When an Intruder Comes Home: GM and GE Strategies to Combat Virus Infection in Plants DOI Creative Commons
Adeeb Rahman, Neeti Sanan‐Mishra

Agriculture, Journal Year: 2024, Volume and Issue: 14(2), P. 282 - 282

Published: Feb. 9, 2024

Viruses are silent enemies that intrude and take control of the plant cell’s machinery for their own multiplication. Infection by viruses resulting damage is still a major challenge in agriculture sector. Plants have capability to fight back, but ability mutate at fast rate helps them evade host’s response. Therefore, classical approaches introgressing resistance genes breeding obtained limited success counteracting virus menace. Genetic modification (GM)-based strategies been successful engineering artificial plants. Several different based on pathogen-derived resistance, antisense constructs, hairpin RNAs, double-stranded RNA, etc., used enhance plants’ viruses. Recently, genome editing (GE) mainly involving CRISPR/Cas-mediated modifications being control. In this review, we discuss developments advancements GM- GE-based methods tackling viral infection

Language: Английский

Advancing genome editing with artificial intelligence: opportunities, challenges, and future directions DOI Creative Commons

Shriniket Dixit,

Anant Kumar, Kathiravan Srinivasan

et al.

Frontiers in Bioengineering and Biotechnology, Journal Year: 2024, Volume and Issue: 11

Published: Jan. 8, 2024

Clustered regularly interspaced short palindromic repeat (CRISPR)-based genome editing (GED) technologies have unlocked exciting possibilities for understanding genes and improving medical treatments. On the other hand, Artificial intelligence (AI) helps achieve more precision, efficiency, affordability in tackling various diseases, like Sickle cell anemia or Thalassemia. AI models been use designing guide RNAs (gRNAs) CRISPR-Cas systems. Tools DeepCRISPR, CRISTA, DeepHF capability to predict optimal a specified target sequence. These predictions take into account multiple factors, including genomic context, Cas protein type, desired mutation on-target/off-target scores, potential off-target sites, impacts of on gene function phenotype. aid optimizing different technologies, such as base, prime, epigenome editing, which are advanced techniques introduce precise programmable changes DNA sequences without relying homology-directed repair pathway donor templates. Furthermore, AI, collaboration with precision medicine, enables personalized treatments based genetic profiles. analyzes patients' data identify mutations, variations, biomarkers associated diseases Cancer, Diabetes, Alzheimer's, etc. However, several challenges persist, high costs, suitable delivery methods CRISPR cargoes, ensuring safety clinical applications. This review explores AI's contribution CRISPR-based addresses existing challenges. It also discusses areas future research AI-driven technologies. The integration opens up new genetics, biomedicine, healthcare, significant implications human health.

Language: Английский

Citations

41
TemStaPro: protein thermostability prediction using sequence representations from protein language models DOI Creative Commons
Ieva Pudžiuvelytė, Kliment Olechnovič, Eglė Godliauskaitė

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(4)

Published: March 18, 2024

Abstract Motivation Reliable prediction of protein thermostability from its sequence is valuable for both academic and industrial research. This problem can be tackled using machine learning by taking advantage the recent blossoming deep methods analysis. These facilitate training on more data and, possibly, enable development versatile predictors multiple ranges temperatures. Results We applied principle transfer to predict embeddings generated language models (pLMs) an input sequence. used large pLMs that were pre-trained hundreds millions known sequences. The such allowed us efficiently train validate a high-performing method over one million sequences we collected organisms with annotated growth Our method, TemStaPro (Temperatures Stability Proteins), was CRISPR-Cas Class II effector proteins (C2EPs). Predictions indicated sharp differences among groups C2EPs in terms largely tune previously published our newly obtained experimental data. Availability implementation software related are freely available https://github.com/ievapudz/TemStaPro https://doi.org/10.5281/zenodo.7743637.

Language: Английский

Citations

22
CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks DOI
Delight Hwarari,

Yasmina Radani,

Yongchao Ke

et al.

Functional & Integrative Genomics, Journal Year: 2024, Volume and Issue: 24(2)

Published: March 5, 2024

Language: Английский

Citations

13
Crop Improvement: Comparison of Transgenesis and Gene Editing DOI Creative Commons
Natalya V. Permyakova, Е. В. Дейнеко

Horticulturae, Journal Year: 2024, Volume and Issue: 10(1), P. 57 - 57

Published: Jan. 6, 2024

The development and improvement of molecular biology methods have led to the creation new technologies that make it possible modify plant genomes by transferring integrating into genomes’ heterologous genes from various expression systems (genetic engineering), as well inducing knockouts one or more target interest (genomic editing). genome-editing is a milestone in modern breeding certainly relies on knowledge developed for transgenesis. This review will discuss issues related advantages disadvantages both improving economically valuable traits important crops.

Language: Английский

Citations

9
Plant protection from virus: a review of different approaches DOI Creative Commons
Irina Anikina, Aidana Kamarova, Kuralay Issayeva

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: June 12, 2023

This review analyzes methods for controlling plant viral infection. The high harmfulness of diseases and the peculiarities pathogenesis impose special requirements regarding developing to prevent phytoviruses. control infection is complicated by rapid evolution, variability viruses, their pathogenesis. Viral in plants a complex interdependent process. creation transgenic varieties has caused much hope fight against pathogens. disadvantages genetically engineered approaches include fact that resistance gained often highly specific short-lived, there are bans many countries on use varieties. Modern prevention methods, diagnosis, recovery planting material at forefront main techniques used healing virus-infected apical meristem method, which combined with thermotherapy chemotherapy. These represent single biotechnological method from viruses vitro culture. It widely uses this obtaining non-virus various crops. tissue culture-based health improvement possibility self-clonal variations resulting long-term cultivation under conditions. possibilities increasing stimulating immune system have expanded, results in-depth study molecular genetic bases toward investigation mechanisms induction protective reactions organism. existing phytovirus ambiguous require additional research. Further genetic, biochemical, physiological features development strategy increase will allow new level be reached.

Language: Английский

Citations

20
Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests DOI Creative Commons

Jocelyn Reynolds,

Reid S. Loeffler,

Preston J. Leigh

et al.

Biosensors, Journal Year: 2023, Volume and Issue: 13(9), P. 885 - 885

Published: Sept. 15, 2023

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify amplification. Recently, numerous attempts been made to incorporate paper microfluidics into these isothermal tests. Paper (including lateral flow strips) used extract acids, amplify the target gene, detect amplified products, all toward automating process. We investigated literature from 2020 present, i.e., since onset of COVID-19 pandemic, during which significant surge in has observed. microfluidic detection extensively for recombinase (RPA) its related methods, along with loop-mediated (LAMP) rolling circle (RCA). Detection was conducted primarily colorimetric fluorometric although few publications demonstrated distance- surface-enhanced Raman spectroscopic (SERS)-based detection. A good number could be found that both on platforms. small showed extraction or three procedures (i.e., fully integrated systems) platforms, necessitating need future work.

Language: Английский

Citations

15
Advancements in the synergy of isothermal amplification and CRISPR-cas technologies for pathogen detection DOI Creative Commons

Xiaolei Mao,

Minghui Xu,

Shuyin Luo

et al.

Frontiers in Bioengineering and Biotechnology, Journal Year: 2023, Volume and Issue: 11

Published: Oct. 10, 2023

In the realm of pathogen detection, isothermal amplification technology has emerged as a swift, precise, and sensitive alternative to conventional PCR. This paper explores fundamental principles recombinase polymerase (RPA) recombinase-aid (RAA) reviews current status integrating CRISPR-Cas system with RPA/RAA techniques. Furthermore, this confluence technology, providing comprehensive review enhancements existing combined methodologies such SHERLOCK DETECTR. We investigate practical applications in conjunction for highlighting how integrated approach significantly advances both research clinical implementation field. aims provide readers concise understanding fusion offering insights into their utility, ongoing enhancements, promising prospects detection.

Language: Английский

Citations

15
Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica) DOI Creative Commons
Yihui Gong, Xuan Luo, Ting Zhang

et al.

Genomics, Journal Year: 2024, Volume and Issue: 116(3), P. 110859 - 110859

Published: May 1, 2024

Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate functions mitochondrial (mt) genome Luffa cylindrica. The mt L. cylindrica contained two chromosomes with lengths 380,879 bp 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA 3 rRNA 1 pseudogene, were identified. About 90.63% codons ended A or U bases, 98.63% monomers A/T, which contributed high A/T content (55.91%) complete genome. Six (ATP8, CCMFC, NAD4, RPL10, RPL5 RPS4) showed positive selection. Phylogenetic analysis indicates that is closely related acutangula. present results provide cylindrica, may facilitate possible variation, evolutionary, molecular breeding studies

Language: Английский

Citations

4
CRISPR/Cas9 opens new horizon of crop improvement under stress condition DOI
Sanjib K. Patra,

Debdatta Chatterjee,

Shrabani Basak

et al.

Biochimica et Biophysica Acta (BBA) - General Subjects, Journal Year: 2024, Volume and Issue: 1868(10), P. 130685 - 130685

Published: July 28, 2024

Language: Английский

Citations

4
CRISPR/Cas in Grapevine Genome Editing: The Best Is Yet to Come DOI Creative Commons
Chong Ren,

Mohamed Salaheldin Mokhtar Mohamed,

Nuremanguli Aini

et al.

Horticulturae, Journal Year: 2024, Volume and Issue: 10(9), P. 965 - 965

Published: Sept. 11, 2024

The advent of Clustered Regularly Interspaced Palindromic Repeat (CRISPR)/CRISPR-associated (Cas) proteins as a revolutionary innovation in genome editing has greatly promoted targeted modification and trait improvement most plant species. For grapevine (Vitis vinifera L.), perennial woody species, CRISPR/Cas is an extremely promising technique for genetic short period. Advances have been achieved by using CRISPR technology recent years, which promises to accelerate grapevine. In this review, we describe the development advances CRISPR/Cas9 its orthologs variants. We summarize applications discuss challenges facing well possible strategies that could be used improve addition, outline future perspectives model system, precise editing, accelerated improvement, transgene-free editing. believe will play more important role exciting bright expected economically significant

Language: Английский

Citations

4