New Breakthroughs In DNA Editing

scripssAccording to the scientists working at The Scripps Research Institute, there is a new way of broadly applying a new and powerful DNA-editing technology. According to Carlos F. Barbas, the tool is among the most popular in biology, as it is a way of targeting it to any DNA sequence.

It is a breakthrough which has to do with TALEs, the group of designer DNA-binding proteins, which is increasingly uses by biologists to turn off, turn on, insert, rewrite or even delete specific genes within cells—for potential medical and biotech applications, including genetic disease treatments, and also for scientific experiments.

It is believed that the TALE-based methods are useful against only a small fraction of the possible DNA sequences found in plants and animals. However, that limitation is removed by the new finding.

For many years, it has been the dream of biologists to manipulate DNA in with precision.  Thanks to leading organizations such as The Scripps Research Institute and Greg Lucier ‘s Life Technologies to name a few, scientific breakthroughs are beginning to happen more often.

Some years ago, when the TALE-based designer proteins were introduced, they could be considered to be the most precise DNA-directed and user-friendly tools ever invented.

DNADesigner transcription-activator-like effectors (TALEs) are based on natural TALE proteins certain plant-infecting bacteria produce, and these natural TALEs are helping bacteria in subverting their plant hosts as they bind to certain sites on plant DNA and boosting certain genes’ activities, thus making the growth and survival of the invading bacteria to be enhanced.

According to the findings of scientists, it is possible to easily engineer the TALE proteins’ DNA-grabbing segment to precisely bind to a DNA sequence of interest. This is done by joining that DNA-binding segment to another protein segment which is capable of performing a specific function desired, and at the site of interest—for instance, the enzyme which can cut through DNA. In this field, the Barbas laboratory and others have collectively already engineered thousands of the powerful TALE-based DNA-editing proteins.

The Limitations

TALE-based DNA-editing is believed to have a limitation. Almost all the natural TALE proteins so far discovered target sequences of nucleoside thymidine DNA. According to various structural studies, natural TALE proteins are not capable of binding well to DNA without that initial T (note the letter “T” in the 4-letter DNA code). Biologists who study molecules have thus widely assumed that the same rule applying to the “T restriction” can be found in any artificial TALE protein engineered.

Questioning Assumptions

Scientists started their evaluation by determining if TALE-based proteins function well against their normal DNA targets when the first letter of the DNA is switched from a “T” to one of the other three nucleosides (C, G or A). Using a library of engineered and natural TALE proteins, there was strong evidence supporting the “T restriction” rule. However, they are not yet giving up on the possibility of more broadly designing useful TALE proteins. For this, a “directed evolution” technique developed was adapted last year by Andrew C. Mercer, another scientist. His colleagues generated a large and new library of TALE proteins randomly varying in the structures hypothesized for the initial nucleoside grabbing. These new TALEs were then put through a series of tests, to (in a speeded up version of natural evolution) select, those at the start of their target DNA sequence adequately working even with a non-T nucleoside.

Through the method, it was possible to discover various new TALE protein architectures that the T restriction is not holding back. It is preferred to bind to DNA beginning with a G (guanosine), and not with a T nucleoside. There are those binding well enough to sequences starting with any of the 4 DNA nucleosides, and according to one scientist, these non-T-restricted TALEs, when conjoined, work as designed, for instance, when they are conjoined to enzyme fragments cutting through the DNA.

How To Properly Store Your Laboratory Chemicals

storageWhether you are a chemistry student working on a project or a chemist for a company, it is important that you store lab chemicals properly so you will avoid hazardous incidents in the lab that could harm your health. If you have large quantities of hazardous chemicals in the lab that are more than a gallon in size, you need to store those in a different room of the lab apart from the other chemicals. Never store the chemicals neat heated objects or near direct sunlight as this is dangerous. Chemists must date all chemicals that they receive and open, and periodically the chemist should examine his inventory of chemicals. The things he should look out for include cloudiness, color changes, and pressure inside the container.

Additional Things to Keep in Mind

You do not want to keep chemicals in unprotected and open areas of the lab because it is dangerous when accidents or fires occur in the lab due to negligence or a natural disaster. The shelves in the lab should also have protection in the design so that the chemicals will not fall. You also should not leave any containers near the end of the shelves. You do not want any chemicals stored on the floors and if there are chemicals that you no longer need, ask your supervisor about the required method of disposal to reduce toxic waste.

OSHA Regulations on Storing Lab Chemicals

According to OSHA, all lab chemicals must be stored in a separate area that is not easily prone to flooding and they should never be stored near hallways or staircases in the building. The lab itself should have 20 feet of lights all around so that the chemists can safely do experiments and store chemicals. The ventilation in the bio storage areas should be at a certain level where it will be safe to walk in the room without having to inhale too much of the chemicals.

Acid Storage Guidelines

When you store acids, you should always label and to keep acid from accidentally spilling on your body or the surface, you should pour the acid in the container through a funnel. You want to tightly secure the lid on the containers of acid to prevent the spread of hazardous fumes throughout the lab. Because not all acids are flammable, it is important to store flammable acids in a well-ventilated room and the remaining acids in another area.

Proper storage of chemicals is important because it is a matter of life and death for those who work with or near the chemicals. Always pay attention to your company’s requirements for chemical storage and also refer to local and state regulations concerning this action. When you work with chemicals you should always wear safety goggles, a lab coat and gloves to reduce bodily harm, and a safety mask is also important. Finally, you want to ask questions if you are unsure about certain types of chemicals and how they should be stored.

The Basics Of Antibodies

antibodies1Antibodies are immunoglobulin proteins that come from B lymphocytes in serum and body fluids. These antibodies will combine with antigens, which are substances that create an immune response. Immunogens are antigens that create an immune response and they can be created to make antibodies with specific proteins. When antibodies are created to fight specific proteins, those antibodies are utilized to research protein functions in dynamic life forms.

Antibodies will bind to the epitope, which the antigenic determinate. These epitopes are 5 to 8 amino acids in length on the protein, which are three-dimensional structures. Epitopes can be linear or discontinuous so that the antibodies will bind in a variety of different ways.

Antibody Characteristics

Antibodies are used to immunize and when an animal is immunized, antibodies do the job. There are five different classes of special immunoglobins which are IgA, IgD, IgE. IgG, and IgM. People who have allergies recognize these as the triggers for major allergens.

Antibodies work in the immune system to bind foreign objects to remove them from the body. The ability to bind is determined by the ability to interact with an antigen. The strength of their relationship is based on the number of binds on the antigen and the bond that they form together. Once they bind, the bind cannot be undone. When antigens have many epitopes, different antibodies can bind with the antigen. When antigens have many binding sites, they are multivalent and the bond is stronger. Binding strength is called avidity.

Monoclonal AntibodiesAntibody Production

The first immune response generates IgM antibodies and the second generates the IgG antibodies. The IgG molecules are the most common antibodies that are researched by cell biologists. Immunoglobin is created in B cells and when there are many cloned B cells, it is a polyclonal antiserum

There are antibodies that come from one B cell that creates a monoclonal antibody with a homogenous population. These will comes from a hybridoma technique fusing a B cell to a myeloma cell creating a hybrid cell. When a mouse is immunized, scientists remove the spleen to isolate B cells to join with myeloma cells. The myeloma cells will grow antibody B cells to fight the myeloma cells with clones of hybridomas and monoclonal antibodies. Scientists have figured out how to grow these antibodies and then inject the mixture of the hybridoma in place of the monoclonal antibodies to fight the cancer cell.

Antibody Purification

Immune responses can create monoclonal hybridomas that are unpurified antisera. These also may become monoclonal hybridomas as ascites fluids or supernatant cultures. In these cases, the affinity chromatography will mop up the antibodies as they bind as a matriculated format to creates a loose bond that washes away the nonspecific immunoglobins. These antibodies are cleansed using an A protein or G protein mixed to a sepharose bead. The proteins are taken from bacteria and they are needed because they have a special, internal antibody-binding quality.

Immunoaffinty is another way to purify antibodies to protect them from immunogens linked to the sepharose bead.

As neuroscientists understand more and more of the qualities of immunogens, antibodies, and antigens, they can begin to understand the reasons that people suffer from debilitating neurological diseases, severe allergies, and immune deficiencies. Scientists will be able to use this knowledge to improve the quality of life for many people for many years to come.

How Computer Science Is Shaping The Future of Biology

biologyDuring an experiment with mouse cells, David Harel began with a petri dish. The procedure included expressing genes, making proteins, and perfusing oxygen-rich blood into the mouse cells.

Eventually, the cells began to move across the dish. The cells differentiated and some became thymus gland T cells. These changes happened much quicker than anyone expected, but the experiment was actually occurring in a computer with virtual organs behaving as if they were in the real-world, but in faster time.

David Harel conducts these experiments at Israel’s Weizmann Institute as a Professor of Computer Science. He is noticing that his team’s studies are at the forefront of a change in scientific thought. The shift is moving from simple analysis to synthesis, which is where the observations are no longer just looked at, but they are put together with other ideas to create something unique and whole. His goal is to look holistically at how all of the little pieces work together, rather than pulling them apart and looking at them individually.

The trend in science, especially biology, is to break everything down into the smallest possible components. As biologists examine plants and animals, they found cells, and then DNA, then genes, proteins, and antibodies. Harel suggests looking the other way at how those small parts create a whole which creates life as we know it. This idea is designed to complement the trend and this complementary path can really only be tested on a computer, because it is too much to test in a laboratory setting.

So, Harel has to be sure that he uses the best data he can find. He has created models of organs, worms, and now, cancerous tumors. His computer models are based on the science that has come before, so he knows he has the best to use. His models end up being useful because they are so realistic and they are interactive so they can be changed when more data is ready for his use. He uses the models to uncover new discoveries and to make inferences that have never been realized before he brought biology to the computer screen.

Harel appreciates when the computer models have a unpredicted experience. He appreciates having to think through the troubles that occur when the biological computer models have faulty gene circuits or nutrient limitations. When his biological models overcome those challenges, the biologists get frustrated and make the attempt to prove the computer wrong, which is where new thinking comes into play and makes the computer work even more exciting.

For example, there was a unconventional stage of development in his worm model. When he added something completely unexpected and the worm model behaved normally. This was not expected, so biologists worked to uncover the reason why the model behaved the way that it did and they made some unusual discoveries during their research sessions.

Harel enjoys that he get to play with living things in a virtual setting. As he ponders the idea of modeling living things, he thinks about the fact that he gets to understand how life works. He also gets to work through errors, rather than being stumped by them and by doing this, he realizes new theories. Playing with biology on a virtual set makes it easier to fix mistakes and learn new things.

Genetic Disorders and Disease

geneticsWhen Tate Asher was born, he seemed perfectly normal. He did everything a baby should do during his first three months of life. However, at three months, he began to show signs that something was wrong.

While his mother, Michelle, was bathing him, he went completely stiff with his back arched like a banana. His right eye started to tic and it seemed that the eye would not focus, even though the left one was looking a his mother.

Tate is now four and since that episode in the bath tub, he has had several more. After that first episode, Michelle and her husband Rob took little Tate to the doctor who first thought it was epilepsy.

The episodes occurred every 10 to 14 days, but around the time that he was eight months old, he had an episode that led doctors to believe that he was not having epileptic seizures. Every 10 to 14 days, Asher was experiencing an episode, and when he was about 8 months old, it was determined by doctors that they were not seizures.

He would crawl, but he would often drag one of his arms. Even when he was 15 months old, he still was not letting go of the props that kept him standing. This made doctors believe that he had a disease called “alternating hemiplegia of childhood, which about one in every one million babies develops at birth. This disease causes neurological problems and developmental problems. A specialist confirmed the diagnosis when Tate was two.

Along with Tate, there are approximately 30 million Americans with diseases that most people have never heard of before. In the United States, a rare disease is one affecting less than 200,000 people and when diseases are rare, the companies that do research to find medications and treatments do not find it worth their money and time.

Many of the diseases are genetic disorders and as more scientists are beginning to understand what creates these problems, there are possible treatments on the horizon for those with rare disorders.

In order to better understand what was happening to their son, Tate’s parents worked with other parents to earn a grant to complete the genetic sequencing for children like Tate. Researchers at Duke University found that 74 percent of children had a similar mutation. Tate did not have the mutation, but the researchers found that the gene is involved in regulating sodium and potassium which are responsible for creating neurological impulses in the body.

Now that researchers understand what the mutation is, they can begin to learn how the disease is created and what causes the mutation. More research will come from the research that Tate’s parents spearheaded in 2010. The Ashers hope that the research will help find a treatment or a way to end the disease completely.

Even though the pharmaceutical companies will not create a drug that can only help a few children, researchers can look into other drugs that could help treat similar symptoms in other diseases and disorders. Once the researchers understand more about the disease, they can begin to turn to medicine that is already available to help with the treatment.

It takes people like Michelle Asher and her son to create the incentive for research scientists to begin looking for ways to treat people who are often forgotten.

Pacemakers Moving From Artificial To Biological

pacemakerPeople with pacemakers should take notice because scientists have recently figured out how to replace artificial pacemakers with biological pacemakers from the heart muscle cells of guinea pigs.

People who need pacemakers need the machine to create the electric pulses that keep the heart beating in a rhythmic pattern. The sinoatrial node in the upper right corner of the heart is where the small percent of pacemaker cells are located and there are only about 10,000 of these cells out of the 10 billion cells that make up the human heart.

Those who need an artificial pacemaker have faulty natural cells that do not help the heart to pump on a regular, rhythmic pace. Candidates for pacemakers must be healthy enough to have the required surgery to place the pacemaker inside of the body. Unfortunately, many pacemakers have to be replaced because their batteries die after time.

Pacemakers have other potential complications, too. They can move from their implanted spot. They can also break and the wires that connect the device to the heart muscle can become tangled. These problems can result in the death of the person with the pacemaker, and they do happen more often than most people would think they happen.

Pacemakers are not adaptive to heart rate changes. This means that people with pacemakers need to be careful not to overexert themselves in challenging exercise that can increase their heart rates. Many people are also having troubles with bacterial infections at the site of the incision and the location of the artificial device. If doctors could use biological pacemakers at the cellular level, these problems would not occur.

Researchers have tried to make new pacemakers by changing heart muscle cells at the genetic level. However, the cells do not end up resembling the pacemaker cells, but the basic muscle cells in the heart. Researchers have also tried to use stem cells, but stem cells can potentially become cancerous, which create a new cadre of problems.

Now, scientists have created a new way to create cells that resemble the ones that are naturally in the human body. These genetically modified cells are the safest cells because the cells seem to be free from the potential development of cancer.

It has taken nearly 10 years of lab work to create a biological pacemaker that can be safely used instead of the battery-powered devices that people are using today. Researchers use a gene called Tbx18. They inject this gene into the heart muscle and the gene begins to create embryonic pacemaker cells. Interestingly, the gene is injected in the form of a virus, so it creates new cells and spreads them around the heart.

Although primitive biological pacemakers had been created by Cho’s team and others before, this study is the first showing that the conversion of heart muscle cells can be directed by a single gene to genuine pacemaker cells. Electrical impulses were generated by the new cells spontaneously and were not distinguishable from native pacemaker cells.

In future therapies, there could be the use of Tbx18 injection into the heart of a patient; another idea is to create pacemaker cells in the laboratory and transplant them into the heart. However, additional studies of effectiveness and safety must be carried out before the start of human clinical trials, the scientists cautioned. In addition, it is not known how long the effects of the gene therapy would last.