My Association with HIV Reverse Transcriptase

 My Association with HIV Reverse Transcriptase:

Just saw on linkedin: Dr. David Baltimore, Nobel prize winner  & co-discoverer of HIV-1 Reverse Transcriptase, passes away at 87.

The central dogma of molecular biology involves DNA-the molecule which contains genes, that is    transcribed into RNA, which is eventually made into protein. However an enzyme (proteins that speed up or catalyze reactions within cells) in human immunodeficiency virus (HIV) reverse transcribed RNA into DNA. This went against the central dogma of molecular biology. Researchers Howard Temin & David Baltimore were awarded the Nobel prize for this discovery (1975) , https://www.nobelprize.org/prizes/medicine/1975/baltimore/facts/  

My tryst with HIV Reverse Transcriptase began  in 1999, when I joined Prof. Monica Roth's Laboratory as a graduate research fellow, post a successful laboratory rotation. This was in the Molecular Biosciences program jointly hosted by Rutgers-UMDNJ, New Jersey USA. I picked a project which involved HIV-1 Reverse Transcriptase. It was a protein modeling project.

HIV-1 Reverse Transcriptase has two functional domains: a polymerase which makes the double stranded DNA polymer and an Rnase H domain which breaks down the RNA component (derived from HIV and also the tRNA primer) of the RNA-DNA hybrids, so as to form a full double stranded DNA genome ,that can integrate into the host cell DNA and remain as a provirus. Prof. Roth had designed a polypeptide minus the polymerase domain, so as to  screen for inhibitors of HIV-1 RNaseH enzyme only.

It took 6 months to clone the polypeptide. This was followed by purification  and testing activity of this polypeptide on hybrid RNA-DNA substrates, in the presence of manganese, which took two and a half years. These findings culminated in a paper in 2004, and the design made to the cover of the  journal: Protein Engineering Design & Selection (PEDS):

https://academic.oup.com/peds/article-abstract/17/7/581/1553405

This designed polypeptide formed the precursor to an RnaseH  polypeptide that functioned in the physiological cation, Magnesium, and a subsequent paper from Prof. Roths laboratory.

Interestingly , when I co-wrote a book chapter , on DNA viruses containing reverse transcriptases;

https://www.taylorfrancis.com/chapters/edit/10.1201/9781003369349-15/dna-viruses-containing-reverse-transcriptase-sonali-sengupta-baibaswata-nayak ,we included the Baltimore classification of viruses.

So Prof. David Baltimore has indirectly played an invaluable role in catalysing my growth as a researcher , and this blogpost is in memory of this great scientist. I bow to him with humility.

AI & 3D bioprinting

 A combination of Artificial Intelligence (which has learned how to assemble an artificial cell) that  gives instructions to the 3D Bioprinter with an input of  cellular constituents, can in theory build cellular machines.

Combinations of cells with vasculature can give rise to 3D bioprinted tissues,organs, organ systems & eventually organisms.

If Consciousness (Awareness) is Fundamental & Universal then it will express itself to a greater degree manifesting enhanced capabilities with increasing complexity of 3D- bioprinted  agents.

What do I mean by increasing complexity? 

A salt crystal is formed by repeating units of sodium and chlorine atoms to form a regular lattice. The coat of a virus called an "icosahedron" is made of repeating units of protein, with the smallest shape being a triangle which arranges itself with increasing complexity in terms of numbers. Bacteria have repeating units of coat protein surrounded by a lipid envelope. As one moves to yeast, there are fission yeasts (yeasts that split) and budding yeasts. Suddenly "things start to look different". There are fungi-zygomycetes that form round spores, ascomycetous fungi where spores are enclosed in a sac like structure and basidiomycetous fungi where spores are arranged on club shaped structures.

Then we move to the plant kingdom, where the common factor is photosynthesis-but plants look different. Can you really visually compare a weed, shrub, herb or a creeper ? Things get more interesting in the animal kingdom where each species looks different from the other. But with more complex forms, there is more complex regulation and greater variety of functions for example it is no more about eating to reproduce and survive, but there are more complex inter-species interactions for mutual benefits, or antagonistic relationships such as that of a prey and a predator, or a combination of both , for example commensalism. So with increasing complexity of a species, interactions between species become more important giving rise to food chains and food webs. 

The prediction is that 3D bio-printed agents directed by Artificial Intelligence involving Machine Learning Algorithms, will show greater manifestation of Consciousness with increasing complexity, if Consciousness/Awareness is the underlying substratum/field of the Universe. With greater manifestation of conscious agents there will be more interactions of the 3D bioprinted agents, from which will emerge the sculpting of local ecosystems as we humans aong with our related species have sculpted the planet earth. So, the cycle of manifestation and interactions continues. 

I end with the following:

   

 All manifest forms and life-forms which are infinite, arise from the unmanifest which is also infinite. When one takes away the infinite manifest from the infinite unmanifest, the infinite still remains.

                   II SHANTIH II 

Cancer Vaccine-ADJUVANT THERAPY

 Assumption 

The theoretical assumption is that,   neo-antigens in tumor cells are probably oncogenes which may be poorly presented on the cell surface. This could be due to low expression levels, or inappropriate interaction of cell-surface neo-antigens, with MHC II molecules, more specifically the  inhibitory peptide. This inhibitory peptide, could form unstable complexes with the neo-antigen and MHC II, resulting in failed neoantigen-presentation. Thus the tumor survivesthe   immunosurveillance process.

The tumor suppressor polypeptide (based on the amino acid sequence) could fold in such a way that it forms stable complexes with MHC II, that is not inhibited by the inhibitory peptide. This leads to proper antigen-presentation. In this instance, the tumor is targeted by the immune system (cell-defense mechanism) and gets eliminated.

A successful cancer vaccine would override the above biology, for example an adjuvant such as an emulsion, could cloak the inhibitory peptide in the case of a neo-antigen/oncogenic polypeptide resulting in stable complexes, that leads to successful antigen-presentation, and elimination of the tumor.

Therapy/Cure ensues.      

Cellular_Metastasis

THEORY Of METASTASIS  : (Metastatic Cancer is the NEMESIS) 

Tumorigenesis :

During tumor initiation, cells intially divide, to form a cluster of cells. This cell division, is based on the evolutionary theory of Darwin, i.e. natural selection.

Tumor cell circulation :

 These cluster of cells, circulate through blood in inhospitable environments, to newer sites. At the newer sites, they secrete tumor-suppressive molecules which block inhibitory factors, that prevent the seeding of cancer seed cells in newer environments. This leads to the hypothesis that the transcriptional machinery (involving RNA and transcriptional factors),  adsorbed by the promoters of tumor-suppressors. The assumption is that, the quantitative relation between oncogenes and tumor-suppressors is an inverse one. 

Metastasis :

With excessive levels of tumor suppressors, a negative feedback loop functions to prevent apoptosis (programmed cell death), of cells  in-order that cell survival ensues. This leads to the increase in levels of oncogenes to counteract the excessive levels of tumor-suppressors,that could be termed as ADAPTATION (Jean-Baptiste Lamarck; French Natural Philosopher); further increase in oncogenic levels/activity ensues, leading to cell division and and metastatic tumors at secondary sites. 

Nomenclature (Terminology)

This progress of events could be termed Dar-Lam-Da or alternatively Darwinian survival-Lamarckian Adaptation followed by Darwinian survival.          

 

(Lyrics):

https://www.youtube.com/watch?v=S4kzGhDEURA

Tumorigenesis-Tumor as a Condensate

 A tumor is like a condensate, analogous to the precipitation of de-differentiated cells. 

Differentiated cells, overcome some kind of energy barrier (Waddingtons epigenetic landscape) and de-differentiate from defined structure to an un-defined mass of cells.

These mass of cells lose their definitive interactions (epithelial mesenchymal transition) and condense to a solid mass.

Mapping the Mind

 In the psychology tradition, there are 16 personality types, based on the following characteristic traits in various permutations:

Introversion/Extroversion, Intuitive/Logical, Thinking/Feeling, Judging/Perceiving.

In the yoga tradition, there are three attributes of the mind: Sattva (Calmness/Balance), Rajas (Energy/Activity), Tamas (Dullness/Laziness).

In the Vedanta Tradition there are five sheaths from the depth to the surface: They are annamayakosha (food sheath), pranamayokosha (vital energy sheath), manomayakosha (mind sheath), vigyanmayokosha (intellect sheath), anandamayokosha (bliss sheath). 

The three gunas of Sattva, Rajas, Tamas belong to manomayokosha. These three gunas in various permutations are expressed as the personality types.

For example Introversion is correlated with Sattva, Extroversion with Rajas. Clear thinking with Sattva and feeling or emotions with Rajas; Judging with tamas and Perceiving with sattva. Intuitive,Logical both with Sattva. 

So an INTP (Introversion, Intuitive, Thinking, Perceiving) personality trait has the predominant qualities of Sattva.

The above-mentioned correlations can be used as a technique for mapping the human mind and its expression as personality traits.

Activity and Stillness

 Anaesthetic mediated stilling of brain activity versus non-anaesthetic mediated stillnes

 

The Prior - Consciousness expresses itself in and via dynamically functioning neurons.

The floor of a neuronal cell, consists of microtubules and actin filaments. The microtubules intercalate to form a dynamically functioning network, that expands and contracts according to cell activity. This is analogous to sarcomere filaments in contracting and expanding muscle.

The expansion and contraction of the microtubule filaments, lead to a rhythmic oscillation pattern, that manifests itself in a dynamically functioning neuronal cell, transmitting information via secreted neurotransmitters. In other words microtubules act upstream of nerve impulse transmission.

When anaesthesia is administered to a living organism, the anaesthetic treatment locks the intercalation, inhibiting nerve impulse transmission, resulting in progressive diminishment  of the rhythmic oscillation pattern of neuronal firing.

This anaesthesia mediated diminshment of neuronal firing, is different from stillness acquired through meditation. The anaesthetic treatment physically affects the neuronal network architecture, which leads to involuntary collapse of the brain. Meditation is the voluntary stilling of neuronal activity by affecting neurotransmitter mediated nerve firing, without affecting neuronal architecture.

The former leads to collapse of the living organism if administered in excess. The latter in the case of a human being, leads to illumination of mind activity in a still background, which in other words is called liberation of the mind via enlightenment