Hey guys,
Welcome to Internship 2017 Blogger page! This is where you will be posting our weekly blogs and be able to see what your fellow classmates are doing in their various labs. Your logs don't have to be long, but they should be a minimum of 4-5 sentences. Remember, the more you write here, the more materials you will have to reference later when you're making your poster!
Things you can blog about:
-How your lab went this week
-Things that you learned/still don't understand
-Updates on what you accomplished this week
-Tell us about your upcoming tasks
-Struggles that you're having
-Instruments you got to use
-Draft up sections for your poster
-All the good and bad of your lab this week!
If you see someone struggling with something you know about, REPLY! Even if you're in different labs, you are all in this together!
Each week, we will post a question in which to guide some of your posts. Respond to the question and feel free to expand on it with your own thoughts and feelings. Here's your first one!
Training 1: June 10th & 14th
You need to research your PI's and their specific area of research. Find an article that was recently published by them (within the last 5 years) related to your work this summer and summarize the introduction.
Questions to address:
-What is your PI's specific area of research?
-What did you learn from the article you picked?
-After reading the introduction, what are you still confused about?
-Pick 5 vocabulary terms that are commonly used in the article that you didn't know coming in and give its definition
Due: Prior to the next time you come in for Training 2 (either June 16th or 17th)
Article Title: Temperate radiations and dying embers of a tropical past: the diversification of Viburnum
ReplyDeletePatrick Sweeney is the Collections Manager at the Yale University Herbarium in the Peabody Museum of Natural History. Among his interests, Dr. Sweeney primarily focuses on North American flora. Recently his most recent research is focused on Viburnum and the mangosteens.
An article that Dr. Sweeney collaborated on was: Temperate radiations and dying embers of a tropical past: The Diversification of ‘Viburnum’. After reading this article, the information that I was able to gather was that Viburnum, has shifted from living in the environment and conditions that it originally thrived in, to conditions that it was later introduced to. While I understand the premises of the research that was conducted, I struggle to understand whether all the different species of Viburnum were tested in the entire experiment.
Before reading this article I did not know what Viburnum was. In the introduction it is defined as “...a clade of c. 165 species of shrubs and small trees that are mainly distributed in temperate forests around the Norther Hemisphere.” (340) Despite the definition, I found it easier to understand as I read through the remainder of the article. Another word that was used repeatedly twas ‘diversification.’ This term refers to the various species of Viburnum that researchers focused on in the study. While I did not find there to be too many unfamiliar words, I did find that there were a few outstanding concepts and phrases. For example, the idea of a ‘dying embers hypothesis’ did not become clear to be until I reached the end of the article. Another phrase that I had trouble understanding at first was when the authors mentioned ‘repeated pulses’-- it just means that the event being investigated has happened before or in a similar manner.
After my reading I was very interested to learn how the investigation done on the Viburnum species could compare or contrast to other kinds of species. I was also wanted to understand if any effects on the species adaptation could be due to human activity.
That's pretty interesting! I wonder if they can have some type of dangers unknown to humans yet. How important are those plants to the ecosystem in the northern hemisphere??
DeleteMy PI is Gregory J. Watkins-Colwell and he is a collection Manager who is in the division of vertebrate zoology. He is interested in the biogeography and systematics of lizards. He is mostly interested in the herpetology (reptiles and amphibians) in New England, Southwest, and Appalachia.
ReplyDeleteThe article I read was: The Amphibians and Reptiles of the 1962-1965 Yale University Prehistoric Expedition to Nubia. I learned that the Nile River was going to be flooded so archeologist were sent out to preserve things and while they were out there they brought back specimens which are important to the Egyptian culture. Each specimen were analyzed carefully and were classified. However, there were many errors and they were incorrectly classified and most of them actually came out to be Lacertidae and Gekkonidae (type of reptile families).
After reading the introduction I was confused about what was happening in the Nile River that caused the United States Department of State send many people out. But as I got further in the article it all started to make much more sense although more difficult words kept appearing.
In this article I came across taxonomy and what this mean is classifying organisms in different categories. This was a word that helped me understand because this is what they were trying to do with the specimens that were brought back. Another word was macroecology meaning the study of spatially large ecosystems. Then there was herpetological specimens meaning reptiles and amphibians. There were two other words that I did not know which were fauna and amphibians. Fauna means the animals or wildlife in a given area while amphibians are cold blooded vertebrates.
This makes me curious as to how those errors were made, and if the process has changed any to make these errors less likely. I also think it's amazing how this research takes people all over the world! The research done in my article was done in the Bahamas, your PI went to Egypt, and another went to the Caribbean Islands. It makes me think about how important this research is and how important it is to study other environments.
DeleteMy PI is Dr. Susan Butts. She is the Senior Collections Manager in the Division of Invertebrate Paleontology. Her work is currently focusing on the factors that influence the silica replacement of shell fossils.
ReplyDeleteArticle Title: Silicification
Alright so silica is a common compound of sediments. And the article basically talks about silicification (when the original skeletal material is replaced because calcium carbonate is reacting with CO2 filled water and silica produced by precipitation are reacting at the same time). There are 3 ways to fossilize with silica: permineralization, entombment, and replacement. This paper specifically talks about the replacement of silica. A big thing that stood out to me was that to preserve it, the organic matter has to degrade which allows for the silica to go to the next step and to preserve the architecture of the skeletal material.
The introduction talks a lot about the taphonomic biases and how silicification introduces those biases. I think that's the thing I'm having the most trouble understanding in my introduction. Like if I'm correct, a taphonomic bias is any factor that affects the likelihood that an organism is preserved as a fossil. And silicification is biased by both the organism and the local controls. Are environmental factors a taphonomic bias? It says there are problems with linking the temporal pattern to the environmental biases. I'm not sure if anyone could clear that up for me, but nevertheless I think I get the gist of the article without it.
There were a couple words/ phrases that I didn't know the definition of prior to reading my article and I put them in my own kind of definition. They are as follows:
* Matrix- surrounding environment where something develops
* Clastic Material- new rocks that come from older rocks
* Nodules- abnormal tissue growth
* Temporal- timing or relating to time
* Precipitation of Silica- how silica goes through materials (like rain going through a cloud)
This seems like a fascinating process! After reading your summary I was tempted to look up some of the terms and ideas you mentioned. Your ideas regarding taphonomic bias were right, it's any factor that influences the likelihood an organism is preserved as a fossil. I found it particularly interesting that there is even a human bias, which influences what fossils we decide to extract and study. From my rudimentary understanding, environmental factors are a common taphonomic bias. There are definitely difficulties when it comes to identifying and classifying fossils because of a certain bias called temporal pattern. Because the population turnover of some organisms is less than the rate of sediment accumulation, fossil remains from different species that did not live at the same time can be present in the same fossil bed. This could lead researchers to believe that these organisms coexisted, even if they didn't.
DeleteThis summary was very interesting to read! After reading your synopsis, I felt like I genuinely understood the basis of the research paper.
My PI is Doctor Pincelli Hull, a postdoctoral associate and professor of geology and geophysics at Yale University. Specifically, Professor Hull studies ocean ecosystems, using fossils found there to further explore environmental changes such as mass extinctions and climate change.
ReplyDeleteI chose the article Investigating controls on boron isotope ratios in shallow marine carbonates, and although the reading was rather challenging, I managed to pick up on some interesting information.
This article describes an experiment done to test the reliability of the boron isotope-pH proxy as a tool to measure the pH of seawater. Apparently, borate contributes to the formation of biogenic carbonates meaning that there is a connection between the ocean’s pH and the levels of this chemical compound. However, there are many other biotic factors that may impact these measurements, for instance, the involvement of cyanobacteria in micrite and peloids. I also learned that these pH ratings are important because they can be used to calculate CO2 concentrations in the air, therefore offering a better understanding of the correlation of between CO2 levels and global climate.
While reading this introduction, I often got stuck on the different types of carbonates and minerals that were identified. I am confused about the significance that the different minerals have when using this method of pH measurement. In addition, I feel like I may have interpreted some of the information in this article incorrectly when attempting to draw conclusions. Lastly, the information on how the boron ratios are applied to an equation was very perplexing to me.
Peloids: Grains made of micrite that are found in carbonates
Ooids: Sedimentary grains commonly comprised of calcium carbonate, but are occasionally composed of iron- or phosphate-based minerals
Aragonite: A common mineral and the second most common naturally occurring calcium carbonate
Calcite: A polymorph of aragonite, calcite being more stable and the most common
Pore Water: The water found in pockets (or pores) of earth
My PI Is Dr. Todd Schwendemann. He is the Associate professor of Physics at Southern Connecticut State University. His specific study of research is Nano-scale friction/adhesion . Also know as Nanotribology.
ReplyDeleteEven though the article that I picked was not written by Dr.Schwendemann, I learned about Iron sucrose. Specifically how it can be used to help our bodies absorb iron. This was the first time I ever heard of iron sucrose. I never knew that this has been used since the early fifties and sixties.
After reading the abstract and introduction, I would still like to learn more about how this actually works. How does our body actually go about breaking down iron sucrose? Also, How does our body use iron and sucrose to function? Does it work differently when the two are combined? These are some of the question that I will seek to find the answer to in the next couple of weeks or from the paper.
Vocabulary:
Iron Sucrose- is a form of the mineral iron. Iron is important for many functions in the body, especially for the transport of oxygen in the blood. Iron sucrose injection is used to treat iron deficiency anemia in people with kidney disease.
Nanotribology-is the branch of tribology that studies friction, wear, adhesion and lubrication phenomena at the nano-scale, where atomic interactions and quantum effects are not negligible.
Microscopy-is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye
Anaphylactoid reactions-are defined as those reactions that produce the same clinical picture with anaphylaxis but are not IgE mediated, occur through a direct non-immune-mediated release of mediators from mast cells and/or basophils or result from direct complement activation.
Exanthema-a skin rash accompanying a disease or fever
I have been reading an article about a fairly new drug called Lanreotide. This drug is currently being used to treat certain hormonal diseases. One rare disease it is being used to treat is Acromegaly, which is a rare disease. Patients suffer excessive skeletal growth, and even soft tissue enlargement. Death is very likely with patients who have this disease. Many patients die from cardiovascular problems. Lanreotide is released into the patient via injection. An injection is required every seven-14 days. The drug is 30 mg.
ReplyDeleteMy PI is Dr. Gregory Watkins- Colwell of the Vertebrate Zoology team. He works specifically in the Herpetology and Ichthyology collections, studying the biogeography and systematics of lizards (especially geckos). New England herpetology is a special interest of his, as is herpetology of the Southwest and Appalachia. Dr. Watkins- Colwell recently published a paper alongside other researchers, titled "Disentangling the Influence of Urbanization and Invasion on Endemic Geckos in Tropical Biodiversity Hot Spots: A Case Study of Phyllodactylus martini (Squamata: Phyllodactylidae) along an Urban Gradient in Curaçao". This publication details a study conducted on how urbanization affects endemic (native) gecko species. The researchers found that the marked decline of a specific gecko species can be attributed to competitive exclusion and top-down control on population growth through interaction with an invasive tropical house gecko. The study found that interaction with invasive domesticated geckos negatively affects endemic gecko populations that would otherwise be able to adapt and survive in increasingly urbanized environments.
ReplyDeleteThe study was conducted on a specific type of endemic gecko, Phyllodactylus martini, along an urban gradient in the Caribbean island of Curacao. The researchers explored P. martini’s ability to adapt to urbanization through the examination of available/consumed prey, sexual dimorphism, and functional morphology. They then examined the competitive relationships between P. martini and Hemidactylus mabouia, a synanthropic (domesticated) reptile common to the urbanized area. They found that P. martini has the ability to adapt to urbanized environments, but the population is significantly endangered by competitive exclusion and top- down control on population growth, both results of P. martini’s interaction and territorial overlap with H. mabouia.
Personally, I enjoy learning about species' adaptations in response to an increasingly changing world. Recently in school I have chosen to research and create reports on both ecological imperialism and the Anthropocene, and I have also recently met with researchers that conducted a study on climate change’s effect on phytoplankton biodiversity at varying longitudes. As our climate drastically changes and we continue to develop and urbanize natural environments, it is important to understand how our actions influence other organisms and ecosystems. The conservation of other species is essential if we intend to retain a certain level of biodiversity on our planet, and it was very interesting to read a paper on the factors that underlie population declines of reptiles, a “particularly nebulous” area of research.
There were some unfamiliar vocabulary words present in this article. An example of this was the term ecomorphology, or ecological morphology. This is the study of the relationship between the ecological role of an individual and its morphological adaptations. Another new vocabulary term was sexual dimorphism, which is when there is a distinct difference in size or appearance between the sexes of an animal in addition to differences between the sexual organs themselves. Another term was synanthropic, which is a synonym for domesticated and refers to a member of a species of wild animals and plants of various kinds that live near, and benefit from, an association with humans and the somewhat artificial habitats that humans create around them. I also encountered the term arthropod, which is an invertebrate animal having an exoskeleton, a segmented body, and jointed appendages, used throughout the paper to refer to the geckos’ prey. Finally, when examining the “Methods” section of the paper, I encountered the term stochastic, which I found to mean randomly determined, or having a random probability distribution or pattern that may be analyzed statistically but may not be predicted precisely.
"Temperate radiations and dying embers of a tropical past: the diversification of Viburnum" is an article that is written by my PI, Patrick W. Sweeney; he is also the collection manger for the Botany collection. He recently took interest in the diversification of Viburnum.
ReplyDeleteSomething I learned from this article is the "dying embers" hypothesis, which is where the speciation rates have decreased and extinction rates have increased toward the present. He believes that Viburnum diversification can be applied quite broadly to distribution patterns to familiar northern temperate plant lineage.
-heterogeneity: Th quality or state of being diverse in character or content
-phylogeny: the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism
-depauperate: imperfectly developed
-subclades: the SNP furthest down in the Y chromosome phylogenetic tree.
-biome: a large naturally occurring community of flora and fauna occupying a major habitat, e.g., forest or tundra.