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The snail gets up
And goes to bed
With very little fuss

 -Kobayashi Issa (1763– 1828)

 
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Posted by on March 4, 2014 in Uncategorized

 

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Substrate Level Phosphorylation

Several processes occur during normal eukaryotic metabolism to create ATP. During glycolysis (the breaking of sugar) both prokaryotes and eukaryotes use energy from the chemical bonds in the sugar to make ATP by directly transferring phosphates from the substrate molecule to ADP, resulting in ATP. Predictably, this process became known as ‘substrate-level phosphorylation. Both Cell Respiration, occurring in the mitochondria, and the light reactions of photosynthesis, occurring in the chloroplasts, also made ATP, however, no one understood how this occurred as no intermediate substrate molecule bearing the phosphates groups was known.

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1978 Nobel Prize in Chemistry winner

The Peter Mitchell, working at his own, privately funded research foundation, tackled this problem and determined that the power to make ATP came from two processes linked indirectly. For his work in this area, Mitchell won the 1978 Nobel Prize in Chemistry “for his contribution to the understanding of biological energy transfer through the formulation of the chemiosmotic theory”.

Model diagram of electron transport and H+ translocation across the membrane

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Electron flow carries H+ across the membrane

Process#1: One of these processes is the electron transport chain (E.T.C.) during which a high-energy, excited electron is passed down a series of membrane proteins. As the electron is passed, it sometimes pulls hydrogen ions (H+) along and passes them across the membrane (see the cartoon illustration of this model by Mitchell). As a result, this process creates an electrochemical gradient across the membrane with more H+ on one side compared to very few on the other.

Process #2: As we know, these gradients will ‘want’ to resolve themselves and move towards equilibrium (by diffusion). There exists a special channel protein that H+ may pass through from the side of the membrane with a high concentration of these ions to the other.

“Each chemical species (for example, “water molecules”, “sodium ions”, “electrons”, etc.) has an electrochemical potential (a quantity with units of energy) at any given location, which represents how easy or difficult it is to add more of that species to that location. If possible, a species will move from areas with higher electrochemical potential to areas with lower electrochemical potential; in equilibrium, the electrochemical potential will be constant everywhere for each species”

                         -from the wiki page on electrochemical potential

I prefer to imagine the membrane and ions as a hydroelectric dam with water building up on one side and a relief passage through the dam.Image

Just as energy is captured when water rushes through the dam, H+ ions coming through the channel protein are used to power an enzymatic subunit that synthesizes ATP.

Sigma-Aldrich provides an excellent animation illustrating how ATP Synthase operates as both a H+ channel and an enzyme making ATP.

http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/metabolic-pathways/atp-synthase/atp-animation.html

A conceptually simple set of experiments provides the evidence supporting this model. Here, an artificial membrane is made incorporating ATP synthase and bacteriorhodopsin. The rhodopsin molecule is capable of transporting H+s across the cell membrane when it is struck by light. Given sufficient supplies of H+ ions, ADP and Pi, ATP will be formed when a light source is present. In the absence of light, no H+ is transported and no ATP is made.

When a H+ carrier molecule that can diffuse through the membrane is introduced, this carrier maintains equal amounts of H+ on both sides of the membrane. Further, even when light is present, H+ is pumped across the membrane and then re diffuses back creating little or no ATP. This is illustrated in a cartoon from Albert’s Essential Cell Biology:

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Chemiosmosis defined experimentally

Chemiosmosis and the work of Peter Mitchell

 
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Posted by on October 5, 2013 in Uncategorized

 

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RadioLab: Source of great conversations

I wasn’t searching for a way to talk about death and the end of life discussions that families must have about it. I was just transporting my son from our home in Paola, KS to his gymnastics class in Lenexa. It’s a thirty minute drive – give or take. Perfect for a good conversation or a couple songs – perfect for a RadioLab Short.

My son is seven and we both like listening to these programs on our drives. I know he’s a little young for much of the material, but it always makes him ask such good questions. It challenges him in his thinking and he gets to see a parent consider and turn over new ideas too.

I wasn’t paying strict attention. I was driving. I was zoning. I was in the audiobook / NPR / Podcast Groove. My eyes on the road, my mind on a walk with the program. We were driving North at about 70 mph and absorbing the program as it pulled us in, bit by bit.

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Doctors who would accept given care options if they were in a state of advanced illness

The Bitter End – a short about how doctors and lay people see end of life care through very, VERY different eyes. To be honest, there was nothing very surprising in the discussion on the radio. Despite the fact that I am not a clinician, my viewpoint of end-of-life care was precisely in line with that of most medical professionals that were surveyed in this report.1 But, that’s a completely reasonable consequence of the proximity of my work to the medical field, having many close friends who are physicians -even my wife in a clinician.

The reality is, people who work in and around hospitals and people who’s impression of hospital care is shaped as much or more by real hospitals than those in TV land, have clear, unromantic ideas about what end of life is like. Also, we have seen more and talked about more situations of ‘heroic’ interventions and know what those outcomes look like.

For instance, my aunt had a heroic intervention by a neurosurgeon following her seizure and fall on the stairs that resulted in a severe head injury, best left to its natural conclusion. Instead, I listened to the doc pat himself on the back for his ability to save her life and turn a sudden trauma with a virtual DOA arrival at the hospital into a yearlong struggle with finding her care as she remained in an unresponsive coma. Oh, and I almost forgot, that meant that we had to actively make the decision to withdraw her feeding tube and fluids so she could die slowly over a number of days in the only legal outlet from this terminal condition. So,… thanks, Mr. Surgeon. Good work.

As I said, I was sort of in the zone and not thinking until we came to a stop at a red light and I suddenly remembered my seven-year-old passenger and thought about what we were listening to.

I don’t believe that there is anything wrong with talking about death – even with children. Death comes to us all in time and we all lose parents and friends and other family. Nevertheless, I thought I might want to take a quick exit before the story went too far. But to turn it off, I had to ask if he had been listening (yes) and would he like to talk about what we heard? (also, yes)

I was relieved when he told me that if I was in the hospital and going to die that he would tell the doctors to give me a ‘sleep shot.’ Then he thought about it … and thought about it some more… And then the waterworks started and he was wailing about how I couldn’t even die, nor his mother, nor his grandmother (Oma) – who would mend his blankie?! No. None of us could ever die. And he would tell the doctors to do anything and everything they could to keep us alive for one more day, one more hour, or minute, or second. And when we died, he wanted to die as well.

fortune-cookie

Are you feeling lucky?

I let him cry a bit and brought him back from the brink with some cuddling in the parking lot of the Chinese restaurant we were headed for. Then we had a nice talk about cognitive dissonance before we drowned our sorrows in wonton soup.

Reference

1. http://www.jhu.edu/jhumag/0601web/study.html

End of Life Care: A RadioLab discussion

 
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Posted by on January 17, 2013 in Uncategorized

 

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Counties Declared in Drought Emergency Summer 2012 (4)

It would be easy to forget that we are still in a fairly severe drought in the midwest. Over the summer of 2012 82 counties in Kansas were declared as federal drought emergencies in early July 2012. Just two weeks later governor Sam Brownback declared every county in the state to be in a drought emergency. Each declaration has different meanings as the first allows for federal aid for agriculture and related industries, while the second allowed water to be taken from lakes in state parks to aid the same industries(1,2). 

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100% of Kansa counties in drought emergency August 2012

This summer the drought was hard to miss. Ponds were down to puddles, crops were failing and getting tilled back into the soil all around, trees were turning autumn colors and dying in July and lawns were dead with the ground dry and cracked.

Personally, I’ve never seen anything like it. Apparently, this was the worst drought in 25 years, if not more. Not long after, the East coast was getting hit by freakishly early winter storms and ‘superstore Sandy’. (I got regular updates from my family, who all live in the mid-Atlantic region).

Now, on the last days of December, the drought feels like a thing of the past, however, we are still in severe conditions here in the Midwest (I live in Kansas). I heard yesterday on NPR that Kansas is still 17″ below normal rainfall, and a quick look to the NOAA shows that the entire state is somewhere between ‘severe’ and ‘exceptional’ conditions (3). 

With luck, I will be shoveling endlessly this winter and we can recover somewhat by spring.

 

I want to apologize, I haven’t been posting much lately because my family has been away and I have spent most of every day outside working on the shop from first light until dark and then collapsed exhausted inside. 

I did have some time while waiting for my wife’s car in the shop yesterday to get a simple children’s book I wrote for/with my son put together as an iBook. It was submitted yesterday and will likely be available for free download sometime this coming week. I’ll post again when that’s available. (Don’t expect much though, the original was a hand-drawn mini book that I redrew using Fifty Three, Inc.’s ‘Paper’ App and an artist’s stylus… and I’m not that much of an artist)

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1. http://www.ksda.gov/news/id/472

1. http://blogs.kansas.com/weather/2012/07/26/kansas-governor-declares-entire-state-is-in-drought-emergency/

3.http://www.crh.noaa.gov/eax/?n=drought

4. http://www.kwo.org/reports_publications/Drought.htm

 
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Posted by on December 30, 2012 in Uncategorized

 

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Aside

In class this week we will be continuing our discussion of genetics / inheritance by completing chapter 23. We will also take a timeout to watch a short clip from a movie I enjoy that ties into the topic of probability that we will discuss in association with the coin toss lab (in your handbook).

We will then finish class by talking about Your Inner Fish, the ‘Making Scents’ chapter. 

 

Altogether, this should put us on schedule to have a quiz on inheritance as it was known by Mendel on Thursday.Image

 
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Posted by on November 12, 2012 in Uncategorized

 
Aside

The Human Microbiome Project is an NIH-sponsored initiative with the goal of identifying all of the many kinds of micro-organisms that we harbor in our bodies as healthy individuals. This is an interesting project for a number of reasons. First and foremost, because we have long assumed that micro-organisms are present only when we are sick – not healthy. Also, what we learn from this project can have a great impact on how we use antibiotics to treat many of the infections we get that do make us ill (often demanding them as patients even when they will do no good as when we have a viral infection like flu or the common cold). Lastly, we are now learning that alterations in the microbiome of our gut or elsewhere may contribute to more subtle changes in our health, like the incidence of allergy, asthma or obesity.

There have been a number of articles on this topic since the publication, in June 2012, a reference database of what constitutes a healthy microbial population. An excellent thorough examination of these data and their application was published in The New Yorker’s Annals of Science column by Michael Specter, ‘Germs are Us, Bacteria make us sick? Do they also keep us alive?’ Therein, Mr. Specter examines the impact of many modern developments that may be tweaking the population of microbiota that we harbor (especially in our gut), from the use of antibiotics, to the fiber content of the food we eat, to our obsession with cleanliness.

H. pylori

Amongst the scientists doing work that Mr. Specter refers to is Dr. Martin Blaser of New York University’s Langone Medical Center. Much of Dr. Blaser’s work has focused on the role of Helobacter pylori in health and disease. This organism is of special interest because a number of years ago this very organism was identified as causing gastric ulcers. In fact, I use this year after year in my own class as an example of how Koch’s Postulates were applied to pinpoint the cause of these ulcers. In those experiments it was shown that many ulcers have populations of H. pylori growing in them and that these organisms can be transplanted into the gut of a healthy patient and cause the same disease. Further, treatment that kills H. pylori results in amelioration of the ulcers.

Nevertheless, Dr. Blaser’s work does not focus on the role of H. pylori in disease, but rather on its role in maintaining the health of the organism. He, and others, have shown that ridding the body of H. pylori may result in an increased incidence of gastric reflux, asthma and obesity. This relationship is discussed in a short article in The New York Times from 2011. It may not be that H. pylori itself is responsible for all of these conditions, but perhaps other organisms that are eliminated by the same drugs that kill H. pylori contribute to these conditions.

Obviously, there is a lot going on within our bodies and a holistic view of how our actions impact a wide variety of systems may be required in order to successfully design treatments that target the ill-effects of some micro-organisms while preserving the health-promoting effects of others.

I’m definitely going to put some more work into researching this topic so I can incorporate a discussion of it in my microbiology class next semester, so don’t be surprised if you read more about this here in the future.

The Human Microbiome Project at Work

 
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Posted by on October 21, 2012 in Education

 

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Aside

A static view of the tree of life

Onezoom.org is an effort o display all of life and its relationship with one another in a single ‘zoomable’ phylogenetic tree. Currently one the mammalian branch of this tree is available, but it is still extraordinarily interesting and gives an idea of the grand scope of the project. Here’s an introductory video showing the intent of the project and why the organizers developed it in the way that they did.

Here’s a link to the site itself where you can try out the viewer. — By the way, +1 point on the upcoming chapter 5 quiz for any of my students who try this out and can email me a screenshot of where humans fit into this tree. I realize this requires you to go to the site, try out the viewer, find humans AND work out a way to visually document that -but there it is.

http://www.onezoom.org

I would like to thank nothinginbiology.org for pointing me toward this resource. I tried to reblog their post, but I ran into some silly technical problems and found it easier just to write up something myself.

OneZoom

 
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Posted by on October 20, 2012 in Education, Uncategorized

 

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