Analyze, describe and interpret the clinical findings given in the case study using appropriate techniques. The introduction should briefly state what the poster is about in approximately 250 words. State what the subject is, why it’s important and give some background information.

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A1 format, portrait orientation poster and 10 minutes presentation

Analyze, describe and interpret the clinical findings given in the case study using appropriate techniques. The introduction should briefly state what the poster is about in approximately 250 words. State what the subject is, why it’s important and give some background information. Use references to support your document. Use BLAST and ORF Finder ( to identify the mutation in a given sequence (Fig. 3) and analyze the resulting amino acid sequence, respectively.

The numerical data should be analyzed and presented graphically along with any statistical analysis of the data you perform. The photomicrographs should be labelled. The poster should contain 6 figures presenting the data with clear and concise figure legends you write yourself expressing your understanding of what is being shown and its meaning.

The poster should conclude with a section on the observations made, the likely prognosis and treatments possible for the individual and conclusions that can be drawn. Any references used should be listed at the end of the poster. Prepare an A1 poster and 10 minutes speech draft. The poster can brief and presentable and the speech draft needs to contain all the information.

.Early in the pandemic, researchers suspected that COVID-19 was caused by a virus. What are some ways that they could confirm that a virus, and not bacteria, was responsible for this disease? What type of microscopy would be needed to view SARS-CoV-2? Why? What cell type or organelle would be of an equivalent size to this virus?

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COVID-19 and SARS-CoV-2.

Using your textbook and the resources listed below, answer the following questions regarding COVID-19 and SARS-CoV-2.

Centers for Disease Control: COVID-19
World Health Organization: Coronavirus disease (COVID-19) pandemic
In addition to the links provided(I provided links at bottom of paper details), include at least two additional sources, one of which must be peer-reviewed, to write a paper that addresses the questions.
Your paper should be formatted in APA style and should include an introduction, conclusion, and a references section.

SARS-CoV-2 Identification

1.Early in the pandemic, researchers suspected that COVID-19 was caused by a virus. What are some ways that they could confirm that a virus, and not bacteria, was responsible for this disease?

2.What type of microscopy would be needed to view SARS-CoV-2? Why? What cell type or organelle would be of an equivalent size to this virus?

3.Based on the Baltimore classification of viruses, which groups would SARS-CoV-2 fall within? What type of genetic material does it contain? Are there any related viruses that cause disease in humans?

SARS-CoV-2 Replication and Genetics

4.Based on your response to question three, draw the replication cycle of SARS-CoV-2.

5.How could SARS-CoV-2 be cultivated? What biological materials would be needed?

6.If viruses such as SARS-CoV-2 are unable to metabolize organic molecules, where do they get the energy to undergo replication?

7.As discussed above, SARS-CoV-2 has an RNA genome. Discuss three differences between RNA and DNA.

8.During the course of the pandemic, several variants of the original SARS-CoV-2 virus have become dominant strains circulating through human populations. Discuss the steps that are involved with the formation of a variant and its increase in prevalence.

COVID-19 Treatments

9.One of the few drugs that have been found to be effective against SARS-CoV-2 is remdesivir. How does this drug inhibit viral replication?

10.Predict which physical or chemical methods of control would be effective against viruses like SARS-CoV-2. List two physical or chemical methods and their mechanism of action.

11.What are at least two suspected reservoirs for SARS-CoV-2, besides humans?

12.How can SARS-CoV-2 be transmitted? For each of the possible transmission mechanisms, discuss whether or not this is a potential source of transmission.

Direct contact
Indirect contact
Vehicle
Vector

13.Why is quarantine an important tool used by public health to reduce the spread of COVID-19?

14.How can herd immunity prevent the spread of viruses within a human population?

15.Some of the first vaccines developed for COVID-19 were RNA vaccines. After the administration of the vaccine, how does this result in an immune response if exposed to the actual virus?

Resources Provided:
https://www.cdc.gov/coronavirus/2019-ncov/index.html
https://www.who.int/emergencies/diseases/novel-coronavirus-2019

List the three ‘factors’ you think need to be considered in the analysis based on the initial set of data in order to improve this organization’s ability to study how pollution influences the development of allergic diseases, such as asthma.

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N/A

Part 1: Hypothesis/Answer (~150 characters)

List the three ‘factors’ you think need to be considered in the analysis based on the initial set of data in order to improve this organization’s ability to study how pollution influences the development of allergic diseases, such as asthma.

Part 2: Main Reason(s) (~450 characters)

Explain the main reason(s) why these are the three factors that you feel need to be considered. You can simply list a main reason for each factor, or if 2-3 of the factors connect with a common theme, you can also address it this way. Think very deeply about these factors to ensure they are unique to you in some way.

Part 3: Supporting Arguments(~550 characters)

Explain the main reason(s) why these are the three factors that you feel need to be considered. You can simply list a main reason for each factor, or if 2-3 of the factors connect with a common theme, you can also address it this way. Think very deeply about these factors to ensure they are unique to you in

Part 5: So What? (~350 characters)

Relate it back to the overarching purpose/goal of this study (in your opinion) and why looking at these factors will not only support this, but also help guide the future of this research in the right direction.

Why does glucose uptake by a skeletal muscle cell require a transporter such as GLUT4? In other words, why isn’t simple diffusion possible? What stimulates the insertion of GLUT4s into the sarcolemma?

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NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE “I Hate Running!” by Rhodes, Rozell, & Wilson

Part I — Blood, Skeletal Muscle Cells, and Glucose Uptake

To untangle the misconceptions in the conversation between Shelby and Patrick, let’s begin by looking at the structures
within skeletal muscle cells that are involved in energy production at a submaximal level of exercise in an untrained
person. This would be the case for Shelby, who is just beginning an aerobic exercise program that includes mostly
endurance training occurring in 20–30 minute bouts. In addition, let’s examine some common metrics such as lactate
threshold and blood pH to assess what is happening in an untrained person during exercise.
During the first 30 minutes of Shelby and Patrick’s run at a submaximal level (40–70% VO2 max), blood glucose levels
increase due to glucose release from the liver (Zinker et al., 1990), providing skeletal muscle cells with a concentration
gradient of glucose for uptake and subsequent ATP production. However, glucose is a large polar molecule and cannot
simply diffuse unaided into the sarcoplasm through the phospholipid bilayer comprising the sarcolemma of skeletal
muscle cells. Instead, to take up blood glucose, skeletal muscle cells must produce and insert glucose transporters,
commonly referred to as GLUTs, into their sarcolemma. These GLUTs are a diverse family of large, integral membrane
proteins that permit facilitated diffusion of glucose down its concentration gradient. Skeletal muscle cells can express
several different forms of GLUTs, but the most common form is GLUT4 (Gaster et al., 2000; Goodwin, 2010;
Richter & Hargreaves, 2013). Interestingly, the insertion of GLUT4 into the sarcolemma can either be stimulated by
insulin binding to its receptor on skeletal muscle cells that are resting, or by an insulin-independent mechanism during
contraction of the skeletal muscle cells (Richter & Hargreaves, 2013).

Activity 2
Using the information above, complete the flow chart (Figure 1) on the following page to get a better understanding
of the sequence of events that occurs during exercise. Then label all structures shown in the diagram (Figure 2), which
represents a portion of a skeletal muscle cell’s sarcolemma during exercise. Also label the extracellular fluid compart–
ment, blood, and sarcoplasm. Indicate where in the body glucose and insulin would have come from and how they are
transported to the skeletal muscle cell.

Questions
1. Why does glucose uptake by a skeletal muscle cell require a transporter such as GLUT4? In other words, why isn’t
simple diffusion possible?

2. What stimulates the insertion of GLUT4s into the sarcolemma?

3. The existence of GLUT4s in the sarcolemma does not guarantee glucose uptake into the cell. Why? What else is
required?

4. Exercise helps reduce blood glucose levels in people, even if they are insulin resistant and thus their cells can no
longer respond to insulin efficiently. How is this possible?

What is the question being addressed by the modellers in Coopey 2007 & what is their hypothesis? How do the equations in the paper enable the group to address their question? Why are there two phases in the model? Describe the biological motivation for the phases and explain how they are realised in the model.

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Essay on research papers

Consider Coopey et al’s 2007[1] & 2008[2] papers. Write a series of paragraphs addressing the following points:

1) What is the question being addressed by the modellers in Coopey 2007 & what is their hypothesis?

2) How do the equations in the paper enable the group to address their question? Give a general description of the model. Then describe the meaning of each term in equations (1) and (2).

3) Why are there two phases in the model? Describe the biological motivation for the phases and explain how they are realized in the model.

4) Why were partial differential equations chosen instead of Boolean networks?

5) What prediction did the model make about the biological system and how could this be tested experimentally?

6) Describe the work in Coopey 2008 and discuss the implications of this study on work in Coopey 2007.

 

[1] Coppey, M. et al. (2007) Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein. Developmental Biology 312. DOI 10.1016/j.ydbio.2007.09.058

[2] Coppey, M. et al. (2008) Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Embryo. Current Biology 18. DOI 10.1016/j.cub.2008.05.03

Describe the principles of the ‘maquette’ approach to de novo protein design. Describe in vitro compartmentalisation used in directed evolution experiments. What are the advantages of using this technique over in vivo experiments?

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Advanced Biotechnology

Instructions

– Maximum of 500 words for each question

– Write a well-structured answer in a series of paragraphs answering points asked in the question. The answer should correctly use the appropriate terminology and referencing.

– When you address the question, you should interpret and discuss the data provided.

– You should also use relevant literature to add a different perspective and/or more detail.

– Include diagrams where appropriate, but these must be referred to in the text.

– Element of criticality and synthesis are a must.

– A well-founded conclusion should also be included

Questions to be answered

Question 1. Describe in detail the pathways for engineering functional CO2 -concentrating mechanisms into plant chloroplasts.

Question 2. This question is in two parts, each carrying equal marks.

(a) The formal definitions for metabolite identifications have been defined by the Metabolite Standards Initiative.  With particular reference to the identification of tryptophan using GC-MS discuss how Level 2 identification is achieved and how this can be improved to Level 1.

(b) Now that you know you can detect tryptophan with GC-MS; how can its level in a yeast culture be quantified?

Question 3. This question involves genetic engineering and is in three parts, each carrying equal marks.

(a) Describe the principles of the ‘maquette’ approach to de novo protein design.

(b) Describe in vitro compartmentalisation used in directed evolution experiments. What are the advantages of using this technique over in vivo experiments?

(c) What is the difference between non-homologous end-joining and homology-directed repair of a nuclease-induced double-strand break? How can each be used in genome editing to introduce mutations?

Question 5. This question involves genetic modification and is in three parts, each carrying equal marks.

(a) What are the differences between rational design and directed evolution approaches to protein design?

(b) You want to introduce an indel into a gene encoding a eukaryotic protein of known structure to disrupt the gene’s function. Where in the gene sequence should you target, and why?

(c) How does off-target nuclease activity with CRISPR-Cas9 occur? Why is this a problem? How is this most-commonly minimised?

Describe where and how the termination of Polymerase II takes place across the genome at the molecular level. Explain the biological significance of the regulation of transcription termination in regard to gene expression.

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Reference to the Research Article

With reference to the research article from Nojima et al., Cell 2015 [1], discuss the relevant data and write a series of paragraphs addressing the following points:

a. Briefly describe the mNET-seq technique and explain two advantages and two disadvantages compared to

i) RNA Pol II ChIP-seq method and

ii) PRO-seq assays. (30%)

b. Describe where and how the termination of Polymerase II takes place across the genome at the molecular level. Explain the biological significance of the regulation of transcription termination in regard to gene expression. (40%)

c. With reference to the paper, explain how Polymerase pausing proximally to promoters and at the transcription termination site (TES) are linked to mechanisms of transcription termination. What was the phosphorylation status of the CTD of Pol II molecules found by the authors to be associated with promoter-proximal pausing, splicing sites and the TES? How, in your opinion, can differential phosphorylation of the CTD dictate and control the different co-transcriptional activities of transcriptional termination and splicing that take place across the gene? (30%)

Reference: Nojima, T. et al. Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell 161, 526-540, doi:10.1016/j.cell.2015.03.027 (2015).

Instructions

– write a well-structured answer in a series of paragraphs answering points asked in the question. The answer should correctly use the appropriate terminology and referencing.

– To provide context, you should give background information.

– When you address the question, you should interpret and discuss the data provided.

– You should also use relevant literature to add a different perspective and/or more detail.

– Include diagrams where appropriate, but these must be referred to in the text.

– Element of criticality and synthesis is a must.

– A well-founded conclusion should also be included

Draw and briefly discuss the signalling pathway delineated in this study and how this adds to what was previously known about HIF regulation. What are the physiological, pathophysiological and therapeutic implications of this study? 

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Structured evaluative piece of writing based on a research paper.

Structured evaluative piece of writing based on this research paper: UCHL1 provides diagnostic and antimetastatic strategies due to its deubiquitinating effect on HIF-1α Goto, Y., Zeng, L., Yeom, C. et al. UCHL1 provides diagnostic and antimetastatic strategies due to its deubiquitinating effect on HIF-1α. Nat Commun 6, 6153 (2015).

Full paper:

 

Questions to be answered;

1. Briefly summarise the main findings described in this paper   (Indicative length approx. 150 words)

2. In Figure 1C the authors use siRNA to reduce UCHL1 levels in cells. Briefly describe how siRNA can reduce UCHL1 expression and suggest two alternative approaches the authors could have used, outlining how they work, their benefits and their limitations.   (Indicative length approx. 250 words)

3. Pick the figure (relates to an entire figure (e.g Fig 1 or Fig 2 etc) and not the individual panels (e.g 1A, 1B or 1C etc)) that you think is the most important. Describe the results, the experimental approach(es) used and why you think that it is the key figure in the paper.   (Indicative length approx. 300 words).

4. Draw and briefly discuss the signalling pathway delineated in this study and how this adds to what was previously known about HIF regulation.   (Indicative length: Figure plus approx. 300 words)

5. What are the physiological, pathophysiological and therapeutic implications of this study?  (Indicative length approx. 300 words)

 

Instructions

– Answer the five questions separately.

– When writing your answers for the 5 separate questions, it is important to ensure that each individual answer is well structured, coherent and well-argued. This may involve including short introductory or concluding statements in some answers, but this will likely not be necessary for all of the questions. Indeed, having an introduction and conclusion for each question would probably result in a lot of unnecessary repetition.

 

 

Provide a narrative with logical flow, connections, and transitions. Explain the issue so that a non-science major with an interest in learning about the issue should be able to comprehend the story.

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Biology terms

To help the reader (and evaluator), identify the ten selected biology terms with underline.
Provide a narrative with logical flow, connections, and transitions.
Explain the issue so that a non-science major with an interest in learning about the issue should be able to comprehend the story.
Use first person (I, me, we) and second person (you) throughout your writing in order to maintain the story line as a personal dialogue between you and the intended audience.
Use FOREIGN DNA, GENE TARGETING, HOST DNA, GENOME ANNOTAION, METABOLOME, PROTEOME, GENETICALLY MODIFIED ORGANISM, GENETIC MARKER, GENETIC ENGINEERING, and POLYMERASE CHAIN REACTIONas the ten terms.
In this scenario, you are a Bt toxin in a corn plant cell. A ribosome calls out to you, saying “hey, I haven’t seen a protein like you before, what’s your story?”.

Your job is to introduce yourself to the ribosome. Explain what a Bt toxin is, where Bt toxins exist naturally, and how and why a Bt toxin came to live in a corn cell.