Heterologous expression of NoxA confers aerotolerance in Clostridium sporogenes

Clostridium is a genus of gram-positive obligate anaerobic bacteria. Some species of Clostridium, including Clostridium sporogenes, may be of use in bacteria-mediated cancer therapy. Spores of Clostridium are inert in healthy normoxic tissue but germinate when in the hypoxic regions of solid tumors, causing tumor regression. However, such treatments fail to completely eradicate tumors partly because of higher oxygen levels at the tumor's outer rim. In this study, we demonstrate that a degree of aerotolerance can be introduced to C. sporogenes by transfer of the noxA gene from Clostridium aminovalericum. NoxA is a water-forming NADH oxidase enzyme, and so has no detrimental effect on cell viability. In addition to its potential in cancer treatment, the noxA-expressing strain described here could be used to alleviate challenges related to oxygen sensitivity of C. sporogenes in biomanufacturing.

A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater

As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.

Expression of Interleukin-1β protein in vitro,exvivo and in vivo salmonid models

Interleukin-1β (IL-1β) is one of the first cytokines expressed during immune responses, and its levels are affected by many factors, including stress. To date, it has only been possible to measure IL-1β transcript (mRNA) expression quantitatively in fish using qPCR. This is because previous studies that measured IL-1β protein concentrations in these taxa used western blotting, which only provides qualitative data. To advance our knowledge of fish IL-1β biology, and because post-translational processing plays a critical role in the activation of this molecule, we developed a quantitative enzyme-linked immunosorbent assay (ELISA) to accurately measure the concentration of IL-1β protein in several cell cultures and in vivo in salmonids. We compared changes in IL-1β protein levels to the expression of its mRNA. The developed ELISA was quite sensitive and has a detection limit of 12.5 pg/mL. The tools developed, and information generated through this research, will allow for a more accurate and complete understanding of IL-1β's role in the immune response of salmonids.The assay described here has the potential to significantly advance our ability to assess fish health and immune status.

A sensitive assay for scrutiny of Autographa californica multiple nucleopolyhedrovirus genes using CRISPR-Cas9

Baculoviruses have very large genomes and previous studies have demonstrated improvements in recombinant protein production and genome stability through the removal of some nonessential sequences. However, recombinant baculovirus expression vectors (rBEVs) in widespread use remain virtually unmodified. Traditional approaches for generating knockout viruses (KOVs) require several experimental steps to remove the target gene prior to the generation of the virus. In order to optimize rBEV genomes by removing nonessential sequences, more efficient techniques for establishing and evaluating KOVs are required. Here, we have developed a sensitive assay utilizing CRISPR-Cas9-mediated gene targeting to examine the phenotypic impact of disruption of endogenous Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genes. For validation, 13 AcMNPV genes were targeted for disruption and evaluated for the production of GFP and progeny virus - traits that are essential for their use as vectors for recombinant protein production. The assay involves transfection of sgRNA into a Cas9-expressing Sf9 cell line followed by infection with a baculovirus vector carrying the gfp gene under the p10 or p6.9 promoters. This assay represents an efficient strategy for scrutinizing AcMNPV gene function through targeted disruption, and represents a valuable tool for developing an optimized rBEV genome. KEY POINTS: [Formula: see text] A method to scrutinize the essentiality of baculovirus genes was developed. [Formula: see text] The method uses Sf9-Cas9 cells, a targeting plasmid carrying a sgRNA, and a rBEV-GFP. [Formula: see text] The method allows scrutiny by only needing to modify the targeting sgRNA plasmid.

Evaluation of Virus-Free Manufacture of Recombinant Proteins Using CRISPR-Mediated Gene Disruption in Baculovirus-Infected Insect Cells

The manufacture and downstream processing of virus-like particles (VLPs) using the baculovirus expression vector system (BEVS) is complicated by the presence of large concentrations of baculovirus particles, which are similar in size and density to VLPs, and consequently are difficult to separate. To reduce the burden of downstream processing, CRISPR-Cas9 technology was used to introduce insertion-deletion (indel) mutations within the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) gp64 open reading frame, which encodes the major envelope protein of AcMNPV. After comfirming the site-specific targeting of gp64 leading to reduced budded virus (BV) release, the gag gene of human immunodeficiency virus type 1 was expressed to produce Gag VLPs. This approach was effective for producing VLPs using the BEVS whilst simultaneously obstructing BV release.

Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae

The overuse and misuse of antibiotics has led to the emergence of antibiotic-resistant bacterial species which remain a challenge to treat therapeutically. Novel and efficacious drugs are desperately needed to combat pathogens. One method to facilitate these discoveries is the use of in silico methods. Computational biology has the power to scan large data sets and screen for potential molecules with antibacterial function. In the current study, an in silico approach was used to identify an antimicrobial peptide (AMP) derived from rainbow trout von Willebrand Factor. The AMP was tested against a panel of aquatic bacterial pathogens and was found to possess antibacterial activity against Streptococcus iniae (S. iniae). Since S. iniae is a zoonotic pathogen, this may be useful in other species as well. The peptide was non-hemolytic and non-cytotoxic at the concentrations tested in rainbow trout cells. Pre-treatment of rainbow trout cells with the peptide did not result in an upregulation of immune genes but stimulating the rainbow trout macrophage/monocyte-like cell line, RTS11, with heat-killed S. iniae, did result in a significant upregulation of the tumor necrosis factor alpha (tnfa) gene. In this study, a new AMP has been identified but its expression, synthesis and role in vivo remains unknown. Nevertheless, the findings presented improve our understanding of fish gill and macrophage responses towards this important zoonotic pathogen.

Utility of Alternative Promoters for Foreign Gene Expression Using the Baculovirus Expression Vector System

The baculovirus expression vector system (BEVS) is a widely used platform for recombinant protein production for use in a wide variety of applications. Of particular interest is production of virus-like particles (VLPs), which consist of multiple viral proteins that self-assemble in strict stoichiometric ratios to mimic the structure of a virus but lacks its genetic material, while a significant amount of effort has been spent on optimizing expression ratios by co-infecting cells with multiple recombinant BEVs and modulating different process parameters, co-expressing multiple foreign genes from a single rBEV may offer more promise. However, there is currently a lack of promoters available with which to optimize co-expression of each foreign gene. To address this, previously published transcriptome data was used to identify promoters that have incrementally lower expression profiles and compared by expressing model cytoplasmic and secreted proteins. Bioinformatics was also used to identify sequence determinants that may be important for late gene transcription regulation, and translation initiation. The identified promoters and bioinformatics analyses may be useful for optimizing expression of foreign genes in the BEVS.

Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media

In this study, a chemically defined, animal component-free media was developed to promote Vero growth in suspension. Key media compounds were screened using Plackett–Burman styled experiments to create a media formulation to support suspension growth. Vero cells remained viable in suspension, but their growth rate was extremely low, conversely, other cell types such as CHO-K1, MDCK and HEK293T were able to grow in single cell suspension in the same media. To investigate the slow growth of Vero cells, RNA-seq analysis was conducted. Vero cells were cultured in three different conditions: adherently in serum-containing medium, adherently in in-house medium, and in suspension in low calcium and magnesium in-house medium. This study illustrates that adherent cells maintain similar gene expression, while the suspension phenotype tends to overexpress genes related to renal tubules.

Antimicrobial Polymeric Composites for High-touch Surfaces in Healthcare Applications

Antimicrobial polymer composites have long been utilized in the healthcare field as part of the first line of defense. These composites are desirable in that they pose a minimal risk of developing contagions with antibiotic resistance. For this reason, the field of antimicrobial composites has seen steady growth over recent years and is becoming increasingly important during the current COVID-19 pandemic. In this article, we first review the need of the antimicrobial polymers in high tough surfaces, the antimicrobial mechanism, and then the recent advances in the development of antimicrobial polymer composite including the utilization of intrinsic antimicrobial polymers, the addition of antimicrobial additives, and new exploration of surface patterning. While there are many established and developing methods of imbuing a material with antimicrobial activity, there currently is no standard quantification method for these properties leading to difficulty comparing the efficacy of these materials within the literature. A discussion of the common antimicrobial characterization methods is provided along with highlights on the need of a standardized quantification of antiviral and antibacterial properties in testing to allow ease of comparison between generated libraries and to facilitate proper screening. We also discuss and comment on the current trends of the development of antimicrobial polymer composites with long-lasting and specific antimicrobial activities, nontoxic properties, and environmental friendliness against a broad-spectrum of microbes.

Droplet formation of biological non-Newtonian fluid in T-junction generators. II. Model for final droplet volume prediction

This work represents the second part of a two-part series on the dynamics of droplet formation in a T-junction generator under the squeezing regime when using solutions of red blood cells as the dispersed phase. Solutions containing red blood cells are non-Newtonian; however, these solutions do not behave in the same way as other non-Newtonian fluids currently described in the literature. Hence, available models do not capture nor predict important features useful for the design of T-junction microfluidic systems, including droplet volume. The formation of a red blood cell-containing droplet consists of three stages: a lag stage, a filling stage, and a necking stage, with the lag stage only observed in narrow dispersed phase channel setups. Unlike other shear-thinning fluids, thread elongation into the main channel at the end of the necking stage is not observed for red blood cell solutions. In this work, a model that predicts the final droplet volume of a red blood cell containing droplets in T-junction generators is presented. The model combines a detailed analysis of the geometrical shape of the droplet during the formation process, with force and Laplace pressure balances to obtain the penetration depth (b_{fill}^{*}) and the critical neck thickness (2r_{pinch}^{*}) of the droplet. The performance of the model was validated by comparing the operational parameters (droplet volume, the spacing between the droplet, and the generation frequency) with the experimental data across a range of the dimensionless parameters (flow rate ratios, continuous phase viscosities, and channel geometries).

Droplet formation of biological non-Newtonian fluid in T-junction generators. I. Experimental investigation

The extension of microfluidics to many bioassay applications requires the ability to work with non-Newtonian fluids. One case in point is the use of microfluidics with blood having different hematocrit levels. This work is the first part of a two-part study and presents the formation dynamics of blood droplets in a T-junction generator under the squeezing regime. In this regime, droplet formation with Newtonian fluids depends on T-junction geometry; however, we found that in the presence of the non-Newtonian fluid such as red blood cells, the formation depends on not only to the channel geometry, but also the flow rate ratio of fluids, and the viscosity of the phases. In addition, we analyzed the impact of the red blood cell concentration on the formation cycle. In this study, we presented the experimental data of the blood droplet evolution through the analysis of videos that are captured by a high-speed camera. During this analysis, we tracked several parameters such as droplet volume, spacing between droplets, droplet generation frequency, flow conditions, and geometrical designs of the T junction. Our analysis revealed that, unlike other non-Newtonian fluids, where the fourth stage exists (stretching stage), the formation cycle consists of only three stages: lag, filling, and necking stages. Because of the detailed analysis of each stage, a mathematical model can be generated to predict the final volume of the blood droplet and can be utilized as a guide in the operation of the microfluidic device for biochemical assay applications; this is the focus of the second part of this study [Phys. Rev. E 105, 025106 (2022)10.1103/PhysRevE.105.025106].

Pseudomonas Exotoxin-Based Immunotoxins: Over Three Decades of Efforts on Targeting Cancer Cells With the Toxin

Cancer is one of the prominent causes of death worldwide. Despite the existence of various modalities for cancer treatment, many types of cancer remain uncured or develop resistance to therapeutic strategies. Furthermore, almost all chemotherapeutics cause a range of side effects because they affect normal cells in addition to malignant cells. Therefore, the development of novel therapeutic agents that are targeted specifically toward cancer cells is indispensable. Immunotoxins (ITs) are a class of tumor cell-targeted fusion proteins consisting of both a targeting moiety and a toxic moiety. The targeting moiety is usually an antibody/antibody fragment or a ligand of the immune system that can bind an antigen or receptor that is only expressed or overexpressed by cancer cells but not normal cells. The toxic moiety is usually a protein toxin (or derivative) of animal, plant, insect, or bacterial origin. To date, three ITs have gained Food and Drug Administration (FDA) approval for human use, including denileukin diftitox (FDA approval: 1999), tagraxofusp (FDA approval: 2018), and moxetumomab pasudotox (FDA approval: 2018). All of these ITs take advantage of bacterial protein toxins. The toxic moiety of the first two ITs is a truncated form of diphtheria toxin, and the third is a derivative of Pseudomonas exotoxin (PE). There is a growing list of ITs using PE, or its derivatives, being evaluated preclinically or clinically. Here, we will review these ITs to highlight the advances in PE-based anticancer strategies, as well as review the targeting moieties that are used to reduce the non-specific destruction of non-cancerous cells. Although we tried to be as comprehensive as possible, we have limited our review to those ITs that have proceeded to clinical trials and are still under active clinical evaluation.

Effectiveness of antiviral metal and metal oxide thin-film coatings against human coronavirus 229E

Virucidal thin-film coatings have the potential to inactivate pathogens on surfaces, preventing or slowing their spread. Six potential nanoscale antiviral coatings, Cu, Cu2O, Ag, ZnO, zinc tin oxide (ZTO), and TiO2, are deposited on glass, and their ability to inactivate the HCoV-229E human coronavirus is assessed using two methods. In one method, droplets containing HCoV-229E are deposited on thin-film coatings and then collected after various stages of desiccation. In the second method, the thin-film coatings are soaked in the virus supernatant for 24 h. The Cu and Cu2O coatings demonstrate clear virucidal behavior, and it is shown that controlled delamination and dissolution of the coating can enhance the virucidal effect. Cu is found to produce a faster and stronger virucidal effect than Cu2O in the droplet tests (3 log reduction in the viral titer after 1 h of exposure), which is attributed, in part, to the differences in film adhesion that result in delamination of the Cu film from the glass and accelerated dissolution in the droplet. Despite Ag, ZnO, and TiO2 being frequently cited antimicrobial materials, exposure to the Ag, ZnO, ZTO, and TiO2 coatings results in no discernible change to the infectivity of the coronavirus under the conditions tested. Thin-film Cu coatings are also applied to the polypropylene fabrics of N95 respirators, and droplet tests are performed. The Cu fabric coating reduces the infectivity of the virus; it results in a 1 order-of-magnitude reduction in the viral titer within 15 min with a 2 order-of-magnitude reduction after 1 h.

Virus matrix interference on assessment of virucidal activity of high-touch surfaces designed to prevent hospital-acquired infections

Objectives/purpose

High-touch surfaces are a critical reservoir in the spread of nosocomial infections. Although disinfection and infection control protocols are well developed, they lack the ability to passively reduce the pathogenic load of high-touch surfaces. Copper and its alloys have been suggested as a surface that exhibit continuous biocidal effects. Antimicrobial studies on these surfaces are prevalent, while virucidal studies are not as well explored. The goal of this study was to first determine the virucidal activity of a copper–nickel–zinc alloy and to then examine the effect of soiling and virus preparation on virucidal activity.

Methods

A baculovirus vector was used as an easily quantifiable model of an infectious enveloped animal cell virus. Droplets containing virus were deposited on surfaces and allowed to stay wet using humidity control or were dried onto the surface. Virus was then recovered from the surface and assayed for infectivity. To examine how the composition of the droplet affected the survival of the virus, 3 different soiling conditions were tested. The first two were recommended by the United States Environmental Protection Agency and the third consisted of cell debris resulting from virus amplification.

Results

A copper–nickel–zinc alloy was shown to have strong virucidal effects for an enveloped virus. Copper, nickel, and zinc ions were all shown to leach from the alloy surface and are the likely cause of virucidal activity by this surface. Virucidal activity was achieved under moderate soiling but lost under high soiling generated by routine virus amplification procedures. The surface was able to repeatably inactivate dried virus droplets under moderate soiling conditions, but unable to do so for virus droplets kept wet using high humidity.

Conclusion

Ion leaching was associated with virucidal activity in both wet and dried virus conditions. Soiling protected the virus by quenching metal ions, and not by inhibiting leaching. The composition of the solution containing virus plays a critical role in evaluating the virucidal activity of surfaces and surface coatings.

Characterizing internal cavity modulation of corn starch microcapsules

Swelling of normal corn starch granules through heating in water leads to enlargement of the starch particles and a corresponding increase in internal cavity size. Through control of the swelling extent, it is possible to tune the size of the internal cavity for the starch microcapsules (SMCs). The swelling extent can be controlled through regulation of the swelling time and the swelling temperature. Since the swelling extent is correlated with particle size and solubility, these aspects may also be controlled. Imaging the SMCs at increasing levels of swelling extent using scanning electron microscopy (SEM) allowed for the internal cavity swelling process to be clearly observed. Brightfield and polarizing light microscopy validated the SEM observations. Confocal laser scanning microscopy provided further validation and indicated that it is possible to load the SMCs with large molecules through diffusion. The highly tunable SMCs are novel microparticles which could have applications in various industries.

A critical evaluation of current protocols for self-sterilizing surfaces designed to reduce viral nosocomial infections

BACKGROUND

Biocidal high-touch surfaces contact surfaces can be used to help reduce healthcare-acquired infections (HAIs). While the bactericidal protocols are well developed, there remains high variability in the methods used to evaluate the virucidal properties of such surfaces. This paper seeks to identify the most commonly used methods and critically evaluate the strengths of each method by comparing tests from standard testing organisations and related bactericidal protocols.

METHODS

Three databases and grey literature were queried using a key-word search for relevant articles. Articles were selected if they met the criteria of virucidal properties of self-sterilizing surfaces designed to prevent HAIs. Of the resulting 177 articles, 38 met the inclusion criteria.

RESULTS

The resulting papers varied greatly in their testing methods and recommendations. Further, no standard test adequately meets the needs for specifically testing virucidal properties of self-sterilizing surfaces.

CONCLUSIONS

Studies have shown that temperature and humidity can affect the performance of virucidal touch-surfaces, but no standard protocols were found to test these factors.

1D 1 H NMR as a Tool for Fecal Metabolomics

Metabolomic studies allow a deeper understanding of the processes of a given ecological community than nucleic acid-based surveys alone. In the case of the gut microbiota, a metabolic profile of, for example, a fecal sample provides details about the function and interactions within the distal region of the gastrointestinal tract, and such a profile can be generated in a number of different ways. This unit elaborates on the use of 1D ¹ H NMR spectroscopy as a commonly used method to characterize small-molecule metabolites of the fecal metabonome (meta-metabolome). We describe a set of protocols for the preparation of fecal water extraction, storage, scanning, measurement of pH, and spectral processing and analysis. We also compare the effects of various sample storage conditions for processed and unprocessed samples to provide a framework for comprehensive analysis of small molecules from stool-derived samples. © 2020 Wiley Periodicals LLC Basic Protocol 1: Extracting fecal water from crude fecal samples Alternate Protocol 1: Extracting fecal water from small crude fecal samples Basic Protocol 2: Acquiring NMR spectra of metabolite samples Alternate Protocol 2: Acquiring NMR spectra of metabolite samples using Bruker spectrometer running TopSpin 3.x Alternate Protocol 3: Acquiring NMR spectra of metabolite samples by semiautomated process Basic Protocol 3: Measuring sample pH Support Protocol 1: Cleaning NMR tubes Basic Protocol 4: Processing raw spectra data Basic Protocol 5: Profiling spectra Support Protocol 2: Spectral profiling of sugars and other complex metabolites.

Limitation in Controlling the Morphology of Mammalian Vero Cells Induced by Cell Division on Asymmetric Tungsten-Silicon Oxide Nanocomposite

Engineered nanomaterials are often used in tissue engineering applications to influence and manipulate the behavior of cells. Recently, a number of tungsten-silicon oxide nanocomposite devices containing equal width (symmetric) tungsten and silicon oxide parallel line comb structures were developed and used by our group. The devices induced over 90% of seeded cells (Vero) to align within ±20° of the axes of 10 µm wide tungsten lines. Furthermore, a mathematical model was successfully developed to predict this alignment behavior and forecast the minimum width of isolated tungsten lines required to induce such behavior. However, the mechanism by which the widths of the symmetrical tungsten and silicon oxide lines induce the alignment behavior is still unknown. Furthermore, the model was never tested on more complex asymmetrical structures. Herewith, experiments were conducted with mammalian cells on complex asymmetrical structures with unequal tungsten and silicon oxide line widths. Results showed that the model could be extended to more complex pattern structures. In addition, cell morphology on the patterned structures reset during cell division because of mitotic rounding, which reduced the population of cells that elongated and aligned on the tungsten lines. Ultimately, we concluded that it was impossible to achieve a 100% alignment with cells having unsynchronized cell cycles because cell rounding during mitosis took precedence over cell alignment; in other words, internal chemical cues had a stronger role in cell morphology than external cues.

Targeted Diphtheria Toxin-Based Therapy: A Review Article

Cancer remains one of the leading causes of death worldwide. Conventional therapeutic strategies usually offer limited specificity, resulting in severe side effects and toxicity to normal tissues. Targeted cancer therapy, on the other hand, can improve the therapeutic potential of anti-cancer agents and decrease unwanted side effects. Targeted applications of cytolethal bacterial toxins have been found to be especially useful for the specific eradication of cancer cells. Targeting is either mediated by peptides or by protein-targeting moieties, such as antibodies, antibody fragments, cell-penetrating peptides (CPPs), growth factors, or cytokines. Together with a toxin domain, these molecules are more commonly referred to as immunotoxins. Targeting can also be achieved through gene delivery and cell-specific expression of a toxin. Of the available cytolethal toxins, diphtheria toxin (DT) is one of the most frequently used for these strategies. Of the many DT-based therapeutic strategies investigated to date, two immunotoxins, Ontak^TM and Tagraxofusp^TM, have gained FDA approval for clinical application. Despite some success with immunotoxins, suicide-gene therapy strategies, whereby controlled tumor-specific expression of DT is used for the eradication of malignant cells, are gaining prominence. The first part of this review focuses on DT-based immunotoxins, and it then discusses recent developments in tumor-specific expression of DT.

Ultraviolet irradiation of trypsin, lysozyme and β-galactosidase: how does UVC affect these enzymes when used as a secondary barrier against adventitious agents?

Trypsin is one of the essential raw materials used in the manufacturing of biopharmaceutical products. As an animal derived product, it can potentially carry a serious risk of contamination with adventitious agents that can result in production shut down and lost product. To mitigate these risks, several methods are currently being used in the industry to remove contamination including physical and chemical methods. Ultraviolet-C (UVC) light is known to inactivate adventitious agents that are resistant to physical and chemical methods and could be a secondary barrier strategy. In this study, we investigated the effect of UVC irradiation on the activity and structure of trypsin. Extreme doses of UVC light were applied to trypsin using a collimated beam apparatus. The effect of UVC light on trypsin enzymatic activity was measured using a colorimetric activity assay and the effect on structure was analyzed by spectrophotometry, gel electrophoresis, and mass spectrometry. To broaden the scope, the effect of UVC light on the activity of two additional enzymes, lysozyme and β-galactosidase, was also examined. At high doses of UVC light, changes to protein structure and protein fragmentation resulted in decreased trypsin activity. However, minimal damage was observed at doses applicable to inactivating adventitious agents, making UVC a feasible treatment for viral inactivation of trypsin products.

What's Happening on the Other Side? Revealing Nano-Meter Scale Features of Mammalian Cells on Engineered Textured Tantalum Surfaces

Advanced engineered surfaces can be used to direct cell behavior. These behaviors are typically characterized using either optical, atomic force, confocal, or electron microscopy; however, most microscopic techniques are generally restricted to observing what's happening on the "top" side or even the interior of the cell. Our group has focused on engineered surfaces typically reserved for microelectronics as potential surfaces to control cell behavior. These devices allow the exploration of novel substrates including titanium, tungsten, and tantalum intermixed with silicon oxide. Furthermore, these devices allow the exploration of the intricate patterning of surface materials and surface geometries i.e., trenches. Here we present two important advancements in our research: (1) the ability to split a fixed cell through the nucleus using an inexpensive three-point bend micro-cleaving technique and image 3D nanometer scale cellular components using high-resolution scanning electron microscopy; and (2) the observation of nanometer projections from the underbelly of a cell as it sits on top of patterned trenches on our devices. This application of a 3-point cleaving technique to visualize the underbelly of the cell is allowing a new understanding of how cells descend into surface cavities and is providing a new insight on cell migration mechanisms.

Nanoscale-Textured Tantalum Surfaces for Mammalian Cell Alignment

Tantalum is one of the most important biomaterials used for surgical implant devices. However, little knowledge exists about how nanoscale-textured tantalum surfaces affect cell morphology. Mammalian (Vero) cell morphology on tantalum-coated comb structures was studied using high-resolution scanning electron microscopy and fluorescence microscopy. These structures contained parallel lines and trenches with equal widths in the range of 0.18 to 100 μm. Results showed that as much as 77% of adherent cell nuclei oriented within 10° of the line axes when deposited on comb structures with widths smaller than 10 μm. However, less than 20% of cells exhibited the same alignment performance on blanket tantalum films or structures with line widths larger than 50 μm. Two types of line-width-dependent cell morphology were observed. When line widths were smaller than 0.5 μm, nanometer-scale pseudopodia bridged across trench gaps without contacting the bottom surfaces. In contrast, pseudopodia structures covered the entire trench sidewalls and the trench bottom surfaces of comb structures with line-widths larger than 0.5 μm. Furthermore, results showed that when a single cell simultaneously adhered to multiple surface structures, the portion of the cell contacting each surface reflected the type of morphology observed for cells individually contacting the surfaces.

Pattern-Dependent Mammalian Cell (Vero) Morphology on Tantalum/Silicon Oxide 3D Nanocomposites

The primary goal of this work was to investigate the resulting morphology of a mammalian cell deposited on three-dimensional nanocomposites constructed of tantalum and silicon oxide. Vero cells were used as a model. The nanocomposite materials contained comb structures with equal-width trenches and lines. High-resolution scanning electron microscopy and fluorescence microscopy were used to image the alignment and elongation of cells. Cells were sensitive to the trench widths, and their observed behavior could be separated into three different regimes corresponding to different spreading mechanism. Cells on fine structures (trench widths of 0.21 to 0.5 μm) formed bridges across trench openings. On larger trenches (from 1 to 10 μm), cells formed a conformal layer matching the surface topographical features. When the trenches were larger than 10 μm, the majority of cells spread like those on blanket tantalum films; however, a significant proportion adhered to the trench sidewalls or bottom corner junctions. Pseudopodia extending from the bulk of the cell were readily observed in this work and a minimum effective diameter of ~50 nm was determined for stable adhesion to a tantalum surface. This sized structure is consistent with the ability of pseudopodia to accommodate ~4–6 integrin molecules.

Supplementing glycosylation: A review of applying nucleotide-sugar precursors to growth medium to affect therapeutic recombinant protein glycoform distributions

Glycosylation is a critical quality attribute (CQA) of many therapeutic proteins, particularly monoclonal antibodies (mAbs), and is a major consideration in the approval of biosimilar biologics due to its effects to therapeutic efficacy. Glycosylation generates a distribution of glycoforms, resulting in glycoproteins with inherent molecule-to-molecule heterogeneity, capable of activating (or failing to activate) different effector functions of the immune system. Glycoforms can be affected by the supplementation of nucleotide-sugar precursors, and related components, to culture growth medium, affecting the metabolism of glycosylation. These supplementations has been demonstrated to increase nucleotide-sugar intracellular pools, and impact glycoform distributions, but with varied results. These variations can be attributed to five key factors: Differences between cell platforms (enzyme/transporter expression levels); differences between recombinant proteins produced (glycan-site accessibility); the fermentation and sampling timeline (glucose availability and exoglycosidase accumulation); glutamine levels (affecting ammonia levels, which impact Golgi pH, as well as UDP-GlcNAc pools); and finally, a lack of standardized metrics for observing shifts in glycoform distributions (glycosylation indices) across different experiments. The purpose of this review is to provide detail and clarity on the state of the art of supplementation strategies for nucleotide-sugar precursors for affecting glycosylation in cell culture processes, and to apply glycosylation indices for standardized comparisons across the field.

Evaluating ultraviolet sensitivity of adventitious agents in biopharmaceutical manufacturing

Incidents of contamination in biopharmaceutical production have highlighted the need to apply alternative or supplementary disinfection techniques. Ultraviolet (UV) irradiation is a well-established method for inactivating a broad range of microorganisms, and is therefore a good candidate as an orthogonal technique for disinfection. To apply UV as a safeguard against adventitious agents, the UV sensitivity of these target agents must be known so that the appropriate dose of UV may be applied to achieve the desired level of inactivation. This document compiles and reviews experimentally derived 254 nm sensitivities of organisms relevant to biopharmaceutical production. In general, different researchers have found similar sensitivity values despite a lack of uniformity in experimental design or standardized quantification techniques. Still, the lack of consistent methodologies has led to suspicious UV susceptibilities in certain instances, justifying the need to create a robust collection of sensitivity values that can be used in the design and sizing of UV systems for the inactivation of adventitious agents.

Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips

Tungsten chemical-mechanical polished integrated circuits were used to study the alignment and immobilization of mammalian (Vero) cells. These devices consist of blanket silicon oxide thin films embedded with micro- and nano-meter scale tungsten metal line structures on the surface. The final surfaces are extremely flat and smooth across the entire substrate, with a roughness in the order of nanometers. Vero cells were deposited on the surface and allowed to adhere. Microscopy examinations revealed that cells have a strong preference to adhere to tungsten over silicon oxide surfaces with up to 99% of cells adhering to the tungsten portion of the surface. Cells self-aligned and elongated into long threads to maximize contact with isolated tungsten lines as thin as 180 nm. The orientation of the Vero cells showed sensitivity to the tungsten line geometric parameters, such as line width and spacing. Up to 93% of cells on 10 μm wide comb structures were aligned within ± 20° of the metal line axis. In contrast, only ~22% of cells incubated on 0.18 μm comb patterned tungsten lines were oriented within the same angular interval. This phenomenon is explained using a simple model describing cellular geometry as a function of pattern width and spacing, which showed that cells will rearrange their morphology to maximize their contact to the embedded tungsten. Finally, it was discovered that the materials could be reused after cleaning the surfaces, while maintaining cell alignment capability.

Production of Virus-Like Particles for Vaccination

The ability to make a large variety of virus-like particles (VLPs) has been successfully achieved in the baculovirus expression vector system (BEVS)/insect cell system. The production and scale-up of these particles, which are mostly sought as vaccine candidates, are currently being addressed. Furthermore, these VLPs are being investigated as delivery agents for use as therapeutics. The use of host insect cells allows mass production of VLPs in a proven scalable system.

A correction method for systematic error in (1)H-NMR time-course data validated through stochastic cell culture simulation

Background

The growing ubiquity of metabolomic techniques has facilitated high frequency time-course data collection for an increasing number of applications. While the concentration trends of individual metabolites can be modeled with common curve fitting techniques, a more accurate representation of the data needs to consider effects that act on more than one metabolite in a given sample. To this end, we present a simple algorithm that uses nonparametric smoothing carried out on all observed metabolites at once to identify and correct systematic error from dilution effects. In addition, we develop a simulation of metabolite concentration time-course trends to supplement available data and explore algorithm performance. Although we focus on nuclear magnetic resonance (NMR) analysis in the context of cell culture, a number of possible extensions are discussed.

Results

Realistic metabolic data was successfully simulated using a 4-step process. Starting with a set of metabolite concentration time-courses from a metabolomic experiment, each time-course was classified as either increasing, decreasing, concave, or approximately constant. Trend shapes were simulated from generic functions corresponding to each classification. The resulting shapes were then scaled to simulated compound concentrations. Finally, the scaled trends were perturbed using a combination of random and systematic errors. To detect systematic errors, a nonparametric fit was applied to each trend and percent deviations calculated at every timepoint. Systematic errors could be identified at time-points where the median percent deviation exceeded a threshold value, determined by the choice of smoothing model and the number of observed trends. Regardless of model, increasing the number of observations over a time-course resulted in more accurate error estimates, although the improvement was not particularly large between 10 and 20 samples per trend. The presented algorithm was able to identify systematic errors as small as 2.5 % under a wide range of conditions.

Conclusion

Both the simulation framework and error correction method represent examples of time-course analysis that can be applied to further developments in ¹H-NMR methodology and the more general application of quantitative metabolomics.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-015-0197-4) contains supplementary material, which is available to authorized users.

Temporal characterization of protein production levels from baculovirus vectors coding for GFP and RFP genes under non-conventional promoter control

The ease of use and versatility of the Baculovirus Expression Vector System (BEVS) has made it one of the most widely used systems for recombinant protein production However, co-expression systems currently in use mainly make use of the very strong very late p10 and polyhedron (polh) promoters to drive expression of foreign genes, which does not provide much scope for tailoring expression ratios within the cell. This work demonstrates the use of different Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) promoters to control the timing and expression of two easily traceable fluorescent proteins, the enhanced green fluorescent protein (eGFP), and a red fluorescent protein (DsRed2) in a BEVS co-expression system. Our results show that gene expression levels can easily be controlled using this strategy, and also that modulating the expression level of one protein can influence the level of expression of the other protein within the system, thus confirming the concept of genes "competing" for limited cellular resources. Plots of "expression ratios" of the two model genes over time were obtained, and may be used in future work to tightly control timing and levels of foreign gene expression in an insect cell co-expression system.

Critical assessment of influenza VLP production in Sf9 and HEK293 expression systems

Background

Each year, influenza is responsible for hundreds of thousand cases of illness and deaths worldwide. Due to the virus’ fast mutation rate, the World Health Organization (WHO) is constantly on alert to rapidly respond to emerging pandemic strains. Although anti-viral therapies exist, the most proficient way to stop the spread of disease is through vaccination. The majority of influenza vaccines on the market are produced in embryonic hen’s eggs and are composed of purified viral antigens from inactivated whole virus. This manufacturing system, however, is limited in its production capacity. Cell culture produced vaccines have been proposed for their potential to overcome the problems associated with egg-based production. Virus-like particles (VLPs) of influenza virus are promising candidate vaccines under consideration by both academic and industry researchers.

Methods

In this study, VLPs were produced in HEK293 suspension cells using the Bacmam transduction system and Sf9 cells using the baculovirus infection system. The proposed systems were assessed for their ability to produce influenza VLPs composed of Hemagglutinin (HA), Neuraminidase (NA) and Matrix Protein (M1) and compared through the lens of bioprocessing by highlighting baseline production yields and bioactivity. VLPs from both systems were characterized using available influenza quantification techniques, such as single radial immunodiffusion assay (SRID), HA assay, western blot and negative staining transmission electron microscopy (NSTEM) to quantify total particles.

Results

For the HEK293 production system, VLPs were found to be associated with the cell pellet in addition to those released in the supernatant. Sf9 cells produced 35 times more VLPs than HEK293 cells. Sf9-VLPs had higher total HA activity and were generally more homogeneous in morphology and size. However, Sf9 VLP samples contained 20 times more baculovirus than VLPs, whereas 293 VLPs were produced along with vesicles.

Conclusions

This study highlights key production hurdles that must be overcome in both expression platforms, namely the presence of contaminants and the ensuing quantification challenges, and brings up the question of what truly constitutes an influenza VLP candidate vaccine.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-015-0152-x) contains supplementary material, which is available to authorized users.

Profiling convoluted single-dimension proton NMR spectra: a Plackett-Burman approach for assessing quantification error of metabolites in complex mixtures with application to cell culture

Single-dimension hydrogen, or proton, nuclear magnetic resonance spectroscopy (1D-(1)H NMR) has become an attractive option for characterizing the full range of components in complex mixtures of small molecular weight compounds due to its relative simplicity, speed, spectral reproducibility, and noninvasive sample preparation protocols compared to alternative methods. One challenge associated with this method is the overlap of NMR resonances leading to "convoluted" spectra. While this can be mitigated through "targeted profiling", there is still the possibility of increased quantification error. This work presents the application of a Plackett-Burman experimental design for the robust estimation of precision and accuracy of 1D-(1)H NMR compound quantification in synthetic mixtures, with application to mammalian cell culture supernatant. A single, 20 sample experiment was able to provide a sufficient estimate of bias and variability at different metabolite concentrations. Two major sources of bias were identified: incorrect interpretation of singlet resonances and the quantification of resonances from protons in close proximity to labile protons. Furthermore, decreases in measurement accuracy and precision could be observed with decreasing concentration for a small fraction of the components as a result of their particular convolution patterns. Finally, the importance of a priori concentration estimates is demonstrated through the example of interpreting acetate metabolite trends from a bioreactor cultivation of Chinese hamster ovary cells expressing a recombinant antibody.

Manipulating the sleeping beauty mutase operon for the production of 1-propanol in engineered Escherichia coli

BACKGROUND

While most resources in biofuels were directed towards implementing bioethanol programs, 1-propanol has recently received attention as a promising alternative biofuel. Nevertheless, no microorganism has been identified as a natural 1-propanol producer. In this study, we manipulated a novel metabolic pathway for the synthesis of 1-propanol in the genetically tractable bacterium Escherichia coli.

RESULTS

E. coli strains capable of producing heterologous 1-propanol were engineered by extending the dissimilation of succinate via propionyl-CoA. This was accomplished by expressing a selection of key genes, i.e. (1) three native genes in the sleeping beauty mutase (Sbm) operon, i.e. sbm-ygfD-ygfG from E. coli, (2) the genes encoding bifunctional aldehyde/alcohol dehydrogenases (ADHs) from several microbial sources, and (3) the sucCD gene encoding succinyl-CoA synthetase from E. coli. Using the developed whole-cell biocatalyst under anaerobic conditions, production titers up to 150 mg/L of 1-propanol were obtained. In addition, several genetic and chemical effects on the production of 1-propanol were investigated, indicating that certain host-gene deletions could abolish 1-propanol production as well as that the expression of a putative protein kinase (encoded by ygfD/argK) was crucial for 1-propanol biosynthesis.

CONCLUSIONS

The study has provided a novel route for 1-propanol production in E. coli, which is subjected to further improvement by identifying limiting conversion steps, shifting major carbon flux to the productive pathway, and optimizing gene expression and culture conditions.

Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks

The baculovirus expression vector system (BEVS) is a versatile and powerful platform for protein expression in insect cells. With the ability to approach similar post-translational modifications as in mammalian cells, the BEVS offers a number of advantages including high levels of expression as well as an inherent safety during manufacture and of the final product. Many BEVS products include proteins and protein complexes that require expression from more than one gene. This review examines the expression strategies that have been used to this end and focuses on the distinguishing features between those that make use of single polycistronic baculovirus (co-expression) and those that use multiple monocistronic baculoviruses (co-infection). Three major areas in which researchers have been able to take advantage of co-expression/co-infection are addressed, including compound structure-function studies, insect cell functionality augmentation, and VLP production. The core of the review discusses the parameters of interest for co-infection and co-expression with time of infection (TOI) and multiplicity of infection (MOI) highlighted for the former and the choice of promoter for the latter. In addition, an overview of modeling approaches is presented, with a suggested trajectory for future exploration. The review concludes with an examination of the gaps that still remain in co-expression/co-infection knowledge and practice.

An initiative to manufacture and characterize baculovirus reference material

This letter to the editor brings to the attention of researchers an initiative to develop a baculovirus reference material repository. To be successful this initiative needs the support of a broad panel of researchers working with baculovirus vectors for recombinant protein production and gene delivery for either therapy or vaccination. First there is a need to reach a consensus on the nature of the reference material, the production protocols and the baculovirus characterization methods. It will also be important to define repository and distribution procedures so that the reference material is available to any researcher for calibrating experimental data and to compare experiments performed in the various laboratories. As more and more baculovirus-based products are licensed or in the final stages of development, the development of a repository of baculovirus reference material is timely. This letter describes the requirements for the reference material and for the project as a whole to be successful and calls for a partnership that would involve academic, industrial laboratories and governmental organizations to support this international initiative.

Bioprocessing of baculovirus vectors: a review

The baculovirus/insect cell expression system is best known, and used, as a research tool for the production of recombinant proteins often requiring post-translational modifications. Although studies on the larger scale use of the system have been reported on for three decades, the recognition of this system as an industrially relevant platform for the production of biologics has only been recently achieved with the approvals of baculovirus-derived human and veterinary vaccines for commercialization. The full utility of baculoviruses, however, does not end with the production of recombinant proteins; baculoviruses are increasingly being studied for their ability to transduce mammalian cells and use as a therapeutic themselves. There is, therefore, a need to revisit the current state of the art in the bioprocessing of baculoviruses as the product. This paper is an extensive review of what is currently known about the amplification and recovery of baculoviruses and highlights the gaps that have not been focused on in the midst of optimizing this system for protein production.

Virus-like particle and viral vector production using the baculovirus expression vector system/insect cell system: adeno-associated virus-based products

The ability to make a large variety of virus-like particles (VLPs) has been successfully achieved in the baculovirus expression vector system (BEVS)/insect cell system. The production and scale-up of these particles, which are mostly sought as candidate vaccines, are currently being addressed. Furthermore, these VLPs are being investigated as delivery agents for use as therapeutics. Recently, adeno-associated viral (AAV) vectors, which can be potentially used for human gene therapy, have been produced in insect cells using three baculovirus vectors to supply the required genes. The use of host insect cells allows mass production of VLPs in a proven scaleable system. This chapter focuses on the methodology, based on the work done in our lab, for the production of AAV-like particles and vectors in a BEVS/insect cell system.

Primary recovery and chromatographic purification of adeno-associated virus type 2 produced by baculovirus/insect cell system

Adeno-associated virus (AAV) is making its place in gene therapy applications; however, the industry is still facing obstacles in producing a large quantity of highly purified material for clinical studies. Insect cell technology can be used to produce AAV to meet the current demand. During the purification process it was observed that there was a reduced recovery of AAV produced in insect cells, Spodoptera frugiperda (Sf9). It was assumed that the formation of AAV agglomerates and the interaction of AAV with other cellular components were major contributors to this loss. After studying different systems of extraction a sequence of treatment for primary recovery of AAV from cell paste was developed. This sequence was necessary to reduce the AAV losses and to increase the recovery. The purification method avoided the use of ultracentrifugation and adopted chromatographic methods for the purification of AAV. Primary recovery, ion exchange chromatography and hydrophobic interaction chromatography gave an overall yield of 75% from the extracted AAV. The purification process was based on chromatographic methods; therefore, it can be scaled up. Although this method was developed for AAV type 2, it is believed that this method could be modified easily to purify other AAV serotypes.

Improving AAV vector yield in insect cells by modulating the temperature after infection

Vectors based on adeno-associated viruses (AAV) are sought for therapeutic gene delivery because of their ability to transduce a variety of tissues with no significant immunological response. Production using the baculovirus expression vector (BEV)/insect cell system has the potential to meet the needs for pre-clinical and clinical trials. In this co-infection system, three baculoviruses are used to produce the AAV vector. A strategy aimed at increasing encapsidation/maturation of the viral vector involved varying the temperature over the course of the process. Cultures were subjected to temperature changes at various times pre- and post-infection (up to 24 h post-infection). It was found that raising the culture temperature to 30 degrees C at the time of infection nearly tripled the infectious titer. In fact, increasing the temperature to 30 degrees C at any time in the process investigated resulted in an increase in titer. Also, raising the culture to 33 degrees C or lowering the temperature to 24 degrees or 21 degrees C resulted in lower titers. The rise in infectious titer was also confirmed by an increase in DNase resistant particles (DRPs). Varying the temperature, however, did not affect the total amount of capsids significantly. Therefore increasing the culture temperature resulted in better encapsidation as determined by the ratio of capsids to DRPs to infectious particles. It is believed that an increase in early proteins and possibly a quicker cascade of baculovirus infection events resulted in this increased packaging efficiency.

Identifying conditions for inducible protein production in E. coli: combining a fed-batch and multiple induction approach

BACKGROUND

In the interest of generating large amounts of recombinant protein, inducible systems have been studied to maximize both the growth of the culture and the production of foreign proteins. Even though thermo-inducible systems were developed in the late 1970's, the number of studies that focus on strategies for the implementation at bioreactor scale is limited. In this work, the bacteriophage lambda PL promoter is once again investigated as an inducible element but for the production of green fluorescent protein (GFP). Culture temperature, induction point, induction duration and number of inductions were considered as factors to maximize GFP production in a 20-L bioreactor.

RESULTS

It was found that cultures carried out at 37 degrees C resulted in a growth-associated production of GFP without the need of an induction at 42 degrees C. Specific production was similar to what was achieved when separating the growth and production phases. Shake flask cultures were used to screen for desirable operating conditions. It was found that multiple inductions increased the production of GFP. Induction decreased the growth rate and substrate yield coefficients; therefore, two time domains (before and after induction) having different kinetic parameters were created to fit a model to the data collected.

CONCLUSION

Based on two batch runs and the simulation of culture dynamics, a pre-defined feeding and induction strategy was developed to increase the volumetric yield of a temperature regulated expression system and was successfully implemented in a 20-L bioreactor. An overall cell density of 5.95 g DW l(-1) was achieved without detriment to the cell specific production of GFP; however, the production of GFP was underestimated in the simulations due to a significant contribution of non-growth associated product formation under limiting nutrient conditions.