Improved yields of full-length functional human FGF1 can be achieved using the methylotrophic yeast Pichia pastoris

We have produced human fibroblast growth factor 1 (hFGF1) in the methylotrophic yeast Pichia pastoris in order to obtain the large amounts of active protein required for subsequent functional and structural characterization. Four constructs were made to examine both intracellular and secreted expression, with variations in the location of the His6 tag at either end of the peptide. hFGF1 could be produced from all four constructs in shake flasks, but production was optimized by growing only the highest-yielding of these strains, which produced hFGF1 intracellularly, under tightly controlled conditions in a 3 L fermentor. One hundred and eight milligrams of pure protein was achieved per liter culture (corresponding to 0.68 mg of protein per gram of wet cells), the function of which was verified using NIH 3T3 cell cultures. This is a 30-fold improvement over previously reported yields of full-length hFGF1. © 2006 Elsevier Inc. All rights reserved.

The effect of lignin and inorganic species in biomass on pyrolysis oil yields, quality and stability

This paper investigates four reference fuels and three low lignin Lolium Festuca grasses which were subjected to pyrolysis to produce pyrolysis oils. The oils were analysed to determine their quality and stability, enabling the identification of feedstock traits which affect oil stability. Two washed feedstocks were also subjected to pyrolysis to investigate whether washing can enhance pyrolysis oil quality. It was found that the mineral matter had the dominate effect on pyrolysis in compared to lignin content, in terms of pyrolysis yields for organics, char and gases. However the higher molecular weight compounds present in the pyrolysis oil are due to the lignin derived compounds as determined by results of GPC and liquid-GC/MS. The light organic fraction also increased in yield, but reduced in water content as metals increased at the expense of the lignin content. It was found that the fresh oil and aged oil had different compound intensities/concentrations, which is due to a large number of reactions occurring when the oil is aged day by day. These findings agree with previous reports which suggest that a large amount of re-polymerisation occurs as levoglucosan yields increase during the aging progress, while hydroxyacetaldehyde decrease. In summary the paper reports a window for producing a more stable pyrolysis oil by the use of energy crops, and also show that washing of biomass can improve oil quality and stability for high ash feedstocks, but less so for the energy crops.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

The effect of antifoam addition on protein production yields

Pichia pastoris is a widely used host for recombinant protein production. The foaming associated with culturing it on a large scale is commonly prevented by the addition of chemical antifoaming agents or "antifoams." Unexpectedly, the addition of a range of antifoams to both shake flask and bioreactor cultures of P. pastoris has been shown to alter the total yield of the recombinant protein being produced. Possible explanations for this are that the presence of the antifoam increases the total amount of protein being produced and secreted per cell or that it increases the density of the culture. Antifoaming agents may therefore have specific effects on the growth and yield characteristics of recombinant cultures, in addition to their primary action as de-foamers.

Improving recombinant eukaryotic membrane protein yields in Pichia pastoris:the importance of codon optimization and clone selection

In the last 15 years, 80% of all recombinant proteins reported in the literature were produced in the bacterium, Escherichia coli, or the yeast, Pichia pastoris. Nonetheless, developing effective general strategies for producing recombinant eukaryotic membrane proteins in these organisms remains a particular challenge. Using a validated screening procedure together with accurate yield quantitation, we therefore wished to establish the critical steps contributing to high yields of recombinant eukaryotic membrane protein in P. pastoris. Whilst the use of fusion partners to generate chimeric constructs and directed mutagenesis have previously been shown to be effective in bacterial hosts, we conclude that this approach is not transferable to yeast. Rather, codon optimization and the preparation and selection of high-yielding P. pastoris clones are effective strategies for maximizing yields of human aquaporins.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

Pyrolysis of Napier grass in a fixed bed reactor:effect of operating conditions on product yields and characteristic

This study presents a report on pyrolysis of Napier grass stem in a fixed bed reactor. The effects of nitrogen flow (20 to 60 mL/min), and reaction temperature (450 to 650 degrees C) were investigated. Increasing the nitrogen flow from 20 to 30 mL/min increased the bio-oil yield and decreased both bio-char and non-condensable gas. 30 mL/min nitrogen flow resulted in optimum bio-oil yield and was used in the subsequent experiments. Reaction temperatures between 450 and 600 degrees C increased the bio-oil yield, with maximum yield of 32.26 wt% at 600 degrees C and a decrease in the corresponding bio-char and non-condensable gas. At 650 degrees C, reductions in the bio-oil and bio-char yields were recorded while the non-condensable gas increased. Water content of the bio-oil decreased with increasing reaction temperature, while density and viscosity increased. The observed pH and higher heating values were between 2.43 to 2.97, and 25.25 to 28.88 MJ/kg, respectively. GC-MS analysis revealed that the oil was made up of highly oxygenated compounds and requires upgrading. The bio-char and non-condensable gas were characterized, and the effect of reaction temperature on the properties was evaluated. Napier grass represents a good source of renewable energy when all pyrolysis products are efficiently utilized.

Synthesis of aromatic monothiols to increase the folding rate and yields of disulfide-containing proteins

Almost all pharmaceutically relevant proteins and many extracellular proteins contain disulfide bonds, which are essential for protein functions. In many cases, disulfidecontaining proteins are produced via in vitro protein folding that involves the oxidation of reduced protein to native protein, a complex process. The in vitro folding of reduced lysozyme has been extensively studied as a model system because native lysozyme is small, inexpensive, and has only four disulfide bonds. The folding of reduced lysozyme is conducted with the aid of a redox buffer consisting of a small molecule disulfide and a small molecule thiol, such as oxidized and reduced glutathione. Herein, in vitro folding rates and yields of lysozyme obtained in the presence of a series of aromatic thiols and oxidized glutathione are compared to those obtained with reduced and oxidized glutathione. Results showed that aromatic thiols significantly increase the folding rate of lysozyme compared to glutathione.

Foraminiferal faunal estimates of paleotemperature: Circumventing the no-analog problem yields cool ice age tropics

The sensitivity of the tropics to climate change, particularly the amplitude of glacial-to-interglacial changes in sea surface temperature (SST), is one of the great controversies in paleoclimatology. Here we reassess faunal estimates of ice age SSTs, focusing on the problem of no-analog planktonic foraminiferal assemblages in the equatorial oceans that confounds both classical transfer function and modern analog methods. A new calibration strategy developed here, which uses past variability of species to define robust faunal assemblages, solves the no-analog problem and reveals ice age cooling of 5° to 6°C in the equatorial current systems of the Atlantic and eastern Pacific Oceans. Classical transfer functions underestimated temperature changes in some areas of the tropical oceans because core-top assemblages misrepresented the ice age faunal assemblages. Our finding is consistent with some geochemical estimates and model predictions of greater ice age cooling in the tropics than was inferred by Climate: Long-Range Investigation, Mapping, and Prediction (CLIMAP) [1981] and thus may help to resolve a long-standing controversy. Our new foraminiferal transfer function suggests that such cooling was limited to the equatorial current systems, however, and supports CLIMAP's inference of stability of the subtropical gyre centers.

(Table 1) Lipid yields for samples across the Cretaceous/Tertiary boundary in DSDP Hole 86-577

Core samples of calcareous sediments taken from above and below the proposed Cretaceous/Tertiary boundary (Sample 577-12-5, 130 cm) were examined for geochemical evidence of the mass extinctions and faunal successions that marked this period. The lipid compositions of the six core samples examined were virtually identical and were characterized by a large component of unresolved naphthenic hydrocarbons and a homologous series of an/mo-alkanes, both presumably of bacterial origin. The results of this preliminary study suggest that the lipids of sediments deposited over a several million year period encompassing the Cretaceous-Tertiary extinctions have been almost completely recycled by bacterial metabolism, which occurred under oxic depositional and/or diagenetic conditions and which left a unique bacterial signature with only minor traces of the original sedimentary lipids.

(Table 1) Sample descriptions, carbon contents, and lipid yields across the K/T boundary at DSDP Hole 93-605 and at Stevns Klint, Denmark

This reconnaissance study was undertaken to determine whether the mass extinctions and faunal successions that mark the Cretaceous/Tertiary (K/T) boundary left a discernible molecular fossil record in the sediments of this period. Lipid signatures of sediments taken from above and below the K/T boundary were compared in core and outcrop samples taken from two locations: the U.S. east coast continental margin (western Atlantic Ocean, DSDP Site 605) and Stevns Klint, Denmark. Four calcareous sediments taken from above and below the K/T boundary in DSDP Hole 605, Section 605-66-1, revealed changing lipid signatures between above and below that are characterized by a large component of unresolved naphthenic hydrocarbons and a homologous series of n-alkanes ranging from Ci6 to C33. These lipid signatures are attributed to an influx of a terrestrial higher plant component and to bacterial reworking of the sediments under partially anoxic depositional and/or diagenetic conditions. The outcrop samples from Stevns Klint had extremely low concentrations of indigenous lipids. The fish clay at the K/T boundary contained traces of microbial hydrocarbons and fatty acids, whereas the carbonates above and below had only microbial fatty acids and additional terrestrial resin acids. The data from both sites indicate a perturbation in the deposition of lipid compound classes across the K/T boundary.

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.