Writing in Biology

Spinacia oleracea L., commonly known as spinach is widely used in the scientific world as a model organism for many areas of study such as DNA synthesis and cellular respiration. Spinach is a good model system due to its cheap price, accessibility, rich chloroplast content, and easiness to handle and maintain. Like all plants, spinach uses photosynthesis in order to create energy and sustain life.

Photosynthesis occurs in the chloroplast and has two sequential stages; light-dependent reactions and light independent reactions.  Light dependent reactions take place in the thylakoid membrane, and use the light energy photons from the sun to excite pigment in the cell and activate a high energy electron transport chain. ATP, O2, and NADPH are the products of the reactions that occur in the light-dependent stage of the photosystem. These products then are used in the light-independent stage, or the Calvin Cycle, which takes place in the stroma and creates GA3P and CO2.

Different types of plants and leaves experience different levels of chlorophyll. Because of this, it is thought that the amount of photosynthesis would increase in leaves with higher levels of chlorophyll, as chloroplasts are the main component of photosynthesis (Emerson, 1929). Spinach is a dark green leaf, containing high levels of chlorophyll. Conversely, Lactuca sativa L., romaine lettuce is a medium to light green leaf, containing medium to low levels of chlorophyll. Based on this knowledge, it can be predicted that spinach will photosynthesize faster than romaine lettuce. If this is correct, the data will show a higher change in absorbance over time in spinach than in romaine lettuce.

For the research proposal, our group wants to look at microclimates in the soil under various trees on the UMASS campus. There is very few research on the microclimates present under trees on the campus. Some research states that natural forests have greater invertebrate diversity than managed trees (https://www.sciencedirect.com/science/article/pii/000632079500015V). However, since all of the trees on campus are considered “managed” we will not be considering this factor in our prediction. Other research suggests that ants are great ecological indicators of the microclimate found in the soil under trees (https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/1540-9295%2...) therefore ants will be one type of invertebrate that we are going to consider when measuring diversity under various trees across campus. Other research uses invertebrate diversity as a indicator of sustainability however invertebrates are not known as well and are too diverse to create a proper report. (https://link.springer.com/article/10.1023/A:1013397410297) “In ecology, sustainability (from sustain and ability) is the property of biological systems to remain diverse and productive indefinitely. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. In more general terms, sustainability is the endurance of systems and processes” (Wikipedia). The sustainability of the tree could be measured by collecting/recording the species diversity and comparing it to other trees on campus. Some factors we can consider are: the distance of the tree from the road, from a body of water, the diameter and height of the tree and which side the tree is facing the sun vs which side isn’t.

Cyclohexanol (1.99 g, 19.8 mmol) was measured into a 5mL round-bottomed (rb) flask.  85% phosphoric acid (0.5 mL) was added to the rb flask.  The system was heated and the product was collected through fractional distillation.  The temperature plateau occurred at 64 °C and the product was obtained in a collection vial.  The product was transferred to a reaction tube.  The reaction tube was washed with water (1 mL).  The procedure was repeated with sodium hydroxide (1 mL) followed by saturated sodium chloride (1 mL).  The product was then dried with calcium chloride pellets (5 min).  The remaining product yielded (0.77 g, 47%).  The product was tested for the compounds it contained with infrared spectroscopy and gas chromatography (one peak) with a retention time (RT) of 0.435.  A bromine solution was added drop-wise to (0.5 mL) of the product and the prescence of cyclohexene was indicated by a color change of the bromine from reddish-orange to colorless.  A potassium permanganate reagent was added drop-wise to (0.3 mL) of the product and the presence of cyclohexene was indicated by a color change from purple to clear with a dark brown precipitate.  These tests were then compared to cyclohexane, which did not react with the reagents.

What were the authors trying to test, and what predictions did they make?

The authors were trying to test the effects of road networks on genetic diversity and connectivity of populations. They predicted that roads and highways would reduce connectivity among populations of flora and fauna. The large number of roads is expected to hinder gene flow, and facilitate genetic drift. Under these conditions, species isolated by roads would likely lose genetic diversity. Population extinction rates are also expected to increase due to inbreeding and reduced evolutionary potential.

What, exactly, did the authors do?

    The authors studied 27 populations of desert bighorn sheep. Over three years genetic samples of the sheep were collected across the study area, primarily by means of fecal pellets. Fourteen different microsatellite loci were genotyped. Female dispersal rates were also studied by examining mitochondrial DNA. Female bighorn sheep are less likely to disperse, so maternally transmitted mitochondrial DNA was used to study dispersal rates.

What did the authors find (i.e, what were their data)?

    The authors found that “the amount of gene flow among populations was strongly and negatively correlated with barriers at interpopulation distances of less than 15 km.” Furthermore, gene flow was weakly and negatively correlated with barriers at distances between 15 and 30 km. The two variables were not correlated after distances of 30km. There was a low correlation of mitochondrial DNA diversity with both barriers and distance. Genetic simulations were also used, and showed that the genetic distance between populations could be influenced by barriers constructed only 40 years ago.

How did the authors interpret their findings?

The authors concluded that genetic diversity for bighorn sheep was negatively correlated with barriers, such as roads and highways. From the results, the authors estimate that genetic diversity had decreased by 15%, for populations completely isolated by barriers. The low correlation of mitochondrial DNA diversity with both barriers and distance may be due to low dispersal rates of the female sheep. Finally, the authors highlight the significance of their finding in a world with a rapidly increasing number of man made barriers “These results suggest that anthropogenic barriers constitute a severe threat to the persistence of naturally fragmented populations.” Underpasses and overpasses have been used successfully to aid in gene flow and help mitigate this issue.

As many know, reaction time is the time that your brain can react to a stimulus. Three main stimulouses are visual, auditory, and tactile. The quickest reaction time of the three usually being tactile. A tactile stimulus this is the fastest is because we have many sensors on our body which enable us to react faster when we receive a stimulus compared to auditory and visual which both require more processing done by the brain. An examply of this is when we place our hand on a hot stove and almost immediately rectract our hand before serious damage can be done. Visual and auditory stimulous has a larger processing time than tactile because for each, you first need to recieve the stimulus and then the information has to be processed by the brain and differentiate between a danger stimulus or a regular stimulus. Reaction time is also influenced by many factors. Sleep could impact the reaction time of an individual. If an individual is not getting enough, their reaction time will decrease because their body is lacking awareness and energy needed for the reaction time. Stimulants such as caffeine or drugs that increase your alertness or heart rate will have the opposite of lack of sleep. These will increase your reaction time because it increases your alertness which makes you more susceptible to processing stimulus faster.

The system the authors use to answer the question is optogenetics. Optogenetics is when

one controls cells that have been injected with ion channels that respond to light. These ion channels are called light-sensitive ion channels. This system allows for gene disruption within the targeted cells in order to provide stimulus to the synaptic terminals to have dopamine released into them. While this is taking place scientists can then record the postsynaptic currents within the synapses that have dopamine in them. This can be specifically used to target the dopamine neurons in the dorsal striatum and nucleus accumbens. This can also target the cells in mice that do not have VGLUT2 in their neurons that still produce dopamine. VGLUT2 stands for vesicular glutamate transporters. They allow glutamate to be put into synaptic vesicles along with secretory vesicles. This is so that glutamate can be released into the synaptic terminals.

Over thirty years ago the idea of stem-cell research was introduced to the scientific world, now thirty years later the research and the technology for stem cells has advanced tremendously. Stem cells have the amazing potential ability to develop into many different stem cells in the body, and due to its regenerative abilities stem cell research offers promises of disease treatment for diseases such as diabetes, spinal cord injury, Parkinson’s disease, and heart disease. However the true potential for stem cell research has not been fully reached, as obstacles regarding ethical permissibility, moral rights, and political justice have introduced controversy to the topic.

Intrinsic hemolytic anemia develops when the red blood cells produced by your body are defective. This condition is often inherited, such as in people with sickle cell anemia or thalassemia. Some types of hemolytic anemia are hereditary-- specifically spherocytosis. This supports our diagnosis because the patient’s father also had occasional anemia. The hereditary spherocytosis is also more probable because the direct Coombs test was negative. Hemolytic anemias can have positive direct Coombs tests but hereditary spherocytosis would present a negative Coombs test. This negative test means that meaning fetus is not in danger and the mother has not developed antibiodies against fetus’s blood.

By using phosphoric acid, dehydration of cyclohexanol was possible. Also, to determine if it was whether alkene or alkane, bromine was used to yield a trans- 1,2-dibrominated product. Oxidizing cyclic alkene to a dicarboxylic acid. Having used all the procedures done before this experiment such as finding melting points, densities, molecular weights, and more combination of extraction, distillation, recrystallization, chromatography was done. Chromatography displays how polluted it is with different liquids. It was about 85% cyclohexanol and 15% something else. In its cyclohexene at about 2900 and 1440, there was a scan done. Higher the temperature of the liquid was, the longer the compounds need which results in better separation. Exactly 2.02 grams of cyclohexanol was used and having to find % yield, different combinations of methods were used to recover. Boiling points were at 63 to 69 degrees as first drop occurred at 66 degrees. At the end, 0.313 grams were recovered which is about 15.5% recovered from the total 2.02 grams used. The second part of the experiment was with cyclohexene and cyclohexane. Depending on which liquid was used, the colors were changed. Bromine in dichloromethane and 1% potassium permanganate and 10% sulfuric acid were used. The only unaffected color was cyclohexene with bromine in dichloromethane. All the other three tested were affected. Using cyclohexene with potassium permanganate with sulfuric acid turned it dark purple. Cyclohexane made the two given liquids either reddish-orange (with bromine in dichloromethane) and dark purple (with 1% potassium permanganate and 10% sulfuric acid).

Most basic of all procedures and involves purification of DNA. An important step within organic extraction is the removal of proteins. Can be done by extracting aqeous solutions of nucleic acids with phenol or chloroform. There are pros and cons when dealing with organic extraction. The pros are it yields relatively pure, high molecular weight DNA. In addition, DNA is double stranded. This means it is good for RFLP and PCR. The cons are it is time consuming and there is the increase risk of contamination. It also involves use of hazardous chemicals.