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.
RNA-binding protein (RBP) has a highly dynamic spatiotemporal regulation process and important biological functions. They are critical to maintain the transcriptome through post-transcriptionally ...controlling the processing and transportation of RNA, including regulating RNA splicing, polyadenylation, mRNA stability, mRNA localization, and translation. Alteration of each process will affect the RNA life cycle, produce abnormal protein phenotypes, and thus lead to the occurrence and development of tumors. Here, we summarize RBPs involved in tumor progression and the underlying molecular mechanisms whereby they are regulated and exert their effects. This analysis is an important step towards the comprehensive characterization of post-transcriptional gene regulation involved in tumor progression.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The catalyst was synthesized by a two-step calcination method. Advances of the in-situ growth allow intimate and enhanced the interfacial separation of charge carriers. At the same time, Co ...modification was introduced to regulate the adsorption energy of N2 and NH3 to achieve adsorption equilibrium. The obtained catalyst had high activity and stability in photocatalitic nitrogen fixation.
Display omitted
Modulation of the binding of the reactant or product species with catalysts is an effective approach to optimize the photocatalytic activity. Herein, we explored the relationship between the binding of reactant (N2) and product (NH3) with catalyst and the photocatalytic nitrogen fixation activity. The surface reactivity of nitrogen with water was tuned by introducing Co into the MXene@TiO2 catalysts, which the TiO2 nanoparticle derived from the in-situ growth on the surface of MXene nanosheets. Co modified adjusted the chemisorption equilibrium of the catalyst for reactant (N2) and product (NH3), thus promoted product desorption and efficiency of the active site. Remarkably, the optimal catalyst (MXene/TiO2/Co-0.5%) exhibited outstanding NH4+ production rate (110 μmol g−1 h−1) and excellent stability in pure water without any hole sacrificial agent under Ultraviolet–Visible (UV–vis) light in N2 and air ambient.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cancer stem cells (CSCs) contribute to the initiation, recurrence, and metastasis of cancer; however, there are still no drugs targeting CSCs in clinical application. There are several signaling ...pathways playing critical roles in CSC progression, such as the Wnt, Hedgehog, Notch, Hippo, and autophagy signaling pathways. Additionally, targeting the ferroptosis signaling pathway was recently shown to specifically kill CSCs. Therefore, targeting these pathways may suppress CSC progression. The structure of small-molecule drugs shows a good spatial dispersion, and its chemical properties determine its good druggability and pharmacokinetic properties. These characteristics make small-molecule drugs show a great advantage in drug development, which is increasingly popular in the market. Thus, in this review, we will summarize the current researches on the small-molecule compounds suppressing CSC progression, including inhibitors of Wnt, Notch, Hedgehog, and autophagy pathways, and activators of Hippo and ferroptosis pathways. These small-molecule compounds emphasize CSC importance in tumor progression and propose a new strategy to treat cancer in clinic via targeting CSCs.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Photocatalytic nitrogen fixation has become a hot topic in recent years due to its mild and sustainable advantages. While modifying the photocatalyst to enhance its electron separation, light ...absorption and nitrogen reduction abilities, the role of the active sites in the catalytic reaction cannot be ignored because the N&z.tbd;N nitrogen bond is too strong to activate. This review summarizes the recent research on nitrogen fixation, focusing on the active sites for N
2
on the catalyst surface, classifying common active sites, explaining the main role and additional role of the active sites in catalytic reactions, and discussing the methods to increase the number of active sites and their activation ability. Finally, the outlook for future research is presented. It is hoped this review could help researchers understand more about the activation of the nitrogen molecules and lead more efforts into research on nitrogen fixation photocatalysts.
The common active sites of photocatalysts for nitrogen fixation are mainly vacancy defects and doped metal.
Ammonia synthesis under mild conditions is of supreme interest. Photocatalytic nitrogen fixation with water at room temperature and atmospheric pressure is an intriguing strategy. However, the ...efficiency of this method has been far from satisfied for industrialization, mainly due to the sluggish cleavage of the N≡N bond. Herein, we report a carbon–tungstic‐acid (WO3⋅H2O) hybrid for the co‐optimization of N2 activation as well as subsequent photoinduced protonation. Efficient ammonia evolution reached 205 μmol g−1 h−1 over this hybrid under simulated sunlight. Nitrogen temperature‐programmed desorption revealed the decisive role of carbon in N2 adsorption. Photoactive WO3⋅H2O guaranteed the supply of electrons and protons for subsequent protonation. The universality of carbon modification for enhancing the N2 reduction was further verified over various photocatalysts, shedding light on future materials design for ideal solar energy utilization.
Photocatalyzed nitrogen fixation: A carbon–tungstic‐acid hybrid for the co‐optimization of N2 activation as well as subsequent photoinduced protonation has been developed. Efficient ammonia evolution was achieved over this hybrid under simulated sunlight (see figure).
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
For staring infrared sensors in geostationary orbit, the clutter caused by the high-frequency jitter and low-frequency drift of the sensor line-of-sight (LOS) is the impact of background features, ...sensor parameters, LOS motion characteristics, and background suppression algorithms. In this paper, the spectra of LOS jitter caused by cryocoolers and momentum wheels are analyzed, and the time-related factors such as the jitter spectrum, the detector integration time, the frame period, and the temporal differencing background suppression algorithm are considered comprehensively; they are combined into a background-independent jitter-equivalent angle model. A jitter-caused clutter model in the form of multiplying the background radiation intensity gradient statistics by the jitter-equivalent angle is established. This model has good versatility and high efficiency and is suitable for the quantitative evaluation of clutter and the iterative optimization of sensor design. Based on satellite ground vibration experiments and on-orbit measured image sequences, the jitter-caused clutter and drift-caused clutter models are verified. The relative deviation between the model calculation and the actual measurement results is less than 20%.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
PDF
