Article
Biotechnology & Applied Microbiology
Sevahn K. Vorperian, Mira N. Moufarrej, Stephen R. Quake
Summary: Cell types affected by diseases can be identified by analyzing cell-free RNA, allowing the determination of their tissue of origin. By utilizing various databases and transcriptomic cell atlases, cell type signature scores can be used to infer cell types contributing to cell-free RNA in different diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Yuling Han, Xiaohua Duan, Liuliu Yang, Benjamin E. Nilsson-Payant, Pengfei Wang, Fuyu Duan, Xuming Tang, Tomer M. Yaron, Tuo Zhang, Skyler Uhl, Yaron Bram, Chanel Richardson, Jiajun Zhu, Zeping Zhao, David Redmond, Sean Houghton, Duc-Huy T. Nguyen, Dong Xu, Xing Wang, Jose Jessurun, Alain Borczuk, Yaoxing Huang, Jared L. Johnson, Yuru Liu, Jenny Xiang, Hui Wang, Lewis C. Cantley, Benjamin R. TenOever, David D. Ho, Fong Cheng Pan, Todd Evans, Huanhuan Joyce Chen, Robert E. Schwartz, Shuibing Chen
Summary: Researchers have developed lung and colonic organoid models using human pluripotent stem cells, which demonstrate susceptibility to SARS-CoV-2 infection. These models are valuable for studying the infection of the virus and screening drugs, with potential therapeutic implications for COVID-19.
Article
Biochemistry & Molecular Biology
Anna Hendrika Cornelia Vlot, Setareh Maghsudi, Uwe Ohler
Summary: Identification of cell identity markers is crucial in single-cell omics data analysis. Existing methods rely on cluster assignments, but this approach is challenging for developmental data and often requires prior knowledge. In this study, we propose SEMITONES, a cluster-free marker identification method, and demonstrate its superior performance on multiple single-cell datasets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Anne Sophie Reuter, David Stern, Alice Bernard, Chiara Goossens, Arnaud Lavergne, Lydie Flasse, Virginie Von Berg, Isabelle Manfroid, Bernard Peers, Marianne L. Voz
Summary: ARP/ASCL transcription factors play a crucial role in cell fate determination. This study investigates the specific activities of these factors, recognizing highly similar DNA motifs. Overexpressing different factors in zebrafish embryos reveals their ability to rescue different secretory cell lineages. The functional divergence is encoded by a 19-aa ultra-conserved element (UCE) found in Neurod members. The UCE acts as a goblet cell fate repressor by inhibiting gfi1aa expression.
Article
Biochemistry & Molecular Biology
Maria A. Gomez-Munoz, Diana Aguilar-Morante, Ana Colmenero-Repiso, Aida Amador-Alvarez, Monica Ojeda-Puertas, Juan Antonio Cordero Varela, Ismael Rodriguez-Prieto, Ricardo Pardal, Francisco M. Vega
Summary: Neuroblastoma is a pediatric tumor with high heterogeneity and poor outcome. Patient-derived xenografts (PDXs) have been found to be useful models for studying neuroblastoma biology. In this study, we analyzed consecutive PDX passages to identify potential changes and correlations with neuroblastoma aggressiveness. We observed changes in gene expression and identified new genes and miRNAs that could be used for patient stratification and understanding tumor aggressiveness.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Jing Zhou, Xingli Zhang, Jiajia Hu, Rihao Qu, Zhibin Yu, Hao Xu, Huifang Chen, Lichong Yan, Chenbo Ding, Qiang Zou, Youqiong Ye, Zhengting Wang, Richard A. Flavell, Hua-Bing Li
Summary: The m(6)A eraser ALKBH5 plays a crucial role in controlling the pathogenicity of CD4(+) T cells during autoimmunity, as its deficiency results in weakened immune responses and reduced recruitment of neutrophils into the central nervous system.
Review
Biochemistry & Molecular Biology
Gustavo D. Campagnaro, Edward Nay, Michael J. Plevin, Angela K. Cruz, Pegine B. Walrad
Summary: A large number of eukaryotic proteins are regulated by various post-translational covalent modifications, with arginine methylation playing a significant role in affecting protein interactions. Kinetoplastids, with their unique genetic features, serve as excellent models for studying post-transcriptional regulation of gene expression. The roles of PRMTs in controlling RBPs in pathogenic kinetoplastids have been extensively studied, with important discoveries made in recent years.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Cuili Pan, Zhaoxiong Lei, Shuzhe Wang, Xingping Wang, Dawei Wei, Xiaoyan Cai, Zhuoma Luoreng, Lei Wang, Yun Ma
Summary: The study identified 185 CDK genes in Bovidae, grouped into eight distinct clades, showing extensive homology. Analysis of global expression in different bovine tissues revealed potential roles of CDK4, CDK7, CDK8, CDK9, and CDK14 in bovine adipocyte differentiation.
Article
Agriculture, Dairy & Animal Science
Mackenzie A. Marrella, Fernando H. Biase
Summary: This study suggests that it is not necessary to transform RNA-sequencing data to fit a normal distribution prior to eQTL analysis, and the differential gene expression framework can be used instead. This approach can detect biologically relevant variants that might be missed with data transformation.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(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
Yaara Finkel, Avi Gluck, Aharon Nachshon, Roni Winkler, Tal Fisher, Batsheva Rozman, Orel Mizrahi, Yoav Lubelsky, Binyamin Zuckerman, Boris Slobodin, Yfat Yahalom-Ronen, Hadas Tamir, Igor Ulitsky, Tomer Israely, Nir Paran, Michal Schwartz, Noam Stern-Ginossar
Summary: The study reveals that SARS-CoV-2 infection leads to a global reduction in translation and accelerated degradation of cytosolic cellular mRNAs. It also impairs the translation of transcripts induced in response to infection, probably mediated by inhibition of nuclear mRNA export.
Article
Plant Sciences
Qun Feng, Junxing Yu, Jie Yu, Mingyang Hu, Lei Gu, Hongcheng Wang, Xuye Du, Bin Zhu, Mengxian Cai
Summary: This study identified a natural trisomy plant in Chinese kale, which exhibited smaller plant architecture compared to normal plants and had an extra chromosome copy identified as chromosome C2. The trisomy plant showed generally upregulated gene expression on chromosome C2 and whole-genome expression perturbation. The upregulated differentially expressed genes were enriched in stress response pathways, while the downregulated genes were related to DNA synthesis.
Article
Immunology
Antoine Freuchet, Payel Roy, Sujit Silas Armstrong, Mohammad Oliaeimotlagh, Sunil Kumar, Marco Orecchioni, Amal J. Ali, Amir Khan, Jeffrey Makings, Qingkang Lyu, Holger Winkels, Erpei Wang, Christopher Durant, Yanal Ghosheh, Rishab Gulati, Felix Nettersheim, Klaus Ley
Summary: In atherosclerosis, some regulatory T cells lose FoxP3 expression and become exT(reg) cells. The study identified exT(reg) cell signature genes and characterized human exT(reg) cells as cytotoxic CD4(+)T cells. This finding suggests that exT(reg) cells play a role in inflammation and contribute to the progression of atherosclerosis.
Article
Genetics & Heredity
Zhiyun Hao, Xiayang Jin, Jiqing Wang, Yuzhu Luo, Jiang Hu, Xiu Liu, Shaobin Li, Fangfang Zhao, Mingna Li
Summary: The differentiation of preadipocytes is crucial for lipogenesis, and understanding the molecular mechanisms of lipogenesis can improve meat quality and commercial income. This study used RNA-seq technology to analyze gene expression profiles at different stages of preadipocyte differentiation in sheep. The study identified a set of differentially expressed genes (DEGs) and found that they were enriched in several biological processes. A regulatory network of DEGs related to preadipocyte differentiation in sheep was constructed, revealing potential key genes involved in this process. This study provides a deeper understanding of the roles of genes in sheep lipogenesis.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Cell Biology
Cheng Yang, Shiming Pu, Huan Zhu, Wanying Qin, Hongxia Zhao, Ziqi Guo, Zuping Zhou
Summary: Neural stem cells play an important role in maintaining the nervous system and repairing damages, offering a potential solution for treating neurodegenerative diseases. This study identified a rare population of neural stem cells in the aging mouse brain, finding that their function and cell number decrease with aging.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2022)
Review
Parasitology
Clare Halliday, Artur de Castro-Neto, Carolina L. Alcantara, Narcisa L. Cunha-e-Silva, Sue Vaughan, Jack D. Sunter
Summary: There are differences in morphology and function of the flagellar pockets among different trypanosomatids, with their life cycles and ecological niches likely influencing these differences.
TRENDS IN PARASITOLOGY
(2021)
Article
Cell Biology
Carlos Cordon-Obras, Claudia Gomez-Linan, Sara Torres-Rusillo, Isabel Vidal-Cobo, Diana Lopez-Farfan, Alicia Barroso-del Jesus, Domingo Rojas-Barros, Mark Carrington, Miguel Navarro
Summary: This study reveals the transcription initiation mechanism of genes in trypanosomes, identifying sequence-specific promoters that regulate the transcription of protein-coding genes, and demonstrates the conservation of this promoter-mediated regulation in eukaryotes.
Article
Microbiology
Lara Lopez-Escobar, Benjamin Hanisch, Clare Halliday, Midori Ishii, Bungo Akiyoshi, Samuel Dean, Jack Daniel Sunter, Richard John Wheeler, Keith Gull
Summary: ESB1, a specific protein found in the expression site body (ESB) of Trypanosoma brucei, is crucial for the activation of monoallelic VSG gene transcription and antigenic variation. It associates with DNA near the active VSG promoter and recruits RNA polymerase I, indicating its role as a transcription regulator.
NATURE MICROBIOLOGY
(2022)
Article
Entomology
Jessica Carreira De Paula, Kevin Doello, Cristina Mesas, Garyfalia Kapravelou, Alberto Cornet-Gomez, Francisco Jose Orantes, Rosario Martinez, Fatima Linares, Jose Carlos Prados, Jesus Maria Porres, Antonio Osuna, Luis Miguel de Pablos
Summary: The study utilized Micro-CT and novel staining methods to characterize the morphoanatomical features of the worker honeybee abdomen, identifying a new cell type known as ventricular telocyte. This method is proposed to be useful in further investigating the structure of honeybee abdomen under various environmental conditions. Continuous improvements in morphological and histochemical analyses of Apis mellifera could enhance the understanding of their anatomy and physiology at cellular and tissue levels.
Article
Cell Biology
Milad Jeilani, Karen Billington, Jack Daniel Sunter, Samuel Dean, Richard John Wheeler
Summary: By analyzing the protein localization properties of Trypanosome brucei, an early-branching eukaryote, this study reveals that nucleolar proteins in T. brucei share similar characteristics with those in common model eukaryotes, particularly basic amino acids. Experimental evidence showed that both homopolymer runs and distributed basic amino acids contribute to nucleolar targeting, along with a nuclear localization signal. These findings support the phase separation models of nucleolar formation and suggest a conserved mechanism for eukaryotic nucleolar targeting from the last eukaryotic common ancestor. Furthermore, the adaptation of physicochemical properties, such as an increase in basic residues, in cytoplasmic ribosome proteins may aid in their segregation.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Laura Smithson, Pearl Ihuoma Akazue, Lucy Findlater, Theresa Manful Gwira, Sue Vaughan, Jack D. Sunter
Summary: The parasites Trypanosoma brucei, T. congolense, and T. vivax, which are closely related, cause neglected tropical diseases known as African Trypanosomiasis. This study identified 13 proteins that localize to the flagellar groove, with three of these proteins shown to play a key role in the attachment of the new flagellum tip. Interestingly, T. congolense and T. vivax did not assemble a canonical groove around the new flagellum tip. This suggests rapid evolution of membrane-cytoskeleton structures and reflects the niche specialization of each species.
MOLECULAR MICROBIOLOGY
(2022)
Review
Parasitology
Laryssa Vanessa de Liz, Patricia Hermes Stoco, Jack D. Sunter
Summary: A key morphological feature of kinetoplastid parasites is the position and length of flagellum attachment to the cell body. The flagellum attachment zone (FAZ), a large complex cytoskeletal structure, mediates this lateral attachment and is essential for parasite morphogenesis and pathogenicity. Despite its complexity, only two transmembrane proteins, FLA1 and FLA1BP, have been identified to interact and connect the flagellum to the cell body. However, the genes for these proteins have undergone expansion in Trypanosoma brucei and Trypanosoma congolense, raising questions about the selection pressure and impact on host-parasite interactions.
TRENDS IN PARASITOLOGY
(2023)
Editorial Material
Parasitology
Jack D. Sunter, Samuel Dean, Richard John Wheeler
Summary: TrypTag was a 4-year project to tag the N- and C-termini of almost all Trypanosoma brucei proteins with a fluorescent protein and record the subcellular localisation through images and manual annotation. We highlight the new routes to cell biological discovery this transformative resource is enabling for parasitologists and cell biologists.
TRENDS IN PARASITOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Amanda T. S. Albanaz, Mark Carrington, Alexander O. Frolov, Anna I. Ganyukova, Evgeny S. Gerasimov, Alexei Y. Kostygov, Julius Lukes, Marina N. Malysheva, Jan Votypka, Alexandra Zakharova, Kristina Zahonova, Sara L. Zimmer, Vyacheslav Yurchenko, Anzhelika Butenko
Summary: This study conducted genome sequencing and analysis on previously overlooked trypanosomatid species, revealing their genomic diversity and chromosomal variations. The findings provide a solid foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in this species.
Article
Parasitology
Alexander D. Cook, Mark Carrington, Matthew K. Higgins
Summary: This article reviews decades of evidence on the effect of complement on African trypanosomes, focusing on the discovery of a trypanosome receptor for complement C3. It critically assesses three recent studies that attempt to provide a structural and mechanistic view of how this receptor helps trypanosomes survive in the presence of complement.
TRENDS IN PARASITOLOGY
(2023)
Review
Microbiology
Anna Barcons-Simon, Mark Carrington, T. Nicolai Siegel
Summary: Antigenic variation is a strategy used by pathogens to evade the host immune system. This Review discusses the impact of nuclear organization on antigenic variation in protozoan parasites, specifically Trypanosoma brucei and Plasmodium falciparum. It highlights the relevance of nuclear organization in both mutually exclusive antigen expression and genome stability, which are essential for antigenic variation.
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Clare Halliday, Laryssa Vanessa de Liz, Sue Vaughan, Jack D. Sunter
Summary: The flagellar pocket, a cell membrane invagination at the base of the flagellum, is tightly associated with cytoskeletal structures in Leishmania and other kinetoplastid parasites. In this study, the localization and function of Leishmania orthologues of Trypanosoma brucei FAZ proteins were screened and analyzed. Deletion of two FAZ proteins, FAZ27 and FAZ34, in the flagellum resulted in reduced cell body size and flagellum loss in some cells. Moreover, distinct changes in cell shape were observed after generating the null mutant, demonstrating the parasite's ability to adapt to morphological perturbations resulting from gene deletion.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Rupa Nagar, Isobel Hambleton, Michele Tinti, Mark Carrington, Michael A. J. Ferguson
Summary: In this study, the surface glycoconjugates of T. theileri were purified and partially characterized using biochemical and mass spectrometry-based approaches. It was found that the surface glycoconjugates consist of glycoproteins and glycolipids, including MSPs and TTPSPs. Furthermore, the glycolipids of T. theileri were shown to be larger and more diverse than those of its phylogenetic relative T. cruzi.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2023)
Article
Veterinary Sciences
Maria Buendia-Abad, Pilar Garcia-Palencia, Luis Miguel de Pablos, Raquel Martin-Hernandez, Mariano Higes
Summary: The trypanosomatid species Crithidia acanthocephali, initially found in the digestive tract of Hemiptera, was recently detected in honey bee colonies in Spain, leading to questions about bees as potential hosts for this parasite. Experimental infection of worker bees with choanomastigotes resulted in the differentiation of the parasites and the adoption of a haptomonad morphology, attaching to the gut walls via hemidesmosomes-like junctions. These findings suggest that insect trypanosomatids may have a wider range of hosts than previously thought.
VETERINARY SCIENCES
(2022)
Article
Cell Biology
Madison Atkins, Jiri Tyc, Shahaan Shafiq, Manu Ahmed, Eloise Bertiaux, Artur Leonel De Castro Neto, Jack Sunter, Philippe Bastin, Samuel Dale Dean, Sue Vaughan
Summary: CEP164C contributes to the locking mechanism at the base of the flagellum in Trypanosoma brucei, with its localization to mature basal bodies of fully assembled old flagella. Inhibiting cytokinesis results in CEP164C acquisition on the new flagellum once it reaches the old flagellum length. These findings provide insight into the molecular mechanisms regulating flagella growth in maintaining existing while growing new flagella.
JOURNAL OF CELL BIOLOGY
(2021)