User:Elizabeth Pouya/Notebook/Biology 210 at AU

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(New page: '''1/29''': The transect is slightly elevated and on a slope. Part of it is adjacent to the sidewalk and directly across Kogod School of Business. Immediately next to the boundaries of the...)
Current revision (10:55, 1 May 2014) (view source)
(PHOTOS FROM LAB WITH DESCRIPTIONS: http://www.flickr.com/photos/116740424@N07/)
 
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'''1/29''': The transect is slightly elevated and on a slope. Part of it is adjacent to the sidewalk and directly across Kogod School of Business. Immediately next to the boundaries of the transect, there is a sewage drain. There is some shade from very large trees that are approximately 20 feet away, however, most of the transect is exposed to the sun when present. Majority of the plants within the transect are dry and unlively however the area under all of the little rocks is very damp.  Within this transect, there is a variety of plants (as shown in the picture.) The transect is also an area that is maintained by the university so fertilizers are used on the plants and the grass is cut by a lawnmower.  
+
== PHOTOS FROM LAB WITH DESCRIPTIONS: http://www.flickr.com/photos/116740424@N07/ ==
 +
 
 +
'''3/4:''' LAB 6
 +
Retinoic acid (Retinoid A) is a small molecule that mediates the functions of vitamin A (retinol) – pertinent to growth and development. It's present in chordate animals. In early stages of embryonic development, Retinoic acid guides the development of the posterior of the embryo.
 +
 
 +
Objective: Our goal in conducting this experiment was to observe the effects that excess retinoic acid has on the growth and development of zebrafish embryo.
 +
 
 +
Hypothesis: WIf we treat our zebrafish with an excess of retinoic acid, then we will observe abnormalities* in their development when compared to the control group of embryos. Abnormalities include: reduced body length, increased heart rate, irregular posterior development
 +
 
 +
Experimental Design:
 +
Control Group: ~20 healthy zebrafish embryo in 20 mL Deerpark water in a petri dish. The petri dish was placed in a dark drawer (RA is light sensitive).
 +
Treatment Group: ~20 healthy zebrafish embryo in 20 mL Deerpark water treated with retinoic acid. Petri dish was placed in a dark drawer.
 +
 
 +
Observed the fish on Days 1, 2, 4, 7, and 14.
 +
 
 +
*Day 1: We're testing the effect of Retinoid A on zebrafish emrbyos. Because Retinoid A is sensitive to light we are placing both of the zebrafish petri dishes in a dark environment (drawer) and so it is a controlled variable. On the first day we simply created the culture for the treated and non-treated zebrafish. Majority of them were in the 10 to 12 hour stage.
 +
*Day 2: When they were checked on the next day only one from zebrafish had died from the treated group and only one from the non-treated group. At this point, the zebrafish in both groups were mostly in the 14-16 hour stage.
 +
*Day 4: None had died when these were check on this day! The zebrafish were in the 48 hr-72 hr phase at this point.
 +
*Day 7: The zebrafish were all in the 120 hour phase with the exception of one in the 16 hr phase. 1 had died in the treatment group and three had died in the non-treatment group.
 +
 
 +
Observations: no discernible physical differences between treatment and control group (negligible differences in body length which was surprising because retinoic acid usually helps aid in the growth of this). Heart rate of control was 116 beats/min vs. heart rate of treatment which was 140 beats/min which was the only noticeable difference between the treatment and control group.
 +
 
 +
Possible sources of error: Water wasn't changed in a consistent interval and retinoic acid exposed to light when counting zebra fish.
 +
 
 +
'''2/28:''' LAB 5
 +
This Lab was modified and narrowed down to just analyzing vertebrates in our transect because of the Snow Day.
 +
 
 +
We looked at dead and preserved unidentified arthopods in their respective glass jars. It was relatively easy to classification each group because they all had distinct characteristics. The only tricky part was trying to tell the difference between a centipede and millipede. It was eventually noticed that centipedes have ''visible'' antennae and whereas millipededes have antennae but they're not instantly noticeable.
 +
 
 +
After analyzing our invertebrates from the B-funnel. We were only able to find one: an ant. A picture is on the Flickr.
 +
Phylum: Arthopoda
 +
Class: Insecta
 +
Order: Hymenoptera
 +
Family: Formicidae
 +
Genus: Dorylus
 +
Species: acutus (among others)
 +
 
 +
It is likely that this ant in addition to the other ants most likely in the transect, it fed of natural sugars, seeds, and the wide variety of plants.
 +
 
 +
'''2/21:''' LAB 4
 +
 
 +
Plant #1: Cat tails: a gymnosperm located in a bush approximately in the center of the transect which was above ground. The bush appeared to be tall and dry. The plant has a long, wide base and stems of about one inch long. Its leaves have densely packed spores. This was the coolest plant because the bushy cat tail part of the plant was actually disected - we found that it was composed of SUPER densely-packed fluffy seeds! These plants also survive through the winter.
 +
 
 +
Plant #2: This plant looked like twiggy dry stuff. It was loosely spread out around the surface of the transect but there wasn't much of it. It possibly came from a very fragile push with thin, short branches. This particular plant did not have any leaves.There is some vascularization at the root of the plant.
 +
 
 +
Plant #3: There was a small green plant with short, yet thick and wide leaves. It had a thick branch from which the leaves grew, it was directly rooted into the ground. It was near the cat tails and rocks. This plant had a lot of vascularization within the stem. A microscope was not necessary to see this because the tubes were about 1 cm wide in diameter! (dycot)
 +
 
 +
Plant #4: Typically known as grass. There was little within the transect itself, but a lot surrounding the areas of the transect. It was short, in-ground (has roots).
 +
 
 +
Plant #5: There was a large bush with only skinny red stems that had no leaves on it (possibly because of current climate). At the end of some of the stems, there were seeds and berries.
 +
 
 +
*Note: The plants were growing in less than ideal conditions (cold, winter climate) and as described, appeared to be very dry. The unhealthy plants may not have been producing seeds or flowers, or may have been producing very few. The lack of observable reproductive structures made identifying the plants very difficult. It was assumed that all plants, were flowering plants. Due to lack of identifying features the genera of the plants was not able to be determined.
 +
 
 +
Fungi sporangia: are the parts within the fungi where asexual pores are reproduced. These are important so that the Fungi continue to grow, otherwise without it, it would not.
 +
 
 +
The cells of fungi tend to be tubular, elongated, and thread-like (filamentous) and they continue multiple nuclei at their tips. Which is why the sample that was example was most likely a fungus (see Flickr).
 +
 
 +
'''2/15''': LAB 3
 +
It is not likely that Archaea species will grow on the agar plates because they don’t provide suitable living conditions for them. For example: extremophiles which require a climate of extremely hot or extremely cold temperatures; the agar plates were placed in room temperature. The agar gel only supports the growth of certain types of prokaryotic colonies.
 +
The appearance/smell of the hay infusion might change from week to week because mold/fungi may start to develop which requires food but may also be a food source to the bacteria. So cycle of food within the ecosystem is constantly adjusting due to the growth of new organisms.
 +
*TABLE SHOWN IN FLICKR
 +
Bacterial growth appears to be evident on both the regular agar plates and the ones with antibiotic. However, the plates without antibiotic appear to have more growth. There was only growth on one of the plates with antibiotic (10-7).This indicates that the bacteria on the 10-7 were antibiotic resistant whereas the other two plates with antibiotic on them (10-3 and 10-5) were unable to grow in the presence of bacteria.Overall, the tetracycline either causes zero colonies to grow in its presence or it allows bacteria to grow if it is resistant to it. Only one species was unaffected by tetracycline (the plate with 10-7 dilution) - the one plate that did grow bacteria in the presence of tetracycline grew more colonies of bacteria than any of the other non-tetracycline plates (as shown in the table). Tetracycline mainly works by interfering with the ability of bacteria to produce proteins that are essential for their growth and replication (prevents introduction of new amino acids to the peptide chain). So tetracycline does not kill bacteria, it simply inhibits them from reproducing. Mammalian cells are less vulnerable to the effect of tetracyclines, because bacteria actively pump tetracycline into their cytoplasm – whereas mammalian cells do not. Tetracyclines are effective against both Gram-positive and Gram-negative cells, more specifically: ''H. pylori, E. Coli, M. tuberculosis, and P. aerugonisa.''
 +
10-5 : branches, entire edge, and no elevation
 +
10-7 :circular form, colonies are an orange color, filamentous form and margin, raised elevation
 +
107 :circular form, entire margin, raised elevation
 +
10-3: irregular form, undulate edge, no elevation
 +
 
 +
 
 +
'''2/7''': LAB 2
 +
The culture is not completely lacking in scent—it’s faint, but slightly there. There appears to be a very thin layer of ‘film’ on top (show in the pictures). The rest of the culture is mainly a muddy color; there is a lot of dirt collected on the bottom along with the leaves and a few branches.
 +
Colpidium ~45µm, mobile, looks as if it is vibrating back and forth very fast, have cilia
 +
Paramecium aurelia ~130µm, mobile and moves slowly and demonstrates inching motion (contracts horizontally and vertically in order to move itself – uses ATP for this process)
 +
Chlamydomonas ~4.5µm, mobile, has two flagella that propel it very quickly
 +
Middle of Culture:
 +
Unknown Organism ~75µm, has a single long flagella that is attached to a plant leaf. The flagella contracts as the rest of the organism is pulled in and let go. Possibly Parenema sp.
 +
Paramecium multimicronucleatum ~200µ, mobile and moves slowly (floats)
 +
Colpidium ~45µm
 +
Top of Culture:
 +
Clamydomonas ~6µm
 +
Paramecium caudatum ~250µm, mobile and moves slowly (floats)
 +
Colpidium ~50µm
 +
The chlamydomas was a species that appeared frequently within all layers of our hay infusion culture. The chlamydomonas is a genus of green algae that has unicellular flagellates/ It’s typically found in stagnant water and damp soil (both a part of our hay infusion culture.) The chlamydomas uses energy, specifically ATP in order to power its flagella. It is also made of a single cell which includes chloroplasts (has the ability to photosynthesize – ATP also required). This organism hosts information within the cell because it has DNA which is capable of replicating itself.  And lastly, chlamydomonas’ lineage diverged from land plants over 1 billion years ago so it had demonstrated that it is capable f evolving.
 +
Had the hay infusion culture been observed for another two months then I would predict that different types of organisms would continue to grow. For example, given the diversity of bacteria and nutrients found in the culture (large food supply) it is possible that mold or possibly even fungi would begin to grow. And with the presence of new organisms, we would also be able to observe new kinds of bacteria.
 +
Selective pressures that affected could have affected the composition of our sample are the availability and variety of nutrients available for the organisms. Also, the number of leafs plant-type factors that were initially put into the hay infusion culture.
 +
 
 +
'''1/29''': LAB 1
 +
Transect: Mini Marsh
 +
The transect is slightly elevated and on a slope. Part of it is adjacent to the sidewalk and directly across Kogod School of Business. Immediately next to the boundaries of the transect, there is a sewage drain. There is some shade from very large trees that are approximately 20 feet away, however, most of the transect is exposed to the sun when present. Majority of the plants within the transect are dry and unlively however the area under all of the little rocks is very damp.  Within this transect, there is a variety of plants (as shown in the picture.) The transect is also an area that is maintained by the university so fertilizers are used on the plants and the grass is cut by a lawnmower.  
Abiotic Factors: little rocks, big rocks, cement brick. Random piece of metal, gum wrapper, and a cigarette.
Abiotic Factors: little rocks, big rocks, cement brick. Random piece of metal, gum wrapper, and a cigarette.
Biotic Factors: cat tails, grass, leaves,  bushes, soil, squirrels, snakes, rates, worms, and trees in close proximity
Biotic Factors: cat tails, grass, leaves,  bushes, soil, squirrels, snakes, rates, worms, and trees in close proximity
 +
We sampled some of the dirt, grass roots, leaves, and different plants in order to make our Hay Infusion culture.
 +
Although now covered in snow, pictures of the Mini Marsh transect are shown below.
 +
EP
EP

Current revision

PHOTOS FROM LAB WITH DESCRIPTIONS: http://www.flickr.com/photos/116740424@N07/

3/4: LAB 6 Retinoic acid (Retinoid A) is a small molecule that mediates the functions of vitamin A (retinol) – pertinent to growth and development. It's present in chordate animals. In early stages of embryonic development, Retinoic acid guides the development of the posterior of the embryo.

Objective: Our goal in conducting this experiment was to observe the effects that excess retinoic acid has on the growth and development of zebrafish embryo.

Hypothesis: WIf we treat our zebrafish with an excess of retinoic acid, then we will observe abnormalities* in their development when compared to the control group of embryos. Abnormalities include: reduced body length, increased heart rate, irregular posterior development

Experimental Design: Control Group: ~20 healthy zebrafish embryo in 20 mL Deerpark water in a petri dish. The petri dish was placed in a dark drawer (RA is light sensitive). Treatment Group: ~20 healthy zebrafish embryo in 20 mL Deerpark water treated with retinoic acid. Petri dish was placed in a dark drawer.

Observed the fish on Days 1, 2, 4, 7, and 14.

  • Day 1: We're testing the effect of Retinoid A on zebrafish emrbyos. Because Retinoid A is sensitive to light we are placing both of the zebrafish petri dishes in a dark environment (drawer) and so it is a controlled variable. On the first day we simply created the culture for the treated and non-treated zebrafish. Majority of them were in the 10 to 12 hour stage.
  • Day 2: When they were checked on the next day only one from zebrafish had died from the treated group and only one from the non-treated group. At this point, the zebrafish in both groups were mostly in the 14-16 hour stage.
  • Day 4: None had died when these were check on this day! The zebrafish were in the 48 hr-72 hr phase at this point.
  • Day 7: The zebrafish were all in the 120 hour phase with the exception of one in the 16 hr phase. 1 had died in the treatment group and three had died in the non-treatment group.

Observations: no discernible physical differences between treatment and control group (negligible differences in body length which was surprising because retinoic acid usually helps aid in the growth of this). Heart rate of control was 116 beats/min vs. heart rate of treatment which was 140 beats/min which was the only noticeable difference between the treatment and control group.

Possible sources of error: Water wasn't changed in a consistent interval and retinoic acid exposed to light when counting zebra fish.

2/28: LAB 5 This Lab was modified and narrowed down to just analyzing vertebrates in our transect because of the Snow Day.

We looked at dead and preserved unidentified arthopods in their respective glass jars. It was relatively easy to classification each group because they all had distinct characteristics. The only tricky part was trying to tell the difference between a centipede and millipede. It was eventually noticed that centipedes have visible antennae and whereas millipededes have antennae but they're not instantly noticeable.

After analyzing our invertebrates from the B-funnel. We were only able to find one: an ant. A picture is on the Flickr. Phylum: Arthopoda Class: Insecta Order: Hymenoptera Family: Formicidae Genus: Dorylus Species: acutus (among others)

It is likely that this ant in addition to the other ants most likely in the transect, it fed of natural sugars, seeds, and the wide variety of plants.

2/21: LAB 4

Plant #1: Cat tails: a gymnosperm located in a bush approximately in the center of the transect which was above ground. The bush appeared to be tall and dry. The plant has a long, wide base and stems of about one inch long. Its leaves have densely packed spores. This was the coolest plant because the bushy cat tail part of the plant was actually disected - we found that it was composed of SUPER densely-packed fluffy seeds! These plants also survive through the winter.

Plant #2: This plant looked like twiggy dry stuff. It was loosely spread out around the surface of the transect but there wasn't much of it. It possibly came from a very fragile push with thin, short branches. This particular plant did not have any leaves.There is some vascularization at the root of the plant.

Plant #3: There was a small green plant with short, yet thick and wide leaves. It had a thick branch from which the leaves grew, it was directly rooted into the ground. It was near the cat tails and rocks. This plant had a lot of vascularization within the stem. A microscope was not necessary to see this because the tubes were about 1 cm wide in diameter! (dycot)

Plant #4: Typically known as grass. There was little within the transect itself, but a lot surrounding the areas of the transect. It was short, in-ground (has roots).

Plant #5: There was a large bush with only skinny red stems that had no leaves on it (possibly because of current climate). At the end of some of the stems, there were seeds and berries.

  • Note: The plants were growing in less than ideal conditions (cold, winter climate) and as described, appeared to be very dry. The unhealthy plants may not have been producing seeds or flowers, or may have been producing very few. The lack of observable reproductive structures made identifying the plants very difficult. It was assumed that all plants, were flowering plants. Due to lack of identifying features the genera of the plants was not able to be determined.

Fungi sporangia: are the parts within the fungi where asexual pores are reproduced. These are important so that the Fungi continue to grow, otherwise without it, it would not.

The cells of fungi tend to be tubular, elongated, and thread-like (filamentous) and they continue multiple nuclei at their tips. Which is why the sample that was example was most likely a fungus (see Flickr).

2/15: LAB 3 It is not likely that Archaea species will grow on the agar plates because they don’t provide suitable living conditions for them. For example: extremophiles which require a climate of extremely hot or extremely cold temperatures; the agar plates were placed in room temperature. The agar gel only supports the growth of certain types of prokaryotic colonies. The appearance/smell of the hay infusion might change from week to week because mold/fungi may start to develop which requires food but may also be a food source to the bacteria. So cycle of food within the ecosystem is constantly adjusting due to the growth of new organisms.

  • TABLE SHOWN IN FLICKR

Bacterial growth appears to be evident on both the regular agar plates and the ones with antibiotic. However, the plates without antibiotic appear to have more growth. There was only growth on one of the plates with antibiotic (10-7).This indicates that the bacteria on the 10-7 were antibiotic resistant whereas the other two plates with antibiotic on them (10-3 and 10-5) were unable to grow in the presence of bacteria.Overall, the tetracycline either causes zero colonies to grow in its presence or it allows bacteria to grow if it is resistant to it. Only one species was unaffected by tetracycline (the plate with 10-7 dilution) - the one plate that did grow bacteria in the presence of tetracycline grew more colonies of bacteria than any of the other non-tetracycline plates (as shown in the table). Tetracycline mainly works by interfering with the ability of bacteria to produce proteins that are essential for their growth and replication (prevents introduction of new amino acids to the peptide chain). So tetracycline does not kill bacteria, it simply inhibits them from reproducing. Mammalian cells are less vulnerable to the effect of tetracyclines, because bacteria actively pump tetracycline into their cytoplasm – whereas mammalian cells do not. Tetracyclines are effective against both Gram-positive and Gram-negative cells, more specifically: H. pylori, E. Coli, M. tuberculosis, and P. aerugonisa. 10-5 : branches, entire edge, and no elevation 10-7 :circular form, colonies are an orange color, filamentous form and margin, raised elevation 107 :circular form, entire margin, raised elevation 10-3: irregular form, undulate edge, no elevation


2/7: LAB 2 The culture is not completely lacking in scent—it’s faint, but slightly there. There appears to be a very thin layer of ‘film’ on top (show in the pictures). The rest of the culture is mainly a muddy color; there is a lot of dirt collected on the bottom along with the leaves and a few branches. Colpidium ~45µm, mobile, looks as if it is vibrating back and forth very fast, have cilia Paramecium aurelia ~130µm, mobile and moves slowly and demonstrates inching motion (contracts horizontally and vertically in order to move itself – uses ATP for this process) Chlamydomonas ~4.5µm, mobile, has two flagella that propel it very quickly Middle of Culture: Unknown Organism ~75µm, has a single long flagella that is attached to a plant leaf. The flagella contracts as the rest of the organism is pulled in and let go. Possibly Parenema sp. Paramecium multimicronucleatum ~200µ, mobile and moves slowly (floats) Colpidium ~45µm Top of Culture: Clamydomonas ~6µm Paramecium caudatum ~250µm, mobile and moves slowly (floats) Colpidium ~50µm The chlamydomas was a species that appeared frequently within all layers of our hay infusion culture. The chlamydomonas is a genus of green algae that has unicellular flagellates/ It’s typically found in stagnant water and damp soil (both a part of our hay infusion culture.) The chlamydomas uses energy, specifically ATP in order to power its flagella. It is also made of a single cell which includes chloroplasts (has the ability to photosynthesize – ATP also required). This organism hosts information within the cell because it has DNA which is capable of replicating itself. And lastly, chlamydomonas’ lineage diverged from land plants over 1 billion years ago so it had demonstrated that it is capable f evolving. Had the hay infusion culture been observed for another two months then I would predict that different types of organisms would continue to grow. For example, given the diversity of bacteria and nutrients found in the culture (large food supply) it is possible that mold or possibly even fungi would begin to grow. And with the presence of new organisms, we would also be able to observe new kinds of bacteria.

Selective pressures that affected could have affected the composition of our sample are the availability and variety of nutrients available for the organisms. Also, the number of leafs plant-type factors that were initially put into the hay infusion culture.

1/29: LAB 1 Transect: Mini Marsh The transect is slightly elevated and on a slope. Part of it is adjacent to the sidewalk and directly across Kogod School of Business. Immediately next to the boundaries of the transect, there is a sewage drain. There is some shade from very large trees that are approximately 20 feet away, however, most of the transect is exposed to the sun when present. Majority of the plants within the transect are dry and unlively however the area under all of the little rocks is very damp. Within this transect, there is a variety of plants (as shown in the picture.) The transect is also an area that is maintained by the university so fertilizers are used on the plants and the grass is cut by a lawnmower. Abiotic Factors: little rocks, big rocks, cement brick. Random piece of metal, gum wrapper, and a cigarette. Biotic Factors: cat tails, grass, leaves, bushes, soil, squirrels, snakes, rates, worms, and trees in close proximity We sampled some of the dirt, grass roots, leaves, and different plants in order to make our Hay Infusion culture. Although now covered in snow, pictures of the Mini Marsh transect are shown below.

EP

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