Papers December 2024

• The emerging roles of multimolecular G-quadruplexes in transcriptional regulation and chromatin organization.
  • Antariksa NF, di Antonio M
  • Accounts of Chemical Research
  • doi: 10.1021/acs.accounts.4c00574
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• Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.
  • Blears D, Lou J, Fong N, Mitter R, Sheridan RM, He D, Dirac-Svejstrup AB, Bentley D, Svejstrup JQ
  • Molecular Cell
  • doi: 10.1016/j.molcel.2024.10.012
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• Regulation of inflammation by Interleukin-10 in the intestinal and respiratory mucosa.
  • Branchett WJ, Saraiva M, O'Garra A
  • Current Opinion in Immunology
  • doi: 10.1016/j.coi.2024.102495
  • PDF

• Regulation of ROS signaling by TIGAR induces cancer-modulating responses in the tumor microenvironment.
  • Cheung EC, Strathdee D, Stevenson D, Coomes J, Blyth K, Vousden KH
  • Proceedings of the National Academy of Sciences of the United States of America
  • doi: 10.1073/pnas.2416076121
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• Sharp habitat shifts, evolutionary tipping points and rescue: Quantifying the perilous path of a specialist species toward a refugium in a changing environment.
  • Dekens L
  • Theoretical Population Biology
  • doi: 10.1016/j.tpb.2024.09.001
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• Generation of TWO iPSC lines (CRICKi009-A; CRICKi010-A) from patients with type 1 von Hippel-Lindau (VHL) and histopathologically confirmed renal cell carcinoma (RCC).
  • Devito LG, Lim ES, O'Toole SM, Shepherd STC, Deng D, Feng H, Barber T, Drake WM, Turajlic S, Healy L
  • Stem Cell Research
  • doi: 10.1016/j.scr.2024.103611
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• User-centred design and development of a smartphone application (OverSight) for digital phenotyping in ophthalmology
  • Devraj K, Jones L, Higgins B, Thomas PBM, Moosajee M
  • Healthcare
  • doi: 10.3390/healthcare12242550
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• Spatiotemporal dynamics of the oropharyngeal microbiome in a cohort of Ivorian school children.
  • Diallo K, Missa KF, Tuo KJ, Tiemele LS, Ouattara AF, Gboko KDT, Gragnon BG, Bla KB, Ngoi JM, Wilkinson RJ, Awandare GA, Bonfoh B
  • Scientific Reports
  • doi: 10.1038/s41598-024-81829-6
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• Hybrid dark-field and attenuation contrast retrieval for laboratory-based X-ray tomography.
  • Doherty A, Buchanan I, Roche I Morgó O, Astolfo A, Savvidis S, Gerli MFM, Citro A, Olivo A, Endrizzi M
  • Optica
  • doi: 10.1364/OPTICA.525760
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• High throughput application of the NanoBiT Biochemical Assay for the discovery of selective inhibitors of the interaction of PI3K-p110α with KRAS.
  • Ismail M, Davies G, Sproat G, Monteverde T, Tart J, Acebrón-García-de-Eulate M, Gohlke A, Hancock D, Adhikari S, Stefanovic-Barrett S, Smith DM, Flemington V, Gleave-Hanford ES, Holdgate GA, Kettle JG, Downward J
  • SLAS Discovery
  • doi: 10.1016/j.slasd.2024.100197
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• TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations.
  • Laddach A, Pachnis V, Shapiro M
  • NAR Genomics and Bioinformatics
  • doi: 10.1093/nargab/lqae139
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• IFN-γ-dependent regulation of intestinal epithelial homeostasis by NKT cells.
  • Lebrusant-Fernandez M, ap Rees T, Jimeno R, Angelis N, Ng JC, Fraternali F, Li VSW, Barral P
  • Cell reports
  • doi: 10.1016/j.celrep.2024.114948
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• Imperfect wound healing sets the stage for chronic diseases.
  • Martin P, Pardo-Pastor C, Jenkins RG, Rosenblatt J
  • Science
  • doi: 10.1126/science.adp2974

• Discovering covalent cyclic peptide inhibitors of peptidyl arginine deiminase 4 (PADI4) using mRNA-display with a genetically encoded electrophilic warhead.
  • Mathiesen IR, Calder EDD, Kunzelmann S, Walport LJ
  • Communications Chemistry
  • doi: 10.1038/s42004-024-01388-9
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• Oxidative stress, inflammation and altered glucose metabolism contribute to the retinal phenotype in the choroideremia zebrafish
  • Méjécase C, Nair N, Sarkar H, Soro-Barrio P, Toms M, Halliday S, Linkens K, Jaroszynska N, Maurer C, Owen N, Moosajee M
  • Antioxidants
  • doi: 10.3390/antiox13121587
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• Epi-microRNA mediated metabolic reprogramming counteracts hypoxia to preserve affinity maturation.
  • Nakagawa R, Llorian M, Varsani-Brown S, Chakravarty P, Camarillo JM, Barry D, George R, Blackledge NP, Duddy G, Kelleher NL, Klose RJ, Turner M, Calado DP
  • Nature Communications
  • doi: 10.1038/s41467-024-54937-0
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• Cancer-induced systemic pre-conditioning of distant organs: building a niche for metastatic cells.
  • Rabas N, Ferreira RMM, Di Blasio S, Malanchi I
  • Nature Reviews Cancer
  • doi: 10.1038/s41568-024-00752-0

• Quantitative perturbation-phenotype maps reveal nonlinear responses underlying robustness of PAR-dependent asymmetric cell division.
  • Rodrigues NTL, Bland T, Ng K, Hirani N, Goehring NW
  • PLoS Biology
  • doi: 10.1371/journal.pbio.3002437
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• Assessing contrast sensitivity function in CRB1-retinopathies: Exploring child-friendly measures of visual function.
  • Rodriguez-Martinez AC, Tailor-Hamblin VK, Crossland MD, Higgins BE, Blindow E, Dekker TM, Greenwood JA, Henderson RH, Jones PR, Moosajee M
  • Translational Vision Science & Technology
  • doi: 10.1167/tvst.13.12.33

• Using embryo models to understand the development and progression of embryonic lineages: a focus on primordial germ cell development
  • Rodriguez-Polo I, Moris N
  • Cells Tissues Organs
  • doi: 10.1159/000538275
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• Cell-autonomous timing drives the vertebrate segmentation clock’s wave pattern
  • Rohde LA, Bercowsky-Rama A, Valentin G, Naganathan SR, Desai RA, Strnad P, Soroldoni D, Oates AC
  • eLife
  • doi: 10.7554/elife.93764.3
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• A combined NMR and deep neural network approach for enhancing the spectral resolution of aromatic side chains in proteins.
  • Shukla VK, Karunanithy G, Vallurupalli P, Hansen DF
  • Science Advances
  • doi: 10.1126/sciadv.adr2155
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• Paracrine rescue of MYR1-deficient Toxoplasma gondii mutants reveals limitations of pooled in vivo CRISPR screens.
  • Torelli F, da Fonseca DM, Butterworth SW, Young JC, Treeck M
  • eLife
  • doi: 10.7554/eLife.102592
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• STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair.
  • van den Heuvel D, Rodríguez-Martínez M, van der Meer PJ, Nieto Moreno N, Park J, Kim H-S, van Schie JJM, Wondergem AP, D'Souza A, Yakoub G, Herlihy AE, Kashyap K, Boissière T, Walker J, Mitter R, Apelt K, de Lint K, Kirdök I, Ljungman M, Wolthuis RMF, Cra
  • Cell
  • doi: 10.1016/j.cell.2024.10.018

• Space synthetic biology: A paradigm for sustainability on earth and beyond
  • Vora TJ, Averesch NJH, DeBenedictis EA, Rothschild LJ
  • New Space
  • doi: 10.1089/space.2024.0002
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• Resolving chaperone-assisted protein folding on the ribosome at the peptide level.
  • Wales TE, Pajak A, Roeselová A, Shivakumaraswamy S, Howell S, Kjær S, Hartl FU, Engen JR, Balchin D
  • Nature Structural & Molecular Biology
  • doi: 10.1038/s41594-024-01355-x
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• MCM double hexamer loading visualized with human proteins.
  • Weissmann F, Greiwe JF, Pühringer T, Eastwood EL, Couves EC, Miller TCR, Diffley JFX, Costa A
  • Nature
  • doi: 10.1038/s41586-024-08263-6
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• Structural insight into the function of human peptidyl arginine deiminase 6
  • Williams JPC, Mouilleron S, Trapero RH, Bertran MT, Marsh JA, Walport LJ
  • Computational and Structural Biotechnology Journal
  • doi: 10.1016/j.csbj.2024.08.019
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• Short-range Fgf signalling patterns hindbrain progenitors to induce the neurogenesis-to-oligodendrogenesis switch.
  • Yeung TJ, Wilkinson DG
  • Development
  • doi: 10.1242/dev.204256
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Preprints December 2024

• Gene network architecture, mutation and selection collectively drive developmental pattern evolvability and predictability
  • Booth H, Hadjivasiliou Z
  • doi: 10.1101/2024.12.23.630099

• Type I interferons induced upon respiratory viral infection impair lung metastatic initiation
  • Farias A, Bridgeman V, Rodrigues FS, Owen A, Ruhland S, Ferreira R, Mack M, Malanchi I, Johansson C
  • doi: 10.1101/2024.12.23.630113

• HIV PrEP programmes as a framework for diagnosing and treating HBV infection in adolescents and young adults in KwaZulu-Natal, South Africa
  • Sukali G, Busang J, Dreyer J, Khoza T, Delphin M, Okesola N, Herbst C, Waddilove E, Upton J, Seeley J, Iwuji C, Anderson M, Matthews PC, Shahmanesh M
  • doi: 10.1101/2024.11.29.24318178

• Hepatitis B Virus (HBV) treatment eligibility in the UK: retrospective longitudinal cohort data to explore the impact of changes in clinical guidelines
  • Campbell C, Wang T, Stockdale AJ, Todd S, Jaworski J, Glampson B, Papadimitriou D, Mayer E, Salih H, Roadknight G, Little S, Noble T, Várnai KA, Davis C, Heinson AI, George M, Borca F, Roberts T, Ribeyre BB, English L, Zhu L, NIHR HIC Viral Hepatitis and Liver Disease Consortium, Woods K, Davies J, Cooke GS, Nastouli E, Khakoo SI, Gelson W, Elsharkawy A, Barnes E, Matthews PC
  • doi: 10.1101/2024.12.02.24318329

• Dominant RDH12-retinitis pigmentosa impairs photoreceptor development and cone function in retinal organoids
  • Méjécase C, Zhou Y, Owen N, Soro-Barrio P, Cheloni R, Nair N, Sarkar H, Toualbi L, Moosajee M
  • doi: 10.1101/2024.12.11.627489

• Modelling co-development between the somites and neural tube in human Trunk-like Structures (hTLS)
  • Makwana K, Tilley L, Chakravarty P, Thompson J, Baillie-Benson P, Rodriguez-Polo I, Moris N
  • doi: 10.1101/2024.12.16.628661

• HIFα isoform specific activities drive cell-type specificity of VHL-associated oncogenesis
  • Lima JDCC, Hooker M, Li R, Barros AB, Masson N, Pugh CW, Mole DR, Adam J, Ratcliffe PJ, Kurlekar S
  • doi: 10.1101/2024.11.28.625663

• The essential host genome for Cryptosporidium intracellular survival exposes metabolic dependencies that can be leveraged for treatment
  • Marzook NB, Song O-R, Baumgärtel L, Bernitz N, Mkandawire TT, Watson LC, Nunes V, Warchal S, MacRae JI, Howell M, Sateriale A
  • doi: 10.1101/2024.12.04.626561

• Structural and functional characterization of the KHNYN extended-diKH domain for mediating ZAP antiviral activity
  • Youle RL, Lista MJ, Bouton C, Kunzelmann S, Wilson H, Cottee MA, Purkiss AG, Morris ER, Neil SJD, Taylor IA, Swanson CM
  • doi: 10.1101/2024.12.23.630104

• Mechanistic studies of autophagic cargo recruitment and membrane expansion through in vitro reconstitution
  • Zhang W, Litschel T, D'Antuono R, Davis C, Schreiber A, Tooze SA
  • doi: 10.1101/2024.12.24.630225

• Are the latent representations of foundation models for pathology invariant to rotation?
  • Elphick M, Turajlic S, Yang G
  • Available at: http://arxiv.org/abs/2412.11938v1

• Cardiometabolic biomarkers and systemic inflammation in US adolescents and young adults with latent tuberculosis infection: a population-based cohort study
  • Magodoro IM, Ntusi NAB, Jao J, Heather JZ, Claggett BL, Siedner MJ, Wilkinson KA, Wilkinson RJ
  • doi: 10.1101/2024.12.25.24319620