simeiosis – BioQuakes

Author: simeiosis

Cancer most commonly is defined as a “perpetuating mass of dystregulated cells growing in an uncontrolled manner”, however the meaning can be further related to epigenetics, for they appear to be very much interconnected. Another definition of cancer goes on to note this relationship as the “dynamic genetic and epigenetic alterations that contribute to cancer initiation and progress.” Recent research shows that if epigenetics is disrupted, it might switch to oncogenes or shut down tumor suppressors. Either way, this would lead to the development of tumor cells that would cause cancer. We are already aware of the fact that chemical modification affecting the packaging of our DNA can switch genes on and off. The first time that became aware of an epigenetic code, we learned that that code chemically labels active or inactive genetic information. The focus of epigenetics is on the change caused by the modification of gene expression, not the alteration of the code itself. With recent discoveries through research on epigenetics and its relation to cancer, we learned that there must be a balance of “writers” and “erasers” for the cells. Recent data has shown that methyltransferase EZH2 is an epigenetic writer that is hyperactivated in many cancers, specifically melanomas and lymphomas. This recent research also shows KDM3A (member of the jumonji histone lysine demthylase family) as an epigenetic eraser. KDM3A fulfills an oncogenic role by activating a network of tumor promoting genes. Epigonomic changes also allow tumor cells to evade the immune system so that these cells can thrive and divide without the disruption of the immune system. Ultimately, there are two potential pathways that epigenomic regulators can cause cancer. The first is the result of too much epigenetic activation, which can lead to oncogenes. The second is too much epigenetic protection that conversely blocks tumor suppressor genes. DNA hypermethylation causes the silencing of tumor suppressor genes.

Both of these methods would lead to the development of cancer. Epigenetic regulation involves methods including histone regulation, DNA methylation, and changes in noncoding RNAs such as miRNAs. One of the challenges of studying cancer and researching possible vulnverabilities in pathways is that they are often disrupted by epigenetics. The recent studies also have shown that there are close ties between epigenomic (analysis of global epigenetic changes across many genes) changes and metabolites, or human cellular chemistry. Metabolites initiate, target, or maintain epigenetic factors with the transcriptional complex, and cooperation with them metabolites can target, amplify or mute these coded responses. Since the fields of both epigenetics and metabolism are still developing a great deal, there is hope that these insights with regards to cancer and regulating gene expression to prevent the development of cancer will allow for more precision in targeting cancer, specifically when existing methods of therapy fail to work sufficiently.

Seagrasses: Benefitting the Ecosystem

By simeiosis

On March 1, 2017

In Student Post

Seagrasses have been known to improve water quality greatly, however it was only recently that scientists discovered other major benefits of the plants that reside in the ocean. The name seagrasses is a misnomer, for they are actually plants that grow in shallow ocean water. Seagrasses are one of the largest stores of carbon in the ocean, and they also remove excess nitrogen and phosphorous from the water.

A few years however, ecologist Joleah Lamb’s colleagues fell ill with amoebic dysentery. This is an intestinal illness that they contracted while conducting research on coral reefs in Indonesia. The illness can be caused by the release of raw sewage into the ocean by a city, which leads to a drastic increase in the populations of shoreline bacteria. The water collected close to the shore had been compared to offshore tidal flats and coral reefs with seagrass beds. The two different sites were very close to one another, yet the water where the seagrass was had a significantly smaller amount of Enterococcus bacteria. The bacteria in areas with seagrass was only 1/3 of that in other areas that did not have the plants. This bacteria is not only dangerous for humans, but is harmful for fish and other species as well.

While at this moment it is uncertain how the seagrasses clean the water, we know that seagrasses trap small particulates and prevent them from flowing on in the ocean. It is believed that the plants would catch the bacteria in the same way, or that the leaves might emit antimicrobial compounds that directly kill the bacteria. Another possibility could be that seagrasses release oxygen made during photosynthesis, and the oxygen is toxic to pathogens. Also, it is noted that seagrass meadows often are located next to coral reefs, so some suggest that they work together to protect one another from bacteria and other possible dangers.

New Reason to Watch Your “Diet”: The Human Gut Microbiome and Competition

By simeiosis

On January 16, 2017

In Student Post

The human body consists of approximately 100 trillion microbes, and in the digestive tract of the human gut alone it is estimated that there are trillions of microbes. Recent studies done by Athena Aktipis, a researcher at Arizona State University’s Biodesign Institute, have shown that people’s dietary choices either help to increase the cooperation between gut microbes and their human hosts, or they could potentially lead to conflict between the two.

The microbiota consists of bacteria, and the human microbiota contains about 500 different species of microbes. There is a possibility that the composition of these microbes could affect behavior, susceptibility to allergies, and even likelihood for obesity. According to several previous studies, exposure to intestinal bacteria prevents allergies in infants and young children. This has been determined by examining the noticeable difference between the compositions of intestinal bacteria in children who have developed allergies and children who have not. The current study further looks at cooperation and competition between human cells and other cells that coexist with them. Cells are cooperative between the human cells and gut microflora when bacterial cells produce energy and vitamins. It also is beneficial when bacterial cells help to detect pathogens that are dangerous to the host. Conflict on the other hand is more likely to occur when the needs of microbes and the needs of the host are at “cross-purposes”, or they contradict one another. This internal conflict could lead to chronic afflictions such as inflammatory diseases that are caused directly by the body’s attempt to maintain dominance in this “power-struggle” within the host.

These recent studies have also shown that sugar and fat are most likely contributors to conflicts that arise between host cells and microbes. This is due to the fact that fats and simple sugars also can be used by microbes such as E. coli, which further contributes to the conflict. The results of these studies suggest that a diet consisting of low fiber and abundant sugar leads to the conditions where conflict takes place between human cells and microbes. When their interests clash or coincide, the cells in the body trigger immune responses that lead to different afflictions that include a wide range of diseases, some of them being inflammatory. Similar to fats and simple sugars, iron is also potentially dangerous in the sense that a pathogen could steal iron from host cell proteins which would ultimately compromise the health and nutrition of the host. According to the studies, it is recommended to maintain a diet that has high nutritional density but also low concentrations of pathogens in order to promote cooperation and prevent any competition or conflict that could damage your overall health and wellness.

Probiotics: The Real Brain Food

By simeiosis

On November 28, 2016

In Student Post

While it is nearly common knowledge that probiotics give partial protection against certain colds, allergies, infectious diarrheas, and other health issues, scientists were not able to prove until recently that probiotics can potentially improve cognition. This is possible since there is communication between the gastrointestinal tract and the brain via the nervous system, the immune system, and hormones.

Scientists have seen that in mice, probiotics have caused an improvement in learning and memory. Researchers from Kashan University of Medical Sciences, Kashan, and Islamic Azad University, Tehran, Iran, completed a double-blind experiment where 52 men and women with Alzheimers (between 60 and 95 years old) either received milk enriched with four probiotic bacteria, or untreated milk. As predicted by several researchers, by the end of the 12 week period, those who received the milk with Lactobacillus acidophilus, L. casei, L. fermentum, and Bifidobacterium Bifidum displayed an improvement in cognition. To determine these results of the study, the scientists asked the participants of the study to complete tasks such as giving the current date, repeating a phrase, and counting backwards from 100 by sevens. Those who received the probiotics earned a “score” on these tasks ranging from 8.7 to 10.6 on the scale out of 30, whereas the participants who did not receive the probiotics scored slightly lower ranging from 8.5 to 8.0. Despite the seemingly minute difference, these results provide scientists with an insight as to the fact that probiotics can improve human cognition.

In the near future, scientists hope to test these results based on longevity of their intake to test whether or not the effects of probiotics grows throughout prolonged treatment. The patients who received the probiotics also demonstrated lower levels of triglyceride, Very Loy Density Lipoprotein (VLDL), high sensitivity C-Reactive protein (hs-CRP) in the blood of the Alzheimer patients, and a reduction in two common measures of insulin resistance and the activity of the insulin-producing cells in the pancreas. These results also signify that this change in metabolic adjustments might be a way that the probiotics impacts other cognitive and neurological disorders.

A Second Theory: Is the RNA World Hypothesis Wrong?

By simeiosis

On October 18, 2016

In Student Post

Introduction

Prior to recent research, scientists strongly supported the “RNA world” hypothesis, a theory that claims that DNA derived from RNA, and that RNA therefore provided the basis for life as we know it. The evidence of this new study under scientists at The Scripps Research Institute leads to an alternate theory that challenges this previous mode of thinking. This study is intriguing not only because it challenges what has mostly been accepted as factual truth by most scientists, but also because it attempts to solve the question of where and how first life developed.

Background: The “RNA world” hypothesis

The “RNA world” hypothesis dates back to over 30 years ago. Proposed independently by Carl Woese, Francis Crick, and Leslie Orgel, it essentially is a theory that states that RNA existed before modern cells, and stored genetic information and catalyzed chemical reactions within earlier cells. This theory further claims that DNA came later and only then contained the genetic material. It also infers that proteins served as a catalyst much later, only fulfilling this role once RNA evolved. The evidence that supports this theory lies with the chemical differences that distinguish RNA from DNA. RNA can be formed from formaldehyde (HCHO) which is chemically simple, especially in comparison to the much more complicated sugar deoxyribose. In a reaction catalyzed by a specific enzyme, deoxyribose is produced from ribose which also indicates the possibility that DNA comes directly after the structurally more simple and single helix RNA.

Recent Studies

Researchers believe that if this theory is correct, RNA nucleotides and DNA backbones would have mixed to create “heterogeneous” (or a product resulting from differing “parents” with unique charateristics) strands. The resulting “chimeras” (an organism composed of cells from different zygotes leading to subtle variations in form) would be an intermediate step in the transition to RNA if stable, however the study shows a decrease in stability (specifically in thermal stability or the ability to function at high temperatures) when the backbone is shared between the two nucleic acids. The researchers attribute this instability to a slight difference between the sugar in RNA and the sugar in DNA. As a result, if the RNA theory had been true, the chimeras would have died off. This proves that evolution has lead to a system where enzymes have developed to maintain the system of “homogenous” molecules, keeping RNA and DNA separate since they function much better separate from one another. Since these enzymes are fairly “new” in terms of the span of the existence of DNA and RNA, it is highly unlikely that RNA was able to transition to newly developed DNA. Without any mechanisms to keep DNA and RNA separate, it is logical to conclude that RNA does not predicate DNA. This concept is reminiscent of the endosymbiont theory that discusses the possible reason for the unique qualities of mitochondria and chloroplasts in that both theories rely on existing knowledge about these unique structures and how each component might contribute to a different function. Similar to the endosymbiont theory, there is no exact answer as to whether this theory is correct, however through challenging the theory and conducting experiments, we can further develop our understanding of certain biological phenomena.

Conclusion

This alternate theory, on the other hand, proposes a different view that RNA and DNA have coexisted and that one therefore did not develop from the other. While this theory is not completely new, these recent findings regarding instability for a backbone shared between the two nucleic acids provide more evidence for this secondary theory (to the RNA world theory). If this theory is accurate, DNA could have developed its homogenous system much earlier than scientists have predicted up until this point. According to this second theory, after RNA first interacted with DNA it still could have evolved to create DNA. Although scientists will never be able to discover life’s exact origin, these findings can provide insights for biology overall.

https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-23

http://www.sciencemag.org/news/2016/05/rna-world-inches-closer-explaining-origins-life

https://www.sciencedaily.com/releases/2016/09/160928153357.htm

http://www.medicinenet.com/script/main/art.asp?articlekey=8905

BioQuakes

AP Biology class blog for discussing current research in Biology

Author: simeiosis

The Role of Metabolism and Epigenetics in Cancer Development

Seagrasses: Benefitting the Ecosystem

New Reason to Watch Your “Diet”: The Human Gut Microbiome and Competition

Probiotics: The Real Brain Food

A Second Theory: Is the RNA World Hypothesis Wrong?

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