Month: October 2016

A Reflection on Antoni van Leewenhoek’s Birthday

Today marks the 384th Birthday for the Father of Modern Microbiology. Many things have changed but many things still remain. We have DNA sequencing, genetic engineering, and other sort of marvelous technology yet, there are estimates that we only know less than 1 thousandth of  1% of all micro-organisms out there – http://www.newsweek.com/new-estimate-there-are-1-trillion-species-microbes-earth-454714   .  This fact is lost on most lay people. For all our advances, there is a whole universe out there that we know nothing about.

We also think we are the masters of this planet and that is probably far from the truth. Micro-organisms multiply and adapt much more quickly than we can. If you want proof, look the anti-biotic Staphlylococcus strains out there. They are getting increasingly more resistant to all the powerful antibiotics we can produce. Maybe this is a sign we need to co-exist in this world rather than trying to bend it to our will.  After all, there are more of them, then are are of us.  🙂

David Slomczynski, Ph.D; GeoMetrick Enterprises

Literature Searches – Where Computers have Failed Us

This topic really is tough for people to understand.  It is so easy just to go into various search engines and type in a topic and get out information but,  that is only PART of the information out there. So much information is located in physical media (books, journals, etc) that people have ignored by it not being ‘convenient’.  In the science fields, many researchers do not go back far enough in the literature and this is to their detriment. There have been some amazing science problems worked out and discussed in older papers. Just using only the last 20 years of research or so, means people are using an arbitrary point of reference. Yes, older literature means you have to look through actual physical media and not on a computer screen. I think researchers should not be intimidated by it, after all, the earlier researchers had to do it that way also.

I will give an example. In my MS and PhD theses, I referenced a paper from 1883. This was the first scientific paper describing the actual enzyme I was working on. Why was that important? The researcher, Yoshida, described the enzymatic reaction in a very succinct and beautiful way. Remember, this paper was published before the term ‘Enzyme’ was coined, so Yoshida used the term ‘diastase’. Beyond being historical, using this reference also showed how much interest there was in this research topic.

In another example, I found work that was done in the 1940’s by the USDA that superseded some of the research I was involved with which proved it was not unique or novel. Going back to the original literature, showed how people have misinterpreted the original work and did not read the original close enough to actually understand the research.

Literature research is important for both research and for patent purposes. This has to be one of the most important of all the work the researcher has to do. “Due Diligence” in literature search can save researchers time from re-inventing the wheel.  This is why it is important for researchers to do as much literature research as possible.

David Slomczynski, Ph.D; Geometrick Enterprises

HPLC Method Development around the World: Why it is so hard

Taking a method that was developed and published from another country and trying to use it in another country – why should that be so hard? Well, once, I was trying to reproduce an HPLC method from a Japanese group published in an Analytical Chemistry Journal (Honda et al 1991 Anal Biochem 199: 256). It turns out the columns used, in the paper, were not available NOR for sale in the US. I tried many columns, with similar characteristics (packing material, coating, etc.) and none worked (even with help from companies selling columns based on their knowledge). I basically had to start from scratch and develop my own system, which I did and it was totally different and more complex.

Another time, I was using an older method, which used high pressure solvent mixing, versus what I had, which was low pressure mixing and could not reproduce the separation. Again with modifications, I was able to get the right results. As it turns out, high pressure mixing, involves solvent compressibility calculations in its mixing algorithm and if not calculated properly can actually throw off the solvent mix the column sees.

So the take home points:

  1. Make sure all the instruments are the same (avoids void volume issues, etc.)
  2. Make sure Solvent and water quality are the same (this is easier now).
  3. Make sure the columns are the same and available.
  4. Use set standards and if possible the same standards

David Slomczynski, Ph.D; Geometrick Enterprises

B. cereus about contamination – Part 3

In part 2  (  http://wp.me/p7I0V6-1l  ) I covered problems with equipment. This post will cover cleaning. As was once told me by my graduate advisor, ‘Cleanliness is next to Godliness’. So, protocols for cleaning are important. Too many times people get accustomed to CIP (Clean In Place) but do not check whether or not the procedure actually works.

There are many tools to check for issues, one is from Hygienia and there are many others. This is a basic test to determine if there are intact bacteria, mold, etc. Then further tests, like culturing, etc. will determine what the microorganism is and what to do about it.

At one particular job, I was working on a project where sterility was important, since we were doing a continuous fermentation to a slow growing culture. It was important that the initial sterility and cleanliness were paramount. All the issues with dead spot, etc. were in place but how to clean was not discussed. We started with a CIP (Clean In Place) system but determined that the system caused issues, namely some Bacillus sp. that was found in the CIP (Clean In Place) material. We had to switch and tried several different vendors until one solution was found of a different make up.

In another instance, a simple brush was found to be the culprit in scoring the inside of a fermentor. It was these scratches, that allowed contamination to build up. We had dismantle the fermentor and polish the inside to remove these scratches before continuing with our process.

Cleaning protocols are not infallible and need to be tested to make sure they work properly.

All 3 posts show how important being observant and diligent in dealing with contamination can be.

David Slomczynski, Ph.D; Geometrick Enterprises