Monday, August 15, 2016

Last Universal Common Ancestor

It has long been suspected that the progenitor of life on planet earth most likely came from the sea.  It has been proposed that the possible origins of life could have been in shallow pools or under more extreme conditions such as within deep-sea vents or proximal to active volcanoes.
The current domains of life consist of bacteria –prokaryotes, the archaea -found in deep sea vents and the eukaryotes that comprise all the animal and plant life on the planet.  It has also been proposed that the archaea and the bacteria preceded the more complex eukaryotic cell type.
William F. Martin, an evolutionary biologist, from Heinrich Heine University in Düsseldorf, Germany, focused his research efforts on finding the progenitor of archaea and bacteria.  To do this, the known genetic structure of members of the archaea and bacteria domains were extensively examined.  This involved the examination of some six million genes representing thousands of microbes.
From these data, Martin and his colleagues were able to construct evolutionary family trees and were able to deduce that 355 gene families originated from single cell bacteria-like organism.  That organism is referred to as the Last Universal Common Ancestor (LUCA).  Furthermore, it is believed that LUCA lived some four billion years ago when the young earth was barely 500 million years old.
If this conclusion is correct, it clearly proposes that life began very early in the evolution of the planet earth and that the evolution of life was a much longer process than previously envisioned.

Wednesday, July 13, 2016

Myelodysplastic Syndromes (MDS)

Myelodysplastic syndromes (MDS) represent a disease state that has its origin in the bone marrow.  Within the bone marrow are resident stem cells that are the progenitors of the circulating white and red cells and platelets that play vital roles in immune function (white cells), oxygenation of the tissues (red cells) and the ability of blood to clot as the result of trauma (platelets) - see diagram below.  The wide range of types of human leukemia are cancers of these progenitor stem cells.

In the case of MDS, these stems fail to mature and produce cells that are referred to as blasts and so-called dysplastic cells.  As a result, the number of mature stem cells are diminished in number; a state that results in diminished numbers of circulating white (neutropenia) and red cells (anemia) and platelets (thrombocytopenia).  It is this diminished cell count that produces the symptoms associated with MDS.  These symptoms may include –
·         Fatigue
·         Weakness
·         Easy bruising or bleeding
·         Fever
·         Bone pain
·         Shortness of breath
·         Frequent infections.

There are also cases in which the overall cell counts appear normal, but the circulating cells are abnormal.  Chromosomal abnormalities have also been found associated with MDS.  What makes MDS particularly significant from a human health perspective, is that certain subtypes of MDS have been shown to be a precursor to acute myeloid leukemia (AML) – a particularly aggressive form of leukemia

From the perspective of scientific research, the question that remains to be answered is what are the cause(s) of MDS.  This question has been and continues to be the focus of a concerted and intense collaborative effort.

Monday, June 6, 2016

A Very Promising Treatment for Patients with Glioblastoma

Glioblastoma is an exceedingly aggressive cancer of the brain that usually leads to death within months of its initial diagnosis. However, in clinical trials conducted by Drs Gordana Vlahovic and Matthias Gromeier at the Preston Robert Tisch Brain Tumor Center at Duke University in Durham, NC, amazing results have been achieved in patients with this disease using a human-engineered polio virus that has been stripped of its ability to cause disease. This modified virus with the ability to kill cancer cells (oncolytic) is referred to as PVS-RIPO (see illustration below). The results to-date have been so impressive, that the Federal Drug Administration (FDA) has accelerated the approval process for its use in clinical settings opening up its application to perhaps hundreds of patients who would otherwise face a grim future.


PVS-RIPO was engineered by removing the genes that are responsible for causing the neuronal damage that produces the deleterious effects of polio in humans and added in its place a portion of the genetic code of the ubiquitous cold-causing rhinovirus.

The rationale for this approach is multi-faceted. The polio virus has a natural receptor that can attach to many different forms of cancer. This receptor binds to CD155. CD155 is a cell surface glycoprotein that spans the outer cell membrane (transmembrane). It is often referred to as the Poliovirus Receptor (PVR). It has been established that CD155 plays a role in the establishment of intercellular junctions between epithelial cells. It seems that CD155 is over-expressed and abundant in various kinds of cancers including glioblastoma and pancreatic cancer.  The strategy employed was to use PVS-RIPO to preferentially infect the patient's cancerous glioblastoma cells.

In the case of the patients involved in clinical trials suffering advanced stages of glioblastoma as mentioned above, PVS-RIPO was infused directly into the tumor in order to maximize exposure to the virus. It seems that the amazing success of this treatment is due not only to successful infection with PVS-RIPO but also the subsequent mobilization of the immune system against the cancer cells.

This approach to treating advanced glioblastoma may ultimately extend to the treatment of other intractable cancers such as pancreatic cancer. This is an exceedingly exciting development that may have broad application in the treatment of and ultimate cure of cancer.

Thursday, May 26, 2016

Origin of Life on Planet Earth

A question that has plagued scientists for a long time is centered around the question as to how life began on planet earth.  It is well known that life is found even under the most inhospitable conditions – a stunning example of this is that life exists within the deep sea hydrothermal vents that are found on the ocean floor.  In addition, microorganisms such as Hormoconis resinae contaminate jet fuel – using this hydrocarbon source as a vital nutrient – and are known to cause corrosion in the tanks that hold this fuel.

Therefore, it can be reasonably postulated that simple life forms could thrive in the harsh conditions of prebiotic earth when oxygen was not present within the atmosphere at that time.  But the question remains as to how did life begin – what was the process by which self-sustaining living organisms were formed from rudimentary compounds.

It has been shown that in an artificial environment created in the laboratory  in which an atmospheric environment was created to simulate the conditions believed to have existed in the prebiotic world, the addition of an energy source – such as lightening – produced rudimentary organic compounds found in living cells.  These experiments were conducted in the 1950's, by the biochemists Stanley Miller and Harold Urey.  These results are only suggestive evidence that organic compounds could have been created spontaneously in the early-earth environment.  It is, of course, far from the complete story.

Since DNA and RNA are fundamental ingredients to all of life as we know it and capable of self-replication, a key step in the evolution of life would be the conversion of simple organic compounds to purines that are some of the important building blocks for both DNA and RNA and for the synthesis of Adenosine Triphosphate (ATP) – the molecule that is responsible for trapping energy derived from metabolism for all of life.

Furthermore, the preponderance of evidence now suggests that RNA may have preceded DNA as the repository of genetic information capable of self-replication.  Certain forms of RNA also demonstrate catalytic properties (ribozymes) that are essential to sustain life.  Of course, contemporary advanced cell structure uses a host of enzymes to accomplish essential catalytic functions.
RNA is made of four different nucleobases  -two pyrimidines – cytosine and uracil – and two purines adenine and guanine.  Previous work done by John D. Sutherland from the School of Chemistry, University of Manchester, UK has shown a plausible synthetic route to pyrimidines in an abiotic environment.  But the route to purines has been more elusive.

Recent work by T. Carell from the Department of Chemistry, Ludwig-Maximilians University Munich, Germany and fellow investigators has recently demonstrated a mechanism that could account for spontaneous creation of purines from simpler compounds readily available within the natural environment of early earth.  The pathway involves the spontaneous synthesis of aminopyrimidines from hydrogen, cyanide and water – compounds readily available in the early earth environment.  Although aminopyrimidines can produce a wide range of synthetic products, in an environment of formic acid, the predominant product is formamidopyrimidine (FaPy) known to readily produce purines.  Furthermore, formic acid has been shown to be present in comets that collided frequently with earth during the early stages of its evolution.


Although this work is very significant, it does not explain how purines and pyrimidines would lead to the creation of more complex and sophisticated RNA molecules.  Nor does it shed any real light on the requisite formation of a cellular environment for biosynthetic reactions so necessary for the containment and sustenance of life processes.

Wednesday, May 4, 2016

Successful Treatment of B-Cell ALL Using Adoptive Cell Transfer

The standard treatment of cancer patients has consisted of an approach involving some combination of surgery, chemotherapy and radiation.  Admittedly, these methodologies have grown sophisticated over the years especially in the areas of surgery and radiation.  However, chemotherapy is a “shotgun approach” employing powerful drugs that target any dividing cells.  The nature of these drugs cause significant side-effects in the patients that they are administered to.

There are a new family of drugs that have been developed to combat certain types of cancers that are more highly targeted.  Among these are Imatinib Mesylate – Gleevic –(see illustration below).  Gleevic has been used in the treatment of acute lymphoblastic leukemia (ALL) and gastrointestinal stromal tumor.  This drug specifically targets the enzyme tyrosine kinase that has been implicated in certain cancers. 


Another drug that has shown promise in trastuzmab – Herceptin (see illustration below).  Herceptin has been used to treat patients with HER2+ breast cancer and adenocarcinoma of the stomach, for example.  Herceptin is a monoclonal antibody (mAb) that targets the HER2 protein found on certain types of cancer cells.


The new approach to fighting certain types of cancers involves a methodology referred to as adoptive cell transfer (ACT).  ACT actually employs the patient’s own immune system in fighting the cancer cells.  Impressive results using this methodology has been shown in clinical trials involving patients with advanced B-cell ALL.

The cancerous B-cells in ALL have a protein on their cell surface that is referred to as CD19.  This protein makes an appropriate target for immunotherapy.  The rationale behind ACT is to utilize the patient’s own T-cells to selectively kill ALL B-cells bearing this marker.  The following steps have been successfully employed in this treatment –

  • CD4 and CD8 lymphocytes are harvested from the patient’s blood.  CD4 T-cells are so-called helper cells and the CD8 T-cells are the cytotoxic cells.
  • These cells are genetically modified using an engineered retrovirus.  The genetic information that is introduced results in the production of a protein referred to as a chimeric antigen receptor (CAR) that binds to a specific cancer cell surface protein (see illustration below).  Structurally, CARS are modified mAbs.  In the case of ALL, the target protein is CD19.
  • Once the patient’s CD4 and CD8 lymphocytes have been successfully modified in the laboratory, they are grown out into billions of cells.  These are the cells that are reintroduced into the patient via infusion.  

CAR Signaling

There is one significant side effect from this approach; it is referred to as cytokine release syndrome that is a direct result of the modified T cells actively involved in killing their cancerous targets.  However, this is a manageable condition.

The results to date in clinical trials have been extraordinary.  This methodology shows great promise that eventually may have broader applications in the treatment of cancer.

Thursday, April 7, 2016

New Danger Posed by the Increasing Abuse of the Opioid Drug - Fentanyl

Opioids are a class of compounds that relieve pain by binding to opioid receptors found on neurons that send signals to the brain that the brain interprets as pain; this binding results in a significant reduction in these signals.  In addition, opioids also bind to analogous receptors within the brain that reduces the emotional response to painful stimuli.
According to the National Institute of Drug Abuse, “Medications that fall within this class (opioids) include hydrocodone (e.g., Vicodin), oxycodone (e.g., OxyContin, Percocet), morphine (e.g., Kadian, Avinza), codeine, and related drugs. Hydrocodone products are the most commonly prescribed for a variety of painful conditions, including dental and injury-related pain. Morphine is often used before and after surgical procedures to alleviate severe pain. Codeine, on the other hand, is often prescribed for mild pain. In addition to their pain-relieving properties, some of these drugs—codeine and diphenoxylate (Lomotil) for example—can be used to relieve coughs and severe diarrhea.”

These receptors pre-exist in nature for they bind to certain endogenous opioids such as dynorphins, enkephalins and endorphins.  The structures of morphine and an endorphin are shown below



Opioids are readily found in nature and, as such, have been used to relieve for thousands of years within human populations.  Biochemically, opioids receptors (see illustration below) that are imbedded in the outer cell membranes of target cells are G-protein coupled, and activate inhibitory G-proteins. Once bound to the appropriate receptor, they trigger a series of cascading chemical events within the cell resulting in the suppression of neuronal signaling.

Opioid Receptor

Although opioids play a very important role in modern medicine for the relief of acute pain, there is an alarming rise of abuse of these substances especially since they are highly addictive.  Of special concern is the increased street-use of a very potent opioid – fentanyl (see structure below)
Fentanyl is, often used in anesthesia to prevent pain after surgery or other procedures.  According to DEA administrator Miechele M. Leonhard "Drug incidents and overdoses related to fentanyl are occurring at an alarming rate throughout the United States and represent a significant threat to public health and safety."

"Often laced in heroin, fentanyl and fentanyl analogues produced in illicit, clandestine labs are up to 100 times more powerful than morphine and 30 to 50 times more powerful than heroin," she added.  In addition, the DEA has noted that, “ingestion of even small doses ― as small as 0.25 mg ― can be fatal. Its euphoric effects are indistinguishable from those of morphine or heroin.”

Of additional concern is the fact that fentanyl can be absorbed directly through the skin, or unknowingly inhaled as an airborne powder; this is especially of critical importance for law enforcement personnel.  Another cause for concern is that fentanyl - like other compounds in the opioid class - can be readily synthesized. In an appropriately equipped laboratory.

The abuse of opioid substances, especially fentanyl is a very real, immediate and important public health issue and deserves the attention of not only government agencies but concerned citizens.  Rather than focusing on criminal punishment of offenders, greater emphasis and resources should be brought to bear on drug rehabilitation and education as a way to help prevent such abuse from happening in the first place.

Monday, April 4, 2016

Creation of a Synthetic Organism with the Smallest Complement of Genes

The tools available to molecular biologists especially in regard to gene sequencing and assembly allow investigators to produce nucleotide sequences that incorporate specific genes and gene clusters into DNA created in-situ.  A team of investigators headed by Craig Venter from the J. Craig Venter Institute in La Jolla California in effect created a microorganism containing 473 genes (Syn 3.0).  The purpose of this investigation was to determine the minimal amount of genetic material required to sustain life as an autonomous organism and successfully reproduce. 

In 2010, Venter and his colleagues created an entire chromosome from the bacterium, Mycoplasma mycoides (this organism has only one chromosome) and demonstrated that this synthetic chromosome was completely functional.  They did this by stripping out the naturally occurring DNA from the mycoplasma, M. capricolum and replacing it with the synthetic chromosome.  The modified organism was called Syn 1.0 and with its complement of 901 genes was shown to be completely viable and capable of reproduction.

With this material in hand, the investigative group sought to assemble Syn 3.0 by methodically whittling down the DNA in Syn 1.0 to the smallest number of genes required to sustain life. The result of this painstaking work was Syn 3.0

What makes this current result so remarkable is that this organism is entirely new.  Of the 473 genes, 149 (31.5%) are of unknown function; therefore, additional work will focus on the discovery of the function of these apparently essential genes.  Syn 3.0 may prove to be an invaluable tool in understanding the evolution of life on planet earth.