bacteria

tags: Microcosm, microbiology, bacteria, E coli, evolution, Carl Zimmer, book review I lived through Seattle's outbreak of the "killer E. coli strain O157:H7" that charged into the world's consciousness after it mercilessly destroyed the kidneys and other vital organs of hundreds of children and adults who consumed contaminated fast food. During this time, I worked as a lab microbiologist in several human and veterinary hospitals in the Seattle area while I earned my bachelor's degree in microbiology, so I have a strong background in both the practical realities and the scientific lore of…
tags: researchblogging.org, evolution, experimental evolution, adaptation, mutation, natural selection, Richard E. Lenski The common gut bacteria, Escherichia coli, typically known as E. coli. Image: Dennis Kunkel. Evolution is a random process -- or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent…
When it comes to evolution, a species' past has a massive bearing on what it might become. That's the latest message from a 20-year-long experiment in evolution, which shows how small twists of fate can take organisms down very different evolutionary paths. The role of history in evolution is a hotly debated topic. The late Stephen Jay Gould was a firm believer in its importance and held the view that innocuous historical events can have massive repercussions, often making the difference between survival and extinction. To him, every genetic change is an "accident of history" that makes some…
Our bodies are rife with genes and the majority of them aren't even ours. We all have a strong sense of our own individuality, but the truth is that our bodies are hotels for a diverse array of microbes including bacteria and fungi. The numbers are simultaneously creepy and humbling. Tot up all the cells in our bodies and the microbial ones would outnumber our own by a factor of ten. The five feet of our large intestine houses the majority of these microorganisms and contain up to 100 trillion of them. These single-celled tenants are known as the microbiota and they carry their own sets of…
As far as humans are concerned, sexually-transmitted infections are things to avoid. But imagine if these infections didn't cause death and disease, but gave you superpowers instead. It may sound like a bizarre fantasy, but it's just part of life for aphids. Aphids mostly reproduce without sex, giving rise to many all-female generations that are exact copies (clones) of their parents. They only have sex once in autumn, the only time when mothers give birth to males. Asexual reproduction makes sense for aphid mothers since they pass on all of their genes to their daughters. If they…
They say that size doesn't matter, but try telling that to bacteria. Most are very small, for they rely heavily on passive diffusion to ferry important nutrients and molecules across their membranes. To ensure that this happens quickly enough, bacteria need to ensure that their surface area is large enough relative to their volume - become too big and they won't be able to import enough nutrients to support their extra size. These constraints greatly limit the size of bacteria. The larger ones solve the problem by being extremely long and slender, or by using an internal compartment called…
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes. Now, in one of our last projects we are determining where…
For comic book characters, big doses of radiation are a surefire way of acquiring awesome superpowers, but in real life, the results aren't quite as glamorous. A victim of acute radiation poisoning can look forward to hair loss, bleeding, the destruction of their white blood cells and bone marrow, and severe damage to their spleen, stomach and intestines. Radiation doesn't kill cells directly, but it can cause so much damage that they commit suicide, by enacting a failsafe program called apoptosis.  Now, Lyudmila Burdelya and colleagues from Roswell Park Cancer Institute have found a way to…
Humans have been blamed for the disappearance of species before but never quite like this. Scientists at the University of Oxford have found evidence that two species of bacteria are merging into one. The two species are swapping genetic material at such a high rate that they are on the road to sharing a single, common genome. Their genetic merger is probably the result of being thrust into a new environment - the intestines of heavily farmed chickens, cattle and other domesticated livestock. The two bacteria in question - Campylobacter jejuni and Campylobacter coli - are two of the most…
Antibiotics are meant to kill bacteria, so it might be disheartening to learn that some bacteria can literally eat antibiotics for breakfast. In fact, some species can thrive quite happily on nothing but antibiotics, even at high concentrations. The rise of drug-resistant bacteria poses a significant threat to public health and many dangerous bugs seem to be developing resistance at an alarming rate. The headline-grabbing MRSA may be getting piggybacks from livestock to humans, while several strains of tuberculosis are virtually untreatable by standard drugs. But a startling new study…
Some of us have enough trouble finding the food we want among the ordered aisles of a supermarket. Now imagine that the supermarket itself is in the middle of a vast, featureless wasteland and is constantly on the move, and you begin to appreciate the challenges faced by animals in the open ocean. Thriving habitats like coral reefs may present the photogenic face of the sea, but most of the world's oceans are wide expanses of emptiness. In these aquatic deserts, all life faces the same challenge: how to find enough food. Now, a couple of interesting studies have shed new light on the…
The next time you watch a snowfall, just think that among the falling flakes are some that house bacteria at their core. It's a well known fact that water freezes at 0°C, but it only does so without assistance at -40&#176C or colder. At higher temperatures, it needs help and relies on microscopic particles to provide a core around which water molecules can clump and crystallise. These particles act as seeds for condensation and they are rather dramatically known as "ice nucleators". Dust and soot are reasonable ice nucleators but they are completely surpassed by bacteria, which can kick…
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that we can have a visual picture of which bacteria live in each environment. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three). II. Cleaning up the data…
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three). II. Cleaning up the data III. Counting all the bacteria IV. Counting the bacteria by biome Part III. Pivot tables from Sandra Porter on…
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three). II. Cleaning up the data III. Counting all the bacteria…
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every year, I collect the data from her students' experiments. Then, in the bioinformatics classes I teach, we work with the chromatograms and other data to see what we can find. This is the first part of a four part video series…
or E. coli, or perhaps a little Giardia (just to loosen things up, of course), or maybe even Herpes. All these scary pathogens become works of art, when Infectious Awareables puts the images on neckties. And what could be funnier than a pair of boxer shorts full of Gonorrhea?
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles. The general process is this: 1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
For the record: Chlamydia is NOT a virus. I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun. But I was perusing the archives and I found this: I could ignore this if it came from a different source, but MicrobeWorld is produced with funding from the American Society for Microbiology! Microbiologists are supposed to know the difference between bacteria and viruses. It's part of our training and big part of what we do. I know, as scientists we're always supposed to follow the mantra of "buyer beware" and "be skeptical of everything…
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify 16s ribosomal DNA by PCR, and check their PCR results by gel electrophoresis. DNA samples are next sent to the university's Genetic Resources Core Facility , where scientific staff, in…