The U.S. Army Contracting Command announced its intent to enter into an Agreement (Section 815 Other Transaction (OT)) with the National Chemical and Biological Defence Consortium (NCBDC).
The NCBDC is an industry consortium that is forming, of which Ubiquitome is a member, specifically in response to the agreement. It is a collaborative group of professionals who can bring their knowledge and expertise together to answer problems that the government poses (specific to chemical and biological).
The consortium encompasses the expertise, knowledge, technologies and innovation that the government requires in terms of the technological advancements needed to enhance the mission effectiveness of military personnel.
As a member of the consortium, Ubiquitome is excited about the opportunities that this will present. For Ubiquitome, this opens doors to provide technology and expertise to the U.S. Army on some of the biggest chemical and biological defence projects in the world.
To be able to have Ubiquitome’s technology used by one of the largest military groups in the world would boost interest and provide further opportunities for development of current technologies.
It also exposes Ubiquitome to the other members of the consortium, some of the best and brightest in chemical and biological defence. This provides opportunities for information sharing and collaborations as well as opening up themselves to a wider target market.
The Special Notice released by the army cites: “Only one such consortium, the National Chemical and Biological Defence Consortium, encompasses the expertise, knowledge, technologies, and innovation to meet the program objectives and goals of the coordinated research and development program designed to support the Department of Defence’s medical, pharmaceutical, and diagnostic requirements as related to enhancing the mission effectiveness of military personnel. The consortium is comprised of a well-balanced and uniquely qualified mixture of traditional and non-traditional contractors, small and large business, for-profit and not-for-profit entities, and academic organizations.”
For more information on the consortium, visit their website here or view the full announcement can be viewed here.
Our partners at IDT (Integrated DNA Technologies) have published an article on the Freedom4 and it's applications in researching the Adélie Penguins in Antarctica. To find the full article click here or else here is a summary of the article.
Developing onsite genotyping of Antarctic penguins
Clade-specific PrimeTime® Custom qPCR Assays
Adélie penguins live on sea ice but breed on ice-free land in Antarctica.
The challenges of developing a conservation program for Adélie penguins
Adélie penguins live only along the coastline of Antarctica and are considered “Near Threatened” , in part, because their sea-ice habitat is vulnerable to changes from global warming. Two genetic variants, or clades, of Adélie penguins have been identified. Understanding population trends across these clades will aid the design of conservation programs for these penguins.
Dr Jonathan Banks, Senior Scientist at the Cawthron Institute (see the Researcher profile), is studying the mating behaviors of Adélie penguins that live around the Ross Sea, approximately 4000 km south of New Zealand. Dr Banks can use DNA samples from feathers to determine whether selected mating pairs of Ross Sea penguins are from one or both Adélie clades. This process is complicated as the mating season is short and usually one of the mating pair feeds at sea while the other incubates the pair’s eggs on land. Having access to onsite molecular testing would simplify sample processing and ultimately increase the number of mating pairs that could be included in this project.
Selecting robust qPCR assays for a mobile PCR thermal cycler
In collaboration with Dr Jo-Ann Stanton (University of Otago; Otago, New Zealand) and Dr Elisabeth Wagner (IDT; Coralville, IA, USA), Dr Banks has validated qPCR assays that distinguish the two Adélie penguin clades. By comparing genetic sequences from the two penguin types, Dr Wagner helped identify potential primer sites targeting the penguin mitochondrial genome. They identified a 138 nucleotide sequence within the d-loop region that varied between the two Adélie penguin groups and designed qPCR primers specific for each clade. Before use in the field, Drs Stanton and Banks validated the rigor of the SYBR® Green–based assays using archived penguin DNA stored under variable conditions. High resolution melt curves distinguished true positive results from amplification of primer-dimers. Clade identification results using the selected PrimeTime qPCR Assays completely corroborated data obtained by DNA sequencing. Full details of the assays are to be published in the New Zealand Journal of Zoology.
As a finalist of the Freedom for You grant sponsored by Ubiquitome, Dr Banks wants to use the Ubiquitome Freedom4 device (see the sidebar, From benchtop to handheld, battery-operated instrument) with the PrimeTime®qPCR Assays to perform onsite molecular genotyping in Antarctica. “Significant time and resources can be saved by eliminating the long, complex transport chain. Helicopters, light aircraft, and intercontinental aircraft are all required just to get samples to the New Zealand laboratory, and then return results to me in Antarctica,” notes Dr Banks.
Field testing around the world
Several researchers around the world wish to incorporate the Freedom4 device into field testing projects. To learn more about Dr Banks’ research and additional field application stories that use the Freedom4 device, visitwww.UbiquitomeBio.com.
To read about the successful use of PrimeTime qPCR Assays with different species, instruments, and probe and intercalating dyes, see the list of peer-reviewed research articles on the PrimeTime citations page. The Related reading section below provides qPCR education and support materials for both novice and experienced qPCR researchers.
Campylobacter is the most common food-bourne infection in the world, and this is especially true in Europe with hundreds of thousands of cases of campylobateriosis seen each year. From a significant increase in cases in 2013, incident rates have been falling and, thankfully, are now back under the 2012 level. However campylobacter infection rates are still significantly higher than salmonella infection which sees only around 80,000 cases each year throughout Europe. New proactive testing methods for campylobacter are being brought in to test poultry, the principal source of infection, prior to slaughter and this can account for the reduction in incident rates since 2013.
These new proactive testing methods are as follows: Samples are taken from poultry and transported to nearby laboratories where they undergo PCR testing to determine whether or not campylobacter is present. The results of positively identified samples are returned to the farm sites where corresponding animals are separated from the main flock and instead of these animals being slaughtered for mass fresh chicken distribution they are utilised as processed meats. This method of testing has shown good results, but there are some major issues with it. The turnaround times for sample results are fine when testing laboratories are close to the farm. But for more remote farms, this is not a viable option, unless animals are placed in holding cages for quite a long time. There are also accuracy issues with quite a few infected animals being missed or misidentified. Misidentification has been attributed to the transportation of the samples or the initial sample gathering.
TNO lead researcher, Jos van der Vossen is investigating ways to speed up the testing process and improve the accuracy of identifying campylobacter in poultry through the use of mobile PCR testing.
By utilising a mobile qPCR testing device, remote locations would have the same access to fast results, better incentivising the testing process. It would also improve the overall accuracy with equivical samples able to be retaken immediately combined with the accuracy of qPCR itself being very high.
Campylobacter is an infectious disease that can incapacitate someone for a week or more with diarrhoea, vomiting and abdominal cramps. By providing accurate on-farm testing methods, the incident rate of campylobacter can be reduced even further, helping to control or eliminate this common food-bourne infection. Rather than testing the meat once it has been processed and distributed, testing the poultry while still alive can ensure that no part of an infected animal is used unprocessed. Effective implementation of animal testing can give people better peace of mind that the food they are eating is disease free, with an overall reduction in health costs throughout Europe.
Ubiquitome is running a grants program for research groups who would benefit from a mobile qPCR device. Jos van der Vossen has been chosen as one of the finalists. To find out more about the program and view the other finalists, visit the website here.
In January, Ubiquitome announced the finalists of the Freedom For You grants program. The program was designed to provide support for remote qPCR projects, with each winner receiving a Freedom4 device. The ten selected finalists are receiving support from Ubiquitome in the form of Freedom4 qPCR reagents and consumables, project design consultation, and technical support, including wet lab processing. Three grant winners will receive a Freedom4 gold standard qPCR mobile device worth USD$25,000.
Postdoctoral research associate, Diwaker Tripathi, from Washington State University, is one of the selected finalists for the grants program based on his research into PCR testing to aid detection and management of Iris yellow spot tospovirus (IYSV) infected onion crops in the United States.
Tripathi is using PCR analysis to test and identify IYSV infected crops growing in Washington State, one of the largest suppliers of onions in the United States both by pound and by acreage. A molecular biologist by trade, Tripathi has been researching and working in the agricultural and plant based fields for his whole career, starting with a Master’s of Science from East Tennessee State University.
For the past few years, his focus has been on testing IYSV infected samples through PCR analysis. The main issue facing the research is the fast spreading nature of the virus and the associated time taken to confirm the full area of infected crops. Currently samples are taken back to a central lab to undergo PCR analysis. The time required to complete testing allows the virus to continue to spread, sometimes wiping out entire crops before a complete picture of the extent of infection has been built.
Tripathi’s focus is now on incorporating mobile molecular testing into his research as a means of speeding up the testing process and reducing the subsequent spread of the virus through crops. This would allow for samples to be tested on site and infected plants removed, if not immediately then within a couple of days, as opposed to the week it can take with traditional methods.
Onion crops are worth millions of dollars to the US economy with millions of pounds exported around the world every year. Every field of onions infected and destroyed by IYSV represents hundreds to thousands of dollars’ worth of value lost. The fast spreading nature of the virus means that the cost to the growers and the economy is substantial if the virus is not caught early.
Tripathi has contributed to several publications across the agricultural and molecular biology topics with his most recent discussing resistance methods against the Iris yellow spot tospovirus:
Tripathi, D., Pappu, H. R. (2015) Evaluation of acibenzolar-S-methyl-induced resistance against iris yellow spot tospovirus. European Journal of Plant Pathology.
The use of mobile molecular testing would increase the effectiveness of the testing by allowing for onsite identification of the virus and immediate removal of infected plants, reducing the further spread of the virus. This in turn would save thousands of crops and hundreds of thousands of dollars to the growers and the economy each year. With similar viruses affecting other crops throughout the United States, Tripathi’s research is a potential model for others to use both nationally and internationally.
For more information on Tripathi’s research click here or to view a full list of the finalists visit our website www.ubiquitomebio.com.
The United States produces 4% of the annual global onion supply with 125,000 acres planted across the country. This accounts for billions of dollars’ worth of produce with Washington and Idaho/Oregon producing the highest numbers of onions. Tospoviruses are enveloped viruses that infect plants, leading to tissue necrosis. The Iris yellow spot tospovirus (IYSV) is one variety of tospovirus and is the most common virus found in food crops in the United States, particularly in onion supplies. IYSV affects onion fields throughout the country but has the greatest impact in Washington, Oregon and California where a large portion of the country’s onion supplies originate. The virus causes multimillion dollar crop losses worldwide and it is often difficult to make diagnoses based on symptoms alone.
The Washington State University is home to a strong agricultural science division who have been investigating ways to minimise the spread of IYSV and in some places to eliminate it completely. One team, led by postdoctoral research associate Diwaker Tripathi, are using PCR analysis to detect and treat infected crops in the Washington area.
Conducting PCR analysis on onion crops requires fields to be identified as ‘potentially affected’ in the first place through visual clues such as lesions on leaves. From there, samples are taken for further analysis to determine whether the visible symptoms are false positives or if the crops are actually infected. To do this PCR analysis conducted in the central lab determines whether or not the virus is present. Positive results require immediate remedial action as IYSV is a fast spreading virus, wiping out entire crops in the couple of days. Removing infected plants is the best way to ensure the least impact possible. To do this however, the area of infection is determined through additional PCR analysis. This means samples are tracked back and forward from the lab over some days to ensure the total infected area is identified. With a fast moving target, this can be a very difficult task.
Tripathi has recognised an opportunity in mobile molecular testing to increase the effectiveness of IYSV identification and removal. Being able to test samples in near real time would allow infection areas to be quickly identified and infected crops to be removed immediately. This would stop virus spread then and there, rather than allowing up to a week during sample testing and mapping for the virus to continue to spread.
By reducing the time taken to test and identify infected crops, hundreds of thousands of dollars’ worth of onion crops could be saved throughout the United States. Current lengthy lab-based methods potentially permit whole crops to become infected leading to them being destroyed. The use of mobile molecular testing would prevent this destruction by rapidly containing virus spread. This benefits both the growers as well as the hundreds of importers and exporters of onions.
Ubiquitome is running a grants program for research groups who would benefit from a mobile qPCR device. Diwaker Tripathi has been chosen as one of the finalists. To find out more about the program and view the other finalists, visit the website here.