2021 SCEP Symposium Archive

Keynote Speaker

Jane Carlton, Ph.D.

Jane Carlton
Julius Silver, Roslyn S. Silver, and Enid Silver Winslow Professor at NYU Department of Biology

Faculty Director of Genomics at the Center for
Genomics & Systems Biology

"The trickiness of Trichomonas genomes"
After graduating with a Ph.D. in Genetics from Edinburgh University in 1995, Professor Carlton took up research positions at the University of Florida, then NCBI at NIH, and then TIGR (The Institute for Genomic Research, founded by J. Craig Venter and Claire Fraser).


Since 2006, her group has been at New York University undertaking research into the biology and evolution of important human parasites. She is Program Director of the Center for the Study of Complex Malaria in India, an NIH-funded International Center of Excellence for Malaria Research. In 2010 she was awarded the Stoll-Stunkard Award from the American Society for Parasitologists; in 2012 she was elected a Fellow of AAAS; and in 2018 she was honored with a Julius Silver, Roslyn S. Silver, and Enid Silver Winslow endowed chair from NYU.

Research Description

In the Carlton lab  we use the tools of comparative genomics – whole genome sequencing and genomics, bioinformatics, molecular biology and population genetics – to study the biology and evolution of closely related strains or species of parasite. In medicine and global public health, the term parasite is used to describe a group of eukaryotic microbes and helminths that cause some of the world’s most devastating diseases. The parasites that we study include:

(1) Species of the malaria parasite Plasmodium: more than half the world’s population is at risk from malaria, and the disease causes ~216 million cases and ~655,000 deaths per year. The most deadly form of the parasite, Plasmodium falciparum, is found mostly in sub-Saharan Africa where it causes the deaths of children < 5 years old. Plasmodium vivax is the most common species outside Africa in South America and Southeast Asia, and is closely related to a group of species that infect Asian Old World monkeys from Taiwan to Sri Lanka, called the monkey malaria clade.

(2) The sexually transmitted parasite Trichomonas vaginalis and related trichomonads: T. vaginalis is the most common non-viral STI, and causes ~249 million cases per year world-wide. It is associated with increased risk of HIV-1 infection, and serious complications during pregnancy. Other trichomonads include Trichomonas tenax found in the mouth, Pentatrichomonas hominis a zoonotic gut parasite, and Tritrichomonas foetus a serious venereal pathogen that causes abortion in cattle.

(3) Other fascinating parasites such as species of the enteric pathogen Cryptosporidium, the bovine parasite Theileria, and Babesia.

Our research often begins with generation of a resource such as sequencing, assembly and annotation of a parasite’s genome. For example, we have been involved in the sequencing of P. falciparum [1], species of rodent malaria (Plasmodium yoelii yoelii [2], Plasmodium chabaudi chabaudi and Plasmodium berghei [3]), several strains of P. vivax [4, 5], several strains of the monkey malaria Plasmodium cynomolgi [6], and the first T. vaginalis genome [7].

Selected Publications

1. Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis. Warring SD, Blow F, Avecilla G, Orosco JC, Sullivan SA, Carlton JM. mSphere. 2021 Jan 6;6(1):e01061-20. doi:10.1128/mSphere.01061-20. PMID: 33408230; PMCID: PMC7845603.

2. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax. Hupalo DN, Luo Z, Melnikov A, Sutton PL, Rogov P, Escalante A, Vallejo AF, Herrera S, Arévalo-Herrera M, Fan Q, Wang Y, Cui L, Lucas CM, Durand S, Sanchez JF, Baldeviano GC, Lescano AG, Laman M, Barnadas C, Barry A, Mueller I, Kazura JW, Eapen A, Kanagaraj D, Valecha N, Ferreira MU, Roobsoong W, Nguitragool W, Sattabonkot J, Gamboa D, Kosek M, Vinetz JM, González-Cerón L, Birren BW, Neafsey DE, Carlton JM. Nat Genet. 2016 Aug;48(8):953-8. doi: 10.1038/ng.3588. Epub 2016 Jun 27. PMID: 27348298; PMCID: PMC5347536.

3. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum.  Neafsey DE, Galinsky K, Jiang RH, Young L, Sykes SM, Saif S, Gujja S, Goldberg JM, Young S, Zeng Q, Chapman SB, Dash AP, Anvikar AR, Sutton PL, Birren BW, Escalante AA, Barnwell JW, Carlton JM. Nat Genet. 2012 Sep;44(9):1046-50. doi: 10.1038/ng.2373. Epub 2012 Aug 5. PMID: 22863733; PMCID: PMC3432710.

4. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM. Nature. 2008 Oct 9;455(7214):757-63. doi:10.1038/nature07327. PMID: 18843361; PMCID: PMC2651158.

5. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ. Science. 2007 Jan 12;315(5809):207-12. doi: 10.1126/science.1132894. PMID: 17218520; PMCID: PMC2080659.

Schedule of Event

Schedule subject to change

9:00 — 9:15 a.m.

Welcome to 11 years of SCEP

Opening remarks for the 11th Annual SCEP symposium

9:15 — 9:30 a.m.
Morning Session: Chair, Dr. Emma Wilson
Angeline Wijono (UCLA, HIll lab)
 "Identification of Lineage-Specific Microtubule Inner Proteins (MIPs) in Trypanosoma brucei"
9:30 — 9:45 a.m.
Melvin Williams (CSUF, Jimenez lab)
"Mitochondrial function is regulated by mechanosensitive channels in Trypanosoma brucei"
9:45 — 10:00 a.m.
Lucy Paddock (HMC, Schulz lab)
"Bromodomain proteins show increased occupancy at binding sites as African trypanosomes differentiate from bloodstream to procyclic forms"

10:00 — 10:15 a.m.

Todd Lenz (UCR, Le Roch lab)
"Chromatin structure and var2csa – a tango in regulation of var gene expression in the human malaria parasite Plasmodium falciparum?"
10:15 — 10:30 a.m.
SCEP Lightning Talks

Akshara Kannan (CSUF, Jimenez lab)
"Regulation of the contractile vacuole function and flagellar homeostasis by mechanosensation"
Izra Abbaali (UCI, Morrisette lab)

"Analysis Pipeline for Candidate Apicomplexan Parasite-Selective Microtubule-Targeting Agents"

Skylar Rains (UCR, SOM)
"There’s a Fungus Afoot! A Case Study of Disseminated Coccidioidomycosis"
Michelle Shimogawa (UCLA, Hill lab)
"Developing a microfluidic-based chemotaxis assay for Trypanosoma brucei"
Stephanie Orchanian
"Defining the Molecular Basis of Immune Cell Recruitment to the Central Nervous System"
10:30 — 10:45 a.m. BREAK
10:45 — 11:00 a.m.
Nelly El-Sakkary (UCSD, Caffrey lab)
"High-Content (HC) Imaging and Gene Expression Profiling (GEP) in a Flatworm Parasite"
11:00 — 11:15 a.m. Ivan Chavez (UCLA, Hallem lab)
"Parasitic nematodes exhibit life stage-specific interactions with host-associated and   environmental bacteria"
11:15  — 11:30 a.m.
Suhani Bhakta (Cal Poly, Mercer lab)
"Determining how protozoan parasite Trichomonas vaginalis is degraded and digested during trogocytosis"
11:30  — 11:45 a.m. William Maciejowski (U of A, Decks lab))
"Evolution of Membrane Trafficking Machinery in Tritrichomonas foetus"
11:45 a.m. — 12 p.m. Break and ready for Keynote!

12:00 — 1 p.m.

Keynote Speaker

Jane Carlton, Ph.D. - Julius Silver, Roslyn S. Silver, and Enid Silver Winslow Professor at NYU Department of Biology

The trickiness of Trichomonas genomes"

1 — 2:30 p.m.

Lunch. Poster Viewing and interactions in SLACK

2:30 — 2:45 p.m.

Afternoon Session: Chair, Dr. Meera Nair
Sarah Bobardt (UCR, Nair lab)
"Endocannabinoid Receptor-Signaling Regulates Host-Parasitic Nematode Interactions"
2:45 — 3:00 p.m. Kristina Bergersen (UCR, Wilson lab)
"Chronic Brain Neutrophils Protect Against Toxoplasma gondii Infection"
 3 — 3:15 p.m.
Peter Back (UCLA, Bradley lab)
"An essential IMC protein complex governs Toxoplasma invasion and egress"
3:15 — 3:30 p.m. Stephanie Matsuno (UCI, UCI Lodoen lab)
"The inflammatory role of caspase-8 during T. gondii infection of human monocytes"

3:30 — 3:45 p.m.


3:45 — 4:00 p.m.

Chandrasekaran “Arun” Sambamurthy (Arizona, Koshy lab)
"Using Toxoplasma gondii to redefine the neuronal innate immune response"
Awards and Thank you's!