An overview of mechanistic modeling of liquid chromatography

Abstract

Liquid chromatography is considered to be the bottleneck for purification of therapeutic proteins. Development and optimization of chromatography process is a cumbersome activity due to the increasing complexities in the types and content of impurities present in the high product titer cell culture harvest obtained from the upstream processing. Further, regulatory expectations are continuously rising with the recent initiatives of quality by design and process analytical technology expecting the manufacturer to have a deeper understanding of the process and the product. Mechanistic modeling is one approach to gain this deeper understanding of a process step. It involves modeling of the underlying physicochemical processes. A well calibrated model with acceptable predictability can be very effective in both process optimization and process characterization activities. In this paper we provide an overview of mechanistic modeling of liquid chromatography. We discuss the various components that such a model entails and also presents the status quo of this area.     

Somitogenesis

A segmented body plan is fundamental to all vertebrate species and this bestows both rigidity and flexibility on the body. Segmentation is initiated through the process of somitogenesis. This article aims to provide a broad and balanced cross-species overview of somitogenesis and to highlight the key molecular and cellular events involved in each stage of segmentation. We highlight where our understanding of this multifaceted process relies on strong experimental evidence as well as those aspects where our understanding still relies largely on models.     

灵长类动作理解的镜像神经机制研究进展

灵长类动作理解(understanding of actions)的神经机制是认知神经科学研究的重要内容,它的阐明对于揭示灵长类特有的一些高级认知行为的本质和过程具有重要意义。就灵长类动物而言,个体对其同类做出动作的识别以及理解是其一切社会行为的基础,但是迄今为止我们对其动作理解的神经机制还知之甚少。随着镜像神经元成为近年来国外认知神经科学与认知人类学研究的热点,人们通过神经生理学和脑成像等技术,陆续发现和证明了其在灵长类动作理解过程中的重要作用。本文综述了近年来关于灵长类动作理解的镜像神经机制的研究成果,介绍了镜像神经元在灵长类动作理解过程中的一些新认识及其在该能力进化和发育等方面的作用,并对当前一些实验中遗留的问题与灵长类动作理解领域的未来研究方向作了反思与展望。     

The forensic analysis of foodborne bacterial pathogens in the age of whole‐genome sequencing

The forensic evaluation of bacterial pathogens presents new challenges to the forensic science community. This review examines bacterial pathogens as objects of forensic comparison, focusing on their nucleic acid sequences as an important aspect of the comparison process. Because of the clonal propagation of most bacterial pathogens, a phylogenetic approach to understanding the diversity and using this understanding to address common forensic questions is explored. As a general phylogenetic framework is now employed in human mitochondrial DNA analysis, we will use the relevant concepts and approaches common in this area to develop this approach further. We also address the impact of the current ease and prevalence of whole‐genome DNA sequence analysis in the forensic comparison process.     

Process validation: achieving the Operational Qualification phase

The OQ phase of process validation is very important and is where the complete understanding of the process is determined by experimentation. This understanding is useful to: * establish optimal process parameters * understand variation that affect the process * aid in investigating process deviations. OQ is an important part of the entire process validation activity and essential to understanding a manufacturing process. The benefits of completing the OQ and overall process validation are the reasons that it makes business sense and receive the long-term benefits of producing high quality product and achieving customer satisfaction.     

Visualising chromosomal replication sites and replicons in mammalian cells

The precise regulation of DNA replication is fundamental to the preservation of intact genomes during cell proliferation. Our understanding of this process has been based traditionally on a combination of techniques including biochemistry, molecular biology and cell biology. In this report we describe how the analysis of the S phase in mammalian cells using classical cell biology techniques has contributed to our understanding of the replication process. We describe traditional and state-of-the-art protocols for imaging sites of DNA synthesis in nuclei and the organisation of active replicons along DNA, as visualised on individual DNA fibres. We evaluate how the different approaches inform our understanding of the replication process, placing particular emphasis on ways in which the higher order chromatin structures and the spatial architecture of replication sites contribute to the orderly activation of defined regions of the genome at precise times of S phase.     

The status of membrane bioreactor technology

In this article, the current status of membrane bioreactor (MBR) technology for wastewater treatment is reviewed. Fundamental facets of the MBR process and membrane and process configurations are outlined and the advantages and disadvantages over conventional suspended growth-based biotreatment are briefly identified. Key process design and operating parameters are defined and their significance explained. The inter-relationships between these parameters are identified and their implications discussed, with particular reference to impacts on membrane surface fouling and channel clogging. In addition, current understanding of membrane surface fouling and identification of candidate foulants is appraised. Although much interest in this technology exists and its penetration of the market will probably increase significantly, there remains a lack of understanding of key process constraints such as membrane channel clogging, and of the science of membrane cleaning.     

Insights on membrane fusion

Membrane fusion is a fundamental cellular process regulating intracellular transport, neurotransmission, enzyme secretion, hormone release, and the entry/exit of viruses, to name a few. Knowledge of how opposing bilayers fuse, besides advancing our understanding of these cellular processes, will provide us with the facts to ameliorate secretory defects and prevent cellular entry or exit of pathogenic viruses. In the last few years, great strides have been made in our understanding of the molecular machinery and mechanism of membrane fusion. In this Special Issue of Cell Biology International, entitled 'Membrane fusion: machinery and mechanism', we have tried to cover several aspects of this vital cellular process, providing insights on the machinery, mechanism and dynamics of the process. Membrane fusion studies reported in this Special Issue have been performed on whole cells, synaptic terminals, viruses, and fusion proteins.     

A neural network model of metaphor understanding with dynamic interaction based on a statistical language analysis: targeting a human-like model

The purpose of this paper is to construct a model that represents the human process of understanding metaphors, focusing specifically on similes of the form an "A like B". Generally speaking, human beings are able to generate and understand many sorts of metaphors. This study constructs the model based on a probabilistic knowledge structure for concepts which is computed from a statistical analysis of a large-scale corpus. Consequently, this model is able to cover the many kinds of metaphors that human beings can generate. Moreover, the model implements the dynamic process of metaphor understanding by using a neural network with dynamic interactions. Finally, the validity of the model is confirmed by comparing model simulations with the results from a psychological experiment.     

The true face of JNK activation in apoptosis

Age-associated changes in apoptotic rates have been observed in a number of different tissues. While the implications of these findings remain unclear, a better understanding of how apoptosis is regulated may further our understanding of the aging process. The role of the JNK pathway in apoptosis has been highly controversial with studies suggesting that it plays a pro-apoptotic, anti-apoptotic or no role in this process. Here we discuss what is currently known about JNK's role in apoptosis, highlighting recent findings regarding NF-kappaB-mediated inhibition of JNK activation and its impact on TNF-alpha induced apoptosis.     

Mapping Electromechanical Coupling Pathways in Voltage-Gated Ion Channels: Challenges and the Way Forward

Inter- and intra-molecular allosteric interactions underpin regulation of activity in a variety of biological macromolecules. In the voltage-gated ion channel superfamily, the conformational state of the voltage-sensing domain regulates the activity of the pore domain via such long-range allosteric interactions. Although the overall structure of these channels is conserved, allosteric interactions between voltage-sensor and pore varies quite dramatically between the members of this superfamily. Despite the progress in identifying key residues and structural interfaces involved in mediating electromechanical coupling, our understanding of the biophysical mechanisms remains limited. Emerging new structures of voltage-gated ion channels in various conformational states will provide a better three-dimensional view of the process but to conclusively establish a mechanism, we will also need to quantitate the energetic contribution of various structural elements to this process. Using rigorous unbiased metrics, we want to compare the efficiency of electromechanical coupling between various sub-families in order to gain a comprehensive understanding. Furthermore, quantitative understanding of the process will enable us to correctly parameterize computational approaches which will ultimately enable us to predict allosteric activation mechanisms from structures. In this review, we will outline the challenges and limitations of various experimental approaches to measure electromechanical coupling and highlight the best practices in the field.     

Are proteins made from a limited parts list?

Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture?     

Life Cycle Perspectives to Achieve Business Benefits: From Concept to Technique

The purpose of this paper is to describe how one pollution prevention tool, life-cycle assessment, can be used to identify and manage environmental issues associated with product systems. Specifically, this paper will describe what life-cycle assessment is, determine the key players in its development and application, and present ideas on how life-cycle assessment can be used today. LCA provides a systematic means to broaden the perspective of a company's decisionmaking process to incorporate the consideration of energy and material use, transportation, post-customer use, and disposal, and the environmental releases associated with the product system. LCA provides a framework to achieve a better understanding of the trade-offs associated with specific change in a product, package, or process. This understanding lays the foundation for subsequent risk assessments and risk management efforts by decision-makers.     

Myoblast fusion in Drosophila

Somatic muscle formation is an unusual process as it requires the cells involved, the myoblasts, to relinquish their individual state and fuse with one another to form a syncitial muscle fiber. The potential use of myoblast fusion therapies to rebuild damaged muscles has generated continuing interest in elucidating the molecular basis of the fusion process. Yet, until recently, few of the molecular players involved in this process had been identified. Now, however, it has been possible to couple a detailed understanding of the cellular basis of the fusion process with powerful classical and molecular genetic strategies in the Drosophila embryo. We review the cellular studies, and the recent genetic and biochemical analyses that uncovered interacting extracellular molecules present on fusing myoblasts and the intracellular effectors that facilitate fusion. With the conservation of proteins and protein functions across species, it is likely that these findings in Drosophila will benefit understanding of the myoblast fusion process in higher organisms.     

Chemometrics applications in biotech processes: a review

Biotech unit operations are often characterized by a large number of inputs (operational parameters) and outputs (performance parameters) along with complex correlations amongst them. A typical biotech process starts with the vial of the cell bank, ends with the final product, and has anywhere from 15 to 30 such unit operations in series. The aforementioned parameters can impact process performance and product quality and also interact amongst each other. Chemometrics presents one effective approach to gather process understanding from such complex data sets. The increasing use of chemometrics is fuelled by the gradual acceptance of quality by design and process analytical technology amongst the regulators and the biotech industry, which require enhanced process and product understanding. In this article, we review the topic of chemometrics applications in biotech processes with a special focus on recent major developments. Case studies have been used to highlight some of the significant applications.     

Identified ion channels in the squid nervous system

Our modern understanding of channels as discrete voltage-sensitive and ion-selective entities comes largely from a series of classical studies using the squid giant axon. This system has also been critical for understanding how transporters and synaptic transmission operate. This review outlines attempts to assign molecular identities to the extensively studied physiological properties of this system. As it turns out, this is no simple task. Molecular candidates for voltage-gated Na(+), K(+), and Ca(2+) channels, as well as ion transporters have been isolated from the squid nervous system. Both physiological and molecular approaches have been used to equate these cloned gene products with their native counterparts. In the case of the delayed rectifier K(+) conductance, the most thoroughly studied example, two major issues further complicate the equation. First, the ability of K(+) channel monomers to form heteromultimers with unique properties must be considered. Second, squid K(+) channel mRNAs are extensively edited, a process that can generate a wide variety of channel proteins from a common gene. The giant axon system is beginning to play an important role in understanding the biological relevance of this latter process.