Article
Biotechnology & Applied Microbiology
Arkadiy I. Garber, Catherine R. Armbruster, Stella E. Lee, Vaughn S. Cooper, Jennifer M. Bomberger, Sean M. McAllister
Summary: SprayNPray is a fast and user-friendly software tool for taxonomic classification of assembled sequences, reducing barriers for biologists beginning to analyze genomes and metagenomes.
Article
Engineering, Environmental
Qiqi Fu, Zhiqiang Chen, Zhigang Yu, Yiqi Wu, Huanyu Bao, Jianhua Guo, Qinxue Wen
Summary: This study analyzed the variations of intracellular antibiotic resistance genes (iARGs) and extracellular antibiotic resistance genes (eARGs) in swine manure composting. The abundance of ARGs rebounded from the thermophilic phase to the mature phase due to the release of persistent eARGs and the increase of certain iARGs during cell proliferation. The conjugative transfer frequencies of ARGs in composting communities were comparable to pre-composting frequency, and ozone treatment was optimized to suppress the rebound and spread of ARGs, resulting in significant reduction of iARGs and decreased possibilities of conjugation and transformation among the composting products.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Kyoung-Su Choi, Seonjoo Park
Summary: The study assembled the complete chloroplast and mitochondrial genomes of Aeginetia indica, revealing that its chloroplast genome shows massive plastid genes with the loss of one IR, while the mitochondrial genome encodes 53 genes and evidence of intracellular and horizontal gene transfers. Potential candidate gene for causing cytoplasmic male sterility (CMS) development in A. indica is Cox2 (orf43).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Michelle T. Hulin, Mojgan Rabiey, Ziyue Zeng, Andrea Vadillo Dieguez, Sophia Bellamy, Phoebe Swift, John W. Mansfield, Robert W. Jackson, Richard J. Harrison
Summary: Through examining the genomic diversity of Pseudomonas syringae in the cherry phyllosphere, it was found that nonpathogenic strains contain reservoirs of T3SE genes and there may be horizontal gene transfer of different T3SE genes in cherry pathogens. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the emergence of new pathotypes. Genome-based epidemiological surveillance can be used to apply timely control measures to prevent disease.
Article
Engineering, Environmental
Cong Zhang, Xin Zhao, Can Wang, Israel Hakizimana, John C. Crittenden, Azhar Ali Laghari
Summary: This study investigates the effects of ARB disinfection on the risk of HGT, with an electrochemical flow-through reactor (EFTR) being used to inactivate E. coli and remove ARGs. Results show that EFTR effectively reduces ARGs concentration and decreases HGT frequency, making it a promising technology for preventing the spread of antibiotic resistance.
Article
Microbiology
Min Jin Kwon, Charlotte Steiniger, Timothy C. Cairns, Jennifer H. Wisecaver, Abigail L. Lind, Carsten Pohl, Carmen Regner, Antonis Rokas, Vera Meyer
Summary: Fungal secondary metabolites are important for drug discovery, but their biosynthetic pathways are often transcriptionally silent in typical laboratory conditions. Utilizing gene coexpression network approaches can predict global and pathway-specific transcription factors, advancing the discovery and activation of fungal secondary metabolic pathways.
MICROBIOLOGY SPECTRUM
(2021)
Review
Biochemistry & Molecular Biology
Anton E. Shikov, Yury Malovichko, Anton A. Nizhnikov, Kirill S. Antonets
Summary: Genetic exchanges, including homologous recombination (HR) and horizontal gene transfer (HGT), play a crucial role in bacterial evolution and adaptation. Tracking the signs of recombination and HGT events is important for both fundamental and applied science. Although there are existing bioinformatics tools for revealing recombination signals, their advantages, disadvantages, and applicability have not been systematically reviewed. In this review, a classification of novel instruments for HR and HGT detection based on genomic consequences is proposed, and available methodologies are summarized with a focus on traceable event types.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Alma Morogovsky, Mariana Handelman, Ammar Abou Kandil, Yona Shadkchan, Nir Osherov
Summary: This study provides experimental evidence for horizontal gene transfer (HGT) mediating antifungal resistance in the pathogenic fungus Aspergillus fumigatus, shedding light on a possible route for HGT of antifungal resistance in the environment and during host infection.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Gang Wang, Huomiao Ran, Jie Fan, Nancy P. Keller, Zhiguo Liu, Fan Wu, Wen-Bing Yin
Summary: This study reveals the widespread alteration of secondary metabolites (SMs) during fungal-fungal interactions. Cocultivation of an endophytic fungus Epicoccum dendrobii with Aspergillus nidulans and other filamentous fungi activates multiple silent biosynthetic gene clusters in A. nidulans. The loss-of-function VeA1 protein, transcription factor SclB, and velvet complex members LaeA and VelB are found to be responsible for the SM changes in A. nidulans. This research provides new insights into the mechanisms that trigger metabolic changes in fungal-fungal interactions.
Article
Microbiology
Maria Uzun, Veronika Koziaeva, Marina Dziuba, Pedro Leao, Maria Krutkina, Denis Grouzdev
Summary: This study discovered new man genes and inferred that the last common ancestor of magnetotactic bacteria may not have been magnetotactic. The transmission of magnetosome synthesis genes was mediated by horizontal gene transfer (HGT), and the interphylum transfer of magnetosome genes was detected for the first time.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Joshua G. Philips, Elena Martin-Avila, Andrea V. Robold
Summary: This review provides updated evidence on the likelihood, factors, and barriers for horizontal gene transfer in genetically modified plants, and presents the legislation and frameworks followed by the Australian Gene Technology Regulator in considering the risks posed by horizontal gene transfer.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Virology
Assane Hamidou Abdoulaye, Jichun Jia, Aqleem Abbas, Du Hai, Jiasen Cheng, Yanping Fu, Yang Lin, Daohong Jiang, Jiatao Xie
Summary: This article describes the genome and evolutionary position of the fusarivirus Rhizoctonia solani fusarivirus 4 (RsFV4). The results show that RsFV4 is related to other fusariviruses of R. solani, and one of its coding regions is closer to helicases of potyviruses and hypoviruses, suggesting an evolutionary link between these three virus groups.
Article
Plant Sciences
Grzegorz Goralski, Magdalena Denysenko-Bennett, Anna Burda, Natalia Staszecka-Moskal, Dagmara Kwolek
Summary: Horizontal gene transfer (HGT) is a process allowing genetic material flow between distantly related organisms, primarily observed in bacteria, protists, and various lineages of eukaryotes. Recent research has focused on HGT in plants, particularly parasitic plants, with close physical contact believed to facilitate the transfer. The mechanisms and future research areas in this field remain to be further explored.
ACTA BIOLOGICA CRACOVIENSIA SERIES BOTANICA
(2021)
Article
Biology
Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel, Fabian Staubach
Summary: The study reveals the significant impact of microbial genomic variation on host fitness, with the thiamine biosynthesis pathway playing a role in the variation of offspring production in Drosophila. Horizontal gene transfer can enhance microbiome flexibility and potentially contribute to host adaptation.
Article
Microbiology
Gaurav Agarwal, Ronald D. Gitaitis, Bhabesh Dutta
Summary: This study revealed the genomic structure and evolution pattern of Psi through whole genome sequencing and phylogenetic analysis, identifying pathogenicity genes of Psi in onions. Horizontal gene transfer analysis demonstrated gene transfer between different Pantoea species, with frequent gene transfer events observed between the two pathovars of Psi.
Article
Biochemistry & Molecular Biology
Catherine Ausland, Jinfang Zheng, Haidong Yi, Bowen Yang, Tang Li, Xuehuan Feng, Bo Zheng, Yanbin Yin
Summary: PULs are gene clusters containing CAZymes and other genes that digest and utilize carbohydrate substrates, and dbCAN-PUL is an online database displaying experimentally verified CAZyme-containing PULs with metadata, sequences, and annotation. Compared to other resources, dbCAN-PUL offers new features such as batch download, annotation, external links, homologous gene cluster display, and BLASTX query service.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Bo Zheng, Yinchao He, Pengxiang Zhang, Yi-Xin Huo, Yanbin Yin
Summary: This study curated experimentally characterized polyphenol utilization proteins (PUPs) and their homologs, identified potential players in polyphenol metabolism in the human gut microbiome, and found that Africans have higher abundance and prevalence of PUP homologs and gene clusters than other populations.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Xiao Wang, Jia Wang, Han Zhang, Shenwei Huang, Yanbin Yin
Summary: Researchers propose a novel deep learning approach, which is a hierarchical distribution-matching framework assisted with contrastive learning, to address batch effects in single-cell RNA sequencing data. This method effectively reduces distribution differences between different batches and aligns samples from different batches to recover cell type clusters.
Article
Biochemical Research Methods
Chuanze Kang, Han Zhang, Zhuo Liu, Shenwei Huang, Yanbin Yin
Summary: This paper presents a novel GNN method LR-GNN based on link representation learning for accurately predicting molecular associations. Experimental results show that LR-GNN outperforms state-of-the-art methods and demonstrates robust ability to predict unknown associations. Visualizations also validate the effectiveness of the link representation used in LR-GNN.
BRIEFINGS IN BIOINFORMATICS
(2022)
Letter
Plant Sciences
Jinfang Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin
HORTICULTURE RESEARCH
(2022)
Article
Biochemical Research Methods
Tang Li, Yanbin Yin
Summary: The pan-genome analysis of metagenome-assembled genomes (MAGs) can be affected by issues such as fragmentation, incompleteness, and contamination. In this study, the researchers conducted a critical assessment of pan-genomics by comparing the results of complete bacterial genomes and simulated MAGs. The findings show that incompleteness leads to significant loss of core genes, while contamination mainly affects accessory genomes. Lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes can alleviate the loss, but to a limited extent. The study concludes that new pan-genome analysis tools specifically for MAGs are needed.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Engineering, Environmental
Hong-yu Wei, Yi Li, Jiao Yan, Shuai-ying Peng, Sai-jin Wei, Yanbin Yin, Kun-tai Li, Xin Cheng
Summary: This study found that EPS from Lactobacillus plantarum LPC-1 has a regulating effect on cell wall remodeling in rice roots and enhances plants' resistance to heavy metals.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Jinfang Zheng, Boyang Hu, Xinpeng Zhang, Qiwei Ge, Yuchen Yan, Jerry Akresi, Ved Piyush, Le Huang, Yanbin Yin
Summary: The updated dbCAN-seq database provides predictions of glycan substrates for CGCs from microbiomes. New features include graphical display of CGC gene compositions, alignment of query CGC and subject PUL, and a statistics page.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Bowen Yang, Jinfang Zheng, Yanbin Yin
Summary: This paper introduces AcaFinder, the first tool for Aca genome mining. AcaFinder can predict Acas and their associated acr-aca operons, identify homologs of known Acas, and analyze potential prophages, CRISPR-Cas systems, and self-targeting spacers (STSs) in input genomes. The tool was applied to mining prokaryotic and gut phage genomes, resulting in the identification of 36 high-confident new Aca families. The study also reveals a complex association network between Acrs and Acas.
Article
Computer Science, Artificial Intelligence
Mingjing Han, Han Zhang, Wei Li, Yanbin Yin
Summary: In this paper, a novel method called Semantic-guided Graph Neural Network (SGNN) is proposed to address the semantic confusion problem in heterogeneous graph embedding. The proposed SGNN utilizes two-level fusion mechanisms to enhance the local representation and extract jumping knowledge from multiple semantics. Experimental results demonstrate the effectiveness of SGNN in real-world tasks.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin
Summary: dbCAN is an online web server for automated annotation of carbohydrate active enzymes (CAZymes). dbCAN3 is an updated version of this server with three new methods for predicting glycan substrates, as well as improved data browsing and visualization features.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Yanbin Yin, Zhiqiang Yan, Jianing Guan, Yiqiong Huo, Tianqiong Wang, Tong Li, Zhibo Cui, Wenhong Ma, Xiaoxue Wang, Wenfu Chen
Summary: Hd1 binding protein 1 (HBP1) and Partner of HBP1 (POH1) were identified as transcriptional regulators of Heading date 1 (Hd1), which is a key factor in the photoperiodic control of flowering time in rice. HBP1 and POH1 physically interacted to form homo- or heterodimers and directly activated the expression of Hd1 by binding to its promoter region. Knockout mutations of HBP1 accelerated flowering time, while overexpression of HBP1 and POH1 delayed flowering time by regulating the expression of Hd1 and other related genes.
Article
Biochemistry & Molecular Biology
Yuchen Yan, Jinfang Zheng, Xinpeng Zhang, Yanbin Yin
Summary: In this study, we developed dbAPIS as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include experimentally verified APIS genes with their protein sequences, functional annotation, structures, genomic context, homologs, classification of APIS proteins, and user-friendly web interface for data browsing, searching, and batch downloading. The current release of dbAPIS contains 41 verified APIS proteins and a large number of sequence homologs of different families and clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Bowen Yang, Minal Khatri, Jinfang Zheng, Jitender Deogun, Yanbin Yin
Summary: Recent studies have shown that known anti-CRISPR (Acr) genes often exist in the same operons as other Acr genes and phage structural genes. However, current Acr prediction tools do not take this important genomic context into consideration. Researchers have developed a new software tool called AOminer, which exploits the genomic context of known Acr genes and their homologs to facilitate the discovery of novel anti-CRISPR operons.
Article
Biology
Nina Rittmeier, Andreas Holzinger
Summary: This study investigated the chromosome visualization methods in the filamentous green alga Zygnema. Existing protocols were modified to allow reliable chromosome counting in this genus. The challenges of interference from cell wall components and random cell divisions were addressed.
