Metapopulation Microcosm Plates (MMP) are devices which resemble 96-well microtiter plates in size and shape, but with corridors connecting the wells in any configuration desired. They can be used to culture microbial metapopulations or metacommunities with up to 96 habitat patches.
In these two video tutorials, Helen Kurkjian explains how you can assemble, fill and clean MMPs in your lab.
Our recent Methods in Ecology and Evolution paper – ‘Imaging biological surface topography in situ and in vivo‘ – shows how to use gel-based profilometry to image various biological surfaces. To start you need to press a gel into a surface of interest. The bottom surface of the gel is coated in a paint to create an impression of the surface that has standard optical properties (not clear, shiny, or coloured). Then lights are shone on the gel at different angles and photographs are taken at six different lighting angles. These photographs allow us to study the surface in incredible detail. The following images give more information on how we can do this and the benefits of it.
To find out more, read our Methods in Ecology and Evolution article ‘Imaging biological surface topography in situ and in vivo’. And to find out more about Dylan’s research, visit his website.
Below is a press release about the Methods paper ‘Integrating evolutionary biology with digital arts to quantify ecological constraints on vision-based behaviour‘ taken from the La Trobe University.
Ctenophorus fionni (Peninsula Dragon), male push up display. © Jose Ramos, La Trobe University
Many animals rely on movement to find prey and avoid predators. Movement is also an essential component of the territorial displays of lizards, comprising tail, limb, head and whole-body movements.
For the first time, digital animation has been used as a research tool to examine how the effectiveness of a lizard’s territorial display varies across ecological environments and conditions. The new research was published today in the journal Methods in Ecology and Evolution.
A team from La Trobe University’s School of Life Sciences, led by Dr Richard Peters, worked with academics from Monash University’s Faculty of IT to create, using 3D animation, a series of varied environmental settings and weather conditions, comprising different plant environments and wind conditions, to quantify how lizard displays are affected by this variation. Continue reading
A salamander having its skin swabbed to test for Bsal infection.
Imagine you’re at the doctor’s office. You’re waiting to hear back on a critical test result. With recent emerging infectious diseases in human populations, you are worried you may be infected after a sampling trip to a remote field site. The doctor walks in. You sit nervously, sensing a slight tremble in your left leg. The doctor confidently declares, “Well, your tests results came back negative.” In that moment, you let out a sigh of relief, the kind you feel throughout your body. Then, thoughts start flooding your mind. You wonder– what are the rates of false negatives associated with the test? How sensitive is the diagnostic test to low levels of infection? The doctor didn’t sample all of your blood, so how can they be sure I’m not infected? Is the doctor’s conclusion right?
Now, let’s say I’m the doctor and my patient is an amphibian. I don’t have an office where the amphibian can come in and listen to me explain the diagnosis or the progression of disease − BUT I do regularly test amphibians in the wild for a fatal fungal pathogen, known as Batrachochytrium dendrobatidis (commonly known as Bd). Diseases like Bd are among the leading causes of the approximately one-third of amphibian species that are threatened, near threatened, or vulnerable to extinction. To test for Bd, and the recently emerged sister taxon Batrachochytrium salamandrivorans (hereafter referred to as: Bsal), disease ecologists rely on non-invasive skin swabs. Continue reading
The sand lizard (Lacerta agilis).
Many researchers, breeders and hobbyists need to know sex of their animals. Sometimes it’s easy – in sexually dimorphic species you only have to look. In other species or juveniles it’s often not so straightforward though. And it’s often impossible – but sometimes essential – in embryos or in tissue samples. Determining sex from DNA is the most practical option, or sometimes even the only possibility, in these cases.
Molecular sexing is routinely used in mammals and birds, but until now it has only been available for a handful of reptile species. Many people didn’t believe that this situation would improve considerably any time soon. But why? Continue reading
Many things can negatively affect stream ecosystems – water abstraction, eutrophication and fine sediment influx are just a few. However, only intact freshwater ecosystems can sustainably deliver the ecosystem services – such as particle filtration, food biomass production and the supply of drinking water – that we rely on. Because of this, stream management and restoration has often been in the focus of environmental legislation world-wide. Macrozoobenthic communities are often key biological components of stream ecosystems. As many taxa within these communities are sensitive to negative stressors introduced by humans, they’re ideal for assessing the quality of water.
Unfortunately, most macrozoobenthic taxa – such as stone-, may-, and caddisflies as well as most other invertebrates – are often found in juvenile larval life stages in these ecosystems, so they’re often difficult to identify based on morphology. With the DNA based metabarcoding method though, almost all taxa in a stream can be reliably identified up to species level using a standardised gene fragment. One key component of this strategy is the development of universal markers, which allow detection of the diverse macrozoobenthic groups.
Our new R package PrimerMiner provides a framework for obtaining sequence data from available reference databases and identifying suitable primer binding sites for marker amplification. The package makes this process quicker and easier. In the following pictures, we summarise the key steps of DNA metabarcoding.
To find out more about PrimerMiner, read our Methods in Ecology and Evolution article ‘PrimerMiner: an r package for development and in silico validation of DNA metabarcoding primers’. Like all Applications articles, this paper is freely available to everyone.
Lizards, such as these South African armadillo lizards, serve an important role as model organisms for various ecological and evolutionary studies. © Chris Broeckhoven
X-ray micro-computed tomography – or µCT – is a technique that uses x-rays to create high resolution cross-sections of samples. Virtual 3D models can be made from these cross-sections without destroying the original samples. Micro-CT has important applications in medical imaging and, in the biomedical field, in vivo µCT allows researchers to make virtual 3D models of the skeleton and organs of live small animals. Three-dimensional models like these could provide insight into diseases and guide the development of medicines and therapies.
In vivo µCT holds three major advantages over other methods:
A variety of commercially available µCT scanners that are optimised for scanning live animals are now available. The use of in vivo µCT in ecological and evolutionary studies, however, has greatly lagged behind its use in biomedical studies. Continue reading
