Science experiment report Assignment | Custom Assignment Help
science biology experiment report all of the steps are on the powerpoint I also attached files which show samples of how its supposed to look likeCellular Respiration Thought Experiment
Stefanie Bautista
Professor Porter Morgan
General Biology SCB 201 600B
Cellular Respiration Thought Experiment
Sick Pisaster Ochraceus consume less oxygen then healthy Pisaster Ochraceus.
All living organisms use cellular respiration to produce adenosine triphosphate (ATP).
There are two ways in producing ATP through cellular respiration and fermentation. Thus, we will
be focusing on cellular respiration. This process has four steps, glycolysis, pyruvate processing,
Krebs cycle and the electron transport chain. Glycolysis is when glucose is broken down to two
pyruvates creating acetyl Coenzyme A (CoA). Acetyl CoA then enters the citric cycle completing
glucose oxidation. The Electron transport chain carries electrons, and O2 is the final electron
acceptor.
In class we learned how to measure the respiration rate of germinated peas, the way we did
this was by measuring the amount of glucose they used. The hypothesis my group and I constructed
was germinating peas are going to consume the most O2.. We tested our hypothesis by having
3 different chambers. Each chamber contained nongerminating peas, germinating peas and glass
beads and drops of NaOH to eliminate any CO2 being produced, this was added with cotton balls.
Therefore, they all received one color dye drop, they were all observed at the same time and were
all set up the same for 30 minutes. Our independent variable was time and our dependent variable
was the amount of oxygen consumed and the control was glass beads. The experiment supported
our hypothesis because the germinating peas did consume the most O2, the nongerminating
cmed le ad he gla bead did cme O2 a all. In finishing up some possible errors
that may have occurred were to not add the same amount of colored drops in each pipette, not
inserting the pipette into the rubber stopper correctly or maintain the apparatus in a horizontal
position these errors can change our results.
The experiment I will be conducting can relate the to the process of cellular respiration
since Pisaster Ochraceus organisms consume oxygen and produce carbon dioxide. It has been said
that there is a wasting disease going on affecting many species underwater causing them to die.
Such as sea stars, sea urchins and sea cucumbers. (Bates, A. E. etc., all 2009). One class of star
fish are Pisaster Ochraceus. Therefore, the question I will be addressing is If a healh Ochace
and sick Ochraceus are both exposed to air would there be factors that the sick Ochraceus can
consume the same amount of oxygen as a healthy Ochraceus? Thus, I will be proposing, If a
regular starfish Pisaster Ochraceus and a sick Pisaster Ochraceus consume oxygen when it has
submerged, then the starfishes with wasting disease will consume less oxygen. This question
comes to mind since wasting disease starfish tend to increase pathogens at higher temperature.
(Bates A. E., et., all 2009). So, would pathogens affect their breathing when they submerge? The
independent variable will be at 30 Celsius when exposed to air and the dependent variable will be
the oxygen rate.
The way this experiment will be designed is by collecting one wasting diseased starfish
and place it in a plastic container without water, placing one regular starfish in another plastic
container. Both starfishes should be about the same weight and shape. My control group will be a
fake starfish and should also have the same weight as the other two. The temperature should be
about 30 Celsius for all three variables. Each star fish should be put on seawater at 15 Celsius for
30 minutes. Once those 30 minutes pass they should be exposed to air for 30 minutes. Within the
30 min I will measure the rate of oxygen consumption by drilling a whole on the lid and inserting
Cellular Respiration Thought Experiment
the pipette. Using cotton and NaOH will prevent CO2 from intervening with O2. A drop of colored
dye should be inserted to the pipette and then recording should begin.
Data 1
Time Regular Ochraceus Sick
Ochraceus
Fake star fish
30 °C at 0 min. -3 -2 0
30 °C at 5 min. -2 -1 0
30 °C at 10 min. -1 1 0
30 °C at 15 min. 2.5 1.5 0
30 °C at 20 min. 3 2 0
30 °C at 25 min. 4.75 2.5 0
30 °C at 30 min. 5.5 3 0
Above are the amounts of oxygen consumed from all three variables within 30 minutes.
Graph 1
Graph 1 above explains the ratios of each Pisaster Orchaceus being exposed to air. As it is seen
the healthy Orchaceus shows more significance than the sick Orchaceus.
Cellular Respiration Thought Experiment
Having a sick ochraceus decreases the amount of oxygen consumed while a healthy
ochraceus increases. My independent variable affected my dependent variables since Pisaster
Ochraceus body temperature should be in a temperature range of 30 °C (McGaw, I. J. etc., all
2015). Since wasting disease Ochraceus are more susceptible to become ill when exposed to stress
and heat, then their interactions with consuming oxygen may vary. The rapid wasting disease can
rapidly cause death (Bates, A. E. etc., all 2009) therefore to prevent it from dying we will use a
constant temperature. This would also explain how the dependent variable impacts the independent
variable since each starfish is being measured every 5 minutes for 30 minutes. A cell structure that
may be affected by the independent variable is the mitochondria since that is where cellular
respiration for organisms occurs. The mitochondria is known to produce ATP. As us human, when
one becomes ill our bodies become vulnerable and aibdie d function properly. Thus,
my prediction is, Ochraceus may function similarly. If my graph does not support, my claim than
the rate of respiration can either be the same for both Ochraceus or can be the opposite of my
hypothesis.
What I have completed can be connected to a different piece of chemistry since chemistry
involves organic chemistry. Most of our body functions through organic compounds such as
Phospholipids, proteins, and sugars. We also have elements that impact our lives every day. A
significant piece that I learned from this assignment is how to create a hypothetical experiment
using methods that have been used in real life. It has also taught me how to format a graph
indicating my dependent and independent variables. I can then connect these skills to SCB 202
and later in life since my career is based on conducting research.
The connection between cellular respiration and climate change are directly comparative
if cellular respiration is high then the temperature increases as well. Although aquatic ecosystems
release more CO2 than land ecosystems do. There can be possibilities that this can worsen climate
changes. However, further studies must be investigated in temperature. This situation touches
bases on enzymes, if there is an excessive amount of temperature than the enzymes will become
denatured and no longer function properly.
The main idea to form a hypothetical experiment is to improve my skills when it comes to
conducting experiments. One must think critically on how many factors such as environment other
organisms, and food can help us maintain a stable health. Thus, I focused on how cellular
respiration functions through an Ochraceus system. I gathered all my information and then created
questions forming them to a claim. Another thing that is very important is to Research articles to
build upon explanations. Science gives us a variety of explanations on how things function in life.
For instance, when we consume food it is broken down into simpler sugars. Most of our energy is
produced through cellular respiration. One possible problem that can occur in my hypothetical
experiment is not using a consistent temperature. If we were to accidently use 37 °C then there will
be a high chance of the wasting disease ochraceus to die.
Cellular Respiration Thought Experiment
References
Bates, A. E., Hilton, B. J., & Harley, C. D. (2009, November 09). Effects of temperature, season
and locality on wasting disease in the keystone predatory sea star Pisaster ochraceus. Retrieved
from https://www.int-res.com/abstracts/dao/v86/n3/p245-251/
McGaw, I. J., Clifford, A. M., & Goss, G. G. (2015, April 16). Physiological responses of the
intertidal starfish Pisaster ochraceus, (Brandt, 1835) to emersion at different temperatures.
Retrieved from https://www.sciencedirect.com/science/article/pii/S0022098115000805
Bacterial Community and Pollutants
Final Research Paper
SCB 201
Instructor Prof. M. Entezari
Group 1
Aayusna Poudel
Sonam Sherpa
Aastha Budhathoki
Babita Jamkatel
ABSTRACT:
Ecological indicators greatly impact the standards of the marine ecosystem. Fluctuation in the quantity physico-chemical indicators and biological indicators not only degrades the marine health, but also results to alteration in population of tiny microbial community. In addition to that, human activities (excessive sewage dumping, nitrogen pollution, fecal contamination, drainage flow) creates certain changes in Ph, salinity, amount of dissolved oxygen which results to low water quality and excessive abundance of the bacterial population. The East River being the receptacle of New York city’s garbage and sewage is home to thousands of bacterial communities. What kind of bacterial community and why are they highly abundant on different parts of East River is a question of high concern. To test this, four different samples of water from the depth and surface of East river and Long island were studied. Metagenomic analysis is the effective approach to study the whole microbial community, with broad access to the functional gene composition and broader description. DNA extraction and sequencing provided us with the statistical data of types of bacterial community abundant on the four different parts of the East River. Bacterial community are the biological indicators of water quality. After weeks of experimentation, the parameters of water quality such as salinity, pH, dissolved CO 2, dissolved oxygen levels and temperature has been determined. Our DNA sequencing shows the presence of four highly abundant bacterial community which are Proteobacteria (, and © Proteobacteria), Flavobacteria, Actinobacteria and Planctomycete. Our research on these bacteria shows that they can be highly pathogenic to human being and to the aquatic life as well.
INTRODUCTION:
The water quality degradation of East River is directly linked to the urbanization, increased population, Combined Sewage Overflows (CSO), pumping stations bypasses, storm water runoff and illegal connection to storm drain system. Mercury is another prolific pollutant in East River. (Greening the Gap, 2013). The pollutants have risen up many microbial communities in the surfaces and depth of East River. Although initiatives have been taken and the quality has been preserved in last couple of decades, there are areas of East River that are of high concern in terms of safety for aquatic life and humans in the abundance of many bacterial community, some of them being known as pathogenic. Enterococcus bacteria levels are monitored in swimming areas throughout Long Island Sound. These bacteria are an indicator of fecal contamination, and high concentrations of bacteria suggest a potential risk to human health while swimming or recreating on the water. (Long Island Sound | Eco Health Report Cards, 2015). Bacteria such as Enterococcus can be monitored by simply culturing the bacteria but other bacterial can only be the monitored by the 16s ribosomal gene sequencing. In order to detect the whole bacterial community(whether pathogenic or free living), 16s ribosomal sequencing method is effective. In our study of DNA sequencing of the samples collected from surfaces and depths of East River and Long Island, the most abundant bacterial community were of , and © Proteobacteria, Flavobacteria, Actinobacteria and Planctomycetia. The bacterial community of a very wide range in our project was obtained through isolating DNA from water sample by MoBio WaterPower Kit and DNA sequencing was done after amplifying via Polymerase Chain Reaction procedure.
Department of Environmental Protection and many other initiators have worked on improving water quality. A significant amount positive changes has been recorded. However, the changing of statistics is not sufficient and cannot be relied to ensure its safety for public consumption or its safety for water ecosystem. The abundance of the particular bacterial community in East River and Long Island is reflected by the type and amount in each area. The aim of this investigation is generally reporting of cumulative findings of bacterial community present in the East River water samples to provide an overview of how safe it is for human consumption but also how safe are our water ecosystem. We are presenting the abundance of three different types of Proteobacteria, Flavobacteria, Actinobacteria and Planctomycetes in East River water samples and in this report we are summarizing the analysis of how these communities can be linked to the water quality parameters .The findings of our project serves the purpose of creating a scope for future researchers in terms of what more can be done to improve the current status of East River.
METHODS AND MATERIALS:
The DNA extraction procedure is done with the use of The PowerWater DNA Isolation Kit. Four water samples (East River Deep and Surface, Long Island Deep and Surface) were filtered using a reusable or disposable filter funnel attached to a vacuum source. The filter then inserted into 5ml PowerWater Bead Tube. The tube allows for bead beating and homogenization. 1 ml of PW1(lysing agent with detergent) is added to the bead tube to break the cell walls. This step also removes non-DNA materials. The Bead Tube is then vortexed at maximum speed for 5 minutes in a Vortex Adapter. The vortex action helps break apart any cells and helps in cell lysis. Next step is followed by centrifuging the tubes to let debris and beads precipitate. This left supernatant with DNA. The supernatant is removed and transferred to a clean collection tube and centrifuged again for a minute to remove any remaining beads, proteins and cell debris. 200 μl of PW2 is added and vortexed to remove any additional organic and inorganic non DNA material. The solution is incubated for 5 minutes at 4°C followed by another centrifuge for a minute. The supernatant is transferred to 2 ml collection tube. 650 μl of Solution PW3 (high concentration salt) is added to the solution and vortexed. High concentration of salt helps to neutralize the negative charge on the nucleic acid backbone, causing the DNA to become less hydrophilic and fall out of solution. It is then centrifuged for a minute in a Spin Filter in which later 650 μl of Solution PW3 of Solution PW4(alcohol-based wash) is added to further purify the DNA. It is centrifuged for 1 minute again. This wash solution removes the residual salt and other contaminants while allowing the DNA to stay bound to the silica membrane in spin filter. The flow is discarded removing the spin filter which is then placed back into the tube. A solution of 650 μl of PW5 (ethanol) is then added and centrifuged for 1 minute. This ensures the complete removal of PW4 solution. After discarding the flow through it is centrifuged again for 2 minutes. The second spin is mandatory to ensure removal of traces of all wash solution or else it would interfere in Polymerase Chain Reaction and gel electrophoresis procedure. The Spin Filter basket is then placed in 2 ml collection tube and 100 μl PW6(Sterile elution buffer) is added. This resulted in complete release of DNA from the silica spin filter membrane. The final step is to centrifuge for 1 minute and discard the spin filter basket. The remaining filtrate has DNA which was stored frozen for further use in any downstream application. (Entezari, Fuentes,2018)
The extracted DNA is as then studied for DNA profiling to determine the genotype of our samples. In order to do that the 16s rRNA gene from the DNA traces in our samples are replicated to large number by using Polymerase Chain Reaction. The amplification is done under three main principles. Denaturation which is melting the double stranded DNA template into single strands. Annealing, a complementary DNA hybridization via DNA primers and Extension which is synthesizing DNA strands via DNA polymerase.
The obtained DNA sequence is then analyzed using the software called BLAST which is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences
RESULTS :
I. DNA Sequence of all four samples
Fig I. Long Island Surface
Fig II. LONG ISLAND DEEP
FIG III. EAST RIVER DEEP
FIG IV. EAST RIVER SURFACE
The results obtained from the sequencing are narrowed down to top 3 most abundant bacterial community in the samples from depth and surfaces of East River and Long Island River.
FIG I. Long Island Surface: 36% Alphaproteobacteria
18% Gammaproteobacteria
16% Flavobacteria
FIG II. Long Island Deep: 32% Gammaproteobacteria
29% Flavobacteria
22% Actinobacteria
FIG III. East River Deep: 30% Alphaproteobacteria
19% Gammaproteobacteria
18% Planctomycetes
FIG IV. East River Surface: 28% Alphaproteobacteria
26% Gammaproteobacteria
18% Flavobacteria
DISCUSSION:
Water bodies like river, lakes, wetlands play significant role in maintaining ecosystem. As a vital part of human ecosystem, these blue bodies remain as a source of drinking water, recreation and irrigation purpose. But human activities and industrial sewages greatly the affected the water sources resulting to fluctuation of the microbial ecosystem some of which are pathogenic as well as free living. Based upon water quality parameters like Ph, dissolved oxygen, salinity, common microbial species were observed in the different water sample. With abnormal ph. ranging from 6-8, salinity 30- 50 mg/l and dissolved oxygen of 5 ppm to 6 ppm, our bacterial samples can perfectly adjust to water sample for their existence. Long Island being the receptacle of water from all areas of east river is most likely to be mixed up with all kinds. Salinity affects the abundance of betaproteobacteria. As we can see from our lab results of salinity, east river deep has the highest salinity. The most abundant percentage of proteobacteria in deep water such as. beta proteobacteria and Bacteroidetes are often the numerically dominant groups inhabiting the upper waters and organic particles in freshwater lakes. (Lemarchand C, et al 2006). Studies identifies some of the species of , and © Proteobacteria are the signature of diseases in human. (Rizzatti,Lopetuso,Gibiino,Binda & Gasbarrini,2017). Flavobacteria in aquatic environment is a serious fish pathogen and the agents of bacterial Coldwater disease (Barnes, 2011.Especially if we look in this analysis, Flavobacteria can be seen in high abundance in Long Island River sample mainly because Long Island River area is also receptacle of Hospital sewage. Hospital sewage mainly contains high nitrogen pollutants which causes toxic algal blooms and leading to
eutrophication of water. Actinomycetes has higher abundance in deep water as they can sustain under nutrient limited conditions. The Actinomycetes have long been recognized as sources of severe earthy-musty tastes and odours in drinking water (Mara & Horan,2003).Planctomycetes abundance have been linked with acidification of ocean.(Farfan, Cordes, Waller, Decarlo, & Hansel, 2018)Similarly some Halophiles in Phylum Actinobacteria finds in growth environment even in high salt concentration and high acidity.These bacterias have proved to be the causal agents of many human and animal infections, which include a number of common and intensively studied diseases, such as diphtheria, tuberculosis, and leprosy. There is also a wide range of infections that are less well known; some, like actinomycosis and nocardiosis, are proving to be more clinically significant than previously thought. (Anandan, Dharmadurai, & Manogaran,2016).Although no Enterococcus suggesting fecal contamination were found in the water sample, the bacterial community that are found residing are alarming. The different forms of pollutants that goes into East River are the cause of degrading parameters which is in detail explained by other group working on this project focusing on specific parameters determining East River water quality but what we found is these degrading parameters to be a sustainable environment for our bacterial communities. The presence of its existence is a great deal considering their pathogenic characteristics. The Department of Environmental Protection says its safe for consumption and recreation. However, contamination could still take place.
The research was done using DNA isolation and Polymerase Chain Reaction for amplification and some of the pros and cons were:
● easily detected bacteria and viruses compared to other cloning methods.
Drawbacks:
● it was a little steady and required more samples of DNA.
● Cross contamination would occur.
● amplification only occurs if the target is exactly or closely related to the DNA sequence of the expected causative agent
● Can’t diagnosis prions.
● High cost and skilled required to performed tests
Many initiatives
