Posts about virus

Should Giant Viruses Be Included on the Tree of Life?

A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants. The study may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life. But I am not sure that makes sense. The reason given for viruses not being “life” is that they cannot reproduce themselves – they hijack living cells to reproduce. The research in the past history of viruses as they evolved into current viruses is interesting but I don’t see the reason to classify current viruses as life.

The researchers used a relatively new method to peer into the distant past. Rather than comparing genetic sequences, which are unstable and change rapidly over time, they looked for evidence of past events in the three-dimensional, structural domains of proteins. These structural motifs, called folds, are relatively stable molecular fossils that – like the fossils of human or animal bones – offer clues to ancient evolutionary events, said University of Illinois crop sciences and Institute for Genomic Biology professor Gustavo Caetano-Anollés, who led the analysis.

“Just like paleontologists, we look at the parts of the system and how they change over time,” Caetano-Anollés said. Some protein folds appear only in one group or in a subset of organisms, he said, while others are common to all organisms studied so far.

“We make a very basic assumption that structures that appear more often and in more groups are the most ancient structures,” he said.

Most efforts to document the relatedness of all living things have left viruses out of the equation, Caetano-Anollés said.

“We’ve always been looking at the Last Universal Common Ancestor by comparing cells,” he said. “We never added viruses. So we put viruses in the mix to see where these viruses came from.”

The researchers conducted a census of all the protein folds occurring in more than 1,000 organisms representing bacteria, viruses, the microbes known as archaea, and all other living things. The researchers included giant viruses because these viruses are large and complex, with genomes that rival – and in some cases exceed – the genetic endowments of the simplest bacteria, Caetano-Anollés said.

Related: Plants, Unikonts, Excavates and SARsBacteriophages: The Most Common Life-Like Form on Earth8 Percent of the Human Genome is Old Virus GenesMicrobes Retroviruses

Open access paper: Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

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Bacteriophages Enter Bacteria Using an Iron Tipped Spike

Bacteria-Killing Viruses Wield an Iron Spike

Forget needles in haystacks. Try finding the tip of a needle in a virus. Scientists have long known that a group of viruses called bacteriophages have a knack for infiltrating bacteria and that some begin their attack with a protein spike. But the tip of this spike is so small that no one knew what it was made of or exactly how it worked. Now a team of researchers has found a single iron atom at the head of the spike, a discovery that suggests phages enter bacteria in a different way than surmised.

Wherever there are bacteria you will find bacteriophages; digestive tracts, contaminated water, and feces are usually a good start. These viruses begin their dirty work by drilling into the outer membrane of bacteria. Once completely through all of a bug’s defenses, the phages inject their DNA, which essentially turns the bacterium into phage-producing factories. Eventually, the microbes become filled with so many viruses that they burst, releasing a new horde of phages into the environment.

Bacteriophages are amazing. It is so interesting to learn about amazingly creative solutions that have evolved over time. Real-life science is not easy to match with fiction that springs from our imaginations.

Related: Bacteriophages: The Most Common Life-Like Form on EarthViruses Eating BacteriaWhere Bacteria Get Their Genes

Our Genome Has Adopted Virus Genes Critical to Our Survival

Mammals Made By Viruses by Carl Zimmer

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years. They typically have gotten there by infecting eggs or sperm, inserting their own DNA into ours. There are 100,000 known fragments of viruses in the human genome, making up over 8% of our DNA. Most of this virus DNA has been hit by so many mutations that it’s nothing but baggage our species carries along from one generation to the next. Yet there are some viral genes that still make proteins in our bodies. Syncytin appeared to be a hugely important one to our own biology. Originally, syncytin allowed viruses to fuse host cells together so they could spread from one cell to another. Now the protein allowed babies to fuse to their mothers.

The big picture that’s now emerging is quite amazing. Viruses have rained down on mammals, and on at least six occasions, they’ve gotten snagged in their hosts and started carrying out the same function: building placentas.

Some mammals that scientists have yet to investigate, such as pigs and horses, don’t have the open layer of cells in their placenta like we do. Scientists have come up with all sorts of explanations for why that may be, mainly by looking for differences in the biology of each kind of mammals. But the answer may be simpler: the ancestors of pigs and horses might never have gotten sick with the right virus.

More amazing facts from science. This stuff is so interesting. Carl Zimmer is a fantastic science writer and he has written several great science books.

Related: Amazing Science, RetrovirusesMicrocosm by Carl ZimmerTen Things Everyone Should Know About ScienceParasite Rex

Cool Animation of a Virus Invading a Person’s Body

Flu Attack! How A Virus Invades Your Body

First, some new viruses get caught in mucus and other fluids inside your body and are destroyed. Other viruses get expelled in coughs and sneezes. Second, lots of those new viruses are lemons. They don’t work that well. Some don’t have the right “keys” to invade healthy cells so they can’t spread the infection. And third, as the animation shows, your immune system is busy attacking the viruses whenever and wherever possible.

That is why most of the time, after a struggle (when you get a fever and need to lie down), your immune system rebounds, and, in time, so do you.

A health body with a strong immune system is able to fight off viruses, and other health issues more easily. Also when you body has run across a specific virus before it is ready to fight it. It has cataloged that virus and is on the look out for it and is prepared to produce specialized cells to attack it. The flu vaccinations you get are priming your body to be ready to attack if that virus is found. Those antibodies take about 2 weeks to build up in sufficient numbers to offer protection against the flu. Viruses are constantly mutating which helps them evade your detectors. This stuff is so amazing. And your body is just doing this stuff every day while you watch youtube or play basketball or…

Related: Antigen Shift in Influenza VirusesLearning How Viruses Evade the Immune SystemHow to Stay Healthy: Avoiding the Flu

Using a Virus to Improve Solar-cell Efficiency Over 30%

Solar and wind energy are making great strides, and are already contributing significantly to providing relatively clean energy.

Researchers at MIT have found a way to make significant improvements to the power-conversion efficiency of solar cells by enlisting the services of tiny viruses to perform detailed assembly work at the microscopic level.

In a solar cell, sunlight hits a light-harvesting material, causing it to release electrons that can be harnessed to produce an electric current. The research, is based on findings that carbon nanotubes — microscopic, hollow cylinders of pure carbon — can enhance the efficiency of electron collection from a solar cell’s surface.

Previous attempts to use the nanotubes, however, had been thwarted by two problems. First, the making of carbon nanotubes generally produces a mix of two types, some of which act as semiconductors (sometimes allowing an electric current to flow, sometimes not) or metals (which act like wires, allowing current to flow easily). The new research, for the first time, showed that the effects of these two types tend to be different, because the semiconducting nanotubes can enhance the performance of solar cells, but the metallic ones have the opposite effect. Second, nanotubes tend to clump together, which reduces their effectiveness.

And that’s where viruses come to the rescue. Graduate students Xiangnan Dang and Hyunjung Yi — working with Angela Belcher, the W. M. Keck Professor of Energy, and several other researchers — found that a genetically engineered version of a virus called M13, which normally infects bacteria, can be used to control the arrangement of the nanotubes on a surface, keeping the tubes separate so they can’t short out the circuits, and keeping the tubes apart so they don’t clump.

The system the researchers tested used a type of solar cell known as dye-sensitized solar cells, a lightweight and inexpensive type where the active layer is composed of titanium dioxide, rather than the silicon used in conventional solar cells. But the same technique could be applied to other types as well, including quantum-dot and organic solar cells, the researchers say. In their tests, adding the virus-built structures enhanced the power conversion efficiency to 10.6% from 8% — almost a one-third improvement.

Read the full press release

Related: Using Virus to Build BatteriesUsing Viruses to Construct ElectrodesUsing Bacteria to Carry Nanoparticles Into Cells

Grauer’s Gorilla (Eastern Lowlands Gorilla)

The Grauer’s Gorilla (Eastern Lowlands Gorilla) is closely related to the endangered mountain gorilla and is found in the Congo. The eastern lowland gorilla is actually the largest gorilla; males can weigh over 500 pounds. As you can guess from the name, these gorilla’s prefer lowlands to the mountains.

Sadly the eastern lowland gorilla wild population is estimated to have fallen below 8,000 due to warfare (intruding on their territory), agriculture, mining, logging and hunting gorilla’s for meat. The Wildlife Conservation Society is helping preserve habitat for these wonderful creatures.

Related: Massive Western Lowland Gorilla Population in Northern Republic of CongoSavanna Chimpanzees Hunt with ToolsOrangutan Attempts to Hunt Fish with SpearInsightful Problem Solving in an Asian Elephant

Molecule Found in Sharks Kills Many Viruses that are Deadly to People

photo of 3 dogfish sharks
Shark Molecule Kills Human Viruses, Too

“Sharks are remarkably resistant to viruses,” study researcher Michael Zasloff, of the Georgetown University Medical Center, told LiveScience. Zasloff discovered the molecule, squalamine, in 1993 in the dogfish shark, a small- to medium-size shark found in the Atlantic, Pacific, and Indian Oceans.

“It looked like no other compound that had been described in any animal or plant before. It was something completely unique,” Zasloff said. The compound is a potent antibacterial and has shown efficacy in treating human cancers and an eye condition known as macular degeneration, which causes blindness.

By studying the compound’s structure and how it works in the human body, Zasloff thought it might have some antiviral properties. He saw that the molecule works by sticking to the cell membranes of the liver and blood vessels. While there, it kicks off other proteins, some of which are essential for viruses to enter and survive in the cell.

The researchers decided to test the compound on several different live viruses that infect liver cells, including hepatitis B, dengue virus and yellow fever. They saw high efficacy across the board.

Zasloff hopes to start human trials in the next few years.

Marc Maresca, a researcher at Paul Cézanne University in Aix-en-Provence, France, who wasn’t involved in the study, agreed that the concentrations used were quite high, possibly in toxic ranges for some cells, but in an email to LiveScience Meresca also called the study “very exciting.”

Related: Alligator Blood Provides Strong Resistance to Bacteria and VirusesFemale Sharks Can Reproduce AloneMonarch Butterflies Use Medicinal Plants

MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

image showing the results of cultures treated with DRACO v. those not treated

Related: Science Explained: RNA Interference8 Percent of the Human Genome is Old Virus GenesVirus Engineered To Kill Deadly Brain Tumors
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Cancer Vaccines

A reader commented on a previous post (MIT Engineers Design New Type of Nanoparticle for Vacines) asking about how vaccines can fight cancer. Preventative vaccines can build up immune response to viruses which cause cancer. So the vaccine actually works against the virus which prevents the virus from causing cancer.

The U.S. Food and Drug Administration (FDA) has approved two vaccines, Gardasil® and Cervarix®, that protect against infection by the two types of human papillomavirus (HPV) – types 16 and 18 – that cause approximately 70% of all cases of cervical cancer worldwide. At least 17 other types of HPV are responsible for the remaining 30% of cervical cancer cases. HPV types 16 and/or 18 also cause some vaginal, vulvar, anal, penile, and oropharyngeal cancers.

Many scientists believe that microbes cause or contribute to between 15% and 25% of all cancers diagnosed worldwide each year, with the percentages being lower in developed than developing countries.

Vaccines can also help stimulate the immune system to fight cancers.

B cells make antibodies, which are large secreted proteins that bind to, inactivate, and help destroy foreign invaders or abnormal cells. Most preventive vaccines, including those aimed at hepatitis B virus (HBV) and human papillomavirus (HPV), stimulate the production of antibodies that bind to specific, targeted microbes and block their ability to cause infection. Cytotoxic T cells, which are also known as killer T cells, kill infected or abnormal cells by releasing toxic chemicals or by prompting the cells to self-destruct (a process known as apoptosis).

Other types of lymphocytes and leukocytes play supporting roles to ensure that B cells and killer T cells do their jobs effectively. These supporting cells include helper T cells and dendritic cells, which help activate killer T cells and enable them to recognize specific threats.

Cancer treatment vaccines are designed to work by activating B cells and killer T cells and directing them to recognize and act against specific types of cancer. They do this by introducing one or more molecules known as antigens into the body, usually by injection. An antigen is a substance that stimulates a specific immune response. An antigen can be a protein or another type of molecule found on the surface of or inside a cell.

Related: National Cancer Institute (USA)Nanoparticles With Scorpion Venom Slow Cancer SpreadUsing Bacteria to Carry Nanoparticles Into CellsGlobal Cancer Deaths to Double by 2030
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Web Gadget to View Cell Sizes to Scale

graphic of red blood cellImage of cell size gadget from University of Utah

The Genetic Science Learning Center, University of Utah has a nice web gadget that lets you zoom in on various cells to see how large they are compared to each other. Above see a red blood cell, x chromosome, baker’s yeast and (small) e-coli bacterium.

A red blood cell is 8 micron (micro-meter 1/1,000,000 of a meter). E coli is 1.8 microns. Influenza virus is 130 nanometers (1/1,000,000,000 a billionth of a meter). Hemoglobin is 6.5 nanometers. A water molecule is 275 picometers (1 trillionth of a meter).

Related: Red Blood Cell’s Amazing FlexibilityHemoglobin as ArtAtomic Force Microscopy Image of a MoleculeNanotechnology Breakthroughs for Computer Chips

Antigen Shift in Influenza Viruses

Antigenic shift is the process by which at least two different strains of a virus, (or different viruses), especially influenza, combine to form a new subtype having a mixture of the surface antigens of the two original strains.

Pigs can be infected with human, avian and swine influenza viruses. Because pigs are susceptible to all three they can be a breeding ground for antigenic shift (as in the recent case of H1N1 Flu – Swine Flu) allowing viruses to mix and create a new virus.

Related: Swine Flu: a Quick OverviewOne Sneeze, 150 Colds for CommutersWashing Hands Works Better than Flu Shots (study results)Learning How Viruses Evade the Immune SystemAlligator Blood Provides Strong Resistance to Bacteria and Viruses

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