Sunday, December 16, 2018

The Impact of Climate Change on the Alaskan Permafrost

The process by which the earth transfers heat has led to an acceleration of warming in the northern climes caused by the unabated increase in greenhouse gases in the atmosphere. This effect has been particularly felt in Alaska. As a result, the heretofore permanent nature of the Alaskan permafrost is changing. This is particularly troublesome in that locked within this permafrost is organic material that is ,by its nature, rich in carbon and greenhouse gases. This process by which melting permafrost leads to increased release of greenhouse gases that subsequently leads to increased melting of permafrost represents a disturbing feedback loop mechanism with inherently dangerous consequences.

A Report from the New York Times helps elucidate the real gravity of this change.

Saturday, October 6, 2018

RNA Modifications Regulate Gene Expression During Development

RNA plays a critical role in gene expression within the cellular environment. Both messenger RNA (mRNA) and transfer RNA (tRNA) are involved in translating the instructions encoded in the DNA sequence of expressed genes into the manufacture of protein products at the site of the ribosomes. This process is, of course, happening continually throughout the life cycle of the cell. In the development of the human embryo in utero, the timing and orchestration of gene expression is vitally important; the precision of these processes is an absolute requirement for the successful creation of a viable individual at birth. The timed expression of development-related genes is determined by gene expression programs.

There is current evidence that there are modifications of RNA that function as post-transcriptional regulators of these gene expression programs. These regulators apparently impact a wide variety of eukaryotic biological processes. Michaela Frye from the Department of Genetics at the University of Cambridge, UK and her scientific collaborators stated in a recent article in the publication, Science, that “N6-methyladenosine affects the translation and stability of the modified transcripts, thus providing a mechanism to coordinate the regulation of groups of transcripts during cell state maintenance and transition. Similarly, some modifications in transfer RNAs are essential for RNA structure and function. Others are deposited in response to external cues and adapt global protein synthesis and gene-specific translation accordingly and thereby facilitate proper development.”


Gene expression in multicellular organisms is determined by a complex set of interacting and dynamic processes that require the coordination of mRNA metabolism and protein synthesis. There has been considerable investigation into the mechanism of transcriptional networks related to tissue-specific stem cell differentiation. However, the regulation of gene expression programs during development is especially crucial and must be unerringly precise. The recent evidence points to specific modifications of RNA as crucial to the regulation of cellular transcriptomes and proteomes during development.

At present there are over 170 modifications in RNA reported, but it is only following the relatively recent development of precise analytical tools that these modifications can be identified and quantified with precision. In addition to the N6 methyladenosine modification of mRNA as a crucial regulator of gene expression, other modifications including 5-methylcytosine and N1-methyladenosine are involved in the modification of both noncoding RNA and mRNA.

A detailed examination of some of these changes has been reported in the Science publication authored by Michaela Frye as noted above. These findings help to elucidate the molecular and cellular mechanisms that are involved in the intricate process of development.

Sunday, July 29, 2018

An Elegant and Monumental Experiment

The year is 1952 – two years prior to the discovery of the three-dimensional structure of DNA.  At that time there were essentially two schools of thought regarding the class of organic compounds responsible for heredity, namely, proteins or nucleic acids.  Two researchers Alfred Hershey (1908 – 1997) and his assistant Martha Chase (1923 – 2003) collaborated on a research project that they felt could unambiguously provide the answer to this fundamental question.  The experiment described below is remarkably simple, precise and elegant; the ramifications of their results speaks for itself in regards to the discoveries that would follow including Watson and Crick’s elucidation of the structure DNA and ultimately the complete sequence of the human genome (2003).

Hershey and Chase focused their attention upon the bacteriophage – a type of virus that preferentially attacks bacterial cells.  Like all viruses, the phage is made up of two distinct classes of compounds – a protein coat that surrounds a DNA core (there is also a class of viruses that use RNA as the infecting agent, the AIDS virus, for example).

Their experimental approach involved two precise steps outlined below
  •          They labeled the phage (T2) with radioactive Phosphorus (P32) prior to introducing T2 to bacterial host.  Phosphorus is predominantly found in DNA where it is a major constituent and found in protein in insignificant amounts.  After infection, they found that P32 was no longer in the phage, but was found in the host indicating the phage DNA was transferred to the host. 
  •          In the second experiment, they preferentially labeled the phage protein with radioactive Sulfur (S35).  Sulfur is a significant part of the composition of proteins but does not exist in nucleic acids (DNA).  In their analysis subsequent to infection, they found that S35 remained with the phage but was not found in the bacterium.

The results from these experiments, clearly demonstrated that the infectious agent was DNA and not protein.  This conclusion was so significant at the time that James Watson stated that, “the Hershey-Chase experiment had a much broader impact than most confirmatory announcements and made me ever more certain that finding the three-dimensional structure of DNA was biology's next important objective.

Note, that Hershey won the Nobel Prize for his work in 1969 along with Max Delbruck and Salvador Luria.  This kind of experimental approach also demonstrates the roles that imagination, dedication, persistence and creativity play in conducting scientific research. 

Saturday, July 7, 2018

A Rationale for the High Mortality Rate of Pancreatic Cancer

Pancreatic cancer is an especially aggressive cancer with a high mortality rate – only 6% of those affected survive beyond 5 years.  It is also the fourth most common death from cancer worldwide.  Even under conditions when it was supposedly caught early on, the adenocarcinoma was successfully resected and the liver was deemed to be free of the presence of metastatic legions, patients, nonetheless suffered from subsequent metastatic disease.  The obvious conclusion from this observation is that there are latent metastases that persist and that are only detectable microscopically.
Furthermore, these latent metastases were believed to represent a balance between cancer cell growth and cancer cell death precipitated by the participation of the immune system in countering this growth.  More recent evidence has indicated, however, that quiescent single disseminated cancer cells (DCCs) are involved.  An explanation for this quiescence has been elusive: although involvement of the immune system is suspected.  Of course, the question remains that if the immune system is involved why is it not able to eliminate these DCCs entirely.
Douglas T. Fearon and his colleagues from the John Hopkins University School of Medicine studied the role of adaptive immunity in response to DCCs using the mouse model.  Both mice and humans with pancreatic duct adenocarcinoma (PDA) show DCCs resident in liver.  in both cases, these cells display unusual phenotypic characteristics – negative for cytokeratin (CK) 19 and major histocompatibility complex class I (MHCI).

According to the authors, “The absence of MHCI and the occurrence of specific CD8+ T cells in the genetically engineered mouse model of PDA, and possible in patients with PDA, suggested that DCCs may be selected by an anticancer immune response during the metastatic process.” This rationale is represented by the image below.

The lack of the expression of MHCI in DCCs is indicative of Endoplasmic Reticulum (ER) stress.  ER stress occurs within cells in certain pathological conditions when there is an accumulation of unfolded proteins.  Many proteins vital to cell viability are maintained in precise folded configurations.  If the mechanism responsible for maintaining proteins in the folded state is disrupted, this results in so-called ER stress.  In this model, quiescent DCCs lacking the expression of MHCI elude destruction by the CD8+ T cells.  These surviving DCCs can then grow out into full blown metastases if the immune response is subsequently disrupted.  In other words, it is the immune response that selects for quiescent DCCs.  To test this hypothesis, the investigators used a mouse model that would allow them to introduce immunogenic PDA cells into seeded mice livers that were pre-immunized and contained only quiescent DCCs lacking MHC1 and CK19.  Those recipients that were not pre-immunized developed macro-metastases.   As a result, a subpopulation of PDA with the phenotypic characteristics of DCCs were found in vitro and those cells proved to be the precursors of DCCs in vivo.

The authors of this study conclude that, “A PDA-specific adaptive immune response selects DCCs, in which the ER stress response accounts for both quiescence and resistance to immune elimination. Accordingly, outgrowth of DCCs to macro-metastases requires not only relief from the cancer cell–autonomous ER stress response, but also suppression of systemic immunity. Thus, the ER stress response is a cell-autonomous reaction that enables DCCs to escape immunity and establish latent metastases.”

This finding may prove important in developing more effect therapeutic strategies for combating pancreatic cancer that currently has an unacceptably high mortality rate.  

Saturday, June 23, 2018

Somatic Mosaicism

A central concept in modern biology has been that in any individual, all cells contain identical copies of the DNA that establishes the phenotype of that individual.  This assumption seemed so critical to the life of the organism that it has never been routinely tested.  Current research challenges this assumption.

There is a condition referred to as Long QT Syndrome (LQTS).  The genetic form of this disease can result in life-threatening arrythmias of the heart.  In spite of the genetic correlation, only 30 percent of the patients studied tested positive for the genetic markers associated with LQTS.
Stephen R. Quake and his colleagues at Stanford University performed a detailed mosaic DNA analysis of an infant with perinatal LQTS.  As a result of this analysis, it was discovered that 8% of the heart cells were capable of arrythmia.   To further study this intriguing result, 7500 patients presenting with LQTS were studied for mosaicism.

Somatic mosaicism represents the occurrence and subsequent proliferation of DNA variants in cell lineages resulting from differentiation after fertilization.  It is now believed that this mosaicism may play a causal role in a variety of human ailments.  Furthermore, in the case of LQTS, a variant in the sodium channel protein NA 1.5 that is encoded by the SCN5A gene located on chromosome 3 may be the causative factor.

According to the authors, “One report suggests that 6.5% of de novo mutations presumed to be germline in origin may instead have arisen from postzygotic mosaic mutation events, and recent genetic investigations directly interrogating diseased tissues in brain malformations, breast cancer, and atrial fibrillation have revealed postzygotic causal mutations absent from germline DNA. Pathogenic mosaic structural variation is also detectable in children with neurodevelopmental disorders. However, a consequential category of genetic variation has not been surveyed systematically in clinical or research studies of other human diseases.”
These surprising results not only challenge the accepted assumption regarding the homogeneity of genetic information in every cell of the individual, it also may have profound implications for the etiology and treatment of human disease.

Saturday, May 26, 2018

Impact of the Changing Climate on Rio Grande

The current state of the Rio Grande as reported in the New York Times

Friday, May 11, 2018

The FOXG1 Syndrome

The so-called “FOXG1 Syndrome,” is a rare birth defect in which the infant who presents with this condition is abnormally small at birth and during the early stage of neuronal development, the head grows slowly; this eventually leads to an unusually small head in early childhood – a condition referred to as microcephaly.  Upon close examination there are number of brain anomalies that are present in patients with this condition –
  • thin or underdeveloped corpus collosum that connects the left and right hemispheres of the brain
  • reduction in the number of anatomical folds (gyri) that are present on the brain’s surface
  • reduced amount of white matter in the brain.  White matter is composed of the Axon bodies of the neurons (see diagram below) that connect the cell bodies of the neurons that make up the so-called grey matter.

Structure of the  Human Neuron

On account of the profound anomalies in brain structure associated with this syndrome, affected individuals present with severe and wide-ranging intellectual disabilities.  These can include involuntary muscular movements, difficulties walking, sleep disturbances, seizures and general irritability.  In addition, abilities in speech and language are often seriously impaired adversely affecting social interactions.  The FOXG1 syndrome has been grouped as an autistic-like disorder.  Although the range of impairments evident closely mirrors that of Rett syndrome, it is now classified as a distinct disease.

In terms of the etiology the FOXG1 syndrome, it is believed to be caused by a mutation in the FOXG1 gene.  The normal gene encodes for a the Forkhead Box G1 protein (see diagram below).  this protein seems to play an essential role in brain development where it functions as a transcription factor that normally represses the activity of certain genes when they are not required.  Extensive research has demonstrated that the FOXG1 gene product is involved in the development of the brain in early embryonic life.  The particular site of action of this transcription factor is the telencephalon that ultimately develops into the cerebrum that is involved in so many critical high-order functions in the human brain including language, sensory perception, learning and memory.

Artistic Rendering of the Forkhead Box G1 Protein

Finally, Rett syndrome is also believed to be caused by a different mutation in the FOXG1 gene leading to a dysfunctional Forkhead Box G1 protein.  Since the origin of these diseases are genetic in origin and impose their deleterious effects during embryonic development, a cure may ultimately reside in the introduction of the normal FOXG1 gene in utero.  This may indeed become a reality at some future time.

Friday, April 20, 2018

A Possible Effective Treatment for Ulcerative Colitis Using a Monoclonal Antibody

Ulcerative Colitis is serious ailment that has been shown to be an auto-immune disease that involves an attack by the ulcerative colitis patient’s own immune system against intestinal tissue.   According to a description of this disease as shown on the Mayo Clinic website –

“Ulcerative colitis is an inflammatory bowel disease (IBD) that causes long-lasting inflammation and ulcers (sores) in your digestive tract. Ulcerative colitis affects the innermost lining of your large intestine (colon) and rectum. Symptoms usually develop over time, rather than suddenly.

“Ulcerative colitis can be debilitating and can sometimes lead to life-threatening complications. While it has no known cure, treatment can greatly reduce signs and symptoms of the disease and even bring about long-term remission.

“Ulcerative colitis symptoms can vary, depending on the severity of inflammation and where it occurs. Signs and symptoms may include:
·         Diarrhea, often with blood or pus
·         Abdominal pain and cramping
·         Rectal pain
·         Rectal bleeding — passing small amount of blood with stool
·         Urgency to defecate
·         Inability to defecate despite urgency
·         Weight loss
·         Fatigue
·         Fever
·         In children, failure to grow

“Most people with ulcerative colitis have mild to moderate symptoms. The course of ulcerative colitis may vary, with some people having long periods of remission.”

As stated above, this disease has no known cure.  However, there is strategy that is being investigated by Wendy J. Komocsar. and her colleagues in the laboratories of Eli Lilly and Company, Indianapolis, IN that utilizes the production of a monoclonal antibody that blocks the activity of BAFF.  BAFF is a natural B-cell activating factor – this factor effectively enhances B-cell survival.  B cells are a subset of the immune repertoire of circulating lymphocytes that are responsible for the production of antibodies.  In addition, it has been demonstrated that the overexpression of BAFF results in severe autoimmune disorders in mice.  Furthermore, elevated levels of BAFF have been shown to be present in some patients with autoimmune diseases.  The monoclonal antibody that has bee produced that blocks BAFF is a potential drug referred to as tabalumab.

This type of approach may provide the potential for providing relief for individual’s suffering from a variety of autoimmune disorders.

Tuesday, February 27, 2018

The Molecular Biology of Celiac Disease

Celiac disease is a so-called, “autoimmune disease” that impacts an estimated one percent of the population.  An auto-immune disease is caused by an individual’s immune system attacking its own tissue.  Other examples of diseases that fit this classification are multiple sclerosis (MS), pemphigus, rheumatoid arthritis and systemic lupus.

In Celiac disease, the tissue that is impacted involves the microscopic villi that line the lumen of the small intestine.  These structures provide the surface area through which digested nutrients are absorbed (see image below).  The patient with celiac disease presents with unexplained loss of weight and fatigue, anemia and constipation for example.  The destruction of these highly complex structures is irreversible; if, this condition is left untreated, it can be deadly.

The trigger for this auto-immune response is the presence of gluten - a protein found in wheat and related plants.  Gluten is a protein that is prevalent in Western diets.  In addition, research studies have demonstrated that the agent (antigen) that induces the autoimmune response is not the intact gluten protein but the protein after it is modified by the enzyme transglutaminase 2 (TG2) within the small intestine.  It seems that in normal tissues, although TR2 is an abundant enzyme, it exists primarily in the inactive state.
Chaitan Khosla and his colleagues at the University of California at Stafford have recently demonstrated that there is a cellular enzyme protein 57 (ERp57) that inactivates TG2.  Normally, ERp57 is involved in the process of protein folding within the cell.  Furthermore, it has been established that ERp57 inactivates TG2 outside the cell within the extra-cellular environment.  These data suggest that the etiology of celiac disease may relate to the functionality of ERp57.

These findings are significant; for, a more detailed understanding of the biological chemistry of celiac disease may open avenues of therapy that have heretofore remained elusive. 

Saturday, February 17, 2018

Stem Cells and the Risk of Atherosclerotic Cardiovascular Disease

Atherosclerosis is a condition often associated with age that involves a narrowing of the lumen of the arteries usually associated with age (see image below).  This condition often leads to coronary heart disease.  Traditionally there are a number of risk factors that are generally associated with this syndrome – high blood pressure (hypertension), high cholesterol, heredity, life style, diet etc.  However, a significant percentage of those individuals that show evidence of atherosclerosis have no known risk factors.  Research done by Dr. Siddhartha Jaiswal and his colleagues that has been published in the New England Journal of Medicine (July, 2017) sheds significant light on the possible etiology of this perplexing reality.

Within the bone marrow, reside stem cells that are so-called, pluripotent cells; they are responsible for the production of the body’s complement of immune-competent cells such as red blood cells, white blood cells including lymphocytes, neutrophils etc.  It has been well documented that over the lifetime of the individual these stem cell undergo mutations that can lead to blood – hematopoietic – cancers such as leukemia.
According to Jaiswal, “Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of an expanded somatic blood-cell clone in persons without other hematologic abnormalities, is common among older persons and is associated with an increased risk of hematologic cancer.”

Jaiswal and his associates now have evidence that CHIP may be the underlying cause of atherosclerotic cardiovascular disease of no known etiology.  The results of their studies indicate that the presence of CHIP in the cell population of circulating blood was associated with a near doubling of the incidence of atherosclerotic cardiovascular disease.  Furthermore, the common mutations that were present in CHIP were found to be in the genes DNMT3A, TET2 AND ASXL1.  These genetic mutations have also been shown to be associated myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML).   These clones seem to be more prevalent with age – more that 10% of persons older than 70 years carry such a mutation.

This finding is significant in that it shed further light upon the etiology of atherosclerosis.

Tuesday, January 16, 2018

The Scientific Method

The scientific method is a proven way to find answers to questions regarding particular aspects of the natural world. It can be summarized in the following way –

• Question arises from known information – data
• Hypothesis proposed to explain data
• Experiment(s) conducted to prove or disprove the working hypothesis
• Experimental approach is precisely documented
• Results are reported
• Results are subject to peer-review.
• To be correct, the conclusion must explain all the data
• If correct, findings must be repeatable.

The following information is presented to highlight the theories that have been effectively discredited using the scientific method, the advances made through the application of the scientific method and the potential disasters that have been effectively averted through its application.

The Homunculus -There was a theory (proposed in the 16 century and popularized in the 19 century) that human sperm carried a miniature human (Homunculus) than subsequently developed into a fully developed infant at birth following fertilization

Image of Homunculus

 Image of an actual human spermatozoa showing DNA


The Martial Canals - Percival Lowell (1855 – 1916) proposed that there was intelligent life on Mars based upon sighting of purported Martian Canals

Image of Martian Canals as reported by Lowell

Image of Mars from space telemetry data

Spontaneous Generation – Theory that living organisms can arise spontaneously from decaying organic matter

Louis Pasteur’s (1822 1895) Classic Experiment that effectively refuted this belief.

The diagram below outlines his elegant approach

Earth’s Place in the Solar System – It was believed for many centuries that the earth was the center of the cosmos

Ptolemy’s (140 AD) Earth-Centric Model

Copernicus’ Model (1543) – Current Model

Ptolemy generated this convoluted model in attempting to fit the available astronomical data into the accepted belief that the earth was the center of the known universe.

HIV AIDS – In the early 1980’s a new, infectious and deadly disease appeared within human populations. In a just a few short years and with intense research efforts spear-headed by the Center for Disease Control (CDC), the cause was determined to be a so-called“retrovirus” (see diagrams below)– a discovery that ultimately averted a world-wide pandemic.

Image of an HIV virus

HIV AIDS Virus infecting human T-cell

George Washington’s Death (1799): An Example of Unscientific Medicine
His death was ultimately attributed to standard medical practice of that era. Washington came down with a respiratory infection. He underwent the following procedures via 3 different physicians –

• A half-pint of blood was extracted via leeches (see diagram below)

• Blisters were created on his throat to balance body fluids”
• Vinegar and sage tea mixtures were administered
• Emetics were given to induce vomiting.

The current understanding is that he died of iatrogenic causes – (caused by physician). His actual death was apparently caused by hypovolemic shock – a condition that occurs when more than 20% of the body’s fluid is lost. As a result, his heart was unable to pump sufficient blood volume to effectively deliver oxygen and nutriment to all the cells.
Rachel Carson – The Silent Spring (August 1972): The Inter-Connected Nature of the Natural World

In the 1950’s, DDT was sprayed to control beetles that are responsible for Dutch Elm Disease. Rachel Carson book documented the impact of DDT pesticide on natural environment especially on bird mortality. This book awakened the scientific community and the public to the ecological implications of human-caused environmental pollution. The Environmental Protection Agency was created in 1970 as a direct result of the growing concerns about the health of the natural environment.

Models of the DDT molecule

Ecological Implications –
• Earthworms ingest DDT from contaminated soil
• Robins (as an example) eat earthworms and concentrate DDT (biological magnification)
• DDT impacts shell production in the eggs – proves fatal to developing embryos
• DDT is an example of poly-chlorinated hydrocarbon (see diagrams above) that is fat
soluble with a long biological half-life.

DDT was ultimately banned for agricultural use – a policy that averted a catastrophic decline in bird populations due to DDT’s insidious effects.

Ozone Depletion - Ozone (O3) is a pollutant in the lower atmosphere. However, in the upper atmosphere, this molecule is vital for the filtering of dangerous UV radiation that normally bombards the earth. Holes in this protective layer was first report in 1985. As a result of intense scientific study, it was soon discovered that ozone was being destroyed by a by-product of a human-produced pollutant, chlorofluorocarbons (CFC - see diagram below). CFCs were once commonly used in refrigerants; until, they were banned in 1995. This ban ultimately helped replenish the ozone concentration in the upper atmosphere.

Diagram Illustrating this Process


The Examples cited above have been included in order to demonstrate the importance and relevance of science and the scientific method in everyday existence.

The End

Monday, January 8, 2018

The Bomb Cyclone

In the winter of 2018, the American Northeast was struck by fierce and extreme winter weather. This apparent weather anomaly was referred to as the “Bomb Cyclone.” It was characterized by a sudden and precipitous drop in barometric pressure accompanied by strong winds and cold arctic air.

Climate scientists have long predicted that accompanying the warming of the lower atomosphere and the oceans, one would expect an increase in the severity and frequency of extreme weather conditions...In a report found in the science section of Time magazine written by Bryan Walsh, the author suggests just such an explanation of this weather phenomenon.

"Sea ice is vanishing from the Arctic thanks to climate change, which leaves behind dark open ocean water, which absorbs more of the heat from the sun than reflective ice. That in turn is helping to cause the Arctic to warm faster than the rest of the planet, almost twice the global average. The jet stream—the belt of fast-flowing, westerly winds that essentially serves as the boundary between cold northern air and warmer southern air—is driven by temperature difference between the northerly latitudes and the tropical ones. Some scientists theorize that as that temperature difference narrows, it may weaken the jet stream, which in turns makes it more likely that cold Arctic air will escape the polar vortex and flow southward. Right now, an unusually large kink in the jet stream has that Arctic air flowing much further south than it usually would."

It should be kept in mind that this conclusion is preliminary: climate scientists would be first to admit that there is not enough accumulated data to unambiguously make this connection, However, numerous examples of extreme weather patterns have already been cited in the scientific literature.