Article
Multidisciplinary Sciences
Michelle M. Conti, Rui Li, Michelle A. Narvaez Ramos, Lihua Julie Zhu, Thomas G. Fazzio, Jennifer A. Benanti
Summary: The authors developed a high-throughput approach to quantitatively evaluate the contribution of each phosphosite within a multisite phosphorylated domain. They applied this method to study the yeast transcription factor Hcm1, revealing a complex CDK-regulatory circuit that mediates its activation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Noriko Suzuki, Tatsuya Abe, Shunji Natsuka
Summary: This study analyzed N-glycan structures in chicken respiratory tracts and found that avian influenza A viruses preferentially bind to glycans with Sia alpha 2-3Gal. The results showed that chicken trachea had a high abundance of fucosylated alpha 2,3-Sia, while no fucosylation was detected in the lung. Additionally, lung tissue contained a small amount of N-glycans with 6-sulfo sialyl LacNAc. These findings suggest that avian influenza A viruses do not evolve to bind to alpha 2,6-Sia, regardless of its abundance.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Liyun Miao, Yin Tang, Ashley R. Bonneau, Shun Hang Chan, Mina L. Kojima, Mark E. Pownall, Charles E. Vejnar, Feng Gao, Smita Krishnaswamy, Caroline E. Hendry, Antonio J. Giraldez
Summary: This study reveals the function of NPS in chromatin reprogramming and genome activation in zebrafish. NPS individually or redundantly open chromatin, regulate histone acetylation, and the position of nucleosomes is influenced by different transcription factors.
Article
Multidisciplinary Sciences
Antony D. St-Jacques, Joshua M. Rodriguez, Matthew G. Eason, Scott M. Foster, Safwat T. Khan, Adam M. Damry, Natalie K. Goto, Michael C. Thompson, Roberto A. Chica
Summary: This study presents a computational method to tune the conformational landscape of enzymes for enhanced catalytic efficiency with non-native substrates. By redesigning the conformational states and equilibria of an aminotransferase, the authors achieved customized biocatalysts with increased activity and altered substrate selectivity.
NATURE COMMUNICATIONS
(2023)
Article
Neurosciences
Kazuya Nozawa, Taku Sogabe, Ayumi Hayashi, Junko Motohashi, Eriko Miura, Itaru Arai, Michisuke Yuzaki
Summary: Excitatory synapses are formed and matured by the cooperative actions of various synaptic organizers, and recent super-resolution nanoscopy developments have revealed the existence of nanoclusters within synapses. These nanodomains interact with each other to organize excitatory synapses, with Nrxns regulating the postsynaptic nanoscopic architecture of glutamate receptors through competition and coordination of Nrxn ligands.
Review
Biochemistry & Molecular Biology
Dylan R. Weaver, Gavin M. King
Summary: The translocation of specific polypeptide chains across membranes is a vital process in all life forms. Atomic force microscopy (AFM) can be used to directly visualize the dynamic structure of the membrane-external protein topography of Sec system components, providing insights into the translocation process. AFM investigations have revealed the association of SecA with SecYEG, forming membrane-bound translocases, and suggested that the mechanism of translocation may vary depending on the hydrophobic content of precursor sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jiwei Luo, Xinglin Ruan, Zhijie Huang, Zekai Li, Le Ye, Yongyu Wu, Xiangkai Zhen, Songying Ouyang
Summary: Legionella pneumophila extensively exploits the ubiquitin pathway in infected host cells, and the Dot/Icm system secretes certain virulence effectors that act as Ub ligases or deubiquitinases. This study focuses on LotA, a unique deubiquitinase from the OTU domain family, and reveals the structural basis for its dual catalytic activity. The study provides insights into the molecular mechanism of LotA's function.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
Matthew J. Niederhuber, Daniel J. McKay
Summary: Genomic assays such as FAIRE-seq, ATAC-seq, and CUT&RUN have revealed that sequential changes in chromatin accessibility play a crucial role in mediating stage-specific cis regulatory module activity and gene expression during insect metamorphosis. Evidence indicates that systemic hormone signaling triggers genome-wide shifts in accessibility patterns and cis-regulatory module usage.
CURRENT OPINION IN INSECT SCIENCE
(2021)
Article
Immunology
Yuhan Wei, Jianwei Zhang, Xueke Fan, Zhi Zheng, Xiaoyue Jiang, Dexi Chen, Yuting Lu, Yingrui Li, Miao Wang, Min Hu, Qi Du, Liuting Yang, Hongzhong Li, Yi Xiao, Yongfu Li, Jiangtao Jin, Deying Wang, Xiangliang Yuan, Qin Li
Summary: The composition of the tumor immune microenvironment plays a critical role in the progression of gastric cancer. In this study, we used mass cytometry to analyze the immune landscape of GC patients and identified a unique tumor-immune signature. We found that T cell frequencies and the presence of regulatory T cells and TAMs were significantly altered in tumor tissues compared to adjacent tissues, suggesting a suppressive immune landscape in GC. Additionally, we discovered that specific oncogenic genomic traits interactively shaped the immunophenotype across tumor progression, providing insights for the development of novel immunotherapy strategies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Environmental Sciences
Amanda K. Suchy, Peter M. Groffman, Lawrence E. Band, Jonathan M. Duncan, Arthur J. Gold, J. Morgan Grove, Dexter H. Locke, Laura Templeton
Summary: This study found that topographic gradients play a significant role in influencing the hydrobiogeochemistry of lawns, with effects varying among different lawn types. Fertilizer application did not affect the properties of lawns, but rather suburban front yards were identified as being at greatest risk of nitrogen mobilization due to a combination of landscape characteristics and human behaviors.
Article
Microbiology
Yakun Fang, Fan Liu, Yi Shi, Ting Yang, Yu Xin, Zhenghua Gu, Guiyang Shi, Liang Zhang
Summary: TrLipE is a thermophilic lipase with potential commercial applications due to its catalytic ability under extreme conditions. By constructing chimeras between TrLipE and structurally similar enzymes, it was found that these chimeras had similar pH range and optimum pH as TrLipE but a narrower temperature range of 40-80 degrees C. Most chimeras showed lower Km and higher kcat values compared to TrLipE when using p-nitrophenol esters as substrates.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ben E. Clifton, Muhammad A. Fariz, Gen-Ichiro Uechi, Paola Laurino
Summary: This study investigated the essential function of tRNA modification m(1)G37 introduced by TrmD in bacteria. Experimental evolution of trmD mutant strains of E. coli revealed that the loss of m(1)G37 could be tolerated due to rapid recovery of growth rate via duplication or mutation of the proline-tRNA ligase gene proS. The inefficient aminoacylation of tRNA(Pro) was identified as the main reason for growth defects in trmD mutant strains, and proS was suggested to act as a gatekeeper of translational accuracy.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Agronomy
Rafael de Almeida Barros, Yaremis Merino-Cabrera, Camilo E. Vital, Neilier R. da Silva Junior, Caue N. de Oliveira, Samuel Lessa Barbosa, Joao Marques Goncalves Assis, Humberto J. O. Ramos, Maria G. de Almeida Oliveira
Summary: The results suggest that the peptides GORE1 and GORE2, designed to inhibit trypsin-like enzymes in Anticarsia gemmatalis, show potential as candidates for pest management and provide valuable information for the development of new inhibitors based on peptidomimetic tools.
PEST MANAGEMENT SCIENCE
(2021)
Article
Biology
Kevin A. Peterson, Sam Khalouei, Nour Hanafi, Joshua A. Wood, Denise G. Lanza, Lauri G. Lintott, Brandon J. Willis, John R. Seavitt, Robert E. Braun, Mary E. Dickinson, Jacqueline K. White, K. C. Kent Lloyd, Jason D. Heaney, Stephen A. Murray, Arun Ramani, Lauryl M. J. Nutter
Summary: Genome editing using CRISPR-associated (Cas) proteins has the potential to correct genetic disease-causing variants. A study compared the genomes of 50 Cas9-edited founder mice to untreated control mice using whole genome sequencing to investigate the occurrence of off-target mutagenesis induced by S. pyogenes Cas9. Computational analysis detected 26 unique sequence variants at 23 predicted off-target sites. Only 38% of the variants identified by computational analysis were validated by Sanger sequencing. In vitro assays showed the presence of two unpredicted off-target sites. The overall off-target rate was 4.9% for the guides tested. These findings suggest that off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bryan J. Visser, Sonum Sharma, Po J. Chen, Anna B. McMullin, Maia L. Bates, David Bates
Summary: DNA supercoiling is a key regulator of DNA metabolic processes, but a reliable genomic assay for supercoiling is lacking. In this study, a high-resolution method (Psora-seq) is presented to measure whole-genome supercoiling, and it is applied in Escherichia coli to observe a supercoiling landscape that is well correlated to transcription. The results indicate that transcription is the major determinant of chromosome supercoiling, while DNA replication also strongly influences supercoiling.
NUCLEIC ACIDS RESEARCH
(2022)
