Showing papers by "Northeast Agricultural University published in 2011"

osa - MIR393 : a salinity- and alkaline stress-related microRNA gene

Abstract: Salinity and alkalinity are the two main environmental factors that limit rice production. Better understanding of the mechanisms responsible for salinity and alkaline stress tolerance would allow researchers to modify rice to increase its resistance to salinity and alkaline stress. MicroRNAs (miRNAs) are ~21-nucleotide RNAs that are ubiquitous regulators of gene expression in eukaryotic organisms. Some miRNAs acts as an important endogenous regulator in plant responses to abiotic stressors. miR393 is a conservative miRNA family that occurs in a variety of different plants. The two members of the miR393 family found in rice are named osa-MIR393 and osa-MIR393b. We found that the osa-MIR393 expression level changed under salinity and alkaline stress, whereas that of osa-MIR393b did not. Target genes of osa-MIR393 were predicted, and some of these putative targets are abiotic related genes. Furthermore, we generated transgenic rice and Arabidopsis thaliana that over-expressed osa-MIR393, and the phenotype analysis showed that these transgenic plants were more sensitive to salt and alkali treatment compared to wild-type plants. These results illustrate that over-expression of osa-MIR393 can negatively regulate rice salt-alkali stress tolerance.

Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa).

Abstract: A Gram-positive, aerobic actinomycete, designated strain NEAU 119T, was isolated from the rhizosphere of a fig tree and was characterized using a polyphasic approach. The isolate formed branching, non-fragmenting vegetative hyphae and produced black pigment on yeast extract/malt extract (ISP medium 2). The G+C content of the DNA was 76.6 mol%. The organism had chemotaxonomic characteristics typical of the genus Actinoalloteichus and was closely related to the type strains of Actinoalloteichus cyanogriseus, Actinoalloteichus spitiensis and Actinoalloteichus hymeniacidonis, currently the only three recognized species of the genus Actinoalloteichus, sharing 16S rRNA gene similarities of 96.4, 96.6 and 98.1 %, respectively. However, the results of DNA–DNA hybridization studies demonstrated that the novel strain showed only 46.8 % relatedness with the type strain of A. hymeniacidonis. In addition, a set of phenotypic characteristics also readily distinguished strain NEAU 119T from the type strains of recognized species of the genus Actinoalloteichus. According to the above data, it is proposed that strain NEAU 119T represents a novel species, Actinoalloteichus nanshanensis sp. nov. The type strain of Actinoalloteichus nanshanensis is NEAU 119T ( = CGMCC 4.5714T = NBRC 106685T).

Soil erosion control practices in Northeast China: A mini-review

Abstract: Soil erosion is of great concern in every agricultural region of the world due to its long-term negative effects on soil productivity. Agricultural management strongly affects soil erosion, and thus agricultural sustainability. The control of soil erosion is the top environmental issue, and has been proposed as a bottleneck to the sustainable development of agriculture in Northeast China. This region is the bread basket of China where the fertile and productive Mollisol soil is primarily distributed. The advances in agronomic, biological and engineering practices including several tillage managements, terraces and strip cultivation, and soil amendments are summarized and discussed. Proposed strategies for erosion control in particular urgent government policies to maintain or restore the productivity of severely eroded farmland are emphasized in the context of agricultural sustainability for Northeast China and similar Mollisol regions.

Arabidopsis ovate family proteins, a novel transcriptional repressor family, control multiple aspects of plant growth and development.

Abstract: Background The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs), a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAIN PROTEIN 7 (KNAT7), and AtOFP5 has been shown to regulate the activity of a BEL1-LIKEHOMEODOMAIN 1(BLH1)-KNAT3 complex during early embryo sac development, but little is known about the function of other AtOFPs.

Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes

Abstract: Oil content of soybean was a valuable quantitative trait controlled by multiple genes. Eleven QTLs were detected by both CIM and MIM method with the population crossed between Charleston and Dong nong594 in recent 3 years (2007, 2008, 2009). Combining the QTLs collected over the past 20 years, an integrated map of oil-content major QTLs in soybean was established using soymap2, which was published in 2004, as a reference. Using the software BioMercator ver.2.1, QTLs were projected from their own maps onto the reference map. In total, ninety-eight QTLs were integrated into soymap2. A meta-analysis method was used to narrow down the confidence interval, and 20 consensus QTLs and their corresponding markers were obtained. Using a local version of GENSCAN, 10,137 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted genes were compared to the International Protein Index database to mine the related genes. The results offer a basis for gene mining and molecular breeding in soybean.

Comparative Studies on the Interaction of Genistein, 8-Chlorogenistein, and 3′,8-Dichlorogenistein with Bovine Serum Albumin

Abstract: Chlorination can significantly enhance the antioxidant and antitumor activity of genistein. In this paper, genistein, 8-chlorogenistein, and 3',8-dichlorogenistein were selected to investigate the binding to bovine serum albumin (BSA) using fluorescence spectroscopy and circular dichroism (CD). The results showed that chlorination, especially at position 3', had significant effects on the binding constant value of chlorinated genistein derivatives to BSA; however, the binding site and the binding number were slightly affected. The thermodynamic parameters indicated that hydrophobic and electrostatic forces played important roles in the binding process and the enhanced binding affinity mainly associated with the increase of the hydrophobicity caused by the chlorine atom substitution. Furthermore, the CD data demonstrated that the conformation of BSA was slightly altered in the presence of genistein, 8-chlorogenistein, and 3',8-dichlorogenistein, with different reduced α-helix contents. The results obtained herein will be of biological significance in toxicology investigation and genistein derivative drug design.

Sample preparation method for isolation of single-cell types from mouse liver for proteomic studies

Abstract: It becomes increasingly clear that separation of pure cell populations provides a uniquely sensitive and accurate approach to protein profiling in biological systems and opens up a new area for proteomic analysis. The method we described could simultaneously isolate population of hepatocytes (HCs), hepatic stellate cells (HSCs), Kupffer cells (KCs) and liver sinusoidal endothelial cells (LSECs) by a combination of collagenase-based density gradient centrifugation and magnetic activated cell sorting with high purity and yield for the first time. More than 98% of the isolated HCs were positive for cytokeratin 18, with a viability of 91%. Approximately 97% of the isolated HSCs expressed glial fibrillary acidic protein with a viability of 95%. Nearly 98% of isolated KCs expressed F4/80 with a viability of 94%. And the purity of LSECs reached up to 91% with a viability of 94%. And yield for HCs, HSCs, LSECs and KCs were 6.3, 1.3, 2.6 and 5.0 million per mouse. This systematic isolation method enables us to study the proteome profiling of different types of liver cells with high purity and yield, which is especially useful for sample preparation of Human Liver Proteome Project.

A model and experimental study of phosphate uptake kinetics in algae: considering surface adsorption and P-stress.

Abstract: Phosphorus is an important limiting nutrient in many ecosystems. Consequently, there is increasing interest on phosphate uptake and algal growth due to the increasing frequency and magnitude of algal blooms induced by eutrophication. The co-existence of surface adsorbed and intracellular phosphorus pools indicate that phosphate uptake by phytoplankton is, to some extent, a two-stage kinetic process. However, almost all previous uptake models considered the internal uptake stage only and ignored the possible impact of surface adsorption. In this article, a two-stage kinetic uptake model considering both surface adsorption and P-stress on phosphate uptake by algae was constructed and compared to conventional one-stage models, based on experimental data on short-term uptake kinetics of a green algae S. quadricauda. Results indicated that with suitable parameters, the two-stage uptake model not only fit the experimental data better, but also gave more reasonable and realistic explanations to the phosphate uptake process. The results are meaningful as surface-adsorption of phosphate may affect the uptake process of phosphate and assist in understanding realistic phosphate uptake kinetics in phytoplankton.

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping.

Abstract: Cucumber, Cucumis sativus L (2n = 2 × = 14) and melon, C melo L (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae) Both species have an Asian origin that diverged approximately nine million years ago Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F2- and RIL-based genetic maps, respectively A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber

MiR-126-3p regulates progesterone receptors and involves development and lactation of mouse mammary gland

Abstract: MicroRNAs (miRNAs) are small (18–22 nucleotide) non-coding, endogenous regulatory RNA molecules, and they regulate gene expression at the post-transcriptional level through binding to their target mRNAs by base-pairing and subsequently inducing either translational repression or mRNA destabilization by plants, animals, and some viruses. In this study, combining microarray techniques with qRT-PCR, we found that miR-126-3p expression showed significant difference in the mouse mammary cycle during pregnancy, particularly on transition from pregnancy to lactation. Bioinformatics were used to predict target gene of miR-126-3p, and luciferase activity assay to test it, it showed that the progesterone receptor (PGR) 3′UTR is directly targeted by miR-126-3p. In this study, mouse mammary epithelial cells as cell model in vitro were used to study the function of miR-126-3p. Using gene silencing and over-expression for miR-126-3p, the expression of PGR protein and the secretion of casein were detected by western blotting and HPLC, respectively. To determine whether miR-126-3p can affect mouse mammary epithelial cells viability, cells were analyzed by CASY-YY. In conclusion, PGR gene confirmed miR-126-3p target genes through luciferase activity and western blotting. And miR-126-3p could also inhibit proliferation of mouse mammary epithelial cells (P < 0.01) and expression of β-casein (P < 0.01), and down-regulate PGR protein (P < 0.05). Our results suggested that miR-126-3p inhibited expression of PGR protein level as well as the proliferation of mammary epithelial cells, therefore miR-126-3p could play an important role in the process of mammary gland development.

Liver fatty acid composition in mice with or without nonalcoholic fatty liver disease

Abstract: Background Nonalcoholic fatty liver disease (NAFLD) is one of the most frequent causes of abnormal liver function. Because fatty acids can damage biological membranes, fatty acid accumulation in the liver may be partially responsible for the functional and morphological changes that are observed in nonalcoholic liver disease. The aim of this study was to use gas chromatography-mass spectrometry to evaluate the fatty acid composition of an experimental mouse model of NAFLD induced by high-fat feed and CCl4 and to assess the association between liver fatty acid accumulation and NAFLD. C57BL/6J mice were given high-fat feed for six consecutive weeks to develop experimental NAFLD. Meanwhile, these mice were given subcutaneous injections of a 40% CCl4-vegetable oil mixture twice per week.

MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs.

Abstract: Background MicroRNAs (miRNAs) are a set of short (19∼24 nt) non-coding RNAs that play significant roles as posttranscriptional regulators in animals and plants. The ab initio prediction methods show excellent performance for discovering new pre-miRNAs. While most of these methods can distinguish real pre-miRNAs from pseudo pre-miRNAs, few can predict the positions of miRNAs. Among the existing methods that can also predict the miRNA positions, most of them are designed for mammalian miRNAs, including human and mouse. Minority of methods can predict the positions of plant miRNAs. Accurate prediction of the miRNA positions remains a challenge, especially for plant miRNAs. This motivates us to develop MaturePred, a machine learning method based on support vector machine, to predict the positions of plant miRNAs for the new plant pre-miRNA candidates. Methodology/Principal Findings A miRNA:miRNA* duplex is regarded as a whole to capture the binding characteristics of miRNAs. We extract the position-specific features, the energy related features, the structure related features, and stability related features from real/pseudo miRNA:miRNA* duplexes. A set of informative features are selected to improve the prediction accuracy. Two-stage sample selection algorithm is proposed to combat the serious imbalance problem between real and pseudo miRNA:miRNA* duplexes. The prediction method, MaturePred, can accurately predict plant miRNAs and achieve higher prediction accuracy compared with the existing methods. Further, we trained a prediction model with animal data to predict animal miRNAs. The model also achieves higher prediction performance. It further confirms the efficiency of our miRNA prediction method. Conclusions The superior performance of the proposed prediction model can be attributed to the extracted features of plant miRNAs and miRNA*s, the selected training dataset, and the carefully selected features. The web service of MaturePred, the training datasets, the testing datasets, and the selected features are freely available at http://nclab.hit.edu.cn/maturepred/.

Effect of microbiological inocula on chemical and physical properties and microbial community of cow manure compost

Abstract: The effect of the microbiological inocula to efficiently decompose animal manures into mature compost was studied. In general, TOC, water contents and C/N ratio decreased during decomposition in two composts and those properties dropped faster in the microbiological inocula compost than the natural compost. The total nitrogen content and NO 3 − –N behaved in the opposite manner and those properties increased faster in the microbiological inocula compost than the natural compost. The pH and NH 4 + –N increased first, and then decreased in two composts. The microbiological inocula showed a more rapid rate of temperature elevation at the start of composting and prolonged the time of high-temperature process. The microbiological inocula were able to facilitate the microbial diversity of the compost. Based on germination assays, the microbiological inocula seems to be advantageous in reducing the maturation time of cow manure compost.

Effects of Aluminum Exposure on Bone Mineral Density, Mineral, and Trace Elements in Rats

Abstract: The purpose of the study was to investigate the effects of aluminum (Al) exposure on bone mineral elements, trace elements, and bone mineral density (BMD) in rats. One hundred Wistar rats were divided randomly into two groups. Experimental rats were given drinking water containing aluminum chloride (AlCl3, 430 mg Al3+/L), whereas control rats were given distilled water for up to 150 days. Ten rats were sacrificed in each group every 30 days. The levels of Al, calcium (Ca), phosphorus (P), magnesium (Mg), zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), selenium (Se), boron (B), and strontium (Sr) in bone and the BMD of femur were measured. Al-treated rats showed lower deposition of Ca, P, and Mg compared with control rats. Levels of trace elements (Zn, Fe, Cu, Mn, Se, B, and Sr) were significantly lower in the Al-treated group than in the control group from day 60, and the BMD of the femur metaphysis in the Al-treated group was significantly lower than in the control group on days 120 and 150. These findings indicate that long-term Al exposure reduces the levels of mineral and trace elements in bone. As a result, bone loss was induced (particularly in cancellous bone).

Detection of sugar accumulation and expression levels of correlative key enzymes in winter wheat (Triticum aestivum) at low temperatures.

Abstract: Carbohydrate accumulation is common in frost-resistant plants, and many enzymes participate in this process. The sugar content and expression levels of metabolic enzymes related to sugar biosynthesis in response to drops in temperature were measured in two cultivars of winter wheat (Triticum aestivum) with different cold tolerances. The results indicate that the two cultivars examined, Dongnongdongmai 1 and Jimai 22, accumulated high levels of carbohydrate before November 4 (above 0 °C), and that accumulation decreased as temperatures fell. However, this decrease was more modest in Dongnongdongmai 1, which had a higher sugar content. Sucrose and fructose were the main soluble sugars, indicating an important role in freezing tolerance. Gene expression studies revealed that expression of the genes encoding chloroplastic enzymes was significantly upregulated in the tillering nodes. Expression upregulation of TaSS and TaTPT may be helpful for sugar accumulation before November 4.