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Jumat, 19 Juni 2009

Urban Myth Disproved: Fingerprints Do Not Improve Grip Friction


Fingerprints mark us out as individuals and leave telltale signs of our presence on every object that we touch, but what are fingerprints really for? According to Roland Ennos, from the University of Manchester, other primates and tree-climbing koalas have fingerprints and some South American monkeys have ridged pads on their tree-gripping tails, so everyone presumed that fingerprints are there to help us hang onto objects that we grasp.


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This theory that fingerprints increase friction between the skin and whatever we grab onto has been around for over 100 years, but no one had directly tested the idea. Having already figured out why we have fingernails, Ennos was keen to find out whether fingerprints improve our grip, so he recruited Manchester undergraduate Peter Warman to test out fingerprint friction.

Because the friction between two solid materials is usually related to the force of one of the materials pressing against the other, Ennos and Warman had to find a way of pushing a piece of acrylic glass (Perspex®) against Warman's finger before pulling the Perspex® along the student's finger to measure the amount of friction between the two. Ennos designed a system that could produce forces ranging from a gentle touch to a tight grip, and then Warman strapped his index finger into the machine to begin measuring his fingerprint's friction.

But after days of dragging the Perspex® along Warman's fingers and thumbs, it was clear that something wasn't quite right. Instead of the friction between each finger and the Perspex® increasing in proportion to the amount that the Perspex® pushed against Warman's fingers, it increased by a smaller fraction than Ennos had expected. Ennos realised that instead of behaving like a normal solid, the skin was behaving like rubber, where the friction is proportional to the contact area between the two surfaces.

To check that skin behaves more like rubber than a normal solid, the duo varied the area of each fingerpad that came into contact with the surface by dragging narrow and wide strips of Perspex® along Warman's fingerpads. They found that the friction did increase as more of the fingerprint came in contact with the surface, so the skin was behaving just like rubber.

Finally, the friction issue was clinched when Warman measured his fingerprints' surface area. The area of skin in contact with the Perspex® was always 33% less than if the fingerpads were smooth resulting in the maximum contact area. Fingerprints definitely don't improve a grip's friction because they reduce our skin's contact with objects that we hold, and even seem to loosen our grip in some circumstances.

So if fingerprints don't tighten our grasp on smooth surfaces, what are they for? Ennos explains that our fingerprints may function in other ways. They might have evolved to grip onto rough surfaces, like tree bark; the ridges may allow our skin to stretch and deform more easily, protecting it from damage; or they may allow water trapped between our finger pads and the surface to drain away and improve surface contact in wet conditions. Other researchers have suggested that the ridges could increase our fingerpads' touch sensitivity. Whatever our fingerprints are for, it seems that the idea that they provide friction for grip is just another urban myth

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Biology - The Study of Life


What is biology? Simply put, it is the study of life -- life in all of its grandeur. From the very small algae to the very large elephant, life has a certain wonder about it. With that in mind, how do we know if something is living? Is a virus alive or dead? What are the characteristics of life? These are all very important questions with equally important answers.


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Characteristics of Life

Living things include both the visible world of animals and plants, as well as the invisible world of bacteria. On a basic level, we can say that life is ordered. Organisms have an enormously complex organization. We're all familiar with the intricate systems of the basic unit of life, the cell.

Life can also "work." No, not the daily employment variety, but living creatures can take in energy from the environment. This energy, in the form of food, is transformed to maintain metabolic processes and for survival.

Life grows and develops. This means more than just getting larger in size. Living organisms also have the ability to rebuild and repair themselves when injured.

Life can reproduce. Have you ever seen dirt reproduce? I don't think so. Life can only come from other living creatures.

Life can respond. Think about the last time you accidentally stubbed your toe. Almost instantly, you flinched back in pain. Life is characterized by this response to stimuli.

Finally, life can adapt and respond to the demands placed on it by the environment. There are three basic types of adaptations that can occur in higher organisms.
  • Reversible changes occur as a response to changes in the environment. Let's say you live near sea level and you travel to a mountainous area. You may begin to experience difficulty breathing and an increase in heart rate as a result of the change in altitude. These symptoms go away when you go back down to sea level.

  • Somatic changes occur as a result of prolonged changes in the environment. Using the previous example, if you were to stay in the mountainous area for a long time, you would notice that your heart rate would begin to slow down and you would begin to breath normally. Somatic changes are also reversible.

  • The final type of adaptation is called genotypic (caused by mutation). These changes take place within the genetic makeup of the organism and are not reversible. An example would be the development of resistance to pesticides by insects and spiders.
In summary, life is organized, "works," grows, reproduces, responds to stimuli and adapts. These characteristics form the basis of the study of biology.

Basic Principles of Biology

The foundation of biology as it exists today is based on five basic principles. They are the cell theory, gene theory, evolution, homeostasis, and laws of thermodynamics.
  • Cell Theory: all living organisms are composed of cells. The cell is the basic unit of life.

  • Gene Theory: traits are inherited through gene transmission. Genes are located on chromosomes and consist of DNA.

  • Evolution: any genetic change in a population that is inherited over several generations. These changes may be small or large, noticeable or not so noticeable.

  • Homeostasis: ability to maintain a constant internal environment in response to environmental changes.

  • Thermodynamics: energy is constant and energy transformation is not completely efficient.
Subdiciplines of Biology

The field of biology is very broad in scope and can be divided into several disciplines. In the most general sense, these disciplines are categorized based on the type of organism studied. For example, zoology deals with animal studies, botany deals with plant studies, and microbiology is the study of microorganisms. These fields of study can be broken down further into several specialized sub-disciplines. Some of which include anatomy, cell biology, genetics, and physiology.

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Rabu, 10 Juni 2009

How Proteins Find The Right DNA Sequences

Illustration of how proteins find the right DNA sequences. (Credit: Image courtesy of Uppsala University)


Researchers at Uppsala University and Harvard University have collaboratively developed a new theoretical model to explain how proteins can rapidly find specific DNA sequences, even though there are many obstacles in the way on the chromosomes.





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In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands.
"By also taking into consideration the fact that there are many obstacles in the way when proteins are to diffuse along DNA strands, we can now calculate more exactly how long it takes them to find their way," says Johan Elf, associate professor of molecular biotechnology at the Center for Bioinformatics.
Besides offering a more precise prediction regarding the time needed to find the right site on DNA, the new theoretical model explains why there is an optimal total concentration of DNA-binding proteins. If there were more, it would simply be impossible for them to find a binding place in a reasonable time, since the proteins would be in each other's way. If there were fewer it would go slower as well, since not enough proteins would be searching. Finally, the new model provides an explanation why so many DNA-binding proteins also bind auxiliary binding sites close to the regulatory site, thus forming DNA loops. It turns out that this can shorten the time to find the right sites.
"This more detailed understanding of gene regulation is important, since it can ultimately provide a better understanding of diseases that occur as a result of problems in the control functions of cells, such as in cancer" says Johan Elf.
The researchers behind the study are Gene-Wei Li, Otto G. Berg, and Johan Elf. The findings are being published March 16 in the scientific journal Nature Physics.
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New Antibiotics Could Come From A DNA Binding Compound That Kills Bacteria In 2 Minutes

A synthetic DNA binding compound has proved surprisingly effective at binding to the DNA of bacteria and killing all the bacteria it touched within two minutes. The DNA binding properties of the compound were first discovered in the Department of Chemistry at the University of Warwick by Professor Mike Hannon and Professor Alison Rodger (Professor Mike Hannon is now at the University of Birmingham). However the strength of its antibiotic powers have now made it a compound of high interest for University of Warwick researchers working on the development of novel antibiotics.

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Dr Adair Richards from the University of Warwick said: "This research will assist the design of new compounds that can attack bacteria in a highly effective way which gets around the methods bacteria have developed to resist our current antibacterial drugs. As this antibiotic compound operates by targeting DNA, it should avoid all current resistance mechanisms of multi-resistant bacteria such as MRSA."
The compound [Fe2L3]4+ is an iron triple helicate with three organic strands wrapped around two iron centres to give a helix which looks cylindrical in shape and neatly fits within the major groove of a DNA helix. It is about the same size as the parts of a protein that recognise and bind with particular sequences of DNA. The high positive charge of the compound enhances its ability to bind to DNA which is negatively charged.
When the iron-helicate binds to the major groove of DNA it coils the DNA so that it is no longer available to bind to anything else and is not able to drive biological or chemical processes. Initially the researchers focused on the application of this useful property for targeting the DNA of cancer cells as it could bind to, coil up and shut down the cancer cell's DNA either killing the cell or stopping it replicate. However the team quickly realised that it might also be a very clever way of targeting drug-resistant bacteria.
New research at the University of Warwick, led by Dr Adair Richards and Dr Albert Bolhuis, has now found that the [Fe2L3]4+ does indeed have a powerful effect on bacteria. When introduced to two test bacteria Bacillus subtilis and E. coli they found that it quickly bound to the bacteria's DNA and killed virtually every cell within two minutes of being introduced - though the concentration required for this is high.
Professor Alison Rodger, Professor of Biophysical Chemistry at the University of Warwick, said: "We were surprised at how quickly this compound killed bacteria and these results make this compound a key lead compound for researchers working on the development of novel antibiotics to target drug resistant bacteria."
The researchers will next try and understand how and why the compound can cross the bacteria cell wall and membranes. They plan to test a wide range of compounds to look for relatives of the iron helicate that have the same mechanism for action in collaboration with researchers around the world.


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Glutamate Receptor Believed Dead Comes To Life

Schematic presentation of the exchange of the delta2 receptor's intrinsic ligand recognition site (red). The recognition site from another glutamate receptor (blue) enables conversion of chemical into electrical signals: the reputedly dead ion channel springs to life. (Credit: Image courtesy of Ruhr-Universitaet-Bochum)


To all intents and purposes, the delta2 receptor is an unequivocal member of the family of glutamate receptors, the most important receptors for excitatory neurotransmitters in our brain. To date, however, this receptor has been considered the “black sheep” of the family because it does not react to glutamate, which, by definition, a glutamate receptor ought to do.


This riddle fascinated the neuroscientists working with Prof. Michael Hollmann (Chair of Biochemistry I – Receptor Biochemistry) at the Ruhr University.
To unlock the secret of this receptor, they “crossed” it with another glutamate receptor that functions normally. The resulting chimera is functional and opens an ion channel. The task now at hand is to identify a transmitter that triggers this mechanism in an unchanged, physiological delta2 receptor. The scientists have published their observations in the current edition of the Proceedings of the National Academy of Sciences, USA (PNAS).



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Lively communication between brain cells




Our brain consists of a gigantic network of about 100 billion neurons. Every one of them is linked to other neurons by more than ten thousand contact sites. The universal language within this network consist of electrical impulses, the sum of which lead to the development of our world of thought in a hitherto completely unknown manner. The majority of contacts between neurons are not direct, as a few millionth of a cm separate the cells from one another. This distance must be overcome if a signal from a transmitting cell is to reach a receptor cell.
This occurs at special contact sites, so-called synapses, which conduct incoming signals with the assistance of a chemical messenger, a so-called neurotransmitter. The activated transmitting cell discharges the messenger, which then crosses the synaptic cleft and is recognized by the receiving cell. This is where the glutamate receptors come into play. Protruding from the plasma membrane into the synaptic cleft they are specialized in registering the messenger most frequently found in the brain, namely glutamate – the well-known flavor enhancer in Chinese dishes, and subsequently convert the chemical signal into an electrical signal.



Conversion of chemical into electrical signals



Key to the secret of conversion of chemical into electrical signals is the structure of the receptors. They consist of three important parts: a glutamate recognition site, a joint, and a channel. The extracellular, bipartite recognition site protruding from the plasma membrane recognizes glutamate, binds it and then snaps shut like a mouse trap. Via a sophisticated joint mechanism, this closing movement is transmitted to the channel that traverses the cell membrane and causes the channel to open. Positive ions that have accumulated outside the cell can now flow into it and thereby generate an electrical signal.



Important but mysterious role



The delta2 receptor also has the three elements discussed above. Why then is it not activated by glutamate? Prof. Hollmann summarizes the problem by stating: "We know that the delta2 receptor is located at specific sites within the cerebellum, that it plays an extremely important role for the fine coordination of motor behaviour, and that it evidently contributes to the correct circuitry of the neurons during development of the cerebellum. What we don't know is just how the receptor fulfils these functions". The scientists thus decided to pursue the principal question whether the delta2 receptor is at all capable of functioning in a manner similar to that of the other glutamate receptors, namely as a neurotransmitter-activated ion channel.



Greek mythology helps



To answer this question the scientists recalled a very old idea: they produced a chimerical receptor. In Greek mythology, the chimera is a monstrous figure with a lion’s head, the body of a goat, and a snake's tail. Within the framework of her dissertation at the IGSN (International Graduate School of Neuroscience), Sabine Schmid created a chimeric delta2 receptor with the joint and channel of the delta2 receptor, but the ligand recognition site transplanted from a normally functioning relative.
This chimeric receptor did indeed react to glutamate and opened its ion channel, which had previously been belived to be dead. Prof. Hollmann comments: "We thus have developed a tool that, for the first time, enables us to investigate of the unique properties of the joint and the ion channel of the delta2 receptor. Moreover, our results suggest that the secret of the delta2 receptor is to be found in the difference in its recognition site for neurotransmitters". To a certain degree, the scientists have thus managed to unveil the function of the “black sheep.” The next step is to determine to which signal the actual recognition site of the delta2 receptor reacts and which role this plays for its essential function in the cerebellum.

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Circadian Rhythm: How Cells Tell Time

The fuzzy pale mold that lines the glass tubes in Dr. Yi Liu’s lab doesn’t look much like a clock.
But this fungus has an internal, cell-based timekeeper nearly as sophisticated as a human’s, allowing UT Southwestern Medical Center physiologists to study easily the biochemistry and genetics of body clocks, or circadian rhythms.
In a new study appearing online this week in the Proceedings of the National Academy of Sciences, Dr. Liu and his co-workers have found that this mold, which uses a protein called FRQ as the main gear of its clock, marks time by a sequence of changes in the protein’s chemical structure.
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Dr. Liu said the new finding might someday help researchers develop treatments for human sleep disorders and other problems associated with a faulty biological clock.
“This timekeeping protein is really the core component of the circadian clock,” said Dr. Liu, professor of physiology at UT Southwestern and senior author of the study.
Despite the evolutionary distance from mold to man, mechanisms controlling their circadian clocks are very similar. In both, circadian rhythms control many biological processes, including cell division, hormonal release, sleep/wake cycles, body temperature and brain activity.
The researchers employed a fungus called Neurospora, an organism frequently used in studies on genetics and cell processes, especially circadian rhythms. It reproduces in the dark and rests in the light.
A decade ago, Dr. Liu discovered that FRQ controlled the cellular clock in Neurospora by chemical changes of its protein structure. As the day goes on, the cell adds chemical bits called phosphates to the protein. Each new phosphate acts like a clock’s ticking, letting the cell know that more time has passed.
When the number of phosphates added to FRQ reaches a certain threshold, the cell breaks it down, ready to start the cycle again.
The researchers, however, did not know where the phosphates attached to FRQ, how many got added throughout a day, or how they affected the protein’s ability to “tell” time.
In the current study, the researchers used purified FRQ to analyze the specific sites where phosphate groups attach. In all, the researchers found 76 phosphate docking sites.
“This is an extremely high number,” Dr. Liu said. “Most proteins are controlled by only a handful of phosphate sites.”
They also studied how these phosphates are added to FRQ daily and found that two enzymes are responsible for adding most of the phosphate groups in Neurospora. They also found that the total number of phosphates oscillates robustly day by day.
In addition, the researchers created a series of mutations in many of the phosphate docking sites, creating strains of mold that had abnormally short or long daily clocks.
In upcoming studies, the researchers plan to identify which enzymes add phosphates to specific sites and exactly how changes in a particular site affect a cell’s clock.
Other UT Southwestern physiology researchers contributing to the work were co-lead authors Dr. Chi-Tai Tang, postdoctoral researcher, and Dr. Shaojie Li, former postdoctoral researcher; Dr. Joonseok Cha, postdoctoral fellow; Dr. Guocun Huang, assistant instructor; and Dr. Lily Li, former postdoctoral researcher. Researchers from the National Institute of Biological Sciences in China and the Chinese Academy of Sciences also participated.
The study was supported by the National Institutes of Health and the Welch Foundation.


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Stem Cells Cultured On Contact Lens Restore Sight In Patients With Blinding Corneal Disease

In a world-first breakthrough, University of New South Wales (UNSW) medical researchers have used stem cells cultured on a simple contact lens to restore sight to sufferers of blinding corneal disease.

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Sight was significantly improved within weeks of the procedure, which is simple, inexpensive and requires a minimal hospital stay.
The research team from UNSW’s School of Medical Sciences harvested stem cells from patients’ own eyes to rehabilitate the damaged cornea. The stem cells were cultured on a common therapeutic contact lens which was then placed onto the damaged cornea for 10 days, during which the cells were able to re-colonise the damaged eye surface.
While the novel procedure was used to rehabilitate damaged corneas, the researchers say it offers hope to people with a range of blinding eye conditions and could have applications in other organs.
A paper detailing the breakthrough appears in the journal Transplantation this week.
The trial was conducted on three patients; two with extensive corneal damage resulting from multiple surgeries to remove ocular melanomas, and one with the genetic eye condition aniridia. Other causes of cornea damage can include chemical or thermal burns, bacterial infection and chemotherapy.
“The procedure is totally simple and cheap,” said lead author of the study, UNSW’s Dr Nick Di Girolamo. “Unlike other techniques, it requires no foreign human or animal products, only the patient’s own serum, and is completely non-invasive.
The surgeon who carried out the procedure and managed the patients was UNSW senior lecturer, Dr Stephanie Watson.
"The operation is relatively non-invasive. The patient merely comes into the hospital for a couple of hours to have their eye prepared and the lens put in place, and then they're able to go home," she said.
“There’s no suturing, there is no major operation: all that’s involved is harvesting a minute amount – less than a millimeter – of tissue from the ocular surface,” said Dr Di Girolamo.
“If you’re going to be treating these sorts of diseases in third world countries all you need is the surgeon and a lab for cell culture. You don’t need any fancy equipment.”
Because the procedure uses the patient’s own stem cells harvested from their eye, it is ideal for sufferers of unilateral eye disease. However, it also works in patients who have had both eyes damaged, Dr Di Girolamo said.
“One of our patients had aniridia, a congenital condition affecting both eyes. In that case, instead of taking the stem cells from the other cornea, we took them from another part of the eye altogether – the conjunctiva – which also harbours stem cells.
“The stem cells were able to change from the conjunctival phenotype to a corneal phenotype after we put them onto the cornea. That’s the beauty of stem cells,” Dr Di Girolamo said.
The therapeutic contact lens used in the trial was of a type commonly used worldwide after ocular surface surgery. However, of the several brands on the market, only one was suitable for growing the stem cells.
“We don’t know why. It’s probably to do with the components the manufacturers have used in that particular lens,” Dr Di Girolamo said.
The researchers are hopeful the technique can be adapted for use in other parts of the eye, such as the retina, and even in other organs. “If we can do this procedure in the eye, I don’t see why it wouldn’t work in other major organs such as the skin, which behaves in a very similar way to the cornea,” Dr Di Girolamo said.


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Bacteria and Food Poisoning

The U.S. Centers for Disease Control and Prevention (CDC) estimates that around 80 million people a year in the U.S. alone contract food poisoning or other foodborne diseases.
Foodborne illness is caused by eating or drinking food that contains disease causing agents. The most common causes of foodborne diseases are bacteria, viruses, and parasites. Foods containing toxic chemicals can cause foodborne diseases as well.
There are over two hundred types of bacteria, viruses and parasites that can cause foodborne diseases. Reactions to these germs can range from mild gastric discomfort to death. The easiest way to prevent foodborne illness is to properly handle and cook foods. This includes washing your hands and utensils carefully and cooking meat thoroughly.
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Below is a list of a few bacteria that cause foodborne diseases, along with the foods that are associated with them, as well as symptoms that are likely to develop from ingesting the contaminated foods.

Bacteria and Food Poisoning
Microbe - Aeromonas hydrophila
Affiliated Foods - Fish, Shellfish, Beef, Pork, Lamb, and Poultry

Diseases - Gastroenteritis, Septicemia
Symptoms - Diarrhea, Blood and Mucus in Stool


Microbe - Bacillus cereu
Affiliated Foods - Meats, Milk, Rice, Potato, and Cheese Products
Diseases - B. cereus Food Poisoning
Symptoms - Diarrhea, Abdominal Cramps, Nausea

Microbe - Campylobacter jejuni
Affiliated Foods - Raw Chicken, Unpasteurized Milk, Non-chlorinated Water
Diseases - B. cereus Campylobacteriosis
Symptoms - Diarrhea, Abdominal Cramps, Nausea and Fever, Headache and Muscle Pain

Microbe - Clostridium botulinum
Affiliated Foods - Canned Foods Including: Vegetables, Meats, and Soups
Diseases - Foodborne Botulism
Symptoms - Weakness, Double Vision and Vertigo, Difficulty in Speaking, Swallowing, and Breathing, Constipation

Microbe - Clostridium perfringens
Affiliated Foods - Non-refrigerated Prepared Foods: Meats and Meat Products, Gravy
Diseases - Perfringens Food Poisoning
Symptoms - Severe Abdominal Cramps, Diarrhea

Microbe - Escherichia coli O157:H7
Affiliated Foods - Undercooked Meats, Raw Ground Beef
Diseases - Hemorrhagic colitis
Symptoms - Severe Abdominal Pain, Watery and Bloody Diarrhea, Vomiting

Microbe - Listeria monocytogenes
Affiliated Foods - Dairy Products, Raw Vegetables, Raw Meats, Smoked Fish
Diseases - Listeriosis
Symptoms - Flu-like Symptoms, Persistent Fever, Nausea and Vomiting, Diarrhea

Microbe - Salmonella spp.
Affiliated Foods - Poultry and Eggs, Milk and Dairy Products, Raw Meats, Fish, Shrimp, Peanut Butter
Diseases - Salmonellosis
Symptoms - Nausea, Vomiting, Abdominal Pain, Fever, Headache, Diarrhea

Microbe - Shigella spp
Affiliated Foods - Poultry, Milk and Dairy Products, Raw Vegetables, Fecally contaminated water, Salads: Potato, Chicken, Tuna, Shrimp
Diseases - Shigellosis
Symptoms - Diarrhea, Abdominal Pain, Fever, Vomiting, Blood or Mucus in Stool

Microbe - Staphylococcus aureus
Affiliated Foods - Poultry and Egg Products, Meat Products, Dairy Products
Diseases - Staphyloenterotoxicosis, Staphyloenterotoxemia
Symptoms - Abdominal Cramping, Nausea and Vomiting, Prostration

Microbe - Vibrio cholerae
Affiliated Foods - Contaminated Water, Shellfish
Diseases - Cholera
Symptoms - Watery Diarrhea, Abdominal Pain, Dehydration, Vomiting, Shock
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