Predictive glycoengineering of biosimilars using a Markov chain glycosylation model

Biosimilar drugs must closely resemble the pharmacological attributes of innovator products to ensure safety and efficacy to obtain regulatory approval. Glycosylation is one critical quality attribute that must be matched, but it is inherently difficult to control due to the complexity of its biogenesis. This usually implies that costly and time‐consuming experimentation is required for clone identification and optimization of biosimilar glycosylation. Here, a computational method that utilizes a Markov model of glycosylation to predict optimal glycoengineering strategies to obtain a specific glycosylation profile with desired properties is described. The approach uses a genetic algorithm to find the required quantities to perturb glycosylation reaction rates that lead to the best possible match with a given glycosylation profile. Furthermore, the approach can be used to identify cell lines and clones that will require minimal intervention while achieving a glycoprofile that is most similar to the desired profile. Thus, this approach can facilitate biosimilar design by providing computational glycoengineering guidelines that can be generated with a minimal time and cost.     

EFFECTS OF A HAEMATOPHAGOUS MITE ON THE BARN SWALLOW (HIRUNDO RUSTICA): A TEST OF THE HAMILTON AND ZUK HYPOTHESIS

I tested three assumptions of the Hamilton and Zuk hypothesis (1982), which suggests that the extravagant male plumage of many bird species allows females to choose mates that are resistant to the parasites exploiting the host population at a given time. By choosing such males as mates, females will rear offspring carrying the genes for resistance. I tested three necessary conditions for the Hamilton and Zuk model: (1) whether parasites affect the fitness of their hosts; (2) whether there is heritable variation in parasite resistance, and (3) whether the expression of the sexual ornament varies with parasite burden. The haematophagous mite Ornithonyssus bursa (Macronyssidae, Gamasida) sucks blood from their Barn Swallow (Hirundo rustica) hosts. Experimental manipulation of mite loads and partial cross-fostering experiments on Barn Swallows, where half of the nestlings in the brood were exchanged with nestlings from another nest, shows that parasite burdens and origin, but not rearing conditions, of Bam Swallow nestlings, affected their adult tarsus length and maximum body weight shortly before fledging. Mite loads of adult Barn Swallows at spring arrival were more similar to mite loads of their own offspring, whether reared in their own or in foster nests inoculated with mites, than to loads of foster offspring. Parent Barn Swallows with long tail ornaments had offspring with smaller mite loads in the partial cross-fostering experiments. The amount of increase in male tail ornaments from one year to another was negatively related to experimentally manipulated mite loads of Barn Swallow nests during the preceding breeding season. In conclusion, the three assumptions of the hypothesis were supported by the experimental tests.     

Prevalence and Incidence of Diabetes in Stockholm County 1990-2010

Background

Diabetes is on the rise in the western world, but data from Scandinavia are inconsistent with indications of stable or even reverse trends. To shed new light on this issue, we investigated diabetes trends in Stockholm County 1990–2010, taking into account trends in risk factors and mortality.

Methods

We used data from a large population-based quadrennial public health survey conducted between 1990 and 2010 in Stockholm County (∼2.1 million inhabitants), supplemented with data from national registers. The age-standardized prevalence and incidence rates of diabetes and related risk factors 1990–2010 were estimated in adult inhabitants. We also modelled the influence of potential risk factors on the diabetes trends and estimated the life time risk of diabetes.

Results

The prevalence of diabetes was 4.6% (95% confidence interval (CI); 4.5–4.8%) in 2010 compared to 2.8% (95% CI; 2.3–3.5%) in 1990. Between 1990 and 2002 the prevalence rose annually by 3.8% (95% CI; 2.1–5.5). Incidence rates showed a similar pattern and rose by 3.0% (95% CI; 0.3–5.7%) annually 1990–2002. The rising incidence was mainly attributable to increasing prevalence of overweight/obesity, which rose by 46% during the observation period. In 2010, the lifetime risk of adult onset diabetes was 28% (95% CI; 26–31%) in men and 19% (95% CI; 17–21%) in women.

Conclusions

Diabetes rates have been increasing in Stockholm over the last decades, both in terms of incidence and prevalence, and this development is most likely the result of increasing overweight and obesity in the population.     

Isolation of Phages for Phage Therapy: A Comparison of Spot Tests and Efficiency of Plating Analyses for Determination of Host Range and Efficacy

Phage therapy, treating bacterial infections with bacteriophages, could be a future alternative to antibiotic treatment of bacterial infections. There are, however, several problems to be solved, mainly associated to the biology of phages, the interaction between phages and their bacterial hosts, but also to the vast variation of pathogenic bacteria which implies that large numbers of different phages are going to be needed. All of these phages must under present regulation of medical products undergo extensive clinical testing before they can be applied. It will consequently be of great economic importance that effective and versatile phages are selected and collected into phage libraries, i.e., the selection must be carried out in a way that it results in highly virulent phages with broad host ranges. We have isolated phages using the Escherichia coli reference (ECOR) collection and compared two methods, spot testing and efficiency of plating (EOP), which are frequently used to identify phages suitable for phage therapy. The analyses of the differences between the two methods show that spot tests often overestimate both the overall virulence and the host range and that the results are not correlated to the results of EOP assays. The conclusion is that single dilution spot tests cannot be used for identification and selection of phages to a phage library and should be replaced by EOP assays. The difference between the two methods can be caused by many factors. We have analysed if the differences and lack of correlation could be caused by lysis from without, bacteriocins in the phage lysate, or by the presence of prophages harbouring genes coding for phage resistance systems in the genomes of the bacteria in the ECOR collection.     

Deletion of a lectin gene does not affect the phenotype of the nematode-trapping fungus Arthrobotrys oligospora

A number of filamentous fungi are known to produce high levels of saline-soluble and low-molecular-mass lectins. The function of these proteins are not clear but it has been proposed that they are involved in storage of nutrients, development, recognition of other organisms, and defense reactions. A gene encoding such a lectin (AOL) was deleted in the nematode-trapping fungus Arthrobotrys oligospora by homologous recombination. The deletion mutants did not express any hemagglutinating activity or protein cross-reacting with AOL antibodies. There were no significant differences between the DeltaAOL and wild-type strains in spore (conidia) germination, saprophytic growth, and pathogenicity. Furthermore, there was no significant difference in the growth and reproduction of collembolan feeding on the various strains of A. oligospora. Thus either the previous proposed functions of AOL are not correct, or the fungus can compensate for the absence of the lectin by expressing other proteins with similar function(s) as AOL.     

Improving odour assessment in LCA—the odour footprint

Purpose

Odour is an important aspect of systems for human and agricultural waste management and many technologies are developed with the sole purpose of reducing odour. Compared with greenhouse gas assessment and the assessment of toxicity, odour assessment has received little attention in the life cycle assessment (LCA) community. This article aims to redress this.

Methods

Firstly, a framework for the assessment of odour impacts in LCA was developed considering the classical LCA framework of emissions, midpoint and endpoint indicators. This suggested that an odour footprint midpoint indicator was worth striving for. An approach to calculating an areal indicator we call “odour footprint”, which considers the odour detection threshold, the diffusion rate and the kinetics of degradation of odourants, was implemented in MATLAB. We demonstrated the use of the characterisation factors we calculated in a case study based on odour removal technology applied to a pig barn.

Results and discussion

We produced a list of 33 linear characterisation factors based on hydrogen sulphide equivalents, analogous to the linear carbon dioxide equivalency factors in use in carbon footprinting, or the dichlorobenzene equivalency factors developed for assessment of toxic impacts in LCA. Like the latter, this odour footprint method does not take local populations and exposure pathway analysis into account—its intent is not to assess regulatory compliance or detailed design. The case study showed that despite the need for materials and energy, large factor reductions in odour footprint and eutrophication potential were achieved at the cost of a smaller factor increase in greenhouse emissions.

Conclusions

The odour footprint method is proposed as an improvement on the established midpoint method for odour assessment in LCA. Unlike it, the method presented here considers the persistence of odourants. Over time, we hope to increase the number of characterised odourants, enabling analysts to perform simple site-generic LCA on systems with odourant emissions.     

Fibroblasts Isolated from Human Middle Turbinate Mucosa Cause Neural Progenitor Cells to Differentiate into Glial Lineage Cells

Transplantation of olfactory ensheathing cells (OECs) is a potential therapy for repair of spinal cord injury (SCI). Autologous transplantation of OECs has been reported in clinical trials. However, it is still controversial whether purified OECs or olfactory mucosa containing OECs, fibroblasts and other cells should be used for transplantation. OECs and fibroblasts were isolated from olfactory mucosa of the middle turbinate from seven patients. The percentage of OECs with p75^NTR+ and GFAP⁺ ranged from 9.2% to 73.2%. Fibroblasts were purified and co-cultured with normal human neural progenitors (NHNPs). Based on immunocytochemical labeling, NHNPs were induced into glial lineage cells when they were co-cultured with the mucosal fibroblasts. These results demonstrate that OECs can be isolated from the mucosa of the middle turbinate bone as well as from the dorsal nasal septum and superior turbinates, which are the typical sites for harvesting OECs. Transplantation of olfactory mucosa containing fibroblasts into the central nervous system (CNS) needs to be further investigated before translation to clinical application.     

Ecosystem respiration depends strongly on photosynthesis in a temperate heath

We measured net ecosystem CO₂ flux (F _n) and ecosystem respiration (R _E), and estimated gross ecosystem photosynthesis (P _g) by difference, for two years in a temperate heath ecosystem using a chamber method. The exchange rates of carbon were high and of similar magnitude as for productive forest ecosystems with a net ecosystem carbon gain during the second year of 293 ± 11 g C m⁻² year⁻¹ showing that the carbon sink strength of heather-dominated ecosystems may be considerable when C. vulgaris is in the building phase of its life cycle. The estimated gross ecosystem photosynthesis and ecosystem respiration from October to March was 22% and 30% of annual flux, respectively, suggesting that both cold-season carbon gain and loss were important in the annual carbon cycle of the ecosystem. Model fit of R _E of a classic, first-order exponential equation related to temperature (second year; R ² = 0.65) was improved when the P _g rate was incorporated into the model (second year; R ² = 0.79), suggesting that daytime R _E increased with increasing photosynthesis. Furthermore, the temperature sensitivity of R _E decreased from apparent Q ₁₀ values of 3.3 to 3.9 by the classic equation to a more realistic Q ₁₀ of 2.5 by the modified model. The model introduces R _photo, which describes the part of respiration being tightly coupled to the photosynthetic rate. It makes up 5% of the assimilated carbon dioxide flux at 0°C and 35% at 20°C implying a high sensitivity of respiration to photosynthesis during summer. The simple model provides an easily applied, non-intrusive tool for investigating seasonal trends in the relationship between ecosystem carbon sequestration and respiration.     

Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris)

The aim of the present study was to investigate the genetic variation in Danish populations of the endangered European crab apple (Malus sylvestris). Special emphasis was given to hybridization between the wild species and its cultivated relative Malus ×domestica. A total of 178 wild individuals from four Danish populations were studied along with a reference sample of 29 old cultivars. The genetic variation within and among samples was studied at ten microsatellite marker loci. Additionally, a morphological analysis was carried out to identify hybrids and test for correspondence between phenotypic and genotypic indices of hybridization. From application of ordination and a model-based cluster analysis to the molecular data, two clusters were identified consisting of wild and cultivated individuals, respectively. This indicates that pronounced admixture between the two species is not present. At the population level, a high correspondence was found between geographic isolation from M. ×domestica and genotypic and morphological indices of hybridization. As expected, isolated populations appeared less affected by hybridization than poorly isolated populations. Isolated “pure” M. sylvestris populations could thus be identified. However, morphological and molecular evidences of hybridization were found to be divergent at the individual level. This is suggestive of some historical introgression into the M. sylvestris gene pool and indicates that relying exclusively on either morphological or molecular characters as diagnostic markers in studies of hybridization between M. ×domestica and M. sylvestris might lead to fallible results. Combined application of genetic and morphological markers is therefore recommended.     

Disturbance and predation risk influence vigilance synchrony of black‐necked cranes Grus nigricollis,but not as strongly as expected

Animals monitor surrounding dangers independently or cooperatively (synchronized and coordinated vigilance), with independent and synchronized scanning being prevalent. Coordinated vigilance, including unique sentinel behavior, is rare in nature, since it is time‐consuming and limited in terms of benefits. No evidence showed animals adopt alternative vigilance strategies during antipredation scanning yet. Considering the nonindependent nature of both synchronization and coordination, we assessed whether group members could keep alert synchronously or in a coordinated fashion under different circumstance. We studied how human behavior and species‐specific variables impacted individual and collective vigilance of globally threatened black‐necked cranes (Grus nigricollis) and explored behavior‐based wildlife management. We tested both predation risk (number of juveniles in group) and human disturbance (level and distance) effects on individual and collective antipredation vigilance of black‐necked crane families. Adults spent significantly more time (proportion and duration) on scanning than juveniles, and parents with juveniles behaved more vigilant. Both adults and juveniles increased time allocation and duration on vigilance with observer proximity. Deviation between observed and expected collective vigilance varied with disturbance and predation risk from zero, but not significantly so, indicating that an independent vigilance strategy was adopted by black‐necked crane couples. The birds showed synchronized vigilance in low disturbance areas, with fewer juveniles and far from observers; otherwise, they scanned in coordinated fashion. The collective vigilance, from synchronized to coordinated pattern, varied as a function of observer distance that helped us determine a safe distance of 403.75 m for the most vulnerable family groups with two juveniles. We argue that vigilance could constitute a prime indicator in behavior‐based species conservation, and we suggesting a safe distance of at least 400 m should be considered in future tourist management.