Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Article
Biochemistry & Molecular Biology
Minju Joo, Ji-Hyun Yeom, Younkyung Choi, Hyeon Jun, Wooseok Song, Hyun-Lee Kim, Kangseok Lee, Eunkyoung Shin
Summary: The ribosome, once considered homogeneous, is now known to be highly heterogeneous and plays specialized roles in translational regulation. This review provides an overview of the current understanding of ribosome heterogeneity and their specialized functions, as well as discussions on specific translation systems that utilize orthogonal ribosomes.
Article
Biochemistry & Molecular Biology
Ivan A. Bychkov, Elena S. Pojidaeva, Anastasia S. Doroshenko, Vladimir A. Khripach, Natalia V. Kudryakova, Victor V. Kusnetsov
Summary: The coordination of activities between nuclei and organelles in plant cells is important and involves information exchange. Phytohormones play essential roles in this process. This study found that multiple hormones can cause changes in the expression of mitochondrial and nuclear genes in plant cells, which affect the cell's functions. These changes may be mediated through various pathways and genes, indicating the complex response to hormones.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Michael Levy, Reuven Falkovich, Ohad Vonshak, Dan Bracha, Alexandra M. Tayar, Yoshihiro Shimizu, Shirley S. Daube, Roy H. Bar-Ziv
Summary: The research focuses on creating artificial cell models based on minimal surface-bound transcription-translation reactions to mimic the compartmentalization in living cells through dense DNA brushes. The study successfully demonstrated the compartmentalization of ribosomes and transcription-translation coupling on the surface using evanescent field fluorescence. By immobilizing ribosomes next to DNA brushes, protein synthesis was achieved, allowing for the formation of subcompartments with active ribosome patterns induced and regulated by the DNA brush layout of coding and inhibitory genes.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Cell Biology
Rachel L. Cohn, Nathan S. Gasek, George A. Kuchel, Ming Xu
Summary: Senescent cells play a significant role in aging and disease, and targeting them could slow down the aging process. The commonly used marker p16 has led to important discoveries, but new markers and investigating heterogeneity are crucial. Advanced technologies like single-cell RNA-seq can help uncover new markers and the urgent need to investigate senescence heterogeneity.
TRENDS IN CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
T. Darriere, E. Jobet, D. Zavala, M. L. Escande, N. Durut, A. de Bures, F. Blanco-Herrera, E. A. Vidal, M. Rompais, C. Carapito, S. Gourbiere, J. Saez-Vasquez
Summary: This article investigates the effects of heat stress on the nucleolus in Arabidopsis thaliana plants, and demonstrates that it disrupts nucleolar structure, inhibits pre-rRNA processing, and leads to imbalanced ribosome profiles. However, the accuracy of transcription initiation and cleavage at specific sites are not affected. The study also shows that the nucleolar structure, pre-rRNA processing pathway, and ribosome profiles can be restored after returning to optimal conditions.
Article
Pathology
Nathaniel K. Mullin, Andrew P. Voigt, Erin A. Boese, Xiuying Liu, Edwin M. Stone, Budd A. Tucker, Robert F. Mullins
Summary: This study identified the regulatory differences in gene expression in human RPE in specific regions and subpopulations, providing insights into the molecular basis of macular diseases.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Article
Cell Biology
Tzu-Ling Shao, Ruei-Teng Ting, Ming -Chia Lee
Summary: This study investigates the interaction between Lsd1 and lncRNAs and its role in ovarian development and cell differentiation using fly ovaries as a model.
Article
Multidisciplinary Sciences
Z. Jafarian, S. Khamse, H. Afshar, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: In late-onset neurocognitive disorders, dysregulation of the neuron-specific gene RASGEF1C is associated with a higher frequency of genotype lacking the 6-repeat allele in patients compared to controls. Evolutionary and pathological consequences of predominantly abundant STR alleles and divergent genotypes are underappreciated features in the study of NCDs.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Felix Naef
Summary: Research on single-cell mRNA dynamics of core clock genes in mouse fibroblasts using single-molecule fluorescence technology revealed significant variability between cells. A probabilistic model was developed to account for transcriptional bursting, circadian time, and cell-to-cell heterogeneity, with clock time contributing only a small fraction to mRNA number variability between cells.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Environmental Sciences
Ana-Belen Muniz-Gonzalez, Marta Novo, Jose-Luis Martinez-Guitarte
Summary: Exposure of Chironomus riparius larvae to endosulfan resulted in significant alterations in different metabolic pathways at the molecular level, as well as modifications in all measured enzymatic activities, despite the absence of lethality. These findings highlight the need to consider effects at the sub-organismal level in addition to traditional ecologically relevant parameters in new risk assessment strategies for toxicants in the environment.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Review
Genetics & Heredity
Cecilia Pessoa Rodrigues, Maria Shvedunova, Asifa Akhtar
Summary: Hematopoiesis is the process of deriving all blood cells from a single multipotent progenitor cell, hematopoietic stem cells, in both fetal and adult organisms. The correct execution of this process relies on the interaction between genetically encoded differentiation programs and various cell-intrinsic and cell-extrinsic factors. Recent studies have highlighted the significant contributions of epigenetic modifiers to HSC self-renewal and lineage specification.
TRENDS IN GENETICS
(2021)
Article
Plant Sciences
Haiying Geng, Meng Wang, Jiazhen Gong, Yupu Xu, Shisong Ma
Summary: The study presents a computational approach named EXPLICIT to predict gene expression in Arabidopsis using transcription factors, demonstrating better accuracy in predicting transcriptomes compared to existing tools and offering new insights into transcriptional regulation in diverse plant pathways.
Article
Plant Sciences
Hulya Turk
Summary: This study found that progesterone stimulates mitochondrial respiration in germinating maize seeds, promoting seed germination through increased gene expression levels and enzyme activities.
Article
Cell Biology
Jessica Denise Schwarz, Soeren Lukassen, Pranjali Bhandare, Lorenz Eing, Marteinn Thor Snaebjoernsson, Yiliam Cruz Garcia, Jan Philipp Kisker, Almut Schulze, Elmar Wolf
Summary: Cellular growth in multicellular organisms needs to be precisely controlled, with the number of functional ribosomes playing a crucial role. The study identified two novel regulators of cell growth genes, RBM8A and ALDOA. RBM8A was found to be an important global regulator of ribosomal protein transcription, while ALDOA was unexpectedly found to regulate the expression of ribosomal biogenesis factors, possibly connecting growth gene transcription to metabolic processes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Microbiology
Jaejin Lee, Minho Lee, Kangseok Lee
Summary: RNA metabolism requires tight regulation to respond to changes in cellular physiology, with ribonucleases playing a crucial role. Living systems have evolved mechanisms to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. Various trans-acting regulators of RNase activity have been discovered in recent years.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Microbiology
Minho Lee, Minkyung Ryu, Minju Joo, Young-Jin Seo, Jaejin Lee, Hong-Man Kim, Eunkyoung Shin, Ji-Hyun Yeom, Yong-Hak Kim, Jeehyeon Bae, Kangseok Lee
Summary: Recent studies have revealed that pathogenic bacteria with ribonuclease mutations exhibit attenuated virulence, impaired mobility, and decreased proliferation in host cells. This study demonstrates that the coordinated modulation of endoribonuclease activity in Salmonella Typhimurium plays a crucial role in virulence, with RNase G impacting hns mRNA stability to regulate pathogenicity. Under anaerobic conditions, the FNR-mediated transcriptional repression of RNase III and simultaneous induction of RNase G result in rapid degradation of hns mRNA and activation of the SPI-1 T3SS in Salmonella.
Article
Chemistry, Multidisciplinary
Uisung Lee, Tae-Il Kim, Sungjin Jeon, Yongyang Luo, Siyoung Cho, Jeehyeon Bae, Youngmi Kim
Summary: meso-Carboxyl-BODIPY exhibits significant changes in fluorescence in response to small electronic changes during acyl substitution reactions, making it useful for constructing fluorescent probes for specific detection of cysteine and aminopeptidase N in live cancer cells.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Microbiology
Ji-Hee Yoon, Min-Seung Jeon, Seong-il Eyun, Yeong-Jae Seok
Summary: The bacterial PTS system is precisely regulated in response to the availability of PTS sugars, and the membrane sequestration of Mlc and induction of its regulon genes differ between different bacterial species. This study sheds light on the coevolutionary dynamics between a transcription factor and its cognate regulator in bacterial natural habitats.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
Summary: This study demonstrates that AuNP-Apt loaded with Lys AB2 P3-His can effectively inhibit Acinetobacter baumannii infection in mice, leading to increased survival.
JOURNAL OF MICROBIOLOGY
(2022)
Article
Immunology
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Summary: This study demonstrates that the expression levels of STRraA, a protein regulator of STRNase E activity, affect Salmonella enterica serovar Typhimurium pathogenicity by protecting fliDST mRNA from STRNase E cleavage, leading to enhanced flagellar assembly.
MICROBIAL PATHOGENESIS
(2022)
Article
Engineering, Marine
Hyeongwoo Choi, Sang Lyeol Kim, Man-Ki Jeong, Ok Hwan Yu, Seongil Eyun
Summary: Chitin, an abundant biopolymer, plays a crucial role in providing rigidity to exoskeletons. This study investigated chitin synthesis in a parasitic species inhabiting a hydrothermal vent, and identified multiple gene copies of chitin synthase. The findings contribute to our understanding of the evolutionary adaptation of organisms to deep-sea environments.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Yuri Choi, Yongyang Luo, Seunghwa Lee, Hanyong Jin, Hye-Jin Yoon, Yoonsoo Hahn, Jeehyeon Bae, Hyung Ho Lee
Summary: This study reveals the cooperative binding of FOX family proteins to the TP53 promoter, which regulates the transcription activity of p53 tumor suppressor. The findings also show distinct dimerization patterns of FOXA1 and FOXL2 in recognition of p53-DNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Minju Joo, Ji-Hyun Yeom, Younkyung Choi, Hyeon Jun, Wooseok Song, Hyun-Lee Kim, Kangseok Lee, Eunkyoung Shin
Summary: The ribosome, once considered homogeneous, is now known to be highly heterogeneous and plays specialized roles in translational regulation. This review provides an overview of the current understanding of ribosome heterogeneity and their specialized functions, as well as discussions on specific translation systems that utilize orthogonal ribosomes.
Article
Genetics & Heredity
Jimoon Jun, Hyeon Gyeong Jeong, Hyeongwoo Choi, Hyunmin Woo, Donggu Jeon, Young-Jin Seo, Seong-il Eyun
Summary: The complete mitochondrial genome of the copepod Labidocera rotunda collected from Jeju, Korea was sequenced in this study. The results showed that the mitochondrial genome was 16,564 bp in length and contained 13 protein-coding genes (PCGs) and 22 transfer RNAs. Phylogenetic analysis revealed that L. rotunda was closely related to the family Temoridae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Biology
Min-Seung Jeon, Da Min Jeong, Huijeong Doh, Hyun Ah Kang, Hyungtaek Jung, Seong-il Eyun
Summary: Assembling fragmented whole-genomic information is necessary for further genome-wide research. Our study focused on selecting the appropriate assembly pipeline for unknown species, using repetitive yeast genome as a model. Our results showed that Oxford Nanopore with R7.3 flow cells generated more continuous assemblies compared to PacBio Sequel. We also found that Illumina NovaSeq 6000 provided more accurate and continuous assembly in the second-generation-sequencing-first pipeline, while MGI DNBSEQ-T7 provided a cheap and accurate read in the polishing process.
LIFE SCIENCE ALLIANCE
(2023)
Article
Microbiology
Jaemin Lee, Minkyung Ryu, Dayeong Bae, Hong-Man Kim, Seong-il Eyun, Jeehyeon Bae, Kangseok Lee
Summary: Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to target molecules with high affinity and specificity. They are widely used in the biomedical field due to their durability and ease of synthesis. Researchers have developed a modified SELEX method that efficiently produces high yields of aptamers, allowing for the selection of an aptamer that specifically binds to an antimicrobial peptide. This method holds potential for the development of therapeutic agents utilizing small therapeutic peptides.
JOURNAL OF MICROBIOLOGY
(2022)
