Top Research Papers on CRISPR

This Perspective presents a detailed summary of which micro/nanotechnologies play roles in the advancement of CRISPR diagnosis and how they are involved, and discusses upcoming opportunities and improvements and how micro-nanoteschnologies will continue to play key roles.

The CRISPR/Cas9-mediated lateral flow nucleic acid assay satisfies some of the characteristics of a next-generation molecular diagnostics tool due to its rapidity and accuracy, allowing for point-of-care use without the need for technical expertise and complex ancillary equipment.

Following the above attempts, the developed CRISPR/Cas12a biosensors not only present an ultrasensitive assay behavior toward these model non-nucleic acid analytes but also can serve as a formidable toolbox for determining real samples including single cell lysates and human plasma, proving a good practical application capacity.

A clustered regularly interspaced short palindromic repeats-mediated surface-enhanced Raman scattering (SERS) assay for multidrug-resistant (MDR) bacteria is reported, which may prove effective for the accurate diagnosis of MDR bacterial pathogens, thus preventing severe infection by ensuring appropriate antibiotic treatment.

A novel design for a colorimetric gene-sensing platform based on the CRISPR/Cas system shows superior characteristics, such as probe universality, compatibility with isothermal reaction conditions, on-site detection capability, and high sensitivity; thus represents a robust next-generation gene detection platform.

It is suggested that this ultrasensitive amplification-free detection system for nucleic acids can be widely applied to the precise and early diagnosis of viral infections, cancers, and several genetic diseases.

This work presents the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea, and highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination.

This paper proposes an Efficient and Effective Incomplete Multi-view Clustering (EE-IMVC) algorithm, which proposes to impute each incomplete base matrix generated by incomplete views with a learned consensus clustering matrix to address issues of intensive computational and storage complexities, over-complicated optimization and limitedly improved clustering performance.

It is shown that LNP delivery of CRISPR-Cas9 enables repeated injections into skeletal muscle and leads to restored dystrophin expression in multiple muscle groups.

The fast locality-sensitive hashing–based clustering (FLSHclust) algorithm is developed, which performs deep clustering on massive datasets in linearithmic time, and uncovered more than 200 new functional systems linked to CRISPR, a technology editing DNA.

This work describes the proposed method as Structurally Regularized Deep Clustering (SRDC), where it enhances target discrimination with clustering of intermediate network features, and enhance structural regularization with soft selection of less divergent source examples.

ABSTRACT Current stellar evolution models predict a dearth of black holes (BHs) with masses $\gtrsim \! 50\, \rm M_\odot$ and $\lesssim \! 5\, \rm M_\odot$, and intermediate-mass black holes (IMBHs; $\sim \! 10^2\!-\! 10^5\rm\, M_\odot$) have not yet been detected beyond any reasonable doubt. A natural way to form massive BHs is through repeated mergers, detectable via gravitational wave emission with current LIGO/Virgo or future LISA and ET observations. Nuclear star clusters (NSCs) have masses and densities high enough to retain most of the merger products, which acquire a recoil kick at the...

A genetically encoded model in which L1 and B1/Alu repeats blueprint chromatin macrostructure is proposed, which explains the robustness of genome folding into a common conserved core, on which dynamic gene regulation is overlaid across cells.

A robust bi-stochastic graph regularized matrix factorization (RBSMF) framework for data clustering is proposed, which is more robust than the commonly used general loss function.

Abstract Many prokaryotes employ CRISPR–Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5 , against a panel of six type I systems: I–F ( Pseudomonas , Pectobacterium , and Serratia ), I–E ( Pseudomonas and Serratia ), and I–C ( Pseudomonas )...

It is found that STRs can modulate transcription factor (TF)-DNA affinities and on rates by up to 70-fold by directly binding TF DNA-binding domains, with energetic impacts approaching or exceeding mutations to consensus sites.

This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems.

Four ongoing research hotspots in molecular diagnostics-target preamplification-free detection, microRNA (miRNA) detection, non-nucleic-acid detection, and SARS-CoV-2 detection-are also covered.

The study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits and finds properties, such as length of variation, that affect the association.

Abstract LIGO and Virgo have reported the detection of GW190521, from the merger of a binary black hole (BBH) with a total mass around 150 M ⊙ . While current stellar models limit the mass of any black hole (BH) remnant to about 40–50 M ⊙ , more massive BHs can be produced dynamically through repeated mergers in the core of a dense star cluster. The process is limited by the recoil kick (due to anisotropic emission of gravitational radiation) imparted to merger remnants, which can escape the parent cluster, thereby terminating growth. We study the role of the host cluster metallicity and escap...

A deep sparse regularizer learning model that learns data-driven sparse regularizers adaptively and applies this model to multi-view clustering and semi-supervised classification tasks to learn a latent compact representation.

Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion.

Approaches of Acr proteins for post-translational control of CRISPR-Cas systems in prokaryotic and mammalian cells, organisms and ecosystems are discussed.

A novel method called correntropy-based hypergraph regularized NMF (CHNMF) is proposed to solve the complex optimization problem of non-negative matrix factorization and extensive experimental results indicate that the proposed method is superior to other state-of-the-art methods for clustering and feature selection.

This Review focuses on the potential applications of CRISPR to treat diseases that cannot be overcome by inducing frameshifts or premature stops in coding genes and discusses Cas protein engineering andCRISPR systems beyond Cas9 that create a toolbox to engineer the human genome.

A rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, are provided and their main applications in the sensing of a wide range of molecular targets relevant to human health are highlighted.

It is found that short walks in blue spaces can benefit both well-being and mood, but there was not a positive effect of blue spaces for any of the cardiovascular outcomes assessed in this study.

Analysis of real and simulated data shows that the ExpansionHunter Denovo method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference repeat expansions not discoverable via existing methods.

A new family of viral anti-CRISPR enzymes that rapidly degrade cyclic tetra-adenylate (cA4) is identified and biochemically and structurally described, highlighting the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts.

The regularity of sound change as set out by the scholars of the late nineteenth century is a fundamental principle of historical linguistics. The principle as recognized by the Neogrammarian linguists states that once a sound change has begun, it affects every word in the vocabulary that contains the sound in question. The principle has been disputed by many linguists and especially dialectologists, who argue that ‘every word has its own history’. This article demonstrates how the Neogrammarian principle operates in one prototypical change in progress, the raising of the mid front long vowel ...

It is uncovered that the prices of BEVs are more dependent on the reduction of carbon emissions and government subsidy than FVs, and the adjustment speed of the eco-friendly level of BEV has the most significant impact on the vehicle market.

The engineering of CRISPR Artificial Splicing Factors (CASFx) based on RNA-targetingCRISPR-Cas systems are reported and it is shown that simultaneous exon inclusion and exclusion can be induced at distinct targets by differential positioning of CASFx.

Recent advances in CRISPR–Cas regulation mechanisms by natural biomolecules that enhance or inhibit CRIPSR–Cas immunity, as well as their applications inCRISPR biology and technologies are summarized.

This Primer describes the main concepts of CRISPR screening and gives examples of its application as a method for biological discovery, with a focus on the use of high-content read-outs.

Significant challenges remain before CRISPR/Cas technology can be routinely employed in the clinic for treating different genetic diseases, which include toxicity and immune response of treated cells to CRISpr/Cas component, highly throughput delivery method, and potential off‐target impact.

CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer s...

The enormous progress that has been made in the application of CRISPR tools to the study of cancer is outlined and the potential use of these technologies in clinical cancer management including diagnosis and treatment is described.

A caged RNA strategy that allows Cas9 to bind DNA but not cleave until light-induced activation is developed, referred to as very fast CRISPR (vfCRISPR), which enables DNA repair studies at high resolution in space and time at specific genome locations.

A listeriaphage encoding an anti-CRISPR protein that inactivates the type VI-A CRISPR system of Listeria seeligeri is described and it is found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation.

This review aims to provide a mechanistic insight into the working mechanism of Cas12a, comparing it with Cas9, and eventually provide an overview of its current applications in genome editing and biotechnology applications.