Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on ...splice sites with important biological functions. Meanwhile, the dinucleotides occur frequently at the sequences without splice sites, which makes the prediction prone to generate false positives. Most existing tools select all the sequences with the two dimers and then focus on distinguishing the true splice sites from those pseudo ones. Such an approach will lead to a decrease in false positives; however, it will result in non-canonical splice sites missing.
We have designed SpliceFinder based on convolutional neural network (CNN) to predict splice sites. To achieve the ab initio prediction, we used human genomic data to train our neural network. An iterative approach is adopted to reconstruct the dataset, which tackles the data unbalance problem and forces the model to learn more features of splice sites. The proposed CNN obtains the classification accuracy of 90.25%, which is 10% higher than the existing algorithms. The method outperforms other existing methods in terms of area under receiver operating characteristics (AUC), recall, precision, and F1 score. Furthermore, SpliceFinder can find the exact position of splice sites on long genomic sequences with a sliding window. Compared with other state-of-the-art splice site prediction tools, SpliceFinder generates results in about half lower false positive while keeping recall higher than 0.8. Also, SpliceFinder captures the non-canonical splice sites. In addition, SpliceFinder performs well on the genomic sequences of Drosophila melanogaster, Mus musculus, Rattus, and Danio rerio without retraining.
Based on CNN, we have proposed a new ab initio splice site prediction tool, SpliceFinder, which generates less false positives and can detect non-canonical splice sites. Additionally, SpliceFinder is transferable to other species without retraining. The source code and additional materials are available at https://gitlab.deepomics.org/wangruohan/SpliceFinder.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle ...diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs. The transcription activity decreased with development, and the high-resolution transcriptome precisely captured the characterizations of skeletal muscle with distinct biological events in four developmental phases: Embryonic, Fetal, Neonatal, and Adult. A divergence in the developmental timing and asynchronous development between the two breeds was observed; Landrace showed a developmental lag and stronger abilities of myoblast proliferation and cell migration, whereas Tongcheng had higher ATP synthase activity in postnatal periods. The miR-24-3p driven network targeting insulin signaling pathway regulated glucose metabolism. Notably, integrated analysis suggested SATB2 and XLOC_036765 contributed to skeletal muscle diversity via regulating the myoblast migration and proliferation, respectively. Overall, our results provide insights into the molecular regulation of skeletal muscle development and diversity in mammals.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Photocatalysis has been proved to be a promising approach in wastewater purification. However, it is hard to recycle powdery photocatalysts from wastewater in industry, but immobilizing them ...using larger materials can overcome this drawback. For that reason, TiO2@g-C3N4 was embedded into chitosan to synthesize a highly reusable and visible-light-driven chitosan/TiO2@g-C3N4 nanocomposite membrane (CTGM). CTGM showed enhanced photoactivity and the photocatalytic efficiencies of the toxic water pollutants methyl orange (M.O.), rhodamine B (Rh.B), chromium (VI) (Cr (VI)), 2,4-dichlorophenol (2,4-DCP) and atrazine (ATZ) were more than 90% under visible light at ambient conditions. Significantly, CTGM was easy to recycle and showed excellent reusability: there was no decrease in the photocatalytic decolorization efficiency of Rh.B throughout 10 cycles. A continuous-flow photocatalysis system was set up and 90% of Rh.B was effectively decolorized. A simple approach was developed to prepare a novel, effective and visible-light-driven membrane that was easy to reuse, and a feasible photocatalysis continuous-flow system was designed to be a reference for wastewater treatment in industry.
Although Sn–Pb perovskites sensing near-ultraviolet–visible–near-infrared light could be an attractive alternative to silicon in photodiodes and imaging, there have been no clear studies on such ...devices constructed on metal/silicon substrates, hindering their direct integration with complementary metal-oxide semiconductor (CMOS) and silicon electronics. Typically, high surface roughness and severe pinholes of Sn-rich binary perovskites make it difficult for them to fulfill the requirements of efficient photodiodes and imaging. These issues cause inherently high dark current and poor (dark and photo-) current uniformity. Herein, we propose and demonstrate the room-temperature crystallization in the Sn-rich binary perovskite system to effectively control film crystallization kinetics. With experimental and theoretical studies of the crystallization mechanism, we successfully tune the density and location of nanocrystals in precursor films to achieve compact nanocrystals, which coalesce into high-quality (smooth, dense, and pinhole-free) perovskites with intensified preferred orientation and decreased trap density. The high-quality perovskites reduce dark current and improve (dark and photo-) current uniformity of perovskite photodiodes on CMOS-compatible metal/silicon substrates. Meanwhile, self-powered devices achieve a high responsivity of 0.2 A/W at 940 nm, a large dynamic range of 100 dB, and a fast fall time of 2.27 μs, exceeding those of most silicon-based imaging sensors. Finally, a 6 × 6 pixel integrated photodiode array is successfully demonstrated to realize the imaging application. The work contributes to understanding the fundamentals of the crystallization of Sn-rich binary perovskites and advancing perovskite integration with Si-based electronics.
Single-cell RNA-sequencing (scRNA-seq) is becoming indispensable in the study of cell-specific transcriptomes. However, in scRNA-seq techniques, only a small fraction of the genes are captured due to ..."dropout" events. These dropout events require intensive treatment when analyzing scRNA-seq data. For example, imputation tools have been proposed to estimate dropout events and de-noise data. The performance of these imputation tools are often evaluated, or fine-tuned, using various clustering criteria based on ground-truth cell subgroup labels. This limits their effectiveness in the cases where we lack cell subgroup knowledge. We consider an alternative strategy which requires the imputation to follow a "self-consistency" principle; that is, the imputation process is to refine its results until there is no internal inconsistency or dropouts from the data.
We propose the use of "self-consistency" as a main criteria in performing imputation. To demonstrate this principle we devised I-Impute, a "self-consistent" method, to impute scRNA-seq data. I-Impute optimizes continuous similarities and dropout probabilities, in iterative refinements until a self-consistent imputation is reached. On the in silico data sets, I-Impute exhibited the highest Pearson correlations for different dropout rates consistently compared with the state-of-art methods SAVER and scImpute. Furthermore, we collected three wetlab datasets, mouse bladder cells dataset, embryonic stem cells dataset, and aortic leukocyte cells dataset, to evaluate the tools. I-Impute exhibited feasible cell subpopulation discovery efficacy on all the three datasets. It achieves the highest clustering accuracy compared with SAVER and scImpute.
A strategy based on "self-consistency", captured through our method, I-Impute, gave imputation results better than the state-of-the-art tools. Source code of I-Impute can be accessed at https://github.com/xikanfeng2/I-Impute .
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers ...have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation.
Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page.
MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Skeletal muscle myogenesis hinges on gene regulation, meticulously orchestrated by molecular mechanisms. While the roles of transcription factors and non-coding RNAs in myogenesis are widely known, ...the contribution of RNA-binding proteins (RBPs) has remained unclear until now. Therefore, to investigate the functions of post-transcriptional regulators in myogenesis and uncover new functional RBPs regulating myogenesis, we employed CRISPR high-throughput RBP-KO (RBP-wide knockout) library screening. Through this approach, we successfully identified Eef1a1 as a novel regulatory factor in myogenesis. Using CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) technologies, we successfully established cellular models for both CRISPRko and CRISPRi. Our findings demonstrated that Eef1a1 plays a crucial role in promoting proliferation in C2C12 myoblasts. Through siRNA inhibition and overexpression methods, we further elucidated the involvement of Eef1a1 in promoting proliferation and suppressing differentiation processes. RIP (RNA immunoprecipitation), miRNA pull-down, and Dual-luciferase reporter assays confirmed that miR-133a-3p targets Eef1a1. Co-transfection experiments indicated that miR-133a-3p can rescue the effect of Eef1a1 on C2C12 myoblasts. In summary, our study utilized CRISPR library high-throughput screening to unveil a novel RBP, Eef1a1, involved in regulating myogenesis. Eef1a1 promotes the proliferation of myoblasts while inhibiting the differentiation process. Additionally, it acts as an antagonist to miR-133a-3p, thus modulating the process of myogenesis.
MicroRNAs (miRNAs), which are short (22-24 base pairs), non-coding RNAs, play critical roles in myogenesis. Using Solexa deep sequencing, we detected the expression levels of 229 and 209 miRNAs in ...swine skeletal muscle at 90 days post-coitus (E90) and 100 days postnatal (D100), respectively. A total of 138 miRNAs were up-regulated on E90, and 31 were up-regulated on D100. Of these, 9 miRNAs were selected for the validation of the small RNA libraries by quantitative RT-PCR (RT-qPCR). We found that miRNA-21 was down-regulated by 17-fold on D100 (P<0.001). Bioinformatics analysis suggested that the transforming growth factor beta-induced (TGFβI) gene was a potential target of miRNA-21. Both dual luciferase reporter assays and western blotting demonstrated that the TGFβI gene was regulated by miRNA-21. Co-expression analysis revealed that the mRNA expression levels of miRNA-21 and TGFβI were negatively correlated (r = -0.421, P = 0.026) in skeletal muscle during the 28 developmental stages. Our results revealed that more miRNAs are expressed in prenatal than in postnatal skeletal muscle. The miRNA-21 is a novel myogenic miRNA that is involved in skeletal muscle development and regulates PI3K/Akt/mTOR signaling by targeting the TGFβI gene.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Drift-diffusion model is an indispensable modeling tool to understand the carrier dynamics (transport, recombination, and collection) and simulate practical-efficiency of solar cells (SCs) through ...taking into account various carrier recombination losses existing in multilayered device structures. Exploring the way to predict and approach the SC efficiency limit by using the drift-diffusion model will enable us to gain more physical insights and design guidelines for emerging photovoltaics, particularly perovskite solar cells. Our work finds out that two procedures are the prerequisites for predicting and approaching the SC efficiency limit. First, the intrinsic radiative recombination needs to be corrected after adopting optical designs which will significantly affect the open-circuit voltage at its Shockley–Queisser limit. Through considering a detailed balance between emission and absorption of semiconductor materials at the thermal equilibrium and the Boltzmann statistics at the nonequilibrium, we offer a different approach to derive the accurate expression of intrinsic radiative recombination with the optical corrections for semiconductor materials. The new expression captures light trapping of the absorbed photons and angular restriction of the emitted photons simultaneously, which are ignored in the traditional Roosbroeck-Shockley expression. Second, the contact characteristics of the electrodes need to be carefully engineered to eliminate the charge accumulation and surface recombination at the electrodes. The selective contact or blocking layer incorporated nonselective contact that inhibits the surface recombination at the electrode is another important prerequisite. With the two procedures, the accurate prediction of efficiency limit and precise evaluation of efficiency degradation for perovskite solar cells are attainable by the drift-diffusion model. Our work is fundamentally and practically important to mathematical modeling and physical understanding of solar cells.
Single-cell RNA-seq studies profile thousands of cells in developmental processes. Current databases for human single-cell expression atlas only provide search and visualize functions for a selected ...gene in specific cell types or subpopulations. These databases are limited to technical properties or visualization of single-cell RNA-seq data without considering the biological relations of their collected cell groups. Here, we developed a database to investigate single-cell gene expression profiling during different developmental pathways (SCDevDB). In this database, we collected 10 human single-cell RNA-seq datasets, split these datasets into 176 developmental cell groups, and constructed 24 different developmental pathways. SCDevDB allows users to search the expression profiles of the interested genes across different developmental pathways. It also provides lists of differentially expressed genes during each developmental pathway, T-distributed stochastic neighbor embedding maps showing the relationships between developmental stages based on these differentially expressed genes, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analysis results of these differentially expressed genes. This database is freely available at https://scdevdb.deepomics.org.
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