Friday, May 31, 2013

Petri and his dishes (and then some)

I was inspired by today's Google doodle, honoring Julius Richard Petri's birthday, to discuss the Petri dish.

A Petri dish culture of a Legionella sp. The genus includes Legionella pneumophila which causes Legionnaires' disease. This is a streak plate, a method used to dilute down a sample to the point where individual colonies can be seen and then counted. 
In modern science, Petri dishes have become a vital tool. Of course, much has changed since the days of Julius Richard Petri. Though the concept of the Petri dish is rather simple--a small isolated environment used for growing whatever small organism the scientist desires--these dishes are used quite widely. Most important, perhaps, are the uses in microbiology, especially in relation to the study of disease.

Bacteria, fungi, and other life cannot simply be grown in a plastic dish. They need a source of food and water. This is provided through some sort of growth medium that is added prior to the addition of the bacteria or other lifeforms. This medium is usually agar-based, agar being an extract from red algae that gels in a similar manner to gelatin. Nutrients are added to the mix, the types of nutrients depending on what is being grown on the plate. Trypticase soy agar, for example, is a very basic medium that a lot of bacteria will readily grow on. After the addition of the growth medium, Petri dishes can referred to as Petri plates.

There are a variety of specialized nutrient media that are used when more information is needed beyond a basic "yep, it's a bacterium." There are selective media, which will prevent the growth of certain lifeforms. This can be helpful when, for example, a scientists wants to know what bacteria are present in a soil sample. Fungi in the soil can overwhelm a plate unless the sample is grown on a medium that inhibits fungal growth.

A plate showing Alpha, Beta, and Gamma hemolysis
Differential media are especially helpful when trying to identify a specific species. Bacteria can show widely different characteristics when grown in contact with various nutrients. A blood plate, one type of differential media, is often used to identify whether bacteria can digest blood cells. This is especially useful when diagnosing infection diseases. Streptococcus pneumoniae, a species that causes one type of pneumonia, can be identified partly thanks to its hemolytic activity, hemolysis being the breakdown of red blood cells. There are three different characteristic types of hemolysis that can be seen by growing bacteria on blood agar: alpha, beta, and gamma. Alpha hemolytic bacteria will only affect the medium that the colony is touching, turning the agar from red to green. Beta hemolytic bacteria cause a rather more dramatic change, removing the color from the media for some distance around each colony. Alpha hemolysis is only a partial digestion of the blood cells, while beta is a complete breakdown of the blood; thus the difference in the results. Gamma hemolytic bacteria, in contrast, cannot digest blood at all. They will feed on the other nutrients in the medium, but the blood will be completely unaffected. The results of growing a pathogen on blood agar can help provide a diagnosis for a sick patient.

One of the most important parts of the process of growing something in a Petri plate is cleanliness. Aseptic technique is vital to prevent contamination of samples, which would skew results. This includes everything from flame sterilization to autoclaving materials; anything that can possibly be done to keep unwanted contaminants away from the sample. I'll never forget the hours I spent in the laboratory during my days learning Microbiology, going through the procedures for aseptic technique over and over again.

Interestingly enough, after an inoculum is added dishes are actually incubated upside down, which may surprise many of you. One of the main reasons for this is to prevent contamination, as spores from various living things then cannot fall down onto the growth medium. Also, condensation cannot drip down from the lid, which would interfere with the otherwise rather stable conditions the Petri dishes provide.

Source is Microbiology with Diseases by Taxonomy, 2nd edition. Images are from Wikimedia Commons and are under Creative Commons licensing or are copyright free: one, two.

Friday, May 24, 2013

The Role of Fire

Generally when people hear the word "fire" all they think of is devastation. However, in nature fire is a complex thing that brings many changes to the environment, not all of which are negative.

Fire can be a great source of good in environments. It cuts back on plant growth, clearing out underbrush. This provides open space for young plants to receive enough sun to grow. Some young plants are even fire resistant and will thrive after others burn. In addition, fire is actually a requirement for certain plants to reproduce. The cone of the jack pine (Pinus banksiana), for example, will only open after they have been exposed to the heat only a fire can provide. There is a natural fire cycle, with the fire clearing out space that plants will then quickly colonize. This is why some plants reproduce only after a fire sweeps through an area: it gives their offspring a better chance of survival.

New life sprouting after a controlled burn
For a very long time the prevailing view concerning fire was that all fire was bad and must immediately be extinguished. This led to some very costly lessons being learned nearly twenty-five years ago.

The fairly recent history of Yellowstone National Park tells how blanket fire suppression can be a very dangerous policy. Many years of suppression combined with a drought in the summer of 1988 turned the park into a tinderbox. The forest ignited and by the time an early September snowfall finally brought the fires down enough to be controlled over one million acres had been touched by flames. Hundreds of large animals died, including over three hundred elk. Dozens of buildings had been destroyed and all told there was approximately $3 million in property damage. $120 million had been spent fighting the fires. Up to nine thousand firefighters at a time had battled the flames.

Perhaps the most tragic aspect to the devastation that hit such a large part of the National Park is the fact that it was largely preventable. Fire management policies have changed significantly since the Yellowstone "Summer of Fire" and for very good reason. The natural fire cycle cuts back on underbrush, preventing it from building up too much. A great many tree species have fire-resistant trunks, so if underbrush is fairly sparse and low to the ground flames can never reach high enough to kill the life that makes a forest a forest: the trees.  If there is a large amount of underbrush, on the other hand, the flames can burn hotter and higher, potentially reaching all the way up to the crown of a tree. Crown fires are far more devastating than fires that stay low to the ground as they can jump from one crown of a tree to the next. This is especially true in areas where the trees grow very close together.  Crown fires can lead to the complete devastation of a forest.

Many small fires will keep a huge, terrible fire from happening in the future.

I have concentrated on forests here, but any environment can be affected by flames. In the future I plan to discuss the link between fire and mudslides in California.

Sources are the Florida Forest Service, National Park Service, and PBS NOVA Online. Image was taken by me.

Thursday, May 23, 2013

Running Free in North Carolina

Finally posting these. I went to North Carolina with my family over the weekend. My father found us a series of trails through a forested area that was surrounded by fencing where we let the dogs go. This is the first time I've seen the greys have a chance to do this.

Happy dogs
It was a warm day after a lot of heavy rain and Ebon took a dip in every patch of water we came across. Willow was having an absolute blast. We don't trust her off lead very much yet, for good reason, so this was a treat for her. She saw the long stretch of sand that was the trail and decided it was a good day to run, probably recalling her track days. All three of them ran while we were there. Willow was by far the most entertaining. She was the first to run, and the other two would take off after her. Then, when they got too far away I was very happy to see how quickly she responded to a whistle. Her recall is surprisingly good, but I have no idea how that would change if there was something interesting to chase. Ebon was keeping up with the greyhounds rather well, but they weren't really even trying to run as fast as they can.

Willow also found a huge mud puddle that she decided was a fun thing to run through. The thing was pretty shallow for the most part and she was having a blast running through it until the water deepened and then she froze, not knowing what to do. I don't think she knows how to swim very well. The boys seemed like they rushed to her aid, though Siggy wasn't so sure about the deeper water either. Ebon happily joined her in the puddle and they both then made their way to dry ground.

Poor Willow doesn't know her limits, unfortunately. Her poorly healed back leg is a frequent issues since she just wants to go and go, but the more she runs the more likely it will hurt. She ran until she limped and my father carried her much of the way back to the car.

Monday, May 13, 2013

Dog Park Day

The always ball-obsessed Ebon with Ebon Look-a-Like, Momma and Daughter Shepherds, Pekinese Mix, The Catahoula Leopard Dog, and Ebon's Chuckit
Ebon and I went to the dog park today, along with Siggy, Willow, and my mom. This is the first time I've remembered to try to take pictures of dogs in general. I've failed miserably other times. I swear today was the Day of the Retrievers as there were, proportionately, about five times more retrievers and retriever mixes there than I've seen in the past. There's been a Day of the Pit Bulls too. I've also discovered I tend to give dogs descriptive names while I'm there, partly so I know who to keep my eyes on I think.

One of the watering stations. Siggy's the white blob to the right and Willow's drinking in the middle. Also included are Mini Ebon, Very Noisy Beagle, Chocolate Lab, and Blue Pit with Block Head
Also at the park today: Ball Thief Husky, Isabella Doberman with Alopecia, Very Dark Golden, Cattle Dog Mix the Owner Swears is a Catahoula, Basenji Mix, Intact Pit that Really Needs to be Neutered, Scaredy Cat Lab/Pit, Pointer with Blue Eye, Constantly Muddy Golden, Pug with a Death Wish, Black Norwegian Elkhound, Humpy Beagle, Collie with Frisbee, and many more.

Saturday, May 11, 2013

What's the Difference between a Possum and an Opossum?

Possums, opossums, or both?
Though some people view these terms as interchangeable, at least in the United States, they actually aren't. In fact, they describe quite distinct groups of animals.

Common brushtail possum (Trichosurus vulpecula), native to Australia
Possums are a group of marsupials found only in the Eastern hemisphere, mainly in Australia and New Guinea. All species that can technically be called possums are included in the Suborder Phalangeriformes, which includes six different Families: Phalangeridae, Acrobatidae, Petauridae, Burramyidae, Tarsipedidae, and Pseudocheiridae. There are also a number of species in this Suborder that don't include "possum" in their common names: the gliders and cuscuses.

Suborder Phalageriformes is included in the Order Diprotodontia, one of the many Orders to be found in Class Mammalia, and one of seven orders of marsupials. Order Diprotodontia includes the largest number of marsupial species, including wombats, bettongs, and the ever-charismatic kangaroos and koalas. Often, a diprotodont will be the first thing someone thinks of when they hear the word "marsupial."

Elegant fat-tailed mouse opossum (Thylamys elegans), native to Chile
Opossums, in contrast, are different enough from possums that they are classified in a completely separate order: Order Didelphimorphia. This Order has only one Family: Family Didelphidae. This group includes all of the marsupials to be found in the Americas. Though most of the species are found in Southern and Central America, there is a single species that lives quite happily farther north: the Virginia opossum (Didelphis virginiana).

What are some of the differences between possums and opossums? Beyond a number of morphological differences, possums are mainly herbivorous, nectivorous, or insectivorous while opossums are mostly omnivorous or carnivorous. This ties into the morphological differences, as the teeth of the two groups are quite different.

It remains true, however, that opossums are colloquially referred to as possums by many people. Some consider all of these species to be possums, with just the American species being opossums. However, since there are significant differences between the two groups I don't think this is appropriate.

Sources are Animal Diversity Web and Merriam-Webster. Images are from Wikimedia Commons under Creative Commons licenses: one, two, three.

Friday, May 10, 2013

Wildlife Dangers and Safety

A sign at one of the local parks. The park includes a large ring of pavement that cuts through a former rice farm. The land now includes a very large swathe of tidal marsh and forest.
Warnings are something that shouldn't be taken lightly. If you see one, pay attention. They've been placed there for a reason.

Like many people, I enjoy the outdoors. I'm a relatively frequent visitor to local parks, a number of which are fairly untouched patches of wilderness with unpaved trails. As such, it is vital for me to be aware of what dangers there may be on those trails. I live in a city where you can go maybe a mile in one direction or another and come across a place where you can possibly come across some quite dangerous animals.

Some people may be surprised by how pervasive alligators are, for example. A lot of people think they're only found in Florida or Louisiana. That, however, is a mere fraction of their range. The American alligator (Alligator mississippiensis) has a range along the coast of the United States all the way from a very small part of Virginia to Texas, extending north into Arkansas and Oklahoma. The only real restrictions to their range are cold winters and the salt content of a body of water. They can tolerate short periods in salty water, but are not adapted to deal with long-term exposure to high levels of salt.

A young alligator found at the same park as the sign above
Where I am, alligators are a rather frequent sight. They thrive in the moist environments that are so common in the area. I have seen a number of them varying in size from three feet or so, like the one seen here, to about eight feet in length. I also know a number of people who have seen far larger gators. My father, for example, came across one that was over twelve feet long when he was out kayaking.

Though small alligators are unlikely to kill you, they can still do quite a bit of damage if they bite. Even worse, very young alligators emit a distinctive cry when they feel threatened that will cause mother alligators to come investigating. Someone who made the very bad decision of messing with a baby alligator could quite easily find themselves facing a very large, very dangerous adult.

So, how to you keep yourself safe around alligators? The main way is to keep your distance. Don't feed, touch, or otherwise bother the animal in any way. Do not swim where alligators are known to live. They can be quite fast over short distances on land, and a distance of at least sixty feet should be maintained with adults. They're even faster in the water. Don't corner the gator, as it may feel that it is in danger and can become dangerous fast. If you are boating nearby, do not panic if an alligator on a bank enters the water. It likely feels threatened and is looking for safety. Also, I repeat, for goodness sake don't bloody feed the thing! I have expressed before my opinions on feeding wild animals, and alligators are one of those animals that should never, ever, EVER be fed. An alligator that views humans as a source of food is extremely dangerous.

A water moccasin, also known as a cottonmouth, found at the same park as the alligator
Snakes may or may not be dangerous, depending on what species you're dealing with. There are about forty species of snake to be found in my area, some with far greater frequency than others. Of those snakes, six species are venomous: the timber rattlesnake (Crotalus horridus), copperhead (Agkistrodon contortrix), Eastern diamondback rattlesnake (Crotalus adamanteus), water moccasin (Agkistrodon piscivorus), pigmy rattlesnake (Sistrurus miliarius), and Eastern coral snake (Micrurus fulvius).

One of the most important parts of snake safety is identification. While I may not be able to always recall all of their common names off the top of my head, I know what all of the local venomous species look like. I remember well the lessons I learned many years ago at the Georgia Southern University Center for Wildlife Education. Except for the coral snake, which is a highly unusual species to come across, all of these snakes have arrow-shaped heads with distinct necks rather than the rounded heads of all the native non-venomous species. Luckily, all of these species are also fairly small compared to snakes that are found in other areas. This means that the safe distance for these species is less than with other, larger snakes. However, this doesn't mean you should approach a venomous snake. Indeed, it is best not to approach any wild snake as you are likely to be perceived as a threat. Even the smallest non-venomous snakes can cause quite painful bites. 

Of course, this is another case where keeping your distance is the easiest way to stay safe around venomous snakes. However, being fairly small creatures, snakes can hide quite easily. A number of species prefer to tuck themselves into holes for various reasons, including temperature regulation and hunting purposes. This is one major reason why debris should be cleared from yards, especially in areas that children or pets frequent. In addition, caution must be taken during treks outside. Don't stick your hands in holes without looking first and be careful where you step, especially around logs and other places where snakes are known to be found. Light your path at night so that you can see what's on the ground, including any snakes you may come across.

If you do happen to come across a snake, it's best to calmly step back and walk around it. Snakes really just want to go about their business and, most often, bites occur when someone messes with the snake. If you don't pose a threat to the animal, it shouldn't pose a threat to you. Stepping on the snake is also a reason people are bit, which is one of many reasons why you should wear closed-toed shoes and long pants in the wilderness.

It also must be noted that pets can potentially be in more danger from wild animals than humans. They are curious creatures and it isn't uncommon for them to stick their noses where they shouldn't. They should always be under supervision in potentially dangerous areas. If the dog is approaching a wild animal, especially a potentially dangerous one, it should be removed immediately for the safety of everyone involved. Also, there is an option for concerned dog owners living in areas with a lot of dangerous snakes known as "snake proofing." It is a form of training that will give a dog a healthy fear of snakes.

Snakes and alligators are perhaps the greatest concerns in my area, but they are definitely not the only potentially dangerous animals to be found. We also have American black bears, alligator snapping turtles, bobcats, wild boar, whitetail deer, coyotes and a number of smaller animals that can deliver a nasty bite or potentially carry diseases like rabies.

While this information is most relevant for my area, everyone who intends to spend a lot of time in the wilderness should be aware of the dangers they may come across.

Sources are Animal Diversity Web, Savannah River Ecology Laboratory: How to be safe around alligators, and Savannah River Ecology Laboratory: How to be safe around snakes. Images are from myself, my significant other, or are copyright free from Wikimedia Commons: one by myself, two from Wikimedia, three and four by my SO.

Thursday, May 9, 2013

Adventures in Petsitting

The closest thing I got to a clear picture of all four dogs
Simmie meeting Albus
This past weekend I was petsitting three dogs and two cats. So, all told, I was caring for six animals including Ebon. Most of those animals were owned by members of my family: Willow, Siggy, Albus, and Ginny. I also watched the neighbor's dog, Simmie, short for Seminole if I'm remembering right. Simmie is a golden retriever who's about two years old. He's quite the puppy still.

In many ways, Simmie reminds me of Ebon as a young fella. The major difference? Simmie is WAY calmer.  Ebon was far more energetic at the same age. The difference is rather remarkable. I suppose that's what you get, though, when you compare a dog that was bred to work and one that was bred to be either a pet or a show dog. This is honestly the first time I've spent enough time with a non-field-bred retriever to notice the difference. Ebon's energy level now at age eight is about equal to Simmie's, he just controls it a lot better.

The remains of my laptop cable
The weekend was interesting, complete with a few minor disasters. The first was someone chewing my laptop cable into dozens of pieces. In all likelihood, it was one of "the blonds": Willow or Simmie. I'm getting a new one, but it was a frustrating surprise.

Siggy being anxious
It also rained almost the entire weekend, which caused a lot of drama with the greyhounds. As I've mentioned several times before on the blog, Siggy has serious issues with thunder and heavy winds. When it's noisy outside there is no way to possibly get him to move from whatever corner he curls up in. He'll even refrain from eating, and in fact I couldn't get him to eat for an entire day. Then once the rain was gone he was understandably starving. Willow isn't bothered by the noise, but refuses to walk on wet grass. That combined with Siggy's want to walk as little as possible made walking the dogs quite...interesting. The retrievers, of course, were more than happy to walk as long as I wanted them to.

Simmie and his butt fluff. He happy dances just like Ebon: toy in mouth, wriggling on back
The retrievers
Then, there's Ebon. He's such an easy dog most of the time, partly because I know his quirks so well now, but that doesn't mean he's perfect by any means. I let him run around off lead a couple of times while I walked the others since his recall's pretty darn sound and he's not one to run across the street if I ask him not to. It also made dealing with four dogs easier. However, at some point when I didn't have my eyes on him he ate something. When he threw it up it looked like a plastic food wrapper of some sort. It wouldn't be the first time some sort of trash found its way into the yard for whatever reason. I also think whatever he ate is responsible for the diarrhea that he started having at the same time. He spent a day without food before I put him on a bland diet. He's not showing any signs that there's any more stuff bothering his gut, but I'm continuing to watch him just in case he's trying to pass any leftovers. Now, though, after several days, he should have expelled anything that may have been left. He's transitioning back to kibble now.

Willow roaching. Unlike Siggy, she sleeps on her back fairly regularly. You can see her bald belly from her spay
Of course, there was no drama with the cats. Cats are so easy. Ironically, one of the main reason I was petsitting is that Albus, the grumpy twelve-year-old tom, can't be left alone due to concerns regarding his urinary health. He's had two urinary blockages so far, which can result in dangerous spikes in blood toxicity and possible death if not quickly treated. Ginny, now eleven, is still healthy as can be. Being born feral, I think she has better genes than Mr. Bad Teeth and Bladder Issues. A feral cat with poor genetics would probably die fairly young.

Thursday, May 2, 2013

The Dog Park!

I'm pretty sure it's obvious who's happy about this
Me giving Siggy love at the park
After my complete and utter failure to find the local dog park on my own, my mother and I went hunting and, amazingly, found it fairly easily. It's tucked away, so I'm really not that surprised that I would have missed it. There's some awkward turns on poorly aligned roads involved. It also happens to be behind the stadium that the local minor league baseball team uses. The enclosure is full of pine trees, and includes several picnic tables and raised gravel beds for the pools and water buckets.

We've been going at least once a week since.

Willow after numerous rounds of fetch
Unfortunately, I have noticed a few issues with Ebon now that we've been a handful of times. He's almost anti-social. If I have a ball with me, which I always do as I want to tire him out while we're there, he doesn't care about anything else. The other dogs could be puffs of smoke for all that dog cares. He follows me around, staring at me, growing more and more excited until I throw the ball. If I put the ball away in my bag he starts jumping on me as if putting the ball out of his line of sight is too much for him. If I sit down, he decides to climb onto the picnic bench.

Ebon jumping to catch a ball

Next time I go I might just leave the ball at home. Part of the reason I'm there is so that he'll get social interaction, after all. Sure, he'll sniff a dog or two every once in a while, but unless a dog approaches him he generally will ignore them. Amazingly, even if a dog is in his face sometimes he still ignores them. One day, a deaf double merle great Dane even decided to hump Ebon and all Ebon did was sit down and act like the Dane wasn't even there.

I think part of it is that Ebon is just an absurdly tolerant dog. He is pretty darn tolerant. He's also never been one to get snappy if another dog snaps at him. In fact, when growled at his first reaction is to back away and crouch down, ears back and tail down. When that Dane wouldn't leave him alone, he did eventually bark at him, though of course it doesn't do any good to bark at a deaf dog.
Ebon and a corgi who wanted to herd everything

I also suspect that Ebon might be growing less playful with age. When he was younger he regularly engaged other dogs in play when given the chance. When Charlie was still alive and fit enough for it, he would play almost daily with Ebon, who was just a puppy at the time. Ebon was always the instigator in the play, bouncing around the then ten-year-old Charlie like there were springs in his paws. He would literally run laps around the house while Charlie would stand there, panting, waiting for Ebon to come back so that they could wrestle.

Things have changed a lot since then, though. Eight years is pretty old for a dog Ebon's size. I find it quite possible that his choice to completely ignore behaviors that are impolite in canine society may be like an old man going, "Those rude young people. Best not even acknowledge their deplorable behavior!" Some dogs grow less tolerant with age, Ebon might be going in the other direction.

Then again, the truth of the matter is likely that Ebon just has an unhealthy obsession with tennis balls.

Yeah, I'm pretty sure that's it.

Wednesday, May 1, 2013

Say Hello, Willow

Willow on her first day in Georgia
It was tough to decide what topic I wanted to cover on the blog after being gone for so long. After some thought, I thought I should go with something simple.

My parents did a lot of talking about the possibility of getting a second greyhound after Siggy. There was a fair amount of looking through adoptable dogs and back and forth about what sort of dog to get. In the end, Willow was the one who came home.

Siggy, Willow, and Ebon at the big part downtown. The bandage on Willow's leg was from one of the cats deciding he didn't particularly like her. A bit mean of him to come up behind her out of the blue like he did
Willow is only two years old and a tiny little grey, only about 50 pounds when she was pulled from the track. Like Siggy, she was injured some time during her career, but the injury was quite different. Her right rear hock was broken and healed crookedly, so now she doesn't like to bear all of her weight on that side. Also, unfortunately, if she spends too much time running around it starts to hurt and causes her to limp a little.

Ebon and Willow retrieving simultaneously
Despite all of that, Willow is an absolute joy! She's just the happiest little dog. She loves practically everything. Food? Awesome! People? Great! Playtime? The best! Other dogs? Well, only if they don't immediately get in her face when meeting the first time. Amazingly, she even loves playing fetch. Ebon, though at first a little unsure about the whole thing due to his instinctual need to return virtually anything that is thrown, has adapted pretty well to her greater speed. He's pretty okay with her getting to the ball before him. It is kinda of funny to see him pull up short when she goes sprinting away, though. It'as almost like he says, "Nope. Not worth it."

Unlike Siggy, Willow does have a rather high chase drive. It's probably why she loves fetch so much. She learned her name pretty quickly and will come when called within limits. She's the sort of grey I would absolutely love to have when I eventually get one. Not as difficult to tire out as Ebon, but far more energetic than Siggy, who would spend all day sleeping if we let him. He has his moments, especially if other dogs are running around, but golly is he lazy. Willow also doesn't have any of Siggy's quasi-PTSD, so that's always a plus.

I'm pet-sitting everyone this weekend: the two cats and all of the dogs. I might be watching one of the neighbor dogs as well. It should be fun!