Biology 2581B Lecture Notes - Lecture 19: Blast, Bioinformatics, Genomics

18 views4 pages

greenporpoise254

18 Apr 2017

School

Department

Course

Professor

For unlimited access to Class Notes, a Class+ subscription is required.

Document Summary

Personalized genomics in healthcare are going to become hugely influenced by bioinformatics. Really easy to get the sequence read, but we really only get small pieces. We have all this data but how do we put it together. You start looking for overlaps to put things together. 25 nucleotides that match - a pretty good bet that they belong together. But now we have repeats in there. You can put them together since they share identical repeats. To put them together, the computer looks for overlaps. As the sequencing reads come off the machine, some are good but some are bad. The key is to find sequences that span the repeat. Algorithms used to evaluate how good they are. Blast - the database that you use to figure out what you"re looking at: against a database of known dna. Tblastx - take unknown sequence: translate all 6 frames and then search those against the data base of the same thing.

Related Questions

Please answer the question after reading the paragraph.

We have a global health challenge in our hands today, and that is that the way we currently discover and develop new drugs is too costly, takes far too long, and it fails more often than it succeeds. It really just isn't working, and that means that patients that badly need new therapies are not getting them, and diseases are going untreated. We seem to be spending more and more money. So for every billion dollars we spend in R&D, we're getting less drugs approved into the market. More money, less drugs. Now we have a whole pipeline of different organ chips that we are currently working on in our labs. Now, the true power of this technology, however, really comes from the fact that we can fluidically link them. There's fluid flowing across these cells, so we can begin to interconnect multiple different chips together to form what we call a virtual human on a chip. Now we're really getting excited.We're not going to ever recreate a whole human in these chips, but what our goal is is to be able to recreate sufficient functionality so that we can make better predictions of what's going to happen in humans. For example, now we can begin to explore what happens when we put a drug like an aerosol drug. Those of you like me who have asthma, when you take your inhaler, we can explore how that drug comes into your lungs, how it enters the body, how it might affect, say, your heart. Does it change the beating of your heart? Does it have a toxicity? Does it get cleared by the liver? Is it metabolized in the liver? Is it excreted in your kidneys? We can begin to study the dynamic response of the body to a drug. Organs on chips could also change the way we do clinical trials in the future. Right now, the average participant in a clinical trial is that: average. Tends to be middle aged, tends to be female. You won't find many clinical trials in which children are involved, yet every day, we give children medications, and the only safety data we have on that drug is one that we obtained from adults. Children are not adults. They may not respond in the same way adults do. There are other things like genetic differences in populations that may lead to at-risk populations that are at risk of having an adverse drug reaction. Now imagine if we could take cells from all those different populations, put them on chips, and create populations on a chip. This could really change the way we do clinical trials. And this is the team and the people that are doing this. We have engineers, we have cell biologists, we have clinicians, all working together. We're really seeing something quite incredible at the Wyss Institute. It's really a convergence of disciplines, where biology is influencing the way we design, the way we engineer, the way we build. It's pretty exciting.

Question: For years, technology and medicine have joined together to pave the way or even solve some of the worldâs greatest issues in healthcare. These issues include but are not limited to incurable diseases and disorders like AIDS and cancer. According to Geraldine Hamilton however, we as a population are spending too much money to develop drugs and solutions to these issues, only to be at a deficit with the drugs actually produced. She believes that one of the keys is how we test these drugs and finding more efficient ways to do so. As a result, she suggests the use of organs on chips, an innovation created and pioneered by her lab. The use of organs on chips could change the way new drugs are released and tested, thus possibly furthering the process of creating solutions to healthcareâs problems. Where is the fine line between technology and human innovation? Is human innovation gradually becoming depending on technology? (At least two paragraphs, a paragraph is at least 5 sentences long.)

As you may recall in the work of Triplett (1898), the presence of others in a bicycle race was found to enhance individual performance. This is called social facilitation (Williams, Harkins, & Karau, 2007). At times, however, the presence of others can detract from individual performance, which is termed social inhibition (Crisp & Turner, 2007). Similarly, social loafing can occur when an individualâs performance within a group decreases due to his or her reliance on others in the group (Crisp & Turner, 2007).

For this Discussion, review the media program, Week 5: The Virtual Office. Focus on the characters in the media and determine which characters displayed social facilitation, social inhibition, and social loafing.

With these thoughts in mind:

Post by Day 3 a description of the characters in the media program demonstrating social loafing, social inhibition, and social facilitation. Explain how you identified them. Then, select one of the characters and, using the current literature, explain two ways you might mitigate their behavior.

Media Program

(Onscreen Text: The employees at the United Cardboard Company often work individually on projects, but as with most environments, they are occasionally asked to participate in group projects. One such group is about to meet right now to plan a presentation for the Board of Directors. Observe the conversation and reactions of various group members to determine which group members exhibit signs of the following: Social Loafing, Social Inhibition, and Social Facilitation.)

(Interior of an office. Ken stands at the front of the conference room.)

KEN: OK, I guess we might as well all get started. As we all know, the big man has requested the five of us to get together and write and conceptualize a presentation to the board on our new packaging system. Maybe we can start by going around and throwing out some initial ideas.

KATHY: Sounds good to me. I think a PowerPoint presentation would do the job well.

GAVIN: I agree. We could follow it up with a physical demonstration of how the packaging looks and folds-- maybe a video of the larger pieces that won't fit into the boardroom.

KEN: Sounds perfect to me. Amanda, Brian, what do you guys think?

BRIAN: Yeah, what you guys said sounds fine.

(Amanda thinks, âI donât know what to say!â)

KEN: Amanda?

AMANDA: I don't know. I didn't really get much chance to think about this. We only found out we needed to do this together three days ago.

KEN: OK, no worries. Let's focus on the PowerPoint idea. I've been doing a lot of them lately, so I'm happy to take the lead on the design aspect. What do you guys think we should all incorporate into the slides?

GAVIN: I think we should start with where we got the idea for this new packaging -- the company that designed it and the different sizes that it comes in.

KATHY: We should follow that with a graph comparing the old prices to the new ones to illustrate how much we'll be saving over time. Amanda, didn't you have most of that information collected at some point?

(Amanda thinks, âOh no! What if I deleted that?)

AMANDA: I don't know, maybe, it's been so long. I didn't think I'd need it again for a group project like this.

(Gavin thinks, âI wonder whatâs gotten into her. Sheâs not usually this tense.â)

KEN: That's OK, Amanda, I'm sure we can easily dig it up again. Brian, do you have any other ideas for the PowerPoint slides?

BRIAN: Nah, I think what you guys mentioned sounds right.

(Kathy thinks, âWow. Way to contribute Brian.â)

KEN: OK then, Kathy and Gavin why don't you send me all of the info and I'll write it up and make the slides. Amanda, don't worry about the cost saving document, I'm sure I can dig it up from my old emails and put it into that slide too.

AMANDA: Are you sure? I'm happy to look. I mean I'm sure I have it somewhere. (Kathy thinks, âShe really needs to get it together. Why is she so nervous?â) At least I think I have it somewhere. You won't tell the Board of Directors if I lost it, will you?

KEN: Of course not, we're in it together. So as I was saying, I'll write up and prepare all the PowerPoint slides. Then we can start our presentation with reading and explaining each slide. Then, what?

KATHY: Well, and then I think we should show them the packaging live, and the quick deconstructing techniques.

KEN: Great idea. You and Amanda can demonstrate the folding, while I narrate what you're doing.

(Amanda thinks, âIs he doing too much of the work? And what if I drop everything while heâs talking?â)

GAVIN: And after you all demonstrate the smaller packaging, we could show a quick video of how the really big ones function down at the warehouse. Brian, would you be able to go film that quickly one of these days?

BRIAN: I don't really have any experience with video cameras or anything like that, so...

(Gavin thinks, âI should have seen that one coming.â)

KEN: That's OK. My wife actually just got me this great little camera for our anniversary. It takes great videos. So I can just run down to the warehouse, get some footage, then put it together on this new editing software I just downloaded. Maybe add a little music. It's going to be really slick!

KATHY: Are you sure, I wouldn't mind doing that too.

KEN: Oh no, it's fine. I love this kind of stuff; just leave it to me. But I suppose that's enough planning. Now it's time to get to work and make the presentation a knock out. Go team!

Check the Course Announcements at the beginning of the week following the deadline for Part 1 to discover exactly what happened to the deer population on the Kaibab plateau. This information is essential for completion of Part 2.

The second part of your project is to take what you've learned about the Kaibab forest ecosystem and write an accurate description of the boom and bust of this deer population, using correct ecological language. Consider as many of the aspects of these events as you can. Be sure to consider the effects on the other species in the ecosystem as well.

Refer to your on-line materials and the appropriate sections of your textbook. Your discussion should include (but not be confined to) consideration of all of the following concepts: carrying capacity, predator/prey relationships, population cycling, resource partitioning, competitive exclusion, fundamental and realized niches, food chains, food webs and trophic pyramids.

Note that the purpose of this exercise is for you to demonstrate to me that you understand these important concepts of ecology by utilizing them accurately and appropriately in the description of the disaster in the Kaibab forest. Your essay must include both clear indications that you understand the meanings of these principles and clear indication that you understand how these principles can be used to describe what happened to the ecosystem on the Kaibab plateau.

information given of part one: On the north rim of the Grand Canyon, an area called the Kaibab plateau, there is a conifer forest called the Kaibab forest. The forest's trees include pine, fir and spruce. Shrubbery includes a variety of willows, raspberries, etc. A hundred years ago, this forest was a stable ecosystem, housing, among other species, a population of about four thousand mule deer.

These deer were hunted by local Native Americans, who used them for food and other materials. They were also hunted by predators like pumas, wolves and coyotes.

In 1906, the US made this region into a National Game Preserve. With the intent of protecting the deer, hunting was forbidden. Bounties were paid for killing the pumas, wolves and other large animals that preyed on the deer. By 1925, more than 6000 predators had been killed, virtually wiping out the ecosystem's large predators.

*Read the instructions* for Part 2, then consider this additional information about the Kaibab forest.
There are some hints in here to suggest the *minimum* range of the subjects you need to discuss to explain this; You will need to read the chapters and the course materials to understand the meanings of these concepts, and to be able to use them to explain the Kaibab disaster. There are other important concepts as well--so keep your eyes open as you read. It wouldn't hurt to go back and read the original description in Part 1, either. And you may find it necessary to do some quick browsing in areas of your book not directly related to ecology. (For instance, you might just want to do some looking into the nature and importance of the bark and twig ends on a tree.) Do not neglect the on-line essays which are provided for you in this Unit. What you should *not* do is Google the Kaibab, or look it up on a source like Wikipedia. This is not about what you can *discover* about the Kaibab forest.
Your grade will depend upon how completely you convince me you understand the concepts involved in this description. This is your test on ecology--your goal is to convince me that you understand the concepts and terminology of the subject, and can apply them to a real life situation.
Before we go on to the new information, there are a few things that came up as I was grading the Part 1 submissions which I think I should mention, just to keep you from straying in some incorrect directions.
First, remember that your concern is the fate of the Kaibab forest in the *immediate* sense--over tens of years, not thousands. There are no evolutionary issues here, at least in the short term (and that's your concern right now). So we won't be talking about adaptive radiation.
Also, keep your focus on the *Kaibab forest*, not on other ecosystems. Oh, and remember that the Kaibab is pretty isolated--emigration really isn't a reasonable alternative for the species living in this forest.
And finally, until we get to Part 3, the only human interaction we are considering is the initial decision to put bounties on those large predators, which led to their near-extinction in the area. You will be thinking a bit about human hunters trying to control the deer population toward the end, but the rest of the time you're just concerned with the natural processes going on in the ecosystem.
Okay, now on to the actual description of what happened in the Kaibab Forest as a result of killing almost all of the large predators. Remember, your task in Part 2 is going to be to describe and explain all of this using the concepts of ecology which you are learning in Unit 2 of the course.
*****
The primary, most immediate outcome of the removal of the predators from the ecosystem was that the deer population exploded, because the loss of the normal predator populations removed a primary source of population control. And the expanding deer population ate a *lot.* [Hint: explaining this requires discussion of population cycling, predator prey relationships and carrying capacities.]
As the deer population got larger and larger, their impact upon their favored food plants became extreme. They ate a much larger percentage of each year's plant populations, and they ate a larger portion of each individual plant. They also began to eat more from the plants which they didn't like so well--plants normally consumed by other herbivores in the ecosystem. In the winter, the starving deer ate about anything remotely resembling food, including twigs and bark from trees. As a result of the destruction of many of the twig ends of the trees, the spring tree growth was inhibited (why?). The stripping of the bark caused the death of some of the trees (why?). The extreme browsing on the herbaceous plants caused shifts in the plant population diversity, as the deer drove many of their favored plants into extinction within the ecosystem. [Hint: Explanation here will need to include discussion of resource partitioning, competitive exclusion, and realized vs. fundamental niches.]
All of this also impacted upon the rest of the animals in the ecosystem, since many of them depended upon the same kinds of food the deer ate, or depended upon the foods that the deer were eating because they could no longer get the food they favored. Then of course, the smaller predatory species (like foxes and owls) depended upon the health of those populations of small herbivores (like rabbits and mice). [Hint: sounds like food chains, food webs and trophic pyramids come into this part.]
After a couple of decades, the ecosystem was quite altered. The plant community was very different from what it had been before, and the deer herd, though not extinct, was composed of significantly smaller and weaker deer than the herd from the 1890s. (This was partially due to their straightened circumstances re. food, but also partially due to the absence of predators. Why would the removal of the natural predators cause this change in the general vigor of the deer in the herd (and why would the substitution of *human* hunting not exert the same positive influence)?)
Okay, the next phase of your assignment is to describe all the things going on in this ecosystem using the proper terminology that you should be learning from studying this unit of the course. Note that your use of terms like, for instance, "resource partitioning" needs to show that you understand not just what the concept means, but how it is reflected in this specific ecological disaster. Feel free to discuss this as much as you want to on your Discussion Board. Don't ignore the little questions tucked into the above description, and pay attention to those hints. Your response must demonstrate proper understanding of these concepts and how they are demonstrated by the disaster in the Kaibab forest.
This is the largest part of your exam project; your response should reflect the fact that this is a 50 point "essay" question. You are given a lot of organizational clues and hints about what issues you need to include in the information above. Make use of those things.

Biology 2581B Lecture Notes - Lecture 19: Blast, Bioinformatics, Genomics

Document Summary

Get access

Related Documents

Biology 2581B Lecture Notes - Lecture 19: Contig, Genbank, Bioinformatics

Biology 2581B Lecture Notes - Lecture 18: Blast, Joint Genome Institute, Genome Editing

Biology 2581B Lecture Notes - Lecture 18: Blast, Bioinformatics, Genomics

Related Questions