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Basic Gene Structure

It’s tempting to think of genes as simply a series of nucleotides beginning with a START codon and ending with one of the three STOP codons. However, there are a number of additional regulatory elements that must be present in order for a gene to be transstopstartcribed and translated appropriately.

Transcription is regulated by signals for the DNA-dependent RNA Polymerase ( or simply ‘RNA Polymerase’) to attach and detatch from the DNA in the nucleus.

The attachment point is known as the promoter, and ‘Initiation’ of transcription is characterized by the recruitment of the RNA polymerase to the DNA upstream of the coding sequence. Polymerase engagement unwinds the DNA allowing for recruitment of ribonucleotides and the start of RNA synthesis (Elongation). There may be a number of false starts until a sufficiently long RNA is made to stabilize the enzyme, and even after elongation begins, it may stall and restart until the polymerase reaches a termination signal. There are a number of different kinds of termination signals, but they all occur downstream of the stop codon and serve to disengage the polymerase from the DNA (Termination) so that it is free to recycle back to the promoter.

There are some key differences between the ways that prokaryotes and eukaryotes perform these operations, but all the above elements occur in each system. The key to understanding this clearly is that transcription must occur before translation, and therefore, the transcribed region must have all the translated region within it. This sounds obvious, but can be helpful in order to envision the gene correctly as a physical object.BasicGeneStructure

 
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Posted by on September 26, 2018 in Uncategorized

 

Directional Cloning: a quick description

PrintImagine that you are a scientist interested in cloning gene A. You’ve just amplified the entire gene A including some flanking sequence by PCR and run the resulting amplicon onto a 2% gel with a 100 bp ladder. See the results in Figure 1.

figure1Happy with your result, you clone the DNA into a cloning vector, pCR2.1 where you can make up tons of DNA to work with. These cloning vectors are great for making lots of DNA, but they do not express any of the genes as proteins (i.e. the DNA is replicated, but not transcribed and translated.) Because you do want to express protein, you need to subclone your gene from the cloning vector into an expression vector. To complicate matters, the gene needs to go into the expression vector with the promoter upstream of the gene and the poly A signal downstream of the gene (See Figure 2). The promoter is the location that the RNA polymerase binds to transcribe the gene, the polyA site is what signals the polymerase to add a polyA tail to the mRNA.

Figure2In order to clone your gene into the expression vector, you decide to determine the direction that your gene has inserted into pCR2.1. To do this, you take advantage of the fact that there is a NotI site off-center in the insert and also one in the plasmid (See Figure 3). Gene A is just under 900bp long in total, the Not I site is located at position 800bp.Figure3

You cut the plasmid with NotI expecting either an ~800bp band or a ~100bp band depending upon the orientation of the insert. The results of your digest are seen in figure 4, leading you to believe that your insert is in the direction seen in figure 5.

Figure 4Figure 5In order to subclone from the cloning vector into the expression vector (figure 6), you cut the gene out of pCR2.1 with SpeI and NsiI and isolate the ~900 bp fragment. The same two enzymes can be used to open the expression vector and isolate the linear plasmid. The two fragments can then be combined in the presence of DNA ligase to complete the subcloning.

Figure6

 
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Posted by on September 17, 2018 in Uncategorized

 

Aliens: Covenant. Je ne sais pas

What was it that made Alien more gripping, more terrifying, less …known than Covenant?

Was it character development?

Perhaps something about the grit of the Nostromo?

Maybe working with a much more limited budget spurred creativity in response to necessity.

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from Benjamin F. Jones “AGE AND GREAT INVENTION” The Review of Economics and Statistics,
February 2010, 92(1): 1–14

Or maybe it’s just that we do our most creative works when we’re young?

 

Quite simply, at least in the sciences, if you haven’t contributed a great work to society by age 40, the likelihood of doing so is about to quickly drop. By 60, it’s vanishingly small (first figure).

There’s some adjustment allowed for those who have earned their terminal degree later in life, possibly accounting for many of the late achievers above (second figure).

 

Artists and writers reach their peaks at about the same time in their lives according to an article by Christopher Ingraham of the Washington Post.

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Benjamin F. Jones and
Bruce A. Weinberg
Age dynamics in scientific creativity PNAS 2011 108 (47) 18910-18914; published ahead of print November 7, 2011

Sir Ridley Scott fits the pattern perfectly. Born in 1937, he was 42 when he made the original Alien in 1979.  Three years later he released his other opus, Blade Runner, and although he continued to make greatly successful films throughout his long career, few have been as widely regarded as groundbreaking.

Screenwriter, Dan O’Bannon was 33 when he wrote the script for Alien; H.R. Giger was also 40 at the time he was producing the art design for the film. For completeness sake, Philip K Dick was 40 when he wrote Do Androids Dream of Electric Sheep, the novel that later became Blade Runner.

So, perhaps it should come as no surprise that Scott’s return (now at 79 years old) to the franchise with Prometheus in 2012 and Covenant in 2017 was unlikely to achieve the success of the original.

Prometheus and Covenant represent prequels meant to explore the origins of the aliens – and – why not explore the origins of all humanoid life? They also continue the cautionary tale of AI being the end of us which started in the original, took a break in the first sequel (apparently, James Cameron doesn’t share Scott’s feelings about technology) only to return with Fassbender’s David & Walter.

Prometheus begins with allusions to a prior race seeding the galaxy (?) with its DNA – a difficult pill to swallow as it suggests an origin of humanity unique from the other life on Earth. This may be fascinating as a science fiction premise, but completely absurd biologically. Nevertheless, the connection to Prometheus, the rogue Titan, makes sense thematically.

Similarly, Covenant begins with speculation about creation as the android, David, awakens to the world in a room that makes the monolith room from 2001 look cluttered with junk. “So, you made me. But who made you?” Deep thoughts, David. Already, David moved from infant to irritating college freshman just out of the first class of intro to philosophy. You can see Weyland already annoyed by his creation, “Play the Piano, David.”

David doesn’t appear scarred in the moment, but obviously, it’s had some effect. Many years later David’s still hung up on being creative and has filled his whole playhouse with sculptures, sketches all over the walls of his creations like a psychotic Leonardo DaVinci, and undoubtedly some angst-ridden poetry amongst his piles of scrolls.

But this is ultimately a film about these two androids – ‘artificial persons,’ as Bishop, the artificial person from Aliens, prefers.

David, the original, is all too human: creative, self-serving, and cruel. Walter, the modern model, is none of these. Walter tells us that David’s individualism scared the humans in charge and they made modifications to prevent these characteristics from emerging in newer models.

Screen Shot 2017-05-29 at 1.36.53 PM“You have symphonies inside you,” David tells Walter while teaching him to play a flute. He can play, but not compose. The whole scene reminds us of Scott’s other masterpiece, BladeRunner, as Rutger Hauer telling Harrison Ford of seeing “… things you people wouldn’t believe. Attack ships on fire off the shoulder of Orion. I watched C-beams glitter in the dark near the Tannhäuser Gate. All those moments will be lost in time, like tears in rain.”

Here we have the director’s real passion. The nature of life. The futility of mortality. We’re even given a recitation of Shelley’s Ozymandias. Only Gather Ye Rosebuds could be plainer in giving us insight into Sir Scott’s mind. After all, are we not looking out over a plain that could easily be the crumbled remains of the King of Kings’ empire? Could it be that Scott is recognizing his age and taking time to reflect on the meaning of it all? Or, is this just an eternal question that he has pondered all his life? The Ozymandias scene is one of the best in the film, despite the similarity to his other work.

“We are food for worms, lads.”

Another improvement is that Walter can heal himself immediately, while David either cannot, or heals slowly, like the humans he is designed to replicate. We’re shown this ability early and it’s obvious later, when it should be much subtler.

As a fan of the franchise, I was going to see this film no matter what, but I also had to come home and watch Alien and Aliens over the next two nights to remember why.

 
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Posted by on May 30, 2017 in Uncategorized

 

By any other Name …

In January 2017, the SciFlix film was John Carpenter’s ‘The Thing’. I considered using this film to discuss questions of exobiology, but decided that a more terrestrial topic was a propos. That evening we invited the regional director of NOAA, a scientist who did her PhD work in Antarctica, and a state legislator to talk about arctic science, climate science, and how policy is influenced (or not) by science.

Antarctica

The lands of Antarctica were first charted in 1820 by Captain Thaddeus

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Bellingshausen. Over the following decades, the continent was aggressively explored, including the first landing on the continent by Capt. John Davis in the Cecilia at Hughes Bay, Antarctic Peninsula. Sir James Clark Ross’ expedition aboard the ships Erebus and Terror occurred in the early 1840s.

In 1853, the first documented landing on the vast East Antarctica was at Victoria Land by the American sealer Mercator Cooper on 26 January 1853. (Antarctic Circle—Antarctic First. Antarctic-circle.org)

Everest

In a similar spirit of adventure, Radhanath Sikdar was the first to identify Mt. Everest as the world’s highest peak in 1852.

Prior to 1852, what mountain was the world’s highest?

Questions like these are designed to fool the hasty who will rack their brain for some other highest mountain. Perhaps Denali in Alaska; Aconcagua in the Andes; Matterhorn in Switzerland?

Of course, the answer is …

Everest.

Reality didn’t change, only our awareness and acceptance of it.

 

Similarly, the reality of the world’s climate doesn’t change simply because we don’t make ourselves aware of the best data describing it. The March for Science, no matter what you think of it, is a response to the science community’s feeling that policy maker no longer concern themselves with evidence when making decisions that affect us all.

The 2016 NOAA report card for Arctic contains the most reliable data for knowing what is really happening at the Earth’s poles. And Frankly, it’s startling.

Included are a few highlights from the Executive Summary:

The mean annual surface air temperature (SAT) anomaly (+2.0° C relative to the 1981-2010 mean value) for October 2015-September 2016 for land stations north of 60° N is the highest value in the record starting in 1900. These data show the artic temperature change as even more drastic than the global averages, which are also increasing over the same period. (Changes of ~1.5 degrees C globally vs 3.5 degrees in the arctic)

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Atmospheric Carbon

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University of Washington – Department of Atmospheric Sciences – Dennis L. Hartmann

 

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Data for the recent era post industrial revolution

Carbon Dioxide Information Analysis Center

 

These are not political postures, they are data collected around the world and presented in good faith to represent the best picture of reality that we can assemble. They don’t tell us why things are the way they are, but they do paint a reasonably clear picture.

A worst case scenario would place a planet at risk of a runaway greenhouse effect similar to what has happened on Venus, although this is unlikely to happen given the Earth’s position relative to the sun and its current brightness – something we can rely on for about another billion years.

Images of the Venus surface, temperature a balmy 462 degrees C collected by the Soviet Union’s Venera missions, which remain the only missions to ever land on Venus.

A different question that may be more important to us in the short term (only hundreds or thousands of years) is what will the changes in climate mean for farming and its support of a rather large global population. Of value in learning to take control of a changing climate is understanding what contributes to it, and presently the best models are that we are doing this through the release of fossil CO2 into the atmosphere.

Everest was the Earth’s highest peak, even prior to 1852. We’re pumping a lot of CO2  from the ground into the air and the climate is changing.

So, what do we do about it?

 
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Posted by on April 8, 2017 in Uncategorized

 

Some notes from the panel discussion at SciFlix: The Imitation Game

During the Panel Discussion for The Imitation Game SciFlix Event, panelist Dr. Hossein Saiedian presented some ideas on how to generate passwords that were not easy to guess, yet complicated enough to foil a brute force, dictionary attack.

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Image 1

 

He also listed some good practices and things to avoid. Because I don’t expect many attendees came armed with their note pads, I wanted to post some excerpts from that presentation.

By the way, can you identify the two photos in image 1 & 2  and explain their relevance and origins?

 

Pencil.png

Image 2

 

Key/password selection

  • ‘Key’ to good encryption: a good password (or key)
  • Passwords (pass phrases) are used for encryption and authentication
  • Key to maintaining security, privacy, and preventing identity theft
  • Objective: avoiding guessable passwords while selecting passwords that are strong and memorable

 

Common recommendations

    • 12 characters or longer
    • A combination of lowercase and uppercase letters, digits and special symbols
    • Formed from characters from an obscure phrase
    • Easily remembered by you but difficult for others to guess
    • Monitor for possible eavesdroppers during password entry

Things to avoid

  • Reusing passwords
  • Recording (writing down) passwords
  • Using the same password on two or more systems/contexts

Bad password practices facilitate two common password vulnerabilities: dictionary attacks and social engineering

Spicer.png
Posting passwords to Twitter accounts with 1.7M followers

Some short phrase ideas

  • Phrase association: Icw82Cmd!

    I can’t wait to see my dog!

  • Letter/number combination: Mocbd=0520

    My older child’s birthday = May 20

  • Letter/number sequence association especially when you are requested to change password at intervals: 89-93GhwB(41)

   Pres from 89-93:George Herbert Walker Bush (41st)

 

Some Free Encryption Tools

Personally, I (Jack), have used Dashlane as a password manager and generator since its inception. I’m not certain what my panelists would think of this, but I invite them to post their opinion here.

 

If you don’t know the images identified above, go here to learn about Image 1. For Image 2, you may need to think a while. In the meantime…

Shall we play a game?

 
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Posted by on April 8, 2017 in Uncategorized

 

SciFlix Movie of the Month: Soylent Green

SciFlix Movie of the Month: Soylent Green

Relax. It’s just people.

This month’s film will be the 1973 adaptation of Harry Harrison’s novel, Make Room! Make Room! Charleton Heston plays a 21st-century police detective working the massively overpopulated New York City. A murder sparks an investigation that cuts to the heart of the world’s population problem: How to feed it?

The Soylent Corporation just released its new product, a plankton-based biscuit made from a harvest from the world’s oceans, Soylent Green. Nutritious! Delicious! Friday, February 10th is Soylent Green Day.

Film Starts at 6:30pm

Regnier Auditorium

12610 Quivira Rd., Overland Park, KS 66213

Discussion to follow – What is the role of the government in providing food safety and biosecurity to a growing population? And what ethics govern a runaway population? Come hear Professors from KU and K-State discuss these questions and answer your questions.

 
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Posted by on February 5, 2017 in Education, tv, Uncategorized

 

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The Great American Melting Pot

After searching for the Schoolhouse Rock episode on base-12 mentioned in the previous post, I was reminded of this other episode that still resonates today.

Music & lyrics by Lynn Ahrens. Vocals by Lori Lieberman. ABC-TV, 1977

 
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Posted by on December 28, 2016 in Uncategorized