Magez, S. et al. The position of B-cells and IgM antibodies in parasitemia, anemia, and VSG switching in Trypanosoma brucei-infected mice. PLoS Pathog. 4, e1000122 (2008).
Cross, G. A. M., Kim, H. S. & Wickstead, B. Capturing the variant floor glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427. Mol. Biochem. Parasitol. 195, 59–73 (2014).
Müller, L. S. M. et al. Genome group and DNA accessibility management antigenic variation in trypanosomes. Nature 563, 121–125 (2018).
Hertz-Fowler, C. et al. Telomeric expression websites are extremely conserved in Trypanosoma brucei. PLoS ONE 3, e3527 (2008).
Cosentino, R. O., Brink, B. G. & Nicolai Siegel, T. Allele-specific meeting of a eukaryotic genome corrects obvious frameshifts and divulges an absence of nonsense-mediated mRNA decay. NAR Genom. Bioinform. 3, lqab082 (2021).
Corridor, J. P. J., Wang, H. & David Barry, J. Mosaic VSGs and the dimensions of Trypanosoma brucei antigenic variation. PLoS Pathog. 9, e1003502 (2013).
Mugnier, M. R., Cross, G. A. M. & Papavasiliou, F. N. The in vivo dynamics of antigenic variation in Trypanosoma brucei. Science 347, 1470–1473 (2015).
Jayaraman, S. et al. Utility of lengthy learn sequencing to find out expressed antigen range in Trypanosoma brucei infections. PLoS Negl. Trop. Dis. 13, e0007262 (2019).
Capewell, P. et al. The pores and skin is a big however neglected anatomical reservoir for vector-borne African trypanosomes. eLife 5, e17716 (2016).
Camara, M. et al. Extravascular dermal trypanosomes in suspected and confirmed circumstances of gambiense human African trypanosomiasis. Clin. Infect. Dis. 73, 12–20 (2021).
Trindade, S. et al. Trypanosoma brucei parasites occupy and functionally adapt to the adipose tissue in mice. Cell Host Microbe https://doi.org/10.1016/j.chom.2016.05.002 (2016).
Carvalho, T. et al. Trypanosoma brucei triggers a marked immune response in male reproductive organs. PLoS Negl. Trop. Dis. https://doi.org/10.1371/journal.pntd.0006690 (2018).
De Niz, M. et al. Organotypic endothelial adhesion molecules are key for Trypanosoma brucei tropism and virulence. Cell Rep 36, 109741 (2021).
Management and Surveillance of Human African Trypanosomiasis: Report of a WHO Knowledgeable Committee. WHO Technical Report Sequence (WHO, 2013).
Crilly, N. P. & Mugnier, M. R. Pondering exterior the blood: views on tissue-resident Trypanosoma brucei. PLoS Pathog. 17, e1009866 (2021).
Kamper, S. M. & Barbet, A. F. Floor epitope variation by way of mosaic gene formation is potential key to long-term survival of Trypanosoma brucei. Mol. Biochem. Parasitol. 53, 33–44 (1992).
Seed, J. R. & Effron, H. G. Simultaneous presence of various antigenic populations of Trypanosoma brucei gambiense in Microtus montanus. Parasitology 66, 269–278 (1973).
Seed, J. R., Edwards, R. & Sechelski, J. The ecology of antigenic variation. J. Protozool. 31, 48–53 (1984).
Barry, J. D. & Emery, D. L. Parasite improvement and host responses through the institution of Trypanosoma brucei an infection transmitted by tsetse fly. Parasitology 88, 67–84 (1984).
Tanner, M., Jenni, L., Hecker, H. & Brun, R. Characterization of Trypanosoma brucei remoted from lymph nodes of rats. Parasitology 80, 383–391 (1980).
Vickerman, Okay. Trypanosome sociology and antigenic variation. Parasitology 99, S37–S47 (1989).
Barry, J. D. & Turner, C. M. R. The dynamics of antigenic variation and development of African trypanosomes. Parasitol. Immediately 7, 207–211 (1991).
Engstler, M. & Boshart, M. Chilly shock and regulation of floor protein trafficking convey sensitization to inducers of stage differentiation in Trypanosoma brucei. Genes Dev. 18, 2798–2811 (2004).
Turner, C. M., Hunter, C. A., Barry, J. D. & Vickerman, Okay. Similarity in variable antigen sort composition of Trypanosoma brucei Rhodesiense populations in numerous websites throughout the mouse host. Trans. R. Soc. Trop. Med. Hyg. 80, 824–830 (1986).
Turner, C. M. R. & Barry, J. D. Excessive frequency of antigenic variation in Trypanosoma brucei rhodesiense infections. Parasitology 99, 67–75 (1989).
Salanti, A. et al. Proof for the involvement of VAR2CSA in pregnancy-associated malaria. J. Exp. Med. 200, 1197–1203 (2004).
Duffy, P. E. & Fried, M. Plasmodium falciparum adhesion within the placenta. Curr. Opin. Microbiol. 6, 371–376 (2003).
Jonsson, A. ‐B., Ilver, D., Falk, P., Pepose, J. & Normark, S. Sequence adjustments within the pilus subunit result in tropism variation of Neisseria gonorrhoeae to human tissue. Mol. Microbiol. 13, 403–416 (1994).
Nassif, X. et al. Antigenic variation of pilin regulates adhesion of Neisseria meningitidis to human epithelial cells. Mol. Microbiol. 8, 719–725 (1993).
Rudel, T., van Putten, J. P. M., Gibbs, C. P., Haas, R. & Meyer, T. F. Interplay of two variable proteins (PilE and PilC) required for pilus-mediated adherence of Neisseria gonorrhoeae to human epithelial cells. Mol. Microbiol. 6, 3439–3450 (1992).
Virji, M. & Heckels, J. E. The position of widespread and type-specific pilus antigenic domains in adhesion and virulence of gonococci for human epithelial cells. J. Gen. Microbiol. 130, 1089–1095 (1984).
Dean, S., Marchetti, R., Kirk, Okay. & Matthews, Okay. R. A floor transporter household conveys the trypanosome differentiation sign. Nature 459, 213–217 (2009).
McWilliam, Okay. R. et al. Excessive-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes. Preprint at bioRxiv https://doi.org/10.1101/2024.03.22.586247 (2024).
Smith, J. E. et al. DNA injury drives antigen diversification by means of mosaic VSG formation in Trypanosoma brucei. Preprint at bioRxiv https://doi.org/10.1101/2024.03.22.582209 (2024).
Calvo-Alvarez, E., Cren-Travaillé, C., Crouzols, A. & Rotureau, B. A brand new chimeric triple reporter fusion protein as a software for in vitro and in vivo multimodal imaging to watch the event of African trypanosomes and Leishmania parasites. Infect. Genet. Evol. 63, 391–403 (2018).
Hutchinson, S. et al. The institution of variant floor glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei within the tsetse fly salivary glands. PLoS Pathog. 17, e1009904 (2021).
Savage, A. F. et al. Transcript expression evaluation of putative Trypanosoma brucei GPI-anchored floor proteins throughout improvement within the tsetse and mammalian hosts. PLoS Negl. Trop. Dis. 6, 1708 (2012).
Schopf, L. R., Filutowicz, H., Bi, X. J. & Mansfield, J. M. Interleukin-4-dependent immunoglobulin G1 isotype swap within the presence of a polarized antigen-specific Th1-cell response to the trypanosome variant floor glycoprotein. Infect. Immun. 66, 451 (1998).
Liu, G. et al. Distinct contributions of CD4+ and CD8+ T cells to pathogenesis of trypanosoma brucei an infection within the context of gamma interferon and interleukin-10. Infect. Immun. 83, 2785–2795 (2015).
Reinitz, D. M. & Mansfield, J. M. T-cell-independent and T-cell-dependent B-cell responses to uncovered variant floor glycoprotein epitopes in trypanosome-infected mice. Infect. Immun. 58, 2337–2342 (1990).
Radwanska, M. et al. Comparative evaluation of antibody responses in opposition to HSP60, invariant floor glycoprotein 70, and variant floor glycoprotein reveals a posh antigen-specific sample of immunoglobulin isotype switching throughout an infection by Trypanosoma brucei. Infect. Immun. 68, 848–860 (2000).
Robbiani, D. F. et al. AID is required for the chromosomal breaks in c-myc that result in c-myc/IgH translocations. Cell 135, 1028–1038 (2008).
Hector, R. F., Collins, M. S. & Pennington, J. E. Therapy of experimental Pseudomonas aeruginosa pneumonia with a human IgM monoclonal antibody. J. Infect. Dis. 160, 483–489 (1989).
Barth, W. F., Wochner, R. D., Waldmann, T. A. & Fahey, J. L. Metabolism of human gamma macroglobulins. J. Clin. Make investments. 43, 1036 (1964).
Mehlitz, D. & Molyneux, D. H. The elimination of Trypanosoma brucei gambiense? Challenges of reservoir hosts and transmission cycles: anticipate the sudden. Parasite Epidemiol. Management 6, e00113 (2019).
Larcombe, S. D., Briggs, E. M., Savill, N., Szoor, B. & Matthews, Okay. The developmental hierarchy and shortage of replicative slender trypanosomes in blood challenges their position in an infection upkeep. Proc. Natl Acad. Sci. USA 120, e2306848120 (2023).
Morrison, L. J., Majiwa, P., Learn, A. F. & Barry, J. D. Probabilistic order in antigenic variation of Trypanosoma brucei. Int. J. Parasitol. 35, 961–972 (2005).
Pinger, J., Chowdhury, S. & Papavasiliou, F. N. Variant floor glycoprotein density defines an immune evasion threshold for African trypanosomes present process antigenic variation. Nat. Commun. 8, 828 (2017).
Trindade, S. et al. Gradual rising conduct in African trypanosomes throughout adipose tissue colonization. Nat. Commun. 13, 7548 (2022).
Shimogawa, M. M. et al. Parasite motility is essential for virulence of African trypanosomes. Sci. Rep. 8, 9122 (2018).
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq utilizing the Trinity platform for reference era and evaluation. Nat. Protoc. 8, 1494–1512 (2013).
Grabherr, M. G. et al. Full-length transcriptome meeting from RNA-seq information and not using a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of brief DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Cock, P. J. A. et al. Biopython: freely out there Python instruments for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).
Camacho, C. et al. BLAST+: structure and functions. BMC Bioinf. 10, 421 (2009).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Primary native alignment search software. J. Mol. Biol. 215, 403–410 (1990).
Quinlan, A. R. & Corridor, I. M. BEDTools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing information. Bioinformatics 28, 3150–3152 (2012).
Li, W. & Godzik, A. CD-hit: a quick program for clustering and evaluating massive units of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Krueger, F. et al. FelixKrueger/TrimGalore: v.0.6.4 – add default decompression path. Zenodo https://doi.org/10.5281/zenodo.5127898 (2023).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
So, J. et al. VSGs expressed throughout pure T. b. gambiense an infection exhibit in depth sequence divergence and a subspecies-specific bias in direction of sort B N-terminal domains. mBio 13, e02553-22 (2022).
Gruszynski, A. E., DeMaster, A., Hooper, N. M. & Bangs, J. D. Floor coat reworking throughout differentiation of Trypanosoma brucei. J. Biol. Chem. 278, 24665–24672 (2003).
Lee, J.-Y. & Kitaoka, M. A newbie’s information to rigor and reproducibility in fluorescence imaging experiments. Mol. Biol. Cell https://doi.org/10.1091/mbc.E17-05-0276 (2018).
Wirtz, E., Leal, S., Ochatt, C. & Cross, G. A. M. A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol. 99, 89–101 (1999).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Dobin, A. et al. STAR: ultrafast common RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Shanmugasundram, A. et al. TriTrypDB: an built-in purposeful genomics useful resource for kinetoplastida. PLoS Negl. Trop. Dis. 17, e0011058 (2023).
Ramírez, F. et al. deepTools2: a subsequent era internet server for deep-sequencing information evaluation. Nucleic Acids Res. 44, W160–W165 (2016).
Track, Y. & Wang, J. ggcoverage: an R package deal to visualise and annotate genome protection for varied NGS information. BMC Bioinf. 24, 309 (2023).
Moloo, S. Okay. A man-made feeding method for Glossina. Parasitology 63, 507–512 (1971).
MacLeod, E. T., Maudlin, I., Darby, A. C. & Welburn, S. C. Antioxidants promote institution of trypanosome infections in tsetse. Parasitology 134, 827–831 (2007).
Beaver, A. mugnierlab/Beaver2022: Launch for publication. Zenodo https://doi.org/10.5281/zenodo.13684001 (2024).
Barnett, S. A. The pores and skin and hair of mice residing at a low environmental temperature. Q. J. Exp. Physiol. Cogn. Med. Sci. 44, 35–42 (1959).
