Editing HIV out of our genome with CRISPR

crispr-pathwayThis is very cool! CRISPR is the system that excises foreign DNA out of bacterial genomes. It’s the equivalent of a bacterial immune system. Where we have a very complicated and extensive immune system that protects us from foreign pathogens (viruses, bacteria and others), it protects us even form poison, venom, foreign things and it is instrumental in healing us when we get cut or injured in some way. For a long time it was thought that bacteria had no such defense mechanism, then surprisingly CRISPR was found! It is the system that protects bacteria form bacteriophages, which are viruses that infect bacteria. If a virus successfully inserts its DNA into the chromosome of a bacterium, it will use the bacterial enzyme systems to make millions of copies of it self, eventually lysing and killing the bacterium to release all those copies of virus, and these viruses will then infect other bacteria. Bacteriophages are viruses that infect bacteria. There are other viruses which infect animals or people, such as the chicken pox virus, aka varicella, the AIDS virus aka HIV (human immunodeficiency virus,) Herpes virus, Hepatitis virus, many many viruses. Retroviruses such as the HIV (AIDS) virus also incorporate themselves into the DNA of in this case T cells, and they incapacitate T cells which are part of our immune system. Thereby we get acquired immunodeficiency or AIDS. Now researchers have developed a new technique using CRISPR, the bacterial “immune system” to excise the HIV virus out of the DNA of human cells that it had infected. Although at this time, this technique can only be used in vitro, CRISPR isn’t specific enough to use in humans. It can cut large regions of DNA in cells, in a nonspecific manner. So CRISPR has to be made more specific before it can be used as a therapy, for HIV or anything else.

Read the article, it is really cool!

http://www.umassmed.edu/news/news-archives/2015/04/editing-hiv-out-of-our-genome-with-crispr/

The virus that causes AIDS is an efficient and crafty retrovirus. Once HIV inserts its DNA into the genome of its host cells, it has a long incubation period, and can remain dormant and hidden for years. And while physicians can mix a cocktail from a variety of antiretroviral drugs to keep it in check, the virus can reactivate if treatment is stopped.

In an attempt to render latent HIV completely harmless, UMass Medical School researchers are using CRISPR/Cas9, a powerful gene editing tool, to develop a novel technology that can potentially cut the DNA of the latent virus out of an infected cell.

“On the simplest level, we’re employing a very precise pair of scissors to go in and clip out all, or part of, the HIV genome and reattach the severed ends of the human genome,” said principal co-investigator Scot Wolfe, PhD, associate professor of molecular, cell & cancer biology. “If we could do that, the hope is that this would be a step on the road to getting a functional cure for HIV.”

CRISPR is a component of the immune system found in normal bacteria. In its natural state, it protects bacteria from viral invasion. Since its discovery, researchers have been seeking ways to program this system to quickly and selectively edit specific genetic sequences for study.

For all its versatility, applications for the CRISPR system remain confined to the lab. Despite recent advances showing that CRISPR/Cas9 can edit HIV from an infected cell in culture, this technique remains too imprecise to be used clinically because of its tendency to cut into random regions of the genome, producing deleterious, off-target effects.

To improve the fidelity and precision of the CRISPR/Cas9 gene editing system for this project, Dr. Wolfe has proposed fusing it with an additional domain that improves its specificity. This would conceivably allow the CRISPR system to edit out only the HIV DNA without the potential for stray cuts in the human genome.

The other hurdle to using current CRISPR/Cas9 technology against HIV is that while researchers have some notions where the virus might be hiding, they still don’t know how to find the virus in latently infected cells.

“Cells that are infected with HIV are permanent carriers of the viral genome. They are a kind of time bomb that can be reactive at any time if a patient stops taking their antiretroviral treatment,” said principal co-investigator Jeremy Luban, MD, the David J. Freelander Professor in AIDS Research and professor of molecular medicine. “In order to attack the virus in its latent state, we really need to understand where the virus lives and what it needs to survive.”

Dr. Luban and Wolfe will use a combination of innovative technologies to describe and model HIV DNA integrated into the genome of reservoir cells, also known as provirus. Characterizing the genomic landscape of these latently infected cells will allow the researchers to identify vulnerable and accessible genetic sequences that can be potentially cut out of the HIV virus to make it permanently inactive.

“Many scientists are looking for tools that will activate the virus so it will be visible to the immune system or drugs. We’ve chosen a different approach that looks to isolate and excise the provirus directly from resting cells,” said Luban.

With a model of the latently infected cells’ genome from which to work, Wolfe hopes to use his precise gene editing tool to excise the latent virus from cells. Part of the project will be to assess whether the precision of the system has improved enough to allow for selected removal of the HIV genome in humanized mouse models and cells from infected patients without causing collateral damage to the human genome.

“The underlying premise of this project that Scot has pushed forward using new technologies that he has developed, is to genetically engineer a system that can potentially remove the HIV genome from infected cells,” said Luban. “The hope is that one might develop the tools to deliver these agents to cells of the human immune system and actually eliminate the virus from where it is hiding.”

Joining Luban and Wolfe on the five-year, $4.6 million National Institute of Allergy and Infectious Diseases funded project are Dale Greiner, PhD, the Dr. Eileen L. Berman and Stanley I. Berman Foundation Chair in Biomedical Research and professor of molecular medicine; Oliver J. Rando, MD, PhD, professor of biochemistry & molecular pharmacology; Job Dekker, PhD, professor of biochemistry & molecular pharmacology; and Manuel Garber, PhD, associate professor of molecular medicine. Each will lend their respective expertise in developing humanized mouse models; mapping chromatin structure; modeling 3D chromosome organization; and computational biology. Additionally, Katherine Luzuriaga, MD, professor of molecular medicine, pediatrics and medicine, and Thomas C Greenough, MD, assistant professor of medicine, will provide clinical expertise on the project.

“We’ve assembled a team of researchers here at UMass Medical School with the goal of better understanding the intricate structure of the latent HIV virus when integrated into immune cells because we believe that will allow us to better target it with CRISPR for gene editing,” Wolfe explained.

Prozac in the Water Makes Fighting Fish More Mellow (What?!?!?!)

http://blogs.discovermagazine.com/inkfish/2016/03/23/prozac-water-makes-fighting-fish-mellow/#.VvXXTYwrLpA

Siamese Fighting Fish

Prozac in the Water Makes Fighting Fish More Mellow

By Elizabeth Preston | March 23, 2016 2:00 pm 156

Had Teresa Dzieweczynski chosen to publish her recent findings as an updated children’s classic, rather than as a research paper, she could have titled it If You Give a Fish an Antidepressant. The book would probably be less charming than If You Give a Mouse a Cookie. But it would also be, unfortunately, more realistic. Our pharmaceuticals are steadily trickling into the homes of fish and other animals. And—as the hero of the original book could have told us, his house in disarray after fulfilling the whims of a hungry rodent—there are consequences.

Dzieweczynski, a psychologist at the University of New England, looked at just one of the drugs that’s crept into American waterways: fluoxetine, better known as Prozac. It’s an antidepressant that makes the hormone serotonin linger in the brain for a longer time. Antidepressants of this type are commonly prescribed, and they commonly get into the water as a result. They’ve turned up in wastewater, drinking water, and other aquatic environments.

She tested fluoxetine on male Siamese fighting fish, or Betta splendens. No one knows how much Prozac is in the water in Thailand, where these fish live naturally. But they make a good model, Dzieweczynski explains, because scientists already understand a lot about their brains, behavior and hormones.

Dzieweczynski and her coauthors put the fighting fish into three different lab environments. Some of the fish swam in tanks with clean water. Others swam in water with a low concentration of fluoxetine—0.5 micrograms per liter, which is at the higher end of what’s been found in U.S. waterways. The third group of fish swam in a stronger dose of fluoxetine, 5 micrograms per liter.

The researchers gave the fish behavioral tests to see how bold they were. In one test, they put a fish into a big empty tank and watched how far it roamed. In another test, they dropped a fish into a tank with rocks and artificial plants it had never seen before, and observed it again. How much did the fish explore? Was it curious about its new environment, or cautious and still? Finally, researchers put a fish into a clear tank adjacent to one that held three other fighting fish. Did the subject approach the strangers, or stay at the opposite end of its tank?

After getting baseline behavioral scores for all their fish, the researchers started dosing them with fluoxetine. They retested the fish after a day of drug exposure. After a week of drug exposure, they tested them again. Then they put all the fish into clean water for a week and tested them a final time.

Across all the behavioral tests, fish exposed to the antidepressant were less bold. They stayed in one place, explored their environment less, and were more hesitant to approach other fish. Their behavior was also more erratic. A higher dose of the drug caused a more dramatic effect.

“Perhaps most importantly and alarmingly,” the authors write, they could still see these effects after the fluoxetine was gone. Even after a week of swimming in clean water, drugged fish behaved less boldly than normal.

In an earlier study, Dzieweczynski drugged female fighting fish with fluoxetine and saw similar results. The effect was a bit stronger in male fish, she says—maybe because they have higher levels of serotonin or testosterone to begin with.

Dzieweczynski didn’t test her “fighting” fish to see how much they actually fought each other. She says other studies have shown that fluoxetine makes them less aggressive. When the fish in this study approached strange fish from across their tank, they may have been seeking a fight, a potential mate, or just safety in numbers.

But no matter what the fishes’ intentions, acting less boldly could hurt their odds of survival in the wild. If fish are less eager to explore their environments, they might have trouble searching for food. Shyer behavior could also make it harder for fish to defend their environments, migrate, or escape predators.

That means letting our drugs get into the water could have a cascade of consequences throughout an ecosystem. And if even temporary drug exposures can have lasting effects, it might be hard to turn the story back to page one. (Can someone bring that mouse back now?

Making Peace With Me

“Making peace with your shortcomings has nothing to do with thinking you are beautiful or perfect or brilliant, and everything to do with putting down your weapons of self-destruction and refusing to fixate on what is missing. Like many things on this journey called life, this is about changing how you think, not how you look.
So go ahead, crow!”
Brilliant blogpost! Thank you! I intend to take your advice!

Scott Williams's avatar

I remember, as a young child, being told, “quit bragging!”. Adults told me, told you, not to brag, because bragging about yourself was very, very, wrong. Be humble, I was taught. People who talk about themselves are egomaniacs. We tell our kids they are amazing, but don’t really want it to go to their head.
Psychology is cool. If you take the time to learn about people you begin to understand that it’s possible to like yourself without turning into a jerk. The science on this is fairly straightforward, insecure people brag too much. People who have made peace with themselves and have a decent self-image tend to be humble, and for one very obvious reason: the more you learn about life, the more you understand how much you still do not know. Most of us struggle with crippling self-esteem issues and if we do not deal with this lack…

View original post 361 more words

Is ‘Cat Litter’ Parasite Making You a Rageaholic?

Oh boy! Say it ain’t so! I’ve had cats since 1986. I love cats! I wonder what you do if toxoplasma really does cause anger issues, why don’t cat owners get tested and treated? Apparently, Azithromycin, a common antibiotic, treats toxoplasmosis.

http://www.livescience.com/54141-toxoplasmosis-parasite-linked-with-rage-disorder.html?cmpid=514627_20160323_59692236&adbid=10153328679641761&adbpl=fb&adbpr=30478646760

Uncontrollable, explosive bouts of anger such a road rage might be the result of an earlier brain infection from the toxoplasmosis parasite, an organism found in cat feces, a new study finds.

In the study of more than 350 adults, those with a psychiatric disorder called Intermittent Explosive Disorder, or IED, were twice as likely to have been infected by the toxoplasmosis parasite compared with healthy individuals with no psychiatric diagnosis.

The study adds to a growing body of evidence suggesting that toxoplasmosis — usually a mild or nonsymptomatic infection from a protozoan parasite called Toxoplasma gondii — may somehow alter people’s brain chemistry to cause long-term behavior problems. Previous studies have linked toxoplasmosis to schizophrenia, bipolar disorder, impulsivity and suicidal behavior.

The researchers stressed, however, that they merely have identified an association between toxoplasmosis and rage, and cannot say that toxoplasmosis causes rage — or that people should get rid of their cats, for that matter.

“Not everyone that tests positive for toxoplasmosis will have aggression issues,” said Dr. Emil Coccaro, a professor and chairman of psychiatry and behavioral neuroscience at the University of Chicago, who led the study. But exposure to the parasite does appear to “raise the risk for aggressive behavior,” and more research is needed to determine whether the link is causal, and what, if any, the underlying biological mechanism may be, he said.[The 10 Most Diabolical and Disgusting Parasites]

The study was published today (March 23) in the Journal of Clinical Psychiatry.

More than 20 percent of the U.S. population has been infected by theToxoplasma parasite, according to the Centers for Disease Control and Prevention. Cats are the only known host in which this parasite reproduces; cats shed the parasites’ eggs, called oocysts, in their feces. Humans can become infected after unintentionally ingesting the microscopic oocysts, primarily from not their washing hands after cleaning a cat’s litter box or working in a garden with contaminated soil. Other sources of Toxoplasma are undercooked meat or unwashed vegetables that have been contaminated.

Toxoplasma can cause severe neurological problems and death in infants infected through their mothers during pregnancy, which is why pregnant women are advised not to change a cat’s litter box.

Coccaro told Live Science he was intrigued by the body of scientific literature linking toxoplasmosis with psychiatric disorders. For this study, his research team recruited 358 adults. About one-third had IED, defined by the Diagnostic and Statistical Manual of Mental Disorders as recurrent, impulsive, problematic outbursts of verbal or physical aggression disproportionate to the situations that trigger them. Another one-third were individuals diagnosed with another psychiatric disorder (not IED). And the remaining third were healthy controls with no psychiatric history.

The research team found that 22 percent of the people with IED tested positive for toxoplasmosis exposure, compared with only 9 percent of the healthy control group. About 16 percent of the group with other psychiatric disorders tested positive for toxoplasmosis, too.

Jaroslav Flegr, a professor of biology at Charles University in Prague in the Czech Republic who was not involved in the study, said this was a confirmation observations made by his research team over the last two decades.

“We have found that prevalence of toxoplasmosis correlate positively with violence-associated injuries and mortality in particular countries,” said Flegr, who was among the first to propose that Toxoplasma can alter the brain. “It correlate also with diseases burden associated with bipolar disorder, obsessive compulsive disorder, and epilepsy. [10 Things You Didn’t Know About the Brain]

All the researchers were at a loss, however, to explain how the infection could be tied to behavior.

“We don’t yet understand the mechanisms involved,” said Dr. Royce Lee, also of the University of Chicago, a co-author on the report. “It could be an increased inflammatory response, direct brain modulation by the parasite, or even reverse causation where aggressive individuals tend to have more cats or eat more undercooked meat.”

Coccaro said that inflammation is a leading theory. Toxoplasmosis triggers the body to create antibodies, which are proteins that recognize specific pathogens and initiate the natural inflammation process to fight infections. After being ingested, Toxoplasma can travel to the muscles and the brain. In the brain, Toxoplasma can hide inside cells, and trigger an inflammatory response that damages nerve cells as the immune system attempts to kill the Toxoplasma.

One of the limits of the study, he said, was that his team could only assess the presence of antibodies in a blood sample, not a brain fluid sample. Future research may reveal the presence of Toxoplasma in the brain of those with IED, which could point in the direction of causation.

Or, conversely, doctors could treat IED patients for Toxoplasma infection to see if their symptoms reverse, Coccaro said.

Follow Christopher Wanjek @wanjek for daily tweets on health and science with a humorous edge. Wanjek is the author of “Food at Work” and “Bad Medicine.” His column, Bad Medicine, appears regularly on Live Science.

A sad old Urdu song :-/

Jaane Woh Kaise Log Lyrics and Translation

Jaane woh kaise log the jinke pyaar ko pyaar mila
I wonder what kind of people find their love reciprocated
Humne to jab kaliyaa.N maangii kaa.NTo.N kaa haar milaa
Whenever I asked for flowers, I received a garland of thorns

Bichharh gayaa har saathii dekar pal do pal kaa saath
Every companion gave me a few moments of company, and left
Kisko fursat hai jo thaame diiwaano.N kaa haath
After all, who has the time to hold a crazy person’s hand?
Humko apnaa saayaa tak aksar bezaar milaa
Even my own shadow is often weary of me

Isko hii jiina kehte hai.N to yuu.N hii jii le.Nge
If this is what they called life, then I will live like this
Uff na kare.Nge, lab sii lenge, aa.Nsuu pii lenge
I will not sigh, I will seal my lips, and swallow my tears
Gham se ab ghabraana kaisaa, gham sau baar milaa
After all, how can I be concerned by sadness? I have met sadness a hundred times

Humne to jab kaliyaa.N maangii.N kaaTo.N kaa haar milaa
When I asked for flowers, I found a garland of thorns
Jaane woh kaise log the jinke pyaar ko pyaar mila
I wonder what kind of people find their love reciprocated

Osteoporosis meds, terrible!

Medication for osteoporosis, such as Fosamax, Prolia, and Boniva actually make your bones weaker and more brittle, and women who are on them experience breaks in bones such as the femur, the thigh bone, one of the strongest, thickest bone in the human body.

Why do they do that? Well these medications inhibit a class of cells called “Osteoclasts.” Osteoclasts are the cells in our bodies that eat away old brittle bones and they are needed to do that before “Osteoblasts” can put down new, fresh bone. So when osteoclasts are inhibited, old, brittle bones are not eaten away, and fresh new bone cells cannot be put down. So taking these “medications” effectively makes your bones old and brittle while the turnover to fresh, new bone is inhibited. So people get very old brittle bones and things like breakage of femurs (previously unheard of) and osteonecrosis of the jaw (https://www.drugwatch.com/fosamax/side-effects/) this is bone death of the jaw and can lead to horrible disfigurement, can occur.

These are horrible side effects and are exactly the opposite of what a medication for osteoporosis should do! I am totally beside myself that knowing these things can happen, people are still being told to take these awful “meds!” It’s like handing someone a hammer and telling them to hit themselves till their femur breaks as a treatment for osteoporosis!

I grant that the idea to suppress osteoclasts (cells that eat bone) may have originally been a good one. No osteoclasts, no bone thinning, that may well have been the logic. But when it was seen what was actually happening, they should have stopped prescribing these awful “meds” but they haven’t. They continue to prescribe them.

I was given a prescription for Fosamax and Prolia. Prolia was going to cost me $400 for one 6 mont shot. Prolia (Amgen) was willing to cover my copay, all except $25. But I refused to take them after I read what I have just told you.

Still can’t believe they are still prescribing these awful compounds.

 

 

Why Acting Strong Is Really Weak

A troubling theme that I come across in my work as a therapist—and in observation of people in general—is the belief that we should always act strongand hide our insecurities and fears. The damage that this “common wisdom” perpetrates is incalculable. It decimates true self-esteem and damages our relationships.

Acting strong is still acting. When we act or pretend to be different than who we truly are, we abandon our real self by putting on a mask. We do this in an attempt to control what we hope others will think of us. So we manipulate and camouflage our self as we seek the approval of others, or at the least try to avoid their disapproval. This sets up our primary betrayal of our genuine self.

We derive authentic self-esteem from our relationship with our own self. If we contort our personality to seek recognition or approval from others, we’re pursuing what I call other-esteem, because it doesn’t come from within, but is sought from outside of us. We’re trying to feel better about ourselves by being disingenuous. How do you think that’s going to work out? The more we do this, the further we move from genuine self-esteem. This is the opposite of what we should be doing. We should be embracing our vulnerability.

What do I mean by vulnerable? For me the word vulnerable doesn’t elicit weakness, butopenness. Don’t construe it to mean fragile. As humans we all experience vulnerable feelings, like insecurity, doubt and fear. In moderation these are common emotions. But due to our misinformed cultural meta-narrative that demands the appearance of strength, we decide to hide these feelings from one another. So we live out our lives falsely thinking that our shortcomings or self-doubts are unique to us. The sad irony is that those same individuals whose opinions we are so worried about are very likely doing the same thing. So the vast majority of people are disempowering themselves, thinking that others are more confident and secure. This tragic myth terribly limits our lives.

Hiding our true self from others is what makes us fragile. Being yourself makes you strong. When I encourage this transition people may ask, “but what will they think of me?” How will they see me? This is a common concern for people who grapple with revealing their genuine self. I’d offer that I want to be seen—as I truly am—as my authentic self.This is the path to a powerful self-esteem.

When we accept our vulnerability, we have nothing to hide from others and this in turn makes us genuinely powerful. You can find the key to a resilient self-esteem by embracing your vulnerability; your fears and insecurities. In doing so, you liberate yourself from setting up others as your judge, as you have nothing to hide. You must embrace your vulnerability to attain inner strength. Releasing your concerns by bringing them into the light allows them to dissipate, masking them cements them into your being.

Who is my judge? Why is it more important to us what someone else thinks of us than what we think of ourselves? When we subordinate our self-worth by setting up another person as our judge, we perpetuate emotional abuse on ourselves. Other people aren’t your judge; why appoint them that power? Everyone has opinions for sure, but to elevate someone’s opinions to the power of a judgment is irrational and without merit. What you’re doing is judging yourself and then projecting that power of judgment onto someone else. I’m fond of saying that the only person who has the right to literally judge me wears a long black robe and presides in a courthouse.

For relationships to thrive we must experience emotional intimacy(link is external). What I mean by this is a transparent and safe sharing of our feelings. When we obscure feelings that we think others will criticize or scrutinize, we block emotional intimacy.

We all just want to be loved, but to be loved you need to be lovable. Most of us struggle in actually being lovable. When you need to act strong, you erect a defensive wall that doesn’t allow others in. You become impenetrable and therefore, unlovable. Others most often see vulnerability—openness—as lovable. In my work with couples and families, when someone expresses their softer vulnerable feelings, others not only listen—they care.

Isn’t it insane that we hide the very qualities that could make us feel validated, affirmed, and loved? Embracing rather than hiding from our vulnerability makes us authentic and powerful. It suggests that we accept and value ourselves as we are, without fear of what we think others may think of us.

We’ve clearly been playing from the wrong game plan.
My forthcoming book, The Possibility Principle: How Quantum Physics Can Improve the Way You Think, Live and Love (Fall 2017, Sounds True) will provide more detail on this subject. In the interim please enjoy related articles atMelschwartz.com(link is external).

Mel Schwartz is a psychotherapist and couples counselor based in Westport, CT. He is the author of The Art of Intimacy, The Pleasure of Passion and his more than 100 articles have been read by over 1 million readers. You can reach him at Mel @melschwartz.com (link is external)He also works globally with people via Skype or telephone.

What are we leaving our children?

What are we leaving our children? In light of the terror attacks, I ask this. We are leaving them isis, a sickening, violent, almost non human group. We are leaving them a horribly unequal world, as far as wealth, as far as education, as far as the comforts of living a long and productive life, and it is this inequality that spawns terror. 

As far as climate, the health of this planet, our home, what are we leaving them? We are leaving them a catastrophe. The 10-20 inch rise in sea levels that was to have taken many decades in which to occur, now climatologists think will happen within a decade. And it will have real and dire consequences. This is what we are leaving for our children to deal with and it is not something that can easily be handled, or perhaps handled at all. 

Terror and climate catastrophe. This is what we are leaving for our children. Sad, incredibly sad. 

How, with the way things are and the way people behave, how can we make things any better? 

Cruz is calling for monitoring of Muslim neighborhoods to make sure that Muslims don’t get radicalized! Trump wants to register Muslims so he can keep tabs on them! Does this not remind you of another awful period in history, targeting and marking a whole group of people. Remember, it did not end well. 

As my brother, who is an Art director of an Institute in Brussels said “Scary times!” Scary because of so many things. 

Unfortunately, fear seems to be winning. 

I ❤️ Ankara. I ❤️ Istanbul. I ❤️ Brussels. 

All three cities have been the target of isis attacks.  I send them all my love.

I hope this abomination known as isis is destroyed with as much alacrity as we can muster!

If Trump could guarantee the annihilation of these monsters, I would vote for him, that is how much I want them gone.

These monstrous inhumans pull out the anger and hate in us, they infect us with their own fear, hatred and violence. We must not give in to them. We must still act with love not fear.

You see, the struggle between love and fear is not some abstract thing, it is played out in the human arena countless times, every day. What we have to do is make sure we act with love and love wins over fear. We can even show our love to our own fear, that is truly grace! If each and every human on this earth does this, then there can be no isis.

With much love from me to all of you.