Process economics evaluation and optimization of adeno-associated virus downstream processing

Adeno-associated virus (AAV) manufacturing has traditionally focused upon lab-scale techniques to culture and purify vector products, leading to limitations in production capacity. The tool presented in this paper assesses the feasibility of using non-scalable technologies at high AAV demands and identifies optimal flowsheets at large-scale that meet both cost and purity targets. The decisional tool comprises (a) a detailed process economics model with the relevant mass balance, sizing, and costing equations for AAV upstream and downstream technologies, (b) a built-in Monte Carlo simulation to assess uncertainties, and (c) a brute-force optimization algorithm for rapid investigation into the optimal purification combinations. The results overall highlighted that switching to more scalable upstream and downstream processing alternatives is economically advantageous. The base case analysis showed the cost and robustness advantages of utilizing suspension cell culture over adherent, as well as a fully chromatographic purification platform over batch ultracentrifugation. Expanding the set of purification options available gave insights into the optimal combination to satisfy both cost and purity targets. As the purity target increased, the optimal polishing solution moved from the non-capsid purifying multimodal chromatography to anion-exchange chromatography or continuous ultracentrifugation.

Environmental life cycle assessment of production of the high intensity sweetener steviol glycosides from Stevia rebaudiana leaf grown in Europe: The SWEET project

PURPOSE

There is an increasing interest in the use of non-nutritive sweeteners to replace added sugar in food and beverage products for reasons of improving consumer health. Much work has been done to understand safety of sweeteners, but very little on sustainability. To address that gap, this study presents the results of a life cycle assessment (LCA) of production of rebaudioside A 60%, 95% pure (RA60) steviol glycoside mix from Stevia rebaudiana leaf grown in Europe.

METHODS

An attributional cradle-to-factory-gate life cycle assessment was conducted on growing of stevia leaves and extraction of steviol glycosides in Europe. Primary data were used from a case study supply chain. Results are reported in impact categories from the ReCiPe 2016 (H) method, with focus given to global warming potential, freshwater eutrophication, water consumption, and land use. Impacts are expressed both in terms of production mass and sweetness equivalence, a common metric for understanding high intensity sweetener potency. Sweetness equivalence of RA60 is typically 200 to 300 times that of sugar. Comparison of environmental impact is made to sugar (sucrose) produced from both cane and beets. The research is part of the EU project SWEET (sweeteners and sweetness enhancers: impact on health, obesity, safety, and sustainability).

RESULTS AND DISCUSSION

Global warming potential for production of RA60 was found to be 20.25 kgCO₂-eq/kg_RA60 on a mass basis and 0.081 kgCO₂-eq/kg_SE on a sweetness equivalence basis. Field production of stevia leaves was found to be the main source of impact for most impact categories, and for all four focus categories. Extraction of the RA60 was the main source of impact for the others. Leaf processing and seedling propagation were minor contributors to life cycle impact. Removal of international transport from the supply chain reduced global warming potential by 18.8%. Compared with sugar on a sweetness equivalence basis, RA60 has approximately 5.7% to 10.2% the impact for global warming potential, 5.6% to 7.2% the impact for land use, and is lower across most other impact categories.

CONCLUSION

This is the first LCA of steviol glycoside mix RA60 produced from leaf in Europe. The results indicate that RA60 can be used to reduce environmental impact of providing a sweet taste by replacing sugar across all impact categories. However, it is important to note that specific formulations in which RA60 is used will have a bearing on the final environmental impact of any food or beverage products. For solid foods, this requires further research.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11367-022-02127-9.

Decisional tool for cost of goods analysis of bioartificial liver devices for routine clinical use

BACKGROUND AIMS

Bioartificial liver devices (BALs) are categorized as advanced therapy medicinal products (ATMPs) with the potential to provide temporary liver support for liver failure patients. However, to meet commercial demands, next-generation BAL manufacturing processes need to be designed that are scalable and financially feasible. The authors describe the development and application of a process economics decisional tool to determine the cost of goods (COG) of alternative BAL process flowsheets across a range of industrial scales.

METHODS

The decisional tool comprised an information database linked to a process economics engine, with equipment sizing, resource consumption, capital investment and COG calculations for the whole bioprocess, from cell expansion and encapsulation to fluidized bed bioreactor (FBB) culture to cryopreservation and cryorecovery. Four different flowsheet configurations were evaluated across demands, with cell factories or microcarriers in suspension culture for the cell expansion step and single-use or stainless steel technology for the FBB culture step.

RESULTS

The tool outputs demonstrated that the lowest COG was achieved with microcarriers and stainless steel technology independent of the annual demand (1500-30 000 BALs/year). The analysis identified the key cost drivers were parameters impacting the medium volume and cost.

CONCLUSIONS

The tool outputs can be used to identify cost-effective and scalable bioprocesses early in the development process and minimize the risk of failing to meet commercial demands due to technology choices. The tool predictions serve as a useful benchmark for manufacturing ATMPs.

Benchmarking biopharmaceutical process development and manufacturing cost contributions to R&D

This study aims to benchmark and analyze the process development and manufacturing costs across the biopharmaceutical drug development cycle and their contribution to overall research and development (R&D) costs. This was achieved with a biopharmaceutical drug development lifecycle cost model that captured the costs, durations, risks and interdependencies of the clinical, process development and manufacturing activities. The budgets needed for process development and manufacturing at each phase of development to ensure a market success each year were estimated. The impact of different clinical success rate profiles on the process development and manufacturing costs at each stage was investigated, with a particular focus on monoclonal antibodies. To ensure a market success each year with an overall clinical success rate (Phase I to approval) of ~12%, the model predicted that a biopharmaceutical company needs to allocate process development and manufacturing budgets in the order of ~$60 M for pre-clinical to Phase II material preparation and ~$70 M for Phase III to regulatory review material preparation. For lower overall clinical success rates of ~4%, which are more indicative of diseases such as Alzheimer's, these values increase to ~$190 M for early-phase and ~$140 Mfor late-phase material preparation; hence, the costs increase 2.5 fold. The costs for process development and manufacturing per market success were predicted to represent 13-17% of the R&D budget from pre-clinical trials to approval. The results of this quantitative structured cost study can be used to aid decision-making during portfolio management and budget planning procedures in biopharmaceutical development.

Process economics evaluation of cell-free synthesis for the commercial manufacture of antibody drug conjugates

Continuous improvements of cell-free synthesis (CFS) systems have generated interest in adopting the technology for the manufacture of biologics. This paper provides an evaluation of the manufacturing cost-effectiveness of CFS for the commercial production of antibody-drug conjugates (ADCs). The evaluation was performed using an advanced techno-economic engine (TEE) built in Python. The TEE is programmed in an object-oriented environment capable of simulating a plethora of process flowsheets and predicting size and cost metrics for the process and the facility. A case study was formulated to compare the economics of whole bioprocesses based on either a CFS system or a mammalian cell system (CHO) for the manufacture of an ADC at a range of product demands. The analysis demonstrated the potential of CFS for the commercial manufacture of biologics and identified key cost drivers related to the system. The CFS system showed an approximately 80% increase in the cost of goods compared to CHO with a significant cost attributed to the in-house manufacture of the bacterial cell extract, necessary for the CFS reaction step in the process. A sensitivity and target analysis highlighted the need for further process improvements especially in the titer for the CFS process to become more competitive against well-established systems.

Evaluating the relationships between aromatic and ethanol levels in gasoline on secondary aerosol formation from a gasoline direct injection vehicle

While the effects of fuel composition on primary vehicle emissions have been well studied, less is known about the effects on secondary aerosol formation and composition. The propensity of light-duty gasoline engines to form secondary aerosol and contribute to regional air quality burdens are of scientific interest. This study assessed secondary aerosol formation and composition due to photochemical aging of exhaust emissions from a light-duty vehicle equipped with gasoline direct injection (GDI) engine. The vehicle was operated on eight fuels with varying ethanol and aromatic levels. Testing was performed over the LA92 cycle using a chassis dynamometer. The aging studies were performed using a mobile environmental chamber. Diluted exhaust emissions were introduced to the mobile chamber over the course of the LA92 cycle and subsequently photochemically reacted. It was found that secondary aerosol mass exceeded the primary particulate matter (PM) emissions. Secondary aerosol was primarily composed of ammonium nitrate due to the elevated tailpipe ammonia emissions. The high aromatic fuels produced greater total carbonaceous aerosol and secondary organic aerosol (SOA) compared to the low aromatic fuels. A clear influence of ethanol for the high aromatic fuels on SOA formation was observed, with greater SOA formation for the fuels with higher ethanol contents. Our results suggest that more SOA formation is expected from current GDI vehicles when operated with gasoline fuels rich with heavier aromatics and blended with higher ethanol levels.

Autologous CAR T-cell therapies supply chain: challenges and opportunities?

Chimeric antigen receptor (CAR) T cells are considered a potentially disruptive cancer therapy, showing highly promising results. Their recent success and regulatory approval (both in the USA and Europe) are likely to generate a rapidly increasing demand and a need for the design of robust and scalable manufacturing and distribution models that will ensure timely and cost-effective delivery of the therapy to the patient. However, there are challenging tasks as these therapies are accompanied by a series of constraints and particularities that need to be taken into consideration in the decision-making process. Here, we present an overview of the current state of the art in the CAR T cell market and present novel concepts that can debottleneck key elements of the current supply chain model and, we believe, help this technology achieve its long-term potential.

Highly Speciated Measurements of Terpenoids Emitted from Laboratory and Mixed-Conifer Forest Prescribed Fires

Wildland fires in the western United States are projected to increase in frequency, duration, and size. Characterized by widespread and diverse conifer forests, burning within this region may lead to significant terpenoid emissions. Terpenoids constitute a major class of highly reactive secondary organic aerosol (SOA) precursors, with significant structure-dependent variability in reactivity and SOA-formation potential. In this study, highly speciated measurements of terpenoids emitted from laboratory and prescribed fires were achieved using two-dimensional gas chromatography. Nearly 100 terpenoids were measured in smoke samples from 71 fires, with high variability in the dominant compounds. Terpenoid emissions were dependent on plant species and tissues. Canopy/needle-derived emissions dominated in the laboratory fires, whereas woody-tissue-derived emissions dominated in the prescribed fires. Such differences likely have implications for terpenoid emissions from high vs low intensity fires and suggest that canopy-dominant laboratory fires may not accurately represent terpenoid emissions from prescribed fires or wildland fires that burn with low intensity. Predicted SOA formation was sensitive to the diversity of emitted terpenoids when compared to assuming a single terpene surrogate. Given the demonstrated linkages between fuel type, fire terpenoid emissions, and the subsequent implications for plume chemistry, speciated measurements of terpenoids in smoke derived from diverse ecosystems and fire regimes may improve air quality predictions downwind of wildland fires.

High throughput process development workflow with advanced decision-support for antibody purification

Chromatography remains the workhorse in antibody purification; however process development and characterisation still require significant resources. The high number of operating parameters involved requires extensive experimentation, traditionally performed at small- and pilot-scale, leading to demands in terms of materials and time that can be a challenge. The main objective of this research was the establishment of a novel High Throughput Process Development (HTPD) workflow combining scale-down chromatography experimentation with advanced decision-support techniques in order to minimise the consumption of resources and accelerate the development timeframe. Additionally, the HTPD workflow provides a framework to rapidly manipulate large datasets in an automated fashion. The central component of the HTPD workflow is the systematic integration of a microscale chromatography experimentation strategy with an advanced chromatogram evaluation method, design of experiments (DoE) and multivariate data analysis. The outputs of this are leveraged into the screening and optimisation components of the workflow. For the screening component, a decision-support tool was developed combining different multi-criteria decision-making techniques to enable a fair comparison of a number of CEX resin candidates and determine those that demonstrate superior purification performance. This provided a rational methodology for screening chromatography resins and process parameters. For the optimisation component, the workflow leverages insights provided through screening experimentation to guide subsequent DoE experiments so as to tune significant process parameters for the selected resin. The resulting empirical correlations are linked to a stochastic modelling technique so as to predict the optimal and most robust chromatographic process parameters to achieve the desired performance criteria.

Cyclocephala (Coleoptera: Scarabaeidae: Dynastinae) evolution in Lesser West Indies indicates a Northward colonization by C. tridentata

A dual cytogenetic and molecular analysis was performed in four species of Cyclocepala (Coleoptera: Scarabaeidae: Dynastinae) from Lesser Antilles (Martinique, Dominica and Guadeloupe). Two species/sub-species, C. mafaffa grandis and C. insulicola, are endemic to Guadeloupe. They have their own non-polymorphic karyotype and a fairly homogeneous haplotype of the COI gene. C. melanocephala rubiginosa has a distinct karyotype. Its COI haplotype is homogeneous in Guadeloupe and heterogeneous in Martinique. Finally, C. tridentata has highly different karyotypes and haplotypes in the three islands. In Martinique, its karyotype, composed of metacentrics, is monomorphic while its haplotype is fairly heterogeneous. Both are close to those of other Cyclocephala and Dynastinae species, thus fairly ancestral. In Guadeloupe, its karyotype is highly polymorphic, with many acrocentrics, and its haplotype fairly homogeneous. Both are highly derived. In Dominica, both the karyotype and the haplotype represent intermediate stages between those of Martinique and Guadeloupe. We conclude that several independent colonization episodes have occurred, which excludes that C. insulicola is a vicariant form of C. tridentata in Guadeloupe. Both chromosome and COI gene polymorphisms clearly indicate a recent colonization with a northward direction for C. tridentata.

Evolution of European cockchafers (Melolonthinae: Scarabaeidae: Coleoptera): a morphological, molecular and chromosomal study of intra- and inter-specific variations

In cockchafers of the genus Melolontha, there is a marked intraspecific polymorphism for morphological characters, making some specimens of one species resemble another. A cytogenetic and molecular (mitochondrial COI gene sequence) study of typical and atypical forms of M. melolontha and M. hippocastani, captured at the same period and area, was performed. Karyotypes and haplotypes clearly characterize each taxon, placing atypical specimens in one or the other species unambiguously. This formally discards the role of hybridization in phenotypic resemblance, as usually proposed. Karyotypes and haplotypes were compared to those of M. pectoralis and Phyllophaga pleei, a more distantly related Melolonthinae, and some Dynastinae species, to reconstruct their ancestral karyotype. The karyotype of M. melolontha is the most derivative and that of P. pleei the most conserved among the Melolonthinae studied, which fits with the phylogeny established by COI gene analysis. Both karyotypes and COI haplotypes demonstrate the proximity of M. pectoralis and M. melolontha. The karyotype of M. melolontha is polymorphic, without relationship with morphological variations. Finally, the existence of similar morphological variations in different Melolontha species and chromosomal polymorphism in M. melolontha is discussed in relation with a network (reticulated) mode of speciation.

Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus)

The major histocompatability complex (MHC) is a multigene family of receptors that bind and present antigenic peptides to T-cells. Genes of the MHC are characterized by an outstanding genetic polymorphism, which is considered to be maintained by positive selection. Sites involved in peptide binding form binding pockets (P) that are collectively termed the peptide-binding region (PBR). In this study, we examined the level of MHC genetic diversity within and among natural populations of brown hare (Lepus europaeus) from Europe and Anatolia choosing for analysis of the second exon of the DQA locus, one of the most polymorphic class II loci. We aimed at an integrated population genetic analysis of L. europeaus by (i) correlating MHC polymorphism to genetic variability and phylogenetic status estimated previously from maternally (mtDNA) and biparentally (allozymes, microsatellites) inherited loci; and (ii) comparing full-length exon amino acid polymorphism with functional polymorphism in the PBR and the binding pockets P1, P6 and P9. A substantial level of DQA exon 2 polymorphism was detected with two completely different set of alleles between the Anatolian and European populations. However, the phylogeny of full-length exon 2 Leeu-DQA alleles did not show a strong phylogeographic signal. The presence of balancing selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous in the PBR and a trans-species pattern of evolution detected after phylogenetic reconstruction. The differentiating patterns detected between genetic and functional polymorphism, i.e. the number and the distribution of pocket variants within and among populations, indicated a hierarchical action of selection pressures.

Mitochondrial DNA variation in Northeast Atlantic and Mediterranean populations of Norway lobster, Nephrops norvegicus

Analysis of the genetic structure of the Norway lobster (Nephrops norvegicus), a marine crustacean with high commercial value, was undertaken to gain information regarding the differentiation of Atlantic from Mediterranean populations of marine invertebrates. Restriction fragment length polymorphism analysis of two mitochondrial DNA segments, 3.6 kilobases in total, was performed. Twelve populations from the North Sea, Irish Sea, Portuguese coast and Aegean Sea were analysed. Low levels of differentiation were found among them (F(ST) = 0.018, P < 0.001) and there were no signs of an Atlantic-Mediterranean divide or of an isolation-by-distance scheme of differentiation. Possible reasons for these low levels of differentiation can be found in the recent expansion of N. norvegicus populations. This is supported by the mismatch distribution of pairwise haplotype differences, as well as by the high mean haplotype diversity (h = 0.93) combined with medium nucleotide diversity (pi = 0.0057) (in comparison to values for marine crustaceans or teleosts) found in this study. This combination of high levels of haplotype diversity with moderate to low levels of nucleotide diversity has also been frequently attributed to a recent time of divergence for various marine species. No evidence was found for a Mediterranean refugium during glaciation periods, separate from the Atlantic, as has been reported for some marine species. The Irish Sea population was the most differentiated as a result of reduced levels of diversity. Results are also discussed in the light of future management of N. norvegicus stocks.

Discrimination of the closely related biocontrol agents Macrolophus melanotoma (Hemiptera: Miridae) and M. pygmaeus using mitochondrial DNA analysis

The separation of the closely related predatory species Macrolophus melanotoma Costa (= M. caliginosus Wagner) and Macrolophus pygmaeus (Rambur) based exclusively on the different colour pattern of the first antennal segment (white central band in M. melanotoma and entirely black in M. pygmaeus) is rather precarious and their taxonomic status is still in doubt. In the present study their taxonomic status was evaluated by DNA confirmatory analysis and hybridization experiments between M. pygmaeus and a Macrolophus taxon, resembling M. melanotoma, with a first antennal segment entirely black or with a white central band collected from Dittrichia viscosa (L.) W. Greuter (Asteraceae) in southern Greece. Adult females from Dittrichia plants hybridized with males of M. pygmaeus and vice versa did not produce viable eggs. The Macrolophus species from Dittrichia irrespective of the first antennal segment coloration differed from M. pygmaeusin digestive patterns generated by AseI, XbaI, and MseI on 16S rRNA and in RAPD profiles produced by the primers OPA-18 and OPA-20. These results demonstrate that on Dittrichia plants there is a distinct dimorphic taxon, M. melanotoma, as it is the only species of the genus Macrolophus bearing a first antennal segment with a central white band. Given the limitation of the coloration pattern, the mtDNA genetic markers are the appropriate method for the identification of M. melanotomaand M. pygmaeus.

Genetic variation of Marchalina hellenica (Hemiptera: Margarodidae) sampled from different hosts and localities in Greece

Random amplified polymorphic DNA (RAPD) analysis was applied to 120 individuals of Marchalina hellenica (Gennadius) representing six populations collected in northern, central and southern mainland Greece. One population was sampled on one species of fir tree and the others on two species of pine trees. Four random decamer primers were used to evaluate genetic variation among the populations examined. The results revealed intra- and interpopulation polymorphism both related to host type and region of origin. Phylogenetic analysis based on genetic distances estimated by the RAPD frequencies revealed an important genetic differentiation in samples collected on fir trees in southern Greece and to a lesser extent in samples from pine trees in central and northern Greece. Furthermore, considerable subdivision and restricted gene flow among the populations examined were observed. The results are discussed in relation to the biology and geographical distribution of M. hellenica in Greece.

RFLP analysis of mitochondrial DNA to evaluate genetic variation in striped red mullet (Mullus surmuletus L.) and red mullet (Mullus barbatus L.) populations

The genetic differentiation of striped red mullet (Mullus surmuletus) and red mullet (Mullus barbatus) was investigated in 6 Mediterranean populations of each species by means of restriction fragment length polymorphism analysis of mitochondrial DNA. Three segments amplified by polymerase chain reaction (control region, COI, and 12S-16S ribosomal RNA) were digested with 20 restriction endonucleases, revealing 71 haplotypes for M. surmuletus and 30 for M. barbatus. For the two species nucleotide diversity was equally distributed within and among populations, leading to N(ST) values of 0.545 and 0.500 for M. surmuletus and M. barbatus, respectively. However, intrapopulation and interpopulation genetic structuring appeared to be much higher for M. surmuletus than for M. barbatus (1.88% vs. 0.46% of mean intrapopulation nucleotide diversity; 1.94% vs. 0.47% of mean interpopulation nucleotide diversity; 0.055% vs. 0.002% of net interpopulation divergence). Furthermore, 81.69% of the haplotypes observed for M. surmuletus were unique, whereas 70.29% of M. barbatus individuals were grouped in 3 common haplotypes. Given that fishing pressure and population sizes are similar for both species, this differentiation could be attributed to differences in biological parameters and life histories between the two species, coupled with oceanographic conditions prevailing in the studied area.

Isolation and characterization of a protein from Mendole (Spicara maena) eggs that binds to DNA and inhibits its replication as well as its acid precipitation

Proteins that bind and protect nucleic acids from acid precipitation have been characterized from human and mouse plasma. In the present study, one protein from Mendole (Spicara maena) eggs was purified to homogeneity, by means of acetone fractionation and Sephadex G-100 gel filtration. The protein inhibited DNA replication, exerted by various DNA polymerases. Amino-acid sequence analysis in the amino terminus revealed a unique sequence. Its possible physiological role is discussed.