Rock On! (Investigating the Rocky Shore)

On this ecology field trip, I got the chance to visit and study a Rocky Shore ecosystem off the cost of the PranBuri beach. It was a hot and very sunny day, but the sky was clear and the conditions were perfect for a field experiment.

The Rocky shore is a unique ecosystem. It's an ecosystem that is continuously facing changes due to the tidal nature of the water that it's submerged in. Usually the Rocky Shore ecosystem extends many meters out into the ocean from the seashore and faces persistent change in their environment because of the the ocean's high and low tides. Marine organisms can survive in this continuously changing environment because they have unique adaptations that allow for them to withstand the dry conditions during the low tide and saline conditions during high tides. The organisms that live within the intertidal zone have to face these extreme environmental conditions, and thus have developed sufficient adaptations that allow for them to thrive.


The most abundant animal that I saw on the rocks of the shore was the barnacles (seen in the picture on the top right right). They are small marine organisms that thrive by attaching themselves to the walls of the rock. The cone shaped body structure of the barnacles and their hollow middle resembles a volcano. Due to the periodic nature of the tides, the hollow middle is an adaptation against water loss during periods of low tides. The hollow entrance is covered by valves that close to prevent water loss during dry periods. Their hard double layered shells are used as protection during high tides against the strong ocean currents.

The periwinkle snail was another organism that could be easily spotted. They are quite small, much like the barnacles are, and had adaptations that allow for them to thrive within the intertidal range of the rocky shore. Periwinkle have muscular foot that enables them to move and seek shelter from the hot sun during low tides. They seek shelter under and between rocks from the excessive heat. Their thick calcium shells allows for them to withstand the constant crashing of the waves that most rocky shore organisms have to endure. On this ecology field trip, the distribution of periwinkle snails were studied using a continuous transect belt. The data for the distribution of the periwinkles along the transect are shown below.

The graph shows that there is no correlation between the two continuous belt transect. The distribution of mangrove periwinkles ( the side to the left is furthest away from the shore) varied between the two transect. In the transect represented by the pink kite diagram, the majority of the mangroves were concentrated in deeper water. The periwinkles were distributed evenly across the second transect, represented by the orange kite diagram. 

The data collected for the experiment is accurate to merely a certain extent. It's difficult to try and count the number of periwinkles that are submerged in water. As they could be easily miscounted, the distribution of periwinkles along the rocky shore should be further investigated by constructing more transect along the shore to assess whether there is a correlation between the number of periwinkles and the distance from the shore. 

"Seashore - A Rocky Seashore Ecosystem." :: Environmental Facts. Young Peoples Trust for the Environment, n.d. Web. 18 Nov. 2012. <http://www.ypte.org.uk/environmental/seashore-a-rocky-seashore-ecosystem/98>.

The Majestic Mangroves

The Pran Buri River

      The combination of salt water that flows in from the sea and fresh water from the river has fostered a Mangrove ecosystem along the PranBuri River. The Pran Buri Mangrove Reserve protects this Mangrove ecosystem from being cleared away for agricultural and industrial purposes. Last month, I got a chance to visit the Mangrove Reserve, and to study the unique and distinctive characteristics of the Mangroves and the communities that have grown around the forest park.

     The terrestrial plants that grow along the Pran Buri river have to adapt to the tidal nature of the area and the extreme saline conditions of the river. Mangroves have adaptations that allow for them thrive in such a condition. While at the reserve, I saw that the Red Mangroves had spidery roots that protruded out the muddy soil. They have such characteristics because the roots provide a structural support in the soft soils for the plants to grow. These above ground roots are filled with spongy tissues and small holes that allow oxygen to be transfered to the roots trapped below ground, where oxygen is scarce. The leaves on the mangrove trees have adaptations that are suitable for the saline conditions of the water. Mangroves, particularly the Grey mangroves near the cost of the river have leaves with glands that secrete salt. Their leaves can also tolerate the storage of large amounts of salts.     In this ecology field study, the biotic and abiotic factors of the Red and Grey Mangrove communities were measured. Although these two communities of mangroves were relatively close to one another, they have so sufficiently adapted to their environments that each species of Mangrove have developed distinctive characteristics. To collect data for the biotic factors in the Grey Mangroves, a continuos belt transect was laid out along the ground, from the edge of the river to the edge of the forest. The organisms along the transect were then counted, and the abiotic factors such as temperature, water quality, light intensity, and turbidity were measured. The data collected for this community of mangrove is shown in the table below.
Biotic Factors of the Grey Mangrove Community 

Species	Number of Organisms
Big mangroves (mature)	19
Intermediate mangroves	10
Seedlings	55
Moss	53
Red Ants	A lot > 200
Small black ants	A lot >200
Spiders	2
Total	> 539

The biotic characteristics of the Grey Mangroves and the Red Mangroves community were rather different.The continuous belt transect could not be used to collect data for the biotic factors in the Red Mangrove  because of the mangroves' protruding roots. Instead the quadrant sampling method was used. The biotic data collected for this community is shown in the table below. 

Biotic Factors of the Red Mangrove Community 

Species

Number of Organisms

Merder’s Mangrove crabs	4
Spiders	1
Total	5

With every ecology field study comes uncertainty in the data that was collected. Some systematic errors in the sampling method of each mangroves were that the area and transect that were chosen for sampling were not randomly selected. The average number of each species in the sampling area could not be taken either because only one transect and a quadrat were used to sample the area. 

I wanted to compare the relative biodiversity of each of the mangrove community using Simpson's Diversity Index. When calculated, the biodiversity of the Grey Mangroves was 0.297 and the Red Mangroves' was 0.60. Although there were fewer number of organisms and species in the quadrat of the Red Mangroves, because the population of the organisms in the Grey Mangroves is largely concentrated on the ant population, the area of the Red Mangroves is considered to be more diverse. A bar graph comparing the relative biodiversity for each of the mangrove community is shown below. 

From just merely observation alone, I could see that the mangrove ecosystem has unique adaptions that allows for them to thrive in an area where other terrestrial plants cannot. The mangroves and other small animals have found its own unique way to adapt to the environment that they were living in. None of the crabs that lived in the Red Mangrove community could be found where the Grey Mangroves grew because of the difference in quality of soil between the two community. Instead small periwinkles and snails were found along the trunks of the Grey Mangroves where the soil was less moist and condensed.

       Because the Grey Mangrove community was located right at the mouth of the river, the plants and small animals there have adaptations that are different from the organisms that live in the Red Mangroves. But in either community, the organisms have adaptations that are so well suited to the particular environment that their population is able to thrive.

Evolution in Action

As a creationists, Charles Darwin had believed that everything on Earth was the creation of a divine being. But upon his voyage to the Galapagos Islands, he made an unanticipated discovery that changed the course of science. Darwin, in his book "Origin of the Species", proposed a rather controversial idea about how the organisms on Earth came to be as they are. He suggested that, in principle, all life forms on Earth could be traced back to a common ancestor. We diverged from this common ancestor because of the slight variations that each offspring has from their parents. He proposed that no two organisms were alike, and that this slight variation contributed to the process of natural selection.

The concept of natural selection that Darwin proposed contributed to evolution is difficult to observe because it often takes years for the variation in an organism to become truly distinct. But luckily, natural selection can be observed "at a snail's pace" in the little European snail, Cepaea nemoralis. 

The Cepaea nemoralis comes in three different colors, and can have up to five horizontal dark bands going across them. The pattern and color of a shell is dependent on the genetic information that the snails have, and throughout their life span these colors reamin unchanged and unaffected by any environmental factors. In the 1950s and 1960s, a large-scale breeding programme in this snail studied the genetic components that were involved in coding the characteristics of the snail's shells (Patel). Similar to Gregor Mendel's experiment, the phenotypic ratio of these snails were the same as the offsprings in Mendel's pea plants. Gene C, with three alternative alleles contributed as the determining factor for these snail's shell color and band. The phenotypic characteristics varied from one snail to the next, and distribution of the different colored snails across Europe can be studied to observe the process of natural selection occurring over the course of just a few decades.

When Darwin coined the term natural selection, he proposed that organisms that were best suited to their environment would survive to reproduce and produce more offsprings, thus passing on the distinctive trait that helped them survive. The different colored shells in the European snails have different thermal properties. The darker shells can absorb solar radiation more efficiently than yellow shells (Patel). This distinctive characteristics makes the darker snails more suited to a cooler climate, and unsuited to warmer conditions. The yellow shelled snails on the other hand can withstand sunshine without much trouble. Biologists have studied these snails and a significant correlation exists between the color of the their  shells and their distribution pattern across Europe. The population of snails with darker shells are concentrated around areas around northern Europe, because they do better in cooler climate. And the population of snails with yellow shells were found to be most populated in areas around southern Europe, where it's hot and sunny. The maladaptive shell colors are selected against. The darker shelled snails do not survive as well in hot climate, and thus do not reproduce as much as the light colored snails do. Without offsprings they cannot pass on their alleles, and their traits are not passed down to the next generation. The selective process that these snails go through demonstrates to us the process of evolution in a nutshell.  The distinctive adaptive skills that these snails have, over time have caused evolution to occur. The better adapted individuals survive and pass on their traits to the next generations. 

Natural selection sometimes involves many mutations leading to significant changes. In New South Wales, Australia, the yellow bellied three toed skink is able to use reproductive methods that allows it to give live birth to their young or lay eggs. Scientists have discovered that skinks that live near coastal areas, where it's warm, tend to lay eggs as a reproductive method. But move higher up into the colder mountains, the skinks that live there are almost all giving birth to live young. Since the skinks can either lay egg or give live birth it gives scientists a chance to study the conditions necessary for live birth. The deciding factor depends on how the young gets their nourishment before birth. In egg laying species the embryo gets its nutrients from the yolk. In mammalian species, a highly specialized placenta connects the fetus to its mother, allowing the baby to take up oxygen and nutrients from the mother's blood and pass back waste. In reptiles, eggs are formed, and as development of the embryo progresses the shell begins to thin out, until the babies are born covered with only a thin layer of membrane. Both these birthing styles come with an evolutionary trade off, eggs are more vulnerable to the predators and harsh weather, but babies are more physically demanding for the mother. For the skinks, mothers in warmer climate tend to lay eggs onto the ground before the final week of development. Moms that live on the mountains feel that it is necessary to protect their young by keeping them longer inside their bodies. The variation in reproductive style, allows each skink to evolve to use the method which is best suits them. This increases the chances that their young will go on to reproduce. Scientists have predicted that these two populations will at some point, separate into two different species, as each population becomes fixed with its reproductive strategy. 

To survive, a species must find a way to adapt to its physical surroundings. An organism that is able to find the best way to adjust to its environment will be the one that is likely to reproduce and pass on the characteristic traits that they have to their offsprings. Genetic variation from more organism to the next, allows for this to occur. Over time, as the trait becomes more distinct, speciation may occur and a species will diverge into new, and more fit organisms. 

"8 Examples of Evolution in Action." Listverse. N.p., n.d. Web. 07 Oct. 2012. <http://listverse.com/2011/11/19/8-examples-of-evolution-in-action/>

Handwerk, Brian. "Evolution in Action: Lizard Moving From Eggs to Live Birth."National Geographic. National Geographic News, 1 Sept. 2010. Web. 7 Oct. 2012. <http://news.nationalgeographic.com/news/2010/09/100901>.

Patel, Simit. "Evolution at a Snail's Pace." Biological Sciences (2010): 26-29. Biological Sciences Review. Web. 04 Oct. 2012. <http://www.rougemontschool.co.uk/.../938-evolution-at-a-snails-pace>.

Gene Repositioning In Breast Cancer

       Breast cancer is a life threatening disease that has affected many victims and their loved ones in the past, and will continue to do so in the future. One out of every four cancers diagnosed in women is breast cancer. Each year it is estimated that nearly 200,000 women will be diagnosed with breast cancer and more than 40,000 will die. Surprisingly, approximately 1,700 men will also be diagnosed with breast cancer and 450 will die each year. When pathologists analyze a sample of cell for the presence of cancer they routinely discover important large-scale alterations to cancer nuclei, such as the nuclear shape and chromatin texture. The research team at the National Cancer Institute then established the theory that the repositioning of genes in the nuclei is plausible for individuals with breast cancer. The positioning of our genes in the genome is undoubtedly non-random. Each component of the genomic sequence has a place of its own in the nucleus. The research team at the institute used this finding to their advantage and set out to see whether they could pinpoint the specific repositioning of genes in individuals with breast cancer.

       To begin their research, the researchers used an instrument called the Fluorescence in Situ Hybridization, FISH for short. Through the use of florescent tubes these machines can be used to localize DNA sequences on chromosomes. From 11 normal human breast and 14 invasive cancer tissue specimen, the researchers identified eight specific genes that have been significantly altered when comparing the spatial organization of the genes in a cancerous tissue and a normal one. Roughly around 20,000-25,000 genes are in the human body. Only eight out the total were identified to have been notably repositioned, suggesting that the changes are specific and does not reflect large scale alterations in gene organization. Neither did the repositioning of these genes reflect upon the possibility that it was due to genome instability that caused the repositioning. Genome instability is often associated with cancer because the number of genes present in the genome will often vary when the tissue is cancerous, but the repositioning of these genes did not correlate with the changes in the number of genes present in the nuclei.

      Next, the researchers wanted see whether they could use the repositioned gene to distinguish cancerous human cells from healthy ones. If they were to be successful, this method could be used as a replacement to diagnose breast cancer. Tissue specimens were taken and tested. The results were satisfactory when they found that the postion of a specific gene, HES5 could distinguish between a cancerous tissue and a healthy one with almost 100 percent accuracy. The protein that this gene codes for regulates cell differentiation in multiple tissues. Disruption of this gene has been associated as a source of cancer. A few other genes out of the total eight could be used as identification for cancerous tissues with a low false-negative and false-positive rate. This means that this gene combination identified most of the cancerous tissue to be cancerous and a few of the non-cancerous tissue as cancerous.

The data that was collected for the gene HES5 is shown in the graph above. A cumulative RRDs (Relative Record Data Set) organized the data of around 88-220 nuclei per sample of HES5 gene randomly selected from regions of the tissue sample. It displays the frequency of occurrence of the gene at a specific location in the nucleus. The left side of the graph is where the genes closets to the nuclear envelope was found, and the right side of the graph consists of genes that were closer to the center. The black line indicates the genes that were from cancerous tissues, and the red from healthy tissues. A noteworthy difference between the two type of tissues can be seen.

Data was collected for several other genes using the same cumulative RRDs. Although the difference in  the positioning of the genes are noticeable, several of the two colored lines overlap. This is an indication that these genes, although they show some repositioning, cannot be used to distinguish the cancerous tissues from the healthy ones.

    The current breast cancer diagnostic test involves poking and prodding large needles to retrive a small amount of tissues for a biopsy. Differential repositioning of these genes gives way to a new method of identifying cancerous tissues, and possibly usage for diagnostic applications. The researchers concluded that in this study, they have identified several genes that are differently positioned in invasive breast cancer compared with normal tissue. The data and method used also show that the positioning of the genes can reliably detect cancerous tissues. "We find that the repositioning of many genes is specific to cancer and does not occur in noncancerous breast tissue nor within the normal tissue adjacent to the tumor"

    These findings have significant usage for diagnostic applications. This approach reduces the current rate of false detection, and is preferable to the present method of diagnosis. A distinct advantage in using this method is that it requires a very small amount of materials. The use of spatial genome positioning can possibly reduce human errors when making the diagnosis because the approach provides pathologists with qualitative data. Subjective criteria or the individual experience of the pathologists is ruled out.


"If validated in a larger number of samples, we envision that this approach may be a useful first molecular indicator of cancer after an abnormal mammogram," said Misteli (research scientist at the National Cancer Institute) "Our method of cancer diagnosis is not limited to breast cancer and may be applied to any cancer type in which repositioned genes can be identified."






MLA Citations:


"Breast Cancer." National Foundation® Official Site. Web. 30 Apr. 2012. <http://www.nationalbreastcancer.org/>.


"Gene’s Position in the Nucleus." U.S National Library of Medicine. U.S. National Library of Medicine. Web. 30 Apr. 2012. <http://www.nih.gov/news/health/dec2009/nci-07.htm>.


Meaburn, Karen J., Prabhakar R. Gudla, Sameena Khan, Stephen J. Lockett, and Tom Misteli. "Disease-specific Gene Repositioning in Breast Cancer." The Journal of Cell Biology. 7 Dec. 2009. Web. 30 Apr. 2012. <http://jcb.rupress.org/content/187/6/801.full.pdf html?sid=77645108-526c-4aa6-bafa-d494ed8708b0>.


O'Connor, Clare. "Fluorescence In Situ Hybridization." Nature.com. Nature Publishing Group. Web. 30 Apr. 2012. <http://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327>.

Star Struck!

Astronomers turn their telescopes to the unbounded beauty of the Milky Way, By: Ken Croswell

It's hard to be modest when you live in the Milky Way. Our galaxy is huge. Much larger and more massive than any other galaxy known to astronomers. It spans out across 120,000 light years, and is so big it has dozens of smaller galaxies scurrying about, like the moon orbiting our planet. The heavy elements necessary for life on Earth is forged by the Milky Way's 's abundant stars. When a star explodes in the lesser galaxy these essential elements such as the iron, calcium, and oxygen (all necessary for the different functions in our body) shoots out into space at a million miles per hour and is lost. When a star in the Milky Way explodes, the elements do not disperse but are restrained by the immense gravitational pull of the galaxy. The gravitational pull allows for the elements to form clouds of dust and eventually the new generations of planets and stars. That's what happend 4.6 billion years ago, when the sun and the Earth emerged from a now-vanished nebula.

Have you ever realized that you know your friend's and family's faces better than your own's ? Similarly we know less about the overall appearance of the galaxy we live in than we do about distant galaxies. Nevertheless, scientists have discovered significant phenomenons that inhabit the Milky Way, including the revelations about the huge black hole at its heart.

Every star in the Milky Way revolves around this black hole, named Sagittarius A-star. Earth revolves around the Sun every 365 days. Whereas the Sun completes it's revolution around Sagittarius A-star once every 230 million years. The path of the orbits of the stars reveals that Sagittarius A-star is four million times the mass of the sun! Ever so often it'll swallow up bits of gas or even an entire star. With the immense heat, gravity, and friction present around the hole the remains of the stars is let out as a scream of X-rays. These light up nearby gas clouds, keeping track of the the hole's past feasts. Surprisingly, moving towards the black hole is not the only direction a star can travel. In 2005 astronomers reported an extraordinarily fast-moving star at 200,000 light years from the galactic center. The star, Hydra, was moving at 709 kilometers per second, or 1.6 million miles an hour.

Despite it' violent reputation, areas our the black hole are relatively fertile. Whereas if you traveled many, many light years towards the rim of our galaxy, you'd find it to be a place relatively bleak for prospects of spotting clusters of planets. But these stars, can offer us an insight into the birth of the galaxy itself. Galactic halos inhibit the edge of our galaxy. Dating these stellar halos can lead an astronomer to discover the age of the entire galaxy. In 2005, Anna Frebel began looking for individual stars in the halo. She discovered a supernova, that emitted lots of heavy radio active elements, such as thorium and uranium. Lucky for her, because radioactive elements decay at a steady rate, she could compare it's abundance to the star's today. She estimated that the Milky Way is around 13.2 billion years old, not much younger than the universe it self- which is 13.7 billion years.

Our universe is so big and so old. It provides us with the countless numbers of star make life possible on Earth

The Milky Way is around 13.2 billion years old. The Earth in comparison to the age of the universe is young, only 4.5 billion years old.

Modern human, the Homo Sapiens, are even younger. We were discovered to have originated from Africa only 200,o00 years ago.

We have made it through so many milestones and discovered so many things, it's hard to imagine just how young we are.

In the book "The God of Small Things" that I had read no long ago, a man named Chacko was trying to give his niece and nephew a

sense of historical perspective about the Earth. He told them about the Earth Woman. He made them imagine that the earth- 4.6 billion

years old- was a forty six year old woman.

"It had taken the whole of the Earth Woman's life for the earth to become what it was. For the oceans to part.

For the mountains to rise. The Earth Woman was eleven years old, Chacko said, when the first single-celled organisms appeared.

The first animals, creatures like worms and jellyfish, appeared only when she was forty. She was forty-five- just eight months ago-

when dinosaurs roamed the earth. The whole human civilization as we know it, began only two hours ago in the Earth Woman's life.

The whole of contemporary history, the World Wars, the War of Dreams, the Man on the Moon, science, literature, philosophy, the pursuit

of knowledge- was no more than a blink of the Earth Woman's eye. And we, my dear, everything we are and ever will be-

are just a twinkle in her eye"