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Novozyme 234 is the best enzyme for the isolation of protoplast but in recent days the Novozyme 234 are not commercially available. So is there any other method (enzymatic) for this isolation?
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You can use chitinase and cellulase CP.
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In my idea, it can be possible to set a grid on the surface of the liquid but I don't find any information about this.
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I would like to quantify the OTR and the oxygen demand in different cultures and rpm of shaker by the method of gas in and gas out, but is not very clear which formulas used, and which measurement magnitude are replaces the variables in the formulas.
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I have studied energetic optimization and adaptive control of the dissolved oxygen concentration in aerobic fermenters having air flow and/or agitation rate as manipulated variable(s). The parameters from the usual KLa correlation were estimated through the recursive least squares algorithm with forgetting factor, thus allowing for on-line estimation of KLa in real-time. A sinusoidal disturbance was imposed to manipulated variables:
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I am working to find a bioactive compound from a bacterial source which can show antifungal activity. So I have established the bacterial culture in a synthetic medium. What we found that the enzyme/proteinous compound is mainly extracellular in nature. Now I want to go for isolation, extraction and purification of the compound from the liquid culture of bacteria at laboratory scale. So I am asking to share your knowledge about the sort of suitable methods which will be helpful for getting the desired compound.
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Try this website protocols
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As C/N is very critical in the optimization of the Exopolysaccharide production by Microorganisms. My concern is that I have used complex media such as tryptic soy broth (TSB) for other optimization experiments. TSB medium contains glucose as carbon and tryptone as the nitrogen source. Should I use different ratio of glucose and tryptone to optimize C/N ratio? Any suitable reference paper please.
Thanking in anticipation
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Dear Ali. To solve your problem, a multivariate analysis is necessary. And as recommended by Sarmad A. Qamar Response surface methodology (RSM). But in view of the complex substrate, it will be difficult to provide a given level of nitrogen.
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I am performing enzyme assay for ADH. I am confused with what concentration of NAD and Tris Cl can be used.
If any one has a protocol, please provide it for me. 
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I have done this assay for Kluyveromyce marxianus to estimate the activity of alcohol dehydrogenase assay for pentose sugars.
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I am trying to determine the degree of polymerization for bacterial cellulose but I can't find the complete method. Can anyone suggest the suitable method for this test?
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As Srivithya has mentioned, the best method for measuring the degree of polymerization of polymer such as cellulose is Cold Gel Permission Chromatography (GPC). I hope the attached article will be useful.
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As my aim is to study the anti-fungal activity by the bacteria, Is there any expertise member who can explain how to know a bio-active compound(may be protein, enzyme or other molecules) isolated from a bacteria is extracellular or intracellular in nature ?
The literature search could not helped me to find out the appropriate solution for this particular microorganism so I want to go for various experimental methods. So is there any proper step by step procedure for better confirmatory tests ????
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Hello, see attached info.
Good luck!
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Hello Every one,
I have done saccharification with 50 U/ml crude enzyme extract in 50 ml buffer with 5% solid loading. Now I have a doubt at calculation part. If I get released reducing sugar of 1.23 g/ml what is my % of saccharification? I have taken 1 ml of crude enzyme extract for estimation of sugars released. Now I have to calculate it for 1 ml or 50 ml please let me know in detail in this regard. I am using the following formula:
Saccharificatioon (%) = sugars released x 0.9/ cellulose content x 100
Thank you,
Ramanjaneyulu, G.
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You might find the following paper to be of some help.
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Novozyme 188 has been discontinued by Sigma Aldrich.  Is there an alternative supplier?  If not, what is a reasonable replacement for standard enzymatic hydrolysis testing (i.e. NREL protocol, Selig et al. 2008)?  Any help is greatly appreciated!
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The cellulase enzyme blend "Cellic CTec2" from Novozyme also worked very efficient for my saccharification assays, and can be readily purchased from Sigma (product number SAE0020 ). Link provided below:
Cheers,
Rakesh.
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I know about silicone and alcohol waxes.
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Hello Allan, your question was asked 5 years ago and I am surprised to see that it has not been addressed till now. I am just seeing it. It so happens we share similar research interest. Non-toxic antifoam reagents are mostly glycol-based. Antifoam and defoamer for fermentation is a non-toxic, non-silicone defoamer specially designed for fermentation process in distilleries.It is a combination of polyalkylene glycols and fatty acid esters.It is water dispersible and can be applied in natural state by aspersion or by automatic dosing pump. It shows excellent knock-down performance in the control of foam, improves the flow and reduces viscosity of the medium even at very low dosage without leaving residue. The shelf-life is long and therefore recommended.
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What affects the protein quantity from an inclusion body during microbial fermentation? Are there any available resources to quantify the exact protein yield expected from inclusion bodies in E.coli?
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concentration of inducer, pH, time of induction, temp., all play a role. you have to optimized all parameter for getting high quantity of protein. thanks.
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Hello everybody,
I'm currently growing E. coli in bioreactor and I have experience only with P. pastoris in bioreactor, so I'm not sure, how should it behave. With Pichia, one can try hard to imrove the conditions and it will grow very well to very high cell density (something like OD600 of hundreds), so I had similar approach with E. coli.
I usually grow E. coli (in flasks) in LB medium supplemented with 0.1M K-phosphate pH 7.0; 1% glycerol; 2mM magnesium.
I grew it for the first time in this medium, but the pH shifted up to 8.x after switching the temperature to 18°C (after induction). We thought it was because of the phosphate, although from what I found on the internet, the phosphate buffer shall not be so much sensitive to temp change as other buffers. Anyway, we grew it without the phosphate the second time, but the pH increased anyway (not that much though). Moreover, it was slowly increasing over time, rather than decreasing. It was about 7.2 in the morning (maybe more). What could be the cause of the pH increase?
Second- what is the usual OD600 after overnight growth in bioreactor? The first time we got around 8, but the pH was slowly increasing. At that time I thought it's because of cell lysis, but now in retrospect, it could be related to the changes in pH as mentioned above. The second time we got OD600 around 3, but it was after shorter time (because we thought it's lysing) and the culture grew slower in general in comparison with the first one.
Thank you for your suggestions.
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OK, that makes sense. I must admit I also weren't quite sure about requirement of E. coli for oxygen. But it doesn't seem to be limiting factor, as the pO2 decreased only from ~20 % to ~15 %.
However, the main concern is currently about the sudden change of pH upon temperature change. What could that be?
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Hi guys,
I have a P. pastoris MutS phenotype which express very well in shaking flasks. I was trying to scale up the culture in a fermentor.
The culture was behaving normally for most of the fermentation process, but as soon as I started the methanol feeding (after a DO spike to make sure all the glycerol was consumed) the pH started to rise and the acid pump worked for the whole methanol feeding process.
I took samples at different time intervals and check them for protein expression. What I noticed is that the protein started to express as soon as 3 hours after the induction, then the expression increased in the next hours to a peak expression at 9 hours of induction. After that the cells were expressing less and less until the end of the fermentation. 
Comparing the expression level of the peak in the fermentor (9 hours) and the expression in flasks for 48h, in the fermentor I anyway got 5x less protein than flasks.
Do you have any idea how to improve the expression?
Why the pH of  the culture was increasing during methanol feeding?
Decrease in protein expression, could possibly due to no more nitrogen source in the medium?
The medium I used was the "Basal salt medium" as described by the invitrogen guidelines and the only nitrogen source was the ammonium hydroxide also used to keep the pH at 5.0
Thank you very much for your help,
Marco
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At any point of time during induction phase, the methanol concentration needs to be maintained at a sub optimal level & not optimal level. This is because, as most experts have mentioned, excess accumulation of methanol (above 3-5%) leads to toxicity for the cells, more than its utilization by the cells towards protein expression. The pH control herein becomes crucial as cells then begin to die (a possible reason of pH rise during induction). Solution could be, to feed optimal glycerol during growth phase along with a judicious supply of nitrogen source (NH4OH or any such other) till the point of reaching adaptation stage. This ensures reaching culture OD to at least 250-300. During adaptation, have a dual control by acid-alkali addition, by monitoring which way the pH is shifting towards. Have at least 6-8 hours of adaptation, before finally switching to 100% methanol. However, this time period needs to be established experimentally. During induction, keep temperature low (23-25 C). After adaptation, when one sees the normalization of set parameters (pH & DO) go for about 40-45 hrs induction, taking care to check the expression regularly along with the wet cell weight estimation. At one point of time, the expression is bound to dip. That is where take a call to harvest the culture.
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I have seen that both yeasts and filamentous fungi are used for biochemical production in cell factories systems. I am not sure about the differences between the two systems, I mean, are fungi able to produce more complex compounds or are there other reasons? It would be nice is someone could help me to understand it. Thank you so much in advance
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Yeasts are Unicellular and Fungi are filamentous.
Yeasts mainly produce alcohol and carbon dioxide through fermentation.
Fungi produce variety of metabolites which depends on the kind of fungi involved
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Hi, I'm looking to produce a highest biomass production of Saccharomyces cerevisiae in the Laboratory, in a stirred tank bioreactor (with working volume of 3 L), for this purpose, I'm trying to choose the best strain to fulfill my goal.
I appreciate the answers.
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thank you
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I am using 500ml GL45 Media storage bottles. 
I want to be able to collect the gas via ballons or let it run through a scrubbing solution as per my choice. 
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It's not just a  a question of DIY . If you want accurate measures you need
a) Follow an established protocol, like the IWA draft (although it still contains some flaws) http://wst.iwaponline.com/content/early/2016/09/19/wst.2016.336. Otherwise you risk amplifying the instrumental error.
b) It's better to employ an instrument like the AMPTS, that has automatic datalogging and normalization of the volume in real time. If the budget is limited, then the u-Flow cell is a good option. See www.bioprocesscontrol.com . Normalization error can be as high as 12 % if done on manual basis.
c) For a comparative table of commercial and self-made instruments, and their corresponding error margins, see chapter 2 of my book: https://www.crcpress.com/Managing-Biogas-Plants-A-Practical-Guide/Rosato/p/book/9781138626614
d) finally, it's better to buy a reactor kit already done and tested rather than toying to build one oneself. You will save a lot of time and money, not to say the risk of publishing wrong data if you micro-leaks, whicha re always impossible to find when you have handmade reactros. The guys at Bioprocess Control have a good assortment of models from batch 500 ml to continuous 10 liter. I personally work with batch 500 ml for research and batch 2 liters for industrial tests.
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We want to use a fermentation volume of 30/40 L and it would be very labour intensive to centrifuge (using bucket centrifuge) the broth before resuspening and lysating it. After lysation it is still necessary to use the centrifuge but then we would no have to use it twice in one process.
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You can try to cool the whole liquid volume at 4-6 C at the end of cultivation. The cells should be on the bottom and you can remove liquid by decanting and the thick cells suspension (now in the less volume) can be treated (centrifuged) or treated  by other procedures.
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During cascading events of a fermentation, agitation and aeration are at a max. Thus the saturation of air with those conditions give a higher DO value compared to the saturation using basic conditions before inoculation.
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Before autoclave, connect DO probe to the cable for at least 6 hrs.  Check the response of DO with nitrogen; the response of DO when disconnected the cable. Pre-calibrate the DO at 100%.  Check DO slope, raw data to see if everything is in the range.
After autoclave, connect DO with cable to see the response.  It should be around 100%
Add media. Start stirrer, heating, air sparge (2- 5% for equilibration).  When the temperature is 37C+/-0.C (around 1 - 2 hrs).  Calibrate DO at 100%
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mycologist, Fermenter specialist
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clean the filter with a 2 % formaldehyde and then autoclave by packing 
you can add 5ml formaldehyde to the fermenter containing water or remaining fungal culture and sterilize for 10mins keep a mask to your nose while sterilizing
and then clean thoroughly
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I need to selectively isolate fungal cellulase/xylanase producers in a selective medium which supports both bacterial and fungal cellulase/xylanase producing organisms. Tetracycline, a broad spectrum antibiotic, has been shown to inhibit some fungal species. Sodium azide and cyclo-heximide can also prevent both bacterial and fungal growth. This condition is also applicable to some other common antibiotics. I need a more restrictive antibiotic with no known antifungal property so that I will not lose any chance of selecting the best fungal strain.
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streptomycin is good to stop fungus growth ,  I tried.. It should be added in traces.. 
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Hello
I want to ask about using the mixed culture instead of pure culture for syngas fermentation, as I used the pure culture but they did not produce ethanol. Can I use digested manure as mixed culture after killing methanotrophic bacteria on it and it is enough heating it at 100C for 30min or I need another treatment method? And there are any papers about this topic?
Basma
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The first issue is to know what ou want to do with the digested manure. If you want to use it as fertilizer, the termal treatment mentioned befor is Oke by Weldejewergis Gebrewahid is Ok.
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How many days needed for the fermentation of S. commune for schizophyllan production? 
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6-7 days.
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I want to check the interaction between magnetic immobilized enzyme with the nano materials. What are be the reaction parameters should be fixed for this?
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I think two possibilities can occur either the enzyme can increase or decrease in activity. This relate to stereo chemistry between enzyme and substrate. If the magnet can make the stereo binding site of enzyme-subtrate become more "fit", then the enzyme activity increase, and vise-versa.
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Is there any solution to get rid of precipitation or is there any salt which doesn't get precipitated when added with CMC (Carboxy Methyl Cellulose)?
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cmc what concentration you r adding to which salt..... and what is the purpose?
cmc is a surfactant ...need to dissolve in water to get the foam
wheather the salt is added to cmc solution or direct to cmc?
pl make clear.... toanswer
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I am studying the effect of surface active agent concentration (1-50 ppm) on the hold-up and mixing time in an internal loop airlift bioreactors. the surface active agent used is  "Sodium dodecyl sulfonate".
The problem is we have an overflow of foam even at lower concentrations of SDB. 
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Dear Ahmed, the concentration of octanol I used was 20 ppm, about the maximal solubility for octanol.
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The media consists of:
1.0% peptone, 2.1% yeast extract, 4.0% glycerol, 2.0% Agar, Sea water.
pH adjusted to 6.5.
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Thanks all for your replies!
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for fermentation of yogurt culture  inside an incubator it needs constant temperature condition for some period of time eg 37 degrees for 4 hours without changing.Hence how can i maintain constant temperature for a period of time inside the incubator ?
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I think you mean uniform temperature inside an incubator. Well, we all know that air is a bad conductor of heat and therefore, to get even distribution of heating or cooling in any closed chamber, you must have a blower (may be for an incubator it may be a gentle blower type as compared to an oven). To keep the temperature constant your thermostat should be of a good quality.
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During Inclusion body preparation, why is a sodium chloride buffer wash required after detergent washes? 
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Zhao has very rightly answered your question.
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To prove the increase in yield and productivity in a better way, instead just with the metabolite profile.
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Thank you Philippa
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Different kinds of substrates produce different amounts of biogas and have different rates of degradation. They know some method to determine these rates?
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MÉTODOS SUGERIDOS: EMBRAPA Concórdia.
Sólidos Totais (ST): secagem a 105 °C até massa constante.
Sólidos Voláteis (SV): diferença dentre sólidos totais e sólidos fixos (SF) após calcinação a 550 °C até massa constante.
Produção Específica de Biogás (PEB) e Produção Específica de Metano (PEM): ensaio cinético anaeróbio mesofílico, expresso em volume normalizado de gás em relação a massa de sólidos voláteis da amostra (com base nas normas DIN 38414-8, VDI 4630, ISO 11734 e/ou ASTM E2170-01).
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for the production of vitamin B12 from Streptomyces olivaceus (MTCC 1392)
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Thank you so much Dr. Jai sir... But as we all know streptomycese is such a dynamic producers of bio-products. I was working on actinomycetes for their secondary metabolite production and at the same time i found that my culture was very good producers of phenazine , extracellular enzymes and approximately all PGPR traits....
I think krishna must be trying to explore Cynocobalmine production and optimization in streptomyces and if he could succeed then it will be a great  work in Indian Microbiology...
All the best for him..
Wish i could be part of this..
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I found that for different media different sterilization SOP follows. Some passes the pure steam into the media after reaching temperature 95 or 90 through sparger and close the jacket steam and some not passes the steam inside the media and close the exhaust valve after reaching the temperature 95 and continue the sterilization with jacket steam.
which is best?
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In my opinion, it is unnecessary...passing pure steam through the media during sterilization can add an additional quantities of water - after its condensation, to the medium and can alter the concentration of components of the medium, which could be critical to following fermentation process...
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Fermenter specialist
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You may use Ozone CIP process for reactors and piping. You can use a system composed of an ozone generator, a tank and a recirculation pump. The water is fed from the upper part of the tank and the recirculation is placed in the bottom, re-entering in the middle part of the tank, in the recirculation pipe a venturi is installed that will suck out the ozone produced in the generator. The water has to maintain a residual ozone of 1 ppm on the loop of your process or in the inside of the reactor in order to disinfect and remove any organic compound that may remind after your process. I suggest proves to determine the residence time in the tank to reach your needs. 
Saludos amigo.
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I would like to ask about some literature on production of bio-gas from banana waste with and without starter?
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You can also read the following papers:
1-Production of Biogas from Banana and Plantain Peelswww.aensiweb.com/old/aeb/2007/33-38.pdf 
2- Production of biogas from banana and …www.thefreelibrary.com › … › September 1, 2007
3- Production of Bio-ethanol from Banana …
4- Ecuador: Banana waste for bioenergy - european-biogas.eu/2016/06/16/ecuador-banana-waste-for-bioenergy
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Dear Sahil,
The following publication illustrated a design of a relatively low cost MFC chamber:
In this publication, the experiments conducted demonstrated the ability to construct low-cost, effective MFCs. For example, Design 6 was 4.3 times as cost efficient ($/mW) as the typical MFC. Using an MFC such as Design 6 for providing electricity for a city of 100,000 people where electricity costs 9.8 c/KW would save approximately $300,000 a year (Extrapolated from Logan, 2005 estimates).
In addition the use of MFCs for electricity generation can accrue benefits in terms of reduced CO2 emissions and wastewater treatment. MFCs are a largely untapped source of energy. Their application could be useful in the following areas:
1. MFCs could replace current costly secondary wastewater treatment procedures while producing electrical power that could be used both in the wastewater treatment plant and the local community.
2. MFCs constructed from cheap materials may have applications in developing countries both for the treatment of wastewater and the efficient generation of electricity.
3. MFCs can be up to 90% efficient in power production compared to 50% for typical fossil fuel power plants. Furthermore MFCs that treat wastewater would not generate any more CO2 than typical biological wastewater treatment processes. Thus their substitution for fossil fuel power plants would result in a net reduction of CO2 emissions.
For more, please see the publication contained in the attached file.
Hoping this will be helpful,
Rafik
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I transferred Saccharomyces cerevisiae yeast strain optimized to produce precursor of pathway with beta-carotene producing plasmid (CRTE, YB and I). There is constitutive promoter (TDH3)  upstream of all 3 genes. For how many days should I wait  to get orange color? Already the colonies are small but white.Or has some one also faced the same problem? I got some recommendation referring to change the temperature to 4 'C. 
I am looking forward to your advice.
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Dear All,
Final products of Biotech Downstream Separation are  commercially relevant (Insulin, Penicillin, Cephalosporin, Enzymes etc).  Some are within cells coming out of the fermenter and cell-disruption is needed, some are in the liquid phase coming out of the fermenter and don't need cell disruption.
I need some info about commercially relevant downstream products.
Thanks in advance
Lothar
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THANKS A LOT !!
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I want to design citric acid plant by submerged fermentation process with Aspen HYSYS. But the problems are Aspen HYSYS doesn't provide sorghum properties, many unit operations for submerged fermentation process, many intermediate components, and Aspergillus niger microorganism. Are there any simulation software specifically for fermentation industry?
Thank you.
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Aspen HYSYS software is not the proper tool to simulate fermentation processes. I recommend the following software for this purpose:
SuperPro Designer: Fermentation Simulation
For your question on modeling a component that doesn't exit in HYSYS library, you can create a hypothetical component but you need to enter its physical and thermodynamic parameters.
Hope this helps answer your question.
Good luck!
Professor Yehia Khalil
Yale University
USA
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Shake flasks are predominant platform to culture the microbial cells. Precise measurement helps to add external oxygen to provide oxygen enriched environment that will increase the growth of cells and recombinant protein production.
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CO2 production can be measured by offgas analysis. For example from bluesens. In fermenters O2 measurement is done by optical or electrochemical probes by Hamilton for example, but for shakeflasks there are non-invasive oxygen sensors from presens for example.
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I wanted to study the effect of 1 % nitrogen source on the enzyme production via Solid State Fermentation.
Which method is correct?
A). The 1% nitrogen source is determine based on the volume of moisture I provide
or
B). The 1% nitrogen source is determine based on weight of the solid substrate I wanted to use.
Does anyone have experience on this matter? TQ
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I agree with all colegues, I like Rual consideration. I want to add just take into consideration your 5 g as dry basis
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I have produced lipase by solid state fermentation. I extract the fungal lipase after 5 days of fermentation. The highest activity was achieved at 0.113(U/gSB) on the 5th day. Sugarcane bagasse was used as the substrate along with cooking oil. 
I need a supporting evidence on highest lipase recovery on the 5th day. what would be the highest recovery of fungal lipase after 120h? I need to plot a growth curve on this. 
Could anyone help me on this? I would really appreciate it. 
Thanks in advance
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Hello. As you said the optimum lipase was produced on 5th day. It means you extracted and assayed everyday from day 1 to onwards. ??
If not, then do the days optimization test first. So that one can conclude on which day maximum lipase produced. 
If yes, then there are many reasons for getting more production on 5th day like:
1. Growth: Growth of fungi is directly propertional to the production of enzyme. May be after 5th day there is a decline of growth of fungi.
2. pH: As Deyaa Abol Fotouh said pH has more influencing factor for enzyme production as it regulates the fungi growth too. 
3. substrates: Production will be more if the affinity of the microorganism towards the substrate is more. Therfore there will be a process of substrates tretment by alkali so that the substrates can be easily utilized by M.O. 
Hope it will help you. All the best.
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Using DSC can we get the melting point of PHB,
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Hello dear, By DSC you can find the glass transition temperature, melting point, crystalization temperature, melting enthalphy, cristallization entalphy. Furthermore you can make cured kinetic of the polymer and find the crosslinking degree, etc.
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Why beer being alcohol and dhaving hydroxyl group has acidic pH? I came across pH of around 60 different types of commercial beer varieties and the pH ranged to 3-5. What is the possible explanation for the acidic pH of beer?
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Dear Bhuwan,
Beer has acidic pH because during fermentation not only ethanol is produced by the yeast. They produce organic acids (acetic, succinic...) and other metabolites like glycerol esters, higher alcohols, ketones as well. Moreover sometimes beer is acidified in a brewery because yeast grow and live better in sligtly acidic pH. Additionally brewer's wort right after mashing has sligtly acididc pH (for normal, pale malts its normally 5.6-5.9 but for other types it may vary but usually goes lower).
If you are not familiar with fermentation you can read about it in any student's book for brewing/fermentation technology.
Witek
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Crab tree positive effect of Ecoli leads to acetate accumulation. Apart from engineering of Ecoli strains, what are the feeding strategies and process control optimization can be done to avoid acetate (<1g/l)
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Mr Phillip Brumm if you know the correct answer you answer to the question,as per your reply to this question I can quess that you dont have minimum knowledge about fermentation process. Can anybody  in the world maintain DO above  90%  and that too  maintaining DO is no way related to acetate production please mind it.
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Are both same? When an organism is in anoxic condition, does it shift to anaerobic mode of metabolism?
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"Anoxia" (adjective: "anoxic") refers to the condition of an environment where there is no molecular oxygen (O2).
"Anaerobe" (adjective: "anaerobic") refers to the condition of an organism which is able to thrive without molecular oxygen (O2).
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It seems that there may be a confusion stemming from the ambiguity of the term "oxygen", which can refers both to the oxygen atom (O) and to the molecular oxygen (O2).
First, there is virtually no place on Earth with no oxygen atom (O), since water is made up of H2O, air contains 21% (by volume) of O2 (plus minor ammounts of CO2 and water vapor), and the crust contains 46.6% (by weight) of oxygen atom (O). Thus, I think it can be misleading to say that there are environments without any type of oxygen (neither bound or free) on Earth.
Second, terrestrial life is impossible without the oxygen atom (O), since it depends on water (H2O) and all four major classes of biomolecules have the oxygen atom (O) in their chemical composition (nucleic acids, carbohydrates, proteins, and lipids).
In contrast, there are many terrestrial enviroments depleted of molecular oxygen (O2), and there are many organisms that can thrive without molecular oxygen (O2). These organisms are called anaerobes, and the etymology of this word reveals its biological origins: from the French word "anaérobie", coined by Pasteur in "Études sur la bière" (1863):
"On pourrait partager les êtres vivants en deux classes: les aérobies, c'est-à-dire ceux qui ne peuvent vivre sans air, et les anaérobies, qui, à la rigueur et pour un temps, peuvent s'en passer..."
Today, the adjective "anaerobic" is also used to the metabolic processes carried out by anaerobes, such as anaerobic respiration (in which the final electron acceptor is different from O2).
Therefore, one may say that anaerobes are able to carry out anaerobic respiration (or fermentation) under anoxic conditions.
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i wish to know how can i calculate my yeast accumulation.
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I would suggest the following this solution as I have done it before and it works well.
You formulate a general mass balance in the reactor with both inlets and outlets. Said mass balance will feature the terms of inlet and outlet streams, accumulation and reaction rate of all the species in the fermentation. In fact, you should take into account two inlets, one for the reactants and one just for the strain.
Outlet  - Inlet + Accumulation = Generation
For the fermentation of glucose into ethanol with Saccharomyces cerevisiae (the yeast), for example, you may have the following balances:
Glucose
(Fout * Woutglucose) - (Fin * Winglucose) + d/dt(Mglucose) = rglucose * Volume
Cells
(Fout * Woutcells) - (Fin * Wincells)  + (Fincells_inoculum ) + d/dt(Mgcells) = rcells * Volume
 Ethanol
(Fout * Woutethanol) - (Fin * Winethanol) + d/dt(Methanol) = rethanol * Volume
You can operate this as fed-batch by opening an closing the inlets and outlet streams, for fill-up and empty. The kinetic models can be found in the following works. Please do not hesitate to contact me if you require additional information
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I wonder, if the chromosome XII has an Endoglucanase encoding gene and XIV carries a beta-glucosidase gene, then why there isn't any report describing production of these enzymes from Saccharomyces cerevisiae?
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Firstly, we tried preparing feather culture media 1 & 2 using NaCl 0.5g/L, KH2PO4 0.4g/L, K2HPO4 0.3g/L, feather 10g/L, pH 7.5 (Media 1) and Media 1 + NH4Cl 0.5g/L, MgCl2.6H2O 0.1gµl, yeast extract 0.1g/L.
We optimized the temperatures for both media to 40 and 50 Celsius, but did not get satisfactory results. Thanks.
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The keratin  can be dissolved in alkaline buffer at pH 9 and above and used as substrate for keratinase assay. 
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I am going to clone and express a glucoamylase gene in an auxotrophic Saccharomyces cerevisiae using YEp 352 which has a LEU2 and URA3 selective marker, in order to produce a one-step conversion route for ethanol production, therefore a strain which has a strong capability to convert starch to ethanol is much needed. thanks. 
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You need not try to clone and try to make such strains. It will be a waste of time and money. There are several such strains with ATCC. You can see their catalogue and then order for one.
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It is assumed that to be a two stage system, the HRT should be greater in the acidogenic reactor because the hydrolysis step is which required most time.
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HRT should be designed considering the growth kinetics of the microbial consortia. Fermentative consortia have faster growth kinetics compared to methanogens in the second stage, thus the HRT in the methanogenic stage i.e. second stage is higher than the first stage. 
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We use pure oxygen for fermentation, but ordinary air for DO probe calibration. At this moment we set air as 100 % point of calibration (we use only 1 point calibration). Is this correct? Shouldn't it be 21 % point of calibration, since we use pure oxygen as oxygen supply. Can someone help?
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Hi, Jirka
I am using NBS BioFlo 310 for my experiments and we use Air for setting the span of the probe which is 100%.
In my opinion, it should merely influence the time needed to reach the fixed digits otherwise, it won't affect the the amount of DO in the vessel broth.
Good luck
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Hi all,
I am trying to figure out which instrument (micro GC/mass spec) is best suitable for monitoring in- and off-gasses during autotrophic fermentation ? Does Mass spec give quantitative data ? which is more reliable/reproducible  ?
Thank you
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Use Biogas analyzer (BGA) from Siemens
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Process of Fermentation includes the use of microorganisms, like yeast and bacteria for the production of enzymes.. In Submerged fermentation, the production of enzymes is done by microorganisms in a liquid nutrient media. Compounds containing carbon in or on the substrate are busted down by the microorganisms thus producing the enzymes either extracellular or intracellular. The enzymes are isolated by various methods. This approach is used in wine making, brewing, cheese making and baking.
I want to know if the bacteria of yogurt can be used as source for inducing fermentation to produce enzymes. 
Thanks in advance. 
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Dear Alok Nahata as we know many factors are responsible for the induction of fermentation process. Here you want to know if there is an enhancement of enzyme production by bacteria of yogurt? 
It depends on the microorganisms and also depends on the substrates you will use and differ from also enzyme to enzyme. If you specify the enzyme on which you want to focus then there will be another aspect of discussion regarding the above problem. All The Best.
-AKM 
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Dear Colleagues..
I would like to invite you to contribute a book chapters
1. Value addition of waste derived proteins to biofuels and biochemicals
2. Rendering industry wastes- transformation to high value products 
3. Application of waste-derived proteins in animal Feed Industry 
In: Book entitled “Protein by-products: Transformation from environmental burden into value-added products” 1st edition By ELSEVIER publishers, Editor- GS Dhilon, PhD., P. Biol. (ASPB).
=> The preliminary acceptance is only upon submission of the draft abstract.
=> The book will be possibly published in second quarter of 2016.
=> There is no processing/publication fee
=> There are no page charges for black and white figures and illustrations submissions provided they are sent to Elsevier with the source files. Color illustrations are billed at the current rate.
=> An author guidelines will be sent to all authors after acceptance of the abstracts
=> In consideration of your contribution to this book, Elsevier will provide to all authors an electronic edition of the book, besides giving a 30% discount on all Elsevier Science books for life.
Please text me within 2 weeks if you are interested.
Thanks
GS Dhillon, PhD., P.Biol (ASPB)
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DearSir,
I would like to contribute chapter in the above mentioned book chapter of protein by-products. I would like to know till wnen can we likely submit the abstract and what is the word limit of abstract??
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Anyone with links to publications on fermentation of wood based sugars? Specifically I am looking at sugars generated by autohydrolysis during medium density fibreboard manufacturing?
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Thank you guys
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In bioreactors, I maintain a low pH via combination of cell metabolism and base addition. In shake flask, base addition is not possible, and I've been looking for a suitable, biologically compatible buffer system for a pH between 3 and 4. Most biological buffers are designed for much higher pH ranges.
I've tried sodium citrate/citric acid, but my cells grow poorly and lyse.
Any suggestions? I plan to try a glycine-HCl system, but I'm not too confident about it, the HCl doesn't sound cell-culture friendly.
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As an alternative to adding a buffer, you might try using urea rather than ammonium salts as the nitrogen source. This simple replacement strongly decreases acidification of yeast cultures in defined media and, in most yeast strains, has little impact on growth rates. 
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DNS method was used to measure reducing sugar as well as DE value , however, this method is under discussion since the standard curve alters when the degree of polymerization of maltooligosaccharide
changes. How to cope with that problem? the used amylase does
not exclusively releases maltose units, it will also release glucose, and so on
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I have not, but John Robyt and his coworkers have done so. Please see the attached paper.
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I am performing co-fermentation experiment with glucose and xylose and to determine the residual sugar concentration I generally prefer HPLC method but HPLC is not in work for a few days. Can anyone suggest me a way to estimate glucose and xylose concentration separately because I want to see how much xylose has been consumed ?
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A alternative way will be mesuare the reducing sugars by DNS method (for exemple), and the glucose by enzymatic kit (GOD-POD). By difference you will know the quantity of xylose. 
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i am using biomass materials to clean syngas (tar removal) generated from downdraft gasifier and filter medium is connected at the outside.i also want to predict and figure out how long such mediums can be used for the purpose. longer the saturation point, better the filter medium.
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Do not try to design yourself  such biofilters. These are readily available in the market and has been designed with lots of care and repetition. They come with the adsorption capacity mentioned on the labels. 
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I  performed pullulase activity  from fermented broth of fungi, by using DNS method, but each time I got the reverse result. Can any one suggest me why?
Methods used
0.5 ml filterate+ 0.5ml Pullulan incubated for 15 min at 300C.  1 ml DNS Added, then heated in water bath for 10 min . volume made up to 5 ml by distilled water. taken OD at 570 nm or 540 nm.
Substrate is pullullan and product is glucose
Measuring product conc. using DNS
Result obtained each time
Time          O.D.
0 hrs        0.150
24 hrs      0.127
48 hrs      0.106
72 hrs     0.112
96 hrs     0.114
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Try raising the temperature of the assay to 50 °C. Most fungal hydrolytic enzymes act around 50 °C.
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For example if the maximum tolerable temperature of bacteria is 43 degree Celsius, if we increase the temperature to 45 degree Celsius , how does it affect the bacterial growth?
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Hello Dr  Richard, 
I hope you can help me in my question ?
I am doing  changing in temprature and salinity concentration for my isolates that I got them from wastewater. So can you provide me with the best experiment to do it properly.
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I am oxidizing my plant fermented broth by air.I found increase in DO and redox because of more solubility of oxygen in the broth. The dissolved oxygen concentration increases and because the reaction in the broth is an oxidation process, the redox is also increasing.
Oxidation also increases with pH decreasing but why?
When I am supplying oxygen for a long time, redox decreases as well as the pH also behaves the same way.
Why this is happening?
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Hi,
I think what what you mean is that increasing in the DO consumption, it means a related productions in CO2. This can affect the pH of the medium.
Best Regards
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Hie can any one help me out with the step by step protocol for fractionating the polygalacturonase and amylase enzymes using ammonium sulphate present in my fermentation broth. My fermenting organism is a yeast belonging to Geotrichum species. I tried it once I found good amount of protein present at 80% fraction  but it did not show any enzyme activity. My control  OD value was more than my test enzyme value. 
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Use this cchapter book. Regards
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I need to know any further consideration beside the actual area of the biopharma plant.
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You can use the book "Piping and Pipeline Calculations Manual" to me has helped me. In conclusion I think you should consider the following:
- Theoretical needs of the productive system.
- Type of fluid: related to auxiliary systems and process lines.
- Type of material: to define friction losses, pressure drops.
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I have tried to increase molecular weight of poly lactic acid of lower molecular weight by chain extension with di dissociates . It give me weight average molecular weight of 200000 Da. I would like to know does there is any other method to get ultra high molecular weight PLA.
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Helena is completely right with her answer. In order to obtain high Mw PLA, you should use ROP from lactides.
cheers,
Miguel
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I am getting a thick liquid distillate after fungal biosolubilization of sugarcane bagasse in Solid State fermentation conditions. I want to quantify lignin derivatives (if any) in the liquid distillate. Can anyone help me out?
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Hi Abhilash,
I guess that GC based methods would provide you a better answer with this query. I have attached an older paper, although, there might be newer methods since the paper has been published. However, the methods are simpler and a simpler GC based system and protocol is used which is easier to follow. I hope that it helps.
Regards
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I would also appreciate any advise on temperature control for optimal growth at 37ºC.
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Hola Manuel, once the fermentation temperature is achieved, there are small variations during the culture, so little heating inputs would be done, for that any of the heating system is adequate, having in count that sterilization is done in one autoclave. (for bioreactors untill 5 lt.)
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I'm currently conducting research on the production of xylanase, pectinase and protease via solid state fermentation. The crude enzyme I harvested from each set of SSF is my primary source of each enzyme I mentioned earlier.
From my literature review it is okay to use sodium acetate buffer for the extraction of xylanase and pectinase. How about protease? does sodium acetate buffer suitable for the leaching out of protease from the SSF?
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Since most of the pectinase work in acidic pH therefore the extraction buffer used is generally citrate or acetate. Protease can be neutral, acidic or alkaline. Based on type of protease secreted by your fungi during SSF, you need to choose the buffer system. When I was doing my Ph.D. even physiological saline or 1% Tween-80/20 used to be sufficient for leaching out protease from the SSF... 
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We need to separate a mixture in a column distillation using an extractive distillation system.
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Hi Joel
Do you want to break the azeotrope? F.E. a separation of water and alcohol inside a destilliation column or do you want to extract something polar from an aqueos Phase..or maybe both?
To break azeotropes you can try to destill under overpressure, this is a suitable method for some difficult mixtures, even if the boiling points are very close, you might have to optimize or enlarge your theoretical destillation bottoms and look om the capacity of your colon.
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Its useful to study the nutrients behavior (Carbon ,Nitrogen,Phosphate,Magnesium and Inducer effects,Byproducts ), recombinant protein profile, process parameters (Temperature,pH, OD,Viability, Plasmid stability,Biomass growth profile) in high cell density cultivation to understand the process at large scale. 
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For recombinant protein production, we have achieved optical densities of 30 - 60 using baffled shake flasks covered with oxygen permeable membranes (Thompson UltraYield Flasks + AirOTop Seals) and fed-batch medium (EnPresso B, BioSilta Ltd.). Have a look at publications from Kaisa Ukkonen and Jian Li for further details.
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I have an isolate which grows well at 19C. but i have come across literature reporting a growth temperature of 30C.
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The medium I used for Rhodotorula rubra was Sabouraud agar with chloramphenicol and the temperature was 20C. But I isolated my R. rubra strain when carrying out cabbage fermentation. I think the most optimal temperature would be the one of the environment your strains originate from. But making a growth curve would be advisable anyway.
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I want to know if I have a fermentor with plastic tank, can I sterilize it with alcohol(ethanol 70%) instead of autoclave in general fermentors?
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In general, plastic fermentors are recommended for single use as they come in sterile condition for ready use. If they are to be used repeatedly then one has to compromise on certain parameters and deal with the complications that may arise while its usage in the previous runs like damaged surfaces that pose complications in terms of reactivity, deposition of residues, microbes and so on. So one has to rationalize and ensure its intended usage. In such case, the surface sterilization may be recommended with 70% alcohol in water, in the presence of sterile ambient like HEPA  filtered laminar hood, followed by UV sterilization for the better results.
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I am running submerged fermentation of Bacillus with barley husk as carbon source in a bioreactor. When samples are taken, the barley husk particles are also included.However, the amount of barley husk particle that is included in the sampling varies ( not possible to standardise). Problem: The absorbance at OD 610 nm fluctuates too much ( suspected reason: unequal amounts of barley husk particle). I am thinking of filtering the sample with a muslin cloth or a filter paper to remove the barley husk particle before checking of the cell density. Is this a good move?
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You cannot use the colorimeter method in this case. You can go with plate count method or protein estimation method for bacteria growth.
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I am unable to have a definite peak in the chromatogram of the five monomeric sugar and cellobiose analysis using HPLC. All five monomeric sugars, except Glucose, forms tailing peaks while Cellobiose is not detected. This tailing peaks caused overlapping when all sugar standards were run. My sugars and cellobiose were either from Merck or Sigma. 
 HPLC conditions are well stated. Other details are:
The brand and model of HPLC used: -HPLC Type: Fisher Scientific Thermofisher
-Brand: Shidmazu
-Model: RID-10A
Size of column: -Product name: APS-2 Hypersil
Diameter(mm): 250 x 4.6
-Particle size: (micron-N-)
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@ Dr Henrik Romar, in case of further works and a possible column blocking, which alternative mobile phase would you recommend ?
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During recombinant protein expression (RPE) cellular/metabolic stress is developed inside E.coli, which then depresses the RPE over time.
Over the past few decades, several genes have been identified which can be used as a biomarker or probe to monitor this stress e.g. ppGpp, whose expression level increases with increased oxidative stress developed inside cell. Like this there are various stresses e.g. heat stress, osmotic stress etc. which are well correlated with the RPE.
I am trying to catalogue all those genes which can be used to monitor different type of stresses developed during RPE in E.coli.
Your valuable suggestions, ideas or Paper references will be well appreciated.
Regards
Ashish
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In E. coli infact this is a challenge for RPE gene. Note normally heat stress or osmotic stress do not give satisfactory results. You will get good results if you use oxidative stress.
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I am currently conducting a research into fungal enzymes involved in glycosyl hydrolysis. I am to select one of three organisms for enzymes production. The activity of the enzyme produced by the best of these three organisms is twice the second best and three times the least. However, when I used the same enzyme units (30FPU) for the three organism in a target hydrolysis, enzymes from the other two organisms (those with lower activities) had  higher sugar yields (10%  total sugar yield more than the best organism). Of course, I thought that the other two organisms might posses some other complementary enzymes which act in synergy to produce a higher sugar yield but I am concerned that they however require a higher volume of crude enzymes or some expensive enzyme concentration mechanisms that will rather make the hydrolytic process non cost effective. I urgently need a decisive guide about this. 
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Enzyme activity by set protocol and applying these enzymes for particular target reaction are totally different things. Factors influencing the target reaction might have significant effect on the enzyme from your three organisms. So I suggest choose your organism based on the actual performance in your target reaction and then further investigate the parameters influencing the enzyme activity such as temperature, pH, solvents, buffer etc. 
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I have been quantifying PHA produced by the microbes via crotonic acid assay. I had centrifuged 15 ml of medium to obtain a considerable amount of biomass , and I had treated the biomass alone with acetone , methanol and water to remove the cell debris and then I had dissoved the left out pellet in chloroform and boiled it at around 90 degrees and after which 20 microlitre of the chloroform extract was used for crotonic acid analysis by standard protocol.
When I compare the spectral readings with the standard graph and quantify I get a few micrograms in 20 microlitre and when I back calculate there is only a few micrograms in a liter of fermentation medium.
where as when I used thermogravimetric analysis of PHA in biomass I obtain micrograms of PHA / micrograms of biomass. can someone help me out with the back calculation.
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Make sure you follow the exact same procedure for your standard curve. You might be having problems with your extraction step. I dont know what protocol you are using though. Depending on what organism you are using you might need some harsher methods to break open the cells. I would recommend 30% warm NaOH solution treatment and then chloroform extraction at a milder temperature like 37C. Ratio of chloroform phase to sulphuric acid is important as well. I use crotonic acid method all the time and time or reaction is critical. Treat sulphuric acid mixture at 80C for at least an hour. Crotonic acid is usually a very reliable method TGA might need special expertise.  Hope this is useful.
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Ttributyrin agar has been dissolved 20 g in 1 litre distilled water and  sterilized by autoclaving at 121°C for 15 minutes. It has been cooled to 80°C and added 10 g neutral tributyrin. But we couldn't see a clear zone, even by Rhodococcus spp. and Pseudomonas spp.
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Suspend 23 grams (Tributyrin Agar Base) in 990 ml distilled water. Add 10 ml of Tributyrin (FD081, himedia). Mix and heat to boiling to dissolve the medium
completely. Sterilize by autoclaving at 15lbs pressure (121°C) for 15 minutes. Shake the flask and individual plate so as to maintain uniform turbidity.
Note : For proper lipase activity, it is recommended to use glass plates instead of disposable plates. Hence USE ONLY GLASS PLATES. DO NOT USE PLASTIC PLATES.
OR ELSE you can use another method.
Suspend 32.15 grams (Spirit Blue Agar) in 1000 ml distilled water. Heat to boiling to dissolve the medium completely. Sterilize by autoclaving
at 15 lbs pressure (121°C) for 15 minutes. Cool to 50°C and add 30 ml lipase substrate Tributyrin (FD081, himedia) slowly while agitating to obtain an
even distribution.
USE ONLY GLASS PLATES. DO NOT USE PLASTIC PLATES.
For detail composition and principle see the PDFs. All d Best.
-AKM
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Dear all,
I am interested in finding the AT-content of all the genes of Saccharomyces cerevisiae(SC). Is there a tool available that can analyze the entire genome database of SC and can tabulate the genes in the order of their AT-content? Moreover, it would be great if the tool can analyze any fixed sequence length of each gene in the database, say, the first 500bp of all the genes and then tabulate them in the order of their AT-content?
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try generunner, i think it can work. or online expasy repository might help you.