Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18–25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the ...biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA–target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA–target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.
Metabolomics offers a noninvasive methodology to identify metabolic markers for pathogenesis and diagnosis of diseases. This work aimed to characterize circulating metabolic signatures of benign ...thyroid nodule (BTN) and papillary thyroid carcinoma (PTC) via serum‐plasma matched metabolomics. A cohort of 1,540 serum‐plasma matched samples and 114 tissues were obtained from healthy volunteers, BTN and PTC patients enrolled from 6 independent centers. Untargeted metabolomics was determined by liquid chromatography‐quadrupole time‐of‐flight mass spectrometric and multivariate statistical analyses. The use of serum‐plasma matched samples afforded a broad‐scope detection of 1,570 metabolic features. Metabolic phenotypes revealed significant pattern differences for healthy versus BTN and healthy versus PTC. Perturbed metabolic pathways related mainly to amino acid and lipid metabolism. It is worth noting that, BTN and PTC showed no significant differences but rather overlap in circulating metabolic signatures, and this observation was replicated in all study centers. For differential diagnosis of healthy versus thyroid nodules (BTN + PTC), a panel of 6 metabolic markers, namely myo‐inositol, α‐N‐phenylacetyl‐L‐glutamine, proline betaine, L‐glutamic acid, LysoPC(18:0) and LysoPC(18:1) provided area under the curve of 97.68% in the discovery phase and predictive accuracies of 84.78–98.18% in the 4 validation centers. Taken together, serum‐plasma matched metabolomics showed significant differences in circulating metabolites for healthy versus nodules but not for BTN versus PTC. Our results highlight the true metabolic nature of thyroid nodules, and potentially decrease overtreatment that exposes patients to unnecessary risks.
What's new?
When thyroid nodules are classified “indeterminate,” is it better to wait and see, or take out the thyroid? Usually, doctors remove the thyroid, resulting in a lifetime of levothyroxine replacement, yet most often the nodules are not cancerous. Here, the authors investigated whether metabolic profile could give a more accurate prediction of whether a thyroid nodule is cancerous. They tested healthy patients, those with benign nodules, and those with papillary thyroid carcinoma. Healthy patients showed distinct differences from those with benign nodules and those with carcinomas, while significant overlap was observed between circulating metabolites from BTN and PTC patients.
The aim of the present study was to determine the effect of the long non‑coding RNA (lncRNA) bladder cancer‑associated transcript 1 (BLACAT1) in chemoresistance of non‑small cell lung cancer (NSCLC) ...cells. Expression of lncRNA BLACAT1, microRNA (miR)‑17, autophagy‑related protein 7 (ATG7), multidrug‑resistance protein 1 (MRP1), and the autophagy‑associated proteins light chain 3 (LC3)‑II/LC3‑I and Beclin 1 were detected using the reverse transcription‑quantitative polymerase chain reaction and western blot analysis. Cell viability was determined using an MTT assay. The interaction between BLACAT1 and miR‑17 was determined using RNA immunoprecipitation and RNA pull‑down assays. A cisplatin (DDP)‑resistant NSCLC cell A549/DDP xenograft model in nude mice was established to investigate the effect of BLACAT1 on the chemoresistance of NSCLC cells. Compared with in DDP‑sensitive NSCLC cells, expression of BLACAT1, ATG7, MRP1, LC3‑II/LC3‑I and Beclin 1 was significantly upregulated in DDP‑resistant NSCLC cells, whereas miR‑17 was downregulated in DDP‑resistant NSCLC cells. Short interfering RNA against BLACAT1 decreased the viability of DDP‑resistant NSCLC cells. In addition, BLACAT1 interacted with miR‑17, and negatively regulated miR‑17. BLACAT1 promoted ATG7 expression through miR‑17, and facilitated autophagy and promoted chemoresistance of NSCLC cells through miR‑17/ATG7. Finally, in vivo experiments indicated that inhibition of BLACAT1 ameliorated the chemoresistance of NSCLC. BLACAT1 was upregulated in DDP‑resistant NSCLC cells, and promoted autophagy and chemoresistance of NSCLC cells through the miR‑17/ATG7 signaling pathway.
•R. toruloides can use 4–20g/L acetic acid to produce lipids.•Sequencing batch process was developed for lipid production using low-content VFAs.•Different performances were found between media ...containing acetic acid and glucose.•The C/N affects acetic acid utilization ratio and lipid content simultaneously.
Rhodosporidium toruloides AS 2.1389 was tested using different concentrations of acetic acid as a low-cost carbon source for the production of microbial lipids, which are good raw materials for biodiesel production. It grew and had higher lipid contents in media containing 4–20g/L acetic acid as the sole carbon source, compared with that in glucose-containing media under the same culture conditions. At acetic acid concentrations as high as 20g/L and the optimal carbon-to-nitrogen ratio (C/N) of 200 in a batch culture, the highest biomass production was 4.35g/L, with a lipid content of 48.2%. At acetic acid concentrations as low as 4g/L, a sequencing batch culture (SBC) with a C/N of 100 increased biomass production to 4.21g/L, with a lipid content of 38.6%. These results provide usable culture strategies for lipid production by R. toruloides AS 2.1389 when using diverse waste-derived volatile fatty acids.
Abstract
Background
Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target ...interaction of Cas9-sgRNA determines its target binding affinity and modulates its post-cleavage target residence duration and exposure of Cas9-induced DSBs. This exposure, via different mechanisms, may initiate variable DNA damage responses, influencing DSB repair pathway choices and contributing to mutational heterogeneity in genome editing. However, this regulation of DSB repair pathway choices is poorly understood.
Results
In repair of Cas9-induced DSBs, repair pathway choices vary widely at different target sites and classical nonhomologous end joining (c-NHEJ) is not even engaged at some sites. In mouse embryonic stem cells, weakening the target interaction of Cas9-sgRNA promotes bias towards c-NHEJ and increases target dissociation and reduces target residence of Cas9-sgRNAs in vitro. As an important strategy for enhancing homology-directed repair, inactivation of c-NHEJ aggravates off-target activities of Cas9-sgRNA due to its weak interaction with off-target sites. By dislodging Cas9-sgRNA from its cleaved targets, DNA replication alters DSB end configurations and suppresses c-NHEJ in favor of other repair pathways, whereas transcription has little effect on c-NHEJ engagement. Dissociation of Cas9-sgRNA from its cleaved target by DNA replication may generate three-ended DSBs, resulting in palindromic fusion of sister chromatids, a potential source for CRISPR/Cas9-induced on-target chromosomal rearrangements.
Conclusions
Target residence of Cas9-sgRNA modulates DSB repair pathway choices likely through varying dissociation of Cas9-sgRNA from cleaved DNA, thus widening on-target and off-target mutational spectra in CRISPR/Cas9 genome editing.
•Highest lipid was accumulated when mixed VFAs were used.•The lipid produced from mixed VFAs was higher than that from the sole acetic acid.•Both propionic and butyric acids can improve the ...odd-numbered fatty acid content.•The highest odd-numbered FAs yield was achieved when the VFA ratio was 5:15:10.
The oleaginous yeast Cryptococcus curvatus ATCC 20509 can use 5–40g/L of acetic, propionic, or butyric acid as sole carbon source to produce lipids. High concentrations (30g/L) of mixed volatile fatty acids (VFAs) were used to cultivate C. curvatus to explore the effects of different ratios of mixed VFAs on lipid production and composition. When mixed VFAs (VFA ratio was 15:5:10) were used as carbon sources, the highest cell mass and lipid concentration were 8.68g/L and 4.93g/L, respectively, which were significantly higher than those when 30g/L of acetic acid was used as sole carbon source. The highest content and yield of odd-numbered fatty acids were 45.1% (VFA ratio was 0:15:15) and 1.62g/L (VFA ratio was 5:15:10), respectively. These results indicate that adjusting the composition ratios of mixed VFAs effectively improves microbial lipid synthesis and the yield of odd-numbered fatty acids.
Background
Myocardial ischemia–reperfusion injury (MIRI) caused by the reperfusion therapy of myocardial ischemic diseases is a kind of major disease that threatens human health and lives severely. ...There are lacking of effective therapeutic measures for MIRI. MicroRNAs (miRNAs) are abundant in mammalian species and play a critical role in the initiation, promotion, and progression of MIRI. However, the biological role and molecular mechanism of miRNAs in MIRI are not entirely clear.
Methods
We used bioinformatics analysis to uncover the significantly different miRNA by analyzing transcriptome sequencing data from myocardial tissue in the mouse MIRI model. Multiple miRNA‐related databases, including miRdb, PicTar, and TargetScan were used to forecast the downstream target genes of the differentially expressed miRNA. Then, the experimental models, including male C57BL/6J mice and HL‐1 cell line, were used for subsequent experiments including quantitative real‐time polymerase chain reaction analysis, western blot analysis, hematoxylin and eosin staining, flow cytometry, luciferase assay, gene interference, and overexpression.
Results
MiR‐582‐5p was found to be differentially upregulated from the transcriptome sequencing data. The elevated levels of miR‐582‐5p were verified in MIRI mice and hypoxia/reperfusion (H/R)‐induced HL‐1 cells. Functional experiments revealed that miR‐582‐5p promoted apoptosis of H/R‐induced HL‐1 cells via downregulating cAMP‐response element‐binding protein 1 (Creb1). The inhibiting action of miR‐582‐5p inhibitor on H/R‐induced apoptosis was partially reversed after Creb1 interference.
Conclusions
Collectively, the research findings reported that upregulation of miR‐582‐5p promoted H/R‐induced cardiomyocyte apoptosis by inhibiting Creb1. The potential diagnostic and therapeutic strategies targeting miR‐582‐5p and Creb1 could be beneficial for the MIRI treatment.
We used bioinformatics analysis to find significantly different microRNA (miRNA) by analyzing transcriptome sequencing data from myocardial tissue in the mouse myocardial ischemia–reperfusion injury (MIRI) model. Multiple miRNA‐related databases (miRdb, PicTar, and TargetScan) were used to predict the downstream target genes of miRNA. Finally, we demonstrated that upregulation of miR‐582‐5p promotes apoptosis induced by hypoxia/reperfusion (H/R) in HL‐1 cells by inhibiting cAMP‐response element‐binding protein 1 (Creb1). Therapeutic strategies that target miR‐582‐5p and Creb1 could be beneficial for the treatment of ischemia/reperfusion injury after acute myocardial infarction.
Despite many decades of research of diodes, which are fundamental components of electronic and photoelectronic devices with p–n or Schottky junctions using bulk or 2D materials, stereotyped ...architectures and complex technological processing (doping and multiple material operations) have limited future development. Here, a novel rectification device, an orientation‐induced diode, assembled using only few‐layered black phosphorus (BP) is investigated. The key to its realization is to utilize the remarkable anisotropy of BP in low dimensions and change the charge‐transport conditions abruptly along the different crystal orientations. Rectification ratios of 6.8, 22, and 115 can be achieved in cruciform BP, cross‐stacked BP junctions, and BP junctions stacked with vertical orientations, respectively. The underlying physical processes and mechanisms can be explained using “orientation barrier” band theory. The theoretical results are experimentally confirmed using localized scanning photocurrent imaging. These orientation‐induced optoelectronic devices open possibilities for 2D anisotropic materials with a new degree of freedom to improve modulation in diodes.
Orientation‐induced diodes assembled using only few‐layered black phosphorus (BP) materials are developed as novel rectification devices. The key to its realization is to utilize the remarkable anisotropy of BP in low dimensions and change the charge‐transport conditions abruptly along the different crystal orientations. These devices can open possibilities for two‐dimensional anisotropic materials to improve modulation in diodes.
Display omitted
•Four pilot-scale CWs differing in plant species and planting patterns were compared.•Nutrients, antibiotics and ARGs in aquaculture wastewater were efficiently removed.•Microbial ...structure and diversity spatially differed in four CWs.•Treatment performances of CWs attributed to the plant physiological features.
Four horizontal subsurface flow pilot-scale constructed wetlands (CWs) named as S1, S2, M1 and M2 were constructed to treat aquaculture wastewater. And two different plant species (Iris pseudacorus and Phragmites australis) were cultivated in single and mixed planting patterns in these four CWs. The removal rate of conventional pollutants (nutrient and organic compounds), antibiotics including enrofloxacin (ENR), sulfamethoxazole (SMZ), and antibiotic resistance genes (ARGs) were evaluated among those CWs. The total nitrogen and NH4+–N removal rates of all CWs were 73.24%–91.46% and 61.20%–92.27%, respectively. CWs with mixed planting patterns, such as M1 (planted with Iris pseudacorus at the forepart and Phragmites australis at the back) and M2 (alternate cultivation with Iris pseudacorus and Phragmites australis) showed better performances than CWs planted with single plant species, such as S1 (Iris pseudacorus) and S2 (Phragmites australis). However, S1 and S2 exhibited higher removal efficiencies for emerging contaminants: S1 had removal efficiencies of 77.64%, 68.70%, and 58.21% for ENR, SMZ, and total ARGs, respectively, and S2 had removal efficiencies of 81.11%, 64.94%, and 56.26% for ENR, SMZ, and total ARGs, respectively. Compared with single planting, the dominant genera in mixed planting exhibited lower relative abundance in anaerobes and higher percent of bacteria associated with nitrogen metabolism, indicating that different plant physiological characteristics affected the microbial community structures of the CWs.
PDF
