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Shale Gets Another Efficiency Boost – DNA Testing Can Cut Costs By 10% – Seeking Alpha

Posted: March 29, 2017 at 10:48 am

source: Stock Photo

If competitors didn't have enough to worry about concerning U.S. shale, another technological breakthrough has the potential to slash another 10 percent off of production costs for shale companies, further enhancing their ability to boost supply and generate a profit under most oil price points.

Among the more than dozen companies using Biota Technology's DNA testing are Statoil ASA (NYSE:STO) and EP Energy Corp. (NYSE:EPE).

To get an idea of the potential range of costs, shale wells are developed from $4 million to $8 million, depending on a variety of elements involved. Biota's take from those using the technology is under 1 percent, said Ajay Kshatriya, CEO and co-founder of Biota Technology.

Peter Lascelles, a geologist for EP Energy Corp., which was one of Biota's first customers, said DNA testing is superior to seismic and chemical analysis in understanding well performance and their potential.

What DNA testing is and does

The outcome of using DNA testing is it allows drillers to avoid mistakes which could limit the maximum output potential of a given well. It helps to more accurately measure the amount of pressure needed to reach shale oil, as well as allows drillers to know beforehand the distance needed between wells to generate the best results, among other improvements.

"The technique involves testing DNA extracts from microbes found in rock samples and comparing them to DNA extracted from oil. Similarities or differences can pinpoint areas with the biggest potential," according to Reuters.

Not only does this help companies engage in less costly production methods because of less accurate knowledge, but it also helps improve productivity by cutting the time it takes for a company to start pumping oil.

Being skeptical of yet another assertion of technology that can improve costs, EP Energy made Biota participate in a blind test to see how effective the technique was. It asked the company to make a determination on the origination of a specific oil sample from numerous wells in a targeted zone.

Lascelles said the company in fact did pinpoint the wells the oil sample came from and was as a result able to recommend ways it could improve drilling in the area.

At under 1 percent of costs to bring wells into production, it's easy to see why this is a very desirable technology to include in the output process.

source: Reuters via Biota

Concerns over increased supply misguided

Earlier in March, Bloomberg published an article where concern was aired over the lower costs of shale oil bringing more supply to the market, which would drive down the price of oil. In my view this is misguided and the result of not understanding how business works.

It would be no different than Wal-Mart at the height of its power being considered a weak investment because its low prices and margins generated more sales, which in turn may provide it the room to further lower prices. The same could be said about Amazon and it removing a lot of the costs out of distribution and delivery, which increases the sales at the company.

Rising supply is a major problem only if the costs are rising while the price of oil is falling. Otherwise, companies can profitably boost revenue and earnings at a lower price point than in the past.

Just like with retailers that turn over inventory far more than competitors and make money by increased sales, oil producers generate more revenue and earnings by increasing barrels sold, even if the price of oil has dropped. They make less per barrel but more from increased sales. Volume makes up for it.

I'm referring here to the new wells being completed, as the older wells aren't as efficient as the new wells. Once the old wells are worked through, the shale industry will emerge as among the lowest cost producers outside of a few state-owned companies in the Middle East. But even with that in mind, the shale costs are being driven down so much they could come close to those costs within the next year or two.

If you think that's too optimistic of an outlook, at CERAWeek some executives said breakeven was a low as $12 per barrel. Shell (NYSE:RDS.A) has said its new wells start to be profitable at about $20 per barrel. It's not going to be long before even those low numbers are improved.

EP Energy

At the end of 2016 EP Energy had drilling inventory of about 5,200 locations, with 2,900 of them located in the Wolfcamp.

The company noted in its latest earnings report that almost all of its locations are profitable "at today's strip pricing," and over 80 percent of them are profitable under $40 per barrel.

Cash costs in 4Q 2016 dropped 7 percent year-over-year, with most of the expense categories lower. Adjusted EBITDA was $255 million in the fourth quarter.

Also important on the cost side, the company was able to get its lease agreements amended with its landowner, the University Land System, which cut back on the royalty rates it will have to pay.

It's easy to see with increased productivity, lower costs and lower royalties, how the company has positioned itself for stronger earnings. Add to that the improvements it'll get from incorporating DNA testing into its operations, and you can see things are going to get better going forward.

And even if the price of oil finds support and royalties climb once again, it doesn't take away from the benefit it gets on the cost side from DNA testing.

Add to that its hedging of 75 percent of its 2017 oil product at $61.66 and its 76 percent of its natural gas production at $3.28, the company looks like it could outperform through the remainder of 2017.

Further out, the company has hedged about 20 percent of its 2017 production level at $60 per barrel, and over 25 percent of its natural gas swap at $3.11.

Statoil

Statoil doesn't have the same performance outlook at EP or others working shale have, as its locations aren't as profitable as the Permian is. Its major deposits are in the Bakken, Eagle Ford, and Marcellus.

So far Statoil hasn't been able to match many of its competitors on the efficiency side, as its breakeven point at the end of 2016 was a very high $66 per barrel. Even so, that's still an 35 percent improvement over 2015 costs. The company says by 2018 it should be able to cut breakeven down to $50 per barrel.

That is based upon existing inventory. If it were to acquire acreage in the Permian, it would be able to more rapidly lower its outlook for breakeven.

Embracing technology that can improve its cost structure will help Statoil, especially has it plays catch-up with competitors that have rapidly improved their ability to compete at most oil price levels.

Conclusion

Continuing to remove costs out of the production process is a positive for the shale industry, as it can continue to increase production profitably with their new wells.

Not only is this not bad, it's very good, as it puts more pressure on OPEC and Russia, which don't have a lot of room to lower costs. In regard to OPEC, I'm talking about the low-cost leaders, which also happen to be the top suppliers within the cartel. Russia actually has significant shale reserves, but its exposure to high-cost Artic oil and the ongoing restrictions on acquiring Western tech and equipment, which would boost its performance, makes it difficult for Russia to make cost improvements at this time.

Those with exposure to U.S. shale know that it's the future of oil for at least the next couple of decades. Costs are going to continue to improve, and when they're very close to the best OPEC has to offer, they'll crush the cartel. Already the U.S. is the swing producer. What happens when costs are removed to the point of being almost even with the best OPEC has to offer?

We're not going to see shale producers cutting back on production. It'll be measured and disciplined, but not relevant to concerns on rising supply and lower oil prices offsetting lower costs. It's U.S. shale that has the rest of the world on the ropes, not the other way around.

That doesn't mean high-cost shale producers won't come under pressure, because they will. What it means is the very best companies are starting to rise to the surface, and as they take more market share from competitors, the industry will consolidate further, and they will be in almost complete charge of the direction of oil in the not too distant future.

In my view this is OPEC's last time of attempting to manipulate the price of oil by cutting costs. Shale producers have responded to the cuts by ramping up production. The problem is many investors and analysts continue to interpret this as the result of moderately higher oil prices, when the reality is it's because they can generate profits with oil at a much lower level. That's why an increase in supply is to the benefit of shale producers; they don't have to provide for a country like its OPEC competitors do.

As for DNA testing, it's one more arrow in the quiver of shale producers who have another tool to use to cut costs even further.

Disclosure: I/we have no positions in any stocks mentioned, and no plans to initiate any positions within the next 72 hours.

I wrote this article myself, and it expresses my own opinions. I am not receiving compensation for it (other than from Seeking Alpha). I have no business relationship with any company whose stock is mentioned in this article.

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Shale Gets Another Efficiency Boost - DNA Testing Can Cut Costs By 10% - Seeking Alpha

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Watching the passage of knotted DNA slip through nanopores … – Science Daily

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Watching the passage of knotted DNA slip through nanopores ...
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How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of biological systems? Scientists used ...

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Watching the passage of knotted DNA slip through nanopores ... - Science Daily

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New study investigates the passage of knotted DNA through nanopores – Phys.Org

Posted: at 10:48 am

March 29, 2017 How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste who used computer simulations to investigate the options available to the genetic material in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States. Credit: Antonio Suma, SISSA

Anyone who has been on a sail boat knows that tying a knot is the best way to secure a rope to a hook and prevent slippage. Similarly, knots in sewing threads prevent them slipping through two pieces of fabric. How, then, can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste, who used computer simulations to investigate the dynamics of the molecule in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States.

"Our computational study sheds light on the latest experimental breakthroughs on knotted DNA manipulation, and adds interesting and unexpected elements," explains Micheletti. "We first observed how knotted DNA filaments pass through minuscule pores with a diameter of about 10 nanometers (10 billionths of a meter). The behaviour observed in our simulations was in good agreement with the experimental measurements obtained by an international research team led by Cees Dekker, which were published only a few months ago in Nature Biotechnology. These advanced and sophisticated experiments marked a turning point for understanding DNA knotting. However, current experiments cannot detect how DNA knots actually pass through the narrow pore.

"In fact, the phenomenon occurs over a tiny spatial scale that is inaccessible to microscopes. This is why our group resorted to what the great German biophysicist Klaus Schulten called 'the computational microscope,' that is, computer simulations."

Suma and Micheletti explain: "The simulations revealed that the passage of the knot can occur in two distinct ways: One where the knot is tight, and the other where the knot is more delocalised. In both cases, the knot not only passes through the pore, but it does so in a very brief time."

Moreover, the knot usually passes in the final stages of the translocation, when most of the DNA strand has already passed. "But there is something more that is counterintuitive," state the authors. "The size of the knot, whether small or large, does not seem to affect the pore obstruction time by much. The latter depends instead on the translocation speed, which, in turn, depends on the initial position of the knot along the filament." These results, say the researchers, ought to help the design of future experiments probing the spontaneous knotting of DNA, a still largely unexplored venue, especially regarding the size of DNA knots.

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Advancing our current understanding of knots in biological molecules is important to clarify their implications in biological contexts as well as in applicative ones, such as DNA sequencing using nanopores. Suma and Micheletti hope that the promising directions suggested by their study can lead to a more detailed and accurate profiling of entanglement in DNA, RNA and proteins.

Explore further: New study shows that proteins are 'virtually' knotted

More information: Antonio Suma et al. Pore translocation of knotted DNA rings, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1701321114

Journal reference: Proceedings of the National Academy of Sciences Nature Biotechnology

Provided by: Scuola Internazionale Superiore di Studi Avanzati

Many of the processes essential to life involve proteins - long molecules which 'fold' into three-dimensional shapes allowing them to perform their biological role.

DNA has the nasty habit of getting tangled and forming knots. Scientists study these knots to understand their function and learn how to disentangle them (e.g. useful for gene sequencing techniques). Cristian Micheletti, ...

Nanotechnologies require a detailed knowledge of the molecular state. For instance, it is useful to know when and how a generic polymer, a long chain of polymers (chain of beads), knots. The study of molecular entanglement ...

A simple and effective way of unravelling the often tangled mass of DNA is to 'thread' the strand into a nano-channel. A study carried out with the participation of the International School for Advanced Studies in Trieste ...

As sailors and mountaineers know very well, every knot carries out a specific function. There's a knot that slides, one that "floats", and one that comes undone with a single pull. In the field of nanotechnology as well, ...

Scientists at The University of Manchester have produced the most tightly knotted physical structure ever known - a scientific achievement which has the potential to create a new generation of advanced materials.

(Phys.org)Researchers from the University of Sheffield report a new continuous-breathing metal-organic framework (MOF), SHF-61, that has two different solvent-specific forms, a narrow-pore structure that is the result ...

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In order for a fuel cell to work, it needs an oxidizing agent. TU Wien has now found a way to explain why oxygen does not always enter fuel cells effectively, rendering them unusable.

Researchers at the University of York and Simon Fraser University, Canada, revealed the 3-D structure of an enzyme that could provide a crucial step forward in treating neurodegenerative diseases.

The photodissociation of triiodide anion (I3-) is a classic textbook reaction that has been extensively studied both in solution and in gas phase. However, probing the ultrafast dynamics of this reaction in the solid state ...

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New study investigates the passage of knotted DNA through nanopores - Phys.Org

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Scientists predict reading ability from DNA alone – Phys.Org

Posted: at 10:48 am

March 29, 2017 Credit: CC0 Public Domain

Researchers from King's College London have used a genetic scoring technique to predict reading performance throughout school years from DNA alone.

The study, published today in Scientific Studies of Reading, shows that a genetic score comprising around 20,000 of DNA variants explains five per cent of the differences between children's reading performance. Students with the highest and lowest genetic scores differed by a whole two years in their reading performance.

These findings highlight the potential of using genetic scores to predict strengths and weaknesses in children's learning abilities. According to the study authors, these scores could one day be used to identify and tackle reading difficulties early, rather than waiting until children develop these problems at school.

The researchers calculated genetic scores (also called polygenic scores*) for educational achievement in 5,825 individuals from the Twins Early Development Study (TEDS) based on genetic variants identified to be important for educational attainment. They then mapped these scores against reading ability between the ages of seven and 14.

Genetic scores were found to explain up to five per cent of the differences between children in their reading ability. This association remained significant even after accounting for cognitive ability and family socio-economic status.

The study authors note that although five per cent may seem a relatively small amount, this is substantial compared to other results related to reading. For example, gender differences have been found to explain less than one per cent of the differences between children in reading ability.

Saskia Selzam, first author of the study from the Institute of Psychiatry, Psychology & Neuroscience (IoPPN) at King's College London, said: 'The value of polygenic scores is that they make it possible to predict genetic risk and resilience at the level of the individual. This is different to twin studies, which tell us about the overall genetic influence within a large population of people.'

'We think this study provides an important starting point for exploring genetic differences in reading ability, using polygenic scoring. For instance, these scores could enable research on resilience to developing reading difficulties and how children respond individually to different interventions.'

Professor Robert Plomin, senior author from the IoPPN at King's College London, said: 'We hope these findings will contribute to better policy decisions that recognise and respect genetically driven differences between children in their reading ability.'

*Calculating an individual's polygenic score requires information from a genome-wide association study (GWAS) that finds specific genetic variants linked to particular traits, in this case educational attainment. Some of these genetic variants, known as single nucleotide polymorphisms (SNPs), are more strongly associated with the trait, and some are less strongly associated. In a polygenic score, the effects of these SNPs are weighed by the strength of association and then summed to a score, so that people with many SNPs related to academic achievement will have a higher polygenic score and higher academic achievement, whereas people with fewer associated SNPs will have a lower score and lower levels of academic achievement.

Explore further: Scientists herald 'tipping point' in ability to predict academic achievement from DNA

More information: Saskia Selzam et al, Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years, Scientific Studies of Reading (2017). DOI: 10.1080/10888438.2017.1299152

Scientists from King's College London have used a new genetic scoring technique to predict academic achievement from DNA alone. This is the strongest prediction from DNA of a behavioural measure to date.

An international team of scientists, led by researchers at University of California San Diego School of Medicine and University of California San Francisco, has developed a novel genetic score that allows individuals to calculate ...

Psychological characteristics link genes with upward social mobility, according to data collected from almost 1000 individuals over four decades. The data suggest that various psychological factors play a role in linking ...

A study co-led by the University of East Anglia (UEA) has found that people with genes for high educational achievement tend to marry, and have children with, people with similar DNA.

Reading achievement at age 10 influences how much independent reading children do at age 11. However, independent reading doesn't directly improve children's achievement in reading, at least among children at the end of elementary ...

A first-of-its-kind, nationally representative study of siblings supports previously published research on unrelated individuals that links specific genotypes to educational attainment among adults in their mid-20s to early ...

Researchers from King's College London have used a genetic scoring technique to predict reading performance throughout school years from DNA alone.

The Liberty Mutual commercial mentions naming your car Brad and considering him part of your family.

When the Earth is dark, human activity sparkles across the globe. As seen from space, night-time lights tell a story about how we live, correlating to everything from electricity consumption and CO2 emissions, to gross domestic ...

If a Japanese woman were to compliment a friend on her flattering pale-blue blouse, she'd probably employ a word with no English equivalent.

(Phys.org)A pair of archaeologists with the American Museum of Natural History has unearthed a palatial compound in El Palenque's plaza in the Oaxaca Valley in Mexico. In their paper published in Proceedings of the National ...

The science and engineering workforce in the United States is aging rapidly, according to a new study. And it is only going to get older in coming years.

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The reality that will emerge is that it will move to the lowest common denominator aspect, which is identifying and labeling types of people.

Brave new world people. alpha, beta, ceta, delta.... and then gamma.

Fully realized and idealized people sorting.

Human genetic separation into groups of desirables vs baskets of deplorables...

Humans and their rather pronounced unconscious aspects...becoming fully enabled in genetic selection... could easily fall into being a total disaster for forms of continuance in evolution.

And the enabled Alpha aspects will have little to no form of any reasonable impetus to alter that coming path which they create and enable.

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Scientists predict reading ability from DNA alone - Phys.Org

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Cortisol excess hits natural DNA process and mental health hard … – Science Daily

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Cortisol excess hits natural DNA process and mental health hard ...
Science Daily
High concentrations of the stress hormone cortisol in the body affect important DNA processes and increase the risk of long-term psychological consequences.

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Rachel Dolezal on Rihanna, Her DNA Test, ‘Fraud’ Claims and Other Facebook Questions – NBCNews.com

Posted: at 10:48 am

NBCBLK's Amber Payne and Rachel Dolezal John Makely / NBC News

These days, the former Spokane NAACP president unapologetically identifies as trans-Black but distinguishes between that term and transracial.

"Transracial it almost sounds like I'm neutral, and I'm not neutral on political and social issues," Dolezal told NBCBLK while on a press tour for her new memoir, "In Full Color: Finding My Place in a Black And White World."

She added: "If I was allowed a more complex term, I would say I'm pan-African, pro-Black, bisexual, mother, activist, artist, you know that's like too long. So trans-Black is quicker."

Related:

When

I heard from high school pals I hadn't talked to in years. Thousands of miles away, my expat friends in Japan and Berlin wanted to discuss. People of different ages, races, ethnicities, and sexual orientations filled my timeline. Even my mom weighed in.

While some of these eight questions are on the serious side, others more irreverent, all prove that the controversy around Dolezal's identity is also nothing short of fascinating.

I wrote the book to really to encourage and advance the conversation on race and yes to set the record straight about my whole life story. And also to encourage people to be exactly who they really are. And the essential essence of who I am is best defined in culture and in race terms as "Black."

Well I think that in America, even though race is a social construct, I mean, we say this in theory, but I think a lot of people don't believe that it really is. And so it's still a very racialized society. And so there's a line drawn in the sand. And there's a Black and white divide and I stand unapologetically on the Black side of that divide with my own internal sense of self and my values, and with my sons and my sister and with the greater cause of really undoing the myth of white supremacy.

It was actually given to me. Unfortunately, the press said I chose it randomly, which I didn't. And at the end of the book, I discuss that an Igbo man reached out to me and really just said that, "We see you. My tribe sees you for who you are, and you have this high frequency in your soul and you're incarnated into this white envelope. And you were brought here as a gift from the gods to challenge white supremacy spiritually."

That was in January 2016, and I fully embraced the name as my legal name in October, so a few months later.

Yea, I don't know about surprising. I guess have been a little bit surprised just at the polarization because it seems like it's either love or hate, as opposed to just like, OK, just cool be who you are whatever. It's not a big deal. Let's just work together and strive for common goals of freedom, justice, and equity. I mean that was kind of to some extent maybe more of what I anticipated.

Well, I wish that I could have had the chance to tell my whole story and introduce myself to the world instead of being introduced by others in a very negative connotation. So the oppositional people really came out with this narrative of a fraud, a liar and a con and all this kinda stuff before I had a chance to say, "Hello, my name is Rachel and this is who I am."

So I think it just kinda steamrolled and got so much momentum of negativity where my life just got shaped by that, and people's perceptions of me were shaped by that. And I knew very quickly that I wasn't going to be able to really describe my experience in full context in an interview and so I really needed to do that in book form.

I think that it is too common for white feminists to say, "We want some diversity, come join our movement about gender, but we want you to check the class and race at the door." And you can't undo that braid of race, class and gender, all three intersect with each other, so it's important for more education to be done about that. We talk about feminism, but I think even in the male world, that Donald Trump is white, rich, and male, like all those three are working together for his opportunities in his life.

Well, I think that it's important as a mother to support who our children are, and you kind of notice that as they grow and develop, whether it's gender or sexual orientation, culture, the music that they want to listen to, the food that they like, so I'll just be constantly encouraging him [her one-year-old] and guiding him toward what resonates with him. And he's one, so right now, what resonates with him are toys and gadgets and buttons.

Well, what I found was kind of like, there's 10% African ancestry, 35% Iberian peninsula and all these things, and then when I asked the testing facility I'm not gonna reveal who I did the test with but they basically said, oh I asked them to make a certified record and they said, those weren't your real results, you're actually 100% European.

I mean, It was under Rachel Dolezal, as my name when I did that test. And I was asking them to certify the results cause I was gonna include it in the book. And really what it made me do is, I just kind of felt like, you know what, this is just b*******. I don't need a lab to tell me who I am, and if their results are that wishy washy anyway? I mean, we know that race is not biological and we teach this all the time in sociology courses so I just didn't get another one done.

1. As a fellow Black woman can you explain the difference between performative blackface and the experience of being Black?

2. What is your take on

3. Do you have any black friends? If so, are they still down?

4. Is it because you are a white woman that you feel entitled to everything including other people's cultures and experiences?

5. Can I touch your hair?

6. Tupac or Biggie? Prince or Michael Jackson?

7. Have you ever been called the N-word or been eyed as a shoplifter or denied service or strip-searched by a cop or otherwise gotten the "Black experience"?

8. WWWWWWWHHHHHHHHHHHYYYYYYYYYYYYYY?

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Rachel Dolezal on Rihanna, Her DNA Test, 'Fraud' Claims and Other Facebook Questions - NBCNews.com

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Mitochondrial DNA – Wikipedia

Posted: at 10:48 am

Mitochondrial DNA (mtDNA or mDNA)[3] is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also in plastids such as chloroplasts.

In humans, the 16,569 base pairs of mitochondrial DNA encode for only 37 genes.[4]Human mitochondrial DNA was the first significant part of the human genome to be sequenced. In most species, including humans, mtDNA is inherited solely from the mother.[5]

Since animal mtDNA evolves faster than nuclear genetic markers,[6][7][8] it represents a mainstay of phylogenetics and evolutionary biology. It also permits an examination of the relatedness of populations, and so has become important in anthropology and biogeography.

Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. This theory is called the endosymbiotic theory. Each mitochondrion is estimated to contain 210 mtDNA copies.[9] In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.[10]

The reasons why mitochondria have retained some genes are debated. The existence in some species of mitochondrion-derived organelles lacking a genome[11] suggests that complete gene loss is possible, and transferring mitochondrial genes to the nucleus has several advantages.[12] The difficulty of targeting remotely-produced hydrophobic protein products to the mitochondrion is one hypothesis for why some genes are retained in mtDNA;[13]colocalisation for redox regulation is another, citing the desirability of localised control over mitochondrial machinery.[14] Recent analysis of a wide range of mtDNA genomes suggests that both these features may dictate mitochondrial gene retention.[10]

In most multicellular organisms, mtDNA is inherited from the mother (maternally inherited). Mechanisms for this include simple dilution (an egg contains on average 200,000 mtDNA molecules, whereas a healthy human sperm was reported to contain on average 5 molecules[15][16] ), degradation of sperm mtDNA in the male genital tract, in the fertilized egg, and, at least in a few organisms, failure of sperm mtDNA to enter the egg. Whatever the mechanism, this single parent (uniparental inheritance) pattern of mtDNA inheritance is found in most animals, most plants and in fungi as well.

In sexual reproduction, mitochondria are normally inherited exclusively from the mother; the mitochondria in mammalian sperm are usually destroyed by the egg cell after fertilization. Also, most mitochondria are present at the base of the sperm's tail, which is used for propelling the sperm cells; sometimes the tail is lost during fertilization. In 1999 it was reported that paternal sperm mitochondria (containing mtDNA) are marked with ubiquitin to select them for later destruction inside the embryo.[17] Some in vitro fertilization techniques, particularly injecting a sperm into an oocyte, may interfere with this.

The fact that mitochondrial DNA is maternally inherited enables genealogical researchers to trace maternal lineage far back in time. (Y-chromosomal DNA, paternally inherited, is used in an analogous way to determine the patrilineal history.) This is usually accomplished on human mitochondrial DNA by sequencing the hypervariable control regions (HVR1 or HVR2), and sometimes the complete molecule of the mitochondrial DNA, as a genealogical DNA test.[18] HVR1, for example, consists of about 440 base pairs. These 440 base pairs are then compared to the control regions of other individuals (either specific people or subjects in a database) to determine maternal lineage. Most often, the comparison is made to the revised Cambridge Reference Sequence. Vil et al. have published studies tracing the matrilineal descent of domestic dogs to wolves.[19] The concept of the Mitochondrial Eve is based on the same type of analysis, attempting to discover the origin of humanity by tracking the lineage back in time.

mtDNA is highly conserved, and its relatively slow mutation rates (compared to other DNA regions such as microsatellites) make it useful for studying the evolutionary relationshipsphylogenyof organisms. Biologists can determine and then compare mtDNA sequences among different species and use the comparisons to build an evolutionary tree for the species examined. However, due to the slow mutation rates it experiences, it is often hard to distinguish between closely related species to any large degree, so other methods of analysis must be used.

Entities undergoing uniparental inheritance and with little to no recombination may be expected to be subject to Muller's ratchet, the accumulation of deleterious mutations until functionality is lost. Animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. The bottleneck exploits stochastic processes in the cell to increase in the cell-to-cell variability in mutant load as an organism develops: a single egg cell with some proportion of mutant mtDNA thus produces an embryo where different cells have different mutant loads. Cell-level selection may then act to remove those cells with more mutant mtDNA, leading to a stabilisation or reduction in mutant load between generations. The mechanism underlying the bottleneck is debated,[20][21][22][23] with a recent mathematical and experimental metastudy providing evidence for a combination of random partitioning of mtDNAs at cell divisions and random turnover of mtDNA molecules within the cell.[24]

Doubly uniparental inheritance of mtDNA is observed in bivalve mollusks. In those species, females have only one type of mtDNA (F), whereas males have F type mtDNA in their somatic cells, but M type of mtDNA (which can be as much as 30% divergent) in germline cells.[25] Paternally inherited mitochondria have additionally been reported in some insects such as fruit flies,[26][27]honeybees,[28] and periodical cicadas.[29]

Male mitochondrial inheritance was recently discovered in Plymouth Rock chickens.[30] Evidence supports rare instances of male mitochondrial inheritance in some mammals as well. Specifically, documented occurrences exist for mice,[31][32] where the male-inherited mitochondria were subsequently rejected. It has also been found in sheep,[33] and in cloned cattle.[34] It has been found in a single case in a human male.[35]

Although many of these cases involve cloned embryos or subsequent rejection of the paternal mitochondria, others document in vivo inheritance and persistence under lab conditions.

An IVF technique known as mitochondrial donation or mitochondrial replacement therapy (MRT) results in offspring containing mtDNA from a donor female, and nuclear DNA from the mother and father. In the spindle transfer procedure, the nucleus of an egg is inserted into the cytoplasm of an egg from a donor female which has had its nucleus removed, but still contains the donor female's mtDNA. The composite egg is then fertilized with the male's sperm. The procedure is used when a woman with genetically defective mitochondria wishes to procreate and produce offspring with healthy mitochondria.[36] The first known child to be born as a result of mitochondrial donation was a boy born to a Jordanian couple in Mexico on 6 April 2016.[37]

In most multicellular organisms, the mtDNA - or mitogenome - is organized as a circular, covalently closed, double-stranded DNA. But in many unicellular (e.g. the ciliate Tetrahymena or the green alga Chlamydomonas reinhardtii) and in rare cases also in multicellular organisms (e.g. in some species of Cnidaria ) the mtDNA is found as linearly organized DNA. Most of these linear mtDNAs possess telomerase independent telomeres (i.e. the ends of the linear DNA) with different modes of replication, which have made them interesting objects of research, as many of these unicellular organisms with linear mtDNA are known pathogens.[38]

For human mitochondrial DNA (and probably for that of metazoans in general), 100-10,000 separate copies of mtDNA are usually present per somatic cell (egg and sperm cells are exceptions). In mammals, each double-stranded circular mtDNA molecule consists of 15,000-17,000[39]base pairs. The two strands of mtDNA are differentiated by their nucleotide content, with a guanine-rich strand referred to as the heavy strand (or H-strand) and a cytosine-rich strand referred to as the light strand (or L-strand). The heavy strand encodes 28 genes, and the light strand encodes 9 genes for a total of 37 genes.[4] Of the 37 genes, 13 are for proteins (polypeptides), 22 are for transfer RNA (tRNA) and two are for the small and large subunits of ribosomal RNA (rRNA).[40] The human mitogenome contains overlapping genes (ATP8 and ATP6 as well as ND4L and ND4: see the human mitochondrial genome map), a feature that is rare in animal genomes.[citation needed] The 37-gene pattern is also seen among most metazoans, although in some cases one or more of these genes is absent and the mtDNA size range is greater.

Great variation in mtDNA gene content and size exists among fungi and plants, although there appears to be a core subset of genes that are present in all eukaryotes (except for the few that have no mitochondria at all).[10] Some plant species have enormous mitochondrial genomes, with Silene conica mtDNA containing as many as 11,300,000 base pairs.[41] Surprisingly, even those huge mtDNAs contain the same number and kinds of genes as related plants with much smaller mtDNAs.[42] The genome of the mitochondrion of the cucumber (Cucumis sativus) consists of three circular chromosomes (lengths 1556, 84 and 45 kilobases), which are entirely or largely autonomous with regard to their replication.[43]

The smallest mitochondrial genome sequenced to date is the 5967 bp mtDNA of the parasite Plasmodium falciparum.[44]

There are six main genome types found in mitochondrial genomes. These genome types were classified by Kolesnikov & Gerasimov (2012)" and differ in various ways such as a circular versus linear genome, genome size, the presence of introns or plasmid like structures, and whether the genetic material is a singular molecule or collection of homogeneous or heterogeneous molecules.[45]

There is only one mitochondrial genome type found in animal cells. This genome contains one circular molecule with between 11-28kbp of genetic material (type 1).[45]

There are three different genome types found in plants and fungi. The first type is a circular genome that has introns (type 2) and may range from 19-1000kpb in length. The second genome type is a circular genome (about 20-1000kbp) that also has a plasmid-like structure (1kb) (type 3). The final genome type that can be found in plant and fungi is a linear genome made up of homogeneous DNA molecules (type 5).

Protists contain the most diverse mitochondrial genomes, with five different types found in this kingdom. Type 2, type 3 and type 5 mentioned in the plant and fungus genomes also exists in some protist, as well as two unique genome types. The first of these is a heterogeneous collection of circular DNA molecules (type 4) and the final genome type found in protists is a heterogeneous collection of linear molecules (type 6). Genome types 4 and 6 both range from 1-200kbp in size.

Endosymbiotic gene transfer, the process of genes that were coded in the mitochondrial genome being transferred to the cell's main genome likely explains why more complex organisms, such as humans, have smaller mitochondrial genomes than simpler organisms, such as protists.

Mitochondrial DNA is replicated by the DNA polymerase gamma complex which is composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and two 55 kDa accessory subunits encoded by the POLG2 gene.[46] The replisome machinery is formed by DNA polymerase, TWINKLE and mitochondrial SSB proteins. TWINKLE is a helicase, which unwinds short stretches of dsDNA in the 5 to 3 direction.[47]

During embryogenesis, replication of mtDNA is strictly down-regulated from the fertilized oocyte through the preimplantation embryo.[48] The resulting reduction in per-cell copy number of mtDNA plays a role in the mitochondrial bottleneck, exploiting cell-to-cell variability to ameliorate the inheritance of damaging mutations.[24] At the blastocyst stage, the onset of mtDNA replication is specific to the cells of the trophectoderm.[48] In contrast, the cells of the inner cell mass restrict mtDNA replication until they receive the signals to differentiate to specific cell types.[48]

In animal mitochondria, each DNA strand is transcribed continuously and produces a polycistronic RNA molecule. Between most (but not all) protein-coding regions, tRNAs are present (see the human mitochondrial genome map). During transcription, the tRNAs acquire their characteristic L-shape that gets recognized and cleaved by specific enzymes. With the mitochondrial RNA processing, individual mRNA, rRNA, and tRNA sequences are released from the primary transcript.[49] Folded tRNAs therefore act as secondary structure punctuations.[50]

The concept that mtDNA is particularly susceptible to reactive oxygen species generated by the respiratory chain due to its proximity remains controversial.[51] mtDNA does not accumulate any more oxidative base damage than nuclear DNA.[52] It has been reported that at least some types of oxidative DNA damage are repaired more efficiently in mitochondria than they are in the nucleus.[53] mtDNA is packaged with proteins which appear to be as protective as proteins of the nuclear chromatin.[54] Moreover, mitochondria evolved a unique mechanism which maintains mtDNA integrity through degradation of excessively damaged genomes followed by replication of intact/repaired mtDNA. This mechanism is not present in the nucleus and is enabled by multiple copies of mtDNA present in mitochondria [55] The outcome of mutation in mtDNA may be an alteration in the coding instructions for some proteins,[56] which may have an effect on organism metabolism and/or fitness.

Mutations of mitochondrial DNA can lead to a number of illnesses including exercise intolerance and KearnsSayre syndrome (KSS), which causes a person to lose full function of heart, eye, and muscle movements. Some evidence suggests that they might be major contributors to the aging process and age-associated pathologies.[57] Particularly in the context of disease, the proportion of mutant mtDNA molecules in a cell is termed heteroplasmy. The within-cell and between-cell distributions of heteroplasmy dictate the onset and severity of disease [58] and are influenced by complicated stochastic processes within the cell and during development.[24][59]

Mutations in mitochondrial tRNAs can be responsible for severe diseases like the MELAS and MERRF syndromes.[60]

Mutations in nuclear genes that encode proteins that mitochondria use can also contribute to mitochondrial diseases. These diseases do not follow mitochondrial inheritance patterns, but instead follow Mendelian inheritance patterns.[61]

Recently a mutation in mtDNA has been used to help diagnose prostate cancer in patients with negative prostate biopsy.[62][63]

Though the idea is controversial, some evidence suggests a link between aging and mitochondrial genome dysfunction.[64] In essence, mutations in mtDNA upset a careful balance of reactive oxygen species (ROS) production and enzymatic ROS scavenging (by enzymes like superoxide dismutase, catalase, glutathione peroxidase and others). However, some mutations that increase ROS production (e.g., by reducing antioxidant defenses) in worms increase, rather than decrease, their longevity.[51] Also, naked mole rats, rodents about the size of mice, live about eight times longer than mice despite having reduced, compared to mice, antioxidant defenses and increased oxidative damage to biomolecules.[65] Once, there was thought to be a positive feedback loop at work (a 'Vicious Cycle'); as mitochondrial DNA accumulates genetic damage caused by free radicals, the mitochondria lose function and leak free radicals into the cytosol. A decrease in mitochondrial function reduces overall metabolic efficiency.[66] However, this concept was conclusively disproved when it was demonstrated that mice, which were genetically altered to accumulate mtDNA mutations at accelerated rate do age prematurely, but their tissues do not produce more ROS as predicted by the 'Vicious Cycle' hypothesis.[67] Supporting a link between longevity and mitochondrial DNA, some studies have found correlations between biochemical properties of the mitochondrial DNA and the longevity of species.[68] Extensive research is being conducted to further investigate this link and methods to combat aging. Presently, gene therapy and nutraceutical supplementation are popular areas of ongoing research.[69][70] Bjelakovic et al. analyzed the results of 78 studies between 1977 and 2012, involving a total of 296,707 participants, and concluded that antioxidant supplements do not reduce all-cause mortality nor extend lifespan, while some of them, such as beta carotene, vitamin E, and higher doses of vitamin A, may actually increase mortality.[71]

Deletion breakpoints frequently occur within or near regions showing non-canonical (non-B) conformations, namely hairpins, cruciforms and cloverleaf-like elements.[72] Moreover, there is data supporting the involvement of helix-distorting intrinsically curved regions and long G-tetrads in eliciting instability events. In addition, higher breakpoint densities were consistently observed within GC-skewed regions and in the close vicinity of the degenerate sequence motif YMMYMNNMMHM.[73]

Unlike nuclear DNA, which is inherited from both parents and in which genes are rearranged in the process of recombination, there is usually no change in mtDNA from parent to offspring. Although mtDNA also recombines, it does so with copies of itself within the same mitochondrion. Because of this and because the mutation rate of animal mtDNA is higher than that of nuclear DNA,[74] mtDNA is a powerful tool for tracking ancestry through females (matrilineage) and has been used in this role to track the ancestry of many species back hundreds of generations.

The rapid mutation rate (in animals) makes mtDNA useful for assessing genetic relationships of individuals or groups within a species and also for identifying and quantifying the phylogeny (evolutionary relationships; see phylogenetics) among different species. To do this, biologists determine and then compare the mtDNA sequences from different individuals or species. Data from the comparisons is used to construct a network of relationships among the sequences, which provides an estimate of the relationships among the individuals or species from which the mtDNAs were taken. mtDNA can be used to estimate the relationship between both closely related and distantly related species. Due to the high mutation rate of mtDNA in animals, the 3rd positions of the codons change relatively rapidly, and thus provide information about the genetic distances among closely related individuals or species. On the other hand, the substitution rate of mt-proteins is very low, thus amino acid changes accumulate slowly (with corresponding slow changes at 1st and 2nd codon positions) and thus they provide information about the genetic distances of distantly related species. Statistical models that treat substitution rates among codon positions separately, can thus be used to simultaneously estimate phylogenies that contain both closely and distantly related species[60]

Mitochondrial DNA was admitted into evidence for the first time ever in 1996 during State of Tennessee v. Paul Ware.[75]

In the 1998 court case of Commonwealth of Pennsylvania v. Patricia Lynne Rorrer,[76] mitochondrial DNA was admitted into evidence in the State of Pennsylvania for the first time.[77][78] The case was featured in episode 55 of season 5 of the true crime drama series Forensic Files (season 5).[citation needed]

Mitochondrial DNA was first admitted into evidence in California in the successful prosecution of David Westerfield for the 2002 kidnapping and murder of 7-year-old Danielle van Dam in San Diego: it was used for both human and dog identification.[79] This was the first trial in the U.S. to admit canine DNA.[80]

Mitochondrial DNA was discovered in the 1960s by Margit M. K. Nass and Sylvan Nass by electron microscopy as DNase-sensitive threads inside mitochondria,[81] and by Ellen Haslbrunner, Hans Tuppy and Gottfried Schatz by biochemical assays on highly purified mitochondrial fractions.[82]

Several specialized databases have been founded to collect mitochondrial genome sequences and other information. Although most of them focus on sequence data, some of them include phylogenetic or functional information.

Several specialized databases exist that report polymorphisms and mutations in the human mitochondrial DNA, together with the assessment of their pathogenicity.

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Aedes aegypti Genome Assembled From Scratch | The Scientist … – The Scientist

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Aedes aegypti Genome Assembled From Scratch | The Scientist ...
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Aedes aegypti is the main vector of the Zika virus. Now, scientists at the Baylor College of Medicine in Houston, Texas, and their colleagues have successfully ...
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Scientists drastically reduce costs for building and sequencing ...The Tech Portal

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Cellecta, Inc. Launches Driver-Map Human Genome-Wide Gene Expression Profiling Kit for 19000 Human Genes – PR Newswire (press release)

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MOUNTAIN VIEW, Calif., March 29, 2017 /PRNewswire/ --Cellecta, Inc. today announced the launch of the Driver-Map Human Genome-Wide Gene Expression Profiling kit, a targeted RNA expression profiling assay designed to easily provide a molecular snapshot of all known 19,000 human protein-coding genes from complex samples starting from as little as 10 pg of total RNA.

The multiplex RT-PCR-based, followed by next-generation sequencing (NGS) method used in the Driver-Map Expression Profiling kit allows researchers access to the specially designed and experimentally validated gene-specific primer pairs to run samples in their own laboratories. This enables them to generate data that is more sensitive and easier to analyze when compared to conventional genome-wide expression profiling approaches such as RNA-Seq and microarray platforms.

"The simple, robust Driver-Map assay is ideal for use in characterization of complex biological samples," said Alex Chenchik, Ph.D., president and chief scientific officer of Cellecta. "Some novel applications for this gold-standard RT-PCR technology include biomarker discovery with whole blood without a globin or rRNA depletion step, detection of circulating tumor cells (CTC) in whole blood without previous CTC enrichment, high sensitivity profiling of tumor, stromal and infiltrating immune cell types from a complex tumor microenvironment, and expression profiling of patient-derived xenograft (PDX) models without interference from mouse background cells."

The Driver-Map Expression Profiling assay is highly reproducible, even starting with minimal amounts of RNA sample. Noteworthy features of this assay include:

The Driver-Map assay kit includes a complete set of gene-specific and PCR-NGS primers, buffers, spike-in ERCC and positive control RNAs as well as all other reagents required to profile 24 samples and prepare them for digital expression profiling using NGS on an Illumina sequencing platform. NGS reagents are not included in the Driver-Map assay kit.

The Driver-Map Human Genome-Wide Gene Expression Profiling kit (Catalog # DM-hgw) is available now. For more information, please visit http://www.driver-map.com

About Cellecta:

Cellecta, Inc., a trusted provider of genomic products and services, is an industry leader in RNAi and CRISPR technologies for the discovery and characterization of novel therapeutic targets, and genetic profiling for biomarker discovery. Numerous scientific papers have been published citing Cellecta's functional genomics portfolio offering gene knockout and knockdown screens, custom and genome-wide RNAi and CRISPR libraries, cell engineering, RNAi and CRISPR construct services, and mutation and expression profiling of disease samples.

Cellecta, Inc. is headquartered in Mountain View, California. Further information about the company and its functional genomic products and services may be found online at http://www.cellecta.com

Cellecta, Inc. Paul Diehl, 650-938-4050 152593@email4pr.com or Media: Ruth Mercado, 650-938-4080 152593@email4pr.com

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Cellecta, Inc. Launches Driver-Map Human Genome-Wide Gene Expression Profiling Kit for 19000 Human Genes - PR Newswire (press release)

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STEMCELL Technologies to Launch CloneR to Facilitate Genome Editing of Human Pluripotent Stem Cells – Business Wire (press release)

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VANCOUVER, British Columbia--(BUSINESS WIRE)--STEMCELL Technologies announces the development of CloneR, a novel medium formulation to aid researchers in their ability to successfully genome edit human pluripotent stem cells. This supplement represents a dramatic improvement over existing technologies.

Editing the pluripotent stem cell genome relies heavily on the survival of single cells to establish clonal cell lines. CloneR is a medium supplement designed for greatly enhancing the cloning efficiency and single-cell survival of pluripotent stem cells. Unlike current methods, CloneR will enable the robust generation of clonal cell lines without single-cell adaptation, thus minimizing the risk of acquiring genetic abnormalities. Such irregularities bear a close resemblance to those found in many human cancers, raising safety concerns for the use of these cells in regenerative medicine.

As the market-leader for the development of innovative products for pluripotent stem cell research, we are delighted to announce the imminent launch of CloneR, says Dr. Allen Eaves, CEO and President of STEMCELL Technologies. We are confident that this new invention will enable researchers by improving their capacity for disease modeling, drug screening and the development of cell and gene therapies for regenerative medicine.

CloneR will build upon STEMCELLs extensive portfolio of products to support pluripotent stem cell research, including mTeSR1, the most widely published feeder-free maintenance medium on the market. The CloneR supplement will be manufactured using STEMCELLs rigorous raw material screening and quality control processes certified under ISO 13485, Medical Devices Standards. This will ensure that the final product is of the highest quality, with maximal performance and minimal lot-to-lot variability.

To receive a notification of the product launch, sign up here: http://www.stemcell.com/CloneR

About STEMCELL Technologies

STEMCELL Technologies helps power leading-edge life science research globally. The company offers highly specialized cell culture media, cell separation products, instruments, accessory products and educational tools that support scientists performing stem cell, immunology, cancer, regenerative medicine and cellular therapy research.

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STEMCELL Technologies to Launch CloneR to Facilitate Genome Editing of Human Pluripotent Stem Cells - Business Wire (press release)

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