Metaheuristic approaches in biopharmaceutical process development data analysis

Bioprocess and Biosystems Engineering - There is a growing interest in mining and handling of big data, which has been rapidly accumulating in the repositories of bioprocess industries....     

The relationship between pheromone trap catch and local population density of the oak processionary moth Thaumetopoea processionea (Lepidoptera: Thaumetopoeidae)

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Lianas as a food resource for herbivorous insects: a comparison with trees

Woody climbers or, ‘lianas’, are one of the features that characterise rainforests. They contribute substantially to plant diversity and leaf biomass which makes them a potentially important food source for herbivores. Here, we focus on insect herbivores, folivores in particular, to show how disparities in the quantitative and qualitative availability of leaves between lianas and trees may differentially influence insect folivory and the herbivore communities themselves. We develop a conceptual model and show that lianas in general have lower structural and chemical defences, a greater nutritional profile and a preferable phenology in comparison with trees, which, contrary to our expectations, has led to assemblages of more‐specialised insects. The impacts this has on higher trophic levels and broader ecological networks, however, are poorly known. We show through a study of four tropical floras from different biogeographic realms that lianas are likely to be a target for a wide range of insect herbivore taxa as they are a phylogenetically diverse group and increase diversity of higher taxa at local scales. This, in combination with their highly palatable leaves, may also make them a suitable temporary food source for insects during times when preferred host plants are scarce. This phenomenon has been observed in mammalian herbivores but awaits investigation in insects as does the effects this may have on survival and fitness. Apparent recent increases in liana abundances in some forests, likely due to climate change, makes understanding their role in supporting and maintaining biodiversity an increasingly important and necessary challenge. Since trees or saplings have usually been the subject of studies on insect herbivory, major knowledge gaps remain about the ways in which lianas contribute to, support and maintain the ecosystems in which they exist. We use our conceptual model to guide future research directions and express the necessity for caution when extrapolating explanations of herbivory derived from data on trees to growth forms with fundamentally different ecologies.     

Factors affecting protein refolding yields in a fed-batch and batch-refolding system

The refolding of recombinant protein from inclusion bodies expressed in Escherichia coli can present a process bottleneck. Yields at industrially relevant concentrations are restricted by aggregation of protein upon dilution of the denatured form. This article studies the effect of five factors upon the dilution refolding of protein in a twin impeller fed-batch system using refold buffer containing only the oxidized form of the redox reagent. Such a buffer is easier to prepare and more stable than a buffer containing both reduced and oxidized forms. The five factors chosen were: bulk impeller Reynolds number, mini-impeller Reynolds number, injection rate of denatured protein, redox ratio, and guanidine hydrochloride (GdHCl) concentration. A 2(5) factorial experiment was conducted at an industrially relevant protein concentration using lysozyme as the test system. The study identified that in the system used, the guanidine hydrochloride concentration, redox ratio, and injection rate were the most important factors in determining refolding yields. Two interactions were found to be important: redox ratio/guanidine hydrochloride concentration and guanidine hydrochloride concentration/injection rate. Conditions were also found at which high refolding yields could be achieved even with rapid injection and poor mixing efficiency. Therefore, a comparative assessment was carried out with minimal mixing in a simple batch-refolding mode of operation, which revealed different behavior to that of fed-batch. A graphical (windows of operation) analysis of the batch data suggested that optimal yields and productivity are obtained at high guanidine hydrochloride concentrations (1.2 M) and redox ratios of unity or greater.     

DNA sequences from Arabidopsis, which encode protein kinases and function as upstream regulators of Snf1 in yeast

Sucrose nonfermenting-1 (Snf1)-related protein kinase-1 (SnRK1) of plants is a global regulator of carbon metabolism through the modulation of enzyme activity and gene expression. It is structurally and functionally related to the yeast protein kinase, Snf1, and to mammalian AMP-activated protein kinase. Two DNA sequences from Arabidopsis thaliana, previously known only by their data base accession numbers of NM_ 125448.3 (protein ID NP_200863) and NM_114393.3 (protein ID NP_566876) each functionally complemented a Saccharomyces cerevisiae elm1 sak1 tos3 triple mutant. This indicates that the Arabidopsis proteins are able to substitute for one of the missing yeast upstream kinases, which are required for activity of Snf1. Both plant proteins were shown to phosphorylate a peptide with the amino acid sequence of the phosphorylation site in the T-loop of SnRK1 and by inference SnRK1 in Arabidopsis. The proteins encoded by NM_125448.3 and NM_114393.3 have been named AtSnAK1 and AtSnAK2 (Arabidopsis thaliana SnRK1-activating kinase), respectively. We believe this is the first time that upstream activators of SnRK1 have been described in any plant species.     

Plant–pollinator interactions in a Mexican Acacia community

Competition for pollination is thought to be an important factor structuring flowering in many plant communities, particularly among plant taxa with morphologically similar and easily accessible flowers. We examined the potential for heterospecific pollen transfer (HPT) in a community of four Acacia species in a highly seasonal tropical habitat in Mexico. Partitioning of pollen flow among sympatric species appears to be achieved, in part, through segregation of flowering in seasonal time, and interspecific differences in pollinator guilds. However, two coflowering species (Acacia macracantha and Acacia angustissima) shared multiple flower visitors, raising the possibility of HPT. Each of these coflowering species showed high intraspecific daily synchrony in pollen release, but dehisce at different times of day. Pollinators rapidly harvested available pollen from one species before abandoning it to visit the flowers of the second later in the day. The activity of shared pollinators, predominantly bees, is thus structured throughout the day, and potential for HPT reduced. Suggestive evidence in favour of a resource partitioning explanation for this pattern is provided by the fact that A. macracantha showed significantly greater intraspecific synchrony when coflowering with a potential competitor (A. angustissima) than when flowering alone. We discuss our results in light of previous work on coflowering acacia assemblages in Tanzania and Australia. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes

Electron transferring flavoproteins (ETFs) are soluble heterodimeric FAD-containing proteins that function primarily as soluble electron carriers between various flavoprotein dehydrogenases. ETF is positioned at a key metabolic branch point, responsible for transferring electrons from up to 10 primary dehydrogenases to the membrane-bound respiratory chain. Clinical mutations of ETF result in the often fatal disease glutaric aciduria type II. Structural and biophysical studies of ETF in complex with partner proteins have shown that ETF partitions the functions of partner binding and electron transfer between (a) a 'recognition loop', which acts as a static anchor at the ETF-partner interface, and (b) a highly mobile redox-active FAD domain. Together, this enables the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. This 'conformational sampling' enables ETF to recognize structurally distinct partners, whilst also maintaining a degree of specificity. Complex formation triggers mobility of the FAD domain, an 'induced disorder' mechanism contrasting with the more generally accepted models of protein-protein interaction by induced fit mechanisms. We discuss the implications of the highly dynamic nature of ETFs in biological interprotein electron transfer. ETF complexes point to mechanisms of electron transfer in which 'dynamics drive function', a feature that is probably widespread in biology given the modular assembly and flexible nature of biological electron transfer systems.     

Moving targets: collective decisions and flexible choices in house-hunting ants

Many decisions involve a trade-off between commitment and flexibility. We show here that the collective decisions ants make over new nest sites are sometimes sufficiently flexible that the ants can change targets even after an emigration has begun. Our findings suggest that, in this context, the ants’ procedures are such that they can sometimes avoid ‘negative information cascades’ which might lock them into a poor choice. The ants are more responsive to belated good news of a higher quality nest than they are when the nest they had initially chosen degraded to become worse than an alternative. Our study confirms, in a new way, that ant colonies can be very powerful “search engines”.     

Evaluation of a novel agarose-based synthetic ligand adsorbent for the recovery of antibodies from ovine serum

This paper evaluates a prototype agarose-based affinity adsorbent utilizing a bound synthetic ligand designed to replace Protein A as an IgG-affinity capture resin and compares its purification characteristics with four commercially available matrices for the recovery of polyclonal antibodies from crude hyperimmune ovine serum. The novel adsorbent was found to show the highest dynamic capacity (29.2 mg/mL) of all matrices under evaluation--30% higher than the other commercial adsorbents evaluated. When using a post-load caprylic acid wash, IgG yields of over 85% and purities of over 90% were achieved consistently over multiple loading cycles. To evaluate bead diffusion, inverted confocal microscopy was used to visualise fluorescent antibody binding on to individual adsorbent beads in real time. The results indicate that the binding characteristics of the prototype adsorbent are similar to those obtained with Protein G Sepharose. This study indicates that the high-capacity prototype matrix is a feasible and potentially cost-effective alternative for the direct capture of antibodies from crude ovine serum and may therefore also be applicable to the purification of other complex industrial feedstocks such as transgenic milk or monoclonal antibodies expressed using recombinant technologies.