A Blast from the Past

A hot button microbe right up there with MRSA, I’m sure nearly every one of us is mindful of Human Immunodeficiency Virus or HIV. HIV has found our Achilles Heel, as it targets the very cells we trust to protect us from invading microbes and viruses such as itself. But the ingenious of this virus is beyond even these tactics, as HIV is a retrovirus.

This designation does not simply mean that HIV is keeping it fresh with style from the 70s, but rather that HIV has some sweet dance moves that can turn everything we thought we knew on its head!

Retroviruses fall within the virus family, Retroviridae, and typically have a single strand of RNA as their genetic blueprint. While RNA genes instead of DNA genes might seem strange for cellular life, viruses bend the rules a bit. In other words, it is not rebellious for a virus to chose RNA rather than DNA; in fact, it is quite hip. HIV acts as a typical RNA virus, dormant and zombie-like until it snags its favorite flavor of cell surface protein. And just as soon as HIV finagles its way inside its new host, is when the magic happens. The ace hidden up HIV’s sleeve is an enzyme known as RT or reverse transcriptase. As hinted by its name, this is the enzyme that turns the beat around!

Reverse transcriptase begins by taking the single strand of viral RNA and using it to fashion a new strand of DNA. But hold up: this seemingly innocent process is actually quite the stunt! In biology, DNA is used to make RNA, not the other way around. But since reverse transcriptase doesn’t seem to subscribe to the “save the best for last” mentality, it pulls this showstopper seemingly from nowhere. This opening trick, leaves one strand of RNA and one strand of DNA in a hybrid molecule of sorts. This is definitely something you don’t see every day, but if you blink you might miss it, as reverse transcriptase keeps the show entertaining by making the RNA strand disappear.

But RT is a performer of many talents, so it wraps up with a spectacular finale: crafting a new DNA strand from the lone DNA strand to fashion a double-stranded DNA molecule.

And just like that, the magnificent reverse transcriptase has transformed one measly strand of RNA into two DNA strands. But besides the wow-factor, why would HIV want this spectacle? I mean, RNA viruses can replicate themselves perfectly adeptly without reverse transcriptase. The secret that answers this inquiry is that this double-stranded DNA molecule is a clandestine operative that sneaks into a host chromosome and implants itself. Reminiscent of a “prophage,” this viral spy is known as a “provirus” and lays low until it is activated. The provirus unwinds itself and proceeds with copying itself and building new virus particles as any other RNA virus.

This show is full of awe-inspiring surprises, but also chock full of implications. For one, antivirals are few and far between, as when viruses replicate, they use enzymes and machinery from a host cell, and we do not want to inhibit something that might hurt our own cells. But reverse transcriptase is specific to retroviruses such as HIV. This means that even though RT is HIV’s secret agent, it is also its Achilles Heel. AZT is a potent inhibitor of HIV replication as it is able to grab onto and block its reverse transcriptase.

Either way, reverse transcriptase and retroviruses are super fascinating!

Beware the Cooties!

I thought we had left “cooties” behind in elementary school, but they’re making a repeat appearance nearly 15 years later in college!

 

Photo by Ed Uthman.

But, of course, these cooties are none other than the “kissing virus,” Mono, itself. And Epstein-Barr Virus or EBV, the tiny tyrant behind Mononucleosis, is astoundingly widespread. According to the CDC, nearly everyone has a run in with EBV at some point in their lives. In fact, 85% of 40-year-old United States residents have already been infected with EBV. It just happens to be that EBV infection in childhood is frequently asymptomatic. In other words, this infection might have snuck past us in childhood.

When it comes to our friendly, neighborhood rhinoviruses, it turns out that you can never suffer through the same cold twice! Our immune system learns from its mistakes; if it has already had to fight a specific microbe before, it keeps a few antibodies hanging around so that it can effortlessly spot and eradicate a repeat offender even several decades later. Talk about an impressive memory! But for EBV it is quite the opposite; you never seem to quite get rid of it.

EBV is a herpesvirus, a family notorious for viral latency. When EBV becomes latent, it just fundamentally comes to be that mooching roommate that seems to be constantly asleep. If you don’t take a close enough look, you might miss it! In latency, the virus slips an entire copy of its blueprints into the DNA of one of our cells but keeps itself under such tight lock and key that no more than a few viral proteins can be produced, not to mention an entire viral particle! But EBV can only stay under the radar behind enemy lines for so long; instead, it often rebounds and comes to be an active virus again! This latency might sound nearly identical to lysogeny in bacteriophages, and while it is quite similar, latency in mammalian viruses is much more rare, with herpesviruses and retroviruses being the only two substantial cliques of peek-a-boo fanatics among them.

EBV is spread effortlessly via bodily fluids including blood and saliva, hence its “kissing virus” moniker. But EBV can be acquired just as easily by sharing toothbrushes, utensils, food, or drinks! When EBV is latent, virus is not being churned out by our resident cellular virus factories to any detectable extent, and consequently a carrier of latent EBV (that is: most of us) is unable to spread the virus. But EBV is quite the surprise-party enthusiast, and if reactivated decades later, can begin to be spread yet again, even though our handy-dandy immune systems’ “second time is the charm” mentality keeps us from having outward symptoms.

Plus, symptoms of Mononucleosis vary drastically, but also typically include fatigue, sore throat, and swollen lymph nodes. Some symptoms can keep an individual bedridden for several weeks, but others might not trigger any perceptible symptoms. And even though most Mono cases persist for 2-4 weeks, others can take up to 6 months.

But keep yourself safe and healthy, by keeping your toothbrush and your fork to yourself and  the smooching to uninfected persons!

Take Care of that Lettuce!

I’m sure you’ve heard the iconic analogy between brains and Jell-O, or hesitantly reached a hand into a brown-paper bag containing “brains” only to find that it must have been mislabeled since it is just spaghetti! But the brain is a bit reminiscent of lettuce as well! The meninges, delicate layers of tissue that bear hug the brain, enfold the brain in much the same fashion as each leaf in a head of lettuce wraps around and looks out for those beneath it. When this tight-fitting, multi-piece lettuce suit gets rumpled or agitated, meningitis takes the stage!

 

Image of Jell-O brain by Angel Schatz.

And young adults between 16 and 25 (i.e. us!) happen to be one of the most affected groups! Just since we’re young and healthy, does not mean we can’t get meningitis. In fact, living in dorms and with roommates boosts our chances of being a not-so-lucky winner of this uber-contagious “vacation.”

Meningitis is just inflammation of the brain’s lettuce layers. This disease takes the “your greatest enemy is yourself” idea to heart, as the immediate antagonist is your own immune system! When the immune system, our own microbial Ghostbusters, replies to a call for help, it loosens up our capillaries and makes them ultra-leaky. This means that more blood can find the problem area quicker and more fluid gushes from capillaries into afflicted tissues. This slackening of TSA for our blood allows more white blood cells and other fighter cells to report to the battlefront asap! But this excess fluid and blood causes swelling, reddening, and heat and the immune system booby traps the area with pain signals to ensure that you baby that body part.

In other words, the immune system is the puppeteer behind inflammation! Now before you call mutiny, the immune system is on your side! Inflammation, although inconvenient, is a sign that your body is fighting back against an invader and is typically helpful. But in meningitis, it is a reckless move.

For one, the brain and its meninges room together in our one-bedroom skull, so when the meninges swell up, the brain gets squished, meaning it is under more pressure. This compression, although slight, of perhaps our single most important, and certainly irreplaceable (imagine a brain transplant!), organ is dangerous. Plus, since capillaries now lose fluid left and right and blood pressure has eased, less blood and consequently less oxygen is getting to the brain. A brain hungry for oxygen throws temper tantrums in the form of seizures and can also have nerve damage.

But as usual, the true culprit for meningitis is a microbe. Bacteria, viruses, fungi, parasites, and even amoebas (tiny, single-cell organisms that thrive in geothermal pools) can cause meningitis. But so long as you keep from dunking your head in hot springs (because we have so many in State College), I’d say you’re fairly safe from amoebas.

While viral meningitis is the most frequent, bacterial meningitis is direr, and on some occasions, even fatal. Bacteria such as Streptococcus pneumoniae (yep, the same big bad behind pneumonia!) and Neisseria meningitides tend to infect the respiratory tract before spreading via the blood to the brain.

Neisseria meningitides, in particular, causes meningococcal meningitis, the highly contagious form we face as college students. Scarily enough, some meningococcal cases cause severe, adverse side effects including brain damage, and 10-15% wind up being fatal. If that’s not incentive to always wash your hands, I’m not sure what is!

So how do we avoid getting our lettuce layers all rumpled?

Foremost, get the meningitis vaccine. Most of you likely have it already since Penn State requires it to live in undergraduate housing. But there is an additional vaccine for another type of meningococcal bacteria that is not required.

Plus, even if vaccinated, be sure keep an eye out for any symptoms that might peek out. And if you have any reason to believe that you might have meningitis, seek medical attention as soon as possible. Cases caught early tend to lack severe side effects and nerve damage.

Just look at Haemophilus meningitis, once the leading type, but today it is no more than a footnote in most meningitis articles. Why? Thank the Haemophilus Influenza B vaccine!

In other words, get vaccinated, be aware, and you’ll be a-okay!

Ancient Egyptians Know What's Up!

I assume everyone has had a scratch or even worse: the deadly papercut, before. Before Band-Aids and Neosporin, the ancient Egyptians’ go-to for healing the nefarious papyrus-cut was some good old mold. According to a publication in the Mycologist, Imhokep, a legendary Egyptian healer (later worshiped as a god of medicine), used mashed up moldy bread to treat skin wounds. While this might sound crazy, or at least counterintuitive when you consider ringworm and other fungal infections, it is actually way ahead of its time.

Named from the Latin word for paintbrush, Penicillium notatum (aka P. chrysogenum) is quite the artist. A fungus with the mycelium, hyphae, spores, and so on, it is particularly fond of decorating bread with some blue, green, and sometimes even yellow spores. And since Penicillium notatum is not prone to infecting us, although some can have allergic reactions to its spores, it is often used for student microbiology labs here at Penn State! In my Microbiology 203 lab class, our first experiment investigated ideal growing conditions for P. notatum. So, I speak from experience, when I say that this fungus is partial to room temperature and damp conditions!

 

Photo of Penicillium by AJC1.

But as you can guess from Penicillium’s spoiler of a genus name, we have this pesky, bread-poaching fungus to thank for one of the most important discoveries in microbiology. Ever.

What do you get when you cross a two-week vacation and a messy scientist? Apparently, the advent of antibiotics.

Alexander Fleming, a not-so-tidy lab technician, neglected to clean his lab bench before taking a two-week leave, and when he returned he noticed a bunch of white fuzz in one of his Staphylococcus cultures. Of course, this was our friendly neighborhood bread mold, Penicillium notatum! It was not P. notatum that made Fleming take another look; rather, it was how it seemed almost as if the fungus kept the Staph bacteria at arm’s length, not allowing it to come near! Plus, when Fleming took a closer look with a microscope, the bacteria seemed to be “lysing” or dying.

In the end, Fleming found that P. notatum secreted a substance able to kill Staph and a slew of other bacterial species. Upon isolating and examining the properties of this secretion, Fleming promptly passed it off to Howard Florey and Ernst Boris to tackle the impossible task of purifying it as a stable compound. And some 10-20 years later, we had Penicillin, the world’s first, and now the most widely used, antibiotic!

Ironically enough, in his initial publication about Penicillin, Fleming didn’t even mention using it for therapeutics! Instead, he focused on its ability to help identify bacteria since it could inhibit some bacteria but not others.

Speaking of inhibition, how precisely does Penicillin play bacteria’s kryptonite?

Penicillin’s claim to fame lies in its special “beta-lactam” ring of three carbons and one nitrogen atom. This ring is the lock pick to a bacterium’s ability to build cell wall. The beta-lactam ring grabs onto a specific type of transpeptidase (called Penicillin-binding proteins or PBPs), the enzyme that weaves strands of cell wall material together. Penicillin then becomes clingy and controlling, keeping a transpeptidase from binding to other molecules and doing its job, and allowing new cell wall to unravel.

But Penicillin is not only the granddaddy of antibiotics, but also a more select class known as Beta-lactam Antibiotics. The Beta-lactam club includes other antibiotic celebrities like methicillin, ampicillin, and amoxicillin!

And since our cells oh-so-conveniently missed the boat on getting a cell wall, Penicillin can keep who is the rival bacteria and who is the home team straight!

But why does bread mold even produce this medical wonder child?

Penicillium notatum evidently does not see anything wrong with playing dirty! When there is nutrients and space on the line, why not take out the competition? Penicillium notatum might be a friend to us, but not so much to the bacteria it is contending with!

It sounds like the ancient Egyptians were actually on the right track!

Mycelium, Hyphae, Spores, Oh My!

As hygienic, tidy college students, surely, we have never found our only slightly stale bread bedazzled with blue and green fuzz or our carpet (that hasn’t seen a vacuum since September) accented with a tasteful, mottled blemish. Right?

Photo by Helena Jacoba.

Enter fungi, the final member of microbiology’s big three! Both abundant and diverse, fungi range from the yeasts used in winemaking, to lichens that festoon trees, to mold on fossilized leftovers from the back of the fridge, and sometimes we even eat fungi on our Pizza!

And although we know upwards of 99,000 different fungal species, scientists find nearly 1200 new species each year! So, let’s touch on the criteria for a fungus.

Foremost, fungi is a eukaryote-exclusive club. To get in, you must show nucleus at the door. Accordingly, no one from the microbes we have been meeting and greeting with thus far even has a change! Viruses, for one, do not even have a cell, not to mention a nucleus, and as hinted by the designation “prokaryotic” or “before the kernel,” bacteria came before the nucleus. But since eukaryotic cells tend to be of larger volume and higher complexity, order is vital. To avoid losing enzymes within the vast cytoplasm or having a million and one different tasks going on simultaneously and interfering with one another (a metaphor for college life?), cells embraced a control freak approach. Each eukaryotic cell has everything for a specific process sorted and painstakingly packaged into tiny compartments or “organelles.”

Yet despite this additional nucleus and a handful of organelles, fungal cells tend to be fairly simple. Fungi have only 1% of the quantity of DNA we have and only 1.3 three times the largest known bacterial genome.

Fungi also value vintage and friends in high places! Not quite as ancient as bacteria, it is still estimated that fungi have been around for roughly 450 million years, about 25 million years before plants. Although an early species, fungi have actually been found to be more related to animals than to plants.  

And fungi have a few fun quirks and handy superpowers!

For one, a fungus does not digest its food within the cell, but rather, does so externally. The tiny molecules produced by this out-of-body digestion absorb into the cell via its walls.

So, how do fungi look?

Well, each genus and each species appears a bit different beneath a microscope, but the style that is simply all the rage among fungi is mycelium. Mycelium refers to the fungal body with branching thread-like protrusions. These ever-growing tentacles form from tube-like cells, known as hyphae.

But fungi also largely reproduce via spores. Spores, the survival kits of the microbial world, consist of only the necessities to whether a storm and pass on your genes: a cell or two carrying the genetic material of the fungus, some food, and any protective measures. Spores produced by fungi can withstand dry, hot environments before kickstarting growth upon reaching a favorable environment, but bacterial spores put them to shame with their incredible ability to withstand harsh environments. Yet, whereas these bacterial endospores serve merely as a survival mechanism, fungal spores predominately play a role in replication.

Photo by Nick Bramhall.

“Fruiting bodies” that produce these spores range from a variety of microscopic options to the shelf fungi and mushrooms we know so well! The diversity and unique nature of fungi (even when it has laid siege to your last slice of bread) is simply astounding!

Not Just a Passing Phage

Now let’s take a step back. Pathogenic bacteria. Antibiotic resistance. How do we evade this doom and gloom?

Well, someone is here to lend us a helping hand: the big, bad “bacteria-eater!”

In fancy (but, nonetheless cool) science mumbo-jumbo, this translates to “bacteriophage,” or just phage, for short. Funnily enough, phages were first discovered by two different scientists, in two different countries, around the same time! But considering that we now know that there exist more bacteriophages on Earth than stars in the galaxy, maybe it isn’t so astounding that two minds would stumble upon them simultaneously!

So, what exactly is this mysterious “bacteria-eater?”

A bacteriophage is simply a virus that infects bacteria. And just like our other favorite microbial “undead,” a bacteriophage is acellular, and thus not considered alive.

Photo by Drew March.

 But bacteriophages are not nearly as scary as zombies (save for the fact that some resemble microscopic spiders!) Rather, phages just boil down to a handful of proteins and your choice of nucleic acid for the assembly instructions. The DNA or RNA is kept within a hardy protein covering, studded with different surface proteins for some bling (and to perform important biological functions, of course! Talk about a two-for-one deal!) This is called the capsid or head of the virus.

Phages largely also have a slim protein tube or tunnel that nucleic acid dashes through to wiggle its way into a bacterium during infection. And in more complex phages, this tail sheath can be decked out with tail fibers: long, threadlike protein filaments that resemble the lanky, spindly legs of a daddy-longlegs!

Bacteriophages have breathtaking diversity! Some may be teeny-tiny, plain-Jane RNA phages with nothing more than a simple capsid and a hunk of RNA, while others may have gizmos and doodads such as baseplates, tail fibers, and an array of surface proteins sprucing up their already intricate capsid, out the wazoo!

But phages can be picky eaters (a phenomenon almost unheard of among college students!) For a phage to be able to grab onto a bacterium, there must be a painstakingly precise molecular interaction between a surface protein in the bacterial cell wall and the tail of the virus. Since this attachment is so tightly under lock and key, a given phage typically has an exclusive VIP list of hosts it can party with. Just look at “coliphages” like T2 and T4 that selectively infect E. coli.

 

Photo courtesy of  MicrobiologyBytes.

But once a phage has hitched itself a ride on a bacterium, it injects its DNA or RNA into the cell and right into a “choose your own adventure” book. If the environment is good to go, the nucleic acid launches its sneak attack and hijacks the cell to copy itself and use itself as a blueprint for new infant viruses. But the virus also has genes for the ace up its sleeve: lysosome. This enzyme is essentially a wrecking ball to a bacterial cell wall, all but obliterating it, to allow fledgling phages to burst free and infect nearby hosts. Since this option demolishes or “lyses” the host bacterium, it is fondly named the lytic cycle.

But the flip scenario is in an environment with a red flag, a bacteriophage will instead initiate stealth mode. In this undercover state, that is: the lysogenic cycle, the phage slips its DNA into the DNA of the bacterium so that when the bacterium divides future generations also get the bonus phage DNA. But if the environment were to somehow shift, it can activate the phage DNA, throwing the unsuspecting bacteria right into the midst of the lytic cycle! Espionage at its finest, if I do say so! But not all phages have these sneaky spy skills; rather, these tricksters get a special code name: temperate phages.

Although we can thank phages for a multitude of scientific discoveries and our comprehensive understanding of molecular biology, since their discovery was followed closely by that of Penicillin and thus the advent of antibiotics; we have rarely seen them in therapeutic use, especially in the western scientific community. But as more and more bacterial strains acquire handy-dandy antibiotic resistance, some scientists have begun turning to our friendly neighborhood bacteriophages!

Not only do bacteriophages mutate and evolve with bacteria, but there exist literally countless phages capable of lysing a single strain of bacteria.

Promising, no? Maybe the natural predators of bacteria should take the wheel!

Beware the Escape Artist!

MRSA, the marvelous Houdini of bacteria, has taken the stage yet again! 

For its debut stunt, staph aureus faced down the fearsome antibiotic, penicillin, and miraculously, it managed to evade this formidable foe! But how, you might ask? Staph aureus had an ace up its sleeve: penicillinase! This enzyme breaks the chemical bonds in penicillin, rendering it inept. So, scientists drew up a new challenge for the master illusionist. When bulky side chains were added to a penicillin molecule, turning it into methicillin, it befuddled penicillinase. But staph aureus still had a few more tricks up its sleeve.

Antibiotics such as methicillin and penicillin bind to proteins called PBPs or penicillin binding proteins. Staph aureus has four of these PBPs that happen to be critical in building new cell wall. When penicillin latches onto these proteins, it leaves them useless, causing cell wall upkeep and growth to plummet.

But staph aureus refused to be outsmarted. Not only has it pulled “methicillin-hydrolyzing beta lactamase,” a novel form of penicillinase that disrupts the bonds in methicillin, seemingly out of thin air, but it also has come up with a never-before-seen version of its second PBP! PBP2a is far less receptive to binding methicillin, so when methicillin stops the other PBPs in their tracks, PBP2a can pick up the slack and keep cell wall construction humming along!

It is simply astounding how staph aureus, the modest round bacterium behind many skin infections, has tamed the impossible and come to be the infamous methicillin resistant staph aureus (MRSA)!

Photo courtesy of NIAID. 

In fact, nearly one-third of us carry staph aureus in our nose or on our skin without harm. It is only able to cause more severe infections along the lines of pneumonia or even life-threatening sepsis, if it finagles its way inside, such as via a cut or surgical incision.

And as its name implies, MRSA can no longer be subdued with methicillin. But this just scratches the surface. The magician is resistant to a plethora of other antibiotics including penicillin, amoxicillin, oxacillin, and on and on! And it just keeps doing the impossible and finding ways to dodge any antibiotics we throw at it!

Recall me citing antibiotics as saving the day in last week’s post about pneumonia? Well, superbugs like MRSA have become our antibiotics’ kryptonite.

On the bright side, however, through much research, we have come to understand the tricks and sleight of hand behind antibiotic resistance.

Bacteria reproduce extraordinarily quickly, “doubling every 4 to 20 minutes” according to PNNL. This means that bacteria can evolve new genes with a breathtaking velocity. All it takes is a single mistake in copying the cell’s DNA, generating a slightly different protein. Just look to PBP2a. This penicillin-binding protein is a barely distinct form of PBP2, but it is different enough to keep from binding methicillin!

And once these resistant proteins have come to be, their blueprint DNA is often kept in small circles of DNA, called plasmids, that float around in a bacterial cell. These “DNA bubbles” can be copied and shared with other bacteria, spreading resistance in a flash.

Antibiotic resistance is an enormous issue for medicine and consequently a vast field of research in microbiology right now, especially since MRSA and other resistant bacteria can be spread through contact so effortlessly!

But MRSA does not only affect hospital patients; rather, it can sweep through a community through shared equipment and spaces such as gyms. In fact, the average age of a patient with community-associated MRSA is 23 years old.

Image by Arlington County. 

Harrowing isn’t it? Just remember to be diligent about washing your hands, covering open cuts and scrapes, and keeping your clothes clean. And while you are at it, check out some of the cool research going on with combating resistance and finding antibiotic alternatives!