RNA-guided programmable nucleases from CRISPR systems generate precise breaks in DNA or RNA at specified positions. In cells, this activity can lead to changes in DNA sequence or RNA transcript ...abundance. Base editing is a newer genome-editing approach that uses components from CRISPR systems together with other enzymes to directly install point mutations into cellular DNA or RNA without making double-stranded DNA breaks. DNA base editors comprise a catalytically disabled nuclease fused to a nucleobase deaminase enzyme and, in some cases, a DNA glycosylase inhibitor. RNA base editors achieve analogous changes using components that target RNA. Base editors directly convert one base or base pair into another, enabling the efficient installation of point mutations in non-dividing cells without generating excess undesired editing by-products. In this Review, we summarize base-editing strategies to generate specific and precise point mutations in genomic DNA and RNA, highlight recent developments that expand the scope, specificity, precision and in vivo delivery of base editors and discuss limitations and future directions of base editing for research and therapeutic applications.
Programmable gene-editing tools have transformed the life sciences and have shown potential for the treatment of genetic disease. Among the CRISPR-Cas technologies that can currently make targeted ...DNA changes in mammalian cells, prime editors offer an unusual combination of versatility, specificity and precision. Prime editors do not require double-strand DNA breaks and can make virtually any substitution, small insertion and small deletion within the DNA of living cells. Prime editing minimally requires a programmable nickase fused to a polymerase enzyme, and an extended guide RNA that both specifies the target site and templates the desired genome edit. In this Review, we summarize prime editing strategies to generate programmed genomic changes, highlight their limitations and recent developments that circumvent some of these bottlenecks, and discuss applications and future directions.
We present two CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems that use base editors and Cas9 nucleases to record cellular events in bacteria and mammalian cells. The devices ...record signal amplitude or duration as changes in the ratio of mutually exclusive DNA sequences (CAMERA 1) or as single-base modifications (CAMERA 2). We achieved recording of multiple stimuli in bacteria or mammalian cells, including exposure to antibiotics, nutrients, viruses, light, and changes in Wnt signaling. When recording to multicopy plasmids, reliable readout requires as few as 10 to 100 cells. The order of stimuli can be recorded through an overlapping guide RNA design, and memories can be erased and re-recorded over multiple cycles. CAMERA systems serve as "cell data recorders" that write a history of endogenous or exogenous signaling events into permanent DNA sequence modifications in living cells.
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in ...the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
Transforming growth factor β (TGF-β) is the most potent and ubiquitous profibrogenic cytokine, and its expression is increased in almost all the fibrotic diseases and in experimental fibrosis models. ...TGF-β increases reactive oxygen species production and decreases the concentration of glutathione (GSH), the most abundant intracellular free thiol and an important antioxidant, which mediates many of the fibrogenic effects of TGF-β in various types of cells. A decreased GSH concentration is also observed in human fibrotic diseases and in experimental fibrosis models. Although the biological significance of GSH depletion in the development of fibrosis remains obscure, GSH and
N-acetylcysteine, a precursor of GSH, have been used in clinics for the treatment of fibrotic diseases. This review summarizes recent findings in the field to address the potential mechanism whereby oxidative stress mediates fibrogenesis induced by TGF-β and the potential therapeutic value of antioxidant treatment in fibrotic diseases.
The smoothed finite element methods (S-FEM) are a family of methods formulated through carefully designed combinations of the standard FEM and some of the techniques from the meshfree methods. ...Studies have proven that S-FEM models behave softer than the FEM counterparts using the same mesh structure, often produce more accurate solutions, higher convergence rates, and much less sensitivity to mesh distortion. They work well with triangular or tetrahedral mesh that can be automatically generated, and hence are ideal for automated computations and adaptive analyses. Some S-FEM models can also produce upper bound solution for force driving problems, which is an excellent unique complementary feature to FEM. Because of these attractive properties, S-FEM has been applied to numerous problems in the disciplines of material mechanics, biomechanics, fracture mechanics, plates and shells, dynamics, acoustics, heat transfer and fluid–structure interactions. This paper reviews the developments and applications of the S-FEM in the past ten years. We hope this review can shed light on further theoretical development of S-FEM and more complex practical applications in future.
The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this Review, we ...summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and we highlight some of the remarkable advancements in basic research, biotechnology, and therapeutics science that these developments have facilitated.
CRISPR-based genome-editing technologies provide powerful tools to study basic biology and may lead to new treatments for human disease.
Summary Articular cartilage degeneration is hallmark of osteoarthritis (OA). Low-grade chronic inflammation in the joint can promote OA progression. Emerging evidence indicates that bioenergy sensors ...couple metabolism with inflammation to switch physiological and clinical phenotypes. Changes in cellular bioenergy metabolism can reprogram inflammatory responses, and inflammation can disturb cellular energy balance and increase cell stress. AMP-activated protein kinase (AMPK) and sirtuin 1 (SIRT1) are two critical bioenergy sensors that regulate energy balance at both cellular and whole-body levels. Dysregulation of AMPK and SIRT1 has been implicated in diverse human diseases and aging. This review reveals recent findings on the role of AMPK and SIRT1 in joint tissue homeostasis and OA, with a focus on how AMPK and SIRT1 in articular chondrocytes modulate intracellular energy metabolism during stress responses (e.g., inflammatory responses) and how these changes dictate specific effector functions, and discusses translational significance of AMPK and SIRT1 as new therapeutic targets for OA.
In January 2013, Beijing experienced several serious haze events. To achieve a better understanding of the characteristics, sources and processes of aerosols during this month, an Aerodyne ...high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) was deployed at an urban site between 1 January and 1 February 2013 to obtain the size-resolved chemical composition of non-refractory submicron particles (NR-PM1). During this period, the mean measured NR-PM1 mass concentration was 89.3 ± 85.6 μg m−3, and it peaked at 423 μg m−3. Positive matrix factorization (PMF) differentiated the organic aerosol into five components, including a highly oxidized, low-volatility oxygenated organic aerosol (LV-OOA), a less oxidized, semi-volatile oxygenated OA (SV-OOA), a coal combustion OA (CCOA), a cooking-related OA (COA), and a hydrocarbon-like OA (HOA), which on average accounted for 28%, 26%, 15%, 20% and 11% of the total organic mass, respectively. A detailed comparison between the polluted days and unpolluted days found many interesting results. First, the organic fraction was the most important NR-PM1 species during the unpolluted days (58%), while inorganic species were dominant on polluted days (59%). The OA composition also experienced a significant change; it was dominated by primary OA (POA), including COA, HOA and CCOA, on unpolluted days. The contribution of secondary OA (SOA) increased from 35% to 63% between unpolluted and polluted days. Second, meteorological effects played an important role in the heavy pollution in this month and differed significantly between the two types of days. The temperature and relative humidity (RH) were all increased on polluted days and the wind speed and air pressure were decreased. Third, the diurnal variation trend in NR-PM1 species and OA components showed some differences between the two types of days, and the OA was more highly oxidized on polluted days. Fourth, the effects of air masses were significantly different between the two types of days; air was mainly transported from contaminated areas on the polluted days. The comparison also found that the aerosol was more acidic on polluted days. Additionally, the variation trends of the mass concentration and mass fractions of NR-PM1 species and OA components were more dramatic when the NR-PM1 mass loading was at a higher level. The serious pollution observed in this month can be attributed to the synergy of unfavorable meteorological factors, the transport of air masses from high-pollution areas, emission by local sources, and other factors.
Smoothed particle hydrodynamics (SPH) is a meshfree particle method based on Lagrangian formulation, and has been widely applied to different areas in engineering and science. This paper presents an ...overview on the SPH method and its recent developments, including (1) the need for meshfree particle methods, and advantages of SPH, (2) approximation schemes of the conventional SPH method and numerical techniques for deriving SPH formulations for partial differential equations such as the Navier-Stokes (N-S) equations, (3) the role of the smoothing kernel functions and a general approach to construct smoothing kernel functions, (4) kernel and particle consistency for the SPH method, and approaches for restoring particle consistency, (5) several important numerical aspects, and (6) some recent applications of SPH. The paper ends with some concluding remarks.
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