Friday, September 30, 2016

CRISPR: The kinder, safer, risk-proof version of GMO ?

Hashtag Alerts:  #SmokeScreening  -  #MarketingPloys -   #UnintendedConsequences - #Bioethics - #ArcticApples            #UnregulatedMushrooms - #PolyphenolOxidase - #Fungi - #CRISPR                      

Well, it seems more controversy is brewing over other varieties of Apples by Okanagan Specialty Fruits Company by introducing other varieties as GMO. My point here is not whether the fruit is safe or not, but rather focus on the not so well thought out consequences of editing out the gene which produces something called, "Polyphenol Oxidases" or (PPOs). This is the enzyme which causes browning when you bite into it. Same thing with potatoes or bananas. But while this has been marketed as yucky and disgusting by their own advertising on their website, is this browning really all that bad ? Frankly, humans seem to have an aversion to things being brown. Other consumable products like Sugar or Flour have been promoted with idea that they are only good when they are white (bleached). It would seem this is mostly some sort of handed down cultural flaw humans have invented. Look how humans view each other. I don't really want to go here, but you understand what I mean. It has gone as far as to effect some people of darker colour (whom I admire & jealous of their darker brown skin tone) who go as far as to look more white, even to the point of commercial bleaching products. But let's get back to something important that Okanagan Specialty Fruit Company says about "Polyphenol Oxidase" on their very own website. They admited the benefits of Polyphenol Oxidase in apples. Please take note of the very last two paragraphs of their page which is titled:
"How’d we “make” a nonbrowning apple?"
"What role does PPO play in the plant, you might ask? In some plants, PPO plays a defensive role – for example, tomatoes produce high levels of PPO when attacked by pests or pathogens. In contrast, apples produce very low levels of PPO, and only in very young fruit.  Its presence is probably left over from apples of ages ago, playing no role in today’s apples."   
"I always close my talk with friends with this intriguing sidebar to the story: When eaten by humans, polyphenolics may have health-promoting benefits. For example, phenolics are believed to act as antioxidants, fighting the well-documented damaging effects that oxidation can have on the heart, other organs and throughout the body. Not enough is known yet about phenolics for the health community to suggest a recommended intake amount, as for other vitamins and nutrients such as Vitamin C (the best-known antioxidant), fiber and so on – but they are certainly worth watching!"
There was an article today EcoWatch called, Third GMO Arctic Apple Gets USDA Approval which fired up controversy from many readers who really missed the main point there. This is really all about companies indoctrinating and marketing by further exacerbating the ignorance of the consumer. People creeped out by brown spots on any produce. This was Not about higher yields or built in pesticides. This had zero to do with inserting foreign genes, but rather using a technology called CRISPR which recently Monsanto has acquired the license for. Many mistakenly accused Monsanto as being behind this GMO apple and that is wrong. This admittedly incredible technological tool can be used to either edited out a specific gene or switch it off. In this case the gene that produces Polyphenol Oxidase which cause things to turn brown. But as the Okanagan's website admits, there are potential consequences. This was also brought out by Mycologist, Paul Stamets, who wrote a short article about the article published in Nature where they had published an article titled, "Gene-edited CRISPR mushroom escapes US regulation." The point of the article was that White Button Mushrooms could be engineered with the CRISPR–Cas9 technique, cultivated and sold without any further government oversight. They basically were given a "Get out of Jail Free Card" which allows them to "Pass 'Go' and collect $200." That's monopoly lingo for legal loophole. Not one word on Nature's article on the unintended consequences of this stuff causing an increase with regards pesticides or what would happen in nature if similar species acquired this trait in their own genomes where loss of information would make wild plants vulnerable to disease, infection and insect pests. In other words, we'd see defenseless plants and total collapse of whole plant ecosystems. Not one word. Below is what Mycologist Paul Stamets had to say on this subject.

Jose A. Bernat Bacete/Getty Images

Common white button mushroom (Agaricus bisporus)
has been modified to resist browning.
"Note: Although heralded by some scientists as a breakthrough, re: “The research community will be very happy with the news,” says Caixia Gao, a plant biologist at the Chinese Academy of Sciences’s Institute of ‪#‎Genetics‬ and Developmental ‪#‎Biology‬ in Beijing."  "I am one researcher who does not agree. I strongly recommend caution. Using ‪#‎Crispr‬ gene editing, scientists interfered with polyphenol oxidase (tyrosinase) production to produce a button (Agaricus bisporus) strain that does not brown. What these researchers apparently did not know is that my research has found that this pathway is responsible for many novel antivirals."  
"Mushrooms‬ have developed novel antivirals that protect them, and by extrapolation us. By interfering with this polyphenol pathway, I am concerned that they have defeated the endogenous natural antiviral defenses. What does this mean? Time will tell. I hope this does not lead to new reservoirs of hyper-viruses that can now emerge unchecked by the natural genome. In scientific terms, this could be a big "OOPS" ! The hubris of scientists playing with such powerful technology without consideration of downstream consequences is potentially dangerous. Genes code for many activities. Defeating them for one purpose may cause unforeseen consequences far more important than creating cosmetically beautiful mushrooms that will sell longer in the grocery stores."
These unforeseen consequences have never really seriously be dealt with nor considered when it comes to this irresponsible, "WE aren't going to regulate CRISPR Technology," push which itself is as much based on lack of information as much as the genomes of organisms being edited. But this doesn't seem to bother anybody or at least very few because they basically have little understanding of how seriously complex and sophisticated DNA is in all life forms. As long as it is not a foreign gene being inserted into another organisms, people are willing to give this a pass. Follow any of the comments section under these topics and gross ignorance is on both sides when it comes to knowledge on the potential for harm. Here is a quick video on how CRISPR is supposed to work and potential for mistakes as a result of lack of bioethics.

In an article titled, "Understanding the Unintended Effects of Genetic Manipulation," the online journal 'Nature Institute' gave a number of examples worthy of consideration. Whether it's called genetic engineering or genetic modification or CRISPR gene editing to change an organism, they generally have a specific objective or goal in mind. Often times this involves the motivation of profit which can effect something what we call Bioethics. Monetary motivate always colours everything. Here are a couple of important paragraphs from the Nature Institute's article:
Unintended (or, as I will sometimes say here, "nontarget") effects are those experimental results that appear in addition to or, in some cases, instead of the intended results. Within the scientific literature a variety of virtually synonymous terms and expressions point to such unintended effects of genetic manipulation. Scientists speak of nontarget effects, unexpected effects, unintended consequences, or the pleiotropic effect of the gene. (Pleiotropy means that a gene affects more than one characteristic.) Sometimes a research report will signal unintended effects with a phrase such as, "Surprisingly, we found . . " or "Unexpectedly, the plants . . " An instructive analogy is the common occurrence of drug "side effects." Here, too, the intended effect of the drug is often accompanied by numerous, sometimes harmful, effects arising from the drug's unanticipated action on nontarget tissues or processes.
Seriosuly, many science journals or research papers use such phrases irrespective of the topic or subject matter which reveals a gross lack of understanding on the part of the researcher from the outset. Unfortunately, with such sensitive technology, we don't have the luxury for mistakes here. And I could careless about someone's pride or ambition for attaining celebrity status among this world's elites. The natural world can't afford serious mistakes.
Unintended Effects of Genetic Manipulation in the Scientific Literature
"Of course, such nontarget effects are not always reported in research reports. As Dougherty and Parks (1995) write, 'Organisms that do not perform as expected are discounted as defective or atypical in some way, are not the subject of study, and frequently are not reported in the literature. It is important, therefore, to recognize that most published works represent a selected subset of transgenic organisms that have been produced. These built-in biases have hindered our understanding of how transgene expression impacts the endogenous [host] gene' and, I would add, how the organism as a whole can be affected by the genetic manipulation." 
(Source: Nature Institute)
The other scary thing here is that with this new CRISPR technology, they often ignore epigenetic effects and eventual side effect consequences. I'll post some examples below which have already exposed the seriousness of this ignorance or deliberate turning of a blind eye. But on another positve note, many studies are coming out with information on how Polyphenols are really good and beneficial for people. More on this down below.

You should also know that Okanagan Specialty Fruit Company has provided some research data on testing results with regards their Arctic Apples. The part I was most interested in were effects of immune system mechanisms being shut down and attacked from diseases and insect pests. They claimed there were attacks, but they were negligible. But they also admitted the reason was that conventional Insecticide & Fungicide sprayings were employed. That to me that is still the problem as proper set up of other biological component mechanisms can be utilized to trigger immune responses of the tree's own defenses and encourage beneficial predator insects to control pests and create balance. More and more Vineyard & Winery owners are doing this all the time. With this Pholyphenol producing gene removed or shut down, there appears no way for soil micro-organism components to trigger positive epigenetic responses to the tree's immune system.
Okanagan Fruit Company - Petition for Determination of Nonregulated Status: ArcticTM Apple (Malus x domestica) Events GD743 and GS784
October 6th, 2016 Breaking News Headlines 
Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard ?
Seriously ? This Biotech industry believes they should receive no oversight regulation with regards gene editing or RNAi technology because there is no danger ? ? ?
The Role & Purpose of  Polyphenol oxidase (PPO) as found in Nature

I appreciate ahead of time that many folks will take acception to the use of the term role or purpose, but there is no way to get around that. This browning effect is marketed from a big agribusiness viewpoint to the average consumer who generally does not do their own personal homework. This enzyme is advertised as an evil thing that simply makes some fruits and vegetables look Yucky. Seriously, many of the GMO proponents (including Okanagan) have actually used the word "Yucky"! The Arctic Apple folks themselves being the very one's in the promotion of this product on their own website. So to highlight, the message here once again is, "nature is flawed and Biotechs can fix the flaws." So how important exactly is Polyphenol oxidase (PPO) to the Earth's plant ecosystem world ? You'll be amazed and it will shine an unwelcomed spotlight on the CRISPR defense team.
Polyphenol oxidase as a biochemical seed defense mechanism
Abstract: "Seed dormancy and resistance to decay are fundamental survival strategies, which allow a population of seeds to germinate over long periods of time. Seeds have physical, chemical, and biological defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. Here, we hypothesize that seeds also possess enzyme-based biochemical defenses, based on induction of the plant defense enzyme, polyphenol oxidase (PPO), when wild oat (Avena fatua L.) caryopses and seeds were challenged with seed-decaying Fusarium fungi. These studies suggest that dormant seeds are capable of mounting a defense response to pathogens. The pathogen-induced PPO activity from wild oat was attributed to a soluble isoform of the enzyme that appeared to result, at least in part, from proteolytic activation of a latent PPO isoform. PPO activity was also induced in wild oat hulls (lemma and palea), non-living tissues that cover and protect the caryopsis. These results are consistent with the hypothesis that seeds possess inducible enzyme-based biochemical defenses arrayed on the exterior of seeds and these defenses represent a fundamental mechanism of seed survival and longevity in the soil. Enzyme-based biochemical defenses may have broader implications since they may apply to other defense enzymes as well as to a diversity of plant species and ecosystems."
Wow, how many of you knew this about seed dormancy and defense mechanisms still being activated even while the seed technically is asleep ? I didn't. Take away those valuable PPOs and clearly there is a significant reduction in length of dormancy or even viability. 

image -

Red Clover (Trifolium pratense L.)
Polyphenol oxidase affects normal nodule development in red clover
Conclusion: "All these data point to a major change in oxido-reduction status of plants lacking normal high level of PPO, resulting in destabilized redox pathways. Lack of PPO in red clover plants does not have an obvious effect on plants grown under optimal, stress-free N2-fixation conditions. However, the normal WT biochemistry, chemical composition, and developing morphology/anatomy of nodules were significantly altered."
Red Clover is a forage plant in the bean or legume family and very important in nitrogen fixation in soils. On the roots of such plants there are root nodules where beneficial bacteria help transfer atmospheric nitrogen into something solid and available to plants. So taking this into consideration that Polyphenol Oxidase (PPO)  belongs to the oxidoreductase class of enzymes, these researchers wanted to know exactly what effect, if any, would the lack of plant PPO have on the nodule’s redox potential, normal nodule development and ultimately on N2-fixation ? Take note of the term, "redox potential" and it's definition. This plant redox signaling is  the complex interface between the redox and hormone-signaling pathways that allow precise control of plant growth and immune system defense in response to metabolic triggers and environmental constraints and/or cues. These pathways contribute to specific signaling systems in plant cells that convey information to the nucleus to regulate gene expression. This was something I wrote about on the effects of root colonization by two different species of the same type of mycorrhizal fungi, Trichoderma virens & Trichoderma harzianum for which there are inumerable beneficial epigenetic triggers that can be signaled and switched on within their host plant's genes governing the immune system. To sum up, there were distinct changes to both wild type Red Clover and the low PPO, GM Red Clover with or without these PPOs.
Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnuts
Take special note of how silencing the gene expression for PPO allows not only facilitated pathogen attacks but also cell death in the leaves of Black Walnut that has had it's Polyphenol Oxidase gene silenced.
Image - American Society of Plant Biologists

Silencing of jrppo1 induces a lesion mimic phenotype
A, Wild-type walnut leaf.
B, PPO-silenced line, early season (June). Inset, magnified view
 of necrotic lesions from abaxial side of leaf.

, PPO-silenced line, late season (September). The development
of the necrotic lesions was not associated with the presence
 of any detectable pathogen.
Walnut (Juglans regia) produces a rich array of phenolic compounds and possesses a single PPO enzyme, rendering it an ideal model to study PPO. We generated a series of PPO-silenced transgeni "c walnut lines that display less than 5% of wild-type PPO activity. Strikingly, the PPO-silenced plants developed spontaneous necrotic lesions on their leaves in the absence of pathogen challenge (i.e. a lesion mimic phenotype)."
Antisense downregulation of polyphenol oxidase results in enhanced disease susceptibility.
"As previously discussed, many PPO genes are up-regulated upon pathogen challenge, and overexpression of a potato (Solanum tuberosum) PPO in tomato (Solanum lycopersicum) resulted in decreased susceptibility to Pseudomonas syringae pv tomato (Li and Steffens, 2002). Likewise, silencing of PPOs in tomato led to increased disease susceptibility (Thipyapong et al., 2004). Similarly, overexpression of PPO genes in tomato and hybrid aspen (Populus tremula × Populus alba) resulted in increased insect resistance, and silencing of PPOs resulted in increased susceptibility to insect herbivory."
 For the moment this is enough info on what happens when the gene expression is deliberately silenced or edited out of a plants genome and the consequences of potential increase of using both Insecticides & Fungicides in the absence of fully functional immune systems in plants. I'll post more as necessary in the future.
So what are Polyphenols and how they work us ? (Video only six minutes)
So why should human beings care whether or not apples have PPOs present in their DNA ? Because there are a number of health benefits to Polyphenol Oxidase or PPOs because they act as good antioxidants as even Okanagan Specialty Fruit Company admitted on their website. Take just one example of the GMO Arctic Granny Smith Apple they've created. Granny Smith Apples are excellent for gut health. Of all apples they are one of the longest keepers in storage. They mostly go through the small intestine undigested as far as fiber and other properties, but in the large intestine ferment and help produce many beneficial gut flora population increases.
"An apple a day may keep the doctor away, but – as an added bonus – Granny Smith apples will greet good gut bacteria with open arms. And, that’s because, researchers recently uncovered evidence that this tart green variety is superior to other types of apples in building a community of healthy bacteria in the colon. This is due to their high content of non-digestible compounds, including fiber and polyphenols." 
Granny Smith apples improve gut bacteria and reduce inflammation
Here is a list of other studies on the importance of Polyphenol Oxidase PPOs to human health benefits:

What's the best kind of Apple Juice or Cider you look for in the stores ? Is it not the brown cloudy variety (loaded with Polyphenols). Guess what, new research suggests that a daily glass of cloudy apple juice may decrease body fat in obese people, compared to another control beverage, with greater effects noted in individuals with certain genetic profiles. This is actually a win win for people interested not only in health, but a far better tasting product.
“This is the first intervention study that addressed the question whether a polyphenol-rich cloudy apple juice shows bioactivity on obesity-associated biomarkers also including the potential role of genetic polymorphisms regarding a potential diet–gene interaction,”   
“Although cloudy apple juice compared to the control beverage failed to modulate plasma parameters related to the obesity phenotype, cloudy apple juice induced a significant reduction in the percent body fat in obese men.” 
Since the subject here wasn't just about CRISPR & Gene Editing Apples because brown is considered a marketing failure, here is a little something interesting with regards another marketing tool used on apples and other fruits. No doubt since the 1960s - Wax

And last but not least  . . . . 

image - Naturopathic Currents

If you think CRISPR's usage will stop with plants, think again.

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