Category Archives: Microbe Life

Inbreeding, Invading & Pacemaking || Labrat’s Digest

Aaaaannd I’m baaacck with The Labrat’s Digest! Happy new year to all, and it’s time to see what’s in store for science in 2019. This week, we’re taking a trip back in time to the Tudor years, checking out some of the critters in our homes, and finally, can scientists create a pacemaker for the brain?

Keeping it in the Family

It’s a poorly kept secret that many of the European royal dynasties believed in keeping their power concentrated within the bloodline. And a big part of “keeping it all in the family” has always included members of these ruling houses marrying and having offspring with their distant or close cousins, aunts, sometimes even their siblings! This way, they could make sure that the bloodline was kept “pure” and fit for ruling the kingdom.

This practice isn’t ancient history either. Queen Elizabeth II of England married her third cousin, Prince Phillip, and they’re still married to this day!

It’s also a poorly kept secret that inbreeding can be dangerous for the child;
you see high rates of miscarriages, stillbirths, deaths, or genetic deficiencies that manifest as physical deformities or mental disabilities. One particular deformity that was common among royals was known as the “Habsburg jaw“.

The Habsburgs were a powerful Austrian family that ruled over various parts of Europe during the 14th, 15th and 16th centuries. They were also notorious for their incestuous relationships: nine out of eleven royal marriages during their reign were between family members. The Habsburgs did this in a desperate bid to maintain power, but it backfired in a very unpleasant way.

The “Habsburg Jaw”, which is a condition correctly known as “mandibular prognathism,” is characterized by a long chin, jutting lower jaw and an abnormally large tongue. Sometimes, it can affect one’s ability to speak properly and make it difficult to fully close one’s mouth.

Take a look at these portraits of the Habsburgs, and this defining feature will quickly become obvious:

The Hapsburgs didn’t feel the need to stop marrying their family members, so their medical issues only proceeded to get worse.

Charles II was the last Habsburg ruler of Spain; his father, Philip IV, married his own sister’s daughter. Charles was nicknamed El Hechizado (Spanish for “the hexed one”), as his lower jaw was so pronounced that he struggled to speak, eat solid food, and his oversized tongue caused him to drool.

On top of this, he was short, lame, impotent and mildly retarded, and the icing on the cake: Charles II was sterile. Unable to produce any more heirs, the Habsburg’s rule finally came to an end in 1700, when Charles died a few days before his 39th birthday.

But why does inbreeding cause these sorts of deformities? Well, let’s learn about a phenomenon is known as genetic variation, which is crucial for the survival of any species.

When a sperm cell and an egg cell combine, they each come with their own set of 23 chromosomes which contain genes which code for different characteristics. The alleles of the genes randomly assemble so you inherit a mix of characteristics from your mother and your father. Because of this, if you have a defective gene from one parent, it’s likely that a working gene from your other parent will cancel this defect out.

But when your parents are related, chances are they’re carrying around similar copies of the genes that they would have inherited from their parents. So, if you inherit a defective gene from your mother, and your father is related to her….CHANCES AAARRRE you’re getting two copies of this defective gene.

So when the genetic variation is decreased, the chances of inheriting defective genes are increased. This is why inbreeding leads to so many different types of deformities. Sometimes, “keeping it in the family” isn’t always the best idea.

Rare bacteria popping up in your home?

Among the many different types of bacteria, extremophiles are definitely the daredevils. As their name suggests, these bacteria thrive in extreme environments: inside of volcanoes, hot springs glaciers, the Dead Sea…

So what are these bacteria doing in our homes?

A recent study showed that some extremophile species of bacteria are popping up inside of water heaters in the Unites States and Puerto Rico. One such species is Thermus scotoductuswhich is usually found in hot springs such as those in the Yellowstone National park.

The same microbes from these hot springs ending up in your home?

The temperature and organic environment inside the water heaters make them an ideal home for these types of bacteria, so it’s no surprise that these critters have taken up residence there.

But the real question, which still remains unanswered, is how did these rare bacteria get there in the first place?

A pacemaker for the brain?

Just like we’ve seen pacemakers work to keep the heart going, could we also see the same kind of technology to keep the brain working?

Scientists have developed a new neurostimulator which can listen to and stimulate electric current in the brain at the same time. This has potential for treating neurological diseases such as Parkinson’s and epilepsy.

The device is known as the WAND (wireless artifact-free neuromodulation device). It monitors the brain’s electrical activity, then gives off an electrical stimulation if it detects something’s going wrong.

The WAND is very effective at preventing tremors or seizures in patients with neurological conditions. It learns to recognize the signs of tremor or seizure, then adjusts its stimulation to prevent the unwanted activity.

The device is wireless, autonomous and closed-loop (can stimulate and record simultaneously), so it’s everything you’d need to respond and adjust to seizures happening in real time. Additionally, when compared to other closed-loop systems which can record electrical activity from 8 points in the brain, WAND can record from over 128 points in the brain!

As science goes, WAND is not quite ready to be the solution to all our problems yet. Work is still being done to enable the device to figure out the best way to stimulate a patient for the best outcome.

Best Podcasts This Week

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4 Familiar Scents You Probably Didn’t Know Were Caused by Microbes


What do microbes smell like?

Have you ever smelled bacteria? Would you even know if you had? I bet you’re imagining that all bacteria or fungi smells funky or nasty, but do they even have a smell?

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Many microbes have a characteristic smell that is used to identify them in nature. These smells come in handy for diagnosing illnesses or figuring out which bacteria might be present. But what you probably don’t realize is….we come into contact with many of these microbe-y odours on a daily basis.

Here are a few familiar scents that you probably didn’t know were caused by microbes:

  1. Rain

We’re all familiar with the smell of rain – that earthy scent that wafts through the air a few minutes before or after a heavy shower. Many of us use that smell to predict an imminent downpour (and as the perfect warning to run and take your clothes off the line). But what causes that distinctive smell?

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The smell of rain is known as petrichor, and it is created from a combination of compounds. The most common are compounds called geosmins. Geosmin is produced by Actinomyces, a group of soil-dwelling bacteria, and is responsible for the smell of freshly turned soil. This same earthy smelling compound is emitted from wet soil into the atmosphere and is carried by wind to reach our noses, letting us know that rain is near.

  1. Baked Bread

Mmmmmmm…… 🙂 Have you ever stepped into a bakery and been consumed by the beautiful warm smell of freshly baking bread? It’s actually the same thing you would smell if you stepped into a brewery that was brewing beer.bread-2193537__340.jpg

What you’re actually smelling is the smell of yeast. Yeast, although classified under fungi and not bacteria, is still a type of microbe that is responsible for some of our familiar scents. This same yeasty smell can also be detected if you’re suffering from a Candida (yeast) infection, and is useful in distinguishing yeast infections from other types of bacterial infections. Even though baking yeast (Saccaharomyces cerivisae) is different from pathogenic yeast, they both carry similar distinctive smells.

  1. Poop

kot-3101851__340.jpgThis is definitely a much less pleasant one, but…well…everybody knows what poop smells like. The smell of faeces is primarily caused by the production of a compound known as indole within the digestive tract. Indole is produced by Escherichia coli (E. coli) producing an enzyme called tryptophanase, which breaks down tryptophan (an amino acid found in most foods) to produce indole:

L-tryptophan + H2O —> indole + pyruvate + ammonia

Also produced in this reaction is ammonia (NH3) which has a distinctive smell of its own.

  1. Body Odor

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Electron micrograph of S. epidermidis

Another unpleasant smell we’re all familiar with is that old BO – the reeking scent of “old sweat” is caused by Staphylococcus epidermidis. S. epidermidis is found all over the body, in particular in stinky areas like under the arm and between the toes.

In fact, it’s not actually your sweat that stinks at all, but once bacteria begin to break it down, that’s when the problem begins. S. epidermidis and other bacteria break down the sugars in your sweat to produce a number of different compounds – and it’s these compounds that can have you reeking to high heaven.

Curious about the source of other scents around you? Chances are many more of them are the fault of some kind of microbe activity. Share this article with your friends and together see how many microbe scents you can identify on a daily basis.


On Viruses & Vaccines

So now that we understand what viruses are and how they work, and we’ve looked at some of the most common viruses affecting us today, we can now take a look at some of the treatment methods we can use to fight these guys off.

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Not Antibiotics

Despite growing concerns, antibiotics are the go-to defence for bacterial infections. download (25).jpgHowever, because viruses and bacteria are so different, antibiotics don’t have the same effect on viruses. For this, a special class of drugs has been developed known as antivirals. Usually antibiotics work to kill their target bacteria. However, antivirals simply work to impair the function of the virus to prevent it successfully infecting its host.

If you recall the Virus Life Cycle (attachment, penetration, uncoating, replication, assembly and release), different antivirals target each stage of the life cycle.  Antivirals can either:

  1. Prevent the virus from entering the host cell in the first place. Antivirals do this by either physically blocking entry into the cell, or by altering the protein on the particle that usually recognizes the host cell the virus is targeting. Some antivirals also prevent the virus from shedding its outer coat and injecting itself into the cells.
  2. Antivirals can also work to disable the genetic machinery of the virus particle. Doing this prevents the virus from replicating its DNA and inserting it into its host’s genome.
  3. Other antivirals work to prevent assembly of the new viral particles after they’ve been replication, and finally some prevent the release of new viral particles out of the host cell and into the rest of the body.

Why Vaccines Matter

Recently, a new wave of the “anti-vax” movement has become popular in the parts of the US and the rest of the world. This paranoia is based on pseudo science linking vaccines to autism in children. (As in literally: the anti-vax movement is based on a 1998 study by a UK researcher named Andrew Wakefield. The study has since been disproven and Wakefield was struck off the UK medical register for lying and abusing the children in the study. Yet, people still believe it.)

download (26).jpgVaccines are based on a concept known as passive acquired immunity (There are 4 types of immunity, but that’s for another day). Acquired immunity basically happens when you are exposed to a virus or bacteria, so your body produces antibodies to fight it off. Once these antibodies are produced, they remain in your body to recognize the virus if it comes around again, and protect you from future infections.

Vaccines involve injecting small amounts of a modified version of the virus into the body in order to allow it to produce the defending antibodies. The virus is usually attenuated (disabled) or killed to prevent the vaccination causing actual infection. Occasionally, live viral particles are also used but in very small concentrations. Some vaccines actually inject artificially synthesized antibodies into your system, rather than leaving your body to create them.

By ensuring you are up to date on your vaccinations (this also includes regular adult vaccinations e.g. yearly flu vaccines) you are making yourself less susceptible to some of the most common (and deadly) viruses.  download (27).jpgOne of the trickiest things about viruses, however, is their rapid mutation rate. This means that scientists are always working to come up with new vaccines because the viruses keep changing, rendering the old treatment ineffective. This is seen especially in the treatment of HIV infections as HIV has a very high mutation rate.

Why Don’t We Have A Vaccine For Everything?

This question comes up every time there’s a new viral outbreak. The truth is, vaccines take a pretty long time to develop.  virus.jpgAfter researchers have grown the vaccine and figured out the best strategy to combat it, extensive testing and trials must be done to determine the safety of the vaccine before it can be released for human use. Some of these trials can take up to 2 years, which is why this type of drug development usually takes so long. And for some viruses, no suitable vaccine has yet been found.


Exploring Viruses: Those Among Us

Now that we understand what viruses are and how they work, let’s take a look at some of the most common types of viruses affecting us today:

Cold or Flu?

Do you know the difference between the flu and the common cold? How often do we claim “flu” as our diagnosis, but it is really?

The most common viruses that affect humans are rhinoviruses. These guys live in the upper respiratory tract and are responsible for causing the common cold. There are 99 different types of rhinoviruses, and they are among the smallest viruses in existence. They are RNA viruses, and have a protein coat (capsid) and are covered with proteins on the outside.

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Rhinoviruses are transmitted via person-to-person contact, and by interaction with fomites. (Nerd Tip: If you haven’t get watched it, Contagion is a great movie about how disease outbreaks affect us in this century). Fomites refer to contaminated surfaces, and can include doorknobs, tabletops, faucets…pretty much everything we touch. . Symptoms of the common cold are sore throat, runny nose, nasal congestion, sneezing and cough, muscle aches, fatigue, malaise, headache, muscle weakness, or loss of appetite. Sounds familiar?

Influenza on the other hand is a much more serious disease, caused by the influenza virus, or the  group of Orthomyxoviridae. While the common cold generally resolves on its own, influenza outbreaks can results in the deaths of tens of millions of people. There are seven types of influenza virus, with influenza A, B and C being the groups that attack humans. Influenza viruses are also RNA viruses, generally spherical in shape with 500 distinct spike-like surface projections on its envelope.

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Each Influenza virus contains different subtypes, which came about when the virus mutated to a new form. For example, the Influenza V virus has 3 subtypes that are currently in circulation: H1N1 (Spanish Flu/2009 “Swine Flu” Outbreak), H1N2, H3N2 (“Hong Kong Flu”). Human flu symptoms usually include fever, cough, sore throat, muscle aches, conjunctivitis and, in severe cases, severe breathing problems and pneumonia that may be fatal.

Vector-Borne: Dengue & ZikAdengue.jpg

Both dengue fever and ZikA are mosquito borne viruses transmitted by the Aedes aegypti mosquito. Dengue virus is an RNA virus that can prevent the functioning of your immune system that Is necessary to fight off the disease. There are 47 strains of the dengue virus. Dengue fever can cause high fever, headache, vomiting, muscle and joint pains, and a characteristic skin rash.

Image result for zika virusThe ZikA virus is an RNA virus that has recently caused a new pandemic in some parts of the world. The ZikA virus is found in the mosquito’s saliva, so when the mosquito bites, some of the ZikA virus is introduced into skin cells and the blood stream. Zika usually causes no or only mild symptoms, similar to a very mild form of dengue fever. However, ZikA can be transmitted from mother to foetus, and can result in microcephaly, severe brain malformations, and other birth defects.


download (22).jpgThe human immunodeficiency virus (HIV) is a retrovirus that causes HIV infection and AIDS. Retroviruses are able to insert themselves into your cells and use its own machinery to read the genetic information on the virus and create a copy that integrates into your DNA. This is why the HIV virus is so hard to treat. The HIV virus is generally spherical on the outside, with a cone shaped capsid inside storing the genetic material. It also contains proteins on the outside of the viral envelope that give it a sort of spiky appearance.

HIV also has a very high mutation rate, which has given it much genetic variability – many many different strains and subtypes exist, making it much harder to design a treatment for all infections. The HIV virus is transmitted via bodily fluids such as blood, semen, vaginal fluid and breast milk. By attacking your immune system, it directly attacks the defence system of your body, crippling your ability to fight off diseases.

The human papillomavirus is a small DNA virus that causes HPV infections. HPV infections cause genital warts and precancerous lesions, and is generally spreaddownload (23).jpg by sustained direct skin-to-skin contact. So obviously, during sex is pretty likely. HPV is the most common sexually transmitted infection globally, but luckily the HPV vaccine prevents the most common types of HPV infection.

Over 170 types of HPV have been detected, of which above 12 of these are considered “high risk” because they can cause cancer. The HPV virus cannot attach to live cells, so instead it waits till you get a tiny little cut or some trauma deep within your skin, and it moves through your skin membranes.

Exploring Viruses: An Introduction

Do you know the difference between viruses and bacteria? Is there even a difference at all? Outside of the scientific community, I’ve heard the two used interchangeably so many times, much to the chagrin of the scientists I know. Even though they are both too small for us to see, viruses and bacteria are two completely different beasts – in fact, they’re not even related. This month, we’ll be looking at some of the features of viruses and how these critters affect us.

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Alive or Nah?

One of the biggest debates in the scientific community is the classification of viruses as living things. All living things must satisfy 7 criteria:

  • They eat/feed
  • They move
  • They breathe/respire
  • They excrete
  • They grow
  • They respond to stimulus
  • And of course, they reproduce.

While plants, animals, bacteria, fungi and archaea all satisfy these 7 characteristics, viruses don’t. Viruses also can’t exist as free living organisms (we’ll discuss a bit more soon) which means that technically, viruses are NON-LIVING things. However, viruses do display some of the characteristics of living things, e.g. they’re able to  move and replicate/reproduce, which creates some confusion around the issues. This confusion led one researcher known as Rybicki to create a description for viruses as “organisms at the edge of life”. This classification in particular is the biggest distinction between viruses and other living things like bacteria.

So what exactly is a virus?

Well, a virus is a “small infectious agent that replicates only inside the living cells of other organisms.” This means that viruses can only survive if they have a HOST (like a plant or animal) to replicate inside of. They do not have their own metabolism, so they cannot exist on their own.

A single virus particle is called a virion, and it’s made up of three parts:

  • Long molecules of DNA or RNA that carry genetic information
  • A protein coat called the capsid, which surrounds and protects the genetic material
  • Some virions have a protective envelope made up of fat molecules that surrounds the protein coat when they are outside a cell

stock-vector-viral-shapes-vector-illustration-showing-that-there-are-many-different-shapes-and-sizes-of-viruses-210660664.jpgThese virions can exists in various shapes, ranging from simple helical/icosahedral forms to more complex structures. And viruses are really really really small:  the average virion is about one one-hundredth the size of the average bacterium. Viruses are so small that most virus species have virions that are too small to be seen even with an optical microscope!

A very important feature of viruses is their ability to easily mutate, and the vast number of ways that viruses are actually able to mutate. This is very important medically, as it has implications for the treatment of viruses. If they are always mutating, it’s difficult to create treatment techniques that can keep up with these mutations. For some viruses like HIV, as soon as one treatment is found to work, the virus mutates to another form that is no longer susceptible to this treatment.

Virus Life Cycle

Viruses have a specific life cycle with a number of different steps:

  • Attachment – the proteins on the outside coating (capsid) of the virus are compatible with receptors on the outside of the cell of the host. These proteins are usually specific to a particular cell type (e.g. HIV virions have proteins that are specific for human white blood cells)
  • Penetration – once attached, virions enter the host cell. Some viruses have evolved where they can just inject their DNA into the host through a special needle-like structure, while the rest of the virion stays outside.
  • Uncoating – the viral capsid is removed and just the DNA/RNA remains
  • Replication – the genome of the virus contained on the DNA/RNA begins to multiply, making multiple copies of itself.
  • Assembly – these copies of the genome begin reassembling into new virus particles that can then be released to form an army and go on to infect more cells.
  • Release – these new virus particles are then either (i) released from the host cell by bursting it open and killing the host cell (lysis) or (ii) the virus genome is incorporated into the DNA of the host cells (lysogeny). By doing this, every time the host cell replicates itself, it will also be replicating a copy of the virus DNA.


This life cycle underscores why viruses can be so dangerous, because it results in either the production of multiple viruses which kill a bunch of the host cells, or the viruses ingrains itself into your DNA – which means you never truly get rid of it. Remember, as well that your body is making multiple copies of your DNA every single day, so these viruses basically exploit their host by using your existing replication machinery to create copies of itself.

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Hopefully now you have a better idea of what viruses are, and why they can prove to be so dangerous. Next week we’ll look more on how viruses affect us and cause diseases, and what differences we have to look at when treating them.