Our Changing World

Thursday 25 September 2014, with Alison Ballance, Ruth Beran & Veronika Meduna

On This Programme

Life and Death of a Cell

Beautiful diamond-shaped protein crystals that have been prepared from purified protein (left), and researchers Catherine Day and Adam Middleton in front of an electron density map

Protein crystals that have been prepared from purified protein (left), and researchers Catherine Day and Adam Middleton in front of an electron density map.

Photo: Josh Wright (left) RNZ / Alison Ballance (right)

Human beings are made up of billions of cells, and those cells need to communicate amongst themselves and also within themselves.

“We’re a big collection of millions and billions of cells, and they have to be good citizens really, and talk to their neighbours,” says Catherine Day. “And they all need to communicate, and effectively they need to know when to divide, and when to respond in a given way, for example when we’ve just eaten. They need to respond to stresses like viruses, and then sometimes they need to die. And we’re particularly interested in the dying cells. So dying is good. Every day about 60 billion cells in you and I die.”

Protein biochemist Catherine Day from the Biochemistry Department at the University of Otago studies how molecules interact and how they regulate signalling pathways. She says that a lot of diseases, such as cancer, are a case of cells not dying when they should, and that her research focuses on understanding the processes that cause cells to die.

A 3D electron density map of a protein produced after the protein crystal has been x-rayed from 360 different angles (left), and protein structures represented in a ribbon diagram.

A 3D electron density map of a protein produced after the protein crystal has been x-rayed from 360 different angles (above), and protein structures represented in a ribbon diagram (below) which shows how they link or bind to each other.

Photo: Martina Foglizzo (left) Adam Middleton (right)

Much of the communication by cells is done by proteins, which Catherine describes as the ‘machines’ of the cell. “They’re the enzymes and a lot of the signalling molecules within a cell.”

“At the heart of what we do is working out the three-dimensional molecular structure of proteins,” says Catherine. “And then that tells us a lot about the functions, how they interact and how they are folded up. Their function is strongly related to their structure.”

Catherine and her team, including post-doctoral researcher Adam Middleton, spend much of their time using x-ray crystallography to work out the structure of different proteins. They are particularly interested in a common regulatory protein called ubiquitin that is found in almost all living tissue.

They begin by concentrating protein and creating crystals, which are then examined under x-ray. They are x-rayed from 360 different angles which creates a 3D electron density map that allows the researchers to see how different proteins bind to one another. The end result of their work is a simple ribbon diagram which illustrates the structure and linkages of different proteins.

This work helps in understanding what happens with diseases such as cancer at a cellular level, and provides a base from which to develop anti-cancer drugs.

“If we want to disrupt a particular interaction between proteins, then by understanding how they bind then you can think about ways to design molecules to block that interaction,” says Catherine.

Catherine Day is talking on 'The life and death of a cell' in Nelson on Tuesday 30 September. her talk is part of the Royal Society of New Zealand's Ten By Ten lecture series being held to celebrate 20 years of Marsden-funded research.


Meet the Tyrannosaur Family

by Veronika Meduna Veronika.Meduna@radionz.co.nz

There was a whole diversity of of tyrannosaurs, and T. rex was just the end product of a hundred million years of evolution.  _ Alan Tennyson

Te Papa curator Alan Tennyson with the skulls of several tyrannosaurs.

Te Papa curator Alan Tennyson with the skulls of several tyrannosaurs.

Photo: RNZ / Veronika Meduna

Tyrannosaurus rex is undoubtedly the most famous member of a group of carnivorous theropod, or "beast"-footed, dinosaurs that lived during the Jurassic. But the evolutionary origins of the tyrannosaur family began some 160 million years ago, spanned several continents and included many small, feathered creatures that look only vaguely related to the finely-tuned killing machine Steven Spielberg portrayed in Jurassic Park.

Tyrannosaurs: Meet the Family, an exhibition that opens at Te Papa Tongarewa this weekend, traces the evolutionary development from smaller, feathered varieties discovered in China to the mighty T. rex, which disappeared along with all large dinosaurs about 65 millions years ago.

The small and feathered Dilong paradoxus

The small and feathered tyrannosaur Dilong paradoxus

Photo: Wikimedia Commons

The earliest tyrannosaurs were tiny, such as the cat-sized Dilong paradoxus with its unusual skull crest or the oldest tyrannosaur Guanlong wucaii. Some recently discovered specimens were found covered in proto feathers, providing evidence that at least some tyrannosaurs had a fluffy coat of down.

Te Papa curator Alan Tennyson says the feathers were useless for flying but have strengthened the evolutionary link between dinosaurs and birds. "“When I was a little kid, noone realised that dinosaurs had feathers at all. There was a link made between Archaeopteryx, the earliest bird, and dinosaurs. But then about 20 years or so ago a lot of dinosaurs with feathers started to be discovered and the link between dinosaurs and birds became even more obvious. Now we know that a lot of dinosaurs had feathers."

The use of feathers for flight was a mere byproduct of evolution, he says, and the primary function was most likley to provide warmth, suggesting that the smaller tyrannosaurs were active and warm-blooded, rather than cold-blooded like modern reptiles. One of the groups of theropods, the microraptors, are now thought to be the ancestors of modern birds.

‘Today we refer to birds as avian dinosaurs, and all the other ones that we traditionally think of as dinosaurs, as non-avian dinosaurs.'

Another feature of early tyrannosaurs is that they had much longer and stronger arms with three fingers. Alan Tennyson says the reason for T. rex's puny arms had a lot to do with balance. "There is one theory, and that is that because of the size of the large tyrannosaurs ... they couldn’t have too much weight at the front of their body, especially with their large heads."

Tyrannosaurs are known only from the Northern Hemisphere, with T. rex in north America and his similarly large cousin Tarbosaurus bataar in central Asia. This exhibition, which was originally designed by the Australian Museum, has been adjusted to include the discoveries, mostly by "dinosaur lady" Joan Wiffen, of large terrestrial dinosaurs in New Zealand.

Here you can listen to our earlier stories about Joan Wiffen's legacy and my own dinosaur hunt with a team of palaeontologists from GNS Science.

Joan Wiffen and her Dinosaurs ( 15 min 24 sec )

Dinosaur Fossils ( 13 min 17 sec )

Recently, science writer and editor of the Australian Geographic John Pickrell has delved into the latest discoveries of feathered dinosaurs in his book Flying Dinosaurs: how fearsome reptiles became birds, and you can listen to his interview with Nine to Noon here. 

John Pickerell - Are birds really dinosaurs? ( 23 min 43 sec )

 


Great Kereru Count

During the breeding season, kereru make spectacular display dives high above the forest canopy (left photo). Kereru were once commonly seen in very large flocks, but such flocks are a rare sight these days (right photo).

During the breeding season, kereru make spectacular display dives high above the forest canopy (left). Kereru were once commonly seen in very large flocks, but such flocks are a much rarer sight these days.

Photo: Tony Stoddard / Kereru Discovery

A citizen science project to count kereru, or New Zealand native wood pigeons, has just kicked off, and over the next two weeks organisers are hoping people from around the country will count kereru in their garden, local park or nearby park. The Great Kereru Count runs from 22 September until midday on 5 October, and builds on two previous counts carried out by the Kiwi Conservation Club, the junior naturalist club run by conservation organisation Forest and Bird.

“We are asking everyone in New Zealand to go out and spend at least 5 minutes looking for kereru,” says event organiser and Kiwi Conservation Club Manager, Tiff Stewart. “And then hop online and tell us how many kereru you saw.”

“The kereru is an incredibly important bird - it plays a crucial role in seed dispersal,” says Tiff. “It is the only bird that can swallow large berries like tawa, puriri, miro and karaka, so it plays a key role in regenerating our broadleaf forests.

Kereru or New Zealand native pigeon sitting in a tree showing its highly visible white chest.

Kereru or New Zealand native pigeon.

Photo: Tony Stoddard / Kereru Discovery

Tiff Stewart says the event will help build a detailed picture of kereru distribution across the country, and the information collected will be shared with scientists, local bodies and community groups. The count is a collaboration between the Kiwi Conservation Club and Kereru Discovery, which is based in Wellington and is a collaboration between WWF-NZ and the Wellington City Council.

Alison Ballance joined Tiff Stewart and the pupils from Room 2 at Tainui School in Dunedin to carry out two five-minute counts in the school grounds, and even though no kereru were seen Tiff says this is still a significant result. She says that it’s important that people record if they don’t see any kereru, as zero counts will identify where kereru are absent or in very low numbers.

To report your sighings visit kererucount.org.nz  or download the free Kereru Count app, so you can report your sightings via mobile phone or tablet on the spot.

Research on urban kereru in Wellington featured in a previous Our Changing World story.

Kereru in Wellington ( 12 min 41 sec )

GREAT KERERU COUNT AUDIO


The Spine and Slipped Discs

The bones of the spine are joined together by little flexible discs which are tough and strong but also flexible. However, if something goes wrong with the discs, it can cause incredible back and lower limb pain.

Professor Neil Broom and his team from the University of Auckland’s Chemical and Materials Engineering department are looking at these discs to better understand their structure and how they interact with the vertebra.

A picture of a skeleton, with the lumbar region of the spine (the five lower vertebrae) highlighted in red

A skeleton, with the lumbar region of the spine (the five lower vertebrae) highlighted in red

Photo: Anatomography (CC BY-SA 2.1 JP)

In particular, he’s looking at discs in the lumbar region of the spine, which consists of the lower five vertebrae.

“You have to think of the disc as a kind of squat cylinder with a very strong wall made up of multiple layers,” says Neil. “The internal part is what we call the nucleus, and that looks like a soft jelly. And then round the outside, containing that, is the annulus, which is the really strong part.”

The experiments conducted in the lab are on tissue taken from sheep and when Ruth Beran visited, she discovered that the annulus feels quite solid and fibrous, and looks like tree rings, while the nucleus feels somewhat slimy. Both are white in colour.

PhD student Samantha Rodrigues is looking at how these annular fibres anchor to the bone and the end plate, a transitional region between the disc and vertebra.

“It is a mechanically complex junction,” says Samantha. “You have this change from soft to hard which means that if you’re trying to do anything with the disc it is possible that it can break just because you have that change in properties.”

On the other hand, research fellow Kelly Wade is looking at the disc nucleus.

“When I started, the nucleus was thought of as like this gel. But it’s quite a lot firmer than that.” Kelly Wade

Acccording to Neil, Kelly’s work has shown that the nucleus has a definite structure. “The nucleus is definitely not just a passenger in the disc, it’s there definitely attached to the vertebra,” says Neil.

And because the nucleus has a lot of fluid in it, it gives the disc a lot of resilience under compression .

Given the structural knowledge of spinal discs, Neil and his team are now moving into loading the disc in various postures to see when it is most vulnerable to failure.

A picture of Neil Broom, Kelly Wade and Samantha Rodrigues with a model of a human spine

From left to right: Neil Broom, Kelly Wade and Samantha Rodrigues with a model of a human spine

Photo: RNZ / Ruth Beran

These experiments have shown that flexion (or bending forward) is an issue when loaded and can lead to disc extrusion, and “damage of the nerve fibres, irritation within that region and leading to basically low back pain and certainly lower limb radiating pain which can be extremely distressing,” says Neil.

While it’s difficult to translate laboratory work directly into real-life recommendations, Neil says: “certainly this is warning us, I think, that flexion is potentially dangerous when you overload, and that loading doesn’t necessarily have to be traumatic."

“And if it’s overloading and flexion over a significant period of time, where you’ve got repeated loading, this can lead potentially to problems that cause disc destruction or disc damage,” says Neil.


Coming Up - Thursday 2 October

We’re at New Zealand IceFest, an Antarctic celebration in Christchurch, which runs until the 12th of October, we’re off to some road works to find out about the science of geodesy, and then we’re in the Water Lab seeing how waves move sediment along the Canterbury coast.