Monday, 19 February 2018 10:57

Tea with a purpose

When you design for a specific action or purpose, a significant plan and thought goes into coming up with a piece of software or instrument or device. This works well for most products. But sometimes for prototypes, or to prove a concept, some really creative people can adapt a concept that did not exist before and take it to a different level.
Consider the picture above. This is a CD drive from a PC that is not been used and is used to brew tea by dipping in the bag a specific number of times. The unique part here is the adaptability of something that is unused and using it for another purpose. Is this the best thing for the job? No. However, it works for the short time and proves the concept and is completely out of the box thinking.
The author here has also created a github page that gives you all the diagram’s and details on how to create it.
What problem do you have that can be solved with a kludge to prove that you need a solution?

Tuesday, 13 February 2018 15:26

Patents are important to give companies exclusivity in the business of biotechnology. In the patent court a “natural product” is not considered patentable since it is the act of nature and not necessarily an invention. However, one Japanese man – Jokichi Takamine, the first pioneer in Biotechnology nearly 120 years ago, patented a natural product an enzyme that he isolated. His first patent on the isolation of an amylase was the first patent granted for the process of separating a microbial enzyme from Koji that was called Taka-diastase. He then licensed this to Parke-Davis and generating a good amount of revenue that not only made him very prosperous but was the start of the Biotechnology industry. He then continued his research to isolate and patent adrenaline and that led to significant patent discussion when challenged in court. The history is that since the patent examiner’s objected that this was a simple isolation of a natural product – he countered by making the molecule a base instead of a salt. The history is more complex and can be read in the link below.


These discoveries set the precedence for the patenting of streptomycin by Waksman at Rutgers and other molecules after that such as Taxol covered in the previous blog which was another natural product that was patented by BMS.
Each of these patents, made the patent holder very rich from the licensing activity and continue to this day with supreme court evaluating the patent for testing BRCA gene mutations by Myriad. These were challenged in court lead to a reversal of the ability to patent natural products.
This discussion on patents stems from 35 U.S.C SS 101 which declares that abstract ideas, laws of nature and products of nature are unpatentable.
So, even though many products that were patented were natural products isolated from nature an exception was made until recently that purified and isolated substances could be patented. The Myriad ruling on non-patentability of natural products confirms that much more strongly – though it took about 120 years! To be clear, a patent holder can still claim a novel use of the product or process for isolation of the product.

Monday, 12 February 2018 16:49

Most analysis whether they are analyzing data from a clinical trial or whether they are trying to analyze images. Similarly, analysis of data requires separation of noise from the signal. In imaging one of the newer techniques of segmenting images is called Multicut. This is best explained in an article that was written for the ilastik framework to analyze images.

While there also check out the video to do real time segmentation of tracking objects or animals.

These same methods may be applicable to analyzing complex data sets is two dimensions since the method has the ability to sort through neighbors. It would be great to see other applications of multicut to analyze complex data sets that are NOT images.

Sunday, 11 February 2018 19:55

World wide internet network

Often times, it is difficult to understand the role of a biomarker in a disease process. The signaling and biochemical networks within the cell are complex but when paired with other networks between cells and in a whole organism, the complexity goes up by significant dimensions.
To understand networks, there are various institutes using the network paradigm to understand stock markets social networks, and economic markets. Do the models developed with one of the networks help understand another network? Maybe not, though there are significant research dollars going into determining whether there is a crossover between internet networks and social networks or biological networks…. For example, understanding all the physical underpinnings of the neuronal pathways does not necessarily predict behavior. However, obvious breaks in networks might make the task easier to predict.
The one area that is fascinating is the internet. It is a complex network that is controlled by individual rules that helps derive the state but does it help predict any one server activity in a network?  Probably not…
In a biological network, a drug that disrupts the network may change the function of the network but is it possible to predict the change? Scientists hope that a subtle change in the network may be determined by observing a few key characteristics (biomarkers). However, it would be a computationally interesting problem to predict biomarkers without necessary knowing all the nodes in the network or very specific characteristics. Unfortunately, the current state of knowledge is to disrupt the network and analyze everything. Then hope you find the key characteristic that represents the altered state of the network.

 

Thursday, 08 February 2018 22:16

Natural products have an interesting story. The story of Taxol or Paclitaxel is interesting from its discovery as a natural product extracted from the bark tree to use as a cancer therapeutic. This compound came out of a screening effort in 1962 and it took until 2001 to become the highest selling cancer therapeutic. Now, this  did arise from a National Cancer Institute funding for a screening of natural products but it was manufactured from the bark of the tree till very recently since the chemical synthesis was too expensive in time and money. What is also interesting is the role that endophytes play in the manufacture of paclitaxel, since one hypothesis is that the  fungus living inside the plant makes the actual molecule. However, there has been doubt that it can do the production by itself.
Currently the largest manufacturer of paclitaxel is a company called Phyton Biotech that performs plant cell fermentation reaction to produce the molecule in the presence of the fungus.
Endophytes fungi were covered in a movie about Dr. Gary Strobel called “Jewels of the Jungle” who discovered the science of endophytes and collected plants from various locations and extracted useful molecules from them. Dr Strobel’s paper referenced below highlights some of his remarkable discoveries and combining a biomarker study with treatment may help understand the diverse function of these complex molecules.

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