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Turk Patoloji Dergisi 2020Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically... (Review)
Review
Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically recorded and stored, is a unique resource for the study of the pathophysiology of disease, the development of diagnostic biomarkers, and working with human tissues for the potential discovery of targeted therapeutic agents. At this point, the pathology unit plays a unifying and complementary role between the clinical and core disciplines and offers optimal management of the patients' biomaterials for diagnostic and research projects. The aim of this article is to present general information with regard to a biobank constructed for the storage of tumor tissue and blood biospecimens. Ethical issues (informed consent, protection of confidentiality and privacy, and secondary use of biospecimens) and the information technology system (collection, systematic recording, backup and protection of clinical information) are important issues in biobanking. The selection of freezers to be used in storage (mechanical freezers, liquid-vapor nitrogen tanks), and if mechanical freezers are preferred the establishment of the relevant infrastructure and support team (such as additional power units for protection from power outages), the preservation of materials by aliquoting in different freezers, ensuring financing so as to afford the cost of the infrastructure, and implementation of all these dynamics while adhering to international guidelines are of the utmost importance.
Topics: Biological Specimen Banks; Humans; Pathology
PubMed: 32189322
DOI: 10.5146/tjpath.2020.01482 -
Journal of Extracellular Biology Sep 2023Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach...
Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients.
Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.
PubMed: 38046436
DOI: 10.1002/jex2.108 -
Methods in Molecular Biology (Clifton,... 2019Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste... (Review)
Review
Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste products. CSF has long been utilized to confirm clinical suspicion of various infectious and inflammatory disorders, such as meningitis and multiple sclerosis. However, there has been increasing interest in collecting CSF in order to study the clinical significance of additional biomarkers. This chapter outlines the procedures necessary to collect, process, store, and utilize CSF obtained for the purposes of biobanking from both living and deceased patients.
Topics: Biological Specimen Banks; Biomarkers; Brain; Cerebrospinal Fluid; Humans; Meningitis; Multiple Sclerosis; Specimen Handling
PubMed: 30539439
DOI: 10.1007/978-1-4939-8935-5_11 -
FEMS Microbiology Reviews Aug 2017First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of... (Review)
Review
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
Topics: Cryopreservation; Cryoprotective Agents; Feces; Gastrointestinal Microbiome; Humans; Intestines
PubMed: 28830090
DOI: 10.1093/femsre/fux027 -
Pediatric Quality & Safety 2023Sugammadex is a medication that may have cost considerations with the potential for waste of unused product in pediatric patients due to the vial size and its single-use...
UNLABELLED
Sugammadex is a medication that may have cost considerations with the potential for waste of unused product in pediatric patients due to the vial size and its single-use limitation. Therefore, exploring the potential of vial-splitting for perioperative use may be beneficial.
METHODS
The study was a retrospective, quality improvement study using the electronic medical record to identify every sugammadex administration over the last five years in a tertiary care pediatric institution. We divided patients into groups depending on the dose of sugammadex administered. The cost of sugammadex was calculated under three scenarios: (1) only 200-mg vials available; (2) 100-mg aliquots available; and (3) 50-mg aliquots. We then calculated the total money spent per patient in the 3 scenarios.
RESULTS
31,063 patients received sugammadex over the study period, of whom 23.6% received 151-200 mg. The greatest percentage of patients received ≤50 mg (32.9%). The average cost per patient was $113.58, $81.61, and $68.83 if 200 mg, 100 mg, and 50 mg doses were available, respectively. Over the last 5 years, $1,390,110.13 could have been saved by having 50 and 100 mg aliquots available.
CONCLUSIONS
Pediatric patients generally receive lower doses of sugammadex due to weight-based dosing, leading to increased waste and cost when using only 200-mg vials. Vial-splitting into smaller aliquots can significantly cut costs for healthcare centers and patients while decreasing waste.
PubMed: 37051405
DOI: 10.1097/pq9.0000000000000646 -
Analytical Sciences : the International... 2016A simple potentiometric method for determining the free acidity without complexation in the presence of hydrolysable metal ions and sequentially determining the...
A simple potentiometric method for determining the free acidity without complexation in the presence of hydrolysable metal ions and sequentially determining the plutonium concentration by a direct spectrophotometric method using a single aliquot was developed. Interference from the major fission products, which are susceptible to hydrolysis at lower acidities, had been investigated in the free acidity measurement. This method is applicable for determining the free acidity over a wide range of nitric acid concentrations as well as the plutonium concentration in the irradiated fuel solution prior to solvent extraction. Since no complexing agent is introduced during the measurement of the free acidity, the purification step is eliminated during the plutonium estimation, and the resultant analytical waste is free from corrosive chemicals and any complexing agent. Hence, uranium and plutonium can be easily recovered from analytical waste by the conventional solvent extraction method. The error involved in determining the free acidity and plutonium is within ±1% and thus this method is superior to the complexation method for routine analysis of plant samples and is also amenable for remote analysis.
PubMed: 27063711
DOI: 10.2116/analsci.32.401 -
Micromachines Jul 2023The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop...
The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop assays to a lab-on-a-chip format demands huge efforts of integration and automation. The present work is motivated by a strong requirement often posed by molecular assays that combine isothermal amplification and CRISPR/Cas-based detection: after amplification, a 2-8 microliter aliquot of the reaction products must be taken for the subsequent reaction. In order to fulfill this technical problem, we have designed and prototyped a microfluidic device that is able to meter and aliquot in the required range during the stepped assay. The operation is achieved by integrating a porous material that retains the desired amount of liquid after removing the excess reaction products, an innovative solution that avoids valving and external actuation. The prototypes were calibrated and experimentally tested to demonstrate the overall performance (general fluidics, metering, aliquoting, mixing and reaction). The proposed aliquoting method is fully compatible with additional functions, such as sample concentration or reagent storage, and could be further employed in alternative applications beyond molecular diagnosis.
PubMed: 37512736
DOI: 10.3390/mi14071425 -
JBRA Assisted Reproduction Jul 2021Lyophilization is potentially more practical and cost-effective alternative for sperm preservation. However, there are no studies that evaluate the ultrastructure of...
OBJECTIVE
Lyophilization is potentially more practical and cost-effective alternative for sperm preservation. However, there are no studies that evaluate the ultrastructure of human spermatozoa after lyophilization. Therefore, the aim of our study was to evaluate the ultrasctructure of lyophilized spermatozoa using Transmission Electron Microscopy.
METHODS
From a total of 21 donated seminal samples, 30 aliquots were originated and divided into two aliquots so that one could have been submitted to cryopreservation/thaw and the other for lyophilization/rehydration. The liquefied aliquots were homogenized at room temperature. Samples assigned for cryopreservation were placed in straws and samples assigned for lyophilization were placed in the appropriate vials. Cryopreservation samples were placed at -30oC for 30 minutes subsequently for 30 minutes at vapour phase and then plunged into liquid nitrogen. Lately, were warmed in water bath at 37oC for 10 minutes followed by 10 minutes centrifugation. The pellet was resuspended and analysed in a Makler chamber. The semen vials assigned for lyophilization were loaded into a pre-fixed freeze-drying chamber. Following lyophilization, vials were removed from the freeze-drying chamber and kept at 4oC until rehydration. TEM was performed after rehydration and thawing. Sperm samples were fixed, rinsed in buffer, post fixed and dehydration was carried out in escalating concentrations of alcohol solution, acetone and then, embedding in Epon resin. Ultrathin sections were stained and examined in a Transmission Electron Microscope.
RESULTS
Analysis of sperm after freezing/thawing using Transmission Electron Microscopy showed lesions to the midpiece, with some mitochondria degeneration and random rupture of plasma membrane. In the head, we identified intact plasma membrane, nucleus and acrosome, as in the flagellum all main structures remained intact including the plasma membrane, the longitudinal columns of dense fibers and the semicircular fibers. Analysis by Transmission Electron Microscopy showed that spermatozoa heads had ruptured plasma membranes, absence of acrosomes, nuclei with heterogeneous and decompressed chromatin. Mitochondria were deteriorated in the midpiece. Longitudinal columns of dense fibers were absent in the flagellum. Axonemes, in cross-sections, were disrupted with disorganized structures.
CONCLUSIONS
To our knowledge, our study demonstrated, for the first time, the structure of the human spermatozoa after lyophilization using Transmission Electron Microscopy. The use of a fixed lyophilization protocol with media containing cryoprotectants might explain the damage to the structures. More studies are necessary to improve the results of sperm lyophilization. In the future, the use of lyophilization of spermatozoa might reduce the costs of fertility preservation, since there will be no need for storage space and transportation is simpler.
Topics: Acrosome; Cryopreservation; Humans; Male; Semen; Semen Preservation; Sperm Motility; Spermatozoa
PubMed: 34286941
DOI: 10.5935/1518-0557.20210028 -
Journal of the International Society of... Feb 2021Chocolate milk has gained recent scientific support as a recovery drink. However, it is known that high exercise-demand triggers gastrointestinal discomfort which...
Low-fat, lactose-free and leucine-enriched chocolate cow milk prototype: A preliminary study on sensorial acceptability and gastrointestinal complaints following exhaustive exercise.
BACKGROUND
Chocolate milk has gained recent scientific support as a recovery drink. However, it is known that high exercise-demand triggers gastrointestinal discomfort which continues post-exercise, thereby hindering this nutritional strategy. In addition, those who are lactose intolerant cannot benefit from a milk-based beverage. Thus, the aim of this preliminary study was to develop a low-fat, lactose-free, and leucine-enriched chocolate cow milk prototype (CML) representing nutrition-related recommendations for football players, as well as assess athletes' individual subjective outcomes for gastrointestinal complaints and sensorial acceptability in a field-based setting following strenuous team-sport physical demands.
METHODS
This study followed a single group and repeated-measured design with 10 football players (23 ± 2 yrs., 74 ± 14 kg, 174 ± 5 cm) who consumed CML following a 90-min football match simulation protocol (FMP). The total CML intake to achieve 0.150 g leucine·kg [BW]·h occurred in aliquots of 50, 30 and 20% at 0-, 45- and 75-min post-FMP, respectively. Athletes were evaluated by the prevalence, the type and severity (bloating, nausea, flatulence, and gastric reflux) of gastrointestinal complaints and sensorial acceptability (overall perception, appearance, consistency, and flavour) after drinking each aliquot in a 4-h recovery period.
RESULTS
The CML showed higher scores for "Product Acceptability Index" (88%) and sensorial acceptability (~ 8 in 9-point hedonic scale). Kendall's W with bootstrapped resample (95%CI) revealed agreement among respondents as "moderate" (overall perception, flavour) to "strong" (appearance, consistency) and with no significant agreement differences between rater response in the timeline analysis (0.57 up to 0.87; p > 0.05). Agresti-Caffo add-4 analysis (95% confidence interval, [95%CI]) revealed no differences in each time-point analysis versus baseline for athletes classified as having severe gastrointestinal symptoms, but confirmed concern with bloating (three athletes showed a transient response at 2-h and only one continued until 3-h; p = 0.051).
CONCLUSIONS
These preliminary findings suggest that CML presents good taste and high acceptability by the sampled athletes. Thus, CML may be an alternative sport drink for immediate post-workout supplementation to overcome the energy deficit, offer co-ingested leucine, maintain palatability and adherence including lactose intolerance following a team sport-specific fatigue.
TRIAL REGISTRATION
RBR-2vmpz9 , 10/12/2019, retrospectively registered.
Topics: Animals; Cattle; Chocolate; Energy Intake; Flatulence; Food, Fortified; Gastroesophageal Reflux; Gastrointestinal Diseases; Humans; Lactose; Lactose Intolerance; Leucine; Male; Milk; Nausea; Soccer; Sports Nutritional Physiological Phenomena; Taste; Young Adult
PubMed: 33568169
DOI: 10.1186/s12970-020-00406-0 -
General and Comparative Endocrinology May 2024Fecal samples are a non-invasive and relatively accessible matrix for investigating physiological processes in resident killer whale (Orcinus orca) populations. The high... (Review)
Review
Fecal samples are a non-invasive and relatively accessible matrix for investigating physiological processes in resident killer whale (Orcinus orca) populations. The high lipid content of the diet (primarily salmonids) leads to lower density fecal material and slower dispersion, facilitating sample collection. As fecal discharge is relatively infrequent and the volume of sample is variable, maximizing analytical options is an important consideration. Here we present an extraction methodology to measure hormones and lipid content from the same fecal aliquot. Lipid extractions are commonly conducted using chloroform and methanol from Folch or Bligh and Dyer (B&D), while alcohol is the primary solvent for hormone extraction. We evaluated the possibility of using the methanol layer from lipid extractions to assess fecal steroid hormone levels. Folch and B&D methanol residues were assayed form metabolites of progesterone (PMs) and corticosterone (GCs), and results were compared to aliquots extracted in 70 % ethanol. Hormone concentrations measured in the methanol layer from Folch and B&D extractions were 55 % to 79 % lower than concentrations in 70 % ethanol. We developed mathematical corrections, using linear regression models fitted to Folch or B&D methanol vs 70 % ethanol hormone concentrations (p < 0.01). Fecal concentrations of PMs and GCs from methanol extractions were biologically validated and are significantly higher in confirmed pregnant females compared to non-pregnant individuals (p < 0.05). This study demonstrates that lipid extraction protocols may be used for the analysis of multiple biomarkers, maximizing the use of small-volume samples.
PubMed: 38705419
DOI: 10.1016/j.ygcen.2024.114544