Gradients in gene essentiality reshape antibacterial research

AM Hogan, ST Cardona - FEMS Microbiology Reviews, 2022 - academic.oup.com
Essential genes encode the processes that are necessary for life. Until recently, commonly
applied binary classifications left no space between essential and non-essential genes. In …

[HTML][HTML] Visualizing translation dynamics at atomic detail inside a bacterial cell

L Xue, S Lenz, M Zimmermann-Kogadeeva, D Tegunov… - Nature, 2022 - nature.com
Translation is the fundamental process of protein synthesis and is catalysed by the ribosome
in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram …

Transposon sequencing: A powerful tool for the functional genomic study of food-borne pathogens

X Liu, G Liu, Y Wu, X Pang, Y Wu, J Niu, Q Chen… - Trends in Food Science …, 2021 - Elsevier
Background Genome-wide functional genetic studies of food-borne pathogens could
provide a comprehensive understanding of the mechanisms underline their survival and …

SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome

C Pinero-Lambea, E Garcia-Ramallo… - Nucleic Acids …, 2022 - academic.oup.com
The development of advanced genetic tools is boosting microbial engineering which can
potentially tackle wide-ranging challenges currently faced by our society. Here we present …

The predicting public sentiment evolution on public emergencies under deep learning and internet of things

M Chen, W Du - The Journal of Supercomputing, 2023 - Springer
With the Internet's rapid development and the increasing amount of netizens, social
contradictions frequently manifest over the Internet. Public emergencies develop and spread …

ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs

S Miravet-Verde, R Mazzolini, C Segura-Morales… - nature …, 2024 - nature.com
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a
technique designed to characterize proteomes by sequencing transposon insertions …

[PDF][PDF] Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification

H Zhang, T Lu, S Liu, J Yang, G Sun… - NAR genomics and …, 2021 - academic.oup.com
Tn5 transposase, which can efficiently tagment the genome, has been widely adopted as a
molecular tool in next-generation sequencing, from short-read sequencing to more complex …

[HTML][HTML] Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome

A Broto, C Piñero-Lambea, C Segura-Morales… - Microbes and …, 2024 - Elsevier
A non-pathogenic Mycoplasma pneumoniae-based chassis is leading the development of
live biotherapeutic products (LBPs) for respiratory diseases. However, reports connecting …

Identification of putative essential protein domains from high-density transposon insertion sequencing

ASMZ Rahman, L Timmerman, F Gallardo… - Scientific Reports, 2022 - nature.com
A first clue to gene function can be obtained by examining whether a gene is required for life
in certain standard conditions, that is, whether a gene is essential. In bacteria, essential …

LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions

D Shaw, S Miravet‐Verde… - Microbial …, 2021 - Wiley Online Library
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts
and often requires preliminary knowledge of which genomic regions are dispensable …