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Biotechnology & Applied Microbiology
Danny Bergeron, Laurence Faucher-Giguere, Ann-Kathrin Emmerichs, Karine Choquet, Kristina Sungeun Song, Gabrielle Deschamps-Francoeur, Etienne Fafard-Couture, Andrea Rivera, Sonia Couture, L. Stirling Churchman, Florian Heyd, Sherif Abou Elela, Michelle S. S. Scott
Summary: Small nucleolar RNAs (snoRNAs) are noncoding RNAs involved in ribosomal RNA maturation. A recent study has shown that many intronic snoRNAs interact with their host transcripts near alternative exons, indicating a potential role in splicing regulation. This study also provides evidence that snoRNA-host interactions can affect the expression and splicing of host genes, suggesting a more widespread role for intronic snoRNAs in gene regulation.
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Plant Sciences
Wei-Bo Xu, Lei Zhao, Peng Liu, Qian-Huan Guo, Chang-Ai Wu, Guo-Dong Yang, Jin-Guang Huang, Shu-Xin Zhang, Xing-Qi Guo, Shi-Zhong Zhang, Cheng-Chao Zheng, Kang Yan
Summary: This study reports a stress-responsive RNA splicing mechanism for intronic miR400 production, whereby miR400 modulates reactive oxygen species (ROS) accumulation and improves plant tolerance by downregulating its target expression. The study also highlights the function of intronic miRNAs as a 'signal transducer' in enhancing plant stress tolerance.
Article
Biochemistry & Molecular Biology
Shang Wang, Yuqing Li, Li Zhong, Kai Wu, Ruhua Zhang, Tiebang Kang, Song Wu, Yuanzhong Wu
Summary: The group has developed GEIS as an improved HDR gene editing technology that can achieve a DsRed positive rate as high as 87.5%. The method has the potential to edit approximately 97% of gene editing targets in human and mouse cells, and may be useful for introducing multiple DNA variations in cells.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
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Genetics & Heredity
Li Zhang, Minna Shen, Xianhong Shu, Jingmin Zhou, Jing Ding, Chunjiu Zhong, Baishen Pan, Beili Wang, Chunyan Zhang, Wei Guo
Summary: This study aims to reveal the characteristics of intronic variants in whole exome sequencing (WES) data and improve its clinical diagnostic value. Analysis of 269 WES data showed that intronic variants were most abundant in the regions flanking exons. The study found that the +9 and -9 positions may serve as potential splicing site boundaries, and the +5 and -5 positions were important sites affecting splicing or gene expression.
BMC MEDICAL GENOMICS
(2023)
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Genetics & Heredity
Chuang Yin, Chuandong Wang, Chen Wang
Summary: This study examines the differential expression of small noncoding RNAs in keloid skin tissue (KST) and reveals potential targets for the development of new treatment for keloids.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Susanna Szakats, Alice McAtamney, Megan J. Wilson
Summary: Recent advances in small RNA-seq technology and bioinformatics pipelines have allowed for the discovery of novel miRNAs in the E15.5 mouse brain. A high-quality small RNA-seq dataset was used to identify 50 putative novel miRNAs, with 6 of them further validated. Conservation analysis and target functional prediction were used to determine the authenticity of these novel miRNA candidates.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Immunology
Ding Ma, Xing Zhou, Yu Wang, Liming Dai, Jie Yuan, Jianping Peng, Xiaoling Zhang, Chuandong Wang
Summary: In this study, we investigated the expression changes of small noncoding RNAs during macrophage polarization using high-throughput sequencing analysis and qPCR. Our results showed that miRNAs, piRNAs, snoRNAs, snRNAs, and repeat RNAs exhibited altered expression patterns during different polarization states, suggesting their potential roles in regulating macrophage function.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Aijaz Parray, Fayaz Ahmad Mir, Asmma Doudin, Ahmad Iskandarani, Ibn Mohammed Masud Danjuma, Rahim Ayadathil Thazhhe Kuni, Alaaedin Abdelmajid, Ibrahim Abdelhafez, Rida Arif, Mohammad Mulhim, Mohammad Abukhattab, Shoukat Rashhid Dar, Ala-Eddin Al Moustafa, Eyad Elkord, Abdul Latif Al Khal, Abdel-Naser Elzouki, Farhan Cyprian
Summary: This study identified microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) as potential biomarkers of COVID-19 severity through differential expression analysis of microarray data, and found that they are significantly correlated with white blood cell count, neutrophil count, lymphocyte count, red blood cell count, hemoglobin, etc. The study provides a unique miRNA and snoRNA profile associated with a higher risk of severity in SARS-CoV-2 infected patients, highlighting the importance of these molecules in SARS-CoV-2 infection.
Review
Biochemistry & Molecular Biology
Alexander Bishop Coley, Jeffrey David DeMeis, Neil Yash Chaudhary, Glen Mark Borchert
Summary: In the past decade, sdRNAs derived from snoRNAs have emerged as important regulators in cancer gene expression. They possess miRNA-like functions and can act as oncogenic or tumor-suppressing RNAs depending on the tissue context. Despite being frequently overlooked in non-coding RNA analyses, sdRNAs represent a subclass of miRNAs that deserve further study to uncover their underlying biology and identify potential biomarkers and therapeutic targets for various human cancers.
Review
Cell Biology
Manisha Deogharia, Priyatansh Gurha
Summary: This article explores the prevalence of noncoding RNAs in the human genome, which play a crucial role in regulating cellular processes through base pairing interactions with proteins. The mechanisms of RNA-RNA or RNA-DNA pairing are discussed, highlighting the shared evolutionary mechanisms of ncRNAs and their diverse base pairing interactions.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Cell Biology
Soomin Son, Baekgyu Kim, Jihye Yang, V. Narry Kim
Summary: In this study, the researchers explore the role of the N-terminal proline-rich disordered domain (PRD) of DROSHA in miRNA processing. They find that the PRD specifically promotes the maturation of intronic miRNAs, independent of splicing reactions. They also discover that PRD is more important for rapidly evolving miRNAs, suggesting a role in miRNA evolution.
GENES & DEVELOPMENT
(2023)
Review
Cell Biology
Jaclyn M. Fingerhut, Yukiko M. Yamashita
Summary: Satellite DNAs are repetitive sequences found in the genome and have been mistakenly considered as junk. Recent studies have started to uncover their function. In the case of intron gigantism, satellite DNAs are found within introns, resulting in large introns that require specialized mechanisms to overcome the burden of repetitive DNA. However, it remains unclear whether intron gigantism has any benefits or serves any functional purpose for cells and organisms.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Microbiology
Yong Nie, Heng Zhao, Zimin Wang, Zhengyu Zhou, Xiaoyong Liu, Bo Huang
Summary: The study sequenced six mitochondrial genomes of the genus Conidiobolus s.s., revealing the characteristics of these genomes and the sorting of 14 core protein-coding genes. Phylogenomic analysis confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Orthopedics
Hui Wang, Guiquan Cai, Fengbin Yu, De Li, Chenglong Wang, Ding Ma, Xiuguo Han, Jiajia Chen, Chuandong Wang, Jiye He
Summary: Osteosarcoma, the most common malignant bone tumor, primarily affects adolescents and the elderly. Bone marrow mesenchymal stem cells (BMSCs) are believed to be a potential source of osteosarcoma cells. Understanding the gene expression differences between BMSCs and osteosarcoma cells, specifically in small noncoding RNAs, provides valuable insights into the pathogenesis and early diagnosis and treatment of osteosarcoma.
JOURNAL OF ORTHOPAEDIC SURGERY AND RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Ryo Kurosawa, Kei Iida, Masahiko Ajiro, Tomonari Awaya, Mamiko Yamada, Kenjiro Kosaki, Masatoshi Hagiwara
Summary: PDIVAS is a tool for detecting disease-causing deep-intronic variants, trained using ensemble machine learning algorithms with high precision and maximum MCC value. In genome sequencing analysis, PDIVAS prioritizes pathogenic variants more efficiently than previous predictors.
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Genetics & Heredity
Yan-Cong Zhang, Yan Zhang, Bi-Ru Zhu, Bo-Wen Zhang, Chuan Ni, Da-Yong Zhang, Ying Huang, Erli Pang, Kui Lin
STANDARDS IN GENOMIC SCIENCES
(2015)
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Biochemistry & Molecular Biology
Jiwon Jang, Yidi Wang, Matthew A. Lalli, Elmer Guzman, Sirie E. Godshalk, Hongjun Zhou, Kenneth S. Kosik
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Engineering, Environmental
Lijuan Zhao, Cruz Ortiz, Adeyemi S. Adeleye, Qirui Hu, Hongjun Zhou, Yuxiong Huang, Arturo A. Keller
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2016)
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Engineering, Environmental
Lijuan Zhao, Yuxiong Huang, Jerry Hu, Hongjun Zhou, Adeyemi S. Adeleye, Arturo A. Keller
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2016)
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Biochemistry & Molecular Biology
Matthew A. Lalli, Jiwon Jang, Joo-Hye C. Park, Yidi Wang, Elmer Guzman, Hongjun Zhou, Morgane Audouard, Daniel Bridges, Kenneth R. Tovar, Sorina M. Papuc, Andreea C. Tutulan-Cunita, Yadong Huang, Magdalena Budisteanu, Aurora Arghir, Kenneth S. Kosik
HUMAN MOLECULAR GENETICS
(2016)
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Neurosciences
Neha Rani, Tomasz J. Nowakowski, Hongjun Zhou, Sirie E. Godshalk, Veronique Lisi, Arnold R. Kriegstein, Kenneth S. Kosik
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Chemistry, Multidisciplinary
Lijuan Zhao, Yuxiong Huang, Hongjun Zhou, Adeyemi S. Adeleye, Hongtao Wang, Cruz Ortiz, Susan J. Mazer, Arturo A. Keller
ENVIRONMENTAL SCIENCE-NANO
(2016)
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Cell Biology
Gongping Sun, Elmer Guzman, Varuzhan Balasanyan, Christopher M. Conner, Kirsten Wong, Hongjun Robin Zhou, Kenneth S. Kosik, Denise J. Montell
JOURNAL OF CELL BIOLOGY
(2017)
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Biochemistry & Molecular Biology
Xuemei Zhang, Yanxian Lin, Neil A. Eschmann, Hongjun Zhou, Jennifer N. Rauch, Israel Hernandez, Elmer Guzman, Kenneth S. Kosik, Songi Han
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Neurosciences
Tomasz J. Nowakowski, Neha Rani, Mahdi Golkaram, Hongjun R. Zhou, Beatriz Alvarado, Kylie Huch, Jay A. West, Anne Leyrat, Alex A. Pollen, Arnold R. Kriegstein, Linda R. Petzold, Kenneth S. Kosik
NATURE NEUROSCIENCE
(2018)
Article
Biochemical Research Methods
Jindan Guo, Erli Pang, Hongtao Song, Kui Lin
Summary: The study presents a new method called colored superbubble (cSupB) for organizing and analyzing spatial structure of genome graphs, proposing a novel tri-tuple coordinate system. The method efficiently detects small indels and can adapt to complex cycle structures.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Xinrui Lin, Ning Zhang, Hongtao Song, Kui Lin, Erli Pang
Summary: This study identified population-specific recent positive selection in cultivated cucumber populations using genomic variation data. The selected sites were associated with reproduction, stress response, and developmental regulation processes. Genes related to fruit traits were also observed, and soft sweeps were common in certain populations. These findings provide valuable insights into the biological mechanisms of cucumber adaptation and domestication.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Mingzhu Sun, Erli Pang, Wei-Ning Bai, Da-Yong Zhang, Kui Lin
Summary: Polyploidy is common and its effects are complex and variable. Computational tools for ploidy estimation are urgently needed to avoid cumbersome experiments. We developed ploidyfrost, a method for estimating ploidy levels without a reference genome, and evaluated its performance using different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin
BMC BIOINFORMATICS
(2017)
Article
Developmental Biology
Elijah J. Spina, Elmer Guzman, Hongjun Zhou, Kenneth S. Kosik, William C. Smith
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)