Issues of banking breast cancer cells to generate mammospheres

Identification of breast cancer stem cells, within the context of the tumor tissue, requires an efficient and standardized method to preserve the functional features of living cells. Although isolating cancer stem cells can be laborious and time-consuming, minimal processing may be advantageous for the banking of specimens from which cultures are not immediately needed. Homogenization of banking procedures will result in a reliable network of biorepositories for cooperative studies and several research groups are focusing on the issues of tissue banks for translational medicine. Most tissue banks collect and freeze unprocessed cancer specimens, which cannot therefore be used to generate viable cells. We discuss the principal issues of biobanking breast cancer living cells and protocols for mammospheres formation from single cell suspension of tumor cells.     

Bacterial and eukaryote microbiomes of mosquito habitats in dengue-endemic southern Taiwan

Mosquitoes interact with the microbiome of the waters where they oviposit in several ways. Past work suggests adult mosquitoes can detect certain microbes that stimulate oviposition. The presence or absence of certain microbes in water containers thus can attract or repel mosquito species to different containers. I hypothesized that these relationships could be detected via metagenomics. I focused on two container breeders that coexist in Southern Taiwan: the dengue vector Aedes aegypti and the less competent vector Ae. albopictus. In addition to culturing, I performed 16S and 18S rDNA metagenomics assays, the latter of which had never been applied to mosquito waters before, to identify the microbial diversity of artificial containers with and without mosquito larvae. I found no correlation between mosquito presence to any features of the containers or to their microbiomes, which instead correlated strongly with location. Microbial diversity across containers was highly variable, even within the same location, with multiple taxa only found in single containers. This variability is reasonable, because mosquito gut microbiomes are also extremely variable. The possibility remains that microbes in natural containers differ significantly from those in artificial containers, and that these differences drive Aedes preferences for human-associated containers. Broad, single-microbe experimental work is recommended to identify possible attractant or repellent microbial taxa.     

The importance of establishing an international network of tissue banks and regional tissue processing centers

During the past four decades, many tissue banks have been established across the world with the aim of supplying sterilized tissues for clinical use and research purposes. Between 1972 and 2005, the International Atomic Energy Agency supported the establishment of more than sixty of these tissue banks in Latin America and the Caribbean, Asia and the Pacific, Africa and Eastern Europe; promoted the use of the ionizing radiation technique for the sterilization of the processed tissues; and encouraged cooperation between the established tissue banks during the implementation of its program on radiation and tissue banking at national, regional and international levels. Taking into account that several of the established tissue banks have gained a rich experience in the procurement, processing, sterilization, storage, and medical use of sterilized tissues, it is time now to strengthen further international and regional cooperation among interested tissue banks located in different countries. The purpose of this cooperation is to share the experience gained by these banks in the procurement, processing, sterilization, storage, and used of different types of tissues in certain medical treatments and research activities. This could be done through the establishment of a network of tissue banks and a limited number of regional tissue processing centers in different regions of the world.     

Investigating seed bank potential of crustose coralline algae using DNA metabarcoding

To examine the potential for the autogenic ecosystem engineers, crustose coralline algae (CCA), to serve as seed banks or refugia for life stages of other species, it is critical to develop sampling protocols that reflect the diversity of life present. In this pilot study on two shallow water species of CCA collected from Raoul Island (Kermadec Islands; Rangitāhua) New Zealand, we investigated two preservation methods (ethanol vs. silica gel), sampled inner and outer regions of the crusts, and used DNA metabarcoding and seven genes/gene regions (16S rRNA, 18S rRNA, 23S rRNA, cox1, rbcL, and tufA genes and the ITS rRNA region) to develop a protocol for taxa identification. The results revealed immense diversity, with typically more taxa identified within the inner layers than the outer layers. As highlighted in other metabarcoding studies and in earlier work on rhodoliths (nodose coralline algae), reference databases are incomplete, and to some extent, the use of multiple markers mitigates this issue. Specifically, the 23S rRNA and rbcL genes are currently more suitable for identifying algae, while the cox1 gene fares better at capturing the diversity present inclusive of algae. Further investigation of these autogenic ecosystem engineers that likely act as marine seed banks is needed.     

A banking strategy toward customized therapy in breast cancer

In breast cancer, various clinical parameters are assessed to define clinical stage and thus obtain a more accurate prognosis. However, banks of tumor tissues are an important source of material for studies of risk of recurrence and of features governing clinical outcome in breast cancer. Although the heterogeneous characteristics of individual tumors, subtle phenotypes and stem cells can only be identified in viable cells, tissue banks often give low priority to the preservation of living cells because it is labor-intensive and expensive. The present study was designed to evaluate the feasibility of introducing, within the routine procedures of tissue preservation, a cryopreservation protocol that allows the recovery of living cells after storage. We analyzed the effect of storage time on cell viability, growth rates, and protein expression of ten human breast cancer specimens subjected to various cryopreservation techniques. Cryopreservation of cancer tissue specimens for 12 months allowed protein characterization but not the recovery of living cells. Here we show that enzymatic digestion immediately before slow freezing, and storage in liquid nitrogen permits the recovery and expansion of living cells that can be tailored to specific requirements and projects.     

Uniaxial tensile testing approaches for characterisation of atherosclerotic plaques

The pathological changes associated with the development of atherosclerotic plaques within arterial vessels result in significant alterations to the mechanical properties of the diseased arterial wall. There are several methods available to characterise the mechanical behaviour of atherosclerotic plaque tissue, and it is the aim of this paper to review the use of uniaxial mechanical testing. In the case of atherosclerotic plaques, there are nine studies that employ uniaxial testing to characterise mechanical behaviour. A primary concern regarding this limited cohort of published studies is the wide range of testing techniques that are employed. These differing techniques have resulted in a large variance in the reported data making comparison of the mechanical behaviour of plaques from different vasculatures, and even the same vasculature, difficult and sometimes impossible. In order to address this issue, this paper proposes a more standardised protocol for uniaxial testing of diseased arterial tissue that allows for better comparisons and firmer conclusions to be drawn between studies. To develop such a protocol, this paper reviews the acquisition and storage of the tissue, the testing approaches, the post-processing techniques and the stress–strain measures employed by each of the nine studies. Future trends are also outlined to establish the role that uniaxial testing can play in the future of arterial plaque mechanical characterisation.     

Comparison of three multi-cryoprotectant loading protocols for vitrification of porcine articular cartilage

Vitrification is a cryopreservation technique for the long-term storage of viable tissue, but the success of this technique relies on multiple factors. In 2012, our group published a working vitrification protocol for intact human articular cartilage and reported promising chondrocyte recovery after using a four-step multi-cryoprotectant (CPA) loading method that required 570 min. However, this protocol requires further optimization for clinical practice. Herein, we compared three multi-step CPA loading protocols to investigate their impact on chondrocyte recovery after vitrification of porcine articular cartilage on a bone base, including our previous four-step protocol (original: 570 min), and two shorter three-step protocols (optimized: 420 min, and minimally vitrifiable: 310 min). Four different CPAs were used including glycerol, dimethyl sulfoxide, ethylene glycol and propylene glycol. As vitrification containers, two conical tubes (50 ml and 15 ml) were evaluated for their heat transfer impact on chondrocyte recovery after vitrification. Osteochondral dowels were cored into two diameters of 10.0 mm and 6.9 mm with an approximately 10-mm thick bone base, and then allocated into the twelve experimental groups based on CPA loading protocol, osteochondral dowel size, and vitrification container size. After vitrification at −196 °C and tissue warming and CPA removal, samples in all groups were assessed for both chondrocyte viability and metabolic activity. The optimized protocol proposed based on mathematical modelling resulted in similar chondrocyte recovery to our original protocol and it was 150 min shorter. Furthermore, this study illustrated the role of CPA permeation (dowel size) and heat transfer (container size) on vitrification protocol outcome.     

Scaled-down purification protocol to access proteomic analysis of 20S proteasome from human tissue samples: comparison of normal and tumor colorectal cells

The proteasome is a proteolytic complex that constitutes the main pathway for degradation of intracellular proteins in eukaryotic cells. It regulates many physiological processes and its dysfunction can lead to several pathologies like cancer. To study the 20S proteasome structure/activity relationship in cells that derive from human biopsy samples, we optimized an immuno-purification protocol for the analysis of samples containing a small number of cells using magnetic beads. This scaled-down protocol was used to purify the cytoplasmic 20S proteasome of adjacent normal and tumor colorectal cells arising from tissue samples of several patients. Proteomic analyses based on two-dimensional gel electrophoresis (2DE) and mass spectrometry showed that the subunit composition of 20S proteasomes from these normal and tumor cells were not significantly different. The proteasome activity was also assessed in the cytoplasmic extracts and was similar or higher in tumor colorectal than in the corresponding normal cells. The scaled-down 20S proteasome purification protocol developed here can be applied to any human clinical tissue samples and is compatible with further proteomic analyses.     

Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing

In this study, two highly specific quantitative PCR assays targeting the bacterial genera Burkholderia and Pseudomonas were developed and evaluated on soil samples. The primers were targeting different multivariate regions of the 16S rRNA gene and designed to be compatible with quantitative PCR and the high throughput 454 pyrosequencing technique. The developed assays were validated using the standard methods. All tests with the new developed assays showed very high specificity. Pyrosequencing was used for direct analysis of the PCR product and applied as a specificity measurement of the primers. The Pseudomonas primers showed a 99% primer specificity, which covered 200 different Pseudomonas sequence clusters in 0.5 g of soil. In contrast to that the same approach using the genus-specific Burkholderia primers showed only 8% primer specificity. This discrepancy in primer specificity between the normal procedures compared with pyrosequencing illustrates that the common validation procedures for quantitative PCR primers may be misleading. Our results exemplify the fact that current 16S RNA gene sequence databases might lack resolution within many taxonomic groups and emphasize the necessity for a standardized and functional primer validation protocol. A possible solution to this could be to supplement the normal verification of quantitative PCR assays with a pyrosequencing approach.     

Assessing the impact of plant invasions on soil seed bank communities: use of univariate and multivariate statistical approaches

Questions: Are soil seed banks affected by invasions of alien plants? How can we rigorously assess alterations in seed bank communities associated with invasive species and account for the high spatial variability of seed bank data? How do multivariate approaches compare with more traditional approaches based on analysis of variance? Location: Three riparian sites, Ireland. Methods: A protocol based on a combination of multivariate techniques was used to characterize soil seed bank communities associated with the herbaceous invasive species Heracleum mantegazzianum in May and October. Permutational multivariate analysis of variance (PERMANOVA) was used to test the effects of the factors “invasion”, “site”, “plot” and “depth” on the soil seed bank, while multivariate analysis of dispersion (PERMDISP) provided a measure of the variability of seed bank data at different spatial scales. Similarity percentages analysis (SIMPER) was used to identify the species that contributed most to the differences between invaded and uninvaded communities. A comparison between the results of PERMANOVA and ANOVA analyses was also made. Results: The composition of seed bank communities invaded by H. mantegazzianum differed significantly from that of uninvaded seed banks. Invaded seed banks were less diverse and had reduced abundance, and were dominated by only a few species, such as Urtica dioica and Juncus effusus. Such patterns were recorded at each of three depth categories, indicating that invasive plants can affect both the transient and the more persistent component of the soil seed bank. Seed bank variability was significantly higher within uninvaded areas, supporting the notion that invasions tend to lead to more homogeneous communities. Conclusion: The analytical protocol used in this study was effective in quantifying the effect of plant invasions, at different spatial scales, providing a statistically robust analysis of alterations in soil seed bank communities. Compared to ANOVA, this protocol provided more biological information and was more appropriate for analysis of the data. This approach is therefore recommended in soil seed bank and invasion ecological studies.     

Advances of radiation sterilisation in tissue banking

Under the auspices of the IAEA tissue banking programme on “Radiation Sterilisation of Tissue Graft” conducted from 1985 to 2004, many scientists and surgeons were involved in various regional research and development (R&D) projects mainly in dealing with radiation dose selection, radiation effects on human tissues and quality system in radiation sterilisation. New findings on radiation effects, tissue processing and preservation were shared during the regional and interregional meetings and workshops. Many tissue banks started to use radiation (25 kGy) to sterilize tissue grafts for tissue safety and efficacy and still continue to use it. The IAEA Code of Practice for Radiation Sterilization of Tissues Allografts developed in 2007 offered simpler methods to conduct radiation dose setting and dose validation experiments for tissue grafts. Advances in dose selection and dose mapping are continued under the quality management system when banks need to be certified to continue their operation. The combination of good tissue processing and preservation as well as good radiation practice will ensure the tissue products are properly sterilised thus safe and of high quality. Experience in meeting challenges in using radiation sterilisation and achievements reported by the tissue bankers are shared here.     

A practical validation approach for virus titer testing of avian infectious bursal disease live vaccine according to current regulatory guidelines

The method for virus titer determination of avian infectious bursal disease (IBD) live vaccine, developed long before regulatory validation guidelines is a cell culture based biological assay intended for use in vaccine release testing.The aim of our study was to perform a validation, based on fit-for-purpose principle, of an old 50% tissue culture infectious dose (TCID₅₀) method according to Guidelines of the International Cooperation on Harmonization of Technical Requirements for Registration of Veterinary Medicinal Products (VICH).This paper addresses challenges and discusses some key aspects that should be considered when validating biological methods. A different statistical approach and non-parametric statistics was introduced in validation protocol in order to derive useful information from experimental data. This approach is applicable for a wide range of methods.In conclusion, the previous virus titration method had showed to be precise, accurate, linear, robust and in accordance with current regulatory standards, which indicates that there is no need for additional re-development or upgrades of the method for its suitability for intended use.     

Tissue engineering: generation of differentiated artificial tissues for biomedical applications

A new field in biomedical science has been established. Cell biologists, engineers, and surgeons now work within a team. Artificial connective, epithelial, or neuronal tissues are being constructed using living cells and different kinds of biomaterials. Numerous companies and laboratories are presenting dynamic developments in this field. Prognoses predict that, at the beginning of the coming century, the industry of tissue engineering will reach the importance of the present genetic technology. An enormous demand for organ and tissue transplants motivates research activities and drives the acquisition of innovative techniques and creative solutions. At the front of this development is the creation of artificial skin for severely burned patients and the generation of artificial cartilage for implantation in articular joint diseases. Future challenges are the construction of liver organoids and the development of an artificial kidney on the basis of cultured cells. In this paper we show strategies, needs, tools, and equipment for tissue engineering. The presupposition for all projects is the induction, development, and maintenance of differentiation within the tissue under in vitro conditions. As experiments in conventional culture dishes continued to fail, new cell and tissue culture methods had to be developed. Tissues are cultured under conditions as close as possible to their natural environment. To optimize adherence or embedding, cells are grown on novel tissue carriers and on individually selected biomatrices or scaffolds. The tissues are subsequently transferred into different types of containers for permanent perfusion with fresh culture medium. This guarantees constant nutrition of the developing tissue and prevents the accumulation of harmful metabolites. An organo-typical environment for epithelial cells, for example, is obtained in gradient containers, which are permanently superfused at the apical and basal sides with different media. Long term experiments result in cultured tissues in a quality thus far unreached.     

Context-oriented model validation of individual-based models in ecology: A hierarchically structured approach to validate qualitative,compositional and quantitative characteristics

Validation constitutes a vital process in model development and application, as it ensures the applicability of a model for the intended purposes and trustworthy results within the range of model assumptions. Commonly, independent empirical data sets are statistically compared with the generated model results, which is an adequate approach for models which operate on a single hierarchical level, such as most equation-based models. Individual-based models (IBM) can operate on different organisational levels synchronously and have an inherent complex and variable interaction structure for many applications. Thus a plain comparison of data congruity on the result levels might leave too many questions unanswered. However, a more comprehensive assessment of model validity can require additional investigations which encompass also qualitative and structural relationships.Here we describe a hierarchically structured validation which is oriented towards the investigated context of the model and allows organising the validation process in close relation to the different hierarchical levels which are covered in the model. The context oriented organisation protocol for validation includes the following steps: (1) assessing the different model levels separately, then, (2) applying a set of different techniques such as visual inspection, statistical comparison, involvement of experts, aggregation of data on higher integration levels and experimental validation.The context oriented approach accounts for the specificity of individual-based models – i.e., the dynamic self-organisation of model outcomes from biologically underpinned individual interactions without an inherent determination of properties on higher hierarchical levels – and extends the potential of the validation process qualitatively, as it allows to assess complex structural and causal relations and multi-level feedback processes of the developed models.     

The evolution and impact of the International Atomic Energy Agency (IAEA) program on radiation and tissue banking in Asia and the Pacific region

The Asia and the Pacific region was within the IAEA program on radiation and tissue banking, the most active region. Most of the tissue banks in the Asia and the Pacific region were developed during the late 1980s and 1990s. The initial number of tissue banks established or supported by the IAEA program in the framework of the RCA Agreement for Asia and the Pacific region was 18. At the end of 2006, the number of tissue banks participating, in one way or another in the IAEA program was 59. Since the beginning of the implementation of the IAEA program in Asia and the Pacific region 63,537 amnion and 44,282 bone allografts were produced and 57,683 amnion and 36,388 bone allografts were used. The main impact of the IAEA program in the region was the following: the establishment or consolidation of at least 59 tissue banks in 15 countries in the region (the IAEA supported directly 16 of these banks); the improvement on the quality and safety of tissues procured and produced in the region reaching international standards; the implementation of eight national projects, two regional projects and two interregional projects; the elaboration of International Standards, a Code of Practice and a Public Awareness Strategies and, the application of quality control and quality assurances programs in all participating tissue banks.     

Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray

Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe the protocol used to develop and validate an MDM method for the semiquantification of a range of functional genes--in this case, particulate methane monooxygenase (pmoA)--and we give an example of its application to the study of the community structure of methanotrophs and functionally related bacteria in the environment. The development and validation of an MDM, following this protocol, takes ～6 months. The pmoA MDM described in detail comprises 199 probes and addresses ～50 different species-level clades. An experiment comprising 24 samples can be completed, from DNA extraction to data acquisition, within 3 d (12-13 h bench work).     

Establishing a procedure for dimethyl sulfoxide removal from cardiovascular allografts: a quantitative study

The success of allotransplants is critically dependent on both tissue viability and efficient removal of potentially toxic cryopreservants. In this study we analysed the dimethyl sulphoxide (Me2SO) content of cardiovascular tissue samples stored in tissue banks and optimized a washing protocol to be used before surgical implant. We compared the Me2SO content of heart valves, arteries and veins and quantitatively determined by HPLC the washing kinetics of each group of tissue samples under strictly controlled conditions using an industrial washing medium (BASE). Our results showed that heart valves and arteries have significantly slower Me2SO release kinetics than veins. Approximately 20 % of the initial content of cryopreservant could still be detected in the valves and arterial tissue after 15 min of continuous washing. Conversely, veins were almost completely cleared of the cryoprotectant under the same conditions. We propose a washing protocol consisting of two sequential washing with BASE for a total of 25 min for valves and arteries and 15 min for veins. In our hands, this protocol reliably ensures the removal of more than 95 % of the initial Me2SO content.     

The challenges of litigation in US courts and the actions tissue banks can take to meet those challenges

The growth of tissue banking from local non-profit organizations to national and multi-national corporations has increased the likelihood of litigation against tissue banks. The acquisition of tissue banks by corporate entities, many of whom are based in the US, means that tissue banks need to be prepared for the challenge of litigation in the US courts. The purpose of this paper is to help tissue banks meet those challenges by describing the nature of US litigation, the most common types of lawsuits against tissue banks and the steps that tissue banks can take to prepare for litigation in the US.     

Measuring Myeloperoxidase Activity in Biological Samples

Background

Enzymatic activity measurements of the highly oxidative enzyme myeloperoxidase (MPO), which is implicated in many diseases, are widely used in the literature, but often suffer from nonspecificity and lack of uniformity. Thus, validation and standardization are needed to establish a robust method that is highly specific, sensitive, and reproducible for assaying MPO activity in biological samples.

Principal findings

We found conflicting results between in vivo molecular MR imaging of MPO, which measures extracellular activity, and commonly used in vitro MPO activity assays. Thus, we established and validated a protocol to obtain extra- and intracellular MPO from murine organs. To validate the MPO activity assays, three different classes of MPO activity assays were used in spike and recovery experiments. However, these assay methods yielded inconsistent results, likely because of interfering substances and other peroxidases present in tissue extracts. To circumvent this, we first captured MPO with an antibody. The MPO activity of the resultant samples was assessed by ADHP and validated against samples from MPO-knockout mice in murine disease models of multiple sclerosis, steatohepatitis, and myocardial infarction. We found the measurements performed using this protocol to be highly specific and reproducible, and when performed using ADHP, to be highly sensitive over a broad range. In addition, we found that intracellular MPO activity correlated well with tissue neutrophil content, and can be used as a marker to assess neutrophil infiltration in the tissue.

Conclusion

We validated a highly specific and sensitive assay protocol that should be used as the standard method for all MPO activity assays in biological samples. We also established a method to obtain extra- and intracellular MPO from murine organs. Extracellular MPO activity gives an estimate of the oxidative stress in inflammatory diseases, while intracellular MPO activity correlates well with tissue neutrophil content. A detailed step-by-step protocol is provided.