Inner Mongolia Academy of Agricultural and Animal Husbandry science

Hohhot, China

Inner Mongolia Academy of Agricultural and Animal Husbandry science

Hohhot, China
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Zheng Y.,Inner Mongolia University of Technology | Li H.,Inner Mongolia University of Technology | Li H.,Inner Mongolia University | Wang Y.,Inner Mongolia University of Technology | And 3 more authors.
Chromosome Research | Year: 2017

The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality. It followed that we proposed two theoretical conjectures: (1) CG1 motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG2 motifs (8-mers including two or more than two CG) are the modular units of CpG islands. Our conjectures were confirmed in yeast by the following results: a maximum of average area under the receiver operating characteristic (AUC) resulted from CG1 information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG1 signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG1 signals; and the AUC value of 0.986 was based on CG2 information when CpG islands and non-CpG islands were distinguished by the three CG subsets. © 2017 Springer Science+Business Media Dordrecht

An Y.,Shanghai JiaoTong University | An Y.,Key Laboratory of Urban Agriculture South | Zhou P.,Shanghai JiaoTong University | Xiao Q.,Inner Mongolia Academy of Agricultural and Animal Husbandry science | Shi D.,Heze University
Journal of Plant Nutrition and Soil Science | Year: 2014

Organic acids (OA) may affect plant resistance to aluminum (Al) toxicity in acidic soils. However, limited information is available on the effects of different organic acids on Al resistance in alfalfa. We investigated the effects of foliar application of organic acids (succinic acid, citric acid, malic acid, and oxalic acid) to alfalfa (Medicago sativa L.) under Al stress. Seedlings were grown in pH 4.5 nutrient solution containing Al at 0 or 100 μM, and were sprayed with water or 100 μM of oxalic acid, malic acid, citric acid, or succinic acid every 3 d during a 10 d experiment. Aluminum stress caused significant reduction in alfalfa growth (reflected by above-ground biomass, root weight and root length), root activity, mineral nutrient concentrations (Ca, K, Mg, Mn and Zn), and a significant increase in leaf membrane lipid peroxidation. Foliar application of the four organic acids, especially succinic acid, alleviated Al toxicity, as demonstrated by the increase in plant growth and root activity, as well as reduction in lipid peroxidation. Oxalic acid and malic acid treatments significantly increased oxalate exudation and decreased Al concentration in roots exposed to Al stress. Succinic acid treatment significantly increased accumulation of all four organic acids in roots, accumulation of Ca, K, Mg, Mn and Zn, and up-regulated the gene transcription of malate dehydrogenase (MDH) and phosphoenolpyruvate carboxylase (PEPC) in roots. Our results suggest that the promotion of oxalate exudation from roots through exogenous application of oxalate and malate could contribute to the improvement in Al resistance of alfalfa, and the positive effects of exogenous application of succinate on Al resistance may be associated with the increased endogenous accumulation of all four organic acids in roots, which may constitute an organic-acid detoxification system in alfalfa. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zhang F.,Inner Mongolia University | Zhang F.,Inner Mongolia Academy of Agricultural and Animal Husbandry science | He J.,Inner Mongolia University | Yao Y.,Inner Mongolia Academy of Agricultural and Animal Husbandry science | And 5 more authors.
Environmental Monitoring and Assessment | Year: 2013

The spatial variability and temporal trend in concentrations of the organochlorine pesticides (OCPs), hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT), in soils and agricultural corps were investigated on an intensive horticulture area in Hohhot, North-West China, from 2008 to 2011. The most frequently found and abundant pesticides were the metabolites of DDT (p,p′-DDE, p,p′-DDT, o,p′-DDT and p,p′-DDD). Total DDT concentrations ranged from ND (not detectable) to 507.41 ng/g and were higher than the concentration of total HCHs measured for the range of 4.84-281.44 ng/g. There were significantly positive correlations between the ΣDDT and ΣHCH concentrations (r 2>0.74) in soils, but no significant correlation was found between the concentrations of OCPs in soils and clay content while a relatively strong correlation was found between total OCP concentrations and total organic carbon (TOC). β-HCH was the main isomer of HCHs, and was detected in all samples; the maximum proportion of β-HCH compared to ΣHCHs (mean value 54%) was found, suggesting its persistence. The α/γ-HCH ratio was between 0.89 and 5.39, which signified the combined influence of technical HCHs and lindane. Low p,p′-DDE/p,p′-DDT in N1, N3 and N9 were found, reflecting the fresh input of DDTs, while the relatively high o,p′-DDT/p,p′-DDT ratios indicated the agricultural application of dicofol. Ratios of DDT/(DDE+DDD) in soils do not indicate recent inputs of DDT into Hohhot farmland soil environment. Seasonal variations of OCPs featured higher concentrations in autumn and lower concentrations in spring. This was likely associated with their temperature-driven re-volatilization and application of dicofol in late spring. © 2013 Springer Science+Business Media Dordrecht.

Hou D.,Inner Mongolia University | He J.,Inner Mongolia University | Lu C.,Inner Mongolia University | Sun Y.,Inner Mongolia University | And 3 more authors.
The Scientific World Journal | Year: 2013

Surface sediment and water samples were collected from Daihai Lake to study the biogeochemical characteristics of nitrogen and phosphorus, to estimate the loads of these nutrients, and to assess their effects on water quality. The contents and spatial distributions of total phosphorus (TP), total nitrogen (TN), and different nitrogen forms in sediments were analyzed. The results showed that concentrations of TN and TP in surface sediments ranged from 0.27 to 1.78 g/kg and from 558.31 to 891.29 mg/kg, respectively. Ratios of C: N ranged between 8.2 and 12.1, which indicated that nitrogen accumulated came mainly from terrestrial source. Ratios of N: P in all sampling sites were below 10, which indicated that N was the limiting nutrient for algal growth in this lake. Effects of environment factors on the release of nitrogen and phosphorus in lake sediments were also determined; high pH values could encourage the release of nitrogen and phosphorus. Modified Carlson's trophic state index (TS I M) and comprehensive trophic state index (TS I C) were applied to ascertain the trophic classification of the studied lake, and the values of TS I M and TS I C ranged from 53.72 to 70.61 and from 47.73 to 53.67, respectively, which indicated that the Daihai Lake was in the stage of hypereutropher. © 2013 Dekun Hou et al.

Bai Y.,Indiana State University | Ding L.,Indiana State University | Baker S.,Indiana State University | Bai J.M.,Terre Haute South Vigo High School | And 5 more authors.
BMC Bioinformatics | Year: 2016

Background: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples. Moreover, a deep investigation of miRNA-mRNA target and biological relationships across multiple cancer types by integrating web-based analysis has not been thoroughly conducted. Results: We developed an interactive visualization tool called MMiRNA-Viewer that can concurrently present the co-relationships of expression between miRNA-mRNA pairs of both tumor and normal samples into a single graph. The input file of MMiRNA-Viewer contains the expression information including fold changes between normal and tumor samples for mRNAs and miRNAs, the correlation between mRNA and miRNA, and the predicted target relationship by a number of databases. Users can also load their own input data into MMiRNA-Viewer and visualize and compare detailed information about cancer-related gene expression changes, and also changes in the expression of transcription-regulating miRNAs. To validate the MMiRNA-Viewer, eight types of TCGA cancer datasets with both normal and control samples were selected in this study and three filter steps were applied subsequently. We performed Gene Ontology (GO) analysis for genes available in final selected 238 pairs and also for genes in the top 5 % (95 percentile) for each of eight cancer types to report a significant number of genes involved in various biological functions and pathways. We also calculated various centrality measurement matrices for the largest connected component(s) in each of eight cancers and reported top genes and miRNAs with high centrality measurements. Conclusions: With its user-friendly interface, dynamic visualization and advanced queries, we also believe MMiRNA-Viewer offers an intuitive approach for visualizing and elucidating co-relationships between miRNAs and mRNAs of both tumor and normal samples. We suggest that miRNA and mRNA pairs with opposite fold changes of their expression and with inverted correlation values between tumor and normal samples might be most relevant for explaining the decoupling of mRNAs and their targeting miRNAs in tumor samples for certain cancer types. © 2016 The Author(s).

Liu J.,Chinese Academy of Agricultural Sciences | Liu J.,Inner Mongolia Academy of Agricultural and Animal Husbandry science | Zhang L.,Chinese Academy of Agricultural Sciences | Xu L.,Chinese Academy of Agricultural Sciences | And 8 more authors.
BMC Genomics | Year: 2013

Background: In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.Results: Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.Conclusions: In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future. © 2013 Liu et al.; licensee BioMed Central Ltd.

Sun J.,Inner Mongolia Academy of Agricultural and Animal Husbandry Science | Nie L.,Inner Mongolia Academy of Agricultural and Animal Husbandry Science | Sun G.,Inner Mongolia Academy of Agricultural and Animal Husbandry Science | Guo J.,Inner Mongolia Academy of Agricultural and Animal Husbandry Science | Liu Y.,Inner Mongolia Academy of Agricultural and Animal Husbandry Science
Molecular Biology Reports | Year: 2013

Based on the sequence of an expressed sequence tag, the full-length cDNA of 1,008 nucleotides was cloned from Ammopiptanthus mongolicus by rapid amplification of cDNA ends. It was designated as AmDHN, encoding a protein of 183 amino acids. The calculated molecular weight of the AmDHN protein is 18.4 k Da, and theoretical isoelectric point is 5.78. The AmDHN localized in nucleus. Under normal growth conditions, differential expression of AmDHN exhibited that the expression was the highest in seeds and the lowest in flowers. AmDHN could be induced by NaCl, PEG6000, ABA and drought treatments. Salt and drought resistances of transgenic plants with overexpression of AmDHN are improved. Taken together, these results demonstrated that AmDHN could regulate the expression of abiotic-responsive genes and plays important roles in modulating the tolerance of plants to abiotic stresses. © 2012 Springer Science+Business Media Dordrecht.

Hou D.,Inner Mongolia University | He J.,Inner Mongolia University | Lu C.,Inner Mongolia University | Dong S.,Inner Mongolia University | And 3 more authors.
Environmental Earth Sciences | Year: 2014

Concentrations and vertical distributions of total nitrogen (TN), total phosphorus (TP) and their different forms in sediments obtained from nine locations of Lake Dalinouer in September 2008 were analyzed. The results demonstrated that TP in surface sediments ranged from 0.493 to 0.904 g/kg, and inorganic phosphorus was the main fraction of total phosphorus, ranging from 335 to 738 mg/kg. Simultaneously, the autogenetic calcium phosphorus (ACa-P) was the main fraction of inorganic phosphorus, ranging from 145.4 to 543.2 mg/kg. Vertical distribution of different phosphorus forms in different sediment cores was distinguishing, and most of them tended to increase toward the surface sediment, indicated that the phosphorus concentration was related to the humanity with a certain extent. The relationships between TP and occluded phosphorus and ACa-P were significant. Nitrogen in the sediment was composed mainly of organic nitrogen, accounting for grater than 80 % of TN. NO3 --N was the dominate fraction of inorganic nitrogen in the surface sediment, ranging between 51 and 346 mg/kg (151.1 ± 104.4 mg/kg), and accounting for between 2.2 and 17.7 % of total sediment nitrogen (6.2 ± 5.6 %). The ratio of organic carbon and TN in sediment was in range of 6.0-25.8 and presented a tendency of lake centre >lake sides, indicating that nitrogen accumulated in the sediments from lake sides came mainly from terrestrial source and nitrogen was mainly autogenetic in lake centre. Ratio of N:P in all sampling sites was below 14, indicated that N was the limiting nutrient for algal growth in this lake. © 2013 Springer-Verlag Berlin Heidelberg.

PubMed | Sino United States SiChuan Nabii Bio Technology Co., Ustar Biotechnologies Hangzhou Ltd., Chinese Academy of Agricultural Sciences and Inner Mongolia Academy of Agricultural and Animal Husbandry science
Type: | Journal: Scientific reports | Year: 2016

Porcine epidemic diarrhea virus (PEDV) is a highly transmissible coronavirus that causes a severe enteric disease particularly in neonatal piglets. In this study, a rapid method for detecting PEDV was developed based on cross-priming amplification and nucleic acid test strip(CPA-NATS). Five primers specific for the N gene sequence of PEDV were used for the cross-priming amplification. Detection of amplification products based on labeled probe primers was conducted with strip binding antibody of labeled markers. The CPA method was evaluated and compared with a PCR method. The reverse transcription CPA system was further optimized for detecting PEDV RNA in clinical specimens. Results showed that the method was highly specific for the detection of PEDV, and had the same sensitivity as PCR, with detection limit of 10(-6) diluted plasmid containing the target gene of PEDV. It was also successfully applied to detecting PEDV in clinical specimens. The reverse transcription CPA-NATS detection system established in this study offers a specific, sensitive, rapid, and simple detection tool for screening PEDV, which can contribute to strategies in the effective control of PEDV in swine.

PubMed | Inner Mongolia University, Inner Mongolia Academy of Agricultural and Animal Husbandry Science and Inner Mongolia University of Technology
Type: | Journal: Journal of theoretical biology | Year: 2016

Introns after splicing still play an important role. Introns can accomplish gene expression and regulation by interaction with corresponding mRNA sequences. Based on the Smith-Waterman method, local comparing makes us get the optimal matched segments between intron sequences and mRNA sequences. Analyzing the distribution regulation of the optimal matching region on mRNA sequences ofribosomal protein genes about 27 species, we find a strong interaction between UTR region sequences and introns. There are a lot of the optimal matching regions and low matching ones, and the latter are supposed to be the combined regions of protein complexes. The optimal matching frequency distributions have obvious differences nearby the mRNA functional sites such as translation initiation and termination sites, exon-exon joints and EJC regions. This conclusion shows that intron sequences and mature mRNA sequences are co-evolved and interactive to play their functions.

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