Posts about virus

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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Swine Flu: a Quick Overview

World Health Organization on Swine influenza

After reviewing available data on the current situation, Committee members identified a number of gaps in knowledge about the clinical features, epidemiology, and virology of reported cases and the appropriate responses. The Committee advised that answers to several specific questions were needed to facilitate its work.

The Committee nevertheless agreed that the current situation constitutes a public health emergency of international concern.

Based on this advice, the Director-General has determined that the current events constitute a public health emergency of international concern, under the Regulations.

Swine flu: a quick overview–and new New York and Kansas cases by Tara Smith

while the cases in the US have been mild and no deaths have occurred that we’re aware of, it seems in Mexico that young people are dying from this–a group that is typically not hard-hit by seasonal influenza viruses. Readers familiar with influenza and know the history of the 1918 influenza pandemic will recall that the “young and healthy” were disproportionally struck by that virus as well–so this knowledge is currently disconcerting and worrisome, but there are so many gaps in our information as far as what’s really going on in Mexico that it’s difficult to make heads or tails out of this data right now.

Third, is this really a new virus? So few influenza isolates are actually analyzed each year (in proportion to the number of people infected) that we aren’t sure yet whether this is something brand-new, or something that has been circulating at a low level for awhile, but just hadn’t been picked up. After all, H1N1 is a common serotype, so additional molecular testing is needed to determine that it’s “swine flu” versus “human” H1N1.

this is a fast-developing story, and it will take much more investigation and field work to determine the true extent of the virus’s spread in the population; to figure out… how efficiently it’s transmitted…

This is very early in the scientific inquiry process looking into what exactly is going on. It is too early to tell how serious a threat this is. The reaction of WHO, CDC though shows they are taking the threat seriously. By far the biggest danger in such situations, is reacting too slowly to serious and contagious threats. If you wait to react until proof exists that the situation is very serious the situation can be almost impossible to control. So you need to react quickly to shut down the spread of the threat, hopefully before it has spread too far.

Related: CDC site on Human Swine Influenza InvestigationInterview with Dr. Tara SmithReducing the Impact of a Flu PandemicH5N1 Influenza Evolution and Spread
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Using Virus to Build Batteries

MIT researchers have shown they can genetically engineer viruses to build both the positively and negatively charged ends of a lithium-ion battery. We have posted about similar things previously, for example: Virus-Assembled BatteriesUsing Viruses to Construct Electrodes and Biological Molecular Motors. New virus-built battery could power cars, electronic devices

Gerbrand Ceder of materials science and Associate Professor Michael Strano of chemical engineering, genetically engineered viruses that first coat themselves with iron phosphate, then grab hold of carbon nanotubes to create a network of highly conductive material.

Because the viruses recognize and bind specifically to certain materials (carbon nanotubes in this case), each iron phosphate nanowire can be electrically “wired” to conducting carbon nanotube networks. Electrons can travel along the carbon nanotube networks, percolating throughout the electrodes to the iron phosphate and transferring energy in a very short time. The viruses are a common bacteriophage, which infect bacteria but are harmless to humans.

The team found that incorporating carbon nanotubes increases the cathode’s conductivity without adding too much weight to the battery. In lab tests, batteries with the new cathode material could be charged and discharged at least 100 times without losing any capacitance. That is fewer charge cycles than currently available lithium-ion batteries, but “we expect them to be able to go much longer,” Belcher said.

This is another great example of university research attempting to find potentially valuable solutions to societies needs. See other posts on using virus for productive purposes.

Image of the Common Cold Virus

image of the rhino virus (human cold)image created by Dr. Jean-Yves Sgro, Institute for Molecular Virology, University of Wisconsin-Madison, from published X-ray data. larger image

Sequences capture the code of the common cold

Conducted by teams at the University of Maryland School of Medicine, UW-Madison and the J. Craig Venter Institute, the work to sequence and analyze the cold virus genomes lays a foundation for understanding the virus, its evolution and three-dimensional structure and, most importantly, for exposing vulnerabilities that could lead to the first effective cold remedies.

“We’ve had bits and pieces of these things for a long time,” says Ann Palmenberg, of UW-Madison’s Institute for Molecular Virology and the lead author of the new study. “Now, we have the full genome sequences and we can put them into evolutionary perspective.”

As its name implies, the common cold is an inescapable, highly contagious pathogen. Humans are constantly exposed to cold viruses, and each year adults may endure two to four infections, while schoolchildren can catch as many as 10 colds.

“We know a lot about the common cold virus,” Palmenberg explains, “but we didn’t know how their genomes encoded all that information. Now we do, and all kinds of new things are falling out.”

The newly sequenced viruses also show, says Palmenberg, why it is unlikely we will ever have an effective, all-purpose cold vaccine: The existing reservoir of viruses worldwide is huge and, according to the new study, they have a tendency to swap genetic sequences when cells are infected by more than one virus, a phenomenon that can lead to new virus strains and clinical manifestations.

The ability of different cold virus strains to swap genes and make entirely new strains was thought to be impossible, notes Claire M. Fraser-Liggett, a co-author of the new study and director of the Institute for Genome Sciences and professor of medicine and microbiology at the University of Maryland School of Medicine. “There is the possibility that this could lead to the emergence of a new rhinovirus strain with fairly dramatic properties,” says Fraser-Liggett.

Related: Common Cold Alters the Activity of GenesLearning How Viruses Evade the Immune SystemLethal Secrets of 1918 Flu Virusimages of snowflakes

Image of Viral Coat

image of exterior of virus - made up of 5 million atomsHigh-energy X-ray diffraction was used to pinpoint some 5 million atoms in the protective protein coat of the PsV-F virus. The coat’s symmetrical features are shared by hundreds of viruses. The red and yellow sections illustrate how building blocks of four proteins come together to form the spherical shell.

The image reveals the structure of a type of protein coat shared by hundreds of known viruses containing double-stranded RNA genomes. The image was painstakingly created from hundreds of high-energy X-ray diffraction images and paints the clearest picture yet of the viruses’ genome-encasing shell called a “capsid.”

Viruses can reproduce themselves only by invading a host cell and highjacking its biochemical machinery. But when they invade, viruses need to seal off their genetic payload to prevent it from being destroyed by the cell’s protective mechanisms. Though there are more than 5,000 known viruses, including whole families that are marked by wide variations in genetic payload and other characteristics, most of them use either a helical or a spherical capsid.

“Spherical viruses like this have symmetry like a soccer ball or geodesic dome,” Pan said. “The whole capsid contains exactly 120 copies of a single protein.” Previous studies had shown that spherical capsids contain dozens of copies of the capsid protein, or CP, in an interlocking arrangement. The new research identified the sphere’s basic building block, a four-piece arrangement of CP molecules called a tetramer, which could also be building blocks for other viruses’ protein coats.

Full press release

Related: Viruses and What is LifeViruses Eating BacteriaMRI That Can See Bacteria, Virus and ProteinsFinding the Host Genes Viruses Require

Resurrection of the Human IRGM Gene

Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:

The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn’s disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys.

Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.

Related: 8 Percent of the Human Genome is Old Virus GenesOld Viruses Resurrected Through DNAOne Species’ Genome Discovered Inside Another’sposts on genesGene against bacterial attack unravelledGene Duplication and Evolution

MRI That Can See Bacteria, Virus and Proteins

IBM team boosts MRI resolution

The researchers demonstrated this imaging at a resolution 100 million times finer than current MRI. The advance could lead to important medical applications and is powerful enough to see bacteria, viruses and proteins, say the researchers.

The researchers said it offered the ability to study complex 3D structures at the “nano” scale. The step forward was made possible by a technique called magnetic resonance force microscopy (MRFM), which relies on detecting very small magnetic forces.

In addition to its high resolution, MRFM has the further advantage that it is chemically specific, can “see” below surfaces and, unlike electron microscopy, does not destroy delicate biological materials.

Now, the IBM-led team has dramatically boosted the sensitivity of MRFM and combined it with an advanced 3D image reconstruction technique. This allowed them to demonstrate, for the first time, MRI on biological objects at the nanometre scale.

That is very cool.

Related: IBM Research Creates Microscope With 100 Million Times Finer Resolution Than Current MRIMagnetic Resonance Force Microscopy (from Stanford)Nanotechnology Breakthroughs for Computer ChipsSelf-assembling Nanotechnology in Chip ManufacturingNanoparticles to Aid Brain Imaging

One Sneeze, 150 Colds for Commuters

One sneeze, 150 colds for commuters

An analysis of the germs unleashed from a single commuter’s sneeze showed that within minutes they are being passed on via escalator handrails or seats on trains and underground carriages. At the busiest stations, one sneeze not smothered by a tissue or handkerchief will provide enough germs to infect another 150 commuters.

A single sneeze expels 100,000 droplets of germs into the air at 90mph. Individual droplets get transferred to handles, rails and other areas frequently held or touched. Up to 10 per cent of all commuters will come into contact with an area infected by that one sneeze, Dr Henderson calculated.

Researchers asked 1,300 workers about their health and found 99 per cent of commuters suffered at least one cold last winter. In contrast, just 58 per cent of those who work from home and 88 per cent of those who walk to work regularly caught a cold last winter.

It is amazing (or maybe not but I find it amazing) how well cold viruses have evolved to have us sneeze and send out personal virus jet packs to spread them all over and let them infect others. It is sad how impolite some people are as they go around potentially infecting hundreds of other people. Partially their ignorance of basic science may also be to blame for their behavior. It is too bad others have to suffer due to their bad manners and ignorance.

Related: Study Shows Why the Flu Likes WinterEmployees That Telecommute are the Most LoyalCommon Cold Alters the Activity of GenesStudy Finds No Measurable Benefit to Flu Shots

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