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How can I find some pieces of the genome of a microorganism?

How can I find some pieces of the genome of a microorganism?


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I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant extraction of those genomes - say, some important gene, some mutation, some protein that occurs in a microorganisms genome. What should I look for, and how can I find it in genbank?


You can use already available tools to extract information from available database. For finding specific genes, use this. For protein, use this. There are lot more tools. Just explore NCBI, EMBL or DDBJ sites. All information is self explanatory. If you want specialized information for specific organism, you can use specialized database ( like Flybase for flies, SGD for common yeast, EnsemblBacteria for bacteria and archaea or HGMD for human mutations. Best way is to search in Google. You will get everything you want :D


I guess you have found the Genome entry of your favourite genomes in Genbank and got the FastA.

Dexter is completely right, you can just search your genes in the databases and filter them for your genomes of interest.

Another possibility is to get the GenBank-formated file "GenBank (full)", instead of the FastA, then use a Genome Browser (for example Artemis) which allows you to search for genes/proteins in a genome and save them as separate FastA files.

Generally it is a good thing to get the GenBank format file for an organism you are interested in, as you can extract the complete genome sequence as FastA easily, but also keep all the other information you might need later.


Biology 171


The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. DNA sequencing technology has contributed to advances in genomics. Just as information technology has led to Google maps that enable people to obtain detailed information about locations around the globe, researchers use genomic information to create similar DNA maps of different organisms. These findings have helped anthropologists to better understand human migration and have aided the medical field through mapping human genetic diseases. Genomic information can contribute to scientific understanding in various ways and knowledge in the field is quickly growing.

Learning Objectives

By the end of this section, you will be able to do the following:

  • Define genomics
  • Describe genetic and physical maps
  • Describe genomic mapping methods

Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of finding the locations of genes on each chromosome. The maps that genome mapping create are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to an interstate highway map) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. Early geneticists called this linkage analysis. Physical maps present the intimate details of smaller chromosome regions (similar to a detailed road map). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a genome’s complete picture. Having a complete genome map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis. We can use genome mapping in a variety of other applications, such as using live microbes to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to producing higher crop yields or developing plants that better adapt to climate change.

Genetic Maps

The study of genetic maps begins with linkage analysis , a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. Scientists used the term linkage before the discovery of DNA. Early geneticists relied on observing phenotypic changes to understand an organism’s genotype. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what we now call genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by their location on the same chromosome. Gene mapping relative to each other based on linkage analysis led to developing the first genetic maps.

Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in garden pea experiments, researchers discovered, that the flower’s color and plant pollen’s shape were linked traits, and therefore the genes encoding these traits were in close proximity on the same chromosome. We call exchanging DNA between homologous chromosome pairs genetic recombination , which occurs by crossing over DNA between homologous DNA strands, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. (Figure) shows two possibilities for recombination between two nonsister chromatids during meiosis. If the recombination frequency between two genes is less than 50 percent, they are linked.


The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Scientists based early genetic maps on using known genes as markers. Scientists now use more sophisticated markers, including those based on non-coding DNA, to compare individuals’ genomes in a population. Although individuals of a given species are genetically similar, they are not identical. Every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for genetic mapping purposes. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population.

Some genetic markers that scientists use in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms , and the single nucleotide polymorphisms (SNPs). We can detect RFLPs (sometimes pronounced “rif-lips”) when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which we can then analyze using gel electrophoresis. Every individual’s DNA will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases. Scientists sometimes refer to this as an individual’s DNA “fingerprint.” Certain chromosome regions that are subject to polymorphism will lead to generating the unique banding pattern. VNTRs are repeated sets of nucleotides present in DNA’s non-coding regions. Non-coding, or “junk,” DNA has no known biological function however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active, and it may be involved in regulating coding genes. The number of repeats may vary in a population’s individual organisms. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small. SNPs are variations in a single nucleotide.

Because genetic maps rely completely on the natural process of recombination, natural increases or decreases in the recombination level given genome area affects mapping. Some parts of the genome are recombination hotspots whereas, others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods.

Physical Maps

A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods scientists use to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information from microscopic analysis of stained chromosome sections ((Figure)). It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. We can adjust the radiation amount to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping, and we can adjust the radiation so that increased or decreased recombination frequency does not affect it. Sequence mapping resulted from DNA sequencing technology that allowed for creating detailed physical maps with distances measured in terms of the number of base pairs. Creating genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped the physical mapping process. A genetic site that scientists use to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that we can identify with cDNA libraries, while we obtain SSLPs from known genetic markers, which provide a link between genetic and physical maps.


Genetic and Physical Maps Integration

Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both genome mapping technique types are important to show the big picture. Scientists use information from each technique in combination to study the genome. Scientists are using genomic mapping with different model organisms for research. Genome mapping is still an ongoing process, and as researchers develop more advanced techniques, they expect more breakthroughs. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world goes into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Researchers are making efforts for the information to be more easily accessible to other researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process.

How to Use a Genome Map Viewer

Problem statement: Do the human, macaque, and mouse genomes contain common DNA sequences?

To test the hypothesis, click this link.

In Search box on the left panel, type any gene name or phenotypic characteristic, such as iris pigmentation (eye color). Select the species you want to study, and then press Enter. The genome map viewer will indicate which chromosome encodes the gene in your search. Click each hit in the genome viewer for more detailed information. This type of search is the most basic use of the genome viewer. You can also use it to compare sequences between species, as well as many other complicated tasks.

Is the hypothesis correct? Why or why not?

Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping information, and also details the history and research of each trait and disorder. Click this link to search for traits (such as handedness) and genetic disorders (such as diabetes).

Section Summary

Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for locating genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Researchers combine information from all mapping and sequencing sources to study an entire genome.

Free Response

Why is so much effort being poured into genome mapping applications?

Genome mapping has many different applications and provides comprehensive information that can be used for predictive purposes.

How could a genetic map of the human genome help find a cure for cancer?

A human genetic map can help identify genetic markers and sequences associated with high cancer risk, which can help to screen and provide early detection of different types of cancer.

Glossary


New sequencing technology

The newly sequenced genome — dubbed T2T-CHM13 — adds nearly 200 million base pairs to the 2013 version of the human genome sequence.

This time, instead of taking DNA from a living person, the researchers used a cell line derived from what’s known as a complete hydatidiform mole, a type of tissue that forms in humans when a sperm inseminates an egg with no nucleus. The resulting cell contains chromosomes only from the father, so the researchers don’t have to distinguish between two sets of chromosomes from different people.

Miga says the feat probably wouldn’t have been possible without new sequencing technology from Pacific Biosciences in Menlo Park, California, which uses lasers to scan long stretches of DNA isolated from cells — up to 20,000 base pairs at a time. Conventional sequencing methods read DNA in chunks of only a few hundred base pairs at a time, and researchers reassemble these stretches like puzzle pieces. The larger pieces are much easier to put together, because they are more likely to contain sequences that overlap.

T2T-CHM13 is not the last word on the human genome, however. The T2T team had trouble resolving a few regions on the chromosomes, and estimates that about 0.3% of the genome might contain errors. There are no gaps, but Miga says quality-control checks have proved difficult in those areas. And the sperm cell that formed the hydatidiform mole carried an X chromosome, so the researchers have not yet sequenced a Y chromosome, which typically triggers male biological development.


How is DNA Manipulated?

1. Explain the following terms and their role in recombinant DNA technology

Here are some restriction enzymes and their sites.

BAMHI G / G A T C C PstI C T G C A / G
HindIII A / A G C T T HhaI G C G / C
EcoRI G / A A T T C HpaII C / C G G
SalI G / T C G A C
HindII G T C / G A C
C A G / C T G (blunt ends)

2. On each of the sequences below, determine which restriction enzyme could be used to splice the DNA and indicate where the cut will be made and the enzyme used.

1. 5' T T T G A A T T C A G A T 3'
3' A A A C T T A A G T C T A 5'
Enzyme:
2. 5' G T G G G A T C C C T T A 3'
3' C A C C C T A G G G A A T 5'
Enzyme:
3. 5' A C G C C T C C G G A G A 3'
3' T G C G G A G G C C T C T 5'
Enzyme:
4. 5' T T A A G C T T A A G A A G C T T 3'
3' A A T T C G A A T T C T T C G A A 5'
Enzyme:
5. 5' A A G C G C G T C G A C T T A T A 3'
3' T T C G C G C A G C T G A A T A T 5'
Enzyme:

3. Create a restriction enzyme that will remove the gene of interst. Give it a name too!

4. The following DNA sequence is from a virus that is dangerous, scientists want to use a restriction enzyme to cut the virus into bits. They do not need sticky ends because the do not plan to combine it with other DNA. Use HindII to show how this DNA would be cut. How many pieces would you have? ____


DNA 'Printing' A Big Boon To Research, But Some Raise Concerns

Cambrian Genomics says that what it calls a DNA printer is essentially a DNA sorter — it quickly spots and collects the desired, tailored stretch of DNA.

Courtesy of Cambrian Genomics

Here's something that might sound strange: There are companies now that print and sell DNA.

This trend — which uses the term "print" in the sense of making a bunch of copies speedily — is making particular stretches of DNA much cheaper and easier to obtain than ever before. That excites many scientists who are keen to use these tailored strings of genetic instructions to do all sorts of things, ranging from finding new medical treatments to genetically engineering better crops.

"Many of the figures in the synthetic biology field are not shy at all about embracing that prospect that we're going to use synthetic biology to redesign humanity and to engineer the traits in our children. And that I find extremely disturbing."

Marcy Darnovsky, Executive Director, Center for Genetics and Society

"So much good can be done," says Austen Heinz, CEO of Cambrian Genomics in San Francisco, one of the companies selling these stretches of DNA.

But some of the ways Heinz and others talk about the possible uses of the technology also worries some people who are keeping tabs on the trend.

"I have significant concerns," says Marcy Darnovsky, who directs the Center for Genetics and Society, a genetics watchdog group.

A number of companies have been taking advantage of several recent advances in technology to produce DNA quickly and cheaply. Heinz says his company has made the process even cheaper.

"Everyone else that makes DNA, makes DNA incorrectly and then tries to fix it," Heinz says. "We don't fix it. We just see what's good, what's bad and then we use the correct pieces."

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The company does that by putting chunks of their DNA on tiny metal beads that emit different colors. That lets a computer scan millions of pieces of DNA to find the right ones.

"So we just take a picture, change a filter, take a picture, change a filter, take a picture, change a filter. And we read the sequences," he says.

It's basically a high-tech version of a spell-checker.

Then Cambrian chooses and "prints" the correct stretch of DNA by firing a computer-controlled laser beam at a glass tray holding millions of these tiny metal beads, each one coated with DNA. The impact of the laser propels the bead carrying the correct DNA into a tray.

"The DNA laser 'printer' is essentially a sorter," he says. It can produce any strand of DNA, made to order, and Heinz can crank out a lot of DNA this way.

"We can make DNA that would be used to make a virus that could target your cancer cells. And I think it can be helpful for dealing with some of the problems that humans have created. If we can make plants that can suck more carbon out of the atmosphere, we can deal with global warming."

Austin Heinz, CEO, Cambrian Genomics

So far, the company's main customers are drug companies, which use the strings of DNA Cambrian Genomics makes to do things like genetically engineer microbes to try to find new medicines.

"They may be interested in making a protein that attacks a cancer cell with some kind of killer payload," he says.

Other users are genetically engineering plants to try to make them grow better. But Heinz envisions a day when mass-produced DNA can genetically engineer people — or let anyone use DNA like computer code to design their own organisms.

"I think some people will find the process of designing and making organisms just fun, in and of itself," he says.

But this sort of talk makes some people nervous.

"Heinz talks openly about everybody being able to create entirely novel creatures," Darnovsky says. "Is that what we want? Do we want anybody, including potential terrorists, to be able to create entirely novel life forms — new creatures? Do we want the teenager next door to be creating Godzilla in the bathtub? I don't want that."

She also worries about genetically engineered plants running amok, ruining the environment. And, she says, genetically engineering people would be even worse.

"Many of the figures in the synthetic biology field are not shy at all about embracing that prospect that we're going to use synthetic biology to redesign humanity and to engineer the traits in our children," she says. "And that I find extremely disturbing."

But others say those kinds of fears are exaggerated.

"Like every other technology, we need to be paying attention to how it's used," says Rob Carlson, a biotechnology analyst at Seattle-based Biodesic. But "it is not intrinsically more dangerous than other technologies," he adds. "And, in fact, if you wanted to do harm, there are many easier ways to go about causing harm than using synthetic DNA."

Heinz says his company is being very careful. It won't sell DNA to just anyone. And the potential benefits to society, he thinks, are huge.

"We can make DNA that would be used to make a virus that could target your cancer cells. And I think it can be helpful for dealing with some of the problems that humans have created. If we can make plants that can suck more carbon out of the atmosphere, we can deal with global warming," he says.

In addition, Heinz says he thinks "in general most people want children that are healthier than they were — maybe better. I think as a race, or as a species we have a goal of improving who we are."

Already, Cambrian Genomics and other companies are scaling up their operations to meet what many expect to be a growing demand for synthetic DNA.


Humans may harbor more than 100 genes from other organisms

You’re not completely human, at least when it comes to the genetic material inside your cells. You—and everyone else—may harbor as many as 145 genes that have jumped from bacteria, other single-celled organisms, and viruses and made themselves at home in the human genome. That’s the conclusion of a new study, which provides some of the broadest evidence yet that, throughout evolutionary history, genes from other branches of life have become part of animal cells.

“This means that the tree of life isn’t the stereotypical tree with perfectly branching lineages,” says biologist Alastair Crisp of the University of Cambridge in the United Kingdom, an author of the new paper. “In reality, it’s more like one of those Amazonian strangler figs where the roots are all tangled and crossing back across each other.”

Scientists knew that horizontal gene transfer—the movement of genetic information between organisms other than parent-to-offspring inheritance—is commonplace in bacteria and simple eukaryotes. The process lets the organisms quickly share an antibiotic-resistance set of genes to adapt to an antibiotic, for instance. But whether genes have been horizontally transferred into higher organisms—like primates—has been disputed. Like in bacteria, it’s been proposed that animal cells could integrate foreign genetic material that’s introduced as small fragments of DNA or carried into cells by viruses. But proving that a bit of DNA in the human genome originally came from another organism is tricky.

Crisp and his colleagues analyzed the genome sequences of 40 different animal species, ranging from fruit flies and roundworms to zebrafish, gorillas, and humans. For each gene in the genomes, the scientists searched existing databases to find close matches—both among other animals and among nonanimals, including plants, fungi, bacteria, and viruses. When an animal’s gene more closely matched a gene from a nonanimal than any other animals, the researchers took a closer look, using computational methods to determine whether the initial database search had missed something.

In all, the researchers pinpointed hundreds of genes that appeared to have been transferred from bacteria, archaea, fungi, other microorganisms, and plants to animals, they report online today in Genome Biology. In the case of humans, they found 145 genes that seemed to have jumped from simpler organisms, including 17 that had been reported in the past as possible horizontal gene transfers.

“I think what this shows it that horizontal gene transfer is not just confined to microorganisms but has played a role in the evolution of many animals,” Crisp says, “perhaps even all animals.

The paper doesn’t give any hints as to how the genes—which now play established roles in metabolism, immune responses, and basic biochemistry—may have been transferred or the exact timeline of the jumps, he says. That will take more work.

The findings are critical to understanding evolution, says Hank Seifert, a molecular biologist at the Northwestern University Feinberg School of Medicine in Chicago, Illinois. “This is a very well-done paper. They used all the latest data they could find, all the genomes in the databases,” he says. “It makes it clearer than ever that there has been a history, throughout evolution, of gene transfer between organisms.”

But not all agree that the new evidence is indisputable. “I see little here that is particularly convincing evidence for horizontal gene transfer,” says microbiologist Jonathan Eisen of the University of California, Davis. He doesn’t rule out that horizontal gene transfer between bacteria and animals is possible, but says that there are other explanations for the identified genes being present in only some branches of the evolutionary tree—a gene that existed in a far-off ancestor could have simply been lost in many relatives other than two seemingly unrelated species, for instance. “It is up to [the researchers] to exclude other, more plausible alternatives, and I just do not think they have done that.”


B. The viral way of life

When genetic information is encoded in double-stranded DNA, the enzyme RNA polymerase copies the information from DNA into messenger RNA, which then directs the synthesis of proteins that are responsible for traits of an organism. This flow of information, DNA —> RNA —> protein, is often referred to as the “central dogma.” Because viruses use the host cell’s translational machinery to make viral proteins, they too must use mRNAs to guide the production of proteins. Viruses containing dsDNA will use the host RNA polymerase to produce mRNA (Figure 1 category I).

What happens when information is stored in ssDNA or in ssRNA or dsRNA? When the viral genome is ssDNA, a viral enzyme (or polymerase) must first synthesize a complementary strand of DNA to produce dsDNA from which mRNA is generated (Figure 3 category II). When the viral genome is dsRNA, mRNA is produced by a viral RNA polymerase that the virus carries into the cell (Figure 3 category III).

Viruses with ssRNA can be one of three types:

  1. positive-strand ssRNA (+ssRNA) viruses in which the viral genome serves directly as mRNA for protein synthesis (Figure 1 category IV). Additionally, the + ssRNA genome serves as a template for producing a negative-strand ssRNA (-ssRNA) via the viral RNA polymerase. The resulting - ssRNA then serves as a template for the production of more + ssRNA again via the viral RNA polymerase. These new + ssRNA can serve as mRNA and also will be encapsulated as the genome of the progeny virus.
  2. negative-strand ssRNA (-ssRNA) viruses in which the RNA genome is copied into mRNA for protein synthesis by the viral RNA polymerase (Figure 1 category V). Additionally, the - ssRNA serves as a template for synthesis of a +ssRNA via the viral RNA polymerase. The resulting +ssRNA then itself serves as a template for production of more - ssRNA, again via the viral RNA polymerase. These - ssRNA genomes can again be copied to mRNA by the viral RNA polymerase or encapsulated as the genome for the progeny virus.
  3. negative-strand ssRNA-reverse transcriptase (-ssRNA-RT) viruses in which a double stranded DNA is synthesized from the viral RNA strand by the enzyme reverse transcriptase. This double stranded DNA molecule is then inserted into the host DNA where it is transcribed into mRNA (Figure 1 category VI)

See Table 3 for examples of viruses with the different types of nucleic acids.

The ways different viruses invade and take over a cell varies to some degree but all demonstrate a common pattern. A virus enters the cell and, using different mechanisms depending on the kind of virus it is, takes over the cellular protein synthesis machinery to generate the proteins it needs for itself to reproduce. Like an unwanted guest who eats everything in the refrigerator, uses every clean towel in the house, and on leaving reduces your house to a pile of rubble, the virus utilizes the building blocks and energy stored that the cell has generated for its own growth and reproduction.

The cell is depleted of the materials and energy it needs to repair the damage. The machinery the cell needs to make more of itself is no longer under its control. As a result, the cell often dies from this invasion. A virus may exit a cell by simply lysing (blowing up) the cell or by budding from the cell, picking up some host membrane as it exists. As you will see in the measles and Ebola viruses, a virus that buds from a cell rather than exploding the cell can spread throughout the body efficiently by traveling in infected cells.

Table 3. Examples of viruses

Virus Structure Mode of Transmission Disease Caused Damage Symptoms
SARS-CoV-2 person-to-person apread contact with contaminated surfaces or objects COVID-19 damages the wall and lining cells of the alveolus as well as the capillaries provokes a destructive immune response cough, fever, tiredness, difficulty breathing
Polio Water, oral Poliomyelitis Destroys motor neuron cells Fever, sore throat, headache, vomiting, fatigue, muscle pain and weakness, paralysis
Influenza Aerosol, Inhalation of infectious droplets Direct contact with respiratory fluids Flu Death of epithelial cells in nose, throat, and lungs Fever, cough, sore throat, runny or stuffy nose, muscle aches, headaches, fatigue
Ebola Direct contact with body fluids Hemorrhagic fever Infects cells of immune system and endothelial cells of vascular system causing blood leakage Nausea, high fever, muscle pain, malaise, diarrhea, red eyes,, severe weight loss, occasionally bleeding from eyes, ears nose, rectum
Measles Aerosol, inhalation of infectous droplets Rubeola (measles) Infects cells of immune system and epithelial cells High fever, cough, runny nose, red and watery eyes, rash
HIV Sexual contact blood AIDS Destroys immune cells (CD4 cells) Lack of energy, weight loss, fevers and sweats, frequent yeast infections, skin rashes or flaky skin, short-term memory loss, mouth, genital, or anal sores
Rotavirus Direct contact with contaminated surfaces fecal-oral Gastroenteritis Epithelial cells of the gastrointestinal tract Severe diarrhea, vomiting, fever, dehydration
Canine Parvovirus Direct contact with contaminated surfaces fecal-oral Gastroenteritis Epithelial cells of the gastrointestinal tract Severe bloody diarrhea, lethargy, anorexia, fever, vomiting, severe weight loss
Vaccinia Direct contact with contaminated objects and people airborne with infected droplets of saliva Smallpox Epithelial cells lining respiratory tract and other organs including skin High fever, fatigue, headache, backache, rash with flat red sores
Adenovirus Direct contact with contaminated objects and people airborne with infected droplets fecal-oral Common cold, sore throat, bronchitis, pneumonia, diarrhea, pink eye (conjunct-tivitis), gastro-enteritis Inflammation and destruction of epithelial cells Fever, cough, runny nose, bladder inflammation or infection (cystitis), inflammation of stomach and intestines

Measuring Inhibition Zones

You will need to know:

How to measure the area of inhibition zones and compare the effectiveness of antibiotics

The larger the inhibition zone, the more effective the antibiotic is to that particular strain of bacteria. You can usually just see which inhibition zone is the largest, but it’s more reliable and accurate to calculate the __areas __of the inhibition zones and compare them.

To do this you’ll need to:

  1. Measure the diameter of the zone you’re interested in, with a ruler.
  2. Half to diameter to get the radius, r.
  3. Use the equation: Area = πr2 to find the Area. (If you don’t already know from maths lessons, π is just a number that is found on your calculator, it’s usually one of the buttons.)

You can also use this technique to measure the area of colonies. A colony is just a build up of bacteria (like when you leave an old mug out and it goes moldy!)


About the Author – Sagar Aryal

My name is Sagar Aryal and I’m a passionate microbiologist and a scientific blogger. I did my Master’s Degree in Microbiology and currently doing my Ph.D. from Tribhuvan University in collaboration with Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Germany. I am particularly interested in research related to actinomycetes, myxobacteria and natural products. You can learn more about me, my credentials, publications and awards on my personal website.


In &lsquoMoon Landing of Genomics,&rsquo Scientists Sequence Ancient DNA From Dirt

Scientists have achieved a breakthrough they&rsquore comparing to the moon landing: sequencing a full ancient genome from soil samples.

How&rsquos that on par with humans touching down on the lunar surface? Well, the research team from the University of Copenhagen found the entire genetic code of an ancient bear species without obtaining it from fossils, marking the very first time scientists have found genes outside the fossil record. And by gathering the DNA from the soil, these researchers gathered a bunch of examples, rather than just one single specimen&rsquos genome.

➡ You think science is badass. So do we. Let&rsquos nerd out over it together.

The scientists found the ancient bear genetic material in the soil of Chiquihuite Cave in rural Mexico. Like the ancient Chauvet Cave in France, Chiquihuite contains some of the oldest human evidence in the world&mdashbut humans weren&rsquot the only ones to use the caves.

The ancestral bear DNA dates back to about 16,000 years ago, and it comes from an unsavory, but logical source: bear waste.

&ldquoWhen an animal or a human urinates or defecates, cells from the organism are also excreted,&rdquo geneticist Eske Willerslev told ScienceAlert. &ldquoWe have shown that hair, urine, and feces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years.&rdquo

From there, the researchers assembled the pieces of environmental DNA (eDNA). &ldquoStandard eDNA techniques allow species to be determined [without] macrofossils across a variety of environments including sediments, ice cores, lakes, rivers, and oceans,&rdquo the scientists explain in their paper, which appears in Current Biology.

So how did the team assemble the bears&rsquo genome from these environmental scraps?

Basically, the scientists patched together the complete ancient genome using modern and extinct bears as templates&mdashthink about using a model of a bottlenose dolphin as a guide to assemble the body parts of a killer whale. The parts aren&rsquot exactly alike, but both animals have a dorsal fin and a blowhole.

Fossils offer scientists a huge amount of information, but the fossil record is spotty by nature, and doesn&rsquot make sense to rely on as something to fully inform us about everyday activities and whole populations of animals. For example, one full T. rex specimen, while spectacular, doesn&rsquot explain what the whole species&rsquo genetic information was like.

Willerslev told ScienceAlert this research is &ldquothe moon landing of genomics&rdquo because it allows study of the genome without any fossil findings&mdashbringing with it a vast wealth of new genetic information that can be gleaned fully from soil and other sediment.


Watch the video: Δημιουργία και εκτροφή ΕΜ ενεργών μικροοργανισμών (October 2022).