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Biology

Introduction Objectives 1. To understand the concept of species diversity, inc

Introduction
Objectives
1. To understand the concept of species diversity, including the contribution of both species richness and “evenness” to it.
2. To understand some of the ways in which species diversity is measured and/or quantitatively modeled.
3. To understand the relationship between species diversity and area sampled.
4. To understand how the equilibrium theory of island biogeography can apply to the design of nature preserves.
5. To gain some familiarity with identification of leaf litter fauna.
Background
If Stafford County had some money to buy land for new parks, would you suggest that they spend it all on one big parcel or on several smaller ones having the same total area?
One of the primary purposes of national parks and other kinds of nature reserves is to protect and conserve biological diversity – different kinds of living things. And while we all agree that conserving biological diversity is a good thing, we also realize that doing so comes only at some cost – development, timber harvest, mining, etc. all promote economic well-being, at least over the short term. So we have to be able to give more practical advice to policy makers than “protect everything!” This two-week field/lab problem is meant to give you some basic background on species diversity and island biogeography, as well as to get you to think about the above problem. In doing so, you should see some important contributions that ecological theory can make to very practical problems. Such contributions form the basis of conservation biology.
To understand the factors affecting diversity, we must first decide how we’ll measure and analyze diversity. This lab will ask you to apply a few common approaches:
Species Richness (S): This is simply the number of different species present in a given area. This is a good first approximation to diversity, but it doesn’t allow us to distinguish between a community that has 10 species represented by 10 individuals each, and one that has one species represented by 91 individuals and nine other species represented by one individual each. To do that, ecologists have developed approaches that incorporate the “evenness” of abundances, because we feel that the former community is more “diverse.”
Shannon Index: Shannon’s index (H’) is a calculation that takes into account both the number of species found (S) and the “evenness” or “equitability” of distribution of total individuals among the species. Values of H’ tend to range between 1.5 (lower diversity) and 3.5 (higher diversity). The Shannon index is given by the equation: where , the proportion of total individuals in the sample made up by individuals of species i.
Dominance-diversity curves: A graphical way of representing species diversity is to plot the log of each species’ abundance vs. its rank (from most abundant to least abundant). If we had 10 species, represented by 100, 80, 53, 41, 35, 33, 29, 14, 9, and 6 individuals, respectively, our dominance-diversity curve would look like Figure 1. Though it doesn’t yield a simple number for comparison, this way of representing diversity conveys more information. Note that the greater the slope of the line, the less “even” the sample, and the smaller the slope, the more “even” the sample.
Applying island biogeography to forest litter communities
The Equilibrium Theory of Island Biogeography (MacArthur and Wilson 1967) predicts the species diversity of islands as a function of their size and distance from the mainland. Reserves are often isolated patches of natural habitat surrounded by human-altered landscapes (i.e., they are effectively islands). Animals living under cover objects are similarly isolated from similar habitats, so we can use them to consider how island biogeography might relate to reserves.
The essence of MacArthur and Wilson’s idea is simple. They assume that the number of species on an island is determined by a balance between the rate of immigration of new species from the “source pool” (generally the nearby mainland) and the rate of local extinction. Both processes are assumed to be continuous, with species continually going (locally) extinct and being replaced through immigration, although not necessarily by the same species. The balance of extinction and immigration results in an equilibrium species richness () for the island (Figure 2).
Consider immigration first. At first, the immigration rate will be high, since each new individual reaching the island will represent a new species. As more and more individuals arrive, however, fewer and fewer represent new species. The immigration rate reaches zero when all of the “source pool” species (i.e., those present on the adjacent mainland) are present on the island. Immigration rate should also vary as a function of the island’s isolation, i.e., its distance from the mainland. So the graph has two immigration curves – one for a near island and one for a far one.
Now consider extinction rate. It is bound to be zero when there are no species present, but will increase in proportion to the number of species already present, due to there being more opportunities for extinction and the exclusion of species that are poor competitors. Extinction should also be a function of island size, both because larger islands support larger populations, which makes them less vulnerable to “bad luck” extinction events, and because larger islands are likely to contain a greater diversity of habitats than small ones. We can now predict that:
1) Species richness will become roughly constant through time, even though there will be continual turnover in species composition. Thus, the equilibrium reached is dynamic rather than static.
2) Large islands should support more species than small islands.
3) Near islands (to the mainland source pool) should support more species than far islands.
There are lots of data from real communities that support the above predictions. The potential application of this for the design of nature reserves is not so simple, however, as highlighted by the “single large or several small” (SLOSS) debate on this issue. On the one hand, it seems very clear that we should expect a decline in species diversity when a patch of land is separated from the “mainland” by human-altered habitat, since distance from the mainland is by definition increased from zero. In addition, a larger preserve should support more species than a smaller one. On the other hand, if we consider the question of whether to make a single large reserve or several smaller ones with the same total area, things get complicated. Small reserves might be more insulated against the spread of an epidemic disease. Small reserves might also allow for survival of poor competitor species in patches that just happen (by chance) to be without superior competitors. Similarly, small reserves might allow for the survival of prey species in patches that happen to lack major predators (Huffaker 1958). Given these tradeoffs, it’s clear that island biogeography theory shouldn’t be the sole factor in designing reserves. Other factors, like the biological needs of all the species involved and the physical features (e.g., topography, habitat diversity, spatial position) of the land in question, must also be considered. Procedure for week 1
We’re going to survey the animal community living under fallen logs and compare it to the community found in nearby open areas that lack a distinct cover item. The procedure is simple: you will flip the log and count and/or collect all the animals you find living within its footprint. You may use hands, forceps, aspirators, or nets to capture animals. Physical variables to collect for each log will include the length and width of the item (in meters), its proximity to the nearest other cover item (also in meters), and any other characteristics that seem relevant. You will then repeat that procedure in a nearby uncovered area that is a similar distance from neighboring logs. Our goal is for each group to survey at least three log-open site pairs. Aim to include both logs that are “isolated” (>3 m from another cover item) and “well-connected” (<1 m from another item) in your samples. To be confident of our identifications, we will collect examples of each invertebrate we find, and take photos of any vertebrates we find. Be sure to keep samples from each site separate and label them appropriately. We will complete identification of the samples in week 2.
Procedure for week 2
Your goal this week is to identify as many distinct “morphospecies” as you can within your samples. While it would be good to identify each animal to species, it is more important for our purposes is to accurately assess how many distinct taxa are present in the samples. As a result, you may identify species as “red centipede” or “striped brown spider” as you go. The key is for the names used by each group to be consistent. To encourage consistency, we will maintain a collection of examples of each species we identify. Before you record an animal as a new morphospecies, check whether that animal has already been given a name in the collection. Enter your group’s data into the Excel template your instructor provided and email it to them. As you're identifying and recording the morphospecies present in your sample, give some thought to the trophic habits (i.e., detritivore (consumer of rotting vegetation, bacteria, fungi, etc.), herbivore (living plants), or carnivore (other animals)) of each species encountered. Doing so will help you to interpret your results (e.g., you might find that spiders, which are carnivores, correlate with high diversity under a log). Write-up: Use the full class data for your Figures.
1. Use island biogeography theory[1] to form good scientific hypotheses for each of the following questions. Remember that good hypotheses are testable explanations for an observation.
How will the species diversity under large items differ from smaller ones?
How will the species diversity under isolated items differ from more-connected ones?
How will the species diversity and trophic habits of animals in “under log” samples differ from “open” samples?
2. For two samples, __CH1c____ and_____TS2c_, show how you’d calculate S and H’. Compare your results to the values your instructor calculated for those samples. The following example should help: Suppose our samples contained 400 individuals in 10 species, and that taxa 1 through 10 were represented by 100, 80, 53, 41, 35, 33, 29, 14, 9 and 6 individuals, respectively. Table 1: Sample calculation of Shannon index (H’)
3. Figure 1: Plot the relationship of the Shannon index (y-axis) versus the area of cover item for each sample. For this and the other figures, you can plot the “under log” and “open” samples as different plots, or as two data series on the same plot.
4. Figure 2: Plot the relationship of the Shannon index (y-axis) versus the “isolation” (distance from nearest cover item) for each sample. 5. Figure 3: Make dominance-diversity curves for “covered” and “open” samples. Place the log (Abundance) for each species on the y-axis, and the species’ rank in terms of abundance on the x-axis. To make this plot, you’ll first have to sort the data with the most common species [2] first and the rarest species last. 6. Do Figures 1 and 2 support the predictions from island biogeography theory (see #1A and #1B)? Explain.
7. Do the data in Figure 3 support your hypothesis in #1C? Describe the ecological reasons (not methodological or error[3] ) why you think the dominance- diversity curves are different (if they are) for “under log” and “open” samples. Be sure to compare both the richness and evenness of the samples. Consider things like: degree of isolation from similar habitat, rate of desiccation of habitat, abundance or lack of food, abundance or lack of predators, abundance or lack of plants, etc. Be specific and refer to the names of actual taxa, rather than generalizing over all species. Spiders are very different ecologically from roaches!
References
Diamond, J.M., and R.M. May. 1981. Island biogeography and the design of natural reserves. Pages 228-252 In R.M. May, editor. Theoretical ecology: principles and applications. Blackwell scientific publications, Oxford, U.K.
Dunn, G.A. and D.K. Dunn. 1998. The insect identification guide. Fourth edition. Special Publication No. 6 of the Young Entomologists' Society, Inc., 1915 Peggy Place, Lansing, MI 48910-2553.
Gibb, T., & Oseto, C. (2010). Arthropod Collection and Identification: Laboratory and Field Techniques. Burlington: Elsevier Science.
Harris, L.D. 1984. The fragmented forest: island biogeography theory and the preservation of biotic diversity. Univ. of Chicago press, Chicago, IL.
Huffaker, C.B. 1958. Experimental studies on predation: dispersion factors and predator-prey oscillations. Hilgardia 27: 343-383.
Knowlton, N. 2001. Coral reef biodiversity – habitat size matters. Science 292: 1493-1495.
MacArthur, R.H. 1965. Patterns of species diversity. Biological Review 40: 510-533.
MacArthur, R.H., and E.O. Wilson. 1967. The theory of island biogeography. Princeton Univ. Press, Princeton, NJ.
Meffe, G.K., and C.R. Carroll, eds. 1994. Principles of conservation biology. Sinauer Associates, Sunderland , MA.
Simberloff, D., and L.G. Abele. 1976. Island biogeography theory and conservation practice. Science 191: 285-286.
Simberloff, D., and L.G. Abele. 1982. Refuge design and island biogeography theory: effects of fragmentation. American Naturalist 120: 41-50.
Watchman, L., M. Groom and J.D. Perrine. 2001. Science and uncertainty in habitat conservation planning. American Scientist 89: 351-359.
Explanations for your hypotheses should be based in IBT, especially in A and B
Note that the rankings will be different for the Covered and Open samples. In other words, you'll have to sort those data separately.
Not measurement error!

Categories
Biology

Post-lab Questions: 1. Describe the difference in thickness between the walls of

Post-lab Questions:
1. Describe the difference in thickness between the walls of the atria and ventricles. What is
the reason for the difference in thickness? (2 marks)
2. Describe the reason for the difference in the thickness between the walls of the left and right ventricles. What is the reason for this difference in thickness? (2 marks)
3. Which chamber is the largest and strongest? (1 mark)
4. Describe the difference in the thickness between the walls of the arteries and veins. What is the reason for the difference in thickness? (2 marks)
5. What is the function of the coronary vessels on the surface of the heart? (1 mark)

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Biology

First open then HW-Diversity file and follow the instructions in the file and an

First open then HW-Diversity file and follow the instructions in the file and answer all of the 7 questions. Once done then open the forestlitter_community file and read the instructions. Once done readinh the instructions then open the rank abundance file and read that. Then open the data file and go over that and then start working on the lab report. At the end you will be submitting two files. One will be the lab report and one will be the HW diversity. Make sure to read the instructions carefully and follow the instructions carefully please. Make sure you answer accordingly. Please let me know if you have any questions or concerns. Thank you so much.

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Biology

Following all the rules and guidelines, deal with one of the following topics: C

Following all the rules and guidelines, deal with one of the following topics:
Cellular structure and function;
Evolution and natural selection;
Heredity and genetics;
Ecosystems and interdependence
1Page Required

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Biology

Bacterial secretion systems (Type I, Type II, Type III, Type IV, Type V and Type

Bacterial secretion systems (Type I, Type II, Type III, Type IV, Type V and Type VI) are used by Gram-negative bacteria to secrete proteins outside the cell, or in some cases into another bacterial or eukaryotic cell.
Vibrio parahaemolyticus is a Gram-negative bacterium that inhabits warm, brackish coastal waters. It is found as a free-swimming organism in these waters, or attached to sediments, zooplankton, fish, or shellfish. V. parahaemolyticus is a human pathogen and can cause acute gastroenteritis due to the consumption of contaminated raw or undercooked seafood. In common with many Vibrio species, V. parahaemolyticus strains contain a number of secretion systems that are important for their free-living and pathogenic lifestyles. You are researching the V. parahaemolyticus strain ATCC 17802. The genome of this strain has been sequenced and is available in IMG (Genome ID = 2721755783). As part of your research you decide to analyse the secretome of this strain: that is, the set of proteins that are expressed by ATCC 17802 and secreted into the extracellular space. ATCC 17802 was cultured in Luria-Bertani broth (pH 8.5, 3% NaCl) at 37°C to mid-logarithmic phase. The bacterial cells were then removed by centrifuging and the extracellular proteins in the supernatant media were precipitated, separated by 2D PAGE and identified by LC-MS/MS Analysis. Table 1 (below) contains a subset of the identified extracellular proteins.
Table 1. Subset of proteins identified in the secretome of Vibrio parahaemolyticus strain ATCC 17802.
IMG Gene Locus Tag
Protein name
Ga0174928_112082
Asparaginase
Ga0174928_112444
Dihydrolipoyl dehydrogenase
Ga0174928_112183
Flagellar protein FliS
Ga0174928_121489
Flagellar protein FliS
Ga0174928_111901
Haemolysin-type calcium-binding repeat-containing protein
Ga0174928_12327
Putative exonuclease SbcC. Putative effector protein.
Ga0174928_111601
Type III secretion protein C (YscC outer membrane pore)
Ga0174928_111590
Type III secretion effector protein VopS (Vibrio outer protein S)
Ga0174928_111343
Type VI secretion system secreted protein Hcp
Ga0174928_12322
Type VI secretion system secreted protein Hcp
Ga0174928_111344
Type VI secretion system secreted protein VgrG
Ga0174928_12323
Type VI secretion system secreted protein VgrG
Ga0174928_12324
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain-containing protein, incolved in TypeVI secretion
Question 3.1. The haemolysin-type calcium-binding repeat-containing protein encoded by Ga0174928_111901 is a serralysin-like metalloprotease that contains several haemolysin-type calcium-binding repeat motifs (repeats-in-toxin (RTX) motifs) in the carboxy-terminal portion of the protein. Which type of bacterial secretion system is most likely used to secrete this protein? Briefly explain your choice. (2 marks)
Question 3.2.
The Hcp and VgrG proteins identified in the ATCC 17802 secretome are proteins that are exported via the Type 6 secretion system (T6SS). The proteins that make up the T6SS machinery have been characterised in the Cluster of Orthologous Groups (COG) categories. Table 2 is a list of the required Type VI Secretion System (T6SS) proteins and COG descriptors for each protein. Use the COG descriptors in Table 2 and the Function Cart tool in IMG to fill in Table 3 to identify genes encoding these T6SS components within the genome of ATCC 17802. (5 marks)
Table 2. List of the required Type VI Secretion System (T6SS) proteins, alternative names and Cluster of Orthologous Groups (COG) descriptors.
Tss/Tag
Alternative Name
COG
TssH
Clp, VasG
0542
TssD
Hcp
3157
TssL
IcmH, DotU, ImpK, VasF
3455
TssI
VgrG
3501
TssA
ImpA, VasJ/VasL
3515
TssB
ImpB, VipA
3516
TssC
ImpC, ImpD, VipB
3517
TssE
HsiF, ImpF
3518
TssF
ImpG, VasA
3519
TssG
ImpH ,VasB
3520
TssJ
Lip, SciN, VasD
3521
TssK
ImpJ
3522
TssM
IcmF, ImpL, VasK
3523
TagD
PAAR domain protein
4104
Table 3: List of genes that encode T6SS components in the genome of Vibrio parahaemolyticus strain ATCC 17802.
Tss/Tag descriptor
Alternative name
COG descriptor
IMG Locus Tag
TssH
Clp, VasG
0542
TssD
Hcp
3157
TssL
IcmH, DotU, ImpK, VasF
3455
TssI
VgrG
3501
TssA
ImpA, VasJ/VasL
3515
TssB
ImpB, VipA
3516
TssC
ImpC, ImpD, VipB
3517
TssE
HsiF, ImpF 3518
TssF
ImpG, VasA
3519
TssG
ImpH ,VasB
3520
TssJ
Lip, SciN, VasD
3521
TssK
ImpJ
3522
TssM
IcmF, ImpL, VasK
3523
TagD
PAAR domain protein
4104
Question 3.3. V. parahaemolyticus strain ATCC 17802 contains components for more than one T6SS. What information from Table 1 (Subset of proteins identified in the secretome of Vibrio parahaemolyticus strain ATCC 17802) indicates that both these T6SSs are functional and genes encoding both these T6SSs are expressed under laboratory conditions? (2 marks)
Question 3.4. Figure 1 (below) is a diagram of the T6SS. Identify the components that are indicated at the following places: (5 marks)
A. B.
C. D.
E.F. G.H.
I. J.
Figure 1. Diagram of the Type Six Secretion System
Question 3.5. Is the target cell illustrated in Figure 1 likely to be a Gram-negative bacterial cell or a eukaryotic cell? Explain your answer. (2 marks)
Question 3.6. The V. parahaemolyticus strain ATCC 17802 gene with locus tag Ga0174928_12327 encodes a putative exonuclease SbcC. This locus is downstream of the vgrG1 gene (locus tag Ga0174928_12323) in an operon. This putative exonuclease SbcC is present in the secretome of ATCC 17802 (Table 1) and has been identified as a putative effector protein. It is not present in the secretome of a ΔT6SS1/ ΔT6SS2 mutant of ATCC 17802.
You have created a knockout mutation in the gene encoding the exonuclease SbcC. Describe how you would set up an experiment to determine whether this protein is a bactericidal effector protein.

Categories
Biology

Advances in Biotechnology Over the last thirty years, our understanding of DNA h

Advances in Biotechnology
Over the last thirty years, our understanding of DNA has led to incredible advances in biotechnology. Genetic engineering involves altering an organism’s genes, adding new genes and traits to microorganisms, plants and even animals.
During this week’s discussion, you will choose to evaluate one of the following advances and respond to the questions listed.
Option 1: Cloning. In the mid-1990s, scientists proved convincingly that after decades of trying, we could indeed clone mammals — and even possibly, human beings. Learn about cloning, starting with the following resource:
National Human Genome Research Institute. (2020). Cloning Fact Sheet. http://www.genome.gov/25020028
Option 2: CRISPR-Cas9. CRISPR is one of the most fascinating breakthroughs in genetic engineering. This technology allows scientists to manipulate specific DNA sequences in the genome of an organism. Learn about gene editing and CRISPR, starting with the following resource:
Medline Plus. (2020, September 18). What are genome editing and CRISPR-Cas9? https://medlineplus.gov/genetics/understanding/gen…
Address the following questions based on the option you selected above. Then, throughout the week, review your classmates’ posts and comment as appropriate on at least two other posts per the Discussion Guidelines:
Provide a brief overview of the technology you selected.
What are the risks and benefits of the technology?
What are some potential uses for the technology?
Could you envision using cloning technology in your own life? If so, how?
What are some of the ethical problems with the use of the technology?
How do you feel about using this technology in humans?
Should the technology be regulated? Why or why not? If so, by whom?

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Biology

Provide the class with a brief overview of the article contents and then discuss the implications of the information presented.

Unit 6 Discussion
Seek out a current news article related to genetics. Try to find something that is new to science or breakthrough research. Provide the class with a brief overview of the article contents and then discuss the implications of the information presented.
Unit 7 Discussion
Watch the video, How we Study the Microbes Living in your Gut (https://www.ted.com/talks/dan_knights_how_we_study_the_microbes_living_in_your_gut ), by Dan Knights. Seek out information on what types of roles our gut flora plays regarding our health and well-being.

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Biology

Describe the difference between a zygote, embryo, and fetus.

Directions – Provide complete, thoughtful, and concise responses to the following prompts. Each of your responses should be approximately half a page in length and should demonstrate your understanding of the material to indicate your level of mastery of the concepts. (10 points each)
Define and describe the various types of symmetry found in animals. Which one is most associated with cephalization and why?
Animals reproduce both sexually and asexually. Define these terms and describe the advantages and disadvantages of each reproductive strategy. Although mollusks, nematodes, and arthropods have very different biology, each of these phyla are considered to be remarkably successful. Compare and contrast these organisms and discuss why these are successful?
Compare and contrast the quadrupedal vertebrates.
Animals are known for having highly differentiated tissue. Define and describe these and how they function together.
There are five major functions carried out by animals. What organ systems are involved in each of these functions?
Like plants, animals use hormones to direct growth processes. One important function of this is in sexual reproduction. What hormones are associated with female sexual function and how do they work in concert with one another?
Compare and contrast positive feedback loops and negative feedback loops with regard to homeostasis.
Describe the difference between a zygote, embryo, and fetus. What demarcates the difference in these stages of development?
How do ectothermic and endothermic organisms differ? What are the advantages and disadvantages of each?

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Biology

Consider all three genetic disorders, their symptoms, their severity, how likely each is to inherit, etc.

Attached is a case study also given at the end of Chapter 4 of your textbook. Read the case study carefully, trying to put yourself into the shoes of either Adam or Sarah. Consider all three genetic disorders, their symptoms, their severity, how likely each is to inherit, etc. Then answer the three questions at the end of the case study, following my guidelines below. This assignment involves both writing skills and pedigree analysis skills. Actions
For question 1: For the first question make sure you include Punnett square(s) and the math to determine the answer (Use whatever letters you’d like in your Punnett Squares, I used C and c for the cancer allele, and H or h for the heart disease allele.). You could either do 2 Punnett squares separately and then multiply the chance of each disease together OR combine the alleles into one Punnett square to determine the answer. If you need help, come to office hours. Are these good odds? Explain why you answered the way you did. For question 2: Write a well-written, thoughtful paragraph to answer these questions. Make sure you explain why you said yes or no to the two questions. It should contain no spelling or grammar errors, no run-on sentences, and make sense to the reader. Many of you struggle with these writing skills, so make sure you have someone else (a tutor, a friend, a family member) read your essay before you turn it in. (This answer is your opinion and you will not be graded on your opinion. I respect your right to feel the way that you do.)
For question 3: Again, in a well-written paragraph, answer each question here separately, supporting each answer with the chances of having a child in each situation.

Categories
Biology

Here is the website link about the beetle nursery “cribs” and the way they use dead animals to feed their young offspring larvae

Feel free to ask me any questions for clarification. We should work together to get a decent answer.
I will send you more helpful documents that will help you answer the questions.Introduction to the study and definition of animal behavior
Tinbergen’s four questions
Question: (a) State what you think is the scientific question the researchers were trying to answer with the data they collected in Figure A.
(b) State a realistic hypothesis they may have used to answer that question.
(c) In 1-2 sentence(s), what is the take-home message of Figure A?
I can provide all of the needed documents to answer this question. Here is screenshot from the textbook of Tinbergen’s Four questions
Here is the website link about the beetle nursery “cribs” and the way they use dead animals to feed their young offspring larvae
MACABRE STUDY SHOWS HOW BEETLES TURN CORPSES INTO NURSERIES THAT NEVER ROT
Some mothers will do anything for their kids.
https://www.inverse.com/article/49899-burying-beet…
Feel free to ask me any questions for clarification. We should work together to get a decent answer.
I will send you more helpful documents that will help you answer the questions.