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ikwana's Content

There have been 27 items by ikwana (Search limited from 21-November 18)



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#115466 validate pour plate method

Posted by ikwana on 18 July 2011 - 05:22 PM in Microbiology

i'm validating the spread plate method and pour plate method.. by using chromocult agar.. i found out, pour plate is the best.. it gives perfect single colony... now i have to validate this method.. how? i use c.freudii and e.coli..



#102864 how to design a drug?

Posted by ikwana on 06 March 2011 - 05:47 AM in General Biology Discussion

my lect told us to do esei on how to design a drug.. we need to describe the R&R, disease, and animal choose for pre-clinical test.. i dont understand ... what this question want..
she said we must find one drug and explain on how do they design it..



#102284 how to check the secondary metabolites?

Posted by ikwana on 01 March 2011 - 05:23 AM in Botany and Plant Biology

currently, I do tissue culture on garlic tissue.. my lect said that, if the tissue grow some roots or shoots, it means, the plant has the secondry metabolites.. is it true?
and, from what i have read from internet, secondary metabolite have the antioxidant properties..

i'm kinda confius on have no idea what is my objective and significance of study on doing this tissue culture..



#98496 HELP ME!! i need a simple protocol

Posted by ikwana on 25 January 2011 - 06:28 AM in Research Idea, Design and Collaboration

Three major question come to my mind:
1. What purity you need to get? Is this project have to end with very high (eg. 90-99%) purity or is it just an attempt to purify to test your skills?
2. What equipment, materials, and methods do you have access to?
- chromatography - what systems (gravity flow, low pressure, SPE, FPLC, HPLC?) and columns (size exclusion, ion exchange, reversed phase?) do you have?
- electrophoresis?
- ultrafiltration and/or dialysis?
- lyophilization?
- centrifugation?
3. Do you have established protocol to test for this enzyme activity?


1. the purification is for determination of its antioxidant activity. i dont know the percentage
2. i think the system is gravity flow, and using size exclusion column. i only have polyacrylmide gel but i dont have the HiLoad 26/60 superdex 200 prep grade
i'm going to blend my sample and seive it and undergo centrifugation before separate in the column

3. i do refer to one journal.. i refer all the procedure from this journal..
u may download the attachment to read the journal..



#98439 HELP ME!! i need a simple protocol

Posted by ikwana on 24 January 2011 - 06:20 PM in Research Idea, Design and Collaboration

i need to purify n isolate allinase enzyme from garlic... BUT! from all jurnal that i've read, a lot of chemical are not available in my campus..

for example:-pefabloc,PLP,PEG-800, methyl-alpha-D-mannoside, HiLoad 26/60 superdex 200 prep grade,alpha-globulin, racemic alliin,lactate dehydrogenase, NADH

i really need any other procedure that only use simple chemical which all lab must have.. i can't order all the chemical above because the shipping time takes about 6 month n i have to finish this project this june..

i don't know what to read anymore.. help me plzz.. this is my final year project...



#98438 any idea what can replace this chemical?

Posted by ikwana on 24 January 2011 - 06:10 PM in Chemistry

i want to isolate allinase from garlic.. n do column chromatography... but, i do not have these chemical..
-pefabloc,PLP,PEG-800, methyl-alpha-D-mannoside, HiLoad 26/60 superdex 200 prep grade,alpha-globulin, racemic alliin,lactate dehydrogenase, NADH


do u have any idea how to replace all these? or how to make it?



#97681 garlic tissue culture final project

Posted by ikwana on 16 January 2011 - 05:05 AM in Botany and Plant Biology

erm, i hv problem to determine concentration of my ms agar.. what i know, i do mix 0.44g of ms powder in 100ml.

i need to know the concentration becoz i need to add growth hormone.

is this correct :

stock solution hormone = ms agar
(M1)(V1)=(M2)(V2)
thats why i need to know my ms concentration, but i dont know how..

and one thing, is hormone BAA is thermobile?



#96863 need protocol on purfication of allinase from raw garlic

Posted by ikwana on 07 January 2011 - 12:48 AM in Protein Expression and Purification

that depends on what your first column will be.

if it is gel filtration then pbs or tbs should be okay (you may want to add 0.5-1mM dtt to keep sulfhydryls reduced).

if it is ion exchange then you may want to use 20-50mM tris or 10-20mM phosphate at an appropriate pH (with dtt).


hey,thank u 4 ur concern..

owh... i so the gel filtration.. but i've the protocol to purify the enzyme (alliinase)

this the link of the journal
http://www.sciencedi...b8&searchtype=a


to blend it,
i have all the material, except
-pefabloc,PLP,PEG-800, methyl-alpha-D-mannoside, HiLoad 26/60 superdex 200 prep grade,alpha-globulin, racemic alliin,lactate dehydrogenase, NADH

do u have any idea, any other chemical that can replace these?

thank u =>



#96682 need protocol on purfication of allinase from raw garlic

Posted by ikwana on 04 January 2011 - 09:51 PM in Protein Expression and Purification

i need to isolate enzyme allinase from raw garlic. i need to use column chromatography.. what reagent i have to mix with the raw garlic ( for crushing, blend, homogenization)before pouring into column? what kind of gel that i have to use in the column? how am i gonna isolate only the allinase?

thank u.. =>



#96574 why genomic can't be use for pcr?

Posted by ikwana on 04 January 2011 - 01:01 AM in PCR, RT-PCR and Real-Time PCR

its about my science project.

i have to search for allinase gene from garlic.

from what i understand, i have to extract the raw garlic and obtain its whole genome.

and then, from the whole genome, i do the pcr to amplify allinase gene.

but my lecturer said, "we can't isolates gene from whole genomic" why??? then how am i going to get the gene if it is not from whole genome?

my idea is like searching for a word from a dictionary.. is my concept wrong?

i only have plant mini kit( to obtain the whole genome from the garlic clove)and PCR kit (to amplify the allinase gene)
is there any other kit that i can use?

help me please... i'm confusedddddddd....



#88553 help me on strawberry perl =(

Posted by ikwana on 01 October 2010 - 06:40 AM in Bioinformatics and Biostatistics

where must i save the hello.pl?

i don understand, wut do u mean by go to the same folder in cmd window? cmd is wut? command?



#88457 help me on strawberry perl =(

Posted by ikwana on 30 September 2010 - 10:11 AM in Bioinformatics and Biostatistics

how to use perl?

i've already install this perl.. then how to use it?
i have some code to be use by using this perl.. but where must i write the coding?

i use devc++.. but when i compiling, it says, 'sub' does not name a type

what does it mean???



#87938 how to extract enzyme allinase from garlic

Posted by ikwana on 24 September 2010 - 09:12 PM in Protein and Proteomics

how to extract allinase from garlic? and how to purify it?

how to determine its concentration?
im going to incubate garlic in different temperature.. how is it to determine whether there is changes in the behaviour of enzyme..

allin will interact allinase to become allicin.. do i have to use allicin to observe the reaction of the allinase?



#84056 Diluting Ampicillin into LB Agar

Posted by ikwana on 18 August 2010 - 10:16 PM in General Lab Techniques

i'm now trying to find how to determine the standard concentration (dially disulphide, diallyl sulphide, ajoene) for Gas chromatography analysis.

and.. sumbody told me to find it, u must calculate from Rf factor..

then i go..." what da heck is Rf? how to calculate it??" :o

i try to find from the internet.. but.. nothin.. <_<

my fren said.. rf is sumthing u must calculate from the graph... then i go..."wut? :o graph? :huh: ?"

GC... for chemistry student... not me.. i havent learn it.. i've only use it twice.. :(

please guys.. help me..... how? how? how?



#84055 Gas chromatography for garlic

Posted by ikwana on 18 August 2010 - 10:03 PM in General Lab Techniques

Looks ok to me, but then I've only done a couple of GC runs before.


really?
actually, this preparation is for HPLC analysis, but is it possible to be used on GC?



#84054 how to prepare garlic extract for GC?

Posted by ikwana on 18 August 2010 - 09:59 PM in Research Idea, Design and Collaboration

how to prepare extraction of garlic before undergoe Gas chromatography?

is this correct?

Preparation of extracts:
Fresh garlic cloves were peeled, coarsely chopped with a knife and a 10 g sample homogenised for 2 min with 100 ml distilled water in a food blender (Kenwood). The homogenate was allowed to stand at room temperature for 15 min to ensure the complete enzymatic transformation of thiosulphinates before being filtered through 4 layers of cheesecloth.
A 50 ml sample of the filtrate was pipetted to a 500 ml conical flask and 15 g sodium chloride (NaCl) added to saturate the solution. After ensuring complete dissolution of the NaCl, 50 ml cold dichloromethane (CH2Cl2) was added and the stoppered flask agitated vigorously for 3 min. The resultant emulsion was centrifuged at 4000 rpm for 15 min, the lower solvent layer removed and dried twice with anhydrous sodium sulphate (Na2SO4).
A 10 ml sample of the dry extract was then pipetted to a 10 l measuring cylinder. This was placed in a water bath at 25C 5C, and the extract was rapidly concentrated by bubbling dry nitrogen through it. The solvent was evaporated to < 1 ml final volume and then adjusted accurately to 1 ml with dichloromethane. The concentrated extract was taken up in a glass syringe and injected directly through a 0.2 m in-line nylon filter into a 10 m fixed sample loop.
Due to the instability of thiosulphinates in organic solvents all HPLC runs were undertaken within 45 min of extraction.



#83916 compound in garlic

Posted by ikwana on 17 August 2010 - 08:20 PM in Botany and Plant Biology

can sumbody tel me, where can i find all the compund garlic and its percentage?

:P



#83909 Gas chromatography for garlic

Posted by ikwana on 17 August 2010 - 07:59 PM in General Lab Techniques

how to prepare extraction of garlic before undergoe GC?

is this correct?

Preparation of extracts:
Fresh garlic cloves were peeled, coarsely chopped with a knife and a 10 g sample homogenised for 2 min with 100 ml distilled water in a food blender (Kenwood). The homogenate was allowed to stand at room temperature for 15 min to ensure the complete enzymatic transformation of thiosulphinates before being filtered through 4 layers of cheesecloth.
A 50 ml sample of the filtrate was pipetted to a 500 ml conical flask and 15 g sodium chloride (NaCl) added to saturate the solution. After ensuring complete dissolution of the NaCl, 50 ml cold dichloromethane (CH2Cl2) was added and the stoppered flask agitated vigorously for 3 min. The resultant emulsion was centrifuged at 4000 rpm for 15 min, the lower solvent layer removed and dried twice with anhydrous sodium sulphate (Na2SO4).
A 10 ml sample of the dry extract was then pipetted to a 10 l measuring cylinder. This was placed in a water bath at 25C 5C, and the extract was rapidly concentrated by bubbling dry nitrogen through it. The solvent was evaporated to < 1 ml final volume and then adjusted accurately to 1 ml with dichloromethane. The concentrated extract was taken up in a glass syringe and injected directly through a 0.2 m in-line nylon filter into a 10 m fixed sample loop.
Due to the instability of thiosulphinates in organic solvents all HPLC runs were undertaken within 45 min of extraction.



#83803 gas chromatography and its standard??

Posted by ikwana on 17 August 2010 - 05:55 AM in Chemistry

how to determine the concentration for standard to be use on gas chromatography?

what i want to detect in my mixture is diallyl sulfide, diallyl disulfide and ajoene

i only know about their boiling point..

what else do i hv to know about these compound b4 proceeding the GC?

:blink: :blink: :blink:



#83599 sequence assembly using CAP

Posted by ikwana on 15 August 2010 - 07:36 PM in Bioinformatics and Biostatistics

are these homework or test questions?


its homework.. i've already answered some of them.. so, i just wana compare my answer wit others..

these is my answer:

1. By using the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing. To know the sequence that the primer should be made to match, primer pairs are selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving sequencing success rate, which currently exceeds 95% for exons, they have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.


4.
The coverage should occur between 5- and 8-fold for maximum benefit and minimum overall cost.


is it correct? :(



#83543 sequence assembly using CAP

Posted by ikwana on 14 August 2010 - 11:52 PM in Bioinformatics and Biostatistics

1. DNA sequencing requires a primer, which must be made with a specific sequence that can bind to an already known sequence on the molecule to be sequenced. in the case of directed sequencing, how do we know the sequence that the primer should be made to match? in the case of shotgun sequencing, how do we know the sequence of the primer to use?

2. in any sequencing project, errors occur in the actual synthesis of the DNA fragments and in the process of reading the fragment from the gel and base-calling. what is the main way of correcting those error in a large-scale sequenccing project?

3.what is the minimum coverage for shotgun contig?

4. why high coverage can be considered to represent a low error rate?

5.what reverse complement for? where is it to use?



#83500 allium sativum (garlic) and its antioxidant

Posted by ikwana on 14 August 2010 - 10:02 AM in Biology Science Fair Projects

Those genes are ones from Fusarium, which is a fungus (sinorhizobium is a bacterium) and will not be the same as the one found in garlic, though there may well be some similarities.

Try http://www.ncbi.nlm....orgn:__txid4682 for the alliinase genes. Look for complete cds.


ok thx.. i saved dat sequnce.. but now i want to find sequence for alliin.. when i search allin at NCBI, it comes out the allin lyase.. from what i know, allin lyase is another name for alliinase rite?



#83492 boiling point of allicin, diallyl sulphide, diallyl disulphide and ajoene

Posted by ikwana on 14 August 2010 - 08:14 AM in Biochemistry

who knows the boiling point of allicin, diallyl sulphide, diallyl disulphide and ajoene?

can enzyme like allinase be detected by gas chromatopragphy method? :(



#83218 allium sativum (garlic) and its antioxidant

Posted by ikwana on 11 August 2010 - 10:24 PM in Biology Science Fair Projects

http://www.ncbi.nlm....y/?term=ALLICIN Have a look at the Nucleotide link.


:D yeaaa!! got the sequence! it codes for allinase rite?
but why the source of organism is fusarium? :huh:
when i blast the sequence, it comes out the sinorhizobium, wuts their correlation? :blink:
i hv another problem, when i click for pick primer, it says that "Primer specificity cannot be properly determined as sequences from the specified organism (Fusarium sp.) are not present in selected database: refseq_rna. " :o

should i go to protein sequence instead of nucleotide.. cuz i hv to do pcr for gene responsible codes for allinase? or should i search for allin? its kinda confuse :unsure:



#83075 allium sativum (garlic) and its antioxidant

Posted by ikwana on 11 August 2010 - 01:49 AM in Biology Science Fair Projects

As far as I can see there is no gene for Allicin, it is produced by the enzyme Alliinase acting on Alliin which is a modified cysteine. There are two entries on NCBI for Allicin production from bacteria and fungus respectively.



the production is in wut category? nucleotide or jurnal? how am i going to get the sequence of allinase production? :blink:




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