Posts Tagged ‘bacteria’

You Know Your Blood Type. What About Your Gut Bug Type?

By AMIE NINH, courtesy of TIME

Veronika Burmeister via Getty Images


Consider this: of the trillions upon trillions of cells in the human body, only about 1 in 10 is actually human. The rest belong to microbes, which colonize every inch of you, from the inside of your mouth to the skin between your toes. It’s no wonder, then, that research is increasingly finding that the diversity of these microbes has important effects on health.

The vast majority of microbes — perhaps up to 100 trillion of them — live in our guts. So-called gut bugs help digest our food, assist our immune systems, maintain the health of the intestines, produce vitamins, aid metabolism and extract calories from food (which is why much research has associated gut bugs with obesity).

To better understand the way gut bugs work, a new study has aimed to categorize the lot of them. The study, led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, found that the bacteria in our guts falls into one of three distinct ecosystems, or "enterotypes."

"The three gut types can explain why the uptake of medicines and nutrients varies from person to person," Jeroen Raes, a bioinformatician at Vrije University in Brussels and coauthor of the new study, said in a statement. Which means that knowing a person’s enterotype could someday help doctors tailor drug treatments or diets to suit them better.

The New York Times reports:

Or, [Bork] speculated, doctors might be able to use enterotypes to find alternatives to antibiotics, which are becoming increasingly ineffective. Instead of trying to wipe out disease-causing bacteria that have disrupted the ecological balance of the gut, they could try to provide reinforcements for the good bacteria. "You’d try to restore the type you had before," he said.

For the new study, the research team evaluated stool samples from 22 European individuals, extracted the DNA and determined its composition by using DNA analysis and computers. They also compared the results to other published findings from Japanese and American subjects.

Scientists found that each of the three enterotypes was composed of a unique balance of microbe species. The team named each type after its dominant bacteria: Bacteroides, an enterotype that’s known to break down carbohydrates and is better at making vitamins B2, B5, C and H; Prevotella, which degrades mucus and produces more B1 and folic acid; and Ruminococcus, which…
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Good News for a Change? A Newly-Discovered Species of Bacteria May Be Breaking Down Oil in Deepwater Plumes in the Gulf

Good News for a Change? A Newly-Discovered Species of Bacteria May Be Breaking Down Oil in Deepwater Plumes in the Gulf

Courtesy of Washington’s Blog

DULARGE, LA - AUGUST 16: Daniel May runs his small shrimping skiff through a bayou on August 16, 2010 near DuLarge, Louisiana. Today marks the beginning of the shrimping season for white shrimp in Louisiana, the first since the Deepwater Horizon accident in the Gulf of Mexico. (Photo by Win McNamee/Getty Images)

A team of scientists published a paper today in the journal Science which provides some hopeful news.

Specifically, a team of scientists have discovered a new species of oil-eating microbes which thrive in the deepwater of the Gulf of Mexico:

The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown due to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous {gamma}-proteobacteria that are closely related to known petroleum-degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrate faster-than-expected hydrocarbon biodegradation rates at 5°C.

Even better, the scientists believe that this new species (pronounced "gamma-proteo-bacteria") may not suck up as much oxygen as previously-discovered species:

Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.

This discovery is especially important given that a leading expert on oil-eating microbes – Dr. David Valentine – failed to find any of the leading known oil-eating bacteria in the deepwater plumes.

As AP notes:

A newly discovered type of oil-eating microbe is suddenly flourishing in the Gulf of Mexico.


Their findings are based on more than 200 samples collected from 17 deepwater sites between May 25 and June 2. They found that the dominant microbe in the oil plume is a new species, closely related to members of Oceanospirillales.


[Lead author Dr. Terry Hazen, co-director of the Earth Sciences Division of the Lawrence Berkeley National Laboratories], suggested that the bacteria may have adapted over time due to periodic leaks and natural seeps of oil in the Gulf.

Scientists also had been concerned that oil-eating activity by microbes would consume large amounts of oxygen in the water, creating a "dead zone" dangerous to other life. But the new study found that oxygen saturation outside the oil plume was 67-percent while within the plume it was 59-percent.

Many well-known bacteria – such as Salmonella,
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Scientist Creates Life. That’s a Good Thing, Right?

Scientist Creates Life. That’s a Good Thing, Right?

By Alice Park, courtesy of TIME 

It’s the ultimate science experiment, really — taking a handful of chemicals, mixing them in just the right combination and presto — life!

And after nearly 15 years of such toiling in his labs in Rockville, Md., J. Craig Venter, co-mapper of the human genome, has done just that. Reporting in the journal Science, he describes a remarkable experiment in which he and the team at his eponymous institute have pieced together the entire genome of a bacterium and then inserted those genetic instructions into another bacterium. The cell booted up, and life — by nearly any definition — was created. 

"We’re basically getting new life out of the computer," Venter says. "We started with a genetic code in the computer, wrote the ‘software,’ put it into the cell and transformed it biologically into a new species. We’re still stunned by it as a concept."

With Venter’s breakthrough it’s now possible to splice and snap together genetic material to create a Legoland’s worth of new genetic combinations. Ideally, some of these would have robust industrial purposes, such as manufacturing bacteria that can churn out valuable vaccine components to shorten production times during an epidemic, or co-opting organisms such as algae to pump out new sources of biofuel-based energy. 

"Just imagine these cells where all we do is put in a new piece of chemical software and all the characteristics of the cell start changing to become what was dictated by the new software," says Venter. "These are biological transformers."

The paper is the final and most critical step toward realizing what began as scientific curiosity among the scientists at the J. Craig Venter Institute back in the early 1990s, when many of the same researchers first succeeded in sequencing the entire genome of a self-replicating organism, the bacterium Haemophilus influenzae. That led to the generation of the complete sequencing of the smallest known genome, at 582,000 base pairs, belonging to another bacterium, Mycoplasma genitalium. Such smallness was intriguing because it led Venter to the philosophical question that inspired the current research — what was the minimum genome required to create life in the lab? 

For the study just released, the answer turned out to be about 1 million, and the paper describes how he did it. DNA is made up of millions of…
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Bacteria, Boids and Market Instability

Here’s some weekend reading in advance. Consider throwing away economic models based on the misconception that people behave rationally and start anew with the premise that we are like mindless bacteria. – Ilene

Bacteria, Boids and Market Instability

bacterial behaviorCourtesy of Tim at  The Psy-Fi Blog

The Gaps Between People

Old-time economics saw investors as rational individuals, all behaving autonomously in a logical fashion, rather like Mr. Spock umbilically attached to Deep Thought. Today not even economists really believe that this is how people actually operate, but figuring out something better is a not insignificant task. Psychologists, however, have long known that what happens in the gaps between people is as important as what happens in the gaps between their ears – so is there something going on in the interactions between investors, which causes market instability?

One possible answer comes from the study of bacteria. Just as we might have suspected all along, stockmarket investor behaviour can be modelled by examining the way a bunch of brainless, single celled and barely animate creatures interested only in food and reproduction disport themselves on a Petri plate. Sometimes analogies are just too sweet.

Investing Earthquakes

The critical thing about any economic model is that it arrives at results that look like what we actually see in markets. Mostly the jargon fixated commentators who dominate the media are happy to talk in terms of business cycles when, in reality, the only cycles seen in most investing circles are the ones used by the boys and girls delivering lunchboxes. What we actually get, if we look at stockmarkets and stock prices, is something that looks like the readout we see from a seismograph when an earthquake occurs.

If we start by making a few assumptions about what investors actually do in real life – like, for instance, that they don’t behave rationally and that they tend to copy successful behaviour from people they’re closely connected to – we can rapidly create a model that produces outputs that look very different from those generated by models of people who behave independently and rationally. In fact the output of these models looks a lot like the readout we see from a seismograph when an earthquake occurs.

So it seems that the interactions between investors and how these interactions affect their willingness or otherwise to invest is the critical thing in these models.…
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Phil's Favorites

Bernanke's Balderdash


Bernanke’s Balderdash

Courtesy of David Stockman

The US and world economies are drifting inexorably into the next recession owing to the deflationary collapse of commodities, capital spending and world trade. These are the inevitable “morning after” consequence of the 20-year global credit binge which has now reached its apogee.

The apparent global boom during that period was actually a central bank driven excursion into the false economics of household borrowing to inflate consumption in the DM economies; and frenzied, uneconomic investing to inflate GDP in China and the EM.

The common denominator was falsification of financial prices. By destroying honest price discovery...

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Market News

News You Can Use From Phil's Stock World


Financial Markets and Economy

Bond Funds Have Been Borrowing to Boost Returns (Bloomberg)

For more than two decade, Bill Gross did the seemingly impossible, according to Bill Gross.

Drug that rose 5,000% hasn't come down in price (CNN)

Remember the drug used by cancer and AIDS patients that skyrocketed from $13.50 to $750 a pill? Well, the price has yet to come back to earth.

The company still has not cut the price below $750 even thoug...

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Zero Hedge

The Deep State: Source Of All Negativity

Courtesy of ZeroHedge. View original post here.

Submitted by Tyler Durden.

Submitted by Doug Casey via,

I’d like to address some aspects of the Greater Depression in this essay.

I’m here to tell you that the inevitable became reality in 2008. We’ve had an interlude over the last few years financed by trillions of new currency units.

However, the economic clock on the wall is reading the same time as it was in 2007, and the Black Horsemen of your worst financial nightmares are about to again crash through the doors and end the party. And this time, they won’t be riding children’s ponies, but armored Percherons.


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Kimble Charting Solutions

Free Premium Trail Offer & Free Webinar Viewing Available Now!

Courtesy of Chris Kimble.


Ryan Detrick and I produced a webinar this week, covering some new indicators we created, which we shared publicly for the first time.

We also shared two new Buy & Hold indicators we created, as well as two short-term trades, that look goo...

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Chart School

Bulls Keep Buying Into The Close

Courtesy of Declan.

Good stuff for bulls as resistance levels get ticked off on the advance. There breathing room for many indices and a chance for consolidation. Nit pickers could point to light volume, but it would be hard for buyers to be coming in here given the sequence of gains.

The Nasdaq 100 still remains tagged to resistance. Can it break tomorrow or will sellers make an appearance. All I know is yet another short trade of mine is stopped out. I should add, I haven't touched my investment account. I would be looking to buy if I had the funds available.

The S&P made a decisive push past its 50-day MA. Next resistance is up at 2,044. Tech...

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All About Trends

Mid-Day Update

Reminder: David is available to chat with Members, comments are found below each post.

Click here for the full report.

To learn more, sign up for David's free newsletter and receive the free report from All About Trends - "How To Outperform 90% Of Wall Street With Just $500 A Week." Tell David PSW sent you. - Ilene...

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Whitney Tilson On LL, EXACT, And Martin Shkreli


Whitney Tilson On LL, EXACT, And Martin Shkreli

Courtesy of Value Walk

1) The shares of one of my largest short positions (~3%), Exact Sciences, crashed by more than 46% yesterday. Below is the article I published this morning on SeekingAlpha, explaining why I think it’s still a great short and thus shorted more yesterday. Here’s a summary:

  • The U.S. Preventative Services Task Force’s Colorectal Cancer Screening Draft Recommendation issued yesterday is devastating for Exact Sciences’ only product, Cologuard.
  • I think this is the beginning of the end for the company.
  • My price target for the stock a year from now is $3, so I shorted more yes...

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Sector Detector: Searching for solid support in the face of global headwinds

Reminder: Sabrient is available to chat with Members, comments are found below each post.

Courtesy of Sabrient Systems and Gradient Analytics

Uncertainty about the health of the global economy led investors to flee U.S. equities during Q3, primarily driven by worries about China's growth prospects and the Federal Reserve’s decision to not raise rates. Sure, there are plenty of real and perceived headwinds, but on balance it seems that a recession here at home is not in the cards. And when you consider sentiment and the technical picture, it appears that a continuation of Friday’s bounce is in store. The question remains as to whether the seasonally strong Q4 will be able to propel the bulls through levels of resistance that have built up.

In this weekly update, I give my view o...

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Swing trading portfolio - week of October 5th, 2015

Reminder: OpTrader is available to chat with Members, comments are found below each post.


This post is for all our live virtual trade ideas and daily comments. Please click on "comments" below to follow our live discussion. All of our current  trades are listed in the spreadsheet below, with entry price (1/2 in and All in), and exit prices (1/3 out, 2/3 out, and All out).

We also indicate our stop, which is most of the time the "5 day moving average". All trades, unless indicated, are front-month ATM options. 

Please feel free to participate in the discussion and ask any questions you might have about this virtual portfolio, by clicking on the "comments" link right below.

To learn more about the swing trading virtual portfolio (strategy, performance, FAQ, etc.), please click here ...

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Baxter's Spinoff

Reminder: Pharmboy and Ilene are available to chat with Members, comments are found below each post.

Baxter Int. (BAX) is splitting off its BioSciences division into a new company called Baxalta. Shares of Baxalta will be given as a tax-free dividend, in the ratio of one to one, to BAX holders on record on June 17, 2015. That means, if you want to receive the Baxalta dividend, you need to buy the stock this week (on or before June 12).

The Baxalta Spinoff

By Ilene with Trevor of Lowenthal Capital Partners and Paul Price

In its recent filing with the SEC, Baxter provides:

“This information statement is being ...

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Mapping The Market

An update on oil proxies

Courtesy of Jean-Luc Saillard

Back in December, I wrote a post on my blog where I compared the performances of various ETFs related to the oil industry. I was looking for the best possible proxy to match the moves of oil prices if you didn't want to play with futures. At the time, I concluded that for medium term trades, USO and the leveraged ETFs UCO and SCO were the most promising. Longer term, broader ETFs like OIH and XLE might make better investment if oil prices do recover to more profitable prices since ETF linked to futures like USO, UCO and SCO do suffer from decay. It also seemed that DIG and DUG could be promising if OIH could recover as it should with the price of oil, but that they don't make a good proxy for the price of oil itself. 


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Watch the Phil Davis Special on Money Talk on BNN TV!

Kim Parlee interviews Phil on Money Talk. Be sure to watch the replays if you missed the show live on Wednesday night (it was recorded on Monday). As usual, Phil provides an excellent program packed with macro analysis, important lessons and trading ideas. ~ Ilene


The replay is now available on BNN's website. For the three part series, click on the links below. 

Part 1 is here (discussing the macro outlook for the markets) Part 2 is here. (discussing our main trading strategies) Part 3 is here. (reviewing our pick of th...

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Help One Of Our Own PSW Members

"Hello PSW Members –

This is a non-trading topic, but I wanted to post it during trading hours so as many eyes can see it as possible.  Feel free to contact me directly at with any questions.

Last fall there was some discussion on the PSW board regarding setting up a YouCaring donation page for a PSW member, Shadowfax. Since then, we have been looking into ways to help get him additional medical services and to pay down his medical debts.  After following those leads, we are ready to move ahead with the YouCaring site. (Link is posted below.)  Any help you can give will be greatly appreciated; not only to help aid in his medical bill debt, but to also show what a great community this group is.

Thank you for you time!

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About Phil:

Philip R. Davis is a founder Phil's Stock World, a stock and options trading site that teaches the art of options trading to newcomers and devises advanced strategies for expert traders...

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About Ilene:

Ilene is editor and affiliate program coordinator for PSW. She manages the site market shadows, archives, more. Contact Ilene to learn about our affiliate and content sharing programs.

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