Bacteria [Communications]
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deleted-2131
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Re: Bacteria [Communications]
ISEF doesn't have a specific format for bibliographies; however, using a format that is standard in your particular field of research is expected. I'm sure that one that Donna suggested will work well. As she said, it is very important to have references on your board and in your write up (if you have one).
All the best,
Terik
Terik
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Re: Bacteria [Communications]
OK, I've received confirmation of my registration -- I think I'm all done!
Now I've started the preparation work for running just two tests for the spectrophotometer growth curves and was making petri plates, and when I incubated some of them there were contaminants! In all of them!
This is a bit unfortunate because I know that when I did my first batch probably 3 months ago, this did not happen O=. (This is especially discouraging -- I'm moving backwards! o=).
I had a roll of plastic sterilized petri plates, and I made the nutrient agar, let it cool to when its cool to handle, and then poured it into the plates. I know I did that. I think I should actually be letting the nutrient agar in the Erlenmeyer flask cool under the UV light -- this would be sufficient enough right?
Here is a photo of the board -- I'll definitely edit the right panel -- that was printed out last minute
. And I could definitely add more graphs and make them more prominent in the board. Ahh, so little space to display things in!:
http://www.flickr.com/photos/tiseagles/3408261107/ > My board
http://www.tiseagles.com/extracurricular.php?id=18 > Photos of all the projects in my fair.
Now I've started the preparation work for running just two tests for the spectrophotometer growth curves and was making petri plates, and when I incubated some of them there were contaminants! In all of them!
This is a bit unfortunate because I know that when I did my first batch probably 3 months ago, this did not happen O=. (This is especially discouraging -- I'm moving backwards! o=).
I had a roll of plastic sterilized petri plates, and I made the nutrient agar, let it cool to when its cool to handle, and then poured it into the plates. I know I did that. I think I should actually be letting the nutrient agar in the Erlenmeyer flask cool under the UV light -- this would be sufficient enough right?
Here is a photo of the board -- I'll definitely edit the right panel -- that was printed out last minute
http://www.flickr.com/photos/tiseagles/3408261107/ > My board
http://www.tiseagles.com/extracurricular.php?id=18 > Photos of all the projects in my fair.
Trader - scientist wannabe =)
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Re: Bacteria [Communications]
Hi Trader,
I'm glad that you got all the forms and paperwork completed! It must be frustrating for you to have found contaminants in your petri dishes; I'm sure that Donna will have some advice on how to resolve that particular issue. The pictures of your display board and science fair were interesting to see. Your board looks quite nice. You will need to update it with your new data, so I would wait to make a detailed plan of how you want to alter sections of your board until after you have completed your latest batch of experiments. You are absolutely right -- you have a lot of information to display in a confined space.
Keep up the good work!
I'm glad that you got all the forms and paperwork completed! It must be frustrating for you to have found contaminants in your petri dishes; I'm sure that Donna will have some advice on how to resolve that particular issue. The pictures of your display board and science fair were interesting to see. Your board looks quite nice. You will need to update it with your new data, so I would wait to make a detailed plan of how you want to alter sections of your board until after you have completed your latest batch of experiments. You are absolutely right -- you have a lot of information to display in a confined space.
Keep up the good work!
All the best,
Terik
Terik
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
Thanks so much for sending all of the pictures. It was very interesting to see all of the projects. The variety and presentation of the science fair projects was typical and I thought your project was outstanding. And, I'm so glad you completed all of the forms.
Welcome to the world of research. Experiments occasionally fail for some reason, and it always seems to happen at a deadline. Your experience with contamination is unfortunately, a problem that occurs occasionally. You can't do any experiments with contaminated media. You need to think about where the contamination came from. If everything was grossly contaminated, then it is likely that the agar was not autoclaved long enough. Spore formers are very heat resistant and the autoclave cycle has to be at 121 degrees Centigrade for 15-20 minutes. You have to let the agar cool before you pour it, but if the top is covered with a sterile plug, then bacteria should not be able to get in before you pour the plates. If the roll of Petri dishes had been opened previously, it's possible that some dust had gotten in and contaminated all of the plates. A drop of non-sterile water could contaminate an entire flask of medium. Before you pour plates, you should wipe the counter top with 70% ethanol or other disinfectant. If you don't have any idea what happened, then just make the medium again the same way, and hope it doesn't happen again.
It's very important not to worry too much when things like this happen. In scientific research, experiments don't always work perfectly, and the best thing to do is to concentrate on what do to next to avoid repeating the problem. A failed experiment is never the end of the world. In your case, your goal is to redo your board for the ISEF fair, so you may need to do this without getting more data. Or, you may have time to repeat the experiment with only one temperature instead of two. Plan out your time, and budget enough time to plan you layout and finish everything without having too much to do at the last minute. You do want to have time to enjoy the experience of going to ISEF.
Donna Hardy
Thanks so much for sending all of the pictures. It was very interesting to see all of the projects. The variety and presentation of the science fair projects was typical and I thought your project was outstanding. And, I'm so glad you completed all of the forms.
Welcome to the world of research. Experiments occasionally fail for some reason, and it always seems to happen at a deadline. Your experience with contamination is unfortunately, a problem that occurs occasionally. You can't do any experiments with contaminated media. You need to think about where the contamination came from. If everything was grossly contaminated, then it is likely that the agar was not autoclaved long enough. Spore formers are very heat resistant and the autoclave cycle has to be at 121 degrees Centigrade for 15-20 minutes. You have to let the agar cool before you pour it, but if the top is covered with a sterile plug, then bacteria should not be able to get in before you pour the plates. If the roll of Petri dishes had been opened previously, it's possible that some dust had gotten in and contaminated all of the plates. A drop of non-sterile water could contaminate an entire flask of medium. Before you pour plates, you should wipe the counter top with 70% ethanol or other disinfectant. If you don't have any idea what happened, then just make the medium again the same way, and hope it doesn't happen again.
It's very important not to worry too much when things like this happen. In scientific research, experiments don't always work perfectly, and the best thing to do is to concentrate on what do to next to avoid repeating the problem. A failed experiment is never the end of the world. In your case, your goal is to redo your board for the ISEF fair, so you may need to do this without getting more data. Or, you may have time to repeat the experiment with only one temperature instead of two. Plan out your time, and budget enough time to plan you layout and finish everything without having too much to do at the last minute. You do want to have time to enjoy the experience of going to ISEF.
Donna Hardy
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Re: Bacteria [Communications]
So from what I gather, the spectrophotometer can estimate the population of a bacteria by using this standard? I'm a bit confused because my teacher says that apparently we should be able to first know what turbidity = X amount of bacteria, what turbidity = Y amount of bacteria and then we'll be able to estimate the number of bacteria.Here is information on McFarland standards, which are used as turbitity standards to estimate concentrations of bacteria. You do not have to make these standards, so this is for your information. If it turns out you can't use the spectrophotometer at 600 nm, however, you could use these to estimate numbers of bacteria, if barium and sulfuric acid are available. And if a judge happens to ask you about this, you'll understand the question.
http://en.wikipedia.org/wiki/McFarland_standard
Unfortunately, my dilution platings only give the doubling time -- would I have to inoculate broth, use dilution plating to count how many bacteria it has, and then read the optical density at 600 nm? (ALSO -- why is it at 600 nm and not at any other optical density reading?)
I checked the link, and I'm not too sure > does
In microbiology, McFarland standards are used as a reference to adjust the turbidity of bacterial suspensions so that the number of bacteria will be within a given range.
Mean that we will be able to directly estimate the population from the turbidity after preparing this McFarland standard? (Sorry, I've never used/seen a spectrophotometer before, but I have time to work on the project now
Thanks.
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Re: Bacteria [Communications]
Trader,
I can't answer this particular question as certainly as I'm sure that Donna can, but I can explain a bit about spectrophotometry and how it relates to the amount of bacteria. Speaking in fairly broad generalizations, a spectrophotometer sends a beam of light through the sample that is in the cuvette and then tells you about how the light is affected by the sample. Transmittance, for example, is a measure of how much of the light makes it through to detector on the other side of the sample compared to the amount that was sent into the sample. The way that the light is affected by the sample will, in your case, depend on the amount of bacteria in the suspension. The more bacteria that is in the suspension, the more strongly the light will be affected. I can't comment on the McFarland standards, but I'm sure Donna will be able to provide a more rigorous technical answer.
Keep up the good work!
I can't answer this particular question as certainly as I'm sure that Donna can, but I can explain a bit about spectrophotometry and how it relates to the amount of bacteria. Speaking in fairly broad generalizations, a spectrophotometer sends a beam of light through the sample that is in the cuvette and then tells you about how the light is affected by the sample. Transmittance, for example, is a measure of how much of the light makes it through to detector on the other side of the sample compared to the amount that was sent into the sample. The way that the light is affected by the sample will, in your case, depend on the amount of bacteria in the suspension. The more bacteria that is in the suspension, the more strongly the light will be affected. I can't comment on the McFarland standards, but I'm sure Donna will be able to provide a more rigorous technical answer.
Keep up the good work!
All the best,
Terik
Terik
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
Thanks to Terik for the explanation about the spectrophotometer.
The McFarland standards are suspensions of barium sulfate, a white insoluble salt that has an appearance that is similar in appearance to a growing culture of bacteria. Different concentrations of barium sulfate will give a visual substitute for the spectrophotometer; you compare the density of the bacterial culture to the McFarland standards to estimate the number of microorganisms per ml. A spectrophotometer at 600 nm will give more accurate results, and your teacher is right; this is the best way to do this. I had just suggested the McFarland standards in case the spectrophotometer was not available for you to use, so don't worry about this option.
I think you should stop doing experiments, and concentrate on writing up your board. Getting some additional results will not be worth it if you sacrifice the time you need to redoing the board. Are you in the middle of an experiment? If so, then finish it, but I would not recommend continuing experiments until the last minute. What do you have left to do?
Donna Hardy
Thanks to Terik for the explanation about the spectrophotometer.
The McFarland standards are suspensions of barium sulfate, a white insoluble salt that has an appearance that is similar in appearance to a growing culture of bacteria. Different concentrations of barium sulfate will give a visual substitute for the spectrophotometer; you compare the density of the bacterial culture to the McFarland standards to estimate the number of microorganisms per ml. A spectrophotometer at 600 nm will give more accurate results, and your teacher is right; this is the best way to do this. I had just suggested the McFarland standards in case the spectrophotometer was not available for you to use, so don't worry about this option.
I think you should stop doing experiments, and concentrate on writing up your board. Getting some additional results will not be worth it if you sacrifice the time you need to redoing the board. Are you in the middle of an experiment? If so, then finish it, but I would not recommend continuing experiments until the last minute. What do you have left to do?
Donna Hardy
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
I didn't answer one question. 600 nm is used to estimate microbial numbers because it works best for this application, and was determined empirically (it works). If you have a spectrophotometer that does not have a 600 nm filter, you could substitute a 570 or 620 filter, if those are available.
Donna
I didn't answer one question. 600 nm is used to estimate microbial numbers because it works best for this application, and was determined empirically (it works). If you have a spectrophotometer that does not have a 600 nm filter, you could substitute a 570 or 620 filter, if those are available.
Donna
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Re: Bacteria [Communications]
OK. So just to make sure:
I'll need the following to make a growth curve with the spectrophotometer.
1) Need to have taken the optical density reading of two nutrient broths with known amounts of population BEFORE
2) I can test for growth curves with the spectrophotometer?
If thats the case then I don't think I've started on the experiment yet
A bit disappointing.
I'll need the following to make a growth curve with the spectrophotometer.
1) Need to have taken the optical density reading of two nutrient broths with known amounts of population BEFORE
2) I can test for growth curves with the spectrophotometer?
If thats the case then I don't think I've started on the experiment yet
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
I'm so sorry I was not clear. You should just take a sample and measure the OD at 600nm periodically as your culture grows; the OD 600 will increase as the population increases. The plate count is the definitive result on a growth curve; the OD 600 nm just gives another measurement to monitor the increase in population. I had suggested this because the plate count results on your original experiment were unexpected. If you had had an OD 600 reading at the same time points as the plate count, it would have helped confirm results, or helped explain why the generation time was so short. However, it's a lot of work for one person with limited lab access to do a plate count and do an OD 600 with a growth curve at the same time, so don't worry if you don't get this done.
If you do have any results, please post the results. If you have not done any more experiments, just start on the revisions of your board and post the copy, and we'll make suggestions. You want to have the best possible presentation of the results you have obtained; it's not worth it to continue experimenting. You have plenty of data now!
Donna Hardy
I'm so sorry I was not clear. You should just take a sample and measure the OD at 600nm periodically as your culture grows; the OD 600 will increase as the population increases. The plate count is the definitive result on a growth curve; the OD 600 nm just gives another measurement to monitor the increase in population. I had suggested this because the plate count results on your original experiment were unexpected. If you had had an OD 600 reading at the same time points as the plate count, it would have helped confirm results, or helped explain why the generation time was so short. However, it's a lot of work for one person with limited lab access to do a plate count and do an OD 600 with a growth curve at the same time, so don't worry if you don't get this done.
If you do have any results, please post the results. If you have not done any more experiments, just start on the revisions of your board and post the copy, and we'll make suggestions. You want to have the best possible presentation of the results you have obtained; it's not worth it to continue experimenting. You have plenty of data now!
Donna Hardy
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Re: Bacteria [Communications]
I think I'll be walking in with the same data that I had for the regional fair
--
I attempted to add to the analysis of the data because that is what I think I'm lacking the most in. For graphs, I wanted to graph the exponential curve of the 3 doubling points I obtained from various temperatures, and I wanted to compare the curves (and coefficients of the curve fit) between the experimental data and the data obtained from aerobic growth.
Graphical analysis allows me to use two types of curve fits: a logarithm base 10 curve and an inverse exponent curve. Both seems to fit the curves really nicely, but they're two separate formulas -- would it make a difference as to which one I use? Given the formula that I mentioned in my materials protocol above, since it mentioned log 2 and that is in base 10, I am leaning towards using a logarithm base 10 curve?
Perhaps for the 600 OD readings I will continue that after the fair... onto next year
Also, I'm worried that the judges might see me testing two different temperatures the wrong way. Since I'm testing the effects of microaerophilic environments on the growth of bacillus subtilis, I wouldn't want to vary temperature, but the levels of oxygen -- would the judges see this the wrong way?
Another thing is that while I like my left panel and my center top, I think that in addition to my graphs problem (I don't know whether to graph the exponential curve and/or the constant growth rate (hopefully) on a log y axis, I'm not sure what to do with the conclusion.
A lot of people say that when I'm going from the regional to the big Intel ISEF I want to "improve" my board. I attempted ot understand more of the reason why, but I'm not sure if I have the space to communicate the "why" through the board -- would the judges think that this is a weakness? I'll aim to show that this isn't true through the presentation, but I think the board has a big part of the judging process...
I'm literally leaving the hypothesis, background research, materials and data untouched going into the Intel ISEF and this somewhat worries me. I'll take a picture of it tomorrow as tomorrow Sunday is one of the first setup days.
As for the concepts, I think I know the using of nitrate as an electron acceptor and not nitrite becuase it cannot be reduced by the structure of b. subtilis? (Does the term redox system have to do with this?) --
I've also seen that in addition to using nitrate as an electron acceptor for anaerobic growth b. subtilis also undergoes fermentative growth. Does b. subtilis use ethanol, lactic acid and hydrogen and convert them into energy through fermentative growth?
Sorry for the last-minuteness. Thanks
Sorry for the last minute-ness.
I attempted to add to the analysis of the data because that is what I think I'm lacking the most in. For graphs, I wanted to graph the exponential curve of the 3 doubling points I obtained from various temperatures, and I wanted to compare the curves (and coefficients of the curve fit) between the experimental data and the data obtained from aerobic growth.
Graphical analysis allows me to use two types of curve fits: a logarithm base 10 curve and an inverse exponent curve. Both seems to fit the curves really nicely, but they're two separate formulas -- would it make a difference as to which one I use? Given the formula that I mentioned in my materials protocol above, since it mentioned log 2 and that is in base 10, I am leaning towards using a logarithm base 10 curve?
Perhaps for the 600 OD readings I will continue that after the fair... onto next year
Also, I'm worried that the judges might see me testing two different temperatures the wrong way. Since I'm testing the effects of microaerophilic environments on the growth of bacillus subtilis, I wouldn't want to vary temperature, but the levels of oxygen -- would the judges see this the wrong way?
Another thing is that while I like my left panel and my center top, I think that in addition to my graphs problem (I don't know whether to graph the exponential curve and/or the constant growth rate (hopefully) on a log y axis, I'm not sure what to do with the conclusion.
A lot of people say that when I'm going from the regional to the big Intel ISEF I want to "improve" my board. I attempted ot understand more of the reason why, but I'm not sure if I have the space to communicate the "why" through the board -- would the judges think that this is a weakness? I'll aim to show that this isn't true through the presentation, but I think the board has a big part of the judging process...
I'm literally leaving the hypothesis, background research, materials and data untouched going into the Intel ISEF and this somewhat worries me. I'll take a picture of it tomorrow as tomorrow Sunday is one of the first setup days.
As for the concepts, I think I know the using of nitrate as an electron acceptor and not nitrite becuase it cannot be reduced by the structure of b. subtilis? (Does the term redox system have to do with this?) --
I've also seen that in addition to using nitrate as an electron acceptor for anaerobic growth b. subtilis also undergoes fermentative growth. Does b. subtilis use ethanol, lactic acid and hydrogen and convert them into energy through fermentative growth?
Sorry for the last-minuteness. Thanks
Sorry for the last minute-ness.
Trader - scientist wannabe =)
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
I think you are setting up today, so I recommend making as few changes as possible. Your project was very good at the regionals, so all of the ideas we had were just suggestions. There was nothing at all wrong with the presentation, and I think you are comfortable with it, so please don't worry about changing anything.
The graphs for the growth curve should be log base 10. This should give a linear curve during the log phase of growth.
Yes, redox reactions refer to the gain and loss of electrons in chemical reactions. Reduction refers to gaining electrons and oxidation is the loss of electrons. So B. subtilis has the ability to give electrons to nitrate, thereby reducing it to nitrite. I’m not absolutely certain, but I think that the medium you used does not contain nitrate.
B. subtilis would convert the glucose to various metabolic products to produce energy. B. subtilis has been shown to use two major pathways to metabolize glucose, the Emden-Meyerhof pathway, in which glucose is converted to pyruvic acid and the hexose –monophosphate pathway, in which glucose (a 6-carbon sugar) is converted to 5 carbon sugars.
http://www.pubmedcentral.nih.gov/articl ... tid=278424
http://en.wikipedia.org/wiki/Metabolic_pathway
http://www.scribd.com/doc/5424827/Hexos ... ay-Pathway
B. subtilis would probably not be able to metabolize ethanol or lactic acid, or oxidize hydrogen.
The biochemistry is really outside the scope of your project, so don’t spend too much time on this. Please don’t put any of these reactions in your write-up, otherwise the judges will ask you questions, and since you haven’t had biochemistry yet, you aren’t quite ready to discuss this topic. You have plenty of information presented in your project, so just focus on that.
Please don’t worry about what the judges will think at this point as you can’t control this. You are jet-lagged, so do make sure you get enough rest so you can focus on what you can control, and present your project as positively as possible.
It’s good you are thinking about next year. You really have developed a good base of knowledge and experience with this project, and what you will need for next year is a really spectacular project that will build on this one, and that you will be able to do with the resources you have available. I’m sure you will think of something.
Donna Hardy
I think you are setting up today, so I recommend making as few changes as possible. Your project was very good at the regionals, so all of the ideas we had were just suggestions. There was nothing at all wrong with the presentation, and I think you are comfortable with it, so please don't worry about changing anything.
The graphs for the growth curve should be log base 10. This should give a linear curve during the log phase of growth.
Yes, redox reactions refer to the gain and loss of electrons in chemical reactions. Reduction refers to gaining electrons and oxidation is the loss of electrons. So B. subtilis has the ability to give electrons to nitrate, thereby reducing it to nitrite. I’m not absolutely certain, but I think that the medium you used does not contain nitrate.
B. subtilis would convert the glucose to various metabolic products to produce energy. B. subtilis has been shown to use two major pathways to metabolize glucose, the Emden-Meyerhof pathway, in which glucose is converted to pyruvic acid and the hexose –monophosphate pathway, in which glucose (a 6-carbon sugar) is converted to 5 carbon sugars.
http://www.pubmedcentral.nih.gov/articl ... tid=278424
http://en.wikipedia.org/wiki/Metabolic_pathway
http://www.scribd.com/doc/5424827/Hexos ... ay-Pathway
B. subtilis would probably not be able to metabolize ethanol or lactic acid, or oxidize hydrogen.
The biochemistry is really outside the scope of your project, so don’t spend too much time on this. Please don’t put any of these reactions in your write-up, otherwise the judges will ask you questions, and since you haven’t had biochemistry yet, you aren’t quite ready to discuss this topic. You have plenty of information presented in your project, so just focus on that.
Please don’t worry about what the judges will think at this point as you can’t control this. You are jet-lagged, so do make sure you get enough rest so you can focus on what you can control, and present your project as positively as possible.
It’s good you are thinking about next year. You really have developed a good base of knowledge and experience with this project, and what you will need for next year is a really spectacular project that will build on this one, and that you will be able to do with the resources you have available. I’m sure you will think of something.
Donna Hardy
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chiazuohui
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Re: Bacteria [Communications]
Good luck for your ISEF!! 
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Re: Bacteria [Communications]
Thanks Chiazuohui! Are you going to the fair as well?
Donna -- I'm finishing up last minute touches now
-- the thing I see with a lot of boards is that they have a LOT of text. Its almost like 12 pt Times New Roman on there, and I have to squint to see their long essays on the background, analysis, etc etc. Though it is printed (I should do that next year)
I know there'll probably be no use worrying or anything, but do you happen to know if the judges would prefer essay boards, or a brief summary of a board that looks like a very simple experiment -- buuut I'm hoping to explain everything in the presentation? It's probably too late to change anything, but it'll be nice to know.
I was just looking over the judging rubric, and a "are all variables correctly identified" is part of the criteria. I'm afraid all I know are dependent and independent variables, and controlled variables -- and I think that for this experiment, there isn't really an independent or dependent variable because I am unable to measure how much oxygen is in the environment to produce the change I see in the growth of bacteria?
As for the changing temperature thing -- should a judge ask "OK, so if you're testing the effect of a microaerophilic environment on b. subtilis, why did you change temperatures through the experiment?" I'm not sure how I would answer -- I hope its not going to be too bad on the judging process (though I shouldn't focus too much on that and have fun
) if I say that I originally planned to check out each growth rate, but I was unable to have the resources to continue that many trial (including time), so I ended up not being able to do it... if I had just 2 more weeks (though even after the regional fair where I did have 2 more weeks... I didn't do anything because it would just take too long to prepare everything, ...) I would be getting growth curves for 37 and 30 C.
For my experiment, would a 2 graphs showing the exponential growth (log) for 37 C, and 30 C as well as a semi-log graph showing the constant linear growth rate be the best representative? That is what I have ...
Thank you for bearing with me
It's already been very fun -- the pin exchange was great! Unfortunately I didn't bring enough pins ... =P so I ended up having to trade some of the ones I have away -- of course, only the ones that I don't like
haha
Donna -- I'm finishing up last minute touches now
I know there'll probably be no use worrying or anything, but do you happen to know if the judges would prefer essay boards, or a brief summary of a board that looks like a very simple experiment -- buuut I'm hoping to explain everything in the presentation? It's probably too late to change anything, but it'll be nice to know.
I was just looking over the judging rubric, and a "are all variables correctly identified" is part of the criteria. I'm afraid all I know are dependent and independent variables, and controlled variables -- and I think that for this experiment, there isn't really an independent or dependent variable because I am unable to measure how much oxygen is in the environment to produce the change I see in the growth of bacteria?
As for the changing temperature thing -- should a judge ask "OK, so if you're testing the effect of a microaerophilic environment on b. subtilis, why did you change temperatures through the experiment?" I'm not sure how I would answer -- I hope its not going to be too bad on the judging process (though I shouldn't focus too much on that and have fun
For my experiment, would a 2 graphs showing the exponential growth (log) for 37 C, and 30 C as well as a semi-log graph showing the constant linear growth rate be the best representative? That is what I have ...
Thank you for bearing with me
It's already been very fun -- the pin exchange was great! Unfortunately I didn't bring enough pins ... =P so I ended up having to trade some of the ones I have away -- of course, only the ones that I don't like
Trader - scientist wannabe =)
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
I can't imagine boards in 12-point, but I can understand why it was necessary to fit into the space. Your board must be clear and readable, so please don't reduce the type size. A summary that looks like a simple experiment would be preferable to one that is unreadable.
I've never judged at ISEF, but I always prefer a presentation that briefly presents the project, followed by details to support the outline. You have to imagine the difficulty of the judges who have to review many projects. Even at ISEF, I imagine they would want to be able to understand the project after 30-45 seconds of looking at the board, or by reading the abstract.
You really know all you need to know, and more about the topic that some of the judges. The temperature (30 and 37 degrees C) is your independent variable; the number of bacteria (your growth curves) are your dependent variable. All other parameters (medium, starting number of organisms, etc.) are controlled, or at least as well as possible, as you know from your experiments.
Good luck at the judging!
Donna
I can't imagine boards in 12-point, but I can understand why it was necessary to fit into the space. Your board must be clear and readable, so please don't reduce the type size. A summary that looks like a simple experiment would be preferable to one that is unreadable.
I've never judged at ISEF, but I always prefer a presentation that briefly presents the project, followed by details to support the outline. You have to imagine the difficulty of the judges who have to review many projects. Even at ISEF, I imagine they would want to be able to understand the project after 30-45 seconds of looking at the board, or by reading the abstract.
You really know all you need to know, and more about the topic that some of the judges. The temperature (30 and 37 degrees C) is your independent variable; the number of bacteria (your growth curves) are your dependent variable. All other parameters (medium, starting number of organisms, etc.) are controlled, or at least as well as possible, as you know from your experiments.
Good luck at the judging!
Donna
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deleted-2131
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Re: Bacteria [Communications]
Trader,
I echo Donna's comments completely. A readable board that summarizes the main points of the project is preferable to a tome of information that is poorly organized and that fails to help me see the most important points. You have spent a lot of time preparing and working for this; now is the time to relax and enjoy it. You will do your best and that is all you can do - relax and have fun. Stressing about these things at the last minute will only frazzle you.
I echo Donna's comments completely. A readable board that summarizes the main points of the project is preferable to a tome of information that is poorly organized and that fails to help me see the most important points. You have spent a lot of time preparing and working for this; now is the time to relax and enjoy it. You will do your best and that is all you can do - relax and have fun. Stressing about these things at the last minute will only frazzle you.
All the best,
Terik
Terik
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Trader
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Re: Bacteria [Communications]
Cool -- I was just unsure about the inconsistency between the title and the focus of the project "effect of microaerophilic environment on growth of facultative anaerobe b. subtilis" and having my independent variable as temperature, which makes it a bit weird.
I can upload a picture very soon -- as for the significance, I was wondering if the significance goes beyond helping better understand / quantitating (even though I dont know the actual oxygen level I used) the effect of less oxygen on b. subtilis. I also have stated in my purpose "to test the definition of b. subtilis as a facultative anaerobe" -- is this risky? I thought that it was shown that it was suggested/shown that b. subtilis wasn't an obligate aerobe at around 1997 which was more than 12 years ago which isn't that recent -- and mentioned in 2000 that it was a facultative anaerobe I think.
So it wouldn't be really significant because it seems like the proposal that it is a facultative anaerobie is well established? Just not sure how definite the classification of b. subtilis as a facultative anaerobe is. If it is definite, I have the time to remove that. I'm not too sure...
As for the significance of the experiment (sorry yet again) -- I know that b. subtilis is used for the fermentative/creation of industrial enzymes -- and I remember that back in the regional fair, I was asked about a specific example that it applied to. I wasn't able to give a specific example, and now I think I have one --
Under this -- "Anaerobic Growth of Bacillus mojavensis and Bacillus subtilis Requires DNA" aem.asm.org/cgi/content/abstract/70/9/5252 it says that one example is for the recovery of petroleum hydrocarbons that "remain entrapped after current recovery technologies reach their economic limit"...microorganisms produce a variety of biosurfactants, several of which generate the ultra-low interfacial tensions needed for hydrocarbon mobilization, and bacillus mojavensis produces this under anaerobic conditions
I'm not sure if this applies to b. subtilis, but is this the around the idea of what b. subtilis does? I also know w/ b. subtilis' use in probiotics -- would the stomach be a microaerophilic environment? =P Back then I wasn't sure, so I didn't use that example, but it'd be interesting to anticipate growth patterns in places where we want the bacteria
Just want to clarify:
There are only TWO ways that b. subtilis grows under anaerobic conditions
> fermentation growth (which is the opposite of cellular respiration, = does not donate electrons to nitrate but instead takes electrons? This is the process of oxidization?"
> using electron acceptors which donates electrons to nitrate and not nitrite.
Finally I was looking at the judging guidelines for the fair and noticed that it called for some things that I don't think I have:
1) creative ability and originality in analysis and interpretation of data (I'm not sure what this means -- I tried to display creativity and analysis through my graphs, with the exponential curve and the semilog graph -- anything else I can add into my presentation and/or to my research paper? I do have one more day of setup...)
2) variables clearly recognized and defined (I'm afraid this isn't the case with the temperature/microaerophilic environment messup
) because changing both the oxygen requirements into microaerophilic and changing temperature, that would be 2 variables right?
and 3) control group -- I know that a control group is to make sure that the results are actuall as a result of the independent variable (which is temperature? But I'm trying to manipulate oxygen level requirements
), so would the control group be when I plated bacteria in a microaerophilic environment in any temperature, any amount, and after dilution plating, there were colonies that occured?
Thank you once again -- last day tomorrow to prepare! I'm terribly sorry for the last minute-ness
I can upload a picture very soon -- as for the significance, I was wondering if the significance goes beyond helping better understand / quantitating (even though I dont know the actual oxygen level I used) the effect of less oxygen on b. subtilis. I also have stated in my purpose "to test the definition of b. subtilis as a facultative anaerobe" -- is this risky? I thought that it was shown that it was suggested/shown that b. subtilis wasn't an obligate aerobe at around 1997 which was more than 12 years ago which isn't that recent -- and mentioned in 2000 that it was a facultative anaerobe I think.
So it wouldn't be really significant because it seems like the proposal that it is a facultative anaerobie is well established? Just not sure how definite the classification of b. subtilis as a facultative anaerobe is. If it is definite, I have the time to remove that. I'm not too sure...
As for the significance of the experiment (sorry yet again) -- I know that b. subtilis is used for the fermentative/creation of industrial enzymes -- and I remember that back in the regional fair, I was asked about a specific example that it applied to. I wasn't able to give a specific example, and now I think I have one --
Under this -- "Anaerobic Growth of Bacillus mojavensis and Bacillus subtilis Requires DNA" aem.asm.org/cgi/content/abstract/70/9/5252 it says that one example is for the recovery of petroleum hydrocarbons that "remain entrapped after current recovery technologies reach their economic limit"...microorganisms produce a variety of biosurfactants, several of which generate the ultra-low interfacial tensions needed for hydrocarbon mobilization, and bacillus mojavensis produces this under anaerobic conditions
I'm not sure if this applies to b. subtilis, but is this the around the idea of what b. subtilis does? I also know w/ b. subtilis' use in probiotics -- would the stomach be a microaerophilic environment? =P Back then I wasn't sure, so I didn't use that example, but it'd be interesting to anticipate growth patterns in places where we want the bacteria
Just want to clarify:
There are only TWO ways that b. subtilis grows under anaerobic conditions
> fermentation growth (which is the opposite of cellular respiration, = does not donate electrons to nitrate but instead takes electrons? This is the process of oxidization?"
> using electron acceptors which donates electrons to nitrate and not nitrite.
Finally I was looking at the judging guidelines for the fair and noticed that it called for some things that I don't think I have:
1) creative ability and originality in analysis and interpretation of data (I'm not sure what this means -- I tried to display creativity and analysis through my graphs, with the exponential curve and the semilog graph -- anything else I can add into my presentation and/or to my research paper? I do have one more day of setup...)
2) variables clearly recognized and defined (I'm afraid this isn't the case with the temperature/microaerophilic environment messup
and 3) control group -- I know that a control group is to make sure that the results are actuall as a result of the independent variable (which is temperature? But I'm trying to manipulate oxygen level requirements
Thank you once again -- last day tomorrow to prepare! I'm terribly sorry for the last minute-ness
Trader - scientist wannabe =)
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
This is good that you are focusing the details of the project. The oxygen levels in your experiment were one of the controlled variables; you grew all of the cultures under microaerophilic conditions (because you did not have a way to continuously aerate them).
There have been several references showing that B. subtilis is a facultative anaerobe, so I think it would be safe to leave this information in. Just leave your write up the way it is. Your results support the literature references.
The use of B. subtilis to produce industrial enzymes and to recover petroleum hydrocarbons are excellent practical examples of the significance of the type of experiment. The use of B. subtilis in probiotics in the treatment of gastrointestinal disorders caused by antibiotic treatment is another good example; the spores survive the acidic environment of the stomach and germinate and grow in the microaerophilic environment of the intestinal tract. These are also excellent topics for future science fair projects. I think that a basic understanding of how microorganisms grow is significant as well, and is intrinsically interesting.
You are correct. B. subtilis has two different metabolic pathways that can be used under anaerobic conditions. If nitrate is present, an enzyme called nitrate reductase is produced and nitrate is used as the final electron receptor. If nitrate is not present, then a fermentative pathway, which requires amino acids, is used and glucose is fermented to produce end products called acetoin and butanediol. Since your medium did not contain nitrate, but did contain glucose and amino acids, your B.subtilis cultures probably were using the fermentative pathway to produce energy needed for metabolism.
Your analysis of your data is very creative and original, and I would definitely not recommend adding anything at this point. Your experiment had only one variable, temperature. The flasks were incubated under identical oxygen levels, and were aerobic initially but rapidly because microaerophilic because you did not have a way to aerate them.
You are well aware of the limitations of your experiment, and the data you were able to obtain with limited resources. However, the strong point about your project is your understanding of the subject and the background reading you have done on current literature references. This shows through on your board write up, and you should use to your advantage when you talk to judges.
Donna Hardy
This is good that you are focusing the details of the project. The oxygen levels in your experiment were one of the controlled variables; you grew all of the cultures under microaerophilic conditions (because you did not have a way to continuously aerate them).
There have been several references showing that B. subtilis is a facultative anaerobe, so I think it would be safe to leave this information in. Just leave your write up the way it is. Your results support the literature references.
The use of B. subtilis to produce industrial enzymes and to recover petroleum hydrocarbons are excellent practical examples of the significance of the type of experiment. The use of B. subtilis in probiotics in the treatment of gastrointestinal disorders caused by antibiotic treatment is another good example; the spores survive the acidic environment of the stomach and germinate and grow in the microaerophilic environment of the intestinal tract. These are also excellent topics for future science fair projects. I think that a basic understanding of how microorganisms grow is significant as well, and is intrinsically interesting.
You are correct. B. subtilis has two different metabolic pathways that can be used under anaerobic conditions. If nitrate is present, an enzyme called nitrate reductase is produced and nitrate is used as the final electron receptor. If nitrate is not present, then a fermentative pathway, which requires amino acids, is used and glucose is fermented to produce end products called acetoin and butanediol. Since your medium did not contain nitrate, but did contain glucose and amino acids, your B.subtilis cultures probably were using the fermentative pathway to produce energy needed for metabolism.
Your analysis of your data is very creative and original, and I would definitely not recommend adding anything at this point. Your experiment had only one variable, temperature. The flasks were incubated under identical oxygen levels, and were aerobic initially but rapidly because microaerophilic because you did not have a way to aerate them.
You are well aware of the limitations of your experiment, and the data you were able to obtain with limited resources. However, the strong point about your project is your understanding of the subject and the background reading you have done on current literature references. This shows through on your board write up, and you should use to your advantage when you talk to judges.
Donna Hardy
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Trader
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- Project Status: I am conducting my research
Re: Bacteria [Communications]
Thank you very much!!! That really clears things up 
One last thing -- I'm not too good at identifying a control group, but if the purpose of a control group is to determine that the results are actually as a result of the independent variable -- would my experiment that grew any amount of bacteria in broth, and then processed it through dilution plating and obtained results be an indicator of this? (My technique isn't that good =P)
Also for the microaerophilic environment, as I was unable to continuously aerate, would there be decreasing oxygen levels throughout the experiment, therefore there might have been a decrease in growth rate throughout the experiment? (then the environment would eventually be anaerobic?)
I'm also adding the last bits of my error analysis. I think that because the smallest increment of the micropipette is 0.01 mL, the uncertainty is 0.005, and the smallest increment of the pipette is 0.1 mL so the uncertainty would be 0.05 mL.
In the case where I use the pipette once, then the micropipette maybe 4 times, would the systematic error % be 0.005 + 0.05 *4? = 0.205 = up to a 20% difference from the actual population?
I also mentioned aerobic conditions of 20 minutes as well as anaerobic conditions in some of the related experiments.
If I can tell that anaerobic growth much slower than and aerobic growth is faster than that in microaerophilic environment (from what I read in the related articles), can I graph my experimental results, the "theoretical" aerobic growth and "theoretical" anaerobic growth? .
Because during practice someone asked me "so how can you just assume that the lower growth was because of some difference in the experimental setup and not because of oxygen??
Also, ONE LAST THING (last post!!! because judging is tomorrow!!) --
I am also a bit worried about the microaerophilic environment. I tried to say that after it starts at aerobic, it eventually goes into microaerophilic, ... BUT!! someone asked me "how much time do you think it'll take until the oxygen reaches microaerophilic levels?.
I have no idea.
One last thing is the practical application -- someone asked me a really good question: given what you now know about b. subtilis, what would you change about its use in probiotics and the creation of industrial enzymes? I wasn't too sure, but I thought that we would be able to change the quantity of it becaues we would be able to anticipate the growth and therefore know how much we should have and when?
Thank you once again. I look forward to seeing you at the fair!!
I'm sleeping early
One last thing -- I'm not too good at identifying a control group, but if the purpose of a control group is to determine that the results are actually as a result of the independent variable -- would my experiment that grew any amount of bacteria in broth, and then processed it through dilution plating and obtained results be an indicator of this? (My technique isn't that good =P)
Also for the microaerophilic environment, as I was unable to continuously aerate, would there be decreasing oxygen levels throughout the experiment, therefore there might have been a decrease in growth rate throughout the experiment? (then the environment would eventually be anaerobic?)
I'm also adding the last bits of my error analysis. I think that because the smallest increment of the micropipette is 0.01 mL, the uncertainty is 0.005, and the smallest increment of the pipette is 0.1 mL so the uncertainty would be 0.05 mL.
In the case where I use the pipette once, then the micropipette maybe 4 times, would the systematic error % be 0.005 + 0.05 *4? = 0.205 = up to a 20% difference from the actual population?
I also mentioned aerobic conditions of 20 minutes as well as anaerobic conditions in some of the related experiments.
If I can tell that anaerobic growth much slower than and aerobic growth is faster than that in microaerophilic environment (from what I read in the related articles), can I graph my experimental results, the "theoretical" aerobic growth and "theoretical" anaerobic growth? .
Because during practice someone asked me "so how can you just assume that the lower growth was because of some difference in the experimental setup and not because of oxygen??
Also, ONE LAST THING (last post!!! because judging is tomorrow!!) --
I am also a bit worried about the microaerophilic environment. I tried to say that after it starts at aerobic, it eventually goes into microaerophilic, ... BUT!! someone asked me "how much time do you think it'll take until the oxygen reaches microaerophilic levels?.
One last thing is the practical application -- someone asked me a really good question: given what you now know about b. subtilis, what would you change about its use in probiotics and the creation of industrial enzymes? I wasn't too sure, but I thought that we would be able to change the quantity of it becaues we would be able to anticipate the growth and therefore know how much we should have and when?
Thank you once again. I look forward to seeing you at the fair!!
I'm sleeping early
Trader - scientist wannabe =)
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Trader
- Posts: 141
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- Project Status: I am conducting my research
Re: Bacteria [Communications]
Thanks Donna Hardy and all the kind mentors who have helped me through the entire experience. I'm really glad to have made it this far.
Thank you ScienceBuddies for the wonderful site and the wonderful compilation of information and this forum -- it took my science fair journey far
I guess this concludes a school year of science fair
.
I've found some contacts that could set me up with a university level research setting (which I hope I can get to the summer)
Unfortunately, I was NOT accepted into the internship in New York -- is there any way any internships or research facilities are still looking for applicants this close to the summer? I really want to be able to start researching right away, I know that I would be able to do more if I am in the right place...
Thank you ScienceBuddies for the wonderful site and the wonderful compilation of information and this forum -- it took my science fair journey far
I guess this concludes a school year of science fair
I've found some contacts that could set me up with a university level research setting (which I hope I can get to the summer)
Unfortunately, I was NOT accepted into the internship in New York -- is there any way any internships or research facilities are still looking for applicants this close to the summer? I really want to be able to start researching right away, I know that I would be able to do more if I am in the right place...
Trader - scientist wannabe =)
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deleted-2131
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Re: Bacteria [Communications]
Hi Trader,
I'm glad that you had a good time at ISEF. It's exciting to have made some contacts that might help you connect with an internship! Off the top of my head I am not aware of any specific summer research programs that still have openings, but there is a fairly comprehensive listing that you can search here: http://societyforscience.org/stp/index.asp.
Congratulations on a job well done this year!
I'm glad that you had a good time at ISEF. It's exciting to have made some contacts that might help you connect with an internship! Off the top of my head I am not aware of any specific summer research programs that still have openings, but there is a fairly comprehensive listing that you can search here: http://societyforscience.org/stp/index.asp.
Congratulations on a job well done this year!
All the best,
Terik
Terik
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deleted-71447
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Re: Bacteria [Communications]
Congrats on a very productive season!
http://ikpe1101.ikp.kfa-juelich.de/brie ... ode72.html
For starters, you need the equation for the final measurement, which is simply the sum of the individual measurements:
Mt=M1+M2+M3+M4+M5
where Mt is the total volume transferred and M1,2,3,4,5 are individual pipette measurements.
From this equation, the derivatives of Mt with respect to M1, 2, 3, and 4 are all 1. Therefore the variance of the final measurement is equal to the sums of the variances of the M1, M2, M3, M4, and M5 measurements. If we assume that your systematic error of 0.05 or 0.005 represents two standard deviations, then the standard deviation of the final volume is
stdev=sqrt(0.025^2+0.0025^2+0.0025^2+0.0025^2+0.0025^2)=0.0255
So, the systematic error (2 standard deviations) of the sum of the 5 pipette measurements is 0.051.
Depending on your level of math, that might be confusing (sorry if it is). I'm glad to explain more if you want. Basically, the end result is that the error of your pipette is so much bigger than the errors of the micropipettes that the latter hardly matters.
Chris
Sorry I didn't get to this earlier. One way to tackle this problem is with error propagation analysis or the "law of error propagation."Trader wrote: I'm also adding the last bits of my error analysis. I think that because the smallest increment of the micropipette is 0.01 mL, the uncertainty is 0.005, and the smallest increment of the pipette is 0.1 mL so the uncertainty would be 0.05 mL.
In the case where I use the pipette once, then the micropipette maybe 4 times, would the systematic error % be 0.005 + 0.05 *4? = 0.205 = up to a 20% difference from the actual population?
http://ikpe1101.ikp.kfa-juelich.de/brie ... ode72.html
For starters, you need the equation for the final measurement, which is simply the sum of the individual measurements:
Mt=M1+M2+M3+M4+M5
where Mt is the total volume transferred and M1,2,3,4,5 are individual pipette measurements.
From this equation, the derivatives of Mt with respect to M1, 2, 3, and 4 are all 1. Therefore the variance of the final measurement is equal to the sums of the variances of the M1, M2, M3, M4, and M5 measurements. If we assume that your systematic error of 0.05 or 0.005 represents two standard deviations, then the standard deviation of the final volume is
stdev=sqrt(0.025^2+0.0025^2+0.0025^2+0.0025^2+0.0025^2)=0.0255
So, the systematic error (2 standard deviations) of the sum of the 5 pipette measurements is 0.051.
Depending on your level of math, that might be confusing (sorry if it is). I'm glad to explain more if you want. Basically, the end result is that the error of your pipette is so much bigger than the errors of the micropipettes that the latter hardly matters.
Chris
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
Welcome back from ISEF, and congratulations again for your outstanding job on a project well done! I think you did an amazing job in a short amount of time. If you can make contact with a local laboratory for your next research project, it will be so much easier to get your experiments done. You need to spend some time identifying a unique topic for next year's project. You should talk to the local lab and find out what they are working on and perhaps pick a related topic as the local researchers will be subject matter experts who will be able to help you.
It's disappointing that you did not get the New York internship. I am not aware of any openings for internships that are still open. There are always very limited openings for these positions, but I was hoping that you would be accepted.
Donna Hardy
Welcome back from ISEF, and congratulations again for your outstanding job on a project well done! I think you did an amazing job in a short amount of time. If you can make contact with a local laboratory for your next research project, it will be so much easier to get your experiments done. You need to spend some time identifying a unique topic for next year's project. You should talk to the local lab and find out what they are working on and perhaps pick a related topic as the local researchers will be subject matter experts who will be able to help you.
It's disappointing that you did not get the New York internship. I am not aware of any openings for internships that are still open. There are always very limited openings for these positions, but I was hoping that you would be accepted.
Donna Hardy
-
Trader
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- Project Status: I am conducting my research
Re: Bacteria [Communications]
I'll be in NYC and Boston, MA (near Emerson College) so I began asking local colleges for possible projects they are working on.
Unfortunately, it seems like most are reluctant to even reply to my email inquiries when I ask them whether any professors would be interested in offering a mentorship for a short period over the summer -- then again, I'm not too sure how this is done ^^.
Donna, do you happen to have any contacts in New York or Boston who may know some of the professors in the area? That might help. There are a LOT of colleges in Boston, so while I'll be having camp at Emerson (not known for science I believe), I can always move around the area and perhaps get some research done!
)
I'll get started on related literature... Especially articles dated 2008/2009...
Unfortunately, it seems like most are reluctant to even reply to my email inquiries when I ask them whether any professors would be interested in offering a mentorship for a short period over the summer -- then again, I'm not too sure how this is done ^^.
Donna, do you happen to have any contacts in New York or Boston who may know some of the professors in the area? That might help. There are a LOT of colleges in Boston, so while I'll be having camp at Emerson (not known for science I believe), I can always move around the area and perhaps get some research done!
I'll get started on related literature... Especially articles dated 2008/2009...
Trader - scientist wannabe =)
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donnahardy2
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Re: Bacteria [Communications]
Hi Trader,
I will look through all my Boston and NYC contacts and see if I can find a referral for you. This sounds like a good plan. What dates will you be in NYC and Boston?
Donna
I will look through all my Boston and NYC contacts and see if I can find a referral for you. This sounds like a good plan. What dates will you be in NYC and Boston?
Donna
-
Trader
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- Project Question: Role of AI-2 in Biofilm Formation of L. monocytogenes
- Project Due Date: Janurary 1, 2010 (2 months!!)
- Project Status: I am conducting my research
Re: Bacteria [Communications]
I'll be in Boston from 7/18 to 8/1 (the camp is only two weeks long)
As for New York, I have yet to finalize everything so I'm very flexible right now but I'm leaning towards 8/1 - 8/17 or so...
It's a bit weird because my home state is NY and I'll have to go to MA for two weeks before moving back.
Thank you very much!! I'm checking out many websites of many colleges in the NY but mostly Boston area... wow
As for New York, I have yet to finalize everything so I'm very flexible right now but I'm leaning towards 8/1 - 8/17 or so...
It's a bit weird because my home state is NY and I'll have to go to MA for two weeks before moving back.
Thank you very much!! I'm checking out many websites of many colleges in the NY but mostly Boston area... wow
Trader - scientist wannabe =)

