Welcome to ecological landscape design. This course is under construction.
Buster Bear was having a lazy day. But as the sun reached higher into the sky, his fur started to get hot and his stomach was starting to growl.
“All right” he said to himself. “Time to get a move on.”
Slowly and methodically, Buster Bear started to head downhill to the Laughing Brook. The movement felt good to his well-rested muscles and the water ahead looked inviting.
As he approached the Laughing Brook, Buster noticed that he wasn’t the only one that had thought about having fish as a mid-morning snack. Once he was close, he realized that it was Little Joe Otter. He also came to realize that the otter had been successful. Little Joe Otter had a nice big trout in his mouth!
Buster Bear crept up to the unsuspecting otter and snarled. As you can imagine, poor Little Joe Otter panicked at the sound, dropped the fish, and dove into the nearby water.
“Just as I had hoped!” Buster Bear thought as he pounced on the trout before it flip-flopped its way down the stream bank.
Little Joe Otter popped his head out of the water of the water and stared coldly at Buster Bear’s mouth.
Buster Bear stubbornly stood there and eventually said, “If you would like the fish back, just come get it.”
This did nothing to get Little Joe Otter to stop his unblinking gaze, so Buster Bear repeated his half-hearted offer. “Come get your fish if you want it.”
Furious, Little Joe Otter dove under the water and slipped downstream until he met Billy Mink. It didn’t take long to tell Billy about his encounter with Buster Bear. Billy Mink listened to Little Joe’s tale and nodded sympathetically. However, being a practical sort of animal, Billy Mink could only say, “There’s not much you can do about it, is there?”
Stewing in his anger, Little Joe Otter thought over his options until a plot for revenge took root in his mind. Without a word, Little Joe Otter took to the water again and made his way upstream until he spotted Buster Bear.
It was clear that one fish did not satisfy the lazy bear’s appetite, so Buster Bear was progressing from one deep pool to the next. Little Joe Otter picked up on Buster’s plan and moved quickly into action. He first went to the pool Buster Bear was going to next. Once there, he swam at a frantic pace in circles to scare away the fish in the pool and disturb the mud to make the water murky.
Buster Bear fished unsuccessfully there for a while and, discouraged, moved on to the next pool only to find the conditions to be similar. All day long, Little Joe Otter sabotaged the lazy bear’s fishing. Buster Bear’s stomach continued to growl and Little Joe Otter’s stomach joined in the chorus.
Biology connection: Food resources, like fish, are prized by many different types of animals. The battle for food is called competition. The population size of one type of animal is often limited not only by the amount of food in an area but also by whether other types of animals eat that food, too.
Re-write of “Thornton Burgess Bedtime Stories” chapter 1.
For Conversational Biology series – topic POLS
To learn a topic, it is nice to have a central framework upon which to build your “mind map”. When it comes to biology, my central framework is called “The Central Dogma of Biology”. To get us started learning about biology, I think it is appropriate to provide this concept for you to use when building your mind map of biology.
If we go back in time to 1956, we would find that Francis Crick was an important figure in biology, particularly molecular biology. Just a few years earlier, he had looked at Rosalind Franklin’s data and, along with James Watson, had described the structure of deoxyribonucleic acid (DNA). This was a big deal because biologist were beginning to come to grips with the idea that DNA is the molecule (a type of macromolecule under the umbrella of “nucleic acids”) that stores genetic information. Prior to this, protein was the top dog in the minds of most scientists. DNA was considered “boring” and proteins (another type of macromolecule) were considered to be more interesting, so it stood to reason that proteins would have been suspected to be the storage molecule for molecular biology.
Anyway, back to the central dogma of biology (aka the central dogma of molecular biology). This concept was proposed by Francis Crick. His framework can be overly simplified to “DNA is transcribed to RNA and RNA is translated to protein” or, even more simply, “DNA à RNA à protein”, where the arrows are steps that read information of one molecule to create the next molecule in the progression.
Let’s back up a step again. What’s RNA? It, like DNA, belongs to the nucleic acid macromolecule class. It looks a lot like DNA, but it is one oxygen molecule short, so RNA (ribonucleic acid) has a similar name to DNA (deoxyribonucleic acid). Notice that the difference in the names is “deoxy”, which is a scientific way of saying “lacks an oxygen”.
Francis Crick had one more arrow in his “DNA à RNA à protein” framework and that was a reverse arrow between DNA and RNA (DNA ß RNA). This left open the possibility that information in the form of RNA could be used to create a new molecule of DNA. This turns out to be true, so this process is called “reverse transcription” since the process of DNA à RNA is called transcription.
One final point, Crick wisely avoided drawing an arrow from protein back to RNA (RNA ß protein). When we get to the topic of the genetic code, we will see why “reverse translation” isn’t a thing.
Previous article: Preface
BRIC Academy- Next Week
- Take everything we need from downstairs lab to upstairs lab on Friday.
Upward Bound Unite Grant (High school kids)
- Possibly two high school students/per 1 undergrad
- Training on Thursday at 1-1:45 pm.
Dr. Graff’s Summer Projects
- Design curriculum for Discover Bio lab and Virology in the fall
- Blog Posts
- Literature Review with Derek
- Look at videos and determine if there is anything extra to add or comments.
- Videos helpful for fall courses and incoming high school students.
- Write up protocols listed on website
- Where is everything in the lab and how to do it.
- Graff will send out an email of techniques, everyone picks one or two protocols and they will be uploaded onto the website.
- Cloning into pGBKT7 isn’t working, so she is making a new batch to start working with.
- 3 dot bacteria is not giving great colonies.
- -Possible errors with TRIM13 into pGADT7.
- -Split cells
- Seed 24 well plate of HEK-293 cells, look up to see what expected TRIM5a localization pattern is and see.
- Working to get group comfortable in the lab.
- Problems cloning TRIM34 with Brittnee’s pGBKT7 plasmid and 3 dot bacteria, switched to Zach’s pGBKT7 plasmid and commercial bacteria.
- Recombination of pGBKT7 for MAGE A1 and A2B.
- Lack of colonies from transformation, going to use commercial bacteria instead of 3 dot.
- Working with POLS phages, making lysates, getting titers, getting streaks for lysogens.
- DNA extractions for OPAD and AbdulJake, low concentrations (Possibly do it again?) Do restriction digest.
- Make a lysogen assay checklist.
Meeting on Next Wednesday at 10 am.
For TRIM Protein Research (TRIM5a, TRIM8, TRIM13, & TRIM58)
- TRIM5a digests confirmed successful insertion into mAzurite and pEGFP-C1.
- Seeded a culture of HEK-293 cells to begin protocols for transfection to determine localization and co-localization of the TRIMs.
- PCR showed bands from Human cDNA and HEK-293cDNA templates for TRIM13 and TRIM8 for insertion into fluorescent plasmids.
- Recombination/Transformation of TRIM8 into pGADT7 did not yield colony formation.
Week 4 “To Do” List
- Gel Pures of TRIM8 and TRIM13 for fluorescence.
- Split HEK-293 cells
- Possible recombination/transformations of TRIM8 and TRIM13 into the fluorescent plasmids.
For TRIM Proteins Research (TRIM5a, TRIM8, TRIM13, & TRIM58)
- Successful transformation of TRIM5a into mAzurite.
- Successful recombination/transformation of TRIM13 into pGADT7.
- PCR produced a band for TRIM5a for insertion into fluorescent plasmids.
- No colony formation from a recombination/transformation of TRIM13 into pEGFP-C1 or mAzurite.
Week 4 “To Do” List
- Get a PCR Product of TRIM8 for insertion into fluorescent plasmids.
- Miniprep of TRIM13 from insertion into pGADT7.
- Transform TRIM5a into mAzurite and pEGFP-C1.
- Expasy’s ViralZone
- ViPR (Virus Pathogen Resource): mostly sequence database?
- Nature Publishing Topic (Virology)
- Science Collection (Virology)
- PLoS Pathogen “Pearls” about Viruses
- virology blog: About viruses and viral diseases (by Vincent Racaniello)
- microbe.tv: science podcasts including This Week in Virology (by VR and friends)
- World of Viruses
- Science Daily: Virology News
- Virology Course Playlist (by Vincent Racaniello)