Wednesday, December 22, 2010


It does appear that the discussion about the size of fermentors is not as simple as it may seem. In fact it is still a very complex issue and the point of contention among many fermentation technologists. Even till today, arguments on the pros and cons of choosing the right size of fermentors is still not settled.
There are generally two schools of thoughts on these matters. The first group who are advocates of going for large size fermentors or the scale up party, and those that goes for small and miniaturized fermentors or the scale down fermentation technologists
In reality both groups have their pros and cons. Every group has their advantages and disadvantages. What is right depends on the situation or the nature of the fermentation problems.
Size of fermentors was not an issue in the early days of fermentation. The simple rule the size of the vessel dictates the volume to be fermented. But with the advent of industrial microbiology where economics dictates everything, size and other parameters as efficiency, energy input suddenly becomes critical.
We have a golden rule in economics called the economics of scale. Where increasing volume produced will result in lowering the cost price of production per unit product. This often explains why fermentation industries have huge fermentors especially those involved in high volume low value products.
This rule could not be similarly applied to low volume high value fermentation products where other factors such as limitations in down stream processing is the constraining factor and purity of product is stringent
Lately in the last few years there have been a trend towards miniaturization of bioreactors or fermentors. This involves the use of fermentors of less than 10 ml or using of microtitreplates
The use of these very small bioreactors offer the main advantage of using small volume of media and allowing multi variate experiments to be easily carried out simulataneously or in parallel configuration. This is almost akin to the advantages of using solid media on petri dishes during primary and secondary screening.
The problem in using these miniaturized bioreactors differ fro the use of petri dishes in that it uses liquid media and tries to mimic what really happened in a liquid fermentation process.
This is not easy as the key issues in any liquid fermentation is attempts to get homogenous mixing, mass transfers and monitoring of the various fermentation process parameters.
The behavior of fluid mixing in miniature fermentors differs greatly from those larger fermentors where mixings can be carried out effectively by various mixing techniques from stirring to even shaking the conical flasks. In microbioreactors due to the small size the mixing of the liquid broth is hard to achieve especially due to the physical interaction between the liquid and the walls of the bioreactors. The phenomenon of surface tension and capillary effect will be significant.
Any new techniques to measure or detect efficacy of mixing in microbioreactors do have to depend in parallel development in techniques such as computational fluid dynamics.
The use of micro fermentor will generate its own set of unique problems not faced significantly when using large fermentors. Small volume of liquid broth will have higher surface area to volume ratio which will affect processes such as evaporation, surface tension. This if not controlled or taken care off will introduce errors in data to be used especially during scale up exercises .It doesn’t matter even if you have come up with miniaturized sensors the problem of mass transfers will be severely affected
Due to poor mixing any samples obtained would be questionable to its representative function. Wrong sample means wrong data despite the use of the most sophisticated microanalysers.
In my own personal view the use of microfermentors are still in the research stage and are of very limited applications in fermentation technology as of now 

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Tuesday, December 21, 2010


Even though all these while we have credited the microorganisms as the transformation agents in the formation of fermentation products from substrates, the REAL heroes are the enzymes themselves that cause the transformation to occur. These enzymes produced or being part of the microorganisms are responsible for the changes
In a simple fermentation carried out in vitro using enzymes obtained from living cells it is possible to cause the desired transformation. In fact this classical observation is the event that gave rise to the birth of enzymology and biochemistry.
As far as the microorganisms are concerned, they are just living sacs full of enzymes that are needed to carry out the various metabolic reactions needed for life. In fact we can envisioned the living cells or cytoplasm containing protein molecules which are just enzymes especially in the cytosol. Its more like a balloon filled with a suspension of enzymes
Therefore to study or understand fermentation technology we need to study the complex interactions that affect enzyme activities.
The complication that arises in comparing enzymes in fermentation technology and simple enzyme reactions in biochemistry is that most enzyme studies in biochemistry are involved with simple enzyme system ( minus the living cell) and they are using pure enzymes and substrates. This simplify a lot of things!
Whereas in the living cell we are involved have many enzymes which influence each other and require the series of enzymes to complete the transformation.
The product of one enzyme is the substrate of the next enzyme. This is further complicated by different kinetics of each enzymes and different control of enzyme activities such as catabolite repression and product inhibition.
A look at the standard metabolic pathway chart will show you the flow of substrates, and points of intermediate diversion far more complicated than the Pudu Raya traffic interchange or London traffic 
The traffic system of the enzymes are not that chaotic as there are rules of enzyme reactions which must be adhered.
Knowing these enzymes are necessary in order for us to appreciate the various fermentation kinetics and to understand fully the importance of such equations such as Michaelis Menten and Monod equation.
So do smile as you try to understand the enzymes. They form the foundation of fermentation technology!

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Tuesday, December 14, 2010


In fermentation technology, we stress in understanding the various process in fermentor and how various intrinsic and extrinsic factors influence the fermentation process. Fermentation technology being an industrial microbiology subject are geared in producing maximum amount of high economical fermentation products
But it is difficult to understand and control the fermentation process as it involves various components such as effect of substrates, products inhibition, conditions and complex microbial interactions
The fermentation process is not only complex but always In a state of flux. Process, We are therefore in a situation to always be adaptive and reactive to these changes so that through out the fermentation process we are always sustaining the conditions in a narrow window of optimal fermentation conditions.
In order to help us to do this we need to know fermentation kinetics. When we talk about fermentation kinetics we are talking about fermentation models. Kinetics and modellings are very useful to us as tools to make fermentation predictions and enhancing our experimental designs to be more focused to the specific problems such as the rate limiting steps or product inhibition
The study of fermentation kinetics help us by providing clear quantitative data for us to understand the process and improve the process accordingly. Peering into observation ports might be good advertising gimmick for fermentation technology but do not really help much in understanding the process or even to control and predict the fermentation outcome. Subjective observations will rarely help in producing optimum fermentation process and thus affect profitability studies and making decisions
Its numbers that count! Real data that can be processed and determine decisions
Thus the importance of the study of fermentation kinetics or models
The first step in the study of fermentation kinetics is to understand the various processes involved in the whole process. Such questions such as inputs and outputs, the metabolic pathways involved and type of products or side products formed. The various individual reactions involved and what factors control the metabolite levels
At the level of the fermentor we need to know the various mass transfers involved, flows and mixing characteristics
Then only after all the relevant data are obtained do we start formulating the models

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In a typical sigmoid growth curve, the first phase is called the lag phase. It has often been accepted by most that the lag phase is the period where there is no net increase in the number of cells. It is the stage where the cells are adapting to the new environment and are busy trying to synthesise new array of enzymes needed.
How true are these ‘allegations’?
As we have said earlier, the microbial growth curve is the graphical representation of the microbial population and not of a single cell. We are talking about millons and millions of cells. If we assume this statement that it is a period of no increase in cell numbers and it is just a period of enzymes induction then it is difficult to accept the idea.
Don’t tell me in the millions of cells there are no cells reproducing?
Even in a drop of culture or microbial suspension, containing millions of cells, each of the cell has different status in terms of its mass transfers exposure. Each cell are in different physiological states from young nd active to old and dormant cells.
Perhaps it might be logical for synchronous cultures to have same starting point in growth or lag phase. Even then synchronocity just last few generations.
We do know however that the length of the lag period is connected to various conditions from short for adapted cultures to long for cultures in a new environment. However that does not mean being in lag phase does not result in non reproduction of new cells. Maybe only the rates might not be significant.

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How do we define microbial growth? To most people when we talk about growth we are always talking about the progression in the development of the organism as a function of time. The progression of growth of the organism or the individual is usually associated with increase in size or biomass of the organism.
The key point here is the INDIVIDUAL organism. However in dealing with microorganisms, most microbiologists tend to picture microbial growth from the view point of the increase in the total population of microorganisms and not the individual unicellular microorganism
The growth of the microbial population at any one time represents the steady state number of cells or growth parameters used as the index of growth. The steady state numbers represent the net number of cells where input of cells and death or loss of cells are taken into considerations
The growth of the cells over time is often conveniently represented in graphs.
These microbial growth curves therefore represent the growth of microbial population rather than the individual cell. So any information derived from studying the growth curve represent understanding the behavior of the population rather than the individual cell.
The behavior of the individual cell differs from the behavior of the population of cells. This must always be bear in mind all the time in interpreting growth curves.
It is one of the weakest link in understanding the behavior of the microbial population to regard it as a simple integration of the activities of the individual cell. This is microbial physiology and not plain mathematics! Everything is not averages or mean values!
It is a gross error or over simplification to regard the microbial growth curve is the popular sigmoid shaped growth curve. In fermentation technology the type of growth curve obtained are determined by many factors and operating regimes. Yet time and time again the error of interpreting the wrong growth curves are continually repeated.

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Thursday, December 9, 2010


It is the purpose in any engineering design of a fermenter to achieve uniform and homogenous mixing. This objective is to ensire that the content of the fermenter is homogenous and good mass transfers occur between the microorganisms and the surrounding environment.
Frequently though this objective is always kept in mind, the weakest link in the process is the failure to understand the rheological properties of each fermentation broth and the provision of unsuitable stirrers or mixers to achieve this end.
Complications arise due to the fact that most if not all fermentation broth are non newtonian and show very complex properties spatially or even temporally during the fermentation run. Just providing any standard stirrer is not the proper solution to this problem. Each fermentation process have its own unique problems and conditions and almost require its own specific stirrer and mixing regime.
One good example often faced in fermentation industries is the problems of mixing viscous broth. This is often encountered in food fermentation such as yogurt fermentation or fermentation of biopolymers or those involving use of sticky sugar substrates.
In theory we expect any mixing of fermentation broth would result in homogenous conditions, improved mass transfers. In viscous broth we expect the effect of stirring would be to stretch and thin out the broth to improve mass transfers
The problem is during the fermentation mixing or stirring there is the tendency for the broth to creep up the stirrer shaft, instead of being dispersed throughout the fermenter. This effect is called the Weisenberg Effect
The Weisenberg effect refers to a common phenomenon when a spinning rod is placed in a solution containg liquid polymers. This will result in the entanglement of liquid polymers to the spinning rod or shaft leaving the free ends of the polymers in the solution. Tensional forces acting on both ends of the biopolymers will try to reduce the distance between the two ends resulting in the polymers to move along the shaft.
Given time a mass of biopolymers will be cumulated at the end of the spinning shaft of the stirrer.
1 Extra load at tip of moving shaft will generate extra torque and if the shaft of stirrer is long will throw out the shaft out of its normal oscilation
1 Inefficient mixing as the impellers will be covered by the cumulated biopolymers
3 Entrapment of biomass that will not contribute to fermentation product
4 more downstream problems and loss of time in cleaning the stirrer system

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Friday, December 3, 2010


Almost everyone knows how to make yogurt. Yogurt is after all a simple fermentation process using milk as the substrate. The microorganisms involved in the process are . S.Thermophilus, L.Actobacillus Acidophilus and B. Bifidum.
In the process the milk sugar or lactose is converted into lactic acid and other fermentation products such as carbon dioxide, acetic acid, diacetyl and acetaldehyde which contribute to yogurt's characteristic taste and aroma.
It does not take a food scientist to make a simple yogurt. A hobbyist who is willing to ‘experiment’ with ingredients and conditions, and after passing through trial and errors will ultimately be an expert in making his own unique yogurt. p(Though others might not like his product)
However, if you are trully interested in making the perfect or standard yogurt that is marketable you do need to really understand the processes ivolved in making high quality yogurt.
Of course, the preference for a particular type of yogurt depends on the individual. But you need to produce a yogurt product of the highest quality, consistency.
A good yogurt is characterised by its flavour, aroma, appearance and texture. The texture of the yogurt itself is important. Many yogurt are designed to help create or maintain a thick texture.
Most people would like to imagine yogurt as viscous but soft enough to flow.The texture of yogurt is measured in terms of its flowability or viscosity.
The manufacture of yogurt itself in reality is complex as the rheology of yogurt fermentation changes with time and stage of process . This would not be a critical issue for home made yogurt involving small volume production
In controlling the viscosity of the yogurt would involve various stages of manipulations such as:
1 The milk used for making yogurt must be standardized and should contain at least 3.3% fat and 12 - 18% Milk Solids
2 Homogenisation should be used to increae the product viscosity
3 Pasteurisation at 98 degrees Centigrade for 3 minutes will help in the coagulation
4 Filtration should be used to removed pockets of whey in the broth
5 Cooling should be carried out in a controlled manner to maintain the integrity of the yogurt viscosity
6 Transfers of yogurt should be carefully carried out by pumping and mixing properly to maintain its viscosity

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Wednesday, December 1, 2010


Milk represents one of the most common source of nutrients used widely in all countries and human cultures. There are many kinds of milk available depending on the type of animals used to produce the milk. However, dairy milk or cow milk represents the most popular type of milk used by man.
Milk is so nutritious that not only its ideal for human nutritional requirements but also for the calves for which nature intended it to be in the first place.
It is a sad and tragic fact that lactating cows are the ones used to produce milk which we need in volumous amounts. To do so, these cows are needed to be fertilized, and only after they give birth to calves would milk be produced. Since the cows are meant to be producing milk, I often wonder what happens to the young calves produced once the dairy cows start lactating. Will they be allowed to grow into maturity or will they be slaughtered young ending up as veals?
My apologies for the temporal distraction from the topic…. Just cannot help it!
Milk being nutritious will also proves to be irresistable to the bacteria. Milk is rich with proteins and various vitamins and growth factors is too good a deal to be rejected by the bacteria. Bacteria especially those that are nutritionally fastidious will grow well in milk.
This nutritional attraction for the bacteria will have serious implications for the humans that drink the milk. Not only will the humans have to compete for the milk with the bacteria but the bacteria will result in the spoilage of the milk itself by its biochemical activities. The bacteria itself will be a source of microbial pathogens and diseases.
One of the consequence of microbial contamination and spoilage of milk will be short shelf life of the milk.Attempts were made to solve the above problem not only due to health but economic consequences.
One of the most common ways to reduce microbial contamination of milk is either by killing or removing the microorganisms in the milk.
There are several methods to achieve this but each method will have its own advantages and limitations.
The use of heat or high temperature is commonly used in pasteurisation or sterilisation of milk.
One of the earliest method used in industries to solve the problem is by the process of pasteuerisation. This process is named after the famous microbiologist Louis Pasteur.
In the pasteurisation process the milk is subjected to a high temperature for a period of time which will allow the killing of some of the microbes without really damaging the quality of the milk
In the Pasteurisation process the presence of microbes is reduced…. (REDUCED) and not completely sterilized! The effect of pasteurisation process will be making the milk safer and prolonged the shelf life of the milk. This is of important consequence to the milk industries as more milk can be distributed wider and more profit
It should be noted the concept of pasteurisation is relevant more in the past when refrigeration is not a common household item.
In pasteurisation we see the reduction of the microbes occurred as the consequence of heat being applied. The MAIN OBJECTIVE in pasteurisation is the reduction or destruction of the microbes in the milk.
Pasteurisation is never seen as what EFFECT the process has on the nature and composition of the milk itself and its nutritional value of the natural milk itself
Milk being dominantly protein and amino acids with vitamins and growth factors are affected by heat. Pateurisation will alter the values of the milk itself.
Heating to this temperature, but no higher, does not change the proteins in the milk or the yoghurt so the taste is not really affected.
The most popular alternative to milk pasteurisation now is using the ultra heat treatment. In UHT the milk is heated to at least 135°C for at least one second. UHT destroys all bacteria in the milk and makes it last much longer than ordinary pasteurised milk. How ever using UHT does cause changes to the taste of the treated milk due to the denaturing of some of the protein components in the milk.

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Monday, October 11, 2010


One of the most fundamental requirements in any type of fermentor is the provision of a device or mechanism to mix the contents of the fermentor. Good mixing will result in homogenous conditions of the fermentation broth which will help improve good mass transfer leading to an efficient fermentation process.
It is therefore not surprising to see in fermentors the provision of a stirrer or some sort of mixing device to execute this important function. Good mixing is not only restricted in liquid fermentation but also in solid substrate fermentation such as cocoa fermentation and even composting.
Many of us are so ingrained by the ‘brainwashing’ of fermentation literature that a standard fermentor is and always must be accompanied by a standard mixing device such as the motor, shaft and impeller combination. To this influence we are also brainwashed that Rushton turbine is the ‘best’ impeller system. Due to this also we dare not think ‘outside the box’ and are happily satisfied with the standard Rushton turbine despite the fact that the kind of fermentation we are using is not the same as those reported for the standard stirrer. Part of the blame for this ignorance is to be blamed on the users for failing to understand themselves the kind of fermentation they are carrying out, their limitations and failing to appreciate the rheology of their own broth.
The only exceptions to this poor thinking which I observed are those involved in disposable bag reactors and those dealing with the cultivation of plant and mammalian cells. In plant cell cultivation the mixing is brought about by the circulation of the fine air bubbles. In the disposable bag fermentation they use gentle waves which help in the mixing of the fermentation broth.
In the market there are various types of stirrers, shafts and impellers. You must be able to choose the right combination for your purpose.
In this aspects it is important that we need to know :
1 What sort of fermentation are we carrying out?
2 What is the size and geometry of the fermentor
3 The rheology of the fermentation broth
4 The kind of flow we expect for the fermentation
It is only after we have considered the above we custom fit the stirring configurations.
The type of flow generated by the stirrer is important. It is easy to get laminar flow or even non laminar flow for Newtonian rheology. Things do becomes complex if the fermentation broth which we are dealing are of the Non Newtonian type. In certain cases, the types of Non Newtonian transformations become even more complex.

The choice of the proper stirrer will have to be seen from:
1 The shaft component
2 The blades or the impellers
If we are dealing with viscous fermentation broth it is advisable we use shafts with bigger diameter. The length of the shaft too is critical to the efficiency of the shaft
The choice of the type of blades will determine if the flow produced will be radial or axial. Propeller stirrer shaft will produce axial flows. Which will result the flow moving away from the shaft? The inclination or direction in change of rotation will have impact on the direction of the flow
In cases where the blades are arranged on the disc will have flow attributes which will show strong shearing properties. The flow will be radial and directed outwards. Such flow will generate strong axial suction ia top and bottom axis
Impeller stirrer shaft will provide strong radial flows .
There are the so called anchor design stirrers with the shaft fitting in the centre of a “U” shape structure. This effective in generating tangential flows but poor axial forces or movement of the fermentation broth
There are also hybrid stirrers where both type of propeller blades and impeller blades share the same shaft. Usually the propeller blade is located at the top to induce downward flow to the blades with radial flows
It is important therefore in decoding the choice of stirrers the user must understand the rheology and viscosity of their fermentation broth before rushing like a fool to carry out just any fermentation using the ‘standard stirrer’ The best part of these fermentation studies not only they will not be able to determine the optimal fermentation conditions for their fermentation study but they have faith in “ stupid data’ their studies generated.
I just love the way the fools rushed in where angels fear to tread.. Read more!

Wednesday, October 6, 2010


I personally think that there is too much of irrelevant engineering in fermentation technology. The obsession with mathematical equations, models by engineers into fermentation technology just add further to the mysticism of fermentation. It only helps in making the subject of fermentation technology so esoteric and beyond the reach and understanding of most people including the engineers themselves. After all, the abuse of irrelevant engineering and mathematics only serve in trying to make “sense” out of “non sense”. The logic is simple enough. How can you ever claim to control and optimize the fermentation process if you have very little understanding of the variability of the process?
Yes! Such mathematical and engineering studies and experiments will still data or rather “erroneous data” which one can still try to make some sense out of it. The end product will yield wrong and erroneous conclusions. At this point I am not saying that all the engineering or mathematical input are useless or irrelevant.
The trouble is there is a persistent and irritating trend by chemical engineers and biochemical engineers trying to justify their intrusion into the field of fermentation technology and not vice versa! Good examples are the adoption of unit processes in downstream processing. In a feeble bid trying to improve the engineering or mathematical input into fermentation technology they even try to apply Monod’s equation, Lineweaver Burke into the fermentation modeling! How relevant or significant input these contributions are is another question.
We are thankful for the engineers in helping build or design the fermentors we have on the market now. But looking with perspective over time we see there is no real significant development or advancement in the design and structure of fermentors from the days of Fleming industrial production of penicillin. What we are having now are in fact “living fossils” of the old antiquated fermentors. Nothing much has really changed!
Let us look at the application and relevance of Reynold’s Number to fermentation technology.
Historically, the exposition of Reynold’s Number is the keystone to fluid mechanics. It is more and observation on the nature of fluid flow which includes air and liquid such as observed in wind tunnel, aerodynamics and in trying to explain the transformation of simple laminar flow to complex flow turbulence
The application of Reynolds number might be of relevance in aerodynamics of flight where it is necessary to understand the behavior of objects exposed to high speed wind velocity and turbulence. But I cannot really see the relevance of Reynolds Number at the level of fermentor where we are really dealing at low rpm. In fact, laminar flow is not really sought after in fermentor as turbulence is needed to improve the various mass transfer processes during fermentation
To complicate things further the behavior of the fermentation broth is complex in terms of its phases and changes that occur as a function of time. The rheology of the fermentation broth is complex and almost no two fermentation broth are the same. In fact there are so many variables involve which will influence the Reynolds number such as size, geometry, broth type, media composition and even the composition of microorganisms used in the fermentation process
There for do we really need to apply Reynolds Number in the study of fermentation process or is it just a vestigial reminder left by the engineers for us just like the mysterious smile of the sphinx?

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Monday, September 6, 2010

Ave Atque Vale there's a time and place for everything. The place is here. I just need to find the right time.

Something to ponder....

Sunday, September 5, 2010
I am...
I am a Malaysian.

With that notion firmly entrenched, I bear witness that my country is now 53 years old. It was an age ripened from the valiant efforts of yesteryears’ soldiers who fought for our country’s independence from both internal forces and foreign masters. Though many lost their lives (and are now remembered in memorials such as God’s Little Acre in Batu Gajah or honoured during Warriors Day), the nation was really one in uniting against the perils of communist and rejoicing together when the Union Jack was lowered many years ago. The Malayans simply lived together as religious and racial differences were assimilated to celebrate independence.

Now, Malaysia is an independent nation and unfortunately, the same ‘independence’ has lost its value. While we no longer have to survive communism or colonialism, we are struggling against new evils that were never there. There is a worrying trend of rising racism and religious intolerance between the different races in Malaysia, no doubt fuelled by unscrupulous parties out to serve their own causes. At the same time, we have leaders who preached about ‘Vision 2020’, ‘Malaysia Boleh’, ‘Cemerlang, Gemilang, Terbilang’ and the latest to join the bandwagon is to point one finger upward and utter ‘One Malaysia’.

I am perturbed by how we’re defined by what our leaders label us to be. Far more amusing is that we allow these linguists, the opportunities to ‘reinvent’ Malaysia time and time again when everybody knows the main problem remains unsolved.

Vision 2020 is fast approaching and Malaysia is nowhere near the intended aim of becoming a first world developed nation. Well, if having the KLIA and hosting the Sepang Grand Prix once a year are the cornerstones of a developed nation, then hooray for us. And perhaps Vision 2010 was also dreamt for moments when we burst with pride that our local universities managed to be in the top 200 universities in the world ranking, one that befits our country’s aim of becoming the region’s top education hub. After all, it’s definitely none of our business that neighbouring countries’ universities are mostly ranked in the top 50! Our consolation (and we’re great at finding excuses) could be in the well known story of the hare and tortoise where the tortoise will eventually win. The problem is, we were actually the hare back in those days when our premier university was racing together with NUS, side-by-side.

What the education system in Malaysia today is, at best, one of a handicapped tortoise. We’re handicapped in every sense of the word, from graduates who can’t string a perfect sentence in English to educators who treat teaching with much passion as a toothache. But don’t let that dampen our spirits as we have thousands of graduates jamming the job market! Seriously, Malaysians are really lucky because we must be the only country where students are treated as the shuttlecock in changing the medium of instruction from English to Bahasa at one’s whim and fancy. And because what could be the next smart move to abolish national examinations in place of ‘assessments’, everyone will probably be assessed as smart because now, everybody gets to enter university. If you’re unable to enter one of the many local universities (I think at last count, there was 17), one can always go to the countless private universities mushrooming in every nook and cranny. It’s your choice whether you want to opt for an internationally branded private university or an education institution located on the first floor of a shop lot. If you’re undecided in pursuing which course to take, there is no need to seek out professional advice. Just read the stacks of brochures hurled at our doorsteps promoting quality education for all (but please excuse their glaring grammatical errors and suspicious contact numbers). Finally, Vision 2020 is also envisaged for the nation’s youngsters to grow up as borrowers (and eventual defaulters) as education loans are readily and easily available. It is indeed a bargain to borrow thousands of Ringgit for a degree that could be, in most cases, not even worth the paper they’re printed on.

Further, who could blame us for reveling in Malaysia Boleh when we won a handful of medals back in the 1998’s Commonwealth Games? We were the proud hosts, eager to show that Malaysia is able to stand in the eyes of the world. Okay, so we hosted but what were the costs involved again? I do not believe the accounts have been tabled for the citizens to see just how much the nation has spent for vanity’s sake. And yes, Thomas Cup belonged to us back in 1992. That was the Malaysia Boleh moment that saw every Malaysian kid picking up the racquet and shuttlecock in their bid to be the next Sidek brothers. But it is now 2010 and 5 successive campaigns have passed without the Cup in our possession.
Malaysia Boleh could probably be the explanation why the old Subang International Airport (an important building in our country’s history) was demolished to build, and this was a shocking surprise, another airport! Well, it’s now named as some sort of Sky Park but hey, Malaysia Boleh spend okay. Other governments think thrice and scrimp to get money but let us show you the way. Boleh demolish, boleh build, vice-versa. Either way, money will line certain already well-lined pockets.

Then there’s Cemerlang, Gemilang, Terbilang. Honestly, I do not even know the meaning of those words. Perhaps it is ‘cemerlang’ that it only took our fifth prime minister a few years in office before retiring. One should really consider the previous prime minister’s tenure (and my God, he could almost rival the reign of Soeharto or if he’s a royal, the revered King Bhumibol of Thailand or English Queen Victoria). Well, most of us viewed the fourth prime minister’s reign as a regime anyway. It could also be ‘gemilang’ that government officers were directed to wear ‘batik’ every 1st and 15th of the month. I may not be fashionably inclined but who will actually do serious work when one is dressed up for a reception? I am lost for words in considering ‘terbilang’. I’m taking a shot here but has it got anything to do with the number of shrimps hurled to court for allegations of graft and corruption? Or maybe it refers to the lobsters tiding their sunset years with huge mounts of cash in Swiss banks, happy in the thought that lady justice will not be catching up on them anytime soon.

Finally, the ideals of ‘1 Malaysia’. I would be driving on highways and I’m forced to read huge billboards stating ‘1 Impian, 1 Harapan, 1 Malaysia’. The thing that struck my curiosity is this. Why the need to brand ourselves as 1 Malaysia? My grandparents and parents experienced a life made complete with their friends of different races. Sure, they worshipped different gods but they were united in friendship that transcended the influences of masjid, church or temple. They had no need to use separate tables, hang out in racially defined groups or view each other in a hateful manner. There were no assaults just because the other person belongs to a different race. Most importantly, there was never the despicable need to shout at someone to ‘balik Tongsan, China, India’ or wherever that our ancestors came from. And yet, those are the very things happening now under ‘1 Malaysia’. Isn’t it ironic and downright absurd to claim 1 Malaysia when racial intolerance has permeated into the social fabric of the Malaysian society?

I am deeply disgusted that a school principal uttered derogatory remarks about our friends of the Chinese heritage. I am more appalled that one race is seen to be protected more than the rest when it should be that all must be protected under the flag. I am saddened that May 13 happened (though there exists an irritating doubt that what I learnt from the history books are formulated truths) but enough is enough. It is time that we need to exist as Malaysians without any labels. By strict definition, I consider myself a Malay-Chinese Malaysian (given my mixed heritage) but I will not, at any time support racial extremists who see Malaysia as part of their God-given land. Nor will I condone any calls asking my Chinese and Indian friends to return elsewhere for I would need to go with them as well.

We are all here on borrowed time and the land where ‘tumpahnya darahku’ belongs either to all of us or none at all. Happy 53rd Merdeka and a wish for the upcoming 1st Malaysia Day.
Written by Raja Syarafina RS at 10:47 PM 0 hand prints to be shared
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Friday, July 2, 2010


I am very sorry for not being able to continue writing fermentation technology articles for some period of time as I am currently too busy with some projects
Will continue once the hectic phase is gone. My apologies again
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Thursday, April 29, 2010


What I gather from the newspapers it is going to be a major project that will swallow billions of RM and carried out over 15 years!! Is it going to be more a pipe dream or a reality? Can the project be guaranteed to be successful or is it going to be more money thrown into the polluted river? 15 years is a very long time…. Wonder if the guarantee if any will hold.
One of the most common erroneous assumption is that if the technology was successful for Thames or for the matter the mighty river Han, it does not mean it will be successfully applied for Sg Klang. (Maybe all the parties concerned have their own expert consultants to vouch that every thing will be ok! As for me it is far better to be realistic and prudent. The River Klang is very complex and have many problems. I for one would like to be proven that the project will work…
Would it not be better if the companies concerned are tested first for their ability by giving certain stretches of the rivers to be handled and their performance monitored? To me it is very logical that if the company cannot manage a small portion of the river, it will be questionable if they can rehabilitate the whole stretch of the rivers.
I would love to see the spirit of competition vying with one another in the race to rehabilitate the stretch of rivers given to them. Nothing could be more wrong if all the companies awarded are working in the same group. That is the reason why I like how the Petronas tenders are being awarded, with the Japanese and Koreans competing with each other to complete their own respective towers!
Rehabilitating the Klang river requires more than just mechanical equipment to remove trash or solid wastes. It is more than just building treatment plants along the river. The solution is complex and requires social engineering too. If not we will be back to square one after billions of RM has been pumped into the project.
I for one would not like to see the rehabilitation of Klang river as a very costly exercise in futility!

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Monday, April 26, 2010


Fermentation technology has been used extensively in the production of microbial enzymes. There are three main objectives in the production of enzymes using microbes:
1 The enzymes must be produced in high volume
2 The enzymes must be pure
3 The enzymes must be stable especially with respect to its structure and functions

The key element in the production of enzymes using fermentation technology is:
1 The presence of microorganisms which have the capability of producing the desired enzymes
2 The choice of suitable bioreactors or fermentors that can be used to support the cultivation of the microorganisms that produce the enzymes
3 The optimum conditions, control and monitoring of the fermentation conditions for maximum enzyme production
In all the above the nature of the enzymes being produced are often the restricting factors in the production of the enzymes. The main problems are enzymes are basically large complex protein molecules which are not stable and easily denatured by certain extreme conditions such as temperature, salt, ph and other factors.
The production of the enzymes by the microbes are basically a physiological or metabolic function of the microbial cells and factors such as feedbacks and catabolite repression or metabolic inhibition will affect the process
The production method of these enzymes is governed primarily by location of the enzymes in the cell and whether the enzymes are inductive or constitutive by nature. Most industries that produce large volumes of enzymes are often involved in inductive enzymes. In such situations there is no need to break the cells or organelles to release the enzymes. As constitutive enzymes are sort of “part of the cell” the amount of enzymes are directly related to the amount of cells produced. In such situations it shows primary metabolites behavior and the growth curve is used to determine the right time to harvest the cells and the constitutive enzymes
In the case of inductive enzymes the process of producing enzymes is simpler. Enzymes that are produced are easily released off the cell into the fermentation media. However, in this method the presents of the substrate or inducer in the media in important to trigger the enzymes production.

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Monday, April 5, 2010


I happened to chance upon the studies on the rehabilitation of Sg Way River project. While the intention to take care of the river is noble, it is of utmost importance that such studies be carried out properly in proper scientific manner. Proper samplings, analyses and interpretation of the results must be carried out for the study to be meaningful.
In order for the study to be meaningful goes far beyond than just taking a few random samples from a few sampling stations along the river. Remember, the results obtained from the few samplings might be valid only for the samples taken but they could not be used to extrapolate to the water quality of the river itself (unless one can guarantee that the composition of the river is homogenous and does not change spatially or temporally)
I am a bit disturbed by the way the sampling plan were carried out ( if there were any?) In my opinion the number of sampling stations is too few in number and too far apart. Determining the number and location of the sampling stations are critical to the success of the study. Prior studies must be carried out on the flow and hydrodynamics of the river in order to come up with the most suitable locations that can yield representative samples of the river water.
Sampling is a science and not determined by the convenience of the samplers such as taking samples from the sides of the embankments! Proper sampling utensils or apparatus must be provided to obtain the proper samples. There are many more other considerations which must be considered….

For the complete data please refer to:

With such few sampling stations, samples, the whole exercise would just remain as a feeble attempt in efforts trying to rehabilitate the river. In my opinion it would have been more proper if the study carried out over the stretch of the driver:
1 Identify the various point source or diffuse source of pollution into the river
2 measure the total maximum daily load from each source
Auditings like this will not only identify the stake holders but also the responsible polluters. It is sad that sometimes the innocent stake holders will have to do the cleaning up of the river while the polluters go away scot free!
I am very disturbed too by the interpretation of the water analyses as provided by the report especially with reference to the Dissolved oxygen, BOD and COD readings. The BOD readings for the three stations W1, W2 and W3 are 5, 4 and 10 mg’litre. Wow! Something is not right here. At such low BOD values the water of Sg Way river is clean and not polluted at all. ( But my eyes see the river as very polluted!) Unless something is wrong or inaccurate in the samples or analyses

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Monday, February 15, 2010


The good thing about the use of enzymes in various industrial processes amenable to enzyme activity is that the reactions are simpler, faster, easier to control and you do not have to worry much about unwanted side products or unwanted products downstream.
However in various industrial fermentations, the use of enzymes are restricted to a few steps which more than often are prelude steps before the real microbial fermentation process. The restrictions in the use of enzymes for industrial processes are often restricted by the type and suitability of the enzymes needed for the various processes in the complete fermentation process.
In industrial fermentations, the use of enzymes is more in the hydrolysis of substrates prior to its fermentation. This stage is often called the liquefaction stage where large molecules are broken down to simpler monomers to be easily used by the fermenting microorganisms. Enzymes too are widely used in the clarification process of various fermentation juices
Using the enzymes therefore help in making the fermentation process more efficient both technically and economically.
Enzymes are basically catalysts, whose main function is to speed up the specific reactions. In a way, the enzymes are no better than the inorganic catalysts used in many of the industrial chemical reactions.
The differences between enzymes and the inorganic catalysts are more in the sense organic enzymes carry out their reactions under a less demanding conditions. Their reactions are more under gentler physiological conditions found in the normal metabolism of the cells.
Organic enzymes are usually large protein structures which are easily denatured by conditions of extreme ph, temperature and salts and metals. The activity of these enzymes are not stable as they are easily denatured . Their active sites where the reactants interact are very sensitive to such conditions
Industrial catalysts operate under very extreme conditions of pressure, temperature, chemical toxicities which would not be suitable for the living microorganisms.
There is high demand today for enzymes to be used in various food and beverage industries among others. One of the biggest outlet for the production of enzymes is by the use of fermentation technology where the enzymes itself is the sought fermentation products.
Before discussing further the production of enzymes using fermentation technology let us acquaint ourselves with the type and location of enzymes in the microbial cells.
Many new students tend to fantasize the enzymes as equivalent to the magic elixir that can transform almost anything to anything. As we have said earlier the function of enzymes are nothing more than speeding up certain biochemical reactions. The living cell which contains cytoplasm within the membrane sac is nothing more than a complex mixture or soup of enzymes. Without enzymes it’s doubtful life will persist!
In reality the function of enzymes are very limited to carry out certain chemical reactions which involve breaking or making new bonds between the chemical groups. We classify enzymes by the nature of the chemical reactions they carry out!
We also classify enzymes by their location that is they intracellular or extracellular. Or we can classify enzymes whether they are constitutive or inductive, or whether they are soluble or attached
The nature of thee enzymes as stated above will determine the conditions for the production of the enzymes and its downstream extraction isolation and purification
Most industrially important enzymes produced by microorganisms are those which are induced and secreted out by the cells into the fermentation broth. It is therefore of great importance and cautions that only suitable microorganisms are used in the production of enzymes using fermentation technology. Common microorganisms used are Bacillus subtilis and Aspergillus oryzae
Much work and research are needed before these microbial enzymes can be used in large fermentors. What is most important is that at least the microorganism chosen must have the ability to produce the desired enzymes. The productivity of the microorganisms can further be enhanced by using various techniques of biotechnology such as gene manipulation
The enzymes produced by these microorganisms do not come in market ready forms! A lot of work needs to be done especially in the downstream activities.

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Monday, February 8, 2010

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Friday, February 5, 2010


One of the first things the students taking fermentation technology will be the outline of the fermentation process flow. He will learn that the complete industrial fermentation process will be made up of three main stages:
1 Upstream activities
2 Midstream activities
3 Downstream activities
In any industrial fermentation process is seen as a pipeline of activities originating upstream with the fermentation products finally being obtained at the end of the pipe or at the downstream stage.
Thus in a simplification in the process flow we see masses being introduced into the process and as it flow down the pipe these masses are being transformed to the desired fermentation products by the fermentation microorganisms.
At each stage of the transformation optimal conditions are implemented not only to obtain the highest yield of the products but also in terms of energy and economic efficiency. This attempts can only be carried out if we assumed that the flow of substrates through the fermentation process will pass through various unit processes which could be identified and optimized.
In such situation, it is important that:
1 The flow of masses from the beginning stages to the final products will be smooth and not interrupted. To achieve this hydrodynamic flow restrictions imposed by various volumetric and hydrodynamic restrictions must be overcome by using different bioreactor or volumetric configurations
2 That each unit process is working under its optimal operating parameters such as temperature, mixing, ph, seeding etc
3 Elimination of physical and physiological bottlenecks in terms of pumping and even removing the effect of catabolite repressions or inhibitions
4 That the impact of any changes in upstream activities will affect the efficiency of the downstream activities. Any improvement or changes in upstream activities will affect downstream and not vice versa
5 That there must be allocation or allowances for changes even within this narrow range of optimized parameters

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Monday, February 1, 2010


The microorganisms are important components in any microbial fermentation. The microorganisms in the fermentation process are either the agents of change which convert the substrate to valuable fermentation products or they themselves are the products sought in the fermentation process.
In either situation the objective of the fermentation process it selves is to obtain the highest number of microbes per unit volume. This trend is termed as achieving high cell density fermentation.
If we can achieve high cell density it is akin to saying that we have higher number of cells to carry out the transformation of substrate to products. More cells mean more “factory workers” to carry out the production. Thus more products will hopefully be produced over the period of fermentation process.
It should be noted although increasing the number of cells can increase the amount of fermentation products formed, that does not mean that the real efficiency of the fermentation process has increased in terms of fermentation yield by the unit cell. It is only the numbers of cells has increased leading to more conversions.
Only new strains or improved strains of producing microorganisms will increase the fermentation yield.
Logically, it is a good option to increase the fermentation product formation by increasing the number of microorganisms that will transform the fermentation substrates to fermentation products. However, this is not easily achieved in reality as there are many physical and physiological constraints that will try to prevent this objective.
The microbial cell is unique in its own right. During the process of fermentation not only it transforms the fermentation substrates to fermentation products, it will in the process of metabolism extract energy and carbon from the substrate to produce new biomass and undergo microbial growth.
In a way this would be ideal in achieving the high cell density fermentation, but such growth is not infinite and will ultimately slow down as in the typical sigmoid growth curve of the batch culture fermentation
Even before achieving this stationary phase the cells will it selves undergoes major changes in its metabolism or physiology will be of negative impact to the fermentation process and product formation
So how can we achieve the optimal high cell density fermentation? How shall we operate so that the fermentation of high cell density will be at optimum fermentation product formation in terms of economic and efficient control?
The whole idea of obtaining high cell density fermentation is ideal when:
1 You can have high density or number of microbial cells in the bioreactor
2 The high density protocol will not negatively affect the fermentation process or the products in terms of the quantity, quality and stability of products
3 That the fermentation process will be able to be carried out efficiently and economically in terms of substrate usage and efficient mass transfers
There are various strategies which could be applied in trying to obtain high density cell fermentation not only through feeding mode but also bioreactor configurations and physiological manipulations of the microbial populations

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Sunday, January 31, 2010


Sometimes we can learn more about the problems of rheology and mixing of fermentation broth by observing simple examples such as a drop of honey. A drop of honey as a rheological model is not truly reflective of the behavior of the fermentation broth but its behavior will allow you insights of mixing non Newtonian fluid.
If we try to stir the drop of honey on a surface using a tooth pick, we will see that it is very difficult to mix the drop of honey homogenously. There is movements by the tooth pick, but in most cases the honey will try to resist the movement and retract elastically back to its mass. Even if mixing occurs temporarily, it only occurs within the close proximity of the stirrer. Increasing the speed of mixing at most times does not increase the mixing of the honey.
Are we trying to say that in fermentors with very viscous broth mixing comes to nothing? Or better still have we come with properly designed stirrers that can really effectively stir the fermentation broth?
The biochemical engineers need to understand more about the properties of the non Newtonian broth and designed new stirrer configurations or even new modes of mixings to overcome this problem. Maybe it is high time or over time that they should start to look at the micromixing aspects rather than be over whelmed by macro mixing properties

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Thursday, January 14, 2010


In the study of fermentation technology, we rely strongly on the understanding and interpretation of the microbial growth curve in making the right decisions for different stages of the fermentation process. We use the growth curve not only to determine the efficiency of the fermentation process but also in trouble shooting exercises
Yet, despite its importance how much do we really understand about the microbial growth curve? In fact, most of us learn about the typical sigmoid growth curve even as early as out initial years in our secondary education and right up to our university days. But really how much do we know about the microbial curve?
Instead we have been indoctrinated by superficial ‘brain washings’ of knowing the lag, log and stationary phase and the verbal description or verbal description of the phases of growth; slow growth, exponential growth and no growth…
They keep telling us the stationary phase is the onset period before the microorganisms die. They tell us that the stationary phase occurs because of lacked of food or toxic conditions. And that the stationary phase is a useless phase of no importance to physiology!
In terms of microbial physiology, the stationary phase is the most important phase when the microbes will undergo huge changes in its metabolism (prior to kicking the bucket!) It is the time for some microbes to produce secondary metabolites such as the antibiotics or even form spores to survive.
Before going into further detail let us try to understand what factors cause the induction of the stationary phase. Bear in mind we are dealing not at the behavior of single cells but a population of millions and millions of cells of diverse types of metabolism and physiology
The stationary phase the growth curve is often visualized as a level phase occurring after the end of the log phase and before the start of the declining or the death phase. Since the growth curve is a graphical representation of mathematical data, we could therefore say that at the stationary phase, the numbers of cells remain constant where either there is no growth or loss of the population of cells or more correctly where the number of new cells added is the same as the number of cells lost. It is hard to imagine that at the stationary phase the cells are not growing at all! It is more of a steady state where the number of cells remained constant
One of the most common explanations to explain the formation of the stationary phase is when substrate becomes the limiting factor. It is a situation where there are not enough nutrients to support the growth and multiplication of all the cells.
Another hypothesis is that stationary phase is induced by the presence of toxic products which reach a certain concentration to inhibit the growth of the microorganisms.
What is often not discussed is the impact of viscosity that might have impact directly or indirectly on the induction of the stationary phase. Then it is quite fair to say that limiting nutrients or substrate are not the only factor initiating the onset of stationary phase.
With regards to toxic products build up inducing stationary phase it might be quite valid in cases where there occurs catabolite repression or the fermentation products itselves are too toxic or too acidic. This argument however does not hold where in aerobic metabolism the end products are just water or CO2
Now let us look closely at the problem. The formation of the stationary phase is commonly associated with the sigmoid growth curve of try phase is commonly associated with the sigmoid growth curve of the microorganisms in general. It is more applied in batch fed mode. Why is this so?
It is more of the continuous washout rate occurring in the fermentor where the growth of the microorganisms is controlled by controlled wasting of cells, raw substrate and waste products. You can initiate continuous phase at various point of the log phase….
I tend too see the onset of stationary phase as a major shift in microbial metabolism rather than the onset of the equivalent of menopause….:) It is a point of intense change in the metabolism of the cell when the microbes are facing extreme stress with regard to their survival. The microorganisms have to carry out drastic changes in structure and function to survive or to insulate the integrity of their metabolism from the normal mode until better conditions will return
However it is during these trying times that the microorganisms will conjure up new compounds which do not seem to serve any functions to them. Initially it seems that these moves are stupid as the microorganisms seemed to waste energy, enzymes and carbon at time when they should be trying to conserve these precious supplies.
Could it be that evolution that took billions of years is stupid or more better we are ignorant of the strategy taken by the microbes? Sometimes we have to change our paradigm and try to see the significance of things from the point of view of the microbes rather than trying to do the thinking for them

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Wednesday, January 13, 2010


Get a large beaker of water. Fill it various strands of fine cotton strings of varying lengths. Then slowly switch on your stirrer. Observe what will happen?
You will observe that as the water starts flowing and mixing, the strings will start getting entangled not only with other strings to form pellets, but also with the spinning shaft and impeller.
This is what will happen too during submerged mycelia fermentation involving fungal or streptomycetes with hyphal structure. Strands of hypha will behave like the strings in forming pellets or getting entangled with the impeller or shaft. The hydrodynamic characteristics of the broth during mixing will cause collision between the various hypha resulting in the formation of pellets.
Of course the use of the string is just a simple model to explain what happens in the broth turbulence. In the real situation involving the mycelia the effect of mixing upon submerged fermentation is far more complex
A lot of submerged fermentation is involved in antibiotic fermentation. Despite the decades of experiences in mycelia antibiotic fermentation, there is relatively poor understanding of the behavior and physiology of mycelia in fermentation which resulted in poor control of the fermention process.The behavior and growth forms of the mycelia in the fermentor affects various mass transfer processes and even the microorganism itself.
The fermentation of the antibiotics initially requires the build up of large amount of biomass in the trophophase before secondary metabolism could be initiated to form antibiotics at the idiophase. Large amount of mycelia will be generated in the log phase prior to the onset of the stationary phase.
Intense aeration and mixing at this stage will result in collisions of the hyphae and mycelia forming fungal mats, pellets and other microbial aggregates. High shear forces are generated at the impeller tips, blades, and fluid turbulence and even at the bubbles paths.
On one hand, such shearing forces will damage the cells or hyphal and thus affecting metabolism and antibiotic formation. While on the other hand such hydrodynamics will form microbial aggregates which will affect the mass transfers across the aggregate and even the viscosity of the broth
The fungal pellets in antibiotic fermentation are interesting in their own way. The morphological and biochemical characteristics of the fungal pellets change as the fermentation progresses
However we can divide the fungal pellets into three classes:
1 Open pellets
2 Semi dense pellets
3 Dense pellets
The open pellets are not dense showing diffuse growth of hyphae,fused together and autolysed while the dense pellets are darker inner mass with thicker hyphae and healthy apical tips. Fungal pellets are larger compared to streptomycete which are smaller and simpler.
Correct shape and form of pellets indicate fermentation going as expected. This is useful diagnostic tool to indicate the onset of secondary metabolite formation during the antibiotic formation

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Sunday, January 10, 2010


In most, if not all of fermentation broth, we are dealing with Non Newtonian fluid. The Non Newtonian nature is due to the composition of a fermentation broth which is not uniform and complex. The fermentation broth often show complex interactions of solid, liquid and gas phases.
To make things worst the rheology of the fermentation broth is always changing as a function of time and with the progress of the fermentation process.
It is more difficult to control and optimize a fermentation process if it is a Non Newtonian fluid! Things would definitely be easier if the fermentation broth is a Newtonian fluid. (But then again there would be no bread, cheese, yogurt, fish sauce and many more fermentation products!)
The main impact of Non Newtonian rheology is that it affect mixings and mass transfers of heat and oxygen and prevent efficient homogenous composition to occur.
We all know that in rheology it is the study of fluid deformation and flow under pressure and the relationship between stress and strain. Through simple observations we can see how difficult it is to mix and aerate viscous fluid. Each rheological type will give different mixing profile.
This has led to the classification of various classes of Non Newtonian fluids such as
1-viscoplastic fluid,
2-bingham fluid,
3-pseudoplastic fluid,
4-dilatant fluid
Non Newtonian rheology curves can be made up of various types. Most of these rhelogical curves are graphs where the x- axis is shear stress and the y- axis is shear rate
The rheological graphs are interesting not only in comparing between the Newtonian and the Non Newtonian but also the varying properties even among the various Non Newtonian fluid
It is interesting to note generally that all Non Newtonian fluids show some similarity in relationship with Newtonian fluid reflecting the effect of shear stress on shear rate. There is roughly a direct linear relationship (with variations) between shear stress and shear rate.
Differences only that Newtonian fluid adhere strictly and very linear and start at point zero of the axis.
1 Viscoplastic and Bingham starts only after certain level of shear stress. This means that the fluid will NOT respond immediately to applied stress and will only react after reaching the critical power point
2 Pseudoplastic and dilatants start at zero point but are curved in their shape. This mean that the fluid will respond immediately to the power or energy input. This is similar to Non Newtonian. However their response will be different in that it is not a linear relationship between stress and shear rate
3 Viscoplastic, pseudoplastic and dilatants are curved in their shapes This means that these fluids react in their yield behavior under stress differently.
So what does these observations mean in fermentation?
These rheological graphs will tell us how to respond efficiently with the type of broth being fermented.By understanding the various rheological changes that occur in the fermentation broth we can:
1 Try to achieve uniform homogenization and optimum mass transfer
2 Try to optimize energy usage in mixing of the fermentation broth
In carrying out the fermentation, we are using the impeller to mix the broth. Energy is transferred and dissipated to the broth by the impeller system. The impeller is in simplicity the shear stress being enforced upon the broth.
The effect of the impeller or mixing on the broth will result in the flow or turbulence of the broth. The broth will respond by exhibiting stress yield properties such as thinning out of the broth to improve mass transfer processes.
So if we know the rheology of the fermentation broth it will help us to adapt to obtain very efficient fermentation by adjusting our mixing regimes. This is especially so when the rheology changes with time and conditions.

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Thursday, January 7, 2010


We have always looked at fermentation process or the formation of fermentation products by microorganisms as something beneficial to man. While we are deriving the benefits from the activities of the fermentation microorganisms, in reality the action of these microorganisms are really not to serve the human masters but more to their selfish ends. To these microorganisms, the fermentation activities are their mode of survival. Fermentation is their metabolic and physiological method of deriving energy from the substrates for their growth.
The fermentation products during their metabolism are just their metabolic waste products which have served their duty. If however, the human beings get their pleasure by consuming their waste products……well and good for these pathetic humans. Nothing is stopping these humans from drinking their metabolic urine or alcohol !
In fact the cornerstone of human civilization in history has always depend on these fermentation products. There is a rich diversity of fermentat ion products as reflected in the culture of various countries. In essence, the diversity is quite limited in terms of the microorganisms and metabolism involved. The fermentation products are just given different brand names in different languages and by the use of different substrates found in the specific countries
The fermentative microorganisms metabolize the substrate to extract their enegy. This is executed by various metabolic pathways found in the microorganisms. It should be stressed that there is a diversity of metabolic pathways available, depending on the type of microorganisms, substrates and physiological environment. What is important to note are:
1 There are a number of fermentation pathways available in a microorganism
2 TCA cycle is only available in aerobic microorganism, BUT at the same time these aerobic microorganisms too have anaerobic or fermentation pathways . These microorganisms too are carrying fermentation process in their metabolism
Most students, in their early stages of learning microbial metabolism erroneously tend to think that only one or two pathways are involved. Or they only tend to think that in the study of fermentation metabolism only carbohydrate catabolism is important! Nothing could be further than truth in these assumptions. It is like saying lipids and proteins are not used as substrates in fermentation.
The beauty about having many fermentation pathways interlinking allows the fermentation microorganisms adaptability in the uncertain environment....and their survival!!!
The changing of tracks in metabolic pathways are achieved by the presence of branch end compounds. Branch compounds are compounds which interlinked two or more metabolic pathways. On reaching a branch end compound the microorganism will have the choice to go for one or other pathway depending on the circumstances. A very central branch end compound is pyruvate. From pyruvate the metabolism can go almost any where.
Such branch end compound such as pyruvate allows the effective linking of carbohydrate, lipid and protein metabolism. It also linked the various anabolic, catabolic and intermediary metabolism.

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Tuesday, January 5, 2010


Everyone knows the greatest power in driving any company is profitability. To increase the company profits and to reduce its risks companies are known to cut corners and finding ways to reduce the taxes they have to pay. Even better if there are other parties who are willing to inject capital especially in their high risk projects! Things simply could not go wrong! It is the ultimate formulae for success at least for the companies
Every body knows that setting up companies involve a lot of risks and it is a well known principle that out of the many new companies formed, many will fail. This failure is attributed to many reasons ranging from poor management, technical problems, and marketing and even from oversight to cash flow problems.
Some projects are even doomed to failure even before taking off, or while still on paper. They just don’t learn!!!. The best advice you can get before starting a company is to try obtaining the fundings from the bank or any other private institutions. They will vet your paper to the dot to see if the project is going to be a liability to their investment
And suddenly in the exciting spin of biotechnology, we have people or bodies who are willing to throw caution to the wind and throw “free or easy” capital to these companies in the name of biotechnology! The only problem is the money they are throwing are not theirs but the taxpayers!
As for me I would not be convinced by hype sounding words or terms, nor promises or potentials! To me I want to see track records. I know there are risks involved in any project but at least I will take calculated risks! I am not convinced at all by the sacks of MOUs but rather by the company performance and profitability.
I fear that in the end all these bionexus exercise will only profit the companies and not the nation

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It is very difficult to imagine running a fermentation plant without a good air supply. Air in various forms and quality are needed to carry out the various activities in the fermentation right from upstream to downstream activities.
Today, we will be discussing about the use of laminar air flows in fermentation activities. Laminar air flow is the term we use to describe the flow of air which occur in parallel layers or sheets just like a laminated sheet in cross section. The easiest way to visualize occurs air flow is to observe the laminar flow in liquid during primary mixing.
Conditions of generating laminar air flows occur under low energy power. High power usage will generate turbulence. Laminar air flow may further be enhanced by the type of nozzle used and by using laminar devices.
Laminar air flow are used more in the belief that such air flow do not create turbulence that might result in increased loading of microparticles in the air.
What is often not appreciated there is turbulence associated with laminar air flows by mechanically disturbing the immediate environment. Second turbulence is created as the laminar flows get mixed and merge. Points of energy cancellations will result in fast sedimentation particles
Laminar air flows do effectively transport microparticles at the zone separating the various layers of air.
The use of laminar flow is usually only effective in small space confinement such as in the inoculation chambers where the positive pressure exerted within the chamber tend to repel any intrusion of particles from the outside.
There is the trend nowadays to incorporate gentle laminar flow on the top surface of the fermentation floor to sweep away the microparticles.
It is regretful despite the understanding of the properties of laminar air flow its incorporation in the architectural design of aseptic areas in sensitive fermentation areas or even in the design of surgical operating theatres are still poorly understood

It is therefore not surprising in surgical operating theatres higher infections are often associated with the use of laminar airflow?

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Monday, January 4, 2010


One of my students used to ask me this question,
“What is the point of trying to understand the complexities of fermentation rheology, when rheology itself is not one of the common parameters used in monitoring the fermentation process?”
I threw this question to the class for deeper discussions..
The general consensus is that:
1 Rheology is an important and relevant parameter of understanding and controlling the fermentation process.
2The use of rheology part could contribute significantly in understanding the changes that occur during the fermentation process.
3 Rheological data could be used in trying to optimize the conditions towards optimum fermentation process.
4 Rheological data could be used to extrapolate the likely event of impending fermentation failure
5 The use of rheology data such as the type of non Newtonian fluid could indicate the right opportunity to change the mixing regime and save energy
6 Operating parameters could be adapted such as mode of feeding to control the rheology of the fermentation broth
7 The failure to use rheology as the online parameter is because there are no sensors that can measure rheology on lines for now, and not because rheology is not an important parameter!

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Sunday, January 3, 2010


In the true tradition and history of fermentation, the reference to fermentation products has always been associated to fermented drinks and foods. These fermentation products are products excreted by various fermentative microorganisms in the absence of oxygen.
These diverse fermentation products have always been characterized by their unique chemical and physical characteristics which give them their own unique taste and odours.
The fermentation products are simple organic compounds usually with carbon skeleton between one and three carbon. The short chain compounds are characterized by their volatility at room or ambient temperature.
The aromatic nature of these fermented products are attributed to their own unique chemical groups such as volatile fatty acids, ketones, aldehydes and even the presence of sulphur containing compounds. It is the interactions of these various volatile which give the unique odour and taste to butter, fish sauce and wine among others.
The problem is that in the age of industrial fermentations there is the need to produce large volumes of these compounds. Some of these fermentation products need to undergo various processing treatments to make the product safe and acceptable. Some of these products need to be modified and repackaged to fulfill the needs of the modern consumers.
What are the effects of these processings and treatments to the quality of the fermentation products? This would not be a problem if the fermentation products are simple compounds produced by single cultures and using modern fermentation technology such as beers. This would however be a problem when the fermentation products are a mixture of volatile organic compounds produced by mixed culture fermentation such as in fish sauce or budu fermentation
Definitely such processing treatments using high temperature will affect the composition and quality of fermented products. The powdered fermentation products when reconstituted will definitely taste different or lost that characteristic bouquet!
Maybe it is for that reason certain fermentation products will always remain traditional…..and tasted better

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