The 6th Edition of Through the Microscope is now complete

Contributed by paustian on Apr 23, 2017 - 02:55 PM

The 6th edition of Through the Microscope is now complete, including hard copy, and ebook versions for Kindle and epub readers. The 5th edition is now officially retired. I was originally going to close the 5th edition, but there are a number of courses and classes still using it. Therefore, it will remain open for at least another year. I still strong encourage any future students to use the 6th edition. In any case, enjoy!

GMO food of no real danger

Contributed by paustian on May 18, 2016 - 09:26 AM

love science and microbiology. I love fitness and nutrition. If you take care of your body and feed it well, it goes a long way to having great quality of life. So I am always interested in fitness and nutrition.

Having the perspective of a scientist, any claims I read for a fitness routine or nutrition regimen have to backed by good solid evidence. This can be very hard to come by. Nutrition research is extremely difficult, because you are dealing with food. The food we eat is incredibly complex, containing hundreds of chemicals that interact with our genetic background and our microbiomes. Even more complexity is added if you are doing the food research using people. Any human subject research will involve hundreds of uncontrollable variables, because you cannot tell a human to only consume leafy greens and broccoli for a year and please stay in this cage the whole time. Where they live, their behaviors and what other food they eat will all influence whatever the research is trying to measure. No matter the nutrition question, finding an answer can be extremely difficult. 

Glyphosate appears to not cause cancer

Contributed by paustian on Nov 14, 2015 - 02:57 PM

Science Insider reports that a recent evaluation from the European Food Safety Authority (EFSA) declares that glyphosate is unlikely to increase the risk of cancer. They also set a limit on what is thought to be a safe does, 0.5 mg per kilogram of body weight. So someone weighing 80 kilograms (166 pounds) could consume 40 mg of glyphosate a day and run no increased risk of cancer. Other agencies have weighed into this in the last few years and concluded that there is some risk. The difficulty comes from assessing the toxicity to humans either based on studies using rats or mice as the model animal, or looking at epidemiological studies. Mice and rats are not humans, really. Our bodies may react differently than a rodents. In the epidemiological studies, large populations have to be examined to detect small risks and often these studies are expensive and fraud with confounding variables. Epidemiological studies can only show correlation, not causation. For right now, it seems glyphosate, such as Roundup, appear to be safe.

Hepatitis C, what was once incurable, can now be cured

Contributed by paustian on Nov 07, 2015 - 11:59 AM

Hepatitis C (HPVC) is a virus that attacks the liver, and will take up residence for the long term. The body is unable to rid itself of the virus and it will continue to replicate in the liver, potentially leading to cirrhosis of the liver, liver cancer and potentially death. Recently some powerful new drugs have won approval that treat various parts of the HPVC replication cycle. Jon Cohen reports in Science Magazine of a new treatment combining the most promising of these drugs into a single therapy that in a small clinical trial cured patients of the virus in just 3 weeks. While the trial tested this idea out on the most treatable patients, it clearly demonstrated the power of the new drugs.

There is a downside to the story in that the drugs developed are prohibitively expensive with some of them selling for $1000 a pill. In addition the various drug companies have not tried these therapies sooner because they seem themselves as competitors, not collaborators. However, physicians are free to prescribe the drugs in combination. It’s a great day for science and drug development.

The 5th edition of Through the Microscope is now available

Contributed by paustian on Jan 15, 2014 - 07:39 PM

After several months of hard work, updating the textbook, working on site design, and upgrading the code, the 5th edition of Through the Microscope is now ready. The new edition includes:

  • New information on bacterial division
  • An updated section describing the bacterial cytoskeleton
  • A completely updated Microbial Ecology section
  • A new more efficient site design that makes using the textbook easier
  • AJAX code that makes available new book tools for working with the textbook
  • and much more

The 5th edition is available by subscription using PayPal (or credit cards). Subscribers to the textbook can also download an eBook version (which has also been updated to a 5th edition). For those that prefer a book they can hold and take with them, you can purchase a print copy of Through the Microscope​ from See the Subscribe to the Book section at the bottom of this page for more information. 

You can learn more by  browsing the table on contents.

Dynamix is Dynamite

Contributed by paustian on Jan 03, 2014 - 07:31 PM

The last day of the week it is an option to take a rest day. If you are feeling good and not hurting too bad, I really recommend you do the Dynamix workout. It is not demanding and is so good for working out the kinks. After a week of P90X3 I was sore all over, not too bad, but I was feeling it. However, I really wanted to explore this DVD so I popped it in and I am glad I did. This is the final workout of the first cycle and it works outs out all your kinks and helps with mobility. It is a recovery workout, giving you a break and not working you too hard. However, I was sweating by the end of it because you do some isometric moves for your core. Dynamix again is all new stuff, and it is based on the latest research about stretching – it is more effective to dynamically stretch your muscles than static stretching alone and that is what this workout teaches you. The cast is great as always. Two people from the test group and an olympic sprinter from England who helped Tony develop this routine.

After the first week, I must say I am really impressed with P90X3. I do hope the next set of workouts will focus a little more on the arms, as I feel that is lacking in these workouts. However, I think I may be wrong about how much my arms were involved, because they are sore after the week, clearly being worked.

The Warrior Workout

Contributed by paustian on Jan 02, 2014 - 08:03 PM

This is the workout that Tony developed for traveling around the country to various Military bases. He was faced with an interesting problem, how do I create a workout that a ton of people can do at once, that doesn't require any equipment, large amounts of space, and is challenging. The answer is, The Warrior. This is an intense workout that challenges all your muscles. It is broken down into 4 complexes of 4 moves each; an upper body move, a lower body move, a core move and a cardio/plyo move. Many of the moves incorporate a stability component, forcing you to recruit muscles along the kinetic chain. For example, Thumbs-Up Push-Up, you do a push-up and then raise your right arm and left leg. This activates the stabilizing muscles in your left arm and right leg, while at the same time working your back, glutes, hamstrings and shoulders. Needless to say, you will be sweating by the time you get to the end of this, but it's fun all the same. Be careful with the sprawl moves (moving to the ground from an upright position) Form is important here to avoid injury. This is a great workout to do on the road, since you don't need any equipment and can do this anywhere.


Contributed by paustian on Jan 01, 2014 - 06:23 PM

When I first saw this I wondered what does CVX stand for? From doing the workout I think it stands for CardioVascular X, and this is Tony's idea of an aerobic workout. I think a better name would be Med Ball Hell. In CVX you do a bunch of moves designed to get your heart rate up and then add a med ball (or dumbbell) to add resistance to what you are doing on the upper body. The combination is a challenge. I started with a 10 pound med ball and after a few exercises I moved down to a 6 pounder. This workout is a testament to how well designed the program is; a difficult move (Press Jacks, Holding a weight at chest level, jump your feet out as you extend the weight upwards. Lower the weight as you return to a normal standing position) is followed by two easier moves (Atlas Twist, a lunging and twisting move) and (March and Reach). The moves come in clusters of 3, you do the first set at a “moderate” pace and pick it up for the second round. In all there are 4 sets of 12 moves, so you end up doing 24 moves. You will be sweating by the end of this, but it's a great cardio workout. Tony is again hilarious (I do like corny humor, you may not). The cast really work well with Tony and you can tell they enjoyed the workout.

Some of CVX grew out of Tony's work in the One-on-One series (for example, Medicine Ball Core Cardio). P90X3 really is a culmination of everything Tony and the rest of the Beach Body team have learned about fitness and nutrition. I loved this workout.  

X3 Yoga

Contributed by paustian on Jan 01, 2014 - 06:20 PM

This is a workout for those who don’t like yoga. You go through some nice poses, and get a little balance work in too. And you are done in no time. Ted comes back from P90X2 yoga, Terry Morrow of P90X2 Plyocide and Stephanie Saunders rounds out the cast. (Stephanie is Tony’s helper in many of his online chats and worked really closely with him developing the whole P90X3 series.)  I really liked the supporting cast, they have a great chemistry and Tony is FUNNY in this one.

Agility X

Contributed by paustian on Dec 30, 2013 - 12:44 PM

I can give you my impression of this workout in one word. Wow! It keeps you moving, its fun, it pushes you in all sort of directions and Tony is his hilarious self. This workout is all about doing cardio type work, yet also working on your balance and precision. You are told in How to Accelerate to create some markings on the floor with Tape, or quarters or something. You are asked to use tape, about 4 foot sizes long, in the middle mark an X and put Xs on each side of it. Make two tape strips like this and then place them about 4 feet apart if you are in pretty good shape and agile, or less if 4 feet is too difficult. This is the first workout that uses them and this is essential. Don't blow it off and say you can imagine it, you need those targets to have your body move in exactly the right way, using the right muscles. I would liken this workout to plyometrics, but it adds a coordination component to it that is really fun. Don't beat yourself up if you can't hit the targets and you find yourself fumbling the first few times in. Just keep trying. This is the stuff that athletes do and if you work on these areas, you will become more athletic yourself. I was drenched in sweat after this one.

New Microbial Ecology Chapter

Contributed by paustian on Dec 30, 2013 - 12:37 PM

A completely reworked and modernized Microbial Ecology Chapter has been published today. Recent advances in DNA isolation and sequencing have made it possible to investigate the microbes present without culturing them. This has completely changed our understanding of the microbial population that is present in the environment and what they are doing. Finally, a clear picture of the environment at the microscopic level is emerging and in the years to come we will learn how it all fits together. It’s an exciting time to be a microbiologist.

P90X3 Impressions

Contributed by paustian on Dec 28, 2013 - 01:45 PM

This series of blog posts are going to be about the new P90X3 workouts. I thought it would be fun to write my impressions of the program as I did it, to give people a taste of what it is like. I just got the P90X3 discs and of course I went through all the material. This looks like it's the same top quality as P90X and P90X2; what else would you expect from Beachbody and Tony Horton? I bought the deluxe package to get the extra workouts. You have a nutrition guide (which I will cover later), the workouts, extra exercise bands, the energy and endurance formula and the DVDs. You also get a workout calendar (and an extra workout calendar for the extra workouts).

Energy and endurance formula

This is advice that I would give anyone, before you start a supplement, read the ingredients. One of the top ingredients is caffeine, and that does not agree with me. If I take in any caffeine it keeps me up at night, and I mean any caffeine. So this is one part of the package I won't be using. Your milage, of course, may vary.

The calendar

This is nicely done, giving you a chance to see what workout you need to do and also having a box to check whether you kept to your diet or not. It's a great motivator for anyone who is just starting out. Seeing those little check marks pile up helps to keep you going and adding the diet check mark is a nice touch. Put the calendar up somewhere and use it.

Why is basic research important? Here is your answer

Contributed by paustian on Sep 17, 2013 - 02:21 PM

In the early 1960's Tom Brock was on vacation in Yellowstone National park. He hit the usual tourist destinations, including the hot springs of the park. To his astonishment, he observed what he was sure were cyanobacteria living at temperatures over 80°C (176°F). Professor Brock went back to his lab and wrote a grant to study the microbes present in this environment. Now many would think that this research is esoteric at best. However, as part of that research, Tom discovered Thermus aquaticus, a microbe that has a optimum growth temperature at 85°C. This was unheard of at the time and it opened up the field of extremophiles, which has let to many important discoveries. 

Fast forward until the 1990's, where Kary Mullis is searching for a replacement polymerase that can withstand the heat of a new reaction cycle he is working out. He decides to use the polymerase from Thermus aquaticus, now known as taq polymerase, instead of the polymerase of E. coli. Taq polymerase can withstand the high temperature his procedure requires. His experiments are a success, the polymerase chain reaction (PCR) is born, and Dr. Mullis wins the nobel prize. PCR is now a powerful technique used in medicine, the food industry, forensics, many types of basic research, and much more.

For his work, Dr. Brock received the golden goose award, celebrating the huge payoff his little experiments in Yellowstone had. Professor Brock was a faculty member here at the University of Wisconsin-Madison.

A measleslike virus is responsible for the recent Dolphin die-off

Contributed by paustian on Sep 06, 2013 - 09:21 AM

Over 300 dolphins have washed up along the eastern coast of the U.S. since July 1st of this year. Scientists at the NOAA declared a Unusual Mortality Event, allowing them to use fund and perform an extensive investigation of the cause. A combination of classic of tissue investigation along with molecular techniques  that assayed for the presence of the virus, revealed the cause to be a Morbillivirus. The Morbillivirus family includes viruses such as measles, that infects humans, and distemper, that infects dogs. The dolphin virus poses no threat to humans.

A similar outbreak in 1987 killed more 700 dolphins. This recent outbreak was probably caused by a large enough population of young, susceptible dolphins being being to now sustain another epidemic of the disease. The virus is likely to continue to cause illness until the population of susceptible individuals declines, either by them gaining immunity to the virus or dying.

Compound Produced by Ocean Microbes Could Treat Anthrax and MRSA

Contributed by vosen on Aug 16, 2013 - 02:23 PM

Researchers at the University of California - San Diego have found a microbe in the Santa Barbara Bay that may produce a compound that could be used to treat anthrax and MRSA (methicillin-resistant Staphylococcus aureus) while conducting research.

The microbe belongs to the Streptomyces family and is found in the sediment close to the shores of Santa Barbara, California. The compound it produces, called “anthracimycin”, was novel in structure, which was solved by spectroscopy. Initial testing of anthracimycin showed it to be a powerful compound against anthrax and MRSA.  Anthracimycin would be a tremendous breakthrough as a drug because anthrax is feared as a possible weapon of bioterrorism and MRSA creates difficult to treat infections, typically in hospitals. In order for anthracimycin to become available as a treatment, more testing and development is needed to ensure the safety of it on people, which may take years.

Gut microbes’ role in species divergence

Contributed by mcoplan on Aug 16, 2013 - 10:01 AM

It is well known that gut microbes play an important role in the health of many organisms.  Seth Bordenstein and Robert Brucker, biologists at Vanderbilt University, were curious to see what other effects these microbes may have on an organism.  They studied the role of microbes in three related species of parasitic jewel wasps.  Two of the species, Nasonia giraulti and N. longicornis, are closely related, whereas the third species, N. vitripennis, diverged about 1 million years ago.  Offspring of  a cross between N. giraulti and N. longicornis generally result in surviving offspring.  However, when either specie was breed with N. vitripennis, almost all male larvae in the second generation die. 

Biofilm matrix gene expression in B. subtilis

Contributed by microsummer2013 on Aug 15, 2013 - 07:11 PM

In a recent paper that was published by the Gourse Lab at the University of Wisconsin-Madison,discusses the biofilm matrix gene expression in Bacillus subtilis. A biofilm matrix is made up of multicellular communities that stick to many types of surfaces in different environments, and the production of extracellular matrix enables the formation of these communities. Once the biofilm matrix forms, the flagella motility is inhibited by the organism. On a molecular level, the eps and tapA-sipW-tasA are two essential operons that enable the production of the biofilm matrix. In addition to the eps and tapA-sipW-tasA operons, SinR and RemA are two DNA-binding proteins that play vital roles in the regulation as well. The Gourse Lab suggested that the DNA-binding protein SinR negatively regulates the eps operon expression by blocking RemA binding. In addition, SinR functions as an anti-activator to the Peps promoter.

'Epilepsy in a Dish': Stem Cell Research Reveals Clues to Disease's Origins and May Aid Search for Better Drugs

Contributed by hmelfman on Aug 14, 2013 - 05:59 PM

Scientists at the University of Michigan Medical School have created an exciting new model called “epilepsy in a dish” to study seizure disorders. It works by converting skin cells from patients harboring an epilepsy disorder to stem cells and then to neurons. The patient specific neurons allow for the study of brain cells and brain activity without the need to perform a brain biopsy. The overall goal of this study is to create induced pluripotent stem cells from cells of patients with different epileptic syndromes in order to understand the mechanisms behind the diseases and for drug development.

Human herpesvirus 6 infection linked to chronic fatigue syndrome (CFS)

Contributed by lyehui on Aug 14, 2013 - 03:59 PM

Chronic Fatigue Syndrome (CFS) is a disorder characterized by extreme tiredness that does not go away with bed rest, lasts for about 6 months in adults. Some of its many other symptoms include cognitive problems, headaches and vertigo. A study in the Journal of Health Psychology also found a high mortality level (12.5%) in CFS patients over the course of 10 years.

Experts believe that CFS has many root causes including psychological factors, pathogens and genetic predisposition.  Recently, a study led by the University of South Florida published under the Journal of Medical Virology suggests that Human Herpesvirus 6 (HHV-6), a common virus, may be a culprit behind some CFS cases.

Inflammatory Response Turned off for Allergic Asthma and CODP Patients

Contributed by sayaovang on Aug 14, 2013 - 12:59 PM

Inflammation is a type of immune system response to injury or irritation.  This response is problematic to the individuals who have asthma and chronic obstructive pulmonary disorder (COPD), though.  Asthma is a lung disease that causes inflammation and narrowing of the bronchi of the lungs, which makes it hard for people with asthma to breathe.  COPD is also a lung disease which causes poor air flow to the lungs due to inflammation, also making it hard for the individual to breathe.  Japanese researchers have gained knowledge on two specific receptors that respond to an inflammatory molecule known as “leukotriene B4,” which is found within individuals who have allergic asthma and COPD.  Prior to their findings, they believed that BLT1 and BLT2 receptors promoted this inflammation, when in fact, they actually have opposite roles.  BLT1 does promote inflammation, but the new finding is that BLT2 weakens the inflammation.

The Microbes in Our Bodies are as Unique as We Are

Contributed by tjtownsend on Aug 14, 2013 - 09:59 AM

In a world of bacteria, the tiny microbes that inhabit the human gut can reveal a lot about an individual.  The human body houses such a high amount of microbes that it significantly outnumbers the number of human cells a person has.  Recently, scientists have sought to better understand the vast number of microbes in the colon, in order to use this information to better human health.

The American Gut Project is dissecting thousands of stool samples to truly understand what microbes exist in the colon, what each microbes function is, and how this information can be used to improve certain diseases linked to the colon.  In the midst of the project, research has shown that the microbes in the human gut are deeply connected to the health of each individual, linking type 2 diabetes, colitis, asthma, depression and weight gain to colon microbes. 

As scientists collect and analyze poop, they have found that no two people contain the same exact makeup of microbes.  The reason the gut microbes differ from individual to individual remains unclear.  However, there are some patterns that are emerging. To create a “supergut” of microbes, one should eat a diet rich in onions, garlic, and leeks.  Cooking vegetables al dente has been shown to increase microbe diversity because the body has to work harder to break down the food so more of that food ends up in the colon.  Like all other diets, the more diverse the plate is, the more diverse fiber that can be consumed, also leading to a healthy, diverse colon.  The scientists of the American Gut Project encourage everyone to get a little dirty and keep windows open, exercise outside and work in a garden.  Those who own dogs have more diverse microbes as well.  Exposure to these environmental microbes helps flourish the colon microbes.  

New Technology Allows Crops to Take Nitrogen from the Air!

Contributed by bgeracie on Aug 13, 2013 - 05:42 PM

The University of Nottingham, located in England, has developed a new technology that would allow all of the crops in the world to take in nitrogen from the air instead of from fertilizers.  During nitrogen fixation, a plant processes nitrogen (which is taken up by the fertilizer and soil) and then converts it into ammonia, which is a form of nitrogen that the cell can utilize. With the conversion of ammonia, the cell adds glutamate, which then creates glutamine. This process is extensive and takes up much energy in cells, but is necessary for growth and survival. 

Diet-Induced Alterations of Host Cholesterol Metabolism Are Likely To Affect the Gut Microbiota Composition in Hamsters.

Contributed by mjwest3 on Aug 13, 2013 - 03:42 PM

While it has been well established that the gastrointestinal microbiota plays a role in the regulation of host metabolism, little is known about the connections between the composition of the gut microbiota and its effect on host metabolic pathways and processes. This is a valuable area of research, as changes in the host gut flora have been linked to various health problems. This knowledge calls for a better understanding of the bacterial patterns and functions associated with and contributing to these health problems.

The Constant Battle of the Common Cold

Contributed by mnjones on Aug 13, 2013 - 12:42 PM

Ever wonder why no matter how hard you try to stay healthy and get plenty of rest, you always seem to get a cold just as winter comes around. One factor of the common cold, recently discovered by Ellen Foxman of Yale University, may be out of your control; the weather. The article, Colder Viruses Thrive in Frosty Conditions, further explains how colder temperatures have been shown to be a reason for the flare up and spread of the common cold.

Recent evidence from rover Curiosity suggests life may have existed on Mars years ago

Contributed by dwaller on Aug 11, 2013 - 09:41 AM

If you ask most people is microbes could survive on Mars, they would answer  "no".  Yet recent evidence from the rover Curiosity suggest that life (microbes) may have existed billions of years ago, when analysis of rock drillings showed traces of some of the most fundamental elements for life (sulfur, hydrogen, carbon, oxygen, nitrogen, etc), in addition to water covering the planet's surface. 

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