Gas-phase cleavage and dephosphorylation of universal linker-bound oligodeoxynucleotides

While base-specific support is commonly used for single-column oligodeoxynucleotide synthesis, the universal linker is critical for high-throughput synthesis of potentially thousands of samples in a single run. Here, we report conditions for cleavage and complete dephosphorylation of two commercial universal linkers, UnySupport and UnyLinker, processed in the gas phase (NH(3)) using our custom device. First, we compared the average yield of T10mers over time (15, 30, 60, 120, and 240 minutes, 40 psi, 80°C and 90°C). For samples processed with water added prior to incubation, we discovered a substantial increase in yield compared to those left dry (up to 55%). This was also the case for samples subjected to increases in chamber pressure (10, 20, 30 and 40 psi, 120 minutes, 80°C and 90°C). Next, we compared the effects of increased temperature, pressure and incubation times on the rates of dephosphorylation. We found the optimum conditions to be either 10 psi, 120 minutes at 80°C or 60 minutes at 90°C; in both cases, water added to columns prior to incubation had a substantial effect on rate of reaction as well as overall yield compared with those left dry. Finally, performance between the two linkers was similar enough to conclude each fulfills the desired requirements for mainstream, high-throughput oligodeoxynucleotide cleavage/deprotection and dephosphorylation in the gas phase.     

OPTIMIZATION OF PROCESSING OF PEANUT BEVERAGE1

Peanut beverages were prepared and homogenized at 2000, 4000, and 6000 psi and processed at 100°C for 10, 15, and 20 min and at 121°C for 5, 10, and 15 min. Sensory analysis, gas chromatographic (GC) analysis, and viscosity measurements were performed on the products. Sulfur aromatic was found sufficient to discriminate between samples processed at 100°C whereas sulfur aromatic, cooked peanut flavor, and bitterness provided the most efficient combination for discriminating between samples processed at 121°C. Processing time had a more significant effect on the sensory attributes of products. Optimum conditions for processing were found to be at homogenization pressure > 3100 psi and process time > 16 min at a processing temperature of 100°C. No sensory characteristic of the peanut beverage correlated with the instrumental analyses done.     

Flow cytometric analysis from fish samples stored at low,ultra-low and cryogenic temperatures

Flow cytometry is a valuable tool in biomedical and animal sciences. However, equipment used for such analysis presents limitations at field conditions, suggesting then preservation procedures for future analysis at laboratory conditions. In this study, freezing at low (−20 °C), ultra-low (−80 °C) and cryogenic temperatures (−196 °C, i.e. liquid nitrogen) were used as preservation procedures of fish tissue. Samples were maintained in 0.9% NaCl or lysing solution, and stored at the temperatures above for 0 (fresh control), 60, 120 and 180 days of storage. After storage, the samples were thawed and proceeded to flow cytometric analysis. Storage at low temperatures (−20 °C), both in lysing and 0.9% NaCl, exhibited poor results when analyzed after 60, 120 and 180 days, showing noisy peaks, deviation in the DNA content and absence of peaks. Ultralow (−80 °C) and cryogenic (−196 °C) temperatures, both in lysing solution and 0.9% NaCl, showed good results and high quality of histograms. Both storage procedures gave similar histograms and DNA content in comparison with control group (fresh) even after 60, 120 and 180 days of storage, exhibiting the main peak at 2C content from diploid cells and a secondary peak at 4C derived from dividing cells. In conclusion, samples may be stored for 180 days at −80 °C and −196 °C in both, 0.9% NaCl or lysing solution. As cryogenic temperatures in liquid nitrogen permits indefinite storage, this procedure should be used for long-term preservation.     

Increased production of PGI2-like activity by frozen-thawed rat aorta

The effects of storage conditions, temperature, and time on the ability of the rat thoracic aorta to produce a platelet aggregation inhibitor were investigated. Aortic fragments were incubated in Tris buffer, aliquots of which were then tested for their ability to inhibit ADP-induced human platelet aggregation. The incubation fluid of samples that had been soaked in Tris buffer at 4°C for 24 hours contained no inhibitor activity, whereas the incubation fluid of similar samples that had been kept at 4°C but not soaked in buffer contained comparable inhibitor activity as that of fresh samples. The incubation fluid of samples that had been kept at ?20°C or ?80°C contained greater inhibitor activity than that of fresh samples, and was maintained in ?20°C samples for 7 days, and ?80° samples for 28 days. The aortic inhibitor had similar properties as PGI₂.     

Effect of pre-treatment and extraction conditions on the antioxidant properties of persimmon (Diospyros kaki) leaves

Persimmon is a very delicious fruit and the leaves of this tree are used as a traditional drug. This study aimed to investigate the effects of drying method (hot air and freeze-drying), extraction temperature (80, 90 and 100 °C) and extraction time (10, 30, 60 and 120 min) and harvest stage (flowering and fruiting) on the antioxidant contents and antioxidant activity of persimmon leaves. The results showed that the highest antioxidants were obtained in both methods of drying. Also, 100 °C for 120 min of extraction gave the highest antioxidant contents, but with no significant difference compared to 90 °C for 60 min of extraction. Persimmon leaves collected during flowering stage had the maximum amount of antioxidants compared to the fruiting stage. Finally, it can be said that persimmon leaves harvested during flowering stage and treated by hot air drying with these extraction conditions (90 °C for 60 min) are richer in bioactive compounds.     

Administration of heparin causes in vitro release of non-esterified fatty acids in human plasma

The objective of this study was to investigate the extent to which $\text{in vitro}$ hydrolysis of endogenous triglycerides contributes to the elevated concentrations of non-esterified fatty acids (NEFAs) which have been reported after heparin administration. Heparin is known to induce the release of lipases which hydrolyze endogenous substrate both $\text{in vivo}$ and $\text{in vitro}$. Four patients undergoing diagnostic cardiac catheterization, who routinely receive heparin, were studied. Blood samples were obtained before and at 5 and 30 minutes after an intravenous bolus of heparin (46 U/kg) was administered. Determinations of NEFAs in plasma were carried out immediately and again various times after the samples had incubated at 24°C and at 0°C. In addition, an aliquot of each sample was frozen quickly, stored for 5–7 days, thawed, and incubated at 24°C for 180 minutes. As expected, there were no significant increases after incubation in the concentrations of NEFAs in the samples obtained before heparin administration. In contrast, in the samples obtained after heparin administration, incubation at 24°C produced significant increases in the concentrations of NEFAs. For example, in the plasma samples obtained 5 minutes after administration of heparin, concentrations of NEFAs increased 50, 160 and 300% after 5, 60, and 180 minutes of incubation compared to pre-heparin concentrations. When assayed immediately, the concentrations of NEFAs increased only 15% over pre-heparin concentrations. Incubating the samples at 0°C slowed lipase activity. Freezing the samples stopped the lipase activity; however, when the thawed samples were incubated at 24°C, concentrations of NEFAs continued to rise. This study suggests that much of the reported increases in the $\text{in vivo}$ concentrations of NEFAs after administration of heparin may be due to $\text{in vitro}$ formation from continued lipase activity on endogenous substrate. Moreover, studies relating increases in the concentrations of NEFAs after administration of heparin to changes in drug binding to plasma proteins should be re-examined for possible $\text{in vitro}$ artifacts.     

Influence of storage condition on exosome recovery

Most of mammalian cells release extracellular vesicles including exosomes which mediate intercellular communication by delivering a variety of molecules. Despite of their importance in normal physiology and disease progression, the standard criteria of storage condition is indefinite and controversial. Therefore, we investigated exosome’s recovery yield and stability by various storage conditions. To investigate the effect of short-term storage temperature on exosome stability, exosomes were incubated at temperatures ranging from -70 to 90°C for 30 min. Immunoblot results showed that all exosome-associated proteins incubated at 90°C were mostly degraded for a short period of time. To examine the effect of long-term storage, isolated exosomes were incubated for 10 days at from -70°C to room temperature (RT), and exosomal protein, RNA and exosome markers were examined. Protein and RNA amounts were most reduced at RT compared with -70 and 4°C. Incubation at 4°C and RT resulted in major loss of CD63, and decreasing level of HSP70 was shown at only RT. In addition, flow cytometry result showed that exosome population became more dispersed after RT incubation for 10 days compared with -70°C incubated or freshly isolated exosomes. In summary, our results indicate that different storage temperature and period influences recovery yield and morphology of exosome, and storage at below -70°C is the favorable condition for preservation of fresh exosomes for clinical application and basic researches.     

Microbial inactivation and shelf life of apple juice treated with high pressure carbon dioxide

Apple juice prepared from 'Annurca' apple puree was treated with a HPCD batch system. The pH, °Brix, color parameters and microbial load of the treated apple juice were compared with those of thermally processed juice. Thermal processes were carried out at 35, 50, 65, 85°C and treatment times ranging between 10 and 140 minutes. Microbial inactivation kinetics indicated that 5-log reduction of natural flora in apple juice was achieved at 85°C and 60 minutes of treatment time for conventional thermal process and at 16.0 MPa, 60°C and 40 minutes for HPCD process. Results suggested that temperature played a fundamental role on HPCD treatment efficiency, with inactivation significantly enhanced when it increased from 35 to 60°C. Less significant was the role of the pressure at the tested levels of 7.0, 13.0 and 16.0 MPa. Also, 5-log reduction of natural flora in apple juice was obtained at lower temperatures by cyclic treatments of six compression and decompression steps. There were no significant differences between treated and untreated samples in °Brix (α = 0.05). Significant differences were detected in pH values between the untreated and HPCD treated samples (α = 0.05). There was a significant decrease in 'L*' and 'b*' values and also differences were detected in 'a*' values between the untreated and the HPCD treated samples (α = 0.05). Statistical analysis for °Brix, pH and color data showed no differences between the untreated and HPCD treated samples in the first 2 weeks of storage at 4°C. These results emphasize the potential use of HPCD in industrial applications.     

Comparison of DNA isolation using salting-out procedure and automated isolation (MagNA system)

Isolation of genomic DNA is a key step in genetic analysis. The aim of the study was to evaluate the suitability of isolation of DNA from peripheral blood with manual salting-out procedure and automated MagNA system under specific conditions. The impact of storage conditions, type of material (whole blood or blood cells), and method used for DNA extraction were evaluated in terms of DNA yield, its purity, and integrity. Fresh material, and material stored at 2–8°C for 1–4 weeks and frozen at ?80°C were tested. For fresh samples, salting-out method gives higher yield than MagNA, irrespectively, on material used. Neither the yield of salting-out method nor its purity decreases during the storage of the samples in the fridge (2–8°C) during 4 weeks. Concerning MagNA, storage of blood cells in the fridge decreases the yield of DNA as well as its purity. For frozen samples, for whole blood, MagNA gives better results while for blood cells, salting-out method seems to be better. For fresh samples, salting-out method is the preferred one, and both whole blood and blood cells can be used. For frozen samples, the preferred method depends on the material.     

Methodology for processing mastectomy and cryopreservation of breast cancer tissue in a resource- poor setting: A pilot study

BackgroundThere is scarcity of breast cancer tissues derived from women of African origin available for patient - derived xenograft and organoid models.ObjectiveWe aim to create a versatile protocol for processing mastectomy and cryopreservation of breast cancer tissue.MethodologyAn immediate collection of breast cancer tissue from mastectomy was bathed in 4 °C HBSS and immediately transferred to 4 °C RPMI1640 containing HEPES, 10% FBS, Streptomycin and Penicillin. Tissues were processed over ice yielding nine samples of cold ischemic time (20–45 min) stored at 3 min interval. Cut samples were transferred into cryovials containing 4 °C cryoprotectant agent (90% FBS +10% Me₂SO) before snap -freezing in liquid Nitrogen vapour and final short-term storage in −80 °C Freezer. The histomorphology, tissue and molecular viability were assessed.ResultsThe cold ischemic times had no detrimental effect to the nine samples despite being processed in a resource poor setting, hence providing a reproducible and reliable protocol.     

植物内生放线菌的选择性分离

[目的]更好地发掘内生菌资源,建立有效的植物内生放线菌分离方法.[方法]比较不同消毒剂和消毒程序、样品预处理、选择性分离培养基等分离内生放线菌的效果,通过形态及16S rRNA基因序列分析进行菌种鉴定.[结果]用5％的次氯酸钠处理样品4-7 min消毒效果最好;100℃处理样品15 min能较好地减少真菌和细菌的干扰.丙酸钠、琥珀酸钠等培养基分离放线菌出菌率较高且类群多样性丰富.[结论]植物样品表面消毒干燥后,100℃处理15 min,用无菌搅拌杯打碎,直接撒植物于分离培养基中的分离方法效果较好.     

Characterization of the Physical State of Spray-Dried Inulin

Modulated differential scanning calorimetry, wide angle x-ray scattering, and environmental scanning electron microscopy were used to investigate the physical and morphological properties of chicory root inulin spray dried under different conditions. When the feed temperature increased up to 80 °C, the average degree of polymerization of the solubilized fraction increased, leading to a higher glass transition temperature (Tg). Above 80 °C, the samples were completely amorphous, and the Tg did not change. The starting material was semicrystalline, and the melting region was composed of a dual endotherm; the first peak subsided as the feed temperature increased up to a temperature of 70 °C, whereas above 80 °C, no melting peak was observed as the samples were completely amorphous. To a lesser extent, the inlet air temperature of 230 °C allowed a higher amorphous content of the samples than at 120–170 °C but induced a blow-out of the particles.     

Temperature-sensitive mutants blocked in the folding or subunit assembly of the bacteriophage P22 tail spike protein: II. Active mutant proteins matured at 30 °C

Little is known of the molecular mechanisms by which temperature-sensitive mutations interfere with the formation of biologically active proteins. We have studied the effects of such mutations at 13 different sites on the properties of the multifunctional tail spike protein of bacteriophage P22, a thermostable structural protein composed of 76,000 M_r chains.Using multiple mutant strains blocked in capsid assembly, we have examined the free mutant tail spikes that accumulate in active form at permissive temperature. When assayed for the ability to bind to phage heads at the restrictive temperature, the mutant proteins were as active as the wild type. Similarly, when assayed for the ability to adsorb to bacteria at restrictive temperature, the mutant proteins were as active as the wild type. Thus the temperature-sensitive phenotypes of the mutants are not due to the thermolability of these functions in the mature mutant protein.The wild-type protein is heat-resistant, requiring incubation at 90 °C, to give a half-time of inactivation of ten minutes. The 13 ts mutant proteins, once matured at 30 °C, were as resistant as the wild-type protein to inactivation at elevated temperatures.Though the mature wild-type protein is heat stable, its maturation is heat-sensitive; the number of polypeptide chains synthesized at 30 °C and 39 °C is the same, but the yield of active tail spikes at 39 °C is only 25% of the yield at 30 °C.The results show that the amino acid substitutions in the mutant proteins, though lethal for the formation of the virus at 39 °C, do not affect the thermostability of the mature tail spike protein formed at 30 °C. They may act by destabilizing thermolabile intermediates in the folding or subunit assembly of the tail spike protein.     

Effect of the addition of IGF-I and vitamin E to stored boar semen

The objective of this study was to evaluate the addition of IGF-I to pig insemination doses stored at 15°C, in conjunction with the addition of different amounts of vitamin E (α-tocopherol). Semen samples (n = 12) from four boars were treated by the addition of different concentrations of vitamin E, ranging up to 400 μg/ml. Immediately after processing and after the doses had been stored at 15°C for 24 or 72 h, samples were warmed at 37°C and 30 ng/ml of IGF-I was added. The assessments were made after 10 and 120 min of IGF-I addition. There was a minor effect of the vitamin E added before cooling and IGF-I added after storage on sperm quality. The addition of 400 μg/ml of vitamin E to diluted semen reduced (P < 0.01) the malondialdehyde (MDA) production in boar semen stored at 15°C for 72 h, regardless of the addition of IGF-I as additive during a 120 min incubation period at 37°C. In these conditions, IGF-I also reduced (P < 0.05) the MDA production in semen samples without addition of vitamin E. IGF-I in the presence of vitamin E reduced (P = 0.03) the glucose intake in freshly diluted boar semen samples before cooling. It was concluded that the addition of 400 μg/ml of vitamin E reduces the MDA production in boar semen stored at 15°C for 72 h, regardless of the presence of IGF-I additive. The addition of IGF-I in doses stored for 72 h with vitamin E ensures higher sperm motility after 120 min of incubation at 37°C.     

Freeze-dried plasma proteins are stable at room temperature for at least 1 year

Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at ?80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at ?20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h. Random and independent sampling by liquid chromatography and tandem mass spectrometry (LC–ESI–MS/MS), as correlated by the MASCOT, OMSSA, X!TANDEM and SEQUEST algorithms, showed that tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature. Random sampling by LC–ESI–MS/MS showed that peptides from C4B were undetectable on ice, but peptides were cleaved from the mature C4B protein including NGFKSHALQLNNR within as little as 1 h at room temperature. The frequency and intensity of precursors within ± 3 m/z of the C4B peptide NGFKSHALQLNNR was confirmed by automated targeted analysis where the precursors from MS/MS spectra that correlated to the target sequence were analyzed in SQL/R. The C4B preproprotein was processed at the N terminus to release the mature chain that was cleaved on the carboxyl side of the isoprene C2 domain within a polar C terminal sequence of the mature C4B protein, to reveal the thioester reaction site, consistent with LC–ESI–MS/MS and Western blot. Random sampling showed that proteolytic peptides from complement component C4B were rarely observed with long term storage at ? 80 °C in a freezer or in liquid nitrogen (LN2), freeze drying with storage at ? 20 °C (FD-20 °C) or freeze drying and storage at room temperature (FDRT). Plasma samples maintained at room temperature (RT) showed at least 10-fold to 100-fold greater frequency of peptide correlation to C4B and measured peptide intensity compared to samples on ice for up to 72 h or stored at ? 80 °C, LN2, FDRT or FD-20 °C for up to a year.     

Production of a Thermostable Lipase by Humicola lanuginosa Grown on Sorbitol-Corn Steep Liquor Medium

For thermostable lipase production by Humicola lanuginosa No. 3, a simple optimized medium consisting of (%, w/v): sorbitol, 1.0; corn steep liquor, 1.0; NaCl, 0.5; CaCl₂–2H₂0, 0.01; Silicone Km-70 (antifoamer), 0.2; and whale oil or castor oil as a lipase inducer, 0.3, was used. The yield of the lipase was about 80 — 120U/ml after 25 hr aerobic cultivation at 45°C when the pH was maintained at 7 to 8. The acetone powder preparation of the enzyme was most active at pH 7.0 and 45°C. The enzyme retained 100% activity on incubation for 20 hr at 60°C. The enzyme was able to hydrolyze almost all forms of natural fats tested (14 kinds), coconut oil being the most rapidly hydrolyzed.     

水柱法场扩大提高CE-UV检测核酸灵敏度

目的：采用水柱法场扩大堆积技术,提高毛细管电泳紫外分析核酸灵敏度。方法：已知浓度的DNA Marker为标准样品,TE缓冲液递度稀释,压力进样前加一段去离子水柱（0.5psi,20s）,观察不同浓度下压力进样紫外检测图谱。结果：在对分离度无明显影响下,将压力进样时间延长至0.5psi,990s,与常规的压力进样（0.5psi,10s）相比,灵敏度提高了94.4倍。与时间延长后的压力进样（0.5psi,90s）相比,灵敏度提高8.2倍,最低检测总浓度为1ng/μl,DNA的检测限降至80ng/ml（S/N=3）,比前人报道的7ng/μl检测限提高了87.5倍。结论：验证了水柱法场扩大堆积注射可以有效提高毛细管电泳紫外检测核酸灵敏度。     

Optimization of the yield and quality of agar from Gracilariopsis lemaneiformis (Gracilariales) from the Gulf of California using an alkaline treatment

The effect of several alkali treatments on the yield, gel strength, rheology, and chemical characteristics (quality) of the agar obtained from Gracilariopsis lemaneiformis from the Gulf of California was analyzed using different alkali concentrations, temperatures and treatment times. In the first stage of the experiment, all treatments lasted 60 min and the NaOH concentrations (2.5, 3.0, 4.0, 5.0, 6.0%) and temperature (80, 90, 100°C) varied. At constant time, temperature played the predominant role, promoting an increase in agar gel strength. Based on the best treatment conditions found (4% and 5% NaOH, and 90°C and 100°C temperature), in the second stage different treatment times (15, 30, 60, 90, 120 min) were used. Since agar yields were not significantly different among temperatures and times, the optimal conditions to obtain best quality agar were those providing the highest gel strength. Treatment time played an important role in increasing gel strength. Maximum gel strength (Nikan, 954 g cm⁻²) was obtained with 5% NaOH at 100°C after 90 min of treatment, though these conditions resulted in an agar yield reduction of 25.5% relative to native agar. This treatment proved to efficiently yield G. lemaneiformis agar that will meet the commercial quality requirements regarding gel strength, 3,6 anhydrogalactose and sulfate content, as well as rheology and hysteresis. Enrique Hernández-Garibay holds a CONACyT scholarship.     

Method for recovery of intact DNA for community analysis of marine intertidal microbial biofilms

A protocol is described for rapid DNA isolation from marine biofilm microorganisms embedded in large amounts of exopolysaccharides. The method is a modification of the hot phenol protocol used for plants tissues, where nonexpensive and easily available enzymes were used. The method is based on the incubation of biofilm biomass samples in an extraction buffer mixed with phenol preheated at 65°C. The procedure can be completed in 2 h and up to 20 samples can be processed simultaneously with ease and DNA of excellent quality, as shown by successfully amplification of polymerase chain reaction (PCR) products. DNA was recovered from a range of intertidal marine biofilms with varying amounts of exopolysaccharides.     

Flavonoids in the Flowers of Gnaphalium affine D. Don

Thermonsenstivie division mutants were derived from Bacillus subtilis Marburg 168 thy trp₂ by means of membrane filtration after nitrosoguanidine mutagenesis. Among them, ts42 requiring uracil for normal growth at 48°C was investigated.

In the absence of uracil, the mutant cells grew normally at 37°C and stopped dividing after temperature shift to 48°C resulting in filaments of two to four times length of normal rods. The total cell number after temperature shift from 37 to 48°C, increased two to three fold in 90 min and remained constant thereafter. The viable count after the temperature shift to 48°C, increased 1.5 to 2 fold in initial 60 min and then decreased exponentially. A rapid restoration of colony forming ability was shown when the mutant cells were shifted back to the permissive temperature after 120 to 180 min of incubation at 48°C or when uracil was introduced to the culture at 48°C. This recovery of viability was partly observed even in the presence of chloramphenicol. The synthesis of RNA of this mutant was shown to decline 20 min after the temperature shift to 48°C whereas the syntheses of DNA and protein proceeded for more than 80 min at that temperature.

No newly isolated uracil requiring mutants formed filaments in the medium lacking uracil or showed growth pattern like ts42.