sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks

Niu, Mengting; Lin, Yanping; Zou, Quan

doi:10.1007/s11103-020-01102-y

Cited by 99 publications

(33 citation statements)

References 77 publications

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“…Furthermore, metallic NPs might exert synergistic effects when combined with anticancer drugs [45][46][47]. Guo et al showed that Ni NPs significantly enhance the permeability of cancerous SMMC-7721 hepatocellular carcinoma cells and increase the accumulation of quercetin in these cells [48].…”

Section: Discussionmentioning

confidence: 99%

CoNi alloy nanoparticles for cancer theranostics: synthesis, physical characterization, in vitro and in vivo studies

et al. 2021

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Nanomaterials are attracting increasing interest in many biomedical fields, including the fight against cancer. In this context, we successfully synthesized CoNi alloy nanoparticles (NPs) by a simple polyol process. The magnetic characteristics of the products were measured by vibration sample magnometry, which revealed that the samples have soft ferromagnetic behavior. The microstructure and morphology were inspected by X-ray diffraction and scanning electron microscopy, respectively. Human cancer cells derived from the breast (MCF7) and oral cavity (C152) and normal cells derived from human umbilical vein endothelial cells (HUVECs) were treated with increasing concentrations of CoNi NPs, and their cytotoxic effect was measured via MTT and lactate dehydrogenase (LDH) leakage assays. We found that treatments by using 12.5 to 400 µg/mL of Co0.5Ni0.5, Co0.6Ni0.4, and Co0.4Ni0.6 NPs were associated with significant concentration-dependent toxicity toward such cell lines and profoundly enhanced LDH leakage following 48 h of exposure (P < 0.05 compared with untreated cells). Besides, a NP dose of 6.25 µg/mL did not affect the survival of HUVECs while leading to marked cell death in MCF7 and C152 cells. In vivo experiments in rats were done to investigate the biochemical and histopathological changes over three weeks, following intraperitoneal administration of Co0.5Ni0.5, Co0.6Ni0.4, and Co0.4Ni0.6 NPs (100 mg/kg). As compared with the controls, the exposure to NPs caused significant elevations in aspartate aminotransferase, alanine aminotransferase, blood urea nitrogen, serum creatinine, serum catalase activity, serum superoxide dismutase, and liver malondialdehyde levels. Also, rats treated with Co0.6Ni0.4 NPs showed more severe histopathological changes of the liver and kidney. Our findings represent an essential step toward developing theranostic nanoplatforms for selective cancer treatment.

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Section: Discussionmentioning

confidence: 99%

CoNi alloy nanoparticles for cancer theranostics: synthesis, physical characterization, in vitro and in vivo studies

et al. 2021

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“…The NBC platform technology has the potential to be used in the development of point-of-care diagnostics for pathogen detection and disease management in developed and developing countries [132]. Of course, new simulation and machine learning approaches can help better optimize these devices [133][134][135]. The schematic representation of the current analytical methods and POC devices applied for the detection of E. coli are shown in Figure 11.…”

Section: Point Of Care (Poc) Devices For Clinical Applicationsmentioning

confidence: 99%

Nanomaterials in the Management of Gram-Negative Bacterial Infections

et al. 2021

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The exploration of multiplexed bacterial virulence factors is a major problem in the early stages of Escherichia coli infection therapy. Traditional methods for detecting Escherichia coli (E. coli), such as serological experiments, immunoassays, polymerase chain reaction, and isothermal microcalorimetry have some drawbacks. As a result, detecting E. coli in a timely, cost-effective, and sensitive manner is critical for various areas of human safety and health. Intelligent devices based on nanotechnology are paving the way for fast and early detection of E. coli at the point of care. Due to their specific optical, magnetic, and electrical capabilities, nanostructures can play an important role in bacterial sensors. Another one of the applications involved use of nanomaterials in fighting microbial infections, including E. coli mediated infections. Various types of nanomaterials, either used directly as an antibacterial agent such as metallic nanoparticles (NPs) (silver, gold, zinc, etc.), or as a nanocarrier to deliver and target the antibiotic to the E. coli and its infected area. Among different types, polymeric NPs, lipidic nanocarriers, metallic nanocarriers, nanomicelles, nanoemulsion/ nanosuspension, dendrimers, graphene, etc. proved to be effective vehicles to deliver the drug in a controlled fashion at the targeted site with lower off-site drug leakage and side effects.

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“…Beyond modifying Cas9 to generate specific types of edits, predicting the on-target efficiency and off-target effects of particular sgRNAs remains challenging. Recently, however, machine learning approaches have been developed to more efficiently predict these two parameters, and can reduce the guesswork required when designing efficient sgRNAs [ 91 , 92 ].…”

Section: Challenges and Emerging Technologies For Crispr/cas9-based Crop Improvementmentioning

confidence: 99%

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

Liu

Lindsay

Jackson

2021

IJMS

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Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.

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sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks

Cited by 99 publications

References 77 publications

CoNi alloy nanoparticles for cancer theranostics: synthesis, physical characterization, in vitro and in vivo studies

CoNi alloy nanoparticles for cancer theranostics: synthesis, physical characterization, in vitro and in vivo studies

Nanomaterials in the Management of Gram-Negative Bacterial Infections

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

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