Why birds are considered living dinosaurs

During week 2, the monophyletic cladogram of the origin of birds was shown in class, so for my topic I decided to find out why exactly birds are considered living dinosaurs themselves. Birds have evolved from a group of theropod, or carnivorous, dinosaurs, the same group that included T.rex (Sereno). The scientific consensus for bird evolution took a while because of many differing hypotheses, including one that thought birds were similar to reptiles. Figuring it out was only made possible because of the discovery of intermediate fossils that showed species of dinosaurs similar to both avian and non-avian dinosaurs. Through these fossils, scientists found skeletal, genetic, and behavioral similarities between the two groups. Similar small genomes and protein sequences have been found between the two, along with popular avian characteristics like wishbones, feathers, and large breastplates (Chiappe). However, they found that the biggest similarity between the two was the ability to fly, made possible in birds by an evolutionary trend of decreased body mass (Sereno). Flight, small size, and diet variability are credited to be the primary reasons birds survived the mass extinction of dinosaurs in the late Cretaceous period (Gregory et al.). They could breed and adapt faster, escape dangers, and didn't have to eat as much. All of this evidence points to the fact that not only are dinosaurs ancestors of the birds, but that birds themselves are a living lineage of the non-avian dinosaurs and are considered avian dinosaurs. 

Citations:

Chiappe, L.M. Downsized Dinosaurs: The Evolutionary Transition to Modern Birds. Evo Edu Outreach 2, 248–256 (2009). https://doi.org/10.1007/s12052-009-0133-4

Gregory, Duncan, et al. “Why Are Birds the Only Surviving Dinosaurs?” YouTube, Natural History Museum, 15 June 2018, www.youtube.com/watch?time_continue=133&v=9GVvtKK5sFw&feature=emb_logo.

Sereno, Paul C. “The Evolution of Dinosaurs.” Science, vol. 284, no. 5423, 25 June 1999, pp. 2137–2147. Science, doi:10.1126/science.284.5423.2137.

Yellowstone's Prismatic Pond

Who doesn't love a good concentric rainbow? I know I do, so this week I decided to look a little bit into the Prismatic Pond in Yellowstone. Specifically, what's living there that makes the pond actually a rainbow? The easy answer is bacteria that contain different pigments, but that's not quite the answer I was looking for. I was more interested in why the bacteria have specialized in such a way that they make a perfect rainbow around the pond. You might say, I was searching for the rainbow connection... I'll see myself out, thanks.

A great article in Smithsonian Magazine by Natasha Geiling explains that the colourful rings correlate with different water temperatures that provide livable conditions for different species of bacteria. So why are they different colours? For photosynthetic genera like Synechococcus, it's largely due to differing levels of carotenoids- you know, those cool pigments that work with chlorophyll and can act as a kind of sunscreen for our little bacteria friends who risk flying too close to the sun? Cyanobacteria like Synechococcus can withstand some of the highest temperatures in the pond, and produce higher levels of yellow carotenoids because of their direct exposure to the sun's damaging UV rays. Hence, the innermost ring of microbial life in the pond is a yellow/green color. As you move from scorching hot water at the inner rings of the rainbow to slightly less scorching temperatures, a greater diversity of microbes can inhabit the area. This increase in diversity results in a new, differently coloured ring that's representative of the new combination of pigments. Synechococcus can still inhabit the area, but now bacteria with other colours of pigments can join them. Hence, why the darkest ring lies closest to the edge of the pond. This comparatively cooler edge can withhold the greatest diversity of organisms, which means a greater diversity of pigments and therefore a dark red colour! 

Geiling, Natasha. 2014. “The Science Behind Yellowstone’s Rainbow Hot Spring.” Smithsonian Magazine, May 7, 2014. https://www.smithsonianmag.com/travel/science-behind-yellowstones-rainbow-hot-spring-180950483/.



Also, since I know this wasn't the most revolutionary or cutting-edge article, I continued searching a bit about microbes in Yellowstone. I found a cool article just published in October last year about sequencing the entire genome of a unique species found in a couple of hot springs. I thought that was cool news, so I'll link it here just in case anybody wants to check that out as well!

Robertson, Sydney, Robert F. Ramaley, Terry Meyer, and John A. Kyndt. 2019. “Whole-Genome Sequence of a Unique Elioraea Species Strain Isolated from a Yellowstone National Park Hot Spring.” Edited by Julia A. Maresca. Microbiology Resource Announcements 8 (44): e00907-19, /mra/8/44/MRA.00907-19.atom. https://doi.org/10.1128/MRA.00907-19.

Blood Falls

     For the third week of CSBIO20, I chose to look into the chemical composition of Blood Falls in Antarctica. In lecture, we learned that Blood Falls is a waterfall that spurs off of an underground lake that emits high iron and sulfur concentrations through interactions of the subglacial brine and iron-rich bedrock beneath the surface. In the journal Applied and Environmental Microbiology, I read an entry called,"Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica." It explored how the subglacial brine of the Taylor Glacier appears to be controlled by the hydrology of the glacier, as well as the preglacial ecosystem. The microorganisms that contribute to the subglacial weathering and carbon cycling also affect the community structure of the ecosystem by influencing electron distribution in the subglacial community (which affects metabolic processes).
     Taylor Falls is a unique glacier in Antarctica because contains a variety of organisms that are both heterotrophic and autotrophic that enrich subglacial brine microorganisms. To this day, it is still unknown how the subglacial brine escapes from the underground lakes, and what triggers this release. Blood Falls in particular is also an enigma because scientists do still not fully understand why the chemistry of this brine differs so dramatically from that derived from other streams that undergo supraglacial melt. The results of this experiment conducted by Mikucki and Priscu uncovered that the, "the ferrihydrite level in the Fe-Rd enrichment medium was reduced after approximately 9 months of incubation," meaning something special about Blood Falls and the subglacial brine of the Taylor Glacier is what maintains the ferrihydrite levels and what keeps Blood Falls looking like blood (4033). Mikucki and Priscu concluded that the growth of the microbes beneath the Taylor Glacier must continue despite absence of sunlight and these extremely cold conditions (chemotrophically or chemoorganotrophically).

Mikucki, J. A. & Priscu, J. C. Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica. Appl. Environ. Microbiol. 73, 4029–4039 (2007).

Engineering the Flagellar Secretion System

For week 2, I decided to look into new and interesting research about the flagellum in prokaryotes. I was really amazed at how prokaryotes use their flagella to move and how John mentioned that they just tumble around until they find what they need. Having learned this, I wanted to see if there were any ways the flagella could be used in biotechnology. After some time browsing on Google Scholar, I found a cool paper titled “Engineering the flagellar type III secretion system: improving capacity for secretion of recombinant protein.”

I learned that biotech companies struggle in harvesting protein products from prokaryotes as they are usually localized in the cytoplasm. This causes problems in protein purification as the cytoplasm is full of many other contaminants. However, researchers found a way to engineer the flagellar type III system into secreting their desired protein into the surrounding media. They do this by removing the flagellin and HAP proteins that compose the flagella. Though the technique needs improvement, researchers think that this could lead to a strain of E.coli that secretes protein product continuously (making biotechnology processes way easier). Although the paper is a bit difficult to understand, I still think that it’s a great read!

Here is the citation and link to the paper!

Link: https://rdcu.be/b0wmm

Citation: Green, C.A., Kamble, N., Court, E. et al. Engineering the flagellar type III secretion system: improving capacity for secretion of recombinant protein. Microb Cell Fact 18, 10 (2019) doi:10.1186/s12934-019-1058-4

Meteorites and the Origin of Life

I decided to search on google scholar for “the origin of life and meteorites” to find articles that talked more about how this could come into being (or possibly not).

After modifying my search a little to aim more at the meteorites, and searching for the year 2017, I found an article detailing in great detail about a certain type of meteorite called the carbonaceous chondrite, and how they could have been able to form certain proteins like glycene.

The article dives deeply into the chemistry side of perhaps an “origin of life,” but it is an interesting read and poses lots of areas for more research and speculation.

Attached is the link: https://link.springer.com/article/10.1007/s11084-016-9530-1

Welcome

Welcome 2020 CS Bio 20 students. You will all shortly receive an invitation to join this blog. Please accept this so you can post here.

Here are the links to chosen topic examples I mentioned in class. These were done a few years ago so there will be more up to date papers to find on some of these topics but I'll leave that exercise to you.

Chosen topic example 1
Chosen topic example 2
Chosen topic example 3