Mechanical/physical methods of cell disruption and tissue homogenization

Navigating the Purification Process: Maintaining the Integrity of Replication-Competent Enveloped Viruses

Replication-competent virus particles hold significant therapeutic potential in application as oncolytic viruses or cancer vaccines. Ensuring the viral integrity of these particles is crucial for their infectivity, safety, and efficacy. Enveloped virus particles, in particular, offer large gene insert capacities and customizable target specificity. However, their sensitivity to environmental factors presents challenges in bioprocessing, potentially compromising high quality standards and cost-effective production. This review provides an in-depth analysis of the purification process steps for replication-competent enveloped virus particles, emphasizing the importance of maintaining viral integrity. It evaluates bioprocessing methods from cell culture harvest to final sterile filtration, including centrifugation, chromatographic, and filtration purification techniques. Furthermore, the manuscript delves into formulation and storage strategies necessary to preserve the functional and structural integrity of virus particles, ensuring their long-term stability and therapeutic efficacy. To assess the impact of process steps on particles and determine their quality and integrity, advanced analytical methods are required. This review evaluates commonly used methods for assessing viral integrity, such as infectious titer assays, total virus particle quantification, and structural analysis. By providing a comprehensive overview of the current state of bioprocessing for replication-competent enveloped virus particles, this review aims to guide researchers and industry professionals in developing robust and efficient purification processes. The insights gained from this analysis will contribute to the advancement of virus-based therapeutics, ultimately supporting the development of safe, effective, and economically viable treatments for various diseases.

Portable and rapid solid sample preparation system utilizing twin-screw mechanism for diagnostic applications

Solid specimens play a crucial role in diagnostic and analytical testing, yet their integration into in vitro diagnostics (IVD) is often limited by lengthy processing times and bulky sample preparation equipment. In this study, we introduce a novel twin-screw mechanical maceration system that enables rapid, continuous, and efficient solid sample preparation within a compact portable platform. By utilizing counter-rotating twin screws, the system generates high shear forces, significantly reducing processing time while maintaining high sample recovery efficiency. We validated its versatility across diverse solid sample types, demonstrating efficient bacterial elution from plant tissues and single-cell dissociation of animal tissues. Our device achieved bacterial elution from plant samples in under 1 min, which is 30 times faster than conventional stomaching, while maintaining a significantly smaller footprint. For animal tissue samples, it dissociated tissue samples of varying sizes (5 g to 100 mg) into single-cell suspensions within 1 min. Furthermore, we explored scalability with a miniaturized device fabricated using 3D printing, which retained comparable performance while reducing volume requirements, expediting processing time, and enabling manual operation without an external power source. This rapid, compact, adaptable, and highly efficient twin-screw system outperforms conventional solid sample processing techniques, making it a promising innovation for a wide range of biomedical applications, from point-of-care diagnostics to tissue biopsies, food hygiene, and agricultural monitoring.

ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias

BACKGROUND

Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies.

RESULTS

We find that all methods that rely on differential lysis of host and microbial cells introduce substantial biases as assessed by 16 S rRNA gene amplicon profiling. However, ChIP enables 10-fold enrichment of microbial DNA while introducing less bias, sufficient to make assessment possible against background, in both pigs and humans.

CONCLUSIONS

We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.

CONCLUSIONS

We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.

Optimization of lung tissue pre-treatment by bead homogenization for subsequent culturomics

The discovery that the lung harbors a diverse microbiome, as revealed by next-generation sequencing, has significantly altered our understanding of respiratory health and disease. Despite the association between the lung microbiota and disease, the nature of their relationship remains poorly understood, and culture isolation of these microorganisms could help to determine their role in lung physiology. Current procedures for processing samples from the lower respiratory tract have been shown to affect the viability of microorganisms, so it is crucial to develop new methods to improve their survival. This study aimed to improve the isolation and characterization of lung microorganisms using a bead-beating homogenization method in a mouse model. Microsphere diameter and bead-beating time affected the survival of the microorganisms (E. coli, S. aureus and C. albicans). Using 2.3 mm diameter microspheres for 60 s of bead-beating promoted the survival of both bacteria and yeast strains. After intratracheal instillation of these microorganisms in mice, approximately 70% of the cells were recovered after the tissue homogenization. To assess the efficiency of the proposed method, the diversity of bacteria was compared between the homogenate and lung tissue samples. Ninety-one genera were detected in the lung tissue, and 63 in the homogenate. Bacterial genera detected in the homogenate represented 84% of the total abundance of the microbiota identified in the lung tissue. Taken together, these results demonstrate that the tissue homogenization process developed in this study recovered the majority of the microorganisms present in the lung. This study presents a bead-beating homogenization method for effective cultivation of lung tissue microorganisms, which may help to improve the understanding of host-microbe interactions in the lung.

Perspective on the influence of suspension manufacturing unit operations on bioburden viability and selection of sampling points at the pilot scale

The suspension wet media milling manufacturing process is a complex multi-unit operation, resulting in drug substance comminution to a target particle size. As a result of this complexity, microbial contamination is of paramount concern, particularly for suspensions dosed for parenteral use. This perspective sought to review the influence of (4) critical manufacturing unit operations using a quality risk management approach to better identify and articulate impact of each unit operation on bioburden viability. The manufacturing unit operations in scope included slurry compounding, deaeration, milling, and filling. Bow tie risk analysis was used as a visual gap analysis tool to evaluate if conventional controls were appropriate to detect and mitigate potential for microbial contamination. A deep dive into these unit operations clarified that mechanisms such as turbohypobiosis, cavitation during deaeration, high energy milling, and inert overlay may have an appreciable influence on bioburden viability and proliferation. The resultant analysis also explicated that endotoxin oversight must be closely monitored through barriers (input material controls, water quality controls) to minimize impact to the product and patient. The identified manufacturing unit operations were not appropriate as mitigating controls for endotoxin. The output of this article relates risk intersections for microbial contamination during wet media milling and offers insights in critical areas for intervention.

Rapid, equipment-free extraction of DNA from skin biopsies for point-of-care diagnostics

Kaposi's sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi's sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process. In this study, a simplified, POC-compatible alkaline DNA extraction, ColdSHOT, was optimized for 0.75 mm human skin punch biopsies. The optimized ColdSHOT extraction consistently produced 40,000+ copies of DNA per 5 µl reaction from 3 mg samples-a yield comparable to standard spin column extractions-within 1 h without significant equipment. The DNA yield was estimated sufficient for KSHV detection from KS-positive patient biopsies, and the LAMP assay was not affected by non-target tissue in the unpurified samples. Furthermore, the yields achieved via ColdSHOT were robust to sample storage in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer prior to DNA extraction, and the DNA sample was stable after extraction. The results presented in this study indicate that the ColdSHOT DNA extraction could be implemented to simplify and accelerate the LAMP-based diagnosis of Kaposi's sarcoma using submillimeter biopsy samples.

REAP+: A single preparation for rapid isolation of nuclei, cytoplasm, and mitochondria

REAP+ is an enhanced version of the rapid, efficient, and practical (REAP) method designed for the isolation of nuclear fractions. This improved version, REAP+, enables fast and effective extraction of mitochondria, cytoplasm, and nuclei. The mechanical cell disruption process has been optimized to cerebral tissues, snap-frozen liver, and HT22 cells with remarkable fraction enrichment. REAP+ is well-suited for samples containing minimal protein quantities, such as mouse hippocampal slices. The method was validated by Western blot and marker enzyme activities, such as LDH and G6PDH for the cytoplasmic fraction and succinate dehydrogenase and cytochrome c oxidase for the mitochondrial fraction. One of the outstanding features of this method is its rapid execution, yielding fractions within 15 min, allowing for simultaneous preparation of multiple samples. In essence, REAP+ emerges as a swift, efficient, and practical technique for the concurrent isolation of nuclei, cytoplasm, and mitochondria from various cell types and tissues. The method would be suitable to study the multicompartment translocation of proteins, such as metabolic enzymes and transcription factors migrating from cytosol to the mitochondria and nuclei. Moreover, its compatibility with small samples, such as hippocampal slices, and its potential applicability to human biopsies, highlights the potential application in medical research.

Scalable Production of 2D Material Heterostructure Textiles for High-Performance Wearable Supercapacitors

Wearable electronic textiles (e-textiles) have emerged as a promising platform for seamless integration of electronic devices into everyday life, enabling nonintrusive monitoring of human health. However, the development of efficient, flexible, and scalable energy storage solutions remains a significant challenge for powering such devices. Here, we address this challenge by leveraging the distinct properties of two-dimensional (2D) material based heterostructures to enhance the performance of wearable textile supercapacitors. We report a highly scalable and controllable synthesis method for graphene and molybdenum disulfide (MoS2) through a microfluidization technique. Subsequently, we employ an ultrafast and industry-scale hierarchical deposition approach using a pad-dry method to fabricate 2D heterostructure based textiles with various configurations suitable for wearable e-textiles applications. Comparative analyses reveal the superior performance of wearable textile supercapacitors based on 2D material heterostructures, demonstrating excellent areal capacitance (∼105.08 mF cm-2), high power density (∼1604.274 μW cm-2) and energy density (∼58.377 μWh cm-2), and outstanding capacitive retention (∼100% after 1000 cycles). Our findings highlight the pivotal role of 2D material based heterostructures in addressing the challenges of performance and scalability in wearable energy storage devices, facilitating large-scale production of high-performance wearable supercapacitors.

Genetically engineered cellular nanoparticles for biomedical applications

In recent years, nanoparticles derived from cellular membranes have been increasingly explored for the prevention and treatment of human disease. With their flexible design and ability to interface effectively with the surrounding environment, these biomimetic nanoparticles can outperform their traditional synthetic counterparts. As their popularity has increased, researchers have developed novel ways to modify the nanoparticle surface to introduce new or enhanced capabilities. Moving beyond naturally occurring materials derived from wild-type cells, genetic manipulation has proven to be a robust and flexible method by which nanoformulations with augmented functionalities can be generated. In this review, an overview of genetic engineering approaches to express novel surface proteins is provided, followed by a discussion on the various biomedical applications of genetically modified cellular nanoparticles.

Rapid nucleic acid extraction from skin biopsies using a point-of-care device

Sample processing is often the rate-limiting step for point-of-care nucleic acid testing, especially for large, robust tissues such as skin biopsies, which can be used to diagnose a variety of dermatological diseases. Extraction of nucleic acids from these samples often relies on lengthy enzymatic digestions, increasing the time to result and reducing the potential impact of rapid molecular diagnostic approaches. To address this, we have developed BLENDER, a device for rapid nucleic acid extraction from tissue biopsies that combines bead-beating homogenization with simultaneous sample heating for enzymatic lysis. Our device can produce a complete DNA yield from a 3 mm cylindrical skin biopsy with only a 15 minute extraction compared to 4 hours when using a commercially available extraction protocol. Decreasing sample-processing time for tissue biopsies could reduce time-to-result for downstream analysis, enabling faster point-of-care diagnosis of solid cancers in limited resource settings.

Mucin 5AC-Mediated CD44/ITGB1 Clustering Mobilizes Adipose-Derived Mesenchymal Stem Cells to Modulate Pancreatic Cancer Stromal Heterogeneity

BACKGROUND & AIMS

Secreted mucin 5AC (MUC5AC) promotes pancreatic cancer (PC) progression and chemoresistance, suggesting its clinical association with poor prognosis. RNA sequencing analysis from the autochthonous pancreatic tumors showed a significant stromal alteration on genetic ablation of Muc5ac. Previously, depletion or targeting the stromal fibroblasts showed an ambiguous effect on PC pathogenesis. Hence, identifying the molecular players and mechanisms driving fibroblast heterogeneity is critical for improved clinical outcomes.

METHODS

Autochthonous murine models of PC (Kras^G12D, Pdx1-Cre [KC] and Kras^G12D, Pdx1-Cre, Muc5ac^-/- [KCM]) and co-implanted allografts of murine PC cell lines (Muc5ac wild-type and CRISPR/Cas knockout) with adipose-derived mesenchymal stem cells (AD-MSCs) were used to assess the role of Muc5ac in stromal heterogeneity. Proliferation, migration, and surface expression of cell-adhesion markers on AD-MSCs were measured using live-cell imaging and flow cytometry. MUC5AC-interactome was investigated using mass-spectrometry and enzyme-linked immunosorbent assay.

RESULTS

The KCM tumors showed a significant decrease in the expression of α-smooth muscle actin and fibronectin compared with histology-matched KC tumors. Our study showed that MUC5AC, carrying tumor secretome, gets enriched in the adipose tissues of tumor-bearing mice and patients with PC, promoting CD44/CD29 (integrin-β1) clustering that leads to Rac1 activation and migration of AD-MSCs. Furthermore, treatment with KC-derived serum enhanced proliferation and migration of AD-MSCs, which was abolished on Muc5ac-depletion or pharmacologic inhibition of CXCR2 and Rac1, respectively. The AD-MSCs significantly contribute toward α-smooth muscle actin-positive cancer-associated fibroblasts population in Muc5ac-dependent manner, as suggested by autochthonous tumors, co-implantation xenografts, and patient tumors.

CONCLUSION

MUC5AC, secreted during PC progression, enriches in adipose and enhances the mobilization of AD-MSCs. On recruitment to pancreatic tumors, AD-MSCs proliferate and contribute towards stromal heterogeneity.

Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine

For investigating the molecular physiology and pathophysiology in organs, the most exact data should be obtained; if not, organ-specific cell lines are analyzed, or the whole organ is homogenized, followed by the analysis of its biomolecules. However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC–MS/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.

Combating Salinity Through Natural Plant Extracts Based Biostimulants: A Review

Enhanced crop growth and yield are the recurring concerns in agricultural field, considering the soaring world population and climate change. Abiotic stresses are one of the major limiting factors for constraining crop production, for several economically important horticultural crops, and contribute to almost 70% of yield gap. Salt stress is one of these unsought abiotic stresses that has become a consistent problem in agriculture over the past few years. Salinity further induces ionic, osmotic, and oxidative stress that result in various metabolic perturbations (including the generation of reactive oxygen, carbonyl, and nitrogen species), reduction in water potential (ψw), distorted membrane potential, membrane injury, altered rates of photosynthesis, leaf senescence, and reduced nitrogen assimilation, among others); thereby provoking a drastic reduction in crop growth and yield. One of the strategies to mitigate salt stress is the use of natural plant extracts (PEs) instead of chemical fertilizers, thus limiting water, soil, and environmental pollution. PEs mainly consist of seeds, roots, shoots, fruits, flowers, and leaves concentrates employed either individually or in mixtures. Since PEs are usually rich in bioactive compounds (e.g., carotenoids, flavonoids, phenolics, etc.), therefore they are effective in regulating redox metabolism, thereby promoting plant growth and yield. However, various factors like plant growth stage, doses applied, application method, soil, and environmental conditions may greatly influence their impact on plants. PEs have been reported to enhance salt tolerance in plants primarily through modulation of signaling signatures and pathways (e.g., Na+, ANNA4, GIPC, SOS3, and SCaBP8 Ca2+ sensors, etc.), and regulation of redox machinery [e.g., superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), non-specific peroxidase (POX), glutathione peroxidase (GPX), peroxiredoxin (Prx), ascorbic acid (AsA), glutathione (GSH), α-tocopherol, etc.]. The current study highlights the role of PEs in terms of their sources, methods of preparation, and mode of action with subsequent physiological changes induced in plants against salinity. However, an explicit mode of action of PEs remains nebulous, which might be explicated utilizing transcriptomics, proteomics, metabolomics, and bioinformatics approaches. Being ecological and economical, PEs might pave the way for ensuring the food security in this challenging era of climate change.

Carotenoid Production from Microalgae: The Portuguese Scenario

Microalgae have an outstanding capacity to efficiently produce value-added compounds. They have been inspiring researchers worldwide to develop a blue biorefinery, supporting the development of the bioeconomy, tackling the environmental crisis, and mitigating the depletion of natural resources. In this review, the characteristics of the carotenoids produced by microalgae are presented and the downstream processes developed to recover and purify them are analyzed, considering their main applications. The ongoing activities and initiatives taking place in Portugal regarding not only research, but also industrialization under the blue biorefinery concept are also discussed. The situation reported here shows that new techniques must be developed to make microalgae production more competitive. Downstream pigment purification technologies must be developed as they may have a considerable impact on the economic viability of the process. Government incentives are needed to encourage a constructive interaction between academics and businesses in order to develop a biorefinery that focuses on high-grade chemicals.

An In Vitro Study of the Effects of Mechanical and Enzymatic Isolation of Stromal Vascular Fraction on Wound Healing

ABSTRACT

The adipose-derived stromal vascular fraction (SVF) is considered to be an attractive source of stem cells in cell therapy. Besides stem cells, it also contains functional cells, such as macrophages, precursor cells, somatic stem cells, and pericytes. Collagenase digestion is the most frequently used method to isolate SVF, but it is time-consuming and costly and has some problems, such as infectious agents and immune reactions. In this research, we compared the yield, cell population ratios, and cell viability when isolating SVF by the ultrasonic physics (U-SVF) method and traditional enzymatic method (E-SVF). Then, we isolated exosomes from U-SVF and E-SVF, respectively, and cocultured them with fibroblasts to investigate the potential of applying this cell secretion in wound repair. The results showed that there was no significant difference between the ultrasonic method and enzymatic method in terms of cell viability, cell numbers, or the expression of CD markers of stem cells. However, exosome analysis identified a greater number and smaller size of exosome particles obtained by U-SVF. In terms of cell proliferation efficiency, although the proliferation efficiency of U-SVF was lower than that of E-SVF. Trilineage differentiation experiments revealed that both E-SVF and U-SVF had good differentiation ability, owing to high stem cell content. Finally, E-SVF and U-SVF exosomes were cocultured with fibroblasts. The efficiency of fibroblast migration increased in the SVF exosome treated groups, and the expression of related genes (integrin α5β1) was slightly upregulated; however, the expression of FAK, AKT, ERK, and RhoA was significantly upregulated at 24 hours. From the abovementioned experiments, we found that there was no significant difference in stem cell-related characteristics between SVF isolated by ultrasonic cavitation and SVF isolated by the enzymatic method. In addition, exosomes secreted by SVF may have excellent therapeutic effect on skin injuries, which provides a new viewpoint and therapeutic strategy for soft tissue repair.

Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis

Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.

Metaproteomics Reveals Alteration of the Gut Microbiome in Weaned Piglets Due to the Ingestion of the Mycotoxins Deoxynivalenol and Zearalenone

The ingestion of mycotoxins can cause adverse health effects and represents a severe health risk to humans and livestock. Even though several acute and chronic effects have been described, the effect on the gut metaproteome is scarcely known. For that reason, we used metaproteomics to evaluate the effect of the mycotoxins deoxynivalenol (DON) and zearalenone (ZEN) on the gut microbiome of 15 weaned piglets. Animals were fed for 28 days with feed contaminated with different concentrations of DON (DONlow: 870 μg DON/kg feed, DONhigh: 2493 μg DON/kg feed) or ZEN (ZENlow: 679 μg ZEN/kg feed, ZENhigh: 1623 μg ZEN/kg feed). Animals in the control group received uncontaminated feed. The gut metaproteome composition in the high toxin groups shifted compared to the control and low mycotoxin groups, and it was also more similar among high toxin groups. These changes were accompanied by the increase in peptides belonging to Actinobacteria and a decrease in peptides belonging to Firmicutes. Additionally, DONhigh and ZENhigh increased the abundance of proteins associated with the ribosomes and pentose-phosphate pathways, while decreasing glycolysis and other carbohydrate metabolism pathways. Moreover, DONhigh and ZENhigh increased the abundance of the antioxidant enzyme thioredoxin-dependent peroxiredoxin. In summary, the ingestion of DON and ZEN altered the abundance of different proteins associated with microbial metabolism, genetic processing, and oxidative stress response, triggering a disruption in the gut microbiome structure.

Alternative Protein Sources as Technofunctional Food Ingredients

Proteins obtained from alternative sources such as plants, microorganisms, and insects have attracted considerable interest in the formulation of new food products that have a lower environmental footprint and offer means to feed a growing world population. In contrast to many established proteins, and protein fractions for which a substantial amount of knowledge has accumulated over the years, much less information is available on these emerging proteins. This article reviews the current state of knowledge on alternative proteins and their sources, highlighting gaps that currently pose obstacles to their more widespread application in the food industry. The compositional, structural, and functional properties of alternative proteins from various sources, including plants, algae, fungi, and insects, are critically reviewed. In particular, we focus on the factors associated with the creation of protein-rich functional ingredients from alternative sources. The various protein fractions in these sources are described as well as their behavior under different environmental conditions (e.g., pH, ionic strength, and temperature). The extraction approaches available to produce functional protein ingredients from these alternative sources are introduced as well as challenges associated with designing large-scale commercial processes. The key technofunctional properties of alternative proteins, such as solubility, interfacial activity, emulsification, foaming, and gelation properties, are introduced. In particular, we focus on the formation of isotropic and anisotropic structures suitablefor creating meat and dairy product analogs using various structuring techniques. Finally, selected studies on consumer acceptance and sustainability of alternative protein products are considered.

Simple and Rapid Non-Enzymatic Procedure Allows the Isolation of Structurally Preserved Connective Tissue Micro-Fragments Enriched with SVF

The stromal vascular fraction (SVF) consists of a heterogeneous population of stem and stromal cells, generally obtained from adipose tissue by enzymatic digestion. For human cell-based therapies, mechanical process methods to obtain SVF represent an advantageous approach because they have fewer regulatory restrictions for their clinical use. The aim of this study was to characterize a novel commercial system for obtaining SVF from adipose tissue by a mechanical approach without substantial manipulations. Lipoaspirate samples collected from 27 informed patients were processed by a simple and fast mechanical system (by means of Hy-Tissue SVF). The Hy-Tissue SVF product contained a free cell fraction and micro-fragments of stromal connective tissue. The enzymatic digestion of the micro-fragments increased the yield of free cells (3.2 times) and CFU-F (2.4 times). Additionally, 10% of free cells from SVF were positive for CD34+, suggesting the presence of endothelial cells, pericytes, and potential adipose-derived stem cells (ADSC). Moreover, the SVF cells were able to proliferate and differentiate in vitro toward adipocytes, osteocytes, and chondrocytes. The immunophenotypic analysis of expanded cells showed positivity for typical mesenchymal stem cell markers. The Hy-Tissue SVF system allows the isolation of stromal vascular fraction, making this product of potential interest in regenerative medicine.

Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis

We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum purity. Similar abundances of endogenous proteins were measured in nine different mouse tissues regardless of the homogenization method used; however, protein precipitation had strong positive effects on several targets. The best throughput was achieved by lyophilizing tissues to dryness, followed by homogenization via bead-beating without sample buffer. Finally, the effect of tissue perfusion prior to dissection and collection was explored in 20 mouse tissues. MRM-MS showed decreased abundances of blood-related proteins in perfused tissues; however, complete removal was not achieved. Concentrations of nonblood proteins were largely unchanged, although significantly higher variances were observed for proteins from the perfused lung, indicating that perfusion may not be suitable for this organ. We present a simple yet effective tissue processing workflow consisting of harvest of fresh nonperfused tissue, novel lyophilization and homogenization by bead-beating, and protein precipitation. This workflow can be applied to a range of mouse tissues with the advantages of simplicity, minimal manual manipulation of samples, use of commonly available equipment, and high sample quality.

Bacterial Lysates as Immunotherapies for Respiratory Infections: Methods of Preparation

Bacterial lysates, prepared from the microorganisms most frequently involved in human Respiratory Tract Infections (RTIs) have been in the market for several decades, and at present, several different brands are available in many countries worldwide. They all claimed to exert local and systemic immunomodulatory effects but different clinical trials show disparate results between them. The lack of consistency of predicted therapeutic effects has undermined their clinical use and hampered licensing in several countries. One explanation for such lack of consistency in the results is that their methods of preparation are also very different. Here, we review the available literature describing methods of preparation of bacterial lysates, including patent disclosure documents. We found a great variety of methodologies of preparation and a lack of standardized procedures among them. The main conclusion of our study is that there is a clear need for standardized protocols of production to obtain comparable results in clinical trials worldwide.

The effect of cytoplasmic crude extracts of Trichophyton verrucosum on cell mediated immunity

OBJECTIVE

Trichophyton verrucosum is a slow growing dermatophyte responsible for a number of skin diseases such as ringworm, and is characterized by patches of hair loss and thick crusts on the host skin in domestic animals. In this study, we examined the immunomodulatory effects of crude extract of Trichophyton verrucosum (TV)cytoplasm in a mouse model.

METHODS

The TV variate was cultured on Sabouraud dextrose agar and the mycelium was grinded by mechanical force. The purified protein was obtained from crude extract of the fungus, and protein concentration was measured by BradFord assay. Six to eight week-female BALB/c mice were divided into three groups: test group, receiving cytoplasmic crude extract plus defibrinated sheep blood; control group, receiving defibrinated sheep blood; and normal group, receiving normal saline. Injections were performed on days 0, 3, 5, 7 and 9 and the mice were sacrificed four days after the last injection. T lymphocyte metabolic activity was examined by methyl thiazol tetrazolium (MTT) assay, and also interleukin-4 (IL-4) and interferon-γ (IFNγ) levels were evaluated by enzyme-linked immunosorbent assay (ELISA).

RESULTS

MTT assay showed that the TV extract stimulated lymphocyte metabolic activity. ELISA results showed that despite increase in the level of IFNγ, no changes were observed in IL-4 level.

CONCLUSIONS

Results indicated that crude extract of TV cytoplasm may probably act as an immune modulator, which affects Th₁ responses. The TV crude extract may be an appropriate agent to induce cellular immunity for combating dermatophytosis infection in animals; and therefore, TV extract may have some potential applications in vaccine/adjuvant technology.

Direct and indirect quantification of phosphate metabolites of nucleoside analogs in biological samples

Nucleoside reverse transcriptase inhibitors (NRTIs) are prodrugs that require intracellular phosphorylation to active triphosphate nucleotide metabolites (NMs) for their pharmacological activity. However, monitoring these pharmacologically active NMs is challenging due to their instability, high hydrophilicity, and their low concentrations in blood and tissues. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the gold standard technique for the quantification of NRTIs and their phosphorylated NMs. In this review, an overview of the publications describing the quantitative analysis of intracellular and total tissue concentration of NMs is presented. The focus of this review is the comparison of the different approaches and challenges associated with sample collection, tissue homogenization, cell lysis, cell counting, analyte extraction, sample storage conditions, and LC-MS analysis. Quantification methods of NMs via LC-MS can be categorized into direct and indirect methods. In the direct LC-MS methods, chromatographic retention of the NMs is accomplished by ion-exchange (IEX), ion-pairing (IP), hydrophilic interaction (HILIC), porous graphitic carbon (PGC) chromatography, or capillary electrophoresis (CE). In indirect methods, parent nucleosides are 1st generated from the dephosphorylation of NMs during sample preparation and are then quantified by reverse phase LC-MS as surrogates for their corresponding NMs. Both approaches have advantages and disadvantages associated with them, which are discussed in this review.

Emerging strategies for the identification of protein-metabolite interactions

Interactions between biological molecules enable life. The significance of a cell-wide understanding of molecular complexes is thus obvious. In comparison to protein-protein interactions, protein-metabolite interactions remain under-studied. However, this has been gradually changing due to technological progress. Here, we focus on the interactions between ligands and receptors, the triggers of signalling events. While the number of small molecules with proven or proposed signalling roles is rapidly growing, most of their protein receptors remain unknown. Conversely, there are numerous signalling proteins with predicted ligand-binding domains for which the identities of the metabolite counterparts remain elusive. Here, we discuss the current biochemical strategies for identifying protein-metabolite interactions and how they can be used to characterize known metabolite regulators and identify novel ones.

Proteomics and Metabolomics for AKI Diagnosis

Acute kidney injury (AKI) is a severe and frequent condition in hospitalized patients. Currently, no efficient therapy of AKI is available. Therefore, efforts focus on early prevention and potentially early initiation of renal replacement therapy to improve the outcome in AKI. The detection of AKI in hospitalized patients implies the need for early, accurate, robust, and easily accessible biomarkers of AKI evolution and outcome prediction because only a narrow window exists to implement the earlier-described measures. Even more challenging is the multifactorial origin of AKI and the fact that the changes of molecular expression induced by AKI are difficult to distinguish from those of the diseases associated or causing AKI as shock or sepsis. During the past decade, a considerable number of protein biomarkers for AKI have been described and we expect from recent advances in the field of omics technologies that this number will increase further in the future and be extended to other sorts of biomolecules, such as RNAs, lipids, and metabolites. However, most of these biomarkers are poorly defined by their AKI-associated molecular context. In this review, we describe the state-of-the-art tissue and biofluid proteomic and metabolomic technologies and new bioinformatics approaches for proteomic and metabolomic pathway and molecular interaction analysis. In the second part of the review, we focus on AKI-associated proteomic and metabolomic biomarkers and briefly outline their pathophysiological context in AKI.

Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics

Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.

Microfluidization of Graphite and Formulation of Graphene-Based Conductive Inks

We report the exfoliation of graphite in aqueous solutions under high shear rate [∼ 10⁸ s^-1] turbulent flow conditions, with a 100% exfoliation yield. The material is stabilized without centrifugation at concentrations up to 100 g/L using carboxymethylcellulose sodium salt to formulate conductive printable inks. The sheet resistance of blade coated films is below ∼2Ω/□. This is a simple and scalable production route for conductive inks for large-area printing in flexible electronics.

A Review on Macroscale and Microscale Cell Lysis Methods

The lysis of cells in order to extract the nucleic acids or proteins inside it is a crucial unit operation in biomolecular analysis. This paper presents a critical evaluation of the various methods that are available both in the macro and micro scale for cell lysis. Various types of cells, the structure of their membranes are discussed initially. Then, various methods that are currently used to lyse cells in the macroscale are discussed and compared. Subsequently, popular methods for micro scale cell lysis and different microfluidic devices used are detailed with their advantages and disadvantages. Finally, a comparison of different techniques used in microfluidics platform has been presented which will be helpful to select method for a particular application.

An overview of technical considerations for Western blotting applications to physiological research

The applications of Western/immunoblotting (WB) techniques have reached multiple layers of the scientific community and are now considered routine procedures in the field of physiology. This is none more so than in relation to skeletal muscle physiology (i.e., resolving the mechanisms underpinning adaptations to exercise). Indeed, the inclusion of WB data is now considered an essential aspect of many such physiological publications to provide mechanistic insight into regulatory processes. Despite this popularity, and due to the ubiquitous and relatively inexpensive availability of WB equipment, the quality of WB in publications and subsequent analysis and interpretation of the data can be variable, perhaps resulting in spurious conclusions. This may be due to poor laboratory technique and/or lack of comprehension of the critical steps involved in WB and what quality control procedures should be in place to ensure robust data generation. The present review aims to provide a detailed description and critique of WB procedures and technicalities, from sample collection through preparation, blotting and detection, to analysis of the data collected. We aim to provide the reader with improved expertise to critically conduct, evaluate, and troubleshoot the WB process, to produce reproducible and reliable blots.

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.

Quantification of the mRNA expression of G protein-coupled receptors in human adipose tissue

G protein-coupled receptors (GPCRs) are important regulators of human physiology and therefore the targets of a large number of modern therapeutics. Although GPCRs are important regulators of adipose tissue endocrine and energy storage functions, the expression and function of a majority of GPCRs in adipose tissue is poorly characterized. A first step in the functional characterization of adipose tissue GPCRs is to accurately quantify the expression of GPCRs in adipose tissue. In this methods chapter, a detailed, step-by-step protocol is presented for the isolation of adipose tissue total RNA, its conversion into cDNA and the real-time PCR quantification of human GPCR mRNA expression relative to the mRNA expression of the stable adipose tissue housekeeping gene peptidylprolyl isomerase A (PPIA). A comprehensive list of 377 manually validated, commercially available GPCR qPCR primers allows facilitated swift quantification of either the entire human GPCRome or individual GPCRs, thus providing a sensitive, flexible, and cost-effective means of determining the mRNA expression of GPCRs in adipose tissue.

Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives

Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.

Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective

Most biomanufacturing systems developed for the production of biocommodities are based on whole-cell systems. However, with the advent of innovative technologies, the focus has shifted from whole-cell towards cell-free enzyme system. Since more than a century, researchers are using the cell-free extract containing the required enzymes and their respective cofactors in order to study the fundamental aspects of biological systems, particularly fermentation. Although yeast cell-free enzyme system is known since long ago, it is rarely been studied and characterized in detail. In this review, we hope to describe the major pitfalls encountered by whole-cell system and introduce possible solutions to them using cell-free enzyme systems. We have discussed the glycolytic and fermentative pathways and their regulation at both transcription and translational levels. Moreover, several strategies employed for development of cell-free enzyme system have been described with their potential merits and shortcomings associated with these developmental approaches. We also described in detail the various developmental approaches of synthetic cell-free enzyme system such as compartmentalization, metabolic channeling, protein fusion, and co-immobilization strategies. Additionally, we portrayed the novel cell-free enzyme technologies based on encapsulation and immobilization techniques and their development and commercialization. Through this review, we have presented the basics of cell-free enzyme system, the strategies involved in development and operation, and the advantages over conventional processes. Finally, we have addressed some potential directions for the future development and industrialization of cell-free enzyme system.

Top-down proteomics: enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection

The large-scale resolution and detection of proteins from complex native mixtures is fundamental to quantitative proteomic analyses. Comprehensive analyses depend on careful tissue handling and quantitative protein extraction and assessment. To most effectively link these analyses with an understanding of underlying molecular mechanisms, it is critical that all protein types - isoforms, splice variants and those with functionally important PTMs - are quantitatively extracted with high reproducibility. Methodological details concerning protein extraction and resolution using 2DE are discussed with reference to current in-gel protein detection limits. We confirm a significant increase in total protein, and establish that extraction, resolution and detection of phospho- and glycoproteins are improved following automated frozen disruption relative to manual homogenisation. The quality of 2DE protein resolution is established using third-dimension separations and 'deep imaging'; substantially more proteins/protein species than previously realised are actually resolved by 2DE. Thus, the key issue for effective proteome analyses is most likely to be detection, not resolution. Thus, these systematic methodological and technical advances further solidify the role of 2DE in top-down proteomics. By routinely assessing as much proteomic data from a sample as possible, 2DE enables more detailed and critical insights into molecular mechanisms underlying different physiological states.

Production of recombinant disulfide-rich venom peptides for structural and functional analysis via expression in the periplasm of E. coli

Disulfide-rich peptides are the dominant component of most animal venoms. These peptides have received much attention as leads for the development of novel therapeutic agents and bioinsecticides because they target a wide range of neuronal receptors and ion channels with a high degree of potency and selectivity. In addition, their rigid disulfide framework makes them particularly well suited for addressing the crucial issue of in vivo stability. Structural and functional characterization of these peptides necessitates the development of a robust, reliable expression system that maintains their native disulfide framework. The bacterium Escherichia coli has long been used for economical production of recombinant proteins. However, the expression of functional disulfide-rich proteins in the reducing environment of the E. coli cytoplasm presents a significant challenge. Thus, we present here an optimised protocol for the expression of disulfide-rich venom peptides in the periplasm of E. coli, which is where the endogenous machinery for production of disulfide-bonds is located. The parameters that have been investigated include choice of media, induction conditions, lysis methods, methods of fusion protein and peptide purification, and sample preparation for NMR studies. After each section a recommendation is made for conditions to use. We demonstrate the use of this method for the production of venom peptides ranging in size from 2 to 8 kDa and containing 2-6 disulfide bonds.

Reproducible method to enrich membrane proteins with high purity and high yield for an LC-MS/MS approach in quantitative membrane proteomics

The proportionately low abundance of membrane proteins hampers their proteomic analysis, especially for a quantitative LC-MS/MS approach. To overcome this limitation, a method was developed that consists of one cell disruption step in a hypotonic reagent using liquid nitrogen, one isolation step using a low speed centrifugation, and three wash steps using high speed centrifugation. Pellets contained plasma, nuclear, and mitochondrial membranes, including their integral, peripheral, and anchored membrane proteins. The reproducibility of this method was verified by protein assay of four separate experiments with a CV of 7.7%, and by comparative LC-MS/MS label-free quantification of individual proteins between two experiments with 99% of the quantified proteins having a CV ≤30%. Western blot and LC-MS/MS results of markers for cytoplasm, nucleus, mitochondria, and their membranes indicated that the enriched membrane fraction was highly pure by the absence of, or presence of trace amounts of, nonmembrane marker proteins. The average yield of membrane proteins was 237 μg/10 million HT29-MTX cells. LC-MS/MS analysis of the membrane-enriched sample resulted in the identification of 2597 protein groups. In summary, the developed method is reproducible, produces a highly pure membrane fraction, and generates a high yield of membrane proteins.

Effect of microfluidization on bioaccessibility of carotenoids from Chlorella ellipsoidea during simulated digestion

This study focused on the bioaccessibility of carotenoids from Chlorella ellipsoidea using a simulated digestion model. To increase the bioaccessibility of carotenoids, C. ellipsoidea was pulverized by microfluidization at pressures up to 20000 psi. The microfluidization treatment significantly reduced mean microalga particle size from 2463 to 361 nm. The major carotenoid in C. ellipsoidea was zeaxanthin, with two minor carotenoids, antheraxanthin and β-carotene. After microfluidization, the zeaxanthin and β-carotene contents in C. ellipsoidea were not changed in comparison to the untreated group, whereas the antheraxanthin content was significantly reduced. The bioaccessibility of carotenoids in untreated C. ellipsoidea was very low (zeaxanthin, 2.60%; β-carotene, 1.69%). Approximately 95% of total C. ellipsoidea carotenoids could not be released and micellized by simulated digestion. The microfluidized microalga (at 20000 psi) was 10 times more effective for zeaxanthin and β-carotene micelle formation compared with untreated C. ellipsoidea, showing higher bioaccessibility of carotenoids (zeaxanthin, 32.60%; β-carotene, 18.19%). These results indicate that microfluidization may be useful for disrupting C. ellipsoidea cell walls and improving zeaxanthin and β-carotene bioaccessibility from C. ellipsoidea during the digestion process.

Perspective: proteomic approach to detect biomarkers of human growth hormone

Several serum biomarkers for recombinant human growth hormone (rhGH) have been established, however, none alone or in combination have generate a specific, sensitive, and reproducible 'kit' for the detection of rhGH abuse. Thus, the search for additional GH specific biomarkers continues. In this review, we focus on the use of proteomics in general and two-dimensional electrophoresis (2-DE) in particular for the discovery of new GH induced serum biomarkers. Also, we review some of the protocols involved in 2-DE. Finally, the possibility of tissues other than blood for biomarker discovery is discussed.

Isolation of subcellular organelles and structures

One of the major challenges in functional proteomics is the separation of complex protein mixtures to allow detection of low abundance proteins and provide for reliable quantitative and qualitative analysis of proteins impacted by environmental parameters. Prerequisites for the success of such analyses are standardized and reproducible operating procedures for sample preparation prior to protein separation. Due to the complexity of total proteomes, especially of eukaryotic proteomes, and the divergence of protein properties, it is often beneficial to prepare standardized partial proteomes of a given organism to maximize the coverage of the proteome and to increase the chance to visualize low abundance proteins and make them accessible for subsequent analysis. In this chapter we will describe with detailed recipes procedures for the enrichment and isolation of the currently most investigated organelles and subcellular compartments in mammalian cells using classical centrifugation techniques to more sophisticated immunoaffinity-based procedures.