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author:("Liu, lizhong")
1.  De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea) 
BMC Genomics  2015;16(1):723.
The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties.
In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers.
This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
PMCID: PMC4580217  PMID: 26395839
Sodom apple; Calotropis gigantea; High throughput sequencing; Transcriptome; Fiber biosynthesis; Secondary metabolite biosynthesis
2.  Recovery from post-traumatic stress disorder after a flood in China: a 13-year follow-up and its prediction by degree of collective action 
BMC Public Health  2015;15:615.
Victims exposed to serious traumatic experiences may develop post-traumatic stress disorder (PTSD) and suffer this mental health problem for a long time. Different types of trauma displayed a chronicity rate of PTSD within the range of 6.3-68.9 %. As one of the most common and severe natural disasters, the natural progression of flood related PTSD has not been revealed. The aim of this study was to estimate the chronicity rate and identify the prognostic factors of PTSD in flood victims.
Flood victims, who were over the age of 16 and diagnosed with PTSD in 2000 in Huarong, Ziyang, and Anxiang counties of Hunan province, China, were enrolled in this survey. Current probable PTSD was analyzed using the PTSD Checklist-Civilian version. Data were collected in face-to-face interviews and analyzed using univariate analysis and multiple logistic regression models.
The rate of current probable PTSD was 15.4 %. The current occurrences of re-experiencing, avoidance/numbing, and hyper-arousal symptom groups were 69.3 %, 17.2 %, and 50.2 %, respectively. Significant prognostic factors for current probable PTSD were flood-related stressors (e.g., life-threatening experiences, extreme physical adversity, and extreme psychological adversity) and frequency of general collective action. The relationships still existed when taking the fluctuation of frequency of general collective action into consideration. Gender and education level showed no influence on the recovery from PTSD. The impact of age in this study was inconsistent; in the 2000 model, around 2006 model, around 2013 model, and all FGCA model, older age was positive prognosis factor for PTSD; in the univariate analysis and fluctuation model, age showed no influence on the recovery from PTSD.
Our findings indicated that PTSD can persist 13 years after a flood. Demographic characteristics (e.g., age, gender, and education level) seem to have no influence on the recovery from PTSD. Trauma-related stressors and social participation are important predictors for remission from chronic PTSD.
PMCID: PMC4491893  PMID: 26148510
Floods; Post-traumatic stress disorder; Chronicity; Prognosis factors; Epidemiology
3.  An ethnobotanical study of the less known wild edible figs (genus Ficus) native to Xishuangbanna, Southwest China 
The genus Ficus, collectively known as figs, is a key component of tropical forests and is well known for its ethnobotanical importance. In recent decades an increasing number of studies have shown the indigenous knowledge about wild edible Ficus species and their culinary or medicinal value. However, rather little is known about the role of these species in rural livelihoods, because of both species and cultural diversity.
In this study we 1) collected the species and ethnic names of wild edible Ficus exploited by four cultural groups in Xishuangbanna, Southwest China, and 2) recorded the collection activities and modes of consumption through semi-structured interviews, 3) investigated the resource management by a statistical survey of their field distribution and cultivation, and 4) compared and estimated the usage intensities by the grading method.
The young leaves, leaf buds and young or ripe syconia of 13 Ficus species or varieties are traditionally consumed. All the species had fixed and usually food-related ethnic names. All four cultural groups are experienced in the collection and use of edible Ficus species as vegetables, fruits or beverages, with the surplus sold for cash income. Different cultural groups use the Ficus species at different intensities because of differences in availability, forest dependency and cultural factors. Both the mountain and basin villagers make an effort to realize sustainable collection and meet their own and market needs by resource management in situ or cultivation.
In comparison with reports from other parts of the world, ethnic groups in Xishuangbanna exploited more edible Ficus species for young leaves or leaf buds. Most of the edible species undergo a gradient of management intensities following a gradient of manipulation from simple field gathering to ex situ cultivation. This study contributes to our understanding of the origins and diffusion of the knowledge of perception, application and managing a group of particular plant species, and how the local culture, economic and geographical factors influence the process.
PMCID: PMC4246566  PMID: 25252723
Ficus; Ethnobotany; Management; Fruit; Vegetables; Xishuangbanna
4.  IRDL Cloning: A One-Tube, Zero-Background, Easy-to-Use, Directional Cloning Method Improves Throughput in Recombinant DNA Preparation 
PLoS ONE  2014;9(9):e107907.
Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.
PMCID: PMC4171505  PMID: 25243603
5.  Transcriptome profiling identifies ABA mediated regulatory changes towards storage filling in developing seeds of castor bean (Ricinus communis L.) 
Cell & Bioscience  2014;4:33.
The potential biodiesel plant castor bean (Ricinus communis) has been in the limelight for bioenergy research due to the availability of its genome which raises the bar for genome-wide studies claiming advances that impact the “genome-phenome challenge”. Here we report the application of phytohormone ABA as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling.
After the application of exogenous ABA treatments, we measured an increased ABA levels in the developing seeds cultured in vitro using the ELISA technique and quantified the content of major biomolecules (including total lipids, sugars and protein) in treated seeds. Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %). To elucidate the possible ABA signal transduction pathways towards overall seed filling, we studied the differential gene expression analysis using Illumina RNA-Sequencing technology, resulting in 2568 (1507-up/1061-down regulated) differentially expressed genes were identified. These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene). Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.
Taken together, metabolite measurements supported by genes and pathway expression results indicated in this study provide new insights to understand the ABA signaling mechanism towards seed storage filling and also contribute useful information for facilitating oilseed crop functional genomics on an aim for utilizing castor bean agricultural and bioenergy use.
PMCID: PMC4109380  PMID: 25061509
ABA signaling; Castor bean; Developing seeds; High throughput RNA-Seq; Storage reserve; ELISA
6.  Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean 
Nucleic Acids Research  2014;42(11):6987-6998.
Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.
PMCID: PMC4066788  PMID: 24799438
7.  Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.) 
BMC Genomics  2013;14(1):785.
The AP2/ERF transcription factor, one of the largest gene families in plants, plays a crucial role in the regulation of growth and development, metabolism, and responses to biotic and abiotic stresses. Castor bean (Ricinus communis L., Euphobiaceae) is one of most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. The available genome provides a great chance to identify and characterize the global information on AP2/ERF transcription factors in castor bean, which might provide insights in understanding the molecular basis of the AP2/ERF family in castor bean.
A total of 114 AP2/ERF transcription factors were identified based on the genome in castor bean. According to the number of the AP2/ERF domain, the conserved amino acid residues within AP2/ERF domain, the conserved motifs and gene organization in structure, and phylogenetical analysis, the identified 114 AP2/ERF transcription factors were characterized. Global expression profiles among different tissues using high-throughput sequencing of digital gene expression profiles (DGEs) displayed diverse expression patterns that may provide basic information in understanding the function of the AP2/ERF gene family in castor bean.
The current study is the first report on identification and characterization of the AP2/ERF transcription factors based on the genome of castor bean in the family Euphobiaceae. Results obtained from this study provide valuable information in understanding the molecular basis of the AP2/ERF family in castor bean.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-14-785) contains supplementary material, which is available to authorized users.
PMCID: PMC4046667  PMID: 24225250
8.  Transcriptome-Wide Identification and Characterization of MicroRNAs from Castor Bean (Ricinus communis L.) 
PLoS ONE  2013;8(7):e69995.
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.
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.
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.
PMCID: PMC3722108  PMID: 23894571
9.  Transcriptome analysis of Sacha Inchi (Plukenetia volubilis L.) seeds at two developmental stages 
BMC Genomics  2012;13:716.
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.
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.
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.
PMCID: PMC3574040  PMID: 23256450
Transcriptome; Unsaturated fatty acids; Omega-3 fatty acids; Triacylglycerols; Gene expression
10.  Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.) 
BMC Plant Biology  2010;10:278.
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.
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.
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.
PMCID: PMC3017068  PMID: 21162723
11.  Prediction of posttraumatic stress disorder among adults in flood district 
BMC Public Health  2010;10:207.
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.
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.
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.
A simple risk score model can be used to predict PTSD among victims of flood.
PMCID: PMC2868002  PMID: 20420677

Results 1-11 (11)