Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays
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{"title"=>"Characterization of mirnas in response to short-term waterlogging in three inbred lines of Zea mays", "type"=>"journal", "authors"=>[{"first_name"=>"Zhijie", "last_name"=>"Liu", "scopus_author_id"=>"55714817900"}, {"first_name"=>"Sunita", "last_name"=>"Kumari", "scopus_author_id"=>"57197190065"}, {"first_name"=>"Lifang", "last_name"=>"Zhang", "scopus_author_id"=>"55709205700"}, {"first_name"=>"Yonglian", "last_name"=>"Zheng", "scopus_author_id"=>"55357332700"}, {"first_name"=>"Doreen", "last_name"=>"Ware", "scopus_author_id"=>"7006205965"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84863107508", "pui"=>"365133221", "doi"=>"10.1371/journal.pone.0039786", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84863107508", "pmid"=>"22768123"}, "id"=>"0f9ab5eb-ec38-3b3b-84b9-35b85bb19ae8", "abstract"=>"Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the microRNA-mediated gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic stress responses. To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and their 92 predicted targets in three inbred Zea mays lines (waterlogging tolerant Hz32, mid-tolerant B73, and sensitive Mo17). Based on our studies, miR159, miR164, miR167, miR393, miR408 and miR528, which are mainly involved in root development and stress responses, were found to be key regulators in the post-transcriptional regulatory mechanisms under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress and development related cis-regulatory elements on the promoters of these miRNAs; and a probable miRNA-mediated gene regulatory network in response to short-term waterlogging stress was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a gene regulatory network; and crosstalk occurs between different biochemical pathways.", "link"=>"http://www.mendeley.com/research/characterization-mirnas-response-shortterm-waterlogging-three-inbred-lines-zea-mays", "reader_count"=>60, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Researcher"=>15, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Master"=>9, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Researcher"=>15, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Master"=>9, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>47, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Argentina"=>1, "Belgium"=>1, "Norway"=>1, "China"=>1, "Philippines"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/614775"], "description"=>"<p>Red octagonal shows all the wet lab experiments. Aqua diamond shows the data analysis method. Blue square shows the computational prediction experiment. T: tolerant line. M: mid-tolerant line. S: sensitive line.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "molecular biology", "Computational biology", "cell biology", "developmental biology"], "article_id"=>285260, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_experimental_design_/285260", "title"=>"Flowchart of the experimental design.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:27:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/614875"], "description"=>"<p>T: Waterlogging treatment. C: Control. RL: Root Length. LL: Leaf Length. RW: Root dry Weight. LW: Leaf dry Weight. TW: Total dry Weight. Error bars show the standard deviation. Student t-test was performed on the tolerant line (Hz32) and mid-tolerant line (B73), comparing with sensitive line (Mo17). ** denotes the p-value below 0.01 and * denotes the p-value below 0.05.</p>", "links"=>[], "tags"=>["waterlogging", "phenotype-screening", "inbred"], "article_id"=>285362, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Short_term_waterlogging_phenotype_screening_results_of_all_three_inbred_lines_/285362", "title"=>"Short-term waterlogging phenotype-screening results of all three inbred lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:29:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/614958"], "description"=>"<p>The flowchart shows the filtering criteria to reduce and refine the numbers of small RNAs to the most interesting subset based on the abundance, removal of repeats (uniqueness), removal of known miRNAs, other ncRNAs, and folding structure. 10 unique sequences were identified as potentially novel miRNA candidates. Light blue squares show the filtered out sequences. Blue squares show the sequences that passed the filter.</p>", "links"=>[], "tags"=>["mirna"], "article_id"=>285451, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_novel_miRNA_prediction_pipeline_/285451", "title"=>"Flowchart of the novel miRNA prediction pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:30:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/615097"], "description"=>"<p>Blue bars show the results of small RNA library in Hz32 under 4 h treatment. Red bars show the results of SLRT-PCR in Hz32 under 4 h treatment at 3 biological replicates. Vertical red line divides the expression profiles of 24 candidate miRNAs with 4 miRNAs (control expression profiles). Error bars show the standard deviation. Chi-square was applied on the small RNA library data and student t-test was performed on SLRT-PCR results. ** denotes the p value <0.01 and * denotes the p value <0.05.</p>", "links"=>[], "tags"=>["profiles", "24", "mirnas", "hypoxia"], "article_id"=>285584, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_profiles_of_24_candidate_miRNAs_under_hypoxia_stress_/285584", "title"=>"Expression profiles of 24 candidate miRNAs under hypoxia stress.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:33:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/615255"], "description"=>"<p>A: Model of miRNA expression pattern. B: Heatmap of miRNA expression profile. The cluster was done on the basis of log<sub>2</sub> (expression level in treatment/expression level in control). Yellow shows down-regulation. Blue shows up-regulation.</p>", "links"=>[], "tags"=>["slrt-pcr"], "article_id"=>285743, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miRNA_expression_profile_by_SLRT_PCR_and_cluster_analysis_/285743", "title"=>"miRNA expression profile by SLRT-PCR and cluster analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:35:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/615421"], "description"=>"<p>A: Model of miRNA target expression pattern. B: Heatmap of miRNA target expression profile. The cluster was done on the basis of log<sub>2</sub> (expression level in treatment/expression level in control). Yellow shows down-regulation. Blue shows up-regulation.</p>", "links"=>[], "tags"=>["mirna", "targets"], "article_id"=>285912, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_miRNA_targets_expression_profile_/285912", "title"=>"Cluster miRNA targets expression profile.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/615548"], "description"=>"<p>A: SLRT-PCR results of miRNA528a/b at 3 biological replicates. B: qRT-PCR results of one of miRNA528a/b targets GRMZM2G039381 at 3 biological replicates. X-axis shows the inbred lines under different time point treatment compared to control. Y-axis shows the expression level. Error bars show the standard deviation. Student t test was performed on qRT-PCR results. ** denotes the p value <0.01 and * denotes the p value <0.05.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "molecular biology", "Computational biology", "cell biology", "developmental biology"], "article_id"=>286032, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_zma_miR528a_b_and_one_of_its_targets_/286032", "title"=>"Expression of zma-miR528a/b and one of its targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:40:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/615639"], "description"=>"<p>Each top strand depicts a miRNA complementary site (targets), and each bottom strand depicts the miRNA. miR159 and miR319 shares the target sequence. Watson-Crick pairing (vertical dashes) and G:U wobble pairing (circles) are indicated. Arrows indicate the 5′termini of mRNA fragments isolated from roots of the maize seedlings, as identified by cloned 5′-RACE products, with the frequency of clones shown. Only cloned sequences that matched the correct target gene and had 5′ ends within a 100 nt window centered on the miRNA complementary site are counted.</p>", "links"=>[], "tags"=>["verification", "mirna"], "article_id"=>286126, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_5_8242_RLM_RACE_verification_of_predicted_miRNA_targets_/286126", "title"=>"5′-RLM-RACE verification of predicted miRNA targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:42:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/615857"], "description"=>"<p>A. TF-miRNA and miRNA-target interactions are shown. B. Probable negative feedback loop between GAMYB and miR319b is shown. Upstream motifs and downstream targets are indicated as circular nodes whereas miRNA are denoted as diamond nodes. Teal color TF nodes represent the upstream motifs, light green nodes represent miRNA targets, whereas royal blue color nodes denote TFs which are involved in both upstream and downstream interactions. Yellow color miRNA shows down regulated miRNAs whereas violet color shows up regulated miRNAs. TF-miRNA interactions are shown as black arrows whereas downstream miRNA-target interactions are shown as red color lines.</p>", "links"=>[], "tags"=>["sub-network", "waterlogging"], "article_id"=>286347, "categories"=>["Biological Sciences", "Developmental Biology", "Plant Biology", "Molecular Biology", "Cell Biology", "Genetics"], "users"=>["Zhijie Liu", "Sunita Kumari", "Lifang Zhang", "Yonglian Zheng", "Doreen Ware"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039786.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miRNA_mediated_gene_regulatory_sub_network_of_short_term_waterlogging_stress_in_B73_/286347", "title"=>"miRNA-mediated gene regulatory sub-network of short-term waterlogging stress in B73.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-29 01:45:47"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[323, 536, 657, 751, 847, 939, 1032, 1114, 1201, 1279, 1355, 1431, 1516, 1582, 1656, 1719, 1791, 1848, 1919, 2000, 2068, 2127, 2208, 2281, 2359]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[316, 541, 663, 766, 856, 950, 1041, 1128, 1218, 1302, 1382, 1456, 1526, 1593, 1657, 1729, 1796, 1862, 1930, 1999, 2065, 2132, 2202, 2261, 2319]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}]}
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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-08-27 18:08:55 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0039786)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'