The Best Australian Science Writing 2014 (16 page)

Planet of the vines

Antarctic ice: Going, going …

From Alzheimer's to zebrafish

Michael Lardelli

The Irish rock band U2 sang that ‘a woman needs a man like a fish needs a bicycle'. In the same way, it is perhaps initially difficult to see how a small, freshwater fish from northern India – the zebrafish – could contribute to our understanding of Alzheimer's disease. But it can.

The zebrafish has some remarkable characteristics that make it especially suitable for studying how genes work normally and in disease situations. Like humans, zebrafish are vertebrates – animals with backbones – and they share many of the same genes. The fish are small, easy to breed and can be kept in small tanks at fairly high density. This makes them relatively cheap to care for which is important when considering how best to spend precious research dollars.

For laboratory-based genetics research, it is important that an organism has a short generation time and produces large numbers of offspring. Zebrafish can produce a new generation in only three months and one female can produce tens of thousands of offspring in a lifetime. But the main advantage of zebrafish is that their embryos are transparent and develop outside the mother's body. This means that the development of living zebrafish embryos can be observed in real time. We can alter the activity of
a gene in zebrafish embryos and then observe how this changes the function of other genes and the way that the embryo develops.

* * * * *

Over 60 000 papers reporting scientific research on Alzheimer's disease have been published. However we still do not have a good understanding of why the disease occurs and what is actually happening in the brains of people with the disease.

The first thing to know about Alzheimer's disease is that it is actually a disease. It is not simply a natural consequence of old age. A change of state of the brain is definitely involved. Age is the greatest risk factor for Alzheimer's disease but it is also possible to develop the disease when young. About 1 per cent of Alzheimer's disease cases are regarded as ‘early onset' because they affect people less than 65 years of age – and sometimes people as young as their late 20s. The early onset cases are usually due to mutations passed down through families.

Mutations in three different genes can cause early onset Alzheimer's disease – the
APP
gene that codes for Amyloid Precursor Protein and two that code for Presenilin proteins,
PSEN1
and
PSEN2
. These three genes are functionally related since they produce proteins that interact within cells. Stated simply, the
PSEN1
and
PSEN2
genes produce two similar Presenilin proteins that are both able to cut the protein produced by
APP
. When the Amyloid Precursor Protein is cut it releases a small protein fragment (a peptide) known as amyloid beta or Aβ.

In brains affected by Alzheimer's disease, the Aβ peptide accumulates and can form small clumps. In the past it has been thought that the accumulation and clumping of Aβ is what drives the disease. Many researchers have regarded the Aβ peptide as toxic and pharmaceutical companies have tried to find
drugs that can reduce the amount of it in the brain. But all of the drugs tested so far have failed, and some have even made the disease worse! We now know Alzheimer's disease develops over decades and it is only when damage to the brain is severe that the symptoms such as loss of memory start to show. For this reason, researchers are now looking at testing their drugs on people who are not yet showing the disease. However a growing group of researchers now doubt that Aβ is the actual cause of Alzheimer's disease and suspect it may be just a symptom.

* * * * *

Studying Alzheimer's disease in humans is not easy since examining the brain in detail can really only be done post-mortem. In the laboratory it is possible to grow living cells from Alzheimer's disease patients in culture systems. However, the environment in which these cells find themselves is so unnatural that their behaviour (including that of their genes and proteins) tends to be abnormal. Also, it is difficult to manipulate gene and protein activity in cultured cells in anything but a very crude fashion. This is where zebrafish embryos can help.

A fertilised zebrafish egg is basically a single, huge cell visible to the naked eye. It behaves normally when alone in an aqueous medium and its patterns of gene and protein activity can be manipulated easily and subtly. For example, we can force an embryo to make various amounts of a particular protein by injecting various amounts of messenger RNA (essentially a template for protein synthesis) into a fertilised egg. As the fertilised egg subsequently divides, the embryo's cells receive the messenger RNA and translate it into protein.

One example of how we have been using zebrafish embryos to gain a greater understanding of Alzheimer's disease involves studying the effects of insufficient oxygen (also known as
hypoxia). Evidence has been accumulating for some time that hypoxia may be an important factor in Alzheimer's disease. By placing zebrafish embryos in water low in oxygen we found that the
APP
,
PSEN1
and
PSEN2
genes in the embryos were all activated, which would cause increased production of Aβ. In fact, increased production of Aβ under hypoxia appears to be a widespread phenomenon among vertebrate animals. This means that Aβ production is probably an advantageous (protective) response to lack of oxygen. So the accumulation of Aβ in the brains of people with Alzheimer's disease may be a sign that their brains are starved of oxygen and the Aβ may actually be protecting their brains from harm rather than causing the disease.

Could mutations in
APP
,
PSEN1
and
PSEN2
cause early onset Alzheimer's disease by disabling this protective mechanism? We don't know, but these small and useful fish might just help us to find out.

The CAVE artists

Massimo's genes

Joseph Jukes' epiphanies

Iain McCalman

In the spring of 1842, the British Admiralty gave orders to the naval corvette the
Fly
to survey the northern end of the Great Barrier Reef and the surrounding waters and reefs of the Torres Strait. The Admiralty wanted particular attention paid to this area because so many British vessels trading in the South Seas or with India had come to grief trying to navigate the uncharted coral reefs and the Strait's perilous narrow entrances. Joseph Beete Jukes, the ship's 31-year-old naturalist, was officially charged with investigating the geological character of the Great Barrier Reef and the structure, origins and behaviour of reef-growing corals – the first scientist ever to be specifically assigned such a task.

Naturally the Admiralty's concern was more practical than scholarly. By the 1840s it was widely recognised that corals were not inert rocks but living organisms, although little was known about the cause, extent and speed of their development. It was thought that dangerous new reefs might suddenly appear in places where previous surveys had shown nothing. The Admiralty hydrographer Francis Beaufort urged the
Fly
's captain to remember that he would be dealing with submarine obstacles ‘which lurk and ever
grow
'.

It was also expected that a geologist would offer advice on suitable sites for future harbours and settlements, and when the captain gave Jukes responsibility for producing the official journal of the voyage, the geologist stressed that he would approach the task as a down-to-earth scientist, conveying ‘plain fact' and ‘simplicity and fidelity'. He claimed he would eschew any ‘selecting for effect', or ‘heightened recollections', or ‘brilliancy, elegance, or graces of style'.

Still, in early January 1843, even this man of plain fact admitted being disappointed on his first inspection of living coral reefs. The fringing reefs off the coral cay Heron Island ‘looked simply like a half drowned mass of dirty brown sandstone, on which a few stunted corals had taken root'. Yet as soon as he broke open some coral boulders that had detached themselves from the main reef and saw their calcareous inner structure, his interest was fired. Jukes decided to throw all his powers of observation and inference into unlocking the mysteries of corals.

The first and most obvious question he needed to answer was how the calcareous fragments of sand, shells and corals had become ‘hardened into solid stone', with a regular bedding and a jointed structure like the blocks making up a rough wall. After considering a variety of hypotheses he concluded tentatively that the core structure of these blocks must have been produced inside a mass of loose sand and corals, and that the latter's calcium skeletons had dissolved to make a liquid limestone binding agent. Having then been pounded by waves, the loose exterior of the blocks must have washed away, leaving the solid inner rock exposed.

On undertaking a minute examination of a smaller coral block raised from underwater on a fishhook, Jukes made another important discovery about the character of this strange organic rock – the property that we would today call biodiversity. The surface was studded with a mosaic of tropical coral types: ‘brown,
crimson and yellow
nulliporae
, many small
actiniae
, and soft branching
corallines
, sheets of
flustra
and
eschara
, and delicate
reteporae
looking like beautiful lacework carved in ivory'. Interspersed with these were numerous species of small sponges, seaweeds, feather stars, brittle stars, and flat, round corals that he'd not seen before.

Breaking open the block, he found, honeycombed inside, several species of boring shells, bristle worms in tubes that ran in all directions, two or three species of tiny transparent marine worms twisted in the block's recesses, and three small species of crab. This single chunk of limestone rock was, he concluded, ‘a perfect museum in itself '. For the first time he allowed a note of excited wonder to creep into his observations, as he reflected on

what an inconceivable amount of animal life must be here scattered over the bottom of the sea, to say nothing of moving through its waters, and this through spaces of hundreds of miles. Every corner and crevice, every part is occupied by living beings, which, as they become more minute, increase in tenfold abundance.

Jukes summarised his conclusions for the benefit of the Admiralty planners and fellow naturalists, estimating that the Great Barrier Reef extended, with relatively few internal breaks, from Sandy Cape in the south for some 1100 miles north, to the coast of New Guinea. It was made up mainly of individual coral reefs, lying side by side in a linear form and running roughly parallel with the coastline, though at distances that varied between ten and several hundred miles. The reefs of ‘the true' Barrier rose on the outer side in a sheer wall from great depths of the ocean floor, while on the inner side lay a shallow lagoon scooped out of the coral that had grown up on a subsided landform. The outer reef sections were usually between three and 10 miles long and
around 100 yards to a mile wide. They took the form of jagged submarine mounds made up of corals and shells compacted into a soft, spongy limestone rock; this was flat and exposed near the lagoon wall's low-water mark, and higher at the windward edge where the surf broke fiercely and the reef plunged down to the ocean floor.

The sheltered lee side of the outer Barrier, where breaks – and thus passages for ships – were likely to be widest, was generally covered in living corals, but these corals could only survive to a depth of 20 or 30 fathoms because of their need for light. Jukes concluded that a coral reef was actually ‘a mass of brute matter, living only at its outer surface and chiefly on its lateral slopes'. Alongside these linked linear reefs were a few detached reefs lying just outside the Barrier, as well as a further scattering of inner reefs between the Barrier and the shore. However, at its southern beginnings near Sandy Cape and at its northern edge in the Torres Strait, the lines of reefs were not ‘true barriers' rising up from deep water, but encrustations of corals growing on shoals or underwater banks and ridges.

For the first time among European commentators, the term ‘barrier' also carried some positive connotations. Unlike Cook and Flinders and others, who'd seen the Reef solely as a terrible obstacle to navigation – something that prevented access to the shore or escape to the open sea – Jukes thought of it as a ‘bastion' that provided the Australian mainland and offshore islands with a protective shield against the massive forces of the ocean. Implicitly he was thinking about the Reef from the perspective of those who lived permanently on its coast, and who benefited from its protection. If laid out dry, he wrote, the Great Barrier Reef would resemble ‘a gigantic and irregular fortification, a steep glacis crowned with a broken parapet wall, and carried from one rising ground to another. The tower-like bastions, of projecting and detached reefs, would increase this resemblance.'