Drifts in ADCC-related quality attributes of Herceptin®: Impact on development of a trastuzumab biosimilar

A biosimilar product needs to demonstrate biosimilarity to the originator reference product, and the quality profile of the latter should be monitored throughout the period of the biosimilar's development to match the quality attributes of the 2 products that relate to efficacy and safety. For the development of a biosimilar version of trastuzumab, the reference product, Herceptin®, was extensively characterized for the main physicochemical and biologic properties by standard or state-of-the-art analytical methods, using multiple lots expiring between March 2015 and December 2019. For lots with expiry dates up to July 2018, a high degree of consistency was observed for all the tested properties. However, among the lots expiring in August 2018 or later, a downward drift was observed in %afucose (G0+G1+G2). Furthermore, the upward drift of %high mannose (M5+M6) was observed in the lots with expiry dates from June 2019 to December 2019. As a result, the combination of %afucose and %high mannose showed 2 marked drifts in the lots with expiry dates from August 2018 to December 2019, which was supported by the similar trend of biologic data, such as FcγRIIIa binding and antibody-dependent cell-mediated cytotoxicity (ADCC) activity. Considering that ADCC is one of the clinically relevant mechanisms of action for trastuzumab, the levels of %afucose and %high mannose should be tightly monitored as critical quality attributes for biosimilar development of trastuzumab.     

Global analysis of the apple fruit microbiome: are all apples the same?

We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.     

Impact of protein fouling on nanoparticle capture within the Viresolve® Pro and Viresolve® NFP virus removal membranes

Virus filtration is a robust size-based technique that can provide the high level of viral clearance required for the production of mammalian-derived biotherapeutics such as monoclonal antibodies. Several studies have shown that the retention characteristics of some, but not all, virus filters can be significantly affected by membrane fouling, but there have been no direct measurements of how protein fouling might alter the location of virus capture within these membranes. The objective of this study was to directly examine the effect of protein fouling by human immunoglobulin G (IgG) on virus capture within the Viresolve® Pro and Viresolve® NFP membranes by scanning electron microscopy using different size gold nanoparticles. IgG fouling shifted the capture location of 20 nm gold nanoparticles further upstream within the Viresolve® Pro filter due to the constriction and/or blockage of the pores in the virus retentive region of the filter. In contrast, IgG fouling had no measurable effect on the capture of 20 nm nanoparticles in the Viresolve® NFP membrane, and IgG fouling had no effect on the capture of larger 40 and 100 nm nanoparticles in either membrane. These results provide important insights into how protein fouling alters the virus retention characteristics of different virus filters.     

Consistency of quality attributes for the glycosylated monoclonal antibody Humira® (adalimumab)

Humira® (adalimumab) is a recombinant human IgG1 monoclonal antibody (mAb) glycoprotein consisting of 1330 amino acids that is specific for human tumor necrosis factor (TNF). The biological activity and clinical profile of mAb therapeutics, including adalimumab, is influenced by their protein structure and glycosylation patterns, which can be affected by the expression system, cell culture conditions and purification process methodology. While clinical outcome cannot yet be attributed to many of the individual structural features that constitute a mAb, it is evident that detailed structural attribute analysis is necessary if structural contributions to function are to be comprehensively defined. Adalimumab product quality data generated from over a decade of manufacturing across multiple production sites and through a series of manufacturing scale changes are presented here. These data reveal a consistent and tightly controlled profile for the product.     

Impact of Pluronic® F68 on hollow fiber filter-based perfusion culture performance

Bioprocess and Biosystems Engineering - High cell density is an important factor in achieving high bioreactor productivity. To meet the oxygen demand with density at...     

Impact of Imitation Processes on the Effectiveness of?Ring Vaccination

Ring vaccination can be a highly effective control strategy for an emerging disease or in the final phase of disease eradication, as witnessed in the eradication of smallpox. However, the impact of behavioural dynamics on the effectiveness of ring vaccination has not been explored in mathematical models. Here, we analyze a series of stochastic models of voluntary ring vaccination. Contacts of an index case base vaccinating decisions on their own individual payoffs to vaccinate or not vaccinate, and they can also imitate the behaviour of other contacts of the index case. We find that including imitation changes the probability of containment through ring vaccination considerably. Imitation can cause a strong majority of contacts to choose vaccination in some cases, or to choose non-vaccination in other cases-even when the equivalent solution under perfectly rational (non-imitative) behaviour yields mixed choices. Moreover, imitation processes can result in very different outcomes in different stochastic realizations sampled from the same parameter distributions, by magnifying moderate tendencies toward one behaviour or the other: in some realizations, imitation causes a strong majority of contacts not to vaccinate, while in others, imitation promotes vaccination and reduces the number of secondary infections. Hence, the effectiveness of ring vaccination can depend significantly and unpredictably on imitation processes. Therefore, our results suggest that risk communication efforts should be initiated early in an outbreak when ring vaccination is to be applied, especially among subpopulations that are heavily influenced by peer opinions.     

Cytogenetics in fruit breeding - localization of ribosomal RNA genes on chromosomes of apple (Malus×domestica Borkh.)

 The localization of rRNA genes was studied by fluorescent in situ hybridization (FISH) on chromosomes of the cultivated apple, M.×domestica ‘Pinova’ (2n=34). The 18S/25S rRNA loci were detected in terminal positions of the short arms of two submetacentric and two metacentric chromosome pairs. One 5S rRNA gene locus was found in the proximal region of the short arm of a small metacentric chromosome pair. Received : 21 June 1996 / Accepted : 28 June 1996     

Impact of β-galactosidase mutations on the expression of the canine lysosomal multienzyme complex

β-galactosidase (GLB1) forms a functional lysosomal multienzyme complex with lysosomal protective protein (PPCA) and neuraminidase 1 (NEU1) which is important for its intracellular processing and activity. Mutations in the β-galactosidase gene cause the lysosomal storage disease G_M1-gangliosidosis. In order to identify additional molecular changes associated with the presence of β-galactosidase mutations, the expression of canine lysosomal multienzyme complex components in GLB1^+/+, GLB1^+/? and GLB1^?/? fibroblasts was investigated by quantitative RT-PCR, Western blot and enzymatic assays. Quantitative RT-PCR revealed differential regulation of total β-galactosidase, β-galactosidase variants and protective protein for β-galactosidase gene (PPGB) in GLB1^+/? and GLB1^?/? compared to GLB1^+/+ fibroblasts. Furthermore, it was shown that PPGB levels gradually increased with the number of mutant β-galactosidase alleles while no change in the NEU1 expression was observed. This is the first study that simultaneously examine the effect of GLB1^+/+, GLB1^+/? and GLB1^?/? genotypes on the expression of lysosomal multienzyme complex components. The findings reveal a possible adaptive process in GLB1 homozygous mutant and heterozygous individuals that could facilitate the design of efficient therapeutic strategies.     

Impact of postharvest exogenous γ-aminobutyric acid treatment on cucumber fruit in response to chilling tolerance

Low-temperature storage is generally used to extend postharvest lifetime and to inhibit decay of cucumber fruit, but it also enhances the intensity of chilling injury. The capability of γ-aminobutyric acid to enhance antioxidant enzyme activities and reduce chilling injury was studied in cucumber (Cucumis sativus L.) fruit stored at 1 °C for 5 weeks. The purpose of this study was to define if the GABA-induced modification in antioxidant system and phospholipase activity is linked to the reduced chilling injury in cold-stored cucumber fruit. Alleviation of chilling injury by GABA treatment was related to increased content of proline, endogenous GABA and enhanced activities of CAT and SOD, together with reduced activities of PLC, PLD and LOX. We suggest that PLC, LOX and PLD are associated with chilling injury initiation by involvement in a signaling pathway and membrane deterioration. Therefore the results obtained in this study suggest GABA’s potential for postharvest applications for reducing chilling injury symptom in cucumber fruit.     

Impact of the ‘tubulin economy’ on the formation and function of the microtubule cytoskeleton

The microtubule cytoskeleton is assembled from a finite pool of α,β-tubulin, the size of which is controlled by an autoregulation mechanism. Cells also tightly regulate the architecture and dynamic behavior of microtubule arrays. Here, we discuss progress in our understanding of how tubulin autoregulation is achieved and highlight work showing that tubulin, in its unassembled state, is relevant for regulating the formation and organization of microtubules. Emerging evidence suggests that tubulin regulates microtubule-associated proteins and kinesin motors that are critical for microtubule nucleation, dynamics, and function. These relationships create feedback loops that connect the tubulin assembly cycle to the organization and dynamics of microtubule networks. We term this concept the ‘tubulin economy’, which emphasizes the idea that tubulin is a resource that can be deployed for the immediate purpose of creating polymers, or alternatively as a signaling molecule that has more far-reaching consequences for the organization of microtubule arrays.     

The Impact of the Species–Area Relationship on Estimates of Paleodiversity

Estimates of paleodiversity patterns through time have relied on datasets that lump taxonomic occurrences from geographic areas of varying size per interval of time. In essence, such estimates assume that the species–area effect, whereby more species are recorded from larger geographic areas, is negligible for fossil data. We tested this assumption by using the newly developed Miocene Mammal Mapping Project database of western North American fossil mammals and its associated analysis tools to empirically determine the geographic area that contributed to species diversity counts in successive temporal bins. The results indicate that a species–area effect markedly influences counts of fossil species, just as variable spatial sampling influences diversity counts on the modern landscape. Removing this bias suggests some traditionally recognized peaks in paleodiversity are just artifacts of the species–area effect while others stand out as meriting further attention. This discovery means that there is great potential for refining existing time-series estimates of paleodiversity, and for using species–area relationships to more reliably understand the magnitude and timing of such biotically important events as extinction, lineage diversification, and long-term trends in ecological structure.     

Chimpanzees’ spontaneous temporal sorting of stimuli on the basis of physical identity

This study asked the question “Would chimpanzees’ choice of stimuli in a sorting task follow any consistent sequence?”. Four stimuli (e.g., two plastic grapes and two hairpins) were presented on each trial. The two chimpanzees were reinforced after placing all four stimuli, one at a time, in a receptacle. The order that stimuli were chosen was classified into one of three sequences: two pairs (e.g., grape, grape, hairpin, hairpin), one pair (e.g., grape, hairpin, hairpin, grape), or no pairs (e.g., grape, hairpin, grape, hairpin). The hypothesis that the number of different sequences would be equal was rejected (p<.001) for both subjects. The sequence of two pairs occurred most frequently. This result was accounted for by two factors: (1) some stimuli were chosen first significantly more often than others, indicating the subjects preferred certain stimuli; (2) when the data reflecting preferences was removed, the hypothesis that the number of different sequences would be equal was rejected again (p<.001) and the sequence of two pairs still occurred most frequently. The results indicate chimpanzees’ choice of stimuli in a sorting task is an organized rather than a random process.     

Impact of tree training system,branch type and position in the canopy on the ripening homogeneity of ‘Abbé Fétel’ pear fruit

In pear, fruit ripening is not homogeneous, which leads to problems in harvest and storage management. To identify factors affecting the ripening homogeneity, structural, biochemical and molecular parameters were investigated. Fruits were sampled from trees trained with three different systems, spindle, V-shaped and bi-axis, and were further grouped on the basis of canopy position (top or bottom) and branch type (short-old-spurs, 3-year-old or older branches, 2-year-old branches and twigs). This study confirmed that the position in the canopy plays a crucial role in fruit ripening in V-shaped and bi-axis training systems. Fruit on the spindle training system was unaffected by the position of the canopy, albeit showing a large variability within the fruit of each part of the canopy. Such variability is much lower in the bi-axis and V-shaped systems. The spindle training system had no similarity in homogeneity indices between the molecular and physiological measurements. Partial least square discriminate analysis (PLS-DA) showed differences in training system, branch type and canopy position separated by the different physiological and molecular parameters. Short-old-spurs and twigs had the highest homogeneity and least variability in all training systems and branch types. In addition, partial least square path modelling (PLS-PM) was able to identify a high correlation between physiological measurements and ripening compared to that of molecular data.     

The effect of bupivacaine·HCl on the physical properties of neuronal membranes

Fluorescent probe techniques were used to evaluate the effect of bupivacaine.HCl on the physical properties (transbilayer asymmetric lateral and rotational mobilities, annular lipid fluidity and protein distribution) of synaptosomal plasma membrane vesicles (SPMVs) isolated from bovine cerebral cortex. An experimental procedure was used based on selective quenching of both 1,3-di(1-pyrenyl)propane (Py-3-Py) and 1,6-diphenyl-1,3,5-hexatriene (DPH) by trinitrophenyl groups, and radiationless energy transfer (RET) from the tryptophans of membrane proteins to Py-3-Py. Bupivacaine.HCl increased the bulk lateral and rotational mobilities, and annular lipid fluidity in SPMVs lipid bilayers, and had a greater fluidizing effect on the inner monolayer than that of the outer monolayer. The magnitude of increasing effect on annular lipid fluidity in SPMVs lipid bilayer induced by bupivacaine.HCl was significantly far greater than magnitude of increasing effect of the drug on the lateral and rotational mobilities of bulk SPMVs lipid bilayer. It also caused membrane proteins to cluster. These effects of bupivacaine.HCl on neuronal membranes may be responsible for some, though not all, of the local anesthetic actions of bupivacaine.HCl.     

AlphaFold – A Personal Perspective on the Impact of Machine Learning

I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on a known structure as a template, the problem of the pathway of protein folding was posed and bets were taken in the emerging field of Machine Learning on whether computers could outplay humans at chess. Half a century later, Machine Learning has progressed from using computational power combined with human knowledge in solving problems to playing chess without human knowledge being used, where it has produced novel strategies. Protein structures are being solved by Machine Learning based on human-derived knowledge but without templates. There is much promise that programs like AlphaFold based on Machine Learning will be powerful tools for designing entirely novel protein folds and new activities. But, will they produce novel ideas on protein folding pathways and provide new insights into the principles that govern folds?     

Climatic factors affecting the occurrence of cloudy stain on the fruit skin of ‘Triumph’ Japanese persimmon

Cloudy stain is a physiological disorder of the Japanese persimmon blemishing the skin and causing a great reduction of fruit quality, thus decreasing its commercial value. The stain starts at or just prior to the fruit colour-break stage, coinciding with the presence of cuticular cracks which increase cuticle water permeability and expose subepidermal cells to air and water, causing oxidation of polyphenol substances of large skin areas that turn almost black. The incidence of the disorder examined over four consecutive years in two growing areas of Spain revealed significant differences from year to year, between areas and even the tree face examined. The data consistently showed that cooler groves and fruit located on the northern face of the canopy were more prone to develop the stain. During the 4 years of the study, the average daily minimum temperature of a period of 15–25 days prior to the onset of staining followed the same order as the yearly staining rate, and accumulated hours below 13°C correlated significantly with the percentage of fruit starting the disorder. No relationship was found between the time-course of relative humidity (RH) and the onset of staining, but once the stain started the lower RH resulted in the lower percentage of affected fruit. Dew point, wind speed, rainfall and evapotranspiration did not correlate either with the onset of staining or with its incidence. Rind of cloudy-stained fruit had higher concentration of N, K, Mg and Fe and lower concentration of Ca than that of healthy fruit, but it is not the cause of the disorder. Accordingly, we conclude that cloudy stain of Japanese persimmon starts after a period of low temperature (≤ 13°C) and, afterwards, RH is responsible for its development and severity.     

Impact of Subunit Composition on the Uptake of α-Crystallin by Lens and Retina

Misfolded protein aggregation, including cataract, cause a significant amount of blindness worldwide. α-Crystallin is reported to bind misfolded proteins and prevent their aggregation. We hypothesize that supplementing retina and lens with α-crystallin may help to delay disease onset. The purpose of this study was to determine if αB-crystallin subunits containing a cell penetration peptide (gC-tagged αB-crystallin) facilitate the uptake of wild type αA-crystallin (WT-αA) in lens and retina. Recombinant human αB-crystallin was modified by the addition of a novel cell penetration peptide derived from the gC gene product of herpes simplex virus (gC-αB). Recombinant gC-αB and wild-type αA-crystallin (WT-αA) were purified from E. coli over-expression cultures. After Alexa-labeling of WT-αA, these proteins were mixed at ratios of 1:2, 1:5 and 1:10, respectively, and incubated at 37°C for 4 hours to allow for subunit exchange. Mixed oligomers were subsequently incubated with tissue culture cells or mouse organ cultures. Similarly, crystallin mixtures were injected into the vitreous of rat eyes. At various times after exposure, tissues were harvested and analyzed for protein uptake by confocal microscopy or flow cytometry. Chaperone-like activity assays were performed on α-crystallins ratios showing optimal uptake using chemically-induced or heat induced substrate aggregation assays. As determined by flow cytometry, a ratio of 1:5 for gC-αB to WT-αA was found to be optimal for uptake into retinal pigmented epithelial cells (ARPE-19). Chaperone-like activity assays demonstrated that hetero-oligomeric complex of gC-αB to WT-αA (in 1:5 ratio) retained protein aggregation protection. We observed a significant increase in protein uptake when optimized (gC-αB to WT-αA (1:5 ratio)) hetero-oligomers were used in mouse lens and retinal organ cultures. Increased levels of α-crystallin were found in lens and retina following intravitreal injection of homo- and hetero-oligomers in rats.     

Impact of Routing Flexibility on the Performance of an FMS—A Simulation Study

The evolving manufacturing environment is characterized by a drive toward increasing flexibility. One possible manifestation of flexibility within an FMS is in the form of routing flexibility. Providing this typically is an expensive proposition, and system designers therefore aim to provide only the required levels commensurate with a given set of operating conditions. This paper presents a framework based on a Taguchi experimental design for studying the nature of the impact of varying levels of routing flexibility on the performance of an FMS. Simulation results indicate that increases in routing flexibility, when made available at the cost of an associated penalty on operation processing time, is not always beneficial. There is an optimal flexibility level, beyond which system performance deteriorates, as judged by the makespan measure of performance. It is suggested that the proposed methodology can be used in practice for not only setting priorities on specific design and control factors but also for highlighting likely factor level combinations that could yield near-optimal shop performance.     

Understanding the pharmacokinetics of Coartem®

Background

During pregnancy, women are more susceptible to Plasmodium falciparum infections and frequently have a higher parasitaemia than non-pregnant women. Several mechanisms are responsible for their increased susceptibility, including down-modulation of immune responses that aid in parasite clearance and sequestration of infected erythrocytes in the placenta. Early in pregnancy, a third mechanism may contribute to higher parasitaemia, since it has been reported that addition of human chorionic gonadotropin (hCG) to in vitro cultures of the NF54-strain of P. falciparum results in increased parasite growth rates. The goal of this study was to further examine the effect of hCG on P. falciparum growth.

Methods

The NF54-3D7, FVO and 7G8 strains of P. falciparum were cultured in vitro with various physiological concentrations of hCG purchased from three sources. Infected erythrocytes were also co-cultured with a human cell line that naturally secretes hCG.

Results

Results from 14 experiments using different combinations of parasite strains and concentrations of hCG from different sources, as well as the co-culture studies, failed to provide convincing evidence that hCG enhances parasite growth in vitro.

Conclusion

Based on these data, it seems unlikely that hCG has a direct effect on the rate of parasite growth early in pregnancy.