ResearchPad - liquid-nitrogen https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Effective coupling of rapid freeze-quench to high-frequency electron paramagnetic resonance]]> https://www.researchpad.co/article/elastic_article_7690 We report an easy, efficient and reproducible way to prepare Rapid-Freeze-Quench samples in sub-millimeter capillaries and load these into the probe head of a 275 GHz Electron Paramagnetic Resonance spectrometer. Kinetic data obtained for the binding reaction of azide to myoglobin demonstrate the feasibility of the method for high-frequency EPR. Experiments on the same samples at 9.5 GHz show that only a single series of Rapid-Freeze-Quench samples is required for studies at multiple microwave frequencies.

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<![CDATA[Effects of different pretreatments on flavonoids and antioxidant activity of Dryopteris erythrosora leave]]> https://www.researchpad.co/article/5c3667dad5eed0c4841a66be

Flavonoids are secondary metabolites of plants that often have medical applications. The influences of different sample drying pretreatments on flavonoids and antioxidant activity of ferns have not studies. Dryopteris erythrosora leaves used to analyze flavonoid alterations resulting from drying pretreatments. The total flavonoid content of D. erythrosora leaves exposed to different pretreatments was significantly different. The total flavonoid content of samples initially air-dried in shade and then oven-dried at 75°C were the highest (7.6%), while samples initially dried at 75°C had the lowest content (2.17%). Antioxidant activities of D. erythrosora leaves with different pretreatments varied. Group B first air-dried in the shade and then oven-dried at 75°C and group C first air-dried in the sun and then oven-dried at 75°C, both showed relatively stronger antioxidant activity. The best pretreatment for preserving the flavonoids was to first dry the plant material in the shade and then complete the drying process in an oven at 75°C. It was tentatively identified 22 flavonoids among the four different pretreatments by HPLC-ESI-TOF-MS.

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<![CDATA[Rigid geometry solves “curse of dimensionality” effects in clustering methods: An application to omics data]]> https://www.researchpad.co/article/5989db5fab0ee8fa60be108e

The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained liquid chromatography-mass spectrometry (LC/MS) data of calculated protein signal intensities in HEK-293 cells. Our first attempt at directly clustering the values failed, most likely due to the so-called “curse of dimensionality”. The clusters were not reproducible, and the outputs differed with different methods. By utilizing rigid geometry with a prime ideal I-adic (p-adic) metric, however, we rearranged the sample clusters into a meaningful and reproducible order, and the results were the same with each of the different clustering methods tested. Furthermore, we have also succeeded in application of this method to expression array data in similar situations. Thus, we eliminated the “curse of dimensionality” from the data set, at least in clustering methods. It is possible that our approach determines a characteristic value of systems that follow a Boltzmann distribution.

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<![CDATA[Biochemical Preparation of Cell Extract for Cell-Free Protein Synthesis without Physical Disruption]]> https://www.researchpad.co/article/5989dac5ab0ee8fa60bb237e

Cell-free protein synthesis (CFPS) is a powerful tool for the preparation of toxic proteins, directed protein evolution, and bottom-up synthetic biology. The transcription-translation machinery for CFPS is provided by cell extracts, which usually contain 20–30 mg/mL of proteins. In general, these cell extracts are prepared by physical disruption; however, this requires technical experience and special machinery. Here, we report a method to prepare cell extracts for CFPS using a biochemical method, which disrupts cells through the combination of lysozyme treatment, osmotic shock, and freeze-thaw cycles. The resulting cell extracts showed similar features to those obtained by physical disruption, and was able to synthesize active green fluorescent proteins in the presence of appropriate chemicals to a concentration of 20 μM (0.5 mg/mL).

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<![CDATA[A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)]]> https://www.researchpad.co/article/5989d9d5ab0ee8fa60b659cc

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53–0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population.

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<![CDATA[Reversible Cryopreservation of Living Cells Using an Electron Microscopy Cryo-Fixation Method]]> https://www.researchpad.co/article/5989d9f3ab0ee8fa60b6f47a

Rapid cooling of aqueous solutions is a useful approach for two important biological applications: (I) cryopreservation of cells and tissues for long-term storage, and (II) cryofixation for ultrastructural investigations by electron and cryo-electron microscopy. Usually, both approaches are very different in methodology. Here we show that a novel, fast and easy to use cryofixation technique called self-pressurized rapid freezing (SPRF) is–after some adaptations–also a useful and versatile technique for cryopreservation. Sealed metal tubes with high thermal diffusivity containing the samples are plunged into liquid cryogen. Internal pressure builds up reducing ice crystal formation and therefore supporting reversible cryopreservation through vitrification of cells. After rapid rewarming of pressurized samples, viability rates of > 90% can be reached, comparable to best-performing of the established rapid cooling devices tested. In addition, the small SPRF tubes allow for space-saving sample storage and the sealed containers prevent contamination from or into the cryogen during freezing, storage, or thawing.

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<![CDATA[Follicular size predicts success in artificial insemination with frozen-thawed sperm in donkeys]]> https://www.researchpad.co/article/5989db5cab0ee8fa60bdfe5b

In asses, semen collection, cryopreservation, and artificial insemination (AI) with frozen-thawed semen have been scarcely described and success rate, particularly following AI, is reportedly low. In the absence of reliable protocols, assisted reproductive technologies cannot support the conservation efforts aimed at endangered wild ass species and domestic donkey breeds. Two experiments were conducted in this study. In experiment 1 we evaluated freezing Abyssinian donkey (N = 5, 4 ejaculates each) spermatozoa using three freezing extenders (Berliner Cryomedium + glycerol, BC+G; BotuCrio, BOTU; INRAFreeze, INRA) and two cryopreservation techniques (liquid nitrogen vapour, LNV; directional freezing, DF). Post-thaw evaluation indicated that BOTU and INRA were similar and both superior to BC+G (P ≤ 0.004 for all motility tests), and that DF was superior to LNV (P < 0.002 for all evaluation parameters). In experiment 2, relying on these results, we used Abyssinian donkey sperm frozen in BOTU and INRA by DF for AI (N = 20). Prior to AI, thawed samples were diluted in corresponding centrifugation media or autologous seminal fluids at 1:1 ratio. No difference was found between BOTU and INRA or between the addition of seminal fluids or media, all resulting in ~50% pregnancy, and no differences were noted between males (N = 4). The size of pre-ovulatory follicle was a significant (P = 0.001) predictor for AI success with 9/10 pregnancies occurring when follicular size ranged between 33.1–37.4 mm, no pregnancy when it was smaller, and only one when larger. A number of ass species face the risk of extinction. Knowledge gained in this study on the Abyssinian donkey can be customised and transferred to its closely related endangered species and breeds.

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<![CDATA[Validation of qPCR reference genes in lymphocytes from patients with amyotrophic lateral sclerosis]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbf9c

Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines—LCLs) were used for qPCR analysis. LCLs were studied before and after liquid nitrogen cryopreservation and culturing (groups LCL1 and LCL2, respectively). qPCR data of 8 ICGs expression was analyzed by BestKeeper, NormFinder and geNorm methods. All studied genes (18SRNA, ACTB, B2M, GUSB,GAPDH, HPRT1, MT-ATP6 and RPS17) were expressed in PBMCs, whereas only first four in LCLs. LCLs cryopreservation had no effect on ICGs expression. Comprehensive ranking indicated RPS17 with MT-ATP6 as the best ICGs for qPCR in PBMCs of control and ALS subjects, and RPS17 with 18RNA or MT-ATP6 in LCLs from ALS. In PBMCs 18RNA shouldn’t be used as ICG.

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