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Applications of ion chromatography for pharmaceutical and biological products
This is a comprehensive source of information on the application of ion chromatography (IC) in the analysis of pharmaceutical drugs and biologicals.This book, with contributors from academia, pharma, the biotech industry, and instrument manufacturing, presents the different perspectives, experience, and expertise of the thought leaders of IC.
eBook
Tutorial: multivariate classification for vibrational spectroscopy in biological samples
Vibrational spectroscopy techniques, such as Fourier-transform infrared (FTIR) and Raman spectroscopy, have been successful methods for studying the interaction of light with biological materials and facilitating novel cell biology analysis. Spectrochemical analysis is very attractive in disease screening and diagnosis, microbiological studies and forensic and environmental investigations because of its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, there is now an urgent need for multivariate classification protocols allowing one to analyze biologically derived spectrochemical data to obtain accurate and reliable results. Multivariate classification comprises discriminant analysis and class-modeling techniques where multiple spectral variables are analyzed in conjunction to distinguish and assign unknown samples to pre-defined groups. The requirement for such protocols is demonstrated by the fact that applications of deep-learning algorithms of complex datasets are being increasingly recognized as critical for extracting important information and visualizing it in a readily interpretable form. Hereby, we have provided a tutorial for multivariate classification analysis of vibrational spectroscopy data (FTIR, Raman and near-IR) highlighting a series of critical steps, such as preprocessing, data selection, feature extraction, classification and model validation. This is an essential aspect toward the construction of a practical spectrochemical analysis model for biological analysis in real-world applications, where fast, accurate and reliable classification models are fundamental.
A tutorial for multivariate classification analysis of vibrational spectroscopy data (Fourier-transform infrared, Raman and near-IR) is presented. Guidelines are provided for data preprocessing, data selection, feature extraction, classification and model validation.
Journal Article
An Acceptor-π-Donor Structured Organic Chromophore for NIR Triggered Thermal Ablation of Tumor via DNA Damage-Mediated Apoptosis
It will be challenging to develop high-performance organic chromophores for light-triggered thermal ablation of the tumor. Besides, the mechanisms of organic chromophores for tumor therapy remain unclear. Herein, an acceptor-π-donor (A-π-D) structured organic chromophore based on 2-dicyanomethylenethiazole named PTM was developed for photothermal therapy (PTT) of tumors.
Biocompatible PTM nanoparticles (PTM NPs) were fabricated by enclosing PTM with Pluronic F-127. The results of optical and photothermal properties of PTM NPs showed robust near-infrared (NIR) absorption, excellent photostability and high photothermal conversion efficiency (56.9%). The results of flow cytometry, fluorescence microscopy, apoptosis, CCK-8 assays and animal experiments showed that PTM NPs had a good killing effect on tumors under NIR laser irradiation. Furthermore, mechanistic studies, RNA-seq and biological analysis revealed that PTM NPs can cause tumor cell death via DNA damage-mediated apoptosis.
Light-induced thermal ablation effects of PTM NPs in vitro and vivo were surveyed. Collectively, our studies provided a new approach to developing a safe and effective photothermal agent for cancer treatment.
Journal Article
Transgene flow in Mexican maize revisited: Socio‐biological analysis across two contrasting farmer communities and seed management systems
The flow of transgenes into landraces and wild relatives is an important biosafety concern. The case of transgene flow into local maize varieties in Mexico (the center of origin of maize) has been intensively debated over the past 15 years, including legal, political, and environmental disputes fanned by the existence of a significant scientific controversy over the methods used for the detection of transgenes. The use of diverse approaches and a lack of harmonized methods specific to the detection and monitoring of transgenes in landraces have generated both positive and negative results regarding contamination of Mexican maize with genetically modified material over the years. In this paper, we revisit the case of transgene contamination in Mexican maize and present a novel research approach based on socio‐biological analysis of contrasting communities and seed management systems. Two communities were used to investigate how different social and biological factors can affect transgene flow and impact transgene spread in Mexico. Our results show the presence of transgenes in one community and thus support the position that transgenes are highly likely to be present in Mexican maize landraces. However, our work also demonstrates that the extent and frequency with which transgenes can be found will significantly depend on the societal characteristics and seed management systems of the local communities. Therefore, we argue that future analysis of transgene presence should include social research on the seed management practices in the sampling area so that more robust and comprehensive understandings and conclusions can be drawn. This paper revisits the controversial case of transgene flow into landraces of Mexican maize and presents results from a novel socio‐biological analysis of contrasting communities and seed management systems. In this study, two different communities were used to investigate how both social and biological factors can affect the ecology of transgene flow and impact the evolution of maize through transgene spread in Mexico.
Journal Article
Points of Significance: Clustering
Many biological analyses involve partitioning samples or variables into clusters on the basis of similarity or its converse, distance. For example, in a gene expression study, we might seek subsets of patients with similar expression, or take a complementary approach and identify similarly expressed genes across patients.
Journal Article
Using Raman spectroscopy to characterize biological materials
Raman microspectroscopy is useful for the analysis of biological samples, because chemical and structural information can be obtained without using labels. This protocol brings together practical guidelines from expert research groups.
Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.
Journal Article
Higher order structure characterization of protein therapeutics by hydrogen/deuterium exchange mass spectrometry
Characterization of therapeutic drugs is a crucial step in drug development in the biopharmaceutical industry. Analysis of protein therapeutics is a challenging task because of the complexities associated with large molecular size and 3D structures. Recent advances in hydrogen/deuterium-exchange mass spectrometry (HDX-MS) have provided a means to assess higher-order structure of protein therapeutics in solution. In this review, the principles and procedures of HDX-MS for protein therapeutics characterization are presented, focusing on specific applications of epitope mapping for protein–protein interactions and higher-order structure comparison studies for conformational dynamics of protein therapeutics.
Figure
HDX of protein backbone amide hydrogen
Journal Article
Functional diversity on rocky shores of the SW Atlantic
Rocky shores are a transitional ecosystem between land and marine environments, and, together with other benthic coastal habitats, have a diverse macrobenthic community. Although there is enough information about the taxonomic diversity of Argentinean rocky shores, studies with a functional approach are scarce. We applied biological traits analysis and functional diversity indices to evaluate the geographic variation of the functional diversity of macrobenthic assemblages on rocky shores along a latitudinal gradient in the SW Atlantic (from 37° to 50° S). A total of 11 beaches with rocky hard substrate belonging to 2 biogeographical provinces (Magellanic and Argentinean) were studied during April 2016. The trait composition of macrobenthic assemblages and functional diversity indices (Rao’s quadratic entropy) varied significantly along the Argentinean coast, suggesting that the latitudinal gradient influences the distribution of species with respect to combinations of trait modalities. Rao’s quadratic entropy, species richness, evenness, and Shannon-Wiener diversity showed a pattern with higher values in the sites located in high latitudes. The functional diversity patterns found coincide with the biogeographical provinces. The presence of intertidal sewage effluents considerably influence functional diversity and mask the effects of the latitudinal gradient on the macrobenthic communities on rocky shores.
Journal Article