INTE 398 Chapter Notes - Chapter 2.8: Window Period, Statistical Hypothesis Testing, Antibody

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lilactiger848

19 Jan 2017

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A simple of blood is taken, either tested immediately called point-of-care (poc) or sent to a lab to be tested for hiv (standard) Most hiv testing of blood samples in done in a lab. If this test shows the person testing does not have hiv no further test and negative result is sent back. If screening indicated the person is infected (hiv+) then a confirmatory test is performed, is that test comes back positive than the positive result is sent. Can take up to 1 2 weeks for a person to receive their result. Test is done at location where blood was taken. If the result is negative then no further testing, if positive then sent to a lab for confirmation. At home tests can be bought over-the-counter in some stores and online in the usa. Some test kits bought online can be of poor quality and provide incorrect results.

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Read the following passage focusing your attention on the scientific procedures and scientific abilities illustrated in it. Think about what types of experiments (observation, testing or application) are described. Identify the hypothesis, predictions, outcomes of experiments and assumptions that appear in the passage. The standard explanation of how humans originally acquired AIDS is that HIV (human immunodeficiency virus) originally was transmitted to humans from monkeys or apes carrying SIV, simian immunodeficiency virus. How could the transmission have occurred? Several similar hypotheses involve an African hunter coming in contact with monkey blood. For example this could have occurred when a hunter butchering a monkey, got some of its blood in a cut, or when a human ate undercooked monkey meat, or when a monkey bit a human. Depending on one's assessment of the genetic diversity of HIV over time, this transmission might have occurred only a few decades ago or, alternatively, hundreds or thousands of years ago. If the latter is correct then AIDS could have been restricted to remote African villages until recent decades when trade and international travel led to the current pandemic. There are however other alternative explanations for the spread of AIDS. One of them is that AIDS arose from contaminated polio vaccines used in Africa from 1957-59. Why is this a plausible explanation? Polio vaccines are cultured on apesâ kidneys, so contamination of a batch of vaccine by an SIV is a possibility. There is a precedent: in the 1950s and early 1960s millions of doses of polio vaccine were contaminated by another simian virus, SV-40. The vaccine alleged to be the origin of AIDS was given to hundreds of thousands of people in central and west Africa from 1957-1959. These locations later had some of the world's highest levels of HIV infection. The timing is also right, since the earliest known cases of AIDS date from the 1960s; the earliest HIV-positive blood sample was collected in Kinshasa in 1959. At the time, there was no way of testing for the presence of SIVs, which were only discovered in the 1980s. Another factor adds plausibility to the theory: the vaccine was given to many infants less than a month old, in an extra high dose. Since the immune systems of infants are not fully developed, this is an excellent way to help a virus jump the species barrier. Some scientists argue that the above explanation is not necessarily correct but that it is worth taking seriously. There are a number of ways to test it. One is to analyze stocks of polio vaccine; if the explanation is correct, then it is probable that some of the vaccines will carry SIV. Another is to scrutinize records of early polio vaccination campaigns in Africa. If it is true that the immunodeficiency virus passed to humans by way of those vaccines, the areas where the campaigns took place would be the same as those where the initial sprouts of the disease occurred and where the larger number of cases occurred during the early stages of the pandemic. Another is to analyze blood samples in Africa from the 1950s and earlier (pre polio vaccination): if the immunodeficiency virus was transmitted via the polio vaccine, HIV should not be found. Adapted from âPolitical refutation of a scientific theory: the case of polio vaccines and the origin of AIDSâ. Brian Martin, published in Health Care Analysis, Vol. 6, 1998, pp. 175-179. Now reread the passage and answer the following questions.

5. For each experiment, write an outcome that would disprove the hypothesis of AIDS passing from monkeys to humans through polio vaccines.

6. What outcomes of the experiments would fail to disprove the hypothesis of AIDS passing from monkeys to humans through polio vaccines?explain.

7.What outcomes would prove the hypothesis? Hint: This is not the same as question 6. Think about what would you need to do to 100% prove a hypothesis.

8. For what reasons do scientists need to conduct testing experiments?

ochrejackal75

BIOTECHNOLOGY

Introduction

In this Experiment we will learn how to identify the unknownbacterium according to the case study given as you start to performyour procedures and following the steps. Also, we will be learningthe outcome of a specific case scenario of immunity. We will beperforming different examples of media and observing the reactionafter inoculation and adding different reagents as it produce somechanging of color diagnose to a negative or positive results. Also,we will conduct different types of biochemical testing includingIndole production, Citrate Utilization, Methyl red test, andMannitol Fermentation.

In this case scenario we are trying to figure out theinfestation of food at the warehouse causing a death of theplaintiff mother. The plaintiff is accusing the warehouse forselling these infested products by insects. At the warehouseinspection is been done by swabbing and acquiring the type oforganism to be identified as evidence for the court finaldecision.

One of the major findings in this experiment is that itwas negative gram stains and the Indole and Methyl Red Test had apositive reaction. Additional testing was perform which show theresult of only negative on Lactose Fermentation and the remainingthree additional testing add up to a positive. The outcome of thisinvestigation scenario could be a negative result to the casescenario presented about infested products by insects since nounknown bacteria was left to bediagnosed.

Procedure

The following steps are requiring completing this labexperimental. First make sure you open the Virtual UnknownSoftware. Complete conducting using Indole production and CitrateUtilization, Methyl Red test choosing from your media option. Alsomake sure you open the reference book for each procedure to beinformed of the lab steps and decision making such as positive ornegative and its color after inoculation.

Observations and Results

	Result + or -	Appearance after Incubation
Gram Stain	- gram rods	N/A
Indole Production	+ positive	Yellowish-after incubation & adding Kovacâs reagent changingto a cherry red color indication of positive
Mannitol Fermentation	- neg	Red
Methyl Red Test	+ pos	Turbid yellowish after incubation and adding methyl red reagentchange to red positive. +
Citrate Utilization	- neg	Greenish after incubation. No reagent added.

Additional tests performed are listed below:

	Result + or -	Appearance after Incubation
Lactose Fermentation	- neg	Red- no reagent added
Sucrose Fermentation	+ pos	Yellowish- no reagent added
Phenol Red Rhamnose (Lactose Steps)	+ pos	Yellow- no reagent
Phenol Red Xylose (Sucrose Steps)	+ pos	Yellow- no reagent

Bacterium identified as: You may want to do some additionaltests to conclusively identify your bacterium. Some good ones to domight be lactose and sucrose fermentation, like you did last week.Remember, they use Phenol Red Lactose Broth and Phenol RedSucrose Broth and yellow= positiveand red =negative. After you do those two tests,you may want to do Phenol Red Rhamnose and Phenol RedXylose, which are set up the same way as the sucrose andlactose tests, they just have different sugars. Be sure to recordyour test results!

Discussion

Identify the bacterium â Make sure you look in the VirtualUnknown lab report to make sure you got the right organism. Afteryou have made your identification, look at the lab report. You cando this by going to the View menu in Virtual Unknown and selectingLab Report. You can double check with me that you are researchingthe right one.

Once all observation was performed including the additionaltesting I was left without an Unknown organism to be identified.This only leave me with a diagnose to state that no evidence wascollected to accused the warehouse as being infested with insectsaccording to the case study.

Explain what features of this organism make it an idealcandidate host for your insecticide. (Hint: remember you will needto infect insects with the bacteria to deliver the insecticide.)âFind out where the unknown organism was isolated from.

Describe in detail the steps you will take to insert the targetgene into the bacterium. - Figure 8.1 of your book should help youwith this.

Conclusion

< Within a few sentences, provide a concluding statementabout the results of your laboratory>

Virtual Lab Report

Student:

Instructor: Test User

Section:

Unknown: BiotechUnknown

Identification Information

Assigned Unknown: Identification not yet complete

Identified Unknown: TBD

Gram Reaction & Morphology: Gram Negative Rods

Auto-Inoculation Used: Yes

Test Detail (Chronological Order):

1 Gram Reaction {-} Eliminated {53}Remaining {71} Recorded 1 time(s)

Observations: none

2 Indole production {+} Eliminated {44}Remaining {27} Recorded 1 time(s)

Observations: none

3 Mannitol fermentation {-} Eliminated {19}Remaining {8} Recorded 1 time(s)

Observations: none

4 Methyl red {+} Eliminated {0} Remaining{8} Recorded 1 time(s)

Observations: none

5 Citrate Utilization (Simmons) {-}Eliminated {2} Remaining {6} Recorded 1 time(s)

Observations: none

6 Lactose fermentation {-} Eliminated {0}Remaining {6} Recorded 1 time(s)

Observations: none

7 Sucrose fermentation {+} Eliminated {4}Remaining {2} Recorded 1 time(s)

Observations: none

8 Rhamnose fermentation {+} Eliminated {2}Remaining {0} Recorded 1 time(s)

Observations: none

9 Xylose fermentation {+} Eliminated {0}Remaining {0} Recorded

goldturtle749

The Case: While Elizabeth is reading the morning newspaper, she notices an ad for a free genetic screening for breast cancer at the clinic next week.The ad specifically invites women of Ashkenazi Jewish ancestry to participate.According to the newspaper ad, subjects will be tested to see whether they have mutations in the BRCA1 gene which would predispose them to breast cancer. Elizabeth, age 27, had heard about the discovery of the gene and about the mutation linked to Jewish women. Her paternal grandmother had been diagnosed with breast cancer at age 51 and died two years later, and Elizabeth worried that she may have inherited a variant that would put her at increased risk. She also worried about her mother, age 52 and apparently cancer-free so far, and her 7- year old daughter. Her daughter is not allowed to participate in the screening, but Elizabeth convinces her mother to go with her to get tested. For the screening, a small amount of blood is drawn. DNA is isolated from the blood, and part of the BRCA1 gene is amplified by PCR. Using a Southern Blot method, the digested DNA is run on a gel, transferred to a neutral membrane. Once on the membrane, the samples are hybridized with specific probes corresponding to deleterous mutations known to be linked to increased breast cancer susceptibility, plus probes for wild type regions of BRCA1. The probe will only bind to the DNA if that mutation is present. Control DNA samples, known to have a specific mutation, are included in the run to verify probe . Probe binding is visualized by labels attached to the probe, and will depend on the lab running the analysis. Probes: 185delAG (AG deletion in exon 2) Normal 185 (no mutation at this site) 4184delTCAA (TCAA deletion in exon 11) Normal 4184 5382insC (C insertion in exon 13) Normal 5382 DNA samples: Elizabeth Mother Unrelated woman Control 185delAG Control 4184delTCAA Control 5382insC Control wild type BRCA1 (no mutations) If either Elizabeth or her mother test positive, is a prophylactic double mastectomy appropriate? (2 marks) What other issues does this type of testing raise, and how should these issues be addressed? (2 marks) What does it mean if a result came back as a Variant of Uncertain Clinical Significance? Provide a peer-reviewed journal article as a reference for this question. (1 mark answer, 1 mark reference) Does the lack of any of these mutations mean that the women will not get breast cancer? (2 marks) Who should have access to the test results? (2 marks) Does the daughter have the right to know the results? She is only seven now, but what about when she is 16? (3 marks) Should this type of screening be mandatory? (3 marks)

INTE 398 Chapter Notes - Chapter 2.8: Window Period, Statistical Hypothesis Testing, Antibody

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