Article
Chemistry, Multidisciplinary
Hrishikesh Gupta, Payal Gupta, Manikyaprabhu Kairamkonda, Krishna Mohan Poluri
Summary: The prevalence of drug resistant C. glabrata strains in immune-compromised patients has increased rapidly. To identify the mutations/variations and update antifungal therapy, researchers comprehensively characterized the clinical isolates using molecular and metabolic profiling methods. Significant variations in susceptibility, surface hydrophobicity, and oxidative stress generation were observed. Metabolic profiling revealed differential metabolites, while transcriptional analysis identified major differences in cellular pathways related to stress, metabolism, and biosynthesis. This study provides valuable information for differentiating pathogenic isolates from wild-type and understanding their enhanced pathogenicity.
Article
Multidisciplinary Sciences
Jibin Liu, Anchun Cheng, Mingshu Wang, Mafeng Liu, Dekang Zhu, Qiao Yang, Ying Wu, Renyong Jia, Shun Chen, Xinxin Zhao, Shaqiu Zhang, Juan Huang, Xumin Ou, Sai Mao, Qun Gao, Xingjian Wen, Ling Zhang, Yunya Liu, Yanling Yu, Bin Tian, Leichang Pan, Mujeeb Ur Rehman, Xiaoyue Chen
Summary: This study identified intracellular metabolites in different serotypes of R. anatipestifer using GC-MS, showing differences in metabolite abundance between serotypes. By constructing large-scale metabolic models and combining transcriptomic and metabolomic data, changes in purine metabolism were explained. The research demonstrated the possibility of detecting and differentiating between these two organisms based on their intracellular metabolites.
SCIENTIFIC REPORTS
(2021)
Review
Food Science & Technology
Maria Dyah Nur Meinita, Dicky Harwanto, Jae-Hak Sohn, Jin-Soo Kim, Jae-Suk Choi
Summary: A systematic review was conducted on the nutritional and pharmacological properties of the brown seaweed Hizikia fusiformis between 2010 and 2021, revealing an increase in research publications on the topic over the past 10 years, with a focus on chemical composition and pharmacological effects. Further studies and strategies are needed to develop H. fusiformis as a promising resource for the nutrition and pharmacological industries.
Article
Environmental Sciences
Katie E. Hillyer, Eric Raes, Andrew Bissett, David J. Beale
Summary: The study characterized bacterial communities in a metal-contaminated estuary sediment using multiple methods, and found additional contamination in areas with high metal concentrations. The dominant bacterial phyla included Proteobacteria and Desulfobacteria, and high concentration areas were enriched with metabolically versatile and biofilm forming phyla. The results can be used to inform management decisions and predictive models.
ENVIRONMENTAL POLLUTION
(2023)
Article
Food Science & Technology
Peijun Tian, Thomaz F. S. Bastiaanssen, Linhong Song, Bin Jiang, Xu Zhang, Jianxin Zhao, Hao Zhang, Wei Chen, John F. Cryan, Gang Wang
Summary: The study found that the psychobiotic strain Bifidobacterium breve CCFM1025 has a significant improvement effect on depressive-like behaviors and neurological abnormalities in chronically stressed mice, with superior carbohydrate utilization capacity and production of more neuromodulatory metabolites. Furthermore, administration of CCFM1025 reshapes the gut microbiome of chronically stressed mice, enhancing fatty acid and tryptophan biosynthesis capability in the gut-brain interaction.
MOLECULAR NUTRITION & FOOD RESEARCH
(2021)
Review
Plant Sciences
Federico Scossa, Saleh Alseekh, Alisdair R. Fernie
Summary: Our agricultural systems are facing the urgent challenge of feeding a growing global population, requiring a better understanding of plant genetic and phenotypic diversity. Recent advances in plant genomics, combined with molecular profiling approaches such as genomics, transcriptomics, and metabolomics, offer insights into the complex architecture of agricultural traits and guide crop breeding strategies.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Review
Oncology
Zijian Zou, Wei Sun, Yu Xu, Wanlin Liu, Jingqin Zhong, Xinyi Lin, Yong Chen
Summary: Sarcomas are rare mesenchymal neoplasms with unique genetic characteristics, and their diagnosis relies heavily on pathological examination. Advanced treatments and multi-omics approaches have shown promise in improving outcomes and understanding sarcomas, but further research is needed to optimize their clinical application.
FRONTIERS IN ONCOLOGY
(2022)
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)
Review
Biochemistry & Molecular Biology
Angelika Buczynska, Iwona Sidorkiewicz, Anna Trochimiuk, Slawomir Lawicki, Adam Jacek Kretowski, Monika Zbucka-Kretowska
Summary: Research suggests that evaluating novel prenatal screening biomarkers using advanced technology may improve the diagnostic accuracy of biochemical prenatal screening for Trisomy 21, while potentially uncovering new potential medical targets.
Review
Food Science & Technology
Karolinny Cristiny de Oliveira Vieira, Hevelin Regiane Augusto da Silva, Isabela Poletto Masselli Rocha, Emmanuel Barboza, Lizziane Kretli Winkelstroter Eller
Summary: Outbreaks and deaths related to Foodborne Diseases (FBD) are constantly occurring worldwide, largely due to consumption of contaminated foodstuffs with pathogens. This review discusses the main omic techniques applied in foodborne pathogens and their potential in ensuring food safety. Omics have been shown to integrate variables that contribute to food safety and improve consumer health, costs, and product quality.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Review
Cell Biology
Jia-Chen Liu, Shan-Shan Dong, Hui Shen, Dan-Yue Yang, Bin-Bin Chen, Xue-Ying Ma, Yi-Ran Peng, Hong-Mei Xiao, Hong-Wen Deng
Summary: Sarcopenia is a systemic disease characterized by muscle dysfunction, with its genetic architecture and molecular mechanisms still largely unclear. Recent advancements in multi-omics studies offer new insights into the pathogenesis of sarcopenia and may lead to new clinical applications.
AGEING RESEARCH REVIEWS
(2022)
Review
Plant Sciences
Yamshi Arif, Priyanka Singh, Andrzej Bajguz, Pravej Alam, Shamsul Hayat
Summary: This review discusses the crucial role of silicon in plant development and stress responses, highlighting its interactions with plant hormones and antioxidants, as well as its application in 'omic approaches. Furthermore, it emphasizes the need for further research on the role of silicon during abiotic stress in plants for a better understanding at a broader level.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Mengyuan Kan, Blanca E. Himes
Summary: Glucocorticoid drugs are widely used in the treatment of diseases, but there is still much to learn about their cell type-specific mechanisms and why patients respond differently. Recent studies have used genomics, transcriptomics, and other omics approaches to address these questions, but there are still knowledge gaps to be filled related to glucocorticoid action mechanisms.
PHARMACOLOGY & THERAPEUTICS
(2021)
Review
Plant Sciences
Tiziana M. Sirangelo, Richard A. Ludlow, Natasha D. Spadafora
Summary: This review provides a summary of the molecular resources for cannabis research, focusing on genomics, transcriptomics, and metabolomics approaches. The use of multi-omics methods allows for a better understanding of the relationships between cannabis sub-species and the identification of new metabolites with therapeutic potential. However, further studies are needed to fully elucidate the complex metabolomic matrix of cannabis.
Review
Biotechnology & Applied Microbiology
Ranjna Sirohi, Jaemin Joun, Hong Ii Choi, Vivek Kumar Gaur, Sang Jun Sim
Summary: This article discusses the potential of microalgae as an energy feedstock and the efforts to increase microalgae productivity using various omics techniques, with a particular focus on the application of genome sequencing and metabolic engineering in this field.
MICROBIAL CELL FACTORIES
(2021)
Review
Pharmacology & Pharmacy
Dong Niu, Xiang Ma, Taoyan Yuan, Yifan Niu, Yibin Xu, Zhongxin Sun, Yuan Ping, Weifen Li, Jufang Zhang, Tao Wang, George M. Church
Summary: Xenotransplantation of pig organs offers a potential solution to the shortage of donor organs for human patients but faces challenges such as immune rejection and the risk of porcine endogenous retrovirus transmission. Advances in genome engineering and immunosuppressive medications have the potential to overcome these barriers, leading to promising preclinical results and upcoming clinical trials for organs like islet, kidney, and heart transplantation.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Biotechnology & Applied Microbiology
Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley Chapman, James C. Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad E. Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Alvaro Martinez Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Soylev, Michael C. Schatz, Shilpa Garg, George Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey A. Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark J. P. Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit
NATURE BIOTECHNOLOGY
(2020)
Correction
Biotechnology & Applied Microbiology
Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley Chapman, James C. Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad E. Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Alvaro Martinez Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Soylev, Michael C. Schatz, Shilpa Garg, George Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey A. Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark J. P. Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit
NATURE BIOTECHNOLOGY
(2020)
Letter
Biotechnology & Applied Microbiology
Nikolai Eroshenko, Taylor Gill, Marianna K. Keaveney, George M. Church, Jose M. Trevejo, Hannu Rajaniemi
NATURE BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Jorge A. Marchand, Merrick D. Pierson Smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church
Summary: T-box riboswitches are a large family of tRNA-binding leader sequences that are crucial for gene regulation in many gram-positive bacteria. TBDB is an open-access database that contains a vast collection of T-box riboswitch sequences and provides structural annotations for this important family of regulatory RNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Engineering, Biomedical
Yanan Yue, Weihong Xu, Yinan Kan, Hong-Ye Zhao, Yixuan Zhou, Xiaobin Song, Jiajia Wu, Juan Xiong, Dharmendra Goswami, Meng Yang, Lydia Lamriben, Mengyuan Xu, Qi Zhang, Yu Luo, Jianxiong Guo, Shengyi Mao, Deling Jiao, Tien Dat Nguyen, Zhuo Li, Jacob V. Layer, Mailin Li, Violette Paragas, Michele E. Youd, Zhongquan Sun, Yuan Ding, Weilin Wang, Hongwei Dou, Lingling Song, Xueqiong Wang, Lei Le, Xin Fang, Haydy George, Ranjith Anand, Shi Yun Wang, William F. Westlin, Marc Guell, James Markmann, Wenning Qin, Yangbin Gao, Hong-Jiang Wei, George M. Church, Luhan Yang
Summary: Genetic engineering of pigs using a combination of CRISPR-Cas9 and transposon technologies allows for inactivation of endogenous retroviruses and enhancement of compatibility with the human immune system, providing a potential pathway for safe and effective porcine xenotransplantation.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Mirko Palla, Sukanya Punthambaker, Benjamin Stranges, Frederic Vigneault, Jeff Nivala, Daniel Wiegand, Aruna Ayer, Timothy Craig, Dmitriy Gremyachinskiy, Helen Franklin, Shaw Sun, James Pollard, Andrew Trans, Cleoma Arnold, Charles Schwab, Colin Mcgaw, Preethi Sarvabhowman, Dhruti Dalal, Eileen Thai, Evan Amato, Ilya Lederman, Meng Taing, Sara Kelley, Adam Qwan, Carl W. Fuller, Stefan Roever, George M. Church
Summary: The use of single-molecule DNA sequencing platform allows for rapid screening of polymerase variants, enabling the identification of enzymes with different features. This approach is valuable for applications requiring polymerases with altered physical properties.
Article
Biotechnology & Applied Microbiology
Alex H. M. Ng, Parastoo Khoshakhlagh, Jesus Eduardo Rojo Arias, Giovanni Pasquini, Kai Wang, Anka Swiersy, Seth L. Shipman, Evan Appleton, Kiavash Kiaee, Richie E. Kohman, Andyna Vernet, Matthew Dysart, Kathleen Leeper, Wren Saylor, Jeremy Y. Huang, Amanda Graveline, Jussi Taipale, David E. Hill, Marc Vidal, Juan M. Melero-Martin, Volker Busskamp, George M. Church
Summary: Using a library of human transcription factor genes, this study identified and utilized new transcription factors to directly program human pluripotent stem cells into various cell types, offering a novel approach in the field of cell engineering.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shilpa Garg, Arkarachai Fungtammasan, Andrew Carroll, Mike Chou, Anthony Schmitt, Xiang Zhou, Stephen Mac, Paul Peluso, Emily Hatas, Jay Ghurye, Jared Maguire, Medhat Mahmoud, Haoyu Cheng, David Heller, Justin M. Zook, Tobias Moemke, Tobias Marschall, Fritz J. Sedlazeck, John Aach, Chen-Shan Chin, George M. Church, Heng Li
Summary: The DipAsm method utilizes long, accurate reads and long-range conformation data to generate chromosome-scale phased assembly for single individuals within a day, demonstrating superior performance in both contiguity and phasing completeness compared to other approaches. DipAsm is crucial for the discovery of structural variants and highly polymorphic and medically important regions, facilitating high-quality precision medicine and studies of individual haplotype variation and population diversity.
NATURE BIOTECHNOLOGY
(2021)
Letter
Multidisciplinary Sciences
Lindsey R. Robinson-McCarthy, Alexander J. Mijalis, Gabriel T. Filsinger, Helena de Puig, Nina M. Donghia, Thomas E. Schaus, Robert A. Rasmussen, Raphael Ferreira, Jeantine E. Lunshof, George Chao, Dmitry Ter-Ovanesyan, Oliver Dodd, Erkin Kuru, Adama M. Sesay, Joshua Rainbow, Andrew C. Pawlowski, Timothy M. Wannier, Peng Yin, James J. Collins, Donald E. Ingber, George M. Church, Jenny M. Tam
Article
Multidisciplinary Sciences
Ethan C. Alley, Miles Turpin, Andrew Bo Liu, Taylor Kulp-McDowall, Jacob Swett, Rey Edison, Stephen E. Von Stetina, George M. Church, Kevin M. Esvelt
NATURE COMMUNICATIONS
(2020)
Article
Biology
Pranam Chatterjee, Manvitha Ponnapati, Christian Kramme, Alexandru M. Plesa, George M. Church, Joseph M. Jacobson
COMMUNICATIONS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Boxun Zhao, Jill A. Madden, Jasmine Lin, Gerard T. Berry, Monica H. Wojcik, Xuefang Zhao, Harrison Brand, Michael Talkowski, Eunjung Alice Lee, Pankaj B. Agrawal
Summary: This study reports the discovery of a de novo transposon insertion in the SRCAP gene, which causes neurodevelopmental disorders in a 28-year-old female. The insertion is a full-length antisense-oriented SVA insertion and originates from an intron of a highly expressed long non-coding RNA in testis. The insertion results in significant depletion of SRCAP expression and exon skipping.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Andrew C. Payne, Zachary D. Chiang, Paul L. Reginato, Sarah M. Mangiameli, Evan M. Murray, Chun-Chen Yao, Styliani Markoulaki, Andrew S. Earl, Ajay S. Labade, Rudolf Jaenisch, George M. Church, Edward S. Boydenit, Jason D. Buenrostrot, Fei Chen
Summary: In situ genome sequencing (IGS) allows for sequencing and imaging of genomes within intact biological samples, providing spatial localization of genomic loci and revealing parent-specific changes in genome structure across embryonic stages, single-cell chromatin domains in zygotes, and epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate the capability of IGS to directly connect sequence and structure across length scales from single base pairs to whole organisms.
Letter
Multidisciplinary Sciences
Preston W. Estep, George M. Church