Author: hplcnyoublog

B. cereus about contamination – Part 2

In my previous post (   ), I covered the first on three main types of contamination. I will continue with number 2 in this post.

2. Dead spots in the process loop. This is a very common problem with fermentors and other vessels of similar design. It can also affect other process equipment as well, like ultrafiltration skids, etc. In all cases, areas of slow or no movement can be areas where contamination will build up. An example is a 100 liter sterilized in place fermentor I was working on. The agitation was from the bottom and had a live steam seal (steam is needed to keep the seal in place). Well, there were some small grooves in this seal and the seal (made if high temperature rubber) acted as insulation. This allowed some material to build up and and cause  partial contamination of some broths I was working on. Eventually, I talked to the equipment manufacturer who came up with a new seal design and installed it.

It is important if there is contamination, even a small amount, to evaluate all equipment to discern where it comes from.

In part 3, I will talk about cleaning procedures.

David Slomczynski, Ph.D; Geometrick Enterprises


B. cereus about contamination – part 1

One thing is known, you either admit you have contamination problems or you can bury your head in the sand. It is that simple. Contamination can be minimized and kept to a minimum as long as you know it is there. Many companies won’t admit it and that is a problem. Since this is a big topic I am planning to split this into 3 posts.

Contamination can come from a variety of sources. Some off the top of my head are: 

  1. Raw Material 
  2. Dead spots in the process loop 
  3. Bad cleaning procedures

I will explain some examples and what was done in those instances.

1. In graduate school, we were working with a fungus where we would grow it on a semisolid medium with shredded wheat as the solid support. Well, the first time we made the medium and let it sit for a day, we had bacterial contamination on the medium. As it turns out, there was a Bacillus sp. that contaminated the shredded wheat in very minute quantities. When we sterilized the shredded wheat, it helped the bacterium to grow by reactivating the spores present. To alleviate this issue, we used a process called Tyndallization. Basically, we sterilized the material twice with a 1/2 day pause in between. This allowed the spores present to germinate and then we were able to kill them during the 2nd sterilization step.

I will cover contamination types 2 and 3 in my next 2 posts.

David Slomczynski, Ph.D; Geometrick Enterprises


SOP’s aren’t for SAPS (Why you need SOPs and what they are) part 3

In part 1, I described what SOP’s are and in part 2 covered what they cover and the information included in them. Well, this is Part 3, where I will describe why they are important to you. This is the hardest point to get across to people, in general.

What is so important about SOP’s? EVERYTHING, there, I said it. They help employees, organizations, etc. all follow the same steps in a process, assay, or writing. This helps to make it all more reproducible.

Let’s say you are a multinational company and there is a new assay, that was developed in one lab and you want the rest of the labs, in the company, to use this assay. How best to share it, with an SOP. A good SOP explains everything, making it easier to transfer this assay across the company.

In closing, SOP’s aren’t for SAPS but they are needed for quality and reproducible work.

Geometrick Enterprises can now help companies with SOP writing and review. If you don’t know where to start, how to start, etc. that is where we come in. We will try to make the process as painless and as simple as possible.

David Slomczynski, Ph.D; Geometrick Enterprises

Biofuels: As Bad As Some Say They Are?

Here in Ann Arbor, there have been plenty of fireworks on this press release “Study: Biofuels increase, rather than decrease, heat-trapping carbon dioxide emissions” about a new paper published by the University of Michigan. After reading this paper, I can understand what the brouhaha is about because there are quite a few other factors, for evaluating carbon emissions from bio-fuels, that were not included in the paper. If I were writing it, I would also have included information about carbon sequestration, for example. Plants take up carbon dioxide and expel oxygen. This respiration is what grows the plant and in point of fact, all the carbon in the plant is sequestered from carbon dioxide. If we look at corn, for example, The ear of corn is about 10% of the total biomass of the corn plant and the kernel is about 25-50% of that ear. The rest of the plant is ground up and plowed back into the ground. The point being is that a small portion of the sequestered carbons dioxide is actually used for fuel production. We can never get 100% conversion back into fuel from biomass so our sequestration of carbons dioxide is always net positive. This is, of course, just one example. There are many other factors that could have been included.

David Slomczynski, Ph.D; Geometrick Enterprises


SOP’s aren’t for SAPS (Why you need SOPs and what they are) part 2

In part 1, of my SOP blog post, I described why you need to use SOP’s (SOP’s aren’t for SAPS (Part 1))  and now I will describe what has to be in an SOP and what needs to be documented by an SOP.

An SOP is a living document that describes any process and/or assay. It is a document that
covers anything where standardization is involved.

So, what needs to be in SOP? Think of the SOP as a pedantic, step by step description of your process.  Every little step, detail, manipulation, etc. If you, in a step, stand on one foot and bay at the Moon for 5 minutes, well then that has to be included. Leaving out any step or detail, no matter how trivial, will result in others not being able to exactly reproduce results from your SOP. This is important since an SOP is your document which all employees will refer to.

It can be a daunting task, writing down every step you did in an assay, a fermentation process, or even writing for an SOP, and for most, that is what makes SOP’s such a daunting document. But, once it is written, you have a document that everyone can use and can be trained with. It is basically a little pain at the beginning for a big reward later.

David Slomczynski, Ph.D; Geometrick Enterprises

SOP’s aren’t for SAPS (Why you need SOPs and what they are) part 1

SOP’s (Standard Operating Procedures) seem obvious to many but aren’t understood, utilized, or not even written. Too many times SOP’s seem to be written by lawyer or some savant to whom the language is obvious. That being said, an SOP is important for several reasons. They are:

  1. It standardizes your methods and procedures. (Internal)
  2. It shows there is a standardization in your company (Internal and External)
  3. Makes it easier to train new employees. (Internal)
  4. When an audit is done, SOP’s help with tracing issues. (Internal and External)
  5. Show them to customers and/or Funding  Agencies to indicate your proficiency. (External)
  6. SOP’s should be used when you are involved with one of the various ISO designations. (External)

So, there are reasons to have and to write SOP’s.

In the next part I will describe what is needed in an SOP.

David Slomczynski, Ph.D; Geometrick Enterprises