Willis
Amy D.
Willis
Amy D.
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ArticleSegment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii(Wiley, 2021-11-18) Kuehn, Emily ; Clausen, David S. ; Null, Ryan W. ; Metzger, Bria M. ; Willis, Amy D. ; Ozpolat, B. DuyguDevelopment of sexual characters and generation of gametes are tightly coupled with growth. Platynereis dumerilii is a marine annelid that has been used to study germline development and gametogenesis. P. dumerilii has germ cell clusters found across the body in the juvenile worms, and the clusters eventually form the gametes. Like other segmented worms, P. dumerilii grows by adding new segments at its posterior end. The number of segments reflect the growth state of the worms and therefore is a useful and measurable growth state metric to study the growth-reproduction crosstalk. To understand how growth correlates with progression of gametogenesis, we investigated germline development across several developmental stages. We discovered a distinct transition period when worms increase the number of germline clusters at a particular segment number threshold. Additionally, we found that keeping worms short in segment number, by manipulating environmental conditions or via amputations, supported a segment number threshold requirement for germline development. Finally, we asked if these clusters in P. dumerilii play a role in regeneration (as similar free-roaming cells are observed in Hydra and planarian regeneration) and found that the clusters were not required for regeneration in P. dumerilii, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state of juvenile P. dumerilii leading to substantially increased germline expansion.
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ArticleStructure-informed microbial population genetics elucidate selective pressures that shape protein evolution(American Association for the Advancement of Science, 2023-02-22) Kiefl, Evan ; Esen, Ozcan C. ; Miller, Samuel E. ; Kroll, Kourtney L. ; Willis, Amy D. ; Rappé, Michael S. ; Pan, Tao ; Eren, A. MuratComprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
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ArticleA cryptic plasmid is among the most numerous genetic elements in the human gut(Elsevier, 2024-02-29) Fogarty, Emily C. ; Schechter, Matthew S. ; Lolans, Karen ; Sheahan, Madeline L. ; Veseli, Iva A. ; Moore, Ryan M. ; Kiefl, Evan ; Moody, Thomas ; Rice, Phoebe A. ; Yu, Michael K. ; Mimee, Mark ; Chang, Eugene B. ; Ruscheweyh, Hans-Joachim ; Sunagawa, Shinichi ; McLellan, Sandra L. ; Willis, Amy D. ; Comstock, Laurie E. ; Eren, A. MuratPlasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry “cryptic” plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one’s mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.