Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas

BACKGROUND: Temporal and spatial expression of fatty acid and lipid biosynthetic genes are associated with the accumulation of storage lipids in the seeds of oil plants. In jatropha (Jatropha curcas L.), a potential biofuel plant, the storage lipids are mainly synthesized and accumulated in the endosperm of seeds. Although the fatty acid and lipid biosynthetic genes in jatropha have been identified, the expression of these genes at different developing stages of endosperm has not been systemically investigated. RESULTS: Transmission electron microscopy study revealed that the oil body formation in developing endosperm of jatropha seeds initially appeared at 28 days after fertilization (DAF), was actively developed at 42 DAF and reached to the maximum number and size at 56 DAF. Sixty-eight genes that encode enzymes, proteins or their subunits involved in fatty acid and lipid biosynthesis were identified from a normalized cDNA library of jatropha developing endosperm. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the 68 genes could be collectively grouped into five categories based on the patterns of relative expression of the genes during endosperm development. Category I has 47 genes and they displayed a bell-shaped expression pattern with the peak expression at 28 or 42 DAF, but low expression at 14 and 56 DAF. Category II contains 8 genes and expression of the 8 genes was constantly increased from 14 to 56 DAF. Category III comprises of 2 genes and both genes were constitutively expressed throughout endosperm development. Category IV has 9 genes and they showed a high expression at 14 and 28 DAF, but a decreased expression from 42 to 56 DAF. Category V consists of 2 genes and both genes showed a medium expression at 14 DAF, the lowest expression at 28 or 42 DAF, and the highest expression at 56 DAF. In addition, genes encoding enzymes or proteins with similar function were differentially expressed during endosperm development. CONCLUSION: The formation of oil bodies in jatropha endosperm is developmentally regulated. The expression of the majority of fatty acid and lipid biosynthetic genes is highly consistent with the development of oil bodies and endosperm in jatropha seeds, while the genes encoding enzymes with similar function may be differentially expressed during endosperm development. These results not only provide the initial information on spatial and temporal expression of fatty acid and lipid biosynthetic genes in jatropha developing endosperm, but are also valuable to identify the rate-limiting genes for storage lipid biosynthesis and accumulation during seed development

An improved method for RNA isolation and cDNA library construction from immature seeds of Jatropha curcas L

<p>Abstract</p> <p>Background</p> <p>RNA quality and quantity is sometimes unsuitable for cDNA library construction, from plant seeds rich in oil, polysaccharides and other secondary metabolites. Seeds of jatropha (<it>Jatropha curcas </it>L.) are rich in fatty acids/lipids, storage proteins, polysaccharides, and a number of other secondary metabolites that could either bind and/or co-precipitate with RNA, making it unsuitable for downstream applications. Existing RNA isolation methods and commercial kits often fail to deliver high-quality total RNA from immature jatropha seeds for poly(A)⁺RNA purification and cDNA synthesis.</p> <p>Findings</p> <p>A protocol has been developed for isolating good quality total RNA from immature jatropha seeds, whereby a combination of the CTAB based RNA extraction method and a silica column of a commercial plant RNA extraction kit is used. The extraction time was reduced from two days to about 3 hours and the RNA was suitable for poly(A)⁺RNA purification, cDNA synthesis, cDNA library construction, RT-PCR, and Northern hybridization. Based on sequence information from selected clones and amplified PCR product, the cDNA library seems to be a good source of full-length jatropha genes. The method was equally effective for isolating RNA from mustard and rice seeds.</p> <p>Conclusions</p> <p>This is a simple CTAB + silica column method to extract high quality RNA from oil rich immature jatropha seeds that is suitable for several downstream applications. This method takes less time for RNA extraction and is equally effective for other tissues where the quality and quantity of RNA is highly interfered by the presence of fatty acids, polysaccharides and polyphenols.</p

Multi-disease transcriptomic analysis of sex hormone genes reveals a novel prognostic model for thyroid cancer with breast cancer correlations

BackgroundThere is a potential bidirectional pathogenicity between thyroid and breast cancers. The association between sex hormones and two types of malignant tumors has emerged as a topic of intense academic debate in recent years. However, the role of sex hormone metabolism-related genes in thyroid cancer still needs to be further explored.MethodsWe obtained thyroid and breast cancer transcriptome data from the TCGA database and sex hormone metabolism-related gene sets from the MSigDB database, thus screening for sex hormone metabolism-related genes linked to the two malignant tumors. Univariate cox regression analysis was used for the screening of disease-free survival (DFS)-associated genes. The TCGA-THCA patients were classified as two categories via a consistent clustering algorithm, and the differential genes between the two categories were subsequently screened. A sex hormone metabolism-related prognostic model (TBSMRPM) of thyroid cancer versus breast cancer consisting of 10 genes was developed by Cox regression analyses and least absolute shrinkage with selection operator (LASSO) cox regression analysis. Finally, we performed clinicopathological subgroup analyses to analyze the correlation between TBSMRPM and clinical characteristics, immune infiltration, tumor mutation burden (TMB), and chemosensitivity, and verified the expression of TBSMRPM signature genes by qRT-PCR.ResultsWe identified 2 clusters correlated with sex hormone metabolism, and screened 10 prognostic differential genes related to thyroid cancer, breast cancer and sex hormone metabolism. After establishing the two risk groups for thyroid cancer originated from TBSMRPM, the results showed that the high-risk group exhibited the shorter DFS (P&lt;0.05). In further clinical stratification analysis, immune infiltration analysis, TMB and drug sensitivity analysis, the two TBSMRPM groups showed significant differences. The qRT-PCR results showed that C2CD4A, CERS1, MMP9, SLC5A1, HORMAD2 were highly expressed in the IHH4, KTC-1, and TPC-1 cell lines, while SLITRK2, ARHGEF37, PLP1, RNF223, and F3 were lowly expressed.ConclusionThe TBSMRPM established in this study has a certain value for the prognosis of thyroid cancer and contributes to refine clinicians’ treatment protocols

US News and Social Media Framing around Vaping

In this paper, we investigate how vaping is framed differently (2008-2021) between US news and social media. We analyze 15,711 news articles and 1,231,379 Facebook posts about vaping to study the differences in framing between media varieties. We use word embeddings to provide two-dimensional visualizations of the semantic changes around vaping for news and for social media. We detail that news media framing of vaping shifted over time in line with emergent regulatory trends, such as; flavored vaping bans, with little discussion around vaping as a smoking cessation tool. We found that social media discussions were far more varied, with transitions toward vaping both as a public health harm and as a smoking cessation tool. Our cloze test, dynamic topic model, and question answering showed similar patterns, where social media, but not news media, characterizes vaping as combustible cigarette substitute. We use n-grams to detail that social media data first centered on vaping as a smoking cessation tool, and in 2019 moved toward narratives around vaping regulation, similar to news media frames. Overall, social media tracks the evolution of vaping as a social practice, while news media reflects more risk based concerns. A strength of our work is how the different techniques we have applied validate each other. Stakeholders may utilize our findings to intervene around the framing of vaping, and may design communications campaigns that improve the way society sees vaping, thus possibly aiding smoking cessation; and reducing youth vaping

GPR30 decreases with vascular aging and promotes vascular smooth muscle cells maintaining differentiated phenotype and suppressing migration via activation of ERK1/2

Estrogen receptors, including classic nuclear receptors ERα, ERβ, and membrane receptor GPR30, are expressed in vascular tissues and exert protective actions in vascular diseases. But the expression pattern and functional roles of GPR30 in vascular smooth muscle cells (VSMCs) remain unclear. In this study, we found that ERα, ERβ, and GPR30 were decreased with VSMCs passaging in vitro or growing in vivo and activation of GPR30 promoted ERα expression. Then, we validated that activation of GPR30 significantly decreased migratory capability of VSMCs and suppressed ERα, whereas PDGF-BB (20 ng/mL) treatment caused increase of migration. And activation of GPR30 led to reduction of osteopontin and cellular retinol binding protein 1, enhancement of calponin and 3F8, and upregulation of total and phosphorylated ERK1/2 expression in VSMCs knocked down by GPR30, ERα, and ERβ or treated with PDGF-BB. These data suggest that GPR30 promotes VSMCs reducing migration and maintaining differentiated phenotype via activation of ERK1/2 pathway. Our findings provide novel mechanisms of GPR30 protection of VSMCs as well as a new target for prevention of vascular aging

A First Generation Microsatellite- and SNP-Based Linkage Map of Jatropha

Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation

Critical current density: Measurements vs. reality

Different experimental techniques are employed to evaluate the critical current density (Jc), namely transport current measurements and two different magnetisation measurements forming quasi-equilibrium and dynamic critical states. Our technique-dependent results for superconducting YBa 2Cu3O7 (YBCO) film and MgB2 bulk samples show an extremely high sensitivity of Jc and associated interpretations, such as irreversibility fields and Kramer plots, which lose meaning without a universal approach. We propose such approach for YBCO films based on their unique pinning features. This approach allows us to accurately recalculate the magnetic-field-dependent Jc obtained by any technique into the Jc behaviour, which would have been measured by any other method without performing the corresponding experiments. We also discovered low-frequency-dependent phenomena, governing flux dynamics, but contradicting the considered ones in the literature. The understanding of these phenomena, relevant to applications with moving superconductors, can clarify their dramatic impact on the electric-field criterion through flux diffusivity and corresponding measurements. © Copyright EPLA, 2013