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:Whole-cell immobilization of selenate-respiring Sulfurospirillum barnesii in polyacrylamide gels was investigated to allow the treatment of selenate contaminated (790 microg Se x L(-1)) synthetic wastewater with a high molar excess of nitrate (1,500 times) and sulfate (200 times). Gel-immobilized S. barnesii cells were used to inoculate a mesophilic (30 degrees C) bioreactor fed with lactate as electron donor at an organic loading rate of 5 g chemical oxygen demand (COD) x L(-1) day(-1). Selenate was reduced efficiently (>97%) in the nitrate and sulfate fed bioreactor, and a minimal effluent concentration of 39 microg Se x L(-1) was obtained. Scanning electron microscopy with energy dispersive X-ray (SEM-EDX) analysis revealed spherical bioprecipitates of <or=2 microm diameter mostly on the gel surface, consisting of selenium with a minor contribution of sulfur. To validate the bioaugmentation success under microbial competition, gel cubes with immobilized S. barnesii cells were added to an Upflow Anaerobic Sludge Bed (UASB) reactor, resulting in earlier selenate (24 hydraulic retention times (HRTs)) and sulfate (44 HRTs) removal and higher nitrate/nitrite removal efficiencies compared to a non-bioaugmented control reactor. S. barnesii was efficiently immobilized inside the UASB bioreactors as the selenate-reducing activity was maintained during long-term operation (58 days), and molecular analysis showed that S. barnesii was present in both the sludge bed and the effluent. This demonstrates that gel immobilization of specialized bacterial strains can supersede wash-out and out-competition of newly introduced strains in continuous bioaugmented systems. Eventually, proliferation of a selenium-respiring specialist occurred in the non-bioaugmented control reactor, resulting in simultaneous nitrate and selenate removal during a later phase of operation.
Project description:Papiliotrema huenov was previously reported to be highly tolerant of a range of extremely toxic heavy metals. This study aimed to identify the potential of P. huenov to remove manganese and copper from aqueous solution. Physical conditions which affect removal of Mn(II) and Cu(II) were determined. Optimal temperature for adsorption of both metal ions was 30 °C, and optimal pH for maximum uptake of Mn(II) and Cu(II) were 5 and 6, respectively. Under these conditions, living cells of P. huenov accumulated up to 75.58% of 110 mg/L Mn(II) and 70.5% of 128 mg/L Cu(II) over 120 h, whereas, the removal efficiency of metal ions by dead cells over 1 h was 60.3% and 56.5%, respectively. These results indicate that living cells are more effective than dead biomass for bioremediation, but that greater time is required. The experimental data extends the potential use of P. huenov in biosorption and bioaccumulation of toxic heavy metals to copper and manganese, two of the most common industrial contaminants.
Project description:This study investigates the effectiveness of biochar immobilized with algicidal Bacillus sp. AK3 and denitrifying Alcaligenes sp. M3 in mitigating harmful algal blooms (HABs) and reducing nitrate pollution in aquatic environments. Over a six-day period, we analyzed changes in algal bloom-forming Microcystis density, chlorophyll-a levels (indicative of algal biomass), nitrate concentration, and microbial community composition in water treated with biochar and Bacillus sp. AK3 and Alcaligenes sp. M3-immobilized biochar. In water treatment using the AK3 and M3-immobilized biochar, Microcystis density decreased from 600,000 cells/mL to 80,000 cells/mL, and chlorophyll-a concentrations also substantially reduced, from 85.7 µg/L initially to 42.8 µg/L. Nitrate concentrations in the AK3 and M3-immobilized biochar treatment significantly decreased from approximately 23 mg/L to around 14 mg/L by Day 6, demonstrating the enhanced denitrification capabilities of the immobilized Alcaligenes sp. M3 and associated bacterial communities. The results also showed significant shifts in bacterial communities, with a decrease in Microcystis, highlighting the specific algicidal activity of Bacillus sp. AK3. The study underscores the potential of biochar-based treatments as a sustainable and effective approach for improving water quality and mitigating the environmental impacts of nutrient pollution and HABs.
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.