Transmission to small animals and cells in culture exposed basic biologic and molecular agent facts most consistent with an exponentially replicating ~25 nm viral particle that contains an essential but unknown nucleic acid for infection.
[citation needed] This contrasts with the assertion that the host encoded amyloid forming prion protein, without nucleic acid, is the infectious agent.
Early in her career, Manuelidis discovered major unknown DNA sequence motifs, and demonstrated their megabase organization in metaphase chromosomes and interphase nuclei.
[7] These late replicating sequences, that contain few if any genes, define all human chromosome centromeres as shown by the development of high resolution in-situ hybridization.
Manuelidis also discovered, isolated, and sequenced the human long interspersed L1 repeats (LINES) and showed they contained a transcriptional open reading frame.
It thus became clear that these ancient large retroviral invaders entered the genome and were symbiotically transfigured, or pathologically tamed, during evolution to attain a structural, and possibly functional role in megabase chromosome band domains.The enormous sizes of L1 and Alu rich domains were also demonstrated by pulse-field electrophoresis.
Manuelidis also opened up the field of 3-dimensional chromosome structure in the interphase nucleus of differentiated cells by combining optical serial sections and high resolution in-situ hybridization of specific DNA sequences.
Previously, interphase compartments were viewed as ill-defined dense heterochromatic blobs beside unorganized euchromatic chromatin spaghetti with no cohesive 3-D structure.
Finally, the insertion of a huge 11 megabase transgene of the globin exon (lacking introns) was recognized by cells, and silenced by compaction together with transcriptionally inert heterochromatic centromeres in neurons.
[22][23][24] This made it possible to demonstrate fundamental mechanisms of infection, including TSE agent uptake and spread via myeloid cells of the blood,[25][26] a common route for most viruses.
[39][40] Manueldis has challenged the dominant assertion that host prion protein (PrP), without any nucleic acid, is the causal infectious agent in TSEs.
[43] Manuelidis stated that "Although much work remains to be done, there is a reasonable possibility these are the long sought viral particles that cause transmissible spongiform encephalopathies".
[45] Later evidence favored the pathological concept, with infectious viral particles binding to and converting receptor PrP to an amyloid form.
[51] On the other hand, all high infectivity scrapie and CJD fractions contain nucleic acids when analyzed using modern amplification strategies.
[53] Novel circular SPHINX DNAs from the microbiome of 1.8kb and 2.4kb have been identified in isolated infectious particles, but their role in infection and/or disease is not yet clear because they are also present at much lower levels in non-infectious preparations.