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Posted by Chris on June 14th, 2018  ⟩  0 comments

It’s summer time again! The temperature has hit “beautiful”, the trees and grass have turned back to their vibrant shades of green, and the birds have begun their annual serenades. Ah, sweet wonderful summer.

Except that we’re all stuck in the same old labs

staring at the same instruments

the same shelves full of bottles and tubes

the same old posters on the walls that we’ve been staring at all through the days of winter

It’s enough to make a scientist go mad! Mad, I say!

But before you let that happen, just go out for a short walk outside (or a long walk, depending on how close you were to mania) and take a deep breath of the sweet, pollen heavy summer air (unless you’re one of the 20 million adults who are hyper-sensitive to the pollen) and relax. We’ve got some fun, low stress, summer-friendly experiments for you to keep your experimental interests fresh without all the stress of those research deadlines.


DIY Earthworm Jar

Have you ever wondered what earthworms actually do in the ground? Worms are some of our best soil “scientists”. They help aerate the soil, break down organic matter and help to turn the soil over in order to mix the layers to provide better plant nutrition. According to the University of Illinois, 500,000 worms on an acre of land will make 50 tons of fertilizer casings and can create a drainage system equal to 2000 feet of 6 inch pipe! This little experiment can help illustrate exactly how worms mix the soil layers.

Materials

Earthworm

  • 2-6 earthworms
  • From the yard: After a rainstorm many will come up to the surface to breathe. Also if there is a part of your garden with good rich soil there are likely worms there that should not be too hard to dig up.
  • From the store: Most bait shops sell both night crawlers and standard earthworms. Some gardening centers sell Red Wrigglers for composting.
  • Two liter soda bottle or similarly sized jar or container (or an ant farm type container might also be good!)
  • Rich Soil – either from the garden or a topsoil mix
  • Sand (not chemically treated) – lighter will show up better
  • Coffee Grounds, Veggie/Fruit Scraps – although stay away from more acidic foods like onions, tomatoes and citrus.

Optional:

  • Cheesecloth and Rubber band or lid with holes for ventilation
  • Thick paper or cloth to cover the sides of the habitat and keep out light
  • Notebook for observations/ drawings
  • Measuring tape/kitchen scale
  • Wire mesh screen/colander
  • Soil Thermometer/Soil pH meter

Prepare Container

  1. Wash out container making sure it’s completely rinsed out with no soap residue.If you’re using an empty two liter cut the top of the bottle off where it starts to slope.
  2. If your container has a lid, poke holes in the top to let in air.
  3. Fill the jar with a layer of sand (½ inch) and soil (2 inches). Make sure you wet the soil and sand so that they are damp but not soaking.Continue layering sand and soil until the jar is full, your last layer should be a soil layer. Make sure to leave an open space of at least 2 inches at the top.

Add worms

  1. Before you put the worms in, count and weigh the worms and measure their average length so you can keep track of their growth.
  2. Put coffee grounds and food scraps on top of the soil.
  3. Add a lid with holes on or cover the top with cheese cloth and secure with a rubber band in order to help keep bugs out.

Keep the worms happy

  1. Worms don’t like light, so either wrap a piece of dark paper around the jar or store the project in a cool, dark place.
  2. Check on the worms every few days to make sure that the soil is still moist.
  3. Give them new food about once a week.
  4. Pretty soon you should be able to see the layers of sand and soil start to mix together and tunnels from the worms traveling through the soil.

Optional Science (for the overachievers)

  • Compare the ambient temperature to the temperature of the soil.
  • Compare the soil pH across the duration of the experiment to see how it has changed.
  • Measure and track the soil migration based on worm number or initial size.

After a few weeks of observing and keeping the worms it’s time to let them go back out into the wild. Use a wire mesh screen to help separate the worms from the dirt.Weigh and measure the worms and compare this to your original measurements and bid them a fond adieu!

References
http://extension.illinois.edu/worms/live/
http://wemadethat.blogspot.com/2013/04/diy-earthworm-habitat.html?m=1
http://www.bbc.co.uk/gardening/gardening_with_children/homegrownprojects_watchworms.shtml#tips_and_advice


Backyard Birding

Birds are the trumpeters of spring and work as one of our greatest natural pest control. To a scientist, they can also be a wonderful subject of exploring animal behavior and genetics. Backyard birding is the idea of not only observing the birds in your area, but also putting things in place to allow them to thrive.

The best resource to explore is the National Audubon Society’s website for tips. There are resources to help you identify different birds through sight or through their calls. They also have guides on different types of feeders and housing you can make. Different seed and nest boxes can attract many different types of birds. You can also buy some great bird observing window feeders, like this one (not sponsored), which offers a 2-way mirror system so that you can watch birds up close at your window without scaring them off. One issue with this bird feeder, however, is that due to the size of a window, all the uncovered area still exposes you and scares the birds away. A way around that is to use Glad Press’n’Seal (or similar) around the other open areas of the window.

Spring is usually the best time to start your observations, with early mornings and late evenings being a great time to watch birds in your yard. But you can also help create a perfect environment for a range of seasonal birds to thrive in your area all year long.


Home Sweet Biome (Biomes in a Bag)

Have you ever wondered exactly how your environment affected the rate of plant growth in your area? Science Buddies has a great experiment procedure to figure that out exactly! This is a quick and simple science experiment that is enlightening and needs very little upkeep.

Materials

  • 2-liter plastic bottles (6), clean and empty
  • Bag of river rock
  • Bag of potting soil
  • Packets of the same type of seeds; vegetables such as beans or peas work well, but flower and grass seeds work, too (need about 20 seeds, total)
  • Resealable food storage bags, 1 gallon-size (6)

Procedure

  1. To model two terrestrial biomes, the temperate forest and the tropical forest, find a place that is sunny (like a sunny windowsill) and another spot that is shady and a bit warmer than the first location.
  2. Cut each of the plastic bottles in half.
  3. Place a handful of river rocks in each plastic half. The rock layer should be 1 inch deep.
  4. Put a layer of potting soil on top of the rocks in all six bottles. There should be twice as much soil as there are river rocks, so approximately 2 inches.
  5. Now, drag your finger in the middle of the soil and make a trench as deep as your fingernail.
  6. Place 3-4 seeds in the trench and then gently replace the soil over the seeds. Spread the seeds out—don't put them all in one pile together. Repeat steps 5-6 for the other five containers.
  7. Fill the measuring cup with water and carefully water one container at a time until you see the water collect at the bottom of the rocks. The amount of water you'll use for each container should be between ¼ cup and ½ cup. The soil should not be soaking wet or soupy, just moist. Make sure that the seeds remain covered after you have watered. Repeat this step for all of the containers.
  8. Now place each container in a resealable plastic bag. Label each bag with the amount of water in that container and the location where it will be placed. Three containers should be in one location and the other three should be at the other location. Carefully and completely seal each plastic bag.

That’s it! You won't have to water the seeds again, because the water in the bag recycles itself! The roots of the plant absorb the water, which then travels up the stem to all the parts of the plant. Some of the water in the leaves evaporates, as does some of the water in the soil. The evaporated water condenses on the inside of the bag and forms water drops. Some of the water drops fall back into the container like rain. Once the water falls back into the plant container, the water cycle starts again.

Observe the biomes twice daily for the next week. Once in the morning and then again in the evening. Try to observe the biomes at the same times each day. Have any seedlings come up? How long did it take for seedlings to come up? Use a ruler to measure how tall the seedlings are. Has water condensed on the inside of the bag? How moist does the soil look?

Reference
Science Buddies Staff. (2017, July 28). Home Sweet Biome: How Do Plants Grow in Different Environments? Retrieved from https://www.sciencebuddies.org/science-fair-projects/project-ideas/EnvSci_p046/environmental-science/biomes


Pollinator Garden

Pollinators are an important part of the ecosystem and a lot of our heavy lifters such as the honeybee and monarch are having a hard time. Help them along this spring by creating a pollinator garden!

One of the biggest ways to really attract pollinators to your hard is to plant milkweed. There is a great video series on Youtube about how to find, germinate and plant milkweed. The first video of the series also lists a few places where you can get free milkweed seeds. Just be careful to manage milkweed because it can get a little out of hand and overrun other bushes and trees. Another great resource for tips on growing a pollinator garden can be found on the USDA’s Forest Service page.

May/June is a great time to get started! Get those seeds and start germinating. While you wait on the little sprouts, carve off some area to dedicate to the garden.


Regrow Celery (Great to do with kids!)

Rather than immediately scrapping or composting that old celery stock, why not save it for regrowth? Children will not only observe plant growth over time, but will also learn an important lesson in sustainability and science.

The best website with information on how to regrow celery from stalk is found here. This page not only shows the initial kitchen growing techniques, but also goes into detail about when to transplant it outside.

Transplanting time will depend on your location. Celery does best in cool weather when nighttime temperatures are around 55°F (13°C) and average daytime temperatures stay between 60-70°F (16-21°C). For more information on optimal, outdoor growing conditions, check out the Aggie Horticulture website.


Water Cycle in a Bag (Great to do with kids!)

Teach your kids about the water cycle in a very fun, hands-on way with this Water Cycle in a Bag activity found on playdoughtoplato’s website. According to the page, it’s quick to prepare and engages kids for a few days.

The instructions on how to set this up is featured on the website. But the basic idea is this: you get a zip up sandwich bag, draw a cloud and sun up top. Fill the bag with just a little water and blue food coloring. Seal it up and tape it to the window. Check it with the kids each day to watch the levels evaporate, condense and trickle down.

This is a great activity when you’re going to have lots of sun. And with school ending soon, late spring and early summer will be a fun time for the kids to do this activity.

And finally...


M&M Hunter Challenge

Camouflage is one of nature’s best defenses for prey species. For this delightful and delicious little “lab” experiment, you might need to get some help from your lab mates. Begin by mixing certain colored M&M’s in a Skittle-based habitat to see how camouflage can help to keep M&M’s “alive” against the hungry lab predators in a set amount of time! You might have to promise to let your lab mates keep any M&M’s they “capture”, but not before you count how well they did. Make it a party and see which researcher is the ultimate M&M predator.

Materials

  • Plastic baggies (6)
  • M&M's, at least 10 of each color
  • Use plain M&M's, which should have six colors: Yellow, blue, green, brown, red, and orange.
  • To make sure you have at least 10 candies of each color, you will want to get at least two 1.69-oz. packages.
  • Skittles®, at least 60 of each color
  • Use plain Skittles, which should have five colors: orange, yellow, green, red, and purple.
  • To make sure you have at least 60 candies of each color, you will want to get at least one 16-oz. package.
  • Metal pie tin or sturdy paper plate
  • Stopwatch or timer
  • 2-4 volunteer predators who like to eat M&M's

Procedure

  • First you will need to prepare a mixed group of "prey." Do this by counting and placing 10 M&M's of each color into a plastic bag.
    • This means you should have one plastic bag with 10 yellow, 10 blue, 10 green, 10 brown, 10 red, and 10 orange M&M's candies in it.
  • Prepare different "habitats" using Skittles candies. Do this by counting and placing 60 Skittles of a single color in a bag. Repeat for each color, in the end you will have 5 bags — each with just one color of Skittles.
    • This means you should have one plastic bag with 60 orange Skittles, one bag with 60 yellow Skittles, one with 60 green Skittles, one with 60 red Skittles, and one with 60 purple Skittles.
  • Gather together your lab of 2-4 volunteer "predators." This can be anybody who likes to eat M&M's.
  • Explain the rules of the game to your predators as follows:
    • The volunteers should pretend to be M&M's birds. They should make a "beak" using their pointer finger and thumb for collecting M&M's candies.
    • You will set a timer (or watch a stopwatch) for 20 seconds. During those 20 seconds, the volunteers will use their beak to quickly pick up M&M's and quickly put them in their other hand.
      • To encourage the volunteers to be fast, tell them that when they are done with the experiment, they can eat the same number of candies as they picked up. (But they should not eat any candies until you are all done testing.)
    • The volunteers should avoid picking up any Skittles candies because Skittles make the M&M's birds sick. The Skittles represent the habitat that the M&M's candies live in.
  • After explaining the rules, pour one prepared bag of Skittles into a metal pie tin or sturdy plate. Mix in the prepared bag of M&M's. Put the pie tin in the middle of your group of M&M's birds. Make sure everyone can reach the pie tin.
  • Set your timer for 20 seconds.
  • Say, Go! And start the timer. When the timer beeps, everyone should stop picking up M&M's.
  • Count the number of each M&M's color that each person collected If any volunteer collected any Skittles, put the number of Skittles they collected in the bottom row of their column, the one labeled "Skittles." Also, re-emphasize that Skittles make the M&M's birds sick and should be avoided.
  • Enjoy your treats!
Posted by unknown on June 7th, 2018  ⟩  0 comments

      Leaving your things lying around is something parents have lectured about forever, but the rule of tidiness is even more important in a laboratory setting. Biochemical products are a bit more volatile than dirty laundry, so it's important to have all of your chemicals accounted for. This article reviews some of the frequently used substances which may be left unattended and concern technicians – are they still functional, or are they damaged beyond repair? It's necessary to understand which substances are sensitive to neglect, but we hope to assuage some unwarranted panic over robust materials.

      Left products on the lab bench - troubleshooting

      What we'll talk about:

      1. Antibodies
      2. Enzymes
      3. DNA
      4. PCR-amplified samples
      5. BSA
      6. ELISA
      7. Bacterial cultures
      8. Slides
      9. Hygroscopic materials
      10. Frozen substances


      Before proceeding, I want to say that this article is intended to be more informative about products that have been accidentally left out. It is not guaranteed that all reagents will behave the same way and other factors can influence performance. Therefore, do not be careless with products in your lab and always store them according to manufacturer or supplier instruction



      1.   Antibodies:

      • The product: Antibodies have variable shelf-life depending on type, but they’re generally kept with glycerol or sucrose to prevent aggregation and promote functional longevity. While shelf-life can differ, many kept at ideal conditions: temperature, pH, desiccation and lighting specifications recommended by the manufacturer can remain functional for more than a year.
      • The situation: You’ve returned to the lab after a weekend and realize you left an entire box of antibodies on the counter, sitting at room temperature. The instructions inform you that storage environment should be 4°C.
      • The diagnosis: There's still hope. Don't throw them out before you test them. Suppliers have done experiments on the storage and shipment of antibodies at various temperatures, and leaving them at ambient temperature even for a week did not decrease their effectiveness. Some companies even subject their antibodies to 37°C and higher temperatures for performance quality testing.
      • The precautions: Purified antibodies have characteristic stability, but it has never hurt anyone to be cautious and run validation tests to be sure.


      2.   Enzymes:

      • The product: Storing enzymes usually involves -20°C temperatures and the addition of glycerol to prevent protein denaturation. Their use in experiments is sometimes cumbersome, because it’s recommended they be kept frozen in the process.
      • The situation: After conducting a reaction, another technician points out your restriction enzyme, no longer in the cooler you used to transport it from the fridge.
      • The diagnosis: Enzymes usually won’t be destroyed by a couple of hours outside a freezer, and they’ll survive a power outage too. A test on a group of 23 unmodified restriction enzymes stored and shipped at ambient temperatures revealed they can remain active without being refrigerated for one to three weeks. We won’t recommend leaving them on the bench for nearly a month, though.
      • The precautions: Enzyme integrity is damaged by temperature fluctuations, so thawing and refreezing products too many times will cause denaturation. Even leaving enzymes in the door of a freezer can be risky due to unmediated temperatures. Avoid protease contamination when enzymes are in open environments.



      3.   DNA:

      • The product: DNA is incredibly complexand has to be treated with care to prevent contamination and denaturation. This is commonly done by keeping it isolated in temperatures of -20°C or lower.
      • The situation: You’ve been using DNA samples since 7:00am. At 5:00pm, you’re struck with the thought that with every minute you’ve had the DNA sample out, the strands have slowly been breaking apart, invalidating the ten hours of work you just put in.
      • The diagnosis: DNA stored in a dry room temperature environment will degrade, but the speed of this process is not as rapid as you might think. Long-term storage can be conducted anywhere between -80°C and 4°C, but room temperature is safe for short-term as long as contamination is not a concern with the addition of EDTA and Tris. Stability is maintained longer by buffers.
      • The precautions: The freezing/thawing process, if repeated often, can damage DNA just as badly as leaving it in unmediated temperatures. Regardless of storage temperature, samples should be tested for concentration and evaporation. 


      4.   PCR:

      • The product: Related to DNA, polymerase chain reaction (PCR) techniques involve mixing DNA with polymerases, primers and other essential compounds to amplify DNA strands. Scientists commonly transfer PCR samples directly to 4°C refrigerators after the thermal cycling process.
      • The situation: You start your PCR and walk away. The last cycle finishes two minutes after you leave for your one-hour lunch break. When you come back to the machine, you see that it’s been waiting for extraction at room temperature.
      • The diagnosis: Inside of a PCR tube, DNA samples can retain their stability. Successful amplification will allow them to resist ambient environments for weeks, if not longer, without noticeable degradation. PCR itself is used to study ancient DNA samples left exposed to the elements for centuries; if that sample can still generate results, so can the one you left on the counter. It's important to note that many thermal cyclers will keep the tubes cool after the cycling process. Even if the machine were somehow unplugged or turned off, your samples should be OK.
      • The precautions: PCR machines must be given the same attention you intend for your samples. If left cooling overnight, the machine's overall lifetime could be impacted. A less reliable device will produce less reliable amplification. 

      5.   BSA:

      • The product: Bovine serum albumin (BSA) is a blocking agent commonly used in experiments detecting the presence and relationships of protein. It is rendered from bovine blood serum, reducing residual binding capacity and nonspecific interactions.
      • The situation: While conducting an ELISA experiment, you had a good number of tubes out. Your dried BSA was in a particularly small tube, and sometime in the process of things it was misplaced among the others you’d finished using. When you clean the bench at the day’s end, you find the unfinished BSA still among the empty bottles.
      • The diagnosis: BSA, especially when dried and used for blocking, will be fine for days without refrigeration. Powders need to be kept dry more than cold. Powder and stock solutions should also be sturdy for a few days if they’re misplaced over the weekend.
      • The precautions: Contamination from fluids is more of a problem than heat with this chemical, so it will be more of a concern if the left out container was also open.


      6.   ELISA:

      • The product: An enzyme-linked immunosorbent assay – ELISA – tests for substances in biochemical fluids via an assay of antibodies and color. Antigens are detected in samples by specifically-targeting antibodies, and serum (like BSA) is commonly screened through ELISA kits.
      • The situation: Testing for the viral antigen in a sample you’ve created, you put together an ELISA kit and go through the complex-forming process. The lab manager calls you away to perform some “housekeeping” tasks. Two days later, you remember your ELISA test.
      • The diagnosis: Whether left on the bench or put in the wrong freezer, ELISA tests are fairly hard to damage in short periods of time. They can sit at ambient temperature without the results degrading, and a kit that has been unintentionally frozen will thaw out with minimal damage.
      • The precautions: Extended periods of time can decrease activity in the test, but results should still be reliable. Avoiding contamination as an overall standard procedure is also important when a kit, used or otherwise, is left unattended.


      7.   Bacterial cultures:

      • The product: Bacteria are finicky; too much heat or cold will degrade their value as scientific subjects, because temperature fluctuations damage cells. The necessary storage conditions are highly dependent on strain, but refrigeration is generally suggested. Frequently used samples are ideally stored at 4°C while those kept for longer periods will be frozen or freeze-dried.
      • The situation: Your bacterial cultures are just starting to show promise in the last minutes of a Friday lab session. You consider leaving them for the weekend rather than making a fresh grouping Monday. There are risks, right? Mutations, contaminations, etc. Your intern says he once left a sample out for a week and came back to find half a dozen strains in one petri dish (though considering the state of his work bench, you aren’t surprised).
      • The diagnosis: Though there are sometimes recommendations to harvest culture DNA or plasmid quite quickly (within 12-24 hours), bacterial strains have been stored for months and years in laboratory settings without adverse effects on their utility. Random mutations will take more than a weekend to transpire. The real concern is contamination or competitive growth in the media if it’s fully exposed to the environment.
      • The precautions: Plasmid yields are more promising in fresher samples. Some strains are more sensitive and conducive to recombination than others, so unwanted developments are more likely to occur with a long, unmediated incubation period. It also isn’t out of the question that a large quantity of pelleted strains, left out for a weekend, will cause quite a smell.


      8.   Slides:

      • The product: Microscopic slides are inseparable from techniques in immunology, cellular cultures and organism selection. Microscopy is associated with slide production for viewing single-celled organisms and other small (but microscopically visible) results of experimentation. Slides themselves are fragile, and sometimes so are the samples they contain.
      • The situation: You’re a technician assigned to the care of several dozen slides from a friend’s month-long cellular immunology project. You leave the samples on a shelf for the week your colleague is on vacation; needless to say their return initiates a rather awkward conversation involving laboratory protocol and sample storage. Was their research ruined?
      • The diagnosis: Slides with properly fixated, embedded and sealed samples can be kept at room temperature as long as the ambient environment is standardly clean and free of agents like persistent mold.
      • The precautions: If the container was left open and exposed to light, this could be more of a problem. Artificial and natural light at high concentrations can harm slide integrity. Compare controls to see if anything has deteriorated.


      9.   Hygroscopic materials:

      • The product: Hygroscopic compounds are defined as such for their water-attracting characteristics. They are able to absorb and hold water molecules from the air. It's important to keep them in desiccated states or in the presence of desiccants.
      • The situation: Your dimethyl sulfoxide (DMSO) has been out in the lab for a good couple of weeks before you notice it sitting on the table. It’s conveniently placed about two feet from the laboratory sink.
      • The diagnosis: Hygroscopic compounds, if encountering high amounts of moisture in an improperly sealed container, are going to be damaged. Even in a properly desiccated environment, leaving these substances for too long without changing desiccants will expose them to excessive moisture. Being attentive to indicators is important, and if they signal compromised material, your product probably isn’t usable anymore.
      • The precautions: Desiccated materials can very sensitive. They require special protection from air, not because of temperature, but because of moisture, and this makes it harder to distinguish good from bad until they're quality-tested.


      10.   Frozen substances:

      • The product: Biochemical samples are almost universally kept cool. Frozen substances are further defended from heat-provoked transformation; they’re thawed before use and returned to consistently low temperatures. This category ranges from bacterial strains to pure compounds.
      • The situation: You have a stock of bacterial plasmids frozen for communal use in the lab. In the course of a day, you’ve removed the stock from the freezer, placed it on the bench, realized you needed to reorganize the entire freezer and come back to the stock seven hours later to find it in liquid form. Are the other techs going to ostracize you?
      • The diagnosis: There is no one answer here. There are circumstances when a chemical or sample is frozen to prevent degeneration, and allowing it to thaw out and maintain an ambient temperature will destroy it. Alternatively, recoveries of frozen E. coli strains after hurricane-produced power outages have been up to 94% successful even after over a month. Your bacterial plasmids should also be fine. Cases must be judged individually based on the substance’s function and traits.
      • The precautions: As previously stated, some chemicals will only function for as long as they are protected from temperature fluctuations. Check the labels to see how they're meant to be stored, and always be aware of your freezer settings.


      A concluding thought: vigilance is essential for chemical preservation and accurate science, but it’s equally as important to consider the durability of accidentally neglected materials. Don’t rush in your panic to discard all evidence of a wandering scientific mind – if you have safe methods, good controls and experience with the substance, you should be able to identify if something is still operable versus when it belongs in the trash.



      Resources

      Best long term storage method for DNA? (2013, July). Retrieved June 28, 2017, from https://www.researchgate.net.

      Clark, J., March, J. B., & Mdegela, R. H. (2000). Extended stability of restriction enzymes at ambient temperatures. Biotechniques, 29(3), 536-542. Retrieved June 19, 2017, from https://www.ncbi.nlm.nih.gov/pubmed.

      Cody, W. L., et al. (2008). Skim Milk Enhances the Preservation of Thawed -80°C Bacterial Stocks. Journal of Microbiological Methods, 75(1), 135-138. doi:10.1016/j.mimet.2008.05.006.

      Johnson, M. (2012). Antibody Shelf Life: How to Store Antibodies. Materials and Methods, 2(120). doi://dx.doi.org/10.13070/mm.en.2.120.

      MiniPCR. Debunking the 4 degree myth: PCR can be left at room temperature overnight. (2016, December 2). Retrieved June 28, 2017, from  http://www.minipcr.com/classroom-tips.

      Moran, E. (2013, May). Using Enzymes at the Bench — Keep it in the cooler? On ice? or at RT? Retrieved June 19, 2017, from http://bitesizebio.com.

      Wu, J., Kim, L., T. K., Huang, C., & Anakella, B. (2009, May). Stability of Genomic DNA at Various Storage Conditions [Scholarly project]. In SeraCare Life Sciences. Retrieved June 19, 2017, from http://www.colorado.edu.



                   Megan Hardie
               GoldBio Staff Writer

      Megan Hardie is an undergraduate student at The Ohio State
      University’s Honors Arts and Sciences program. Her eclectic
      interests have led to a rather unwieldly degree title: BS in
      Anthropological Sciences and BA English Creative Writing,
      Forensics Minor. She aspires to a PhD in Forensic Anthropology
      and MA in English. In her career, she endeavors to apply the
      qualities of literature to the scientific mode and vice versa,
      integrating analysis with artistic expression.

      Category Code: 79104, 88221, 88231, 79109

Posted by Chris on June 1st, 2018  ⟩  0 comments

It’s no secret that animal parts are a big part of the black market trade in our world. Elephants, rhinos, tigers, pangolins and many more animals are routinely targeted, killed and butchered mercilessly and dispassionately without any regard to their preservation or sustainability. These animals continue to become rarer every year and several are approaching numbers that will lead to an extinction level event. As long as these animals continue to be killed beyond reason, all too soon, they will join species like the northern white rhino, now in the twilight of existence, with the death of the last male of the species earlier this year.

Conservationists and activists have warned and warred against poachers for decades, but with the exponential increase in ivory prices, poachers have become highly organized businesses, with resources that often far outstrip the governments and agencies working against them. It’s suggested that some 20,000 elephants and 100 rhinos are killed every year for their tusks and horns. In 2007, elephant herds were estimated to be between 470,000 and 690,000, but in just five years after that, over 100,000 elephants were cut down by poaching to feed the ever-growing ivory frenzy.

Technology has been trying to keep up with the problem, but it’s not necessarily a clear case that things are improving. Professor James J. Spillane from the St. Augustine University of Tanzania outlined several different ways science and technology is fighting to stop the poaching; including advances in communication, satellite mapping and radio technology, drones and aviation, and DNA testing/fingerprinting.

According to a recent article by John Platt in Scientific American, nearly 1,800 smuggled ivory pieces were caught while being smuggled into Singapore, a popular entry point for the black market ivory trade. Using DNA testing, via methods like PCR and DNA fingerprinting, scientists like Samuel Wasser have been able to test elephant feces throughout all of Africa in order to map out each of the elephant herds. Since the feces contains DNA both from the plants that were eaten as well as from the animal eating them, Wasser was able to distinguish between individual elephants and trace their herds using specific, localized DNA mutations, and ultimately track down where those animals lived and died. From that, they are able to match smuggled ivory samples back to a specific region, allowing governments to tag poaching “hotspots” and potentially catch and convict both the poachers in the field and their crime bosses further up the chain. But as Professor Spillane remarked in his paper, the hotspots are liable to change after they are identified, as the poachers become aware of increased scrutiny and move their efforts to keep one step ahead of the agencies targeting them.

So the conservationists continue in their efforts to chase the poachers down, using each and every possible technology to their advantage, working to catch the poachers before they strike. And all the while, these amazing examples of life in the vast variety of our biome suffer for it and decline inch by inch toward the oblivion of extinction until the only way our children’s children will ever see them will be in picture books or museums.

If you would like to help save these endangered animals, there are many international groups that are always in need of additional support, such as: The International Rhino Fund (IRF), the World Wildlife Fund (WWF), the Wildlife Conservation Society (WCS), or the International Union for Conservation of Nature (IUCN), just to name a few. Don’t wait until these animals are a museum relic to wonder how this could have happened and wish you could have done something to help.

Posted by Fernanda on May 16th, 2018  ⟩  0 comments

Sandra’s haunting journey with a deadly flesh-eating parasite started a few years ago while Sandra was enjoying her last day of vacation at a tropical paradise. That day, Sandra decided to walk through the sandy beach one last time. Just as she was about to return to her hotel room, she felt a sting on her left leg and quickly forgot about it. Soon after, the bite developed into a small itchy lump. A month later, the red, itchy lump was still there. Then the lump became a painful ulcer, an open sore in her leg, that slowly kept growing. That day at the beach, Sandra had been bitten by a sandfly infected with leishmaniasis, a disease that can be extremely painful and sometimes fatal for humans.

Fortunately, dangerous diseases, such as leishmaniasis, are being combated by a new emerging field called synthetic biology that is defined as “the design and construction of new biological parts, devices, and systems, or the re-design of existing, natural biological systems for useful purposes,” and requires the merging of biology, mathematics and engineering. But, how is synthetic biology ultimately battling disease?

Synthetic biology is changing how we study disease by redesigning a powerful biological system, the inducible gene expression system. Normally, genes encoded by DNA are transcribed into mRNA by the cell’s molecular machinery. This mRNA is then translated into proteins. This process of manufacturing protein products from DNA is the very definition of a gene expression system. And often, these systems have switches that we can manipulate and control to activate expression of any gene we want by introducing an artificial inducer. It is this introduction of a synthetic activator that makes the gene expression system inducible. We are then able to use the cell’s machinery and switches to generate an artificial system that we can turn on anytime and use to construct complex genetic circuits and networks.

Today, one of the most important inducible gene expression systems being used in synthetic biology is the induction of the lac operon by the compound isopropyl β-D-1-thiolgalactopyranoside (IPTG). IPTG mimics allolactose, a lactose metabolite that activates transcription of the lac operon, and is often used to induce expression of genes under regulation of the lac operator. In the absence of IPTG, the lac repressor (encoded by the lacI gene) binds to the lac operator (lacO), preventing transcription. However, when IPTG is present, it binds to the lac repressor, releasing it from the lac operator in an allosteric manner, allowing the transcription of genes in the lac operon.


This powerful ability to induce gene transcription has made IPTG a technology that has revolutionized biology across many fields, including the study and treatment of diseases. Indeed, the creation of disease models for the study of the pathology observed in complex and devastating human illnesses, including leishmaniasis, is necessary and is becoming achievable with the emergence of synthetic biology and IPTG induction.

Leishmaniasis, the flesh eating disease Sandra contracted, impacts many human populations around the world. This complex infection is not actually caused by the sandfly, but by its protozoan parasite Leishmania. Leishmania has two distinct forms: the amastigote and the promastigote. During transmission, an infected sandfly bites a mammal and passes the promastigote, which is then engulfed by mammalian macrophages. Once in macrophages, the promastigote can either be killed by oxidative mechanisms or it can begin to interfere with the macrophage’s intracellular signaling leading to progression of the disease.

That day at the beach, a chain of events began occurring under the surface of Sandra’s skin to protect the parasite. For its survival, Leishmania interferes with intracellular signaling by ultimately changing the macrophage’s phenotype which leads to progression of disease, and results in ulcerative lesions, mucosal lesions and infection of organs including spleen, liver, and bone marrow, and death. The mechanism behind this signal interference requires the modulation of Nuclear factor-KB (NFKB) and protein kinase C (PKC), two signaling molecules that are essential for an organism’s immune and inflammatory responses. In the case of PKC, leishmaniasis changes the activity of two PKC isoforms: PKC-ς and PKC-α. On one hand, this parasite increases PKC-ς ‘s activity by changing its affinity for substrate in the presence of intracellular ceramide, a lipid whose production increases during infection. On the other hand, this increase in ceramide interferes with PKC-α’s catalytic action by preventing its binding with co-modulators calcium and di-acyl glycerol (DAG). Because NFKB’s activation is dependent upon PKC activity, leishmaniasis’s interference with PKC activity results in aberrant NFKB signaling.

To counteract this cellular signaling manipulation by leishmaniasis, a group of synthetic biologists adopted a similar approach. Milsee Mol and her team engineered PKC to contain domains of both the α and ς isoforms giving rise to PKC_ας under the regulation of the lac repressor and induced by IPTG, resulting in NFκB signaling modulation. They observed that induction of gene expression with IPTG in peritoneal macrophages carrying the engineered PKC_ας led to a change of gene expression in macrophages from an anti-inflammatory phenotype to a pro-inflammatory phenotype, in vitro.

Because inflammation is part of many diseases’ pathology, this finding may present a future way to use IPTG to treat multiple diseases simultaneously, without the addition of other medication or medication that has debilitating side effects.

Another way biologists are currently using IPTG to combat disease is in the regulation of synthetic gene networks in 3-D materials, generating a microenvironment where cellular mechanisms and behavior can be manipulated and studied. In these microenvironments, the biomaterial presents the genetic inducer, IPTG, to cells that contain synthetic gene circuits and are grown and cultured within the biomaterial. This technique is especially exciting because we can have additional ways of controlling gene expression due to materials being able to release inducers, such as IPTG, in many different ways. In addition, we know that cells gain different characteristics and may differentiate into different cells depending on the type of material they are grown in.

In one study coupling synthetic biology and materials science, Tara Deans and her research team aimed to couple inducers, such as IPTG, into biomaterials and create 3-D environments using three different types of materials: polycaprolactone (PCL) electrospun fibers, polyethyleneglycol (PEG) hydrogels, and poly lactic-co-glycolic acid (PLGA) sponges. They observed that IPTG could diffuse in these materials where cells were growing, resulting in gene expression in vitro. Furthermore, Deans and her team also found that modifying the biomaterial by attaching a sugar ring or a peptide sequence affects the structure of cells and how genes are expressed after induction with IPTG. They also found that implanting PLGA sponges containing CHO cells into the abdomen of mice and allowing them to drink water containing IPTG resulted in induction of gene expression. Thus, Deans et al. showed that IPTG is a powerful tool that can be attached to biomaterials and used in to manipulate gene expression networks both in vivo and in vitro and may help in establishing disease models and therapeutic treatments.

As evident in the studies described here, the generation of complex genetic circuits and microenvironments requires the ability to control expression of multiple genes independently of each other. In the past, scientists developed various inducible systems such as the IPTG-inducible lac promoter system. However, this system often interferes with other inducible systems, impeding the creation of a complex genetic circuit. One inducible system that is inhibited by IPTG is the arabinose-inducible araBAD promoter system (PBAD). In this system, when arabinose is not present, the dimeric AraC protein contacts two half-sites on DNA (I1 and O2), creating a DNA loop, which interferes with RNA polymerase binding. Once arabinose binds to AraC, the dimer’s position changes and binds to half-sites I1 and I2, allowing transcription from the PBAD promoter. IPTG inhibition prevents the use of both systems in the same cell.

Fortunately, Lee et al. generated a mutant library of arabinose-binding regulatory protein AraC and identified mutants showing insensitivity to IPTG, leading to the generation of a PBAD system that can be used with the IPTG/lac operon system. So, these two systems can control gene expression in a gene circuit at the same time and independently of each other lending flexibility to their use in the study of cell signaling in cellular microenvironments.

The re-design and application of IPTG induction of gene expression in synthetic biology is certainly promising for our pursuit of understanding biological mechanisms and disease. Perhaps in the near future, our ability to manipulate gene expression, to engineer novel proteins, and to generate cellular microenvironments will help individuals like Sandra heal faster and lead to a better life.

References

Deans, T. L., Singh, A., Gibson, M., & Elisseeff, J. H. (2012). Regulating synthetic gene networks in 3D materials. Proceedings of the National Academy of Sciences, 109(38), 15217-15222. doi:10.1073/pnas.1204705109.

Jensen, P. R., Westerhoff, H. V., & Michelsen, O. (1993). The use of lac-type promoters in control analysis. European Journal of Biochemistry,211(1-2), 181-191. doi:10.1111/j.1432-1033.1993.tb19885.x.

Lee, S. K., Chou, H. H., Pfleger, B. F., Newman, J. D., Yoshikuni, Y., & Keasling, J. D. (2007). Directed Evolution of AraC for Improved Compatibility of Arabinose- and Lactose-Inducible Promoters. Applied and Environmental Microbiology, 73(18), 5711-5715. doi:10.1128/aem.00791-07.

Mol, M., Kosey, D., Bopanna, R., & Singh, S. (2017). Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis. doi:10.1101/151779.

Mol, M., Patole, M. S., & Singh, S. (2014). Immune signal transduction in leishmaniasis from natural to artificial systems: Role of feedback loop insertion. Biochimica Et Biophysica Acta (BBA) - General Subjects,1840(1), 71-79. doi:10.1016/j.bbagen.2013.08.018.

Olivier, M., Brownsey, R. W., & Reiner, N. E. (1992). Defective stimulus-response coupling in human monocytes infected with Leishmania donovani is associated with altered activation and translocation of protein kinase C. Proceedings of the National Academy of Sciences,89(16), 7481-7485. doi:10.1073/pnas.89.16.7481.

Parasites - Leishmaniasis. (2013, January 10). Centers for Disease Control and Prevention. Retrieved May 7, 2018, from https://www.cdc.gov/parasites/leishmaniasis/index.html.

Singh, V. (2014). Recent advancements in synthetic biology: Current status and challenges. Gene,535(1), 1-11. doi:10.1016/j.gene.2013.11.025. 


Categories: 88241, 79102, 79101

Posted by Fernanda on May 14th, 2018  ⟩  0 comments

You may have seen him perched up on tree branches, showing off his bright, red, feathery chest. The male Northern Cardinal, distinguished by his bright red feathers, has fascinated many birdwatchers and scientists alike. And, according to legend, if you see a cardinal flying toward the sun, you will have good luck. Even sports teams have succumbed to the Northern Cardinal’s enchantment. For instance, the name of this striking bird has been adopted by the St. Louis professional baseball team, the St. Louis Cardinals, and Phoenix’s American football NFL team the Arizona Cardinals. But, what is the relevance of the cardinal’s brilliant red feathers?

While pleasing to the human eye, the cardinal’s red plumage has a more specific and important function. Its most important purpose is to serve as a social cue leading to their thriving in the wild. In fact, a 3-year study of this territorial bird, found that redder males have more offspring in a breeding season. Redder males also gain higher quality territories perhaps due to the red hue appearing more dominant to duller male cardinals. These redder cardinals also pair up with earlier breeding females. In addition, the male’s bright colored breast plumage has been positively correlated with parental care. Thus, the redder the male cardinal, the more successful he will be in the wild.

It’s well documented that a male cardinal’s bright red feathers lead to his success, but what really contributes to his coloration? Is it good genes, good health, a certain diet or something else? For many, many years, scientists have mulled over the same question. Long ago, they found that red pigments in birds are produced when they ingest yellow carotenoids found in seeds, and metabolize them into red ketocarotenoids through an enzyme called ketolase. Interestingly, although both red and yellow birds ingest the same seeds, containing the same nutrients, only the red birds are able to metabolize the yellow dietary precursors into red ketocarotenoids, resulting in red plumage.

The identity of the ketocarotenoid-producing ketolase was unknown until the last few years, when scientists began to truly unravel the mechanisms underlying red feather pigmentation in canaries, giving insight into why many birds, including male cardinals, have such striking red plumage. Among these researchers were Lopes et al., who studied red coloration in birds by comparing the genomes of three canaries: red siskins, common canaries, and the product of crossing a red siskin with a canary, the “red factor” canary. They identified two genomic regions necessary to develop the red coloration. Remarkably, one of those regions contained the gene encoding CYP2J19, a cytochrome P450 enzyme, which is known to metabolize carotenoids. They also found that CYP2J19 was strongly expressed in skin and liver of red birds compared to yellow birds, suggesting that this enzyme might be responsible for the red coloration.

Development of red feathers also required a second region located in the epidermal differentiation complex (EDC) in chromosome 25, which contains over 50 genes that encode proteins necessary for feather and skin development in birds. These two genomic regions work together to give rise to red feathers, exactly how is still unknown.

The discovery of these two genomic regions is especially significant given that to other birds, the red feathers in the cardinal appear as a complex and attractive conglomeration of invisible colors. This is because the bird retina has 4 single cone-types (humans have 3) that are sensitive to various types of light, including ultraviolet light, allowing birds to see many more colors that the human eye cannot discern. Interestingly, one of the 4 cones in the avian retina, the red single cone, requires astaxanthin, a ketocarotenoid, to discriminate different colors. Indeed, Lopes et al. found that in addition to CYP2J19 being expressed in the liver and skin, it is also expressed in the red single cone and its levels correlates with astaxanthin production, indicating that CYP2J19 may be involved in ketocarotenoid production in the eye. We may reason that if CYP2J19 is responsible for the red coloration in birds, then it would be found in retinas of red birds and not in those of the yellow birds. However, Lopes et al. found similar levels of CYP2J19 in retinas of both yellow and red birds. Thus, both yellow and red birds have the ability to develop red feathers. The fact that only red birds do suggests CYP2J19 is regulated differently in red-feathered birds, including the cardinal.

Surprisingly, around the same time that Lopes and his team made this discovery, a different group studying color variation in the zebra finch made a similar discovery. Mundy et al. found that a homolog of CYP2J19, CYP2J19B, is found in red beaks of normal zebra finches but not in the beaks of yellow-beaked zebra finches. Now, the next step is to identify the factors regulating the expression of CYP2J19.

Such a discovery may also shed light into why the female cardinal exhibits a subdued tan feather color. Feather color in cardinals, as in other birds, is known to be a sex-limited trait, meaning feather color arises from differential regulation of genes in females and males resulting in sexual dimorphism. Perhaps the next question to answer is if CYP2J19 or its regulators are expressed differently in the female than in male cardinals, causing sexual dimorphism.

So, next time you see a vibrant red cardinal flying around in your backyard, you will not only have good luck, but you will have a better understanding of the complexity of the genetics behind color variation in birds.

References

Barsh, G. (2016). Evolution: Sex, Diet and Red Ketocarotenoids. Current Biology, 26(21). doi:10.1016/j.cub.2016.09.032.

Linville, S. U., Breitwisch, R., & Schilling, A. J. (1998). Plumage brightness as an indicator of parental care in northern cardinals. Animal Behaviour, 55(1), 119-127. doi:10.1006/anbe.1997.0595.

Mundy, N., Stapley, J., Bennison, C., Tucker, R., Twyman, H., Kim, K., . . . Slate, J. (2016). Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster. Current Biology, 26(11), 1435-1440. doi:10.1016/j.cub.2016.04.047.

Stoddard, M. C., & Prum, R. O. (2011). How colorful are birds? Evolution of the avian plumage color gamut. Behavioral Ecology, 22(5), 1042-1052. doi:10.1093/beheco/arr088.

Twyman, H., Andersson, S., & Mundy, N. I. (2018). Evolution of CYP2J19, a gene involved in colour vision and red coloration in birds: Positive selection in the face of conservation and pleiotropy. BMC Evolutionary Biology, 18(1). doi:10.1186/s12862-018-1136-y.

Wolfenbarger, L. L. (1999). Red coloration of male northern cardinals correlates with mate quality and territory quality. Behavioral Ecology, 10(1), 80-90. doi:10.1093/beheco/10.1.80.



Category Code: 79101, 88241