: adams@plessthan.com  
 
MODELS - I am currently exploring two models of nascent RNA-mediated gene transcription regulation:
                                            • Argonaute-linked gene network formation based on precise RNAPII pausing
                                            • Transposable Element remnants in transcription control and evolution

        These basic models are then used as templates for more complex ideas:
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Video animations by Brent Bishop
 
Nuclear RNA Networks - PART 1: Nodes & Edges The Wonders of RNA: RNA Networks
What if genes could communicate directly with each other, guided by fragments of their own RNA? In such a gene-to-gene network, what would function as the informational "nodes" (to borrow the parlance of social networks)? What would form the "edges" connecting each node?

This video, part 1 of Dr. Melanie Adams' 'RNA Networks' series, explores a hypothetical model in which complex RNA Networks use precise communication to establish and maintain accurate gene regulation.

Dr. Melanie Adams discusses cutting edge theories about RNA, its roles, and capabilities.

This segment defines the concept of RNA Networks, drawing comparisons between a social network's nodes and edges and RNA's informational hubs and routes that connect genes that contain homologous sequences transcribed in antisense.

In this model, RNA is capable of maintaining and transmitting complex genetic instructions via argonaute proteins by becoming their small RNA guides.

   
Nuclear RNA Networks - PART 2: Nodes & Cell Differentiation The Wonders of RNA: Pseudogenes & Adapting to Bad Smells
What is the importance of the intricate, specific stem loops - or "flags" - transcribed by RNAPII? What is the importance of RNAPII Pause Points, and what functions do they fulfill?

This video, part 2 of Dr. Melanie Adams' "RNA Networks" series, explores the role of RNAPII Pause Points during cell differentiation - particularly their connection to the release of unique informational "flags" that signal to separate clusters of genes to maintain precise gene-to-gene contact.

This segment explores the implications of bidirectional transcription for adapted behavior, the role of cryptic promoters and retrotransposable elements, and the creation of 'self-pseudogenes' in animals such as C. elegans.

 

   
Nuclear RNA Networks PART 3: Nodes, PIWI, & Junk The Wonders of RNA: Lessons from HIV
How might a differentiating cell know what RNA is "self"? "Other"? Or if it will become a muscle cell or a neuron? What RNA is junk?

This video, part 3 of Dr. Melanie Adams' "RNA Networks" series, further explores the idea that different cell types have different RNA networks, defined by unique RNAPII pauses, or "nodes."

This segment concludes the series by examining RNA Networks in three subchapters: Pause Point Creation & Activation, Jumping Genes & Networks, and Inheritance & Diversity.

This segment describes a trick HIV uses to trigger rapid gene expression - a trick that turns out to be the norm for the majority of human stress response genes. The segment explores how the discoveries in the field of virology can provide insight into our understanding of RNA, DNA, and the evolution of life.
   
Nuclear RIAC: RNA-Induced Activating Complex - PARTS 1-4 The Wonders of RNA: Transposable Elements, Germ Cells, & Evolution
Could small RNAs can be transcriptionally activating as well as suppressing? This film, Dr. Melanie Adams' precursor to her "RNA Networks" series, explores a model termed Nuclear RNA-Induced Gene Activation (Nuc-RIAC), in which intranuclear gene-to-gene signaling via RISC or RIAC allows complex networks to form.

This film also serves as a foundational introduction to the more complex ideas that follow in the "RNA Networks" series.

• Pt 1: Introduction to Transcription
• Pt 2: Promoter Proximal Pausing
• Pt 3: Argonaute
• Pt 4: P-TEFb

This segment explores the possibilities of isolating and examining Transposable Elements such as LTR's in order to determine whether ancient transcriptional elements are truly junk, or perhaps have a deeper function in germ cell development and evolutionary speciation.

 

   
The Wonders of RNA: Visualizing Science Through Animation The Wonders of RNA: Alu Repeats & Inflammation
In this segment, Dr. Adams shares her reflections and insights on expressing scientific models through animation.

Considering the challenge of depicting the unimaginably tiny, yet vastly sophisticated molecular world, Dr. Adams discusses animation's ability to convey complex relationships and systems in ways that transcend language or static imagery.

This segment explores how small RNAs such as the ancient, ubiquitous Alu Repeats affect inflammation and reactions to shock or stress. Traditionally thought of as genetic junk, Alu Repeats are the most abundant transposable elements in the human genome, and may participate as signals in a complex gene-to-gene network, triggering argonaute proteins to turn off remote regions and prompt histone modifiers to methylate nucleosomes.

   
The Wonders of RNA: Smooth vs Punctuate Changes in Evolution The Wonders of RNA: Conventional & Innovative Theories
This segment explores the role that transposable elements have played in the Evolution of Life. Touching on the ongoing debate between a slow, gradual concept of the evolution, and a rapid, punctate vision of the process, Dr. Adams presents the possibility that the presence of flexible, jumping, transposable elements may allow for both: a gradual unfolding of evolution punctuated by bursts of sudden genetic change.

This segment explores RNA's traditionally accepted role as a 'xerox' of DNA, as well as innovative perspectives about its function as an intracellular communicator.
   

If you would like to discuss these topics or their respective presentations, please contact me at adams@plessthan.com. I am passionate about exploring these topics with peers, and I am open to filming the discussion and hosting it on this site and the Nuclear RNA Networks YouTube channel.
       : adams@plessthan.com