News Item
Oncology
Philip Bucher, Judith Feucht
Summary: The lack of tumor-specific surface antigens hampers the use of CAR T cells in solid tumors. A new AND-gated CAR T cell system utilizes proximal T cell signaling proteins to restrict activation only when encountering dual antigens, reducing on-target, off-tumor toxicity and maintaining antitumor efficacy in preclinical models.
Article
Biochemistry & Molecular Biology
Anna Macioszek, Bartek Wilczynski
Summary: The article describes a new method for genome-wide data analysis called HERON, which can detect DNA regions enriched for a certain feature even in long DNA domains, demonstrating good interpretative ability for difficult data such as modified histone variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Ellen Ruth A. Morris, Jing Wu, Angela Bordin, Sara D. Lawhon, Noah D. Cohen
Summary: This study characterized the genomic and methylomic differences of multiple SEE and SEZ isolates from Texas. The results showed that genetic mobile elements in SEE and differential methylation of shared genes between SEE and SEZ might contribute to the host specificity of SEE.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch
Summary: This study utilized a targeted sequencing approach to investigate DNA methylation changes in NSCLC patients, identifying differential methylation regions and confirming potential regulatory elements. The research contributes to understanding the mechanisms of lung cancer initiation and progression, and offers new potential targets for cancer treatment.
Article
Biochemistry & Molecular Biology
Sarah Bailey, Joseph Guhlin, Dinindu S. S. Senanayake, Phoebe Scherer, Patricia Brekke, John G. G. Ewen, Anna W. W. Santure, Annabel Whibley
Summary: By assembling the genome of a threatened passerine bird endemic to New Zealand, high-quality reference genomes were generated to assess the evolutionary potential of the species. The assembled genomes were of high quality and provided valuable information about the DNA methylation patterns and sex-specific evolutionary processes. These reference genomes will help in evaluating the adaptive potential and conservation management of this threatened species.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Marina Pupke Marone, Harmeet Chawla Singh, Curtis J. J. Pozniak, Martin Mascher
Summary: This article describes modifications to the TRITEX genome assembly workflow driven by the rise of fast and easy long-read contig assembly in inbred plant genomes and the routine deployment in pangenome projects. New features include the use of dense genetic maps as surrogates or complements, and the introduction of user-editable tables to facilitate the curation of contig placements.
Article
Oncology
Ariane Hallermayr, Teresa M. Neuhann, Verena Steinke-Lange, Florentine Scharf, Andreas Laner, Roland Ewald, Ben Liesfeld, Elke Holinski-Feder, Julia M. A. Pickl
Summary: Liquid biopsy is a promising method for detecting clinically relevant genetic variants in cancer and mosaic diseases. Researchers developed a cost-efficient workflow that allows analysis of both tissue and liquid biopsy samples and established clinically relevant cutoffs for variant reporting and precise quantification. This approach successfully identified the molecular cause of an asymmetric overgrowth syndrome that would have remained undetected with tissue analysis.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Jeffrey C. Y. Yu, Yixiao Zeng, Kaiqiong Zhao, Tianyuan Lu, Kathleen Oros Klein, Ines Colmegna, Maximilien Lora, Sahir R. Bhatnagar, Andrew Leask, Celia M. T. Greenwood, Marie Hudson
Summary: Using the SOMNiBUS method to re-analyze WGBS data, 131 differentially methylated regions and 125 differentially methylated genes were identified. This method provides a better understanding of the pathogenesis of systemic sclerosis.
CLINICAL EPIGENETICS
(2023)
Article
Food Science & Technology
Joao Carlos Gomes-Neto, Natasha Pavlovikj, Carmen Cano, Baha Abdalhamid, Gabriel Asad Al-Ghalith, John Dustin Loy, Dan Knights, Peter C. Iwen, Byron D. Chaves, Andrew K. Benson
Summary: Incorporating bacterial whole-genome sequencing into Public Health laboratories has improved foodborne outbreak detection and source attribution. Analysis on the populations of three serovars of Salmonella enterica subsp. enterica revealed insights on ecological and epidemiological patterns at different hierarchical scales, demonstrating the potential for using genomics in understanding pathogen populations. Additionally, identification of lineage-specific informative loci that may provide selective advantages in food production environments was achieved.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Medicine, General & Internal
Juan Li, Yuan Liang, Jian Fan, Chunru Xu, Bao Guan, Jianye Zhang, Bin Guo, Yue Shi, Ping Wang, Yezhen Tan, Qi Zhang, Changwei Yuan, Yucai Wu, Liqun Zhou, Weimin Ci, Xuesong Li
Summary: The study found that UTUC and UCB have very similar DNA methylation profiles, and DNA methylation subtypes can be used to predict patient prognosis in UC. The results provide a mechanistic rationale for evaluating SGI-110 in treating UC patients in the clinic.
Article
Environmental Sciences
Yanhong Wang, Xinyan Shi, Xianxin Huang, Chunlei Huang, Helin Wang, Hanqin Yin, Yixian Shao, Ping Li
Summary: This study investigated the microbial community composition and functions in different farming soils and found that the farming patterns influenced the geochemical parameters and microbial communities, subsequently affecting the forms of selenium in soils.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yu Zhang, Ning Lu, Shunchang Pu, Kui Mu
Summary: This study aimed to identify sensitive methylation sites of non-small cell lung cancer through whole-genome sequencing to build an early warning system. Findings indicate that methylation rates of specific genes are associated with patient survival time and tumor characteristics.
CELLULAR AND MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Peng Tian, Xuemei Zhang, Rui Xia, Yang Liu, Meijiao Wang, Bo Li, Tieyan Liu, Jinfeng Shi, Rod A. Wing, Blake C. Meyers, Mingsheng Chen
Summary: Two types of phased, small interfering RNAs (phasiRNAs) are expressed in young anthers of grasses, they are 21 or 24 nucleotides in length. Comparative genomic analysis revealed conservation in genomic positions but rapid divergence in sequences of phasiRNAs. Production of phasiRNAs is under the control of multiple reciprocal regulation mechanisms.
Article
Biochemistry & Molecular Biology
Hong Yu, Tao Lin, Xiangbing Meng, Huilong Du, Jingkun Zhang, Guifu Liu, Mingjiang Chen, Yanhui Jing, Liquan Kou, Xiuxiu Li, Qiang Gao, Yan Liang, Xiangdong Liu, Zhilan Fan, Yuntao Liang, Zhukuan Cheng, Mingsheng Chen, Zhixi Tian, Yonghong Wang, Chengcai Chu, Jianru Zuo, Jianmin Wan, Qian Qian, Bin Han, Andrea Zuccolo, Rod A. Wing, Caixia Gao, Chengzhi Liang, Jiayang Li
Summary: The study presents a strategy for de novo domestication of wild allotetraploid rice and establishes necessary resources for this purpose, demonstrating the rapid improvement of agronomically important traits through gene editing.
Article
Biotechnology & Applied Microbiology
Zhihua Wu, Hong Liu, Wei Zhan, Zhichao Yu, Erdai Qin, Shuo Liu, Tiange Yang, Niyan Xiang, Dave Kudrna, Yan Chen, Seunghee Lee, Gang Li, Rod A. Wing, Jiao Liu, Hairong Xiong, Chunjiao Xia, Yongzhong Xing, Jianwei Zhang, Rui Qin
Summary: Safflower, a popular crop with high linoleic acid and flavonoid content, diverged from artichoke and sunflower millions of years ago. Unique expansions in gene families related to lipid metabolism and flavonoid biosynthesis were found in safflower, with key genes such as FAD2 and CHS exhibiting tandem duplications. This study provides insights into the evolutionary history and molecular basis of fatty acid and flavonoid biosynthesis in safflower.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Correction
Multidisciplinary Sciences
Hyun-Seung Park, Murukarthick Jayakodi, Sae Hyun Lee, Jae-Hyeon Jeon, Hyun-Oh Lee, Jee Young Park, Byeong Cheol Moon, Chang-Kug Kim, Rod A. Wing, Steven G. Newmaster, Ji Yeon Kim, Tae-Jin Yang
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, Yi-Xiong Guo, Dal-Hoe Koo, Dave Kudrna, Chenbo Gong, Yicheng Huang, Jia-Wu Feng, Wenhui Zhang, Yong Zhou, Andrea Zuccolo, Evan Long, Seunghee Lee, Jayson Talag, Run Zhou, Xi-Tong Zhu, Daojun Yuan, Joshua Udall, Weibo Xie, Rod A. Wing, Qifa Zhang, Jesse Poland, Jianwei Zhang, Ling-Ling Chen
Summary: This study reported the assembly and analysis of gap-free reference genome sequences for two elite Oryza sativa rice varieties, providing a global view of the structure and function of rice centromeres. The research found that all rice centromeric regions share conserved centromere-specific satellite motifs, with a higher similarity of CentO repeats within the same chromosome.
Article
Plant Sciences
Karine E. Janner de Freitas, Railson Schreinert dos Santos, Carlos Busanello, Filipe de Carvalho Victoria, Jennifer Luz Lopes, Rod A. Wing, Antonio Costa de Oliveira
Summary: The cooking quality of Common/Asian rice varieties is highly dependent on grain starch composition, which is influenced by genetic factors. Analyzing grain quality genes in wild rice relatives can provide insights into the evolution and potential use of genetic resources. Deletion/mutation of amino acids in active sites may negatively affect specific steps of starch biosynthesis, while complete deletion of certain genes in wild species may not impact amylose content.
Article
Genetics & Heredity
Naveenkumar Athiyannan, Michael Abrouk, Willem H. P. Boshoff, Stephane Cauet, Nathalie Rodde, David Kudrna, Nahed Mohammed, Jan Bettgenhaeuser, Kirsty S. Botha, Shannon S. Derman, Rod A. Wing, Renee Prins, Simon G. Krattinger
Summary: In this study, a chromosome-scale assembly of the South African bread wheat cultivar Kariega was generated, and a disease resistance gene Yr27 was identified. The results demonstrate the feasibility of cloning genes through chromosome-scale assemblies and suggest that highly similar alleles of a single-copy gene can confer resistance to different pathogens.
Review
Plant Sciences
Aseel Alsantely, Rafal Gutaker, Maria E. Navarrete Rodriguez, Griselda Arrieta-Espinoza, Eric J. Fuchs, Antonio Costa de Oliveira, Joe Tohme, Andrea Zuccolo, Rod A. Wing, Alice Fornasiero
Summary: This article reviews the relevance and major outcomes of the Oryza Map Alignment Project (OMAP) to the wild Oryza species in the Americas, with a focus on biodiversity conservation. It also discusses the achievements and future implications of the neodomestication of Oryza alta. The study highlights the importance of the wild relatives of rice in contributing to global food security and the potential for neodomestication in other wild Oryza species in the Americas.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Letter
Biochemistry & Molecular Biology
Zhichao Yu, Yongming Chen, Yong Zhou, Yulu Zhang, Mengyuan Li, Yidan Ouyang, Dmytro Chebotarov, Ramil Mauleon, Hu Zhao, Weibo Xie, Kenneth L. McNally, Rod A. Wing, Weilong Guo, Jianwei Zhang
Article
Multidisciplinary Sciences
Yong Zhou, Zhichao Yu, Dmytro Chebotarov, Kapeel Chougule, Zhenyuan Lu, Luis F. Rivera, Nagarajan Kathiresan, Noor Al-Bader, Nahed Mohammed, Aseel Alsantely, Saule Mussurova, Joao Santos, Manjula Thimma, Maxim Troukhan, Alice Fornasiero, Carl D. Green, Dario Copetti, David Kudrna, Victor Llaca, Mathias Lorieux, Andrea Zuccolo, Doreen Ware, Kenneth McNally, Jianwei Zhang, Rod A. Wing
Summary: Understanding and utilizing genetic diversity is crucial for rice production. A study using 73 high-quality genomes of Asian rice and two wild relatives reveals the prevalence of large inversions across the pan-genome of Asian rice and their potential impact on gene expression, recombination rate, and linkage disequilibrium. The study suggests that the inversion rate in Asian rice is significantly higher than previous estimates for plants.
NATURE COMMUNICATIONS
(2023)
Article
Food Science & Technology
Khalid Sedeek, Andrea Zuccolo, Alice Fornasiero, Annika M. Weber, Krishnaveni Sanikommu, Sangeetha Sampathkumar, Luis F. Rivera, Haroon Butt, Saule Mussurova, Abdulrahman Alhabsi, Nurmansyah Nurmansyah, Elizabeth P. Ryan, Rod A. Wing, Magdy M. Mahfouz
Summary: In this study, genome assemblies of 5 pigmented rice varieties were generated and the genetic variation among 51 pigmented rice varieties was evaluated. Phylogenetic analysis divided the pigmented varieties into four groups. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. A regeneration and transformation system was established and CRISPR-Cas9 was used to create an early maturing, shorter-stature black rice variety. This study provides a multi-omics resource for understanding and improving Asian pigmented rice.
Article
Plant Sciences
Parthiban Thathapalli Prakash, Dmytro Chebotarov, Jianwei Zhang, David A. Kudrna, Rolando O. Torres, Mignon A. Natividad, Marinell R. Quintana, Jiaming Song, Carlos E. Maldonado, Sherry Lou Hechanova, Kshirod Jena, Rod A. Wing, Amelia Henry
Summary: Developing drought-resistant rice is crucial for improving field productivity. Wild relatives of rice have potential traits for drought resistance. This study identified Oryza glumaepatula as a promising source for drought resistance. Multiple genomic loci related to drought resistance traits were detected through whole-genome resequencing and variant calling. These findings provide valuable information for introgressing drought tolerance into O. sativa backgrounds.
Article
Genetics & Heredity
Fabrice Ntakirutimana, Christine Tranchant-Dubreuil, Philippe Cubry, Kapeel Chougule, Jianwei Zhang, Rod A. Wing, Helene Adam, Mathias Lorieux, Stefan Jouannic
Summary: In this study, a genome-wide association study was conducted on four major panicle traits in African rice. A total of 41 stable genomic regions significantly associated with these traits were identified, including 13 previously identified QTLs and 28 unique regions. A genomic region on chromosome 3 associated with spikelet and branch number was also found, with the localization of the O. sativa ortholog of the PHYTOCHROME B gene. The study provides insights into the genetic variation and molecular processes governing panicle architecture in African rice, which may contribute to the breeding of new cultivars.
G3-GENES GENOMES GENETICS
(2023)
Article
Biodiversity Conservation
Muriel Gros-Balthazard, Vincent Battesti, Jonathan M. Flowers, Sylvie Ferrand, Matthieu Breil, Sarah Ivorra, Jean-Frederic Terral, Michael D. Purugganan, Rod A. Wing, Nahed Mohammed, Yann Bourgeois
Summary: This article discusses the impact of development in the al-'Ula oasis on local agriculture and date palm cultivation in Saudi Arabia. The research shows that the barni date palm is propagated clonally and shares genetic characteristics with other West Asian date palms. Understanding local agrobiodiversity and promoting sustainable development is crucial.
PLANTS PEOPLE PLANET
(2023)
Article
Biotechnology & Applied Microbiology
Yanli Zhou, Chengjun Zhang, Li Zhang, Qiannan Ye, Ningyawen Liu, Muhua Wang, Guangqiang Long, Wei Fan, Manyuan Lon, Rod A. Wing
Summary: This study detects new fusion genes that may drive phenotype evolution in Oryza, providing novel insights into the genome evolution of Oryza.