Tiny life sticking to growing green things

Communicating science to non-scientists is important, but often the jargon scientists use makes their work impenetrable, even to other scientists. So how can scientific writing become less obscure and more approachable? Randall Monroe, the creator of xkcd webcomics, gave it a go with his annotation of a Saturn V rocket blueprint. The annotation used only the 1000 most commonly used words, so instead of Saturn V the name of the rocket became Up Goer Five.

So can scientific communication in my field (microbiology and genetics) be effective using only the 1000 most commonly used words? In the interests of simplifying my writing, I wrote a summary of my PhD project using only the 1000 most commonly used words (using this text editor):

This study wants to find the ‘small pieces’ which are important for tiny life (the helping ones) to stick to growing green things. Pseudomonas tiny life are some of the best helping tiny life and one of the most well-known ones, Pseudomonas protegens Pf-5, can control problems in growing green things used for food. But in the field, helping tiny life show does not stick to growing green things very often or very well. This study will look at the whole set of ‘small pieces’ important for P. protegens Pf-5 to stick to growing green things. Making tiny life stick better to growing green things will help lower problems with growing green things and better the return from growing green things used for food, which are important both here and around the world.

This is hilarious and obviously oversimplified (to the point of not making sense in a lot of places). For comparison, this is the ‘normal’ version of my project summary:

The project aims to identify the essential genes for colonisation of plant surfaces by biocontrol bacteria. Pseudomonas bacteria are some of the most successful biocontrol bacteria and one of the most well-known strains, Pseudomonas protegens Pf-5, has the ability to control diseases that affect cotton, wheat, pea, maize, tomatoes and potatoes. Despite this, field trials of biocontrol bacteria show a lack of reliability and persistence on plant surfaces. This project will conduct a genome-wide study of genes essential for P. protegens Pf-5 colonisation of plant surfaces. Enabling reliable colonisation of crop roots by biocontrol bacteria will contribute to lowering plant disease and increasing crop yields, which are important both in Australia and internationally.

From this exercise I learned that some level of complicated language is important to communicate a precise meaning (important in science), but not every complicated word is necessary. Sometimes the language I choose can be off-putting to the reader, make my work harder to understand and appear pretentious even when I don’t mean it to.

So overall, science writing in my field using the 1000 most used words is not practical and makes it harder, not easier to understand (even nonsensical in places). But it’s an interesting exercise to see just how much jargon you’ve used or if a simpler word will do in place of a complicated one. And wouldn’t we all like simpler rather than complex!

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JAMS symposium = ECRs, viruses, bacteria, biocontrol, mining, big data and whale snot

On the 21st of March, over 30 Macquarie University staff and students attended the 7th annual symposium of JAMS, the Joint Academic Microbiology Seminars, at the Australian Museum. JAMS was very popular on Twitter, with the #JAMS7 hashtag trending on the day.

Six students from the Paulsen and Tetu groups presented posters and Vanessa Pirotta won the student poster prize. Congratulations Vanessa!

Our new posters will feature in the corridors of our department to show off the exciting microbiology work happening in our group.

A major topic of the day was remediation of contaminated sites with talks on amending microbial communities to assist with remediation, microbes using atmospheric hydrogen to survive in nutrient depleted environments, and stochastic vs directed assembly of microbial communities in mine tailings.

Continuing the environmental microbiology theme there were also talks on marine viruses in contrasting environments, and the physiology and metagenomics of plant-fungi associations.

On top of all of that it was great to hear about the valuable work the EMCR Forum is doing on behalf of early- and mid-career STEM researchers, and to everyone’s relief it’s free to join.

Thanks to the JAMS organising committee for another excellent microbiology meeting – we’re all looking forward to the next monthly JAMS meeting (for more information visit jams.org.au).

A minefield of data issues?

Even creating a small amount of data for my Masters project has brought home to me some of the issues around data – how to store it, where to store it, in what format to store it, how to ensure the appropriate people have access to it, how to stop people accessing it if they shouldn’t have access to it, how to future proof the storage, how to ensure the data and method used to collect it remain linked, who gets to keep it.

And that’s just for a few small plant biology experiments for my Masters. I’m sure there are many more levels of complexity for confidential data and big data. Some of these issue were discussed briefly with my Masters cohort, but it seems like that short conversation was only scratching the surface. I’m sure that as a (very) early career researcher there are a lot of things I don’t know and even more things I’m not even aware that I need to know.

 

Brightfield microscope image of Australian wild cotton (G. australe) leaf cross-section – one of the types of data from my Masters project (Photo: Belinda Fabian)

During my research break between my Masters and my PhD I’m working on up-skilling in a variety of areas; some directly related to my potential research topic(s), some which are generally related to study and/or my career (e.g. learning to code and using R) and others that just broaden my horizons (both scientifically and personally). One of the general study/career areas I’m learning about is data management through the 23 [research data] things program (see below for more information).

I see the 23 [research data] things program as helping me with generic study/career knowledge and skills and ideally it will will form part of a firm footing for me as a researcher. Awareness of the issues related to data management is important for researchers (and keeping digital data adds more concerns), but from my experience an understanding of it comes in a very piecemeal fashion during research training (as with many other things). So hopefully participating in this program will help me get out in front of the curve and make me aware of issues, solutions and strategies for managing data and where to find information down the track when the need becomes pressing.

Things you need to know:

The 23 [research data] things is a program run through ANDS (Australian National Data Service). More information can be found here. There’s an introductory webinar on tomorrow 1 March, 12.30-1.30 AEDT.

The program is free and runs from March to November 2016 (I know that sounds like a lot, but the FAQs suggest that it will only take about an hour a week and there will be breaks and catch-up opportunities during the year).

The program is advertised as being of interest to lots of different types of people – from the 23 [research data] things website: “If you are a person who cares for, and about, research data and want to fill in some gaps, learn more, find out what others are thinking… then this may be for you!” I’m getting involved as a research who will deal with data in my career, but if you’re a person who creates or cares for data then the program may be of interest to you too.

There’s a Meetup group for discussing the activities and other thoughts about the program and search #23RDThings on Twitter for all the buzz.

Google Scholar is Filled with Junk Science

An interesting commentary on the state of Google Scholar’s search results.

I haven’t personally experienced the junk science results in Google Scholar that this author discusses, but then again my current research may not be attractive for predatory publishers. I’m focusing on plant physiology and biochemistry, which may be less prone to junk science when compared with more controversial areas or topics.

But this problem is very important to keep at the front of your mind if you’re researching a new area and may not have the skills to evaluate the research and determine ‘good science’ from ‘bad science’.

Drought vs Deluge – How Will Grasslands Cope with Climate Change?

Climate change due to human activities is predicted to change many aspects of the environment, from atmospheric carbon dioxide to temperature and rainfall1. Modellers are confident in the projected temperature increases, but the predictions about rainfall are much less certain. Changes in rainfall patterns will impact on many aspects of ecosystems, including how nutrients move.

Associate Professor Sally Power studies how these nutrient cycles are being affected by human-induced changes in the environment. She took up a position two years ago at the Hawkesbury Institute of the Environment, University of Western Sydney after completing her studies and working at the Imperial College in London. She previously completed a post-doctoral position at La Trobe University, Melbourne and loved Australia, so now she’s here permanently. Associate Professor Power is passionate about the understanding the interactive impact of multiple climate drivers on ecosystems.

At a recent seminar at Macquarie University Associate Professor Power spoke about three projects she is involved with at the moment:

  1. Drought and diversity in the UK (DIRECT)
  2. Rainfall extremes (DRI-grass)
  3. Elevated CO2 impacts on forest nutrient cycling (EucFACE)

The DIRECT project (Diversity, Rainfall and Elemental Cycling in a Terrestrial Ecosystem) aims to answer questions about how grassland ecosystems will respond to predicted rainfall changes and whether biodiversity will buffer these effects of a rainfall pattern change2. To test these ideas the research team constructed an array of grassland plots with a range of plants functional groups – perennials, caespitose grasses and annual plants (Figure 1)3.

Figure 1. Plant traits selected for the DIRECT experiment Image: Grantham Institute, Imperial College London (4).

Figure 1. Plant traits selection for the DIRECT experiment
Image: Grantham Institute, Imperial College London (4).

Rainfall predicted for the year 2100 (down 30% in summer, up 15% in winter) was applied to these plots to see how different vegetation communities might respond to rainfall changes2. Key ecosystem processes (such as respiration rate and nutrient cycling) were faster when there were a range of perennial plants present. Process rates in vegetation plots dominated by annual plants or caespitose grasses were not strongly affected by changes in rainfall2. This research showed that plant functional groups are important for maintaining grassland ecosystem function and they need to be considered in future management plans2.

In addition, the researchers used different plots in the same area and changed the rainfall pattern to see if drought and deluge impact differently on the grassland ecosystem. The rainfall treatments used were5:

  • Current levels;
  • Prolonged drought – 30% drop in rainfall; and
  • Reduced frequency – same amount of rain, concentrated into heavier falls less frequently.

The key findings were that changing the frequency of rainfall affected the number of species, especially the perennial species5. Surprisingly the number of species was not affected by the change in the total amount of rain (prolonged drought). The reduced rainfall frequency also lead to an increase in respiration and the grassland ecosystem switched from being a net carbon sink to net carbon source (from overall absorbing carbon to overall emitting carbon; Figure 2)5. The results of this experiment suggest that grassland ecosystems are relatively resistant to predicted rainfall changes5.

Figure 2. Change from carbon sink to carbon source for each of the  rainfall treatments (A = ambient; PD = prolonged drought; RF = reduced frequency). (Adapted from image presented by Associate Professor Sally Power)

Figure 2. Change from carbon sink to carbon source for each rainfall treatment (A = ambient; PD = prolonged drought; RF = reduced frequency; adapted from image presented by Associate Professor Power)

Associate Professor Power is also in the preliminary stages of some large scale experiments in western Sydney. The first of these experiments is DRI-grass (Drought & Root Herbivore Interactions in a Grassland Ecosystem). This study asks whether Australian grassland ecosystems have stronger responses to the amount or frequency of rain and whether these responses are affected by root herbivores6. Associate Professor Power emphasised that root herbivores are very abundant and their weight can exceed the weight of the sheep in a hectare7. Root herbivores can respond directly and indirectly to changes in rainfall patterns and can make it harder for plants to cope with climate change impacts8.

The research team has set up five different rainfall treatments: +50% rain; -50% rain; 3 week rainfall cycle with the same total amount of rain; summer drought; and the ambient conditions (Figure 3). The rainfall treatments only began in June 2013 and the root herbivores are not yet in place. So far the researchers have observed there are lower species abundances under drought conditions and an increase in summer rain has led to the dominance of African lovegrass.

Figure 3. Rainfall shelters for the DRI-grass experiment in the foothills  of the Blue Mountains (Image: The Hermon Slade Foundation; 6)

Figure 3. Rainfall shelters for the DRI-grass experiment in the foothills
of the Blue Mountains (Image: The Hermon Slade Foundation; 6)

The second project in western Sydney is being conducted in the EucFACE facility (Eucalyptus Free Air CO2 Enrichment)9 located in an intact Cumberland Plain Woodland ecosystem. Associate Professor Power and her team are looking at how elevated CO2 increases rates of nutrient cycling in the ecosystem. So far they have noticed there is an increase in available phosphorus, but no change in the amount of available nitrogen in elevated CO2 conditions.

Once the data is collected from these long term experiments, Associate Professor Power aims to understand some of the impacts of climate change on grassland ecosystems and make recommendations about how these systems should be managed to mitigate these impacts.

 

Learn more:

  1. IPCC (2013). Summary for Policymakers. In: Climate Change 2013: The Physical Science Basis. Working Group I Contribution to the IPCC Fifth Assessment Report. Cambridge University Press, Cambridge.
  2. Fry EL, Manning P, Allen DGP, Hurst A, Everwand G, Rimmler M & Power SA (2013). Plant Functional Group Composition Modifies the Effects of Precipitation Change on Grassland Ecosystem Function. PLoS ONE, 8(2): e57027. doi: 10.1371/journal.pone.0057027.
  3. Fry EL, Power SA & Manning P (2014b). Trait-based classification and manipulation of plant functional groups for biodiversity-ecosystem function experiments. Journal of Vegetation Science, 25, 248–261. doi: 10.1111/jvs.12068.
  4. Fry E, Hurst A, Everwand G, Rimmler M, Manning P & Power S (2009). Poster: “Diversity, Rainfall and Elemental Cycling in a Terrestrial ecosystem, (DIRECT)” presented at Committee for Atmospheric Pollution Effects Research AGM. https://workspace.imperial.ac.uk/climatechange/public/pdfs/CAPER_poster.pdf, accessed 25 May 2014.
  5. Fry EL, Manning P & Power SA (2014a). Ecosystem functions are resistant to extreme changes to rainfall regimes in a mesotrophic grassland. Plant Soil, doi: 10.1007/s11104-014-2137-2.
  6. The Hermon Slade Foundation (2014). Drought, deluge and diversity decline – How do root herbivores affect grassland resilience to predicted changes in rainfall patterns? http://www.hermonslade.org.au/projects/HSF_13_12/hsf_13_12.html, accessed 25 May 2014.
  7. Britton E (1978). A revision of the Australian chafers (Coleoptera: Scarabaeidae: Melolonthinae) Vol. 2. Tribe Melolonthini. Australian Journal of Zoology, 26, 1–150, Supplementary Series.
  8. Bardgett RD & Wardle DA (2003). Herbivore-mediated linkages between aboveground and belowground communities. Ecology, 84, 2258-2268. doi: 10.1890/02-0274.
  9. Hawkesbury Institute of the Environment (2014). EucFACE, http://www.uws.edu.au/hie/facilities/face, accessed 25 May 2014.

Synaesthesia – a ‘mixing of the senses’

The 2014 winner of the Paul Bourke Award was Associate Professor Anina Rich, a researcher from Macquarie University. This honour is awarded annually by the Academy of the Social Sciences in Australia to an early researcher who has achieved excellence in their field. As part of the award the winner presents their recent research in a public lecture at their home university. Dr Anina Rich studies how the brain integrates sensory information, particularly focusing on synaesthesia.

People with synaesthesia (synaesthetes) perceive sensory information in a different way. They can experience colours in association with letters, sounds or smells. The most common type of synaesthesia is letter-colour (Figure 1) but there are also other types such as auditory-visual and olfactory-visual synaesthesia. Chiou & Rich (2014) define synaesthesia as a ‘concurrent and distinct experience in a separate or the same modality’.

Figure 1. A representation of the colours one synaesthetes associates with each letter and number.

Figure 1. A representation of the colours one synaesthete associates with each letter and number.

Synaesthesia is present is 0.05-4% of the population and may have a genetic link. Relatives with synaesthesia are common and it is more prevalent in females than males. Many people don’t realise they are a synaesthete as their synaesthetic experience is constant over time and normal for them (perception in general is subjective).

Dr Rich is interested in studying synaesthesia as it may provide information about how information is normally integrated. Synaesthesia is not a medical disorder, there are no deficits associated with it. Many synaesthetes report that the extra sensory information they receive can be used to improve their memory and learning. Dr Rich is interested in seeing if synaesthetes have extra connections in the brain or are just using their connections between brain sections in a different way to the rest of the population.

To test this idea, Dr Rich and her team asked seven auditory-visual synaesthetes to describe the location on a grid of colours and shapes in response to auditory stimulus (Figure 2). Using functional MRI, Dr Rich and her team were able to work out that the occipital lobe in the back of the brain is stimulated when auditory-visual synaesthetes are presented with auditory information.

Figure 2. Examples of the stimuli presented to the auditory-visual synaesthetes (Chiou et al. 2013).

Figure 2. Examples of the stimuli presented to the auditory-visual synaesthetes (Chiou et al. 2013).

In addition, Dr Rich’s team has been investigating the areas of the brain non-synaesthetes use to process information about objects and colours. For example, a lemon is instantly recognisable as a lemon due to its yellow colour. When this colour is changed to something incongruent, like a red lemon, it becomes harder to identify. This object-colour binding is centralised in the anterior temporal lobe of the brain. Dr Rich is now conducting research to see if the same brain location of object-colour binding is seen in synaesthetes and what happens to their synaesthetic experience if the activity of this brain region is temporarily disrupted (Chiou et al. 2014).

Studying synaesthesia and how the brain processes sensory information is important as it can provide information about how learning and experience can alter our perception. As Dr Rich said in her presentation “what we already know has huge influence on what we think we see”. This work has implications for designing environments where people are required to process multiple sources of information, such as airplane cockpits.

To learn more:

Chiou R & Rich AN (2014). The role of conceptual knowledge in understanding synaesthesia: Evaluating contemporary findings from a “hub-and-spokes” perspective. Frontiers in Psychology, 5(105), 2-18. doi:  10.3389/fpsyg.2014.00105.

Chiou R, Stelter M & Rich AN (2013). Beyond colour perception: Auditory-visual synaesthesia induces experiences of geometric objects in specific locations. Cortex, 49(6), 1750-1763.

Chiou R, Sowman PF, Etchell AC & Rich AN (2014).A Conceptual Lemon: Theta Burst Stimulation to the Left Anterior Temporal Lobe Untangles Object Representation and Its Canonical Color. Journal of Cognitive Neuroscience, 26(5) 1066-1074. doi:10.1162/jocn_a_00536.

Prevention is Better Than Cure – Keeping Dementia at Bay

What do we know about dementia?

Recently Associate Professor Michael Valenzuela spoke at Macquarie University’s Australian Advanced School of Medicine about his work with elderly Australians. Associate Professor Venezuela leads a team of researchers at the Brain and Mind Research Institute, part of the University of Sydney. His work is important for determining how elderly people can be productive into old age rather than being confined to institutions or nursing homes. Dementia is not one disease, but a collection of diseases characterised by a decline in brain functions, such as perception, memory, language and cognitive skills1. Research has shown that shrinkage of the hippocampus (a brain section important for memory and spatial skills) is an indicator for dementia (Figure 1)2.

Figure 1. Shrinkage of the hippocampus in healthy elderly people and suffers of  Alzheimer’s Disease (one of the diseases under the umbrella of dementia)2.

Figure 1. Shrinkage of the hippocampus in healthy elderly people and sufferers of Alzheimer’s Disease (one of the diseases under the umbrella of dementia)2.

What are the risk factors?

So what determines whether an elderly person can maintain an independent lifestyle or become dependent on others for care and support? A major risk factor for dementia is being mentally lazy. A person’s cognitive lifestyle across the years of their life is a major factor in the risk of cognitive decline and developing dementia as a person ages. A survey of elderly people in Australia, the UK, the USA and France (Lifetime of Experience Questionnaire) is currently being conducted to find out more about how cognitive lifestyle correlates with risk of dementia3.

One recent finding of the Lifetime of Experience Questionnaire is that managerial experience during a person’s working life is correlated to a bigger hippocampus. Managing at least 10 people can be effective at preventing the onset of dementia4. The researchers analysing the data have postulated that interactions with people and the complex skill set required to successfully perform in a management position are what leads to this reduction in dementia risk.

What can we do to stave off the onset of dementia?

The findings from Associate Professor Valenzuela’s research show that one way to reduce the risk of dementia is to maintain an active cognitive lifestyle (ACL)5. Consistently ‘working out’ your brain can increase the time you live with a clear mind and reduce the amount of time living with dementia6. This pushing back of the onset of dementia is known as compression of cognitive morbidity. Pablo Picasso is a wonderful example of a person who was active and independent into old age. He continued to paint right up to his death at 73 years old (Figure 2).

Figure 2. Pablo Picasso adding paint to an artwork.

Figure 2. Pablo Picasso adding paint to an artwork.

How do we go about promoting active cognitive lifestyles in communities?

Associate Professor Valenzuela’s team has started a Brain Training Lab at the Montefiore Home in Randwick, Sydney (Figure 3). Here the program participants undergo computer-assisted cognitive training for 60 minutes, three times a week over a 12 week program. There are two groups – one does repeated standardized tasks and the other group watches National Geographic videos and answers questions about them. This study aims to answer questions about the minimum/maximum amount of training required to improve cognitive function and how long positive effects from brain training can last7.

Figure 3. Participants undertaking computerised tasks as part of the Brain Training Lab.

Figure 3. Participants undertaking computerised tasks as part of the Brain Training Lab.

Another experiment that has been established is the Study of Mental Activity and Regular Training (SMART) trial. This study combines mental and physical training to see if either type of training in isolation or the combination of both improves cognitive abilities8. The link between exercise and brain health has been observed in rat experiments. Exercise has been shown to improve brain organisation and object/place recognition in aged rats. This link has also been demonstrated in humans; exercise training has been shown to increase the size of the hippocampus9. The SMART study includes 100 Sydneysiders over the age of 55 and they conduct training twice a week for six months. Measurements of cognitive ability before any training, after six months of training and at an 18 month follow-up hope to determine if there are improvements in the brain, general health and quality of life of the participants8.

Wider implications

Only in the past 100 years have people been able to live beyond 65 years of age. The population of the world is aging fast due to the maturing of the baby boomer generation and medical advancements extending life expectancy. The combination of aging populations and increased life expectancy means more people than ever before are soon going to be retired. Retirement design needs to be carefully considered so the development of dementia in aging population doesn’t negatively impact on the economy and health care systems10. Studies on aging and cognitive ability have shown that it isn’t effective to retire and then do no ‘brain work’ for 20-30 years. Associate Professor Valenzuela warns that retirement design needs to take this into account. Opportunities need to be created where elderly people can replace the intensive cognitive and social interactions of a work environment when they retire. Only in this way can the older people retain their cognitive abilities and stave off the onset of dementia.

Want to learn more?

  1. Department of Health, Commonwealth of Australia (2013). Dementia, http://www.health.gov.au/dementia, accessed 23 May 2014.
  2. Thompson PM, Hayashi KM, de Zubicaray GI, Janke AL, Rose SE, et al. (2004). Mapping hippocampal and ventricular change in Alzheimer disease. NeuroImage, 22(4), 1754-1766. doi: 10.1016/j.neuroimage.2004.03.040.
  3. Valenzuela M & Sachdev P (2007). Assessment of Complex Mental Activity Across the Lifespan: Development of the Lifetime of Experiences Questionnaire. Psychological Medicine, 37, 1015-1026. doi: 10.1017/S003329170600938X.
  4. Suo C, Leon I, Brodaty H, Trollor J, Wen W, et al. (2012). Supervisory experience at work is linked to low rate of hippocampal atrophy in late life. NeuroImage, 63, 1542-1551. doi: 10.1016/j.neuroimage.2012.08.015.
  5. Marioni RE, van den Hout A, Valenzuela MJ, Brayne C, Matthews FE, et al. (2012). Active cognitive lifestyle associates with cognitive recovery and a reduced risk of cognitive decline. J Alzheimers Dis, 28(1), 223-230. doi: 10.3233/JAD-2011-110377.
  6. Marioni RE, Valenzuela MJ, van den Hout A, Brayne C, Matthews FE (2012).Active Cognitive Lifestyle Is Associated with Positive Cognitive Health Transitions and Compression of Morbidity from Age Sixty-Five.PLoS ONE, 7(12), e50940.doi: 10.1371/journal.pone.0050940.
  7. Lampit A, Suo C, Gates N, Kwok SSY, Naismith S et al. (2011). Temporal evolution of cognitive training-induced structural and functional brain plasticity. 10th National Emerging Researchers in Ageing Conference, University of New South Wales, Sydney. http://rng.org.au/timecourse/, Accessed 23 May 2014.
  8. Gates NJ, Valenzuela M, Sachdev PS, Singh NA, Baune BT, et al. (2011) Study of Mental Activity and Regular Training (SMART) in at risk individuals: A randomised double blind, sham controlled, longitudinal trial. BMC Geriatrics, 11(19), doi: 10.1186/1471-2318-11-19.
  9. Erickson KI, Voss MW, Prakash RS, Basak C, Szabo A, et al. (2011). Exercise training increases size of hippocampus and improves memory. Proceedings of the National Academy of Sciences of the United States of America, 108(7), 3017-3022. doi: 10.1073/pnas.1015950108.
  10. Brookmeyer R, Johnson E, Ziegler-Graham K & Arrighi HM (2007). Forecasting the global burden of Alzheimer’s disease. Alzheimer’s & Dementia, 3(3), 186–191. doi: 10.1016/j.jalz.2007.04.381.