Perfect Paragraph: Warren Lab

Submitted by danielcosta on Thu, 09/21/2017 - 19:47

The Warren Lab of the UMASS Amherst Environmental Conservation department is currently conducting some extremely interesting research regarding the effects of urbanization on woodthrush populations. The research of this lab is centered around field work that has been conducted during the summer months over the past several years. The field work includes tasks like collecting nest samples and setting up cameras in discrete locations in order to obtain footage of the undisturbed woodthrushes. During the school year, undergraduates are invited to work with the faculty of the lab and help with the research. This is how I am currentley involved with the Warren Lab. My job is to watch videos of woodthrush nests and record their behavior. Another portion of the in-lab research includes sorting through nest samples and identifying the various materials the woodthrushes use to make their nests. The objective of the research is to discover the underlying implications that urbanization has on the native species of that area as well as discovering ways in which these native species adapt to urbanization. 

Perfect Para: Cell signal notes

Submitted by akoundinya on Thu, 09/21/2017 - 19:15

Extracellular signaling is essential to the function of cells in the human body. While transcription of DNA in the nucleus and translation into proteins in the ribosomes are essential drivers of cellular function, signals outside the cell have a major impact on cell signaling. While stimuli such as light, odors, tastes, and mechanical stress all influence cell signaling, specific proteins called Hormones are substances produced within specific cells to regulate the function of other cells in different areas of the body. Extracellular signaling usually starts by a ligand binding to a receptor on the cell membrane of a cell. When a ligand binds to a receptor and causes a biological reaction in the cell, this ligand is known as an agonist. When a ligand binds to a receptor and causes no reaction other than the binding of the receptor, it is called an antagonist. After a ligand binds to the receptor and is absorbed into the cytoplasm, the ligand receptor can now interact with the G Protein. The name G protein came from its ability to bind to guanine nucleotides. After the ligand/receptor interact with the G protein, the G protein becomes activated and starts to activate other intermediate proteins called Secondary Messengers. These secondary messengers perform a variety of functions from aiding with the transcription of certain genes to the translation of specific proteins. Secondary messengers represent the intracellular reaction to the extracellular signal.

Methods Project: Species

Submitted by danielcosta on Thu, 09/21/2017 - 18:19

For my methods project, I have decided to chose the species Pinus densiflora, further specified as "Oculus-draconis". This is a species of pine trees indigenous to Japan, the Korean Peninsula, and northeastern China. The common name for this species is Dragon's Eye Pine, due to its color variation and needle position. The needles form in clusters at the end of the tree's branches. When young, as is the exact species used for my project, their needles open up in a pendulous habit. The bottom quarter of each needle is the dark green color of most pines, then blends into a yellow-green color halfway up the needle, and finally becomes mostly yellow, but may contain hints of white at the end of the needle. The combiation of the end of the dark tree branch that is visible, with the small circle of dark green needling, mixed with the outer edging of the more prevelant, lighter part of the needle ends resemble the look of a big, beautiful eye, giving the tree its common name. The Dragon's Eye Pine is an evergreen and during the winter months, the color of its needles fade. This species can grow up to 40 feet, although my photographed tree is only a maximum of about 10 feet tall. 

I chose the Dragon's Eye Pine because it stood out to me and caught my eye as I walked by it. Its beautiful, bright color make it stand out compared to the other vegetation around it. The tree is planted outside of the DuBois library and will assumingly be in the same place for the next few weeks. This should make it fairly easy to find the Dragon's Eye Pine. As I was walking by the library thinking of what species I might want to photograph for my project, I passed by the Dragon's Eye Pine and immediatley became interested in it. Even after photographing the pine, I stood by for a few more minutes appreciating its beauty and design. I'm excited to see how my methods will be replicated.

Animal Movement Continued

Submitted by brdougherty on Thu, 09/21/2017 - 17:46

Article Summary

Title: Transoceanic Migration, Spatial Dynamics, and Population Linkages of White Sharks

Authors: Ramon Bonfil, Michael Meyer, Michael C. Scholl, Ryan Johnson, Shannon O’Brien, Herman Oosthuizen, Stephan Swanson, Deon Kotze, and Michael Paterson


            In the scientific article Transoceanic Migration, Spatial Dynamics, and Population Linkages of White Sharks published in sciencemag many groundbreaking discoveries about white sharks were discussed. The goals or objectives of this study appeared to be very broad initially because at the time very limited information was known about white sharks. White sharks were previously very hard to study due to restrictions in technology at the time. The initial objective of this study according to Bonfil was to use electronic tagging and photographic identification data in order to observe and show the complex behavioral patterns of white sharks. Using the modern Technology at the time they were able to observe these white sharks and categorize their movements into four distinct behavioral patterns: rapid transoceanic return migrations, frequent long-distance coastal return migrations, smaller-scale patrolling, and site fidelity

            While observing the white sharks in this study revolutionary observations were made. One of the most important observations made was while observing a female shark referred to as P12. This specific shark made a transoceanic migration from South Africa to Australia and back. This shark made the voyage without the aid of oceanic islands, which were previously believed to be necessary for transoceanic migrations. This brings into question how P12 was able to navigate this long journey. Bonfil speculates that it is possible that white sharks use celestial cues as a navigational mechanism instead of, or in addition to Earth’s magnetic field. This specific migration was important because previously it was believed that females didn’t make transoceanic migrations. This also showed a clear direct link to two of the most widely separated white shark populations. This link between the two populations is especially important because it brings into question whether or not the female has a natal homing mechanism. While on this migration voyage this female shark recorded the fastest return migration recorded among marine animals.

            Personally, I thought this study and their findings were very much by chance. The main issue I have with the study is the lack of a goal or clear objective when studying the white sharks. Since the study lacked a clear goal all of their results were pretty much by chance and any knowledge that was found could be labeled groundbreaking. I also believe that since previously there was limited knowledge about this specific shark species any information found was labeled as news worthy. I also feel that this study can be seen as a good starting point and left many questions unanswered. For example, now that we know that female white sharks are capable of making transoceanic migrations why are they doing this? And are all female sharks doing it? If not why?




Bonfil, R., Meyer, M. L., Scholl, M. C., Johnson, R., Obrien, S., Oosthuizen, H., . . . Paterson, M. (2005, October 7). Transoceanic migration, spatial dynamics, and population linkages of white sharks. Science.


Beginning of methods project

Submitted by briangriffin on Thu, 09/21/2017 - 16:06

        For my methods project I will be using the species Tillandsia cyanea. This species is a type of plant found on campus in the Durfee conservatory. I chose this plant because it is relatively easy to find and it is most likely going to be in the same location at a future date when someone replicates my methods. Also there is a placard next to the plant identifying the species. Therefore there less of a chance of someone misindetifying the exact organism described in my project. This orangism lives inside the Durfee greenhouse, this means that time of day wont really affect the shadows and lighting of the photo. But if there's a difference in cloud cover at the time of the photos, this might have an effect on the lighting since the greenhouse is translucent. Factors to control include where the photo is taken from, flash being on or off, and if there is water on the plant if it has recently been watered. 

        This species has many morpholocial characteristics to describe for the purpose of this methods project. The are many leaves on this plant that seem to start at the base. These leaves tend to be about 12-18 inches wide and about .4-.8 inches wide and come to a point at the end. There is a couple brightly pink colored flower stock with a hard exterior. They have an overlapping V shape that seems to get smaller and tighter at the end of the flower stock. The are no actual flowers at the time the photo was taken.

Thin layer chromatography

Submitted by oelbetanony on Thu, 09/21/2017 - 15:33

Thin layer chromatograohy is a three step method used for analyzing mixtures by seprating compunds in the mixture based on polarity. The steps are in order, spotting, develpment, and visualization. Thin layer chromatography can help identify the number of compoubds, the identity, and the purity of a compound. The first step spotting is when you use a pipet to add a spot of the compound you are testing on the powdered silica gel tray. development is when you place the tray in a jar with a developing solvent in it. The solvent will eventually travel up the silica gel and thats when we know its been developed. Visulaiztion of the developed tray can be hard since most organic compiunds are colorless so to be able to see the spots we must use a short wavelength UV light. To calculte the retention factor we take the the distance traveled by the substance and divide by the distance traveld by the solvent. 

Ecology Assignment

Submitted by hamacdonald on Thu, 09/21/2017 - 15:28

The species monito del monte, Dromiciops gliroides,  would most likely shift downward away from the equator. The reason for this being is global warming is slowly warming the earths surface temperatures making this location no longer suitable for the monito del monte. This is proven in the graph, "Change in population size of Dromiciops gliroides in the study area" as the number of  monito del monte drastically declines from around 1600 in 2002 to 600 in 2016. This once suitable location for the species has warmed gradually to a temperature that does not support the needs of the species. Therefore it has caused them to slowly shift downward away from the equator and find a new location with a more suitable to their temperature needs.

Classes Perfect paragraph

Submitted by briangriffin on Thu, 09/21/2017 - 15:28

         As a college student I am enrolled in multiple classes and every day I attend these classes. Classes are blocks of times where I sit in a room with other students and a professor or a teacher’s assistant. During this time we discuss topics taught in the specific class. Yesterday was Thursday so I attended my Thursday classes, which includes Evolutionary genetics, Ecology, and advanced genetics. Evolutionary genetics takes place between 10:00-11:15am and yesterday we discussed a paper that was assigned to us for reading in the previous class. Ecology takes place between 1:00-1:15pm and yesterday we learned about climate change in a lecture format. In a lecture style class I am mostly taking notes and listening to the professor lecture on the subject. But there was discussion when questions were asked by her and by students. My last class of the day was advanced genetics which took place between 2:15-2:30. In this class we are in assigned groups and yesterday we discussed the papers that each member of my group researched prior to that class. Classes have different formats and cover different subjects, this variation is shown by the classes I attended yesterday.

Rough Draft Diabetes

Submitted by dalon on Thu, 09/21/2017 - 15:20

Diabetes is an illness in which the level of glucose in one’s blood is too high. There are two types of diabetes: type 1 and type 2, with type 2 being more common. Type 1 diabetes is when the pancreas is unable to make insulin, while type 2 diabetes is when insulin is not produced or utilized properly or at a high enough efficiency. Type 1 diabetes is a disease that you are born with; you cannot develop type 1 diabetes over time. Type 2 diabetes, on the other hand, can be developed during one’s lifetime. The risk of acquiring type 2 diabetes is increased if you eat poorly, don’t exercise, are older, or have a family history of diabetes. Prediabetes is also a documented condition, in which the blood glucose levels are higher than normal but not high enough to classify the patient as diabetic.


Submitted by briangriffin on Thu, 09/21/2017 - 14:59

               Cytochrome Oxidase 1 (CO1) is a mitochondrial gene referred to as the barcode gene. This gene is used widely in entomology and other fields for identifying species. The reason of its widespread use is due to the fact that it accumulates mutations at a rapid rate among populations. This is because it is a mitochondrial gene with not too many constraints on the gene itself. This means that when a mutation occurs it is less likely to be deleterious. These factors led to its popularity in many fields of biology. The Barcode of Life Database (BOLD) was created for people to upload their CO1 sequences. This database only has CO1 sequences but for many different species and contains more CO1 sequences than NCBI. In my lab we used CO1 to identify a possible new species of Pimpla which is a genus of parasitic wasps. The wasp found parasitizing winter moths was identified by a taxonomist as Pimpla aequalis but when the CO1 sequence of this wasp was compared to that of Pimpla aequalis, there was about a 10% difference in this gene. This demonstrates one use of the Barcode gene in regards to research.


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