Journal: Reading Response

Submitted by abnguyen on Sun, 03/05/2017 - 23:11

For my Advanced Genetics class, I had to read an article and respond to it.  This is my response below.

After reading this article I found it interesting that CRISPR is already being used for experiments like this one.  It did not surprise me that removing transcriptional factors also hindered the expression of certain genes.  However, I was surprised that this retrovirus spanned multiple mammalian lineages.  This is another branch in the evolutionary tree that links us closer to other species.  One question I have about this article is, if these endogenous retroviruses started out as virus, isn't there a chance that the virus used reverse transcriptase to incorporate itself into our genome?

Chuong EB. Elde NC. Feschotte C.  Regulatory evolution of innate immunity through co-option of endogenous retroviruses.  Science.  <  Accessed 2017 Mar 3. 

Journal #16-- Development and Function of Spinal Cord Networks

Submitted by skhall on Sun, 03/05/2017 - 20:36


        While looking at the various research that UMass has to offer, I came upon a type of research that is done by Gerald B. Downes. His lab is interested in the development, organization and function of neuronal networks that involve precise movements of locomotive behavior like walking or swimming. They use zebrafish to study this because they have several characteristics that make them eel-suited for studying this type of information.Their spinal cords are relatively simple compared to mammals and the embryos are transparent which also make it easier to study. These features in the fish allow them to integrate genetic, molecular, cellular and a behavior approach to study the spinal cord network. Specifically they are looking to understand how the hindbrain and spinal cord control this behavior. Using the zebrafish to study this information is broadly conserved among vertebrates, but it might gives good insight about mammalian systems to establish new types of models of human disease. Gerald Downess works with five other researchers to help on this project.

PP wk 6

Submitted by jiadam on Fri, 03/03/2017 - 15:35


There were specific differences in the image B of figure 1 compared to image B of figure 2. Figure 1 has different dimensions compared to figure 2. Figure 1 shows Isenberg School of Management and figure 2 has Isenberg School of and the top of another word but not the bottom. Figure 1 panel letter in the top left covers letters visible in figure 2. There are two visible triangles in figure 1 as opposed to three in figure 2. Figure 1 has an image next to it. The replicated figure has blank white space next to it.

There were specific differences in image C of figure 1 compared to the image C of figure 2. There are four stems in figure 1 compared to 3 stems in figure 2. The pot is shown in figure 1 compared to no pot in figure 2. The arrows are at different angles. Figure 1 has thicker arrows pointing 20-40 degrees away from 90 degree mark (vertical) whereas figure 2 arrows are 20-40 degrees below the 180 degree mark (horizontal). The words Sporophytes and gametophytes are plural in figure 1 compared to Sporophyte and Gametophyte in figure 2. Gametophytes is not capitalized in figure 1 but it is in figure 2. The words Sporophytes and gametophytes are on the figure in figure 1 and are white with a black outline in figure 1 in a word art format. The replicated figure has Sporophyte and Gametophyte off the picture and in a non-word art format. You can see the clay color in figure 1 compared to figure 2.

Week 07: Data Analysis

Submitted by sbrewer on Fri, 03/03/2017 - 15:34

Meeting Location

BCRC (M311S)


This week, we will use the first few minutes in class to work on and share proposal ideas. The rest of the class time will be devoted to a Data Analysis activity.

Required Activities

  1. Find a Research Paper that has methods (related to studying moss) that you believe can be adapted for our class.
  2. Find a review paper that summarizes the topic you've selected for your Research Proposal.
  3. Add both papers as Biblio entries.
  4. Be prepared to briefly report on what data your group plans to collect.

In class, we'll work with these data files.

Observation of the Blue Sky Flower - Durfee Conservatory: Epiphyte/Vine House

Submitted by kcapri on Fri, 03/03/2017 - 14:20

The specimen has five delicate petals that are a light violet shade. The center of the plant has a yellow feature projecting from it. The specimen was about 3.5 inches across. There are green, leathery leaves that surround the specimen. This is the Blue Sky Flower, also known by its scientific name Thunbergia grandiflora.  Their vine can grow from anywhere to three inches to six meters in height. Their hues can vary from sky blue, which is why they are named, to a lighter violet. It is a flowering vine orchid that can be found on the UMass campus in the Durfee Conservatory.


Image 1. Photograph depicting the Blue Sky Flower in the Vine House of the Durfee Conservatory. Taken from the Durfee Conservatory -


The Vine House in Durfee Conservatory had many specimens to observe. This was the second house in Durfee from the campus side door, and it contained epiphytes and vines. Epiphytes are plants that grow on other plants, which is unique to observe. Examples of these include orchids,  and flowers such as the Blue Sky Flower.



Epiphyte/Vine House. Epiphyte/Vine House. 2017 [accessed 2017 Mar 1].  

Kinsey TB. Thunbergia grandiflora. Hawaiian Plants and Tropical Flowers. 2017 [accessed 2017 Mar 1].

Possible in class methods experiment

Submitted by lcampion on Fri, 03/03/2017 - 14:10

Finding scientific article about moss that had a methods section that was possible to replicate in this class. Since many moss species, such as Physcomitrella patens, are considered model organisms, there are hundreds of articles and experiments out there. As a model organism, there is already general understanding about the fundamental processes that plants undergo to survive. It was hard to find a simple experiment concerning moss.

This article discusses an experiment that focused on the effects of temperature on the growth of two specific moss species. The moss were collected and split into 4 temperature blocks and each block contained both mono-species and multi-species cultures. The moss was left to grow in the controlled climates for 154 days. Other factors such as water availability and light and dark periods were also controlled. The growth of the moss was measured by the thickness of the moss cover.

Breeuwer, Angela, et al. "The Effect of Temperature on Growth and Competition between Sphagnum Species." Oecologia, vol. 156, no. 1, May 2008, pp. 155-167. EBSCOhost, doi: 10.1007/s00442-008-0963-8

Moss Journal- Resilience of moss in northern ecosystems

Submitted by rfredericks on Fri, 03/03/2017 - 13:58

In this journal they tested the resiliance of moss and their role in ecological stability. They used model simulations to test this theory. If we were able to grow moss in several different conditions we could replicate this experiment. Some of the moss tested was in northern high lattitude regions, we could likely still preform an experiment but the conditions would be somewhat different as we are not in a boreal/arctic ecosystem.

Geography Paper Excerpt PP

Submitted by sjurgilewicz on Fri, 03/03/2017 - 13:26

The pollution in and around Lake Atitlan is horrifying. The sewage spilling into the lake is a major health hazard to the indigenous people living around the lake. The growth of the cyanobacteria prevents the locals from using the lake for all it is worth; they cannot swim, fish or bathe. The connecting rivers are filled with trash which then flows into the lake. It is obvious that cleanup is needed. The water treatment plant that was present and providing clean water had since been destroyed after Hurricane Stan. There is a dire need for money to be put into the land and lake cleanup, but a severe lack of it. The locals attempt to do their part in the cleanup, but only so much can be done by hand and with limited reasources. 

Moss Experiment

Submitted by dkotorobay on Fri, 03/03/2017 - 13:24

The experiment conducted was done to see what would happen with the spore dispersal of larger capsules in the Sphagnum. Larger capsules are typically better for short range spore dispersal. The experment was conducted from mid to late summer so there isn't really a way for us to duplicate it but it looked interesting.


Bird vs Mammal Respiration Perfect Paragraph

Submitted by kcapri on Fri, 03/03/2017 - 13:23

Respiration is the coordinated process of moving air into and out of internal structures of animals. There are several different types of respiratory systems in nature. Fish, mammals, and birds all have very unique modes of respiration. Mammals have lungs that feature alveoli, sac-like structures that increase surface area and gas exchange. While birds do have lungs, their lungs have parabronchi structures that allow rapid air exchange, in comparison to mammal alveoli structures. Respiration in birds is different from mammal respiration. Birds have several large thin-walled air sacs, such as the cranial thoracic sac, caudal, abdominal sacs.


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