CRISPR/Cas-based genome engineering in natural product discovery

2019 ◽  
Vol 36 (9) ◽  
pp. 1262-1280 ◽  
Author(s):  
Yaojun Tong ◽  
Tilmann Weber ◽  
Sang Yup Lee
Keyword(s):  
Natural Product ◽  
Genome Editing ◽  
Genome Engineering ◽  
State Of The Art ◽  
Natural Product Discovery ◽  
Current State

This review summarizes the current state of the art of CRISPR/Cas-based genome editing technologies for natural product producers.

The Current State-of-the-Art in Therapeutic Genome Editing and the Future

2016 ◽  
Vol 05 (01) ◽  
Author(s):  
Donya Moradi Manesh ◽  
Punam Malik
Keyword(s):  
Genome Editing ◽  
State Of The Art ◽  
Current State ◽  
The Future

scholarly journals Natural product biosynthesis: What's next? An introduction to the JBC Reviews Thematic Series

2019 ◽  
Vol 295 (2) ◽  
pp. 335-336
Author(s):  
Satish K. Nair ◽  
Joseph M. Jez
Keyword(s):  
Natural Product ◽  
State Of The Art ◽  
Data Sets ◽  
Specialized Metabolites ◽  
Current State ◽  
Modified Peptides ◽  
Thematic Review ◽  
Global Threat ◽  
Derivatives Of ◽  
Academic Sector

The diversity of natural products not only fascinates us intellectually, but also provides an armamentarium against the microbes that threaten our health. The increased prevalence of pathogens that are resistant to one or more classes of available medicines continues to be a growing global threat. As drug-resistant pathogens erode the effectiveness of the current reserve of antibiotics and antifungals, methodological advances open additional avenues for discovery of new classes of drugs, as well as novel derivatives of existing (and proven) classes of compounds. In this Thematic Review Series, we aim to provide a snapshot of the current state of the art in natural product discovery. The reviews in this series encapsulate convergent approaches toward the identification of different classes of primary and specialized metabolites, including nonribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides, from all kingdoms of life. Traction in unraveling new and diverse classes of molecules has come largely from the academic sector, which ensures availability of methods and data sets. Such knowledge is needed to thwart serious threats to human health and calls to mind the proverb praemonitus praemunitus (forewarned is forearmed).

Genome engineering for microbial natural product discovery

2018 ◽  
Vol 45 ◽  
pp. 53-60 ◽  
Author(s):  
Si-Sun Choi ◽  
Yohei Katsuyama ◽  
Linquan Bai ◽  
Zixin Deng ◽  
Yasuo Ohnishi ◽  
...  
Keyword(s):  
Natural Product ◽  
Genome Engineering ◽  
Natural Product Discovery

scholarly journals Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Naoki Wada ◽  
Risa Ueta ◽  
Yuriko Osakabe ◽  
Keishi Osakabe
Keyword(s):  
Genome Editing ◽  
Genome Engineering ◽  
State Of The Art

scholarly journals Deep metric learning improves lab of origin prediction of genetically engineered plasmids

2021 ◽  
Author(s):  
Igor Soares ◽  
Fernando Camargo ◽  
Adriano Marques ◽  
Oliver Crook
Keyword(s):  
Dna Sequences ◽  
Genome Engineering ◽  
State Of The Art ◽  
Learning To Rank ◽  
Metric Learning ◽  
Similarity Measures ◽  
Genetically Engineered ◽  
Current State ◽  
Deep Metric Learning ◽  
Lab Associations

Abstract Genome engineering is undergoing unprecedented development and is now becoming widely available. To ensure responsible biotechnology innovation and to reduce misuse of engineered DNA sequences, it is vital to develop tools to identify the lab-of-origin of engineered plasmids. Genetic engineering attribution (GEA), the ability to make sequence-lab associations, would supportforensic experts in this process. Here, we propose a method, based on metric learning, that ranks the most likely labs-of-origin whilstsimultaneously generating embeddings for plasmid sequences and labs. These embeddings can be used to perform various downstreamtasks, such as clustering DNA sequences and labs, as well as using them as features in machine learning models. Our approach employsa circular shift augmentation approach and is able to correctly rank the lab-of-origin90%of the time within its top 10 predictions -outperforming all current state-of-the-art approaches. We also demonstrate that we can perform few-shot-learning and obtain76%top-10 accuracy using only10%of the sequences. This means, we outperform the previous CNN approach using only one-tenth of the data. We also demonstrate that we are able to extract key signatures in plasmid sequences for particular labs, allowing for an interpretable examination of the model’s outputs.CCS Concepts: Information systems→Similarity measures; Learning to rank.

Behavioral Genetics: Concepts for Research and Practice in Language Development and Disorders

1995 ◽  
Vol 38 (5) ◽  
pp. 1126-1142 ◽  
Author(s):  
Jeffrey W. Gilger
Keyword(s):  
Language Development ◽  
Behavioral Genetics ◽  
State Of The Art ◽  
Genetic Research ◽  
Great Promise ◽  
Behavioral Genetic ◽  
Fine Grained ◽  
Future Goals ◽  
Current State ◽  
Research Designs

This paper is an introduction to behavioral genetics for researchers and practioners in language development and disorders. The specific aims are to illustrate some essential concepts and to show how behavioral genetic research can be applied to the language sciences. Past genetic research on language-related traits has tended to focus on simple etiology (i.e., the heritability or familiality of language skills). The current state of the art, however, suggests that great promise lies in addressing more complex questions through behavioral genetic paradigms. In terms of future goals it is suggested that: (a) more behavioral genetic work of all types should be done—including replications and expansions of preliminary studies already in print; (b) work should focus on fine-grained, theory-based phenotypes with research designs that can address complex questions in language development; and (c) work in this area should utilize a variety of samples and methods (e.g., twin and family samples, heritability and segregation analyses, linkage and association tests, etc.).

Schizophrenia Research: Current State of the Art

1976 ◽  
Vol 21 (7) ◽  
pp. 497-498
Author(s):  
STANLEY GRAND
Keyword(s):  
State Of The Art ◽  
Current State

Umbral Calculus

10.37236/24 ◽  
2002 ◽  
Vol 1000 ◽  
Author(s):  
A. Di Bucchianico ◽  
D. Loeb
Keyword(s):  
19Th Century ◽  
Finite Differences ◽  
State Of The Art ◽  
Umbral Calculus ◽  
Current State ◽  
Logical Foundation ◽  
Complete Bibliography ◽  
The 19Th Century ◽  
Mathematical Literature

We survey the mathematical literature on umbral calculus (otherwise known as the calculus of finite differences) from its roots in the 19th century (and earlier) as a set of “magic rules” for lowering and raising indices, through its rebirth in the 1970’s as Rota’s school set it on a firm logical foundation using operator methods, to the current state of the art with numerous generalizations and applications. The survey itself is complemented by a fairly complete bibliography (over 500 references) which we expect to update regularly.

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