Review
Biotechnology & Applied Microbiology
Alexander Arsov, Kaloyan Petrov, Penka Petrova
Summary: This article discusses the potential of microbial production of butanol as a new fuel and the challenge of butanol toxicity to microbes. Modern omics approaches have made significant progress in addressing the issue of low butanol tolerance, but a strain capable of both synthesis and tolerance at commercializable concentrations has yet to be discovered or produced.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Engineering, Chemical
Tao Sun, Shubin Li, Guangsheng Pei, Lei Chen, Weiwen Zhang
Summary: Synthetic biology research has utilized photosynthetic cyanobacteria as autotrophic cell factories for the direct biosynthesis of various biofuels from CO2. However, the low tolerance to toxicity of biofuels restricts the economic application of cyanobacterial hosts. This study investigates the stress responses of Synechocystis sp. PCC 6803 to exogenous n-hexane using RNAseq transcriptomics and identifies a regulatory gene, slr0724, involved in n-hexane tolerance. This research contributes to a better understanding of cellular responses to n-hexane and the potential engineering of n-hexane tolerance in cyanobacteria.
CHINESE JOURNAL OF CHEMICAL ENGINEERING
(2023)
Article
Environmental Sciences
Xiuqi You, Xiaoqiang Cao, Xuan Zhang, Jianhua Guo, Weiling Sun
Summary: The study explores the combined toxicity of antibiotics and nanoplastics/microplastics, revealing an antagonistic effect between antibiotics and NPs/MPs. The toxic effects of NPs/MPs are particle size-dependent, with ROS identified as an important factor for inhibiting cell growth.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Genetics & Heredity
Kaloyan Petrov, Alexander Arsov, Penka Petrova
Summary: The study identified genetic factors involved in the butanol stress response of Lactiplantibacillus plantarum, revealing common species-specific effects of butanol stress such as upregulation of multidrug efflux transporters, toxin-antitoxin system, and transcriptional regulators. The strains differed greatly in DEGs responsible for membrane transport, metabolism, and important transcriptional regulators, with uniquely upregulated genes in the butanol-resistant strain contributing to tolerance. The phosphoenolpyruvate flux and the phosphotransferase system were also found to be major factors in butanol tolerance.
Article
Genetics & Heredity
Jingbo Wang, Chang Su, Zhibo Cui, Lixiang Huang, Shuang Gu, Sixu Jiang, Jing Feng, Hai Xu, Wenzhong Zhang, Linlin Jiang, Minghui Zhao
Summary: Transcriptomics and metabolomics analyses were conducted to investigate the mechanism of aluminum (Al) tolerance in two rice landraces. The results revealed that genes related to phenylpropanoid biosynthesis were highly enriched in both landraces, suggesting the close relationship between phenylpropanoid biosynthesis and Al tolerance. Peroxidase was identified as the most significant enzyme in phenylpropanoid biosynthesis, regulated by multiple genes. Two candidate genes, Os02g0770800 and Os06g0521900, were found to be involved in the regulation of Al tolerance in rice. This study provides insights into the resistance mechanism of rice to Al stress and offers reference for understanding the molecular mechanism of Al poisoning on plants.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Yuntao Wang, Zhen Sun, Qiqi Wang, Jihong Xie, Linqing Yu
Summary: This study integrated transcriptome and metabolome analysis to investigate the mechanism of alfalfa in response to low-temperature stress under different applications of phosphate fertilizer. The results showed that phosphate fertilizer improved the root structure of alfalfa and increased the content of soluble sugar and soluble protein. It also led to differential expression of genes and metabolites related to cold tolerance in alfalfa.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Fisheries
Ruihang Xu, Yufeng Zhai, Jia Yang, Yupei Tong, Peimin He, Rui Jia
Summary: In this study, it was found that the trans-vp28 gene Synechocystis sp. PCC6803 can enhance the immunity of Litopenaeus vannamei. Transcriptomic and metabolomic analysis revealed the differential expression of genes and metabolites related to immune defense, detoxification, and antioxidant systems. This study provides important insights into the defense and immune mechanisms used by invertebrates against pathogens.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Plant Sciences
Gustavo Pedro Javier Oberschelp, Luisina Lourdes Morales, Marina Lucia Montecchiarini, Leonel Harrand, Florencio Esteban Podesta, Ezequiel Margarit
Summary: Eucalypts are widely planted hardwood trees due to their rapid growth, wood quality, and adaptability. However, most commercial species and hybrids are sensitive to frost, which hinders their introduction in warm/temperate climates. In this study, two Eucalyptus species with different frost tolerance were exposed to low temperatures to investigate their acclimation process. The species E. benthamii showed higher basal frost tolerance and a stronger acclimation response compared to the frost-sensitive E. grandis. Metabolome characterization revealed differences between the two species and provided insights into their acclimation dynamics. E. benthamii exhibited early sugar accumulation and the accumulation of other metabolites that may play roles as osmolytes and antioxidants, contributing to its higher frost tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Agriculture, Multidisciplinary
Bingbing Liu, Xiaoxiao Wang, Kun Li, Zongwei Cai
Summary: This study utilized metabolomics, lipidomics, and mass spectrometry imaging to investigate the spatial distribution of different metabolites and lipids in two cottonseed cultivars under drought and salt stress. The findings highlighted the potential roles of these substances in enhancing stress tolerance and provided insights into metabolic and lipidomic regulatory networks in coping with salinity and drought stresses.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Plant Sciences
Dingding Cao, Wenbin Zhang, Nan Yang, Ziling Li, Chaoyue Zhang, Dan Wang, Guiping Ye, Jianjun Chen, Xiangying Wei
Summary: This study analyzed the responses of Sesuvium portulacastrum to salt stress at morphological, physiological, proteomic, and metabolomic levels. The results showed that signal transduction and phenolic acid metabolism were crucial for S. portulacastrum's salt tolerance. The study also identified the coordinated regulation of Ca2+, ABA, and JA signaling pathways in promoting salt tolerance in S. portulacastrum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Hind Emad Fadoul, Felix Juan Martinez Rivas, Kerstin Neumann, Salma Balazadeh, Alisdair R. Fernie, Saleh Alseekh
Summary: This study evaluated the effects of simulated long-term water deficit stress on two contrasting African wheat cultivars. Results showed that Wadielniel exhibited higher tolerance to drought stress with significant changes in metabolites compared to Condor. Metabolites such as amino acids, proline, organic acids, and lipid classes were identified as potentially playing a role in drought stress regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ling Wang, Bilian Qian, Lei Zhao, Ming-Hua Liang, Xiangqiang Zhan, Jianhua Zhu
Summary: Cold stress is a significant abiotic stress condition that hinders plant growth and development. In this study, the negative role of MPL1 and LIP1 triacylglycerol lipases in cold stress response was elucidated. These lipases may serve as potential candidates for breeding cold-tolerant crops through genome editing technology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Xiuqing Yao, Quan Zhang, Yixuan Fan, Xinyang Xu, Ziyong Liu
Summary: This study reports a newly isolated strain of Clostridium beijerinckii XH 0906 capable of oxygen-tolerant butanol and isopropanol fermentation under aerobic conditions. A mutant strain, C. beijerinckii XH 29, obtained by UV mutagenesis, showed improved BI production capacity and could produce high levels of isopropanol through fermentation of a glucose-acetone mix.
Article
Plant Sciences
Wei Zang, Rongqing Miao, Yue Zhang, Yue Yuan, Qiuying Pang, Zhiqiang Zhou
Summary: High salinity and alkalinity are two common abiotic stressors impacting plant growth. While much research has focused on neutral salt stress, the mechanisms underlying plant response to alkali stress are still not well understood. The halophyte Suaeda corniculata shows strong tolerance to both salt and alkali stress, with alkali stress having a more severe effect on plant growth than salt stress. Metabolomic and proteomic analysis revealed distinct regulation patterns in response to salt and alkali in S. corniculata. The study highlights the importance of ROS-scavenging systems, glycine betaine accumulation, and germinlike proteins in conferring alkali tolerance in S. corniculata.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Microbiology
Jonathan M. Conway, William G. Walton, Isai Salas-Gonzalez, Theresa F. Law, Chloe A. Lindberg, Laura E. Crook, Suzanne M. Kosina, Connor R. Fitzpatrick, Adam D. Lietzan, Trent R. Northen, Corbin D. Jones, Omri M. Finkel, Matthew R. Redinbo, Jeffery L. Dangl
Summary: Characterization of bacterial auxin degradation loci and their regulators reveals two distinct types across plant microbiome species, where only one, exemplified in Variovorax species, can interfere with root growth inhibition in a complex synthetic microbial community.
NATURE MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Ruifeng Hu, Guangsheng Pei, Peilin Jia, Zhongming Zhao
Summary: The study introduced and implemented a VAE model to explore large-scale epigenomics data for classification of histone modifications, tissue/cell specificity, and classification of new data with unknown sources.
Article
Biochemistry & Molecular Biology
Guangsheng Pei, Ruifeng Hu, Yulin Dai, Astrid Marilyn Manuel, Zhongming Zhao, Peilin Jia
Summary: The authors used a deep learning convolutional neural network model, DeepFun, to predict the regulatory effects of genetic variants based on epigenomic data, and prioritized trait-associated loci in GWAS studies. By applying this model, they refined important GWAS associations and provided novel insights into understanding the molecular basis of human complex diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Danesh H. Sopariwala, Neah Likhite, Gungsheng Pei, Fnu Haroon, Lisa Lin, Vikas Yadav, Zhongming Zhao, Vihang A. Narkar
Summary: ERR alpha is induced in skeletal muscle by hindlimb ischemia or hypoxia, and its overexpression can drive a switch in myofiber type and activate gene programs related to angiogenesis in muscle. This leads to increased baseline capillarity and arterioles, as well as improved perfusion recovery in ischemic muscle, suggesting ERR alpha as a potential target for treating PAD/CLI.
Article
Biochemistry & Molecular Biology
Nathaniel K. Berg, Jiwen Li, Boyun Kim, Tingting Mills, Guangsheng Pei, Zhongming Zhao, Xiangyun Li, Xu Zhang, Wei Ruan, Holger K. Eltzschig, Xiaoyi Yuan
Summary: The study revealed the crucial role of the neuronal guidance protein netrin-1 in controlling lung inflammation by modulating CCL2-dependent infiltration of NK cells during LPS-induced lung injury. Deletion of netrin-1 in the myeloid compartment led to exacerbated lung inflammation and increased mortality rates.
Article
Multidisciplinary Sciences
Peilin Jia, Ruifeng Hu, Guangsheng Pei, Yulin Dai, Yin-Ying Wang, Zhongming Zhao
Summary: Drug response in cancer patients varies significantly due to tumor heterogeneity, with transcriptome context playing a key role. Researchers developed a deep variational autoencoder model to compress gene signatures into latent vectors and accurately impute drug response.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Xinyu Song, Jinjin Diao, Jiaqi Yao, Jinyu Cui, Tao Sun, Lei Chen, Weiwen Zhang
Summary: The study introduced a synthetic NOG pathway to increase acetyl-CoA pool in Synechocystis 6803, leading to enhanced productivity by eliminating native competing pathways. The integrated approach demonstrated an increase in acetyl-CoA concentration and production of value-added chemicals in cyanobacteria.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mengfan Tang, Guangsheng Pei, Dan Su, Chao Wang, Xu Feng, Mrinal Srivastava, Zhen Chen, Zhongming Zhao, Junjie Chen
Summary: The study identified that CCNC is a critical survival target in cells with BRCA2 loss, potentially contributing to PARPi resistance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Guangsheng Pei, Ruifeng Hu, Peilin Jia, Zhongming Zhao
Summary: The Deep-Fun web server utilizes a convolutional neural network framework and chromatin profiles from ENCODE and Roadmap projects to assess the functional activity of non-coding genetic variants. It expands the functionality of existing non-coding variant prioritizing tools by providing specific functional assessments in a tissue- and cell type-specific manner. The server has been validated with datasets from various GWAS studies and is expected to be widely used in genetics, functional genomics, and disease studies.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Bingrui Li, Guangsheng Pei, Jun Yao, Qingqing Ding, Peilin Jia, Zhongming Zhao
Summary: This study comprehensively characterized cell-type alterations across 18 cancer types and identified myofibroblastic CAF (myCAF) composition as a poor prognostic factor in nine cancer types. Furthermore, genes associated with the differentiation degree of myCAF and inflammatory CAF (iCAF) were identified, highlighting their roles in fibroblast and extracellular matrix-related pathways. These findings provide therapeutic perspectives for targeting CAF subtypes in the tumor microenvironment and arranging treatment schemes based on CAF compositions in different cancer types.
Article
Biochemical Research Methods
Xuyang Sun, Shubin Li, Fenfang Zhang, Tao Sun, Lei Chen, Weiwen Zhang
Summary: In this study, a genetic switch repressed by NanR and induced by N-acetylneuraminic acid (Neu5Ac) was developed in fast-growing cyanobacteria. The switch achieved high induction with minimal leakage through optimization of NanR expression level and introduction of Neu5Ac transporter. The orthogonality between the NanR/Neu5Ac switch and theophylline-responsive riboregulator was also investigated, showing potential for coordinated or binary regulation of target genes.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Oncology
Divya Ravirala, Brandon Mistretta, Preethi H. Gunaratne, Guangsheng Pei, Zhongming Zhao, Xiaoliu Zhang
Summary: Novel chimeric molecules, BiCEP and TriCEP, were constructed and evaluated in this study for their ability to engage both NK and T cells, enhancing antitumor activities. Both molecules showed promising results in engaging immune cells to kill tumor cells, suggesting their potential in oncolytic virotherapy for cancer treatment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Biochemical Research Methods
Jiaqi Yao, Jin Wang, Yue Ju, Zhengxin Dong, Xinyu Song, Lei Chen, Weiwen Zhang
Summary: This study engineered a xylose utilization pathway from Escherichia coli into fast-growing cyanobacteria, enabling photomixotrophic cultivation based on xylose. By rewiring the metabolism and driving more carbon flux from xylose to acetyl-CoA, the biosynthesis of 3-hydroxypropionic acid was significantly improved.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xu Feng, Mengfan Tang, Merve Dede, Dan Su, Guangsheng Pei, Dadi Jiang, Chao Wang, Zhen Chen, Mi Li, Litong Nie, Yun Xiong, Siting Li, Jeong-Min Park, Huimin Zhang, Min Huang, Klaudia Szymonowicz, Zhongming Zhao, Traver Hart, Junjie Chen
Summary: Exploiting cancer vulnerabilities is crucial for finding anticancer drugs. This study used CRISPR screens to uncover genetic interactions between tumor suppressor genes and protein-coding genes, leading to the discovery of high-confidence synthetic lethal interactions and essential paralog gene pairs. It also suggests that targeting certain tumor suppressors could suppress the proliferation of cells lacking other tumor suppressors, providing valuable information for targeted cancer therapy.
Article
Genetics & Heredity
Guangsheng Pei, Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao
Summary: Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and dynamic cellular mechanisms. In this study, the researchers present deCS, an automatic cell type annotation method that enhances annotation accuracy using comprehensive human cell type expression profiles and marker genes. The results show that expanding the references is critical for improving annotation accuracy, and deCS significantly reduces computation time and increases accuracy compared to existing tools. The researchers also demonstrate the broad utility of deCS in identifying trait-cell type associations in human complex traits, providing deep insights into disease pathogenesis.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Danesh H. Sopariwala, Andrea S. Rios, Guangsheng Pei, Anirban Roy, Meiricris Tomaz da Silva, Hao Thi Thu Nguyen, Addison Saley, Rachel Van Drunen, Anastasia Kralli, Kristin Mahan, Zhongming Zhao, Ashok Kumar, Vihang A. Narkar
Summary: In this study, the role of nuclear receptor ERR alpha/gamma in regulating skeletal muscle composition, contractility, and exercise capacity was elucidated. The deletion of ERR alpha/gamma led to decreased expression of genes associated with mitochondrial and oxidative metabolism, resulting in impaired mitochondrial function, angiogenesis, and exercise capacity.