To Pranburi and Back!!

On the 20^th of September, Ruamrudee International School's IB Biology HL year two classes loaded up two buses and drove to Pranburi. Worn out from the long and ever so eventful bus ride where nobody caught a single wink of sleep, we reached the hotel absolutely beat. From there, my roommates (the ever so lovely Om and Pinky) and I climbed up our 3 flights of stairs to our love suite hotel room (honestly, it had such a romantic ambiance that it could have passed for a honeymoon getaway, which was pretty cool). After a 5 minute break, we headed for the beach, were we conducted a short reconnaissance of the beach in search of organisms in the marine ecosystem. Once we'd all thoroughly exhausted our supply of beach biota to photograph, we were treated to a scrumptious dinner, followed by group cheers (hilarity all around--the intense creativity of scientists is truly something to behold!!). By the time we were sent off to bed, nobody even thought about going past curfew--sleep was priority one.

The next day, after another intensely delectable meal of bacon (mmmmm),eggs, and other mouthwatering goodies, we loaded up the buses again and zoomed off to the mangrove forest!! There, we conducted investigations on the ecology of a mangrove forest and the rocky shore area of the nearby beach. The mangrove forest we visited was situated next to Pranburi River, while the rocky shore was a man-made structure protruding from the sandy shore into the ocean. The two aforementioned explorations will be the subject of the following two blogs:

Mangrove Investigation

Top: mangrove A
Bottom: mangrove B

At the mangrove forest, we investigated two areas. One area was next to Pranburi River, which will be referred to as mangrove B for the remainder of the blog, while the other was further inland, and will be referred to as mangrove A. Mangrove B was dominated by yellow mangroves, whereas mangrove A was dominated by grey and red mangroves. 

At each site, both abiotic and biotic factors were observed. With regards to abiotic factors, the temperature, dissolved oxygen, pH levels, salinity, water quality, turbidity, water depth, light intensity, and substrate were tested, and the results were recorded and compared. 

In order to assess the biodiversity of each site, the Simpson’s Diversity Index was used, and the number of organisms present for each species observed was recorded. At mangrove A, the data collected was restricted to a single 1 meter by 1 meter quadrat, while at mangrove B, the data was collected using a perpendicular transect. Approximately 10 meters long and 1 meter wide, the transect ran perpendicular to Pranburi river.

As it was the first time I had ever been in a mangrove forest, everything I saw was new to me. The first lesson I learned was that mangrove ecosystems have amazing biodiversity, and that, although it looks rather serene from the point of view of someone standing on the boardwalk, the roots of the mangroves house multifarious organisms. I also learnt that, while the mangroves by the river were completely different in structure from those inland, they were still all mangroves, but were just of different species. On a lighter yet more traumatic note, I also learned that red ants in mangrove forests are crazily sticky--once they cling onto your shirt, or even PAPER, you'll have a super difficult time getting them off--blowing is futile. Adaptation and natural selection, anyone? 

After our investigations, we were further familiarized with the Pranburi mangroves as we compared the data from the two sites. Our large group was split into smaller groups, with a total of 12 people collecting data in my group (The Red Crabs). Once in that small group, we were split into 2 more groups (R-1 and R-2), so each group of 6 collected data on their own, resulting in two sets of data per site. The data from which we drew our conclusions is represented below.

Table 1: Abiotic Factors in Mangrove A and B--reports the air and water temperature, dissolved oxygen levels, pH levels, salinity, substrate descriptions, water quality, turbidity, depth of water, and light intensity in both sites.

Table 2: Biotic Factors in Mangrove A and B--reports the species present and the abundance of each species in both sites. * The red and yellow coloring indicates the species of mangrove present--red codes for red mangroves (specifically Rhizophora mangle), while yellow codes for yellow mangroves (specifically Cerops tagal).

  

Figure 1: Comparison of Species Abundance in Mangrove A and B--graphically displays the numbers of each species present at each site.

Using this data, we can calculate the biodiversity of each site using the Simpson’s Diversity Index. This uses the formula: Diversity (D) = [N(N-1)]/∑[n(n-1)], where N is the total number of organisms, and n is the number of organism of a particular species. The higher the D value, the higher the diversity. Plugging in our values for the abundance of species at each site, we get 3.88 for site A, and 1.56 for site B, showing that there is a greater biodiversity inland than next to the river.

From the above data, and the Simpson’s Diversity Index calculations, we can conclude that the environment that the inland red mangrove forest provides is more conducive to biodiversity than that which the riverside yellow mangrove forest provides. What must be noted in looking at the results is also that the yellow mangroves are much smaller species which do not sport stilt roots, and thus live in dense clusters, while red mangroves do sport stilt roots and thus cannot be that close together. This is the reason for the small number of mangroves in the quadrat we observed at the inland site (mangrove A).

With regards to abiotic factors, site A (inland) had higher air temperature and turbidity (the lower the turbidity the clearer the water) than site B (riverside), as well as soil that was more moist and muddy, rather than sandy, while site B had higher water temperature, dissolved oxygen, pH, salinity, and nitrate and phosphate levels. The light intensity in both areas was low, as there was thick foliage due to the tall mangroves. This makes sense because it is near the river, which flows rather rapidly and therefore has more dissolved oxygen, and there is a constant flow of nutrients which come with the river’s current. Therefore, technically, mangrove site B should be more conducive to the growth of organisms, as high dissolved oxygen and nutrient levels means fertility and better living conditions for most organisms. It must also be noted, however, that while mangrove A’s ground was submerged in water, mangrove B was completely dry, with the exception of the river. This means that the quality of the river water has little effect on the growth of the organisms in mangrove B, as the mangrove forest was not in the river, but next to it.

Additionally, it must also be noted that site A has many organisms which are adapted to the environment already and can survive perfectly well in the saline, submerged environment. This includes fish, crabs, and tapeworms, all of which would not live amongst the mangroves in site B, but in the river, and as such were not included in our observations. Therefore, I learned, from this investigation, that despite the apparent serenity of the red mangrove forest and the difficult conditions (what with all the water which went up and down with the tides, which I figured would prevent fish and snails from inhabiting the area), it is actually a diverse ecosystem because the organisms living there are adapted for the environment already. Additionally, I learned that the mangrove forests are protectors of the coast, slowing down waves, lessening the impact of natural disasters such as tsunamis and hurricanes, and providing a safe environment for the growth of organisms, so much so that it can be called a nursery.

Rocky Shore Investigation:

After our tumble in the mangrove forest with malicious branches and super-sticky red ants, we had a charming lunch at a beach-side hotel. Lunch itself was awarding enough, but afterwards, we were given free time to frolic on the sandy shore, taking pictures and having a completely carefree break--something that is so hard to come by these days. Although I'm sure we all wanted it to last the rest of the day, we of course had to get back to the point of the field trip and continue our investigation at the nearby rocky shore, which turned out to be really fun anyways.

At the rocky shore, which was essentially a man-made platform extending into the ocean constructed out of rocks piled on top of each other, we used a perpendicular transect to see the abundance of various organisms as we went further into the ocean. As the rocky shoreline had a gentle slope as it went deeper into the ocean, we were able to calculate the slope by using the following set up:

The quadrats, which were 0.5 meters by 0.5 meters, were placed adjacent to each other going from the lowest pole and away from the ocean towards the highest pole. In each quadrat, the number of organisms was counted and recorded. To determine the total distance between the poles, a tape measure was used and the distance was measured perpendicular to the poles (along the red line), which stood straight up. In addition to taking inventory of all the organisms present along the continuous belt transect, we also measured the abiotic factors, which included air and water temperature, wave frequency, wind direction, aspect, and light intensity.

As was earlier mentioned, there were two sub-groups in our Red Crab group, and my group, R-1, went to the open-ocean side of the platform, while R-2 went to the beach-facing side of the platform. As the data for R-2 somehow disappeared, the following comparison will be using R-1's data collection for the open-ocean condition and the pink group's data collection for the beach-side condition. As the quadrats were numbered differently between our two groups, the table below might look flipped compared to the pink group's tables, it had to be reformatted so that each quadrat referred to the same thing. 

Once we collected our materials, we waded into the water (which was hip-deep--which meant that I dunked my camera in the seawater several times--I'm sorry, camera!! >3<) and began our investigation!!

Table 3: Abiotic Factors at Rocky Shoreline--indicates the air and water temperature, wave frequency, wind direction, aspect, and light intensity at both the open-ocean and beach-side sites. 

Table 4: Biotic Factors at Rocky Shoreline for Open-Ocean Site--indicates the abundance of each species according to quadrat.

Table 5: Biotic Factors at Rocky Shoreline for Beach-Side Site--indicates the abundance of each species according to quadrat.

Figure 2: Kite Diagram of Species Abundance at Open-Ocean Site--indicates the abundance of each species observed along the rocky shoreline for the open-ocean site, with quadrat 1 being furthest into the ocean, and quadrat 6 being almost completely out of the water.

Figure 3: Kite Diagram of Species Abundance at Beach-Side Site--indicates the abundance of each species observed along the rocky shoreline for the beach-side site, with quadrat 1 being furthest into the ocean, and quadrat 6 being almost completely out of the water.

As the first kite diagram above (Figure 2) shows, the abundance of rock periwinkles, acorn barnacles, limpets, and knobbed periwinkles increased as we went further from the ocean and up the rock shoreline. However, there appears to be an optimal location for these organisms, as there were 300 acorn barnacles in the 5^th quadrat, and none in the 6^th. The same goes for rock periwinkles, as there were 9 in the 3^rd quadrat, 6 in the 4^th, 5 in the 5^th and none in the 6^th. For limpets and knobbed periwinkles, we can assume that the optimal location is either further inland, as it is not contained in our transect area, or they simply were not abundant at the location which we were investigating.

The second kite diagram shows a slightly different distribution of organisms. The knobbed periwinkles are more widely distributed between the 6 quadrats, with the most at quadrat 5. On the other hand, rock periwinkles were only found in quadrat 6, compared to the wider distribution on the open-ocean side. Acorn barnacles, however, were most abundant in quadrat 5 in both conditions, although the number of acorn barnacles in the open-ocean condition was much higher (300 barnacles) compared to the number of acorn barnacles in the beach-side condition (7 barnacles). Lastly, limpets were apparently much more abundant on the beach-facing side of the platform, although the amounts on each side were difficult to compare accurately, as R-1 counted the number of limpets, while the pink group measured the abundance in percent.

From this investigation, I learned that different organisms are adapted for different environments. The difference in distribution of the organisms on either side of the platform would most likely be due to the different abiotic factors. One obvious difference was wave frequency--which was at 20 waves per minute on the open-ocean side, and 16 waves per minute on the beach-facing side. This might mean that certain organisms which aren't able to deal with the turbulent waters would have to occupy later quadrants which were further from the ocean, so that they wouldn't be hit with the full brunt of the waves and be washed off the rocks or killed. Of course, it’s not like this concept of adaptation affecting habitat hasn’t been taught to biology students again and again, but to see it in nature so obviously like this is still awesome.

In conclusion, I learned a lot about ecology and how to use lots of different equipment throughout the course of our biology field trip. But despite our busy schedule, I had a lot of fun, cooperating with classmates while conducting our investigations, enjoying group activities, and socializing during dinner. Every night my roommates and I got back to our rooms absolutely exhausted and fell asleep as soon as our heads hit the pillow, but it was definitely a trip I’ll always remember fondly!! The most memorable part might have been the present-giving on the last night--everybody's presents and speeches were just so touching and authentic or unique in some way that it was probably the best secret-Santa type activity I'd ever seen.

Evolution, Natural Selection, Snails, and Mice

Evolution is the process in which characteristics of populations change over time, and natural selection is a mechanism by which evolution can occur. Natural selection occurs in a population in which overproduction leads to competition between offspring which exhibit variation in their heritable characteristics. Those who are the most fit to survive and reproduce pass their characteristics down to the next generation, while those which are less fit die out before they can reproduce due to the limited carrying capacity of the ecosystem to which they belong. The characteristics which best promote the survival of the organisms possessing them, giving them an advantage over those who don’t possess those characteristics, get passed down through generations and increase in frequency.

This is the case with Cepaea nemoralis, terrestrial snails which exhibit variable shell color (pink, yellow, or brown) and banding (un-banded or banded). With regards to shell color, brown (C^B) is dominant over pink (C^P), which is dominant over yellow (C^Y), and with regards to banding, band absence (B) is dominant over band presence (b). The relative simplicity with which these characteristics allowed scientists to observe the effect of evolution on Cepaea nemoralis genetics, for example, in dealing with shell color and thermal properties.

Differently colored Cepaea nemoralis shells showing genetic variation.

Brown and pink shells, the darker colors, are more efficient in absorbing solar radiation than yellow shells. Therefore, in areas where temperatures are low would need to absorb as much of the heat around them as possible, snails with dark-colored shells would be more likely to survive long enough to reproduce and pass down their adaptive traits, whereas yellow-shelled snails would be more likely to freeze to death first and are selected against. On the other hand, if these pink- and brown-shelled snails were living warm conditions, they would absorb too much heat and possibly die of heat shock, while yellow-shelled snails would be the best suited and live to reproduce. Consistent with this logic, a study conducted on snail populations across Europe showed that, as climates got warmer to the south, the proportion of yellow shells to pink and brown shells gradually increased.

The same concept of survival of the fittest was shown with respect to shell banding. The song thrush, a predator of Cepaea nemoralis, visually locates its prey. Therefore, snails better camouflaged in their environments would be less likely to be preyed on. In open grasslands, yellow-banded shells are the best camouflaged and most inconspicuous, so more yellow-banded-shelled snails survive and reproduce than do other colored snails. In woodlands, on the other hand, pink- and brown-un-banded shells are less conspicuous, and therefore snails with these characteristics are more likely to survive to pass down these genes. This may also possibly be explained by microclimatic selection (grasslands are warmer than woodlands), and with global warming and declining song thrush populations, the cause of this variation may become clearer.

TOP: Light-colored deer mouse on dark soil
BOTTOM: Dark-colored deer mouse on pale sand

Another case in which the effects of natural selection are apparent is that of the deer mice (Peromyscus maniculatus) in Nebraska. Originally dark-colored and successfully blended in with the dark soil on which they lived, deer mice evolved in terms of coat-color over the past 8,000 years due to the deposition of light-colored sand by glaciers onto their habitat 10,000 years ago and spoiled their camouflage. The deer mice living on Sand Hills, Nebraska, today have very pale, sand-colored coats compared to deer mice living in other areas where glacial deposition hadn’t taken place and soils were dark. In this case, the gene which determined fur-color was called Agouti and the allele for blonde-fur is dominant over that for brown fur. The reason why the coat colors of deer mice are so important for their survival is similar to the suggested reason for the prevalence of yellow-banded snails in grasslands, that is, visual selection--the likelihood of organisms with more camouflaged characteristics to avoid detection by their predators and therefore survive to adulthood and reproduce. Owls, hawks, and the other predators of deer mice locate their prey by sight. Therefore, dark-colored deer mice inhabiting the Sand Hills where the pale quartz grains making up the dunes made their coat color conspicuous are more likely to be eaten before they can reproduce. On the other hand, light-colored deer mice are less conspicuous and therefore can survive long enough to reproduce and pass down their genes. Conversely, dark-colored deer mice are better than light-colored deer mice to the surrounding areas which have darker soils, and therefore are more prevalent in those areas.

As evidenced from the above examples, ecology, evolution, and genetics are inextricably linked. Evolution, the process by which the characteristics of populations change over time as they adapt to their environments, can occur through natural selection. Natural selection, as mentioned earlier, involves the passing on of advantageous traits which enhance the chances of survival for organisms which possess them. The only physical traits which can be passed on are those that are genetic--acquired traits like physical fitness due to constant exercise are not heritable and cannot be passed onto offspring. And as evolution occurs in populations and not individuals, genetic variation and diversity in a population is important. This is in turn related to ecology, the relationship and interactions between organisms and the environments they inhabit, including biotic and abiotic factors, in that species evolve in response to the environments they live in. When a change in the environment a population inhabits takes place, the diversity in the genetic traits of the organisms making up the population ensures that each organism has different chances for survival. Those which have traits which are more suited to the environment after the change are more likely to survive long enough to reproduce and pass on those genes, while those which aren’t as well suited to the new environment tend to die off first. The favoring of certain genes in a population due to differing survival rates results in changes in the characteristics--evolution! For example, animals living in grasslands do best if they have mechanisms to cope with the heat and have inconspicuous characteristics to enhance their camouflage. Therefore, the animals possessing genes which best suit these environments are most likely to survive and reproduce, passing on these heritable genetic traits onto their offspring, and resulting in shifts in the allelic frequency of said traits in the population, and ultimately, evolution of the species. This also highlights the importance of biodiversity--without biodiversity, if a change in the environment takes place, then no organisms would be better suited to the new environment, and species might go extinct! Survival of the fittest and thus evolution can’t take place if none of the organisms in the population are fit enough to compete with other species!

SOURCES:

Bradt, Steve. "Mice living in Sand Hills quickly evolved lighter coloration." Harvard Gazette. Harvard College, 27 Aug 2009. Web. 6 Oct 2012. <http://news.harvard.edu/gazette/story/2009/08/mice-living-in-sand-hills-quickly-evolved-lighter-coloration/>.

"Survival of the blondest: Mice change their coat colour over 8,000 years to fool predators." Daily Mail Online. The Daily Mail, 28 Aug 2009. Web. 6 Oct 2012. <http://www.dailymail.co.uk/sciencetech/article-1209491/Survival-blondest-Mice-change-coat-colour-8-000-years-fool-predators.html>.

IMAGES:

http://idw-online.de/pages/de/newsimage?id=84635&size=screen

http://news.harvard.edu/gazette/story/2009/08/mice-living-in-sand-hills-quickly-evolved-lighter-coloration/

“Jumping Genes”: Our Genetic Sequences Aren't Set in Stone

Our genetic material is complex—so complex that 
even now we’re still discovering new things about it.

When we learned about DNA and genetics in class, we learned that our genomes contain alleles which code for genotypes that determine our phenotypes (our traits). DNA replication is a very delicate process and, although it occurs at rapid rates, there are very few mistakes. Enzymes exist which would correct any mistakes made, as even a simple base substitution mutation—that is, the changing of one nucleotide for another (for example, the change of adenine to thymine, guanine, or cytosine) could result in a disorder that can plague a person their whole life. An example of this is sickle cell anemia. In individuals with sickle cell anemia, the base adenine in the codon GAG which codes for glutamic acid in hemoglobin is exchanged for thymine, so that the codon becomes GTG and codes for valine instead. Hemoglobin is the protein found in red blood cells which is responsible for binding oxygen. Due to the change in amino acid, hemoglobin’s structure is distorted and so is the shape of the red blood cell—changing from the flattened disk shape to a curved, sickle-like shape.  This leads to weakness, fatigue, and shortness of breath because the abnormal hemoglobin doesn’t carry oxygen as efficiently as normal hemoglobin does, and can crystallize in blood vessels. Given that even the change of one base in our DNA can have profound consequences, we would assume that our genomes are, in general, quite fixed throughout our lives, unless we develop a disorder. Recent studies show that that is not the case.

Within our genome, there are DNA molecules that can jump from one locus to another, and might influence brain function and behavior. “Retrotransposons” are one such type of mobile DNA which copy-paste themselves into various areas of the genome, and have been found to compose over 40% of the human genome. In order to investigate this phenomenon, the Roslin Institute in Edinburgh, Scotland, undertook the task of mapping the retrotransposon insertion sites in human brain cells. These brain cells were extracted from the tissue of healthy individuals who showed no sign of disease or abnormality after they passed away.

What they found was that, even when looking at only the hippocampus (which is responsible for memory) and the caudate nucleus, there was a dizzyingly large number of retrotransposon insertion sites—specifically, 25,000 different sites! These genes were found to integrate themselves in “genes that were expressed in the brain.”  This is due to the fact that, normally, our chromosomes are coiled in such a way that they aren’t always accessible for transcription and, in this case, retrotransposon insertion. Examples of such genes include neurotransmitter receptors in neurons, membrane transporters that remove remaining neurotransmitters from the synaptic gap after the signal has been transmitted to the post-synaptic neuron, genes which suppress tumor growth (which are deleted in brain cancer patients) and those which have been linked to psychiatric disorders such as schizophrenia.

As would be expected, retrotransposon activity is normally suppressed in order to prevent mutation that could negatively affect developing gametes, but during brain development, when stem cells are dividing to produce new neurons, they are mobilized and insert themselves into accessible areas of the chromosome during DNA replication when the two strands of the double helix are separated. Since the hippocampus is responsible for learning and memory, and therefore produces new cells throughout the human life span, retrotransposon activity in this area of the brain was found to be higher than in the caudate nucleus.

 Diagram showing retrotransposition

These jumping genes insert themselves into random areas in the genome quite often, occurring several hundred times in most brain cells, and resulting in genetic variability within these cells. When inserted, they can cause mutations which express themselves negatively, but it is also possible that retrotransposon activity could influence our behavior and neural activity in ways that aren’t always bad. As Faulkner says, “it is entirely possible that retrotransposition is generally a good thing but sometimes contributes to disease.”

I find these jumping genes quite interesting and believe that we could better understand brain disorder and behavioral changes from analyzing how and under what conditions will retrotransposition cause harm to brain cells.  It is well understood that human cells are able to replicate masses of DNA within short periods of time with a mechanism to prevent or minimize errors. Understanding how and under what conditions adverse mutation can occur might allow us to help our body deal with retrotransposition so that, when such DNA sequences are copy-pasted into random regions of the genome, they don’t cause harm, and simply give genetic variability in our cell populations.

Genetic variety helps living organisms survive through sometimes drastically changing conditions and environments. Plants cross pollinate in order to create genetic diversity so that disasters like epidemics don’t wipe out the whole species. Humans achieve genetic variety through crossing over and random orientation of homologous chromosomes during meiosis I. Perhaps retrotransposition is another means by which humans have been attempting to achieve genetic variety, so that in survival of the fittest, we are able to deal with harmful external factors and better our chances of not going extinct.

Images:

http://upload.wikimedia.org/wikipedia/commons/thumb/5/50/L1_Retrotransposon.jpg/400px-L1_Retrotransposon.jpg

http://sahavicha.kalasin3.go.th/UserFiles/Image/DNA.jpg

Phototropism, Geotropism….. Scentropism?

Tropisms are directional growth responses to external stimuli. Common tropisms include phototropism and geotropism—both of which we discussed in biology class. Phototropism is positive for plant stems and negative for roots—that is, the stem will lean towards sunlight as the plant grows while the roots will grow away from the light. The opposite is true for geotropism—growth in response to gravity—as the stems grow counter to the force of gravity, and the roots grow in the direction gravity is acting, which is down. These tropisms seem reasonable enough. Plants use sunlight for photosynthesis so it makes sense that they would grow towards it in order to maximize the amount of sunlight they are exposed to. But what of parasitic plants without the ability to photosynthesize?

Cuscuta pentagona—an orange vine with small white flowers—lacks chlorophyll and therefore is unable to convert light energy into chemical energy and make its own food. It would not benefit from phototropism, which leads plants to the light energy source they need to produce sustenance. Sure, the Cuscuta grows its roots into the dirt and its vines upward, like other plants. However, it attains the nutrients it needs by attaching itself to a host plant and sending “microprojections” into the tomato’s phloem - through which the plant transports sugars (mostly sucrose, but also glucose), amino acids, plant hormones, and mRNA—to siphon off the host plant’s photosynthesized sugar supplies. Without a host to live off of, a young Cuscuta plant will inevitably die. To prevent this from happening, the Cuscuta has a plant-detecting mechanism by which it locates the target host plant it will attack through smell.

Cuscuta pentagona commonly latches onto tomato plants. As a Cuscuta pentagona seedling grows, it probes its surroundings, growing and rotating its shoot tip until it finds a tomato (or other) plant in its vicinity, then wraps around this new host’s stem in order to have access to the plant’s phloem. Consuelo De Moraes hypothesized that the Cuscuta or dodder plant detected its host through “chemical signaling.” She noticed that, despite variable conditions—light or shade, in the presence of other plants (specifically, wheat), empty pots, or  pots with fake plants—dodder vines always grew towards the tomato plants! To test her hypothesis, she synthesized a tomato perfume, or “eau de tomato”, with extracts from the stem of a tomato plant. She then soaked cotton swabs with this perfume and placed them on sticks in a pot next to the dodder. As she hypothesized, the dodder indeed grew towards the cotton that gave off the scent of a tomato plant. Dodders grow towards tomato plants because tomato plants contain beta-myrcene, in addition to two other chemicals. All three of these chemicals are easily turned into gases and give off odors which attract dodders.

This is not the only case in which non-tactile plant communication occurs. University of Washington scientists David Rhoades and Gordon Orians, observed that willow trees neighboring those that were plagued by caterpillars were less likely to be attacked by caterpillars. Upon investigation, Rhoades found that the leaves of trees  found next to, but not touching, the infested willows contained phenolic and tannin—chemicals that repel the insects which feed on them. These chemicals were absent in healthy willows which were not surrounded by caterpillar-plagued willows. Since neither the roots nor branches of the damaged and healthy trees had contact with each other, Rhoades proposed that, via pheromones, the infested trees sent a warning message to healthy trees so that they could defend themselves against the impending insect attack.

Plants aren’t as altruistic as they seem, however, as Martin Heil, a Mexican scientist, found. Heil posited that the infected plants didn’t intend on warning their neighbors at all—the pheromones released by damaged leaves were directed at the remaining healthy leaves of the infested plant. Neighboring plants simply detected these pheromones and reacted to protect themselves. To test his hypothesis, Heil isolated damaged leaves in a sealed plastic bag to determine whether this disrupts pheromone communication. As he had suspected, the damaged leaves were unable to transmit their warning message to healthy leaves on the same plant, and these healthy leaves remained the same. Heil concluded that the chemicals released by damaged leaves are necessary for the rest of the plant to defend itself from further attacks.

Of course, plants don’t smell in the same way that we do—with nerves that send signals to our brain and tell us of what scents are around us—but they are most definitely capable of detecting and responding to chemicals in the air around them. This makes a lot of sense. We all know that plants, flowers especially, give off odors and aromas which attract pollinators and vectors, like nocturnal animals, for seed transport. But, just as humans speak and can hear, plants give off odors and can detect scents.

I found this really eye-opening and intriguing. It shows that we can still discover new things about even seemingly simple organisms with which we are familiar. Although we don’t have enough information to conclude definitively the nature of pheromone communication, Heil’s experiment doesn’t rule out the existence of a warning system. The chemicals released by damaged leaves may be necessary for the survival of the healthy leaves, but this fact alone doesn’t preclude the intention of the infected plant to warn neighboring plants of its plight. It would be interesting to explore the details of pheromone communication, how it varies, if at all, among different plant species. Pheromones could be the key to giving us a better understanding of plant communication. Another thing I found ironic is that humans, although thought to be one of the most complex organisms with conscious thought, aren’t capable of understanding the pheromones we release, whereas plants can. Maybe we aren’t as superior to other organisms as some might think.

Image:

http://fnpsblog.blogspot.com/2012/04/cuscuta-pentagona-dodder-that-wont.html

The Elusive Cause of Alzheimer's Disease, Found At Last?

Alzheimer’s disease is an incurable, degenerative form of dementia which eventually leads to death in those affected. Symptoms include loss of memory pertaining to recent events, confusion, irritability, aggression, mood swings, linguistic difficulties, and, in later stages of the disease, long-term memory loss. These symptoms result from accumulation of amyloid plaques and neurofibrillary tangles in the brain. Amyloid plaques are caused by deposits of amyloid-β protein in the brain. This leads to damage to membranes of axons and dendrites of neurons, which combine with amyloid-β protein to form amyloid plaques which gather in between healthy neurons and affect brain function. On the other hand neurofibrillary tangles are formed when a faulty version of tau protein—a protein that supports the structure of neuron—is produced in the brain, resulting in the collapse of neuronal structures.

As can be seen from the picture, the language and memory regions of the brain have atrophied, which leads to the linguistic difficulty and memory loss symptoms of Alzheimer's.
https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzUqsv_SzlCE-YHnqXiMC4NtF8ZxXTayNeSQJkBLvizHLpmk1m0X-ajy-Kqwb7Uyy63NMVurClbN1O8DhioZCEeGpbQNeIi5dsSxoumvZPuD8ffHaZciowuydKf0Mb4iSfJw0kjjGqyXvR/s1600/alzheimersbrain.jpg

Neurofibrillary tangles form in the neurons, while amyloid plaques form in between neurons, both contributing to decreased brain functionality.
http://www.ahaf.org/assets/images/plaques_and_tangles_border.jpg

Almost all of us have heard of Alzheimer’s disease before. We know its general symptoms, and some of us might even have relatives who suffer from it. However, what has eluded us in the past is what causes Alzheimer’s.  Although a family history of Alzheimer's has been identified as a risk factor, other factors appear to be in play as well, as not all members of families with histories of Alzheimer's are affected by it. So what differentiates one person from another in terms of whether or not they will develop the disease, if not the nucleotide sequences in their genes? The study “Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer’s Disease,” conducted by Diego Mastroeni, Ann McKee, Andrew Grover, Joseph Rogers, and Paul D. Coleman, purported to answer just that.

"EPIGENETIC DIFFERENCES IN CORTICAL NEURONS FROM A PAIR OF MONOZYGOTIC TWINS DISCORDANT FOR ALZHEIMER'S DISEASE"

In the past, studies have been done to identify certain genes related to Alzheimer’s. But, although certain genes have been found to be associated with the disease, these genes only indicated the probability of Alzheimer’s, and so could not be the sole cause of the disease. Therefore, Mastroeni and his colleagues toyed with the idea that epigenetic modifications, which result in phenotypic differences in monozygotic twins, could also determine the onset of Alzheimer’s disease. They hypothesized that these epigenetic mechanisms may be responsible for mediating the effects of the environment—external factors—on Alzheimer’s risk. In order to investigate this possible cause, the study examined DNA methylation, in which a methyl group is added to the 5^th carbon of the cytosine pyrimidine ring or 6^th carbon of the adenine purine ring to turn the gene in which methylation occurs "off", altering gene expression without changing the nucleotide sequence itself.

FIGURE 1: A methyl group (CH₃) is added to the C5 on cytosine to block the transcription of the gene, locking the gene in “off” mode so that it is not expressed.

http://www.hgu.mrc.ac.uk/img/researchers_img/meehan/DNA_Methylation_in_Vertebrates_a.jpg

                As in all controlled experiments, there was both a control and experimental condition. Since this approach to finding the cause of Alzheimer’s deals with DNA, the scientists had to find subjects who had identical genetic material in order to ensure that the only differences in gene expression would be due to epigenetic modifications. Therefore, their subjects were a pair of monozygotic twins—twins that were born from the same pregnancy and developed from one oocyte (egg cell)—who were discordant for Alzheimer’s disease.

                Both twins were evaluated before and after their deaths by neurologists as well as neuropathologists in order to diagnose any neurological diseases. Ante-mortem evaluations showed that one twin was positive for AD, while the other was neurologically normal. Both twins were white male chemical engineers, however the twin who developed Alzheimer’s had extensive exposure to pesticides in his work. The affected twin experienced his first symptoms of Alzheimer’s at age 60, his memory loss increasing in severity over the course of the next 16 years, until he passed away at age 76. On the other hand, his identical twin, who underwent the same education and had the same job, but had a different working environment, developed prostate cancer and passed away at age 79, with his cognitive facilities still intact.

                The tissue processing protocols and facility in which the twins were autopsied were the same, with both twins frozen on aluminum plates at -80°C on dry ice immediately after their bodies were recovered, and then transferred to a freezer of the same temperature for storage. The post-mortem examinations of brain tissue for the non-Alzheimer’s twin showed a scant amount of Thioflavin S plaque (top left) and neurofibrillary tangle (bottom left). On the other hand, the Alzheimer’s twin showed high amounts of both (right column), which led to impaired cognitive function.

FIGURE 2: The brain tissues of both twins were analyzed for Thioflavin S plaque and neurofibrillary tangle, with high levels of both indicating Alzheimer’s, whereas low levels indicate normal brain tissue.

"Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer's Disease "

Immunohistochemistry, antigen detection through the use of various antibodies which bind to their specific corresponding antigens, was also used to analyze the twins’ brain tissues, specifically, their temporal neo-cortex, which was cut into 1-cm thick layers. These slabs were then washed, treated with several chemicals, and then further sliced into 40 micrometer pieces, which were then washed again and incubated in various antibody solutions. Afterwards, the brain tissue was again treated with chemicals, dried, rinsed with alcohol, de-fatted, and mounted. Special microscopes that utilized laser scanning were then used to examine the immunostained tissue sections. Under the microscope, the specific immunoreacted substances which were being tested for (in this case, 5-methylcytosine) would exhibit a fluorescence due to the chemicals with which the tissue was treated (ex. fluorophore-conjugated secondary antibody solution). In statistically analyzing the samples, the fluorescence intensities of 5-methylcytosine, the methylated version of the cytosine nitrogen base in DNA, were evaluated (the intenser the fluorescence from the sample, the more methylation of DNA in that region). The anterior temporal neocortex, which is affected by Alzheimer’s, as well as the cerebellum, which is not affected, were processed using antibody concentrations which would detect 5-methylcytosine. As was expected, there was little difference between the cell layers of the cerebellum in both twins (bottom row of fig. 3) and a visible difference between their anterior temporal neocortex cell layers (top row of fig. 3).

FIGURE 3: Immunoreactivity (reactions between an antigen and its particular antibody) for DNA methylation in the anterior temporal neocortex (top row) and cerebellum (bottom row) are shown. The left column shows the results for the non-demented twin, and the right column shows those for the Alzheimer’s twin.
"Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer's Disease "

The results of the DNA methylation immunoreactivity show that there is decreased methylation in the anterior temporal neocortex of the Alzheimer’s twin relative to the unaffected twin, due to the disease’s impact on the region. Using a T-test, Mastroeni found that all markers had significant decreases (P<0.0001) in imunoreactivity in the twin affected by Alzheimer’s than in the non-Alzheimer’s twin, meaning that there was less DNA methylation in the Alzheimer's twin. The implications of this finding can be applied to previous studies on Alzheimer’s disease, which reported either increases or decreases in the expression of certain genes in Alzheimer’s patients. As many genes have methylation sites, the explanation of Alzheimer’s resulting from hypomethylation (decrease in methylation) could perhaps account for the complexity of the disorder and serve as an all-encompassing explanation for the various biological characteristics of the disease. These findings also show that epigenetic mechanisms may very well also be the means by which life events (ex. exposure to pesticides, or work environment) are translated into effects on our physiology (ex. increased risk for developing Alzheimer’s).

OTHER RESEARCH:

Prior to the aforementioned study, scientists had already established quite an extensive database of Alzheimer’s related research. One risk factor in developing Alzheimer’s is genetics. Two kinds of genes were found to be associated with Alzheimer’s which increased the risk of the disease being passed down in the family—ApoE4, which increases risk of Alzhiemer’s, and deterministic genes, which are very rare but, if inherited, inevitably result in early onset Alzheimer’s. These genes can contain mutations which result in heightened risk for Alzheimer’s, but even this does not explain the whole picture, which is why the investigation into possible epigenetic causes for Alzheimer’s was needed to further illuminate the issue.

 A research study published two years after Mastroeni’s study further explored epigenetics as a marker of Alzheimer’s disease. As ribosomal insufficiencies have also been observed in Alzheimer’s patients, Pietrzak hypothesized that genes which code for rRNA (which is required in the synthesis of ribosomes, which make protein) are being methylated and thus turned “off”, effectively decreasing ribosome production. The findings of the study supported his hypothesis that rDNA (DNA which codes for rRNA) hypermethylation could be another epigenetic marker of Alzheimer’s disease. This again puts an emphasis on the complexity of Alzheimer's disease, as it is characterized by the hypomethylation of certain genes and the hypermethylation of others.

A 2012 research study on mice with Alzheimer’s disease showed that the memory loss typical to Alzheimer’s cases result from methylation of genes involved in neuronal communication. By blocking the enzyme which catalyzes the methylation of the genes, HDAC2, scientists were able to restore the function of the neurons which had been turned “off.” If drugs could be made to inhibit the enzyme in humans, it could possibly be used as a treatment for the disease in the future. In this instance, as well as the studies mentioned above, an epigenetic approach was taken to understanding Alzheimer’s.

These recent studies go to show the importance of gene regulation in Alzheimer’s disease, and, although we are still not 100% sure as to the cause of Alzheimer’s disease, much progress has been made and the beginnings of a potential treatment have appeared. The next steps the scientific community must take include bringing this drug which could hinder the effects of Alzheimer’s into existence, and continuing its research into the causes of Alzheimer’s. Although we definitely know more about the disease than we did 10 years ago, we must know even more in order to identify a cure for the currently incurable disease, and eradicate today’s most prevalent form of dementia.


For MORE information about DNA methylation, please view 24:20-28:19 of this youtube video: 

BIBLIOGRAPHY:

1.       "Alzheimer's & Dementia Causes." Alzheimer's Association. Alzheimer's Association, 2011. Web. 28 Apr 2012. <http://www.alz.org/research/science/alzheimers_disease_causes.asp>.

2.       "Alzheimer's Disease." Science Daily. Science Daily, n.d. Web. 19 Apr 2012. <http://www.sciencedaily.com/articles/a/alzheimer's_disease.htm>.

3.       Mastroeni, Diego, Ann McKee, Andrew Grover, Joseph Rogers, and Paul Coleman. "Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer's Disease."Epigenetic Differences in Cortical Neurons from a Pair of Monozygotic Twins Discordant for Alzheimer's Disease 4.8 (2009): 1-6. PLoS One. Web. 16 Apr 2012.

4.       Pietrzak, Maciej, Grzegorz Rempala, Peter Nelson, Jing-Juan Zheng, and Michal Hetman. "Epigenetic Silencing of Nucleolar rRNA Genes in Alzheimer's Disease." Epigenetic Silencing of Nucleolar rRNA Genes in Alzheimer's Disease 6.7 (2011): 1-6.PLoS One. Web. 18 Apr 2012.

5.       Tsai, Li-Huei. "HHMI News: REAWAKENING NEURONS - Researchers Find an Epigenetic Culprit of Memory Decline." HHMI. Howard Hughes Medical Institute, 29 Feb 2012. Web. 27 Apr 2012. <http://www.hhmi.org/news/tsai20120229.html>.

The Flood of 2011

As soon as the school canceled parent teacher conferences, my parents and I drove north to my grandmother’s house in Nong Khai—a town in northeastern Thailand. Until today, the fact that vicious torrents of floodwater were overwhelming many civilian areas felt unreal to me. The flood was but a secondhand experience that I could only witness through at TV screen; I was completely alienated from what was happening.

I find it difficult to write a blog on the current flood, because I do not feel like I am a victim in the same sense as those who lost their homes or livelihoods. I feel as though I am not qualified to speak to the suffering and destruction caused by the flood, because I do not know what it is like to go through that. Today, however, as my parents and I made our way back to Bangkok, I got a glimpse of the true nature of the flood. I saw a wheat field under murky water, with the occasional half submerged tree or lamppost. The farmers had taken to their homes, and the usually lively landscape seemed absolutely lifeless. But faded lines on the electricity poles at the side of the road indicated that water in the area had subsided, leading us to believe that the danger had passed, and the situation had calmed. Instead of taking the safer, roundabout route that we had taken on our way out of Bangkok, my parents chose to take a shortcut through Wang Noi, an area that had recently suffered from severe flooding. The traffic at Wang Noi was nearly unbearable. Every two minutes or so, our car crawled forward one meter. Frustrated and with only 600 meters left before we were to turn right and leave the town, my parents attempted to avoid the congestion by veering off the main road and onto a flooded strip of lower ground. Although the water started out quite shallow, the further we went, the higher it rose. As we sloshed sluggishly through the water, I heard an ominous gurgling coming from the trunk of our car. Water had seeped through the doors at an alarming speed, so that, within a few minutes, my shoes were bobbing up and down in flood water.

This morning, when I started my blog, I had planned to write a generic, and rather impersonal, piece about how the flood caused much hardship to the citizens of Thailand and how it could be symbolically represented by the furniture in my house—our sofa precariously balanced on the coffee table represented the people displaced from their homes, forced by nature to seek refuge in flood shelters. But now I realize that it’s more than just a severe case of inconvenience that plagues flood victims. By no means am I trying to say that I know fully the feelings of those whose houses and livelihoods were destroyed by the flood. This experience simply gave me a taste of what others had taken on at full steam. I chose this picture because the moment I took it, which was a little while before our car was half submerged in floodwater, was the first time that I had seen with my own eyes the disaster caused by the flood. It embodies, for me, the unease a flood victim faces as he chooses a limited number of belongings to bring with him, if he even has the time to bring anything at all, and the panic that consumes him as the water level rises constantly and unpredictably. Just looking at the picture, one could see that the water level is unbelievably high, and having to be stuck in the middle of that must have been absolutely terrifying for the flood victims.

I now realize just how fortunate I am that my house and those of my relatives are safe and dry. Now that I’m back in Bangkok and have a chance to help with flood relief efforts, I know that, instead of helping out of obligation, I’ll be helping with the sincere hope that I can alleviate the suffering of the flood victims, and that means a lot to me.