Optimising fed-batch production of recombinant proteins using the baculovirus expression vector system

Fed-batch culture can offer significant improvement in recombinant protein production compared to batch culture in the baculovirus expression vector system (BEVS), as shown by Nguyen et al. (1993) and Bedard et al. (1994) among others. However, a thorough analysis of fed-batch culture to determine its limits in improving recombinant protein production over batch culture has yet to be performed. In this work, this issue is addressed by the optimisation of single-addition fed-batch culture. This type of fed-batch culture involves the manual addition of a multi-component nutrient feed to batch culture before infection with the baculovirus. The nutrient feed consists of yeastolate ultrafiltrate, lipids, amino acids, vitamins, trace elements, and glucose, which were added to batch cultures of Spodoptera frugiperda (Sf9) cells before infection with a recombinant Autographa californica nuclear polyhedrosis virus (Ac-NPV) expressing beta-galactosidase (beta-Gal). The fed-batch production of beta-Gal was optimised using response surface methods (RSM). The optimisation was performed in two stages, starting with a screening procedure to determine the most important variables and ending with a central-composite experiment to obtain a response surface model of volumetric beta-Gal production. The predicted optimum volumetric yield of beta-Gal in fed-batch culture was 2.4-fold that of the best yields in batch culture. This result was confirmed by a statistical analysis of the best fed-batch and batch data (with average beta-Gal yields of 1.2 and 0.5 g/L, respectively) obtained from this laboratory. The response surface model generated can be used to design a more economical fed-batch operation, in which nutrient feed volumes are minimised while maintaining acceptable improvements in beta-Gal yield. (C) 1998 John Wiley & Sons, Inc.

Factors controlling the origin of gas in Australian Bowen Basin coals

Open system pyrolysis (heating rate 10 degrees C/min) of coal maturity (vitrinite reflectance, VR) sequence (0.5%, 0.8% and 1.4% VR) demonstrates that there are two stages of thermogenic methane generation from Bowen Basin coals. The first and major stage shows a steady increase in methane generation maximising at 570 degrees C, corresponding to a VR of 2-2.5%. This is followed by a less intense methane generation which has not as yet maximised by 800 degrees C (equivalent to VR of 5%). Heavier (C2+) hydrocarbons are generated up to 570 degrees C after which only the C-1 (CH4, CO and CO2) gases are produced. The main phase of heavy hydrocarbon generation occurs between 420 and 510 degrees C. Over this temperature range,methane generation accounts for only a minor component, whereas the wet gases (C-2-C-5) are either in equal abundance or are more abundant by a factor of two than the liquid hydrocarbons. The yields of non-hydrocarbon gases CO2 and CO are greater then methane during the early stages of gas generation from an immature coal, subordinate to methane during the main phase of methane generation after which they are again dominant. Compositional data for desorbed and produced coal seam gases from the Bowen show that CO2 and wet gases are a minor component. This discrepancy between the proportion of wet gas components produced during open system pyrolysis and that observed in naturally matured coals may be the result of preferential migration of wet gas components, by dilution of methane generated during secondary cracking of bitumen, or kinetic effects associated with different activations for production of individual hydrocarbon gases. Extrapolation of results of artificial pyrolysis of the main organic components in coal to geological significant heating rates suggests that isotopically light methane to delta(13)C of -50 parts per thousand can be generated. Carbon isotope depletions in C-13 are further enhanced, however, as a result of trapping of gases over selected rank levels (instantaneous generation) which is a probable explanation for the range of delta(13)C values we have recorded in methane desorbed from Bowen Basin coals (-51 +/- 9 parts per thousand). Pervasive carbonate-rich veins in Bowen Basin coals are the product of magmatism-related hydrothermal activity. Furthermore, the pyrolysis results suggest an additional organic carbon source front CO2 released at any stage during the maturation history could mix in varying proportions with CO2 from the other sources. This interpretation is supported by C and O isotopic ratios, of carbonates that indicate mixing between magmatic and meteoric fluids. Also, the steep slope of the C and O isotope correlation trend suggests that the carbonates were deposited over a very narrow temperature interval basin-wide, or at relatively high temperatures (i.e., greater than 150 degrees C) where mineral-fluid oxygen isotope fractionations are small. These temperatures are high enough for catagenic production of methane and higher hydrocarbons from the coal and coal-derived bitumen. The results suggests that a combination of thermogenic generation of methane and thermodynamic processes associated with CH4/CO2 equilibria are the two most important factors that control the primary isotope and molecular composition of coal seam gases in the Bowen Basin. Biological process are regionally subordinate but may be locally significant. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

Continental extension: From core complexes to rigid block faulting

Extension of overthickened continental crust is commonly characterized by an early core complex stage of extension followed by a later stage of crustal-scale rigid block faulting. These two stages are clearly recognized during the extensional destruction of the Alpine orogen in northeast Corsica, where rigid block faulting overprinting core complex formation eventually led to crustal separation and the formation of a new oceanic backarc basin (the Ligurian Sea). Here we investigate the geodynamic evolution of continental extension by using a novel, fully coupled thermomechanical numerical model of the continental crust. We consider that the dynamic evolution is governed by fault weakening, which is generated by the evolution of the natural-state variables (i.e., pressure, deviatoric stress, temperature, and strain rate) and their associated energy fluxes. Our results show the appearance of a detachment layer that controls the initial separation of the brittle crust on characteristic listric faults, and a core complex formation that is exhuming strongly deformed rocks of the detachment zone and relatively undeformed crustal cores. This process is followed by a transitional period, characterized by an apparent tectonic quiescence, in which deformation is not localized and energy stored in the upper crust is transferred downward and causes self-organized mobilization of the lower crust. Eventually, the entire crust ruptures on major crosscutting faults, shifting the tectonic regime from core complex formation to wholesale rigid block faulting.

Synchronization of mutually coupled chaotic systems

We report on the experimental observation of both basic frequency locking synchronization and chaos synchronization between two mutually coupled chaotic subsystems. We show that these two kinds of synchronization are two stages of interaction between coupled chaotic systems. in particular the chaos synchronization could be understood as a state of phase locking between coupled chaotic oscillations.

The influence of age on reproductive performance in the Brown Thornbill

I examined age effects on reproduction in the Brown Thornbill Acanthiza pusilla in Canberra, Australia. I found that the reproductive performance of both males and females improved with age, although only age-related improvement in male performance had a significant effect on annual reproductive success. Reproductive success improved with male age as a result of improved performance during two stages of the breeding cycle: first-year males were less likely to fledge young than those aged two or more, while both first and second-year males were less successful at raising fledglings to independence than males of three or more. Male performance appears to improve over three years as they gain experience at provisioning nestlings and caring for fledglings without attracting predators, rather than as a direct result of improved foraging skills. In contrast, reproductive success only improved slightly with female age, although females of two or more years initiated their first clutch earlier in the season than one-year-old females, and tended to be mure likely to re-nest if a breeding attempt failed. The poor performance of young females appears unlikely to be related to their foraging ability but may be associated with costs imposed by dispersing to a breeding vacancy earlier in the year. Although the reproductive performance of Brown Thornbills improves considerably with age 1 found no evidence that performance improved as a result of repeated breeding attempts with the same partner.

Ancient mitochondrial DNA and morphology elucidate an extinct island radiation of Indian Ocean giant tortoise (Cylindrapsis)

Ancient mitochondrial DNA sequences were used for investigating the evolution of an entire clade of extinct vertebrates, the endemic tortoises (Cylindraspis) of the Mascarene Islands in the Indian Ocean. Mitochondrial DNA corroborates morphological evidence that there were five species of tortoise with the following relationships: Cylindraspis triserrata ((Cylindraspis vosmaeri and Cylindraspis peltastes) (Cylindraspis inepta and Cylindraspis indica)). Phylogeny indicates that the ancestor of the group first colonized Mauritius where speciation produced C. triserrata and the ancestor of the other species including a second sympatric Mauritian form, C. inepta. A propagule derived from this lineage colonized Rodrigues 590 km to the east, where a second within-island speciation took place producing the sympatric C. vosmaeri and C. peltastes. A recent colonization of Réunion 150 km to the southwest produced C. indica. In the virtual absence of predators, the defensive features of the shells of Mascarene tortoises were largely dismantled, apparently in two stages. 'Saddlebacked' shells with high fronts evolved independently on all three islands. This and other features, such as a derived jaw structure and small body size, may be associated with niche differentiation in sympatric species and may represent a striking example of parallel differentiation in a large terrestrial vertebrate. The history of Mascarene tortoises contrasts with that of the Galápagos, where only a single species is present and surviving populations are genetically much more similar. However, they too show some reduction in anti-predator mechanisms and multiple development of populations with saddlebacked shells.

Latent inhibition and schizophrenia: Pavlovian conditioning of autonomic responses

Latent inhibition (LI) is an important model for understanding cognitive deficits in schizophrenia, Disruption of LI is thought to result from an inability to ignore irrelevant stimuli. The study investigated LI in schizophrenic patients by using Pavlovian conditioning of electrodermal responses in a complete within-subject design. Thirty-two schizophrenic patients, ( 16 acute. unmedicated and 16 medicated patients) and 16 healthy control subjects (matched with respect to age and gender) participated in the study. The experiment consisted of two stages: preexposure and conditioning. During preexposure two visual stimuli were presented, one of which served as the to-be-conditioned stimulus (CSp +) and the other one was the not-to-be-conditioned stimulus (CSp -) during the following conditioning ( = acquisition). During acquisition. two novel visual stimuli (CSn + and CSn -) were introduced. A reaction time task was used as the unconditioned stimulus (US). LI was defined as the difference in response differentiation observed between proexposed and non-preexposed sets of CS + and CS -. During preexposure. the schizophrenic patients did not differ in electrodermal responding from the control subjects, neither concerning the extent of orienting nor the course of habituation. The exposure to novel stimuli at the beginning of the acquisition elicited reduced orienting responses in unmedicated patients compared to medicated patients and control subjects, LI was observed in medicated schizophrenic patients and healthy controls. but not in acute unmedicated patients. Furthermore LI was found to be correlated with the duration of illness: it was attenuated in patients who had suffered their first psychotic episode. (C) 2002 Elsevier Science B.V. All rights reserved.

Bridging the gap between different statistical approaches: An integrated framework for modelling

This paper proposes a template for modelling complex datasets that integrates traditional statistical modelling approaches with more recent advances in statistics and modelling through an exploratory framework. Our approach builds on the well-known and long standing traditional idea of 'good practice in statistics' by establishing a comprehensive framework for modelling that focuses on exploration, prediction, interpretation and reliability assessment, a relatively new idea that allows individual assessment of predictions. The integrated framework we present comprises two stages. The first involves the use of exploratory methods to help visually understand the data and identify a parsimonious set of explanatory variables. The second encompasses a two step modelling process, where the use of non-parametric methods such as decision trees and generalized additive models are promoted to identify important variables and their modelling relationship with the response before a final predictive model is considered. We focus on fitting the predictive model using parametric, non-parametric and Bayesian approaches. This paper is motivated by a medical problem where interest focuses on developing a risk stratification system for morbidity of 1,710 cardiac patients given a suite of demographic, clinical and preoperative variables. Although the methods we use are applied specifically to this case study, these methods can be applied across any field, irrespective of the type of response.

Sentinel node biopsy for breast cancer: Using local results for estimation of risk to the patient

Background: Sentinel node biopsy (SNB) is being increasingly used but its place outside randomized trials has not yet been established. Methods: The first 114 sentinel node (SN) biopsies performed for breast cancer at the Princess Alexandra Hospital from March 1999 to June 2001 are presented. In 111 cases axillary dissection was also performed, allowing the accuracy of the technique to be assessed. A standard combination of preoperative lymphoscintigraphy, intraoperative gamma probe and injection of blue dye was used in most cases. Results are discussed in relation to the risk and potential consequences of understaging. Results: Where both probe and dye were used, the SN was identified in 90% of patients. A significant number of patients were treated in two stages and the technique was no less effective in patients who had SNB performed at a second operation after the primary tumour had already been removed. The interval from radioisotope injection to operation was very wide (between 2 and 22 h) and did not affect the outcome. Nodal metastases were present in 42 patients in whom an SN was found, and in 40 of these the SN was positive, giving a false negative rate of 4.8% (2/42), with the overall percentage of patients understaged being 2%. For this particular group as a whole, the increased risk of death due to systemic therapy being withheld as a consequence of understaging (if SNB alone had been employed) is estimated at less than 1/500. The risk for individuals will vary depending on other features of the particular primary tumour. Conclusion: For patients who elect to have the axilla staged using SNB alone, the risk and consequences of understaging need to be discussed. These risks can be estimated by allowing for the specific surgeon's false negative rate for the technique, and considering the likelihood of nodal metastases for a given tumour. There appears to be no disadvantage with performing SNB at a second operation after the primary tumour has already been removed. Clearly, for a large number of patients, SNB alone will be safe, but ideally participation in randomized trials should continue to be encouraged.

Behaviour state analysis in Rett syndrome: Continuous data reliability measurement

Awareness of optimal behaviour states of children with profound intellectual disability has been reported in the literature as a potentially useful tool for planning intervention within this population. Some arguments have been raised, however, which question the reliability and validity of previously published work on behaviour state analysis. This article sheds light on the debate by presenting two stages of a study of behaviour state analysis for eight girls with Rett syndrome. The results support Mudford, Hogg, and Roberts' (1997, 1999) concerns with the pooling of participant data. The results of Stage 2 also suggest, however, that most categories of behaviour state can be reliably distinguished once definitions of behaviours for each state are clearly defined.

Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy

The advent of molecular markers as a tool to aid selection has provided plant breeders with the opportunity to rapidly deliver superior genetic solutions to problems in agricultural production systems. However, a major constraint to the implementation of marker-assisted selection (MAS) in pragmatic breeding programs in the past has been the perceived high relative cost of MAS compared to conventional phenotypic selection. In this paper, computer simulation was used to design a genetically effective and economically efficient marker-assisted breeding strategy aimed at a specific outcome. Under investigation was a strategy involving the integration of both restricted backcrossing and doubled haploid (DH) technology. The point at which molecular markers are applied in a selection strategy can be critical to the effectiveness and cost efficiency of that strategy. The application of molecular markers was considered at three phases in the strategy: allele enrichment in the BC1F1 population, gene selection at the haploid stage and the selection for recurrent parent background of DHs prior to field testing. Overall, incorporating MAS at all three stages was the most effective, in terms of delivering a high frequency of desired outcomes and at combining the selected favourable rust resistance, end use quality and grain yield alleles. However, when costs were included in the model the combination of MAS at the BC1F1 and haploid stage was identified as the optimal strategy. A detailed economic analysis showed that incorporation of marker selection at these two stages not only increased genetic gain over the phenotypic alternative but actually reduced the over all cost by 40%.

Cyclopropane-1,1-dicarboxylate is a slow-, tight-binding inhibitor of rice ketol-acid reductoisomerase

Ketol-acid reductoisomerase (EC 1.1.1.86) catalyses the second reaction in the biosynthesis of the branched-chain amino acids. The reaction catalyzed consists of two stages, the first of which is an alkyl migration from one carbon atom to its neighbour. The likely transition state is therefore a cyclopropane derivative, and cyclopropane-1,1-dicarboxylate(CPD) has been reported to inhibit the Escherichia coli enzyme. In addition, this compound causes the accumulation of the substrate of ketol-acid reductoisomerase in plants. Here, we investigate the inhibition of the purified rice enzyme. The cDNA was cloned, and the recombinant protein was expressed in E. coli, purified and characterized kinetically. The purified enzyme is strongly inhibited by cyclopropane-1,1-dicarboxylate, with an inhibition constant of 90 nM. The inhibition is time-dependent and this is due to the low rate constants for formation (2.63 X 10(5) M-1 min(-1)) and dissociation (2.37 x 10(-2) min(-1)) of the enzyme-inhibitor complex. Other cyclopropane derivatives are much weaker inhibitors while dimethylmalonate is moderately effective. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

Bajo de la Alumbrera copper-gold deposit: Stable isotope evidence for a porphyry-related hydrothermal system dominated by magmatic aqueous fluids

Alteration zones at the gold-rich Bajo de la Alumbrera porphyry copper deposit in northwestern Argentina are centered on several porphyritic intrusions. They are zoned from a central copper-iron sulfide and gold-mineralized potassic (biotite-K-feldspar +/- quartz) core outward to propylitic (chlorite-illite-epidote-calcite) assemblages. A mineralized intermediate argillic alteration assemblage (chlorite-illite +/- pyrite) has overprinted the potassic alteration zone across the top and sides of the deposit and is itself zoned outward into phyllic (quartzinuscovite-illite +/- pyrite) alteration. This study contributes new data to previously reported delta(18)O and delta D compositions of fluids responsible for the alteration at Bajo de la Alumbrera, and the data are used to infer likely ore-forming processes. Measured and calculated delta(18)O and delta D values of fluids (+8.3 to +10.2 and -33 to -81 parts per thousand, respectively) confirm a primary magmatic origin for the earliest potassic alteration phase. Lower temperature potassic alteration formed from magmatic fluids with lower delta D values (down to -123 parts per thousand). These depleted compositions are distinct from meteoric water and consistent with degassing and volatile exsolution of magmatic fluids derived from an underlying magma. Variability in the calculated composition of fluid associated with potassic alteration is explained in terms of phase separation (or boiling). if copper-iron sulfide deposition occurred during cooling (as proposed elsewhere), this cooling was largely a result of phase separation. Magmatic water was directly involved in the formation of overprinting intermediate argillic alteration assemblages at Bajo de la Alumbrera. Calculated delta(18)O and delta D values of fluids associated with this alteration range from +4.8 to +8.1 and -31 to -71 per mil, respectively Compositions determined for fluids associated with phyllic alteration (-0.8 to +10.2 and -31 to -119 parts per thousand) overlap with the values determined for the intermediate argillic alteration. We infer that phyllic alteration assemblages developed during two stages; the first was a high-temperature (400 degrees-300 degrees C) stage with D-depleted water (delta D = -66 to -119 parts per thousand). This compositional range may have resulted from magma degassing and/or the injection of new magmatic water into a compositionally evolved hydrothermal system. The isotopic variations also can be explained by increased fluid-rock interaction. The second stage of phyllic alteration occurred at a lower temperature (similar to 200 degrees C), and variations in the modeled isotopic compositions imply mixing of magmatic and meteoric waters. Ore deposition that occurred late in the evolution of the hydrothermal system was probably associated with further cooling of the magmatic fluid, in part caused by fluid-rock interaction and phase separation. Changing pH and/or oxygen fuoracity may have caused additional ore deposition. The ingress of meteoric water appears to postdate the bulk of mineralization and occurred as the system at Bajo de la Alumbrera waned.

Assortative Mating for Cigarette Smoking and for Alcohol Consumption in Female Australian Twins and their Spouses

Background Non-random mating affects population variation for substance use and dependence. Developmentally, mate selection leading to positive spousal correlations for genetic similarity may result in increased risk for substance use and misuse in offspring. Mate selection varies by cohort and thus, assortative mating in one generation may produce marked changes in rates of substance use in the next. We aim to clarify the mechanisms contributing to spousal similarity for cigarette smoking and alcohol consumption. Methods Using data from female twins and their male spouses, we fit univariate and bivariate twin models to examine the contribution of primary assortative mating and reciprocal marital interaction to spousal resemblance for regular cigarette smoking and nicotine dependence, and for regular alcohol use and alcohol dependence. Results We found that assortative mating significantly influenced regular smoking, regular alcohol use, nicotine dependence and alcohol dependence. The bivariate models for cigarette smoking and alcohol consumption also highlighted the importance of primary assortative mating on all stages of cigarette smoking and alcohol consumption, with additional evidence for assortative mating across the two stages of alcohol consumption. Conclusions Women who regularly used, and subsequently were dependent on cigarettes or alcohol were more likely to marry men with similar behaviors. After mate selection had occurred, one partner's cigarette or alcohol involvement did not significantly modify the other partner's involvement with these psychoactive substances.

Evaluation of unsupervised semantic mapping of natural language with Leximancer concept mapping

The Leximancer system is a relatively new method for transforming lexical co-occurrence information from natural language into semantic patterns in an unsupervised manner. It employs two stages of co-occurrence information extraction-semantic and relational-using a different algorithm for each stage. The algorithms used are statistical, but they employ nonlinear dynamics and machine learning. This article is an attempt to validate the output of Leximancer, using a set of evaluation criteria taken from content analysis that are appropriate for knowledge discovery tasks.