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This is a longer question i know, but if you could help me out with this, it would be much apreciated.

READ ALL THESE INSTRUCTIONS BEFORE BEGINNING! There is no time limit, but there is a due date!

You will be provided with a prokaryotic DNA sequence. It is formatted in a way that provides an easier way to keep track of which base you are looking at. That is all the numbers are there for.

You need to locate the CORRECT protein coding region (the upstream sites, start codon, etc.) and submit the corresponding amino acid sequence using the single-letter abbreviations without spaces or hyphens (ie, KDELHDN....) in the submission box provided.

As this is computer-graded, you MUST enter the information correctly as instructed above!!

Some reminders:

Never assume that the only place ATG appears is at the beginning of a coding sequence. Many proteins include methionine as part of their internal sequence.

Finding an ORF (open-reading frame) does not mean that it is a functional gene. Those must have the upstream elements- promoter, ribosome binding site, etc.

For the purposes of this exercise, you may assume that the start codon is 10 bases downstream of the +1 site.

You may also assume that other upstream elements are centered at exactly -10 and -35, but may not be exactly the same as the consensus sequences.

You may use any resources to complete this assignment.

You may attempt this twice.

QUESTION (The teacher said that when it is finishe it should spell out and write some type of sentence

1 ATGAAACGAA AGCGATGCGC GCGAAAGAAC

31 TCATGCATCG CGATAATCTG ATGGAAAGCA

61 ACGCGGGCGA AAGCGCTGAC GAAGTGGAAC

91 ACTGAACCGT CGAAAGCAAA ACACCGCGAT

121 AAGCGGTTGA CAGACGGGCG AGACGACAAA

151 ATATAATCGT GTCTAAGGAG GTCCATGGCG

181 AACTATATTA ACACCGAACG CAACGAAACC

211 AGCATTACCG AAAGCGCGCG CGAAATGATT

241 AACGATCTGG AAAGCAGCTT TCGCATTCCG

271 CCGGAACGCT ATTGATAACA AGTATCCGTA

301 CTGGAAGAGC CCCCGCTATA GATGCCACAC

331 TGTTCAATTT TGGACTAATC TGAATACTTT

361 TCAGCTTGAC AGTATCAAAC CGGCAACGTG

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Jamar Ferry
Jamar FerryLv2
28 Sep 2019

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Related questions

About Gene Cloning - EMERGENCY :(!!

Hello I have to write a report about the experiment I did aboutgene cloning and also have to answer few qns from the prof. I woudreally appreciate if anybody can help me and will thank you in apossible way. I am that desperate since this would be veryimportant for my grade :(

I don't know the insert gene and have to figure it out on NCBIBLAST search using the sequence.( I tried but I couldnt find onNCBI)

The cloning was with pGEX-4T-1 vector and unknown gene which isabout 700bp.

It says by using pGEX_3_primer, got the sequence, which would bereverse sequnece so I did reverse and it is

AAAATTAGTTTGTTTTAAAAAACGTATTGAAGCTATCCCACAAATTGATAAGTACTTGAAATCCAGCAAGTATATAGCA

TGGCCTTTGCAGGGCTGGCAAGCCACGTTTGGTGGTGGCGACCATCCTCCAAAATCGGATCTGGTTCCGCGTGG

ATCCACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCA

AGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGA

GGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTC

AGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCG

AGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCT

GCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAA

GAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAG

CAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGT

GCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAA

CAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGTAGCGGCCGC

Then the qn is,

1.What is this gene? Where is the start and stop codon of thisgene coding sequence?

2.Would this gene translated in in-frame? Gst fusion?

3.What is the partial expected amino acid sequence of GST-YFPprotien?

4.Can you find the restriction enzyme site that we used? (BamHI,NotI)

5.To check weather the cloning was done or not, it is better touse one restriction enzyme that is on vector and the other is oninsert. In this case we used the same emzyme as we used for cloningwhich are BamHI and NotI. If we want to still use NotI but changeBamHI as different enzyme, what could it be?

You need to devise a cloning scheme to solve the following problem. An insert is available and it contains a gene within it, whose exact position and orientation within the insert are unknown. This gene contains a sequence for an important small peptide hormone. No DNA sequence information is available. The insert is shown below with a strategic restriction site indicated. The specific task to be set out as an experimental strategy is as follows:

You have accepted a consultancy contract to provide a large amount of the purified peptide to a new medical centre that needs the peptide to treat patients. It is a new peptide on a DNA fragment just isolated and provided to you and is therefore not yet in commercial production. Of course it would be a simple task to sequence the insert and go from there, but for the purpose of this hypothetical exercise sequencing is unavailable.

Set up an experimental scheme that takes into account the task described above, beginning with the insert and the expression vector pUC18. A map of pUC18 with all features indicated, including the multi-cloning site, may be easily obtained by typing the vector name into Google.

The insert containing the peptide gene is a blunt-ended fragment of 1.8 kb that was not generated with a restriction enzyme. A single unique restriction site is indicated on the fragment. The size of the gene is unknown, but what is known is: (a) the orientation, which is right to left in the drawing below; (b) the gene does not have a promoter; and (c) there is a 6x His tag at the C-terminus of the Open Reading Frame (ORF).

BamHI

======================== I =====

(Sorry for the poor drawing, cant seem to upload the image; Bam HI is supposed to be at the "I")

For this assignment, Part One of your course project, assume the role of Dr. Madness. Your rogue nation seeks global domination. With a bare bones laboratory and your exhaustive microbiological and epidemiological knowledge, you (Dr. Madness) decide that the best way to rule the world is to create and disseminate the perfect biological weapon.

For this part of the assignment, you will develop your weapon from the ground up. Discuss nearly all of the epidemiological criteria related to it, and justify and discuss why it is used and how effective it is. This agent could be a hybrid of other biological pathogens or an entirely new one. If the agent is newly created, there must be some basis and epidemiological support of a similar agent by which you can base your justification. In other words, it will be unrealistic to create an airborne virus that inoculates and kills within one hour. There must be a realistic exposure and incubation time and must be supported through current agent biology or biochemistry (for example, influenza exposure and incubation takes 1–4 days).

Name of Agent: Explain why you chose the name. If it is a biological agent, be sure to provide a taxonomic name

Etiology: This will talk about the genesis of your agent. Where was it discovered? How was it made? How long has it been around? Why was this agent created? What were the social and economic factors of your rogue nation that made Dr. Madness focus on this element of the agent? What are the environmental precursors to this agent? Discuss the interaction among agent, host, and environment.

Identification: This will describe the basics of the agent. Is it a bacteria, virus, toxin, parasite, hybrid, or something else? Discuss how your agent presents within the human population. What are the symptoms in humans? What are the (zoonotic) symptoms in animals? How does the disease progress? Are there stages? Discuss the various stages including length of infection, severity, and the like. What are the diagnostic indicators? How would a doctor be able to identify this agent in a clinic or emergency room?

Laboratory Analysis: How will the agent be identified? Can it be grown in media? What type of laboratory methods can be used to identify the agent (microscopy, chromatography, PCR, and so on)?

Occurrence: This is the epi: who, what, when, where, how, and why of the disease. Where does it happen? When can it be found? Who is most and least susceptible to the agent (risk factors). More exotic and hard to find agents are harder to prevent and control but are also more difficult to initiate an epidemic or pandemic, whereas more generalized and known agents may be easier to cure, but have a much wider swath of causing pandemics. How do socioeconomic factors foster or inhibit the spread of disease?

Reservoir: What is the natural reservoir of the agent? Are there other organisms where this agent can reside without causing disease? Increasing the reservoir can enhance transmission but can also allow for easier identification and treatment in response to it.

Mode of Transmission: Consider inhalation, absorption, digestion, contact, and so forth. If you use multiple modes, justify your selections.

Incubation Period: Provide the range with an average (median) day of disease onset. Does the period change in different socioeconomic status identifiers (sex, age, race, creed, and so on)? Why or why not?

Period of communicability: How long is a person with this agent contagious? Increasing this period also increases the opportunity for study and thus treatment and control.

Susceptibility: Is the agent susceptible to reinfection of the same person? Allowing for this increases morbidity but usually mortality wanes in subsequent infections.

Taking on the role of Dr. Madness, generate your superweapon and describe the weapon using the above mentioned criteria. Remember, the focus in on creating something that becomes difficult to identify, monitor, or treat with prophylaxis. You will write out the proposal as Dr. Madness submitting this to his lead researcher to develop. This proposal should be approximately 6–8 pages in length, but some submissions may be longer.

Submit your Bioweapons and Epidemiology Part One proposal in the assignment area.

Please be sure to review the Bioweapons and Epidemiology Part One Scoring Guide for information on how this assignment is graded.

Project Requirements

To achieve a successful project experience and outcome, you are expected to meet the following requirements.

Written communication: Written communication is free of errors that detract from the overall message.

APA formatting: Resources and citations should be formatted according to current APA style and formatting.

Resources: Include all literature cited in the project.

Length of paper: 6–8 typed, single-spaced pages, not including cover page and resource list.

Font and font size: Arial, 10 point.

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