Friday, May 27, 2022

The Beginning of Cellular Life on Planet Earth

A Possible Structure for a Primitive Cell- Biology Libre Texts

A necessary first step in examining the evolution of cellular-based life from the pre-biotic world is to discern what constitutes the makeup of cells in the broadest possible terms. In deconstructing cell structure from the viewpoint of prokaryotes, I propose the following necessary prerequisites for a living cell:

· Cell Membrane to delineate the cell and protect it from the local environment

· Cell infrastructure composed of the most basic structural components including actin, myosin, etc.

· Source of readily available energy

· Proteins especially enzymes involved in catabolic and anabolic activities

· Signal transduction pathways that allow for both intracellular and extra-cellular communication.

· Nucleic Acids: DNA and RNA to serve as information stores for the cell.

· Mechanisms for DNA and cellular replication.

Any attempt to propose a mechanism by which primordial cell-like structures evolved into the complex cells that exist today, strongly suggests a gradual stepwise process that took eons to accomplish. It also suggests, in my mind, that the process would involve steps in which cellular organization would grow in complexity from the level of simple molecules (substrates) through proteins and nucleic acids and finally through protein-nucleic acid interaction to the encoding of the genetic material. In this way, selection pressures and processes would enhance each succeeding step.

Taking all this into account, I propose the following model for the evolution of cellular life from primordial beginnings.

Elements of the Hypothesis:

There existed an aqueous environment (possibly shallow ponds or along coastal regions or possibly the sea floor) where there was an abundance of nucleotides, fatty acids, amino acids, peptides and polypeptides. It is possible that some of this organic material may have been seeded by meteorites.
In these organic-enriched regions, conditions were appropriate for the spontaneous formation of cell-like structures.
 
These cell-like structures developed semi-permeable membranes formed from the spontaneous assembly of proteins and lipids (probably a more primitive structure than found in present day cells) and highly permeable to dissolved organic matter in the local environment.
 
The local environment was such that amino acids, nucleotides, fatty acids and carbohydrates could readily penetrate the cell membranes of these primordial cells and concentrate there.
 
Ambient conditions including oxygen concentration, temperature, abundance of ammonia and methane made the spontaneous synthesis of proteins and nucleic acids not only possible but highly likely.
Assuming that spontaneous formation of tRNAs were a likely scenario, these tRNAs could bind to their appropriate amino acids. These amino acid carriers collided with each other and result in the formation of random polypeptide chains. Subsequently, Polypeptides that were capable of binding to carbon sources such as glucose stabilized these small proteins and gave them a competitive advantage over more non-specific proteins. Since the metabolic pathway for glucose metabolism is universal to all life, one must assume that glucose was abundant in pre-biotic times. This same argument can be applied to the presence of ADP/ATP, since this molecule is the essential ingredient for all energy sustaining life activities.
 
Some of these selected proteins also possessed catalytic capabilities and were able to breakdown carbon rich substrates and ultimately capture energy in ATP molecules. This energy may have been used in accelerating the synthesis of more complex molecules and intra-cellular structures, the precursors of cellular organelles.  
 
There is mounting evidence that strongly suggests that RNA may have played a pivotal role in information storage in the early evolution of cellular life. As I have postulated above, tRNAs may have been abundant. Additionally, evidence for the role of RNA in information storage includes:
 
  • The discovery of RNA that possesses catalytic activity referred to as ribozymes. There is a ribozyme that has been found in the core of ribosomes.   
  • The discovery of small pieces of RNA that can readily bind to a variety of organic molecules and that are found on the ends of mRNA in prokaryotes. These pieces function as switches that can turn translation on or off and are referred to as riboswitches. 
  • Double-stranded RNA that can silence gene transcription in a complex referred to as RISC.
  • What is now referred to as the anti-codon region of tRNA may have been used to make mRNA possibly happening spontaneously utilizing an environment rich in small pieces of RNA or assisted by a ribozyme. These nascent mRNAs served as templates for the further synthesis of specific and biologically valuable proteins. Whether or not such associations are possible today in conditions that simulate the pre-biotic environment would need to be tested. It is possible that “ancient” RNA had a different structure than the current form. This early mechanism was probably inefficient and prone to error.
 
These early cells were infiltrated by a competing entity that gradually assumed a symbiotic relationship and was to become what is now referred to as ribosomes. These structures contributed a much more efficient mechanism for the synthesis of proteins.  In addition, the mitochondria found in eukaryotic cells and the chloroplasts found uniquely in plant cells have their own nucleic acid and most probably were once independent organisms that also assumed a symbiotic relationship with their host cells.
 
Messenger RNAs were no longer able to sustain the growing complexity of cell life as embodied in metabolism and energy transfer mechanisms. A more highly conserved store of information was required. The appearance of an enzyme capable of using mRNA as a template to make highly stable double-stranded DNA encouraged the further development of cellular complexity and evolution. This transition was necessitated by the fact the extra-cellular environment was no longer as rich in nutrients and building materials as was previously the case. It has become clear that large portions of the genome of humans and other complex organisms are made up of retrotransposons. There are relatively small pieces of DNA that code for reverse transcriptases that allow for copying of these segments and ultimately inserting them in other places in the genome. These were originally discovered by McClintock and referred to as so-called “jumping genes.” Integration of these pieces in the promoter or structural regions of active genes can have profound impacts on gene expression. Certain diseases have been associated with this process. Furthermore, there are retrotransposons that have been conserved among and between organisms. This suggests that the increasing complexity of the genome as seen in evolution may be in large due to retrotransposons. In addition, retrotransposons have many characteristics similar to retroviruses suggesting that retroviruses may have played a significant role in delivering novel genetic material to the genome.
In conclusion, the particular scenario I have outlined represents one possible pathway that may have taken place that was responsible for the evolution of cellular life as we know it from prebiotic conditions that existed on planet Earth billions of years ago.

Wednesday, May 18, 2022

The Impact of Sunscreen Products Upon the Viability of Coral

It has been reported that the compound oxybenzone (shown below) that is the active ingredient in sunscreen preparations exhibits a toxicity to corals. The mechanism of this toxicity has not been fully understood.


Oxybenzone

William Mitch and his colleagues at Civil and Engineering at Stanford University, California have successfully delineated the mechanisms involved in regard to this toxicity. They have established that oxybenzone caused increased mortality of a sea anemone under conditions that simulated the natural (UV) radiation (290 to 370 nanometers). Furthermore they found that both the anemone and a mushroom coral formed oxybenzone–glucoside conjugates (see image below) that were powerful auto-oxidants. Corals are composed of layers, of calcium carbonate secreted by soft bodied animals called coral polyps. These polyps live in a symbiotic relationship with a host zooxanthellae such as algae that gives the coral its color. Corals devoid of algae are bleached as a consequence of climate change.




Algal symbionts took up these conjugates, and their mortality correlated well with the corresponding concentration of oxybenzone glucosides within the animal cells. Since many commercial sunscreens preparations contain compounds structurally analogous to oxybenzone, an understanding of the mechanism of this toxicity should enable the synthesis of more eco-friendly sunscreen products.

According to the authors of a paper published in a recent article in the prestigious journal, Science, “Research in the US Virgin Islands found no substantial settlement of coral larvae, survival of juvenile corals, or regeneration of adult tissue in induced lesions over a 5-year period in Trunk Bay, where high levels of recreational swimming resulted in up to 1.4 mg of oxybenzone per liter of seawater. Meanwhile, a thriving coral community was found at neighboring Caneel Bay, with lower recreational use but presumably the same impacts from global stressors. Exacerbation of coral declines by sunscreens washed off tourists would be ironic and particularly pernicious, given the promotion of ecotourism in the interest of protecting coral reefs.”

Finally, the authors go on to say that, “With recent moves by regulatory authorities in Hawaii and elsewhere to ban oxybenzone, understanding the mechanism(s) of its phototoxicity is important to ensure that the sunscreen components that are selected as alternatives are truly safer for corals.”

The ecological factors that promote and sustain the delicate balance in the natural world can easily be disrupted by human encroachment. It is vitally important to support the kind of scientific investigations that uncover these human factors and find ways to mitigate their impact.




Sunday, May 15, 2022

The Filovirus

One of the suspected and postulated origins of COVID-19 virus in human populations is the transfer of the virus across the species barrier i.e. from bats. This capacity to “jump” across species is of added concern given the severity of illness originating from human infection by a family of viruses referred to as filoviruses. A filovirus is a filamentous RNA virus (see image below).



 

Infection by this virus is the causative agent of so-called “hemorrhagic fevers” in humans and primates, that includes the Ebola and Marburg viruses. These viruses can result in multiple organ system involvement. The Marburg virus, for example, can produce nausea, vomiting, chest pain, a sore throat, abdominal pain, and diarrhea may appear. Symptoms become increasingly severe and can include jaundice, inflammation of the pancreas, severe weight loss, delirium, shock, liver failure, massive hemorrhaging, and multi-organ dysfunction. These diseases are most prevalent in sub-Saharan Africa.



 

In 2002, the Lloviu filovirus was found in Schreiber bats (Miniopterus schreibersii) in northern Spain. This infection resulted in a massive die-off of these animals. Gabor Kemenesi and his colleagues from the National Laboratory of Virology at Szentagothai Research Center at the University of Pecs, Hungary successfully isolated and sequenced the Lloviu filovirus from Schreiber bats in Hungary. During a active surveillance of these bats, they found the Lloviu virus resident in these dead and living cave-dwelling bats.

Furthermore, antibody testing detected nine seropositive bats out of 74 live bats and four positives among 351 live bats sampled. The Lloviu virus is known to infect human cells in culture, but unlike the Ebola virus appears to be nonpathogenic to humans, at least for the time being.


Sunday, January 23, 2022

Epstein Barr Virus Infection May be Associated with the Onset of Multiple Sclerosis

Multiple Sclerosis (MS) is a chronic and debilitating disease that is a result of the destruction of the myelin sheath that serves as insulation for the peripheral nerves within the central nervous system (CNS).  The loss of myelin has serious implications for the patient suffering from this syndrome – it results in a gradual deterioration of motor function. 

To date the etiology of this disease has been unclear.  It has long been suggested that Infection with the Epstein-Barr virus (EBV) may be responsible for triggering the onset of MS.  In a recent issue of the prestigious publication Science (January, 2022), Kjetil Bjornevik, from the Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, has provided compelling statistical evidence that EBV infection triggers the onset of MS.  According to the author, “analyzed EBV antibodies in serum from 801 individuals who developed MS among a cohort of >10 million people active in the US military over a 20-year period (1993–2013). Thirty-five of the 801 MS cases were initially EBV seronegative, and 34 became infected with EBV before the onset of MS. EBV seropositivity was nearly ubiquitous at the time of MS development, with only one of 801 MS cases being EBV seronegative at the time of MS onset. These findings provide compelling data that implicate EBV as the trigger for the development of MS.” 

EBV (see diagram below) preferentially attacks B cells; B cells are the part of the immune system repertoire responsible for the production of antibodies.   In MS the myelin sheath is degraded through an inflammatory response.  It has been shown that in MS the B cells responsible for this inflammatory are derived from plasmablasts that are generated in the marrow and take residence inside the brain and its internal lining.  These plasmablasts divide and produce clusters of daughter cells that produce immunoglobulins.  These immunoglobulins contain specific antibodies that target myelin-producing glial cells within the central nervous system (CNS).

EBV Virus


One of the accepted therapies that attempt to take advantage of this etiology is the use of monoclonal antibodies that target CD20 - a protein preferentially found on the surface of B cells.  However, it has significant drawbacks in so far as these monoclonals do not readily pass through the blood brain barrier (BBB) and they are unable to bind to plasmablasts.

What remains unclear, however, is the mechanism through which EBV triggers this sequence of events in MS patients.  One possibility involves what is referred to as molecular mimicry in which some EBV proteins may be similar enough in structure to myelin that the immune system is induced to produce antibodies against the infected individual’s myelin and CNS antigens – this would represent an autoimmune response.  In addition, EBV encodes an interleukin-10–like protein, which activates B cells.  The author of this study, reports that recent evidence seems to suggest that molecular mimicry may be the actual mechanism underlying the association between EBV infection and MS.

The results of these kind intensive studies of the etiology of MS are extremely important in that the product of this work may finally produce effective therapies for MS patients.

Thursday, October 28, 2021

What drives Cancer?

In a recent article in the Science, a prestigious scientific journal published by the American Association for the Advancement of Science (AAAS), Dr. Arianna Baggiolini and her colleagues, from the Memorial Sloan Kettering Cancer Center In New York, NY, proposed a model to explain why some melanocytes preferentially transform into the cancerous state while other melanocytes do not.

Melanoma is a cancer that preferentially arises from cells of the melanocyte lineage.  Melanocytes (see image below) are responsible for   skin pigmentation through the production of melanin so that skin cells, especially keratinocytes, are protected from UV-induced DNA damage.  Melanoma typically resides in the skin.  It has been well established that a so-called “founder mutation” is required to initiate uncontrolled proliferation of cells – a phenomenon that is characteristic of all cancers.  Interestingly, these mutations, also referred to as driver mutations (oncogenes), are also found in healthy skin.  The question arises – why is it that oncogenesis preferentially arises in in some melanocytes and not others.


Dr. Baggliolini and her group of investigators conducted an experimental study in an attempt to explain this behavior.  The animal they chose for their studies was genetically modified zebra fish deficient for the tumor suppressor p53 to drive expression of the BRAFV600E oncoprotein in each stage of melanocyte differentiation.  The evidence they obtained led to a concept they refer to as oncogenic competence – an additional variable is present that renders the melanocytes more susceptible to transformation to tumor cells.

In regard to Melanoma, to give rise to cancer, melanocytes require a driver mutation. For melanoma, such mutations frequently occur in proteins of the mitogen-activated protein kinase (MAPK) pathway, with the BRAFV600E mutation (in which Val600 is replaced with Glu) being most prevalent.  Furthermore in normal human skin, individual melanoblasts and neural crest cells also possess this driver mutation.

Human skin contains many individual melanocytes harboring potentially oncogenic driver mutations. However, what determines which of those cells can evolve to produce melanoma has not been unambiguously determined. Baggiolini and her experimental team found that both neural crest cells and melanoblasts were capable of giving rise to melanomas but, surprisingly, that melanocytes were somewhat resistant. These findings from zebrafish were confirmed in a parallel study using human pluripotent stem cells (hPSCs) rendered deficient for the tumor suppressors retinoblastoma (RB), p53, and p16 and in which the precursor cell line was induced at various stages of melanocytic differentiation.  The results show that melanocytes, but not neural crest cells or melanoblasts, were largely incapable of forming tumors when subcutaneously transplanted into immunodeficient mice.

The result of these experimental studies has clearly shown that the additional factor required to explain why some melanocytes do go on to produce cancer while other melanocytes with the driver mutation do not, is the enzyme ATAD2.  This enzyme is responsible for chromatin reorganization.  In those melanocytes in which this enzyme is expressed at lower levels, the likelihood of transformation of melanocytes into the cancerous state is increased.

This is a very interesting finding for it establishes a link between tumorigenesis and chromatin organization.

Friday, June 11, 2021

Biology of a Virus


 

It has been over a year since the world population has been dealing with the COVID-19 pandemic.  As a result of intense scientific investigation and study, effective vaccines have been developed and are being distributed worldwide.  

Given this reality, it would be of value to more fully understand what viruses are and how they function.

The following document may be of some help in this regard.

Sunday, February 7, 2021

The Basis of Antiviral Immunity

     Models of COVID-19 and the Spike Protein

The human immune system is a highly sophisticated and powerful system that the body utilizes on an ongoing basis in order to ensure the continued survival of the individual in a hostile environment. It is comprised of a heterogeneous population of cells, factors and organs that function together to maintain the general health of the individual. The immune system is, in fact, a product of millions of years of evolution. Rudimentary immune systems and processes can be found in many more primitive forms of life including single-celled organisms.

Immunologists have delineated two arms of the human immune system – innate and adaptive. The innate branch of the immune system possesses pattern recognition mechanisms designed to recognize any non-self antigen – an antigen is any substance, usually protein, that can elicit an immune response. When an antigen is recognized as foreign, the innate immune system is designed to mobilize quickly to neutralize the foreign organism that carries this antigen.

The other part of the immune system is referred to as the adaptive immune system. As the name infers, the adaptive immune system can adapt to new foreign invasive bacteria and viruses that find their way into the host. It is precisely this arm of the human immune system that responds to SARS-COV-2 (COVID-19). It is this system that neutralizes virally-infected cells and can induce the production of so-called, “memory cells.” It is this capability that is exploited and enhanced by vaccination strategies.

Both T-cells and B cells represent the primary cellular arsenal for the adaptive immune system essential for the eradication of invading viruses. The progenitors of the cellular components of the human immune system originate in the bone marrow. The COVID-19 pandemic has revealed the wide variability of the immune response to the COVID-19 virus ranging from an asymptomatic response to an acute and sometimes life threatening severe acute respiratory syndrome. This apparent variability has raised questions regarding the mechanisms through which antiviral responses are employed and the nature of the longevity of immunological memory.

As we are well aware, viral infections often lead to disease states within the impacted host. Viruses occupy a special place in regard to life on planet earth. They are essentially inert when outside a living cell showing no properties that are ordinarily assigned to living things. However, once they gain entry into a host cell, they subvert the cellular machinery, effectively diverting ordinary cell processes to a singular goal – the production of viral particles. This usually leads to the death of the host cell facilitating the release of new viral particles that go ahead and infect neighboring cells within the target tissue – in the case of COVID-19 its target tissue is found in the lungs.

The dynamics of the human body’s response to an invasion by a virus is intricate, immediate, and multi-faceted. The current understanding of this process is that it involves the integration of the two arms of the immune system we have previously referred to i.e. the innate and the adaptive. The first and rapid response is that of the innate system. The innate immune responses result in the production of factors that lead to inflammation at the site of entry – this is the so-called “inflammatory response.” This response leads to the activation of the adaptive immune system.

Viral particles are essentially composed of an inner core of either DNA or RNA and an outer shell of protein. It is the proteins on the viral surface that are potential antigens. Viral proteins and particles are subsequently taken up by specialized cells in the immune repertoire that are called dendritic cells (DCs) These cells transport the ingested antigen(s) to the lymphoid organs (lymph nodes and spleen for example), where they are specifically recognized by T and B cells. The T cells constitute the cellular branch of the adaptive system and the B cells represent the humoral branch responsible for the production of specific antibodies against the viral intruder. It is the cellular (T cell) and humoral (B cell) branches of adaptive immunity that collaborate to enable highly specific defenses against diverse viruses.

According to Dr. Linda Bradley from the Tumor and Microenvironment and Cancer Immunology Program at Sanford Burnham Prebys Medical Discovery Institute at La Jolla in a recent report in the prestigious journal, Science, “The magnitudes of the T and B cell responses are determined by such factors as the pathogenicity of the virus, the extent of inflammation, the frequencies of virus-specific T and B cells, and the kinetics of viral replication. CD8+ T cells differentiate into effector cells that limit viral replication through production of cytokines and direct killing of infected cells."

Furthermore, in regard to immune responses to COVID-19, this report goes on to state that, “Viral recognition elicits cytokine-producing effector cells, such as T helper 1 (TH1) cells, which inhibit viral replication and support CD8+ T cell as well as B cell differentiation. Effector T cells can enter the circulation and relocate to tissue sites of infection, where they mediate local antiviral responses. CD4+ T cells also differentiate into T follicular helper (TFH) cells that are crucial for the development of antibody-producing B cells (plasma cells) in lymphoid tissues and support memory B cell development. Antibodies can neutralize viruses by preventing host cell entry or promoting the lysis of infected cells. As a result of the coordinated interplay of innate and adaptive responses, the peak T and B cell responses lead to decreasing viral load and subsiding inflammation, often within 1 week of infection."

It is an understanding of the mode of action of a particular virus and the immune system’s responses to it, as outlined above, that plays a critical role in developing a vaccine that can effectively augment the natural immunity. For a virus to successfully infect a host it must gain entry to the host, successfully evade the immune response, gain entry into the host cell, and successfully commandeer the host cells machinery to make more viral particle and spread the infection. Any vaccine that successfully interdicts any of these mechanisms will necessarily prove efficacious.