Review of computational fluid dynamics applications in biotechnology processes

Computational fluid dynamics (CFD) is well established as a tool of choice for solving problems that involve one or more of the following phenomena: flow of fluids, heat transfer,mass transfer, and chemical reaction. Unit operations that are commonly utilized in biotechnology processes are often complex and as such would greatly benefit from application of CFD. The thirst for deeper process and product understanding that has arisen out of initiatives such as quality by design provides further impetus toward usefulness of CFD for problems that may otherwise require extensive experimentation. Not surprisingly, there has been increasing interest in applying CFD toward a variety of applications in biotechnology processing in the last decade. In this article, we will review applications in the major unit operations involved with processing of biotechnology products. These include fermentation,centrifugation, chromatography, ultrafiltration, microfiltration, and freeze drying. We feel that the future applications of CFD in biotechnology processing will focus on establishing CFD as a tool of choice for providing process understanding that can be then used to guide more efficient and effective experimentation. This article puts special emphasis on the work done in the last 10 years.     

RECENT DEVELOPMENTS IN MEMBRANE-BASED SEPARATIONS IN BIOTECHNOLOGY PROCESSES: REVIEW

Membrane-based separations are the most ubiquitous unit operations in biotech processes. There are several key reasons for this. First, they can be used with a large variety of applications including clarification, concentration, buffer exchange, purification, and sterilization. Second, they are available in a variety of formats, such as depth filtration, ultrafiltration, diafiltration, nanofiltration, reverse osmosis, and microfiltration. Third, they are simple to operate and are generally robust toward normal variations in feed material and operating parameters. Fourth, membrane-based separations typically require lower capital cost when compared to other processing options. As a result of these advantages, a typical biotech process has anywhere from 10 to 20 membrane-based separation steps. In this article we review the major developments that have occurred on this topic with a focus on developments in the last 5 years.     

Recent developments in membrane-based separations in biotechnology processes: review

Membrane-based separations are the most ubiquitous unit operations in biotech processes. There are several key reasons for this. First, they can be used with a large variety of applications including clarification, concentration, buffer exchange, purification, and sterilization. Second, they are available in a variety of formats, such as depth filtration, ultrafiltration, diafiltration, nanofiltration, reverse osmosis, and microfiltration. Third, they are simple to operate and are generally robust toward normal variations in feed material and operating parameters. Fourth, membrane-based separations typically require lower capital cost when compared to other processing options. As a result of these advantages, a typical biotech process has anywhere from 10 to 20 membrane-based separation steps. In this article we review the major developments that have occurred on this topic with a focus on developments in the last 5 years.     

Automation in cervical cytology: an overview.

Cancer of the uterine cervix is one of the more common female cancers and a major source of premature female mortality. UK deaths in 1987 exceeded 2000. To reduce these rates, national screening programmes have been introduced using the Papanicolaou method. In screening for cancer, the examination of specimens is an intensive and expensive task. Its high cost has led to a number of attempts to automate the process, either fully or partially. Over the last 30 years, various experimental prescreening systems have been developed for the diagnosis of cytological samples including the use of image processing techniques. This paper presents a historical overview of automation in cervical cytology and the status of current developments for automated cytological diagnosis.     

Continuous Processing for Production of Biopharmaceuticals

The merits of continuous processing over batch processing are well known in the manufacturing industry. Continuous operation results in shorter process times due to omission of hold steps, higher productivity due to reduced shutdown costs, and lowers labor requirement. Over the past decade, there has been an increasing interest in continuous processing within the bioprocessing community, specifically those involved in production of biotherapeutics. Continuous operations in upstream processing (perfusion) have been performed for decades. However, recent development of continuous downstream operations has led the industry to envisage an integrated bioprocessing platform for efficient production. The regulators, key players in the biotherapeutic industry, have also expressed their interest and willingness in this migration from the traditional batch processing. This paper aims to review major developments in continuous bioprocessing in the past decade. A discussion of pros and cons of the different proposed approaches has also been presented.     

Pool‐less processing to streamline downstream purification of monoclonal antibodies

With cell culture titers and productivity increasing in the last few years, pressure has been placed on downstream purification to look at alternative strategies to meet the demand of biotech products with high dose requirements. Even when the upstream process is not continuous (perfusion based), adopting a more productive and/or continuous downstream process can be of significant advantage. Due to the recent trend in exploring continuous processing options for biomolecules, several enabling technologies have been assessed at Biogen. In this paper, we evaluate the capability of one of these technologies to streamline and improve our downstream mAb purification platform. Current conventional downstream polishing steps at Biogen are operated in flow‐through mode to achieve higher loadings while maintaining good selectivity. As titers increase, this would result in larger columns and larger intermediate product pool holding tanks. A semicontinuous downstream process linking the second and third chromatography steps in tandem can reduce/eliminate intermediate holding tanks, reduce overall processing time, and combine unit operations to reduce validation burdens. A pool‐less processing technology utilizing inline adjustment functionality was evaluated to address facility fit challenges for three high titer mAbs. Two different configurations of polishing steps were examined: (i) anion exchange and hydrophobic interaction and (ii) anion exchange and mixed mode chromatography. Initial laboratory scale proof of concept studies showed comparable performance between the batch purification process and the pool‐less process configuration.     

Economic and Societal Changes in China and their Effects onWater Use A Scenario Analysis

China's development over the last few decades has been characterized by high rates of economic growth, large-scale migration from rural areas to the fast-growing cities accompanied by changes in lifestyles, and steady population growth. These developments have left deep marks on resource availability and quality. In this article we conduct a scenario analysis of how lifestyle changes and other major developments might affect water resources.
China has the longest tradition in river and water resource management in the world. Its civilization has sought to control the effects of floods and drought for thousands of years and has utilized water flows for irrigation and navigation. In the last century, competing uses such as domestic, municipal, and industrial water consumption have also become reasons for the regulation of and large-scale abstraction of water.
To investigate the major changes in economy and society and their effects on the water situation in China, a set of scenarios is developed and analyzed within a structural economics framework. A hydrological model that represents water flows in the major watersheds is linked to a regional input-output model that represents socioeconomic activities in the major economic-administrative regions of China. The regional analysis shows that the North and Northwest regions are water-scarce and that lifestyle changes and technical shifts are the most important factors driving future water consumption.     

Glycosylation of monoclonal antibody products: Current status and future prospects

Protein based therapeutics have started to dominate the pharmaceutical landscape primarily due to the high efficacy that they have demonstrated against complex diseases. Despite the significant success, issues with regards to safety, efficacy and quality of biotherapeutics have been a point of considerable debate and concern among the various stakeholders. The correlation between the glycoform profile and the safety and efficacy of a drug, in particular, has garnered significant attention of researchers worldwide. An escalated emphasis is presently given to develop an understanding of how the various process parameters as well molecular biology considerations contribute to glycan heterogeneity. This paper aims to review the major developments that have occurred in this area over the last decade. The impact of the various process parameters on glycan expression, methods for obtaining a pre‐determined glycan levels/profiles of a protein therapeutic and developments in the area of real‐time glycan monitoring and control are discussed. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1091–1102, 2016     

TILLING in extremis

Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.     

Intensified Downstream Processing of Monoclonal Antibodies Using Membrane Technology

The need to intensify downstream processing of monoclonal antibodies to complement the advances in upstream productivity has led to increased attention toward implementing membrane technologies. With the industry moving toward continuous operations and single use processes, membrane technologies show promise in fulfilling the industry needs due to their operational flexibility and ease of implementation. Recently, the applicability of membrane-based unit operations in integrating the downstream process has been explored. In this article, the major developments in the application of membrane-based technologies in the bioprocessing of monoclonal antibodies are reviewed. The recent progress toward developing intensified end-to-end bioprocesses and the critical role membrane technology will play in achieving this goal are focused upon.     

Micro biochemical engineering to accelerate the design of industrial-scale downstream processes for biopharmaceutical proteins

The article examines how a small set of easily implemented micro biochemical engineering procedures combined with regime analysis and bioprocess models can be used to predict industrial scale performance of biopharmaceutical protein downstream processing. This approach has been worked on in many of our studies of individual operations over the last 10 years and allows preliminary evaluation to be conducted much earlier in the development pathway because of lower costs. It then permits the later large scale trials to be more highly focused. This means that the risk of delays during bioprocess development and of product launch are reduced. Here we draw the outcomes of this research together and illustrate its use in a set of typical operations; cell rupture, centrifugation, filtration, precipitation, expanded bed adsorption, chromatography and for common sources, E. coli, two yeasts and mammalian cells (GS-NSO). The general approach to establishing this method for other operations is summarized and new developments outlined. The technique is placed against the background of the scale-down methods that preceded it and complementary ones that are being examined in parallel. The article concludes with a discussion of the advantages and limitations of the micro biochemical engineering approach versus other methods.     

Proteomic reactors and their applications in biology

Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.     

Immunological and functional characterization of Mycobacterium leprae protein antigens: an overview

A major focus of leprosy research in the last 10 years has been the identification and characterization of antigens of Mycobacterium leprae that interact with antibodies and T cells of the host's immune response. Through the combined efforts of many different laboratories, a substantial number of protein antigens have been identified and characterized. In this MicroReview we present an updated list of M. leprae protein antigens, and, with emphasis on recent developments, summarize what is known regarding their functional and immunological features.     

Animal cognition: 1900-2000

During the 20th century there has been considerable progress in the study of animal cognition, based on essential ideas that were developed earlier. These essential ideas include the metaphors of the animal, the questions, the sources of hypotheses, and the types of explanations. The progress cannot be generally characterized as continuous improvement, cyclic changes, or discrete steps, but the quality of the empirical results has increased substantially since the first experiments in the field. Improvements in research methods have been primarily responsible for this progress. These have included improvements in animal husbandry, stimulus control, apparatus design, the measurement of behavior, experimental procedures, and data analysis. In the last third of the century the computer has led to major improvements in all stages of the research process in animal cognition. Although they have greatly improved the quality of the empirical results, they have not led to a general theory of animal cognition. In the near future the available research methods are likely to lead to further progress in the developments of quantitative theories of animal cognition.     

Preparative chromatographic separation: Simulated moving bed and modified chromatography methods

Chromatography has been the method of choice for the separation of complex biological mixtures for analytical purposes, particularly for the last fifty years. Its use has recently been extended to preparative separation where the productivity relative to the amount of resin and solvent used is a matter of concern. To overcome the inherent thermodynamic inefficiency of batch chromatography, as exemplified by the partial temporal usage of the resin and dilution of the product with the solvent, chromatography has been continually modified by separation engineers. Column switching and recycling represent some of the process modifications that have brought high productivity to chromatography. Recently, the simulated moving bed (SMB) method, which claims a high separation efficiency based on counter-current moving bed chromatography, has become the mainstay of preparative separation, especially in chiral separation. Accordingly, this paper reviews the current status of SMB, along with several chromatographic modification, which may be helpful in routine laboratory and industrial chromatographic practices.     

Artificial intelligence: Deep learning in oncological radiomics and challenges of interpretability and data harmonization

Over the last decade there has been an extensive evolution in the Artificial Intelligence (AI) field. Modern radiation oncology is based on the exploitation of advanced computational methods aiming to personalization and high diagnostic and therapeutic precision. The quantity of the available imaging data and the increased developments of Machine Learning (ML), particularly Deep Learning (DL), triggered the research on uncovering “hidden” biomarkers and quantitative features from anatomical and functional medical images. Deep Neural Networks (DNN) have achieved outstanding performance and broad implementation in image processing tasks. Lately, DNNs have been considered for radiomics and their potentials for explainable AI (XAI) may help classification and prediction in clinical practice. However, most of them are using limited datasets and lack generalized applicability. In this study we review the basics of radiomics feature extraction, DNNs in image analysis, and major interpretability methods that help enable explainable AI. Furthermore, we discuss the crucial requirement of multicenter recruitment of large datasets, increasing the biomarkers variability, so as to establish the potential clinical value of radiomics and the development of robust explainable AI models.     

Cell sorting in cancer research—Diminishing degree of cell heterogeneity

Increasing evidence of intratumor heterogeneity and its augmentation due to selective pressure of microenvironment and recent achievements in cancer therapeutics lead to the need to investigate and track the tumor subclonal structure. Cell sorting of heterogeneous subpopulations of tumor and tumor-associated cells has been a long established strategy in cancer research. Advancement in lasers, computer technology and optics has led to a new generation of flow cytometers and cell sorters capable of high-speed processing of single cell suspensions. Over the last several years cell sorting was used in combination with molecular biological methods, imaging and proteomics to characterize primary and metastatic cancer cell populations, minimal residual disease and single tumor cells. It was the principal method for identification and characterization of cancer stem cells. Analysis of single cancer cells may improve early detection of tumors, monitoring of circulating tumor cells, evaluation of intratumor heterogeneity and chemotherapeutic treatments. The aim of this review is to provide an overview of major cell sorting applications and approaches with new prospective developments such as microfluidics and microchip technologies.     

Current status of stem cell research: An editorial

The purpose of this editorial is to highlight recent developments in molecular biology tools and techniques in stem cell research and their applications to human diseases. Recent advancements in stem cell research and regenerative medicine are offering immense hope to cure human diseases and injuries, such as cancer, diabetes, Alzheimer's disease, Parkinson's disease, and traumatic brain injuries. In the last three decades, especially in the last decade, major breakthroughs have been seen in the conversion of adult stem cells into induced pluripotent stem cells, which in turn has led the way to developing stem cell therapies for human diseases. This article summarizes contributions of research into stem cell therapies.     

Signaling of a varicelloviral factor across the endoplasmic reticulum membrane induces destruction of the peptide-loading complex and immune evasion

Cytotoxic T lymphocytes eliminate infected cells upon surface display of antigenic peptides on major histocompatibility complex I molecules. To promote immune evasion, UL49.5 of several varicelloviruses interferes with the pathway of major histocompatibility complex I antigen processing. However, the inhibition mechanism has not been elucidated yet. Within the macromolecular peptide-loading complex we identified the transporter associated with antigen processing (TAP1 and TAP2) as the prime target of UL49.5. Moreover, we determined the active oligomeric state and crucial elements of the viral factor. Remarkably, the last two residues of the cytosolic tail of UL49.5 are essential for endoplasmic reticulum (ER)-associated proteasomal degradation of TAP. However, this process strictly requires additional signaling of an upstream regulatory element in the ER lumenal domain of UL49.5. Within this new immune evasion mechanism, we show for the first time that additive elements of a small viral factor and their signaling across the ER membrane are essential for targeted degradation of a multi-subunit membrane complex.