BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Cells

Can your diet’s effect on gut bacteria play a role in reducing Alzheimer’s risk?

Could following a certain type of diet affect the gut microbiome in ways that decrease the risk of Alzheimer’s disease? According to researchers at Wake Forest School of Medicine, that is a possibility.

In a small study, researchers were able to identify several distinct gut microbiome signatures in study participants with mild cognitive impairment (MCI), but not in the other participants with normal cognition. Researchers found that these bacterial signatures correlated with higher levels of markers of Alzheimer’s disease in the cerebrospinal fluid of the participants with MCI. Additionally, through cross-group dietary intervention, the study also revealed that a modified Mediterranean-ketogenic diet resulted in changes in the gut microbiome and its metabolites that correlated with reduced levels of Alzheimer’s markers in the members of both study groups.

“The relationship of the gut microbiome and diet to neurodegenerative diseases has recently received considerable attention, and this study suggests that Alzheimer’s disease is associated with specific changes in gut bacteria and that a type of ketogenic Mediterranean diet can affect the microbiome in ways that could impact the development of dementia,” said Hariom Yadav, Ph.D., assistant professor of molecular medicine at Wake Forest School of Medicine.

The randomized, double-blind, single-site study involved 17 older adults, 11 diagnosed with MCI and six with normal cognition. These participants were randomly assigned to follow either the low-carbohydrate modified Mediterranean-ketogenic diet or a low-fat, higher carbohydrate diet for six weeks then, after a six week “washout” period, to switch to the other diet. Gut microbiome, fecal short chain fatty acids, and markers of Alzheimer’s in the cerebrospinal fluid were measured before and after each dieting period.

The limitations of the study included the subject’s group size, which also accountns for the lack of diversity in terms of gender, ethnicity, and age.

“Our findings provide important information that future interventional and clinical studies can be based on,” Yadav said. “Determining the specific role these gut microbiome signatures have in the progression of Alzheimer’s disease could lead to novel nutritional and therapeutic approaches that would be effective against the disease.”

Each human contains trillions of organisms that influence our metabolism, immune function, weight, and even cognitive health. It is so fascinating to examine the role of gut microbiomes in the progression of Alzheimer’s disease. I believe diets can be very controversial, and I find it interesting to see researchers in this study show how the Mediterranean-ketogenic diet may be effective against Alzheimer’s. However, I am so intrigued to see where these findings may take us with approaches that may be effective against Alzheimer’s, whether they be nutritional or therapeutic approaches.

Nobel Prize awarded to Researchers for Key Discoveries in Cellular Respiration

Recent findings about the change in oxygen levels in cells show new important factors about oxygen that translate to one’s well-being. William G. Kaelin Jr., Sir Peter J. Ratcliffe and Gregg L. Semenza discovered how cells can “sense and adapt to changing oxygen availability,” and are now being awarded the Nobel Prize in Physiology or Medicine. Oxygen is a crucial aspect to how a cell’s functionality. Mitochondria in cells use oxygen to aid in converting food into ATP (energy), a process known as cellular respiration.

A representation of the reaction of cell respiration.

 

Gregg Semenza wanted to further look into the rise of levels of the hormone erythroprotein (EPO), a response to low levels of oxygen, or hypoxia. He found that “oxygen sensing mechanisms were present in virtually all tissues, not only in the kidney cells where EPO is normally produced.” While Semenza analyzing cultured liver cells, Semenza found a protein complex that was unknown to science. He named unidentified DNA segment the “hypoxia-inducible factor (HIF).”

Over the course of 24 years, Semanza continued to explore aspects of HIF and found two different DNA-binding proteins, now named “HIF-1a and ARNT.” Researchers worked with Semanza in finding out which parts of the HIF assist in cellular respiration. While Semenza and Ratcliffe were researching regulation of EPO, Kaelin Jr. was researching von-Hippel-Lindau’s disease (VHL). Kaelin Jr.’s research showed that VHL gene “encodes a protein that prevents the onset of cancer,” and that cancer cells lacking a functional VHL gene have “abnormally high levels of hypoxia-related genes.” But when the VHL gene was reintroduced into cancer cells, “normal levels were restored.” Eventually, Kaelin Jr. and his team found that VHL needs HIF-1a for degradation at normal oxygen levels.

Kaelin Jr. and Ratcliffe both published articles that center around protein modification called prolyl hydroxylation which “allows VHL to recognize and bind to HIF-1α degradation with the help of oxygen-sensitive enzymes.” The papers also wrote that the gene activating function of HIF-1α “was regulated by oxygen-dependent hydroxylation.” The researchers now had a much clearer idea of the effects of how oxygen is sensed within cells.

These groundbreaking finds give the science world more information about how oxygen levels are regulated in cells in physiological processes. Sensing oxygen levels is important for muscles during physical exercise, as well as the generation of blood cells and strength of one’s immune system.

Stem Cells and CRISPR

Many cells can reproduce but there are a few types of cells that are not able to reproduce. One of these types are nerve cells, the cells that cary messages from your brain to your body.  There are many ways nerve cells can be destroyed or damaged, by trauma or drug use.  Millions of people are effected by losing nerve cells and for so long no one could think of a way to recreate them; until the discovery of stem cells.

After fertilization, and when the newly formed zygote is growing, it is made up of a sack of cells.  Some of these cells are stem cells which develop according to their environment. Because of the behavior of stem cells, scientists theorized that if they placed stem cells in the brain or spinal chord, two areas that have an abundance of neurons, the stem cells would turn into a neuron because of the environment it was in.  But, when they tried introducing stem cells into the body, the immune system treated them as an foreign body, as it should. Our immune system has to treat anything that does not come from our body as an enemy or we could get extremely sick.  However, the downside is organ transplants, blood transfusions, etc. are dangerous because they could cause a serious immune rejection.

Someone experiencing a spleen transplant rejection

Cells have a surface protein that displays molecular signals to identify if it is self or foreign.  Removing the protein causes NK (natural killer) cells to target the cell as foreign. Scientist haven’t been able to figure out how to make a foreign cell not seem foreign until Lewis Lanier, chair of UCSF’s Department of Microbiology and Immunology, and his team found a surface protein that, when added to the cell, did not cause any immune response.  The idea would be to use CRISPR/cas9 to edit the DNA of the stem cells, and in doing so would remove the code for the current surface protein and add the code for the new surface protein.

After the scientists had edited the stem cells, to have the correct signal protein, they released them into a mouse and observed that there was no immune rejection. Truly amazing. Maybe brain damage could be helped by this science one day. Tell me your thoughts on Stem Cells in the comments!

For more information, please go check out the primary source of this article.

 

 

Do humans have night vision?

Can humans see in the dark?

If you said yes, you are correct! When I saw the title of Emily Underwood’s article, “How humans- and other mammals- might have gotten their night vision“, it immediately intrigued me. Sight is an amazing gift that we all take for granted. Our eyes are incredible organs, and scientists are now discovering how they work when we see in the dark naturally. That is pretty cool!

Underwood’s article describes a study that gives insight into how our eyes work in the dark. According to her, “On a moonless night, the light that reaches Earth is a trillion–fold less than on a sunny day. Yet most mammals still see well enough to get around just fine—even without the special light-boosting membranes in the eyes of cats and other nocturnal animals.

In broad daylight, mammalian retinas respond to photons, which activate rods, which then send an electrical signal to the brain through a ganglion cell. It was thought that this retinal circuit was the same when the sun went down, but a new study by Greg Field and his colleagues at Duke University proves that the retinal cells adapt when there is no light to create what we know was natural night vision. How?

To understand this new study, we first need to know about direction-selective ganglion cells.

Direction-selective ganglion cells (DSGCs) specialize in motion detection. Depending on the movement of an object, different cells get excited. For example, some DSGCs fire when an object moves up and down and other DSGCs fire when an object moves from left to right. These ganglion cells play an important role in telling the brain where an object is moving towards. By doing this, the brain can make a decision as to how your body should act.

However, in the dark DSGCs behave very differently. Field’s experiments aimed to see how the DSGCs adapt when there is no light. His team examined slices of mouse retinas on glass plates embedded with electrode arrays. In an oxygenated solution, the mouse retinas could still “see” while the arrays recorded the electrical activity of the neurons. They ran the experiment twice: once under a normal “office light” setting, and once by dimming the lights to a moonlight setting. Looking at the results, Field found that three of the four directional DSGCs did not have a response to motion when they dimmed the lights. The only cells that were responding were the ones that usually respond to the motion “up” in daylight. In fact, these cells compensated for the other DSGCs, and were now responding to motions like “down” and “sideways”.

Why were the “up” DSGCs were acting differently? To answer this question, Field genetically engineered mice without intracellular gap junctions to run the experiment again. Gap junctions have previously been associated with night vision, and the results in Field’s experiment confirmed their relationship. The mice lacking gap junctions were not able to adapt to the dark. This shows that gap junctions are critical in boosting motion detection in the “up” cells when there is limited light.

It is still not known why specifically the “up” cells contribute to natural night vision, what do you think?

Field’s findings will be helpful to artificial vision efforts. DSGCs make up 4% of ganglion cells in humans, a small amount compared to 20% in mice. Yet a large part of retinal prosthetics relies on electrically stimulated ganglion cells. Studies like this can fine-tune the technologies that will be able to help visually impaired people, which is why I love reading about them. These experiments are crucial in progressing the future of medicine and the treatment of all kinds of health issues.

Design Your Own Organelle!

What?

All eukaryotic cells consist of compartmentalized organelles, each with a specific function. We’ve all heard of mitochondria, chloroplast, and lysosomes, but, what if we could design a new organelle?! That’s exactly what scientists are working on right now – modifying or hijacking existing organelles to fit new specific functions.

Why?

Scientists currently have the technology to alter the DNA of cells to manufacture proteins they couldn’t “naturally” make. However, this technique has a few flaws. The proteins produced or their intermediates could damage the cell and chemicals in the cell could damage the proteins. If we could compartmentalize the production of these new proteins, this problem would be avoided. So, we look to organelles!

How?

Stuart Warriner, a chemical biologist at the University of Leeds, and his colleagues believe peroxisomes are the key. Current techniques allow scientists to manipulate these organelles. Their experiments show that they could deliver certain proteins into the peroxisomes of most cells. These selective proteins are ones that are not usually made; therefore, we say that humans have “hijacked” the cell.

https://commons.wikimedia.org/wiki/File:OSC_Microbio_03_04_Peroxisome.jpg

What’s Next?

Scientists are hopeful that future research could lead to the ability to use peroxisomes to manufacture compounds by importing specific proteins into them. Currently, when an organelle is modified, every organelle of that type must be modified. Future research could ensure that modified and conventional organelles could coexist in the same cell. In addition, Warriner and his team are working on the modification of peroxisomes in yeast to produce desirable compounds. Despite these studies, Warriner believes that this technique of hijacking organelles will not be implemented in humans for decades, if not never, because it wouldn’t be particularly useful. To learn more, check out their findings!

Who Cares?

We have the ability to alter DNA and cells! That is amazing! Although peroxisome altercation may not prove to be essential to humans, it is still an impressive exploratory feat and a step toward greater modification in microscopic organisms. What do you think similar cell modification research should be focused on?

Our Intestines Cure Cancer??

There are over one hundred trillion organisms- most are bacteria- living in our intestine today. These are referred to as the gut microbiota.

While trillions of bacteria sounds scary, they can actually be very helpful. Research has been done worldwide and the discovery has been that gut microbes actually can kill cancer cells all over the body. (Not just in the intestines) But how? Gut microbes and cancer actually cross paths. Gut microbes can manipulate the immune system and can either increase inflammation or lower it as needed. This means the bacteria can actually work with cancer treatments, boost T-cells, and control other factors that help cancer grow such as fungi, or viruses.

However, this is not all. While some cells help against cancer growth, others do the opposite. It varies cancer to cancer, and all have different results. As said by microbiologist and immunologist Patrick Schloss “What we really need is to have a much better understanding of which species, which type of bug, is doing what and try to change the balance.” So more research is still being done to decide how to control the microbiota, but a possible theory is that because it’s in the intestine it is related to our metabolisms and so what we eat controls the bacterium- this can also then effect the colon, thus effecting more cancer: colon cancer.

 

Stem Cells…Key to Youth and Controversy

Have you ever wondered what it would be like to be young forever? With the help of stem cells, this is possible. Stem cells can regenerate skin tissues and can also be used to treat diseases. However, something as enticing as living forever has its controversies. There are two types of stem cells: embryonic (ES) and adult (iPS); the embryonic stem cells are the controversial type.

Embryonic Stem Cell

Embryonic Stem Cell

The only way to effectively use the embryonic stem cell is to kill a four to six day old embryo. Some people view this act as killing a baby, which sparks ethical arguments about whether or not to utilize embryonic stem cells. To avoid this controversy, scientists have been trying to use stem cells from iPS cells instead of ES cells, but they questioned the power of iPS cells compared to the ES ones.

Because genes may differ in the iPS cells from the its source, the ES cells, there is a possibility that these two cells do not have the same capability. One scientist notes that the source of iPS and ES cells differ, which can lead to differences in gene activity. The ES cells are derived from embryos, which are not completely identical to iPS adult cells.  However, recent scientific research shows that these two types of stem cells have more equal capabilities than scientists’ initially thought.

Scientists conducted an experiment to compare the genetic makeup between the ES and iPS cell. They manipulated the male type of each cell, which eventually allowed the ES cell to transform into the iPS cell. They concluded that the iPS cells genetically matched the ES cells’ parents, and that the iPS cells had more similarities with the ES cells than iPS cells had to each other.

Even though these two experimental cells genetically matched, the two cells were not identical. The experiment showed 49 genes that differed between the two stem cells. Because of this difference, scientists needed to see if this affected the functional capability of the cells. The researchers conducted another experiment that analyzed 2 of the 49 genes. One helps take in glucose, while the other helps break it down. Even though these two genes were more active in the ES cell than the iPS cell, they were equally efficient at their respective jobs. The scientists concluded that these two specific cells were functionally equivalent.

The many experiments that have been conducted on the topic of stem cells contribute to the increase in research for more ways to utilize stem cells, without the ethical controversy. Scientists are starting to employ different technological devices, such as 3-D printers to help develop and build stem cells. This ability to fabricate cells using technology overcomes previous obstacles of limited stem cell resources.

– Source Article

– More fun facts about stem cells here

Do Viruses Make Us Smarter?

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Sanofi Pasteur

A study conducted at the Lund University shows that “inherited viruses” that are millions of years old play an important role in building up the complex networks that characterize the human brain.” It is well known that retroviruses are make up about five percent of our DNA. Research under Johan Jakobsson indicate that retroviruses may play a critical role in the basic functions of the brain, “in the regulation of which genes are to be expressed, and when.”

Studies of neural stem cells show that these cells use a particular molecular mechanism to control the activation processes of the retroviruses. Findings have shown to have increasingly gained control in our cellular machinery. Because tumors are unable to form in nerve cells, different from other teachers, viruses are activated specifically in the brain. The results open up potential for new research paths concerning brain diseases linked to genetic factors.

“I believe that this can lead to new, exciting studies on the diseases of the brain. Currently, when we look for genetic factors linked to various diseases, we usually look for the genes we are familiar with, which make up a mere two per cent of the genome. Now we are opening up the possibility of looking at a much larger part of the genetic material which was previously considered unimportant. The image of the brain becomes more complex, but the area in which to search for errors linked to diseases with a genetic component, such as neurodegenerative diseases, psychiatric illness and brain tumors, also increases”.

Original Article: http://www.biologynews.net/archives/2015/01/12/do_viruses_make_us_smarter.html

For More Info:

http://www.sciencedaily.com/releases/2015/01/150112093129.htm

Human skin cells reprogrammed directly into brain cells

Brain

 

Original article: http://www.sciencedaily.com/releases/2014/10/141022123021.htm

Some key words:

Neurodegenerative diseases: Disease such as Alzheimer’s, Parkinson’s and Huntington’s disease that undergo a neurodegenerative process, specific neurons are targeted for degeneration.

Spiny brain cell: The desired end brain cell in this study, and a brain cell affected by Huntington’s disease

 

In a study by the researchers at Washington University School of Medicine in Saint Louis, they demonstrate a way for human skin cells to be specifically converted to a type of brain cell. This study can help in the rehabilitation of people with Huntington’s disease by turning skin cells in to brain cells that are lost through this neurodegenerative disease. This is all accomplished without passing through the stem cell phase preventing other cell types forming.

This research involved adult skin cells that Yoo, the senior author, and his colleagues reprogrammed by using two microRNAs: miR-9, and miR-124. These micro RNAs open up the otherwise tightly packaged and inactive sections of the gene critical to the formation of brain cells. While the micro RNAs open up genes used for the creation and functionality of neurons, transcription factors taken from a part of the brain where medium spiny neurons are common directs the newly formed brain cells to a specific subunit of brain cells. The researchers then observed that the newly formed brain cells behave and function in a similar way to the native medium spiny neurons in mice, allowing this study to proceed in to further stages of experimentation, and hopefully result in a treatment practical for human use.

This study is very critical in the advancement of the treatment for neurodegenerative disease such as Huntington’s disease. Using different transcription factors from parts of the brain, alternate types of brain cells can be created to replace cells lost from neurodegenerative effects. This form of treatment will also prevent rejection of the transplant because the skin cells can be taken from the patient’s own body. This is a breakthrough in our pursuit of cures for these lethal neurodegenerative diseases.

Coral Reef Bleaching Puts Fish’s Ability to “Just Keep Swimming” in Danger

Coral reefs are vital sources of life for many sea creatures. The diversity of the underwater ecosystems surrounding coral reefs are, unfortunately, being put in danger because of coral bleaching. According to the National Ocean Service, coral bleaching is due in part by a process that is the result of damaged chloroplasts in coral cells which produce “toxic, highly reactive oxygen molecules during photosynthesis.” The main cause of this issue, is temperature; the coral respond to the drastic changes in temperature, whether they be hot or cold, by releasing the symbiotic algae that dwell in their tissues, which result in the coral taking on a white, “bleached” color.

Found on Flickr, Licensed under Creative Commons Licensing

Coral bleaching has both negative internal and external effects. Internally, the coral’s ecosystems are placed at risk because they “rely on live coral for food, shelter, or recruitment habitat.” This is a major issue, as we have the potential to lose certain, diverse, species that live off of and around coral reefs, which, in turn, could negatively influence the food chain. The external effect is that there will not be tourism revenue brought in from people who scuba dive to the coral reefs affected by bleaching. This is due to the fact that they will no longer be aesthetically appealing. Thus, leading to a negative economic state in tourism hot spots.

Unfortunately, the temperature of the Earth is out of human control, so there is little we can do to prevent coral bleaching, but we can use the rapidity of the bleaching as a marker to gauge the temperature of the world.

HeLa Cells Sequenced!

Photo By: University of Arkansas
Wellcome Trust

The immortal cell, also known as HeLa cells, have been used by scientists for years for various medical research. But, until today the genome of HeLa cells was never known. Jonathan Landry and Paul Pyl, from the European Molecular Biology Laboratory in Heidelberg, performed the study to sequence Henrietta Lacks‘ genome, and what they found was quite remarkable. They found striking differences between her cells and the cells of a normal human being. The genome had abnormalities in both chromosome number and structure. They also found that countless regions of the chromosomes in each cell were arranged in the wrong order and had extra or fewer copies of genes, all telltale signs of chromosome shattering. Chromosome shattering has recently been found to be linked to 2-3% of cancers. Seeing as how Henrietta Lacks’ cells were taken from a cervical tumor, this is not a surprising find. However, because her genome had never been sequenced this was all new to Landry and Pyl. They said, “The results provide the first detailed sequence of a HeLa genome. It demonstrates how genetically complex HeLa is compared to normal human tissue. Yet, possibly because of this complexity, no one had systematically sequenced the genome, until now.” Another scientist, Lars Steinmetz, who led the project, added, “Our study underscores the importance of accounting for the abnormal characteristics of HeLa cells in experimental design and analysis, and has the potential to refine the use of HeLa cells as a model of human biology.” Although this study is nowhere near groundbreaking, it still helps to highlight the importance of the extensive differences that cell lines can have from their human references.

For more information on this study and HeLa cells in general, you can go to:http://www.science20.com/news_articles/genome_hela_cell_line_sequenced-106181

 

Magnets: Fun Toy or Deadly Tool?

Taken by: USCPSC

Cancer is one of the most well known diseases, yet it is one of the hardest to treat. The research of different treatments for cancer is ongoing and innovative. According to a recent study in South Korea magnets may be the next step in cancer treatment. A way for magnets to assist the body in targeting and killing off cancer cells has been discovered and is being researched and developed.

A problem with current cancer treatments like chemotherapy or radiation therapy is that they can only be targeted to a certain extent. With this experimental form of cancer treatment, using magnets, the body’s natural functions are used to kill the cells in a tumor. The human body naturally goes through a process called apoptosis, or the process of programed cell death. Apoptosis is used by the body when it is first developing allowing fingers and toes to grow individually, and it is used daily to kill off skin cells that have been damaged by weather. The researchers in South Korea are using this process to target and kill off the cancer cells.

The researchers applied zinc-doped iron oxide nanoparticles to colon cancer cells. This allows for the cells to naturally bind with antibodies, which then bind to the death receptors on the cancer cells. The researchers then applied a magnetic field, which caused  the death receptors to send out a signal telling the system to attack the cell. When this occurs chemicals are sent out and the cells of the tumor that had zinc-doped iron oxide nanoparticles on them were killed.

Sadly this innovative new cancer fighting technique has its downsides. In their experiments only half the exposed cells were killed although none of the cells they weren’t targeting were harmed. And when this method was tested on zebra fish some grew abnormal tails, which means that this method may be innovative but it still has plenty of testing to go through before it will be used on humans.

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