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الحكايات الثراثية الصينية /
دخل الحراس الأربعون الغابة والأمير الصغير بصحبتهم، الغابة موحشة، وأشجارها كثيفة وطويلة تبلغ عنان السماء، وتعج بالحيوانات البرية، صعد الأمير بعدها إلى الجبل تحت حراسة مشددة من قبل الحراس، لم يستل سكينا، ولم يطلق سهما، وما هي إلا لحظات حتى اصطاد الكثير من الحيوانات النادرة بمساعدة الحراس، فسر كثيرا، وفجأة ظهرت أمام أعينهم نمر متوحش ذو عينين مقلوبتين وعلى جبينه خطوط بيضاء، وقبل أن يستوضح الأمير الأمر وسط الحراس، وضع السهم في القوس وأطلقه بكل قوته صوب النمر، إلا أن السهم لم يصب الهدف، فانطلق النمر نحوه قاصدا مهاجمته، إلا أنه استدار بجسمه وفر هاربا حينما شاهد المظهر المهيب لأولئك الحراس الأربعين، ولم يتوقف الأمر عند هذا الحد، بل حدث أمر عجيب آخر!.
Book
LncRNA KLF3-AS1 in human mesenchymal stem cell-derived exosomes ameliorates pyroptosis of cardiomyocytes and myocardial infarction through miR-138-5p/Sirt1 axis
Aim
Myocardial infarction (MI) is a severe disease with increased mortality and disability rates, posing heavy economic burden for society. Exosomes were uncovered to mediate intercellular communication after MI. This study aims to explore the effect and mechanism of lncRNA KLF3-AS1 in exosomes secreted by human mesenchymal stem cells (hMSCs) on pyroptosis of cardiomyocytes and MI.
Methods
Exosomes from hMSCs were isolated and identified. Exosomes from hMSCs with transfection of KLF3-AS1 for overexpression were injected into MI rat model or incubated with hypoxia cardiomyocytes. Effect of KLF3-AS1 on MI area, cell viability, apoptosis, and pyroptosis was determined. The relationship among miR-138-5p, KLF3-AS1, and Sirt1 was verified by dual-luciferase reporter assay. Normal cardiomyocytes were transfected with miR-138-5p inhibitor or sh-Sirt1 to clarify whether alteration of miR-138-5p or sh-Sirt1 can regulate the effect of KLF3-AS1 on cardiomyocytes.
Results
Exosomes from hMSCs were successfully extracted. Transfection of KLF3-AS1 exosome in rats and incubation with KLF3-AS1 exosome in hypoxia cardiomyocytes both verified that overexpression of KLF3-AS1 in exosomes leads to reduced MI area, decreased cell apoptosis and pyroptosis, and attenuated MI progression. KLF3-AS1 can sponge miR-138-5p to regulate Sirt1 expression. miR-138-5p inhibitor transfection and KLF3-AS1 exosome incubation contribute to attenuated pyroptosis and MI both in vivo and in vitro, while transfection of sh-Sirt1 could reverse the protective effect of exosomal KLF3-AS1 on hypoxia cardiomyocytes.
Conclusion
LncRNA KLF3-AS1 in exosomes secreted from hMSCs by acting as a ceRNA to sponge miR-138-5p can regulate Sirt1 so as to inhibit cell pyroptosis and attenuate MI progression.
Journal Article
Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
Journal Article
An enhanced isothermal amplification assay for viral detection
Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. Here we report the development of a molecular diagnostic test for SARS-CoV-2 based on an enhanced recombinase polymerase amplification (eRPA) reaction. eRPA has a detection limit on patient samples down to 5 viral copies, requires minimal instrumentation, and is highly scalable and inexpensive. eRPA does not cross-react with other common coronaviruses, does not require RNA purification, and takes ~45 min from sample collection to results. eRPA represents a first step toward at-home SARS-CoV-2 detection and can be adapted to future viruses within days of genomic sequence availability.
Current state-of-the-art diagnostics for infectious diseases are sensitive but require extensive equipment. Here the authors develop an enhanced recombinase polymerase amplification reaction for SARS-CoV-2 that allows for inexpensive and rapid testing with minimal equipment.
Journal Article
Interaction between Nitrogen and Sulfur in Co-Doped Graphene and Synergetic Effect in Supercapacitor
The co-doping of graphene with nitrogen and sulfur was investigated aiming at understanding their interactions with the presence of oxygen in graphene. The co-doped graphene (NS-G) was synthesized via a one-pot hydrothermal route using graphene oxide as starting material and L-cysteine, an amino acid containing both N and S, as the doping agent. The obtained NS-G with a three-dimensional hierarchical structure containing both macropores and mesopores exhibited excellent mechanical stabilities under both wet and dry conditions. As compared to N or S singly doped graphene, the co-doped sample contains significantly higher concentrations of N and S species especially pyrollic N groups. The co-doped sample considerably outperformed the singly doped samples when used as free-standing electrode in supercapacitors due to enhanced pseudocapacitance. The simultaneous incorporation of S and N species with the presence of oxygen significantly modified the surface chemistry of carbon leading to considerably higher doping levels, although directly bonding between N and S is neither likely nor detected. Hence, the synergetic effect between N and S occurred through carbon atoms in neighboring hexagonal rings in a graphene sheet.
Journal Article
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Significance Alternative splicing (AS) is an important mechanism of eukaryotic gene regulation. Deep RNA sequencing (RNA-Seq) has become a powerful approach for quantitative profiling of AS. With the increasing capacity of high-throughput sequencers, it has become common for RNA-Seq studies of AS to examine multiple biological replicates. We developed rMATS, a new statistical method for robust and flexible detection of differential AS from replicate RNA-Seq data. Besides the analysis of unpaired replicates, rMATS includes a model specifically designed for paired replicates, such as case–control matched pairs in clinical RNA-Seq datasets. We expect rMATS will be useful for genome-wide studies of AS in diverse research projects. Our data also provide new insights about the experimental design for RNA-Seq studies of AS.
Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of transcript splicing (MATS), a statistical method for detecting differential alternative splicing between two RNA-Seq samples. Here we describe a new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The performance of rMATS is evaluated by the analysis of simulated and real RNA-Seq data. rMATS outperformed two existing methods for replicate RNA-Seq data in all simulation settings, and RT-PCR yielded a high validation rate (94%) in an RNA-Seq dataset of prostate cancer cell lines. Our data also provide guiding principles for designing RNA-Seq studies of alternative splicing. We demonstrate that it is essential to incorporate biological replicates in the study design. Of note, pooling RNAs or merging RNA-Seq data from multiple replicates is not an effective approach to account for variability, and the result is particularly sensitive to outliers. The rMATS source code is freely available at rnaseq-mats.sourceforge.net/ . As the popularity of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative splicing in diverse RNA-Seq projects.
Journal Article