Development and application of an analytical approach to assess an antibody's potential for disulfide reduction

Monoclonal antibody (mAb) interchain disulfide bond reduction has been observed in a recent large-scale clinical manufacturing operation. A massive reduction/precipitation at post-clarification steps has occurred. This note presents the development of a novel analytical approach to identify the “potential reduction”—a unique approach to predict the propensity of a monomeric-profiled mAb to be reduced in the post-harvest stage, such as harvest clarification and/or purification steps. The core of this new approach includes comparing the non-reducing capillary electrophoresis profiles of pre- and post-vacuum treated mAb in harvest cell culture fluid (HCCF). Using this approach, the potential reductions of two in-house mAbs in the unclarified and clarified cell culture harvest were assessed.     

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.     

Stepwise Frontal Analysis Coupled with Affinity Chromatography: A Fast and Reliable Method for Potential Ligand Isolation and Evaluation from Mahuang-Fuzi-Xixin Decoction

Mahuang-Fuzi-Xixin Decoction (MFXD) is widely used in the treatment of asthma, however, the functional components in the decoction targeting beta2-adrenoceptor (β₂-AR) remain unclear. Herein, we immobilized the haloalkane dehalogenase (Halo)-tagged β₂-AR on the 6-chlorocaproic acid-modified microspheres. Using the affinity stationary phase, the interactions of four ligands with the receptor were analyzed by stepwise frontal analysis. The association constants were (4.75±0.28)×10⁴ M⁻¹ for salbutamol, (2.93±0.15)×10⁴ M⁻¹ for terbutaline, (1.23±0.03)×10⁴ M⁻¹ for methoxyphenamine, (5.67±0.38)×10⁴ M⁻¹ for clorprenaline at high-affinity binding site, and (2.73±0.05)×10³ M⁻¹ at low-affinity binding site. These association constants showed the same rank order as the radioligand binding assay, demonstrating that immobilized β₂-AR had capacity to screen bioactive compounds binding to the receptor while stepwise frontal analysis could predict their binding affinities. Application of the immobilized receptor in analysis of MFXD by chromatographic method revealed that ephedrine, aconifine, karakoline, and chasmanine were the bioactive compounds targeting β₂-AR. Among them, ephedrine and chasmanine exhibited association constants of (2.94±0.02)×10⁴ M^-1and (4.60±0.15)×10⁴ M⁻¹ to the receptor by stepwise frontal analysis. Molecular docking analysis demonstrated that ephedrine, chasmanine, and the other two compounds interact with β₂-AR through the same pocket involving the key amino acids such as Asn312, Asp113, Phe289, Trp286, Tyr316, and Val114. As such, we reasoned that the four compounds dominate the therapeutic effect of MFXD against asthma through β₂-AR mediating pathway. This work shed light on the potential of immobilized β₂-AR for drug discovery and provided a valuable methodology for rapid screening.     

LABORATORY EXPERIMENTS ON SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS?

We integrate experimental studies attempting to duplicate all or part of the speciation process under controlled laboratory conditions and ask what general conclusions can be made concerning the major models of speciation. Strong support is found for the evolution of reproductive isolation via pleiotropy and/or genetic hitchhiking with or without allopatry. Little or no support is found for the bottleneck and reinforcement models of speciation. We conclude that the role of geographical separation in generating allopatry (i.e., zero gene flow induced by spatial isolation) has been overemphasized in the past, whereas its role in generating diminished gene flow in combination with strong, discontinuous, and multifarious divergent selection, has been largely unappreciated.     

Quantitative imaging approaches to understanding biological processing of metal ions

Faster, more sensitive, and higher resolution quantitative instrumentation are aiding a deeper understanding of how inorganic chemistry regulates key biological processes. Researchers can now image and quantify metals with subcellular resolution, leading to a vast array of new discoveries in organismal development, pathology, and disease. Metals have recently been implicated in several diseases such as Parkinson's, Alzheimers, ischemic stroke, and colorectal cancer that would not be possible without these advancements. In this review, instead of focusing on instrumentation we focus on recent applications of label-free elemental imaging and quantification and how these tools can lead to a broader understanding of metals role in systems biology and human pathology.     

Approximated solution of model for three-phase fluidized bed biofilm reactor in wastewater treatment

An approximated analytical solution of mathematical model for the three phase fluidized bed bioreactor (TFBBR) was proposed using the linearization technique to describe oxygen utilization rate in wastewater treatment. The validation of the model was done in comparison with the experimental results. Satisfactory agreement was obtained in the comparison of approximated analytical solution and numerical solution in the oxygen concentration profile of a TFBBR. The approximated solutions for three modes of the liquid phase flow were compared. The proposed model was able to predict the biomass concentration, dissolved oxygen concentration the height of efficient column, and the removal efficiency.     

Metabolomics and its use in ecology

Metabolomics may be defined as the analysis of thousands of naturally occurring small molecules (metabolites) such as sugars, organic acids, amino acids and nucleotides that are the products of cellular metabolism. As such, it is essentially the study of the complete biochemical phenotype (or metabotype) of any biofluid, cell, tissue or indeed organism, at both the qualitative and quantitative level. Metabolic profiles are context dependent, and will change in response to environmental circumstances. Therefore, while the technique has primarily been used in biomedical research to date, it is also applicable to ecological investigations and shows great promise in measuring the impact of factors such as climate change, disease, food restriction, infection and parasite load. In this review we detail the history and background of metabolomics and discuss examples of previous and potential future metabolic studies and applications in ecological science.     

Real-time quantification and supplementation of bioreactor amino acids to prolong culture time and maintain antibody product quality

Real-time monitoring of cell cultures in bioreactors can enable expedited responses necessary to correct potential batch failure perturbations which may normally go undiscovered until the completion of the batch and result in failure. Currently, analytical technologies are dedicated to real-time monitoring of bioreactor parameters such as pH, dissolved oxygen, and temperature, nutrients such as glucose and glutamine, or metabolites such as lactate. Despite the importance of amino acids as the building blocks of therapeutic protein products, other than glutamine their concentrations are not commonly measured. Here, we present a study into amino acid monitoring, supplementation strategies, and how these techniques may impact the cell growth profiles and product quality. We used preliminary bioreactor runs to establish baselines by determining initial amino acid consumption patterns, the results of which were used to select a pool of amino acids which gets depleted in the bioreactor. These amino acids were combined into blends which were supplemented into bioreactors during a subsequent run, the concentrations of which were monitored using a mass spectrometry based at-line method we developed to quickly assess amino acid concentrations from crude bioreactor media. We found that these blends could prolong culture life, reversing a viable cell density decrease that was leading to batch death. Additionally, we assessed how these strategies might impact protein product quality, such as the glycan profile. The amino acid consumption data were aligned with the final glycan profiles in principal component analysis to identify which amino acids are most closely associated with glycan outcomes.     

A revised equation relating DNA buoyant density to guanine plus cytosine content

An equation relating DNA buoyant density of CsCl to G + C content is given which uses the correct density value of Escherichia coli DNA as the reference. This is done to eliminate the current confusion brought about by two references states.