areas of ALC 5 are only minimally available. Beneficial impacts were found on 146 583 and 71 890 ha when planting Miscanthus or SRC, respectively, under baseline planting conditions rising to 293 247 and 91 318 ha, respectively, under 2020 planting scenarios. The results provide an insight into the interplay between land availability, original land uses, bioenergy crop type and yield in determining overall positive or negative impacts of bioenergy cropping on ecosystems services and go some way towards developing a framework for quantifying wider ES impacts of this important LUC.     

Local contagion and regional compression: habitat selection drives spatially explicit,multiscale dynamics of colonisation in experimental metacommunities

Habitat selection, including oviposition site choice, is an important driver of community assembly in freshwater systems. Factors determining patch quality are assessed by many colonising organisms and affect colonisation rates, spatial distribution and community structure. For many species, the presence/absence of predators is the most important factor affecting female oviposition decisions. However, individual habitat patches exist in complex landscapes linked by processes of dispersal and colonisation, and spatial distribution of factors such as predators has potential effects beyond individual patches. Perceived patch quality and resulting colonisation rates depend both on risk conditions within a given patch and on spatial context. Here we experimentally confirm the role of one context‐dependent processes, spatial contagion, functioning at the local scale, and provide the first example of another context‐dependent process, habitat compression, functioning at the regional scale. Both processes affect colonisation rates and patterns of spatial distribution in naturally colonised experimental metacommunities.