De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis

<p>Abstract</p> <p>Background</p> <p>American ginseng (<it>Panax quinquefolius </it>L.) is one of the most widely used herbal remedies in the world. Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway.</p> <p>Results</p> <p>In this study, a one-quarter 454 sequencing run produced 209,747 high-quality reads with an average sequence length of 427 bases. <it>De novo </it>assembly generated 31,088 unique sequences containing 16,592 contigs and 14,496 singletons. About 93.1% of the high-quality reads were assembled into contigs with an average 8-fold coverage. A total of 21,684 (69.8%) unique sequences were annotated by a BLAST similarity search against four public sequence databases, and 4,097 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Based on the bioinformatic analysis described above, we found all of the known enzymes involved in ginsenoside backbone synthesis, starting from acetyl-CoA via the isoprenoid pathway. Additionally, a total of 150 cytochrome P450 (CYP450) and 235 glycosyltransferase unique sequences were found in the 454 cDNA library, some of which encode enzymes responsible for the conversion of the ginsenoside backbone into the various ginsenosides. Finally, one CYP450 and four UDP-glycosyltransferases were selected as the candidates most likely to be involved in ginsenoside biosynthesis through a methyl jasmonate (MeJA) inducibility experiment and tissue-specific expression pattern analysis based on a real-time PCR assay.</p> <p>Conclusions</p> <p>We demonstrated, with the assistance of the MeJA inducibility experiment and tissue-specific expression pattern analysis, that transcriptome analysis based on 454 pyrosequencing is a powerful tool for determining the genes encoding enzymes responsible for the biosynthesis of secondary metabolites in non-model plants. Additionally, the expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community that is interested in the molecular genetics and functional genomics of American ginseng.</p

Issue of spatial coherence in MQW based micro-LED simulation

In existing flip-chip LED simulations, the light extraction efficiency is related to the multiple quantum well (MQW) to metal reflector distance because of optical interference. We calculate the contrast using several typical light intensity distributions among the several QWs in MQW. The coherence is obtained analytically. When the luminosity of each QW is equal, the contrast is ∼0, meaning the light is incoherent, contrary to traditional studies. The spatial coherence is important only when the light emission comes from just one QW. As the MQW has a not negligible thickness, the traditional single-dipole model is no longer accurate

Scale effect of circularly polarized luminescent signal of matter

Circularly polarized luminescence (CPL) is an important part in the research of modern luminescent materials and photoelectric devices. Usually, chiral molecules or chiral structures are the key factors to induce CPL spontaneous emission. In this study, a scale-effect model based on scalar theory was proposed to better understand the CPL signal of luminescent materials. Besides chiral structures being able to induce CPL, achiral ordered structures can also have a significant influence on CPL signals. These achiral structures are mainly reflected in the particle scale in micro-order or macro-order, i.e. the CPL signal measured under most conditions depends on the scale of the ordered medium, and does not reflect the inherent chirality of the excited state of the luminescent molecule. This kind of influence is difficult to be eliminated by simple and universal strategies in macro-measurement. At the same time, it is found that the measurement entropy of CPL detection may be the key factor to determine the isotropy and anisotropy of the CPL signal. This discovery would bring new opportunities to the research of chiral luminescent materials. This strategy can also greatly reduce the development difficulty of CPL materials and show high application potential in biomedical, photoelectric information and other fields.</p

Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers

<p>Abstract</p> <p>Background</p> <p><it>Panax notoginseng </it>(Burk) F.H. Chen is important medicinal plant of the <it>Araliacease </it>family. Triterpene saponins are the bioactive constituents in <it>P. notoginseng</it>. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the <it>Panax </it>species are largely unknown.</p> <p>Results</p> <p>Using the 454 pyrosequencing technology, a one-quarter GS FLX titanium run resulted in 188,185 reads with an average length of 410 bases for <it>P. notoginseng </it>root. These reads were processed and assembled by 454 GS <it>De Novo </it>Assembler software into 30,852 unique sequences. A total of 70.2% of unique sequences were annotated by Basic Local Alignment Search Tool (BLAST) similarity searches against public sequence databases. The Kyoto Encyclopedia of Genes and Genomes (KEGG) assignment discovered 41 unique sequences representing 11 genes involved in triterpene saponin backbone biosynthesis in the 454-EST dataset. In particular, the transcript encoding dammarenediol synthase (DS), which is the first committed enzyme in the biosynthetic pathway of major triterpene saponins, is highly expressed in the root of four-year-old <it>P. notoginseng</it>. It is worth emphasizing that the candidate cytochrome P450 (Pn02132 and Pn00158) and UDP-glycosyltransferase (Pn00082) gene most likely to be involved in hydroxylation or glycosylation of aglycones for triterpene saponin biosynthesis were discovered from 174 cytochrome P450s and 242 glycosyltransferases by phylogenetic analysis, respectively. Putative transcription factors were detected in 906 unique sequences, including Myb, homeobox, WRKY, basic helix-loop-helix (bHLH), and other family proteins. Additionally, a total of 2,772 simple sequence repeat (SSR) were identified from 2,361 unique sequences, of which, di-nucleotide motifs were the most abundant motif.</p> <p>Conclusion</p> <p>This study is the first to present a large-scale EST dataset for <it>P. notoginseng </it>root acquired by next-generation sequencing (NGS) technology. The candidate genes involved in triterpene saponin biosynthesis, including the putative CYP450s and UGTs, were obtained in this study. Additionally, the identification of SSRs provided plenty of genetic makers for molecular breeding and genetics applications in this species. These data will provide information on gene discovery, transcriptional regulation and marker-assisted selection for <it>P. notoginseng</it>. The dataset establishes an important foundation for the study with the purpose of ensuring adequate drug resources for this species.</p

Detection of copy number variations and their effects in Chinese bulls

BACKGROUND: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. RESULTS: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. CONCLUSIONS: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users

Bidirectional associations between hearing difficulty and cognitive function in Chinese adults: a longitudinal study

BackgroundMiddle-aged and older adults frequently experience hearing loss and a decline in cognitive function. Although an association between hearing difficulty and cognitive function has been demonstrated, its temporal sequence remains unclear. Therefore, we investigated whether there are bidirectional relationships between hearing difficulty and cognitive function and explored the mediating role of depressive symptoms in this relationship.MethodWe used the cross-lagged panel model and the random-intercept cross-lagged panel model to look for any possible two-way link between self-reported hearing difficulty and cognitive function. To investigate depressive symptoms’ role in this association, a mediation analysis was conducted. The sample was made up of 4,363 adults aged 45 and above from the China Health and Retirement Longitudinal Study (CHARLS; 2011–2018; 44.83% were women; mean age was 56.16 years). One question was used to determine whether someone had a hearing impairment. The tests of cognitive function included episodic memory and intelligence. The Center for Epidemiologic Studies Depression Scale, which consists of 10 items, was used to measure depressive symptoms.ResultsA bidirectional association between hearing and cognition was observed, with cognition predominating (Wald χ2 (1) = 7.241, p &lt; 0.01). At the between-person level, after controlling for potential confounders, worse hearing in 2011 predicted worse cognitive function in 2013 (β = −0.039, p &lt; 0.01) and vice versa (β = −0.041, p &lt; 0.01) at the between-person level. Additionally, there was no corresponding cross-lagged effect of cognitive function on hearing difficulty; rather, the more hearing difficulty, the greater the cognitive decline at the within-person level. According to the cross-lagged mediation model, depressive symptoms partially mediates the impact of cognitive function on subsequent hearing difficulty (indirect effect: −0.003, bootstrap 95% confidence interval: −0.005, −0.001, p &lt; 0.05), but not the other way around.ConclusionThese results showed that within-person relationships between hearing impairment and cognitive function were unidirectional, while between-person relationships were reciprocal. Setting mental health first may be able to break the vicious cycle that relates hearing loss to cognitive decline. Comprehensive long-term care requires services that address depressive symptoms and cognitive decline to be integrated with the hearing management

Impact of the COVID-19 lockdown on air pollution in an industrial city in Northeastern China

Many studies in China investigated how the lockdown following the coronavirus disease 2019 substantially affected air quality; however, few were conducted in Northeastern China. Here, the changes in six criteria air pollutants, including particulate matter (PM10 and PM2.5), nitrogen dioxide (NO2), carbon monoxide (CO), sulfur dioxide (SO2), and ozone (O3), were investigated in Shenyang from January to May 2015–2020. Compared with the pre-lockdown, the mass concentrations of PM2.5, PM10, SO2, NO2, and CO during the lockdown decreased by 40.3% to 48.6%, indicating a positive impact of lockdown policies on reducing pollutant emissions. The responses of PM2.5, PM10, and CO to the lockdown measures in downtown areas were more sensitive than in the suburbs. However, the O3 concentration showed the opposite trend, attributed to the drop in NOx and particulate matters. Compared to the same period in 2015–2019, the proportion of days with good air quality increased from 63.2% to 77.2% during the lockdown and Shenyang experienced no severe pollution. Our results suggest that reducing human activities can improve air quality; however, coordinated control policies of O3, PM2.5, and NO2 are imperative.

Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

BACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2)regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.Jingyuan Song, Linchun Shi, Dezhu Li, Yongzhen Sun, Yunyun Niu, Zhiduan Chen, Hongmei Luo, Xiaohui Pang, Zhiying Sun, Chang Liu, Aiping Lv, Youping Deng, Zachary Larson-Rabin, Mike Wilkinson and Shilin Che