Tuesday, December 15, 2015

The Role of ADAR in Mammalian Development

Adenosine deaminase enzymes that act upon RNA (ADAR) have been shown to play a critical role in mammalian development.  ADAR is responsible for the conversion of adenosine to inosine in double-stranded RNA (dsRNA).




Literally hundreds of thousands of these transforming events have been reported within human cells.  This editing appears to occur predominantly in noncoding repetitive elements within the genome.  Additionally, there are three forms of ADAR that have been identified – ADAR1, ADAR2 and ADAR3.  They seem to be widely expressed during early development especially in the embryonic and post-natal development period.  To date, of the three forms of ADAR, only ADAR1 and ADAR2 have been shown to demonstrate enzymatic activity on natural substrates in vitro.

Using the mouse animal model, ADAR2 has been shown to modify an essential receptor in the brain.  Experimental animals who die from seizures have successfully rescued when a genomic substitution mimicked the adenosine to inosine modification of the RNA transcript.  This result proved to be an elegant demonstration of the mode of action of ADAR2 in vivo.

The role of ADAR1 within the living organism remained unknown.  This prompted Dr. Brian J. Liddicoat and his colleagues from the Department of Medicine at St. Vincent’s Hospital University of Melbourne, Australia to engage in an elaborate experimental investigation to uncover its role.

The results of their extensive efforts demonstrated that, “The A-to-I editing of ADAR1 is essential for embryonic development and the maintenance of hematopoiesis in vivo.”  Hematopoiesis refers to the production of viable circulating blood cells.

This is an important finding and is a significant contribution to the overall understanding of the complexities and intricacies of mammalian development.

Wednesday, December 2, 2015

Climate Change Revisited

Despite the anti-science rhetoric that seems to have broad representation in the US Congress, climate change is a very real phenomenon that if unchecked will put the world's people in peril. If our collective behavior in regards to burning of fossil fuels continues unabated it will necessarily have a dramatic impart on peace and security in the world populated by future generations of human beings. The question we must pose to ourselves is, "Is this the legacy we want to leave behind?"

An example of what the future may have in store is what changes are occurring in the lives of the peoples of the Marshall Islands.

Sunday, November 15, 2015

Somatic Mutation and Cancer

Cancer is a disease that can involve any tissue in the human body.  Some cancers, of course, are more common than others such as lung cancer, colon cancer, breast cancer in women and prostate cancer in men.  What all cancers share in common is that the tissue cell involved undergoes a transformation that imparts a selective advantage to that cell allowing it divide outside the normal controls imposed upon that particular cell type.  This process is known as clonal expansion.

It is now clearly understood that this selective advantage is a direct result of somatic mutation of the affected cell’s genetic material – DNA.  This causal relationship was first suspected in 1914 when it was observed that chromosomal abnormalities were present in cancer cells.  Note that this discovery was made even before DNA was known to be substance responsible for carrying hereditary information.    Considerably later, it was found that introducing DNA fragments from a malignant cell into a healthy one led to transformation of the recipient cell into a cancerous one.  Soon after this finding, oncogenes were discovered.  Oncogenes are the result of mutations in a class of genes responsible for cell growth or its modulation as is the case with tumor suppressor genes.

In nature, somatic mutations are common and are harmless for the most part – they do not generally impact genes that are involved in cellular process that would impart a selective advantage to the cell type affected.  These innocuous changes are referred to as “passenger mutations.”  Those rare mutations that do provide a selective advantage to the affected cell are referred to as “driver mutations.”  Ii is this type of mutation chat can lead to cancer – the production of a clone of cells that has the capacity to function autonomously and thereby no longer constrained by the controls normally imposed upon cells of a particular tissue.

Although this evolution of a cell from a normal state to one that is cancerous has been understood in general terms, the underlying process has not been amenable to discovery until the advent of high-throughput DNA sequencing. 

Utilizing this technology, the cancer-associated genes from over 10,000 human subjects have been sequenced along with over 2500 complete genomes from cancerous tissue samples.  Dr. Inigo Marincorena and associate from the Wellcome Trust Sanger Institute in Cambridge, UK have reviewed some of the result obtained from this data.

From this extensive study, new cancer genes have been discovered as well as new kinds of mutational events.    Mutations occur as a result of a number of possible factors.  These include:
  • DNA replication errors
  • DNA damage that is subsequently incorrectly repaired by the normal DNA repair machinery or damage that is left unrepaired
  • DNA damage that is a result of exogenous factors such as mutagens, ultraviolet light and ionizing radiation
  • DNA damage that is a result of endogenous factors such as reactive oxygen species (free radicals), aldehydes or mitotic errors
  • Viruses and endogenous retrotransposons that lead to insertions into the genome.

It seems that the frequency of mutations found in various cancerous cell types vary depending upon the tissue involved.  For example, pediatric brain tumors and various types of leukemia have the lowest numbers of mutations whereas lung and skin cancers show the highest rates.  Furthermore these mutation rates can be greatly enhance if there is definitive loss of DNA repair pathways.

One of the conclusions drawn from the extensive genomic data derived from these studies is that more than one driver mutation is required in order for a clone originating from a transformed cell to successfully evolve into the fully cancerous state with the capability of metastasis.

This report represents a brief and limited overview of the extensive of this work and its significance.  It is fair to say, that future studies of this magnitude will shed greater light on the complex processes that are involved in cellular transformation and oncogenesis.

Thursday, November 5, 2015

Climate Change – An Urgent Call to Action

Humanity does not seem to grasp the dim future that awaits the entire species if the dire warnings issued by climate scientists worldwide are not heeded regarding the absolute necessity to significantly diminish the burning of fossil fuels and thereby slow down the inexorable increase of the concentration of greenhouse gases in the atmosphere.

Ironically, human families work diligently towards fashioning a better life for their children, grandchildren and future descendants, yet their focus has been tilted towards material success and enhanced prosperity.  These are important goals.  However, if this onward rush towards greater and greater prosperity is not tempered by reality, the insidious consequences of climate change will make a significant portion of the planet essentially uninhabitable and rising seas will inundate the habitats of hundreds of millions of human populations wreaking havoc upon centers of economic power where great stores of human wealth reside.  Under such circumstances, such wealth would immediately be rendered quite meaningless.

It is quite absurd at this juncture to argue the merits of the science or allow short-term economic interests to resist the necessity for immediate and significant action.  If we do not act quickly as a world community, our descendants will find themselves marooned on what would increasingly become a hostile planet.  Is this the kind of future we are working so assiduously towards?

Obfuscation and resistance serves no useful purpose – the longer we procrastinate the more impossible it will be to make meaningful corrections on this our spaceship earth.

Tuesday, October 6, 2015

Use of Genetically Modified Yeast in the Production of Opiates

Opiates are pain-relieving drugs that play a vital role in palliative care.  Morphine is a well-known member of this class of compounds.  Opiates have been derived from poppy plants for thousands of years.  The compound thebaine (paramorphine or codeine methyl enol ether) - see structure below -is the natural product that is the precursor for opiates.


Due to the incredible strides that have been made in regards to genetic engineering, a team of researchers headed by Christina Smolke from Stanford University in Palo Alto California has successfully incorporated genes derived from a variety of plants including poppies, bacterial genes from Pseudomonas and rodent genes into the yeast genome and endowed these modified yeast organisms with the capacity to produce thebaine from a sugar source.  This methodology required the successful incorporation of 21 different genes – a monumental enterprise.

This is a significant breakthrough in the area of synthetic biology for it suggests that eventually it will become possible to readily produce large quantities of thebaine that can subsequently be used to produce a variety of opiates.  Smolke and her colleagues avoided producing a modified yeast cell capable of producing morphine directly from sugar in order to forestall the possibility of inadvertently making the illicit production of morphine a practical reality.

Friday, October 2, 2015

The Role of Neutrophils in Guiding the Immune Response to Infection by the Influenza Virus

The influenza is virus has a global impact on human populations. Much research effort has been directed towards understanding how the human immune system combats influenza virus infection. The cellular target of this virus is the epithelial cells of the respiratory tract. In order for the immune system to successfully combat this pathogen, virus specific cytotoxic CD8+ circulating lymphocytes must migrate to the site of infection.

 It has been established that in order for these cytotoxic CD8+ lymphocytes to successfully kill virally-infected cells, it must be preceded by the innate immune response. A key player in this first response are Neutrophils (see image below) These cells are generally the first cell type to cross the blood vessel epithelium into the distressed tissue and are responsible for generating chemical signals that alert different types of immune cells.

 Although this relationship between Neutrophils and aspects of the adaptive immune response has been established, the underlying molecular mechanisms have been unclear. Dr. Kihong Lim and his colleagues at the Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY have investigated the mechanism of this immune response to infection by the influenza virus. What they uncovered was an interesting process.

Their studies have shown that the subset of cytotoxic CD8+ lymphocytes specific for influenza infected epithelium cells is dependent upon the presence of Neutrophils at the site of infection. The migrating Neutrophils leave in their wake a chemical trail; that chemical is a particular chemokine – a class of substances that serves as a powerful attractant to circulating lymphocytes – CXCL12. It is this CXCL12 that is a necessary requirement for the procurement of virus specific CD8+ lymphocytes at the infection site and for their subsequent ability to kill infected respiratory epithelial cells.

The results of this work contribute significantly to the fundamental understanding of the complex interactions that are required to mount a successful immunological assault upon a virus-induced infection.

Thursday, September 24, 2015

Progress in Developing a Vaccine against the Ebola Virus

Progress in Developing a Vaccine against the Ebola Virus
The recent spread of hemorrhagic fever (EHF) in areas of West Africa including Guinea, Sierra Leone and Liberia has placed considerable urgency on the need to develop an effective vaccine against the pathogen responsible for this horrific and highly contagious disease, the Ebola virus (EBOV).  To date, of the approximately 27,200 reported cases, there have been more than 11,100 deaths – a mortality rate of  40.8 percent.   EBOV is so infectious that a high incidence rate has also been reported among health care workers.  It needs to be kept in mind that the health care infrastructure of the countries affected has been severely compromised especially since these so-called, “low resource” countries have budgets inadequate to respond effectively to this challenge.

By way of background EBOV belongs to a class of viruses called filoviruses.   Filoviruses are single-stranded RNA viruses.  This class of viruses possesses a glycoprotein (GP) on its surface that could conceivably make a good candidate as an immunogen – a protein capable of eliciting an immune response.

Dr. Andrea Marzi at the Laboratory of Virology, Division of Intramural Research at the National Institute of Allergy and Infectious Diseases  at the National Institutes of Health in Hamilton Montana.and his colleagues  have helped develop a strategy for developing such a vaccine.  The strategy they employed can be outlined in the following way –
  • A live attenuated stomatitis virus was employed as a viral vector
  • Recombinant technology was employed to modify this virus so that it expresses the Ebola GP on its surface referred to as Viral Stomatitis Vector EBOV (VSV-EBOV)
  • This viral vector was then introduced into experimental animals – the rodent and macaque.

This approach was shown to be highly efficacious in both pre and post exposure vaccinations.  These results were so promising that phase 1 clinical trials in humans  were begun in several  worldwide locations. 

The following is in the author’s own words – “Complete and partial protection was achieved with a single dose given as late as 7 and 3 days before challenge, respectively.  This indicates that VSV-EBOV may protect humans against EBOV infections in West Africa with relatively short time to immunity, promoting its use for immediate public health responses.”

Wednesday, September 2, 2015

Tumor Suppressor p53 and the Clearance of Apoptotic Cells

Within the human body, with its complex array of highly differentiated organs and tissues, it is estimated that more than a billion cells die each day.  Most of these deaths arise from a natural process referred to as apoptosis – programmed cell death.  Since apoptosis is integral to the functioning of a healthy organism, its mechanism has been the focus of study for many years. 

In addition to the process of apoptosis, there also exists a mechanism for the efficient processing and clearance of the cellular debris that is a direct result of apoptosis.  Otherwise, the accumulation of released substances from dead cells could function as autoantigens and elicit an undesirable immune response against normal tissue resulting in autoimmune diseases.  In addition, chronic inflammation and developmental abnormalities could result from the buildup up cellular debris.  It has been established that the immune response to apoptotic cells involves the mobilization of phagocytic cells whose function is to engulf the dead or dying cells.  This process necessarily requires the expression of immune tolerance in order to prevent an autoimmune response.

The tumor suppressor  p53 protein has long been associated with the mechanism of apoptosis.  However, little has been established in regards to the putative role of p53 in the clearance of cellular debris that results from apoptosis.

Dr. Kyoung Wan Yoon and his colleagues from the Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA have focused their research efforts on the elucidation of the role of p53 in the clearance of post apoptotic cells and the establishment of tolerance to self-antigens.

What they have shown is the following.  As a result of stress upon a cell that leads to p53-mediated apoptosis, p53 triggers the production of a protein product from the so-called “Death Domain1a (DD1a)” gene.  DD1a functions as a ligand that is instrumental in the binding of the apoptotic cell to the phagocytic immune cell that will eventually engulf the dead cell.  Once this engulfment occurs it subsequently triggers the binding of an inhibitory T cell that ensures tolerance to self-antigens; thereby, preventing untoward reactions that could lead to a disease state.

This kind of work is extremely valuable in furthering the understanding of the mechanism of self-tolerance.  Such knowledge may prove instrumental in determining the underlying mechanisms involved in auto-immune disease.

Thursday, August 13, 2015

HIV-1 Vaccine Development

It has been over thirty years since the discovery of HIV-1 as the virus responsible for AIDS.  It has been a long-standing goal to produce a vaccine able to induce cross-reactive antibodies that are capable of neutralizing the infectious capability of the HIV-1 virus in all its variant forms.  Progress in this direction has been impeded due to the complexity of the surface envelope glycoprotein (ENV) – a glycoprotein is a class of proteins containing carbohydrate moieties.  ENV is responsible for the process that allows the entry of the HIV-1 virus into its host cell (CD4+ T Helper cells).

ENV is trimer consisting of three glycoproteins with a molecular weight of 160K.  This trimer is split into a 120K surface component and a 41K membrane component.  Together they constitute a moiety that facilitates the entry of the virus into the host cell called the viral spike.  Although the components of the viral spike have long been considered candidates for a vaccine, it has been elusive.  In addition, the viral genes for these components have been discovered and used in vaccine production; this approach has also been shown to be unsatisfactory.  The reason for this failure seems to reside in the fact that many of the regions of the molecular structure of the ENV subunits that are candidates for eliciting a significant immune response lie buried in areas that are effectively hidden from immune-surveillance.

As a consequence, investigators have proposed using the entire ENV trimer as an immunogen – a substance capable of stimulating the immune system to produce humoral antibodies against it.  Unfortunately, the stability of ENV outside the environment of the viral membrane rapidly degrades.  However, this intrinsic difficult has been effectively sidestepped by R.W Sanders and associates (Science 349, aac4223(2015)).  They overcame this obstacle by engineering a molecule with covalent disulfide bonds that held the subunits together.  They subsequently used this modified ENV to immunize rabbits and monkeys.  Although it worked effectively against the same strain of virus from which the ENV was obtained, it was ineffective against heterologous strains of the deadly virus.

Although the problem of creating an effective vaccine against HIV-1 remains intractable, future efforts and innovative approaches similar to ones reported here may finally yield a viable solution.  Progress in science necessarily depends on all the work that has gone on before and the collaborative effort and energy of many. 

Thursday, July 30, 2015

The role of T cells in Establishing Self-Tolerance

The human immune system is a powerful system designed to protect the individual from the onslaught of deleterious microorganisms that populate the natural environment.  Since it is essential that immune-capable cells not attack the tissues of the host, mechanisms for self-tolerance are necessarily implemented early in development.   When this self-tolerance mechanism fails, the result is often expressed as an autoimmune disease.  An example of such an ailment is multiple sclerosis (MS) in which the immune systems produces antibodies against myelin – the proteins that provides insulation for the electrical impulses that travel through the peripheral nerves.

Given the important role that self-tolerance plays in human health, many research laboratories are involved in fully elucidating its mechanism.   It is well known that the thymus gland is the site where self-tolerance is established.    It has also been shown that the immune regulator protein Aire is an important factor in the establishment of immunological tolerance; it operates within a subset of thymic stromal cells and directs T cell selection.  Aire is a transcription factor expressed in the medulla of the thymus and controls the mechanism that prevents the immune system from attacking the body itself.  Individuals with the autoimmune disease polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) have been shown to have a mutation in the AIRE gene.

Since Aire seems to play such a fundamental role in the early development of immuno-tolerance, it would be of extreme interest to delineate the underlying molecular mechanism for this affect.  Dr. Siyoung Yang and his colleagues at the Division of Immunology in the Department of Microbiology and Immunobiology at Harvard Medical School in Boston have made some interesting discoveries in this regard.  They have reported that Aire promotes the creation of a distinct population of regulatory T cells – Foxp3+CD4+ - in the very early stage of development.   Furthermore, they found that these regulatory T cells persist into adulthood and play a pivotal role in self-tolerance.

This is very important that contributes significantly to the understanding immune-tolerance and this kind information may prove invaluable in the understanding and eventual treatment of autoimmune diseases.

Friday, July 10, 2015

Long Term Effects of Measles Infection on the Immune System

It is a well-established that contraction of measles has a lasting impact on the immune system predisposing the individuals affected to opportunistic infections.  The period of vulnerability was thought to last for months.  In fact, it has recently been shown that this deleterious impact on the host’s immune system can persist for over 2 to 3 years.  This is of particular concern to public health professionals especially in those parts of the world where the measles immunization regimen is poorly administered or in those regions where there is a complete lack of infrastructure for the delivery of health care.  Public health data shows that wherever mass measles immunizations are employed childhood mortality is lowered by 30 to 50% in so-called resource-poor countries and up to 90% for impoverished populations.

It has been of interest to determine the mechanistic explanation for this apparent lost in immune-competency in individuals infected by the measles virus.  The suspicion has been that measles infection results in the loss of the host’s immune system memory-cell population – a condition referred to as “immune amnesia.”

Dr. Michael J. Mina and his colleagues at the Department of Ecology and Evolutionary Biology at Princeton University, Princeton NJ were able to confirm through epidemiological data that, in fact, measles infection leads to the ablation of those T and B lymphocytes responsible for immunological memory thereby leaving patients susceptible to opportunistic infections.  Children in this group are particularly prone to increased mortality in this setting.

In addition, the data also unambiguously demonstrated the efficacy of measles vaccination in preventing potentially lethal opportunistic infections that would otherwise spread through susceptible populations impacted by uncontrolled measles infections.  These finding are of particular interest in terms of improving public health on a global basis.

Monday, June 8, 2015

Dermal Adipocytes Involved in the Immune Response against Staphylococcus Infections

There has been some evidence in the scientific literature that adipocytes – cells whose specialized function is the storage of fat – play an immunological role.  Since microbial infection immediately results in the rapid growth of the infectious agent, it is essential that the host tissue mount an immediate immunological defense.  Part of this innate defense involves the mobilization of host cells from the local environment such as epidermal cells, mast cells and locally resident leukocytes – white cells found in the peripheral blood circulation.  This line of defense is especially important during the lag phase before the recruitment of neutrophils and monocytes.  The production of antimicrobial peptides (AMPs) by locally available cells and leukocytes is critical during the initial stage of infection.

In an effort to further elucidate the mechanism of early immunological responses to infection, Dr. Ling-Juan Zhang and fellow researchers from the Division of Dermatology at the University of California in San Diego, examined in detail the initial stages of infection by Staphylococcus aureus - a microorganism responsible for serious skin and soft tissue infections that often results in systemic as well as local disease.  From these studies, they discovered some interesting findings.

What these investigators discovered, using the mouse animal model, was that increased cellular expansion of the subcutaneous adipose layer consisting of adipocytes accompanied infection with Staphylococcus aureus.   Furthermore, these adipocytes were responsible for the production of a potent AMP referred to as cathelicidin.  As further evidence that adipocytes had an immunological role in defending against infection, mice that possessed adipocytes that lacked the ability to produce cathelicidin were unable to inhibit bacterial infection.   Finally, it was also demonstrated that human adipocytes also were responsible for the production of cathelicidin.

Clarifying the role of adipocytes in the initial immunological response to infection is of great interest.  A full understanding of this mechanism may prove to be of immense therapeutic value in the treatment of infection by Staphylococcus aureus. 

Friday, May 22, 2015

The Role of Telomerase Activity in Urothelial Cancer

Telomerase is an enzyme whose activity within a cell leads to cell immortality due to repeated cell divisions.   The telomerase enzyme is highly active in embryonic cells and in stem cells where uninterrupted cell divisions are requisite for the role of these cells in the growth and development of the individual organism.    In addition, telomerase activity is a significant factor in cancer – its activity has been shown to be up-regulated in over 85% of cancers.  However, there is no detectable telomerase activity in most somatic – body – cells.  This lack of activity is due to the suppressed production of telomerase reverse transcriptase (TERT).  It has been suggested that mutations associated with TERT reactivation may be the, “most prevalent of all noncoding mutations in cancer.”

The question, of course, arises as to what is the cellular event that turns on telomerase activity in cancerous cells.  Due to exhaustive genetic analysis, there is evidence of point mutations in the TERT gene promoter in many cancer types including urothelial cancer (UC) – UC ranks five in the number of cancer cases reported in the Western world.  However, it remained unclear as to whether any of these mutations actually results in the reactivation of telomerase.

Dr. Sumit Borah from Howard Hughes Medical Institute at the University of Colorado BioFrontiers Institute in Boulder Colorado and collaborators from other institutions have done genetic studies on cell lines from 23 different UC patients.  They have clearly shown a correlation between these mutations and higher levels of TERT messenger – mRNA -, TERT protein and, most importantly, telomerase enzymatic activity.   Furthermore this group of investigators has established that elevated levels of TERT m-RNA expression is strongly associated with reduced survival in two independent UC patient studies.

These findings are highly significant; because they further elucidate the underlying genetic mechanisms that can transform a normal cell into a cancerous one. 

Thursday, May 14, 2015

How the Ebola Virus Gains Entry into its Target Cell

Many viruses that have been studied require a specific cell surface receptor in order to gain entry to their target cell(s).  To this date, no specific cell surface receptor has been identified for the Ebola virus.   The Ebola virus is responsible for a highly infectious disease referred to as hemorrhagic fever in humans.  However, important strides have been made in understanding the mechanism of Ebola virus infection.

Once the Ebola virus successfully binds specifically to its host cell, it is engulfed by a process known as micropinocytosis that encapsulates the virus in a cell organelle referred to as endosome – a membrane-bound vesicle.  While within this environment, the virus’ surface glycoproteins are cleaved through the action of a protease (an enzyme that degrades proteins).

The process by which the virus is ultimately released from the endosome into the intracellular environment remains to be completely characterized.  However Dr. Yasuteru Sakurai and his colleagues from the Texas Biomedical Research Institute in San Antonio Texas have elucidated an important step in this process.  Through exhaustive and painstaking studies they have shown that endosomal calcium channels – two-pore channels (TPCs) are necessary for the release of the Ebola virus from the endosome that holds it.

More importantly, from a therapeutic standpoint, the investigators used a number of research techniques to disrupt TPC function including gene knockout – where the gene responsible for the production of TPC protein is rendered dysfunctional  - and were able to effectively disrupt virus trafficking and, thereby, prevent infection.  Finally the use of Tetrandrine -  a calcium channel blocker possessing anti-inflammatory, immunologic and antiallergenic effects - inhibited infection of human macrophages; these cells have been shown to be the primary target of the Ebola virus in an in-vitro setting.

These are important findings for a number of reasons.  They demonstrate that TPC-related proteins play an essential role in the Ebola virus infection process.  In addition, their preliminary results using Tetrandrine illustrate how this information may be used to develop effective strategies against hemorrhagic fever. 

Wednesday, April 29, 2015

Revolutionary Advances in Genomic Engineering

The area of study encompassed by genomic engineering has made so many technological advances that the modification of genomes – including the human genome – has rapidly come within the reach of those adequately trained in the techniques and methodologies of molecular biology.

There have been two extraordinary technological advances in the field of molecular biology that have made the ability to modify specific genes a reality.  First of all, the complete sequencing of the human genome in 2003 has made it possible to identify the genes implicated in many cellular and disease processes.  Secondly, the use of cluster regularly interspaced short palindromic repeats (CRISPRs) together with Cas9 has made it possible to specifically engineer the modification of literally any targeted gene.   Cas genes code for proteins that are directly related to CRISPR activity.

The CRISPR-Cas9 system was discovered in prokaryotic cells, bacteria for example.  It has been shown that this system provides protection from foreign genetic elements such as plasmids and phages- phages are viruses that target prokaryotic cells - that often attack prokaryotic cells.  This system has been likened to acquired immunity found in more complex organisms such as human.

CRISPRs are found in approximately 40% of sequenced bacteria genomes.  CRISPRs are, in fact, composed of segments of prokaryotic DNA made up of short repetitions of base sequences followed by segments of so-called, "spacer DNA."   These spacer segments seem to result from the cell’s previous exposure to an invading organism and serve as a template for the production of RNA transcription products that interact with Cas gene – related proteins in a system designed to inactivate invading phages or plasmids.

Since 2013, the CRISPR-Cas9 system has been adapted for use in the specific editing of genes.  When a specifically engineered CRISPR-Cas9 system is introduced into a host mammalian cell such as human it can alter a target gene in a very specific way.  This was amply demonstrated when researches at MIT effectively used this approach to effectively cure mice of a rare genetic liver disorder.   

This is such a powerful technique carrying with it such profound implications for the future of genetic engineering that in January of 2015 a group of those scientists intimately associated with these studies met in Napa, California at the Innovative Genomics Initiative (IGI) Forum on Bioethics to discuss the scientific, medical, legal and ethical implications of their work.

Saturday, April 4, 2015

A Possible New Treatment Option for Patients with Acute Myeloid Leukemia (AML)

AML is the most common form of adult leukemia accounting for some twenty-five percent of adult patients with leukemia.  The standard protocol for treatment involves a shot-gun approach using non- selective chemotherapy to induce successful remission.   Although this clinical methodology has shown to be effective for most patients, other avenues of treatment are needed for those who prove refractory to the standard approach and to those patients who cannot endure high dose chemotherapy.

The biology of cancer cells has progressed dramatically since the complete sequencing of the human genome.  As a result, it has been clearly established that cancer is the result of genetic mutations that involve either/or those genes referred to as proto-oncogenes involved in normal cell division and tumor suppressor genes involved in the normal suppression of cell division The new era of cancer treatment involves the development of methodologies to specifically target these mutations either by developing specialized drugs to target these changes or mobilizing the immune system through targeted immunotherapy.

Dr. Anuradha Illendula and his colleagues from the Department of Molecular Physiology and Biological Physics at the University of Virginia in Charlottesville, using the mouse animal model,  have developed a small molecule referred to as AI-10-49 that effectively binds to a transcription factor subunit referred to as core bind factor β (CBFβ).

Molecular Structure of AI-10-49 -

These investigators were able to show that the use of A!-10-49 not only prolonged the survival of mice transplanted with leukemic cells without any observable toxic effects but was also able to inhibit the proliferation of a sub-type of human AML cells grown in culture.  These findings are of particular importance for this approach may serves as a model for development of drugs specifically targeting "uninhibited cell division resulting from genetically altered transcription factor function."

Saturday, March 7, 2015

Extreme Winter Weather in the Lower Latitudes and Warming of the Arctic Ocean

For the past two winters, the continental United States has experienced harsh weather conditions with unusual amounts of precipitation in the form of snow.  Meteorologists have established that arctic-born weather has been directed to the Northeastern, Midwestern and even Southeastern continental United States as a result of a shift in the direction, depth and pattern of the jet stream described as “wavy.”

Dr. Jennifer Francis, a climatologist, and her colleagues at Rutgers University in collaboration with Dr. Steven Vavrus from the University of Wisconsin at Madison have published data establishing a connection between warming in the Arctic Ocean and the extreme winter weather in the lower latitudes. 
Ordinarily sea ice exerts an influence on global temperature by its ability to reflect back solar radiation into space on account of its whiteness through what is referred to as the albedo effect.  However, as a result of the gradual warming of the planet due to the accumulation of greenhouse gases, the temperature in the Arctic has increased at twice the rate as the rest of the earth.   This increased temperature is accelerating the melting of Artic sea ice.  As this sea ice melts, it reduces the albedo effect and results in increased warming and therefore the further melting of sea ice.  This cycle of increased warming is referred to as negative feedback.
It seems that this warming trend in the Arctic has disrupted normal climate conditions in the following way - cold air that is usually contained within the Arctic region by so-called “polar vortex winds” has moved southward into the mid-latitudes as a result of the high pressure that is a direct consequence of the enhanced melting of the sea ice.   Accordingly, the lower latitudes have experienced unusually extreme winter weather.

If this explanation is proven to be correct for seasonal aberrations in weather in the lower latitudes, then these changes would suggest a permanent alteration in weather patterns for the regions impacted.

Saturday, February 28, 2015

The Frequency of Various Types of Cancers Explained

For more than a century, the medical world has known that certain kinds of cancers are far more prevalent than others.   The question, of course, that comes to mind is why is this so?  There has been much speculation concerning the answer to this important question.

Drs. Cristian Tomasetti and Bert Vogelstein form the Division of Biostatistics and Bioinformatics at the Department of Oncology at the Sidney Kimmel Cancer Center at John Hopkins University School of Medicine and the Department of Biostatistics at the John Hopkins Bloomberg School of Public Health in Baltimore MD conducted an exhaustive statistical analysis of patient data.  The following represents a summary of their results.

 The table below shows the relative lifetime risk of a number of different types of cancers.
Cancer by Tissue Type
Percentage of Lifetime Risk of Cancer
Brain and Nervous System
Pelvic Bone
Laryngeal Cartilage

Although some of these differences can be associated with certain risk factors such a smoking and alcohol use, ultraviolet light exposure and human papilloma virus (HPV) infection, such etiology only applies to specific populations.  In addition, environmental factors cannot explain the wide differences found in lifetime risks involving cancers of the alimentary tract – esophagus .51%, large intestine 4 82%, small intestine .20% and stomach .86%.
Interestingly, cancers of small intestine are three times less common than brain cancers even though the epithelial cells of the small intestine are far more exposed to environmentally dangerous substances than brain cells that are protected by the so-called blood –brain barrier.
Another factor that is often cited to explain differences in risk of various cancers is inherited genetic variation.  The statistical data shows, however, that this risk factor accounts for only between 5 and 10 percent of the etiology of cancer.

Therefore, there must be another cause that accounts for the wide variability shown in the table above.  The investigators went on to demonstrate that a very close correlation (81%) exists between the lifetime risk for a given cancer and the, “total number of divisions of the normal self-renewing cells (stem cells) maintaining the tissue’s homeostasis.”   From this perspective, it is the probability of sustaining deleterious random genetic mutations that transform a cell into a cancerous state that increases with the number of cell divisions of tissue-specific stem cells.

This may prove to be a very important finding in regards to understanding the etiology of cancer. 

Friday, February 13, 2015

A Promising New Class of Antibiotics

As mentioned in an earlier report, the current classes of antibiotics (See table below) being utilized to fight infection are no longer effective in regards to certain diseases, especially since many pathogenic organisms have developed an effective immunity against them. 

Classes of Antibiotics Currently in Use -

Mode of Action
Inhibits bacterial cell wall biosynthesis
Inhibits protein synthesis in Gram-negative bacteria  such as Streptomyces griseus
Inhibits protein synthesis in Gram-positive bacteria such as Streptococcus pneumoniae by preferentially binding to the  50S component of the bacterial ribosome
Inhbits protein synthesis by preferentially binding to the  30S component of the bacterial ribosome
Irreversibly binds to and inactivates key enzymes that maintain bacterial DNA

Note: Antibiotics are of no use in treating viral infections since the biology of the virus is markedly different than that of bacterial agents.

There is, however, some basis for renewed optimism in regard to this global public health concern.  Most antibiotics currently being utilized are natural products produced by cultured soil micro-organisms.  For varied reasons, some economic in nature, the synthetic production of antibiotics has been unable to adequately supply new and effective classes of antibiotics.  Uncultured bacteria, on the other hand, although large in number, have been an untapped resource for new antibiotics.

Dr  Losee Ling and his colleagues at the Novobiotic Team,  NovoBiotic Pharmaceuticals, LLC.  767C Concord Ave, Cambridge, MA have developed specific methodologies to grow uncultured organisms thereby opening up a vast new resource.  As a result of an exhausted screening of uncultured bacteria,  they discovered a new antibiotic that they have called teixobactin (see the structure below).

Teixobactin acts by inhibiting cell wall synthesis.  It  accomplishes this by binding to highly conserved constituents of the bacterial cell wall and, in this way, effectively interfering with cell wall synthesis resulting in bacterial cell death.  The investigators were able to demonstrate that no resistant strains were produced when teixobactin was used to undermine the growth of both Staphylococcus aureus and Mycobacterium tuberculosis- pathogens responsible for Staphylococcus infections and Tuberculosis, respectively .   According to Dr. Ling, “The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.”

This is a very exciting development in regards to global public health.

Wednesday, February 4, 2015

How Cells Overcome Oxidative Stress

At some point in the evolutionary past, living organisms began to use molecular oxygen in cellular respiratory metabolic pathways and therefore gained access to increased amounts of energy to support life.  This was especially important in the evolution of complex multi-cellular organisms.    Along with this new capability came the issue of dealing with the harmful by-products of oxidative respiration.  The most detrimental of these are reactive oxygen species (ROS) that are produced in the mitochondria – those organelles that generate most of the energy required for cellular processes within eukaryotic cells.

ROS can produce oxidative damage and have been shown to be involved in a number of serious human pathologies including Alzheimer’s, cancer, diabetes and Parkinson’s.  These reactive molecular species are also involved in cellular senescence and cell death.
In response to this threat - referred to as oxidative stress - cells have developed mechanisms designed to minimize the damage.   the ROS defense system localized in the mitochondria transforms highly reactive and potentially destructive superoxide anions (O2--)  to hydrogen peroxide (H2O2) that is subsequently broken down to water by ubiquitous peroxidase enzymes that use reduced glutathione (GSH) as their substrate.  Given the essential role that GSH plays in this mechanism, it is crucial that appropriate levels of this substance are maintained.   A key enzyme that is employed in providing high levels of GSH is the nicotinamide nucleotide transhydrogenase (TH) enzyme.

Dr. Leung and his colleagues at the Department of Integrative Structure and Computational Biology at the Scripps Research Institute in La Jolla CA studied the three dimensional structure of TH and elucidated its mechanism of action.  This kind of information is important in so far as it increases the overall understanding of how cells cope with oxidative stress.    

Thursday, January 8, 2015

The Role of Endogenous Retroviruses in B Cell Immune Response to Foreign Antigens

Over the course of evolution, retroviral infections have left remnants of their genetic footprint imprinted within the human genome.  This is believed to play such an important role in human biology that the collective genomes from viruses that innocuously inhabit the human body is referred to as the virome.

The virome is a part of the larger community of microbiota that shares a commensal or symbiotic relationship with the human body.   Important participants in this community are the gut microorganisms that collectively breakdown food, produce important nutrients, inhibit the growth of deleterious organisms and stimulate immune responses.

The immune reaction to an invasive organism typically results in the production of specific antibodies by circulating B cells in response to antigens presented by the offending organism.  There are two arms to B cell involvement – one involving T cell dependent (TD) processes and the other a T cell–independent (TI) response.   This latter response is elicited through the innate immune sensing pathways in antibody production through specific B cell receptor (BCR) cross-linking
Dr. Ming Zeng and his colleagues at the Center for the Genetics of Host Defense at the University of Texas Southwestern Medical Center in Dallas, Texas studied the involvement of endogenous retroviruses (ERV) in innate immune pathways.

In the course of their investigation, they exposed mice to protein molecules ordinarily found on the outer membranes of invasive bacteria and viruses.  These proteins are known to invoke the TI-mediated B cell response.   What they discovered was that immunization with these antigens resulted in the enhanced production of endogenous retrovirus (ERV) RNAs in the responding B cells.  Furthermore, this response apparently triggered a sustained reaction against the specific antigens through enhanced immunoglobulin M production.

These findings are of particular interest, for they offer further validation for the role of endogenous retroviruses in the immune response to invasive and deleterious microorganisms.  A well-functioning immune system is absolutely essential for the individual life of the organism and has been perfected during the evolution of life on the planet.