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.

11.3 The Kidney and Osmoregulation

Curiosity about particular phenomena—investigations were carried out to determine how desert animals prevent water loss in their wastes.

Water, water, every where,
And all the boards did shrink;
Water, water, every where,
Nor any drop to drink.
The Rime of the Ancient Mariner

As a zoology major at university, I spent many hours pouring over Knut Schmidt-Nielsen’s classic text, Animal Physiology. He was  widely regarded as the father of comparative physiology and made groundbreaking contributions to the discipline of  Ecophysiology, the study of how animal physiology is adapted to the environment. A group of animals that came in for particular notice in many of his studies were the desert rats (Dipodomys sp.).

dipomerr
Merriam’s Kangaroo Rat (Dipodomys merriami) (Dr. Lloyd Glenn Ingles, 1999)

These rats eat only dry food, principally seeds, yet almost never drink water, even if it is available. Their habitat, the deserts of SW North America, see little rainfall and baking temperatures. How is this possible?

Firstly, a primer on water balance (adapted from Schmidt-Nielsen, 1962). Animals gain water through either drinking free water, water in their food and the water produced from the oxidation of glucose in respiration (metabolic water). Water is lost from the body by evaporation from the skin and lungs, in urine and in feces.  In order to survive without drinking water and on a dry-food diet, these animals must therefore minimise their water loss. As this topic is linked to 11.3 (Osmoregulation) we will focus on their kidney adaptations.

We learn when studying topic 11.3 that the Loop of Henle is crucial in allowing the development of a urine that is hyperosmotic to the blood plasma. Desert rats have a proportionally very long Loop of Henle and a thicker medulla, which allows for the establishment of even more concentrated urine.  Additionally, as a small animal, their high metabolic rates mean they have more densely packed mitochondria and transport pumps throughout the nephron, allowing the maintenance of a concentration gradient.

The result is that various species of desert rats can excrete a urine that is up to 16 times the concentration of their blood plasma and over four times more concentrated than seawater!

screen-shot-2017-02-09-at-12-17-53-pm
adapted from Willmer et al. 2011

With a greater amount of solute in the urine, proportionally less water is needed to excrete it. These rodents also take it a step further by producing very dry, pellet-like feces.  They also ingest their feces to reabsorb what little water is in them.  They are therefore able to survive only by using metabolic water and the water in their food – a useful adaptation for the desert.

But the curiosity doesn’t end there!  Schmidt-Nielsen wanted to know if they could survive on drinking seawater.  Seawater has a concentration of between 1000-1200 mOsm/L. If a human drank 1 litre of seawater, they would need 2 litres of urine to flush out the excess sodium chloride, thus leading to dehydration very quickly.  But given the ability of the desert rat kidney’s to concentrate the urine, he reasoned that they should be able to do it.

Firstly, to induce thirst, he fed the rats on a diet of soybeans. These are high in protein and produce a lot of urea that needs to be removed.  Normally, the rats don’t drink water so they need to be induced to do this; the high protein diet accomplishes this. He then provided different groups of rats seawater, freshwater and no water. The results are displayed below:

screen-shot-2017-02-09-at-12-58-42-pm
The results of providing sea water to desert rats (Schmidt-Nielsen 1962).

Amazingly, the rats provided with sea water showed no change in body weight after 2 weeks, almost exactly the same as those provided with fresh water.  Proof of the tremendous concentrating power of their kidneys, and more specifically, their loops of Henle.

And remember, should you ever be stuck on a becalmed ship or wrecked on a desert island, don’t drink the water!

Sources

Coleridge, Samuel Taylor. “The Rime of the Ancient Mariner .” Poetry Foundation, Poetry Foundation, http://www.poetryfoundation.org/poems-and-poets/poems/detail/43997.

Ingles, Dr. Lloyd Glenn. “Merriam’s Kangaroo Rat (Dipodomys merriami)”  University of Texas, El Paso. museum2.utep.edu/chih/theland/animals/mammals/dipomerr.htm, 1999. Web. 9 Feb. 2017.

Schmidt-Nielsen, Knut. “Comparative Physiology of Desert Mammals.” Agricultural Experimental Station, vol. 21, Dec. 1962, animalsciences.missouri.edu/research/bec/Brody%20Memorial%20Lectures%201/Lecture%202%20Knut%20Schmidt-Nielsen.pdf.

Willmer, Pat, et al. Environmental Physiology of Animals. 2nd ed., Malden, Mass., Blackwell Publ., 2011.

6.1 Digestion and Absorption

Use models as representations of the real world—dialysis tubing can be used to model absorption in the intestine. (1.10)

Models are an essential part of the scientific method and have been discussed in our biology syllabus in topics ranging from Neural Development, the human brain, DNA structure and membranes.

Models allow scientists to represent an idea that is difficult, or impossible to experience directly. By their nature they are simplifications of the real world processes they describe, but they are still extremely useful as a means of explaining processes, making predictions, testing hypotheses and analysing data. Think of the importance of models of climate change or fisheries populations – these models have direct impacts on economics, politics and society.

In 6.1 we are discussing the use of models in the digestive system.  A classic middle-school demonstration is to use visking, or dialysis, tubing to demonstrate the workings of the digestive system.  An example experiment using starch, iodine and Benedict’s solution shows how this might work. The inside of the model gut originally contains both starch and glucose. However, testing over time shows that after 15 minutes, the gut still contains starch, however the liquid outside the “gut” tests positive for glucose.  The movement of glucose out of the gut and into the surrounding fluid, while the larger starch molecules stay behind, helps demonstrate the need to reduce the size of polysaccharides before they can be absorbed and used by the body.

It would be useful to review the different NOS statements on models and develop some common ideas about the use of models in biology.  Turn each statement into a question using an appropriate command term and try to develop some short-answers. For example:

  1. NOS statement for 6.1 – Use models as representations of the real world—dialysis tubing can be used to model absorption in the intestine.
  2. This becomes: Outline how dialysis tubing can be used to model absorption in the intestine (3).

Sources:

“Evaluating Visking Tubing As A Model For A Gut | Nuffield Foundation”. Nuffieldfoundation.org. N. p., 2016. Web. 11 Dec. 2016.

“Scientific Modelling “. Sciencelearning Hub. The University of Waikato. 2016. Web. 9 Dec. 2016.

2.1 Molecules to Metabolism

Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.

A popular theory during the 18th and 19th centuries, though it can be traced back to the ancient Greeks, was the idea of Vitalism.  Vitalism states that:

…living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things. (Bechtel and Richardson)

It was particularly associated with the idea of a vital force that provided the “spark” of life separating the living from the non-living.

In 1828, the German chemist Friedrich Wöhler synthesised organic urea from inorganic cyanic acid and ammonium. Although it is now doubted that Wöhler expressly set out to falsify vitalism, his results nevertheless showed that organic molecules can be produced without the need for a non-specific “force” – providing an important milestone in understanding quantitative chemistry, isomerism and biochemistry.

As a scientific theory, Vitalism fails on two principal fronts: it offers no predictive value and there are no tests or experiments which could be used to demonstrate its existence or function.

References

Bechtel, W. and Richardson, R. Vitalism. mechanism.ucsd.edu. 1998. Web. May 24, 2016.

Kinne-Saffran and Kinne R.K.H. Vitalism and Synthesis of Urea: From Friedrich Wöhler to Hans A. Krebs. Am J Nephrol 1999; 19:290–294.