Simple Method For Isolation Research Articles

Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses

Cell isolation protocols from brain tissue include prolonged ex vivo processing durations, rendering them suboptimal for transcriptomic studies. Particularly for microglia and vascular cells, current isolation methods produce lower yields, necessitating addition of an enrichment step, and use of large tissue volumes - in most cases whole brain tissue - to obtain sufficient yields. Here, we developed a simple, rapid, and reproducible cell isolation method for generating single-cell suspensions from micro-dissected brain regions, enriched for microglia and vascular cells, without an enrichment step. Cells isolated using this method are suitable for molecular profiling studies using 10 × Genomics Chromium single-cell RNA sequencing with high reproducibility. Our method is valuable for longitudinal unbiased molecular profiling of microglia and vascular cells within different brain regions, spanning multiple time points across physiological development or disease progression.

A Simplified Method for Isolation and Culture of Retinal Pigment Epithelial Cells from Adult Mice

A Simplified Method for Isolation and Culture of Retinal Pigment Epithelial Cells from Adult Mice

A modified CTAB method for the extraction of high-quality RNA from mono-and dicotyledonous plants rich in secondary metabolites

BackgroundHigh-quality RNA extraction from woody plants is difficult because of the presence of polysaccharides and polyphenolics that bind or co-precipitate with the RNA. The CTAB (cetyl trimethylammonium bromide) based method is widely used for the isolation of nucleic acids from polysaccharide-rich plants. Despite the widespread use of the CTAB method, it is necessary to adapt it to particular plant species, tissues and organs. Here we described a simple and generalized method for RNA isolation from mature leaf tissues of several economically important woody (17) and herbaceous plants (2) rich in secondary metabolites. High yields were achieved from small amount (up to 50 mg) of plant material. Two main modifications were applied to the basic protocol: an increase in β-mercaptoethanol concentration (to 10%v/v) and the use of an effective DNase treatment. As opposed to similar studies, we tried to describe a more detailed protocol for isolating RNA, including the exact quantity and concentration of the reagents were used.ResultsOur modified CTAB method is proved to be efficient in extracting the total RNA from a broad range of woody and herbaceous species. The RNA yield was ranged from 2.37 to 91.33 µg/µl. The A260:A280 and A260:A230 absorbance ratios were measured from 1.77 to 2.13 and from 1.81 to 2.22. The RIN value (RNA Integrity Number) of the samples fell between 7.1 and 8.1, which indicated that a small degree of RNA degradation occurred during extraction. The presence of a single peak in the melt curve analyses and low standard errors of the Ct values of replicated measurements indicated the specificity of the primers to bind to the cDNA.ConclusionsOur RNA isolation method, with fine-tuned and detailed instructions, can produce high quality RNA from a small amount of starting plant material that is suitable for use in downstream transcriptional analyses. The use of an increased concentration of the reducing agent β-mercaptoethanol in the extraction buffer, as well as the application of DNaseI-treatment resulted in a method suitable for a wide range of plants without the need of further optimalization, especially in Rhus typhina (Staghorn sumac), for which molecular-genetic studies have not yet been sufficiently explored.

Isolated bovine pancreatic islets as an alternate in vitro model for diabetes research.

Background & objectives Isolation of functional pancreatic islets for diabetes research and clinical islet transplantation stands as a big challenge despite the advancements in the field. In this context, the non-availability of human/animal tissues is one of the major impediments to islet-based research, which has tremendous scope for translation. The current study explores the feasibility of using the bovine pancreas as an alternative source to isolate pancreatic islets and assess its functionality for in vitro studies. Methods The bovine pancreas was collected from a registered slaughterhouse and transported in an ice-cold medium - Hank's Balanced Salt Solution (HBSS) to the laboratory. Islets were isolated by sequential collagenase digestion followed by a two-step filtration and purification by density gradient separation method. After isolation, islets were identified with dithizone staining and the islet function was assayed in vitro for assessing the dynamic insulin secretory function by monitoring the glucose-stimulated insulin secretion (GSIS), in response to low and high glucose. Staining techniques were also used to understand the cytoarchitecture of the bovine pancreas. Results The islet yield was 157±23 islets per gram of pancreas and was viable. The cold ischaemia time was reduced to 60-75 min. The islets released insulin with glucose stimulation. The insulin release was observed more with high glucose (28 mM) than with low glucose (2.8 mM). Dithizone staining confirmed the presence of islets after isolation and the size of islets ranged from 50 to 600 µm size. The mantled islets (islets with acinar tissue) were also noted with the pure islets in culture. Hematoxylin and eosin (H&E) and aldehyde- fuchsin showed islets interspersed in the acinar tissue of the bovine pancreas. Special stain defined the islets better than regular staining. Fluorescent and diaminobenzidine (DAB) staining with insulin, glucagon and somatostatin revealed the arrangement of the cells in each islet. The beta cells were majorly found in the islet core with alpha cells interspersed with the delta cells in the periphery. Interpretation & conclusions The isolation procedure described in this study yielded viable islets for in vitro studies which showed a differential response to glucose challenge, confirming their viability. We provide a simple and reproducible method for small-scale isolation of functional islets from the bovine pancreas. This model proffers the beginner a hands-on in islet experiments and helps to re-iterate the process that could be extrapolated to other pancreatic tissues as well as to expand on diabetes research.

Observation of the Effects of Different Enzyme Digestion Time and Enzyme Digestion Methods on the Extraction of Primary Renal Tubular Epithelial Cells from Sprague-Dawley Suckling Mice.

Renal tubular epithelial cells are one of the essential functional cells in the kidney. Optimizing the isolation and culture method of primary renal tubular epithelial cells from SD mammary rats provides better experimental materials for renal tubule-related studies, which is essential for studying the pathogenesis of renal diseases, especially diabetic nephropathy and drug screening. SD rat renal tubular epithelial cells were isolated and purified by 2.5-mg/ml collagenase II or 2mg/ml trypsin + 2.5mg/ml collagenase II enzymatic digestion. The isolation and purification were observed at different time points (15min, 30min, 45min, and 60min) to determine the optimal extraction time for the enzymatic digestion method. After comparing the two enzymatic methods, it was determined that the trypsin + collagenase II enzymatic method was more effective. The primary renal tubular epithelial cells extracted by the trypsin + collagenase II digestion method were identified by the marker Cytokeratin 18 of renal tubular epithelial cells at 45min of digestion with high purity. We established a simple, efficient, and reproducible method for isolation and culture of renal tubular epithelial cells in SD mammary gland rats.

Development of a high-throughput DNA isolation method for livestock and poultry meat based on mesoporous metal-organic framework-coated solid-phase microextraction device

A rapid, portable, simple, low-cost, and high-throughput DNA isolation method was developed for the quantitative identification of meat adulteration based on mesoporous UiO-66 coated solid phase microextraction (SPME) devices. The high-throughput DNA extraction system consists of 96 UiO-66 SPME devices and a polyformaldehyde plate, which can extract DNA from 96 livestock and poultry meat samples simultaneously. At the same time, several parameters of the high throughput DNA isolation method were optimized, including lysis buffer volume, elution buffer volume, lysis time and elution time, etc. Compared with the single DNA isolation device, the 96-SPME high-throughput extraction system maintains the original good universality, reproducibility, chemical stability, and reusability. On this basis, it obtained higher DNA concentration (80 ± 34 ng μL−1), satisfactory DNA purity (A260/A280=2.4) and shorter extraction time (less than 7.2 s per sample), which are much more convenient and efficient than the conventional kit method and the single SPME DNA isolation method. In addition, the conventional multiplex polymerase chain reaction and real-time polymerase chain reaction techniques were used for the qualitative and quantitative detection of meat adulteration. The DNA obtained from this extraction method is highly reproducible and sensitive for the identification of duck ingredients in beef, with a detection range of 1–100 % and a minimum detection limit of 1 % (w/w).

Isolation of Extracellular Vesicles from Cell Culture and Blood Through Nano-Targeted DLD Microfluidic Device.

Extracellular vesicles (EVs) are secreted by cells and found in biological fluids such as blood, with concentration correlated with oncogenic signals, making them attractive biomarkers for liquid biopsy. The current gold-standard method for EVs isolation requires an ultracentrifugation (UC) step among others. The cost and complexity of this technique are forbiddingly high for many researchers, as well as for routine use in biological laboratories and hospitals. This chapter reports on a simple microfluidic method for EVs isolation, based on a microfluidic size sorting technique named Deterministic Lateral Displacement (DLD). With the design of micrometric DLD array, we demonstrated the potential of our DLD devices for the isolation of nano-biological objects such as EVs, with main population size distribution consistent with UC technique.

Analysis of Purity and Concentration Escherichia coli DNA by Boiling Method Isolation with Addition of Proteinase-K and RNase

Escherichia coli is a leading cause of Urinary Tract Infections (UTIs) in Indonesia, with approximately 180,000 cases reported annually. The more cases of UTIs, the more PCR diagnosis is needed with an accurate, fast, simple, and economical DNA isolation method. However, currently, there is no DNA purification stage from protein and RNA contaminants in the boiling DNA isolation method. This study aimed to investigate the impact of incorporating Proteinase-K and RNase into the boiling DNA isolation method on the purity and concentration of E. coli’s DNA during isolation. The boiling method involved heating to 95°C – 100°C bring to cell lysis and release of cellular components, including DNA. Urine samples were artificially contaminated with E. coli at different McFarland standards (0.25, 0.5, and 1). The boiling DNA isolation method was then performed and then analyzed for purity and concentration using a NanoDrop spectrophotometer. This study demonstrated a positive correlation between Proteinase-K and RNase concentrations used in the boiling DNA isolation method and the subsequent increase in DNA purity and concentration. An increase in DNA purity and concentration was obtained even though it was not statistically significant compared to that without Proteinase-K and RNase addition, with p-values of 0.245 for DNA purity and 0.353 for DNA concentration. Further research is recommended with higher Proteinase-K and RNase concentrations in the boiling DNA isolation method to achieve improved purity and concentration of E. coli DNA. Such enhancements could improve PCR amplification and help diagnose E. coli-related UTIs.

Assessment of Genetic Diversity and Fingerprinting of Sugarcane Varieties Using Simple Sequence Repeat (SSR) Markers

Simple sequence repeat (SSR) fingerprinting was chosen because of its high polymorphism, which enables precise analysis of genetic diversity, for the assessment of genetic variety among several sugarcane varieties. This method focuses on certain areas of the sugarcane genome and offers important insights into the distinctive genetic patterns and relationships between the many sugarcane types under study. To increase sugarcane production and resilience, crop development plans, breeding programmes, and conservation activities must be guided by the data obtained by SSR fingerprinting. This study aimed to assess the genetic diversity and fingerprinting of eight sugarcane varieties (Isd 16, Isd 20, Isd 21, Isd 24, Isd 28, Isd 29, Isd 30, and Isd 31) using four SSR primers. A simple and efficient method for DNA isolation was employed, and the primers successfully amplified a total of 59 bands from the eight varieties. The results showed that the marker SMC687CS exhibited the highest number of alleles and genotypes per locus, followed by SMC336BS and SMC334BS, while SMC119CG showed the lowest. The highest PIC value was obtained from the marker SMC687CS, indicating its high level of polymorphism. The four SSR markers were able to distinguish 56.25% of all the cultivars evaluated, with the highest linkage distance recorded between the varieties Isd 24 and Isd 28. This study identified and classified the eight sugarcane varieties, indicating genetic differences among them that coincide with their field performances.

Umbilical Cord Blood-Derived Monocytes as A Reliable Source of Functional Macrophages for Biomedical Research.

Macrophages are multifunctional immune cells widely used in immunological research. While autologous macrophages have been widely used in several biomedical applications, allogeneic macrophages have also demonstrated similar or even superior therapeutic potential. The umbilical cord blood (UCB) is a well-described source of abundant allogenic monocytes and macrophages that is easy to collect and can be processed without invasive methods. Current monocyte isolation procedures frequently result in heterogenous cell products, with limited yields, activated cells, and high cost. This study outlines a simple isolation method that results in high yields and pure monocytes with the potential to differentiate into functional macrophages. In the experimental study, we describe a simple and efficient protocol to isolate highpurity monocytes. After collection of human UCB samples, we used a gradient-based procedure composed of three consecutive gradient steps: i. Hydroxyethyl starch-based erythrocytes sedimentation, followed by ii. Mononuclear cells (MNCs) isolation by Ficoll-Hypaque gradient, and iii. Separation of monocytes from lymphocytes by a slight hyperosmolar Percoll gradient (0.573 g/ml). Then the differentiation potential of isolated monocytes to pro- and antiinflammatory macrophages were evaluated in the presence of granulocyte colony-stimulating factor (GM-CSF) and macrophage CSF (M-CSF), respectively. The macrophages were functionally characterized as well. A high yield of monocytes after isolation (25 to 50 million) with a high purity (>95%) could be obtained from every 100-150 ml UCB. Isolated monocytes were defined based on their phenotype and surface markers expression pattern. Moreover, they possess the ability to differentiate into pro- or anti-inflammatory macrophages with specific phenotypes, gene/surface protein markers, cytokine secretion patterns, T-cell interactions, and phagocytosis activity. Here we describe a simple and reproducible procedure for isolation of pure monocytes from UCB, which could be utilized to provide functional macrophages as a reliable and feasible source of allogenic macrophages for biomedical research.

Improving of an easy, effective and low-cost method for isolation of microplastic fibers collected in drying machines filters

Microplastic fibers have been found to be a dominant form of microplastics in water matrixes, and textile industry and domestic washing of synthetic textiles as one of its main sources. Additionally, there is a lack of knowlidge about microplastic fiber release during mechanically drying clothes and textiles due to differences in the isolation of microplastic fiber methods. Limited information available in the literature in terms of the isolation of microplastic fibers from organic-rich samples after using different household equipment represents one of the main challenges leading us to our main goal, to optimise an effective, simple, and low-cost method for the isolation of microplastic fibers from textile fibers of different origins without damaging their structure. This is achieved by primarily removing mineral matter by using density separation with a saturated solution of ZnCl2 followed by removal of organic matter by using hydrogen peroxide (H2O2) and FeCl3 as a catalyst. Identification of microplastic fibers was obtained by optical microscope, Fourier-transform infrared spectroscopy and Thermogravimetric analysis. Clear microscope (both optical and SEM) images, high percentage of obtained FTIR spectra overlap with Polymer Sample laboratory, clear TGA of isolated samples confirmed that this method can be used as a simple and effective method for isolation of microplastic fibers from organic components rich samples of different origin.

Direct leaf-peeling method for areca protoplasts: a simple and efficient system for protoplast isolation and transformation in areca palm (Areca catechu)

BackgroundAreca palm (Areca catechu) is a woody perennial plant of both economical and medicinal importance grown in tropical and subtropical climates. Yet, the molecular biology study of areca palm is extremely impeded by its unavailability of a transformation method. An efficient protoplast isolation and transformation system could be highly desirable to overcome this barrier.ResultsHere, we described a simple and efficient method for protoplast isolation and transformation from the perennial plant areca palm. A high yield of protoplasts (2.5 × 107 protoplasts per gram of fresh leaf tissues) was obtained from the fresh light green leaflet from the newly-emerged leaf digested overnight in the enzyme solution [2% (w/v) cellulase R10, 0.5% (w/v) macerozyme R10, 0.7 M mannitol, 10 mM CaCl2, 20 mM KCl, 20 mM MES and 0.1% (w/v) BSA, pH 5.7] by the direct leaf-peeling method. The isolated areca protoplasts maintain viability of 86.6% and have been successfully transformed with a green fluorescent protein (GFP)-tagged plasmid (pGreen0029-GFP, 6.0 kb) via the polyethylene glycol (PEG)-mediated transformation. Moreover, the mannitol concentration (optimal: 0.7 M) was determined as a key factor affecting areca protoplast isolation. We also demonstrated that the optimal density of areca protoplast for efficient transformation was at 1.0–1.5 × 106 cells/ml. With the optimization of transformation parameters, we have achieved a relatively high transformation efficiency of nearly 50%.ConclusionWe have established the first efficient protocol for the high-yield isolation and transformation of areca palm protoplasts. This method shall be applied in various biological studies of areca palm, such as gene function analysis, genome editing, protein trafficking and localization and protein–protein interaction. In addition, the protoplast system offers a great genetic transformation approach for the woody perennial plant-areca palm. Moreover, the established platform may be applied in protoplast isolation and transformation for other important species in the palm family, including oil palm and coconut.

Large-Scale Amide Coupling in Aqueous Media: Process for the Production of Diazabicyclooctane β-Lactamase Inhibitors

Herein, the amide coupling of six primary amines with the sodium salt of diazabicyclooctane acid in an aqueous medium without an additional base/surfactant or organic solvent is described. The product was efficiently isolated from the reaction through simple filtration and recrystallized using hot water treatment as a swift and cost-effective process. The methodology was implemented on a kilogram scale to produce penultimate intermediates for synthesizing β-lactamase inhibitors such as zidebactam, relebactam, and nacubactam. The comparison of green metrics for several previously reported amide coupling methods was discussed. The developed procedure avoids using hazardous organic solvents and provides a simple isolation method at the operational level with high purity and efficiency.

A simple and quick isolation method to obtain a huge number of fibroblasts like mesenchymal stem cells from human umbilical cord

In this publication, we have developed a simple and quick isolation method of stem cells from the umbilical cord. Usually, the umbilical cord is a waste product during the child delivery procedure, but the umbilical cords contain valuable stem cells called mesenchymal stroma stem cells (also called MSCs), which can be the basis for different applications e.g., testing the effect of therapeutic compounds as well as the development of therapeutic applications for the cure of degenerative diseases like bone and cartilage related. These stem cells can be used to create new artificial organs too. The umbilical cord was cut with sterile scissors into small pieces (1-2 mm size) and these pieces were placed on 6 well culture plates. The cell culture media was added to these plates after 5-10 minutes placing these plates in a CO2 incubator. The successful growth of cells was observed after 7 days in wells, where pieces of umbilical cord were implanted. Microscopic observations show how the cells are oozing out from these pieces. These cells were isolated and passaged further. These adhere to the plastic surface, were fibroblast shaped, and were isolated successfully in different experiments.

SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing.

We developed a simple and reliable method for the isolation of haploid nuclei from fresh and frozen testes. The described protocol uses readily available reagents in combination with flow cytometry to separate haploid and diploid nuclei. The protocol can be completed within 1 hour and the resulting individual haploid nuclei have intact morphology. The isolated nuclei are suitable for library preparation for high-throughput DNA and RNA sequencing using bulk or single nuclei. The protocol was optimised with mouse testes and we anticipate that it can be applied for the isolation of mature sperm from other mammals including humans.

Extracellular vesicles derived from microgreens of Raphanus sativus L. var. caudatus Alef contain bioactive macromolecules and inhibit HCT116 cells proliferation

Extracellular vesicles (EVs) are phospholipid bilayer vesicles released from cells, containing natural cargos. Microgreens of Raphanus sativus L. var. caudatus Alef were used in this study as the source of EVs. EVs were isolated by differential centrifugation. The physical properties were determined by dynamic light scattering (DLS) and electron microscopy. The biological and chemical composition were studied by Fourier-transform infrared (FTIR) microspectroscopy and high-performance liquid chromatography analysis, respectively. EVs had a median size of 227.17 and 234.90 ± 23.30 nm determined by electron microscopy and DLS, respectively with a polydispersity index of 0.293 ± 0.019. Electron microscopy indicated the intact morphology and confirmed the size. The FTIR spectra revealed that EVs are composed of proteins as the most abundant macromolecules. Using a curve-fitting analysis, β-pleated sheets were the predominant secondary structure. Notably, the micromolecular biomarkers were not detected. EVs exerted anti-cancer activity on HCT116 colon cancer over Vero normal cells with an IC50 of 448.98 µg/ml and a selectivity index of > 2.23. To conclude, EVs could be successfully prepared with a simple and effective isolation method to contain nano-sized macromolecules possessing anti-cancer activity.

Voltage sensor fault detection, isolation and estimation for lithium-ion battery used in electric vehicles via a simple and practical method

Accurate measurement information, especially precise voltage, is essential for model-based multi-state estimation algorithms of lithium-ion battery. Regarding the shortcomings in existing diagnosis methods, such as the difficulty in threshold value determination, low voltage sensor fault detection efficiency and the assumption of no multiple faults occur simultaneously, a simple and practical voltage sensor fault detection, isolation and estimation method is proposed in this paper. Firstly, the widely used algorithm by fusion of recursive least square and extend Kalman filter is adopted to obtain the measurement innovation (MI) between measured and estimated terminal voltage during online state-of-charge estimation process. Subsequently, focusing on the MI generated under faultless and faulty voltage sensors, a simple feature point (FP) identification-based voltage sensor detection and isolation method is further designed. Finally, with the identified FP's y-coordinate, a three-step based voltage sensor fault estimation method is developed to determine the fault mode and the corresponding fault value. Moreover, the proposed voltage sensor fault diagnosis method is verified by Federal Urban Driving Schedule test, whose results demonstrate that it can still realize immediate voltage sensor fault detection (at the moment of sensor fault occurrence) and accurate voltage sensor fault estimation even though there exist certain current sensor fault.

Combination of Sea Sand Disruption Method and Ion-Pair Solid-Phase Extraction for Effective Isolation and Purification of Chlorogenic Acid from Plants Prior to the HPLC Determination.

Chlorogenic acid (CQA) is one of phenolics commonly found in higher plants, possessing numerous health-promoting effects on humans. Unfortunately, it is easily degraded/transformed into other substances during extraction. Therefore, its reliable analysis requires a special approach that does not involve high temperatures. This paper presents a very simple method of CQA isolation using the sea sand disruption method with subsequent purification of the extract using the ion-pair solid-phase extraction process, followed by HPLC–DAD detection. It was found that control of the ion pairing reagent concentration and sample pH is crucial to improve purification, and that the best results, with recovery exceeding 98%, were obtained for 0.05 M tetrabutylammonium bisulfate at pH 7 when the ion pairs were formed directly in the extract and eluted from the C18 sorbent using an acidified methanol–water mixture. The practical potential of the developed procedure was verified by using it for CQA isolation from different plants. The approach represents one of the contemporary analytical trends and current advances in the solid phase extraction, in which several sorption extraction techniques are combined to ensure high-quality analytical results.

Current status and outlook of advances in exosome isolation.

Exosomes are extracellular vesicles with a diameter ranging from 30 to 150 nm, which are an important medium for intercellular communication and are closely related to the progression of certain diseases. Therefore, exosomes are considered promising biomarkers for the diagnosis of specific diseases, and thereby, treatments based on exosomes are being widely examined. For exosome-related research, a rapid, simple, high-purity, and recovery isolation method is the primary prerequisite for exosomal large-scale application in medical practice. Although there are no standardized methods for exosome separation and analysis, various techniques have been established to explore their biochemical and physicochemical properties. In this review, we analyzed the progress in exosomal isolation strategies and proposed our views on the development prospects of various exosomal isolation techniques.Graphical abstract

Rapid and inexpensive method of PCR ready DNA isolation from human peripheral blood and saliva

BackgroundThe isolation of nucleic acids is a frequently performed procedure in the molecular biology area. Although several rapid DNA isolation techniques from human peripheral blood and saliva have been developed, there are still some disadvantages – volume, time, cost, and yield are a few notable ones. ObjectiveWe aim to develop a rapid and inexpensive method to isolate high-molecular-weight genomic DNA from human peripheral blood and saliva that can be used for molecular biology experiments. MethodsFive DNA isolation methods with slightly varying protocols were used. High-quality DNA obtained from one specific method was further amplified by PCR and the template with good amplification was further used for performing RFLP and sequencing. ResultsOut of 5 different isolation methods (R1 to R5), DNA obtained from the R4 was of good quality (molecular weight is > 10 kb and 260/280 ratio is 1.89 ± 0.2), which allows successful PCR amplification and good separation in Restriction Fragment Length Polymorphism analysis. Sequencing by the Sanger Sequencing produced a good readable sequence of an amplified fragment from Method R4 DNA. ConclusionIn the present study we have developed a simple, rapid, and cost-effective DNA isolation method, which uses low sample volume and yields good quantity and high-quality product. The DNA obtained is highly fit for molecular genetics research applications.