scholarly journals CRISPR/Cas Technologies and Their Applications in Escherichia coli

2021 ◽  
Vol 9 ◽  
Author(s):  
Huina Dong ◽  
Yali Cui ◽  
Dawei Zhang
Keyword(s):  
Escherichia Coli ◽  
Transcriptional Regulation ◽  
Homologous Recombination ◽  
Genome Editing ◽  
State Of The Art ◽  
Bacterial Species ◽  
The State ◽  
Research Progress ◽  
End Joining ◽  
Eukaryotic Organism

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have revolutionized genome editing and greatly promoted the development of biotechnology. However, these systems unfortunately have not been developed and applied in bacteria as extensively as in eukaryotic organism. Here, the research progress on the most widely used CRISPR/Cas tools and their applications in Escherichia coli is summarized. Genome editing based on homologous recombination, non-homologous DNA end-joining, transposons, and base editors are discussed. Finally, the state of the art of transcriptional regulation using CRISPRi is briefly reviewed. This review provides a useful reference for the application of CRISPR/Cas systems in other bacterial species.

scholarly journals Ku Heterodimer-Independent End Joining in Trypanosoma brucei Cell Extracts Relies upon Sequence Microhomology

2007 ◽  
Vol 6 (10) ◽  
pp. 1773-1781 ◽  
Author(s):  
Peter Burton ◽  
David J. McBride ◽  
Jonathan M. Wilkes ◽  
J. David Barry ◽  
Richard McCulloch
Keyword(s):  
Homologous Recombination ◽  
Trypanosoma Brucei ◽  
Antigenic Variation ◽  
Bacterial Species ◽  
Nonhomologous End Joining ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Strand Breaks ◽  
Cell Extracts ◽  
Ligase Iv

ABSTRACT DNA double-strand breaks (DSBs) are repaired primarily by two distinct pathways: homologous recombination and nonhomologous end joining (NHEJ). NHEJ has been found in all eukaryotes examined to date and has been described recently for some bacterial species, illustrating its ancestry. Trypanosoma brucei is a divergent eukaryotic protist that evades host immunity by antigenic variation, a process in which homologous recombination plays a crucial function. While homologous recombination has been examined in some detail in T. brucei, little work has been done to examine what other DSB repair pathways the parasite utilizes. Here we show that T. brucei cell extracts support the end joining of linear DNA molecules. These reactions are independent of the Ku heterodimer, indicating that they are distinct from NHEJ, and are guided by sequence microhomology. We also demonstrate bioinformatically that T. brucei, in common with other kinetoplastids, does not encode recognizable homologues of DNA ligase IV or XRCC4, suggesting that NHEJ is either absent or mechanistically diverged in these pathogens.

Prime editing: The state-of-the-art of genome editing

Meta Gene ◽  
2020 ◽  
Vol 24 ◽  
pp. 100661
Author(s):  
Fatemeh Khatami ◽  
Maryam Aghaii ◽  
Seyed Mohammad Kazem Aghamir
Keyword(s):  
Genome Editing ◽  
State Of The Art ◽  
The State

scholarly journals The Research Progress of SiRNA Targeting Notch1 on Tumor Cells: A Mini Review of the State of the Art

2016 ◽  
Vol 6 (3) ◽  
pp. 163-166
Author(s):  
Lanfen Huo ◽  
◽  
Shaoling Wu ◽  
Zhonghai Chi ◽  
Xindong Zhao ◽  
...  
Keyword(s):  
Tumor Cells ◽  
State Of The Art ◽  
The State ◽  
Research Progress

scholarly journals Next-Generation Gene Therapy for Parkinson’s Disease Using Engineered Viral Vectors

2021 ◽  
pp. 1-9
Author(s):  
Tomas Björklund ◽  
Marcus Davidsson
Keyword(s):  
Parkinson’S Disease ◽  
Gene Therapy ◽  
Parkinson's Disease ◽  
Clinical Trials ◽  
Genome Editing ◽  
Viral Vectors ◽  
State Of The Art ◽  
The State ◽  
Next Generation ◽  
Suitable Vector

Recent technological and conceptual advances have resulted in a plethora of exciting novel engineered adeno associated viral (AAV) vector variants. They all have unique characteristics and abilities. This review summarizes the development and their potential in treating Parkinson’s disease (PD). Clinical trials in PD have shown over the last decade that AAV is a safe and suitable vector for gene therapy but that it also is a vehicle that can benefit significantly from improvement in specificity and potency. This review provides a concise collection of the state-of-the-art for synthetic capsids and their utility in PD. We also summarize what therapeutical strategies may become feasible with novel engineered vectors, including genome editing and neuronal rejuvenation.

CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art

2017 ◽  
Vol 101 (20) ◽  
pp. 7435-7443 ◽  
Author(s):  
Tian-Qiong Shi ◽  
Guan-Nan Liu ◽  
Rong-Yu Ji ◽  
Kun Shi ◽  
Ping Song ◽  
...  
Keyword(s):  
Genome Editing ◽  
Filamentous Fungi ◽  
State Of The Art ◽  
The State

scholarly journals Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla

Microbiology ◽  
2020 ◽  
Vol 166 (11) ◽  
pp. 1047-1064 ◽  
Author(s):  
Deepti Gurung ◽  
Robert M. Blumenthal
Keyword(s):  
Escherichia Coli ◽  
Dna Damage ◽  
Homologous Recombination ◽  
Dna Sequences ◽  
Type Species ◽  
Bacterial Species ◽  
Distribution Patterns ◽  
Content Type ◽  
Link Type ◽  
Open Questions

Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli ; while bacteria in other phyla, like the Firmicute Bacillus subtilis , use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.

scholarly journals Deep Emotion Recognition in Dynamic Data using Facial, Speech and Textual Cues: A Survey

2021 ◽  
Author(s):  
Tao Zhang ◽  
Zhenhua Tan
Keyword(s):  
Deep Learning ◽  
Emotion Recognition ◽  
State Of The Art ◽  
The State ◽  
Research Progress ◽  
Speech Emotion Recognition ◽  
Expression Recognition ◽  
Learning Techniques ◽  
Textual Cues ◽  
Definition Of

With the development of social media and human-computer interaction, video has become one of the most common data formats. As a research hotspot, emotion recognition system is essential to serve people by perceiving people’s emotional state in videos. In recent years, a large number of studies focus on tackling the issue of emotion recognition based on three most common modalities in videos, that is, face, speech and text. The focus of this paper is to sort out the relevant studies of emotion recognition using facial, speech and textual cues due to the lack of review papers concentrating on the three modalities. On the other hand, because of the effective leverage of deep learning techniques to learn latent representation for emotion recognition, this paper focuses on the emotion recognition method based on deep learning techniques. In this paper, we firstly introduce widely accepted emotion models for the purpose of interpreting the definition of emotion. Then we introduce the state-of-the-art for emotion recognition based on unimodality including facial expression recognition, speech emotion recognition and textual emotion recognition. For multimodal emotion recognition, we summarize the feature-level and decision-level fusion methods in detail. In addition, the description of relevant benchmark datasets, the definition of metrics and the performance of the state-of-the-art in recent years are also outlined for the convenience of readers to find out the current research progress. Ultimately, we explore some potential research challenges and opportunities to give researchers reference for the enrichment of emotion recognition-related researches.

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