Double proton transfer and one-electron oxidation behaviors in double H-bonded glycinamide-formamidine complex and comparison with biological base pair

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-formamidine complex have been investigated employing the B3LYP/6-311++G** level of theory. Computational results suggest that the participation of a formamidine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one since no zwitterionic complexes have been located during the DPT process. The barrier heights are 14.4 and 3.9 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.1 and 2.9 kcal/mol to 11.3 and 1.0 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the lower reverse barrier height implies that the reverse reaction should proceed easily at any temperature of biological importance. Additionally, the one-electron oxidation process for the double H-bonded glycinamide-formamidine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycinamide fragment and a proton has been transferred from glycinamide to formamidine fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral double H-bonded complex have been determined to be about 8.46 and 7.73 eV, respectively, where both of them have been reduced by about 0.79 and 0.87 eV relative to those of isolated glycinamide due to the formation of the intermolecular H-bond with formamidine. Finally, the differences between model system and adenine-thymine base pair have been discussed briefly.

Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

The Early Diagenetic Formation of Organic Sulfur in the Sediments of Mangrove Lake, Bermuda

Due to a low mineral content, the sapropelic sediments depositing in Mangrove Lake, Bermuda, provide an excellent opportunity to explore for possible additions of sulfur to organic matter during the early stages of diagenesis. We evaluated early diagenetic organic sulfur transformations by monitoring the concentrations and stable isotopic compositions of a number of inorganic and organic sulfur pools, thereby accounting for all of the sulfur in the sediments. We have identified and quantified the following sulfur pools: porewater sulfate, porewater sulfide, elemental sulfur, pyrite sulfur, hydrolyzable organic sulfur (HYOS), chromium-reducible organic sulfur (CROS), and nonchromium-reducible organic sulfur (Non-CROS). Of the organic sulfur pools, the Non-CROS pool is by far the largest, followed by CROS, and finally HYOS. By 60 cm depth these pools contribute, respectively, to 85, 7.9, and 3.6% of the total solid phase sulfur. The HYOS pool is probably of biological origin and shows no interaction with the sulfur compounds produced during diagenesis. By contrast, CROS is produced, most likely, from the diagenetic addition of polysulfides to functionalized lipids in the upper, H2S-poor, elemental sulfur-rich, region of the sediment. A portion of this sulfur pool is unstable and decomposes on contact with the H2S-rich porewaters. The portion of CROS that remains in the sulfidic waters appears to readily exchange sulfur isotopes with H2S. While some of the Non-CROS pool is of biological origin, some is also formed by the diagenetic addition of sulfur to organic compounds in the upper H2S-poor region of the sediment. By contrast with CROS, Non-CROS is not diagenetically active in the H2S-rich porewaters. Overall, somewhere between 27 and 53 % of the organic sulfur buried in Mangrove Lake sediments is of diagenetic origin, with the remaining organic sulfur derived from biosynthesis. We extrapolate our Mangrove Lake results and calculate that in typical coastal marine sediments between 11 and 29 μmol g−1 of organic sulfur will form during early diagenesis, of which 2–5 μmol g−1 will be chromium reducible.

Methods for physical separation and characterization of soil organic matter fractions

Turnover of soil organic matter (SOM) is coupled to the cycling of nutrients in soil through the activity of soil microorganisms. Biological availability of organic substrate in soil is related to the chemical quality of the organic material and to its degree of physical protection. SOM fractions can provide information on the turnover of organic matter (OM), provided the fractions can be related to functional or structural components in soil. Ultrasonication is commonly used to disrupt the soil structure prior to physical fractionation according to particle size, but may cause redistribution of OM among size fractions. The presence of mineral particles in size fractions can complicate estimations of OM turnover time within the fractions. Densiometric separation allows one to physically separate OM found within a specific size class from the heavier-density mineral particles. Nutrient contents and mineralization potential were determined for discrete size/density OM fractions isolated from within the macroaggregate structure of cultivated grassland soils. Eighteen percent of the total soil C and 25% of the total soil N in no-till soil was associated with fine-silt size particles having a density of 2.07-2.21 g/cm3 isolated from inside macroaggregates (enriched labile fraction or ELF). The amount of C and N sequestered in the ELF fraction decreased as the intensity of tillage increased. The specific rate of mineralization (mug net mineral N/mug total N in the fraction) for macroaggregate-derived ELF was not different for the three tillage treatments but was greater than for intact macroaggregates. The methods described here have improved our ability to quantitatively estimate SOM fractions, which in turn has increased our understanding of SOM dynamics in cultivated grassland systems.

Insulin-like growth factor-binding protein-3 plays an important role in regulating pharyngeal skeleton and inner ear formation and differentiation

Insulin-like growth factor-binding protein (IGFBP)-3 is the major insulin-like growth factor (IGF) carrier protein in the bloodstream. IGFBP-3 prolongs the half-life of circulating IGFs and prevents their potential hypo-glycemic effect. IGFBP-3 is also expressed in many peripheral tissues in fetal and adult stages. In vitro, IGFBP-3 can inhibit or potentiate IGF actions and even possesses IGF-independent activities, suggesting that local IGFBP-3 may also have paracrine/autocrine function(s). The in vivo function of IGFBP-3, however, is unclear. In this study, we elucidate the developmental role of IGFBP-3 using the zebrafish model. IGFBP-3 mRNA expression is first detected in the migrating cranial neural crest cells and subsequently in pharyngeal arches in zebrafish embryos. IGFBP-3 mRNA is also persistently expressed in the developing inner ears. To determine the role of IGFBP-3 in these tissues, we ablated the IGFBP-3 gene product using morpholino-modified antisense oligonucleotides (MOs). The IGFBP-3 knocked down embryos had delayed pharyngeal skeleton morphogenesis and greatly reduced pharyngeal cartilage differentiation. Knockdown of IGFBP-3 also significantly decreased inner ear size and disrupted hair cell differentiation and semicircular canal formation. Furthermore, reintroduction of a MO-resistant form of IGFBP-3 "rescued" the MO-induced defects. These findings suggest that IGFBP-3 plays an important role in regulating pharyngeal cartilage and inner car development and growth in zebrafish.

He, Ne and Ar isotopic composition of Fe-Mn crusts from the western and central Pacific Ocean and implications for their genesis

The noble gas nuclide abundances and isotopic ratios of the upmost layer of Fe-Mn crusts from the western and central Pacific Ocean have been determined. The results indicate that the He and Ar nuclide abundances and isotopic ratios can be classified into two types: low He-3/He-4 type and high He-3/He-4 type. The low He-3/He-4 type is characterized by high He-4 abundances of 191x10(-9) cm(3.)STP(.)g(-1) on average, with variable He-4, Ne-20 and Ar-40 abundances in the range (42.8-421)x10(-9) cm(3.)STP(.)g(-1), (5.40-141)x10(-9)cm(3.)STP(.)g(-1), and (773-10976)x10(-9) cm(3.)STP(.)g(-1), respectively. The high He-3/He-4 samples are characterized by low He-4 abundances of 11.7x10(-9) cm(3.)STP(.)g(-1) on average, with He-4, Ne-20 and Ar-40 abundances in the range of (7.57-17.4)x10(-9) cm(3.)STP(.)g(-1), (110.4-25.5)x10(-9) cm(3.)STP(.)g(-1) and (5354-9050)x10(-9) cm(3.)STP(.)g(-1), respectively. The low He-3/He-4 samples have He-3/He-4 ratios (with RIRA ratios of 2.04-2.92) which are lower than those of MORB (R/R-A=8 +/- 1) and Ar-40/Ar-36 ratios (447-543) which are higher than those of air (295.5). The high He-3/He-4 samples have He-3/He-4 ratios (with R/R-A ratios of 10.4-12.0) slightly higher than those of MORB (R/R-A=8 +/- 1) and Ar-40/Ar-36 ratios (293-299) very similar to those of air (295.5). The Ne isotopic ratios (Ne-20/Ne-22 and Ne-21/Ne-22 ratios of 10.3-10.9 and 0.02774-0.03039, respectively) and the Ar-38/Ar-36 ratios (0.1886-0.1963) have narrow ranges which are very similar to those of air (the Ne-20/Ne-22, Ne-21/Ne-22, Ar-38/Ar-36 ratios of 9.80, 0.029 and 0.187, respectively), and cannot be differentiated into different groups. The noble gas nuclide abundances and isotopic ratios, together with their regional variability, suggest that the noble gases in the Fe-Mn crusts originate primarily from the lower mantle. The low He-3/He-4 type and high He-3/He-4 type samples have noble gas characteristics similar to those of HIMU (High U/Pb Mantle)- and EM (Enriched Mantle)-type mantle material, respectively. The low He-3/He-4 type samples with HIMU-type noble gas isotopic ratios occur in the Magellan Seamounts, Marcus-Wake Seamounts, Marshall Island Chain and the Mid-Pacific Seamounts whereas the high He-3/He-4 type samples with EM-type noble gas isotopic ratios occur in the Line Island Chain. This difference in noble gas characteristics of these crust types implies that the Magellan Seamounts, Marcus-Wake Seamounts, Marshall Island Chain, and the Mid-Pacific Seamounts originated from HIMU-type lower mantle material whereas the Line Island Chain originated from EM-type lower mantle material. This finding is consistent with variations in the Pb-isotope and trace element signatures in the seamount lavas. Differences in the mantle surce may therefore be responsible for variations in the noble gas abundances and isotopic ratios in the Fe-Mn crusts. Mantle degassing appears to be the principal factor controlling noble gas isotopic abundances in Fe-Mn crusts. Decay of radioactive isotopes has a negligible influence on the nuclide abundances and isotopic ratios of noble gases in these crusts on the timescale of their formation.

A bioaugmentation failure caused by phage infection and weak biofilm formation ability

Two biological aerated filters (BAF) were setup for ammonia removal treatment of the circulation water in a marine aquaculture. One of the BAFs was bioaugmented with a heterotrophic nitrifying bacterium, Lutimonas sp. H10, where the ammonia removal was not improved and the massive inoculation was even followed by a nitrification breakdown from day 9 to 18. The nitrification was remained stable in control BAF operated under the same conditions. Fluorescent in situ hybridization (FISH) with rRNA-targeted probes and cultivable method revealed that Lutimonas sp. H10 almost disappeared from the bioaugomented BAF within 3 d, and this was mainly due to the infection of a specific phage as revealed by flask experiment, plaque assay and transmission electron observation. Analyses of 16S rRNA gene libraries showed that bacterial groups from two reactors evolved differently and an overgrowth of protozoa was observed in the bioaugmented BAR Therefore, phage infection and poor biofilm forming ability of the inoculated strain are the main reasons for bioaugmentation failure. In addition, gazing by protozoa of the bacteria might be the reason for the nitrification breakdown in bioaugmented BAF during day 9-18.

Stable Carbon Isotopic Composition in Soil Organic Carbon and C3/C4 Source Variations at the Haibei Alpine Meadow

Stable carbon isotopes of organic matter originated from different soil layers (0～5 cm, 5～15 cm, 15～25 cm, 25～35 cm, 35～50 cm, 50～65 cm) were investigated in the Haibei Alpine Meadow Ecosystem Research Station of the Chinese Academy of Sciences. The preliminary results indicated that δ13C values of soil organic matter increased with increased soil depth. δ13C of soil organic carbon in 0～5 cm layer showed the lowest value, -25.09‰; while 50～65 cm soil layer possessed the lowerδ13C value, -13.87‰. Based on mass balance model of stable isotopes, it was proposed that the percentage of C4 carbon source tend to increase with increased soil depth. The preliminary study indicated that alpine meadow might have undergone a successive process from C4-dominated community to C3-dominated one. However, changing δ13C values in atmospheric CO2 overtime and different processes of soil organic carbon formation (or eluviation) might somewhat contribute to increasing δ13C values. In this case, mass balance model would underestimate C3 community and overestimate C4 community.

Determination of free fatty acids in bryophyte plants and soil by HPLC with fluorescence detection and identification by online MS

A method for the determination of long and short chain free fatty acids (FFAs), using 1-[2-(ptoluenesulfonate)-ethyll-2-phenylimidazole-[4,5-f-9,10-phenanthrene (TSPP) as labeling reagent, has been developed. Identification of FFA derivatives was carried out by HPLC-MS with atmospheric pressure chemical ionization (APCI) in positive ion mode. Gradient elution on an Agilent Eclipse XDB-C-8 column gave good separation of the derivatives. Excellent linear responses were observed and good compositional data could be obtained from as little as 200 mg of bryophyte plants and soil samples. Facile TSPP derivatization coupled with HPLC-APCI-MS analysis allowed the development of a highly sensitive method for the quantitative analysis of trace level of FFAs from biological and natural environmental samples.

Determination of aliphatic amines from soil and wastewater of a paper mill by pre-column derivatization using HPLC and tandem mass spectrometry (HPLC-MS/MS)

A pre-column derivatization method for the sensitive determination of aliphatic amines using the labeling reagent 1,2-benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC) followed by HPLC with fluorescence detection and APCI/NIS identification in positive-ion mode has been developed. The chromophore of 2-(9-carbazole)-ethyl chloroformate (CEOC) reagent was replaced by the 1,2-benzo-3,4-dihydrocarbazole functional group, which resulted in a sensitive fluorescence derivatizing reagent, BCEOC, that could easily and quickly label amines. Derivatives were stable enough to be efficiently analyzed by HPLC and showed an intense protonated molecular ion corresponding m/z [M + H](+) with APCI/MS in positive-ion mode. The collision induced dissociation of the protonated molecular ion formed characteristic fragment ions at m/z 264.1, m/z 246.0 and m/z 218.1, corresponding to the cleavages of CH2CH2O-CO, CH2CH2-OCO, and N-CH2CH2O bonds. Studies on derivatization conditions demonstrated that excellent derivatization yields close to 100% were observed with a 3 to 4-fold molar reagent excess in acetonitrile solvent, in the presence of borate buffer (pH 9.0) at 40 degrees C for 10 min. In addition, the detection responses for BCEOC derivatives were compared with those obtained with CEOC and FMOC as labeling reagents. The ratios I-BCEOC/I-CEOC and I-BCEOC/I-FMOC were, respectively, 1.40-2.76 and 1.36-2.92 for fluorescence responses (here, I was the relative fluorescence intensity). Separation of the amine derivatives had been optimized on an Eclipse XDB-C-8 column. Detection limits calculated from an 0.10 pmol injection, at a signal-to-noise ratio of 3, were 18.65-38.82 fmol (injection volume 10 mu L for fluorescence detection. The relative standard deviations for intraday determination (n = 6) of standard amine derivatives (50 pmol) were 0.0063-0.037% for retention times and 3.36-6.93% for peak areas. The mean intra-and inter-assay precision for all amines were <5.4% and 5.8%, respectively. The recoveries of amines ranged from 96 to 113%. Excellent linear responses were observed with correlation coefficients of >0.9994. The established method provided a simple and highly sensitive technique for the quantitative analysis of trace amounts of aliphatic amines from biological and natural environmental samples.

Determination of free fatty acids in soil and bryophyte plants by precolumn derivatization via HPLC with fluorescence detection and tandem mass spectrometry (HPLC-MS/MS)

A sensitive method for the determination of 30 kinds of free fatty acids (FFAs, C-1-C-30) with 1-[2-(p-toluenesulfonate)-ethyl]-2-phenylimidazole-[4,5-f] 9,10-phenan- threne (TSPP) as labeling reagent and using high performance liquid chromatography with fluorescence detection and identification by online postcolumn mass spectrometry with atmospheric pressure chemical ionization (APCI) source in positive-ion mode (HPLC/MS/APCI) has been developed. TSPP could easily and quickly label FFAs in the presence of K2CO3 catalyst at 90 degrees C for 30 min in N,N-dimethylformamide (DMF) solvent, and maximal labeling yields close to 100% were observed with a 5-fold excess of molar reagent. Derivatives were stable enough to be efficiently analyzed by high performance liquid chromatography. TSPP was introduced into fatty acid molecules and effectively augmented MS ionization of fatty acid derivatives and led to regular MS and MS/MS information. The collision induced cleavage of protonated molecular ions formed specific fragment ions at m/z [MH](+)(molecular ion), m/z [M'+CH2CH2](+)(M' was molecular mass of the corresponding FFA) and m/z 295.0 (the, mass of protonated molecular core structure of TSPP). Fatty acid derivatives were separated on a reversed-phase Eclipse XDB-C-8 column (4.6 x 150 mm, 5 mu m, Agilent) with a good baseline resolution in combination with a gradient elution. Linear ranges of 30 FFAs are 2.441 x 10(-3) to 20 mu mol/L, detection limits are 3.24 similar to 36.97 fmol (injection volume 10 mu L, at a signal-to-noise ratio of 3, S/N 3:1). The mean interday precision ranged from 93.4 to 106.2% with the largest mean coefficients of variation (R.S.D.) < 7,5%. The mean intraday precision for all standards was < 6.4% of the expected concentration. Excellent linear responses were observed with correlation coefficients of > 0.9991. Good compositional data could be obtained from the analysis of extracted fatty acids from as little as 200 mg of bryophyte plant samples.Therefore, the facile TSPP derivatization coupled with HPLC/MS/APCI analysis allowed the development of a highly sensitive method for the quantitation of trace levels of short and long chain fatty acids from biological and natural environmental samples.

Independence of alpine meadow plants from soil organic matter for nitrogen supply: evidence from stable nitrogen isotopes

Stable nitrogen isotope signatures of major sources of mineral nitrogen ( mineralization of soil organic nitrogen, biological N-2 fixation by legumes, annual precipitation and plant litter decomposition) were measured to relatively define their individual contribution to grass assimilation at the Haibei Alpine Meadow Ecosystem, Qinghai, China. The results indicated that delta N-15 values (- 2.40 parts per thousand to 0.97 parts per thousand) of all grasses were much lower than those of soil organic matter (3.4 +/- 0.18 parts per thousand) and mineral nitrogen ( ammonium and nitrate together,7.8 +/- 0.57 parts per thousand). Based on the patterns of stable nitrogen isotopes, soil organic matter (3.4 +/- 0.18 parts per thousand), biological N-2 fixation (0 parts per thousand), and precipitation (- 6.34 +/- 0.24 parts per thousand) only contributed to a small fraction of nitrogen requirements of grasses, but plant litter decomposition (- 1.31 +/- 1.01 parts per thousand) accounted for 67%.