Drafts

    Recently I had just came back from Boston for the weekend, and needed to make myself some sort of meal in order to substitute my dinner (I had volleyball coming up in a few hours, so to eat a whole meal before it would be a bad idea). I remember I had half a loaf of ciabatta sitting in my dresser where I store all my dry ingredients, so I decided to make a bruschetta.
    Unfortunately, when I had began to slice into the bread, it was almost completely stale. This baffled me because I had only been gone for a couple of days. I’ve had bread sit around at home for almost a week and it’s still very fresh.
    This made me wonder, what causes bread to become stale? I know already that some sort of dehydration occurs, so leaving it in a paper bag was probably not the most optimal way of storing it. After some research, it turns out that the water in the starch moves towards the crust, causing the starch to become hard and crunchy. Yet why does the water in the starch move like that? Is it in some way similar to passive diffusion? Or maybe the crust of the bread is very electropositive, causing the water to be attracted and move out of the starch by that kind of interaction? I find it also interesting that the main reason is due to the loss of water in the bread as a whole. I would assume that if a loaf of bread was exposed to air, water would eventually evaporate out of the loaf, causing the bread to become stale overall. If the water moves towards the crust, then why is the crust still really hard as well? Is it because it’s easier for water to evaporate through the crust rather than through the starch itself?
    In my opinion, the entire mechanism of bread becoming stale seems a lot more complex than it actually seems. Is it possible we can use the same mechanism in other scenarios that end up becoming beneficial in a way? Not the dehydration part, because that is already being used in a lot of places (instant ramen, bouillon cubes, etc.) but the mechanism in which water “moves” from the starch to the crust. I feel like a similar mechanism is used for air-dry clay, but I’m unsure if the two are related.

I believe that the most important aspect of the biological world to conserve would be soil fertility. The fertility of the world’s soil is an essential component of the biological world for both humans and other mammalian species. Soil itself is where carbon, nitrogen, phosphorus and many other nutrients are stored, transformed and cycled. All these nutrients are necessary for life on earth.  Soil erosion and degradation has been one of the most pressing issues facing human security in the 21st century. As the global population continues to increase our long term viability of farm land slowly begins to decline. Farming practices being shifted through the years has caused an accelerated loss of soil and this serious decline of fertile soil is threatening food supplies.

The research article is broken up into the level 1 headings of abstract, introduction, methods, results, and discussion. The methods section, for example, has the level 2 headings of study site, field methods, epiphyte field identification and species groupings, and analytical methods. This is particularly useful for clarifying specific parts of a singular experiment. In contrast, the mini-review article has level 1 headings for each question it asks, such as “why should we try to construct models of communities?” and “if press or pulse methods could be applied, could we build a predictive model?” This is useful for addressing broader concepts from multiple different experiments and articles. I am not surprised by this distinction between the two formatting levels, but would also not be surprised to see level 2 headings in other review-style articles for further specification. I think although the formality of many heading levels is more commonplace in research articles than review, it may just be a byproduct of the research articles being more specific about a singular experiment. Depending on the review article, I wouldn’t be surprised to see up to level 3 headings, provided the concepts are multifaceted enough.

The geese have mostly brown feathers on their backs while their undersides are mostly white. While the feathers on its torso are shorter, the featers at its tail are longer and fewer in number. There is a sudden shift in color at its neck, which is black up through its face and beak. Its cheeks remain a clean white. The geese float on the water, with only about a tenth of its body submerged in the water. Some geese lower their body and crane their necks out to peck at food floating on the surface of the water. One goose glides along the water with its neck perpendicular to the surface, looking like it is scoping the surface for any food. The necks of the geese are clearly very flexible. They can bend in a "U" shape before extending to reach for something. The baby geese are smaller, about one fifth the size of their parents. They are mostly brown in color, but it is a light brown that is much softer than the darker gray-brown feathers of the adults. The undersides of the young geese are still white, and the necks and face remain white and light brown. There is no traces of black in the feathers of the young geese, except for their small beaks. They have much shorter necks than the adults, making them resemble ducks more than geese. They too peck at the water for food, cocking back their head and lurching forward to grab anything. Occasionally the adult geese extend their necks straight into the air, although it is unknown why. As the geese move, they create ripples in the water. 

Today in biochemistry we learned about the hydrophobic effect. That is when nonpolar molucules that are exposed to an aqueous environment bunch together. The process is driven by entropy. Because molecules in nature perfer to be disordered, the nonpolar molecule bunch together to minimize interactions with the polar water molecules. The water molecules can form dipole-dipole interactions with one and other because water has permanent, partical charges. The nonpolar molecules form van der waal interactions between themselves. This process can be seen in salad dressing when the bottle is shaken. The bubbles of oil that are formed disperse but reappear after a few minutes. 

Today I performed DNA extraction in a labratory course. We took the leaves of a plant and ground it up using two metal balls inside the 2 mL roundbottom tube. The tube was attached to a machine that shook the tubes rapidly and rigorously for one minute. That was enought to crush the frozen leaves in a fine powder. Detergent and EDTA were added to the powder to break down the cell and nuclear membranes and stop enzymes from breaking down the DNA. The tube was heated and chilled. Next we added a potassium solution to the tubes to cause proteins and carbohydrates to precipitate, which they did. After centrifuging the tube, the supernatant containing the DNA was transferred to a new, clean 2 mL roundbottom tube. Isopronanol was then addded to the solution to cause the DNA precipitate, leaving behind lipids and remaining proteins and carbohydrates in the solution. The content was centrifuged once again, and this time, the pellet was what we wanted to keep, for it was the DNA. The resulting pellet was very small and almost clear. It appeared as a small, cloudy smudge on the bottom of the tube. We extracted the supernatant and washed the DNA pellet with 70% ethanol. The DNA pellet was then dissolved in a solution that would preserve the DNA to be able to be used far in the future. 

     Feather is a derived characteristic specific to Class Aves that is similar to what is known as skin. Feathers act as insulation, communication, defense mechanism, and flight. Feathers come in various patterns and coloration which gives each bird their own specific plumage to be distinguished from one another. The role feathers serve for birds to survival is explained in detail with different situations.

Alpha-keratin is a type of protein found in all vertebrates to form a skin. Birds and reptiles have an additional protein called beta-keratin which is the main structure of feathers and beaks for birds, and reptilian skin and claws for reptiles. The primary feathers, known as contour feathers are the most common type of feathers found in birds. It has the long flat shape with a hollow stick called a calamus supporting the root and connecting to the rachis. Lateral barbs then branches off from the rachis creating the soft and smooth shaft of feather. The inner part of the feather serves as insulation, and the outer part is for different purposes. Barbs can be separated into three structure: barbule, barbicel, and ramus. Barbules is the thin flexible part of the feather which gives the texture. Then from that as the feather goes inward toward the body, it becomes more rigid structure to support the shape and give insulation.

    Feathers can also have a secondary structure. For example the Cedar Waxwing of North America has a modified fused barbs at the terminal with wax-like wing feather tips. The fused barbs allow water to soak the feather to reduce buoyancy but at the same time can air dry fast when coming out of water. Many water birds have feather modification specific for swimming.

A great example of water bird would be the specie called Sandgrouse. They are birds that live in the desert of Africa. From the nearest water the nest is about thirty kilometers away which enables the baby bird from getting the water. The male sandgrouse would go in the water and absorbs it to bring it back to the nest. They have modified barbs where barbules extends to hold water in them.

It is crucial to recognize and understand the different styles of scientific writing when reading articles, integrating concepts, and conducting research. The two articles assigned are of two different types: one classic research and one mini-review. The research article, “Neighbor Relations within a Community of Epiphytic Lichens and Bryophytes,” has a more formal layout than the mini-review article, “Describing and quantifying interspecific interactions: a commentary on recent approaches.” The research article is divided up by formal sections: abstract, introduction, methods, results, and discussion. In contrast, the mini-review article is divided up by different questions, such as “why should we try to construct models of communities?” and “if press or pulse methods could be applied, could we build a predictive model?” The mini-review article has an abstract of its own, but the information within it is different than that of the research article. The abstract of the research article is of a singular experimental nature, while the abstract of the mini-review article addresses multiple research articles and their findings.

Though GABAergic neurotransmission has been found to be most directly affected by the mutations underlying Dravet's syndrome, scientists have explored the potential of other neurotransmitters rescuing the phenotype, relieving mutant zebrafish larvae of epileptic seizures. One of the neurotransmitters that has shown some promise is serotonin (5-hydroxytryptamine). It's been revealed that increasing serotonin levels can reduce epileptic locomotor activity and brain activity. As such, the drug fenafluramine was identified to be capable of targeting serotonin recetor subtypes, acting as agonists for those subtypes and allowing serotonergic neurotransmission. However, this drug does not restore the sodium channels lost in GABAergic neurons. While this drug is effective at targeting the right subtypes, it does have some co-morbidities. It happens to target the serotonin-2B receptor subtype, which leads to cardiac hypertrophy. This has made the drug unfit for use as an effective treatment against Dravet's syndrome.

Wolves (Canis lupus), coyotes (Canis latrans), and domestic dogs (Canis familiaris) are all separate species. Although there are times in which the species interbreed this is because of the fact that all of the species are similar enough. The article mentions that even modern humans today have some traces of Homo neaderthalensisas well as Denisova homininsgenes mixed in their genomes. The fact that they can interbreed with one another does not make them a single species. Their interbreeding occurs when there is not enough of one species in the area and what this leads to is more variation among the species. Although wolves, coyotes, and domestic dogs share very similar genes there still is enough variation to make them separate species.