About
Affiliations:
Lecturer, Microbiology, Immunology, and Molecular Genetics
Research Interests:
Daniel is currently studying the molecular mechanisms between signal transduction and motility of the African trypanosome, Trypanosoma brucei. This organism is the causative agent of sleeping sickness, a vector-borne disease on which the sleep-wake cycle is disrupted. He is also studying the role of cAMP signaling during the intracellular infection cycle of the American trypanosome, Trypanosoma cruzi. This organism is the causative agent of Chagas disease, a vector-borne disease characterized for hypertrophy of the heart, esophagus, and colon. In addition, he mentors students in course-based undergraduate research, focused on virology. Working in teams, students isolate soil bacteriophages, annotate and publish their sequenced genome, and elaborate a comparative genomics project.
Bio:
Daniel’s over fifteen-year experience as a molecular parasitologist started at the end of his first year at university, doing mutagenesis and cloning of a Trypanosoma cruzi gene. Later, during his senior year, he studied Leishmania major RNA polymerase III. L. major is a trypanosome species, causative agent of cutaneous leishmaniasis, a vector-borne disease characterized by ulcerative skin lesions. He used tandem affinity purification to isolate RNA polymerase III, to identify putative transcription factors. During this time, he received three research scholarships to perform as an undergraduate researcher. Furthermore, he received a medal from the university, for being the top student of his class (2008) majoring in Biology.
In graduate school, as well as during his postdoctoral and ongoing research, he has studied Trypanosoma brucei. For his PhD dissertation, he performed the molecular characterization of one of the subunits of the RNA polymerase III transcription factor B, BRF1. His work provided evidence that the transcription of the three nuclear RNA polymerases is co-regulated. He received a five-year fellowship for his PhD research and a dissertation scholarship. Moreover, his research project helped to conceptually frame the analysis of the 5S rRNA gene and transcripts in L. major, and it was the foundation for the molecular characterization of Maf1, a negative regulator of transcription. His PhD thesis was recognized as the third best PhD parasitology thesis nationwide in 2018. After his PhD thesis defense, while he was teaching sciences at a high school, one of the members of his PhD thesis committee, invited him to collaborate on a research project about a flagellar phosphatase in L. major. This was Daniel’s first exploration of flagellum biology in trypanosomes, setting the foundation of his postdoctoral research.
Once again working with T. brucei, but now on his postdoctoral research, Daniel implemented APEX2-mediated proximity labeling in T. brucei to define flagellum subdomains. This approach allowed him to obtain one of the most detailed eukaryotic flagellum proteomes to date, and at sub-organelle resolution. His results provided further evidence that the flagellum is a signaling platform. To study downstream effectors of cAMP signaling, he has combined proximity proteomics and titanium dioxide-mediated phosphoenrichment to obtain a cAMP-dependent flagellar phosphoproteome. This is an example of the emerging field of spatial-phosphoproteomics. During his postdoctoral research he obtained four different scholarships and fellowships. In 2021 and 2022, he was a nominee to receive a UCLA Chancellor’s Award for Postdoctoral Research.
In 2023, Daniel started teaching at the department. He has taught two seminars to undergraduates doing apprentice-based research, and three laboratories to undergraduates doing course-based research. Two of the laboratories are part of the Howard Hughes Medical Institute (HHMI) Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program.
Scientific Production:
Research papers
Andrés Cano-Santiago, Luis E. Florencio-Martínez, Daniel E. Vélez-Ramírez, Adrián J. Romero-Chaveste, Rebeca G. Manning-Cela, Tomás Nepomuceno-Mejía, Santiago Martínez-Calvillo. Analyses of the essential C82 subunit uncover some differences in RNA polymerase III transcription between Trypanosoma brucei and Leishmania major. Parasitology. 1-16.
Vélez-Ramírez, DE, Shimogawa, M., Ray, SS., Lopez, A., Rayatpisheh, S., Langousis, G., Gallagher-Jones, M., Dean, A., Wohlschlegel, J., and Hill, K.L. 2021. APEX2 proximity proteomics resolves flagellum subdomains and identifies flagellum tip-specific proteins in Trypanosoma brucei. mSphere. 6(1).
Escalona-Montaño AR, Pérez-Montfort R, Cabrera-González N, Mondragón-Flores R, Vélez-Ramírez DE, Gutiérrez-Kobeh L, Becker I, Aguirre-Garcia M. 2017. Protein phosphatase PP2C in flagellum of L. major: cloning and characterization. Parasitology Open. 3(e15):1-9.
Romero-Meza G, Vélez-Ramírez DE, Florencio-Martínez LE, Román-Carraro FC, Manning-Cela R, Hernández-Rivas R, Martínez-Calvillo S. 2016. Maf1 is a negative regulator of transcription in Trypanosoma brucei. Molecular Microbiology. 103(3):452-468.
Moreno-Campos R, Florencio-Martínez LE, Nepomuceno-Mejía T, Rojas-Sánchez S, Vélez-Ramírez DE, Padilla-Mejía NE, Figueroa-Angulo E, Manning-Cela R, Martínez-Calvillo S. 2016. Molecular characterization of 5S ribosomal RNA genes and transcripts in the protozoan parasite Leishmania major. Parasitology Press. 143(14):1917-1929.
Vélez-Ramírez DE, Florencio-Martínez LE, Romero-Meza G, Rojas-Sánchez S, Moreno-Campos R, Arroyo R, Ortega-López J, Manning-Cela R, Martínez-Calvillo S. 2015. BRF1, a subunit of RNA polymerase III transcription factor TFIIIB, is essential for cell growth of Trypanosoma brucei. Parasitology. 142(13):1563-73.
Book Chapters
Santiago Martínez-Calvillo, Rodrigo Moreno-Campos, Gabriela Romero-Meza, Saúl Rojas-Sánchez, Daniel E. Vélez-Ramírez, Rebeca G. Manning-Cela, Luis E. Florencio-Martínez. Leishmaniasis. Chapter of the book: Most common parasitosis in the Mexican population. Edited by Jorge Morales Montor, Abraham Landa, Luis Ignacio Terrazas & Romel Hernández Bello. Editorial Universitaria UANL. 2016.
Elisa E. Figueroa-Angulo, Daniel E. Vélez-Ramírez, Gabriela Romero-Meza, Santiago Martínez-Calvillo. Trypanosoma brucei: Atypical mechanisms of genetic expression and antigenic variation. Chapter of the book: Genomic of Parasites: Molecular, Genomic, Proteomic and Virulence Aspects. Edited by: María E. Alvarez-Sánchez & Elisa Azuara. Editorial Académica Española. 2012.
Bacteriophage genomes
Nucleotide [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – . Accession No. PQ844483.1, Arthrobacter phage QuinnAvery; [published 2025 March 10]. Available from: [https://www.ncbi.nlm.nih.gov/nuccore/PQ844483.1]
Nucleotide [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – . Accession No. PV089520.1, Arthrobacter phage IttyBittyPiggy; [published 2025 February 25]. Available from: [https://www.ncbi.nlm.nih.gov/nuccore/PV089520.1]