( Protists ( ( are ( ( eukaryotes , ) ( organisms ( with ( organized nuclei ) ) ) ) ) . ) )
(ROOT (S (NP (NNS Protists)) (VP (VBP are) (NP (NP (NNS eukaryotes)) (, ,) (NP (NP (NNS organisms)) (PP (IN with) (NP (VBN organized) (NNS nuclei)))))) (. .)))
Protists are eukaryotes, organisms with organized nuclei.
(ROOT (S (NP (NNS Protists)) (VP (VBP are) (VP (VBN thought) (S (VP (TO to) (VP (VB be) (NP (DT the) (JJS oldest) (NNS eukaryotes))))))) (. .)))