News Item
Multidisciplinary Sciences
Anil Oza
Summary: The US National Science Foundation plans to utilize the historic site for biology and computer science education.
Article
Multidisciplinary Sciences
Etienne Routhier, Julien Mozziconacci
Summary: This article reviews the new applications of deep learning in the field of genomics, including functional annotation of genomes, sequence determinants of genome functions, and the possibility of writing synthetic genomic sequences.
Editorial Material
Oncology
Kristopher K. Frese, Kathryn L. Simpson, Caroline Dive
Summary: Gay et al. present a molecular classification of small cell lung cancers in Cancer Cell, extending previous studies on personalized treatments. Their identification of an "inflamed" subtype suggests potential susceptibility to immunotherapy after acquired chemoresistance.
Review
Biotechnology & Applied Microbiology
Zhou Li, He Yang, Yifei Wang, Shan-Ho Chou, Jin He
Summary: This article introduces the critical role of microbial cell factories in green biomanufacturing. It proposes the concept of the "spatial position effect" and uses 3D genomics technology to study the spatial structure characteristics of the chassis strain's 3D genome. It also suggests a method to design integration sites for synthetic gene circuits and achieve stable and efficient chassis strains for green biomanufacturing.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Imad Abugessaisa, Jordan A. Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung Chau Hon, Melissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Norio Kobayashi, Jay Shin, Michiel de Hoon, Yoshihide Hayashizakil, Piero Carninci, Hideya Kawaji, Takeya Kasukawa
Summary: The FANTOM Consortium has been dedicated to understanding the transcriptome and transcriptional regulation of mammalian genomes for the past 20 years, focusing on creating new non-coding RNA datasets and resources. The latest edition, FANTOM6, has contributed a large dataset from knock-down experiments of 285 IncRNAs in human dermal fibroblasts, along with updated miRNA and promoter atlases for human, mouse, and chicken genomes. Updated FANTOM resources are publicly available for enhanced accessibility.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Astronomy & Astrophysics
Simon Mueller, Ravit Helled
Summary: Determining the composition of giant exoplanets is essential for understanding their origin and evolution. However, direct measurement is not possible, and instead, it is deduced from mass-radius measurements, planetary age, and evolution simulations. Accurate stellar age determination, mass-radius measurements, and atmospheric compositions from upcoming missions can greatly improve the determination of heavy-element mass in giant planets. This paper emphasizes the importance of accurate age measurement and atmospheric metallicity for revealing the composition of giant exoplanets.
ASTRONOMY & ASTROPHYSICS
(2023)
Review
Immunology
Amber N. Carrier, Anjali Verma, Muhammad Mohiuddin, Manuel Pascual, Yannick D. Muller, Alban Longchamp, Chandra Bhati, Leo H. Buhler, Daniel G. Maluf, Raphael P. H. Meier
Summary: Organ allotransplantation is hindered by the limited supply of human donor organs. Xenotransplantation has the potential to address this shortage by using organs from pigs with gene editing. Recent research progress in the United States includes successful trials of pig-to-human heart and kidney xenotransplantation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Xinxu Zhang, Zongbao Liu, Wei Xu, Jie Pan, Yuhan Huang, Mingwei Cai, Zhuhua Luo, Meng Li
Summary: Metagenomic exploration of the ocean's Yap Trench led to the discovery of three new monophyletic bacterial lineages named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. The genomes of these new lineages suggest a versatile lifestyle and a preference for oxygen-limited or particle-attached environments. Evolutionary analysis indicated the importance of gene gain and loss events, as well as horizontal gene transfer, in shaping the genomic and metabolic features of these new phyla.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Infectious Diseases
Hugo Mathe-Hubert, Rafika Amia, Mikael Martin, Joel Gaffe, Dominique Schneider
Summary: The evolution of persistence in bacteria is influenced by environmental changes but is not solely driven by cellular errors. The persistence level can be maintained in a stable environment over multiple generations. These findings contribute to a better understanding of the phenomenon of bacterial persistence.
Article
Genetics & Heredity
Karen H. Miga, Evan E. Eichler
Summary: Advances in long-read sequencing and assembly allow labs to generate phased genomes that are more accurate and contiguous than the original human reference genome. Complete genome assemblies will become standard in human genetics, even in clinical settings, due to advancements in technology and computational processing.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Environmental Sciences
Chao Guo, Lutz Ahrens, Stefan Bertilsson, Marco J. L. Coolen, Jianhui Tang
Summary: The impact of perfluoroalkyl and polyfluoroalkyl substances (PFAS) on microbial communities in natural ecosystems was investigated in this study. The study found that the distribution of perfluorooctanoate (PFOA) between water and sediment is influenced by iron concentration and salinity. The alpha diversity of bacterial communities was significantly correlated with PFOA concentration, especially in water. Algoriphagus halophilus and Flavobacteriaceae were identified as biomarkers for PFOA exposure in both riverine and marine systems. Temporal variations in PFOA-sensitive bacteria were observed, suggesting the need for further research on using Limnobacter as a bioindicator for temporal monitoring of PFOA pollution.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Andres Andrade-Dominguez, Abigail Trejo-Hernandez, Carmen Vargas-Lagunas, Sergio Encarnacion-Guevara
Summary: The study found that the fungus promotes the growth of the bacterium and that together, these organisms form a mixed biofilm whose biomass is about 3 times greater and more structured than that of either single-species biofilm. Additionally, the study showed that the biofilm traits are dependent on a symbiotic plasmid encoding elements involved in the phenotypic plasticity of the bacterium, mitochondrial function, and in the production of a yeast-secreted sophoroside.
SCIENTIFIC REPORTS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Joe J. Harrison, Matthew R. Parsek, Boo Shan Tseng
Summary: The study shows that adaptive mutations in a key gene in Burkholderia cenocepacia led to lineages with different ecological roles, enabling stable coexistence of multiple genotypes and increasing community productivity.
TRENDS IN MICROBIOLOGY
(2021)
Article
Microbiology
Guangping Huang, Wenyu Shi, Le Wang, Qingyue Qu, Zhenqiang Zuo, Jinfeng Wang, Fangqing Zhao, Fuwen Wei
Summary: This study established a high-quality gut microbiome catalog of giant pandas, uncovering microbial diversity, functions, and resistome landscapes. Wild pandas exhibit host genetic-specific microbial structures and functions, while captive pandas encode more multi-drug resistance genes.
Article
Biochemistry & Molecular Biology
Tobias S. Kaiser, Jule Neumann
Summary: Circalunar clocks, allowing organisms to time reproduction to lunar phase, have been experimentally proven but are still not well understood at the molecular level. A new generation of researchers is using new tools to address this gap. Classic experiments on circalunar clocks highlight potential avenues for molecular research and suggest divergent mechanisms across different organisms.
