User:Qasim Mahmood/Notebook/Biology 210 at AU

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'''Lab 4 Plantae and Fungi'''
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The objectives of this lab were to understand the characteristics and diversity of plants and to appreciate the function and importance of Fungi. The first plant we found was found on the ground and in abundance. It was a tree branch of medium size. We classified the branch by its leaves to be a gymnosperm. The leaves were slender and long/tubular and the seeds were cone like at the base of the leaf. The stem was spiky. We classified this leaf as a eastern pine leaf. The second leaf we found was sharp and pint and smaller then the pine branch. It was a gymnosperm and the leaves were branching out. The leaves were sharp and dark green. The reproductive part of the leaf was at the base of the leaf. We classified this leaf to be a 'holly' leaf. The third plant we found was found on the grown. It was large and a worn down orange color and was deteriating. We classified it as a gymnosperm and the leaves represented a typical leaf found on the ground. No seeds were observed. We classified this leaf to be from a sycamore tree. The fourth plant found was found on the ground in abundance, this was the one plant that we observed to be the most prevalent. It was long and green very firm and strong was hard to break apart. It was a gymnosperm and was a vine. The fifth leaf was found on the ground but barley any were there. The color was red/orange and not as big as the sycamore tree leaf. It was from a gymnosperm and was vascular. We determined it to be a oak leaf that had blown into our transect. All of the leaves/plants found were gymnosperms because they were not flowering, were not non-vascular, were not seedless, and had seeds. The vascularity of a pine tree is xylem same with the holly sycamore and oak however i believe the vine is phloem. However this is based off of research done through wikipedia and outside resources. The oak leaves were scarce, probably blown into the transect the rest of the leaves including the vines were found in heavy abundance, especially the vines. The vines were essentially the ground there was no room to walk. Fungus sporangia are hyphae that grow upward and form small, black, globlelike structures. They are essentially root-like material found underground. The fungi we observed un the microscope looked pinkish and almost like a teardrop but with a half circle base. (Refer to picture 15 in personal notebook).
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'''Lab 5 Invertebrates'''
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The objectives of this lab were to understand the importance of invertebrates and to learn how simple systems (including specialized cells and overall body plan) evolved into more complex systems. The nematodes don't have either cilia or flagella so they move through a thrashing motion by contracting their muscles. Earthworms don't have a cilia or flagella either and move in a  similar manner by contracting and then moving forward. Flat worms move by means of cilia within their body. Thousands of cilia help the flat worm move forward. The largest organism we measured was 2.5cm and the smallest was .4cm ( a centipede and a fruit fly respectively). Our organisms that we observed were the pre-selected organisms since we didn't find any in our transect. We may possibly find centipedes, earthworms, wood-peckers, sparrows, and mice within our transect. Water would benefit the transect deeply but not to much. More abundance of food would be good, the only animals observed truly there were mice one time, sparrows, and the worms. Although it can be assumed squirrels are frequent goers and so are other insects. So anything to improve the nuts available and the nutrients available in the leaves/soil would benefit the transect greatly.
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[[Image:rats.jpeg]]
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[[Image:dididi.jpg]]
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'''Lab 6: Embyology and Zebrafish Development'''
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The objectives of this lab were to learn the stages of the embryonic development, compare embryonic development in different organisms, and to set up and experiment to study how environmental conditions affect embryonic development. The purpose behind this lab was to understand the effects of ratonic acid (Vitamin A) in the development of zebrafish from an embryonic level to their adult stages. Preceding our own experiment we observed the characteristics of a frog, starfish, and chick embryo without the effect of any other variables. Procedure one called for the observation of the starfish embryo. Professor Knight prepared a slide and projected it in which we observed and noted the characteristics of the starfish embryo and compared the starfish zygote to the starfish unfertilized egg. Procedure 2 asked us to examine the development of a frog egg. We observed pre-made slides of the frog eggs under a microscope (I believe one was in the early phase while the other in the late phase). After this step we observed live tadpoles to see how they interact and the difference/similarities to the egg. Procedure 3 called for the observation of the chicken-egg. We observed eggs that had been incubated for 72 hours under a microscope. The fertilized eggs had a specific circle in the middle which we used to identify, additionally we identified individual parts of the egg.
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[[Image:132123]][[Image:Embryo.jpg]]

Current revision

Lab 1: Observing Evolution in regards to The Volvicine line and Defining a Niche at AU Objective: The objective of this lab was to help us better understand natural selection and to help us understand the biotic and abiotic characteristics of a niche. The purpose of the lab was to view a multicellular organism and see how it originated and evolved from once a single celled organism to where it is today. We viewed this from the origin of a volvocine line where we saw the complexity of cells increase from Chlamydomonas to genius's to volvox, the most complex. Additionally we were group #2 so we were in charge of niche #2, we created our hay infusion in order to study bacteria in the following week. If the volvicine line truly does exhibit natural selection and evolution the complexity of the cells ranging from Chlamydomonas to Gonium to Volvox will become increasingly complex. Additionally if the Transect/niche is undisturbed by humans then the niche will provide a more isolated and complex array of bacteria and hay fusion. Steps:

          Procedure 1: The Volvicine Line

1) We took Chlamydomonas and prepared a slide and included Protoslo 2) We observed through a microscope and saw that they were round and not grouped together 3) We prepared our Gonium slide and added protoslo 4) We observed through a microscope and saw that they were some-what grouped up with 4-5 cells per group/colony. 5)We prepared a Volvox slide and added protoslo 6) We observed through a microscope and saw that there were thousands of cells and were grouped together.

          Procedure 2: Defining a Niche at AU

1) We were assigned transect #2 which was near the seminary 2) We traveled to transect #2 3) We observed the niche and saw that this specific niche was more isolated then others 4) We took sample data which was 1/2 soil 1/2 plant matter and took it back to the lab. 5) When we arrived in lab we created a hay fusion which involved: 6) Weighing 11.2 grams of soil/ground sample and placing it in a plastic jar with 500 mld of deer park water 7) adding .1 grams dried milk and mixing for 10 seconds 8)Label Jar 9) Place jar in corner of the room with top off

Raw Data:

Table 1. Shows us the size of each cell and how large colonies are within each organism. Additionally it tells whether an organism is motile or not and the way it reproduces.  Characteristic	Chlamydomonas	Gonium	Volvox
Number of Cells:	13	14	Thousands
Colony Size: # of cells in each colony	1	8	Thousands
Describe any functional specialization of cells	Flagella for movement	Cillia moving in groups and slower	Clumped together, too many to count not high enough magnification
Describe any reproductive specialization (Isogamy vs oogamy)	Isogamy	Isogamy	Ogamy
 

Image:15 40x-2 (c1+c2).TIFThis picture shows us the relative different sizes of the organisms.

(Insert Picture 2) This picture shows the hay fusion and how it looks before water is evaporated

Conclusion and Future Plans:

In conclusion I believe our niche will provide us with valuable data and organisms due to the isolation of the environment. Additionally the niche itself seems to have been untouched by man on a daily basis due to the isolation. Additionally I can conclude that the concept of natural selection and evolution is exemplified by the volvicine line due to the increasing complexity of organisms from the Chlamydomonas to the Gonium and then the Volvox. In future studies it will be cool to compare our bacteria to the bacteria of another niche and see the difference and overarching difference in organisms as well as the abiotic/biotic factors in the niche. The objective and problem were both addressed and were easily seen (the concept of natural selection/evolution as well as the different niches and what categorizes each niche). Very good start. Well described, thorough notes. Ensure that all red text questions and comments are addressed. SK

Lab 2: Identifying Algae and Protists: Objective: The objectives of this lab were to understand how to use a dichotomous key and to understand the characteristics of Algae and Protists. In this lab we set up our lab for future weeks to come so as far as predictions and hypothesis go, I predict that our hay infusion will give us a result of bacteria and animilia that are isolated or abnormal in a populated area since our transect is so secluded. Initially when we brought the transect back to our work station the smell was similar to that of the potomac rivers, there was no mold present but the color of the water was dark green. Animilia or samples that we take from the transect that are further away from the plant matter may rely less on the plant matter for food and in addition the ones farther away from the plant matter may be required to be more mobile due to the less abundance of food. The samples we picked from the middle of the transect were more mobile and showed flagella which increase motility. The three samples we observed were, Ameoba proteus (suspected), Paramecium aurelia (suspected) ,and Euglena from the middle part of the transect and Gonium, Blepharisma (suspected), and chlamydomonas (suspected) from the bottom. The sizes in respected order were about 620 um, 136 um, 45 um, 85 um, 425 um, 6 um. The euglena meets the need for life because they are able to reproduce, have a metabolism, grow, and are mobile due to the environment they are in. I believe if the hay infusion were allowed to be incubated for another 2 months without any more food being put into the environment I believe the smaller organisms will perish and the larger organisms will dominate. A proper food chain will be put into order and the survival of the fittest will essentially be put in place and in addition I believe that this is only possible if oxygen levels stay high enough and there is enough plant matter to sustain the level of reproduction that will occur by the organisms. I believe the selected pressures that would effect our samples would involve availability of food and level of oxygen. A more mobile organism would have an advantage in an environment with less food where as a organism that may be bigger but not have a flagella would have an advantage in a environment with an abidance of food.

Picture of drawings: Picture of diagram:

"Lab 3: Microbiology and Identifying Bacteria with DNA" The objective of this lab was to understand the characteristics of bacteria, to observe antibiotic resistance, and to understand how DNA sequences are used to identify species. I believe their will be archaea species that will grow on the agar plate because some of them may be immune to the agar that kills off bacteria/archaea. The appearance/smell may change week to week because of the growth of bacteria/archaea. Possibly more archaea/bacteria--> More smell. Overall the dishes that did not have the tetercylcine grew more bacteria compared to the ones that didn't. We had no fungi on our plates. The unaffected bacteria are the ones that grew on the tet+ plates. Tet inhibits a lot of enzyme reactions. This link explains in detail what TET does. http://www.chm.bris.ac.uk/motm/tetracycline/antimicr.htm. Of the three bacteria plates we looked at only the -9 non get plate exhibited mobile not grouped bacteria. The other two dishes we looked at (-7 get and -5 NA) were both grouped and non mobile so it seemed. The -7 get were rod+coci shaped and grouped while the 05 NA were grouped together circular and of the color blue. Insert picture of graph Insert pictures of slides

Lab 4 Plantae and Fungi The objectives of this lab were to understand the characteristics and diversity of plants and to appreciate the function and importance of Fungi. The first plant we found was found on the ground and in abundance. It was a tree branch of medium size. We classified the branch by its leaves to be a gymnosperm. The leaves were slender and long/tubular and the seeds were cone like at the base of the leaf. The stem was spiky. We classified this leaf as a eastern pine leaf. The second leaf we found was sharp and pint and smaller then the pine branch. It was a gymnosperm and the leaves were branching out. The leaves were sharp and dark green. The reproductive part of the leaf was at the base of the leaf. We classified this leaf to be a 'holly' leaf. The third plant we found was found on the grown. It was large and a worn down orange color and was deteriating. We classified it as a gymnosperm and the leaves represented a typical leaf found on the ground. No seeds were observed. We classified this leaf to be from a sycamore tree. The fourth plant found was found on the ground in abundance, this was the one plant that we observed to be the most prevalent. It was long and green very firm and strong was hard to break apart. It was a gymnosperm and was a vine. The fifth leaf was found on the ground but barley any were there. The color was red/orange and not as big as the sycamore tree leaf. It was from a gymnosperm and was vascular. We determined it to be a oak leaf that had blown into our transect. All of the leaves/plants found were gymnosperms because they were not flowering, were not non-vascular, were not seedless, and had seeds. The vascularity of a pine tree is xylem same with the holly sycamore and oak however i believe the vine is phloem. However this is based off of research done through wikipedia and outside resources. The oak leaves were scarce, probably blown into the transect the rest of the leaves including the vines were found in heavy abundance, especially the vines. The vines were essentially the ground there was no room to walk. Fungus sporangia are hyphae that grow upward and form small, black, globlelike structures. They are essentially root-like material found underground. The fungi we observed un the microscope looked pinkish and almost like a teardrop but with a half circle base. (Refer to picture 15 in personal notebook).

Lab 5 Invertebrates The objectives of this lab were to understand the importance of invertebrates and to learn how simple systems (including specialized cells and overall body plan) evolved into more complex systems. The nematodes don't have either cilia or flagella so they move through a thrashing motion by contracting their muscles. Earthworms don't have a cilia or flagella either and move in a similar manner by contracting and then moving forward. Flat worms move by means of cilia within their body. Thousands of cilia help the flat worm move forward. The largest organism we measured was 2.5cm and the smallest was .4cm ( a centipede and a fruit fly respectively). Our organisms that we observed were the pre-selected organisms since we didn't find any in our transect. We may possibly find centipedes, earthworms, wood-peckers, sparrows, and mice within our transect. Water would benefit the transect deeply but not to much. More abundance of food would be good, the only animals observed truly there were mice one time, sparrows, and the worms. Although it can be assumed squirrels are frequent goers and so are other insects. So anything to improve the nuts available and the nutrients available in the leaves/soil would benefit the transect greatly. Image:rats.jpeg Image:dididi.jpg

Lab 6: Embyology and Zebrafish Development The objectives of this lab were to learn the stages of the embryonic development, compare embryonic development in different organisms, and to set up and experiment to study how environmental conditions affect embryonic development. The purpose behind this lab was to understand the effects of ratonic acid (Vitamin A) in the development of zebrafish from an embryonic level to their adult stages. Preceding our own experiment we observed the characteristics of a frog, starfish, and chick embryo without the effect of any other variables. Procedure one called for the observation of the starfish embryo. Professor Knight prepared a slide and projected it in which we observed and noted the characteristics of the starfish embryo and compared the starfish zygote to the starfish unfertilized egg. Procedure 2 asked us to examine the development of a frog egg. We observed pre-made slides of the frog eggs under a microscope (I believe one was in the early phase while the other in the late phase). After this step we observed live tadpoles to see how they interact and the difference/similarities to the egg. Procedure 3 called for the observation of the chicken-egg. We observed eggs that had been incubated for 72 hours under a microscope. The fertilized eggs had a specific circle in the middle which we used to identify, additionally we identified individual parts of the egg. Image:132123Image:Embryo.jpg

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