Advanced Biology

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1. Enzymes (30pts).

Embryonic liver tissue contains an enzyme that catalyzes the reaction S→P. Adult liver also displays S→P

activity. Some kinetic data are shown below.

a) (20pts) What conclusion can you draw concerning the identity of the two enzymes?

What is the same or different about them and why might that be. (show all work for full credit)

 

During sever liver damage an enzyme (E1 from above) is released into the blood stream. After severe

exercise a muscle enzyme, Es that catalyzes the same reaction is released into the bloodstream.

Ei and Es can be differentiated easily because they have different Km values The Km of the muscle enzyme

is 2×10-5 M. An assay of the blood sample of a patient gave the results bellow

 

b) (10pts) Is the patient suffering from liver disease or have the simply been exercising two

strenuously, explain your answer (with any plots used for full credit)

 

 

 

 

2. Cell Metabolism (70pts). (refer to the tables at the end of the test to find values for the specific bacteria)

Aerobacter aerogenes is to be cultured aerobically, with glucose (C6H12O6) or pyruvate

(C3H4O3) as the growth substrate. Use the tables below to answer the following questions.

a. Setup (10pts): i) (3pts)Write the general Equation for Biosynthesis

 

 

ii) (3pts) What is the Empirical biomass formula of this species and what is its molecular weight?

 

 

iii) (4pts) What is the biomass degree of reductance of the biomass?

 

b) (15pts) Calculate the biomass yield per mole of glucose (you will need an empirical equation other than YX/S to do so). Show your work for full credit.

 

c) (15pts) Calculate the biomass yield per mole of pyruvate (you will need an empirical equation other than YX/S to do so). Show your work for full credit.

 

 

d) (30pts) i) (10pts)Compare the actual biomass yields per mole glucose or pyruvate to their

respective maximum theoretical yields.

 

ii) (5pts) Which growth substrate is more efficient with respect to biosynthesis?

iii) (10pts) Give two brief explanations why the answer to part a makes sense (or, make an educated guess as to which substrate is more efficient and justify your

answer).

iv) (5pts) Considering the case of growth on glucose, evaluate whether or not one can

expect significant amounts of secreted product(s), why?.

 
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Micro

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Please Pick 2 question to answer from each chapter and provide reference.

2 questions per chapter (chapter 15-20)  10 questions total. Word doc attached.

Chapter 15 

1.Explain the two main features that characterize the third line of host defense mechanisms.

2.Chronic lymphocytic leukemia (CLL) leads to the production of cancerous B cells, and treatment often involves bone marrow transplantation. Based upon your knowledge of lymphocyte development, explain how this procedure can lead to therapeutic effects in some patients.

3.Recently, scientists have been experimenting with using IRA-B cells as a treatment for hospitalized patients in an attempt to prevent them from getting septic infections. Speculate on what the principle behind this might be.

4.Provide an explanation to refute the following statement: Humans would never develop natural immunity to a novel biological agent created in a laboratory.

5.   a.Explain how the anamnestic response is triggered by vaccination. b.Conduct additional research and discuss one current example illustrating how lack of herd immunity within a population has led to localized disease outbreaks in the United States.

Chapter 16

1.Conduct additional research and discuss examples that illustrate how cancer can be both a cause of immune dysfunction and an effect of this process.

2.Summarize the roles of the microbiome and genetics in the development of type I allergic reactions. Discuss how probiotics or gene therapy could be used to alter an individual’s allergic response to antigen.

3.   a.Draw a diagram illustrating whether or not each of the following transfusions would be immunologically compatible. Type A donor into a type B recipient Type B donor into a type AB recipient Type O– donor into a type O+ recipient b.Explain how xenotransplantation might be successful in light of the immune system’s robust ability to recognize foreign antigen.

4.Summarize the role of the immune system in the development of type I diabetes. Propose a strategy that could be used to protect young children from developing an autoimmune reaction, and subsequently type I diabetes, after a viral infection.

5.A patient in your unit exhibits frequent bouts of microbial infections and is found to produce extremely low levels of IgG and IgM antibodies. Your colleague suggests that the patient receive numerous vaccinations against a broad spectrum of common pathogens; you disagree. Why? Explain another treatment that may be beneficial to this patient.

Chapter 17

1.Explain why specimens should be taken aseptically, even when nonsterile sites are being sampled and selective media are to be used, and explain why speed is important in the clinical testing process.

2.In the middle of an outbreak of measles (an infection that is highly communicable), a public health department is using immunologic testing to determine whether sick children have measles or not. If the children test positive, they are quarantined at home, and their contacts are counseled to update their MMR vaccine. In this situation, would you prefer to use a diagnostic test that is highly specific or one that is highly sensitive? Justify your answer.

3.Explain which type of ELISA can be used to determine an individual’s past exposure to a pathogen.

4.You are working at a health clinic, and a woman enters, suspecting that she was exposed to HIV two nights ago. a.Discuss whether or not she can be tested for HIV infection at this point. b.Summarize how you would respond to this patient, providing her with appropriate information regarding testing for HIV infection.

5.Compare and contrast the process of restriction analysis used in traditional DNA fingerprinting with the procedure used in pulse-field gel electrophoresis.

Chapter 18 

1.A young boy was at the playground when he felt a sharp pain on his leg. Upon inspection, his mother realized he had been stung by a bee. They went home and she carefully removed the stinger and washed the site well. Within a week, the site became swollen and painful; a red line appeared at the site, trailing up his leg.

a.Explain what condition the young boy appears to be suffering from and the most likely causative agent involved.

b.Discuss how the microbe may have gained access to the portal of entry.

2.A farmer working on a piece of machinery gets his shirtsleeve caught in a moving piece of the equipment. His shirt is sliced, and a sharp blade covered in mud slices through his upper arm. He attempts to control the bleeding and immediately seeks medical attention. After 3 days, he develops a fever and his arm becomes extremely swollen and painful. Pulling back the bandages, he finds that the wound has become blackened and is leaking a bloody fluid. Microscopic analysis of the fluid reveals the presence of gram-positive bacilli.

a.Discuss what condition the patient is suffering from and the likely causative agent of this infection.

b.Explain how the patient contracted this pathogenic microbe and what virulence factors contributed to the pathogenesis seen at the wound site.

c.In addition to antibiotics, the physician prescribes hyperbaric therapy. Describe what this treatment involves and how it could be therapeutic to this patient.

3.   a.Conduct additional research, and discuss whether “pox parties” represent a safe method of developing immunity to varicella zoster virus.

b.Provide evidence in support of or refuting the following statement: Shingles develops when you are reinfected with varicella zoster virus later on in life.

4.Smallpox has a rich history—from prompting the first vaccine to potential use as a bioterrorism agent. Given what you know about the etiology of the disease and the current state of the world’s immunity to smallpox, discuss how effective (or ineffective) a smallpox biological weapon could be against a human population.

5.Your coworker says that her spouse is in the hospital for elective surgery and his recovery is complicated by two infections: He has chicken pox all over the upper half of his body, and shingles on his legs. What questions will you ask for clarification?

Chapter 19

1.   a.Explain why the nervous system is described as “immunologically privileged,” and discuss whether this provides a beneficial or disadvantageous effect in this system.

b.Discuss the defenses a pathogen encounters as it attempts to gain entry into the nervous system.

2.Conduct research and summarize the causative agent and mode of transmission behind the multistate meningitis outbreak linked to steroid injections that occurred in 2012. How did improper physical and chemical control methods play a major role in this outbreak? Did portal of entry play any role?

3.Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy affecting white-tailed deer and elk. In 2005, venison from a deer testing positive for CWD was served during an annual wild-game dinner in the town of Verona in upstate New York. Based upon your knowledge of vCJD and related spongiform encephalopathies and any additional research you conduct, discuss whether any of the attendees are at risk for developing disease in the future.

4.As you learned in section 8.3, many types of fruits and vegetables can be fermented into alcoholic beverages. Such was the case recently when prisoners in Utah attempted to make an illegal beverage called “pruno”; however, someone added a weeks-old baked potato to the mix, letting a microbe into the party who was clearly uninvited. Consumers of the pruno began to develop difficulty swallowing, vomiting, double vision, and muscle weakness; three required ventilation therapy. No deaths were attributed to the contaminated beverage.

a.What disease were the prisoners suffering from, and what was the causative agent involved?

b.Based upon your knowledge of this disease, what form of treatment was used to successfully avoid the worst outcomes of the disease in these patients?

5.In August 2011, a soldier from Fort Drum in Watertown, New York, tested positive for rabies; he died less than 3 weeks later. Further investigation revealed that he actually became infected when he was bitten by a dog in January of the same year while stationed in Afghanistan. Discuss any risks the soldier posed to his platoon, explaining whether or not this fatal outcome could have been avoided.

Chapter 20 

1.Explain why cases of dengue fever have been observed beyond endemic regions of the world today. Discuss whether or not completely eradicating mosquito (vector) populations from disease-ridden areas is advisable.

2.   a.Discuss whether or

not genetics plays a role in HIV infection, providing at least one example to illustrate your position.

b.Provide evidence in support of or refuting the following statement: An HIV-positive individual will always harbor the virus even if no viral load is detectable by PCR or other methods.

3.Explain why over the years the incidence of HIV infection has declined in the United States while the prevalence of AIDS has increased.

4.   a.Compare and contrast various characteristics of hemorrhagic and non hemorrhagic fever diseases.

b.Provide an explanation for the observed increase in incidence of these zoonotic infections around the world today.

5.Several pathogens in this chapter are listed as Category A bio weapons by the Centers for Disease Control and Prevention (CDC). What characteristics of the pathogens in this chapter make them suited for mass infection with high mortality?

 
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Homework

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Gender is determined by father, because he can give either the X or the Y chromosome.

It is estimated that from 10-20% of all human fertilized eggs contain chromosome abnormalities, and these are the most common cause of pregnancy failure.

These chromosome abnormalities:

● arise from errors in meiosis, usally meiosis I; ● occur more often (90%) during egg formation than during sperm formation; ● become more frequent as a woman ages. ● Aneuploidy – the gain or loss of whole chromosomes – is the most common chromosome

abnormality. ● Aneuploidy is caused by nondisjunction, the failure of chromosomes to separate correctly

o homologues during meiosis I or o sister chromatids during meiosis II

● Zygotes missing one chromosome (“monosomy”) cannot develop to birth (except for females with a single X chromosome).

● Three of the same chromosome (“trisomy”) is also lethal except for chromosomes 13, 18, and 21 (trisomy 21 is the cause of Down syndrome).

● Three or more X chromosomes are viable because all but one of them are inactivated.

X-Inactivation Human females inherit two copies of every gene on the X chromosome, whereas males inherit only one (with 18 exceptions: the 9 pseudoautosomal genes and the 9 “housekeeping” genes found on the Y). But for the hundreds of other genes on the X, are males at a disadvantage in the amount of gene product their cells produce? The answer is no, because females have only a single active X chromosome in each cell. During interphase, chromosomes are too tenuous to be stained and seen by light microscopy. However, a dense, stainable structure, called a Barr body (after its discoverer) is seen in the interphase nuclei of female mammals. The Barr body is one of the X chromosomes. Its compact appearance reflects its inactivity. So, the cells of females have only one functioning copy of each X-linked gene – the same as males. X-inactivation occurs early in embryonic development. In a given cell, which of a female’s X chromosomes becomes inactivated and converted into a Barr body is a matter of chance (except in marsupials like the kangaroo, where it is always the father’s X chromosome that is inactivated). After inactivation has occurred, all the descendants of that cell will have the same chromosome inactivated. Thus X-inactivation creates clones with differing effective

 

 

gene content. An organism whose cells vary in effective gene content and hence in the expression of a trait, is called a genetic mosaic.

X-Chromosome Abnormalities:

As we saw above, people are sometimes found with abnormal numbers of X chromosomes. Unlike most cases of aneuploidy, which are lethal, the phenotypic effects of aneuploidy of the X chromosome are usually not severe. Examples:

● Turner’s syndrome X0 (2n= 45): females with but a single X chromosome. The phenotypic effect is mild because their cells have a single functioning X chromosome like those of XX females. Number of Barr bodies = zero.

● XXX, XXXX, XXXXX karyotypes: all females with mild phenotypic effects because in each cell all the extra X chromosomes are inactivated. Number of Barr bodies = number of X chromosomes minus one.

● Klinefelter’s syndrome (2n= 47): people with XXY or XXXY karyotypes are males (because of their Y chromosome). But again, the phenotypic effects of the extra X chromosomes are mild because, just as in females, the extra Xs are inactivated and converted into Barr bodies.

Genetic Disorders – Diseases resulting from abnormalities in human genes

• Mutation in a single gene – absence or alteration of a protein. Ex. Hemophilia • Chromosomal disorder – Duplication, loss, or breakage. Ex. Down Syndrome

There are many genetic diseases and disorders (See Hand Out). Some are:

• Down Syndrome • Sickle cell anemia • Hemophilia • Fanconi’s anemia • Cystic fibrosis

Many Gross Chromosomal abnormalities don’t cause death and are sex chromosome related. Karyotypes are used to look at chromosome shape and to ensure there are no abnormalities with the fetus. This is done by looking at the embryo’s amniotic fluid (amniocentesis).

 

 
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Need Help With Biology Assignment

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Biodiversity Lab DOMAIN BACTERIA Bacteria are incredibly diverse, but they’re usually really tiny and hard to see, even under a standard microscope. On an agar plate, bacteria have the nutrients to divide quickly, eventually leading to clusters of rapidly dividing cells, or colonies, that are visible to the naked eye. Cyanobacteria, were the only lineage of organisms to evolve the complicated process of photosynthesis from scratch and, in doing so, oxygenated the Earth’s atmosphere paving the way for the evolution of Eukaryotes. Some Cyanobacteria, such as Nostoc and Anabaena, adhere to one another as they divide and form colonies that look like multicellular “algae” to the naked eye, thus leading to the common name “blue-green algae”. In low nitrogen environments, some of the cells in the colony will even change function to become anatomically different cells specialized for nitrogen fixation, which benefits the entire colony. Some other types of Cyanobacteria are

responsible for algal blooms that release toxins and gases that can be fatal to mammals such as dogs and humans. DOMAIN ARCHAEA Archaea are mostly tiny and hard to see, like bacteria. Most are also extraordinarily difficult to cultivate due to their extremophile lifestyles- thriving in extreme conditions that other organisms can’t tolerate. While we can’t replicate an anoxic or deep sea environment in the lab, we can replicate an extremely salty environment that halophilic Archaea such as Halobacterium prefer but which is toxic to nearly all other forms of life.

Many colors of life from left to right: 1. Anabaena, a photosynthetic blue-green alga (Domain Bacteria); 2. Halobacterium, a halophilic

Archaea; 3. Acrochaetium, a multicellular red alga (Archaeplastida); 4. Chlamydomonas, a single-celled, free swimming Chlorophyte

green alga (Archaeplastida); 5. Ectocarpus, a brown alga (Stramenopiles, S.A.R. clade)

 

 

 

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Eukaryotes EUKARYOTE SUPERGROUPS The best evidence from DNA sequences supports 4 major lineages within domain Eukarya; Excavata, S.A.R. Clade, Archaeplastida, and Unikonta. Excavata: -Euglena is a flagellated, photosynthetic Excavata that acquired its chloroplasts by endosymbiosis of a unicellular green alga (see Archaeplastida). They can move surprisingly fast, as you can see in this video: https://youtu.be/upPgx3GyBjQ Other lineages in Excavata cannot photosynthesize and must consume their food as existing organic matter. Some even use humans as food, such as the brain-eating amoeba Naegleria fowleri and the organisms that

cause the diseases African Sleeping Sickness and Chagas. S.A.R. Clade: Stramenopiles: – Diatoms produce cases made of silicon; they are photosynthetic and are important at the base of the food chain in both freshwater and saltwater aquatic environments. Brown algae are also in this group, ranging from single-celled to colonial to filamentous mulicellular organisms all the way to huge kelp almost 200 ft long.

Brown algae are large, multicellular Stramenopiles (S.A.R.)

Alveolates: -Paramecium is a heterotrophic (=must feed on organic matter) ciliate that lacks chloroplasts and uses small hair-like cilia to move around with amazing speed and agility for a single-celled organism as shown in this video: https://youtu.be/mFSIUuT0EgM -Dinoflagellates are photosynthetic flagellates that in high density cause toxic “red tides”. Some are also bioluminescent when agitated, as you can see in this video: https://youtu.be/5MiUxopM5VM

 

 

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Node #4, Stramenopiles+Alveolates, is often referred to as the group Chromalveolata, the ancestor of which likely picked up photosynthetic plastids by engulfing a unicellular Red Alga (see Archaeplastida). Rhizaria: -Foraminiferans most often make shells of Calcium Carbonate. Rhizaria extend long pseudopods out of these shells to gather food. One lineage of Rhizaria is photosynthetic by way of chloroplasts acquired through endosymbiosis of a unicellular green alga (Archaeplastida). Archaeplastida: Includes Red Algae, Green Algae, and plants; all red algae, green algae, and plants descended from a common unicellular ancestor at node 5 that engulfed a photosynthetic Cyanobacterium which became the earliest plastids in eukaryotes.

Embryophytes: (nonvascular) -Liverworts and Mosses spend the majority of their life cycle as haploid gametophyte plants that produce sperm and egg, with a short-lived diploid sporophyte life stage that produces and disperses spores

The diploid sporophytes of mosses (left) often look like upside-down golf clubs, but the main body

of the plant is haploid. In hemisphaeric liverwort (center), the diploid sporophyte

generation only exists as short-lived, round yellow globes that produce spores (right)

 

(vascular spore plants) -Lycophytes and Ferns still reproduce by spores like nonvascular plants and algae, but in vascular plants the diploid sporophyte life stage grows large and the haploid, gametophyte stage of the life cycle is usually small and short-lived

 

 

 

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Spikemosses (left) are diploid and produce spores. Ferns usually produce spores under their leaves (center). On the right, a dark green,

haploid fern gametophyte will soon be overgrown by the light green diploid sporophyte producing its first leaf. (seed plants- Gymnosperms) -Cycads are often called Sago Palms, although real palm trees are angiosperms that flower and fruit. -Ginkgo is represented by a single modern species; 270 million year-old fossils look identical (stasis). -Conifers are the largest group of living gymnosperms; most are needle-bearing evergreens. -Gnetophytes: Welwitschia mirabilis is a Namib Desert plant that only makes two continuously-growing leaves throughout its life

Representatives of the 4 extant Gymnosperm lineages (seed plants-Angiosperms) -Amborella trichopoda: All other 250,000+ species of flowering plant are more closely related to each other than they are to this woody shrub from the south pacific island of New Caledonia. -Monocots usually produce flower parts in 3’s or multiples thereof and parallel-veined leaves. Orchids are the largest family of monocots with over 25,000 species, and grasses are another huge family that provides most calories consumed by the human population (sugarcane, corn, wheat, oats, barley, rice, etc.) -Eudicots: Usually flower parts in 4s and 5s, net-veined leaves. The Sunflower family is the largest family of eudicots (and flowering plants overall) with more than 30,000 species. The “flowers” of members of the sunflower family are actually aggregations of up to hundreds of flowers.

 

 

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Amborella (left); representative eudicot and monocot flowers and fruits (right) Unikonta: The first major division in Unikonta (node 6) separates Amoebozoans from Opisthokonts. -Amoebozoans: Chaos carolinensis is a large amoeba that changes cell shape to extend pseudopods and engulf potential food particles for internal digestion as seen in this video: https://youtu.be/zgtWbJ2wSeg Fungi: Fungi range from unicellular (yeasts) to huge multicellular organisms, most of which grow as long, filamentous strands of cells known as hyphae. Masses of hyphae that are visible macroscopically are known as a mycelium. -Lichens: Lichens are actually a symbiotic relationship between two different supergroups: fungal hyphae (Unikonta) and a unicellular photosynthetic organism, usually a green alga (Archaeplastida). The hyphae farm the green alga as a carbon source while providing inorganic nutrients to the alga by slowly breaking down rock, bark, mineral soil, and other substrates.

(left) Lichens can be found growing on bark, rocks, or bare ground; even though they are given scientific names, they are really an

ecosystem of multiple organisms living together closely. (right) Giant puffball mushroom growing in lawn grass. -Mushrooms: Most mushrooms form from a dikaryotic mycelium; the hyphae forming the mycelium originate from fusion of hyphae from two haploid individuals. After these fuse, each cell of the dikaryotic mycelium contain two separate haploid nuclei and grow into a fruiting body. In surfaces that generate spores, individual

 

 

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cells will fuse the haploid nuclei into a zygote where recombination can occur. The zygote then undergoes meiosis to generate haploid spores that can disperse to grow haploid hyphae with new genetic combinations of both parents. -Molds are mycelia with filamentous hyphae that invade their substrate and secrete digestive enzymes to break down the substrate before absorbing small molecules. Animals: Animal phylogeny and diversity is mapped on its own tree. Keep in mind that the closest relative of animals in Unikonta are single-celled Choanoflagellates, and the closest relatives of fungi are single-celled Nucleariids. Thus, animals and fungi evolved multicellularity independently from one another. Animal lineages represented in the tree are listed below: Phylum Porifera: Sponges Phylum Cnidaria: Jellyfish, Hydra, Corals, etc. Deuterostomes: Phylum Hemichordata: Acorn Worms Phylum Echinodermata: Sea Stars, Sea Cucumbers, Sea Urchins Phylum Chordata: Cephalochordata: Lancelets/Amphioxus Tunicata: Tunicates, Sea Squirts Cyclostomes: Jawless Fish (Hagfish, Lamprey) Chondrichthyes: Cartillaginous Fish (Sharks, Rays) Actinopterygii: Ray-finned Fish, the most diverse lineage of vertebrates Dipnoi: Lungfish Amphibia: Caecilians, Salamanders, Frog & Toads Reptilia: Turtles, Lizards, Snakes, Crocodilians, Birds Mammalia: Mammals Lophotrochozoa: Phylum Platyhelminthes: Flatworms Phylum Mollusca: Clams, Oysters (bivalves), Snails, Slugs (gastropods), Octopus, Squid (Cephalopods) Phylum Annelida: Segmented Worms Ecdysozoa: Phylum Nematoda: Roundworms Phylum Arthropoda: Subphylum Chelicerata: Horseshoe Crabs, Ticks, Mites, Spiders, Scorpions Subphylum Myriapoda: Centipedes, Millipedes Subphylum Crustacea: Crabs, Shrimp, Pillbugs, Barnacles, etc. Subphylum Hexapoda, Class Insecta: Insects (well over half of all described animal species)

(left) Insects like this Pipevine Swallowtail make up more than half of all named animal species. Ray-finned fish, like the Etowah Darter (center) are the most diverse lineage of vertebrates. Birds, including Burrowing Owls (right), are the most diverse land vertebrate lineage.

 

 

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QUESTIONS Use the phylogenetic trees at the end of this pdf to answer the following questions. Clicking on the lineages on the phylogenetic trees will take you to the Wikipedia entry for that group. 1. Which node in the 3-domain supertree (the first tree) represents the common ancestor of eukaryotes and Archaea? Which node in the 3-domain tree represents the common ancestor of all Eukaryotes? What are some characteristics that would have been present in the common ancestor of all eukaryotes? Think about characteristics that are shared between your cells and the cells of all these other groups (2 pts).

2. List all of the acquisitions of photosynthetic found in eukaryotes below (give either the numbered node where it evolved or the name of the lineage in which it occurred) (2 pts). 3. Unikonta don’t have any true chloroplasts or photosynthetic lineages, but describe the similarities and differences between Lichens and chloroplast-containing eukaryote lineages. (1 pt) 4. Identify the node in the Archaeplastida phylogeny where the diploid sporophyte generation became the dominant stage in the life cycle (1 pt). 5. Identify the node in the Archaeplastida phylogeny where land plants evolved. (1 pt) 6. Which node represents the most recent common ancestor of Seed Plants? (1 pt)

 

 

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7. Which node represents the most recent common ancestor of Gymnosperms. Conifers are, by far, the most species-rich lineage of modern Gymnosperms; do you think the most recent common ancestor of seed plants would have had needles like a pine tree or broad leaves more like most angiosperms? (2 pts) 8. Which node is the most recent common ancestor of Angiosperms (flowering plants)? These are now the most species-rich lineage of embryophytes by far with approximately 350,000 species. Most of these species (including all monocots) are herbaceous, meaning they don’t form a woody trunk with internal vascular rings or bark Amborella trichopoda is a shrub from New Caledonia that represents the basal branch of Angiosperms (i.e. all other flowering plants are more closely related to each other than they are to Amborella). Do you think the ancestor of angiosperms was woody or herbaceous? What about the ancestor

of all seed plants? (hint: Amborella, Ginkgo, all conifers, Gnetophytes, and Cycads have woody “trunks”)? (2 pts) 9. Sponges have specialized individual cells but lack true tissue (masses of coordinated cells, like muscle, nerve, etc.). At what node in the animal phylogeny did true tissues evolve? (1 pt) 10. At what node in the animal phylogeny did bilateral symmetry evolve (hint: sponges and cnidarians aren’t bilaterally symmetric, but every other organism on the animal tree technically is)? Bilaterally symmetric animals have a left and right side, as well as a dorsal and ventral side. Based on the organisms on this tree, what do you think this bilateral common ancestor may have looked like? (2 pts) 11. You have two forelimbs (arms) and two hindlimbs (legs). At which node in the phylogeny did these paired appendages evolve? Are there any instances of convergent evolution of paired appendages? Are there any instances of losses of paired appendages? Give the examples, if they exist (2 pts).

 

 

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12. Identify the node in the phylogeny where your ancestor first colonized land (hint: this is also the common ancestor of organisms with fingers and toes). Give an example of a descendant from that ancestor that has gone back to living a fully aquatic lifestyle. List any other examples of animal lineages that appear to have colonized land independently of your ancestor (2 pts). 13. Are fish (i.e. jawless fish, cartilaginous fish, ray-finned fish, and lungfish) monophyletic? i.e. Do they trace

back to a single common ancestor, and are all descendants of that most recent ancestor considered fish? (1 pt). 14. Chambered Nautilus is the first-branching lineage of Cephalopods. Do you think Octopuses/Octopi evolved from a shelled ancestor? Explain why or why not (1 pt). 15. List all of your ancestors (list of node numbers) from both the animal tree and the 3-domain tree. (2 pts). 16. Go outside and take photographs of 4 different organisms, each representing a different terminal group on the tree. Identify where they belong on the tree and submit photographs. A maximum of 2 animals or 2 plants are allowed, and at least one of your selections must be something other than an animal or plant. (2 pts)

 
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Pathophysiology Week 10, Question 1 And 2

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Question 1

Ophthalmic Disorders

Mr. Ally went to the eye doctor and complained about dark areas in his vision. He had never noticed it before. There is no pain.

  • What is the diagnosis?
  • Explain the reason behind floaters and dark areas in the visual field.
  • How should the doctor treat Mr. Ally?

Question 2

Case Analysis:

Ear Disorders

A 32-year-old man has vertigo, nausea, and hearing problems. He was diagnosed with Meniere’s syndrome.

  • What causes the vertigo in this patient?
  • How should this patient be treated?

 

  • Why might there be permanent loss of hearing and loss of equilibrium?
 
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Biology MCQs Test Bank

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1. Overall success rates for clinical research grants are lower than success rates for basic research grants because:
a.  Clinical research grants are assigned to study sections with inappropriate scientific expertise
b.  Clinical research grants are harder to design well and the Principal Investigator may give up rather than revise and resubmit their application
c.  Clinical research grants have higher requested budgets and do not do as well during review
d.  All of the above
e.  None of the above
2. Which of the following statement(s) about the NIH Dual Review System is TRUE?
a.  The Scientific Review Group constitutes the first level of review
b.  The Advisory Council constitutes the second level of review
c.  The Scientific Review Group makes funding decisions
d.  a and b
e.  a, b, and c are all true
3. Which of the following statements about the first level of review is FALSE?
a.  The NIH Scoring Scale goes from 1 to 9
b.  There are five “core” review criteria: Significance, Investigator, Innovation, Approach, Environment
c.  The Overall Impact Score is determined by averaging the sub scores for the five “core” review criteria
d.  Appropriateness of the Budget does not affect the Overall Impact Score
e.  The Review Group can defer the review of an application if they need more information to score it
4. A successful grant submission include(s):
a.  Understanding the psychology of the review process
b.  Beginning the submission process early
c.  Performing a critical self-assessment
d.  Examination of currently funded research in the area
e.  All of the above
5. Which of the following is NOT an example of a source document?
a.  Pathology report
b.  A handwritten daily diary maintained by the patient
c.  Nurse’s notes in the medical record
d.  A worksheet that has recorded a patient’s height and weight abstracted or taken from data in the medical record.
6. An event that prolongs a hospitalization is considered a serious adverse event:
a.  True
b.  False
7. What best describes a properly designed Case Report Form (CRF)?
a.  Collects relevant data in accordance with the protocol
b.  Allows for efficient and complete data processing and analysis
c.  Facilitates the pooling of data across studies
d.  All of the above
8. When collecting key data on the Case Report Form (CRF) for analysis, all of the following are true, EXCEPT:
a.  Provide consistent units of measure to ensure comparable values
b.  Include multiple open ended questions with free-textual responses
c.  Provide choices to questions to allow for efficient summarization
d.  Avoid collecting the same data in different parts of the CRF
9. It is the research nurse’s responsibility to determine whether an adverse event is related to the medical treatment of procedure?
a.  True
b.  False
10. When preparing a budget for a clinical trial, what should you consider?
a.  The effort of the coordinator and Principal Investigator (PI)
b.  The procedures that will be done by another department
c.  The overhead of your organization
d.  All of the above
e.  None of the above
11. To protect the liability of your patient and your organization, what can you do?
a.  Pre-certify each patients insurance coverage as it pertains to research participation
b.  State clearly in the informed consent what items will be paid for by the study budget, and what items will be the patients responsibility
c.  Set up in advance of enrollment a way to capture study patients in the billing system to prevent double billing
d.  All of the above
e.  None of the above
12. What does double dipping refer to?
a.  An ice cream cone dipped in chocolate twice
b.  Placing both feet in the pool at the same time
c.  Having the cost of a research procedure covered in the study budget, and also billing the patient’s insurance
d.  All of the above
e.  None of the above
13. Epidemiology assumes disease has causal and preventative factors that can be identified through systematic investigation.
a.  Yes
b.  No
14. Which of the following is most likely a case series study
a.  Report of 5 cases of pneumocystis pneumonia in previously healthy homosexual men
b.  National survey of health and nutrition
c.  Association study of maternal use of stilbesterol with tumor appearance
d.  Observational study of cardiovascular health in men and women over 65
15. Which of the following statements about control groups or control arms in a study is FALSE
a.  Control groups can take many different forms
b.  The specific question being addressed in the study directs the choice of the control group or groups for the study
c.  All good studies have a placebo control arm
d.  A randomized study’s control group should be an ethical option for study participants
16. Mark the TRUE statement about Blinding/Masking
a.  All of these statements are true
b.  A purpose of blinding or masking is to reduce the possibility of expectancy bias impacting study outcomes.
c.  There are almost always design features that can be implemented to at least partially mask a study.
d.  A few of the different labels applied to studies include double-blind, single-masked, assessor-masked, unmasked, or open-label.
e.  Protocols should clearly specify who is masked, why, to what information each person is masked, and the criteria for unmasking.
17. Which of the following is a type of randomized study
a.  Group sequential trial
b.  Historical control study
c.  Cohort study
d.  Case-control study
18. Which item(s) below are motivations and features of randomization
a.  Helps reduce selection bias when allocating participants to study arms
b.  In double blind studies helps eliminate patient response bias
c.  Attribute causality
d.  Try to ensure only one factor is different between two or more groups
e.  All of the above
19. Which of the following is NOT a legitimate way to randomize
a.  Using stratified randomization by clinical center
b.  Using the last digit of the medical record number
c.  Varying block size while using blocked randomization
d.  Randomizing each patient to a treatment with a known probability
20. What does failing to reject Ho (the null hypothesis) mean?
a.  There is not enough evidence in your sample to reject the null hypothesis
b.  The null hypothesis is true
c.  The deviation from the null might be too small to detect reliably with the study’s sample size
d.  a and c
21. The null hypothesis for a study is the mean systolic blood pressure (SBP) in the control group is equal to (the same) as the mean systolic blood pressure in the experimental intervention group. Which one of the following statements is an accurate interpretation of the p-value that comes from testing this hypothesis?
a.  The p-value is the probability that the null hypothesis is true
b.  The p-value is a measure of the strength of evidence in the study’s data that the null hypothesis is not true
22. What is the positive predictive value?
a.  The probability of testing positive if truly diseased; does not depend on disease prevalence in the population
b.  The probability of being diseased given a positive test result; depends on disease prevalence in the population
c.  The probability of being diseased given a positive test result; does not depend on disease prevalence in the population
d.  A statistic regularly used in the analysis of both cohort and case-control study designs
23. Suppose a study comparing the effects of two treatments on systolic blood pressure requires approximately 50 patients in each treatment arm to statistically detect a TEN point difference (2-sided t-test at significance level of 0.05 and power of 80%). Approximately how many patients in each treatment arm would be required in each treatment arm to detect a FIVE point difference?
a.  100
b.  200
c.  400
d.  Cannot be determined – one needs to know the common standard deviation of the measures
e.  Can be determined, but one needs special power tables to calculate
24. The basic formulas for sample size use which of the following
a.  Type I error
b.  Type II error
c.  Variance
d.  Difference (effect) to be detected
e.  All of the above
25. What can change a study’s power and how is power impacted
a.  Sample size (n): power increases as sample size increases
b.  Difference (effect) to be detected (δ): power increases as this difference increases.
c.  Variation in outcome (σ2): power decreases as an outcome’s variance increases
d.  All of the above
26. In order to define the survival outcome variable we do NOT need to define which of the following?
a.  The event
b.  The time origin
c.  The time scale
d.  The covariates
e.  The time at which an event occurs
27. You are reviewing a manuscript with the results of an observational study that looked at survival for several groups. The statistical methods section states stratified logrank tests were performed to compare overall survival between groups. The figures include several Kaplan-Meier curves and reports the p-values from the logrank tests. The manuscript does not mention any other statistical methods. What other statistical analysis method could you recommend be used before making conclusions about the study results?
a.  The answer is always the same regardless of the statistical analysis method. Kaplan Meier, any type of Cox regression, logistic regression, it does not matter which type of analysis is used to evaluate the time-to-event or survival data
b.  The Cox proportional hazards model is the best method to use for time-to-event analyses. You can always assume proportional hazards
c.  Cox models can be used to analyze the study data. Cox models can be used to make inference about continuous and categorical covariates such as age and gender in time-to-event models. For consistent unbiased estimates the Cox model requires independent censoring, either directly or given the covariates in the model. The proportional hazards assumption should be evaluated because it may not be true. There are Cox models that do not assume proportional hazards. Also, depending on the study design there are other statistical analysis methods that may be appropriate
28. Does the Kaplan Meier have a sensible interpretation for competing risks?
a.  Yes
b.  No
29. When talking to a reporter it is important to be aware of terms of the journalistic trade. What does “On the Record” mean?
a.  This means that a reporter cannot use your information in a story as coming from you; however, the reporter can use it in other ways such as getting another source to respond to your comment
b.  This means that the reporter can use the information you give, including direct quotes, but you are not to be named. You may be identified as a NIH scientist, or a knowledgeable NIH source
c.  This means that a reporter can quote you directly, using your name and title
30. When talking to a reporter it is important to be aware of terms of the journalistic trade. What does “not for attribution and on background” mean?
a.  This means that a reporter cannot use your information in a story as coming from you; however, the reporter can use it in other ways such as getting another source to respond to your comment
b.  This means that the reporter can use the information you give, including direct quotes, but you are not to be named. You may be identified as a NIH scientist, or a knowledgeable NIH source
c.  This means that a reporter can quote you directly, using your name and title
31. When talking to a reporter it is important to be aware of terms of the journalistic trade. What does “Off the Record” mean?
a.  This means that the a reporter cannot use your information in a story as coming from you; however, the reporter can use it in others ways such as getting another source to respond to your comment
b.  This means that the reporter can use the information you give, including direct quotes, but you are not to be named. You may be identified as a NIH scientist or a knowledgeable NIH source
c.  This means that a reporter can quote you directly, using your name and title
32. Despite the ground rules, when talking to a reporter it is always best to be?
a.  On the record
b.  Not for attribution and on background
c.  Off the record
33. The United States’ Freedom of Information Act (FOIA) provides individuals with a right to access records in the possession of the federal government. Which item best describes what may be available under the FOIA?
a.  Minutes of NIH Institution Review Boards
b.  Your computer files
c.  Document drafts
d.  Your e-mail messages
e.  Approved research protocols
f.  All of the above
34. Under the United States’ Freedom of Information Act a document stamped “Confidential” may still be released to the requester
a.  True
b.  False
35. The best response for you to give when a reporter contacts you directly is?
a.  “Sure, I can talk with you right now. What would you like to talk about?”
b.  “I’d be happy to talk with you, but I am not allowed”
c.  “I’d be happy to talk with you. Would you coordinate this with my Communication Office?”
36. Which of the following is a key component of a good outcome measure?
a.  Cohen’s d
b.  Sensitivity to change
c.  Ratio scale
d.  Depression
37. Which of the following characteristics are the most important in determining a good measure?
a.  Cost and categorization
b.  Feasibility and frequency of publication
c.  Scale and specialization
d.  Reliability and validity
38. Community-Based Participatory Research (CBPR) is only applicable to descriptive research to identify the social determinants of health.
a.  True
b.  False
39. CBPR is only qualitative research methods used to study community health problems.
a.  True
b.  False
40. What is the reason NIH requires the inclusion of women and minorities in all clinical research?
a.  Legal requirement as a result of the 1993 NIH reauthorization
b.  NIH policy
c.  Ethical principle of justice
d.  All of the above
41. Since the implementation of the inclusion policy:
a.  Knowledge has been gained about differences in cardiovascular symptoms between men and women
b.  More research participants from minority groups have participated in clinical research
c.  More women than men have participated in clinical research
d.  All of the above
42. A university scientist has discovered a compound that may be an important new drug, the compound has not yet been disclosed publicly, but a manuscript is being prepared. The scientist needs to conduct certain additional experiments, but is unfamiliar with the technical procedures. Fortunately, the scientist knows a colleague, now working at a company, who is an expert at those techniques. The scientist wants to send a sample to the colleague to conduct those tests on the compound. Which one of the following statements is TRUE?
a.  The scientist should send a sample of the compound to the colleague now; any necessary paperwork can be done later, when it is more convenient
b.  The scientist likely is not authorized to send a sample to the colleague until a Material Transfer Agreement has been executed by the scientist’s employer and the colleague’s Company
c.  The scientist and the colleague should personally execute a Confidential Disclosure Agreement before discussing the compound
d.  The colleague, on behalf of the company, must file an Employee Invention Report on the scientist’s compound as quickly as possible
e.  The parties must negotiate a full Cooperative Research and Development Agreement (CRADA) to allow the company to pay for the scientist’s efforts
43. A scientist at NIH wants to get a sample of a patented compound from a company. The company is willing to send the compound if the scientist signs a form. The form says that (1) the recipient may not distribute the materials further, (2) the company owns any inventions the recipient develops, and (3) the recipient agrees to indemnify the company. Which one of the following should the scientist do?
a.  Send the form to the NIH scientist’s Technology Transfer office or General Counsel’s office, and wait for them and the company’s attorneys to work something out
b.  The NIH scientist should sign the company’s form on behalf of the NIH and hope no one at the company realizes the scientist is not authorized to sign to sign the form.
c.  Get the sample from a colleague at a nearby university, who signed the company’s form, if the university colleague will not make the scientist sign anything
d.  File an Employee Invention Report on the compound as quickly as possible, and attach any relevant background materials
e.  Sign a copy of the US Public Health Service (PHS) Model Cooperative Research And Development Agreement (CRADA) and send it to the company for counter-execution
44. A scientist at NIH and a colleague at a company have been working together on a project established under an approved, duly executed CRADA. During the project, the colleague shows the NIH scientist a draft (unfiled) patent application for something the colleague and the NIH scientist both believe they co-invented. The scientist should do which of the following?
a.  Post the draft patent application on the Internet immediately, because NIH policy favors publication at the soonest possible opportunity
b.  Buy stock in the colleague’s company before the invention has been publicly disclosed
c.  Sign a Uniform Biological Material Transfer Agreement immediately to document the transfer rights
d.  Forward the draft to the NIH scientist’s Technology Development Coordinator to determine what the NIH wants to do about the invention
e.  Do nothing – under a CRADA, the company automatically owns all inventions and NIH no longer has to worry about such inventions
45. In order to strengthen certain literature searches for potential side effects, Johns Hopkins University recommended that investigators collaborate with which two of the following: 1) a board-certified physician with a relevant specialty 2) a pharmacist 3) a senior MD/PhD researcher with a relevant specialty 4) a librarian 5) a PhD chemist with a relevant specialty
a.  1 & 2
b.  1 & 4
c.  2 & 3
d.  2 & 4
e.  2 & 5
46. Which of the following is a key clinical information database that is very similar in subject coverage to PubMed, and is particularly valuable for drug, toxicology, conference and international information coverage?
a.  Web of Science
b.  Scopus
c.  Embase
d.  Biosis
e.  Micromedex
47. Implementation studies focus primarily on:
a.  Whether and how an intervention that is known to be efficacious can be implemented in a “real-world” setting
b.  Whether an intervention is efficacious in a highly selected samples of research participants
c.  Whether a treatment can be implemented in a highly selected sample of research participants
d.  Whether and how an intervention that does not have known efficacy can be implemented in a controlled setting
48. The main purpose(s) of establishing exclusionary criteria is:
a.  For balancing between-participant variance
b.  For safety issues
c.  To decrease potential confounding
d.  All of the above
e.  b and c only
49. The risk of Type I error is most likely to occur when:
a.  A researcher has designed a study to maximize control over extraneous factors
b.  A researcher is most concerned about various sources of bias
c.  A researcher is most concerned with maximizing generalizability
d.  A researcher has designed a study to equally balance internal and external validity
50. The name of the conceptual structure of a team made up of people of different disciplines who each report to someone outside the team structure is known as:
a.  Project team
b.  Matrix model
c.  Disconnected team
d.  Clinical team
51. Which is NOT true of the recent trends in project management?
a.  There is a trend toward the project manager being more involved in timeline management
b.  The project manager serves as both a project leader and analyst
c.  The project manager may have duties in managing the company’s pipeline portfolio
d.  Interpersonal skills may be as important to the project manager than analytical skills
52. Disclosure of which of the following items is necessary for an informed consent document?
a.  The diagnosis or identification of a subject’s condition or problem
b.  The nature and purpose of the proposed treatment or intervention
c.  The foreseeable risks and benefits of the proposed treatment or intervention
d.  All of the above
53. An individual enrolled in a protocol at the NIH Clinical Center may appoint a surrogate decision-maker to make medical and/or research decisions in the event s/he becomes incapable through use of a Durable Power of Attorney for Health Care, also known as a DPA?
a.  True
b.  False
54. Authorship is based on significant contribution to?
a.  The conceptualization and design of the research project
b.  The execution of the experiments
c.  Writing of the paper
d.  Assumption of responsibility for the entire study
e.  Any of the above
55. Which of these is NOT considered to be research misconduct?
a.  In your manuscript copying verbatim a paragraph from another scientist’s published manuscript with no attribution
b.  Submitting a previously published table of data without attribution to the original work
c.  Preparing a figure for a paper using only those experiments which had laboratory controls that worked
d.  Changing some of the numbers in a table so that the standard error is smaller
56. In evaluating the ethical aspects of a study, it is important to assess scientific validity. Assessing scientific validity includes consideration of:
a.  Sample size and study design
b.  Costs and budget
c.  Informed consent
d.  Amount of compensation to participants
57. In the proposed ethical framework for clinical research, the final principle “respect for enrolled subjects” is understood to include:
a.  Establishing a contract between the subject and the researcher
b.  Monitoring the subject’s welfare and protecting confidentiality of information
c.  Keeping the financial costs of participation reasonable
d.  Informing the subject of new information only after the study is published
58. If you are conducting clinical research that is funded by the NIH, you are always required to follow the:
a.  CIOMS International Guidelines
b.  Common Rule
c.  Nuremberg Code
d.  Belmont Report

 
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Biology

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· Be a minimum of 75 words in length

· Include at least one in-text citation along with a reference at the end of the post using APA format

Question 1:

Discuss the importance of each step in the scientific method. Why do you think scientists utilize this type of experimentation and reasoning?

Question 2:

Describe the circumstances under which each of the following would be considered to be not sustainable: cutting trees for lumber and paper; use of nuclear energy; use of fossil fuels. How could each activity be managed to make it sustainable?

Study Material 

Title: The Scientific Method After Next

Description: Read “The Scientific Method After Next,” by Stein, from World Future Review (2012).

URL: https://lopes.idm.oclc.org/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=76099699&site=ehost-live&scope=site

Title: Scientific Method

Description: View the “Scientific Method” on YouTube.

URL: http://www.youtube.com/watch?feature=player_embedded&v=wlb7tLJy5AI#t=0

Question 3:

View the Biome Explorer in the topic materials. Click on an ecosystem and a scenario. How might this scenario affect the genetic diversity of the population? Would this be good or bad for the population? Then explain another topic (not listed in the scenarios) that can impact a species population within the ecosystem. Why?

Question 4:

Species differ greatly in birth and death rates, survivorship, and life spans. There must be advantages and disadvantages in living longer or reproducing more quickly. Why hasn’t evolution selected for the most advantageous combination of characteristics so that all organisms would be more or less alike?

 
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Bio 7,8,9

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1. What approach is David Duncan using to analyze “living forever”? What is his background? What is he examining? (2 points)

2. What does mythology tell us about living forever?

3. What are the three ways that David describes that we can extend life?(6 points)

4. What is resveritol? (2 points)

5. What does he suggest are the pros and concs of extending our lives—100, 200, to even 400 years in the future? (2 points)

6. Does Gary want to partake in cryogenics? What is his reasoning at the end of the video? (2 points)

 
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Human Sexuality

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Assignment Instructions

Assignment 1: Human Sexuality Throughout History Time-line

Our readings describe the various historical-cultural influences that have affected human sexuality. These historical-cultural influences include such events as the sexual revolution, the control of conception, the emergence of contraception, as well as the redefining of gender roles throughout history. Many of these events changed the way sexuality is viewed today. Using Prezi (http://prezi.com/), PowerPoint, or Word create a time-line and identify at least 7 important historical events that you believe influence sexuality today. Evaluate each of these events according to its significance in history and culture. Place the date, a brief description, or even a video clip of the historical-cultural influence. Please read the grading rubric below for additional guidance with this assignment.

 
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Genetics

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What type of mutant organism would you make if you had the technology? Would you create a new type of worm with longevity? A mutant rice with increased nutritional value? A dog that glows in the dark? All of these currently exist. Think about it, use your imagination, and be creative!. What unique organism would you create?

1. Decide what type of organism and what type of mutation you would like to create. (You can pick humans, plants, animals, bacteria, whatever you fancy.)

2. Think about what sort of specific technology or techniques you want to use: cloning, molecular gene manipulation, breeding, etc. Be specific about the method (there are many different molecular gene manipulation methods). What genes or proteins will you target to get the phenotype you desire?

3. Explain how your organism will benefit society, i.e., justify the expense of funding your research to create this mutant.

4. Draw a detailed picture of your mature organism (May also make clay or other media model if desired.) Take a picture of your drawing. Convert to PDF with CamScanner or another app.

5. Post the picture and a description of your mutant proposal in the discussion area of Canvas:

Information to include in your post in addition to your picture:
a. Scientific name of your mutant (Genus species)
b. Explanation of its abilities or phenotype.
c. Description of genes/proteins targeted and method used
d. Benefit to society

 
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