Drafts

Today I had a quiz in Bio285, Cell and Molecular Biology I, a class I am in as a senior amongst many sophomores and juniors. The quiz was on basic protein structure and folding, but some of the questions were pretty tricky. The primary structure is the first level of proteins, and it is the sequence of amino acids in a polypeptide held together by peptide bonds. The second level is the secondary structure, which is the folding of the backbone. Secondary structure is held together by hydrogen bonds between amino and carboxyl groups of different amino acids. The third level is the tertiary structure, which is the interacting and folding of R groups. Tertiary structure can be influenced by many types of bonds, covalent and non-covalent, including disulfide, hydrogen, Van der Waal’s interactions, electrostatic interactions, and hydrophobic interactions. The type of bonds formed depends on the polarity and charge of the R groups. The fourth and final level of protein structure is the quaternary structure. This consists of multiple polypeptides interacting together, and they can be different polypeptides or multiple of the same. These are held together by all the bonds mentioned in tertiary structure bonding.

 The selected plant is approximately 3’ 2” tall and bushed out towards the top of the plant. The leaves are small and pointed with purple discoloration on most of the leaves. The stem of the plant is mostly brown with some hints of scarlet where new branches grow out of the stem. Berries represent another unique characteristics of this plant. The dark purple berries grow off the end of the branches. The smooth coat of the berries and the leaves readily reflect the sun. The plant holds some dried berries that hang from the plant, ready to fall off. These berries are crucial to discovering the identity of this plant. The patio of the architecture building contains two different types of plants that can grow berries: huckleberry and shadberry. Due to the pointed structure of the leaves and the scarlet coloration of the stem, the plant could be identified as a shadberry plant. The berries of a shadberry plant have the same distinct, protruding calyx  that are not as present on huckleberries.

Today I attended a general Lab Safety training coordinated by UMass EH&S in order to obtain a certification needed to work in a laboratory. The training started out talking about different hazard signs, including but not limited to: flammable, acutely toxic, environmental toxicity, and physical hazards. The woman then went on to say things about engineering solutions to safety protocol, and how those should be the first line of defense against a harmfl situation. I was surprised to learn that personal protection, aka safety goggles, gloves, and lab coats, are the last line of defense and should only be used when they absolutely need to be. Because these items are personal, there is more of a gray area when it comes to who needs to be protected at which times. Ife negineering allows the whole lab to be safe at once, then steps should be taken to improve that before relying on PPE equipment. At the end of the training I got a free pair of safety glasses, and I have my Fire Safety training on Friday.

Today I went to my independent study for the first time, where I am supposed to work in a microbiology department on Tuesdays and Wednesdays for 3 hours total. My expectations for what a lab should look like was not very off. One thing I did not expect was how messy a lab should be. I understand that a lab can be messy sometimes, with notebooks left open and test tubes all over the place, but the lab I saw today had a very abstract look to it. It was messy but organized at the same time. For example, there are defined drawers to grab gloves, but nothing is labeled. Bottles are not organized in a neat manner, but they still remain on the shelf. The lab I work in is interested in the transfer of electrons to current harvesting electrodes by bacteria named Geobacter sulfurreducens. The bacteria must grow in solution without oxygen in them, so a mix of nitrogen and carbon dioxide is put together in a gas, and is left to bubble inside the water to remove the oxygen. The oxygen above the water level is also removed by spewing out the same gas afterward. This process takes 25 minutes to complete. An anaerobic solution allows for the bacteria to grow, which will then make electrons for which we can manipulate.

As the world population continues to grow in size, issues in food growth and distribution arise. Simply focusing on the issue of food growth, all efforts must be made to produce the highest yields as possible in the arable land we currently use. Doing this allows for more efficient farming, and avoids destructive deforestation that decimates biodiversity and the natural carbon capture that our forests and jungles provide. To maximize yields on our current farmland, GMOs must be used responsibly. While GMOs do assist in higher yields, they also come with additional responsibilities to the farmer. Round-Up Ready seed usually requires specific herbicides-chemicals that are currently being investigated as a carcinogen-to be sprayed to eliminate crowding by weeds. The farmer, seed manufacturer, and herbicide manufacturer must all be responsible for the dangers to human health, as well as avoiding resistance among weed populations. GMOs then may seem to be a much more labor intensive option than simple organic farming. However, when used correctly, GMOs are the only way forward to feed our ever growing population.

Today I learned in my Ecology class the different kind of forests, and a lot about oceans. I specifically was interested by phytoplanktons because they can only live in the euphotic zone. The reason for this is that the water needs to be able to reach sunlight so they are able to do photosynthesis. They are similar to terrestial plants because they need photosynthesis to grow. They remind me of a buoy that you use swimming, because all they do is float and absorb sunlight. They also require nutrients from the ocean such as nitratees, phosphates and sulfur, because they then convert them into proteins, fats and carbohydrates. In a well balanced ecosystem, they provide food for sea animals such as whales and shrimp. The reason why I find them so cool is because they are the foundation of the sea life. They do however have toxis effects to humans!

Today one of my classes discussed GMOs and my professor purposefully made it a point to tip-toe around the debatable aspects of the modifications and methods of use while teaching the topic. Me being an aries would have prefered the debate, so instead I'll write my thoughts here. Firstly, the FDA finding the GMOs are not inherently dangerous and do not need to be regulated proves that the federal goverment needs more education. I agree that GMOs are not inherently dangerous, but they absolutely should be regulated by genetisists because modifying the DNA of an organism to be grown in exposed fields and allowed to contaminate nature and the endogenous genome of other organisms in the proximatey is highly dangerous. It is known that some species of GMOs are able to cross breed with weeds and like organisms in their original environments. This means that another organism's DNA can be crossed into uncontrolled species in the wild. Also, GMOs can cause very legitimate problems in the diversity of a species. If all the different alleles of a farm grown species were cut down to a single allele that was controlled because it produced the most wanted product, it presents real issues. The possibility of complete wipeout from a new disease or virus that affects the plants is a reality that people need to be aware of. 

Kombucha is a fermented tea, usually black or green tea, that has a very low alcohol content of less than 0.5% alcohol by volume. In many cases, it is used for supplemental or medicinal purposes and due to the low alcohol content is commercially sold in many grocery and convenient stores. Kombucha is fermented with several different species of yeasts and acid bacteria such as such as Bacterium xylinum, Bacterium xylinoides, Bacterium gluconicum, Saccharomyces ludwigii, Saccharomyces apiculatus varieties, Schizosaccaromyces pombe, Acetobacter ketogenum , Torula varieties , Pichia fermantans (Gharib, 2009). Research has shown that the organic acids, enzymes, and vitamins produced by the fermentation process have some health benefits. Kombucha may aide digestion, avert cardiovascular disease, reduce inflammation, aide in immune support and even divert some forms of cancer. Overall, kombucha is a new health fad that has some research to support its health benefits.

Gharib, Ola Ali. "Effects of Kombucha on oxidative stress induced nephrotoxicity in rats." Chinese Medicine, vol. 4, 2009, p. 23. Gale OneFile: Health                      and Medicine, https://link.gale.com/apps/doc/A213497834/HRCA?u=mlin_w_umassamh&sid=HRC.... Accessed 17 Sept. 2019.

As soon we take one look at food, our salivary glands are at work to produce saliva mixed with enzymes to start breaking down carbohydrates. Our teeth play a major role in mechanical digestion to form a paste out of the food we are chewing, making it easier for us to swallow the food bolus down our esophagus. Due to peristalsis, the food bolus keeps moving down to the stomach, where gastric acid kills any bacteria or germs and the food is churned to make it more liquid. The food passes down to the duodenum. Pancreatic enzymes further break down carbohydrates, proteins and fats. The fat gets emulsified by the bile from the gall bladder to help in digestion. The smaller molecules move down to the small ileum and get absorbed by the blood vessels and sent to the liver to get sorted. Water is absorbed by the colon and the undigested food is egested through large intestine. 

Sound perception and production in birds, especially oscines, has been the subject of much research. Birds’ singing and song learning systems have been studied from perspectives ranging from mechanical through neurological to social and adaptive. Mechanically speaking, birds produce song via the syrinx, an analog to the human larynx. Found at the entrance of the bronchioles, the syrinx is a group of connective tissues, cartilage rings, and membranes that vibrate in concert to produce sound. Sound itself comes not from the vibration of the medial tympaniform membranes but from connective tissue at the end of each bronchus that sticks into the syringeal lumen. From a neurological point of view, bird song perception, production, and learning originates in a series of neuronal nuclei heretofore referred to as the song pathway. Perception of song begins in auditory field L in conjunction with the NCM and CMM areas. These signals are then passed through the HVC, area X, LMAN, and DLM which all have song selective neurons that discriminate between different song types. Song production also comes from the song pathway and uses the same nuclei. Firstly, main auditory field L projects to both the HVC and RA, and the HVC itself projects to the RA. Secondly, from the RA is a projection to nXIIts, from which there is direct innervation of the syrinx, and thus, song production. Song learning also takes place in the song pathway, though this is less well understood and seems to have to do with the expression of immediate early genes (IEGs) such as ZENK in different neuronal nuclei depending on the acoustic environment.