PP1: An Enzyme that Really Gets Around

        My bogarted zircon article was explored in the comments last week so let's radically switch gears and party on...to the human enzyme PP1, an enzyme I had not even heard of until yesterday.

        [To review from high school biology and chemistry: An enzyme is a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction (such as the generic enzyme shown above).] Enzymes are a complicated-looking group of structures (see above). The Wikipedia introduction to the specific enzyme PP1 is:

         Phosphoprotein phosphatase 1 (PP1) belongs to a certain class of phosphatases known as protein serine/ threonine phosphatases. This type of phosphatase includes metal-dependent protein phosphatases (PPMs) and aspartate-based phosphatases. PP1 has been found to be important in the:

1. control of glycogen metabolism
2. muscle contraction
3. cell progression
4. neuronal activities 
5. splicing of RNA
6. mitosis 
7. cell division
8. apoptosis
9. protein synthesis,
10. and regulation of membrane receptors and channels.

        In other words, this complex, New Year's Eve party-looking enzyme is part of so many processes in the human body that changing one part of PP1 for one disease (such as a cure for cancer) can radically affect the PP1 which is involved in other processes in the body (such as a cure for Alzheimer's disease):

         Brown University researchers yesterday published this press release about PP1 advances yesterday:

PP1 Brown University Research 3-3-14 

         From the photo and gif of enzymes above you'll note these are wildly complicated, interactive human structures. Below is the illustration that accompanies the Brown University article: (The main researcher is Dr. Rebecca Page, though the team includes several Brown scientists).

                                               Credit: Page lab / Brown University

             The enzyme PP1, the tan mass above, is everywhere in the body and has a role in nearly every biological process. That function is shaped by more than 200 regulatory proteins that bind to PP1, including one called PNUTS, the blue/purple and pink structures above. And, certainly learning more about PNUTS will cost significantly more than peanuts. And, note my great restraint in making no PNUTS or PP (1 or otherwise) jokes. I will leave that up to you.


              Unravelling how regulatory proteins bind to PP1 is a large part of understanding and possibly curing diseases like cancer and Alzheimer's. And, yes, it is a very long and winding road from this Brown University research to cures for these human diseases.

 

              This topic is quite new to me. I would appreciate your insights, thoughts, suggestions on this newly developing area of research.


Catalystically,

Word Woman (Scientific Steph)
Agent for Change
    

Barite or Baryte: A View from Cobachi, Sonora, Mexico

          Barite (spelled baryte everywhere besides the U.S) is a heavy, non-magnetic mineral with very high specific gravity of up to 4.5. It is one dense, soft rock. Barite (BaSO4) is useful in the manufacture of paper and rubber, as a tracking agent in medical tests in  the human body, and as the weighting material put into drilling fluid to keep the sides of petroleum drilling casings from collapsing and to prevent blowouts. It is readily used down boreholes as it does not interfere with any magnetic tests associated with drilling. The pinkish crystals pictured below are barite. The darker, smaller mineral is cerussite. The radiating form of barite crystals is sometimes referred to as Bologna Stone (for the town in Italy, not the lunch meat):

 

              The most useful variety for petroleum geologists occurs as thick sedimentary beds of pure barite with little to no silica impurities. Barite often occurs interbedded or interfingering with chert, so pure beds of thick (a meter or more) barite are highly prized:

            Pure barite needs little jigging (essentially shaking the rock in an aqueous solution), washing, heavy media separation, tabling, or flotation to be used down well bores. The barite is merely crushed to a uniform size and put in the drilling mud. 77 percent of barite is used for this purpose. And even though it is a heavy mineral, it is considered non-toxic due to its high insolubility. Deep oceanic BaSO4 deposits are useful in constraining the temperatures of oceanic crust in paleoenvironments.

            Barite in the form of desert roses is also coveted by rock hounds:

             My remarkable six-month, first adventure out of college included mapping a barite deposit in Cobachi, Sonora, Mexico. I lived with two British geologists, Rod and Kevin, and a geologist from North Carolina, Phyllis, in the little white house in the left of the photograph:

           The house had no windows, doors, or running water...but it was just $100 a month to rent. :-) Cobachi is so small (about 300-350 people) that it often does not show up on maps, even in our GPS age (though it does here):

                Mapping the barite deposit including making a grid through the desert (with the help of a local crew of ten men with machetes), scaring cows off the runway so the small plane could land, performing specific density tests, stratigraphy and paleontology including late Paleozoic fusulinids, and learning Spanish. We also hiked to the top of Sierra Cobachi with our friends from the community. They carried thick, heavy Coke bottles up and down the mountain to this stunning cave:

          

          This image of the people in Cobachi reminds me of how warm and kind they were to us very foreign-looking and sounding geologists. We would be treated to tomatoes on our burritos when they could afford none for their own families. They taught us to make tortillas and goat cheese and withstood us asking the same questions countless times as we learned Spanish. We took part in dances, loud wailing funerals, and evening talks about our day's adventures.

           Anaconda Barite just announced they will be upgrading the jigging plant in Cobachi early this year. So the heavy mineral barite (named from the Greek word heavy) will provide more years of economic opportunities to Cobachians. Here's hoping the heavy Coke-bottle carrying is no longer going on, though :-).

           Cobachi surely holds a heavy place in my heart...in a good way.

           Any early career adventures you'd like to share? Or your own favorite barite story?


Sedimentally yours,

Word Woman (Scientific Steph)

           

Ganymede Geology: Cup Bearer (of GanyMead?) to the gods

     Before we head to the largest moon of Jupiter, Ganymede, and leave earth's Iceland, this 1 minute and 13 second BBC clip shows the divergent (pulling apart) sea-floor spreading we discussed last Tuesday:

DIVERGENT SEA-FLOOR SPREADING---BBC CLIP

     The three margins described on earth in the concept of plate tectonics: (1) divergent (seen above), (2) convergent (mountain building or orogeny) and (3) transform or strike-slip often associated with earthquakes, may also play a role in the geologic formation of Ganymede.

      Ganymede, discovered by Galileo in January, 1610, has surface area that is greater than half of the surface area of the land mass on earth. The moon was named for Ganymede, the pretty boy who was taken by Zeus to be cup bearer to the gods (Had they been geologists it may well have been mead in those cups :-) ). Ganymede may be seen this month with binoculars:
 

      NASA released a geologic map of Ganymede this week, the first complete geologic map of Jupiter's seventh moon. The "cup bearer" stands out quite well with a blue, dark green, and purple body and green "crater head" on the right side of the first image:

     The geology of Ganymede is especially interesting to geologists because it appears there were times of tectonic movement on this icy moon. These grooves and ridges point to a similar origin to the earth's plate tectonic movement:

    
     In addition, periods of intense crater impacts are seen in the geologic history:

     One of the more interesting features on Ganymede are palimpsests, derived from the word meaning to write over older writing (similar to pentimento overpainting in art). [The word palimpsest is from the Greek for to scrape]:

   
   Similarly, older craters are "overwritten" by younger ones as the older crater margins are eroded through time:

         There were (and are) quiescent times on this frozen, icy moon (quiescently frozen :)) as well.

          There is also evidence for some cryovolcanism (eruption of  volatiles like ice and water, methane, and ammonia from volcanoes) on Ganymede.


      The link to the NASA article contains a 37 second animation so you can also see the "Dark Side of the Moon" (The Pink Floyd song turns 40 next month!):

GANYMEDE GEOLOGIC MAP NASA 2014 

       Looking forward to discussing Ganymede geology, nomenclature, great music, and some planetary geology jokes and puns. Do you have a favorite?

Palimpsestially,(thanks, Lego)

Word Woman (aka Scientific Steph)

Icelandic Plate Tectonics: No Scree-ching Halt: Give It an Inch and It'll Take A Year

     At long last, we are ready for the trip to Iceland now that the Viking Sunstone (optical Iceland spar or calcite) has been found:

Viking Sunstone--Soap-Bar Sized Optical Calcite 

 

     Optical calcite is rhombohedral and refracts light in a way that Norse explorers of 900-1200 A. D. were likely able to locate the sun even after sunset and on cloudy days. In those pre-GPS days, the calcite rhomb was accurate to within 1 degree:

     Optical calcite is found in abundance in the scree of Iceland, though it is now a protected resource since Icelandic tourism has recently blossomed. You may read more about calcite here, but I want to get us to Iceland, the only place on earth (currently) where a mid-oceanic ridge occurs on land:

Calcite Optics

     To repeat, Iceland is the ONLY place on our planet where one may actually witness oceanic crust being created on land. All other parts of the global mid-oceanic ridges are deep beneath the surface of the ocean. These folks are walking between two tectonic plates, the North American plate and the Eurasian plate, in Iceland:

     The theory of plate tectonics describes the large-scale motions of the lithosphere. A good, general overview of the theory may be found here:

 Plate Tectonics Overview

     The divergent boundaries between plates, known as mid-oceanic ridges, are the places where oceanic crust is created. There is a particularly good color, animated graphic in the link below (and shared here) which shows the new basalt (nicknamed MORB for Mid-Oceanic Ridge Basalt) or gabbro being created:

 Mid-Oceanic Ridges

     Oceanic crust is richer in iron and magnesium making it heavier than continental crust, which is richer in lighter silica. The very newest "skin of the earth"  is created at mid-oceanic ridges. As one moves away from the center of the ridge, the oceanic crust is progressively older on mirroring sides of the ridge. Almost all oceanic crust is 200 million years old or younger, fairly young in geologic terms. Then, at the margins with lighter continental crust, the oceanic crust dives beneath the lighter continental crust and is essentially recycled. The major plates and their current movements are shown below:

     In Iceland, one may witness this new "baby earth skin" creation directly. In the land of fire and ice, you can actually touch this brand new earth as the mid-oceanic Atlantic ridge runs right through Iceland:

       The Eurasian and North American plates are moving apart at the rate of about an inch a year. There is no scree-ching halt to the oceanic plate movement due to the convection currents in the earth. The convection is akin to heating up pudding on the stove. The rising hot pudding comes to the surface then plunges back down again as it cools at the surface. 

        To witness new earth being created is, for me, amazing. After seeing the volcanos, ice, spar, and other Icelandic delights, here's that optional side trip to the Lucky Leif bridge in southwestern Iceland. It's a moment to ponder the earth's dynamic nature while straddling the two tectonic plates. Our trip would have been unabridged without it. :-) Enjoy!

        I welcome your comments, insights, and any sparring. 

      Here's to MORB excitement with all of you gab-BRO and SIS enthusiasts,

      Word Woman (aka Scientific Steph) 

 

Ooids, Pisoids, and Kidney Stones: Concentrate Concretely!

     The trip to Iceland with a discussion of plate tectonics and mid-oceanic rifts has been postponed due to snow. This week's blog will migrate to some more tropical sedimentary features like these ooids (from the Greek for egg-like). I never wondered why Dr. Allen Curran of Smith College chose to study them in the Bahamas:

and pisoids (from the Greek word for pea-like).

      I tried to play the word ooid in a recent Scrabble game; the Official Scrabble Dictionary says it is not a word. Oo id is! Pisoid is also not acceptable~~and it's such a fun word.  .  .

 
     The main difference between the two sedimentary concretions is their size. Ooids are less than 2 millimeters in size and pisoids are 2 millimeters and greater in size. Ooids and pisoids are spheroidal, layered or coated grains, usually composed of calcium carbonate (CaCO3). Some pisoids and ooids contain iron (siderite for you Latin fans) or phosphates as well. They form as a series of concentric layers (see thin section below--crossed nicols or not--you be the judge!) around a nucleus of a crystal, shell fragment, or other small grain in shallow seas where the water is highly concentrated in calcium carbonate.

     And if you use a scanning electron microscope (SEM) to view ooids you will see not only the concretions that mark the growth of ooids, but also the pitting and cracking of the grains caused by various microbes:

     
      Three interesting things you should know about ooids and pisoids:

      (1) They have formed under different conditions called calcite seas (where low-magnesium calcite is the primary CaCO3 precipitate and which occurred during my favorite period, the Jurassic, and the Ordovician period) or aragonite seas (where aragonite and high magnesium calcite is the primary CaCO3 precipitate during most of the rest of geologic time, including now).  Thus, the calcite seas are found in the early Paleozoic time period when life was relatively new and during the middle of the Mesozoic (sometimes called the Age of Dinosaurs). Both of these time periods were time periods of rapid sea-floor spreading. (Ok, a wee bit of plate tectonics today).

       (2) Ooids and pisoids generally require microbial action in their formation.

       (3) They cannot form in areas where a great deal of river runoff occurs as the ooids and pisoids need greatly concentrated waters full of CaCO3 to form. This brings us to the kidney stone tie in:

       It had not occurred to me until today that the process of ooid and pisoid concretion is similar to kidney stone formation (It even says so in Wikiipedia :-)). Kidney stones tend to form in patients with concentrated urine (no extra fresh water running in). 


       Oh, a fourth item:

       (4) Ooids and pisoids ought to be Scrabble-acceptable words. 


       And to bring this concentrated topic concretely back in focus, this view of pisoids shows the highlighted concreted layers that have been colorized to show the structure of the layers.

        

        Looking forward to your crystallized, concentrated comments, diluted not at all by your new-found enthusiasm for the ooid and the pisoid :-)


        Ooidally (but not pisoidally this evening),

        Word Woman (Scientific Steph)

 

Petrographic Thin Sections, Deadlines, and Nature's Stained Glass

     Deciding on this week's Partial Ellipsis of the Sun topic was harder than usual. The genetically modified organisms (GMOs) we saw on the western side of Kaua'i, guarded by several people, trucks and barbed wire, was an option. I decided that topic needed more research than driving past miles of corn (in various developmental stages) where sugar cane and pineapples used to grow ten years ago and reading a few articles. I will also read Frankenstein's Cat: Cuddling up to Biotech's Brave New Beasts by Emily Anthes before addressing this topic. (Great suggestion, Jan).

     So...deadlines to deadliness :-), on this Tuesday I decided to write about petrographic thin sections because they are something I know and they are amazing beautiful.

      Here's a piece of olivine, a magnesium iron silicate (called peridot when of gem quality):

      

     Amazingly beautiful, right? How about cutting a nice, clean, thin slice of this and attaching it to a glass slide. And then, how about looking at this thin slice of rock (or thin section) under a petrographic microscope? Still not impressed?

      Well, how about under crossed Nicols filters (see below) under a petrographic microscope, in thin section?

 
      The  two polarizing filters on a petrographic microscope work similarly to polarizing sunglasses. Each filter allows light vibrating at one particular orientation to pass through. One of the two filters is fixed. The other can be moved in and out of the light path. That filter's  polarizing direction is perpendicular to the fixed filter. 

      If you put a thin section of a rock in between the two polarizing filters (referred to as looking at the section under "crossed Nicols") it creates the stunningly beautiful portraits we see above of olivine and below of  zircon: 

     The uncrossed filter photograph of zircon, a nesosilicate, is below:

      
       Here's one more crossed Nicols thin section of basalt, a fast-cooling, fine-grained volcanic rock from Thailand with two large spectacular olivine crystals in the center.

       And, for completeness, a sample of basalt:

           I will end this week's illustration-rich blog with a photo of one of my favorite thin sections of gabbro, coarser-grained (i.e. slower cooling), intrusive igneous rock found near mid-oceanic rift zones (under crossed Nicols):

         The brightly colored orthopyroxene crystals are surrounded by striped plagioclase feldspar. Slower cooling produces some amazing crystals.

          Stained glass: made by nature.

          Enjoy! Next stop, a field trip to Iceland to see the mid-Atlantic ocean ridge on land to see that basalt and gabbro up close!

Petrographically yours,

Word Woman (Scientific Steph)

      

Fossilized Jurassic Spiders, Other Chelicerata, and Impractical Jokes

     Two weeks ago the horseshoe crab, a marine arthropod, was the topic of Partial Ellipsis of the Sun. This week, another member of the Chelicerata, the spider,  will be the focus.

      Besides the smooth transition from one arthropod to another, I was entranced by this recent large spider discovery from fine volcanic ash beds in Daohugou, China (in Inner Mongolia):

      The giant Jurassic (201-145 million years ago) male spider's body length is 1.65 centimeters long, and its first leg length is 5.82 centimeters, the largest fossilized spider found to date (as of January 8, 2014).  It was significantly different, according to researchers from the University of Kansas, from the female of the species, Nephila jurassica, to warrant an entirely new genus and family. Lots of room for discussion there! :-)

      The researchers believe that this male spider is one of the first orbweaver spiders after a detailed look at foot claws, hairs and genital organs, using a Scanning Electron Microsope (SEM). 

       The full article featuring Paul Selden of the U of Kansas is linked here:

                                     GIANT JURASSIC SPIDER IN VOLCANIC ASH

      So, how to get to impractical jokes from this giant Jurassic spider? Via the Jumping Spider, of course:

     

    

     Jumping spiders make up 13 percent of the entire air-breathing chelicerates. While the marine horseshoe crabs rely on external fertilization, air-breathing spiders use internal (but usually indirect) fertilization. 

      The jumping spider is likely the closest to what I was like after a very impractical joke involving the Jurassic time period.

       I worked on an extensive project using aerial photography and Landsat imagery for one of our biggest clients, Amoco Oil Corporation. I wrote a very detailed 200-page, single-spaced, report on the geologic basin (in the days where we had secretaries to type everything from scratch, no computers of course, and no global replace feature).

       The President of our company, Chuck, called me in one day and showed me a letter, written on very fancy, thicker-than-regular-paper AMOCO Oil Company letterhead. It was addressed to him and said something like: "On page 143 of your report we have just received, I see that Jurassic is misspelled as Jurrassic. Jurassic does not have two r's in it. I cannot believe such unprofessional work is coming to us from your company."

       I was a bit concerned, as a newly-minted 23-year-old geologist.

       "What should we do about this, Steph?" asked my boss, looking very serious. "Termination?"  

       It was only then that I heard the crowd of geologists laughing outside Chuck's door. One of my fellow geologist's girlfriend had gotten the AMOCO stationery from her work there and helped with the elaborate impractical joke.

       Jumping Spider indeed!

        How about you? What are some of the best practical or impractical jokes ever played on you? Did any of them involve words, spiders, or other arachnids?

Jurassically Yours,

Word Woman (Scientific Steph)

      
      

      

      

Kaua'i, Okina, A'a

     Aloha from Hanalei Bay in Kaua'i.

     Due to technical difficulties, Partial Ellipsis of the Sun will be taking the week off.

     There were wonderful things about the okina (the unicameral glottal stop of a "backward apostrophe"), the original unicase or unicameral Hawaiian language (ron, jan---you were made for Hawaiian), and the a'a lava here... but my iPad is not cooperating and will only work in HTML mode. Also, I've been swimming with large sea turtles, fish and eels and need to get back there for the afternoon Anini swim ;-).

     However, there is an interesting NPR story link on the first land-walking fish, Tikaalik (which does incorporate that a'a). :

http://www.npr.org/blogs/thetwo-way/2014/01/14/262464764/first-land-walking-fish-looks-like-it-had-all-wheel-drive?utm_content=socialflow&utm_campaign=nprfacebook&utm_source=npr&utm_medium=facebook


    Until next week, I shall try to embed a few photographs here. We'll see how it goes.

                                                          

                                                           Hanalei Bay "downtown" 

                                                             

                                                              Hibiscus flower

                      

                                                           Anini (not Wanini) Beach

                                                   Hanalei Bay, dragon head to tail...

                                                                  Palm trees, of course

   View from our lanai. . .


  And, lastly, wild roosters everywhere on the island:

Mahalo,

Word Woman (Scientific Steph)

Blue-blooded Horseshoe Crabs, Hemocyanin, and Kenneth Marshall Gordon

     The blood of horseshoe crabs (as well as cuttlefish, squid, lobster, and a variety of other marine animals) contains hemocyanin, which is copper-based, rather than hemoglobin, which is iron-based. They are the blue-bloods of the animal kingdom and their blood has amazing anti-bacterial properties. The blood sloshes around in their bodies, rather than being carried in veins and arteries.

      
        And their blood has powerful acti-bacterial properties that release a mass of blood-clotting granules that instantaneously clot to seal out the bad bacteria, preventing further infection. It is so valuable that pharmaceutical companies are harvesting the horse shoe crabs, removing some of their blood,

     

and then returning them to the sea. The link to the full NPR article (including a video of the process) is here: 


http://www.npr.org/blogs/krulwich/2012/05/31/154095868/what-the-vampire-said-to-the-horseshoe-crab-your-blood-is-blue
 

     Paleontologist Richard Fortey describes the 450,000,000-year-old creatures as being akin to a Volkswagen Beetle:
 

"I saw a damaged horseshoe crab still trundling gamely onwards, even with a great hole punched right though its head. Looking over the beach more carefully, I noticed a lot of these war veterans; lumps out of the thorax, broken tail spikes — clearly, it must take a lot to finish these creatures off."

      Indeed, the amazing blue-blood properties of these relatives of trilobites are what have likely kept the horseshoe crab around for so many millions of years. They have lasted through the massive extinctions at the end of the Paleozoic, Mesozoic, and Cenozoic eras when massive extinctions wiped out large, sweeping amounts of their cousins.

       I don't have a wonderful segue to this next portion. We are all still a bit in shock here in Colorado about Ken Gordon's death last month.

       Today was the memorial service for Kenneth Marshall Gordon, one of Colorado's most respected members of the Colorado House for 8 years and then the Senate for another 8 years. 

     Ken was our neighbor when he first ran in Colorado in 1992 and my son and I put up yard signs for him. Ken introduced my then three-year-old son to then Governor Romer. Ken took no PAC money--ever. He was respected, well-liked, and he listened to everyone. He believed in the power of every voice. The Temple was packed with over 500 people from both sides of the political aisle, with friends, family, and our current Governor Hickenlooper. Ken was one of the really, really good guys.

     I learned at the service today that Ken was from a somewhat "blue-blood" Michigan family but that he preferred to make his own way, working long hours in a meat-packing plant, before he became a lawyer. He did not want help from his family. And, sadly, rather than asking his family for help to get medical care, he drove himself to the local hospital and died, of a massive heart attack, in the parking lot. Ken was 63 years old.

      This is the way I'll remember Ken--out there walking, like the horseshoe crabs. Ken walked across the state of Colorado in support of referenda for education.  If only he'd had the staying power of the horseshoe crab to be able to work more on his life's work, to love and be a loved a little more...and to walk a little further.

 
   

And the walking man walks (James Taylor),

Word Woman (aka Scientific Steph)