Starting college biology this fall? Here are some tips

As someone who’s taught thousands of students, I have a few tips for those of you kicking off the semester. While my focus has always been biology, these pretty much apply to almost any course.

1. Go to class. It’s the number-one thing you can do to do well. Don’t sleep in. Don’t skip just because you got to talking with someone in the coffee shop who’s pretty hot and you’d rather sit there making progress than make progress just at that moment in class. Go. To. Class. Trust me.

2. Take notes in class. Good, thorough notes. If your professor allows it and you learn best through listening, record the class. Always ask permission first.

3. Ask questions in class. How your instructor receives questions may determine how nutty you can get with this. I always welcome questions because my experience tells me that if one student doesn’t understand something, about 12 more who aren’t speaking up don’t get it, either. Consider yourself their spokesperson, raise your hand, and ask.

4. Do readings before class. Even if you don’t understand half of what you read, at least vocabulary won’t be a total shock to you. If you do understand it, then lecture should serve as good reinforcement. Also, I think too many students overlook figures and graphs in reading material. Make sure to review and understand them, as graphic representations in biology are often the most relevant ways to learn the material.

5. Understand your working vs. long-term memory. You must transfer from one memory bank to another. The best reinforcement you can do is to review your notes/reading as soon after lecture as possible. Get that information in there through this second review, whether it’s by re-reading, a study group/partner, or listening to your recorded lecture again.

6. Don’t start studying for an exam the day before the exam. Start studying for the exam whenever you get new material. That means after every class. This isn’t high school. Much of this information is complex and requires time for absorption and real understanding. You’ll do yourself a huge favor if you study every day after class as though you had quiz over new information the very next day.

7. If your instructor indicates being amenable, take advantage of emailing/message boards/other interfaces to ask questions for clarification as you study. My best students often were those who emailed me questions as they went along. These students were not, however, the ones who tried to blanket me with my own review questions the night before a big exam, hoping I’d answer them.

8. Use office hours, especially to clarify last-minute questions or complex information. If your instructor is not a fan of electronic communication, use the office hours.

9. Think like your instructor. What have they emphasized in class? Are there copies of old exams (legally acquired) that might give you an idea of how they ask questions or what depth they’re expecting for answers? If you were writing a test over this material, what would you ask? Ask it, and then answer it.

10. Go to class. Have I mentioned this one yet?

Next up: How to study for biology.

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How Bumpy the Jelly eats without tentacles

Robot explores the deep sea

The deep dark layers of the sea—where sunlight doesn’t penetrate and oxygen levels drop as precipitously as the ocean shelves—may be home to some of the last great mysteries of our planet. New discoveries lie hidden in the depths, but it takes a robot to assist us in uncovering them.

The Monterey Bay Aquarium Research Institute in California has such a robot, Ventana, a deep-diving submarine robot that can roam the dark parts of the ocean where humans cannot go. In 1990, Ventana came across an unusual jelly(fish) in the mesopelagic zone, between 500 and 1800 feet down, where sunlight does not penetrate, but oxygen levels remain relatively high. This jelly was weird among its brethren. It had four fleshy arms that trailed behind its softball-sized gelatinous body (or bell), but no tentacles. Wart-like bumps covered its arms and bell, and as it moved through the water trailing its arms, it looked like a slow-moving meteor or translucent blue shooting star.

An elusive, warty marine invertebrate

Marine scientists at the aquarium were intrigued, but they felt they needed to find out more before introducing the jelly to the world. Over the next 13 years, they had only seven sightings of the animal, five in Monterey Bay, and two sightings 3000 miles away in the Gulf of California. It was the latter two, in 1993, that surprised them, because it demonstrated that the new jelly was not just a local creature endemic to Monterey Bay, but might have a wider distribution.

They captured at least one of the jellies, anxious to find out more about its habits. They placed their captive in a tank with small shrimp and pieces of squid and watched. The bits of squid and hapless shrimp collided with the bumps on the jelly’s bell and stuck there. Over time, the prey moved slowly down the bell, was transferred to one of the “arms,” and then slowly moved up the arm and into the mouth. The “arms” appeared to serve as lip-like extensions for prey, much as pseudopodia serve as prey-capturing extensions for some cells, like macrophages.

The jelly’s feeding mechanism was unusual, as were its choices in prey size. The animal probably dines on some of the many other jellies that inhabit its zone, and it appears to favor prey a little larger—at ¾ to two inches—than the average jelly prefers.

It’s a triple! A brand new subfamily, genus, and species!

Given these unusual characteristics, the scientists who made the discovery designated this jelly—which they had heretofore called “Bumpy” in honor of its appearance—a new subfamily, genus, and species. They assigned it the subfamily, Stellamedusidae, and gave it the species name Stellamedusa ventana. “Stella” derives from “star” because of the jelly’s shooting-star-like appearance as it moves through the water; “medusa” is a common name for jellies; and “ventana” comes from the robot submarine without which the researchers would never have made their discovery. This additional subfamily brings the total number of jelly subfamilies to eight and is quite a find; lions and housecats belong to the same family, but are in different subfamilies, so S. ventana is as distantly related to other jellies as the “king of the jungle” is to Kitty.

Patience: They waited 13 years to report this

Although the jelly is unusual among other jellies in lacking tentacles, the researchers who identified it and published a paper on their discovery in the Journal of the Marine Biological Association of the United Kingdom, say that several deep-sea species have evolved in a similar way, using “arms” instead of tentacles. The researchers waited 13 years to report their find because they wanted to uncover more information about S. ventana, but the creature still remains an enigma. In spite of its potentially wide distribution, it apparently has never turned up in fishermen’s nets and, with only seven sightings in 13 years, remains elusive.

Crazy cat lady may have microbe to blame

Toxoplasma gondii is the cat-borne parasite responsible for causing toxoplasmosis and a host of other problems in humans. This close relative of the malaria-causing protozoan may drive human behavior and immunity, in addition to causing acute illness and devastating birth defects. Recent research points to a single gene underlying this parasite’s virulence in the human host. It’s scary yet fascinating to think that a single gene from a single organism could have such dramatic effects on our species.

Warning pregnant women away from litter boxes

Because T. gondii infection can result in serious fetal defects, many pregnant women have heard of toxoplasmosis, an illness that often goes unnoticed in the afflicted person. Pregnant women are warned away from cat litter boxes and even away from gardening because contact with cat feces can mean contact with the parasite. T. gondii spends the sexual part of its life cycle in cats, but for its asexual life, it can parasitize a number of hosts, from pigs to lambs to mice to people. People also can acquire the infection from eating undercooked meat or drinking contaminated water. In some countries, like Brazil, up to 60% of the population has been exposed to T. gondii; in the United States, about 33% of people tested have antibodies to the parasite, indicating past infection.

Link between parasite and schizophrenia

The “crazy cat lady” has practically become a social stereotype in the United States and other countries, conjuring the image of a woman who lives with 25 cats and talks to herself a lot. But researchers investigating schizophrenia have actually identified a potential link between people who are exposed to Toxoplasma infection and the manifestations of schizophrenia; for example, several studies have identified higher levels of antibodies to the parasite in people with schizophrenia, and infection with Toxoplasma can cause damage to brain cells that is similar to the damage seen in patients with schizophrenia. Toxoplasmosis can also sometimes lead to symptoms of psychosis.

The fact is that most people don’t know they have toxoplasmosis because they have healthy immune systems. In people with compromised immunity, however, such as those with HIV, T. gondii can precipitate an extreme form of dementia that eventually kills them. The dementia is so severe that the sufferer eventually becomes completely unaware of his or her surroundings and lapses into a coma. The bug, however, also can affect the central nervous system in healthy people and is also linked to severe eye problems even in patients who are not immunocompromised. One researcher has claimed that infection with the parasite makes men dumber and women act like “sex kittens.”

ROP18: Watch out for this one

There are different strains of T. gondii, and investigators have noted that the Type 1 strain is most closely associated with disease. Studies of T. gondii, which has a genome with about 6000 genes, have pinpointed the virulence capacity of the strain to a single gene, dubbed ROP18. This gene encodes a kinase, one of a huge class of cell signaling proteins that add phosphates to molecules. Typically in cell signaling, kinases exist in a series, phosphorylating the next protein in the pathway, which helps maintain regulation of the signaling. The most virulent T. gondii strains have a form of the gene that differs from that carried by benign strains. Researchers speculate that this kinase interferes with a cell’s normal signaling, hijacking it for its own purposes, including growth and reproduction. The good news is that because kinases are so important in cell signaling, pharmaceutical companies have developed libraries of molecules that inhibit specific kinases, so one potential path to preventing toxoplasmosis is to discover an inhibitor of ROP18.

Rats get a little nutty from it, too

Not only has this parasite been linked to the ability to alter human behavior, but it also appears to alter rodent behavior in ways that favor its own reproduction. For example, rodents exposed to toxoplasma via cat feces actually become more likely to hang out near cat urine. If a cat eats the infected animal, the toxoplasmosis bug can then move into the sexual phase of its life cycle in the cat.

Magnetic fields and the Q

Sorry, not for Trekkies. This Q is chemical.

People have been concerned for years about magnetic fields having adverse health effects–or even have peddled magnets as being health beneficial. But although scientists have demonstrated repeatedly a chemical response to magnetic fields, no one has ever shown the magnetic fields directly affecting an organism.

The earth’s core is weakly magnetic, the result of the attraction between electric currents moving in the same direction. Nature presents plenty of examples of animals that appear to use magnetic fields. Some bacteria can detect the fields and use them for movement. Birds appear to use magnetic fields to navigate, and researchers have shown that attaching magnets to birds interferes with their ability to navigate. Honey bees become confused in their dances when the earth’s magnetic fields fluctuate, and even amphibians appear to use magnetism for navigation. But no one has clearly demonstrated the mechanism by which animals sense and use magnetic fields.

Do pigeons use a compass?

Some research points to birds using tiny magnetic particles in their beaks to fly the right way. But these particles don’t tell the birds which way is north; they simply help the bird create a topographical map in its head of the earth over which it flies. The magnetic particles tell a pigeon there’s a mountain below, but not that the mountain is to the north. The conundrum has been to figure out how the pigeon knows which way is north in the absence of other pointers, such as constellations.

The answer to the conundrum lies with the bacteria. Scientists in the UK have used the purple bacterium Rhodobacter sphaeroides to examine what magnetic fields do at the molecular level. These bacteria are photosynthetic, and absorb light to convert to energy in the same way plants do. The absorbed light triggers a set of reactions that carry energy via electrons to the reaction center, where a pigment traps it. Under normal conditions, as the pigment traps the energy, it also almost instantaneously converts it to a stable, safe form, but sometimes the energy can form an excited molecule that can be biologically dangerous. As it turns out, these reactive molecules may be sensitive to magnetic fields.

A radical pair…or dangerous triplet

A chemical mechanism called the “Radical Pair Mechanism” is the method by which the potentially dangerous molecules can form. In this mechanism, an electron in an excited state may pair with another type of electron in an excited state. If the two excited molecules come together, they can form what is called a “radical pair in a singlet state,” because they are two singlets that have paired. Under normal conditions, this pairing does not happen; in the photosynthetic bacterium, for example, a compound called a quinone (Q) inhibits formation of this pair or of an equally damaging triplet of one electron type or the other.

But when a Q is not present, the singlet or triplet state results. If the triplet forms, it can interact with oxygen to produce a highly reactive, biologically damaging singlet molecule that we know as a “radical.” You have probably heard of radicals in the context of antioxidants—they are the molecules that antioxidants soak up to prevent their causing harm. You may also have heard of carotenoid, a pigment that is an antioxidant. In a normal photosynthetic bacterium, the carotenoids present serve as the Q, the compound that prevents formation of the damaging radical.

A helpful effect of magnetic fields?

Where do magnetic fields come in? Previous work indicated an influence of magnetic fields on triplet formation, and thus, on radical formation. One excellent model to test the effects of fields in a biological system is to remove the Q, the molecular sponge for the triplets, and then apply magnetic fields to see whether triplets—and radicals—form.

That’s exactly what the researchers did, using a mutated form of R. sphaeroides that did not make carotenoids—the Q. The result? The stronger the field, the less radical product was made. They have demonstrated a magnetic field effect in an organism for the first time, and the effect was helpful, not damaging. Their next step, which they are working on, is examining whether or not the bacteria grow better in the presence of the fields.

Rats are fast, cheap TB detectors

An unpredictable killer continues to kill

Can you name the disease that killed Chopin, Keats, Descartes, Kafka, Florence Nightingale, Eleanor Roosevelt and 200 million more people in the last 100 years? It’s tuberculosis, formerly known as “consumption,” and now known as TB. The tuberculosis bacterium, Mycobacterium tuberculosis, is an airborne pathogen that can be passed on from people with active cases of TB and usually settles in the lungs, where it can flourish and cause infection. It is possible to have what is known as “latent TB,” a situation in which you harbor the bacteria, but do not manifest the disease and are not contagious. Worldwide, World Health Organization predicts that the numbers of people who die from TB will climb to 8 million by 2015.

Experts agree that generally, when TB is caught early and treated, it is curable. But with millions of people suffering from it—including people with suppressed immune systems, such as those with HIV infections—detecting every case of TB is a tough job. Current methods require three saliva samples taken over a two-day period to be prepped on a slide, stained, and examined by a trained technician for the presence of TB bacteria. A good technician can analyze about 20 samples per day; for the 8 million people who may have TB in 2015, it would take 1200 technicians working 365 days to identify them all. One thing desperately needed in nations without the funding for technicians is a fast, accurate, low-tech way to analyze samples for the presence of TB.

Bacteria, explosives…whatever

Enter the rat. Bart J.C. Weetjens, who is not a rat, but a scientist working for Apopo, a Belgian company based in Tanzania, had one of those “chance favors the prepared mind” moments. He realized that the Dutch word for tuberculosis, tering, means something along the lines of “that’s starting to smell like tar.” Given that traditional Chinese medicine includes using smell to diagnose TB, Weetjens concluded that a trained animal might be able to detect TB, much in the way a bomb-sniffing dog detects explosives. It just so happened that Weetjens’ company had already trained a native African giant pouched rat, Cricetomys gambianus, to use its olfactory faculties to sniff out land mines. Weetjens decided simply to substitute TB bacteria for explosives.

The rats were uniquely qualified for the job. Unlike most nocturnal predators, these animals have very small eyes, indicating a strong reliance on olfactory and aural senses. During the day, they seem blind, sniffing the air rather than looking around. They can grow as large as a cat, are omnivorous, easily tamed and trained, and great breeders; a single female can produce 10 litters of up to four young each year. Weetjens took his idea to the World Bank, which agreed to fund a complete study of the rats’ ability to sniff out TB.

HeroRats

Weetjens already reported preliminary results that indicate the rats may be a viable way to ID TB. The rats identified 77 percent of infected saliva samples, and 92 percent of cultured bacteria samples, with a false-positive (indicating bacteria where there were none) rate of 2 percent. The current human-based process has an accuracy rate of about 95 percent, but Weetjens figures that with several rats analyzing samples, the rats’ accuracy will match the humans’. According to Weetjens, the rats can analyze 126 samples in 20 minutes, making them a very cheap, fast diagnostic test. The analysis of 8 million samples that would have taken 1200 humans 365 days would take only two rats working the same period of time. The latest data indicate similar success rates.

Ancient warfare captured in amber

The soldier vs. the cockroach

About 100 million years ago, a soldier beetle of an ancient type found itself under investigation by the antennae of a much larger animal, possibly a giant cockroach. Understandably alarmed, the small soldier beetle, only about a quarter of an inch long, immediately fired off a shot of offensive chemical from one of its rear glands. Just as it released its toxic dose, a wave of sap engulfed it, forever freezing the moment in amber and taking with it the antennae of the larger predator.

We would never know a thing about this tiny event from millions of years ago were it not for the preservative properties of amber. It starts out as sap dripping down a tree but has captured for us some of the most amazing, ancient finds in the history of fossils. Recent reports have included the discovery of the oldest bee species and even the presence of the malaria pathogen in the blood of an amber-preserved mosquito. Finds like this make amber a window into an ancient world showing us things we otherwise would never see.

Small-scale wars in a big world

The scene between the cockroach and the soldier bug would have been lost to history without the amber. But now we know that chemical warfare, today widely practiced by a variety of insect species, existed at the time of the dinosaurs. As Tyrannosaurus rex made its way across the landscape leaving its tri-toed footprints in the mud, soldier beetles were busy waging their war against killers on a much smaller scale.

Insects today employ this tactic so frequently that it featured as the central trait of the most frightful insect villain in movie history, the sulfuric-acid squirting super-killer in the Alien series. Some modern insects do actually shoot acid as a form of defense; in fact, the modern version of the soldier beetle fires off a mean shot of carboxylic acid at anything trying to eat it. Other nasty mixtures insects use today include chemicals that make the predator vomit or at least spit out the intended snack.

The amber that captured the David vs. Goliath battle between the hapless soldier beetle and its cockroach attacker was found in an amber mine in Myanmar, formerly Burma. This mine has been a treasure trove of biological finds trapped in amber, discoveries that tell us things about ancient ecosystems that we otherwise never would know.

What we do know is that this ancient species of soldier beetle liked to eat aphids, other little insects, and plant pollen, which may have been why it was on the tree in the first place. It had seven pairs of chemical-firing glands along its abdomen and was able to pick and choose which ones to use, depending on the angle of the predator. In the case of the amber-encased soldier beetle, it was employing only one gland and had actually achieved a successful shot, engulfing the predator’s antennae in the presumably noxious chemical before succumbing to the flowing sap.

Don’t crack my amber!

No one knows exactly what the chemical was because the person who owns the amber and the scientist who discovered the beetle refuse to allow eager entomologists to examine the encased remains. Many entomologists would be thrilled to extract DNA from this specimen, to be able to compare it to other sequenced ancient and modern samples. Others would like to identify what this earliest known practitioner of chemical warfare was using in those seven accurately firing glands. But to get at these samples, the entire specimen would have to be ground up and completely destroyed, something the amber’s owner, a collector of such pieces, refuses to allow.

And, for the geeks…a new dating for the soldier beetle?

As consolation, entomologists will have to accept another prize. This particular fossil pushes the dating of this species of soldier beetle back by 60 million years, newly placing the little bug squarely in the time of the dinosaurs.

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