Writing in Biology

Birds are bipedal vertebrates that evolved from theropod dinosaurs or reptiles. They are from a new class of vertebrates known as Aves which includes all birds. They have feathers and wings. The main function of their feathers is to maintain body temperature and their wings are used for flight. To maintain balance, birds placed their body in the center of the earth so it can be over and between their feet. When landing, they come closer to the ground and slowly rises to minimize the impact. 

Most birds are arboreal, in other words, tree-dwelling species. They grip on tree branches to keep their body upright and to prevent them from falling. Birds do not have claws, but instead, they have 3 digits or toes that they used to climb up trees. They also don't have teeth but instead, they have gizzards that help them digest hard nuts shell, seeds, and insects. Birds are the only species of its kind to reproduce externally. Most birds provide parental care until the eggs hatch after that the babies are on their own. They use their acute senses to help them navigate and communicate, also, they can hear sounds and see a wide range of colors more than humans. Their brain is about six to eleven time larger than reptiles and has lateralization that resembles primate brain.

Mammal and reptile are morphologically different in a few ways. Mammal skulls are synapsid: they have a single, large opening called a temporal fenestra behind each eye that allows for more attachment of jaw muscles. This muscle attachment gives mammals a larger range of motion in their jaws, which allows them to have stronger bites. Reptiles such as alligators are diapsid, which means they have two temporal fenestrae on each side of their heads, while other reptiles such as turtles do not have any of these openings and are thus referred to as anapsid. Another difference between mammal and reptile skulls is the mammalian middle ear is made up of three bones, the malleus, the incus, and the stapes, whereas the reptilian middle ear is made up of only the stapes. Reptiles have articulate and quadrate bones in their mandibles and skulls respectively, and in mammals these bones have migrated up towards the middle ear and formed the malleus and incus. Mammal skulls also differ from reptile skulls in that they have two occipital condolytes at the articulation between the skull and the cervical vertebrae. This allows mammals to move their heads up and down through, which is beneficial to them because this gives them the ability to further manipulate their food. Reptiles on the other hand only have a single occipital condolyte, which limits their head movements, most of which involve moving the entire body.

Skull morphology differs between mammal and reptile skulls. Mammal skulls are synapsid: they have a single, large opening called a temporal fenestra behind each eye that allows for more attachment of jaw muscles. This muscle attachment gives mammals a larger range of motion in their jaws, while also allowing them to have stronger bites. Reptiles such as alligators are diapsid which means they have not one, but two temporal fenestrae on each side of their heads, while other reptiles—including turtles— do not have any of these openings, and are thus referred to as anapsid. Another difference between mammal and reptile skulls is the mammalian middle ear is made up of three bones, the malleus, the incus, and the stapes, whereas the reptilian middle ear is made up of only the stapes. The malleus and incus however are the result of the migration of the articulate and quadrate bones found in the reptilian mandible and skull respectively.

Birds are very interesting vertebrates, they have feathers and wings that allow them to fly. They are bipedal vertebrates meaning they have 2 legs just like us humans. Some of them eat insects and others eat seeds. Birds can come in different size, shape, colors, and beak sizes. They belong in a class of vertebrates known as Aves which includes all birds. They do have claws but instead, they have toes or digits (3 digits), some birds even have toes in their wings which I think is pretty amazing. Toes from their wings help them climb up trees and they can also use them to hold their preys. 

I am holding a round clear plastic cup with a medium size worm inside that has a yellowish color and It's not pleasant to look at. There is something else inside the cup that I am not sure what it is, I would like to know if they eat whatever is inside the cup. The worm has a dark head and there are lines all over its body. It does not have feet or tail but it has two brown eyes at the back of its body. There is also a circle around the brown eyes with things sticking out of it. When the worm moves, there is a long brownish line connected from the head to the back that looks like its spine.

DNA extraction was performed in the laboratory today. Leaves from the plant Brachypodium distachyon were frozen in liquid nitrogen and placed inside a 2-mL round-bottom tube with two metal balls. A machine was used to shake the tubes vigorously, allowing the balls to grind up the frozen leaves inside into a fine powder. Detergent was added to the powder to break down the cell and nuclear membranes, and ethylenediaminetetraacetic acid was added to stop the cells’ enzymes from degrading the DNA. The tube was then incubated and chilled in ice. A potassium solution was then added to the tube, which caused the proteins and carbohydrates to precipitate. The tube was centrifuged, causing the precipitated contents to form a solid pellet. The supernatant containing the DNA was transferred to a new, clean 2-mL tube, and isopropanol was added to the solution, which caused the DNA to precipitate. The tube was centrifuged, causing the precipitated DNA to form a small, clear pellet at the bottom of the tube. The supernatant was extracted, and the DNA pellet was washed with 70% ethanol. Lastly, the DNA pellet was dissolved in a preservation solution.

https://neurosciencenews.com/memory-flow-neurons-10671/

This study aims to shed light on how the brain remembers certain important locations that contribute to remembering a route of travel.  The study design was a behavioral intervention. The researchers used a two-photon microscope to observe vasoactive intestinal polypeptide-expressing (VIP)-cell activity as mice ran on treadmills while being presented with various sights and sounds.  The researchers focussed on area CA1 of the hippocampus, the area that has previously been shown to be responsible for animal location. The hippocampus at large is responsible for long term memory. It is understood that as an animal learns its route, various excitatory and inhibitory neurons are fired.  What I am left wondering is how the information is stored latently, to be used at a later time.

Covalent bonds occur when atoms share electrons; however, becasue different atoms have different electronegativites, there is often an uneven distribution of electrons between the two that are covalently bonded. This results in polarity, where one atom is slightly positive, while the other atom is slightly negative. This can lead to interactions with other molecules that result in non-covalent bonds. Non-covalent bonds are electrostatic. This does not mean that they are only between fully charged molecules. Non-covalent bonds occur when two molecules have any sort of charge: partial or full or temporary or permanent. They can be intermolecular or intramolecular, meaning two parts of one molecule interact with each other. Noncovalent bonds are classified based on their magnitude and duration. Ionic bonds occur between opposite permanent, full charges. Meanwhile, van der Waals interactions occue between opposite temporary, partial charges. Dipole interactions describe any non-covalent bond in between. Dipole interactions can be dipole-dipole, ion-dipole, etc. A very important dipole-dipole interaction is the hydrogen bond. A hydrogen bond occurs when it is bound to a highly electronegative atom, usually nitrogen or oxygen. This causes the hydrogen atom to hold a permanent, partially positive charge. When it interacts with an atom with a permanent, partially negative charge, it forms a hydrogen bond. 

FISH, flourescent insitu hybridization is a molecular technique used to visaulize expression patterns of genes in a model organism. Knowing where a gene is expressed can give clues as to what role the gene plays in the organism. In fluorescent in situ hybridization, a fluroescent RNA probe is made and introduced into the organism, where it binds the appropriate gene sequence. As you can guess, the sequence of the RNA probe has to be complementary to that of the desired DNA sequence. Probe generation involves DNA extraction, polymerase chain reaction (PCR) to amplify the desired sequence, and then in-vitro transcription to turn DNA to RNA. The probe then has to be labeled. The actual in-situ hybridization process varies depending on the model organism used. In zebrafish, the whole process last about 4 days. The image of the expression pattern can be obtained by using confocal microscopy.

          The protein presenilin 1 is one subunit of a complex known as gamma-secretase. Presenilin 1 carries out the major function of the complex, which is to perform proteolysis on other proteins. The γ-secretase complex is best known for its role in processing amyloid precursor protein (APP), which is made in the brain and other tissues. Gamma-secretase cuts APP into smaller peptides, including soluble amyloid precursor protein (sAPP) and several versions of amyloid-beta peptide. Evidence suggests that sAPP has growth-promoting properties and may play a role in the formation of nerve cells in the brain both before and after birth. Alzheimer's disease patients with an inherited form of the disease have been found to carry mutations in the presenilin proteins or in the APP.