Who's writing, anyways?
it's me, Alex
This is me as an E. coli being infected by a T4-bacteriophage (a type of virus that only infects bacteria). That should be about all you need to know about me.
If you do want to know more, I am a PhD student at the Amsterdam University Medical Center, with a research background in immunology and microbiology. When I was a Master student, I sat down one Monday night after a day in the lab and thought, "Wouldn't it be awesome if more Mondays were microbial?" To answer my own question, yes, it is awesome.
Thus, Microbial Mondays were born. On the first Monday of every month, you can read all about a new microbial topic, written in plain and understandable English by this here enthusiastic PhD student.
So where do I get all this information from? It's a mixture of information from the papers cited in the posts, fun facts I've picked over the years of studying, lecture notes (especially from Dr. Kluftinger and Dr. Plunkett's excellent courses at the University of British Columbia in Canada), and of course some Wikipedia here and there. If you have a question about a source, or if some information is unclear, let me know and I'll be happy to clarify!
Back the Bugs!
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Alex the Academic
01/2020 – Present
Supervision of M.Sc. Internship. Amsterdam University Medical Centers, Amsterdam, The Netherlands.
Interactive Zoom Q&A "Connecting with a Microbiologist" for students Grade 7-9
09/2018 – 01/2019
Supervision of M.Sc. Literature Thesis. Amsterdam University Medical Centers, Amsterdam, The Netherlands.
06/2016 – 05/2017
Delegate Trainer. Leiden Model United Nations Foundation, The Netherlands.
Planned and facilitated mock United Nations meetings and workshops to teach delegates relevant skills, such public speaking, lobbying, and researching.
05/2016 – 07/2016
Undergraduate Teaching Assistant, Biology 116. University of British Columbia (UBC), Canada.
Science Fair Judge, Aberdeen Hall Preparatory School, Canada.
09/2013 – 04/2016
Supplemental Learning Leader. Learning Resources & Support, University of British Columbia (UBC), Canada.
Developed and executed strategies to engage students with course material in weekly interactive sessions for chemistry, psychology, and microbiology.
09/2018 – Present
PhD Candidate, Ribeiro group, Department of Experimental Immunology
Amsterdam University Medical Centers, Amsterdam, The Netherlands
Daily supervisor: Dr. Carla Ribeiro
Topic: Molecular mechanisms of autophagy in the context of viral infections
Key skills: Human cell culture and ex vivo tissue model; work in BSL-2 and BSL-3 lab (virus infections); RNA interference; autophagosome isolation; extracellular vesicle isolation, flow cytometry, ELISA, bacterial cell culture, molecular cloning, PCR
06/2018 – 08/2018
Internship, Jean group, Department of Microbiology & Immunology
University of British Columbia, Vancouver, Canada
Daily supervisor: Dr. François Jean
Topic: Flaviviral hijacking of lipid droplets (literature review)
01/2018 – 06/2018
Internship, Geijtenbeek group, Department of Experimental Immunology
Academic Medical Center Amsterdam, The Netherlands
Daily supervisor: Dr. Carla Ribeiro
Topic: Role of autophagy in virus-induced inflammation
Key skills: Human cell culture and ex vivo explant models; work in BSL-3 lab; RNA interference; autophagosome isolation; flow cytometry
10/2017 – 12/2017
Internship, van Wijk group, Laboratory of Translational Immunology University Medical Center Utrecht, Netherlands
Daily supervisors: Dr. Aridaman Pandit & Abhinandan Devaprasad
Topic: Network analysis of immune cells in juvenile idiopathic arthritis
Key skills: computational methods (R-based) for network analysis of large datasets derived from RNASeq and Luminex assays
10/2016 – 09/2017
Internship, van Strijp group, Department of Medical Microbiology,
University Medical Center Utrecht, Netherlands
Daily supervisor: Dr. Ilse Jongerius
Topic: Bordetella pertussis immune evasion molecules
Key skills: bacterial cell culture, cloning and protein expression in E. coli, protein purification, Western blot, ELISA, circular dichroism spectroscopy
Result: co-authorship of a manuscript and presentation at a congress
03/2016 – 07/2016
School of Nursing, University of British Columbia (UBC), Canada
Focus: Development of outreach programmes to improve Type II diabetes outcomes in Indigenous people.
Result: co-authorship of a manuscript, currently in submission
05/2013 – 12/2014
Institute for Healthy Living & Chronic Disease Prevention, UBC, Canada
Focus: Developing a tobacco reduction and cessation programme for new fathers.
Result: co-authorship of a manuscript and of a programme facilitator manual
AWARDS & SCHOLARSHIPS
Winner of FameLab Netherlands (Dutch Amateur Science Communicator of the Year) (2021)
Dojindo Best Short Talk Prize, Nordic Autophagy Society Conference (2019)
Best Poster Prize, AI&II PhD student retreat (2018)
Academic Medical Center (Amsterdam) PhD Scholarship (2018)
Talma Eykman Prize for Best Master Thesis, Biomedical Sciences, Utrecht University (2018)
Best Presentation in Public Health, International Student Congress of (bio)Medical Sciences (2018)
Utrecht Excellence Scholarship (2016)
Best Presentation, University of British Columbia (UBC) Student Leadership Conference (2016)
UBC Tu’um Est Student Initiative Fund (UBC) (2015)
Best Delegate Award, European Model United Nations Conference (2015)
Best Delegate Award, Model United Nations of the Hague Conference (2015)
UBC Provost Teaching Assistant and Tutor Excellence Award (2015)
Canadian Cancer Society Youth Achievement Bursary (2015)
UBC Deputy Vice-Chancellor Scholarship (2015)
University of British Columbia (UBC) Hugh M. Brock Education Abroad Scholarship (2014)
UBC Tu’um Est Student Initiative Fund (UBC) (2014)
UBC Deputy Vice-Chancellor Scholarship (2014)
UBC Deputy Vice-Chancellor Scholarship (2013)
UBC Deputy Vice-Chancellor Scholarship (2012)
UBC National Entrance Scholarship (2011)
Cloherty APM, Rader AG, Compeer B, Ribeiro CMS (2021). Human TRIM5α: Autophagy Connects Cell-Intrinsic HIV-1 Restriction and Innate Immune Sensor Functioning. Viruses, 13(2), 320. https://doi.org/10.3390/v13020320
Cloherty APM, van Teijlingen NH, Eisden TJTHD et al. (2021). Autophagy-enhancing drugs limit mucosal HIV-1 acquisition and suppress viral replication ex vivo. Sci Rep 11, 4767. https://doi.org/10.1038/s41598-021-84081-4
Cloherty APM, Olmstead AD, Ribeiro CMS, Jean F (2020). Hijacking of Lipid Droplets by Hepatitis C, Dengue and Zika Viruses—From Viral Protein Moonlighting to Extracellular Release. International Journal of Molecular Sciences, 21(21), 7901. https://doi.org/10.3390/ijms21217901
Hovingh ES, de Maat S, Cloherty A, Johnson S, Pinelli E, Maas C, & Jongerius I (2018). Virulence Associated Gene 8 of Bordetella pertussis Enhances Contact System Activity by Inhibiting the Regulatory Function of Complement Regulator C1 Inhibitor. Frontiers in immunology, 9, 1172. https://doi.org/10.3389/fimmu.2018.01172
Bottorff JL, Oliffe JL, Sarbit G, Kelly MT, & Cloherty A (2015). Men's Responses to Online Smoking Cessation Resources for New Fathers: The Influence of Masculinities. JMIR research protocols, 4(2), e54. https://doi.org/10.2196/resprot.4079