2015 Fall

NewsBits 03- Bugs in Your House and Microbes in Antarctica

fullsizeoutput_3cf

Researchers at NC State University surveyed arthropods living in homes and found huge biodiversity. Some of the results can be found here.

A tree frog that was believed to be extinct for 100 years was discovered in abundance in a northeast Indian jungle. The paper published in PLOS ONE can be found here.

If long strands of RNA don’t code for proteins, should they be considered junk? If we don’t know exactly what role DNA between genes plays, should we call them “junk”? This article explores this issue.

Social, but not intelligent? In a paper published in Science on January 22, scientists show that prairie voles console one another in stressful circumstances.

How could a species of beetle help prevent frost on airplane parts? Find out here.

Have you’ve ever wondered about courtship behavior in the mysterious puma? Max Allen explains some of his really cool research here.

Here’s a neat paper on the microbial biodiversity of Antarctica. Could there be implications for how scientists understand the cold limits of terrestrial life on other planets?

Hadrosaurids, the duck-billed dinosaurs, lived in Asia, Europe, and North America. A new study shows they originated in North America.

 

 

 

NewsBits 02- Dwindling seaweed harvests and the oldest mammoth

fullsizeoutput_3cf

The story that found that around 6600 tardigrade genes had come from bacteria and other outside sources is now being questioned. A team from the University of Edinburgh have gotten different results. Read about it here.

If you’re interested in treeshrews, here’s a fascinating natural history account from Darren Naish.

The Yellowstone Wolf Project Annual Report for 2014 is now available. In addition to that, check out Rick Lamplugh’s story of probably the most famous of any of Yellowstone’s wolves, 06.

Have you ever heard of a caterpillar, an ant, and a parasite working together. Here’s your chance.

Bacteria, fungi, and worms can help reveal the time and place of death.

There seems to be a seaweed shortage. That could cause problems for researchers around the world.

Everything’s possible with CRISPR? Even the ability to wipe out malaria?

Confirmed mountain lion sightings in Tennessee, including a female.

A 200 million year-old fossil from Greenland are making some paleontologists doubt the age of mammals. They may be 30 million years older than originally thought.

It looks as though dinosaurs appeared and diversified rapidly.

As many as 17 species of animals were found living in water that was trapped in rock as deep as 1.4 km underground. This is as deep as anyone has found living animals. Microbes have been found as deep as 3 km.

The Steppe Mammoth may have been the largest species of elephant to have ever lived.

This is an interesting read about Lonesome George and possibly bringing back a species of Galapagos tortoise.

NewsBits 01- Jellyfish evolve “backwards” and tardigrades carry alien DNA

fullsizeoutput_3cf

Check out Frontiers for Young Minds to see how scientists and young people are working together to create science articles.

Are some researchers redefining what is means to be an animal? Researchers at The University of Kansas have shown that jellyfish have evolved into microscopic parasites. Why is this significant? Click the link to learn more.

Should scientists practice to improve creative writing and storytelling skills? Find out by examining the life of Oliver Sacks.

There are examples of blue tarantulas scattered throughout the tarantula family tree. Why? Do tarantulas use this color to communicate? Is it simply a result of natural selection. Do they use the color to warn potential predators. No one seems to know.

How do we know how extinct animals fed? We look at their teeth, of course. This article examines tooth morphology and development in therapods, a suborder of dinosaurs that were ancestrally carnivorous.

If you have ever wondered what Einstein’s “General Relativity” was all about, check this out. General Relativity just turned 100.

Tardigrades, also known as water bears, recently won the award for having the most foreign DNA in their genome. Researchers from the University of North Carolina at Chapel Hill have shown that about 17.5% of a tardigrade’s DNA is foreign. Is there a link between foreign DNA and organisms that have the ability to withstand harsh environments?

Is it the sequence and structure of chromatin that determines the shape of an organism or it is physiological networks such as bioelectrical systems that are responsible. This article highlights research in which biologists made a species of flatworm to grow heads and brains from a different species of flatworm without altering the genome.

John Marzluff, an expert on crow behavior and author of Gifts of the Crow, explains where Seattle’s crows go to roost at night. The behavior of these birds show their intelligence, but also leave us with unanswered questions.

Do mass extinctions actually help some species survive? If so, do the extinctions events cause a shift in morphological characteristics. Carl Zimmer writes about it here.

Finally, two new books by noted biologists are due out early next year. One Wild Bird at a Time by Bernd Heinrich highlights the “day-to-day observations of individual wild birds”. E.O. Wilson has a new book called Half Earth: Our Planet’s Fight for Life. Wilson argues that to effectively preserve the biodiversity of our planet, we must dedicate half of the Earth’s surface to nature.

 

DNA Barcoding-> What is it?

How do we identify different species? One obvious way is morphology, the way an organism looks. This may include size, shape, and body color. Field guides or internet sites could be used to help identify a particular organism this way. However, what about organisms, like insects, that are often hard to identify strictly by morphology? That’s where a useful method called DNA barcoding comes into play.

We use the DNA barcoding technique in our lab to sample the biodiversity of insects, but we also use it to train undergraduate students in molecular biology. The purpose of this post is to describe the history as well as the science behind this technique. I will also describe how it works in our lab.

In 2003, Paul Hebert, a professor and current Director of the Biodiversity Institute of Ontario, came up with “DNA barcoding” as a way in which to identify species. DNA barcoding uses a short genetic sequence from an organism’s genome. For almost all animals, the gene region that is used is the mitochondrial cytochrome c oxidase 1 gene, or “CO1”. COI is a 648 base-pair region that codes for an enzyme that plays a major role in cellular respiration (how your body converts glucose to ATP), specifically the last step called oxidative phosphorylation. The COI gene is suitable for barcoding because its rate of mutation is fast enough to distinguish between animal species, even closely related species.

Here’s what our “pipeline” looks like:

Week 1: Students in our lab collect insects from sample plots. We have plots at a section of the city’s greenway trails as well as plots on campus. This way we can compare a disturbed urban area (campus) to a less disturbed area (greenway). After collecting in the field, the students attempt to identify the specimens using field guides and other internet resources. Here’s a great one. The insects are stored either in the freezer or in 70% ethanol.

Week 2: The DNA is extracted from the insects. This process includes initially grinding up certain parts of the insects and then going through a series of steps to isolate the DNA. We use Carolina Biological’s protocol. The samples are then stored in the freezer until the next lab.

Week 3: The DNA is amplified, or copied. During this lab we use a procedure called Polymerase Chain Reaction, or PCR. The small amount of DNA that we have extracted from the insects is replicated. We use a COI primer, which are small pieces of DNA, to amplify the DNA of interest. The PCR machine can make about 68 billion copies! This is a step that also involves using extra deoxynucleotides, a cool enzyme called Taq polymerase, and a loading dye so that we can visualize the results during the next lab. Again, the sample are stored in the freezer until the next lab.

Week 4: The DNA samples are visualized on a gel using a procedure called electrophoresis. In our case, the DNA is separated according to molecular size with the aid of an electrical field. There are many interesting applications of using gel electrophoresis. We use it to determine whether or not we have our gene of interest.

Week 5: In between week 4 and 5, our DNA samples are sequenced. During week 5, we use bioinformatics to determine our species based on our sequence with the help of a database. Students are able to compare the barcoding results with their original identification from the field guides during week 1. Students are also able to measure the biodiversity of each are (campus and greenway) using several biodiversity indices.

Two main objectives are met during this research. One, we are training undergraduate students to actually be scientists. Students need concrete examples of the scientific process from beginning to end. This research project uses a nice blend of field research and laboratory methods. The students are also given autonomy which increases learning. The second objective is to highlight the importance of biodiversity, even if it is local. Biodiversity is crucial for progress in ecological and evolutionary fields of science and also for conservation programs.

Stay tuned for our results.

The Ecology of Fear, Part IV

Since coyotes do inhabit neighborhoods and other urban environments, humans must learn how best to live with them. In Part I of this series, we looked at the specific coyote “problem” in Iredell County. In Part II, we learned about the natural history of coyotes, and in  Part III we attempted to clear up misconceptions about coyote behavior and ecology. With this post, we will explore recommendations and suggestions on how to live with these predators.

Coyotes can be found living in every county in North Carolina yet the state has no formal coyote management plan. The reasons are pretty simple. It can be time-consuming and expensive to try to implement a removal/management plan. Individual coyotes that are found killing livestock will quickly be replaced by other individuals if they are removed from an area. This paper highlights best practices when it comes to managing potential predators of livestock. Several studies have shown that coyotes are far too resilient for periodic eradication programs. In fact, only a 10% survival rate in offspring must survive and reproduce to maintain most coyote populations. It has been estimated that if 75% of coyotes in any given area are killed each year, it would take 50 years to exterminate the population. Coyotes simply increase productivity, survival, and immigration under removal efforts. Since it does not look as if coyotes will disappear from NC any time soon, it is best for both coyotes and us that we learn how to avoid conflicts.

First of all, seeing a coyote is not a cause for concern. If you see a coyote frequently, then you can take steps to decrease the chances of a conflict. The Urban Coyote Project recommends people follow these six steps to avoid conflicts:

1. Do not feed coyotes
2. Do not let pets run loose or be unattended
3. Do not run from a coyote
4. Repellents or fencing may help
5. Report aggressive, fearless coyotes immediately
6. Do not create conflict where it does not exist

Following these steps and using common sense when coming into contact with coyotes will benefit both parties. We certainly benefit from having these predators in our areas. Be smart.

*Since their is no coyote management plan in NC, it is extremely hard to estimate population numbers in the state. However, The North Carolina Wildlife Resources Commission does keep track of the number of harvested coyotes by hunters per year. These numbers could help us understand population dynamics from year to year. These documents can be found here.