May 17

New Writing Gig!

I’m writing for Demand Media now. I’m really excited to be writing nutrition and health articles for them, which will appear on various sites such as SFGate Healthy Living, TheNest Woman, Livestrong.com, AZ Central Nutrition, etc. So far I have two articles up and one pending. Visit demandmedia.ginariggio.com to see my articles!

I’m also hoping to do another article for Bite Size Bio on Roche 454 Sequencing. It will probably be one of my last technical articles for a little while since I’ll be leaving my job at the lab in August to pursue nutrition writing and live in a new city! I suspect I’ll eventually go back to working in a lab but I’m looking forward to my hiatus. It will give me more time for creative pursuits.

So, stay tuned for updates. I’ll let you know when/if my third Demand Media article goes live.

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May 16

Can You Actually Increase Your Metabolism?

While some individuals seem to be able to eat freely and remain slim, others need to monitor their food intake very carefully. One difference between these two extremes is metabolic rate. Metabolism is a term used to describe the process of breaking down fats, carbohydrates and proteins from the food you eat into energy for bodily processes. Certain types of exercise may affect your rate of metabolism and if you are looking for a boost, the right workout regimen can refine your fitness plan [14].

Resting Metabolic Rate

When people say they want to increase their metabolism, they typically mean that they want to increase their body’s resting metabolic rate. Resting metabolic rate (RMR) is the total amount of energy your body uses per some unit of time simply to maintain basic processes like growth and organ function. RMR is the largest part of the body’s total daily energy budget and a strong indicator of how well you burn the calories you eat, so knowing what affects RMR is important when you’re trying to gain or lose weight. [1]

The Effects of Aerobic Exercise

Exercise studies on humans repeatedly show that aerobic exercise such as biking and running does not have a significant impact on resting metabolic rate. [4, 6, 7, 8]. A study of 40 women and 38 men between the ages of 19-87 rode an exercise bike for 20-40 minutes per day 3-4 times per week and no significant changes in RMR occurred after 16 weeks. [8]. A 2010 study published in the International Journal of Sports Medicine on seventeen previously sedentary men and women showed no alterations in RMR even after 1 year of 45 minutes of jogging three times per week. [4]

However, aerobic exercise of moderate intensity does have an impact on how well your body burns fat, which over time can positively impact physical fitness and help with weight goals. [11, 14] To avoid confusion, aerobic exercise does not improve fat burning by increasing RMR. When the body is physically able to sustain low or moderately intense aerobic activity, fat burning increases. [9]. This process happens regardless of your resting metabolic rate. In the 2010 exercise study mentioned above, participants who trained for one year were able to reduce their body fat percentage while their RMR remained the same. [4]

The Influence of Lean Body Mass

Early research in 1986, 1990, 1997, and 2003 on the relationship between RMR and exercise are among many studies that indicate that muscle mass is positively related to RMR. [1,2,3,13] Two studies reveal that increasing muscle mass through weight training may increase metabolic rate by a small amount. At University of Maryland in 2001, a group of 40 men and women both young and old participated in a 24-week strength training program and RMR increased by 9% only in men, independent of age. [5] In an earlier study at University of Maryland in 1995, 15 post-menopausal women between the ages of 50 and 69 gained muscle mass but only slightly increased RMR after a 16-week strength training regimen using weight machines three times per week [10].

The Benefits of Physical Fitness

Although there is no guaranteed method for significantly increasing your body’s resting metabolism, both aerobic and strength training have beneficial effects on health. Both types of exercise can help improve cardiovascular health, increase physical strength, optimize body weight and maximize mental and physical well-being. [12]. Regardless of your age, gender, or genetic makeup, it is a good idea to become more physically fit through a well-rounded workout program that includes both weight training and aerobic exercise.

References

  1. The Proceedings of the Nutrition Society: Physical Activity and Resting Metabolic Rate
  2. Journal of Clinical Investigation: Determinants of 24-hour Energy Expenditure in Man
  3. American Journal of Clinical Nutrition: A new predictive equation for resting energy expenditure in healthy individuals.
  4.  Journal of Sports Medicine: Effects of One Year Aerobic Endurance Training on Resting Metabolic Rate and Exercise Fat Oxidation in Previously Untrained Men and Women
  5. Medicine and Science In Sports and Exercise: Effect of strength training on resting metabolic rate and physical activity: age and gender comparisons
  6. American Journal of Physiology: Age and aerobic exercise training effects on whole body and muscle protein metabolism
  7. The American Journal of Clinical Nutrition: The effects of either high-intensity resistance or endurance training on resting metabolic rate
  8. The American Journal of Clinical Nutrition: The effects of aerobic fitness on resting metabolic rate
  9. American Journal of Physiology: Regulation of endogenous fat and carbohydrate metabolism in relation to exercise intensity and duration
  10. Journal of Applied Physiology: Resistive training increases fat-free mass and maintains RMR despite weight loss in postmenopausal women
  11. European Journal of Clinical Nutrition: Meta-analysis: effect of exercise, with or without dieting, on the body composition of overweight subjects
  12. Psychiatry: Exercise and well-being: A review of mental and physical health benefits associated with physical activity
  13. Metabolism: Relationship between resting metabolic rate and the composition of the fat-free mass
  14. Sports Medicine: The role of diet and exercise for the maintenance of fat-free mass and resting metabolic rate during weight loss
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Feb 06

Introduction to Yttrium

I’ve been told that scientists love corny acronyms, so to name my blog and fulfill my obligation as a scientist to create more corny acronyms I needed a “Y” topic to create the word NIFTY out of my four legitimate interests – neuroscience, infectious diseases and immunology, food, and lab techniques. I have taken it upon myself to learn about yttrium, just for fun. This post will therefore be a brief introduction to yttrium, and I will introduce my readers to a new tidbit about yttrium each month to follow.

Yttrium is an element with atomic number 39 on the periodic table. It got it’s seemingly weird name from a village in Sweden, Ytterby, where it was first discovered. Yttrium touches the modern world in many ways with it’s remarkable versatility, both as a radioactive and non radioactive substance. It’s principle use (according to Wikipedia) is in making the red phosphor (science for “red glowing material”) for cathode ray tube TV monitors as well as LED screens. It is used in the production of synthetic garnet stones for both jewelry and microwave filters. It is also useful in enhancing the performance of other metals and is a component of some types of superconductors.

A radioactive variant of yttrium, Yttrium-90, has been used as a cancer drug that delivers radiation by way of binding to monoclonal antibodies. (I will be doing a post on this topic in more detail in a month.) Needles made of yttrium-90 are known to cut more accurately than scalpels and have been used to perform surgery and to deliver pain treatment.

Is it toxic to humans? Maybe. Water soluble yttrium compounds can be, while insoluble compounds are considered non-toxic. One report stated, however, that exposure to yttrium compounds may cause lung cancer in humans.

You are not likely to find yttrium in your backyard, though. It is rare, and never found sitting alone. It is usually found among rare earth minerals, which are mixtures of rare elements. Although, interestingly, it is 400 times more abundant in the earth’s crust than silver. Yttrium is found in soil in concentrations between 10 and 150 parts per million and in sea water at 9 parts per trillion. The Apollo mission even found some yttrium on the moon!

So, there you have it. A very quick overview of the fabulous, versatile element yttrium. Next month’s post will cover in more detail the use of yttrium as a combination drug/radiation treatment for cancer.

Other Sources:

Yttrium. Wikipedia.org. Retrieved 2/5/2013. http://en.wikipedia.org/wiki/Yttrium

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Sep 25

BiteSize Bio Article: The Pros and Cons of Storing DNA on Cards

I have been very busy in the lab, so I haven’t had much time to review any cool journal articles. About a week ago, my most recent BiteSize Bio article “The Pros and Cons of Storing DNA on Cards” went live. It is about the technology known as Whatman FTA Cards. You can read the article here. For some reason, the article is posted as a members-only article, so you’ll have to create a BiteSize Bio account in order to view it. However, creating an account is pretty easy, so why not? =) It’s a great blog to support, and if you’re interested in science blogging, they are great to work with and will help you get your foot in the door!

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Jul 30

Bitesize Bio Article: A Beginner’s Guide to Storing Biological Materials

I’ve been taking time lately to write technical articles for another blog called Bitesize Bio. It’s one of my favorite biology blogs and Google often brings me there automatically when I search for basic lab knowledge and tips that have helped me through my job.

I thought it would be fun to write up some articles on things I came into the lab being very confused about, and then later cleared up that confusion with experience. While I am still a beginner, I think it is useful to document these questions and answers because they are likely to be at a level that other beginners will understand. The more entrenched I get in the process of academic research, the less I will remember what I once did not understand.

Anyway, the link to the article is here: A Beginner’s Guide to Storing Biological Materials.

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May 30

The Mechanism of Magic Mushrooms

“Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin”

This paper is probably old news by now, published in December 2011 in the Proceedings of the National Academy of the Sciences (PNAS), but worth summarizing nevertheless. The project, aimed at elucidating the mechanism behind the subjective effects of “magic mushrooms,” appears to be a collaborative effort on the part of several universities in the United Kingdom as well as the University of Copenhagen in Denmark.

Admittedly, I don’t usually follow this topic, because I had been under the impression for a while that nobody in the science community had really looked at the subject of “psychedelic drugs” since the 1970s when Tim Leary was running amok. So, it was surprising to see a sentence like the following as an opener to a peer-reviewed original research article put forth by a lab at a mainstream medical school.

“Psilocybin is the prodrug of psilocin (4-hydroxy-dimethyltryptamine), the primary hallucinogenic component of magic mushrooms, and a classic psychedelic (“mind-manifesting”) drug. Psilocybin has been used for centuries in healing ceremonies (1) and more recently in psychotherapy (2); it is capable of stimulating profound existential experiences (3), which can leave a lasting psychological impression (4).”

The researchers took two groups of 15 healthy volunteers (mostly male, on average in their early 30s) and administered psilocybin while their brain activity was measured using BOLD fMRI for one group and arterial spin-labeling perfusion for the other group. All participants had previous experience with psychedelic drugs, but for this placebo-controlled study the drug was administered intravenously instead of it’s more typical oral route.

BOLD fMRI and arterial spin-labeling perfusion are two non-invasive methods by which blood flow in the brain can be tracked, where BOLD fMRI requires a contrast and arterial perfusion does not. [2,3]. Because blood flow in the brain is strongly correlated with metabolism in the brain, it is a useful as a marker for regional brain function [2]. Researchers can then make assumptions about mechanisms of a wide variety of human experiences based on what is known about the function of different regions of the brain.

The researchers found only decreases in blood flow in “switchboard-like” regions of the brain, such as the thalamus and anterior and posterior cingulate cortex. They also found that the magnitude of coordinated decreases in blood flow to the medial prefrontal cortex (mPFC) and the anterior cingulate cortex predicted the intensity of the “trippers’” experiences.

This doesn’t mean much without knowing what neuroscientists currently know about the functions of these regions of the brain. Wikipedia and the articles it references list numerous functions for the thalamus [5]. and the posterior cingulate cortex [4], all of which are related to coordinating the function of other brain regions. Undergraduate level psychology students remember the thalamus as the “switchboard” of the brain, capable of both receiving and relaying information.

Similarly, the prefrontal cortex [7] is considered a source of “executive function.” Tasks under that umbrella include differentiating among conflicting thoughts and impressions and relating present behavior to future consequences or social acceptability. It allows us to know one thing and do another. The anterior cingulate cortex is responsible for autonomic functions like the heartbeat as well as rational decision making, emotion, and empathy.

Remembering before, the most prominent finding in this study is that the coordination between these two brain regions is decreased, and the magnitude of that decrease directly relates to the intensity of the psychedelic experience reported by the subjects. The researchers described this as a perceived state of “unrestrained consciousness,” which does jive to some degree with the way people tend to describe the psychedelic experience. This paper challenges the notion that psychedelics, at least in the case of psilocybin, elevate brain activity. Rather, it seems that it is more accurately described as a suppression of activity in specific types of control regions of the brain.

On the molecular level, the study seems to also support the popular view that psilocybin acts on the serotonin receptors, specifically the 5HT2A receptor. The regions of the brain that were affected by the psilocybin also happened to have very high concentrations of those serotonin receptors.

Another very peculiar and interesting point is that the regions of the brain that are highly active under normal conditions were the ones most dramatically suppressed by psilocybin. For example, the posterior cingulate cortex, mentioned above, has a very high level of metabolism and was suppressed by up to 20% in some subjects. This region of the brain is often considered to be a source of “default mode” where the self or the “ego” is constructed.They cite Aldous Huxley’s metaphor of the brain as a filtering device that manages the flow of information and leads to our perception of the world around us. Perhaps the mechanism of magic mushrooms involves turning off or turning down that filter.

The authors speculated about a number of other claims about psychedelics, including their possible use in treatment of mental illness and ability to reduce cluster headaches. A thorough perusal of this fascinating paper is highly recommended.

References:

1. Robin L. Carhart-Harrisa et al. Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin. PNAS February 7, 2012 vol. 109 no. 6 2138-2143 doi: 10.1073/pnas.1119598109

2. Detre JA, Wang J, Wang Z, Rao H. Arterial spin-labeled perfusion MRI in basic and clinical neuroscience. Curr Opin Neurol. 2009 Aug;22(4):348-55. Review. PubMed PMID: 19491678

3. Wikipedia.org, Functional Magnetic Resonance Imaging.

4. Wikipedia.org, Posterior cingulate cortex.

5. Wikipedia.org, Thalamus function.

6. Wikipedia.org, Medial pre-frontal cortex.

7. Wikipedia.org, Anterior cingulate cortex.

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Mar 25

Studying SIV in it’s Natural Host

See below for image credit

A review paper came out in Science last week that changed my perception of HIV and AIDS. The paper discussed what has been learned about HIV and the immune response by studying the natural hosts of Simian Immunodeficiency Virus (SIV). SIV is the virus from which HIV originated. The term “natural hosts” refers to the carriers of the virus that never develop AIDS. “Natural SIV Hosts: Showing AIDS the Door” by Chahroudhi et al. covers the most recent advances in understanding the mechanisms involved in this protection.

Viruses like HIV and SIV are called “lentiviruses” which are a subfamily of the retrovirus family. The prefix “lenti-” means “slow,” because those infected with HIV can carry the virus for years before developing AIDS. The genome of a retrovirus is made of RNA rather than DNA, and once it is inside the cell of it’s host, it is able to use a host enzyme called a reverse transcriptase to make DNA from it’s genome. Another enzyme called integrase then inserts the newly transcribed virus-derived DNA directly into the host’s genome to be copied indefinitely through normal cell division. In contrast, DNA viruses do not incorporate directly into the host genome in order to replicate. It is for this reason that the host cells usually carry retroviral infections for life.

SIV has infected over 40 species of primates in Africa and is a highly replicating virus. Cross-species transmission of a variant of this virus (called SIVcpz) from chimpanzees to humans, likely through improper handling of infected bushmeat, has been attributed to the HIV-1 epidemic in humans. SIVmac in rhesus macaques is attributed to HIV-2. In order to better understand why the virus causes disease in some hosts but not others, it becomes important to study the conditions where the viral load is quite high but active disease is absent. Because it was thought for a while that high levels of HIV cause AIDS, these types of investigations have been long overdue.

The two natural hosts of SIV are African green monkeys and sooty mangabeys. There are research centers in the United States and Europe dedicated to studying the biological processes that occur in these primates when they are infected with SIV. Because the virus does not give these primates AIDS, researchers are able to infect them with the virus and then extensively monitor how their immune systems respond to the initial infection, or the “acute” phase.

What have the researchers found? In the acute phase of both pathogenic SIV and the benign infection in the natural host, infected cells have a short life span, the viral load is high, and the innate and adaptive immune response is highly active. Also in both systems, the primate suffers a significant loss of a type of immune cell called a CD4+ cytotoxic T-Cell that help the immune system kill off infectious agents.

However, once the acute phase has passed, differences arise. Most significantly, the natural host is usually able to quickly regain it’s healthy CD4+ levels. Evidence of active disease is therefore indicated by a decline in CD4+ levels. According to the paper, many mechanisms for this rapid resolution of immune function in natural hosts have been proposed.

One explanation is that, in response to the virus, the natural hosts initiate processes such as programmed death of immune cells and enzymatic damage of RNA. If there are fewer activated immune cells circulating, then there are fewer immune cells to infect. While high viremia is not associated with the development of active disease, the number of infected cells may matter.

A second hypothesis is that a T-cell receptor called a CD3-TCR is down-regulated in the natural host by a viral protein called Nef. CD3-TCR normally binds a T-cell and allows it to be stimulated by antigens. Infected T-cells with low levels of this receptor will be less prone to stimulation, and therefore less prone to chronic immune activation. The pathogenic virus in the non-natural hosts seems to have lost the ability to down regulate CD3-TCR. (Some researchers have considered a clever experiment to help elucidate this further, in which the benign SIV virus is genetically engineered to produce an HIV-like Nef protein to see if that leads the natural host to develop AIDS.)

A process called bacterial translocation is thought to cause chronic immune activation and progression to disease in HIV and SIV patients. Bacterial translocation is when the integrity of a mucous membrane, such as the intestine, is lost and bacteria present there are able to enter the bloodstream. Another difference between the natural host and the pathogenic case is that the natural host’s mucosal tissue integrity is preserved. Researchers think that this may be protecting the natural host from the bacterial translocation associated with active disease.

Interestingly, it seems that the virus is also less likely to affect the tissues of the natural hosts where the immune responses initiate, such as the lymph nodes, which have shown in experiments to retain normal histology. With lower viral loads in such critical locations, it will become easier for the host to recover it’s CD4+ levels after the acute phase of the infection.

Why would the virus have different tissue specificity in the natural host? While the total number of infected T-cells can impact disease progression, it is thought to be even more important which type of T-cell is affected for AIDS to develop. Different types of T-cells are associated with different tissues.

In the natural host, the more expendable T-helper effector memory cells found in the mucusal tissue called are targeted, and in the pathogenic case, the T-helper central memory cells are targeted. T-helper memory cells are located mostly in the lymphoid tissue, are more long lived in the body. If infected, it becomes more difficult for the host to regain healthy CD4+ levels. This has been shown in measurements of CD4+ infected cells in human HIV sufferers; the infection level of the memory cells is usually the highest of all the T-cells infected.

The central memory cells of the natural host also express much lower levels of the main virus receptor called CCR5 that allows the virus to enter the cell. Also, around 7% of sooty mangabeys actually have a mutant form of the gene that codes for the CCR5 viral receptor, making it less expressed on memory cells, and therefore it is less probable that the virus will enter those cells.

Lastly, there is a small percentage of sooty mangabeys that are born with a naturally low level of CD4+ T-helper central memory cells, and instead have another type of immune cell called a DN (double negative) T-cell that acts as a useful substitute. The naturally low level of CD4+ cells combined with another cell type that produces a productive immune response may protect these animals from AIDS.

In light of all the above evidence, it is believed that the natural hosts of SIV have co-evolved with the virus, where the virus is able to replicate but the host does not suffer disease. Low rates of mother to infant transfer of the virus may also be evidence of this co-evolution. And, infants who do acquire the disease from their mothers usually have relatively low levels of viral replication compared to adults.

A noteworthy observation is that there are rare cases of HIV infected humans who exhibit an immune response very similar to the SIV natural host — stable CD4+ T-cell counts despite high viral load — and never develop AIDS. The authors project that this may lead to new insights in treatment of HIV for humans.

References:

Chahroudi, A; Bosinger S, Vanderford T, Paiardini, M. “Natural SIV Hosts: Showing AIDS the Door” Science. 9 March 2012. Vol 335, 1188-1193. doi: 10.1126/science.1217550

African Green Monkey image: http://naturalunseenhazards.wordpress.com/tag/african-green-monkey/

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