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author:("Liu, lizhong")
1.  Transcriptome-Wide Identification and Characterization of MicroRNAs from Castor Bean (Ricinus communis L.) 
PLoS ONE  2013;8(7):e69995.
Background
MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean.
Results
Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed.
Conclusions
The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae.
doi:10.1371/journal.pone.0069995
PMCID: PMC3722108  PMID: 23894571
2.  Transcriptome analysis of Sacha Inchi (Plukenetia volubilis L.) seeds at two developmental stages 
BMC Genomics  2012;13:716.
Background
Sacha Inchi (Plukenetia volubilis L., Euphorbiaceae) is a potential oilseed crop because the seeds of this plant are rich in unsaturated fatty acids (FAs). In particular, the fatty acid composition of its seed oil differs markedly in containing large quantities of α-linolenic acid (18C:3, a kind of ω-3 FAs). However, little is known about the molecular mechanisms responsible for biosynthesis of unsaturated fatty acids in the developing seeds of this species. Transcriptome data are needed to better understand these mechanisms.
Results
In this study, de novo transcriptome assembly and gene expression analysis were performed using Illumina sequencing technology. A total of 52.6 million 90-bp paired-end reads were generated from two libraries constructed at the initial stage and fast oil accumulation stage of seed development. These reads were assembled into 70,392 unigenes; 22,179 unigenes showed a 2-fold or greater expression difference between the two libraries. Using this data we identified unigenes that may be involved in de novo FA and triacylglycerol biosynthesis. In particular, a number of unigenes encoding desaturase for formation of unsaturated fatty acids with high expression levels in the fast oil accumulation stage compared with the initial stage of seed development were identified.
Conclusions
This study provides the first comprehensive dataset characterizing Sacha Inchi gene expression at the transcriptional level. These data provide the foundation for further studies on molecular mechanisms underlying oil accumulation and PUFA biosynthesis in Sacha Inchi seeds. Our analyses facilitate understanding of the molecular mechanisms responsible for the high unsaturated fatty acids (especially α-linolenic acid) accumulation in Sacha Inchi seeds.
doi:10.1186/1471-2164-13-716
PMCID: PMC3574040  PMID: 23256450
Transcriptome; Unsaturated fatty acids; Omega-3 fatty acids; Triacylglycerols; Gene expression
3.  Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.) 
BMC Plant Biology  2010;10:278.
Background
The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers.
Results
In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean.
Conclusion
Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure analysis, facilitating breeding and crop improvement of castor bean.
doi:10.1186/1471-2229-10-278
PMCID: PMC3017068  PMID: 21162723
4.  Prediction of posttraumatic stress disorder among adults in flood district 
BMC Public Health  2010;10:207.
Background
Flood is one of the most common and severe forms of natural disasters. Posttraumatic stress disorder (PTSD) is a common disorder among victims of various disasters including flood. Early prediction for PTSD could benefit the prevention and treatment of PTSD. This study aimed to establish a prediction model for the occurrence of PTSD among adults in flood districts.
Methods
A cross-sectional survey was carried out in 2000 among individuals who were affected by the 1998 floods in Hunan, China. Multi-stage sampling was used to select subjects from the flood-affected areas. Data was collected through face-to-face interviews using a questionnaire. PTSD was diagnosed according to DSM-IV criteria. Study subjects were randomly divided into two groups: group 1 was used to establish the prediction model and group 2 was used to validate the model. We first used the logistic regression analysis to select predictive variables and then established a risk score predictive model. The validity of model was evaluated by using the model in group 2 and in all subjects. The area under the receiver operation characteristic (ROC) curve was calculated to evaluate the accuracy of the prediction model.
Results
A total of 2336 (9.2%) subjects were diagnosed as probable PTSD-positive individuals among a total of 25,478 study subjects. Seven independent predictive factors (age, gender, education, type of flood, severity of flood, flood experience, and the mental status before flood) were identified as key variables in a risk score model. The area under the ROC curve for the model was 0.853 in the validation data. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of this risk score model were 84.0%, 72.2%, 23.4%, and 97.8%, respectively, at a cut-off value of 67.5 in the validation data.
Conclusions
A simple risk score model can be used to predict PTSD among victims of flood.
doi:10.1186/1471-2458-10-207
PMCID: PMC2868002  PMID: 20420677

Results 1-4 (4)