A case of plant blindness

A case of plant blindness

Most scientist working on plants would have noticed at some time that plants are ignored by a lot of other life science researchers. Sometimes it will be during a talk whereby the presenter say something along the line ‘in all eukaryotes we have gene family X’ while you know gene family X is absent in plants. Other times it will be when reading and article whose topic is spans a broad range of living organisms. The later happened with me lately when reading an interesting article about phosphoinositides. Plant blindness is the term that has been coined for this kind of ignorance and ignoring. And there has a lot of talk on the internet among plant scientists about plant blindness.

At first I did not intend to write about that here so soon, but reading that review article made me change my mind. The thing is a review article is summarising all what is known about the topic, in this case phosphoinositides. A lot of the time when something falls outside the scope of the review the authors will to say so and when possible refer were the reader can go to if they really want to know more about that topic. As a researcher we use review articles to get an overview of the research that has been done. Starting out in a new topic it might be used as a guide to get to know that topic.

So the review that I am reading is talking about phosphoinositides in the context of mammalian cells and assumes that the reader reads the review because it is also interested in phosphoinositides in the context of mammalian cells. So far so good would you think. Except for the nice little summary table about the different phosphoinositides, their abundance and where we can find them in the cell. This table is labelled ‘Abundance, location, measurement and roles of phosphoinositides in eukaryotic cells’, this means that they claim that the data they present here is correct for not only mammalian cells, but also yeast, insect, plant cells, etc.. This, however, turned out not to be true. Working on phosphoinositides in plants have taught me a few things. The over all message is that plants do things slightly differently. Firstly, the abundance for some of the phosphoinositides in plants is different compared to what is known for mammalian cells. And secondly,

some proteins of the phosphoinositide pathway that we known from mammalian cells are absent in plants.

For the phosphoinositides community to belief and accept that things are different in plants took time. After a combination of having multiple plant genomes sequenced, and a number of publications telling things are different in plants. We are finally at a stage that we plant researchers can say with confidence:

‘No, it is not behaving the same as in mammalian cells, we are not sure what is going on in stead but we belief it is like …’.

It takes time to get to this stage. It can also make reading articles from the time when they did not know what was going on confusing. It is therefore damaging to have a new review article just ignoring this difference between plant and mammalian phosphoinositides. Anyone new in the field will come away with the believe that phosphoinositides are organised/regulated similar in mammalian and plant cells, therefore receiving a set back in their research.

So how can we change this. What I would like to see is simply some acknowledgement that things might be different in other organisms. As a writer of a review article you can do this to either check what the recent literature says about your area of interest in other organisms. If you can not find anything recent that your are happy with citing, then get in contact with someone who is actually studying your topic in another organism, I am sure they would be happy to help you. In addition, it would be nice if editors can remind the authors of review articles of this.

Now I would not let you go before telling that plant blindness aside, the authors of that review article on phosphoinositides did actually a good job. The article gives some nice overview of tools that can be used for analysis. It also gives some nice examples of how phosphoinositide protein interactions probably work.

Plants and salt stress

Plants and salt stress

The research project that I am doing at the moment is focussing on identifying lipid protein interactions under abiotic stress conditions like salt and heat stress. Hence I am reading about salt stress to get an idea about how my study fits in the bigger picture that we have about how plants react towards salt stress. Therefore from time to time I will talk about  salt stress, probably getting slowly getting into more details.

First a few facts about salt stress and its effect on plants. More than 6% of the total land area is affected by salt. This is for example land close to the seashore, or land in river delta’s were due to the tides salt water and fresh water mixes. But also land with ancient marine deposits whose natural salt seepage can wash into nearby area’s.  Another way for land to become affected by salt is trough irrigation water, whereby traces of salt remain in the soil after evaporation of the water. Over time these traces of salt can accumulate to high concentrations. The salt NaCl is the major contributor to salinity, although there are other salts like Ca2+, Mg2+ and SO42- that can contribute as well.

Plants can be roughly divided into halophytes (salt plants), which grow well on highly saline soils, and glycophytes (sweet plants) which are more salt sensitive.  Although it has to be said that salt is toxic for all plants, it is just that halophytes are better able to exclude salts up to higher concentrations. Examples of plants that are sensitive to salt are rice, maize and beans, while bread wheat, barley are moderately tolerant, and date palms, mangroves and sugar beets are highly salt tolerant.

The effects of salt stress on plants can be initially seen as a reduction in growth, with slower expansion of young leaves and slower emergence of lateral buds, resulting in fewer branches and lateral shoots. Later on the senescence of mature leaves can be observed. This later response is due to the toxic effect of Na+ ions. The earlier response is due to the osmotic stress caused by the high concentration of salt around the roots. Although, it would be expected for the roots to be more sensitive to high salt concentrations, the roots actually appear to be less affected. The initial response to salt stress in the roots is a complete stop in growth, but they recover quickly, within an hour for moderate stress to within a day for severe salt stress. While root growth recovers, it does not reaches the same rate as before being affected by salt stress. Furthermore, the root will adjust its growth into the direction where the concentration of salt is the lowest.

As salinity is a common occurrence in soils plants have evolved mechanisms to deal with its consequences. Plants can become more tolerant in three ways, firstly by becoming more tolerant to osmotic stress. When plants have a higher tolerance to osmotic stress they can keep up the rate of leaf growth. However, as a larger leaf area would mean more water loss via the leaves, this would only be beneficial when there is enough water in the soil. A second way to become more tolerant to salt stress is to exclude Na+ from the leaves. In this strategy Na+ would be excluded by the roots so it would not be able to accumulate in toxic concentrations the leaves. A third way to become more tolerant is tissue tolerance. Applying this strategy, Na+ and/or Cl– is compartmentalised on cellular or intracellular level. By doing this Na+ or Cl– would not be able to build up to toxic concentrations in the cytoplasm. Of course a plant does apply all these strategies to various degrees depending on the species. The effectiveness of these strategies also depend on the level of salt stress, the developmental stage of the plant and other environmental conditions like soil water level and air humidity.

Mangroves in Kannur, India

A good example of a halophyte are mangrove trees which grow in coastal saline or brackish water. They are more tolerant to osmotic stress by actively limiting the amount of water that  they lose through their leaves. Either by restricting the opening of stomata, or by adjusting the orientation of their leaves so they are not exposed to the midday sun. Both strategies limit the water loss through the leaves.  To avoid Na+ building up in the leaves mangroves actively filter salt from the roots, in Red mangroves this results in 90-97% of salt being excluded.  While mangroves filter out a large proportion of the salt at the roots, the salt that does make it up the shoot is compartmentalised. Either in old ‘sacrificial’ leaves which are shed when the concentration becomes to high. Stored in vacuoles as done by red mangroves. Or secreted through salt glands at the base of the leave, which is done by white or grey mangroves.

References

  • Munns and Tester, 2008,  Mechanisms of Salinity Tolerance, Annual Review of Plant Biology 59:651-681

  • Julkowaska and Testerink, 2015, Tuning plant signalling and growth to survive salt, Trends in Plant Science 20:219-229

  • Galvan-Ampudia et al., 2013, Halotropism is a response of plant roots to avoid a saline environment, Current Biology 23:2044-205

  • “Morphological and Physiological Adaptations: Florida mangrove website”. Nhmi.org.

Resurection number …

Resurection number …

Another attempt to resurrect this blog. This time born out of a desire to get better in science writing as well as wanting to tell the wider world about the fascinating aspects of plant science.

The realisation that I actually like reading and writing about science more than actually doing the experiments myself was a slow one, considering that I am well in my postdoctoral extra time in my fourth postdoctoral position. Over the years I have done widely different research project allowing me to read widely about plant science together with getting a glimpse of the research that people in other groups than my own were doing. All equally fascinating if not more so than the research topic I was pursuing myself at that moment.

It probably speaks about how much at home I felt in the lab together with enough positive results to keep going that I managed to hold on for so long and believe in the dream that if I just work hard enough, with a bit of luck I would be able to make it to a PI position. Even though in hindsight I never had enough publications and data from Friday afternoon projects needed to propel you in that highly dreamed of PI position. However, after struggling to get the assay condition just right, progressing in the style of three steps forward two steps back for about a year now. After just another blot failing to show the results I so desperately want I came to the realization that this in my eyes now tedious labwork is not what I want to do.

For some months now I have been thinking about what it is what I wanted to do as this postdoc ended as I am well aware now that to do another one is no option and the chances of making it into a PI position a practically non existing whatever others might tell me. Number one on that list was that in my next job I wanted to be able to read more about science. Though this in it self would hardly pay the bills, nobody would be so creasy to pay you money so you could just read about science. So vague ideas about how maybe I could then help others doing science while reading about science. Maybe writing a book someday when I have enough spare time and a stable income so not having to worry about paying bills. But then, after that doomed blot , I realized that while I could wait for the perfect time and opportunity to arise for writing that book, I could always just start writing and blogging about the science I read and heard about. So that is what I plan to do, allocating some time at the start of each day to read and write about the science I read and heard about. It probably won’t be perfect, so don’t hesitate to give me some feedback, although preferably in an encouraging way.