9.3 Growth in Plants

Developments in scientific research follow improvements in analysis and deduction—improvements in analytical techniques allowing the detection of trace amounts of substances has led to advances in the understanding of plant hormones and their effect on gene expression.

In this case, the NOS statement is referring to the use of genomics to analyse gene expression in plants. Some of the earliest experiments into tropisms were conducted by none other than Charles Darwin, whose 1880 book The power of movement in plants represented the first attempt to synthesise available evidence on tropisms and included many of his own experiments in this field.  As developments in technology increased, the role of hormones became increasingly important and better understood.

Hormones influence gene expression; by detecting changes in gene expression, we can determine the role of hormones in this process. DNA sequences have been analysed to determine how these change in response to hormone exposure and mRNA levels (evidence of transcription and hence gene expression) can also be detected, pinpointing the cells that are responding to these hormones. Scientists have detected a range of common short sequences of nucleotides, from four to twelve bases in length. Different combinations of these appear to be linked to specific hormones and allow the genes to be affected by different classes of hormones. Details on some of these nucleotide sequences can be seen in the table below (Plants in Action).  Experiments have revealed that plant hormones can act extremely fast – with mRNA changes detected as quickly as 2-5 minutes from exposure.

Table 9.02.png
Image from Plants in Action 1st Ed.

The advances in microarray analysis of DNA and mRNA was thus critical to our improved understanding of how plant hormones work.

Sources:

Jennifer J. Holland, Diana Roberts, Emmanuel Liscum; Understanding phototropism: from Darwin to today, Journal of Experimental Botany, Volume 60, Issue 7, 1 May 2009, Pages 1969–1978, https://doi.org/10.1093/jxb/erp113 Web. Accessed 6 Feb, 2018.

“Modified Gene Expression.” Plants in Action, 1st ed., Australian Society of Plant Physiologists, 1998, plantsinaction.science.uq.edu.au/edition1/?q=content/9-2-4-modi-ed-gene-expression. Web. Accessed 6 Feb, 2018.

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9.2 Transport in the Phloem

Developments in scientific research follow improvements in apparatus—experimental methods for measuring phloem transport rates using aphid stylets and radioactively-labelled carbon dioxide were only possible when radioisotopes became available.

This NOS is another example that fits nicely into the syllabus content.  In 9.2, students are asked to analyse …data from experiments measuring phloem transport rates using aphid stylets and radioactively-labelled carbon dioxide. We can learn about this process through the NOS to understand how it works and why it enables us to understand the flow of sap through the phloem.  Two for the price of one!

Radioisotopes have been encountered before in your IB Biology studies. They become widely available to researchers after the second world war.  As the molecules that are radioactive can be traced, it became possible to track the flow of these molecules through cells, tissues and organisms over time.

Phloem transport is based on high hydrostatic pressure.  Thus if the phloem can be punctured, the contents should continue to exude out. If the plant is exposed to radioactively labelled carbon dioxide, the sap can be tested for the presence of the isotopes and the rate of translocation can then be estimated.

Collecting Phloem Sap using Aphid Stylets (D. Fischer)
Image from D. Fischer, Plants in Action.

The use of the aphids can be summarised as follows (base on the images above; Plants in Action; image D. Fischer):

Top Image: Aphid feeding, inset is the stylet (St) penetrating to the phloem (p)
Image a: feeding aphid with stylet penetrating the plant
Images b-d: the stylet is removed from the aphid (they would be anaesthetised beforehand – there are some links here to the use of animals in experiments)
Image e: phloem sap starts to accumulate from the stylet.

The droplet of phloem sap can then be analysed for traces of the isotope to determine transport rate.  Aphids can be placed along the length of the plant stem to show transport along various distances.

Sources:

Fischer, D. “Collection of Sap from Aphid Stylet.” Plants in Action, University of Queensland, 2018, plantsinaction.science.uq.edu.au/content/522-techniques-collect-phloem-sap. Digital image. Feb 1, 2018.

“5.2.2 – Techniques to Collect Phloem Sap.” Plants in Action, Australian Society of Plant Scientists, 2018, plantsinaction.science.uq.edu.au/content/522-techniques-collect-phloem-sap. Online Textbook. Feb 1, 2018.

11.2 Movement

Developments in scientific research follow improvements in apparatus—fluorescent calcium ions have been used to study the cyclic interactions in muscle contraction

 In a review article of the use of Calcium imaging in physiology studies, Russell notes that calcium ions are:

“…an ubiquitous intracellular messenger that regulates multiple cellular functions such as secretion, contraction, cellular excitability and gene expression in all organ systems.” (Russell, 1605)

We have encountered them in detail in looking at synapses and muscle contraction in animals and also their role in the formation of the cell wall in plants.  Clearly calcium is an important element whose roles range wider than just making healthy bones and teeth!

Advances in technology enable us to collect data that is otherwise outside the the abilities of human perception; this provides the evidence to develop theories.  In 1962 it was reported that scientists had extracted a Ca2+-sensitive bioluminescent protein from the jellyfish, Aequoria victoria.  and gave it the name “aequorin”. Aequorin emits light when it reacts with calcium and this can be detected experimentally by illumination with different types of radiation. In many cases, a light microscope can be used to view it and it can be photographed or filmed as well.

1024px-Aequorea4
Aquorea victoria (Sierra Blakely)

In topic 11.2 we learn about the role of calcium from the sarcoplasmic reticulum binding to troponin and thus triggering the contractile cycle of actin and myosin.  A recent study (Desai et al.) used calcium fluorescence to tag individual molecules of myosin in order to image how single filaments of myosin interact with ATP and Calcium to activate the actin.  The team were able to determine that two myosin heads are needed to activate the actin filament and that 11 Myosins bind as part of a regulatory unit.

As technology advances, our understanding of biological processes grows deeper and more complex. This in turn either provides additional evidence in support of existing theories or may suggest alternative explanations.  And so science moves on….

Sources:

Allott, Andrew, and David Mindorff. Biology: Course Companion. Oxford, Oxford University Press, 2014.

Blakely, Sierra. “ Aequorea Victoria .” Aequorea Victoria , Wikipedia, 17 Feb. 2017, en.wikipedia.org/wiki/Aequorea_victoria. Accessed 20 Apr. 2017.

Desai, Rama, Michael A. Geeves, and Neil M. Kad. “Using Fluorescent Myosin to Directly Visualize Cooperative Activation of Thin Filaments.” The Journal of Biological Chemistry 290.4 (2015): 1915–1925. PMC. Web. 20 Apr. 2017.

Russell, James T. “Imaging Calcium Signals in Vivo: a Powerful Tool in Physiology and Pharmacology.” British Journal of Pharmacology, vol. 163, no. 8, 2011, pp. 1605–1625., doi:10.1111/j.1476-5381.2010.00988.x.

Zimmer, Marc. “Green Fluorescent Protein.” Green Fluorescent Protein – The GFP Site, Connecticut College, 18 Aug. 2015, http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP-1.htm. Accessed 20 Apr. 2017.

1.2 Ultrastructure of Cells

Developments in scientific research follow improvements in apparatus—the invention of electron microscopes led to greater understanding of cell structure.

Although lenses had been used for magnification earlier, it was Anton van Leeuwenhoek, a Dutch draper of the 17th-century, who developed the first true microscope in his workshop in Delft. Cunningly arranged from lenses he polished and ground himself, he was able to view objects at up to 270x magnification and became the first person to observe and describe bacteria, yeast and the microorganisms in water, amongst others.

van-leeuwenhoek-microscope1
Anton van Leeuwenhoek’s microscope. The specimen was placed on the spike and the screw was turned to focus. (History of the Microscope)

Microscope design continued slowly but was radically improved by the discovery in the 1860s by Ernst Abbe of the Abbe sine condition. This is necessary in order for a lens to focus on and produce a very clear sharp image. One of Abbe’s sketches below shows a compound microscope not very different to those we use in the lab today.

abbe1874-refrac
The Abbe refractometer (Paselk)

After WW1 the demand for laboratory work led to an explosion in the production of microscopes and they became indispensable  to the modern lab.  However, as Abbe himself noted, the theoretical resolution of a light microscope is limited to 200nm, owing to the distance of wavelengths of light.  The usual assumptions is a wavelength size of 550nm (now where have we seen that before?!) Thus even with the improvements made in lens quality and construction, a light microscope will always be limited to that resolution and a maximum magnification of somewhere around 1000-2000 times, under the very best circumstances. In order to improve this, an illumination source that could overcome this limitation had to be sourced.

This was overcome in 1931 by Max Knoll and Ernst Ruska at the Berlin Technische Hochschule by using a beam of electrons. By the end of the decade, a resolution of 10nm had been achieved and by 1944, 2nm. This brought closer the goal of atomic resolution. Further developments included the Scanning Electron Microscope (1965) which allowed for precise three-dimensional images and opened up yet further possibilities for research.

With such high resolution, it was now possible to explore a whole new world at the cellular and molecular level, allowing research into some of the very fundamental processes of living organisms. As we have seen before, developments in technology can drive scientific research forwards at a very fast pace. The majority of content learned in IB Biology across nearly all the topics has been informed by the power of electron microscopes.

Possible Questions to think about (Note these are my own and not from any IB exams!):

Outline how technology has improved scientific research using a named example [3].

Compare and contrast the use of light and electron microscopes [4].  (This links to topic 1.2 – Understanding: • Electron microscopes have a much higher resolution than light microscopes)

 

Sources:

Palucka, Tim. “Overview of Electron Microscopy.” History of Electron Microscopy, 1931-2000, History of Recent Science and Technology, 2002, authors.library.caltech.edu/5456/1/hrst.mit.edu/hrs/materials/public/ElectronMicroscope/EM_HistOverview.htm. Accessed 27 Feb. 2017.

Paselk, Richard A. “The Evolution of the Abbé Refractometer.” The Evolution of the Abbé Refractometer, Humboldt State University , Sept. 1999, www2.humboldt.edu/scimus/Essays/EvolAbbeRef/EvolAbbeRef.htm. Accessed 27 Feb. 2017.

“Van Leeuwenhoek Microscope.” A Complete Microscope History – Who Invented the Microscope?, History of the Microscope, 2010, http://www.history-of-the-microscope.org/history-of-the-microscope-who-invented-the-microscope.php. Accessed 23 Feb. 2017.

“Who Invented the Microscope? A Complete Microscope History.” History of the Microscope, History of the Microscope, 2010, http://www.history-of-the-microscope.org/history-of-the-microscope-who-invented-the-microscope.php. Accessed 27 Feb. 2017.

3.5 Genetic modification and biotechnology

Assessing risks associated with scientific research—scientists attempt to assess the risks associated with genetically modified crops or livestock.

Genetically Modified Organisms is a great topic to encourage deeper thinking and to have students consider the impacts of science on society. There is a lot of genuine mistrust and concern with this, but there is also a lot of misinformation and misunderstanding of the science, so it makes a good topic to link to the importance of scientific literacy.

I like to use the different thinking routines created by Project Zero for Visible Thinking and have written about them before when discussing stem cells. For GMOs, we used the Circle of Viewpoints to try to understand the many perspectives on this topic.

Screen Shot 2016-08-15 at 3.18.44 PM
Circle of Viewpoints – Visible Thinking

We came up with a great range of viewpoints:

  • A concerned parent/consumer
  • An FDA spokesperson
  • A worker at Monsanto
  • A large-scale commercial farmer in the US
  • A small-scale organic farmer in the US
  • A subsistence farmer in Cambodia
  • A Greenpeace activist
  • A UN worker
  • the Pope
  • an ecologist
  • a member of the Just Label It coalition

It was a really useful exercise and the students tried to get under the skin of their characters! It helped the students identify the range of viewpoints and we were able to narrow down to some of the key concerns about the technology. To guide our discussion we focused principally on three examples of GMOs: Bt Cotton, Golden Rice and the recently approved AquaAdvantage GM Salmon. The risks we discussed included: possible health concerns/allergies; the risk of genetic contamination of wild organisms; increasing the evolution of Bt resistant pests and risks to non-target species. The role-play allowed us to balance these risks with the possible increases in yield and efficiency, nutritional benefits and less use of pesticides. The issues of labelling and the possible (emotional?) response we have to knowing that the food is GMO could provide the basis for a good TOK lesson as well. We also discussed the extensive testing that the GM salmon has been forced to undergo and that it has been nearly 20 years of research and development – at what point should we accept that something is low-risk? When do we decide that we have sufficient evidence in the natural sciences to support a conclusion?

The main challenge we found was placing a time limit on the discussion, as we could comfortably have debated this for several more lessons.

 

“Circle Of Viewpoints | Project Zero”. Pz.harvard.edu. N. p., 2016. Web. 15 Aug. 2016.

8.3 Photosynthesis

Developments in scientific research follow improvements in apparatus—sources of 14C and autoradiography enabled Calvin to elucidate the pathways of carbon fixation.

At the beginning of the 20th-century, the scientific understanding of photosynthesis was centred on the combination of Carbon Dioxide with chlorophyll to produce formaldehyde as an intermediate before being converted to a carbohydrate (Benson). This view predominated up to the discovery of radioactive Carbon-14 by Kamen and Benson in 1940 (Benson).

In 1945, C14 became readily available to researchers in the US. A young researcher in California, Melvin Calvin, was told by a senior scientist at the University of California-Berkley that he should start to do something interesting with it. So began a research focus that led to the Nobel Prize in Chemistry in 1961 “for his research on the carbon dioxide assimilation in plants” (“Melvin Calvin-Facts”).

The shape of the apparatus Calvin used led to it being called the “lollipop” experiment. The central “lollipop” contained a suspension of algae, to which was introduced the radioactive carbon.  Periodically, a sample of the algae was released into the tube below (the stick of the lollipop) where it was immediately killed by a solution of alcohol.  The compounds could then be analysed through chromatography.  By using the radioactively labelling isotope of carbon, it was possible to trace the path the isotope took and by analysing the intermediate compounds the researchers were able to determine what happened to the carbon – where was it absorbed and what was it used for? The series of experiments helped identify the sequence of carbon compounds produced in the Calvin Cycle and also disproved the idea that chlorophyl fixes carbon.

Lollipop PS
The “Lollipop” apparatus (The Bancroft Library)

These experiments were carried out be many individuals over a period of nearly 15 years and in some ways it seems unfair that Calvin tends to receive all the credit (as well as a solo Nobel Prize). A personal report by Andrew Benson (available here) gives a good idea of the collaborative nature of this process.

Sources:

Benson, A. Following the path of carbon in photosynthesis: a personal story. Photosynthesis Research. 73: 29–49, 2002. Web. April 20, 2016.

Calvin, Melvin. “The Path of Carbon in Photosynthesis.” Nobel Lectures, 1964, pp. 618–644., http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1961/calvin-lecture.pdf. Web. 30, Jan. 2018

“Calvin’s Lollipop Experiment.” The Bancroft Library, The University of Berkeley, California, bancroft.berkeley.edu/Exhibits/Biotech/Images/3-9lg.jpg. Web. Jan 30, 2018.

“Melvin Calvin – Facts”. Nobelprize.org. Nobel Media AB 2014. Web. 19 Apr 2016.

 

8.1 Metabolism

Developments in scientific research follow improvements in computing—developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways.

Bioninformatics is the “Synthesis of molecular biology and computer science that develops databases and computational tools to store, retrieve, and analyze nucleic acid and protein sequence data.” (Pierce, B) and we have encountered it already in 7.3 Translation.

In addition to genes, though, bioinformatics can screen metabolic pathways and protein structures in order to assess potential targets for new drugs. For example, the Malaria Drug Target database allows researchers to search for potential inhibitors and targets in the malarial parasite, based on protein structure and function cross-referenced with genetic sequences. Many of these potential targets are key enzymes within metabolic pathways.  Hasan et al. (2015) used a protein database to investigate the possibility of using the enzyme transketolase as a drug target.  The enzyme is important in the pentose phosphate pathway, which is part of  energy generation and nucleic acid synthesis (Hasan et al.).  Analysis using various databases and computer software allowed the researchers to identify the enzyme, determine its structure and compare it to the human version of the enzyme. The result is a promising avenue for testing drugs to control the spread of Plasmodium falciparum, the malaria parasite.

Hasan , A. et al. Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source Code for Biology and Medicine 2015. 10:7. Web .Accessed April 19, 2016.

Pierce, B. Genetics: A conceptual approach. 2nd Edition. 2005. Web. Accessed April 19, 2016.