Michel, the technician
Oh, hi! Are you also looking for Dr. Champrobacter, the eminent microbiologist from the Institute, an expert in biological soil decontamination? Unfortunately, we have not heard from her in a week. Two weeks ago, Dr. Champrobacter traveled to an equatorial country, El Païs more precisely, to gather soil samples from an area that once served as pasture for sheep.
Unfortunately, for the last 30 years, this land has been used as a dump for various chemical products, most notably hydrocarbons and PCBs. The country’s government was worried about this pollution that may already be contaminating the river that crosses it and that supplies drinking water to the villagers of El Suelo. The government had called upon Dr. Champrobactor to study the situation and suggest a biotechnological solution to remedy it.
She came back last week and dropped off her samples in the refrigerator in the laboratory. She told me that she had had a headache and a fever since the previous day. This is all she told me. She didn’t seem well. Usually, she is so talkative! She worked a little in her office. When she waved goodbye to me with the back of her hand, I noticed that she had a black mark on it as if she were dirty. Since that day, nobody has seen her.
I am worried because maybe over there, in that equatorial country, somebody does not want a foreign scientist to come and put her nose in their affairs… if you want to try and find her I can entrust you with her computer. Maybe it contains information that you will find useful. Oh yes, also, I took this photograph when she came and left her samples. We do this every time she comes back from taking samples.
Using this computer, which belongs to Alvir Champrobacter, you have access to all the information pertaining to the preparation and realization of her sampling trip. Visit the stops along her journey. Look carefully at the clues she left behind her. Some of them could be useful. When you have examined all the files, you can try and solve the enigma of her disappearance. Good luck!
According to you, what happened to Alvir Champrobacter?
As its name implies, the photon microscope uses light, made up of photons, as well as a system of glass lenses to modify the trajectory of the light traveling between the object under study and the eye of the observer. The light source is placed under the object. With this microscope, objects can be magnified from 1000 to 2000 times their original size. We can observe bacteria, such as the tuberculosis bacilli, but they will be very small. Viruses cannot be observed under this microscope because they are too small.
As for the electron microscope, it uses a beam of electrons emitted by a source, generally a tungsten filament heated to incandescence. The beam comes down from the top of the column. It is controlled and directed on the object to be observed by a system of magnetic fields. A lens that serves as the objective magnifies and focuses the image. Finally, a projector does the final magnification on a screen (fluorescent, cathodic, etc.)
The electron microscope presently in use at the INRS-Institut Armand-Frappier has a maximum magnification of 600,000 times on the main screen but with a television camera, it can reach a magnification of 12,000,0000 times. With this very large magnification, we can see the shape and structure of viruses. Today, there are even super microscopes, also called "tunnel effect microscopes," that are even more powerful and with which is it possible to see macromolecules, such as DNA, for example.
Presentation of the project
Project for El Païs: Genetic transformation and symbiotic association (Top secret)
Genes are responsible for the physical and physiological characteristics of living beings. They determine size and shape as well as certain diseases or particular capabilities. Genetic transformation is defined as the action of modifying the genes present in an organism, in order to give it a characteristic it does not already possess. The new microorganism is a GMO, a genetically modified organism.
The capacity to degrade hydrocarbons by oxidation is a physiological characteristic of some microorganisms. Therefore, it is possible to take genes from a microorganism capable of degrading hydrocarbons, a hydrocarbonoclastic microorganism, and transfer them to another microorganism that lives in association with a plant. There is already a symbiotic association between a rhizobium-type bacterium and the legume plant. The plant feeds the microorganisms and they in turn provide the plant with nitrogen.
The proposal for the El Païs project is as follows: take the genes from a microorganism capable of degrading hydrocarbons and transfer them to rhizobium-type bacteria that live in symbiosis with legumes. By transplanting the legumes and their genetically modified associates onto the contaminated field, they will carry out the decontamination work themselves! The legumes would then be harvested and destroyed, by incineration, for example. Considerable benefits could be obtained by patenting the legume plants associated with the genetically modified organisms.
The calendar is an indispensable tool in the planning of any successful project. The one that is posted in Alvir’s laboratory has several uses. It is used to register events that are important for the running of the laboratory and some that are less important!
Vaccination booklet - Clue!
A vaccination aims to show the body what a harmful microorganism looks like without making it sick. To do this, a healthy person is injected with microorganisms that may be alive but attenuated or even dead, with microorganisms similar to the infectious microorganism, or with fragments of microorganisms.
Thanks to the immune system, the body will understand that they are intruders and will eliminate them without being infected. A very important step of this elimination is the manufacture of memory cells that will remember the intruders. Later, if a real infectious microorganism appears, the body will recognize it immediately and eliminate it. The body will therefore avoid the disease!
Vaccines can be used against all types of harmful microorganisms, including viruses and bacteria. Alvir Champrobacter received several vaccines. They are registered in her vaccination booklet. Consult it to know which vaccines she received.
Photo - Clue!
This photo of Alvir Champrobacter was taken the last time she came to the laboratory. She came to leave some soil samples taken during her last trip to El Païs.
This laboratory spatula belonged to Alvir Champrobacter’s grandfather when he was an amateur paleontologist. This spatula is very important to Alvir; it is her lucky charm.
Prescription for antibiotics - Clue!
Antibiotics are molecules produced by microorganisms to defend themselves against other microorganisms. Penicillin-type moulds are big producers of antibiotics.
Human beings have made good use of this particular property to increase their capacity to defend themselves against microorganisms by exploiting antibiotics as medication. Let us specify that antibiotics can only fight against bacteria, as they do not affect viruses.
River - Clue!
Soil sampling is a tough job. One must dig deep, often with a simple shovel. Not accustomed to the equatorial heat, Alvir Champrobacter drinks lots of water from the river to quench her thirst.
Inhabitants in the region mistrust this water. They say it makes them sick. The water from the river contains several microorganisms such as viruses for hepatitis A and B. Although they are usually not fatal, the diseases caused by these microorganisms are nevertheless very uncomfortable and unpleasant.
Hepatitis A can cause fever, nausea, weight loss, and intestinal discomfort from the very first days of the infection, while hepatitis B can take several weeks before manifesting itself. Jaundice is the most revealing symptom.
Shovel - Clue!
On the last day of sampling, Alvir cleans her material to avoid bringing contaminated soil back to Canada. While scraping some shovels, she scratched the inside of her hand on dirty metal. An hour later, remembering the risks of tetanus and anthrax, she decides to take care of her wound, which is bleeding a little. Grumping, she wipes her hands on some wet towels, puts on a bandage, and returns to work because she is in a hurry to leave.
Pails filled with soil - Clue!
When analyzing a problem involving contaminated soil, Alvir Champrobacter must always trace its history: What was it used for in the past? Who was the owner? For how long? Etc. At the village coffee shop in El Suelo, several people told her that shepherds shearing their sheep were dying of a strange disease that they were calling the "black killer". The villagers believed that a spell was cast on the wool. Alvir suspects that the problem is anthrax. In the past, anthrax was often associated with workers who handled sheep’s wool.
Bacillus anthracis can infect the skin, lungs, and intestines. This bacterium is able to produce spores, a resistant form that allows it to remain in soil for several years. The bacterium penetrates the body through a cut or a scratch on the skin, which becomes black, or through the respiratory tract or the mouth.
Hole in soil
Microorganisms are diverse and abundant in all layers of soil. They feed on organic matter that they cut into fine particles; these can then be assimilated by plants of all sizes. True decomposers of organic waste, microorganisms are demineralization agents, responsible for the great cycles of matter.
Layers of varying thicknesses and structures characterize soils. In turn these properties influence the humidity and the gaseous and biological content of the different soil strata. There will be a lot of biological activity in a layer rich in organic matter, whereas a rock layer containing little organic matter will be less biologically active since it contains less food.
For example, some bacteria live thousands of meters under the surface of the Earth in underground petroleum reserves. Using gaseous hydrogen and carbon dioxide as sources of food and energy, they excrete simple organic compounds that are consumed by other bacteria.
Pile of earth - Clue!
Tetanus is a disease caused by a bacterium that can be found in soil, dust, or human or farm animal excrement. The germ can only enter the body through a wound. The mortality rate varies between 30 and 90%.
The first symptoms are cramps and muscle contractions around the wound and a rigidity of the jaw muscles. At an advanced stage, the disease provokes facial muscle contractions that result in an inability to open the mouth. The last symptom is a very intense contraction of the back muscles leading the body to form an arc. Death may occur following involuntary contractions of the respiratory muscles.
The current treatment for the disease is not very effective, which is why vaccination is so important. The vaccine, administered in combination with the vaccines against diphtheria and pertussis during early childhood (DTP and d2T5), must be administered as a recall vaccine at 10-year intervals.
Some pathogenic microorganisms can develop in food that is then ingested by humans. A number of techniques have been developed to preserve the freshness of food longer and establish better quality control to ensure that the population doesn’t consume tainted food.
The cold temperature of the refrigerator (4°C) slows down the metabolism of microorganisms but does not kill them; this is why it is important to respect the conservation temperatures of food, especially meats. With an ice cooler, it may be difficult to respect these conditions.
For example, raw meat that is ground, or in cubes or slices, will keep for a day or two at 4°C. Cooked poultry, without sauce, will keep for three to four days at the same temperature. The time and temperature of conservation will vary depending on whether the food is wrapped or not, whether the wrapping has been opened or not, and whether the food is dehydrated or fresh.
Filtration system - Clue!
The protozoan Giardia lamblia causes a disease known as giardia. This microorganism lives in the environment as a cyst, a very resistant form. Once inside the body, through ingestion of contaminated water, the germ travels down to the intestines where it binds itself to the intestinal wall and invades the intestine by multiplying.
An accumulation of this germ in the intestines can interfere with the digestion of food. Some people are asymptomatic, meaning that they show no signs of the disease they have contracted. However, others have severe diarrhea, cramps, and flatulence, often leading to weight loss. The incubation period of the protozoan is from three to twenty-five days. The only way to protect oneself against this microorganism is to filter contaminated water using an efficient filtering system.
First aid kit - Clue!
A first aid kit is essential when working on soil sampling, especially in cases such as this one where the site is far from emergency services. The risk of injuries such as scratches, cuts, and splinters is high.
The kit prepared for Alvir by her technician, Michael, contains all the products needed to treat small injuries: wet towels, isopropyl alcohol, hydrogen peroxide, antibiotic ointment, bandages, and sterile cotton to disinfect the wounds.
El Suelo hotel
Shower and toilet
Alvir Champrobacter likes to take a good shower after a long hard day of work. She has reserved a room with running water in the village of El Suelo. Being a microbiologist, she knows the importance of good corporal hygiene. Germs are naturally present on and in the human body. Since the skin is a barrier that stops them from entering, a wound becomes an open door for infection. Washing your hands regularly is a good means of preventing infection.
When they are controlled, with good hygiene, for example, and there is a good balance between them, the germs generally are not dangerous for your health. In fact, their simple presence affords a certain protection, preventing the ones that make us sick, the pathogens, from "gaining ground".
Of all the organs of the human body, the large intestine is the one that contains the greatest number of microorganisms. Escherichia coli is an example of a bacterium that lives there. The bacteria of the intestine have an important task to accomplish: finishing digestion of food so that the nutritive elements that it contains can enter the blood circulation and travel to the cells of our body to feed them. Therefore, eating well, drinking water, and exercising regularly are three measures that facilitate the work of the microorganisms.
Peas - Clue!
People involved in fieldwork soil sampling often have to eat in a hurry. Often during her trip, Alvir Champrobacter has to make do with a can of peas for dinner. Beware of bulging cans! This can indicate the presence of Clostridium botulinum, a bacterium that produces spores that allow it to survive for a very long time in canned goods.
This bacterium produces a toxin that provokes food poisoning in people who ingest it. This bacterium’s toxin can lead to paralysis and even death.
The night of her arrival in El Suelo, the owner of the hotel served supper to welcome Alvir Champrobacter. He poured her large servings of local unfiltered beer, accompanied by the national dish: a stew of beef stomach that had simmered all day. Bon appetit, Dr Champrobacter.
During the next night, Alvir did not feel very well. She was asking herself if it was the stew or the beer... The El Suelo local beer is special. After bottling, yeasts and sugar are adding leading to a second fermentation when the bottles are stored in a warm room (25°C). This fermentation raises the quantities of CO2 and alcohol produced. This is how one produces beer called "on lees". The lees are the deposits of yeasts and products of fermentation found at the bottom of the bottle.
Cheese - Clue!
One of the favorite dishes of the villagers of El Suelo is a cheese they make by putting milk in the stomachs of calves. Alvir is a curious woman and this is a great quality for a researcher! She therefore ate some of this cheese that some workers on the sampling site offered her at lunch hour, two days before her departure.
This cheese is made in several steps. First, rennet and lactic bacteria such as Lactobacillus acidophilus curdle the milk. This results in a semi-soft body of cheese. Draining removes the unnecessary liquid and the cheese is then ripened for several days at room temperature.
Cow - Clue!
El Suelo villagers prepare an excellent stew of beef stomach! They wash the stomachs in very salted water and then boil them all day with herbs and spices.
Ruminants such as cows and oxen feed on grass that contains cellulose. This sugar contains energy. The ruminants can digest grass and recover the energy because their stomachs, made up of four compartments, contain a multitude of microorganisms (bacteria, protozoa, and fungi) capable of breaking up the cellulose into very small pieces.
Endodinium simplex, a protozoan, is an example of this type of microorganism. Ruminants can therefore use the energy provided by their diet to move, moo, and graze! Contrary to the cow, human beings can’t eat grass to recover its energy because their digestive systems are not adapted to this food.
Herd of sheep - Clue!
Around the village of El Suelo, herds of sheep are an important source of revenue for the villagers. Unfortunately, these animals are sometimes carriers of a bacterium, Bacillus anthracis, which can be transmitted to human beings and cause a serious disease known as anthrax.
When the disease develops on the skin, the infected wound becomes black and symptoms such as headaches, fever, and nausea can then appear. Death can occur -– in 20% of cases – when the disease is left untreated. Rapid treatment with an antibiotic such as penicillin or streptomycin eliminates the disease.
Anthrax can also develop if the bacteria are inhaled. The symptoms of respiratory anthrax are fever and anaphylactic choc leading to death within 48 hours. If the bacterium is absorbed orally, nausea and vomiting cause death in 60% of cases.
On the morning Alvir Champrobacter was leaving the El Suelo hotel, the owner’s dog, Saxo, was making quite a fuss over our researcher, who just adores animals! Playfully, Saxo licked her hand several times to say goodbye.
The virus that causes rabies is transmitted from the affected animal’s saliva to the person’s blood, generally following a bite, but sometimes just by licking. Foxes, skunks, raccoons, and bats are often rabies carriers but all mammals, including humans, can be victims of the disease.
The first symptoms suggest an impairment of the central nervous system, the respiratory tract, or the gastrointestinal system. The rabies virus attacks the brain and provokes either great agitation (furious rabies) or paralysis (paralytic rabies). Hence, at the acute stage of the disease, the clinical signs can vary: one animal can become paralyzed and die while another will run all over the place and will bite everything in sight before dying. Death occurs in the first seven days of the disease.
Laboratory in El Païs University
Hola my friend! Please forgive me for not getting up but I must finish these observations under the microscope very quickly… my boss is not very easygoing!!! You have come to look at the results of the analyses of the El Suelo project?
I know because Michel sent me an email. I took out the file; it is on the counter next to the medication… That dear Alvir, when she left, she was not well, you know. She had a fever, nausea… I gave her this medication for the return trip but she did not take it, explaining that she needed to have her full wits… She was very stubborn, that woman!
Acetaminophen - Clue!
Acetaminophen poisoning is very frequent. Last year, more than 4,000 cases were recorded by the Quebec anti-poison center. This represents nearly 19% of all medical intoxications and 8% of all intoxications in Quebec, which is enormous.
Caplet - Clue!
Dimenhydrinate belongs to a class of medication known as "antiemetics". It is used to prevent and treat motion sickness as well as nausea and vomiting associated with various disorders.
It is available as a pill, capsule, caplet, syrup, liquid, suppository, or injection. This medication does not require a prescription. It can alter the physical and mental capacities required to carry out certain activities such as driving a vehicle or operating machines.
Alcohol and other sedatives can amplify the risk of sedation after taking dimenhydrinate. A person taking this medication must be careful if he undertakes activities that require vigilance.
DNA molecular model
DNA is the abbreviation for deoxyribonucleic acid, the name of a molecule essential to the life of all living beings. It is a specific constituent of every living being. The study of DNA has shown that from insects to plants and from bacteria to humans, it is always constructed the same way.
The common presence of DNA in all living organisms provides a good foundation to the theory that a common ancestor is at the origin of the diversity of life on Earth. The set of chromosomes, made up of DNA, can be compared to a book of instructions indicating how to construct a human being. Genes, present on each chromosome, determine our characteristics such as the color of our eyes, the length of our nose, etc.
However, while the genes give the directions, proteins are the workers carrying out the instructions to build the human being. Proteins are complex molecules composed of several sub-units called "amino acids". The number and assembling order of these amino acids are specific to each protein; they are also determined by the DNA instructions.
When talking about DNA, the first image that comes to mind is that of a twisted ladder. The sides of the ladder are actually the two nucleotide chains that are attached to one another.The nucleotides are always made up of three parts: a sugar (S), a phosphate group (P), and a base (B). Only the bases can differentiate the nucleotides from one another because the other two elements, the sugar and the phosphate group, are identical for all nucleotides.
There are four different bases, often associated with the letters A, T, C, and G. To form the "ladder," the nucleotides bind to each other through the sugars and phosphate groups. To form the "rungs," the bases bind together. The A always binds with the T and the C with the G. Finally, when the nucleotides are long enough, the DNA starts to fold onto itself and take its familiar snakelike shape.
In the 1960s, a team from the University of Wisconsin-Madison discovered Thermus aquaticus, the first extremophilic bacterium. This bacterium does indeed like extreme conditions, as evidenced by the fact that it lives in thermal waters where the temperature is above 70°C.
The thermostable enzymes produced by this microorganism made possible a technology called "polymerase chain reaction" used in research laboratories since the 1980s. The "PCR" ("Polymerase chain reaction") apparatus that uses this enzyme is used to rapidly multiply or polymerize DNA or RNA chains to facilitate their study. We can thus avoid the long process of cell culturing, for example.
Analyses: soil and water
To determine what chemical products are contaminating the soil of El Solo’s dump, Alvir Champrobacter had some chromatographic chemical analyses done on a few soil samples. The morning of her departure for Montreal, Manolito gave her a folder containing the results. The soils of El Suelo contain petroleum hydrocarbons and PCBs or polychlorinated biphenyls.
The first step of an analysis by chromatography consists in extracting the compounds from the soil using a solvent. The extract is then injected into the chromatograph, which vaporizes the compounds by a gradual increase in the temperature. In gaseous form, the compounds migrate all the way through the long, fine column that separates them according to their size.
The light compounds are the first to come out of the end and be detected; the heavier compounds, which are generally bigger, are retained for a longer time on the column. By comparing the retention times of the unknown compounds with those of known compounds, the unknown compounds can be identified. The results obtained are chromatograms like those shown in the picture. Each peak corresponds to a compound in the mixture of pollutants.
Oh, hi! Thanks for returning Alvir’s computer. The director of the Institute just told me that she telephoned from the hospital a while ago. Sure enough, she was not poisoned! She had been given a prescription for antibiotics, but given the gravity of her infection, she was hospitalized urgently the day after she returned to Montreal. This story is truly mind-boggling! It’s surprising that a microbiologist such as Alvir would be contaminated with soil bacteria such as Bacillus anthracis. I had told her to be careful. She did not disinfect her wound immediately, so hello infection!
Luckily, she received antibiotics as soon as she returned to Montreal! Also, since she had had all the other vaccinations before her departure, especially the ones for tetanus and hepatitis, there was no risk there! When she came to the laboratory, I knew that something was not right … and that black mark on her hand, accompanied by fever and nausea, should have alerted me. Maybe the director is right, I watch too many movies!
Alvir Champrobacter is seriously ill. She was contaminated by Bacillus anthracis.
Here are the clues that could help you solve the mystery:
Prescription for antibiotics
Pails filled with soil
Herd of sheep