Altering the ribosomal subunit ratio in yeast maximizes recombinant protein yield

Background The production of high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences that has yet to be addressed in a truly rational manner. Typically eukaryotic protein production experiments have relied on varying expression construct cassettes such as promoters and tags, or culture process parameters such as pH, temperature and aeration to enhance yields. These approaches require repeated rounds of trial-and-error optimization and cannot provide a mechanistic insight into the biology of recombinant protein production. We published an early transcriptome analysis that identified genes implicated in successful membrane protein production experiments in yeast. While there has been a subsequent explosion in such analyses in a range of production organisms, no one has yet exploited the genes identified. The aim of this study was to use the results of our previous comparative transcriptome analysis to engineer improved yeast strains and thereby gain an understanding of the mechanisms involved in high-yielding protein production hosts. Results We show that tuning BMS1 transcript levels in a doxycycline-dependent manner resulted in optimized yields of functional membrane and soluble protein targets. Online flow microcalorimetry demonstrated that there had been a substantial metabolic change to cells cultured under high-yielding conditions, and in particular that high yielding cells were more metabolically efficient. Polysome profiling showed that the key molecular event contributing to this metabolically efficient, high-yielding phenotype is a perturbation of the ratio of 60S to 40S ribosomal subunits from approximately 1:1 to 2:1, and correspondingly of 25S:18S ratios from 2:1 to 3:1. This result is consistent with the role of the gene product of BMS1 in ribosome biogenesis. Conclusion This work demonstrates the power of a rational approach to recombinant protein production by using the results of transcriptome analysis to engineer improved strains, thereby revealing the underlying biological events involved.

Information and communication technology (ICT) and human development

Using panel data for 41 developed and developing countries over the period 1998-2004, this paper examines the links between ICT diffusion and human development. We conducted a panel regression analysis of the investments in healthcare, education and information and communication technology (ICT) against human development index (HDI). The results show that these variables can be used to predict HDI scores. In agreement with findings of previous research, it is clear from our analysis that the central focus on ICT as a solution for development will not bring the results that the promoters of ICT as an ‘engine of growth’ are expecting. It is unwise to disaggregate the issues of education and healthcare infrastructure from ICT infrastructure development. ICT policies should be integrated with other national policies in order to find a holistic and structural solution to development.

Studies on the deactivation and reactivation of spent hydroprocessing catalyst

A study is reported on the deactivation of hydroprocessing catalysts and their reactivation by the removal of coke and metal foulants. The literature on hydrotreating catalyst deactivation by coke and metals deposition, the environmental problems associated with spent catalyst disposal, and its reactivation/rejuvenation process were reviewed. Experimental studies on catalyst deactivation involved problem analysis in industrial hydroprocessing operations, through characterization of the spent catalyst, and laboratory coking studies. A comparison was made between the characteristics of spent catalysts from fixed bed and ebullating bed residue hydroprocessing reactor units and the catalyst deactivation pattern in both types of reactor systems was examined. In the laboratory the nature of initial coke deposited on the catalyst surface and its role on catalyst deactivation were studied. The influence of initial coke on catalyst surface area and porosity was significant. Both catalyst acidity and feedstock quality had a remarkable influence on the amount and the nature of the initial coke. The hydroenitrogenation function (HDN) of the catalyst was found to be deactivated more rapidly by the initial coke than the hydrodesulphurization function (HDS). In decoking experiments, special attention was paid to the initial conditions of coke combustion, since the early stages of contact between the coke on the spent catalyst surface and the oxygen are crucial in the decoking process. An increase in initial combustion temperature above 440oC and the oxygen content of the regeneration gas above 5% vanadium led to considerable sintering of the catalyst. At temperatures above 700oC there was a substantial loss of molybdenum from the catalyst, and phase transformations in the alumina support. The preferred leaching route (coked vs decoked form of spent catalyst) and a comparison of different reagents (i.e., oxalic acid and tartaric acid) and promoters (i.e., Hydrogen Peroxide and Ferric Nitrate) for better selectivity in removing the major foulant (vanadium), characterization and performance evaluation of the treated catalysts and modelling of the leaching process were addressed in spent catalyst rejuvenation studies. The surface area and pore volume increased substantially with increasing vanadium extraction from the spent catalyst; the HDS activity showed a parallel increase. The selectivity for leaching of vanadium deposits was better, and activity recovery was higher, for catalyst rejuvenated by metal leaching prior to decoking.

The development of a novel in vitro model suitable for the prediction of bioavailability

In vitro studies of drug absorption processes are undertaken to assess drug candidate or formulation suitability, mechanism investigation, and ultimately for the development of predictive models. This study included each of these approaches, with the aim of developing novel in vitro methods for inclusion in a drug absorption model. Two model analgesic drugs, ibuprofen and paracetamol, were selected. The study focused on three main areas, the interaction of the model drugs with co-administered antacids, the elucidation of the mechanisms responsible for the increased absorption rate observed in a novel paracetamol formulation and the development of novel ibuprofen tablet formulations containing alkalising excipients as dissolution promoters.Several novel dissolution methods were developed. A method to study the interaction of drug/excipient mixtures in the powder form was successfully used to select suitable dissolution enhancing exicipents. A method to study intrinsic dissolution rate using paddle apparatus was developed and used to study dissolution mechanisms. Methods to simulate stomach and intestine environments in terms of media composition and volume and drug/antacid doses were developed. Antacid addition greatly increased the dissolution of ibuprofen in the stomach model.Novel methods to measure drug permeability through rat stomach and intestine were developed, using sac methodology. The methods allowed direct comparison of the apparent permeability values obtained. Tissue stability, reproducibility and integrity was observed, with selectivity between paracellular and transcellular markers and hydrophilic and lipophilic compounds within an homologous series of beta-blockers.

The impact on agriculture of the drawdown of shallow watertables

The promoters of the large groundwater developments implemented in the 1970's paid little attention to the effects of pumping on soil moisture. A field study, conducted in 1979 in the Tern Area of the Shropshire Groundwater Scheme, revealed that significant quantities of the available moisture could be removed from the root zone of vegetation when drawdown of shallow watertables occurred. Arguments to this effect, supported by the field study evidence, were successfully presented at the Shropshire Groundwater Scheme public inquiry. The aim of this study has been to expand the work which was undertaken in connection with the Shropshire Groundwater Scheme, and to develop a method whereby the effects of groundwater pumping on vegetation can be assessed, and hence the impacts minimised. Two concepts, the critical height and the soil sensitivity depth, formulated during the initial work are at the core of the Environmental Impact Assessment method whose development is described. A programme of laboratory experiments on soil columns is described, as is the derivation of relationships for determining critical heights and field capacity moisture profiles. These relationships are subsequently employed in evaluating the effects of groundwater drawdown. In employing the environmental assessment technique, digitised maps of relevant features of the Tern Area are combined to produce composite maps delineating the extent of the areas which are potentially sensitive to groundwater drawdown. A series of crop yield/moisture loss functions are then employed to estimate the impact of simulated pumping events on the agricultural community of the Tern Area. Finally, guidelines, based on experience gained through evaluation of the Tern Area case study, are presented for use in the design of soil moisture monitoring systems and in the siting of boreholes. In addition recommendations are made for development of the EIA technique, and further research needs are identified.

A study of new product market search and user adoption

The research was carried out in the Aviation Division of Dunlop Limited and was initiated as a search for more diverse uses for carbon/carbon composites. An assumed communication model of adoption was refined by introducing the concept of a two way search after making cross industry comparisons of supplier and consumer behaviour. This research has examined methods of searching for new uses for advanced technology materials. Two broad approaches were adopted. First, a case history approach investigated materials that had been in a similar oosition to carbon/carbon to see how other material producing firms had tackled the problem. Second, a questionnaire survey among industrialists examined: the role and identity of material decision makers in different sized firms; the effectiveness of various information sources and channels; and the material adoption habits of different industries. The effectiveness of selected information channels was further studied by monitoring the response to publicity given to carbon/carbon. A flow chart has been developed from the results of this research which should help any material producing firm that is contemplating the introduction of a new material to the world market. Further benefit to our understanding of the innovation and adoption of new materials would accrue from work in the followino areas: "micro" type case histories; understanding more fully the role of product champions or promoters; investigating the phase difference between incremental and radical type innovations for materials; examining the relationship between the adoption rate of new materials and the advance of technology; studying the development of cost per unit function methods for material selection; and reviewing the benefits that economy of scale studies can have on material developments. These are all suggested areas for further work.

Placenta growth factor-1 exerts time-dependent stabilization of adherens junctions following VEGF-induced vascular permeability

Increased vascular permeability is an early event characteristic of tissue ischemia and angiogenesis. Although VEGF family members are potent promoters of endothelial permeability the role of placental growth factor (PlGF) is hotly debated. Here we investigated PlGF isoforms 1 and 2 and present in vitro and in vivo evidence that PlGF-1, but not PlGF-2, can inhibit VEGF-induced permeability but only during a critical window post-VEGF exposure. PlGF-1 promotes VE-cadherin expression via the trans-activating Sp1 and Sp3 interaction with the VE-cadherin promoter and subsequently stabilizes transendothelial junctions, but only after activation of endothelial cells by VEGF. PlGF-1 regulates vascular permeability associated with the rapid localization of VE-cadherin to the plasma membrane and dephosphorylation of tyrosine residues that precedes changes observed in claudin 5 tyrosine phosphorylation and membrane localization. The critical window during which PlGF-1 exerts its effect on VEGF-induced permeability highlights the importance of the translational significance of this work in that PLGF-1 likely serves as an endogenous anti-permeability factor whose effectiveness is limited to a precise time point following vascular injury. Clinical approaches that would pattern nature's approach would thus limit treatments to precise intervals following injury and bring attention to use of agents only during therapeutic windows.

Zirconia and alumina based catalysts for steam reforming of naphthalene

The present paper deals with experimentation of ZrO2 and Al2O3-supported catalysts for conversion of naphthalene, chosen as tar model compound of pyrolysis or gasification syngas. In particular, the reforming capacity of active metals and promoters such as Co, Ni, Fe, Cr, Ce and Pt was tested in a fixed bed reactor at temperature from 400 to 900 °C. As regards ZrO2-supported catalysts, the best results were achieved by the Ni/Fe/Pt catalyst with 96% naphthalene conversion, 78% and 280% as CO and H2 production yield at 800 °C. Regarding Al2O3-supported catalysts, they were more active on average than the zirconia ones, achieving a very good performance even at 500 °C (90–100% naphthalene conversion, 30–40% CO yield and 300–350% H2 yield at 550 °C). Influence of different amounts of alumina, montmorillonite and carbon on carrier composition as well as pellets’ size were also studied. Both zirconia and alumina catalysts showed deactivation at higher temperatures due to coke deposition, resulting in a strong H2 production drop. Regeneration of catalysts by O2 and steam as well as activation by H2 were also studied. The activated catalyst was able to convert more than 99% naphthalene at 450 °C with a CO and H2 production yield of 26% and 420%, respectively.

Functional recombinant protein is present in the pre-induction phases of Pichia pastoris cultures when grown in bioreactors, but not shake-flasks

Background - Pichia pastoris is a widely-used host for recombinant protein production; expression is typically driven by methanol-inducible alcohol oxidase (AOX) promoters. Recently this system has become an important source of recombinant G protein-coupled receptors (GPCRs) for structural biology and drug discovery. The influence of diverse culture parameters (such as pH, dissolved oxygen concentration, medium composition, antifoam concentration and culture temperature) on productivity has been investigated for a wide range of recombinant proteins in P. pastoris. In contrast, the impact of the pre-induction phases on yield has not been as closely studied. In this study, we examined the pre-induction phases of P. pastoris bioreactor cultivations producing three different recombinant proteins: the GPCR, human A2a adenosine receptor (hA2aR), green fluorescent protein (GFP) and human calcitonin gene-related peptide receptor component protein (as a GFP fusion protein; hCGRP-RCP-GFP). Results - Functional hA2aR was detected in the pre-induction phases of a 1 L bioreactor cultivation of glycerol-grown P. pastoris. In a separate experiment, a glycerol-grown P. pastoris strain secreted soluble GFP prior to methanol addition. When glucose, which has been shown to repress AOX expression, was the pre-induction carbon source, hA2aR and GFP were still produced in the pre-induction phases. Both hA2aR and GFP were also produced in methanol-free cultivations; functional protein yields were maintained or increased after depletion of the carbon source. Analysis of the pre-induction phases of 10 L pilot scale cultivations also demonstrated that pre-induction yields were at least maintained after methanol induction, even in the presence of cytotoxic concentrations of methanol. Additional bioreactor data for hCGRP-RCP-GFP and shake-flask data for GFP, horseradish peroxidase (HRP), the human tetraspanins hCD81 and CD82, and the tight-junction protein human claudin-1, demonstrated that bioreactor but not shake flask cultivations exhibit recombinant protein production in the pre-induction phases of P. pastoris cultures. Conclusions - The production of recombinant hA2aR, GFP and hCGRP-RCP-GFP can be detected in bioreactor cultivations prior to methanol induction, while this is not the case for shake-flask cultivations of GFP, HRP, hCD81, hCD82 and human claudin-1. This confirms earlier suggestions of leaky expression from AOX promoters, which we report here for both glycerol- and glucose-grown cells in bioreactor cultivations. These findings suggest that the productivity of AOX-dependent bioprocesses is not solely dependent on induction by methanol. We conclude that in order to maximize total yields, pre-induction phase cultivation conditions should be optimized, and that increased specific productivity may result in decreased biomass yields.

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Abolishing the Audit Commission:framing, discourse coalitions and administrative reform

The abolition of the Audit Commission in England raises questions about how a major reform was achieved with so little controversy, why the agency lacked the institutional stickiness commonly described in the literature on organisational reform and why it did not strategise to survive. In this paper, we apply argumentative discourse analysis to rich empirical data to reveal the pattern and evolution of storylines and discourse coalitions, and the ways in which these interact with and affect the practices of Parliament, the media and the Audit Commission itself. Our analysis shows that the politics of administrative reform are as much about discursive framing and the ability of pro-reformers to gain discursive structuration and institutionalisation as they are about the material resources available to a newly elected government and its ministers. Questions of technical feasibility are unlikely to derail a reform initiative once its promoters gain discursive ascendency.

REST is a hypoxia-responsive transcriptional repressor

Cellular exposure to hypoxia results in altered gene expression in a range of physiologic and pathophysiologic states. Discrete cohorts of genes can be either up- or down-regulated in response to hypoxia. While the Hypoxia-Inducible Factor (HIF) is the primary driver of hypoxia-induced adaptive gene expression, less is known about the signalling mechanisms regulating hypoxiadependent gene repression. Using RNA-seq, we demonstrate that equivalent numbers of genes are induced and repressed in human embryonic kidney (HEK293) cells. We demonstrate that nuclear localization of the Repressor Element 1-Silencing Transcription factor (REST) is induced in hypoxia and that REST is responsible for regulating approximately 20% of the hypoxia-repressed genes. Using chromatin immunoprecipitation assays we demonstrate that REST-dependent gene repression is at least in part mediated by direct binding to the promoters of target genes. Based on these data, we propose that REST is a key mediator of gene repression in hypoxia.