Article
Microbiology
Yong Qi, Shan-Shan Wang, Lu-Lin Li
Summary: Late gene expression of baculovirus depends on the virus-encoded RNA polymerase. The immediate-early gene ie1 plays essential roles in viral early gene expression, late gene expression, and DNA replication. IE1 can independently activate late gene expression, showing nonspecific transcription start sites.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Mark R. Bruder, Marc G. Aucoin
Summary: We have developed a sensitive assay using CRISPR-Cas9-mediated gene targeting to evaluate the phenotypic impact of disrupting Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genes. By disrupting 13 AcMNPV genes, we evaluated their performance in terms of green fluorescent protein production and progeny virus yield. This assay provides an efficient strategy for scrutinizing AcMNPV gene function and developing an optimized recombinant baculovirus expression vector (rBEV) genome.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Virology
Jianan Huang, Huanlei Liu, Xiaodong Xu
Summary: The baculovirus expression vector system (BEVS) is widely used for producing recombinant proteins. However, there is a risk of homologous recombination between viral genome and functional baculovirus-derived elements associated with foreign genes, which can lead to defective viruses and decreased recombinant protein yields. Shortening the length of homologous fragments and separating them by point mutations can effectively reduce the unfavorable recombination.
Article
Microbiology
Sandra Yazmin Jimenez-Hernandez, Jonatan C. Rangel-Nunez, Jorge E. Ibarra, Ma Cristina Del Rincon-Castro
Summary: This study characterized PlxyMNPV_LBIV-11 at a biological, morphological, and molecular level and found its similarity with AcMNPV. It showed infectivity and potential as a biological control agent, although its virulence was lower than AcMNPV.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Virology
Jeffrey J. Hodgson, Nicolas Buchon, Gary W. Blissard
Summary: Little is known about the trafficking process of viral envelope proteins in insect cells. In this study, a stable Drosophila cell line was engineered to investigate the host proteins and cellular trafficking pathways involved in the delivery of the baculovirus envelope protein GP64 to the plasma membrane. Through a targeted RNA interference screen, several host genes were identified to be important for the trafficking of GP64 to the cell surface. The findings suggest that recycling plays a role in maintaining GP64 at the cell surface. This study provides insight into the understanding of how insect virus envelope proteins are transported and contributes to the knowledge of virus infection processes.
JOURNAL OF VIROLOGY
(2022)
Article
Entomology
Long Liu, Yu-Shan Wei, Dun Wang
Summary: This study identified and characterized eleven TLRs and five downstream TLR pathway components in Lymantria dispar, and found that upon Lymantria dispar multiple nucleopolyhedrovirus infection, several TLRs and all identified downstream genes of the TLR pathway were significantly up-regulated, suggesting activation of the TLR pathway and its involvement in the insect's immune response.
Article
Fisheries
Chao Li, Jianhu Jiang, Jiasong Xie, Wenge Yang, Yajun Wang
Summary: Goldfish have been used as a model to study the innate immune system and host-pathogen interactions. Transcriptome analysis of goldfish spleen infected with Mycobacterium marinum revealed multiple immune-related pathways, providing valuable information for further investigations on strategies against M. marinum infection in teleosts.
Article
Biotechnology & Applied Microbiology
Shisi Xing, Dan Deng, Wen Wen, Wei Peng
Summary: This study investigated the differences in gene expression in the female midgut between mated and virgin Drosophila suzukii. The results showed that mating had significant effects on metabolism and immune system in the midgut, which may contribute to supplying the female with nutrients and energy required for egg production.
Article
Fisheries
Mateen Nawaz, Xionglin Li, Xinyuan Yue, Moussa Gouife, Kejing Huang, Suyang Chen, Rongrong Ma, Jianhu Jiang, Suming Zhou, Shan Jin, Yajun Wang, Jiasong Xie
Summary: This study conducted transcriptome analysis of silver pomfret infected with Photobacterium damselae subsp. damselae (PDD) to investigate the molecular mechanisms of host defense. Differentially expressed genes and immune-related pathways were identified, providing valuable information for strategies against Photobacterium spp. infection in teleosts.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Huan Yu, Chang-Jin Yang, Yi-Yi Ou-Yang, Yue Tong, Hui-Yu Lan, Jia-Min Gan, Shi-Wei Li, Ding-Yi Bai, Guo-Hua Huang
Summary: Genetic engineering technology was used to introduce six ascovirus genes into Autographa californica nucleopolyhedrovirus (AcMNPV), resulting in increased viral production, improved insecticidal efficiency, and larger occlusion bodies (OBs). This study provides a novel strategy for improving baculoviruses as biological insecticides.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2023)
Article
Mathematical & Computational Biology
Deeksha Malhan, Alireza Basti, Angela Relogio
Summary: Emerging evidence suggests that the circadian clock plays a regulatory role in alternative splicing. This study conducted computational analysis on RNA-seq datasets to investigate the impact of core-clock gene knockout on circadian expression and alternative splicing events in colorectal cancer and Hodgkin's lymphoma cells. The results demonstrate a role for the circadian clock in the regulation of alternative splicing and suggest potential implications for aberrant splicing in cancer hallmark genes.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Fisheries
Mateen Nawaz, Moussa Gouife, Songwei Zhu, Xinyuan Yue, Kejing Huang, Rongrong Ma, Jianhu Jiang, Shan Jin, Junquan Zhu, Jiasong Xie
Summary: Goldfish have been used as a model organism to study the immune system and host-pathogen interactions. A bacterium called Aeromonas hydrophila has been causing mass mortality in fish species. This study observed damages in the head kidney of goldfish infected with A. hydrophila and analyzed the gene expression and enzyme activities related to the immune response. The findings will contribute to a better understanding of the early immune response in goldfish and aid in future research on prevention strategies.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Qing Yuan, Fu-Xing Zuo, Hong-Qing Cai, Hai-Peng Qian, Jing-Hai Wan
Summary: A novel gene signature based on differentially expressed genes (DEGs) between glioblastoma (GBM) and healthy subventricular zone (SVZ) was developed for determining GBM patient prognosis. High-risk patients showed significantly reduced overall survival and were associated with lower immune cell counts and higher PD-L1 expression. Targeting these genes may be a therapeutic strategy for GBM.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: Gene-based transcriptome analysis can identify key factors causing disease production and cell differentiation, but basic life activities are mainly driven by gene interactions, requiring interaction-based transcriptome analysis to investigate insights into differential gene interactions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Agriculture, Dairy & Animal Science
Judith Wilson, Marcos De Donato, Brooke Appelbaum, Carly Turner Garcia, Sunday Peters
Summary: Overtraining syndrome (OTS) is caused by excessive training and inadequate recovery, leading to decreased performance and impaired repair of damage. Acute, intense physical exercise affects the expression of immune genes, and can be used to evaluate OTS indications.
Correction
Multidisciplinary Sciences
Xiaofeng Cai, Xuepeng Sun, Chenxi Xu, Honghe Sun, Xiaoli Wang, Chenhui Ge, Zhonghua Zhang, Quanxi Wang, Zhangjun Fei, Chen Jiao, Quanhua Wang
NATURE COMMUNICATIONS
(2022)
Article
Virology
Jeffrey J. Hodgson, Nicolas Buchon, Gary W. Blissard
Summary: Little is known about the trafficking process of viral envelope proteins in insect cells. In this study, a stable Drosophila cell line was engineered to investigate the host proteins and cellular trafficking pathways involved in the delivery of the baculovirus envelope protein GP64 to the plasma membrane. Through a targeted RNA interference screen, several host genes were identified to be important for the trafficking of GP64 to the cell surface. The findings suggest that recycling plays a role in maintaining GP64 at the cell surface. This study provides insight into the understanding of how insect virus envelope proteins are transported and contributes to the knowledge of virus infection processes.
JOURNAL OF VIROLOGY
(2022)
Article
Plant Sciences
You Qing, Yi Zheng, Sizolwenkosi Mlotshwa, Heather N. Smith, Xin Wang, Xuyang Zhai, Esther van Der Knaap, Ying Wang, Zhangjun Fei
Summary: This study provides comprehensive analysis on small RNAs in tomato and demonstrates the significant role of genomic structural variants (SVs) in the dynamic expression of plant sRNAs. Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to altered mRNA gene expression during tomato domestication, particularly for stress tolerance genes. The study highlights different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs.
Article
Biochemistry & Molecular Biology
Oscar A. Perez-Escobar, Sergio Tusso, Natalia A. S. Przelomska, Shan Wu, Philippa Ryan, Mark Nesbitt, Martina Silber, Michaela Preick, Zhangjun Fei, Michael Hofreiter, Guillaume Chomicki, Susanne S. Renner
Summary: Iconographic evidence suggests that watermelon pulp may have been consumed as a dessert in Egypt 4,360 years ago. Earlier archaeobotanical evidence from seeds in Neolithic settlements in Libya provides some insight, but it is unclear whether these seeds belonged to watermelons with sweet pulp or a different form. Through genomic analysis of ancient seeds from Libya and Sudan, as well as herbarium collections from 1824 to 2019, researchers discovered that the ancient watermelon seeds were more closely related to a West African strain (Citrullus mucosospermus) used for seeds, rather than the domesticated variety (Citrullus lanatus ssp. vulgaris) used for pulp. Additionally, the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh, similar to C. mucosospermus. The genomes of the ancient watermelons also showed evidence of interbreeding between various Citrullus species, including a surprising introgression between the Libyan seed and C. lanatus populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Seunghyun Ban, Islam El-Sharkawy, Jiantao Zhao, Zhangjun Fei, Kenong Xu
Summary: Somatic mutations can alter important traits in tree fruits. This study reveals that a hemizygous deletion of a 2.8 Mb genomic region on chromosome 6, which results in the complete loss of the MdACT7 gene, is largely responsible for the delayed fruit maturation in AGala.
Article
Biochemistry & Molecular Biology
Jingyin Yu, Shan Wu, Honghe Sun, Xin Wang, Xuemei Tang, Shaogui Guo, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Cecilia McGregor, Susanne S. Renner, Sandra Branham, Chandrasekar Kousik, W. Patrick Wechter, Amnon Levi, Rebecca Grumet, Yi Zheng, Zhangjun Fei
Summary: The Cucurbit Genomics Database is an important resource for studying cucurbit plants, providing large-scale genomic data and functionally annotated information. The database contains reference genomes, variome data, and gene expression profiles for multiple cucurbit species, facilitating efficient mining, analysis, and dissemination of these datasets. It plays a significant role in advancing cucurbit research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Honglin Feng, Wenbo Chen, Sonia Hussain, Sara Shakir, Vered Tzin, Femi Adegbayi, Todd Ugine, Zhangjun Fei, Georg Jander
Summary: RNA interference (RNAi)-based technologies are becoming commercialized for agricultural pest control. Horizontally transferred genes (HTGs) are attractive targets for RNAi-mediated pest control. This study identified and confirmed the importance of 30 HTGs for the growth and survival of the green peach aphid.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Philippe Nicolas, Richard J. Pattison, Yi Zheng, Taly Lapidot-Cohen, Yariv Brotman, Sonia Osorio, Alisdair R. Fernie, Zhangjun Fei, Carmen Catala
Summary: Tomato fruits with disrupted starch biosynthesis undergo significant transcriptional and metabolic remodeling, affecting central carbohydrate and lipid metabolism and impacting stress responses. The lack of carbon flow into starch leads to increased levels of soluble sugars, readjustment of metabolism, and activation of growth and stress protection pathways. These findings provide insights into the effects of carbohydrate metabolism perturbations on tomato fruit development and potential implications for enhancing protective mechanisms against abiotic stress in fleshy fruit.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Mei Liu, Baoshan Kang, Huijie Wu, Miguel A. Aranda, Bin Peng, Liming Liu, Zhangjun Fei, Ni Hong, Qinsheng Gu
Summary: This study reveals that SA-induced flavonoid biosynthesis plays a critical role in watermelon development and resistance to CGMMV. Understanding the defense mechanism of watermelon against CGMMV infection is essential for managing viral diseases in agriculture.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Xiaofen Yu, Mengyun Qin, Minghao Qu, Quan Jiang, Sumin Guo, Zhenghai Chen, Yufang Shen, Guodong Fu, Zhangjun Fei, Hongwen Huang, Lei Gao, Xiaohong Yao
Summary: Despite a lack of documented homoploid hybridization events in plants, this study provides insights into the evolutionary consequence of homoploid hybridization in kiwifruit species. Through genome sequencing and population genomic analyses, the study reveals that A. zhejiangensis is mainly composed of F-1 hybrids of A. hemsleyana and A. eriantha, with gene flow initiating about 0.98 million years ago. The study also identifies five inversions containing genes related to pollen germination and pollen tube growth that may account for the fertility breakdown in hybrids. Despite distinct morphological traits, A. zhejiangensis does not initiate speciation.
Article
Plant Sciences
Dong Meng, Hongyan Cao, Qing Yang, Mengxia Zhang, Ewa Borejsza-Wysocka, Huicong Wang, Abhaya M. Dandekar, Zhangjun Fei, Lailiang Cheng
Summary: Sorbitol, a major photosynthate in apple and other tree fruits, stimulates its own metabolism through the SnRK1-mediated phosphorylation of bZIP39. SnRK1 interacts with and phosphorylates bZIP39, a transcription factor that activates the expression of key enzymes in sorbitol metabolism. This study reveals the molecular mechanism of how sorbitol regulates its own metabolism and integrates sorbitol signaling into the sugar signaling network to modulate plant carbohydrate metabolism.
Article
Multidisciplinary Sciences
Heqiang Lou, Lili Song, Xiaolong Li, Hailing Zi, Weijie Chen, Yadi Gao, Shan Zheng, Zhangjun Fei, Xuepeng Sun, Jiasheng Wu
Summary: The authors assembled the genome of Torreya grandis, a gymnosperm species with edible seeds containing sciadonic acid. They identified two key genes involved in sciadonic acid biosynthesis and found that seed development is accompanied by DNA methylation changes. This study provides important genomic resources and insights into the evolutionary mechanism of sciadonic acid biosynthesis in land plants.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Anze Svara, Honghe Sun, Zhangjun Fei, Awais Khan
Summary: In this study, long-read sequencing and in silico gene sequence characterization were used to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Multiple highly homologous DNA sequences were identified on linkage groups 1 and 6, and two candidate genes located close to the scab-resistance marker Ch-Vf1 were found. This study provides novel genomic resources and identifies candidate genes for further resistance characterization.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Ming Chen, Lin Guo, Muthusamy Ramakrishnan, Zhangjun Fei, Kunnummal K. Vinod, Yulong Ding, Chen Jiao, Zhipeng Gao, Ruofei Zha, Chunyue Wang, Zhimin Gao, Fen Yu, Guodong Ren, Qiang Wei
Summary: The rapid growth of Moso bamboo is associated with cell division and elongation, gibberellin, cytokinin, auxin, abscisic acid, and mechanical pressure. This study provides insight into the mechanisms underlying the rapid growth of Moso bamboo.
Article
Plant Sciences
Ning Zhang, Chloe Hecht, Xuepeng Sun, Zhangjun Fei, Gregory B. Martin
Summary: This study discovered that the basic helix-loop-helix (bHLH) transcription factor Nrd1 promotes susceptibility to bacterial speck disease in tomato by suppressing the defense gene Agp1 that encodes an arabinogalactan protein.