Project description:The yeast calibration curve dataset was acquired to compare the accuracy of DIA tools with decreasing contents of target peptides. Four samples (Y1, Y2, Y3 and Y4) with decreasing contents (200, 100, 50 and 25 ng, respectively) of analytes (yeast tryptic peptides) and a high content of background peptides (800 ng human tryptic peptides constantly) were analyzed in triplicate using LC-DIA-MS/MS. The DIA data were processed by different DIA tools based on the spectral library generated from the DDA data. The accuracy of different DIA tools was compared.
Project description:Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. Japan, especially western and central parts, has seen record high temperatures in the last decade, and the rice kernel quality has decreased; specifically a reduction the first-grade of rice has been seen. In this study, we specifically looked at the harvested rice in a town of the central Kanto-plains (Japan) during the year 2010, which saw day-time temperatures go above the critical limits ranging from 34 to 38C at the final stages of seed development and maturity to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial) were obtained Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki prefecture in September 2010, as grade 1 (labeled as Y1), grade 2 (labeled as Y2), and grade 3 (out-of-grade, labeled as Y3). The research objective was to examine in particular alterations in gene expressions genome-wide in grade 2 (Y2) and grade 3 (Y3) seeds over the grade 1 (Y1) following the high-temperature spike using a high-throughput omic-approach DNA microarray (Agilent 4 x 44K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. Rice seed quality analysis revealed, as expected, low quality in Y3 > Y2 over Y1, in taste, amylose, protein and fatty acid degree, but not in water content. Transcriptome profiling data revealed 124 and 373 up-regulated and 106 and 129 down-regulated genes in Y2 and Y3, respectively. Bioinformatics analysis of differentially expressed genes revealed changes in function of genes related to metabolism, including starch metabolism (e.g., alpha amylase), defense/stress response, fatty acid biosynthesis and hormones. This research provides for the first time the seed transcriptome profile for the classified low grades (2 and out-of-grade) of rice under an actual stressed environmental condition of high temperature.
Project description:Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. Whereas, dragon fly also induced higher tail tadpole. The tadpoles revert to a normal phenotype upon removal of the larval salamander or dragon fly threat. The objective of the present study was to use Affymetrix Xenopus Genechip to profile gene expression in the tail tissue by different predation threat. Tadpoles of Rana pirica treated with larvae salamander for 8days (S1, S2, S3) or dragon fly for 8days (Y1,Y2, Y3) were analyzed with triplicate. Removal experiments were also treated with predators for 4days and then removed predators from tadpoles (-S1,-S2, -S3) or (-Y1,-Y2,-Y3). Controls were cultured for 8days without predators (C2, C3). Tails from tadpoles after 8days of each treatment were dissected for RNA extraction and gene expression analysis using Affymetrix Xenopus Genechip arrays.
Project description:MicroRNA profile comparison of the corneal endothelium of young and old mice: implications for senescence of the corneal endothelium We collected the corneal endothelia from 30 mice aged 10-13 weeks and the corneal endothelia from 30 mice aged 2 years. The samples were pooled into six groups (y1, y2, y3 and s1, s2, s3). Each group comprised corneal endothelia from ten mice, and these six groups were used for a genome-wide microRNA microarray study.
Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.
Project description:We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.
Project description:Driven by economic interests, the abuse of antibiotics has become a significant concern for humans worldwide. As one of the most commonly used antibiotics, oxytetracycline (OTC) residue in animal-derived foods occurs occasionally, which has caused danger to humanity. However, there is still no simple and efficient solution to detect OTC residue. Here, an easily-operated colorimetric strategy for OTC detection was developed based on nickel ions (Ni2+) immobilized carboxymethylcellulose/polyacrylonitrile nanofibrous membranes (Ni@CMC/PAN NFMs). Owing to numerous O- and N-containing groups OTC has a strong tendency to complex with Ni2+ on the strips, inducing a color change from light green to yellow visible to the naked eye. The NFMs structural features, CMC functionalization process, and Ni2+ immobilization amount was carefully regulated to assure OTC detection whilst maintaining the inherent characteristics of NFMs. With the benefits of the large specific surface area (SSA) and small pore size of NFMs, the strips not only exhibited a rapid response (2 min), and low detection limit (5 nM) but also performed with good reversibility and selectivity concerning OTC detection over other antibiotics. The successful development of such enchanting nanofibrous materials may provide a new comprehension into the design and improvement of colorimetric strips.
Project description:We report herein a convenient one-pot synthesis for the shelf-stable molecular complex [Mn(NO3)3(OPPh3)2] (2) and describe the properties that make it a powerful and selective one-electron oxidation (deelectronation) reagent. 2 has a high reduction potential of 1.02 V versus ferrocene (MeCN) (1.65 vs normal hydrogen electrode), which is one the highest known among readily available redox agents used in chemical synthesis. 2 exhibits stability toward air in the solid state, can be handled with relative ease, and is soluble in most common laboratory solvents such as MeCN, dichloromethane, and fluorobenzene. 2 is substitutionally labile with respect to the coordinated (pseudo)halide ions enabling the synthesis of other new Mn(III) nitrato complexes also with high reduction potentials ranging from 0.6 to 1.0 V versus ferrocene.
Project description:The yeast Cryptococcus podzolicus Y3 shown the capability to degrade citrinin by the intracellular enzymes. However, the enzymes which is responsible for the degradation process was unknown. Transcriptome change in response to mycotoxin citrinin was analyzed. The molecular mechanism of Cryptococcus podzolicus Y3 withstand citrinin was revealed.