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1.  Improving the accuracy of expression data analysis in time course experiments using resampling 
BMC Bioinformatics  2014;15(1):352.
Background
As time series experiments in higher eukaryotes usually obtain data from different individuals collected at the different time points, a time series sample itself is not equivalent to a true biological replicate but is, rather, a combination of several biological replicates. The analysis of expression data derived from a time series sample is therefore often performed with a low number of replicates due to budget limitations or limitations in sample availability. In addition, most algorithms developed to identify specific patterns in time series dataset do not consider biological variation in samples collected at the same conditions.
Results
Using artificial time course datasets, we show that resampling considerably improves the accuracy of transcripts identified as rhythmic. In particular, the number of false positives can be greatly reduced while at the same time the number of true positives can be maintained in the range of other methods currently used to determine rhythmically expressed genes.
Conclusions
The resampling approach described here therefore increases the accuracy of time series expression data analysis and furthermore emphasizes the importance of biological replicates in identifying oscillating genes. Resampling can be used for any time series expression dataset as long as the samples are acquired from independent individuals at each time point.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0352-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-014-0352-8
PMCID: PMC4220062  PMID: 25344112
Resampling; Gene expression data; ARSER; Biological replicates; Circadian rhythms; HAYSTACK
2.  Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis 
BMC Plant Biology  2014;14:136.
Background
The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level.
Results
We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD.
Conclusion
Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress adaptation in plants. It is also envisioned that alternative splicing of the clock genes plays more complex roles than previously expected.
doi:10.1186/1471-2229-14-136
PMCID: PMC4035800  PMID: 24885185
Arabidopsis thaliana; Circadian clock; Transcription factor; Alternative splicing; Nonsense-mediated decay (NMD); Environmental stress
3.  Natural variation in floral nectar proteins of two Nicotiana attenuata accessions 
BMC Plant Biology  2013;13:101.
Background
Floral nectar (FN) contains not only energy-rich compounds to attract pollinators, but also defense chemicals and several proteins. However, proteomic analysis of FN has been hampered by the lack of publically available sequence information from nectar-producing plants. Here we used next-generation sequencing and advanced proteomics to profile FN proteins in the opportunistic outcrossing wild tobacco, Nicotiana attenuata.
Results
We constructed a transcriptome database of N. attenuata and characterized its nectar proteome using LC-MS/MS. The FN proteins of N. attenuata included nectarins, sugar-cleaving enzymes (glucosidase, galactosidase, and xylosidase), RNases, pathogen-related proteins, and lipid transfer proteins. Natural variation in FN proteins of eleven N. attenuata accessions revealed a negative relationship between the accumulation of two abundant proteins, nectarin1b and nectarin5. In addition, microarray analysis of nectary tissues revealed that protein accumulation in FN is not simply correlated with the accumulation of transcripts encoding FN proteins and identified a group of genes that were specifically expressed in the nectary.
Conclusions
Natural variation of identified FN proteins in the ecological model plant N. attenuata suggests that nectar chemistry may have a complex function in plant-pollinator-microbe interactions.
doi:10.1186/1471-2229-13-101
PMCID: PMC3728157  PMID: 23848992
LC-MS/MS; Nectar protein; Nectarin; Nicotiana attenuata
4.  Biocontrol Characteristics of Bacillus Species in Suppressing Stem Rot of Grafted Cactus Caused by Bipolaris cactivora 
The Plant Pathology Journal  2013;29(1):42-51.
One of the most important limiting factors for the production of the grafted cactus in Korea is the qualitative and quantitative yield loss derived from stem rots especially caused by Bipolaris cactivora. This study is aimed to develop microbial control agents useful for the control of the bipolaris stem rot. Two bacteria (GA1-23 and GA4-4) selected out of 943 microbial isolates because of their strong antibiotic activity against B. cactivora were identified as Bacillus subtilis and B. amyloliquefaciens, respectively, by the cultural characteristics, Biolog program and 16S rRNA sequencing analyses. Both bacterial isolates significantly inhibited the conidial germination and mycelial growth of the pathogen with no significant difference between the two, of which the inhibitory efficacies varied depending on the cultural conditions such as temperature, nutritional compositions and concentrations. Light and electron microscopy of the pathogen treated with the bacterial isolates showed the inhibition of spore germination with initial malformation of germ tubes and later formation of circle-like vesicles with no hyphal growth and hyphal disruption sometimes accompanied by hyphal swellings and shrinkages adjacent to the bacteria, suggesting their antibiotic mode of antagonistic activity. Control efficacy of B. subtilis GA1-23 and B. amyloliquefaciens GA4-4 on the cactus stem rot were not as high as but comparable to that of fungicide difenoconazole when they were treated simultaneously at the time of pathogen inoculation. All of these results suggest the two bacterial isolates have a good potential to be developed as biocontrol agents for the bipolaris stem rot of the grafted cactus.
doi:10.5423/PPJ.OA.07.2012.0116
PMCID: PMC4174789  PMID: 25288927
Bacillus species; biocontrol; Bipolaris cactivora; bipolaris stem rot; grafted cactus
5.  Identification and profiling of miRNAs during herbivory reveals jasmonate-dependent and -independent patterns of accumulation in Nicotiana attenuata 
BMC Plant Biology  2012;12:209.
Background
Plant microRNAs (miRNAs) play key roles in the transcriptional responses to environmental stresses. However, the role of miRNAs in responses to insect herbivory has not been thoroughly explored. To identify herbivory-responsive miRNAs, we identified conserved miRNAs in the ecological model plant Nicotiana attenuata whose interactions with herbivores have been well-characterized in both laboratory and field studies.
Results
We identified 59 miRNAs from 36 families, and two endogenous trans-acting small interfering RNAs (tasiRNA) targeted by miRNAs. We characterized the response of the precursor and mature miRNAs to simulated attack from the specialist herbivore Manduca sexta by quantitative PCR analysis and used ir-aoc RNAi transformants, deficient in jasmonate biosynthesis, to identify jasmonate-dependent and -independent miRNA regulation. Expression analysis revealed that groups of miRNAs and tasiRNAs were specifically regulated by either mechanical wounding or wounding plus oral secretions from M. sexta larvae, and these small RNAs were accumulated in jasmonate-dependent or -independent manners. Moreover, cDNA microarray analysis indicated that the expression patterns of the corresponding target genes were correlated with the accumulation of miRNAs and tasiRNAs.
Conclusions
We show that a group of miRNAs and tasiRNAs orchestrates the expression of target genes involved in N. attenuata’s responses to herbivore attack.
doi:10.1186/1471-2229-12-209
PMCID: PMC3502350  PMID: 23134682
Anti-herbivore defense; Jasmonate; Manduca sexta; miRNA; Nicotiana attenuata; tasiRNA
6.  Identification and characterization of circadian clock genes in a native tobacco, Nicotiana attenuata 
BMC Plant Biology  2012;12:172.
Background
A plant’s endogenous clock (circadian clock) entrains physiological processes to light/dark and temperature cycles. Forward and reverse genetic approaches in Arabidopsis have revealed the mechanisms of the circadian clock and its components in the genome. Similar approaches have been used to characterize conserved clock elements in several plant species. A wild tobacco, Nicotiana attenuata has been studied extensively to understand responses to biotic or abiotic stress in the glasshouse and also in their native habitat. During two decades of field experiment, we observed several diurnal rhythmic traits of N. attenuata in nature. To expand our knowledge of circadian clock function into the entrainment of traits important for ecological processes, we here report three core clock components in N. attenuata.
Results
Protein similarity and transcript accumulation allowed us to isolate orthologous genes of the core circadian clock components, LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1/PSEUDO-RESPONSE REGULATOR 1 (TOC1/PRR1), and ZEITLUPE (ZTL). Transcript accumulation of NaLHY peaked at dawn and NaTOC1 peaked at dusk in plants grown under long day conditions. Ectopic expression of NaLHY and NaZTL in Arabidopsis resulted in elongated hypocotyl and late-flowering phenotypes. Protein interactions between NaTOC1 and NaZTL were confirmed by yeast two-hybrid assays. Finally, when NaTOC1 was silenced in N. attenuata, late-flowering phenotypes under long day conditions were clearly observed.
Conclusions
We identified three core circadian clock genes in N. attenuata and demonstrated the functional and biochemical conservation of NaLHY, NaTOC1, and NaZTL.
doi:10.1186/1471-2229-12-172
PMCID: PMC3489836  PMID: 23006446
Circadian clock; Flowering time; NaLHY; NaTOC1; NaZTL; Nicotiana attenuata; Protein interaction
7.  A simple and efficient micrografting method for stably transformed Nicotiana attenuata plants to examine shoot-root signaling 
Plant Methods  2011;7:34.
To adjust their development to the environment, plants rely on specific signals that travel from shoot to root and vice versa. Here we describe an efficient micrografting protocol for Nicotiana attenuata, a useful tool for identifying these signals and understanding their functions. Additionally we analyzed transcript accumulation profiles of scions and rootstocks of grafts performed with wild-type and stably transformed N. attenuata. Our results are consistent with the source-to-sink movement of an sRNA silencing signal.
doi:10.1186/1746-4811-7-34
PMCID: PMC3207920  PMID: 22014154
Grafting; Nicotiana attenuata; root and shoot signaling; systemic signals
8.  Tissue Specific Diurnal Rhythms of Metabolites and Their Regulation during Herbivore Attack in a Native Tobacco, Nicotiana attenuata 
PLoS ONE  2011;6(10):e26214.
Ecological performance is all about timing and the endogenous clock that allows the entrainment of rhythms and anticipation of fitness-determining events is being rapidly characterized. How plants anticipate daily abiotic stresses, such as cold in early mornings and drought at noon, as well as biotic stresses, such as the timing of pathogen infections, is being explored, but little is known about the clock's role in regulating responses to insect herbivores and mutualists, whose behaviors are known to be strongly diurnally regulated and whose attack is known to reconfigure plant metabolomes. We developed a liquid chromatography-mass spectrometry procedure and analyzed its output with model-based peak picking algorithms to identify metabolites with diurnal accumulation patterns in sink/source leaves and roots in an unbiased manner. The response of metabolites with strong diurnal patterns to simulated attack from the specialist herbivore, Manduca sexta larvae was analyzed and annotated with in-house and public databases. Roots and leaves had largely different rhythms and only 10 ions of 182 oscillating ions in leaves and 179 oscillating ions in roots were rhythmic in both tissues: root metabolites mainly peaked at dusk or night, while leaf metabolites peaked during the day. Many oscillating metabolites showed tissue-specific regulation by simulated herbivory of which systemic responses in unattacked tissues were particularly pronounced. Diurnal and herbivory-elicited accumulation patterns of disaccharide, phenylalanine, tyrosine, lyciumoside I, coumaroyl tyramine, 12-oxophytodienoic acid and jasmonic acid and those of their related biosynthetic transcripts were examined in detail. We conclude that oscillating metabolites of N. attenuata accumulate in a highly tissue-specific manner and the patterns reveal pronounced diurnal rhythms in the generalized and specialized metabolism that mediates the plant's responses to herbivores and mutualists. We propose that diurnal regulation will prove to an important element in orchestrating a plant's responses to herbivore attack.
doi:10.1371/journal.pone.0026214
PMCID: PMC3196511  PMID: 22028833
9.  A Novel Gene, ROA, Is Required for Normal Morphogenesis and Discharge of Ascospores in Gibberella zeae▿† 
Eukaryotic Cell  2010;9(10):1495-1503.
Head blight, caused by Gibberella zeae, is a significant disease among cereal crops, including wheat, barley, and rice, due to contamination of grain with mycotoxins. G. zeae is spread by ascospores forcibly discharged from sexual fruiting bodies forming on crop residues. In this study, we characterized a novel gene, ROA, which is required for normal sexual development. Deletion of ROA (Δroa) resulted in an abnormal size and shape of asci and ascospores but did not affect vegetative growth. The Δroa mutation triggered round ascospores and insufficient cell division after spore delimitation. The asci of the Δroa strain discharged fewer ascospores from the perithecia but achieved a greater dispersal distance than those of the wild-type strain. Turgor pressure within the asci was calculated through the analysis of osmolytes in the epiplasmic fluid. Deletion of the ROA gene appeared to increase turgor pressure in the mutant asci. The higher turgor pressure of the Δroa mutant asci and the mutant spore shape contributed to the longer distance dispersal. When the Δroa mutant was outcrossed with a Δmat1-2 mutant, a strain that contains a green fluorescence protein (GFP) marker in place of the MAT1-2 gene, unusual phenotypic segregation occurred. The ratio of GFP to non-GFP segregation was 1:1; however, all eight spores had the same shape. Taken together, the results of this study suggest that ROA plays multiple roles in maintaining the proper morphology and discharge of ascospores in G. zeae.
doi:10.1128/EC.00083-10
PMCID: PMC2950417  PMID: 20802018
10.  Rocuronium bromide induced anaphylaxis in a child -A case report- 
Korean Journal of Anesthesiology  2010;59(6):411-415.
Anaphylaxis or anaphylactoid reaction in pediatric patient during anesthesia is rare. We report a rocuronium induced anaphylactic reaction in a 33-month-old female. The patient was scheduled to undergo escharectomy due to injuries suffered from a major burn. Shortly after administration of rocuronium, the patient developed severe hypotension, tachycardia, and hypoxia. A similar reaction occurred after administration of rocuronium on subsequent anesthesia. She underwent uneventful anesthesia with volatile induction and maintenance of anesthesia with sevoflurane on her next 7 operations without using of muscle relaxant.
doi:10.4097/kjae.2010.59.6.411
PMCID: PMC3022135  PMID: 21253379
Anaphylactoid reaction; Anaphylaxis; Muscle relaxant; Pediatrics; Rocuronium
11.  Nuclear Import and DNA Binding of the ZHD5 Transcription Factor Is Modulated by a Competitive Peptide Inhibitor in Arabidopsis* 
The Journal of Biological Chemistry  2010;286(2):1659-1668.
Competitive inhibition of transcription factors by small proteins is an intriguing component of gene regulatory networks in both animals and plants. The small interfering proteins possess limited sequence homologies to specific transcription factors but lack one or more protein motifs required for transcription factor activities. They interfere with the activities of transcription factors, such as DNA binding and transcriptional activation, by forming nonfunctional heterodimers. A potential example is the Arabidopsis MIF1 (mini zinc finger 1) protein consisting of 101 residues. It has a zinc finger domain but lacks other protein motifs normally present in transcription factors. In this work, we show that MIF1 and its functional homologues physically interact with a group of zinc finger homeodomain (ZHD) transcription factors, such as ZHD5, that regulate floral architecture and leaf development. Gel mobility shift assays revealed that MIF1 blocks the DNA binding activity of ZHD5 homodimers by competitively forming MIF1-ZHD5 heterodimers. Accordingly, the transcriptional activation activity of ZHD5 was significantly suppressed by MIF1 coexpressed transiently in Arabidopsis protoplasts. Notably, MIF1 also prevents ZHD5 from nuclear localization. Although ZHD5 was localized exclusively in the nucleus, it was scattered throughout the cytoplasm when MIF1 was coexpressed. Transgenic plants overexpressing the ZHD5 gene (35S:ZHD5) exhibited accelerated growth with larger leaves. Consistent with the negative regulation of ZHD5 by MIF1, the 35S:ZHD5 phenotypes were diminished by MIF1 coexpression. These observations indicate that MIF1 regulates the ZHD5 activities in a dual step manner: nuclear import and DNA binding.
doi:10.1074/jbc.M110.167692
PMCID: PMC3020774  PMID: 21059647
Arabidopsis; DNA-binding Protein; Gene Expression; Plant; Transcription Factors; Zinc Finger
12.  Gibberellic acid-mediated salt signaling in seed germination 
Plant Signaling & Behavior  2008;3(10):877-879.
Seed germination initiates the postembryonic development of plants, which determines successful seedling establishment and plant propagation. It is therefore tightly regulated by diverse environmental conditions, including high salinity and drought, as well as by intrinsic developmental programs, among which gibberellic acid (GA) is best understood. Regulatory roles of GA in seed germination have been extensively studied. It is also known that high salinity inhibits germination by repressing genes encoding GA biosynthetic enzymes. However, it is still unclear how salt signals are coordinately incorporated into the GA signaling pathway at the molecular level. We recently demonstrated that a membrane-bound NAC transcription factor, NTL8, mediates salt signaling, primarily through a RGL2-independent GA pathway, in regulating seed germination. High salinity promotes NTL8 transcription and proteolytic activation of NTL8. Notably, the NTL8-mediated salt signaling is independent of abscisic acid (ABA). These observations indicate that membrane-mediated transcription control is an important component of salt signaling during seed germination.
PMCID: PMC2634403  PMID: 19704528
Arabidopsis; gibberellic acid (GA); salt stress; membrane-bound transcription factor; NAC; NTL8; RGL2
13.  Small interfering peptides as a novel way of transcriptional control 
Plant Signaling & Behavior  2008;3(9):615-617.
Transcription factors are key components of transcriptional regulatory networks governing virtually all aspects of plant growth and developmental processes. Their activities are regulated at various steps, including gene transcription, posttranscriptional mRNA metabolism, posttranslational modifications, nucleocytoplasmic transport, and controlled proteolytic cleavage of membrane-anchored, dormant forms. Dynamic protein dimerization also plays a critical role in this process. An exquisite regulatory scheme has recently been proposed to modulate the action of transcription factors. Small peptides possessing a protein dimerization motif but lacking the DNA-binding motif form nonfunctional heterodimers with a group of specific TFs, inhibiting their transcriptional activation activities. Extensive searches for small proteins that have a similar structural organization in the databases revealed that small peptide-mediated transcription control is not an exceptional case but would be a regulatory mechanism occurring widespread in the Arabidopsis genome.
PMCID: PMC2634540  PMID: 19513250
Arabidopsis; flowering time; HD-ZIP III; homodimer; transcription factor; ZPR
14.  Membrane-Mediated Salt Stress Signaling in Flowering Time Control 
Plant Signaling & Behavior  2007;2(6):517-518.
More than 10% of the plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factors have been predicted to have alpha-helical transmembrane (TM) domain in their C-terminal regions, among which at least three members have been proven to be membrane-associated and play a role in cell cycle control and stress responses. These observations suggest that membrane-mediated regulation would be an important molecular mechanism mediating rapid transcriptional responses to internal and external stimuli in plants. Recently, we showed that a salt-responsive NTL (NTM1-Like's) transcription factor NTL8 is localized primarily in plasma membranes as dormant form and subsequently processed into transcriptionally active, nuclear form. Overexpression of an active NTL8 form exhibited delayed flowering as well as reduced growth with small curled leaves. Consistent with this, expression of FLOWERING LOCUS T (FT) and its downstream genes was significantly reduced in the transgenic plants. Furthermore, FT was notably repressed by high salt. These results indicate that NTL8 mediates salt-responsive flowering via FT in Arabidopsis and that membrane-mediated transcription regulation underlies the salt signaling in mediating flowering initiation.
PMCID: PMC2634355  PMID: 19704545
Arabidopsis; flowering time; flowering locus T (FT); membrane-bound transcription factor; NAC; salt stress
15.  Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation 
Nucleic Acids Research  2006;35(1):203-213.
Controlled proteolytic cleavage of membrane-associated transcription factors (MTFs) is an intriguing activation strategy that ensures rapid transcriptional responses to incoming stimuli. Several MTFs are known to regulate diverse cellular functions in prokaryotes, yeast, and animals. In Arabidopsis, a few NAC MTFs mediate either cytokinin signaling during cell division or endoplasmic reticulum (ER) stress responses. Through genome-wide analysis, it was found that at least 13 members of the NAC family in Arabidopsis contain strong α-helical transmembrane motifs (TMs) in their C-terminal regions and are predicted to be membrane-associated. Interestingly, most of the putative NAC MTF genes are up-regulated by stress conditions, suggesting that they may be involved in stress responses. Notably, transgenic studies revealed that membrane release is essential for the function of NAC MTFs. Transgenic plants overexpressing partial-size NAC constructs devoid of the TMs, but not those overexpressing full-size constructs, showed distinct phenotypic changes, including dwarfed growth and delayed flowering. The rice genome also contains more than six NAC MTFs. Furthermore, the presence of numerous MTFs is predicted in the whole transcription factors in plants. We thus propose that proteolytic activation of MTFs is a genome-wide mechanism regulating plant genomes.
doi:10.1093/nar/gkl1068
PMCID: PMC1802569  PMID: 17158162

Results 1-15 (15)