Yunhai Yi

Collection of Open Science practices in a research workflow

Jeroen Bosman, Yunhai Yi, Sarah Coombs, Angelos Konstantinidis et autres

This is a set of files with description of 237 open science practices. It also has formatted cards for all practices that can be printed and used in a variety of settings.

A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems

Yunhai Yi, Lifeng Liang, Anne de Jong, Oscar Paul Kuipers

The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in …

nl (code pays fourni par la source)

Exploring natural product biosynthetic potential in diverse microbial ecosystems

Yunhai Yi

In this thesis, we explore the diverse range of natural products produced by microbes in various ecosystems. By investigating the unique properties of these bioresources, we aim to discover and develop new antibiotics and other drugs. Our studies include examining the gut …

Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains

Patricia Arias-Orozco, Lu Zhou, Yunhai Yi, Rubén Cebrián et autres

ABSTRACT Picocyanobacteria can synthesize a distinctive class of lanthipeptides referred to as prochlorosins. They are classified within the Nif11 family and are subject to post-translational modifications by a solitary promiscuous enzyme from the ProcM group. Their biological function is unknown but highly …

nl, be, es (code pays fourni par la source)

Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products

María Victoria Fernández-Cantos, Diego García-Morena, Yunhai Yi, Lifeng Liang et autres

The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut’s microbial food webs, or …

nl (code pays fourni par la source)

Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM

Patricia Arias-Orozco, Yunhai Yi, Fleur Ruijne, Rubén Cebrián et autres

ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform …

nl, es (code pays fourni par la source)

Biocontrol properties from phyllospheric bacteria isolated from Solanum lycopersicum and Lactuca sativa and genome mining of antimicrobial gene clusters

Claudia Y. Muñoz, Lu Zhou, Yunhai Yi, Oscar Paul Kuipers

BACKGROUND: Biocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed …

nl (code pays fourni par la source)

Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From Pseudomonas mediterranea EDOX

Lu Zhou, Anne de Jong, Yunhai Yi, Oscar Paul Kuipers

The plant microbiome is a vastly underutilized resource for identifying new genes and bioactive compounds. Here, we used Pseudomonas sp. EDOX, isolated from the leaf endosphere of a tomato plant grown on a small farm in the Netherlands. To get more insight …

nl (code pays fourni par la source)

Temporal dynamics of teleost populations during the Pleistocene: a report from publicly available genome data

Jia Li, Chao Bian, Yunhai Yi, Hui Yu et autres

Abstract Background Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection pressures (such as food shortage and habitat loss) and went through population declines. However, …

cn, mo (code pays fourni par la source)

Genome Mining of Antimicrobial Gene Clusters from Phyllospheric Bacteria Isolated from Solanum Lycopersicum and Lactuca Sativa to Identify Biocontrol Properties

Claudia Y. Muñoz, Lu Zhou, Yunhai Yi, Oscar Paul Kuipers

Abstract BackgroundBiocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed …

nl (code pays fourni par la source)

Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter , Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains

Patricia Arias-Orozco, Yunhai Yi, Oscar Paul Kuipers

Species of the Alteromonas and Marinobacter genera are heterotrophic Gammaproteobacteria that are part of the marine microbial ecosystem. In this study, four strains were isolated from two nonaxenic Synechococcus cultures and were sequenced. Few studies of these two genera have been reported. …

nl, cn (code pays fourni par la source)

The first Conus genome assembly reveals a primary genetic central dogma of conopeptides in C. betulinus

Chao Peng, Yu Shu Huang, Chao Bian, Jia Li et autres

Although there are various Conus species with publicly available transcriptome and proteome data, no genome assembly has been reported yet. Here, using Chinese tubular cone snail (C. betulinus) as a representative, we sequenced and assembled the first Conus genome with original identification …

cn, mo (code pays fourni par la source)