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 (NH₃) 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.     

Survival of Campylobacter jejuni in chicken meat at frozen storage temperatures

The aim of this study was to determine the survival of Campylobacter jejuni in chicken meat samples at frozen temperatures and given length of incubation and to determine the impact of aerobic bacteria on the survival of C. jejuni. The chicken meat samples were inoculated with C. jejuni NCTC 11351 suspensions and stored in bags at temperatures of -20°C and -70°C. The mean value of C. jejuni from meat samples decreased from 7.52 log10 CFU/g after 30 minutes of incubation at ambient temperature, to 3.87 log10 CFU/g on the eighth week of incubation at -20°C, and to 3.78 log10 CFU/g at incubation at -70°C after the same incubation period. Both freezing temperatures, -20°C and -70°C, decreased the number of campylobacters. The presence of aerobic mesophilic bacteria did not influence the survival of C. jejuni in chicken meet samples. Keeping poultry meat at freezing temperatures is important for the reduction of C. jejuni, which has a strong influence on the prevention of occurrence of campylobacteriosis in humans.     

Post-irradiation chemical processing of DNA damage generates double-strand breaks in cells already engaged in repair

In cells exposed to ionizing radiation (IR), double-strand breaks (DSBs) form within clustered-damage sites from lesions disrupting the DNA sugar-phosphate backbone. It is commonly assumed that these DSBs form promptly and are immediately detected and processed by the cellular DNA damage response (DDR) apparatus. This assumption is questioned by the observation that after irradiation of naked DNA, a fraction of DSBs forms minutes to hours after exposure as a result of temperature dependent, chemical processing of labile sugar lesions. Excess DSBs also form when IR-exposed cells are processed at 50°C, but have been hitherto considered method-related artifact. Thus, it remains unknown whether DSBs actually develop in cells after IR exposure from chemically labile damage. Here, we show that irradiation of 'naked' or chromatin-organized mammalian DNA produces lesions, which evolve to DSBs and add to those promptly induced, after 8-24 h in vitro incubation at 37°C or 50°C. The conversion is more efficient in chromatin-associated DNA, completed within 1 h in cells and delayed in a reducing environment. We conclude that IR generates sugar lesions within clustered-damage sites contributing to DSB formation only after chemical processing, which occurs efficiently at 37°C. This subset of delayed DSBs may challenge DDR, may affect the perceived repair kinetics and requires further characterization.     

Site-specific laser modification (cleavage) of oligodeoxynucleotides

Sequence-specific photomodification of oligodeoxynucleotide pAGAGTATTGACTTA ("a target") has been carried out with the aid of complementary fluorescent probes. Such a probe consisted of oligodeoxynucleotide pAATACTCT and a chromophore group attached to its 5' end. Three different derivatives of ethidium bromide were used as a chromophore. The photomodification was induced by nitrogen laser radiation (337 nm, 15 MW/cm2). The irradiation induces the following photodamages: target cleavage at the specific binding site with a cutting off of the 8-mer from its 5' end (yield up to 12%), formation of specific covalent adduct target-probe with a yield of 20-70%, and piperidine-sensitive target modifications with a 7-27% yield (for different chromophores). The total yield of specific photodamages of all kinds is 50-80%. The target cleavage and generation of piperidine-sensitive modifications are optically nonlinear processes. Piperidine treatment of the irradiated samples led to specific cleavage of the target with the yield up to 40%. All kinds of observed modifications are not influenced by high concentrations of free radical scavengers: 1.3M tBuOH and 10 mM cystamine. The pattern of cleavage indicates that the most probable position of the chromophore is between T8 and G9 of the target, i.e., the chromophore stacks on top of the last A.T base pair of the duplex. The aggregate of evidence is in agreement with the mechanism of nonlinear photomodification (the cleavage and generation of piperidine-sensitive modifications) based on the transfer of two-photon excitation energy from the chromophore to the target.     

Oligomerization of Glycine and Alanine Catalyzed by Iron Oxides: Implications for Prebiotic Chemistry

Iron oxide minerals are probable constituents of the sediments present in geothermal regions of the primitive earth. They might have adsorbed different organic monomers (amino acids, nucleotides etc.) and catalyzed polymerization processes leading to the formation of the first living cell. In the present work we tested the catalytic activity of three forms of iron oxides (Goethite, Akaganeite and Hematite) in the intermolecular condensation of each of the amino acids glycine and L-alanine. The effect of zinc oxide and titanium dioxide on the oligomerization has also been studied. Oligomerization studies were performed for 35 days at three different temperatures 50, 90 and 120°C without applying drying/wetting cycling. The products formed were characterized by HPLC and ESI-MS techniques. All three forms of iron oxides catalyzed peptide bond formation (23.2% of gly2 and 10.65% of ala2). The reaction was monitored every 7 days. Formation of peptides was observed to start after 7 days at 50°C. Maximum yield of peptides was found after 35 days at 90°C. Reaction at 120°C favors formation of diketopiperazine derivatives. It is also important to note that after 35 days of reaction, goethite produced dimer and trimer with the highest yield among the oxides tested. We suggest that the activity of goethite could probably be due to its high surface area and surface acidity.     

Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysis

Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of the major factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine ( Pinus radiata ), and eucalyptus ( Eucalyptus globulus ), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160 °C for 1, 3, 6, and 12 h. The influence of the pretreatment conditions on the cellulose crystalline structure was analyzed by X-ray diffraction (XRD). On a larger length scale, the impact of ionic liquid pretreatment on the surface roughness of the biomass was determined by small-angle neutron scattering (SANS). Pretreatment resulted in a loss of native cellulose crystalline structure. However, the transformation processes were distinctly different for Avicel and for the biomass samples. For Avicel, a transformation to cellulose II occurred for all processing conditions. For the biomass samples, the data suggest that pretreatment for most conditions resulted in an expanded cellulose I lattice. For switchgrass, first evidence of cellulose II only occurred after 12 h of pretreatment at 120 °C. For eucalyptus, first evidence of cellulose II required more intense pretreatment (3 h at 160 °C). For pine, no clear evidence of cellulose II content was detected for the most intense pretreatment conditions of this study (12 h at 160 °C). Interestingly, the rate of enzymatic hydrolysis of Avicel was slightly lower for pretreatment at 160 °C compared with pretreatment at 120 °C. For the biomass samples, the hydrolysis rate was much greater for pretreatment at 160 °C compared with pretreatment at 120 °C. The result for Avicel can be explained by more complete conversion to cellulose II upon precipitation after pretreatment at 160 °C. By comparison, the result for the biomass samples suggests that another factor, likely lignin-carbohydrate complexes, also impacts the rate of cellulose hydrolysis in addition to cellulose crystallinity.     

Hyperactivation of hamster sperm motility by temperature-dependent tyrosine phosphorylation of an 80-kDa protein.

Protein phosphorylation and dephosphorylation are believed to play key roles in regulation of sperm motility. Here we examine the effect of temperature on hamster sperm motility and protein tyrosine phosphorylation status. As in previous work, a decrease from 37 degrees C to 22 degrees C caused loss of hyperactivated motility. We now find that cooling also produces a dephosphorylation of several 48-80-kDa flagellar peptides. A return to 37 degrees C restored hyperactivation but resulted in rephosphorylation of only an 80-kDa protein. Conversely, hyperactivation and phosphorylation of the 80-kDa component were insensitive to incubation temperature for sperm incubated with the protein phosphatase inhibitor, calyculin A, or for sperm demembranated by detergent extraction. These results strongly indicate that the temperature-sensitive tyrosine phosphorylation status of an 80-kDa sperm flagellar peptide explains the sensitivity of hyperactivation to temperature.     

Highly effective complementary addressed laser modification (cleavage) of oligodeoxynucleotides

Complementary addressed nonlinear photomodification of oligodeoxynucleotide dAGAGTATTGACTTA ("target") has been carried out by means of fluorescent derivatives of oligonucleotide dpAATACTCT ("addressed chromophore"). Three different ethidium derivatives were used as a chromophore. The photomodification was induced by nitrogen laser radiation (337 nm, 15 MW/cm2), which led to the target cleavage in the addressation region with the yield of the main fragment (8 bases long) about 10%, formation of specific covalent adduct target-addressed chromophore with the yield 20-70%, "hidden" (not revealed by gel electrophoresis) target damages with 7-27% yield (for different chromophores). The total yield of specific (i. e. localized in the vicinity of the addressation site) modification was 50-80%. The target cleavage and hidden damage generation are optically nonlinear processes. Piperidine treatment of the irradiated samples caused addressed cleavage of the target with up to 40% yield. All kinds of observed modification are not effected by high concentrations of free radical scavengers, 1,3 M t-BuOH or 10 mM cystamine. The bulk of the data is in agreement with the mechanism of nonlinear photomodification (the cleavage and hidden damage generation) based on the transfer of two-photon excitation energy from the chromophore to the target.     

Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at -70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy.     

小麦白粉病生防菌G-1菌株原生质体诱变育种

以链霉菌G-1(Streptomyces sp.G-1)为出发菌株,通过研究菌株G-1原生质体形成与再生的条件,发现该菌株在含0.5%甘氨酸的菌丝体培养基中经过二次培养后,所得菌丝体用2 mg/mL溶菌酶在30℃下处理90 min,可获得大量原生质体,其再生率可达8.2%。菌株G-1的原生质体经紫外诱变和宁南霉素抗性筛选后,得到一高产突变株G-1-125,其有效组分A的产量达到794mg/L,较出发菌株提高了180%。     

Pretreatment of rice straw using an extrusion/extraction process at bench-scale for producing cellulosic ethanol

A combination of a twin-screw extrusion and an acid-catalyzed hot water extraction process performed at a bench-scale was used to prepare high monomeric xylose hydrolysate for cellulosic production. The influences of the screw speed (30-150 rpm), barrel temperature (80-160 °C) and corresponding specific mechanical energy of the extruder on the structural properties of the pretreated rice straw, sugar concentration and conversion were investigated. The optimal condition for the extrusion step was determined to be 40 rpm with 3% H2SO4 at 120 °C; the optimal condition for the extraction step was determined to be 130 °C for 20 min. After the pretreatment at the optimal condition, 83.7% of the xylan was converted to monomeric xylose, and the concentration reached levels of 53.7 g/L. Finally, after the subsequent enzymatic hydrolysis, an 80% yield of the total saccharification was obtained.     

Preparative-scale kinetic resolution of racemic styrene oxide by immobilized epoxide hydrolase

Epoxide hydrolase from Aspergillus niger was immobilized onto the modified Eupergit C 250 L through a Schiff base formation. Eupergit C 250 L was treated with ethylenediamine to introduce primary amine groups which were subsequently activated with glutaraldehyde. The amount of introduced primary amine groups was 220 μmol/g of the support after ethylenediamine treatment, and 90% of these groups were activated with glutaraldehyde. Maximum immobilization of 80% was obtained with modified Eupergit C 250 L under the optimized conditions. The optimum pH was 7.0 for the free epoxide hydrolase and 6.5 for the immobilized epoxide hydrolase. The optimum temperature for both free and immobilized epoxide hydrolase was 40 °C. The free epoxide hydrolase retained 52 and 33% of its maximum activity at 40 and 60 °C, respectively after 24h preincubation time whereas the retained activities of immobilized epoxide hydrolase at the same conditions were 90 and 75%, respectively. Immobilized epoxide hydrolase showed about 2.5-fold higher enantioselectivity than that of free epoxide hydrolase. A preparative-scale (120 g/L) kinetic resolution of racemic styrene oxide using immobilized preparation was performed in a batch reactor and (S)-styrene oxide and (R)-1-phenyl-1,2-ethanediol were both obtained with about 50% yield and 99% enantiomeric excess. The immobilized epoxide hydrolase was retained 90% of its initial activity after 5 reuses.     

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.     

A new DNA extraction method by controlled alkaline treatments from consolidated subsurface sediments

Microbial communities that thrive in subterranean consolidated sediments are largely unknown owing to the difficulty of extracting DNA. As this difficulty is often attributed to DNA binding onto the silica-bearing sediment matrix, we developed a DNA extraction method for consolidated sediment from the deep subsurface in which silica minerals were dissolved by being heated under alkaline conditions. NaOH concentrations (0.07 and 0.33 N), incubation temperatures (65 and 94 °C) and incubation times (30-90 min) before neutralization were evaluated based on the copy number of extracted prokaryotic DNA. Prokaryotic DNA was detected by quantitative PCR analysis after heating the sediment sample at 94 °C in 0.33 N NaOH solution for 50-80 min. Results of 16S rRNA gene sequence analysis of the extracted DNA were all consistent with regard to the dominant occurrence of the metallophilic bacterium, Cupriavidus metallidurans, and Pseudomonas spp. Mineralogical analysis revealed that the dissolution of a silica mineral (opal-CT) during alkaline treatment was maximized at 94 °C in 0.33 N NaOH solution for 50 min, which may have resulted in the release of DNA into solution. Because the optimized protocol for DNA extraction is applicable to subterranean consolidated sediments from a different locality, the method developed here has the potential to expand our understanding of the microbial community structure of the deep biosphere.     

High-level expression of human insulin-like growth factor II in Escherichia coli.

A gene encoding mature human insulin-like growth factor II (IGF-II) was constructed from the modified IGF-II cDNA sequence and two double-stranded synthetic oligodeoxynucleotide linkers. It was fused to a truncated lacZ gene such that IGF-II was expressed as part of C-terminus of beta-galactosidase. This fused lacZ'-IGF-II gene was under the control of tac promoter and we overproduced the beta-galactosidase-IGF-II fusion protein in the Escherichia coli. The fusion protein formed inclusion bodies inside the cells. The fusion protein was purified from the isolated inclusion bodies and IGF-II protein was obtained from their fusion protein by CNBr cleavage. The released IGF-II was confirmed by its molecular weight as determined by SDS-PAGE and by its ability to bind anti-IGF antibody.     

Simplified construction and performance of a device for particle bombardment

A modified particle inflow gun (PIG), that utilized a plastic vacuum chamber, was compared with a conventional PIG by bombarding cantaloupe (Cucumis melo L.) cotyledon basal quarters with plasmid pBI221 (Clontech Inc.) containing a -glucuronidase (GUS) gene adsorbed onto tungsten particles. Both guns produced an equivalent number of transient GUS foci when tested at 410 kPa (60 psi), 620 kPa (90 psi) or 830 kPa (120 psi) helium and at a 10, 15 or 20 cm gap between the specimen and DNA/particle holder screen. For both guns, treatments utilizing the lower pressure and/or the greater distance generally produced significantly fewer GUS-positive foci. The plastic PIG was convenient to operate and could be built with simple hand tools in less than 40 minutes, using readily available parts.     

Relationship of advanced oxidative protein products in human saliva and plasma: age- and gender-related changes and stability during storage

Abstract The blood levels of advanced oxidative protein products (AOPP) elevate in aging and age-related diseases. However, saliva AOPP in healthy humans have been unexplored. Thus, we investigated 143 Chinese healthy adults to assay age- and gender-related changes in saliva and plasma AOPP levels and the stability of saliva AOPP stored both at -?20°C and -?80°C. We found the mean AOPP levels in saliva and plasma of 119 subjects were 7.51?±?3.20 and 28.31?±?5.53 μmol/L (μM). An age-dependent increase was observed in both saliva and plasma AOPP levels. This increase was particularly significant in the elderly subjects compared with that in the young and middle-aged ones. A significant positive correlation among age, saliva and plasma AOPP levels was observed. No gender-dependent difference was observed in either saliva or plasma AOPP levels during the aging process. Furthermore, AOPP levels in the 24 saliva samples showed no significant change at every successive determination during 4 weeks at -?80°C, whereas those levels significantly increased after 7 days of storage at -?20°C. These results indicate the feasibility to screen aging biochemical indicators using saliva AOPP as an alternative to blood AOPP. Saliva AOPP samples are suitable to be stored at -?80°C.     

Dinucleosome as a product of initial chromatin cleavage by endogenous nucleases

The ability of nucleic endonucleases to recognize dinucleosomal level of chromatin structure was studied. Rat liver chromatin endonucleases were shown to be capable of DNA cleavage at dinucleosome linkers. The cleavage was observed mainly at initial stages of chromatin autohydrolysis, i.e. up to 10-20th min of incubation in the medium containing 5 mmol of magnesium chloride and 2 mmol of calcium chloride. Thus, mononucleosomal DNA in dinucleosomes and other even chromatin subunits was larger and more homogeneous than in odd subunits. The cleavage of autodigested chromatin by bovine spleen and snake venom exonucleases and by nuclease S1 has shown that dinucleosomal structure is independent of differences in the length of internal and external dinucleosome linkers. The initial endonucleolysis appears to be characterized by different accessibility of the linkers for chromatin nucleases.     

Selective cleavage of pepsin by molybdenum metallopeptidase

In this study, the cleavage of protein by molybdenum cluster is reported for the first time. The protein target used is porcine pepsin. The data presented in this study show that pepsin is cleaved to at least three fragments with molecular weights of ～23, ～19 and ～16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH(4))(6)Mo(7)O(24)·4H(2)O) was incubated at 37°C for 24h. No self cleavage of pepsin occurs at 37 °C, 24h indicating that the reaction is mediated by the metal ions. N-terminal sequencing of the peptide fragments indicated three cleavage sites of pepsin between Leu 112-Tyr 113, Leu 166-Leu 167 and Leu 178-Asn 179. The cleavage reaction occurs after incubation of the mixture of pepsin and (NH(4))(6)Mo(7)O(24)·4H(2)O) only for 2h. However, the specificity of the cleavage decreases when incubation time is longer than 48 h. The mechanism for cleavage of pepsin is expected to be hydrolytic chemistry of the amide bonds in the protein backbone.