Monday, August 29, 2011

FDA’s New Strategic Plan for Regulatory Science Includes Rapid Micro Methods

The FDA’s push for the implementation of rapid methods as an alternative to the conventional sterility test (see my previous blog posts FDA Research: Identifying Faster Sterility Tests for Biological Products, and FDA's Proposed Changes Encourage the Use of Rapid Methods for Sterility Testing of Biologics) appears to have been the starting point for a more comprehensive scientific and quality strategy that will allow the Agency both to meet today’s public health needs and to be fully prepared for the challenges and opportunities of tomorrow.

The core responsibility of FDA is to protect consumers by applying the best possible science to its regulatory activities - from pre-market review of efficacy and safety to post-market product surveillance to review of product quality. In the last few years, rapid advances in innovative science have provided new technologies to discover, manufacture and assess novel medical products, and to improve food safety and quality; FDA must both keep pace with and utilize these new scientific advances in order to accomplish its mission to protect and promote the health of the United States.

To meet this need, FDA has developed a strategic plan for regulatory science, the science of developing new tools, standards, and approaches to assess the safety, efficacy, quality, and performance of FDA-regulated products. This plan identifies eight priority areas of regulatory science where new or enhanced engagement is essential to the continued success of FDA’s public health and regulatory mission.

One of the priority areas, Support New Approaches to Improve Product Manufacturing and Quality, outlines the application of novel technologies to product development and innovative analytical approaches, including rapid methods for the detection of microbial contamination. Here is an overview:

Application of novel science and technologies is leading both to innovation in manufacturing and to innovative products that are often complex. In order to foster these innovations, FDA needs to do research—collaborating with industry and academia—to assess how these new technologies affect product safety, efficacy, and quality, and to use the information to inform development of regulatory policy relevant to these innovations.

In addition, analytical technologies are rapidly changing and leading to dramatic improvements in sensitivity, resolution, and precision in the determination of product structure and the detection of contaminants. In order to better reduce the risk of microbial contamination of products, the following needs will be addressed:

a) Develop sensitive, rapid, high-throughput methods to detect, identify, and enumerate microbial contaminants and validate their utility in assessing product sterility;

b) Develop and evaluate methods for microbial inactivation/removal from pharmaceutical products that are not amenable to conventional methods of sterilization;

c) Evaluate the impact of specific manufacturing processes on microbial contamination; and

d) Develop reference materials for use by industry and academia to evaluate and validate novel methods for detecting microbial contamination.

All of these needs fall within the FDA’s Quality by Design initiative, which includes understanding the manufacturing process and identifying the key steps for obtaining and assuring a pre-defined final product quality. FDA is constantly working to identify ways to improve the manufacturing process to ensure consistent product quality throughout the shelf life as well as to identify when contamination or other production failures may occur. Improved quality by design will also lower product development and manufacturing costs by reducing the likelihood of production failures during a long run and by providing opportunities for continuous improvement. As part of its Quality by Design effort, FDA is now working on three new areas to support increased manufacturing quality. The first is a continuous processing where materials constantly flow in and out of equipment. The second is the use of process analytical technology to monitor and control processes, as opposed to the current method of just testing products. The third is the development of new statistical approaches to detect changes in process or product quality.

How does the new strategy impact public health? Regulatory science research on novel manufacturing methods and on the analysis of products during and after manufacture will facilitate adoption of rapid microbiological methods, thus facilitating and lowering the cost of manufacturing and improving FDA’s ability to rapidly evaluate safety, efficacy, and the quality of medicinal products. If there was ever any doubt that the FDA does not embrace the implementation of rapid methods, now is the time to reconsider. The future of microbiology has been set in motion, and with the FDA and other regulatory authority’s acceptance of next generation microbial methods; the use of these technologies will soon become the norm, and not the exception.

The full plan (PDF format) may be downloaded here.

A summary of the Strategic Plan is also available in an audio Podcast. Presented by Vicki L. Seyfert-Margolis, Ph.D., Senior Advisor for Science Innovation and Policy for the FDA Commissioner’s Office, the Podcast may be accessed here.

Monday, August 15, 2011

DNA Readers: Cracking the Epigenetic Code Using Nanoscale Electrodes

Very exciting developments on the detection of DNA markers has recently been published by scientists at Osaka University. Nanowerk News ( has provided an overview of their research, which is provided below. The publication reference, abstract and link to where you can obtain the full publication is also provided.

Overview from Nanowerk News

Decoding some of the subtler information encoded in our DNA could soon become a high-throughput process, a team of researchers in Japan have shown. Masateru Taniguchi and colleagues at Osaka University have shown that DNA-borne chemical markers, which play a key role in gene expression, can be detected electrically using nanoscale electrodes (as DNA is passed through a nanoscale gap between two electrodes, a measurable current is generated allowing the detection of DNA markers).

The team's technology is a step toward understanding the meaning of some of the molecular modifiers that nature uses to annotate DNA strands. These modifiers, also known as epigenetic markers, alter over time and are thought to play a key role in processes ranging from embryo development to aging and disease. But just how the markers work, and what different markers mean, remains to be unraveled.

Deciphering the epigenetic code is a massive mapping exercise, but will provide important information on how epigenetic markers differ among cell types and between healthy and sick individuals. Actually detecting the markers, however, has proved difficult. One of the most common markers is an individual methyl group, which consists of a single carbon atom and three hydrogen atoms, and its detection has previously required the attachment of additional chemical labels. "But such an approach is troublesome and takes a lot of time," says Taniguchi. The ability to detect markers such as methyl groups directly would therefore open up immense opportunities for epigenetic research.

Taniguchi and his colleagues explored the possibility of direct marker detection by analyzing a small strip of DNA as it passes between two electrodes positioned just a nanometer apart (see image). An electrical current flows as the DNA squeezes between the electrodes, and the size of the current depends on the chemical make-up of the DNA within the gap. This allows any molecular marker on the DNA, including individual methyl groups, to be detected electrically.

The key issue for turning the technology into a practical, rapid DNA-reading device is achieving precise control of the movement of the DNA strand through the electrode nanopore. "Recently, we have theoretically proposed a way to control DNA strand flow using a gate," Taniguchi explains. "We are now developing a gating nanopore device as a proof-of-principle demonstration of this electrical gating scheme."


Makusu Tsutsui†, Kazuki Matsubara†, Takahito Ohshiro†, Masayuki Furuhashi†, Masateru Taniguchi*†, and Tomoji Kawai*†‡
† The Institute of Scientific and Industrial Research,Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
‡ Division of Quantum Phases and Devices, Department of Physics, Konkuk University, Seoul 143-701, Republic of Korea.
J. Am. Chem. Soc., 2011, 133 (23), pp 9124–9128.


We report label-free electrical detections of chemically modified nucleobases in a DNA using a nucleotide-sized electrode gap. We found that methyl substitution contributes to increase the tunneling conductance of deoxycytidines, which was attributed to a shift of the highest occupied molecular orbital level closer to the electrode Fermi level by methylation. We also demonstrate statistical identifications of methylcytosines in an oligonucleotide by tunneling current. This result suggests a possible use of the transverse electron-transport method for a methylation level analysis.

Wednesday, August 10, 2011

FDA Research: Identifying Faster Sterility Tests for Biological Products

Tim Sandle's Blog recently made us aware of an FDA scientific poster that considers rapid sterility testing (thanks Tim!). The FDA routinely conducts their own internal studies on new technologies, and to better understand how these programs work, I am providing a brief overview of the Science & Research initiative at FDA, as well as the work being conducted within CBER, the Center that performed the sterility testing studies. Links to the relevant FDA websites, as well as the sterility test study, are also provided below.

Relevant Links (as of August 10, 2011)

About Science & Research at FDA

The mission of the Food and Drug Administration (FDA) is the protection and advancement of public health by helping speed innovation on FDA regulated products. To accomplish this, FDA makes risk assessment/risk management decisions on safety, efficacy, and quality of the products it regulates. Evaluation of FDA regulated products requires application of the latest technology and standards pertinent to the particular regulatory challenges, e.g., in review of new products (drugs, biologics, medical devices or food additives) or in the resolution of compliance/safety issues of a marketed/regulated product.

Underlying FDA regulatory decisions are the application of advanced technology and science based standards. Examples include the pre-market and post-market evaluation and approval of new technologies in the products, in addressing the many compliance issues that arise in the marketed products FDA regulates, and the use of new technologies in the manufacture and evaluation of innovative products. The burden for FDA is to ensure the acceptance of our science-led regulatory decisions by the U.S. consumer and the respective scientific communities and thus maintaining scientific credibility, accuracy and predictability of the decision making process.

Science & Research (Biologics)

In order to provide effective regulatory review of biological products, the Center for Biologics Evaluation and Research conducts active mission-related research programs. This research greatly expands our knowledge of fundamental biological processes and provides a strong scientific base for regulatory review.
A wide variety of changing technical and scientific issues related to the safety, potency and efficacy of novel biological products requires knowledge of new developments and concepts of basic research in the relevant biological disciplines. Because of the rapid advancement in both conventional and new biotechnologies, the scope of research is both diverse and dynamic.

Innovation and Regulatory Science

CBER plays a critical role in the development of biological products that are at the cutting edge of 21st century medicine.

The center regulates preventive and therapeutic vaccines, blood and blood products, and cell, tissue, and gene therapies. Therefore, its research focuses on creating new knowledge in the fields of diagnostic and therapeutic product innovations and the regulatory science needed to ensure those products are safe, effective, and available to the public.
CBER scientists facilitate the development of new and promising biological products and technologies by increasing the understanding of existing products through mission-related research that advances regulatory science. For example, CBER scientists are actively engaged in developing in vitro (“test-tube”) tests and animal models used to study new therapies and product testing methods, assays, and standards. This work supports the development of CBER-regulated products by enabling the development of manufacturing methods and providing tools to assess product safety, efficacy and manufacturing consistency. CBER scientists also evaluate potential methods for improving ongoing monitoring of the safety of products that CBER has approved for use.
The web site provides both summaries of recently published research conducted by CBER scientists, as well as posters developed to highlight some of this work. These web pages will keep you informed of current research being done at CBER that is helping to bring safe and effective products to the public.


Identifying Faster Sterility Tests for Biological Products

Seema Parveen, Simleen Kaur, James L. Kenney, William M. McCormick, Rajesh K. Gupta. Center for Biologics Evaluation and Research, FDA, Rockville, MD.

The two‐week sterility test incubation period can be a significant limiting factor in the timely release of biologicals, particular for pandemic vaccines and products with short shelf lives. Researchers in the Division of Product Quality (DPQ) in the Office of Compliance and Biologics Quality (OCBQ) are working to resolve this problem by evaluating rapid microbial methods that significantly reduce the time needed for sterility testing of biologicals. Several alternative rapid tests to detect microorganisms in either solid or liquid media were compared.

Microorganisms were spiked into 10 ml of Fluid A with & without 100 ppm thimerosal, and then evaluated for detection by Compendial Sterility Methods (Filtration and Direct inoculation method) and Rapid Sterility Methods:

1. Milliflex Detection System (ATP bioluminescence)
2. BacT/Alert (detection of carbon dioxide)
3. BACTEC (detection of carbon dioxide)

Three rapid microbial methods and the compendial sterility method were comparatively evaluated for the sensitivity and speed of detection of spiked

The research team developed criteria for an alternate rapid sterility method to be equivalent in sensitivity and accuracy to the Compendial Method, but provides results within seven days rather than two weeks. To compare the various methods they spiked growth media with various organisms and used the methods to detect, isolate and identity the spiked organisms.


The compendia method, Rapid Milliflex, BacT/Alert, and BACTEC showed equivalent sensitivity at detection of lowest spiked microorganism level.

The Milliflex Detection System detected the lowest spiked of P. acnes and B. vulgatus within 5 days versus 9‐10 days for compendial sterility method, BacT/Alert, and BACTEC.

The Milliflex system consistently detected spiked organisms at 1 CFU/10 ml within 5 days (usually 1‐3 days). Similar results were obtained at 10 and 100 CFU/10 ml.

Solid media (TSA, SDA, and SBA) showed faster growth of spiked organisms (within 5 days) compared to liquid medium.

The Milliflex Detection System appears to be a promising alternative to the compendial sterility test for filterable biological products.

Additional information about the group's RMM research may be obtained by contacting Dr. Rajesh Gupta at

Monday, August 8, 2011

Gold Nanoparticle Based Microbial Detection and Identification

I had an opportunity to read a very interesting and exciting paper on the use of gold nanoparticles for the detection and identification of microorganisms. Below you will find the reference and a brief abstract, and I will be providing a more detailed review of the paper in our next Newsletter, due out later this week. If you would like to read more, please subscribe to our FREE Newsletter by clicking on

Gold nanoparticle based microbial detection and identification. Muhammad Ali Syed, S Habib Ali Bokhari. J Biomed Nanotechnol. 2011 Apr;7(2):229-37.


Microorganisms belong to one of the biggest threats to humanity. Rapid detection and identification of microbes in environmental, food and clinical samples is required for safety purposes as well as diagnosis of infectious diseases. Conventional techniques for microbial detection, though reliable and gold standard, are time consuming, expensive and unsuitable for field situations. Advent of novel techniques involving Nanotechnology has been promising for the development of rapid and low cost strategies for rapid detection and identification of microbes with higher sensitivity. Gold nanoparticles find a significant place in medicine, material sciences as well as diagnostics for their unique optical and physiochemical properties. This review focuses at recent advancements in the development of gold nanoparticle based assays for microbial detection and identification.

Tuesday, August 2, 2011

Microbial growth in pharaoh's tomb suggests burial was a rush job

Recent genetic testing conducted by the Harvard School of Engineering and Applied Sciences suggests that King Tut was buried in an unusual hurry, before the walls of the tomb were even dry. The following story, excerpted from, explains in more detail.
In the tomb of King Tutankhamen, the elaborately painted walls are covered with dark brown spots that mar the face of the goddess Hathor, the silvery-coated baboons--in fact, almost every surface.

Despite almost a century of scientific investigation, the precise identity of these spots remains a mystery, but Harvard microbiologist Ralph Mitchell thinks they have a tale to tell.

Nobody knows why Tutankhamen, the famed "boy king" of the 18th Egyptian dynasty, died in his late teens. Various investigations have attributed his early demise to a head injury, an infected broken leg, malaria, sickle-cell anemia, or perhaps a combination of several misfortunes.

Whatever the cause of King Tut's death, Mitchell thinks those brown spots reveal something: that the young pharaoh was buried in an unusual hurry, before the walls of the tomb were even dry.

Like many ancient sites, Tutankhamen's tomb suffers from peeling paint and cracking walls. In the oppressive heat and humidity, throngs of tourists stream in and out of the cave, admiring it but also potentially threatening it.

Concerned about the tomb's preservation, the Egyptian Supreme Council of Antiquities approached the Getty Conservation Institute for help. The Getty, in turn, had questions for Mitchell.

What are the brown spots? Are visiting tourists making them worse? Most importantly, do they present a health hazard?

In his investigation, Mitchell, the Gordon McKay Research Professor of Applied Biology at Harvard's School of Engineering and Applied Sciences (SEAS), combines classical microbiology with cutting-edge genomic techniques. His research team has been culturing living specimens swabbed from the walls of the tomb as well as conducting DNA sequence analyses.

Meanwhile, chemists at the Getty have been analyzing the brown marks, which have seeped into the paint and the plaster, at the molecular level.

So far, the chemists have identified melanins, which are characteristic byproducts of fungal (and sometimes bacterial) metabolism, but no living organisms have yet been matched to the spots.

"Our results indicate that the microbes that caused the spots are dead," says Archana Vasnathakumar, a postdoctoral fellow in Mitchell's lab. "Or, to put it in a more conservative way, 'not active.'"

Further, analysis of photographs taken when the tomb was first opened in 1922 shows that the brown spots have not changed in the past 89 years.

While the identity of the ancient organism remains a mystery, all of this is good news for tourists and Egyptologists alike, because the evidence suggests that not only are the microbes not growing--they're actually part of the history, offering new clues to the circumstances of King Tut's death.

"King Tutankhamen died young, and we think that the tomb was prepared in a hurry," explains Mitchell. "We're guessing that the painted wall was not dry when the tomb was sealed."

That moisture, along with the food, the mummy, and the incense in the tomb, would have provided a bountiful environment for microbial growth, he says, until the tomb eventually dried out.

Exotic as the project may sound, investigations like this are typical of Mitchell's research in applied microbiology.

In past years, his lab has studied the role of bacteria in the deterioration of the USS Arizona at Pearl Harbor, Hawaii, and the microorganisms living within limestone at Mayan archaeological sites in southern Mexico. Nick Konkol, a former postdoctoral research associate, and Alice DeAraujo, a current research assistant, have developed rapid new ways to detect mold growing within the paper of historical manuscripts, paintings, and museum artifacts.

The field is referred to as "cultural heritage microbiology," and Mitchell literally wrote the textbook on it.

For microbiologists with broad interests, cultural heritage provides an endless supply of surprising, new applications, crossing disciplines and cultures and providing important insight into modern environmental problems.

"This type of research is typical of the interactive activity of SEAS, where modern scientific and engineering techniques are integrated to solve complex problems," Mitchell says.

Just a few years ago, he was called down to the Smithsonian National Air and Space Museum to investigate the collection of Apollo space suits. In the heat and humidity of the museum's Maryland storage facility, black mold was chewing through the many-layered polymers, damaging the priceless suits.

The relatively simple solution in that case was the installation of a climate control system. Unfortunately, however, there is a difference between prevention and treatment. Once a historical artifact has begun to deteriorate, the damage is usually irreversible.

Mitchell points to the example of the cathedral in Cologne, Germany. Built over the course of 632 years and listed as a UNESCO World Heritage site, the walls of the magnificent cathedral feature angels and historical figures carved out of stone.

In just the past 100 years, the angels' faces have been eaten away by air pollution.

"I always use the analogy of cancer," Mitchell says. "You want to get to it early enough that it isn't doing major destruction."

But what to do about King Tut's 3000-year-old microbial vandalism?

The damage is already done, so Mitchell predicts that the conservators will want to leave the spots alone, particularly as they are unique to that site.

"This is part of the whole mystique of the tomb," he says.