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!

Do you like what I do? Consider supporting me on Patreon! You can become a fan of fungus, an algae enthusiast, or a bacterial benefactor with just a few clicks. 

Alex the Academic
A.P.M. Cloherty


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

Research Assistant

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

Research Assistant

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


  • 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

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