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Journal of the Formosan Medical... Feb 2019Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to... (Review)
Review
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts.
Topics: DNA; Feces; Gastrointestinal Microbiome; Humans; Metagenomics; Reagent Kits, Diagnostic; Sequence Analysis, DNA; Specimen Handling
PubMed: 29490879
DOI: 10.1016/j.jfma.2018.02.005 -
Antioxidants (Basel, Switzerland) Sep 2022This study monitored the chemical and biochemical composition of bovine seminal plasma (SP). Freshly ejaculated semen ( = 20) was aliquoted into two parts. The first...
This study monitored the chemical and biochemical composition of bovine seminal plasma (SP). Freshly ejaculated semen ( = 20) was aliquoted into two parts. The first aliquot was immediately assessed to determine the sperm motion parameters. Another motility measurement was performed following an hour-long co-incubation of spermatozoa with SP at 6 °C. The other aliquot was processed to obtain the SP. Seminal plasma underwent the analyses of chemical composition and quantification of selected proteins, lipids and RedOx markers. Determined concentrations of observed parameters served as input data to correlation analyses where associations between micro and macro elements and RedOx markers were observed. Significant correlations of total oxidant status were found with the content of Cu and Mg. Further significant correlations of glutathione peroxidase were detected in relation to Fe and Hg. Furthermore, associations of chemical elements and RedOx markers and spermatozoa quality parameters were monitored. The most notable correlations indicate beneficial effects of seminal Fe on motility and Mg on velocity and viability of spermatozoa. On the contrary, negative correlations were registered between Zn and sperm velocity and seminal cholesterol content and motility. Our findings imply that seminal plasma has a prospective to be developed as the potential biomarker of bull reproductive health.
PubMed: 36139870
DOI: 10.3390/antiox11091796 -
Metabolites Jun 2020Metabolomics can be significantly influenced by a range of pre-analytical factors, such as sample collection, pre-processing, aliquoting, transport, storage and thawing.... (Review)
Review
Metabolomics can be significantly influenced by a range of pre-analytical factors, such as sample collection, pre-processing, aliquoting, transport, storage and thawing. This therefore shows the crucial need for standardizing the pre-analytical phase with the aim of minimizing the inter-sample variability driven by these technical issues, as well as for maintaining the metabolic integrity of biological samples to ensure that metabolomic profiles are a direct expression of the in vivo biochemical status. This review article provides an updated literature revision of the most important factors related to sample handling and pre-processing that may affect metabolomics results, particularly focusing on the most commonly investigated biofluids in metabolomics, namely blood plasma/serum and urine. Finally, we also provide some general recommendations and best practices aimed to standardize and accurately report all these pre-analytical aspects in metabolomics research.
PubMed: 32503183
DOI: 10.3390/metabo10060229 -
Biomarker Insights 2022Biobanks have been supporting longitudinal prospective and retrospective studies by providing standardized services for the acquisition, transport, processing, storage,...
BACKGROUND
Biobanks have been supporting longitudinal prospective and retrospective studies by providing standardized services for the acquisition, transport, processing, storage, and distribution of high-quality biological material and associated data. Here, we describe how the Dog Aging Project (DAP), a large-scale longitudinal study of the domestic dog () with translational applications for humans, developed a biobank of canine biospecimens and associated data.
DESIGN AND METHODS
This was accomplished by working with the Cornell Veterinary Biobank, the first biobank in the world to receive accreditation to ISO 20387:2018-General Requirements for Biobanking. The biobank research team was involved in the early collection stages of the DAP, contributing to the development of appropriate workflows and processing fit-for-purpose biospecimens. In support of a dynamic strategy for real-time adjustment of processes, a pilot phase was implemented to develop, test, and optimize the biospecimen workflows, followed by an early phase of collection, processing, and banking of specimens from DAP participants.
RESULTS
During the pilot and early phases of collection, the DAP Biobank stored 164 aliquots of whole blood, 273 aliquots of peripheral blood mononuclear cells, 130 aliquots of plasma, and 70 aliquots of serum, and extracted high molecular weight genomic DNA suitable for whole-genome sequencing from 109 whole blood specimens. These specimens, along with their associated preanalytical data, have been made available for distribution to researchers.
CONCLUSION
We discuss the challenges and opportunities encountered during the implementation of the DAP Biobank, along with novel strategies for promoting biobanking sustainability such as partnering with a DAP quality assurance manager and a DAP marketing and communication specialist and developing a pilot grant structure to fund small innovative research projects.
PubMed: 36468152
DOI: 10.1177/11772719221137217 -
Journal of Endodontics Jan 2018A biocompatible strategy to promote bacterial eradication within the root canal system after pulpal necrosis of immature permanent teeth is critical to the success of...
INTRODUCTION
A biocompatible strategy to promote bacterial eradication within the root canal system after pulpal necrosis of immature permanent teeth is critical to the success of regenerative endodontic procedures. This study sought to synthesize clindamycin-modified triple antibiotic (metronidazole, ciprofloxacin, and clindamycin [CLIN]) polymer (polydioxanone [PDS]) nanofibers and determine in vitro their antimicrobial properties, cell compatibility, and dentin discoloration.
METHODS
CLIN-only and triple antibiotic CLIN-modified (CLIN-m, minocycline-free) nanofibers were processed via electrospinning. Scanning electron microscopy, Fourier-transform infrared spectroscopy (FTIR), and tensile testing were performed to investigate fiber morphology, antibiotic incorporation, and mechanical strength, respectively. Antimicrobial properties of CLIN-only and CLIN-m nanofibers were assessed against several bacterial species by direct nanofiber/bacteria contact and over time based on aliquot collection up to 21 days. Cytocompatibility was measured against human dental pulp stem cells. Dentin discoloration upon nanofiber exposure was qualitatively recorded over time. The data were statistically analyzed (P < .05).
RESULTS
The mean fiber diameter of CLIN-containing nanofibers ranged between 352 ± 128 nm and 349 ± 128 nm and was significantly smaller than PDS fibers. FTIR analysis confirmed the presence of antibiotics in the nanofibers. Hydrated CLIN-m nanofibers showed similar tensile strength to antibiotic-free (PDS) nanofibers. All CLIN-containing nanofibers and aliquots demonstrated pronounced antimicrobial activity against all bacteria. Antibiotic-containing aliquots led to a slight reduction in dental pulp stem cell viability but were not considered toxic. No visible dentin discoloration upon CLIN-containing nanofiber exposure was observed.
CONCLUSIONS
Collectively, based on the remarkable antimicrobial effects, cell-friendly, and stain-free properties, our data suggest that CLIN-m triple antibiotic nanofibers might be a viable alternative to minocycline-based antibiotic pastes.
Topics: Anti-Infective Agents; Cells, Cultured; Ciprofloxacin; Clindamycin; Dental Pulp; Drug Delivery Systems; Drug Therapy, Combination; Humans; Metronidazole; Nanofibers
PubMed: 29061356
DOI: 10.1016/j.joen.2017.08.024 -
Veterinary Sciences Feb 2023This study aimed to assess the semen quality after the cooling and freezing of the first and second ejaculates of the season, which were collected 1 h apart. After...
This study aimed to assess the semen quality after the cooling and freezing of the first and second ejaculates of the season, which were collected 1 h apart. After collection (n = 40 ejaculates), the gel-free semen volume, concentration, total number of sperm, and sperm morphology were determined. An aliquot of each ejaculate was extended and cooled for 48 h; a second aliquot was cushion-centrifuged and cooled for 48 h; and a third aliquot was processed and then frozen. The total motility (TM) and progressive motility (PM), plasma membrane integrity (PMI), and high mitochondrial membrane potential (HMMP) were assessed pre-(0 h), 24 h, and 48 h post-cooling and before and after freezing. The second ejaculate had a lower gel-free semen volume ( = 0.026). The sperm concentration was greater in the first than in the second ejaculate ( < 0.001). The sperm morphology was similar between the ejaculates ( > 0.05). Cushion-centrifugation prevented a reduction in the TM, PM, and PMI over time ( < 0.05). The TM, PM, and PMI decreased after freezing but not between the ejaculates ( > 0.05). The first and second ejaculates of the season, which were collected 1 h apart, varied in quantity but not in quality after cooling and freezing.
PubMed: 36977212
DOI: 10.3390/vetsci10030173 -
Arthritis Research & Therapy Jan 2022Synovial fluid (SF) is commonly used for diagnostic and research purposes, as it is believed to reflect the local inflammatory environment. Owing to its complex...
BACKGROUND
Synovial fluid (SF) is commonly used for diagnostic and research purposes, as it is believed to reflect the local inflammatory environment. Owing to its complex composition and especially the presence of hyaluronic acid, SF is usually viscous and non-homogeneous. In this study, we investigated the importance of homogenization of the total SF sample before subsequent analysis.
METHODS
SF was obtained from the knee of 29 arthritis patients (26 rheumatoid arthritis, 2 osteoarthritis, and 1 juvenile idiopathic arthritis patient) as part of standard clinical care. Synovial fluid was either treated with hyaluronidase as a whole or after aliquoting to determine whether the concentration of soluble mediators is evenly distributed in the viscous synovial fluid. Cytokine and IgG levels were measured by ELISA or Luminex and a total of seven fatty acid and oxylipin levels were determined using LC-MS/MS in all aliquots. For cell analysis, synovial fluid was first centrifuged and the pellet was separated from the fluid. The fluid was subsequently treated with hyaluronidase and centrifuged to isolate remaining cells. Cell numbers and phenotype were determined using flow cytometry.
RESULTS
In all patients, there was less variation in IgG, 17-HDHA, leukotriene B (LTB), and prostaglandin E (PGE) levels when homogenization was performed before aliquoting the SF sample. There was no difference in variation for cytokines, 15-HETE, and fatty acids arachidonic acid (AA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Between 0.8 and 70% of immune cells (median 5%) remained in suspension and were missing in subsequent analyses when the cells were isolated from untreated SF. This percentage was higher for T and B cells: 7-85% (median 22%) and 7-88% (median 23 %), respectively.
CONCLUSIONS
Homogenization of the entire SF sample leads to less variability in IgG and oxylipin levels and prevents erroneous conclusions based on incomplete isolation of synovial fluid cells.
Topics: Arthritis, Rheumatoid; Chromatography, Liquid; Humans; Hyaluronoglucosaminidase; Synovial Fluid; Tandem Mass Spectrometry
PubMed: 34998422
DOI: 10.1186/s13075-021-02696-4 -
Clinical Biochemistry Mar 2014Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are... (Review)
Review
Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are available, we present a current overview of experimental data regarding procurement, storage, and quality assurance that can inform the handling of frozen biospecimens. Frozen biospecimen degradation can be influenced by factors independent of the collection methodology including tissue type, premortem agonal changes, and warm ischemia time during surgery. Rapid stabilization of tissues by snap freezing immediately can mitigate artifactually altered gene expression and, less appreciated, protein phosphorylation profiles. Collection protocols may be adjusted for specific tissue types as cellular ischemia tolerance varies widely. If data is not available for a particular tissue type, a practical goal is snap freezing within 20min. Tolerance for freeze-thaw events is also tissue type dependent. Tissue storage at -80°C can preserve DNA and protein for years but RNA can show degradation at 5years. For -80°C freezers, aliquots frozen in RNAlater or similar RNA stabilizing solutions are a consideration. It remains unresolved as to whether storage at -150°C provides significant advantages relative to that at -80°C. Histologic quality assurance of tissue biospecimens is typically performed at the time of surgery but should also be conducted on the aliquot to be distributed because of tissue heterogeneity. Biobanking protocols for blood and its components are highly dependent on intended use and multiple collection tube types may be needed. Additional quality assurance testing should be dictated by the anticipated downstream applications.
Topics: Artifacts; Biological Specimen Banks; Cryopreservation; Freezing; Guidelines as Topic; Humans; Protein Stability; Quality Control; RNA Stability; Specimen Handling; Time Factors
PubMed: 24424103
DOI: 10.1016/j.clinbiochem.2014.01.002 -
Journal of Visualized Experiments : JoVE Sep 2016The granulocyte and monocyte phagocytosis and oxidative burst (OB) activity assay can be used to study the innate immune system. This manuscript provides the necessary...
The granulocyte and monocyte phagocytosis and oxidative burst (OB) activity assay can be used to study the innate immune system. This manuscript provides the necessary methodology to add this assay to an exercise immunology arsenal. The first step in this assay is to prepare two aliquots ("H" and "F") of whole blood (heparin). Then, dihydroethidium is added to the H aliquot, and both aliquots are incubated in a warm water bath followed by a cold water bath. Next, Staphylococcus aureus (S. aureus) is added to the H aliquot and fluorescein isothiocyanate-labeled S. aureus is added to the F aliquot (bacteria:phagocyte = 8:1), and both aliquots are incubated in a warm water bath followed by a cold water bath. Then, trypan blue is added to each aliquot to quench extracellular fluorescence, and the cells are washed with phosphate-buffered saline. Next, the red blood cells are lysed, and the white blood cells are fixed. Finally, a flow cytometer and appropriate analysis software are used to measure granulocyte and monocyte phagocytosis and OB activity. This assay has been used for over 20 years. After heavy and prolonged exertion, athletes experience a significant but transient increase in phagocytosis and an extended decrease in OB activity. The post-exercise increase in phagocytosis is correlated with inflammation. In contrast to normal weight individuals, granulocyte and monocyte phagocytosis is chronically elevated in overweight and obese participants, and is modestly correlated with C-reactive protein. In summary, this flow cytometry-based assay measures the phagocytosis and OB activity of phagocytes and can be used as an additional measure of exercise- and obesity-induced inflammation.
Topics: Flow Cytometry; Granulocytes; Humans; Monocytes; Phagocytosis; Respiratory Burst; Staphylococcal Infections; Staphylococcus aureus
PubMed: 27684595
DOI: 10.3791/54264 -
Annals of Laboratory Medicine May 2015The identification of in vitro hemolysis (IVH) using a hematology analyzer is challenging because centrifugation of the specimens cannot be performed for cell counts. In...
BACKGROUND
The identification of in vitro hemolysis (IVH) using a hematology analyzer is challenging because centrifugation of the specimens cannot be performed for cell counts. In the present study, we aimed to develop a scoring system to help identify the presence of hemolysis in anticoagulated blood specimens.
METHODS
Thirty-seven potassium EDTA anticoagulated blood specimens were obtained, and each specimen was divided into 3 aliquots (A, B, and C). Aliquots B and C were mechanically hemolyzed by aspirating 2 and 5 times, respectively, using a 27-gauge needle and then tested; aliquot A was analyzed immediately without any hemolysis. After the cells were counted, aliquots B and C were centrifuged and the supernatants were tested for the hemolytic index and lactate dehydrogenase levels.
RESULTS
The 4 hematologic parameters were selected and scored from 0 to 3 as follows:< 34.0, 34.0-36.2, 36.3-38.4, and ≥38.5 for mean cell hemoglobin concentration (MCHC, g/dL); <0.02, 0.02, 0.03, and ≥0.04 for red blood cell ghosts (10(12)/L); <0.13, 0.13-0.38, 0.39-1.30, and ≥1.31 for difference value (g/dL) of measured hemoglobin and calculated hemoglobin; and <0.26, 0.26-0.95, 0.96-3.34, and ≥3.35 for difference value (g/dL) of MCHC and cell hemoglobin concentration mean. The hemolysis score was calculated by adding all the scores from the 4 parameters. At the cutoff hemolysis score of 3, the IVH of aliquots B and C were detected as 64.9% and 91.9%, respectively.
CONCLUSIONS
The scoring system might provide effective screening for detecting spurious IVH.
Topics: Anticoagulants; Blood Specimen Collection; Edetic Acid; Hemoglobins; Hemolysis; Humans
PubMed: 25932443
DOI: 10.3343/alm.2015.35.3.341