Biomedical Research and the Male Scientist

Mouse behavior in a study may depend greatly on the sex of the researcher.
Courtesy: http://www.allaboutvision.com/conditions/amd_news.htm

           Many scientific fields focus on disease studies in order to develop effective therapies. Before potential remedies are supplied to human subjects, their efficacy and safety must first be tested on animals. Mice have served as suitable subjects for new drugs and treatment options that may potentially alleviate or eradicate human disease; thus, an overwhelming majority of biomedical research projects utilize mice. In these studies, variables need to be considered in order to accurately assess whether the experimental group is truly responding to the administered treatment. Such variables may include the health of the mice, the time of day that the treatment is administered, and the treatment dosage.

            Nevertheless, there may be an additional factor that biomedical researchers are not considering: the sex of the researcher. A report in Nature Methods details this discovery. Jeffrey Mogil's lab specializes in projects relating to pain perception in mice at McGill University in Canada. Interestingly, Mogil noticed that something was amiss with the recent set of experiments done by his students.  A pain-inducing agent was injected into the hind paws of mice, and facial grimaces were measured post-treatment. However, mice showed a significant reduction in facial grimaces in the presence of male researchers compared to that of no researcher, and the number of facial grimaces was not affected by the presence of female researchers. It was hypothesized that the smell of males influence this trend because placing a male's shirt in close proximity to a cage was able to exert this same effect, and surprisingly, this effect was nullified by the placement of a female's shirt nearby. Upon further analysis, the scent of male researchers and males of other species increased the levels of corticosterone, a stress-related hormone, in the blood of mice. This revelation led Mogil's group to postulate that the male scent induces a stress response in mice, which can alter the outcome of administered treatments.

             Though the idea that mice behavior exhibits a sex bias can be comical, this possibility raises a number of concerns. For example, some people wonder whether all past biomedical experiments employing mice are now invalidated. This finding does not necessarily prove this notion for a number of reasons. First, this set of experiments was done solely to measure pain responses; this study does not address sex bias in other types of mouse studies, such as those involving drug responses. Also, some physical characteristics of mice are known to be dependent on genetic background. This means that a particular stimulus may elicit a different behavior in a mouse with brown coat color compared to one with black coat color. Mouse behavior may also exhibit a more pronounced sex bias in response to pain versus other stimuli. Furthermore, we are reminded that there are subtle aspects of scientific studies that may influence their outcome, and we should identify and consider these factors more heavily when evaluating the data of future experiments.

The Mysterious Y Chromosome

        One key difference distinguishes men from women: the Y chromosome. This name is a misnomer, since this chromosome resembles a chromosomal fragment rather than the letter Y. Despite the Y chromosome's small size, its biological function is essential to the survival of species. Several genes on this chromosome are important for initiating the development of male sex organs. For example, the SRY (Sex-determining factor Y) gene is responsible for stimulating the formation of testes during embryonic development.

         Questions surrounding the evolution of the Y chromosome have lingered in the minds of scientists since its discovery in 1905. It has been estimated that the Y chromosome lost 97% of its genes during the course of evolution, and researchers believe that there must be a reason why the remaining 3% of genes on the Y chromosome were retained. Until recently, it was unknown whether these genes possessed a selective advantage over the genes that were no longer present. A study in Nature has conducted rigorous genetic analysis of the Y chromosome to gain a better understanding of the genes that have weathered time. David Page's group at the Massachusetts Institute of Technology (MIT) found that the genes that have been shielded from decay are required to maintain proper levels of proteins essential for viability. In other words, loss of these genes on the Y chromosome would result in deficiencies for proteins involved in important biological processes, which can lead to the death of an organism. Thus, this research group concluded that genes found on the Y chromosome play a role in supporting basic cellular processes as well as determining male sex characteristics.

          This finding is intriguing because it sheds light on possible variables that might not be considered in human diseases and disorders. For instance, loss of the Y chromosome can result in developmental disorders such as Turner syndrome, in which an individual has one X chromosome but lacks another functional X or Y chromosome. These individuals appear to be female but often fail to develop mature ovaries, leading to decreased fertility. Turner syndrome also results in other maladies such as hearing loss, scoliosis, and short stature. It is possible that a deficiency in gene dosage due to the lack of an X or Y chromosome is responsible for sex-independent characteristics of this disease. Many of the genes on the Y chromosome are expressed throughout the body, so they will most likely function in capacities that are independent of male sex organs. Furthermore, future studies should investigate the various functions of these genes in male cells and how they contribute to supporting the lives of male organisms.

A human X chromosome (in red) and Y chromosome (in blue).
Courtesy: SPL, http://www.bbc.com/news/health-24991843

The Ferocity of Amoebae at the Microscopic Level

An amoeba (in green) is eating a human cell (in pink).
Courtesy: Katy Ralston; http://www.npr.org/blogs

        We've all heard the headlines detailing fateful encounters with a dreadful foe, the amoeba. An amoeba is a single-celled organism that can infect a host and cause serious illness, sometimes to the point of death. Amoeba infections tend to be rare, but their effects can be damaging. For example, Naegleria fowleri, an amoeba that is commonly found outdoors in untreated water, can infect humans through the nose. Remarkably, 90% of infected individuals are asymptomatic, but inflammation of the brain can develop in the few cases that do present symptoms. Scientists discovered that this amoeba secretes enzymes that digest brain tissue, which the amoeba then utilizes as sustenance.
         If this occurrence sounds like the makings of a horror film, this is just the tip of the iceberg. Another subtype of amoeba, called Entamoeba histolytica, populates the intestine upon infection and results in severe cases of food poisoning. The mechanism by which E. histolytica causes disease has remained unclear until now. A recent report in Nature describes the methods utilized by this amoeba to antagonize human cells. Dr. William Petri's group at the University of Virginia uncovered the devastating events by imaging E. histolytica activity under a microscope. To the groups' amazement, the amoeba chewed on human cells and regurgitated the cellular debris. Upon making this observation, Petri's group was perplexed. Why would the amoeba destroy human cells in this manner without digesting their material? Their hypothesis states that the amoeba is solely attempting to break through the intestinal wall, rather than consuming intestinal cells. With this revelation, Petri hopes new tactics can be developed to combat the cellular carnage that E. histolytica and similar amoebae  inflict.
        It is common to observe bacteria and other parasites exhibiting aggressive behavior toward each other, but to visualize an amoeba eating a human cell and merely spitting out the remnants evokes a different sense of fear. We like to consider ourselves near the top of the food chain, so to see a microscopic organism challenge that notion is difficult to accept. This story reminds us that vigilance is essential to remaining in good health. So don't forget to boil that water for your neti pot and remember to wash food items in clean water!
        
            

Fertilization Really Isn't Magic!

         The creation of a new life first requires the fusion of an egg with sperm. This initiates a cascade of events that drives the division of the newly fertilized egg. Though this phenomenon is considered to be a fundamental part of biology, there are many aspects of fertilization that are unknown. For example, the mechanism for sperm-egg partnering has been nebulous for many years. In 2006, a breakthrough was made in which a protein called Izumo1 was discovered on the surface of mouse sperm. Inoue and colleagues at Osaka University in Japan found that male mice lacking this protein were sterile. Interestingly, sperm lacking this protein were observed to bind to an unfertilized egg, but they were unable to undergo fusion. These results led the group to conclude that Izumo1 was necessary for sperm-egg recognition, but it also raised a new question surrounding the identity of Izumo1's binding partner on the surface of the egg.

         A new report in Nature has proposed an answer to this question. A study from Dr. Gavin Wright's laboratory at the Sanger Institute in Cambridge, England, have identified a protein on the surface of the egg called Juno. This protein binds to Izumo1, and it is essential for egg-sperm recognition since fertilization does not occur in female mice lacking this protein. An intriguing facet of this report is the disappearance of Juno protein from the egg surface after fertilization. This occurrence may be responsible for limiting eggs to one fertilization event since it takes place within forty minutes of fertilization. These findings led Wright's group to conclude that Juno is the long-lost partner of Izumo1, and the presence of these proteins in humans indicates that identical interactions occur during the inception of human life.

        Both these studies raise a new set of questions. How does binding of Izumo1 to Juno lead to the surface of the egg becoming more permeable? Which signaling events are taking place in the cell to remove Juno from the egg surface after fertilization? More work will have to be done to fully understand all events occurring during the fusion of egg and sperm. It will also be useful to determine whether a reduction of either protein in humans can serve as an underlying cause of infertility. Conversely, it may be possible that an increase in Juno protein on the egg surface can facilitate fertilization. It's a wonder that these protein-binding events spur the wonderful journey that we call life! 

A fertilized human egg after in-vitro fertilization.
Courtesy: Advanced Fertility Center of Chicago; http://www.advancedfertility.com/embryos.htm

Cancer Cells: The Epitome of Greed

         Regulatory networks exist within cells to control behaviors that may potentially become pathogenic, such as migration and division. When these systems are defective, cancer cells arise and wreak havoc in an organism.  Cancer cells have broken free of regulatory constraints to divide uncontrollably and compete with normal cells for nutrients, interfering with tissue function and leading to organ failure. Cancer cells are a unique challenge for treatment because they can evade detection by the immune system, and their elimination can have deleterious effects on neighboring normal cells.

         Over several decades, researchers have studied methods to halt cancer cell growth. One facet of cancer cell physiology was highlighted in the 1920s when Otto Warburg, a German biochemist, noticed that cancer cells consumed significantly more glucose than normal cells. In order for cells to carry out the processes required for life, they must consume and dissemble glucose in a series of steps to extract energy. Increased metabolism in cancer cells indicated to Warburg that the abnormal division rate of cancer cells was driven by their insatiable need for glucose. Fifty years later, attention shifted to genetic alterations that were conducive to cancer progression, and researchers at that time believed that Warburg's observation was a consequence rather than a causative agent of cancer.

         However, the spotlight has once again turned to the metabolic properties of cancer cells due to a recent discovery described in Nature. This report states that cancer cells are highly dependent on a mutation within the enzyme called isocitrate dehydrogenase 2, or IDH2. This enzyme is a component of the citric acid cycle, which facilitates the generation of adenosine triphosphate (ATP), the main energy source in cells. Mutations within this enzyme are significant because they are hypothesized to re-route the metabolic process by favoring a faster, less efficient method of producing ATP in cancer cells. In light of this result, a drug called AG-221 was developed to combat the activity of the abnormal version of IDH2 in cancer cells. Clinical trials for AG-221 have shown great promise in acute myeloid leukemia (AML) patients, raising the possibility that the reliance of cancer cells on particular metabolic pathways can provide drug targets for cancer treatment.

       Metabolism has become a hot topic in the realm of cancer biology because it is a feature of all cells. Every cell in the body must incorporate glucose for ATP production, but cancer cells take advantage of this process to support their constant growth and proliferation. The identification of compounds that block the utilization of alternative metabolic pathways in cancer cells can serve as an innovative method of combating cancer's devastating effects. Nonetheless, more research is needed to ensure that these compounds have a minimal effect on healthy tissue and that these compounds are not a short-term fix. Cancer cells notoriously accumulate additional genetic mutations to circumvent cancer therapies, and this has hampered the formulation of effective anti-cancer drugs. Despite the uncertainties that remain, this new finding sets the stage for a greater emphasis on differential requirements between cancer cells and their normal counterparts, which will increase our knowledge of the aberrations that surface when a normal cell becomes cancerous.

Leukemia cells take advantage of metabolic pathways to support their high division rate.
Courtesy: Charles Hess, MD and Lindsey Krstic, BA; University of Virginia 

Guess That Bacterium!

Salmonella, a potentially dangerous bacterium, is often associated with raw eggs.
Courtesy: Bill Marler, www.marlerblog.com

      Food poisoning is an unconvenient part of life. Though foods can be prepared with the proper guidelines, bacteria and viruses can sometimes evade these safeguards and cause illness upon ingestion. In the case that infections spread through a population, it is the Center for Disease Control and Prevention (CDC) that conducts investigations to identify the sources of foodborne illness.

      For potentially serious outbreaks, whole genome sequencing has recently been adopted to identify causative pathogens. Whole genome sequencing allows for the elucidation of all DNA sequences within an organism, and this method has been a useful tool for distinguishing organisms within a species. Recently, the CDC has embarked on a project to identify several strains of Listeria involved in outbreaks this year. This work will be carried out with whole exome sequencing, and this venture is exciting because Listeria strains responsible for these cases may be detected more accurately. The probability that two bacterial strains will be 100% genetically identical is extremely low; therefore, this testing option may distinguish pathogenic bacteria and viruses more effectively.

       If this project is successful, the CDC will have a robust protocol for identifying the sources of illness within the population. In addition to recognizing bacterial and viral agents efficiently, whole genome sequencing can illuminate the diversity that exists between strains and the mechanisms by which this diversity arose (e.g. genetic mutations). Though this prospect is a step forward in understanding the genetic landscape of pathogens, we should still enjoy that next burger safely!

   

The Publishing Predicament

        The postdoctoral fellow waits anxiously at his computer as time ticks away. His fifth year in the lab is quickly coming to an end, and he has worked tirelessly to produce a cohesive story from his research project of three years. It took a year to prepare the final manuscript, and he is waiting on the email containing the verdict of his last submission attempt. Unfortunately, the paper had already been rejected from four journals, and he is slowly losing hope of his work being published in a highly respected journal. He plans on applying for faculty positions in the fall, but he senses a long journey lies ahead because he lacks one thing: a publication in Cell, Science, or Nature.

        Unfortunately, this situation is not uncommon for those looking to gain tenure-track positions in academia or research scientist positions within industry. Universities and institutions scrutinize the number of publications a candidate has authored in addition to the journals in which those publications appear. As a general rule of thumb, a candidate must have at least one publication in Cell, Science, or Nature. These journals are considered to be elite since they often publicize the most novel and provocative findings. In line with this reputation, these journals are highly selective, often rejecting 90% of submissions.

         Though these three journals are highly respected by the scientific community, researchers know that every piece of scientific work must be evaluated for its merit. In the search for novel discoveries, journals sometimes overlook the scientific reasoning that accompanies the work, leading to errors and faulty logic that may derail the research of others in a particular field. This problem has recently been highlighted by Randy Schekman, one of two scientists recognized for the 2013 Nobel Prize in Physiology or Medicine. In an article for The Guardian, he suggested that researchers boycott submissions to Cell, Science, and Nature and instead publish in open-access journals. Though the journals try to provide the scientific community with novel science, he argued that they often fail to recognize major flaws, which can later lead to retractions.

        Journal editors require a set of criteria for identifying reports that will further scientific progress, and novelty has become a convenient measuring stick. But it has become increasingly clear that this cannot be the main criterion for assessing the quality of scientific work. A new system must be adopted in which the merit and clarity of scientific work is more heavily considered. Not only will this change allow for more young scientists to continue their research pursuits in academia, but it will also encourage them to take more care with their work and present arguments that are sufficiently supported by their experimental results. No consensus has been reached concerning how this change can be effected, but the future of science depends on emphasizing the inherent quality of scientific reports rather than the journals choosing to publish them.

       

                      Randy Schekman, a 2013 Nobel laureate, has called for an end to the elite journal culture.
                          Courtesy: http://newsroom.ucla.edu/portal/ucla/randy-schekman-molecular-biologist-248784.aspx

         

  

Acid Bath Stem Cells: Fact or Fiction?

      Three months ago, the scientific community was rattled by two papers published in Nature. These papers, with Haruko Obokata listed as first author, claimed that subjecting adult mouse white blood cells to acidic conditions converted them into embryonic stem-like cells. Embryonic stem cells have the ability to produce multiple cell types in an organism, and scientists have attempted to find alternative methods for their isolation since the primary method involves the destruction of fertilized embryos. Thus, the publication of these papers excited researchers with the prospect of a relatively easy protocol for creating stem-like cells.

       Unfortunately, the inability of researchers to reproduce Obokata's experiments have raised questions about the validity of her results. Several figures in the papers appeared to be modified or mislabeled, sparking an investigation for scientific misconduct by the RIKEN Center for Developmental Biology. Yesterday, the committee ruled that Obokata was indeed guilty of scientific misconduct due to several inconsistencies in her 2011 paper as well as those found in her most recent publications.

       This situation is a cautionary tale to those that fail to scrutinize sensationalist scientific reports. The results from Obokata's papers seemed reasonable upon second glance, but the idea that adult cells can be converted into stem-like cells with pH stress was outlandish. Editors of scientific journals, in the quest to publish the most novel and insightful papers, can get carried away with a provocative study that may be shown to be fraudulent or non-reproducible in the future. Therefore, the old adage still rings true: "If it seems too good to be true, it probably is."

Mouse embryo supposedly created by Obokata's stress-induced cells, which expressed green fluorescent protein (GFP).
Credit: Nature News http://www.nature.com/news/acid-bath-stem-cell-study-under-investigation-1.14738

Embryonic Stem Cells, Retroviruses, and You

        The human cell contains roughly 25,000 genes, so it is natural to believe
that the majority of the human genome contains protein-coding genes. On the contrary, protein-coding genes only make up about 2% of our genomes. If protein-coding genes constitute a small percentage of the human genome, what is the function of the other subset of genes occupying our cells? Ninety-eight percent of our genomes contain non-coding DNA, which includes DNA sequences that regulate the expression of coding genes, pseudogenes (genes that no longer encode protein due to the acquisition of mutations over time), and transposons (DNA sequences that migrate through the genome). Scientists hypothesize that these non-coding sequences

Embryonic stem cells in the process of generating multiple cell types.
Courtesy: University of California, Merced 

  

originated from retroviruses. Retroviruses are a unique class of virus that convert their RNA sequences into DNA with the aid of an enzyme called reverse transcriptase. They also possess enzymes that facilitate the incorporation of their newly converted DNA into the genome of their host, ensuring that their genetic material will be replicated during the lifetime of the host cell. Retroviruses have received much negative attention due to the devastation caused by HIV, the most infamous retrovirus of all.

         However, retroviruses may have contributed to our evolution. A new study published in Nature Structural and Molecular Biology suggests that a retroviral infection may have bestowed pluripotency (the ability of a cell to generate multiple cell types) on primate embryonic stem cells. This study, led by Huck-Hui Ng's group in Singapore, discovered that sequences belonging to the human endogenous retrovirus H, or HERVH, could be detected in human embryonic stem cells. When mutations were introduced into these sequences, human embryonic stem cells no longer had the capacity to generate multiple cell populations, leading Ng and colleagues to conclude that HERVH infection played an important role in the origins of cell pluripotency.

       Interestingly, these scientists suggested that stem cells from non-primates do not rely on HERVH for pluripotency. This idea implies that primate and non-primate stem cells rely on different evolutionary sources for their pluripotency, and the next logical question concerns how this phenomenon occurred. These studies highlight a crucial role that environmental agents play in our evolution, and it will be fascinating to learn of other important cellular functions that may be dependent on virus-host interactions.