International Journal of Genomics
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Open Access journal
ISSN (Print) 2314-436X - ISSN (Online) 2314-4378
Published by Hindawi [333 journals]
- Temporal Changes in Gene Expression Profile during Mature Adipocyte
Abstract: Objective. To characterize changes in gene expression profile during human mature adipocyte dedifferentiation in ceiling culture. Methods. Subcutaneous (SC) and omental (OM) adipose tissue samples were obtained from 4 participants paired for age and BMI. Isolated adipocytes were dedifferentiated in ceiling culture. Gene expression analysis at days 0, 4, 7, and 12 of the cultures was performed using Affymetrix Human Gene 2.0 STvi arrays. Hierarchical clustering according to similarity of expression changes was used to identify overrepresented functions. Results. Four clusters gathered genes with similar expression between day 4 to day 7 but decreasing expression from day 7 to day 12. Most of these genes coded for proteins involved in adipocyte functions (LIPE, PLIN1, DGAT2, PNPLA2, ADIPOQ, CEBPA, LPL, FABP4, SCD, INSR, and LEP). Expression of several genes coding for proteins implicated in cellular proliferation and growth or cell cycle increased significantly from day 7 to day 12 (WNT5A, KITLG, and FGF5). Genes coding for extracellular matrix proteins were differentially expressed between days 0, 4, 7, and 12 (COL1A1, COL1A2, and COL6A3, MMP1, and TGFB1). Conclusion. Dedifferentiation is associated with downregulation of transcripts encoding proteins involved in mature adipocyte functions and upregulation of genes involved in matrix remodeling, cellular development, and cell cycle.
PubDate: Sun, 19 Mar 2017 00:00:00 +000
- The Promise of Agriculture Genomics
PubDate: Sun, 05 Mar 2017 00:00:00 +000
- Racial Differences in Expression Levels of miRNA Machinery-Related Genes,
Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid
Carcinoma and Comparative Validation Using the Cancer Genome Atlas
Abstract: Aberrant regulation of microRNA (miRNA) machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC), which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC.
PubDate: Thu, 02 Mar 2017 08:26:25 +000
- A Review of Recent Advancement in Integrating Omics Data with Literature
Mining towards Biomedical Discoveries
Abstract: In the past decade, the volume of “omics” data generated by the different high-throughput technologies has expanded exponentially. The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been the promise of the high-throughput experimental techniques. Different bioinformatics approaches have been developed to streamline the downstream analyzes by providing independent information to interpret and provide biological inference. Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles. In this review paper, we discuss the recent advancement in approaches that integrate results from omics data and information generated from text mining approaches to uncover novel biomedical information.
PubDate: Sun, 26 Feb 2017 07:10:14 +000
- Case Study of Somaclonal Variation in Resistance Genes Mlo and Pme3 in
Flaxseed (Linum usitatissimum L.) Induced by Nanoparticles
Abstract: Nanoparticles influence on genome is investigated worldwide. The appearance of somaclonal variation is a cause of great concern for any micropropagation system. Somaclonal variation describes the tissue-culture-induced phenotypic and genotypic variations. This paper shows the results of somaclonal variation in two resistance genes pectin methylesterase and Mlo-like protein in all tissue culture development stages, as donor plant, calluses, and regenerants of Linum usitatissimum induced by gold and silver nanoparticles. In this paper, it was essential to obtain DNA material from all tissue culture development stages from one donor plant to record changes in each nucleotide sequence. Gene region specific primers were developed for resistance genes such as Mlo and Pme3 to define the genetic variability in tissue culture of L. usitatissimum. In recent years, utilization of gold and silver nanoparticles in tissue culture is increased and the mechanisms of changes in genome induced by nanoparticles still remain unclear. Obtained data show the somaclonal variation increase in calluses obtained from one donor plant and grown on medium supplemented by gold nanoparticles (Mlo ; Pme3 ) or silver nanoparticles (Mlo ; Pme3 ) and decrease in regenerants. Morphological parameters of calluses showed a number of differences between each investigated culture group.
PubDate: Thu, 23 Feb 2017 08:20:23 +000
- Genomewide Expression and Functional Interactions of Genes under Drought
Stress in Maize
Abstract: A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
PubDate: Thu, 23 Feb 2017 00:00:00 +000
- Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium
Abstract: Based on the ability of nitrate reductase synthesis, Corynebacterium pseudotuberculosis is classified into two biovars: Ovis and Equi. Due to the presence of nitrate reductase, the Equi biovar can survive in absence of oxygen. On the other hand, Ovis biovar that does not have nitrate reductase is able to adapt to various ecological niches and can grow on certain carbon sources. Apart from these two biovars, some other strains are also able to carry out the reduction of nitrate. The enzymes that are involved in electron transport chain are also identified by in silico methods. Findings about pathogen metabolism can contribute to the identification of relationship between nitrate reductase and the C. pseudotuberculosis pathogenicity, virulence factors, and discovery of drug targets.
PubDate: Mon, 20 Feb 2017 11:44:33 +000
- Integrating Biological Covariates into Gene Expression-Based Predictors of
Abstract: The use of gene expression-based classifiers has resulted in a number of promising potential signatures of patient diagnosis, prognosis, and response to therapy. However, these approaches have also created difficulties in trying to use gene expression alone to predict a complex trait. A practical approach to this problem is to integrate existing biological knowledge with gene expression to build a composite predictor. We studied the problem of predicting radiation sensitivity within human cancer cell lines from gene expression. First, we present evidence for the need to integrate known biological conditions (tissue of origin, RAS, and p53 mutational status) into a gene expression prediction problem involving radiation sensitivity. Next, we demonstrate using linear regression, a technique for incorporating this knowledge. The resulting correlations between gene expression and radiation sensitivity improved through the use of this technique (best-fit adjusted increased from 0.3 to 0.84). Overfitting of data was examined through the use of simulation. The results reinforce the concept that radiation sensitivity is not driven solely by gene expression, but rather by a combination of distinct parameters. We show that accounting for biological heterogeneity significantly improves the ability of the model to identify genes that are associated with radiosensitivity.
PubDate: Wed, 08 Feb 2017 12:44:50 +000
- Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice
Landraces as a Comprehensive Information Resource for Marker-Assisted
Abstract: Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three indica and two japonica with potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes. Over two million and eight hundred thousand single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in indica and japonica lines have been determined, which potentially have significant impacts on multiple transcripts of genes. SNP deserts, contiguous SNP-low regions, were found on chromosomes 1, 4, and 5 of all genomes of rice examined. Based on the distribution of SNPs per 100 kilobase pairs, the phylogenetic relationships among the landraces have been constructed. This is the first step towards revealing several salient features of rice genomes in Vietnam and providing significant information resources to further marker-assisted selection (MAS) in rice breeding programs.
PubDate: Tue, 07 Feb 2017 08:32:54 +000
- The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus
Abstract: The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in contigs with N50 of 4,736, while the transcriptome assembly resulted in contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate the Limulus clock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.
PubDate: Mon, 06 Feb 2017 13:20:51 +000
- The Numerical Predominance and Large Transcriptome Differences of
Neutrophils in Peripheral Blood Together Inevitably Account for a Reported
Pulmonary Tuberculosis Signature
Abstract: Previous transcriptomic analysis revealed a 393-transcript signature (PTBsig), which is dominated by interferon inducible genes, in whole blood of pulmonary tuberculosis (PTB) patients. Comparisons with a limited set of interferon-driven genes among separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils indicated that the signature is due to changes in neutrophils, the overwhelmingly predominant cell type. By extending the analysis to the entire 393 transcripts of PTBsig and by switching the cell proportions between separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils, we create putative PTBsig for whole blood (pPTBsig) in which CD4+ or CD8+ T cells or monocytes predominated or in which the cell proportions were unchanged. These putative signatures are then compared to the actual reported PTBsig. We show that, because of their predominance in peripheral blood and their larger transcriptional responses, neutrophils were indeed almost exclusively responsible for PTBsig. We caution that the functional significance of changes in other cell types might escape notice in transcriptome analysis that is based upon whole blood.
PubDate: Mon, 06 Feb 2017 11:48:06 +000
- Characteristics and Validation Techniques for PCA-Based Gene-Expression
Abstract: Background. Many gene-expression signatures exist for describing the biological state of profiled tumors. Principal Component Analysis (PCA) can be used to summarize a gene signature into a single score. Our hypothesis is that gene signatures can be validated when applied to new datasets, using inherent properties of PCA. Results. This validation is based on four key concepts. Coherence: elements of a gene signature should be correlated beyond chance. Uniqueness: the general direction of the data being examined can drive most of the observed signal. Robustness: if a gene signature is designed to measure a single biological effect, then this signal should be sufficiently strong and distinct compared to other signals within the signature. Transferability: the derived PCA gene signature score should describe the same biology in the target dataset as it does in the training dataset. Conclusions. The proposed validation procedure ensures that PCA-based gene signatures perform as expected when applied to datasets other than those that the signatures were trained upon. Complex signatures, describing multiple independent biological components, are also easily identified.
PubDate: Mon, 06 Feb 2017 09:57:36 +000
- Genetic Diversity and Association Analysis for Solvent Retention Capacity
in the Accessions Derived from Soft Wheat Ningmai 9
Abstract: Solvent retention capacity (SRC) test is an effective method for quality evaluation of soft wheat. Ningmai 9 is a founder in soft wheat breeding. The SRC and genotype of Ningmai 9 and its 117 derivatives were tested. Association mapping was employed to identify the quantitative trait loci (QTL) associated with SRCs. Ningmai 9 had the allele frequency of 75.60% and 67.81% to its first- and second-generation derivatives, respectively, indicating higher contribution than theoretical expectation. Neighbor-joining cluster based on the genotyping data showed that Ningmai 9 and most of its first-generation derivatives were clustered together, whereas its second-generation derivatives were found in another group. The variation coefficients of SRCs in the derivatives ranged from 5.35% to 8.63%. A total of 29 markers on 13 chromosomes of the genome were associated with the SRCs. There were 6 markers associated with more than one SRC or detected in two years. The results suggested that QTL controlling SRCs in Ningmai 9 might be different from other varieties. Markers Xgwm44, Xbarc126, Xwmc790, and Xgwm232 associated with SRCs in Ningmai 9 might be used for quality improvement in soft wheat breeding.
PubDate: Sun, 05 Feb 2017 06:58:38 +000
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High
Throughput Genomic Studies
Abstract: High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
PubDate: Thu, 26 Jan 2017 08:13:45 +000
- Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the
Mammary Tissue of Local Turkish Kivircik Sheep
Abstract: Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST sequences were assembled with the CAP3 software. Putative functions of all unique sequences and statistical analysis were determined by Geneious software. Total 422 ESTs have over 80% similarity to known sequences of other organisms in NCBI classified by Panther database for the Gene Ontology (GO) category. By comparing gene expression profiles, we observed some putative genes that may be relative to reproductive performance or play important roles in milk synthesis and secretion. A total of 2414 ESTs have been deposited to the NCBI GenBank database (GW996847–GW999260). EST data in this study have provided a new source of information to functional genome studies of sheep.
PubDate: Mon, 23 Jan 2017 00:00:00 +000
- Association of PTPN22 Haplotypes (−1123G>C/+1858C>T) with Rheumatoid
Arthritis in Western Mexican Population
Abstract: Rheumatoid arthritis (RA) is an autoimmune disease characterized by the presence of antibodies against cyclic citrullinated peptide (anti-CCP), a consequence of the breakdown of immune tolerance. The lymphoid tyrosine phosphatase (Lyp) protein has significant effects on maintenance of peripheral immune tolerance. Two polymorphic variants (−1123G>C and +1858C>T) at PTPN22 gene that encodes this protein have been associated with autoimmune disorders and found in strong linkage disequilibrium in Caucasian population. We evaluated whether PTPN22 haplotypes (−1123G>C/+1858C>T) are associated with anti-CCP antibodies, as well as susceptibility to RA in a Western Mexican population. A total of 315 RA patients and 315 control subjects (CS) were included. The polymorphisms were genotyped by PCR-RFLP and the anti-CCP antibodies were determined by ELISA. The PTPN22 polymorphisms were in strong linkage disequilibrium (D′ = 1.00 in CS). The susceptibility haplotype CT was significantly more frequent in RA patients than in CS (OR 2.18, 95% CI 1.15–4.16, ). No association between haplotypes and anti-CCP antibodies levels was observed. In conclusion, this study confirmed that −1123G>C and +1858C>T PTPN22 polymorphisms are in strong linkage disequilibrium and the CT haplotype is a susceptibility marker to RA in Western Mexico. However, the PTPN22 haplotypes are not associated with anti-CCP antibodies.
PubDate: Sun, 22 Jan 2017 07:31:46 +000
- Module Anchored Network Inference: A Sequential Module-Based Approach to
Novel Gene Network Construction from Genomic Expression Data on Human
Abstract: Different computational approaches have been examined and compared for inferring network relationships from time-series genomic data on human disease mechanisms under the recent Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge. Many of these approaches infer all possible relationships among all candidate genes, often resulting in extremely crowded candidate network relationships with many more False Positives than True Positives. To overcome this limitation, we introduce a novel approach, Module Anchored Network Inference (MANI), that constructs networks by analyzing sequentially small adjacent building blocks (modules). Using MANI, we inferred a 7-gene adipogenesis network based on time-series gene expression data during adipocyte differentiation. MANI was also applied to infer two 10-gene networks based on time-course perturbation datasets from DREAM3 and DREAM4 challenges. MANI well inferred and distinguished serial, parallel, and time-dependent gene interactions and network cascades in these applications showing a superior performance to other in silico network inference techniques for discovering and reconstructing gene network relationships.
PubDate: Wed, 18 Jan 2017 00:00:00 +000
- Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid
Metabolism in Salvia miltiorrhiza, a Traditional Chinese Medicine Model
Abstract: Salvia miltiorrhiza Bunge is an important traditional Chinese medicine (TCM). In this study, two S. miltiorrhiza genotypes (BH18 and ZH23) with different phenolic acid concentrations were used for de novo RNA sequencing (RNA-seq). A total of 170,787 transcripts and 56,216 unigenes were obtained. There were 670 differentially expressed genes (DEGs) identified between BH18 and ZH23, 250 of which were upregulated in ZH23, with genes involved in the phenylpropanoid biosynthesis pathway being the most upregulated genes. Nine genes involved in the lignin biosynthesis pathway were upregulated in BH18 and thus result in higher lignin content in BH18. However, expression profiles of most genes involved in the core common upstream phenylpropanoid biosynthesis pathway were higher in ZH23 than that in BH18. These results indicated that genes involved in the core common upstream phenylpropanoid biosynthesis pathway might play an important role in downstream secondary metabolism and demonstrated that lignin biosynthesis was a putative partially competing pathway with phenolic acid biosynthesis. The results of this study expanded our understanding of the regulation of phenolic acid biosynthesis in S. miltiorrhiza.
PubDate: Tue, 17 Jan 2017 00:00:00 +000
- Development of a New Marker System for Identification of Spirodela
polyrhiza and Landoltia punctata
Abstract: Lemnaceae (commonly called duckweed) is an aquatic plant ideal for quantitative analysis in plant sciences. Several species of this family represent the smallest and fastest growing flowering plants. Different ecotypes of the same species vary in their biochemical and physiological properties. Thus, selecting of desirable ecotypes of a species is very important. Here, we developed a simple and rapid molecular identification system for Spirodela polyrhiza and Landoltia punctata based on the sequence polymorphism. First, several pairs of primers were designed and three markers were selected as good for identification. After PCR amplification, DNA fragments (the combination of three PCR products) in different duckweeds were detected using capillary electrophoresis. The high-resolution capillary electrophoresis displayed high identity to the sequencing results. The combination of the PCR products containing several DNA fragments highly improved the identification frequency. These results indicate that this method is not only good for interspecies identification but also ideal for intraspecies distinguishing. Meanwhile, 11 haplotypes were found in both the S. polyrhiza and L. punctata ecotypes. The results suggest that this marker system is useful for large-scale identification of duckweed and for the screening of desirable ecotypes to improve the diverse usage in duckweed utilization.
PubDate: Thu, 12 Jan 2017 00:00:00 +000
- Aspectual Fertility Variation and Its Effect on Gene Diversity of Seeds in
Natural Stands of Taurus Cedar (Cedrus libani A. Rich.)
Abstract: There are many environmental and biological factors on forestry practices as known. Aspect called as slope faces is one of the most important environmental factors in these practices because of its easy application for managers. Fertility variation defined as an individual ability to give progeny and gene diversity estimated based on effective number of parents were investigated as the proportion of numbers of cones counted from individuals in natural stands sampled aspectual of Taurus cedar (Cedrus libani A. Rich.) for three consecutive years. The averages of cone number were 19.4, 47.2, and 75.5 for the years. It was the highest in flat (23.5) for 2013, in south (92.1) for 2014, and in flat (95.7) for 2015, while it was lowest in south (16.3), in east (18.2), and in north (39.4) for the years, respectively. Significant correlations were estimated among years for cone production in polled aspect. Estimated fertility variations changed for the years and stands. It could be generally acceptable level for typical natural stands except of west of 2014. Fertility variations were 1.55, 3.05, and 1.64 in polled stands for the years. Gene diversity was 0.99 for the years in polled stands. North aspect could be taken into consideration in establishment and selection of seed sources and gene conservation areas based on fertility variation and gene diversity.
PubDate: Mon, 09 Jan 2017 00:00:00 +000
- Enriching Genomic Resources and Marker Development from Transcript
Sequences of Jatropha curcas for Microgravity Studies
Abstract: Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.
PubDate: Thu, 05 Jan 2017 00:00:00 +000
- Growth and Survival Variation among Scots Pine (Pinus sylvestris L.)
Abstract: Tree height, basal diameter, and survival were examined in thirteen-year-old provenance test established by 30 seed sources of Scots pine (Pinus sylvestris L.) at two exotic sites of the species in Southern part of Turkey. Variations within provenance and among provenances and relations among the traits were estimated to compare Scots pine provenance and two other native species. Averages of tree height and basal diameter were 350 cm and 52.7 mm in Aydogmus site and 385 cm and 51.2 mm in Kemer site, respectively. There were large differences within and among provenances for the characters. Sites were similar () for the characters, while there were significant differences () among provenances within site according to results of variance analysis (ANOVA). Scots pine provenances were higher and had more thickness than that of black pine (Pinus nigra Arnold) and Taurus cedar (Cedrus libani A. Rich.) which were natural species of the region. There were positive and significant () correlations between height and basal diameter in the species. Average survivals were 56% and 35% of the provenances in the sites. They were 71% and 11% in black pine and 53% in Taurus cedar for the sites respectively.
PubDate: Wed, 04 Jan 2017 08:38:02 +000
- Characterization and Expression Analysis of Common Bean Histone
Deacetylase 6 during Development and Cold Stress Response
Abstract: Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants, HDA6 is yet to be validated in common bean. In this study, we show that HDA6 is involved in plant development and stress response. Differential expression of HDA6 was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root. Upregulation of HDA6 gene during cold stress implies its prominent role in abiotic stress. Furthermore, the HDA6 gene was isolated from three common bean genotypes and sequence analyses revealed homology with functionally characterized homologs in model species. The 53 kDa translated product was detected using an HDA6 specific antibody and recombinant protein overexpressed in Escherichia coli showed HDAC activity in vitro. To our knowledge, this is the first report in the agriculturally important crop common bean describing the functional characterization and biological role of HDA6.
PubDate: Tue, 03 Jan 2017 11:07:47 +000
- Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing
Sequence Intrinsic Composition and Open Reading Frame Information
Abstract: More and more studies have demonstrated that long noncoding RNAs (lncRNAs) play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification). The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.
PubDate: Tue, 27 Dec 2016 13:27:00 +000
- Detection of QTLs for Yield Heterosis in Rice Using a RIL Population and
Its Testcross Population
Abstract: Analysis of the genetic basis of yield heterosis in rice was conducted by quantitative trait locus mapping using a set of 204 recombinant inbred lines (RILs), its testcross population, and mid-parent heterosis dataset (). A total of 39 QTLs for six yield traits were detected, of which three were detected in all the datasets, ten were common to the RIL and testcross populations, six were common to the testcross and , and 17, 2, and 1 were detected for RILs, testcrosses, and , respectively. When a QTL was detected in both the RIL and testcross populations, the difference between TQ and IR24 and that between Zh9A/TQ and Zh9A/IR24 were always in the same direction, providing the potential to increase the yield of hybrids by increasing the yield of parental lines. Genetic action mode of the 39 QTLs was inferred by comparing their performances in RILs, testcrosses, and . The genetic modes were additive for 17 QTLs, dominance for 12 QTLs, and overdominance for 10 QTLs. These results suggest that dominance and overdominance are the most important contributor to yield heterosis in rice, in which the accumulative effects of yield components play an important role.
PubDate: Thu, 22 Dec 2016 13:28:27 +000
- The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding
Abstract: Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN) based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding.
PubDate: Tue, 20 Dec 2016 06:43:07 +000
- Identification of Alternative Variants and Insertion of the Novel
Polymorphic AluYl17 in TSEN54 Gene during Primate Evolution
Abstract: TSEN54 encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified an AluSx-derived alternative transcript in TSEN54 of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR) amplification and TSEN54 sequence analysis of primate and human samples identified five novel alternative transcripts, including the AluSx exonized transcript. Additionally, we performed comparative expression analysis via RT-qPCR in various cynomolgus, rhesus monkey, and human tissues. RT-qPCR amplification revealed differential expression patterns. Furthermore, genomic PCR amplification and sequencing of primate and human DNA samples revealed that AluSx elements were integrated in human and all of the primate samples tested. Intriguingly, in langur genomic DNA, an additional AluY element was inserted into AluSx of intron eight of TSEN54. The new AluY element showed polymorphic insertion. Using standardized nomenclature for Alu repeats, the polymorphic AluY of the langur TSEN54 was designated as being of the AluYl17 subfamily. Our results suggest that integration of the AluSx element in TSEN54 contributed to diversity in transcripts and induced lineage- or species-specific evolutionary events such as alternative splicing and polymorphic insertion during primate evolution.
PubDate: Mon, 19 Dec 2016 12:33:06 +000
- Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on
Anthocyanin Biosynthesis during Strawberry Fruit Ripening
Abstract: Anthocyanin in strawberries has a positive effect on fruit coloration. In this study, the role of exogenous hematin on anthocyanin biosynthesis was investigated. Our result showed that the white stage of strawberries treated with exogenous hematin had higher anthocyanin content, compared to the control group. Among all treatments, 5 μM of hematin was the optimal condition to promote color development. In order to explore the molecular mechanism of fruit coloring regulated by hematin, transcriptomes in the hematin- and non-hematin-treated fruit were analyzed. A large number of differentially expressed genes (DEGs) were identified in regulating anthocyanin synthesis, including the DEGs involved in anthocyanin biosynthesis, hormone signaling transduction, phytochrome signaling, starch and sucrose degradation, and transcriptional pathways. These regulatory networks may play an important role in regulating the color process of strawberries treated with hematin. In summary, exogenous hematin could promote fruit coloring by increasing anthocyanin content in the white stage of strawberries. Furthermore, transcriptome analysis suggests that hematin-promoted fruit coloring occurs through multiple related metabolic pathways, which provides valuable information for regulating fruit color via anthocyanin biosynthesis in strawberries.
PubDate: Thu, 15 Dec 2016 13:59:23 +000
- Gene Expression Analysis of Alfalfa Seedlings Response to Acid-Aluminum
Abstract: Acid-Aluminum (Al) is toxic to plants and greatly affects crop production worldwide. To understand the responses of plants to acid soils and Aluminum toxicity, we examined global gene expression using microarray data in alfalfa seedlings with the treatment of acid-Aluminum. 3,926 genes that were identified significantly up- or downregulated in response to Al3+ ions with pH 4.5 treatment, 66.33% of which were found in roots. Their functional categories were mainly involved with phytohormone regulation, reactive oxygen species, and transporters. Both gene ontology (GO) enrichment and KEGG analysis indicated that phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis played a critical role on defense to Aluminum stress in alfalfa. In addition, we found that transcription factors such as the MYB and WRKY family proteins may be also involved in the regulation of reactive oxygen species reactions and flavonoid biosynthesis. Thus, the finding of global gene expression profile provided insights into the mechanisms of plant defense to acid-Al stress in alfalfa. Understanding the key regulatory genes and pathways would be advantageous for improving crop production not only in alfalfa but also in other crops under acid-Aluminum stress.
PubDate: Thu, 15 Dec 2016 12:11:57 +000
- Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and
Enzymes Involved in Triterpenoid Biosynthesis
Abstract: G. pentaphyllum (Gynostemma pentaphyllum), a creeping herbaceous perennial with many important medicinal properties, is widely distributed in Asia. Gypenosides (triterpenoid saponins), the main effective components of G. pentaphyllum, are well studied. FPS (farnesyl pyrophosphate synthase), SS (squalene synthase), and SE (squalene epoxidase) are the main enzymes involved in the synthesis of triterpenoid saponins. Considering the important medicinal functions of G. pentaphyllum, it is necessary to investigate the transcriptomic information of G. pentaphyllum to facilitate future studies of transcriptional regulation. After sequencing G. pentaphyllum, we obtained 50,654,708 unigenes. Next, we used RPKM (reads per kilobases per million reads) to calculate expression of the unigenes and we performed comparison of our data to that contained in five common databases to annotate different aspects of the unigenes. Finally, we noticed that FPS, SS, and SE showed differential expression of enzymes in DESeq. Leaves showed the highest expression of FPS, SS, and SE relative to the other two tissues. Our research provides transcriptomic information of G. pentaphyllum in its natural environment and we found consistency in unigene expression, enzymes expression (FPS, SS, and SE), and the distribution of gypenosides content in G. pentaphyllum. Our results will enable future related studies of G. pentaphyllum.
PubDate: Wed, 14 Dec 2016 14:47:49 +000