The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. ...Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods.
Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision.
The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ CONTACTS: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu
Supplementary data are available at Bioinformatics online.
To determine the effect of thermal maturity on the methane sorption in shale gas system, two different thermal maturity kerogens of type II isolated from Barnett shale of Fort Worth Basin were used ...to measure the methane adsorption amount under the pressure ranging from 0 to 14 MPa at constant temperatures. One kerogen was called Lee C-5-1 with 0.58% of vitrinite reflectance; the other was called Blakely#1 kerogen with 2.01% of vitrinite reflectance. The results suggested that the methane sorption capacity of kerogen Blakely#1 was higher than the immature kerogen Lee C-5-1, and its Langmuir constant and Langmuir maximum sorption amount, which were reached by fitting the measured data for at least square method, greater than the immature kerogen Lee C-5-1. This may be associated with that nanopores opened up during the degradation of organic matter, and which increased the specific surface area of kerogen. Therefore, the over mature kerogen has greater methane adsorption capacity.
The nano-scale pore systems of organic-rich shale reservoirs were investigated from Upper Ordovician Wufeng and Lower Silurian Longmaxi Formations in southeast Sichuan Basin. These two formations are ...the most important target plays of shale gas development in China. The purpose of this article is to assess the geometry and connectivity of multi-scale pore systems, and to reveal the nature and complexity of pore structure for these over-mature gas shales. To achieve these objective, total organic carbon, mineralogy, image analyses by focused ion beam-SEM, low pressure nitrogen adsorption, mercury injection capillary pressure (MICP) and spontaneous fluid deionized (DI) water and n-decane imbibition were performed.
Most of the visible pores from SEM work in Wufeng and Longmaxi shales are within nm- and μm-size regimes and belong to organic matter (OM) pores. The shapes of OM pore in Longmaxi samples are elliptical, bubble-like, irregular or rounded. Wufeng pores are mainly irregular, linear and faveolated, even though two shales have small depth difference, as well as similar thermal maturity, kerogen type and TOC content. Nano-scale pores in Longmaxi are mainly associated with narrow platelike or slitlike pores with pore size of 3–50 nm; while inkbottle pores are dominant in Wufeng samples and over 88% of the pore volume is contributed by pores with diameter <20 nm. Overall, porosity, pore volume and surface area values from Wufeng samples are much higher than those in Longmaxi, which is mainly correlated with the different TOC contents and mineral compositions. MICP tests show that a total of 5 inflection points (indicative of different connected pore networks) are identified in all pressure regions for Longmaxi, while only 2 for Wufeng in high pressure region with the associated permeability at nano-darcy range. Imbibition curves of n-decane are divided into three stages: the initial stage (Stage Ⅰ), linear imbibition stage (Stage Ⅱ) and late imbibition stage (Stage Ⅲ), and the slopes of linear imbibition stage are around 0.5, suggesting well-connected pore spaces for n-decane. In contrast, imbibition curves for DI water are divided in two stages with linear slopes of between 0.25 and 0.5, indicating moderately-connected pore networks for the movement of DI water. This is consistent with the mixed-wet nature of these shales, with observed weak wettability for hydrophilic, while complete wetting for hydrophobic fluids.
•Organic-rich shales from Wufeng and Longmaxi are analyzed for pore structure (geometrical and topological) characteristics.•Multiple approaches (SEM, low pressure N2 sorption, and MICP) indicates the presence of μm-nm pore spectrum.•Permeability for multiple pore networks at μm-nm scale are calculated from MICP tests.•Imbibition of both hydrophilic and hydrophobic fluids indicates that oil-wet regions are better connected than water-wet ones.•Wufeng and Longmaxi shales are mixed-wet.
MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies focus on mature miRNAs, which leaves many unknowns about primary miRNAs (pri-miRNAs). To fill the gap, we attempted to model the ...expression of pri-miRNAs in 1829 primary cell types, cell lines, and tissues in this study. We demonstrated that the expression of pri-miRNAs can be modeled well by the expression of specific sets of mRNAs, which we termed their associated mRNAs. These associated mRNAs differ from their corresponding target mRNAs and are enriched with specific functions. Most associated mRNAs of a miRNA are shared across conditions, while on average, about one-fifth of the associated mRNAs are condition-specific. Our study shed new light on understanding miRNA biogenesis and general gene transcriptional regulation.
With mutations constantly accumulating in bacterial genomes, it is unclear whether the previously identified bacterial strains are really present in an extant sample. To address this question, we did ...a case study on the known strains of the bacterial species S. aureus and S. epidermis in 68 atopic dermatitis shotgun metagenomic samples. We evaluated the likelihood of the presence of all sixteen known strains predicted in the original study and by two popular tools in this study. We found that even with the same tool, only two known strains were predicted by the original study and this study. Moreover, none of the sixteen known strains was likely present in these 68 samples. Our study thus indicates the limitation of the known-strain-based studies, especially those on rapidly evolving bacterial species. It implies the unlikely presence of the previously identified known strains in a current environmental sample. It also called for de novo bacterial strain identification directly from shotgun metagenomic reads.
The tumor stromal microenvironments (TSM) including stromal cells and extracellular matrix (ECM) form an abominable barrier hampering nanoparticles accessibility to cancer cells, significantly ...compromising their antitumor effects. Herein, we report a bioinspired lipoprotein (bLP) that can induce efficient photothermia to remodel TSM and improve second bLP accessibility to cancer cells for antitumor therapy. The multiple stromal cells and ECM components in TSM are remarkably disrupted by bLP-mediated photothermal effects, which cause a 4.27-fold enhancement of second bLP accumulation in tumor, deep penetration in whole tumor mass and 27.0-fold increase of accessibility to cancer cells. Of note, this bLP-mediated TSM-remodeling to enhance cancer cell accessibility (TECA) strategy produces an eminent suppression of tumor growth and results in a 97.4% inhibition of lung metastasis, which is superior to the counterpart liposomes. The bLP-mediated TECA strategy provides deeper insights into enhancing nanoparticle accessibility to cancer cells for antitumor therapy.
Drug delivery systems (DDS) are defined as methods by which drugs are delivered to desired tissues, organs, cells and subcellular organs for drug release and absorption through a variety of drug ...carriers. Its usual purpose to improve the pharmacological activities of therapeutic drugs and to overcome problems such as limited solubility, drug aggregation, low bioavailability, poor biodistribution, lack of selectivity, or to reduce the side effects of therapeutic drugs. During 2015–2018, significant progress in the research on drug delivery systems has been achieved along with advances in related fields, such as pharmaceutical sciences, material sciences and biomedical sciences. This review provides a concise overview of current progress in this research area through its focus on the delivery strategies, construction techniques and specific examples. It is a valuable reference for pharmaceutical scientists who want to learn more about the design of drug delivery systems.
This review makes a concise overview of current progress in the research of drug delivery systems that focused on the delivery strategies, construction techniques and specific representatives. Display omitted
Oxidative stress plays a critical role in cerebral ischemia/reperfusion (I/R)-induced blood-brain barrier (BBB) disruption.
saponins (PNS) possess efficient antioxidant activity and have been used in ...the treatment of cerebral ischemic stroke in China. In this study, we determined the protective effects of PNS on BBB integrity and investigated the underlying mechanism in cerebral microvascular endothelial cells (bEnd.3) exposed to oxygen-glucose deprivation/reperfusion (OGD/R). MTT and LDH release assays revealed that PNS mitigated the OGD/R-induced cell injury in a dose-dependent manner. TEER and paracellular permeability assays demonstrated that PNS alleviated the OGD/R-caused disruption of BBB integrity. Fluorescence probe DCFH-DA showed that PNS suppressed ROS generation in OGD/R-treated cells. Immunofluorescence and western blot analysis indicated that PNS inhibited the degradation of tight junction proteins triggered by OGD/R. Moreover, mechanism investigations suggested that PNS increased the phosphorylation of Akt, the activity of nuclear Nrf2, and the expression of downstream antioxidant enzyme HO-1. All the effects of PNS could be reversed by co-treatment with PI3K inhibitor LY294002. Taken together, these observations suggest that PNS may act as an extrinsic regulator that activates Nrf2 antioxidant signaling depending on PI3K/Akt pathway and protects against OGD/R-induced BBB disruption in vitro.
Abstract
Accurate identification of microRNA (miRNA) targets at base-pair resolution has been an open problem for over a decade. The recent discovery of miRNA isoforms (isomiRs) adds more complexity ...to this problem. Despite the existence of many methods, none considers isomiRs, and their performance is still suboptimal. We hypothesize that by taking the isomiR–mRNA interactions into account and applying a deep learning model to study miRNA–mRNA interaction features, we may improve the accuracy of miRNA target predictions. We developed a deep learning tool called DMISO to capture the intricate features of miRNA/isomiR–mRNA interactions. Based on tenfold cross-validation, DMISO showed high precision (95%) and recall (90%). Evaluated on three independent datasets, DMISO had superior performance to five tools, including three popular conventional tools and two recently developed deep learning-based tools. By applying two popular feature interpretation strategies, we demonstrated the importance of the miRNA regions other than their seeds and the potential contribution of the RNA-binding motifs within miRNAs/isomiRs and mRNAs to the miRNA/isomiR–mRNA interactions.
Osteosarcoma is the most frequent primary bone tumor with poor prognosis. Through RNA-sequencing of 100,987 individual cells from 7 primary, 2 recurrent, and 2 lung metastatic osteosarcoma lesions, ...11 major cell clusters are identified based on unbiased clustering of gene expression profiles and canonical markers. The transcriptomic properties, regulators and dynamics of osteosarcoma malignant cells together with their tumor microenvironment particularly stromal and immune cells are characterized. The transdifferentiation of malignant osteoblastic cells from malignant chondroblastic cells is revealed by analyses of inferred copy-number variation and trajectory. A proinflammatory FABP4
macrophages infiltration is noticed in lung metastatic osteosarcoma lesions. Lower osteoclasts infiltration is observed in chondroblastic, recurrent and lung metastatic osteosarcoma lesions compared to primary osteoblastic osteosarcoma lesions. Importantly, TIGIT blockade enhances the cytotoxicity effects of the primary CD3
T cells with high proportion of TIGIT
cells against osteosarcoma. These results present a single-cell atlas, explore intratumor heterogeneity, and provide potential therapeutic targets for osteosarcoma.
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