Article
Biotechnology & Applied Microbiology
H. B. Mahesh, Meghana Deepak Shirke, Guo-Liang Wang, Malali Gowda
Summary: Transcriptional re-programming occurs in both host and pathogen during leaf and neck infection, resulting in tissue-specific and infection-specific gene expression patterns. Different sets of genes are uniquely expressed in leaf and neck tissues, with certain genes being up-regulated during infection in each tissue. MicroRNA sequencing reveals differential expression of microRNAs targeting specific transcripts in response to infection, providing insights into the dual-epidemics of blast disease.
Article
Multidisciplinary Sciences
Steffen Fuchs, Loelia Babin, Elissa Andraos, Chloe Bessiere, Semjon Willier, Johannes H. Schulte, Christine Gaspin, Fabienne Meggetto
Summary: This article presents an improved protocol for enriching and sequencing full-length circRNAs using the Oxford Nanopore long-read sequencing platform. The protocol involves exonuclease treatment and negative selection to enrich lowly abundant circRNAs, followed by cDNA library creation and PCR amplification. The protocol works well with human cancer cell lines and enables reliable full-length analysis of circRNAs.
Article
Biotechnology & Applied Microbiology
Yen-Wen Kuo, Bryce W. Falk
Summary: This study compares the expression of amiRNAs in plants using different vectors. The research finds that the nucleotide composition of the mature amiRNA region determines the selection of the guide strand, with the strand containing excess purines being preferentially selected. Furthermore, the study shows that only when the intended strand is loaded into AGO can the amiRNA provide the expected RNAi effects.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Karlis Pleiko, Kristina Posnograjeva, Maarja Haugas, Paarn Paiste, Allan Tobi, Kaarel Kurm, Una Riekstina, Tambet Teesalu
Summary: In vivo phage display is commonly used for identification of specific homing peptides, but current methods lack the ability to assess the distribution of specific peptide phages across tissues during screening. By applying bioinformatics tools for RNA sequencing to analyze high-throughput sequencing data, researchers were able to estimate the representation of individual peptides during biopanning in vivo, leading to the identification of novel lung- and brain-specific homing peptides. This approach offers a more efficient and reproducible method for in vivo peptide phage biopanning.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Jiaxing Chen, ChinWang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K. Cheung, Lu Zhang
Summary: Single-cell RNA sequencing has enabled the reconstruction of cell-type-specific gene regulatory networks with the novel DeepDRIM algorithm, which demonstrated superior performance compared to existing algorithms for both simulated and real scRNA-seq data. The method was robust to varying dropout rates, cell numbers, and training data sizes. DeepDRIM was further applied to analyze cell-type-specific GRN alterations in B cells from COVID-19 patients, revealing potential gene targets associated with coronavirus infection.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Zifan Yue, Fei Tong, Chengcheng Zeng, Ruili Wei
Summary: This study systematically investigated the potential regulatory effects of tRNA-related fragments (tRFs) in thyroid-associated ophthalmopathy (TAO). The dysregulation of tRFs and mRNA expression levels in TAO patients were analyzed, and potential therapeutic targets and biomarkers were explored. The results suggest that tRF5-GluCTC may play a role in regulating orbital fibroblast adipogenic response and fibrotic hyperplasia in TAO patients by targeting ATF3, HSD17B2, and PMAIP1.
FRONTIERS IN GENETICS
(2022)
Article
Engineering, Geological
Yang Liu, Di Wang, Jinlong Hu, Guoli Zhu
Summary: This paper proposes a rock fragment classification method based on convolutional neural network (CNN), which uses contrast limited adaptive histogram equalization to enhance fragment edge features and balances the data set through image regeneration. The experiments show that the proposed CNN model achieves high accuracy in classifying various types of fragments and outperforms other classic fragment classification models.
ROCK MECHANICS AND ROCK ENGINEERING
(2023)
Article
Pharmacology & Pharmacy
Yu-Chen Yan, Zhi-Heng Xu, Jian Wang, Wen-Bo Yu
Summary: This study utilized single-nuclei RNA sequencing data for network pharmacology analysis and employed a deep learning algorithm for high-throughput screening of effective drug-target interactions. The strongest interactions between ginkgolides and MAPK14 were validated by molecular docking. This work overcomes the limitations of conventional research, enhances our understanding of the mechanisms of GBE in treating PD, and provides a theoretical foundation for future drug development in PD.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thomas Bridge, Udo Wegmann, Jason C. C. Crack, Kate Orman, Saher A. A. Shaikh, William Farndon, Carlo Martins, Gerhard Saalbach, Amit Sachdeva
Summary: Designing biomolecules with dual photoactivity and photoreactivity remains a challenge. Researchers achieved this by incorporating photocaged tyrosine (pcY) for photoactivity and p-benzoyl-?-phenylalanine (Bpa) for photoreactivity into an epidermal growth factor receptor (EGFR)-targeting antibody fragment, 7D12. They identified a position for incorporating Bpa that had minimal effect on the binding affinity of 7D12 to EGFR. Upon exposure to 365-nm light, this mutant of 7D12 can specifically bind to and form a covalent bond with EGFR.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Siqi Bao, Ke Li, Congcong Yan, Zicheng Zhang, Jia Qu, Meng Zhou
Summary: This study summarizes the recent advances and applications of deep learning-based methods in the analysis of scRNA-seq data and specific tools, and investigates the future perspectives and challenges of deep learning techniques in the appropriate analysis and interpretation of scRNA-seq data.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Pauline Sararols, Isabelle Stevant, Yasmine Neirijnck, Diane Rebourcet, Annalucia Darbey, Michael K. Curley, Francoise Kuhne, Emmanouil Dermitzakis, Lee B. Smith, Serge Nef
Summary: FLCs and ALCs exhibit significant differences in transcriptional and functional features, including gene expression variations and non-transcriptional events such as intron retention. The FLC-specific expression of Crhr1 and Mc2r receptors suggests a dual regulation of steroidogenesis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yan Zhou, Minjiao Peng, Bin Yang, Tiejun Tong, Baoxue Zhang, Niansheng Tang
Summary: In this study, a new deep learning classifier is proposed for large sample scRNA-seq data. The classifier outperforms existing methods in various settings and does not require prior knowledge of the data distribution.
Article
Genetics & Heredity
Takehito Sugasawa, Shin-ichiro Fujita, Tomoaki Kuji, Noriyo Ishibashi, Kenshirou Tamai, Yasushi Kawakami, Kazuhiro Takekoshi
Summary: The study found that specific cfDNA sequences (spcfDNA) levels in healthy individuals significantly increased after extreme exercise, such as running a full marathon, and were strongly correlated with white blood cell and plasma myoglobin concentrations. This suggests that spcfDNA may be highly sensitive markers of extreme physical stress.
Article
Oncology
Jinchun Wu, Haiyan Zhou, Xiaoping Yi, Qiongzhi He, Tianxiang Lei, Fengbo Tan, Heli Liu, Bin Li
Summary: In NF1-deficient GISTs, about 48% of cases have concurrent mKIT mutations, especially in Chinese populations. These gain-of-function mKIT mutations are mostly located in exon 11 of the KIT gene. The presence of mKIT in NF1-associated GISTs is not associated with patient age, gender, or location.
CANCER MANAGEMENT AND RESEARCH
(2021)
Article
Immunology
Sai Pooja Mahajan, Jeffrey A. Ruffolo, Rahel Frick, Jeffrey J. Gray
Summary: Antibodies are important therapeutics for treating cancer, infectious disease, and inflammation, and their target affinity needs to be improved through engineering. This study proposes the F(v)Hallucinator pipeline based on deep learning to design antibody sequences, resulting in the generation of inexpensive, diverse, and targeted antibody libraries enriched in binders for the target antigen. This provides a new approach for antibody affinity maturation.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Cell Biology
Christelle Morris, David Cluet, Emiliano P. Ricci
Summary: Eukaryotic gene expression is regulated by the translation and turnover of mRNAs, with the ribosome playing a central role in this process. The cell has evolved multiple translation-dependent mRNA surveillance pathways to handle specific problematic mRNAs. Current research focuses on translation features, genetic code complexity, and the emerging role of the ribosome as a regulatory hub.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Multidisciplinary Sciences
Philippe E. Mangeot, Laura Guiguettaz, Thibault J. M. Sohier, Emiliano P. Ricci
Summary: The CRISPR-Cas system has brought democratization of genome editing in eukaryotic cells, but the delivery of Cas9 protein and sgRNA into target cells remains a technical challenge. Nanoblades, based on MLV, have been developed to overcome issues with traditional viral vectors and can efficiently deliver Cas9 protein and guide RNA without the need for a coding transgene.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Shilpa Rao, Ian Hoskins, Tori Tonn, P. Daniela Garcia, Hakan Ozadam, Elif Sarinay Cenik, Can Cenik
Summary: Viruses rely on host translation machinery for survival and utilize Nsp1 to suppress host translation. The study reveals that a subset of human genes is preferentially translated in the presence of Nsp1, including genes related to viral pathogenicity. Additionally, the enrichment of 5' terminal oligo-pyrimidine tracts in these preferentially translated genes is uncovered.
Article
Multidisciplinary Sciences
Yu H. Sun, Ruoqiao Huiyi Wang, Khai Du, Jiang Zhu, Jihong Zheng, Li Huitong Xie, Amanda A. Pereira, Chao Zhang, Emiliano P. Ricci, Xin Zhiguo Li
Summary: The ribosome plays a crucial role in mediating piRNA biogenesis from both short and long open reading frames, indicating a general mechanism regardless of precursor ORF length. This pathway is essential for protecting the germline genome and fertility. The study reveals a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes, shedding light on the role of piRNA in fine-tuning protein production.
NATURE COMMUNICATIONS
(2021)
Review
Immunology
Anissa Guillemin, Anuj Kumar, Melanie Wencker, Emiliano P. Ricci
Summary: Innate immunity is the first line of defense against infections and tissue damage, and it relies on a dynamic and coordinated gene expression program. Transcriptional and post-transcriptional regulatory pathways, involving RNA-binding proteins and other effectors, play crucial roles in shaping the innate immune response. Recently, microRNAs and post-transcriptional modification of RNA bases have also emerged as essential players in this process.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Yu Rebecca Miao, Kaushik Thakkar, Can Cenik, Dadi Jiang, Kazue Mizuno, Chenjun Jia, Caiyun Grace Li, Hongjuan Zhao, Anh Diep, Yu Xu, Xin Eric Zhang, Teddy Tat Chi Yang, Michaela Liedtke, Parveen Abidi, Wing-Sze Leung, Albert C. Koong, Amato J. Giaccia
Summary: This study reveals the distinctive requirements for neutralizing TNF receptor ligands APRIL and BAFF in hematological cancers, and demonstrates that an affinity-enhanced mutant sBCMA-Fc fusion molecule (sBCMA-Fc V3) significantly enhances antitumor activity against both MM and DLBCL. The study also shows an adequate toxicity profile and on-target mechanism of action in nonhuman primate studies.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Boris Bonaventure, Antoine Rebendenne, Ana Luiza Chaves Valadao, Mary Arnaud-Arnould, Segolene Gracias, Francisco Garcia de Gracia, Joe McKellar, Emmanuel Labaronne, Marine Tauziet, Valerie Vivet-Boudou, Eric Bernard, Laurence Briant, Nathalie Gros, Wassila Djilli, Valerie Courgnaud, Hugues Parrinello, Stephanie Rialle, Mickael Blaise, Laurent Lacroix, Marc Lavigne, Jean-Christophe Paillart, Emiliano P. Ricci, Reiner Schulz, Nolwenn Jouvenet, Olivier Moncorge, Caroline Goujon
Summary: DDX42 has been identified as an intrinsic antiviral inhibitor, restricting HIV-1 and other RNA viruses. It does not impact the replication of several negative-strand RNA viruses, suggesting a specific mode of action on target cells.
Article
Multidisciplinary Sciences
Sebastien Durand, Marion Bruelle, Fleur Bourdelais, Bigitha Bennychen, Juliana Blin-Gonthier, Caroline Isaac, Aurelia Huyghe, Sylvie Martel, Antoine Seyve, Christophe Vanbelle, Annie Adrait, Yohann Coute, David Meyronet, Frederic Catez, Jean-Jacques Diaz, Fabrice Lavial, Emiliano P. Ricci, Francois Ducray, Mathieu Gabut
Summary: The study reveals that RSL24D1 is highly expressed in both mouse and human pluripotent stem cells and is involved in the biogenesis of 60S subunits. Depletion of RSL24D1 impairs global translation, particularly of pluripotency factors and components from the Polycomb Repressive Complex 2 (PRC2), leading to altered self-renewal and lineage commitment choices in embryonic stem cells.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Hakan Ozadam, Tori Tonn, Crystal M. Han, Alia Segura, Ian Hoskins, Shilpa Rao, Vighnesh Ghatpande, Duc Tran, David Catoe, Marc Salit, Can Cenik
Summary: Translation regulation is crucial for early mammalian embryonic development. However, the previous bulk measurements have limited the precise determination of translation regulation, including allele-specific analyses. In this study, a new microfluidic isotachophoresis (ITP) approach, called Ribo-ITP, was developed to profile translation in single oocytes and embryos during early mouse development. The results revealed differential translation efficiency as an important mechanism for regulating genes involved in centrosome organization and N-6-methyladenosine modification of RNAs. It also led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. Moreover, the Ribo-ITP approach has the potential to enable various applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples, including single cells.
Article
Pathology
Ana Cristina Vargas, Erin E. Heyer, Alison L. Cheah, Fiona Bonar, Martin Jones, Fiona M. Maclean, Anthony J. Gill, James Blackburn
Summary: This study used a 241-gene RNA hybridisation capture sequencing panel to identify unexpected fusions in sarcomas of young individuals. The results showed successful sequencing in 57% of samples, with 16.6% of them harboring translocations. RNA-based sequencing is an important tool for redefining the classification of sarcomas and identifying pathogenic gene fusions.
Article
Multidisciplinary Sciences
Manon Venet, Margarida Sa Ribeiro, Elodie Decembre, Alicia Bellomo, Garima Joshi, Celia Nuovo, Marine Villard, David Cluet, Magali Perret, Remi Pescamona, Helena Paidassi, Thierry Walzer, Omran Allatif, Alexandre Belot, Sophie Trouillet-Assant, Emiliano P. Ricci, Marlene Dreux
Summary: The authors demonstrate that in severe SARS-CoV-2 infection, the function of plasmacytoid dendritic cells (pDC) is impaired, leading to reduced production of type I interferon and possibly lower viral control. This study suggests that pDC activation is essential to control SARS-CoV-2 infection, and failure to develop this response could be important in understanding severe cases of COVID-19.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Ian Hoskins, Song Sun, Atina Cote, Frederick P. Roth, Can Cenik
Summary: satmut_utils is a flexible solution for simulating and quantifying genetic variants, allowing for high-performance analysis of multiplexed assays of variant effect (MAVEs) and revealing the impact of variants on mRNA abundance.
Meeting Abstract
Biotechnology & Applied Microbiology
A. Gutierrez-Guerrero, M. J. Abrey Recalde, S. Perian, P. E. Mangeot, C. Costa, O. Bernadin, F. Fusil, G. Froment, A. Martinez-Turtos, A. Krug, F. Martin, K. Benabdellah, E. P. Ricci, S. Giovannozzi, R. Gijsbers, M. Mevel, E. Ayuso, F. L. Cosset, E. Verhoeyen
HUMAN GENE THERAPY
(2021)
Meeting Abstract
Biotechnology & Applied Microbiology
A. Gutierrez-Guerrero, M. J. Abrey Recalde, S. Perian, P. E. Mangeot, C. Costa, O. Bernadin, F. Fusil, G. Froment, A. Martinez-Turtos, A. Krug, F. Martin, K. Benabdellah, E. P. Ricci, S. Giovannozzi, R. Gijsbers, M. Mevel, E. Ayuso, F. L. Cosset, E. Verhoeyen
HUMAN GENE THERAPY
(2021)
Article
Biotechnology & Applied Microbiology
Alejandra Gutierrez-Guerrero, Maria Jimena Abrey Recalde, Philippe E. Mangeot, Caroline Costa, Ornellie Bernadin, Severine Perian, Floriane Fusil, Gisele Froment, Adriana Martinez-Turtos, Adrien Krug, Francisco Martin, Karim Benabdellah, Emiliano P. Ricci, Simone Giovannozzi, Rik Gijsbers, Eduard Ayuso, Francois-Loic Cosset, Els Verhoeyen
Summary: The use of nanoblades, a new technology, allows efficient delivery of genomic cleaving agents into human T, B, and hematopoietic stem and progenitor cells for gene editing. It achieves high editing efficiency at gene loci like Wiskott-Aldrich syndrome without observed toxicity. The technology also shows promise for clinical translation in gene therapy due to its simplicity and cost-effectiveness.
FRONTIERS IN GENOME EDITING
(2021)
