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  • Hints, Tips & Tricks - Efficient RT

    27 May 2016

    Initially, the RT step should be performed as specified in the supplier protocol. However, the length and the temperature of the RT step can be optimized to increase the efficiency of the reverse transcriptase. The reverse transcriptase should be tested across a range of RNA concentrations to ensure assay linearity.

    Agricultural Biotechnology and Environmental Research (White Paper)

    4 May 2016

    Agricultural Biotechnology and Environmental Research

    Agriculture and the very environments we exist within are undeniably important and there is an interplay between them. Ecosystems not only provide vital life resources such as clean air and water, they also provide healthy land upon which to grow crops or farm livestock – about half of the ‘useable’ land across the globe is currently pastoral or employed in intensive agriculture. Research to support better understanding and management of agricultural practices, in addition to understanding and maintaining the wide variety of global ecosystems, is critical to a sustainable future for our growing population. There are a range of molecular tools available from Bioline to assist investigations within agricultural or environmental systems, whether through PCR, real-time PCR, or sequencing. Bioline also offers sample-to-answer workflows specially formulated for plant samples, streamlining and simplifying your laboratory time and maximizing result quality from these often difficult sample types.

    Agricultural Science
    Agriculture is a broad term encompassing the production, processing and distribution of crops, livestock, feed and other products that support humanity. In addition to traditional crop farming, many other industries fall under the agricultural banner including dairy, livestock, fisheries and forestry. Agriculture is often linked to definitions of civilization and there is evidence of plant breeding and animal domestication going back tens of thousands of years in many cultures.

    From very early on, farmers recognized that desirable traits could be enhanced through breeding strategies – improving yields, disease resistance and other characteristics. It was through the study of plant breeding that Mendel identified the genotype-phenotype connection and described the fundamental laws of inheritance, often described as the founding of genetic science. While conventional breeding techniques have proven effective, results can often take multiple generations to manifest and sometimes it is difficult to identify a desired trait within existing populations. With a growing understanding of the genetic sequences and make-up of selected species, a more targeted approach looks at total genomics - linking complex phenotypic traits to the genetic architecture and underlying molecular mechanisms to better instruct cross breeding and back breeding efforts.

    Genomics Assisted Breeding
    Genomics assisted breeding programs greatly enhance selection efficiency through the construction of comprehensive genetic maps and establishment of marker-trait associations, directing molecular breeding programs for more precise outcomes. Molecular markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) or microsatellites are used to genotype segregating populations. With ongoing advances and applications of next generation sequencing (NGS), understanding of the genetic diversity within breeding material is increasing at a rapid pace, helping to improve knowledge of so-called ‘orphan’ crops and integrate the various core components of molecular breeding programs. Bioline offers a full range of sample preparation, cloning, sequencing and PCR reagents to support molecular breeding research and applications in all areas of agricultural science.

    Breeding and Genetically Modified Organisms
    The latest approach to breeding and agricultural crop improvement uses recombinant DNA techniques to genetically modify plants and animals. Individual genes that confer a desired trait, such as insect resistance or herbicide tolerance, are selected and transferred into the desired organism. Unlike conventional breeding, genetic modification (GM) can occur between completely unrelated species, thus opening access to a broader range of traits. GM breeding holds promise to support the future demands of a growing population and a changing climate, using traits such as drought and frost resistance, elevated iron or vitamin levels, or faster growth and maturation periods.

    In order for transgenic breeding to be successful, it is necessary to have full understanding of the stability of the introduced gene across generations, as well as potential intergenic, intragenic or other interactions within the genome and within the environment where the crop or organism is being introduced. Nations across the Americas, Europe and Asia have embraced GM technology for many core crops. The US has granted approval for use of over 70 different GM varieties, with over 90% of cotton and 80% of corn across the US planted with GM seed. Approval has also been granted for the first use of GM fish – a salmon requiring half the usual time to grow to market size. Controversies surrounding GM technology mainly focus on the broader potential impacts of GM organisms on the surrounding ecosystems. Unknown future stability of engineered traits, the ability of organisms to transfer genes and breed naturally outside of agricultural constraints, competition with native plants and animals and other unintended and poorly understood outcomes, have seen some governments and organisations show caution towards the technology.

    Environmental Research
    Our global environment and the individual ecosystems within are a complex interplay of a multitude of species and ecological processes and our understanding of all of that is limited at best. Our very existence relies on the continuation of healthy biological and ecological global and local systems and much of today’s research looks at how to define a ‘healthy’ system, how to monitor, measure and manage these systems, in order to maximize sustainable interaction. Apart from the intrinsic value of a healthy environment, essentials such as functional water cycles, soil formation and climate regulation, we also gain value from environmental services such as food, raw materials and fuels. Yet our agricultural and harvesting practices reduce the ability of ecosystems to continue to provide these services, thus effective and sustainable management practices and policies are key to our continued survival and sustainable future.

    Although any measurable parameter of an ecosystem will offer valuable information, it is impossible to assess every aspect of complex natural systems, thus researchers look to define ‘indicators’ – biologically relevant measurements or surrogate organisms, that can represent or quantify key measures of an environment and offer insight into potential stress and or resilience of an environment. While typically a small group of key indicator organisms are studied in depth in order to assess ecosystem health, it is well recognized that it is the overall biodiversity within an ecosystem that offers the best opportunity for long-term stability, productivity and maximum functionality. This current epoch has been defined as the Anthropocene, a time when humans are a persistent and driving force of extinction – we are losing species 1,000 times faster than at any other point in history. The true impact of such events is yet to be seen and a sustainable relationship between humans and the global environment is not yet secure. Research efforts continue in an attempt to better define our current and future ecological state, using a range of methods including molecular characterisations of extant diversity and Bioline’s extensive range of molecular tools are well placed to support.

    Methods for Assessing Biodiversity
    Biodiversity can be defined on many different levels: from macro-level ecosystem diversity; species-level diversity of plants, animals or microorganisms; right down to the genetic diversity within individual populations. While species diversity is the most commonly used method for defining or measuring biodiversity in a given ecosystem, it is, in practice, a difficult variable to measure both in terms of appropriate sample size, spatial scale and method of identification, as well as in the very definition of diversity, be it richness, evenness, differentiation, or abundance. While many studies rely on traditional taxonomic identification methods, molecular-based methods are gaining favor representing rapid, less-subjective pathways for assessment of biodiversity. Total DNA from soil, water or invertebrate samples can be isolated and analysed using PCR with restriction enzyme digestion (PCR-RFLP), cloning and pyro-sequencing, or deep sequencing techniques, to establish DNA-based metrics that can then be linked to extant diversity. Whatever the chosen method, Bioline offers a suite of molecular tools to support the rapid characterisation of biodiversity across a range of environmental samples.

    Population Growth and Climate Change– Managing the Future
    One of the major concerns for agricultural and environmental scientist’s alike surrounds the management and support of the growing global population and the resulting impact on the environment and availability and health of environmental resources. Population has more than quadrupled over the past century and continues to rise, with a doubling in global food demand projected for the next 50 years. In addition to the basic challenges of increasing food production, it is the impact on the terrestrial and aquatic ecosystems that is critical to manage to ensure a sustainable future. For too long, humanity has demanded more than the regeneration capacity of the Earth’s biosphere and we are now witnessing the result of this overshoot – carbon-induced climate change, large-scale deforestation, collapsing fisheries, soil erosion and salinization, to name a few.

    Environmental research efforts ultimately aim to integrate ecological studies with socioeconomic policies in order to affect the much needed changes in global and local policies. Meanwhile agricultural scientists are busy identifying ways to breed crops and livestock that are better placed to weather potential increases in temperature – introducing drought tolerance, salinity tolerance and other relevant characteristics to key crops and food supplies.