Plate 1: Airways, arteries and veins of the fowl lung. Credit: John Ndegwa Maina

Birds are extremely important animals. As predators, pollinators, seed dispersers, scavengers and ecosystem bio-engineers, the world’s 11,000 bird species play critical roles in the food chain and therefore the existence of animal life.

They have also shaped the progress of human societies in the cultural, philosophical, artistic, economic and scientific fields. Birds feature prominently in the history of painting, poetry, commerce and music.

Because they can easily escape from unsuitable habitats, birds are important “guard animals”: the number and diversity of species indicate environmental health. BirdLife International’s State of the World’s Birds Report for 2022 says about half of all bird species are in decline and more than one in eight of them are in danger of extinction.

Knowledge of the biology of birds and their place in ecosystems aids in devising conservation efforts. Biology explains why animals behave the way they do and what threatens their survival.

One of the aspects of bird biology that has long interested scientists is their lungs. They are structurally very complex and functionally efficient. Birds can fly with their lungs. Flying takes an enormous amount of energy and some birds fly non-stop over very long distances or at very high altitudes where there is little oxygen.

Even after extensive research, there are still questions about the bioengineering of the respiratory system of birds. They relate to how the airways and blood vessels are formed, arranged and connected, and how air flows around the lung.

To investigate these aspects of the bird’s lung, my colleagues and I used a variety of techniques. Three-dimensional (3D) computer reconstruction with serial sections is one of them.

Using this technique showed us that the tiny structures (air and blood capillaries) between which oxygen is exchanged are not in the shape they long thought they were. Because they are so small and so closely intertwined, it wasn’t possible to see their shapes and connections clearly until we used 3D reconstruction. We were then able to see why the bird’s lung is so efficient at taking in the oxygen needed to release energy – the key to survival.

Plate II. Air capillaries (top) and blood capillaries (bottom). Credit: John N Maina

the approach

For hundreds of years, scientists could only study biological structures in two dimensions: tissue sections were placed under a transmission microscope. In the late 1970s, the South African-born Nobel laureate Sydney Brenner was the first to use computing to reconstruct sequences of sections. More recently, 3D reconstruction methodologies have revolutionized several areas of biology.

3D reconstruction showed us that the airways and blood vessels follow each other and supply specific parts of the bird’s lung. The different branches of the airway system are not connected to each other, and neither are the branches of the blood system. We got a much clearer picture of the shapes and connections of the air capillaries and blood capillaries in the lungs. The compact entanglement of the capillaries increases the respiratory surface area while minimizing the thickness of the blood-gas barrier.

The design of the bird’s lungs forms a highly efficient gas exchange system with a large functional reserve. The lungs are continuously ventilated in one direction (back to front) with “fresh” air through coordinated actions of the very large air sacs. During each breathing cycle, the air in the lungs is replaced with “clean” air. This maintains a high pressure that circulates oxygen in the blood circulating through the lungs. It gives birds their flying power.

Our reconstruction of the serial 3D section provided new details and underlined the value of the technique for investigating complex biological structures.

3D reconstruction

3D reconstruction involves preparing a spatial model of a structure from 2D images. Because it takes time, a lot of material and specialized skills, it is not often used in biological studies.

We used the method on a chicken lung because it is the model animal for studying bird biology.

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Plate IV. Compare images. Credit: John N Maina

We cut 2,689 serial sections from a chicken lung with a thickness of 8 micrometers (each micrometer is one millionth of a meter). We stained and mounted them on glass slides, photographed sections and aligned the images for reconstruction using open-source software.

There are other modern 3D reconstruction methods that are faster, cheaper and easier to use. But 3D histological reconstruction of serial sections (constructing an image from thin slices of tissue) remains a very important technique. The reconstructions have better contrast and a better signal-to-noise ratio (there is less unwanted information). Dyes and markers can also be used to improve the identification of structures.

Bird lung capillaries

The process showed us that the bird’s lung’s extremely small terminal respiratory units — long called “air capillaries” — aren’t like that: they’re rather round structures, interconnected by very narrow passageways.

In addition, the “blood capillaries” are not “true” capillaries like those found in most other tissues and organs that are much longer than they are wide. They consist of clearly separated parts that are about as long as they are wide and connected together in 3D. The air and blood capillaries of the bird’s lung intertwine very closely in a “honeycomb” arrangement.

Knowing the shape and size of these units provides information about the efficiency of the bird’s lung gas exchange, a flow-through system.

More to come

As more efficient ways to apply 3D reconstruction technology are developed, 3D imaging and animation will become an essential research tool in a biologist’s toolbox. It will be possible to fully conceptualize the shapes of structural components and thus provide a better understanding of how they work.

Vital insights into the biology of animals, including birds, will enable us to formulate more effective measures to ensure their conservation in the face of the challenges of global warming and environmental pollution.


Half of the world birds in decline, species that are dying out ‘faster and faster’


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