Tim Freeman, managing director of Freeman Technology, said: “I am delighted to be working with ATS Scientific Inc. whose highly experienced team shares our dedication to customer support. We concluded the distribution agreement in the latter part of 2012 and already we see promising signs of how the market in Canada will develop for us in 2013. It is just one year since we established Freeman Technology Inc. to serve the USA, so it is especially pleasing that we are now able to further extend the support we provide to customers throughout North America.”

ATS Scientific’s National Sales manager Gilles Groulx, said: “Freeman Technology’s FT4 Powder Rheometer is an excellent fit within our portfolio of analytical instruments and materials characterisation systems. We aim to deliver the highest levels of sales and service support to the powder processing community in Canada and very much look forward to working closely with Freeman Technology’s own powder experts and application specialists.”

Freeman Technology provides systems for the measurement of powder flow properties. With a strong process focus and significant commitment to R&D and applications development, the company delivers extensive know-how alongside its universal powder tester, the FT4 Powder Rheometer, with expert teams guiding and supporting users in addressing specific powder challenges.

Freeman Technology’s headquarters are in Gloucestershire, UK, with a wholly owned subsidiary in the USA and distribution partners in China, Ireland, India, Japan, Malaysia, Singapore, Taiwan, Thailand and now Canada. In 2007 the company received the Queen’s Award for Enterprise in Innovation and in 2012 the Queen’s Award for Enterprise in International Trade.

To visit the ATS Scientific website go to www.ats-scientific.com

This application note describes how the Agilent 2100 Bioanalyzer High Sensitivity DNA Kit can be used to provide quantitative and qualitative information about the DNA samples used in the Agilent SureSelect Target Enrichment System.

Introduction:
The Agilent 2100 Bioanalyzer, an automated on-chip electrophoresis system, has already proven to be a valuable tool for automated sizing and quantification of various doublestranded DNA sample types relevant for the next-generation sequencing (NGS) sample preparation workflow.¹

The Agilent 2100 Bioanalyzer with the DNA 1000 kit is recommended by NGS platform providers for measuring DNA sample quality prior to sequencing runs. These quality checks reduce time and resources wasted by low quality samples. Recently, a High Sensitivity DNA kit was developed which offers improved sensitivity for checking the size and quantity of precious low concentrated DNA starting material or DNA libraries down to a concentration of 100 pg/μL.

Next-generation sequencing technology has brought high throughput to genome sequencing, but the new processes lack the ability to target specific areas of a genome. The SureSelect Target Enrichment System, enables genomic areas of interest to be sequenced exclusively. This creates process efficiencies that reduce costs and allow more samples to be analyzed per study.² The Agilent High Sensitivity DNA Kit and the Agilent 2100 Bioanalyzer can be used for quality control at several steps during the SureSelect Target Enrichment workflow. During the sample preparation, the Agilent 2100 Bioanalyzer is used for quality control and sizing selection of the sheared genomic DNA, and to assess the quality and size distribution of the PCR amplified sequencing library DNA. After post-hybridization amplification, the Agilent 2100 Bioanalyzer can be used to determine the quality and the concentration of the PCR-amplified capture DNA before sequencing.

This Application Note describes how the High Sensitivity DNA kit and the Agilent 2100 Bioanalyzer can be used before sequencing to reduce the number of required PCR cycles. This reduces amplification bias, thus improving the quality of DNA libraries created during the SureSelect Target Enrichment workflow.

Experimental:
DNA library preparation
The DNA library was prepared for Illumina’s Genome Analyzer II sequencers according to manufacturer’s instructions.

SureSelect Target Enrichment
The SureSelect Target Enrichment for the Illumina single-end sequencing platform, consisting of three main steps; sample preparation, hybridization and post hybridization amplification, was carried out as described in the manual.³ 16 DNA samples obtained after the post-hybridization amplification with different numbers of PCR cycles (4-18) were used for DNA analysis with the Agilent 2100 Bioanalyzer.

High Sensitivity DNA analysis with the Agilent 2100 Bioanalyzer
The on-chip DNA electrophoresis was performed on the Agilent 2100 Bioanalyzer in combination with the Agilent High Sensitivity DNA kit, according to the High Sensitivity DNA kit guide.⁴ A dedicated High Sensitivity DNA assay is available with the Agilent 2100 Expert software (revision B.02.07 or higher). An integration region from 100 to 2000 bp was used for all samples for smear quantification.

DNA quantification
In addition to the fluorescence-based DNA quantification on the Agilent 2100 Bioanalyzer, the Qubit fluorometer and the Qubit Quant-iT dsDNA BR Assay kit were used for DNA quantification according to the manufacturer’s instructions.

Results and discussion:

Figure 1 PCR-amplified DNA library derived from the SureSelect Target Enrichment workflow, analyzed with the High Sensitivity DNA kit.
(A) Overlay of DNA electropherograms obtained after 4 to 10 PCR cycles as well as TE buffer blank (black). The number of PCR cycles is indicated in the electropherogram overlay.
(B) Overlay of DNA electropherograms obtained after 12 to 18 PCR cycles. The number of PCR cycles and the dilution ratios are indicated in the electropherogram overlay.

This Application Note describes how the Agilent High Sensitivity DNA kit and the Agilent 2100 Bioanalyzer can be used to further improve the quality of DNA sequencing libraries enriched by the SureSelect kit. For this purpose, 16 amplified and purified DNA samples from the post-hybridization PCR amplification step were analyzed with the High Sensitivity DNA kit and the 2100 Bioanalyzer prior to sequencing on the Illumina platform.

Figure 1 shows electropherograms of typical PCR amplified DNA libraries. The electropherograms show a typical smear from 150 to 350 nucleotides. The primers/primer-dimers migrated very close to the lower marker, but did not affect the analysis. The excellent sensitivity of the High Sensitivity DNA kit allowed the amplified DNA to be detected and reliably quantified, even after only four PCR cycles (figure 2). As expected, DNA concentration increased with the number of PCR cycles. Above 14 PCR cycles, the increase in DNA concentration was no longer linear and becomes saturated (figure 1B). When using 10 or more cycles, the DNA concentration was outside the quantitative range of the High Sensitivity assay. These samples were diluted with TE buffer in the indicated dilution ratios (figure 1B) prior to the analysis on the Agilent 2100 Bioanalyzer.

Figure 2 Electropherogram obtained after 4 PCR cycles. The integration region from 100 to 2000 bp was used for smear quantification.

The key observation clearly shown in figure 1B is that the quality of the PCR product depended on the number of PCR cycles performed. After 14 PCR cycles, an additional DNA smear at approximately 500 bp was detected in the electropherogram. This PCR artifact could potentially affect the efficiency of an NGS experiment. When running amplifications with PCR cycles below 14 this PCR artifact was not observed. DNA library analysis with the High Sensitivity DNA kit allows the number of required PCR cycles to be reduced. This results in fewer amplification-related artifacts, significantly improving the DNA sample quality for downstream sequencing. It should be expected that the improved DNA sample quality due to the reduced number of PCR cycles will positively affect the outcome of the downstream sequencing by reducing allelic bias, single-stranded DNA generation, and duplicate sequences.⁵

Table 1 Comparison of DNA quantification with a fluorometer and the Agilent 2100 Bioanalyzer. 16 different DNA samples obtained from the post-hybridization amplification step of the SureSelect Target Enrichment workflow were quantified with the fluorometer and the Agilent 2100 Bioanalyzer. The DNA samples were measured directly (4 to 10 PCR cycles) or after dilution (12 to 18 cycles) as indicated in figure 1. The standard deviation for the total DNA concentration measured with the Agilent 2100 Bioanalyzer was calculated from four data points measured on two different DNA chips.

The DNA concentrations determined with the High Sensitivity DNA kit were also compared with the DNA concentrations measured with a fluorometer (table 1). The DNA samples obtained after 4 to 10 PCR cycles were measured directly without dilution; all other samples were diluted as indicated in figure 1. The selected assay on the fluorometer permitted DNA quantification only after 10 or more PCR cycles. The High Sensitivity DNA kit provided a reproducible DNA quantification after only four PCR cycles. For added confidence in our results, each DNA sample was measured four times on two different High Sensitivity DNA chips with the Agilent 2100 Bioanalyzer.

Above 10 PCR cycles, overall DNA concentrations are generally similar for both methods. Variances in the DNA concentration determined with the fluorometer and the on-chip electrophoresis could be due to the differences in technologies. Different fluorescent dyes are used, and the quantification by the Agilent 2100 Bioanalyzer is preceded by an electrophoretic separation of the sample. Additional variances were introduced by diluting the samples.

Figure 3 Comparison of DNA quantification with a fluorometer and the Agilent 2100 Bioanalyzer. The obtained DNA concentrations (table 1) were plotted against the number of PCR cycles, Agilent 2100 Bioanalyzer (black), fluorometer (blue). The insert shows the same data in double logarithmic scale to demonstrate the linearity of both methods.

Figure 3 graphically summarizes the data from table 1. The DNA concentrations obtained through both DNA quantification methods were plotted against the number of PCR cycles. Both methods, the fluorometer and the on-chip electrophoresis, clearly show the expected sigmoid amplification rate. The results obtained with both methods are in good agreement with each other. The Agilent 2100 Bioanalyzer provides DNA quantification as well as additional valuable information on the quality of the enriched DNA library.

The insert in figure 3 shows the same data in double logarithmic scale to demonstrate the linearity of both methods. The linear dynamic range for the SureSelect DNA samples analyzed with the High Sensitivity DNA assay and the Agilent 2100 Bioanalyzer was determined to be 80 to 5000 pg/μL with r2= 0.9996. The last data point, after 18 PCR cycles, was not taken into account for this linearity analysis, as the PCR begins to saturate after14 cycles.

Conclusion:
Quality control of DNA samples after library generation derived from the SureSelect Target Enrichment workflow can easily be performed with the High Sensitivity DNA kit and the Agilent 2100 Bioanalyzer.

The High Sensitivity DNA kit offers increased sensitivity for DNA analysis down to pg/μL concentrations across a broad linear dynamic range. This enhanced performance allows the number of required PCR cycles to be significantly decreased, eliminating PCR artifacts, while still reliably quantifying the sample. The improved DNA quality will improve the outcome of downstream sequencing analysis, maximizing throughput efficiency while minimizing cost per sample.

Therefore, the number of required PCR cycles can be significantly decreased, eliminating PCR artifacts, while still reliably quantifying the sample.

References:

1. “Performance characteristics of the High Sensitivity DNA assay for the Agilent 2100 Bioanalyzer”, Agilent Technologies Technical Note, publication number 5990-4417EN, 2009.
2. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brokman, W., Fenell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D.B., Lander, E.S. and Nusbaum, “Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing”, C., Nature Biotechnology, 27 (2), 182-189, 2009.
3. “SureSelect Target Enrichment System, Illumina Single-End Sequencing Platform Library Prep”, Agilent Technologies Manual, reference number G3360-90010, 2009.
4. “Agilent High Sensitivity DNA Kit Guide”, Agilent Technologies Manual, reference number G2938-90321, 2009.
5. Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H., and Turner, D.J.; “A large genome center’s improvements to the Illumina sequencing system”; Nature Methods, 5 (12) 1005-10, 2008.

Biobanking throughout the decades

Biobanks are typically cryogenic storage facilities maintained by institutions that manage a collection of biological materials, such as human tissue, serum, plasma, urine, and blood, along with the donors’ data. The majority of biobanks store tissue that will be used in medical research. A small collection of blood samples kept in a freezer can technically be classified as a biobank, but the term is often associated with larger facilities maintaining hundreds of thousands of samples.²

Sample collections must be maintained reliably with minimal deterioration over time, and they must be protected from any physical damage.³ Quality sample management is a well-known challenge facing life science investigators, and the need for biobanks is growing as the pharmaceutical industry shifts toward personalized medicine, which requires more usable, well-maintained biospecimen collections.

Biobanks have been around for at least 50 years. First-generation biobanks stored and retrieved samples manually from liquid nitrogen tanks or -20/-80°C freezers. Sample management and information system standards varied between institutions.

“In existing conventional biological storage, warming events can have significant impact  on the integrity of samples,” explains Matt Hamilton, vice president at Hamilton Storage Technologies. “The opening and closing of a manual freezer door creates the opportunity for extreme and continuous temperature fluctuations inside the entire storage compartment which can adversely affect each sample in the freezer.  The thermostability of each sample, and therefore the potential for damage, is dependent upon the type of tube the sample is stored in, the storage buffer pH and the volume in the storage tube.  It is important to evaluate the storage conditions very closely since multiple factors can impact sample integrity during storage.”⁴

A door held open on a manual freezer for even a short period can result in a significant temperature increase. Data gathered by Hamilton Storage Technologies shows that the temperature of samples taken from -80°C storage to ambient conditions increases by an average of up to 21.5°C per minute (Figure 1). Holding a manual freezer door open for more than one minute can expose some samples to temperatures inside the freezer that are above -60°C depending upon the freezer configuration and sample storage conditions. This can happen countless times over the lifetime of a sample stored and retrieved manually. Accumulated temperature elevations above this level are believed to damage the integrity of many biospecimen types.⁵

Figure 1

Since the late 1990s, biobanks have become a key resource for a growing number of genomics, personalized medicine, and other types of studies. Since the early 2000s and the completion of the Human Genome Project, second-generation biobanks have emerged to meet the needs of modern researchers. One-third of all biobanks have been installed since the early 2000s, after the draft of the human genome was completed. The growing presence of biobanks reflects their growing importance in advancing genetic research and testing.⁶ Second-generation biobanks offered improved operational design through standardized protocols for sample storage and annotation, and began to use automated liquid handling for some tasks.

The gap between second-generation biobank infrastructure and researchers’ needs became apparent in large genetic studies such as The Cancer Genome Atlas (TCGA) program.⁷

TCGA began as a three-year pilot in 2006 with an investment of $50 million from the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). The project’s goal was to create an atlas of genetic changes that manifested as a cell became cancerous.⁸

TGCA characterized more than 20 tumor types, which required the careful collection of thousands of cancer samples.⁹ Dozens of bio-repositories in the US assured the institute that at least 500 samples of each required cancer type could be easily provided. Early in the project, it became clear that many specimens were unfit for analysis due to the lack of sample storage standards. The rate of unacceptable shipments from some institutions ran as high as 99 per cent.^10,11

To achieve their mission of mapping the genetic changes in cancer, the investigators had to elevate the challenges of fixing, storing, and annotating samples. Because of this need, the Office of Biorepositories and Biospecimen Research (OBBR) published its first guidelines for the industry in 2006. During 2007, forums were held to distribute and educate professionals on the guidelines, which increased standards for reliability and sample handling.¹²

The rise of third-generation biobanking technology

Reliability of third-generation biobanks is measured by “uptime.”¹³ Third-generation systems typically include four main building blocks: automated tube storage and retrieval, tube processing assisted by robotic liquid handlers, a plate storage and retrieval system, and a database infrastructure that stores clinical information about the sample.

In a third-generation system, researchers do not open freezer doors; they simply place sample tubes in a temperature-controlled hatch and a robotic arm retrieves the tube and stores it in a unique interior cell. Tubes are barcoded so researchers can use laboratory information management systems (LIMS) to search for appropriate samples. This information system enables the researcher to store and retrieve the sample securely. When a researcher wants to retrieve a sample for a particular study, they transmit their request to the automated biobank’s LIMS and the robotic arm retrieves the sample. The arm deposits the sample in a delivery hatch and an email is sent when the sample is ready to be picked up. The -80°C freezer also records how many times each sample is removed from frozen storage and for how long. The automated system reduces sample retrieval time, preserves the chain of custody, and minimizes the sample’s time outside its optimal storage temperature.

“Removing the uncertainty about storage conditions ensures that data derived from sample testing will be accurate and reliable,” explains Hamilton.¹⁴

Users and technology

The most common laboratories or organizations utilizing this type of automated storage system are those collecting biological samples that need to be stored in large quantities at ultra-low temperatures for a long period. Typically, biobanks support researchers who are performing population- or disease-based studies, or forensic institutions storing samples from crime scenes. Biobanks storing tissue also need to track chain of custody, and virtually all laboratories need to maintain temperature stability and thus the value of their samples.

Hamilton Storage Technologies, a leader in laboratory automation, recently introduced its third-generation BiOS™  automated storage system to meet the demands of today’s labs and clinics.¹⁵ This ultra-low-temperature storage system is designed to store more than 10 million sensitive biological samples in multiple types of labware such as tubes and microplates. All samples within the BiOS system are stored in -85°C freezer compartments to maintain temperature stability even while sample picking. One- and two-dimensional barcode reading and sample tracking provide chain-of-custody documentation, with software tools to support compliance with the FDA’s 21 CFR Part 11 regulations. Multiple redundant backup systems ensure that samples stay at -85°C, even in emergencies.

Along with the BiOS system, Hamilton Robotics provides a fully integrated, automated liquid handling workstation, the Microlab® STAR , which utilizes the Rack Runner™ robot for true hands-free operation, further ensuring integrity of the sample transfer from the BiOS system to finished preparation for analysis.¹⁶ This robot is configurable for almost any sample preparation requirement and supports the speed requirements of high-throughput labs using next-generation sequencing for gene expression and genotyping applications.

Hamilton Storage Technologies’ SAM and Rack Runner systems at the Netherlands Forensic Institute in The Hague. Photo Credit: Netherlands Forensic Institute.

The Netherlands Forensic Institute (NFI) and the LifeLines Biobank at the University Medical Center Groningen (UMCG) in the Netherlands have purchased the new Hamilton BiOS system to store their sample collections.¹⁷

LifeLines is a major, three-generation population-based study of 165,000 residents of the Netherlands’ northern provinces. The study is based on UMCG’s healthy aging program and seeks to identify universal risk factors, and their modifiers, for multifactorial diseases such as cardiovascular disease, diabetes, asthma/COPD, and depression. By 2017, LifeLines expects to collect and store more than 8 million samples in the BiOS system, including urine, plasma, serum, and buffy coat extracts. The BiOS system ensures long-term sample viability and provides redundant cooling along with sample picking at ultra-low temperatures.¹⁸

“Sample safety was our foremost goal when we started the tender process,” explains Marcel Bruinenberg, research laboratory manager at LifeLines. “The technology in the Hamilton BiOS system guarantees that the samples will never go above -65˚C, significantly lowering the risk of degradation. Our goal is to keep samples viable for 30 years or longer.”¹⁹

NFI performs the vast majority of forensic DNA casework in the Netherlands, including providing second opinions and analyses for cold cases. NFI will utilize the BiOS system for long-term storage of DNA extracts from crime scenes. Ultimately, one million crime scene samples will be stored in the system for 80 years, as required by government regulations. NFI will also use a +4°C SAM™ system to store active case samples, providing access without freeze-thaw cycles.²⁰

NFI was impressed with the degree of innovation Hamilton’s biobanking automation solutions offered. Specifically, AutoLys tubes and FlipTubes™ which enable sample lysis to be automated.²¹ Hamilton had identified sample lysis as a major bottleneck in DNA forensics analysis and invested in developing a completely new solution. NFI had been hand-processing the lysis step on critical crime samples to meet quality and yield demands. When validating their new biobanking system, they tested an automated sample lysis and DNA extraction solution. AutoLys tubes are test tubes designed explicitly for automated DNA sample lysis and DNA extraction for forensic studies, and are used with Hamilton Microlab® AutoLys STAR liquid handling instruments. Initial validation work with the AutoLys STAR system produced results at quality levels comparable to the lab’s manual process standards. Automating this process also reduces the possibility of manual errors, lowers contamination risk, and offers the ability to run assays overnight. NFI expects this system to improve overall lab throughput.²²

Expanding markets

More laboratories are adopting third-generation systems, like the Hamilton BiOS system, to keep up with industry standards, increased workloads, tighter regulatory requirements, and data analysis needs. Biobanks are becoming larger, more sophisticated, and more centralized, which improves sample storage economics and concentrates the workload to a few highly skilled workers. The trend toward larger and larger biobanks will continue as genetic testing expands beyond the medical field.

As genetic information becomes more affordable to obtain and analyze, this information can be used to make our environment and our neighborhoods safer. For example, genetic testing has taken off in forensics. Crime statistics indicate that arrests, identifications, and prosecutions double when genetic information is used to solve a crime. All 50 states now mandate the collection of DNA samples from offenders of certain crimes. This policy has had an unintended consequence of creating processing delays. A report from the National Institute of Justice in 2011 indicated that the number of backlogged samples in the US has exceeded 100,000 for several years.²³

Agricultural industries also now employ genetic testing to track outbreaks. Using simple environmental testing methods, FDA field stations use genomic assays to quickly identify the pathogens causing the outbreak. Genomic information can now be used to improve response time to an outbreak and resolve a challenging business problem between food producers and distributors.²⁴

Conclusion

In the future, the biobanking industry will likely include more globally centralized centers for studying specific genetic diseases and monitoring the health of our environment. This shift toward consolidation for the large and mid-sized centers will reduce the number of biobanking facilities that do not meet newer standards and will lower overall storage costs.²⁵ These larger facilities will need to adopt technologies that include complete sample processing, both up- and downstream, using robotic liquid handling systems. Centers will have advanced LIMS that track samples and maintain chain of custody from collection to storage to extraction. By improving the quality of biobanking facilities, precious samples will be protected and more useful to researchers, which will lead to a better understanding of disease biology and improving methods to safeguard our environment.

Martin Frey, Ph.D., is head of the Storage Technology Market Segment at Hamilton Bonaduz. Dr.Frey is currently the acting product manager for the BiOS automated sample storage system.

Annette Summers is a consultant for Hamilton Company and the founder of GeneCom Group, a marketing and public relations firm.

Mary Napier is a consultant for GeneCom Group and provides scientific writing and industry research assistance to the firm.

Sources:

1. Infiniti Research Limited, “Global Biobanking Market: 2011-2015.”(Elmhurst: Inifiniti Research, 2012). np.
2. M. Frey, “Automation Improves Biobanking Efficiency.” Tutotials, Genetic Engineering News Dec. 1, 2010: Vol. 30 (21), http://www.genengnews.com/gen-articles/b-automation-b-b-improves-b-b-biobanking-b-efficiency/3496
3. F. Betsou et al, “What are the Biggest Challenges and Opportunities for Biorepositories in the Next Three to Five Years?”Biopreservation and Biobanking. 8.2 (2010). doi:10.1089/bio.2010.8210.
4. Matt Hamilton, (vice president at Hamilton Storage Technologies), in discussion with the author October 2012.
5. Betsou,  “What are the Biggest Challenges and Opportunities for Biorepositories in the Next Three to Five Years?”
6. Ibid
7. B. Schwarz, “The Challenge for Biobanking.” Opinion, Biotechnologynews.net. May 19, 2011. http://www.bluechiip.com/wp-content/uploads/2011/05/110519_Article  _in_BioTechnologyNews.net
8. National Cancer Institute; The Cancer Genome Atlas; “Program Overview History and Timeline”. http://cancergenome.nih.gov/abouttcga/overview/history
9. Ibid
10. B. Schwarz, “The Challenge for Biobanking” May 19, 2011
11. S. Silberman, “Libraries of Flesh:  The Sorry State of Human Tissue Storage.” Wired, June 2010.  http://www.wired.com/magazine/2010/05/ff_biobanks/
12. National Cancer Institute; The Cancer Genome Atlas; “Program Overview History and Timeline”
13. M. Baker, “Biorepositories: Building better biobanks.” Nature 486, 141–146 (07 June 2012). doi:10.1038/486141a
14. Matt Hamilton, (vice president at Hamilton Storage Technologies), in discussion with the author October 2012.
15. Hamilton Company; Storage; Automated Sample Storage; BiOS system
16. Hamilton Company; Robotics; STAR Line
17. Hamilton Company, “New Hamilton Fully Automated Sample Lysis Solution to be Validated by Netherlands Forensic Institute.” news release, Feb 14, 2012 http://www.evidencemagazine.com/images/Newsletters Feb 2012/HamiltonAutoLysSystem.pdf
18. Lifelines; Lifelines research; the “Study design and organization” http://www.lifelines.nl/lifelines-research/study-design-and-organisation
19. Hamilton Company, “Lifelines Biobank Buys New BiOS System from Hamilton Storage Technologies.” news release, Feb 12, 2012 http://www.hamilton-storage.com/storage-technologies/details/news/lifelines-biobank-buys-new-bios-system-from-hamilton-storage-technologies
20. Hamilton Company, “Lifelines Biobank Buys New BiOS System from Hamilton Storage Technologies.” news release, Feb 27, 2012 http://www.hamilton-storage.com/storage-technologies/details/news/lifelines-biobank-buys-new-bios-system-from-hamilton-storage-technologies
21. Hamilton Company, news release Feb 14, 2012.
22. Tijark Tjin A Tsoi, “Tijark Tjin A Tsoi Speaks About the NFI.” NFI video, 0:59.  April 9, 2012. http://www.forensicinstitute.nl/about_nfi/organisation_profile/
23. US Department of Justice.  NIJ Special Report.  “Making Sense of DNA Backlogs, 2010.  Myths vs. Realities.  Feb. 2011.  NCJ 232197.  Accessed October 2012. https://www.ncjrs.gov/pdffiles1/nij/232197.pdf
24. National Agricultural Genotyping Center.  “Translating Science into Solutions for Agriculture.” Date unknown.  Accessed online October 2012. http://www.ncga.com/uploads/useruploads/nagc_white_paper.pdf
25. M. Lambert, “Biobanking Confronts Growing Pains” Feature Articles,Genetic Engineering News. Vol 32 (16). Sept. 15, 2012. http://genengnews.com/gen-articles/biobanking-confronts-growing-pains/4481

Pittcon Hall of Fame

The Pittcon 2013 program committee has announced the recipients of its 2013 Pittcon awards. The awards honour scientists who have made outstanding contributions to analytical chemistry and applied spectroscopy.

A new award for this year, the Robert Boyle Prize for analytical science, was established by the Royal Society of Chemistry for outstanding contributions to analytical science. It was awarded to Norman Dovichi for pioneering development of ultrasensitive separations, including the first separations at zepto- and yoctomole levels and capillary electrophoresis-based DNA sequencing for the human genome.

Other winners were:

• Pittsburgh Spectroscopy Award: Laurence A. Nafie, Syracuse University

• Pittsburgh Analytical Chemistry Award: David R. Walt, Tufts University

• Pittcon Heritage Award: Posthumously awarded to Guenther Laukien, Founder of Bruker. The award will be accepted by his son, Frank H. Laukien, Bruker Corporation.

• Pittsburgh Conference Achievement Award: Sarah Trimpin, Wayne State University

• ACS Division of Analytical Chemistry Award for Young Investigators in Separation Science: Kevin A. Schug, University of Texas at Arlington

• The Coblentz Society/ABB – Bomem-Michelson Award: Brooks H. Pate, University of Virginia

• Chromatography Forum of the Delaware Valley Dal Nogare Award: Irving W. Wainer, National
Institutes of Health

• SEAC – Charles N. Reilley Award: Andrew G. Ewing, Chalmers University and the University of Gothenburg, Sweden

• SEAC – Young Investigator Award: Bo Zhang, University of Washington

• Ralph N. Adams Award: J. Michael Ramsey, University of North Carolina – Chapel Hill

• The Coblentz Society – Williams Wright Award: John Coates, Coates Consulting LLC

The awards will be presented during a symposium at Pittcon 2013, March 17-21, at the Pennsylvania Convention Center in Philadelphia, PA. The conference will include presentations from scientists in diverse disciplines such as bioanalytical, biomedical, nanotechnology, food science, drug discovery, biomedical, materials science, homeland security, and neurochemistry. Methodologies represented include molecular, vibrational, and mass spectroscopy; capillary electrophoresis; HPLC; infrared and Raman spectrometry; LC/MS; UV/VIS; microfluidics; electrochemistry; and portable instruments.

For complete details and bios of the winners visit the events website at www.pittcon.org.

Saskatchewan is to be home to the new Global Institute for Food Security (GIFS)

The province of Saskatchewan and Potash Corporation of Saskatchewan Inc. are investing $50 million in the new Global Institute for Food Security (GIFS) based out of the University of Saskatchewan.

With an initial investment of up to $35 million from Potash-Corp and $15 million from the province over the next seven years, the new institute will make use of Saskatchewan’s agricultural resources, innovation and expertise to address the ever-increasing global demand for safe, reliable food.

“The plan for growth positions Saskatchewan as a global leader in food security and innovation by 2020,” said Saskatchewan Premier Brad Wall. “Advancing Saskatchewan’s agricultural advantage allows us to significantly increase the global food supply – our moral obligation as a good global citizen – while building the next economy, an innovation economy, here at home.”

As the world’s population is expected to reach nine billion by 2050, global food production will need to increase by an estimated 70 per cent to match the increasing demand. Along with increasing production, the system will also need to change to effectively provide safer, more nutritional food to consumers.

“Food security remains our biggest challenge as populations increase and diets change, putting immense strain on food production,” said Bill Doyle, president and CEO of PotashCorp. “We need to help farmers around the world produce more food, ensure it’s safe and nutritious, and get it efficiently to those who need it. As the world’s largest producer of crop nutrients, supporting food production is a mandate for our company and we believe this institute can play an important role in improving global food security.”

Bill Doyle, President and CEO PotashCorp

PotashCorp’s donation is one of the largest corporate donations for university research in Canada. Its recipient, the new food security centre, will build on Saskatchewan’s strength in crop production systems through investments in technological, economic, nutritional and environmental improvements to the food supply system, at home and abroad.

The institute will also look at new approaches to the food supply system including: breeding for higher yield; improved nutrition and processing traits; examining how soil quality affects the nutritional value of crops; and adapting prairie zone crops to available soil and water.

To do this, the new centre will examine crops grown in Saskatchewan, as well as in other areas of the world, such as wheat, lentils, peas and canola. These are essential food sources for a large portion of the world’s population. The institute will work to develop transferable solutions that can be applied to regions and partnerships around the world.

Research from the new institute will also impact the policy agenda for food security, so that changes can take place to improve how the various parts of the food system interact.

The University of Saskatchewan is proud to be home to the institute: “Over the past century, the University of Saskatchewan has led far-sighted research and innovation to help grow a province and feed a growing nation. Now, through this innovative partnership and its bold vision, we will build on our strengths and provide new research solutions across the food supply system to help feed a growing world,” said Dr. Ilene Busch-Vishniac, president, University of Saskatchewan.

“This collaborative institute will create unique opportunities for cutting-edge science and policy research that will attract top faculty and students and put Saskatchewan on the global map for food security research.”

Jonathan Bramson

Our immune system does not shut down with age, says a new study led by McMaster University researchers.

The study published in PLOS Pathogens shows a specialized class of immune cells, known as T cells, can respond to virus infections in an older person with the same vigour as T cells from a young person.

“For a long time, it was thought the elderly were at a higher risk of infections because they lacked these immune cells, but that simply isn’t the case,” said Jonathan Bramson, the study’s principal investigator. “The elderly are certainly capable of developing immunity to viruses.”

Researchers at McMaster, University of Toronto and the University of Pennsylvania examined individuals younger than 40, between 41 to 59 years of age and older than 60, infected with three different viruses, including West Nile, and found the older group demonstrated perfectly normal immune responses. Both the number of virus-fighting T cells and the functionality of the T cells were equivalent in all three groups.

“So as we age, our bodies are still able to respond to new viruses, while keeping us immune to viruses we’ve been exposed to in the past,” Bramson said.

He added that these results have important implications for vaccination of elderly individuals. Currently, vaccines for the elderly aren’t designed to elicit responses from these immune cells, and this might explain the lack of effective protection from the flu vaccine, he said.

Vaccines specifically designed to generate T-cell immunity may be more effective at protecting older adults, Bramson said.

The research was funded by the Canadian Institutes for Health Research and the U.S. National Institutes of Health.

Their findings, published recently in the journal Proceedings of the National Academy of Sciences, showed the active form of vitamin D acts by several mechanisms to inhibit both production and function of the protein cMYC. This protein, cMYC, drives cell division and is active at elevated levels in over half of all cancers.

“For years, my lab has been dedicated to studying the molecular mechanisms of vitamin D in human cancer cells, particularly its role in stopping their proliferation,” said White. “We discovered that vitamin D controls both the rate of production and the degradation of cMYC. More importantly, we found that vitamin D strongly stimulates the production of a natural antagonist of cMYC called MXD1, essentially shutting down cMYC function.”

Also in the study, the researchers applied vitamin D to the skin of mice and observed a drop in the level of cMYC and evidence of a decrease in its function. Moreover, other mice lacking the specific receptor for vitamin D were found to have strongly elevated levels of cMYC in a number of tissues including skin and the lining of the colon.

“Taken together, our results show that vitamin D puts the brakes on cMYC function, suggesting that it may slow the progression of cells from premalignant to malignant states and keep their proliferation in check. We hope that our research will encourage people to maintain adequate vitamin D supplementation and will stimulate the development of large, well-controlled cancer chemoprevention trials to test the effects of adequate supplementation,” said White.

While vitamin D can be obtained from dietary sources and direct exposure to the sun, the combination of poor diet and sun avoidance has created vitamin D deficiency in large parts of the population worldwide. There is a known link between insufficient amounts of the vitamin and increased incidence in a number of cancers, including colon cancer, cancers in the digestive tract, and certain types of leukemia.

The research was funded by the Canadian Institutes of Health Research and the National Cancer Institute/Canadian Cancer Society Research Institute.

Professor Aaron Slepkov

Two leading publications are drawing attention to a recent discovery by an interdisciplinary team of scientists that includes Dr. Aaron Slepkov, Trent University’s Canada Research Chair in physics of biomaterials.

The group demonstrated that a technique entrenched in the biomedical imaging industry can be used by geologists to analyze pockets of fluid trapped in rock. The article appears in the November 2012 issue of Physics Today and the November 19, 2012 issue of Chemical & Engineering News.

Prof. Slepkov, who is a professor in Trent’s department of physics and astronomy, was integral to the project helping to develop the methodology, design the experiment, collect and analyze the data and write the report. The team included researchers from Canada’s National Research Council and the US Geological Survey.

The team used a technique known as coherent anti-Stokes Raman scattering (CARS) microscopy that has been gaining popularity in the biomedical sciences. CARS microscopy creates high-resolution, chemically specific images, based on bondvibration frequencies. The technique can be used to build up three-dimensional images even in relatively turbid samples.

The breakthrough came when Prof. Slepkov and his fellow researchers saw the potential application in other disciplines. “We wanted to broaden the utility of CARS microscopy, beyond biomedical imaging,” said Prof. Slepkov. “Seeing it as a tool for geologists is an idea that came right out of left field, when Bob Burruss of the US Geological Survey came to the National Research Council for Albert Stolow’s CARS microscopy workshop.”

The researchers demonstrated that the CARS microscopy tool could be used to examine rock samples for pockets of methane gas and other organic matter, without destroying the samples. Previously, one had to crush the samples to examine its contents in this way.

“This is just the beginning,” said Prof. Slepkov. “We are trying to show a range of potential applications that may be of interest to a wide swath of scientists, including mineralogists, archeologists, crystallographers, petroleum chemists, and fluid inclusion researchers.”

Prof. Slepkov sees this discovery as the first step towards creating demand for the technique in the geosciences but he also thinks there are commercial applications.

“This technique allows the petrochemical industry to develop new ideas of what they might be able to do. In the long term, it’s going to assist in surveying and in determining in situ ratios of methane to crude oil content and various other chemical contents of crude oil.”

The technique was largely developed by Ph.D. student and co-author Adrian Pegoraro in Dr. Albert Stolow’s world-class lab at the National Research Council. Prof. Slepkov is currently working to build up research capabilities at Trent, including a laser microscopy lab to investigate biomaterials. Prof. Slepkov plans to continue working with his colleagues at the National Research Council and the US Geological Survey on this work, but he also hopes to collaborate with researchers in other disciplines at Trent.

Computer simulation shows the surfaces of a microscopic crack in metal. The white atoms accumulated around it are hydrogen.

Hydrogen, the lightest element, can easily dissolve and migrate within metals to make these otherwise ductile materials brittle and substantially more prone to failures.

Since the phenomenon was discovered in 1875, hydrogen embrittlement has been a persistent problem for the design of structural materials in various industries, from battleships to aircraft, to nuclear reactors. Despite decades of research, experts have yet to fully understand the physics underlying the problem or to develop a rigorous model for predicting when, where and how hydrogen embrittlement will occur. As a result, industrial designers must still resort to a trial- and-error approach.

Now, Jun Song, an assistant professor in materials engineering at McGill University, and prof. William Curtin, director of the Institute of Mechanical Engineering at École polytechnique fédérale de Lausanne in Switzerland, have shown that the answer to hydrogen embrittlement may be rooted in how hydrogen modifies material behaviours at the nanoscale. In their study, published in Nature Materials, Song and Curtin present a new model that can accurately predict the occurrence of hydrogen embrittlement.

Under normal conditions, metals can undergo substantial plastic deformation when subjected to forces. This plasticity stems from the ability of nano- and micro-sized cracks to generate “dislocations” within the metal – movements of atoms that serve to relieve stress in the material.

“Dislocations can be viewed as vehicles to carry plastic deformation, while the nano- and micro-sized cracks can be viewed as hubs to dispatch those vehicles,” Song explains. “The desirable properties of metals, such as ductility and toughness, rely on the hubs functioning well. Unfortunately those hubs also attract hydrogen atoms. The way hydrogen atoms embrittle metals is by causing a kind of traffic jam: they crowd around the hub and block all possible routes for vehicle dispatch. This eventually leads to the material breaking down.”

State-of-the-art computer simulations were performed by Song to reveal explicitly how hydrogen atoms move within metals and how they interact with metal atoms. This simulation was followed by rigorous kinetic analysis, to link the nanoscale details with macroscopic experimental conditions.

This model has been applied to predict embrittlement thresholds in a variety of ferritic iron-based steels and produced excellent agreements with experiments. The findings provide a framework for interpreting experiments and designing next-generation embrittlement-resistant structural materials.

The research was funded in part by the Natural Sciences and Engineering Research Council of Canada, the U.S. Office of Naval Research and by the General Motors/Brown Collaborative Research Lab on Computational Materials.

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