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PandaCreamPuff's Content

There have been 27 items by PandaCreamPuff (Search limited from 22-July 18)



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#113491 I am just venting some of my worries and frustration here....

Posted by PandaCreamPuff on 24 June 2011 - 04:44 PM in Venting and Counseling

thanks for asking.

Writing is going alright....I have 2-3 publications lined up for my supervisors to read...but they decided that teaching is more important than research at the moment...so they have actually stopped reading emails and turned off their phones....it's SO FRUSTRATING

and never mind about my thesis drafts....it's less than 5 months away and they have only read like 5% of what i have typed...which is probably 80% of the whole thesis >_<


I am at a point where:

1) I have no hope whatsoever about my chances for my degree
2) Even if I failed I would not feel as bad as I know I have tried my best, and I failed based on things outside my control.....hopefully this is not the case in the end though.....



#113272 Terminology Inquiry

Posted by PandaCreamPuff on 22 June 2011 - 07:48 AM in Genetics and Genomics

Hi all

I am writing up my thesis and wrote "islet" on a section of the chromosome containing multiple genes (loci), but then my supervisor circled islet and said "you mean locus? how different?" Therefore, I'd like to make sure that and islet is not just one locus but a region of multiple loci....if that is the case, then what is the difference between an islet and an operon?

Thanks



#109353 BLASTing a limited database

Posted by PandaCreamPuff on 10 May 2011 - 04:55 AM in Bioinformatics and Biostatistics

Hi all

I have nucleotide sequences which I would like to BLAST, however I would not like to BLAST the whole database, instead just a selected series of sequences. I would like to know how to get around that. Can I limit my search to only include some accession numbers?

Thank you so much



#108841 Having a paper translated from a foreign language

Posted by PandaCreamPuff on 04 May 2011 - 02:33 PM in Dissertation and Paper Writing

thanks for the reply.

I am aware of these translators, however I was more asking about whether there are services which are catered to the scientific community. I am not sure how reliable these translation products in terms of accurately conveying the messages in the publication.



#108761 Having a paper translated from a foreign language

Posted by PandaCreamPuff on 04 May 2011 - 05:25 AM in Dissertation and Paper Writing

Dear all

I have this important paper that is published in German. Do you guys know of any translation services out there? I am highly reluctant on using google translation, however I have found this website, and am wondering if any of you has used it before:

http://www.sciencedocs.com/

Thanks



#105159 I am just venting some of my worries and frustration here....

Posted by PandaCreamPuff on 29 March 2011 - 11:53 PM in Venting and Counseling

i tried using Zotero but I do not like the idea of sticking to firefox...

I have been taking notes on different notebooks based on the chapters of my thesis.

:)



#104530 Fisher Exact Test help

Posted by PandaCreamPuff on 23 March 2011 - 07:29 AM in Bioinformatics and Biostatistics

Dear all

I am making a 2 x 4 contingency table, but one of the cells has an expected frequency of less than 5. Therefore I cannot use the chi-square to compare observed vs expected ratio, and will need the use the Fisher's Exact Test.

Most of the Fisher Test tutorials talk about 2 x 2 contingency tables, but I am not sure how to fit this into a 2 x 2 table...

Outcome 1 Expected: 6
Outcome 2 Expected: 4

Outcome 1 Observed: 0
Outcome 2 Observed: 10

Can someone let me know how to get around this?

Thanks so much all



#102102 funny video to cheer us up

Posted by PandaCreamPuff on 27 February 2011 - 04:58 AM in Lab Jokes

that alone deserves a PhD pass



#102101 Regression analysis between two genes

Posted by PandaCreamPuff on 27 February 2011 - 04:55 AM in Bioinformatics and Biostatistics

Hi everyone

I am trying to determine if there is an association between the extent of sequence divergence of gene "A" between two species and the extent of divergence of gene "B." I would have one axis with the number of nucleotide mismatch of gene A, and another axis of gene B.

Is there a software that allows me to put in my sequence data, perform pairwise sequence analysis of both eachs in each paired combinations, and plot that as a regression analysis?

Thank you so much :)



#101751 ClustalW question

Posted by PandaCreamPuff on 24 February 2011 - 01:39 AM in Molecular Biology

Hi all

I would like to generate a tree based on multiple DNA sequence alignment from ClustalW. I have not trimmed my sequences, but under the default ClustalW setting, does it only calculate the similarities on the region where all sequences are aligned? In another words, if I have some sequences that are longer than others, will these regions be calculated as gaps?

I have posted an image of my alignment for visual aid: will the gap seen in sequence 2/1-829 be seen as differing from the other 3 sequences?

Posted Image

Thanks for any input.



#100983 Storing genomic DNA in 4C with PBS?

Posted by PandaCreamPuff on 17 February 2011 - 05:45 AM in Molecular Biology

It should be fine, this is more or less the pH and salt levels inside the cell anyway... however, they are more prone to bacterial/fungal and DNAse digestion if stored in PBS.


Thanks Bob.



#100650 Storing genomic DNA in 4C with PBS?

Posted by PandaCreamPuff on 15 February 2011 - 02:54 AM in Molecular Biology

Hi all

I have been storing genomic DNA after a heat-lysis method in PBS. I have been doing this for some time and my PCR and sequencing seems to work fine. I am just worried that for my thesis this will cause me some mark deduction, as I did not use TE buffer, which is probably the conventional way of storing DNA. Has anyone stored gDNA in PBS?

Thanks



#99075 I am just venting some of my worries and frustration here....

Posted by PandaCreamPuff on 30 January 2011 - 04:18 PM in Venting and Counseling

thanks for the comments. Lately I have been writing the intro section while finishing up my labwork.....still very stressed about the big day.



#92582 Gene borders

Posted by PandaCreamPuff on 18 November 2010 - 09:21 AM in Genetics and Genomics

Hi everyone

I am currently getting my head around some concepts regarding horizontal gene transfer. The following paper looked at recombinational events and have identified an "x" number of gene transfers:

http://www.plosntds....td-0000752-g002

They then address that a big proportion of the recombination breakpoints corresponds to "gene borders," suggesting that both inter and intra species recombination take place.

My question is that what does a "gene border" mean in this sense? Does it relate to sequences bordering homologies to two different species in nucleotide sequences?


Thank you so much



#90970 Molecular Diagnostic Method by PCR

Posted by PandaCreamPuff on 31 October 2010 - 01:02 PM in Molecular Biology

Hi all and happy Halloween. My science life has totally sucked me away from my Halloween night :(

Anyways, I am researching on a PCR-based molecular method for diagnosing etiological bacterial pathogens for mucosal illnesses. One aspect of PCR-based methods is that they do not require viable bacteria, as naked DNA can also be amplified if it's the targeted nucleotide fragment.

So my question is if anyone knows the duration of naked DNA persistence in the mucosal surfaces, specifically the respiratory tract? Because if it persists for a long time, the source of the naked DNA may not be present as an intact cell responsible for illnesses.

Thanks so much.



#88924 I am just venting some of my worries and frustration here....

Posted by PandaCreamPuff on 06 October 2010 - 03:47 PM in Venting and Counseling

So I am in my final year of my PhD. I am writing the discussion of my first publication, and I am extremely worried about my degree. I hate what I am writing. It doesn't sounds flowing and I feel I do not know enough at all about my topic. I believe that at this point I should be able to write 1000 words about my topic easily. However I am still at the point of reading up and feeling I am seriously losing time. I feel completely hopeless and there would be days where I read numerous articles, and the next day forget most of the key points of the papers.

I just don't know what to think. Seems like no matter how hard I work I am not really improving. It's so tempting to just tell everyone I am quitting and forget about this whole annoying degree >_<

:(

*sobs*



#83111 How to keep articles organized

Posted by PandaCreamPuff on 11 August 2010 - 08:10 AM in Reading and Organizing Literature

If you have a Mac do not hesitate: use Papers it is wonderfull!!!! Visit their Website


Wow that looks really amazing. That website has made my otherwise uneventful day B)



#82840 What do you guys eat for lunches?

Posted by PandaCreamPuff on 09 August 2010 - 03:49 AM in Chit Chat

Hi all

I know this may sound absurd and random, but I would like to know what I can eat during lunch times so that I can perform better in consolidating memories when I read scientific papers. Specifially, I think I need food that enhances my concentration. I would think avoiding carbs would help me get less sleepy....

I might just get fruits and vegs for lunch today.

Thanks guys :)

Cheers

PandaCreamPuff

PS: *runs to supermarket to get the freshest fruits now* >_<



#82564 In Vitro Evolution

Posted by PandaCreamPuff on 05 August 2010 - 12:52 PM in Evolution and Darwinism

don't know if it's relevant but there is at least one study working on evolution and adaptation in vitro in bacteria:

http://www3.intersci...ETRY=1&SRETRY=0



#82549 UK English vs. US English

Posted by PandaCreamPuff on 05 August 2010 - 09:46 AM in Dissertation and Paper Writing

Hi everyone!

So I am based in a UK lab trying to submit a paper to an American journal. My boss, by default, encourages me to write in UK English, however would it matter if I am submitting to an American journal? Would they want me to write in American English?

All these "organize" vs "organise" and "colonize" vs. "colonize" is doing my head in lol :angry:

Thanks a munch!

Cheers

PCP!



#82394 very bad signals after sequencing

Posted by PandaCreamPuff on 04 August 2010 - 04:03 AM in Bioinformatics and Biostatistics

does your sequencer get maintainanced according to the suggested timeframe for regular check ups? Our 3130 just had a maintenance done a month ago and had better results than ever before for everyone using it. Before it was alright but sometimes you would get very low signals and even failed sequence analysis. There are also the daily and weekly maintenance which should be done religiously to ensure quality results :)



#82392 Repost: A nice Word Addon for sequence manipulation and analysis

Posted by PandaCreamPuff on 04 August 2010 - 03:56 AM in Bioinformatics and Biostatistics

Looks good but do you have the article in pdf form? Biotechnique website has issues from 2004 in electronic format. I would like to check how to use this one under Mac.


Hi noelmathur try this?

http://www.biotechni...bc01_10422a.pdf



#79676 Inquiry about Obtaining reference bacterial strains

Posted by PandaCreamPuff on 15 July 2010 - 05:16 AM in Microbiology

hi all

I was under the impression that the convention is that bacterial strains can be obtained from ATCC or NCTC, however my boss insisted that I look at CDC. I did not dare asking him why not ATCC/NCTC. I looked at the CDC website and it's more like "oh you should wash your hand before dinner" that sort of website (more for the lay-people).

Does CDC actually have a reserve for bacterial strains where researchers can order? I learned from high school that they have the pox virus on reserve but other than that..... >_<

Thanks so much :)

Cheers

Marc



#78081 Restriction Digest Question

Posted by PandaCreamPuff on 04 July 2010 - 01:21 AM in Molecular Biology

Hi all

I have two sequences of about 700bp, and I would like to see if a particular RFLP enzyme can differentiate them from each other on a gel. Is there a programme that I can use to tell me which enzyme I should use? I am currently tackling NEBcutter but not having much luck.

Thanks all!



#77519 How often do you.....

Posted by PandaCreamPuff on 29 June 2010 - 12:46 PM in Dissertation and Paper Writing

Because I am about to submit my first paper, but then my professor was saying i should verify my data accurately to make sure the data is correct before submission (which I totally agree of course). He then goes on and says how his career is in my hands and if some other lab asks us to give them our samples to run and get different results then we have no more careers in science >_<




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