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Stephen Rhodes Portfolio
Mia's Portfolio
Will's Portfolio
Siwoo's Portfolio
Jason's Portfolio
Will's Portfolio

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Developing Questions to Investigate Phenomena

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Developing a Model of Bacteria (Prokaryotes) Vs Eukaryotic cells.  

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Developing a Model of Bacteria (Prokaryotes) Vs Eukaryotic cells.  

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Develop a Model of Bacteria Cell Size Compared to Eukaryotic Cell Size

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Obtaining Information on Bacteria Cells 

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Obtaining Information on Bacteria Cells 

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Obtaining and Communicating Information_ Learning About Bacteria

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Siwoo's Portfolio

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Some cells are visible to the unaided eye

The smallest objects that the unaided human eye can see are about 0.1 mm long. That means that under the right conditions, you might be able to see an amoeba proteus, a human egg, and a paramecium without using magnification. A magnifying glass can help you to see them more clearly, but they will still look tiny.

Smaller cells are easily visible under a light microscope. It's even possible to make out structures within the cell, such as the nucleus, mitochondria and chloroplasts. Light microscopes use a system of lenses to magnify an image. The power of a light microscope is limited by the wavelength of visible light, which is about 500 nm. The most powerful light microscopes can resolve bacteria but not viruses.

To see anything smaller than 500 nm, you will need an electron microscope. Electron microscopes shoot a high-voltage beam of electrons onto or through an object, which deflects and absorbs some of the electrons. Resolution is still limited by the wavelength of the electron beam, but this wavelength is much smaller than that of visible light. The most powerful electron microscopes can resolve molecules and even individual atoms.

Adenine

The label on the nucleotide is not quite accurate. Adenine refers to a portion of the molecule, the nitrogenous base. It would be more accurate to label the nucleotide deoxyadenosine monophosphate, as it includes the sugar deoxyribose and a phosphate group in addition to the nitrogenous base. However, the more familiar "adenine" label makes it easier for people to recognize it as one of the building blocks of DNA.

How can an X chromosome be nearly as big as the head of the sperm cell?

No, this isn't a mistake. First, there's less DNA in a sperm cell than there is in a non-reproductive cell such as a skin cell. Second, the DNA in a sperm cell is super-condensed and compacted into a highly dense form. Third, the head of a sperm cell is almost all nucleus. Most of the cytoplasm has been squeezed out in order to make the sperm an efficient torpedo-like swimming machine.

The X chromosome is shown here in a condensed state, as it would appear in a cell that's going through mitosis. It has also been duplicated, so there are actually two identical copies stuck together at their middles. A human sperm cell contains just one copy each of 23 chromosomes.

A chromosome is made up of genetic material (one long piece of DNA) wrapped around structural support proteins (histones). Histones organize the DNA and keep it from getting tangled, much like thread wrapped around a spool. But they also add a lot of bulk. In a sperm cell, a specialized set of tiny support proteins (protamines) pack the DNA down to about one-sixth the volume of a mitotic chromosome.

Carbon

The size of the carbon atom is based on its van der Waals radius.

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The smallest objects that the unaided human eye can see are about 0.1 mm long. That means that under the right conditions, you might be able to see an amoeba proteus, a human egg, and a paramecium without using magnification. A magnifying glass can help you to see them more clearly, but they will still look tiny.

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Jake's Portfolio

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Go to www.menti.com and use the code 76 42 99 3

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Why A Faecal Transplant could save your life

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Why A Faecal Transplant could save your life

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The faecal transplant, also known as trans-poo-sion, surely has the title of medicine's most disgusting procedure.

It is pretty much what you are imagining - part of a faecal stool is taken from one person and given to another.

The purpose is to introduce new beneficial microbes to the receiving patient's digestive system.

And it can be life-saving.

It shows just how important microbes, which colonise nearly every surface of our body, are to our health.

The gut is an exceptionally rich world with many different species of micro-organisms interacting with each other and our human tissue.

Down in the dark, oxygen-deprived depths of your bowels is an ecosystem as rich as a rainforest or coral reef.

But a bacterium called Clostridium difficile ( C. difficile) can take over and dominate the bowels.

It is an opportunist and normally takes hold after patients have been treated with antibiotics.

Antibiotic drugs are one of the miracles of the modern age, but they kill good and bad bacteria alike.

They are like a forest fire burning through the gut's microbiome - the collected micro-organisms living down there - leaving behind a scorched microbial earth on which C. difficile flourishes.

The microbiome

You are more microbe than human - if you count all the cells in your body, only 43% are human

The rest is our microbiome and includes bacteria, viruses, fungi and single-celled archaea

The human genome - the full set of genetic instructions for a human being - is made up of 20,000 instructions called genes

But add all the genes in our microbiome together and the figure comes out at between two million and 20 million microbial genes and is known as the second genome

Performing the transplant

The problem with C. difficile is that patients will have multiple bouts of watery and even bloody diarrhoea every day, tummy cramps, fever and in the most severe cases the infection is fatal.

The best that medicine has to offer is more antibiotics; it is the definition of a vicious circle.

A stool transplant - or to give it its full title "a faecal microbiota transplant" - aims to repopulate the patient's gut with the microbes from a healthy person.

A relative is often used as they would have had similar gut bacteria.

After a "sample" is produced, it is mixed with water.

Some techniques break the poo up by hand while others blitz it in a household blender.

There are two routes for getting the sample into the required location - down through the mouth or up through the rectum.

The next episode airs 11:00 BST Tuesday April 24, repeated 21:00 BST Monday April 30 and on the BBC iPlayer

Dr Janet Jansson, a microbial ecologist from Pacific Northwest National Laboratory in Washington State in the US, was part of the team trying to prove trans-poo-sion works.

The patient was a 61-year-old woman who had had chronic diarrhoea for around eight months and had lost 27kg in weight.

"It was really a desperate plea for some kind of solution, she was at risk of dying from this C. difficile infection, all of the antibiotics were ineffective," said Dr Jansson.

A sample of healthy stool was transplanted from her husband.

Dr Jansson told the BBC she was very surprised at its success.

"Amazingly two days after that she was able to have normal stools, normal bowel movements, she was basically cured," she said.

"As a microbial ecologist, this is very unusual.

"We saw she went from a very diseased state, when you look at the microbial species, to a healthy microbiome that was very similar to her husband's," Dr Jansson added.

The excitement in the field has led to some people even performing their own DIY faecal transplants with groups like OpenBiome in the US - essentially a public stool bank - being set up.

But will trans-poo-sions mean anything for medicine beyond C. difficile?

The interaction between our human and microbial selves is being investigated in nearly every disease you can think of.

The microbiome has been linked to diseases including inflammatory bowel disease, diabetes, Parkinson's, whether cancer drugs work and even depression and autism.

But this means there could be unintended consequences of a faecal transplant.

It is possible to make mice thinner or fatter by transplanting into them the microbiome from either a lean or obese human, although the jury is still out on whether the same rules apply in people.

There is also the more obvious risk of transferring dangerous disease-causing microbes.

It is why scientists are trying to move on from donating faeces to donating cocktails of bacteria.

Dr Trevor Lawley, from the Wellcome Sanger Institute, said future treatments had to be more refined and targeted.

"Faeces is an undefined community, and when you develop a drug first and foremost you have to consider the safety of the patient," he said.

"We have an idea of what bugs to put in now, so if you have a defined mixture that's proven safe, we can overcome that."

And that is likely to be the future of microbial medicine - knowing what is the problem in an individual patient's microbiome and being able to address that.

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Why a faecal transplant could save your life

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The faecal transplant, also known as trans-poo-sion, surely has the title of medicine's most disgusting procedure. It is pretty much what you are imagining - part of a faecal stool is taken from one person and given to another. The purpose is to introduce new beneficial microbes to the receiving patient's digestive system.

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There's a report in Nature on the bacteria found in the human gut that's getting a lot of press today (especially for a paper about, well, bacteria in the human gut). A team at the Beijing Genomics Institute, with many collaborators, has done a large shotgun sequencing effort on gut flora and identified perhaps one thousand different species.
I can well believe it. The book I recommended the other day on bacteria field marks has something to say about that, pointing out that if you're just counting cells, that the cells of our body are far outnumbered by the bacteria we're carrying with us. Of course, the bacteria have an advantage, being a thousand times smaller (or more) than our eukaryotic cells, but there's no doubt that we're never alone. In case you're wondering, the average European subject of the study probably carries between 150 and 200 different types of bacteria, so there's quite a bit of person-to-person variability. Still, a few species (mostly Bacteroides varieties) were common to all 124 patients in the study, while the poster child for gut bacteria ( E. coli) is only about halfway down the list of the 75 most common organisms. We have some Archaea, too, but they're outnumbered about 100 to 1.
What's getting all the press is that idea that particular mixtures of intestinal bacteria might be contributing to obesity, cancer, Crohn's disease and other conditions. This isn't a new idea, although the new study does provide more data to shore it up (which was its whole purpose, I should add). It's very plausible, too: we already know of an association between Helicobacter and stomach cancer, and it would be surprising indeed if gut bacteria weren't involved with conditions like irritable bowel syndrome or Crohn's. This paper confirms earlier work that such patients do indeed have distinctive microbiota, although it certainly doesn't solve the cause-or-effect tangle that such results always generate.
The connection with obesity is perhaps more of a stretch. You can't argue with thermodynamics. Clearly, people are obese because they're taking in a lot more calories than they're using up, and doing that over a long period. So what do bacteria have to do with that? The only thing I can think of is perhaps setting off inappropriate food cravings. We're going to have to be careful with that cause and effect question here, too.
One problem I have with this work, though, is the attitude of the lead author on the paper, Wang Jun. In an interview with Reuters, he makes a very common mistake for an academic: assuming that drug discovery and treatment is the easy part. After all, the tough work of discovery has been done, right?

"If you just tackle these bacteria, it is easier than treating the human body itself. If you find that a certain bug is responsible for a certain disease and you kill it, then you kill the disease," Wang said

For someone who's just helped sequence a thousand of them, Wang doesn't have much respect for bacteria. But those of us who've tried to discover drugs against them know better. Where are these antibiotics that kill single species of bacteria? No such thing exists, to my knowledge. To be sure, we mostly haven't looked, since the need is for various broader-spectrum agents, but it's hard to imagine finding a compound that would kill off one Clostridium species out of a bunch. And anyway, bacteria are tough. Even killing them off wholesale in a human patient can be very difficult.
Even if we magically could do such things, there's the other problem that we have no idea of which bacterial strains we'd want to adjust up or down. The Nature paper itself is pretty good on this topic, emphasizing that we really don't know what a lot of these bacteria are doing inside us and how they fit into what is clearly a very complex and variable ecosystem. A look at the genes present in the samples shows the usual common pathways, then a list that seem to be useful for survival in the gut (adhesion proteins, specific nutrient uptake), and then a massive long tail of genes that do we know not what nor why. Not only do we not know what's happening on other planets, or at the bottom of our own oceans, we don't even know what's going on in our own large intestines. It's humbling.
Dr. Wang surely realizes this; I just wish he'd sound as if he does.

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There's a report in Nature on the bacteria found in the human gut that's getting a lot of press today (especially for a paper about, well, bacteria in the human gut).

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Why Antibiotics Don't Antibiotics Anymore?

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Evolution of Bacteria Against Antibiotics

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Evolution of Bacteria Against Antibiotics

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Antibiotic Resistance Game - GameUp - BrainPOP.

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In this free science game, players fight antibiotic resistance by targeting bacteria with antibiotic blasts! But mutations are strong, and they multiply. . .

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Whiteboard.fi - Online whiteboard for teachers and classrooms

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Whiteboard.fi is an instant formative assessment tool for your classroom, providing you with live feedback and immediate overview over your students.

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Cell Structure Review Prokaryotes vs Eukaryotes

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Introduction to Cytology

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Interesting link for understanding antibiotics

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Antibiotics have transformed human health by saving millions of lives and alleviating much human misery. However, in most parts of the world it's easy to take treatment with antibiotics for granted and we tend to forget that the drugs were discovered less than a century ago.

In 1928, the Scottish bacteriologist Alexander Fleming returned from his summer vacation and was met by an unexpected sight in his laboratory at St. Mary's Hospital, London. Some of his Petri dishes containing the bacterium Staphylococcus aureus had been contaminated with a mould. After carefully placing the dishes under a microscope, he observed that the mould had created a germ-free zone in which the bacteria did not grow. Fleming concluded that the mould must be producing an antibacterial agent, which not only inhibited the growth of the staphylococci but, more important, might be harnessed to combat infectious diseases. Fleming famously wrote about this red-letter date:
"When I woke up just after dawn on September 28, 1928, I certainly didn't plan to revolutionize all medicine by discovering the world's first antibiotic, or bacteria killer. But I guess that was exactly what I did."
However, it was not only Fleming's merit that the first antibiotic - which he later named penicillin - came to be one of the world's most widely used drugs. About ten years later, the Australian pathologist Howard Florey and the German-born biochemist Ernst Chain, isolated the active substance of penicillin and carried out the first tests on mice. With promising results, the new drug was ready to be used in humans in 1941.

One of the first patients to receive a treatment with penicillin was a British policeman named Albert Alexander who had developed a deadly infection after scratching himself on a rosebush. After five days of penicillin injections, the infection began to heal but since there was not enough pure penicillin available to complete the cure, Alexander eventually relapsed and died a month later.

Later that year, Florey and Chain succeeded in developing methods for mass production of penicillin, which was just in time to treat the many wounded soldiers during World War II. The following year, 400 million units of pure penicillin were manufactured and by the end of the war, American pharmaceutical companies produced 650 billion units a month. The antibiotic era had truly begun and in 1945 Fleming, Florey and Chain were jointly awarded the Nobel Prize in Physiology or Medicine.

Laboratory workers in the development of penicillin, England (1943). By Ministry of Information Photo Division Photographer, Stone Richard [Public domain], via Wikimedia Commons.

Amid a wave of unbridled optimism, one of the first to urge caution over the new drug was actually Fleming himself. In his Nobel lecture in 1945, Fleming presciently warned about the dangers of misusing penicillin:
"It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body. The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant."
Before long, Fleming's predictions came true. The first case of penicillin resistance was observed in 1947. The period between 1950 and 1960 is often referred to as the golden age of antibiotic discovery, as one-half of the antibiotics commonly used today were discovered during these years.

New possibilities for humanity

With the introduction of antibiotics, infectious diseases that previously got people killed or severely disabled, was now regarded as easily treatable. To give an example, the survival rate of bacterial pneumonia dramatically increased from 20% to 85% between 1937 and 1964.

Without any doubt, antibiotics have revolutionized medicine in many respects and is a prerequisite for today's high-technological healthcare. Perhaps most people associate antibiotics with successful treatment of bacterial respiratory tract infections (e.g., pneumonia, otitis and sinusitis), urinary tract infections (UTIs) or gastrointestinal infections. However, without antibiotics it would no longer be possible to perform organ transplants, cancer chemotherapy, intensive care and other surgical procedures, such as hip replacements. Also the care of preterm babies would become more difficult and potentially life-threatening since these children are less able to fight off infections.

In essence, our misuse of antibiotics accelerates the emergence and spread of antibiotic-resistant bacteria. Today we also see an alarming increase in new bacterial strains resistant to several antibiotics at the same time (known as multidrug-resistant bacteria or superbugs). Such bacteria may eventually become resistant to all existing antibiotics and we will then be entering the post-antibiotic era.

© Uppsala University

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The discovery of antibiotics - Part 1 - ReAct

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In 1928, the Scottish bacteriologist Alexander Fleming returned from his summer vacation and was met by an unexpected sight in his laboratory at St. Mary's Hospital, London. Some of his Petri dishes containing the bacterium Staphylococcus aureus had been contaminated with a mould. After carefully placing the dishes under a microscope, he observed that the mould had...

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Do you have questions or comments about this model? Ask them here!(You'll first need to log in.)

WHAT IS IT?

NOTE: This is a transformed model of the Bacterial Infection model in the NetLogo Models Library. Additional model information can be found in the Info tab in the original model. The model shows bacterial growth and antibiotic resistance through membrane permeability changes. Bacterial mutation rate is very high compared to that of human cells. The administration of antibiotics causes a selection pressure on bacteria and induces the evolution of antibiotic resistance. The model explains how bacteria evolve antibiotic resistance through the mutations which change membrane permeability.

HOW IT WORKS

A patient is infected with four different strains of bacteria, each with different membrane permeability level. The bacterial mutation changes membrane pereability, which is represented by the number of holes in the bacterial cell membrane. Also, the number of holes in the bacterial cell membrane indicates susceptibility to antibiotics. A random mutation can add one hole or remove one hole. Mutations to the number of holes exceeding the range between three and six do not occur.

Bacterial natural death is considered in the model.

A patient can take antibiotics repeatedly. Antibiotic molecules enter the patient's bloodstream and kill bacteria as they travel through the patient's body. The space is the patient's bloodstream. Antibiotics are given by placing moleucles at random positions in the space. The molecules move around the bloodstream until they decompose and exit the space. The half of exising antibiotic molecules decomposes every half-life.

HOW TO USE IT

MUTATION P: During the asexual reproduction, mutations can occur which change the number of holes in the bacterial cell membrane. MUTATION P is a probability of a mutation that changes membrane permeability per reproduction.

BACTERIA-DEATH-PROB: Bacterial natural death occurs with a given probability, BACTERIA-DEATH-PROB at every time point.

HALF-LIFE: When antibiotics enter the patient's bloodstream, the half of the existing antibiotic molecules decompose and are removed from the space at every HALF-LIFE.

THINGS TO TRY

At first, try bacteria reproduction without mutations (set REPRODUCE? to "on" and set MUTATION P to 0). Then, increase MUTATION P and allow bacteria to change their membrane permeability and observe changes in bacterial growth and the distribution of different strains (permeability).

Fix all bacteria traits to represent certain bacteria. Imagine developing new antibiotic treatment. Antibiotics have three parameters: dosage, frequency, and half-life. Change these three parameters to find successful combinations, i.e., successful treatments killing all bacteria.

EXTENDING THE MODEL

Considering that bacteria can move with flagella, the model could be extended to allow bacteria to move in the space.

RELATED MODELS

Bacterial Infection model in the NetLogo Models Library.

CREDITS AND REFERENCES

The original model is authored by Uri Wilensky (Copyright 2016 Uri Wilensky).

References: Novak, M. and Quigley, D and Wilensky, U. (2016). NetLogo Bacterial Infection model. http://ccl.northwestern.edu/netlogo/models/BacterialInfection. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

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Do you have questions or comments about this model? Ask them here!(You'll first need to log in.) NOTE: This is a transformed model of the Bacterial Infection model in the NetLogo Models Library. Additional model information can be found in the Info tab in the original model.

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https://www.sejda.com/pdf-editor
https://www.pdfbuddy.com/

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How the Corona virus is mutating to become more infectious because of weakened immune systems.

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Please Use this to construction how bacteria grow. 

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Please Use this to construction how bacteria grow. 

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Antibiotic suceptibility testing in agar plate.

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ID Laboratory Videos_ Antibiotic susceptibility testing

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Quick addition

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Simulation 1

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Guide the bird to the moths. Click on the moth to eat it. You have one minute to eat as many moths as you can. See what impact eating more light or dark moths has on moth population.

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Evolution is the change in inherited traits over time. There are five forces that can lead to evolutionary change; gene flow, genetic drift, mutation, natural selection, and sexual selection. Some of the virtual labs are inquiry-based, meaning that they allow students to develop and test their own questions through manipulation of variables. Others are more guided labs where students collect data following a structured process. Sample are available for classroom use.

The simulation produces data to analyze a predator that has resistance to a prey species with high toxicity.

The Evolution: 10,000 simulation lets the user track the evolution of a fictional population over 10,000 years.

The Natural Selection simulation allows the user to play the part of a predator eating a prey species that has two color phenotypes. The user can run the simulation in three different environments.

The simulation is based on a bacterial mutagenesis lab. Students can study the effect that UV exposure time has on bacteria survival and mutation rates.

allows students to test how selection, population size, and mutation rates affect allele frequencies. This simulation is conducive to inquiry based virtual labs.

The Sexual Selection simulation explores the how a trait can influence survival and mate selection. This simulation allows for inquiry based activities.

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Evolution is the change in inherited traits over time. There are five forces that can lead to evolutionary change; gene flow, genetic drift, mutation, natural selection, and sexual selection. Some of the virtual labs are inquiry-based, meaning that they allow students to develop and test their own questions through manipulation of variables.

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Vocab list needed for Evolution and Natural selection

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As you've probably noticed, words related to "" are listed above. Hopefully the generated list of term related words above suit your needs.

P.S. There are some problems that I'm aware of, but can't currently fix (because they are out of the scope of this project). The main one is that individual words can have many different senses (meanings), so when you search for a word like mean, the engine doesn't know which definition you're referring to ("bullies are mean" vs. "what do you mean?", etc.), so consider that your search query for words like term may be a bit ambiguous to the engine in that sense, and the related terms that are returned may reflect this. You might also be wondering: What type of word is ~term~ ?

Also check out on relatedwords.io for another source of associations.

Related Words

Related Words runs on several different algorithms which compete to get their results higher in the list. One such algorithm uses word embedding to convert words into many dimensional vectors which represent their meanings. The vectors of the words in your query are compared to a huge database of of pre-computed vectors to find similar words. Another algorithm crawls through Concept Net to find words which have some meaningful relationship with your query. These algorithms, and several more, are what allows Related Words to give you... related words - rather than just direct synonyms.

As well as finding words related to other words, you can enter phrases and it should give you related words and phrases, so long as the phrase/sentence you entered isn't too long. You will probably get some weird results every now and then - that's just the nature of the engine in its current state.

Special thanks to the contributors of the open-source code that was used to bring you this list of term themed words: @Planeshifter, @HubSpot, Concept Net, WordNet, and @mongodb.

There is still lots of work to be done to get this to give consistently good results, but I think it's at the stage where it could be useful to people, which is why I released it.

Please note that Related Words uses third party scripts (such as Google Analytics and advertisements) which use cookies. To learn more, see the privacy policy.

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As you've probably noticed, words related to "" are listed above. Hopefully the generated list of term related words above suit your needs. P.S. There are some problems that I'm aware of, but can't currently fix (because they are out of the scope of this project).

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Create a new document and edit with others at the same time -- from your computer, phone or tablet. Get stuff done with or without an internet connection. Use Docs to edit Word files. Free from Google.

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Please use this as the guide to complete assignment 6

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Gathering Evidence for the Mechanism Natural Selection_ Rock Pocket Mouse 

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Karen's Portfolio

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Portfolio Unit 4_ Why Don’t Antibiotic Work Like They Used To

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Yiran's Portfolio

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https://padlet.com/2234259929/nhndk36t1ncc55az