Phylogenetic structural scaling of the appendicular skeleton: relationship with loading regime and locomotor behaviour

Lead Research Organisation: Royal Veterinary College
Department Name: Comparative Biomedical Sciences CBS

Abstract

Scaling studies examine how structures change in response to increasing animal size. Most previous scaling studies have characterized bone shape with length and midshaft diameter and quantified loading on the bone with the mass of the animal. In this interdisciplinary study we will integrate engineering analyses, including image analysis, detailed mechanics, kinematics measurements and statistical shape modelling to determine how bones change across a range of species and sizes. We will investigate 5 species from each of the following clades: bipedal birds, mammalian carnivores (cats, dogs, wolves, lions), Macropodoidea (kangaroos, wallabies), bovine artiodactyls (hoofed mammals), and catarrhine primates (terrestrial monkeys). We will use computer tomography images, similar to 3D x-rays, to determine the structural characteristics of the bone that affect the bone's mechanical properties and its ability to withstand load. We will measure the locomotor behaviour of each animal using a multi-camera motion analysis system and force plates. This will allow us to determine joint angles, ground contact forces, limb positions, and stride characteristics that are integral components of locomotor behaviour and hence bone loading regimes. Using a range of statistical techniques we will determine the relationship between bone structure and the locomotor behaviour. The shapes of some irregularly-shaped bones, such as the scapula and pelvis, are difficult to quantify. Unlike long bones where structural measures, such as cross-sectional area, are simple to determine, irregular bones have no obvious dimensions to measure. Statistical shape modelling overcomes this difficulty by creating a virtual model of the bone and comparing its shape to an average bone. The technique considers all variability and highlights were the most variability in shape occurs. These statistical shape models can be used to predict the shape of the corresponding bone in a joint. This technique would prove extremely useful for palaeontologists who often have incomplete skeletons and must predict the shapes of missing bones. It will also show how closely the shapes of articulating bones are linked via their interrelated loading regimes. Bone is made up of tiny spicules called trabeculae. The size and orientation of the trabeculae are influenced by the loading on the bone. Few studies have examined how the trabecular structure varies across species. We will obtain trabecular bone samples from each species and image them using microCT, which has a resolution up to 5 micrometers. We will obtain standard 3D measures of the trabecular structure, such as trabecular thickness and orientation. Trabecular structural measures will be correlated with locomotor parameters in order to determine how the loading, size, and locomotor behaviour influences bone micro-structure. Our study will also take research on musculoskeletal scaling into a new, extremely integrative direction. We have designed a study that (1) examines all bones in the appendicular skeleton at multiple structural levels, (2) uses a wide range of taxa and sizes, (3) applies a mechanistic approach to understanding bone structure and locomotor behaviour, and (4) employs rigorous statistical techniques to determine relationships between structure and function.

Technical Summary

Scaling studies examine how structures change size and shape across species with a range of masses. By adding detailed mechanical analysis of bone structure and gait, we hypothesize that a better understanding of the relationship between bone shape and function will be obtained. We will examine the structural and locomotor characteristics of 5 species in each of 5 clades: bipedal birds, Carnivora, Macropodoidea, bovine artiodactyls, and catarrhine primates. We will measure the macro and micro-structure of the bones using CT and micro-CT imaging, respectively. From the images we will construct 3D models of the bones in order to determine macro-structural properties (such as second moment of area) and micro-structural properties (such as trabecular thickness and orientation). We will characterize locomotor behaviour using a multi-camera motion analysis system and force plates to obtain measures of joint angles during gait, ground reaction forces, speed, and stride length. From these measures we will calculate the joint forces and moments, a first approximation of the loading on the bone during gait. To obtain locomotor data for each study animal, we will use previous studies that have extensively studied gait as well as collect our own data at local zoos and wild animal parks. We will additionally measure variability in complex bones such as the pelvis and scapula using statistical shape modelling, which indicate the major modes in shape variability. We will use these models in canonical correlation analysis to determine if bone shape can be predicted across a joint. We will employ advanced statistical techniques to determine how bone structural parameters are related to locomotor behaviour. Our study will take research on musculoskeletal scaling into a new, extremely integrative interdisciplinary direction, by employing detailed rigorous mechanistic analysis to understand locomotor behaviour influences bone shape across species.
 
Description Our project examined scaling across species, including bone structure and locomotor habits. We developed novel techniques in both arenas (analyzing bone structure and quantifying gait patterns) and have also developed a new open-source software platform for analysis of images (boneJ.org). Prior to this project, the majority of scaling studies examined a limited number of variables (mass, length of the bone, and diameter of the bone at mid-shaft), which provide a limited indication of bone mechanics.



Our novel analysis methods of bone structure included 3-dimensional morphology along the entire length of the bone. This revealed that the scaling at the mid-shaft is different than scaling at the ends of bones around the joints. We have analyzed four clades of animals and revealed differences in scaling trends across clades.



Gait analysis was performed in zoos and wild animal parks with marker and markerless systems with a force plate(s) in the ground to record ground reaction forces. Analysis of the kinetics (forces) during animal locomotion is particularly novel across such a wide range of species (28 species, walking and running gaits for multiple individuals). We have developed our own code on a Matlab platform for obtaining joint angles and joint moments from 2D or 3D data.. We will be sharing this code with others in the community once our initial publications are accepted.



The most wide-spread impact of our research has been in the development of BoneJ, an open source plug-in for the imageJ platform that automatically analyzes image data for standard parameters. It was developed because of our frustration with commercial software and is intended to analyze the cross sectional properties of bones from computer tomography images. However, one year after its release, we realize the user group is incredibly diverse ranging from morphology of marine coral to design of nuclear reactors. The adoption of boneJ across many disciplines has happened for a number of reasons: 1) it is free; 2) it is open source so users can see how all calculations are made, 3) it is extendable and allows for other features to be easily added, and 4) we have developed a incredibly responsive user group culture, fostered primarily by the support given by Michael Doube, the PDRA on the grant at Imperial.



These contributions have established a new standard in scaling research, pushing the boundaries of traditional scaling studies to exploit current technical and computing methods, and have assembled a staggeringly large database of bone images and experimental data on locomotion.
Exploitation Route BoneJ software is open source and has been put to broad usage by >8000 others already--
http://bonej.org/
and
https://groups.google.com/forum/#!forum/bonej-users-and-developers
and
http://forum.imagej.net/tags/bonej
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://bonej.org/
 
Description Our bone scaling work has led to a new industry collaboration with F+P (architecture firm), with PhD student starting 1 October 2014. Applying principles of bone biology to architectural design paradigms. BoneJ project which arose from this project was consulted on by Software Sustainability Institute through their 'Open Call for Projects', to enhance its durability and reliability as a community-based scientific software resource. (Successful application to Wellcome Trust for further development of the resource by Michael Doube; former postdoc on project). Further detail on the outputs from this project was provided in a public BBSRC case study of impacts "Open source bone biology software benefits industry and academia", at http://www.bbsrc.ac.uk/news/impact/open-source-bone-biology-software/
First Year Of Impact 2010
Sector Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Manufacturing, including Industrial Biotechology,Other
Impact Types Economic,Policy & public services

 
Description Biomedical resource and technology development grant
Amount £160,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2015 
End 10/2018
 
Description Research Grant (co-I)
Amount £226,493 (GBP)
Funding ID RPG-2013-124 
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2014 
End 09/2016
 
Description Research Grant (co-I)
Amount £192,009 (GBP)
Funding ID RPG-2014-350 
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2015 
End 05/2018
 
Title BoneJ software 
Description bone measuring software for ImageJ; open source-- details www.bonej.org 
Type Of Material Improvements to research infrastructure 
Year Produced 2010 
Provided To Others? Yes  
Impact >8000 users and numerous follow-on studies; >335citations to main Doube et al. paper in Bone since 2010-BoneJ is getting used a lot, cited about 2-3 times per week: https://scholar.google.com/citations?view_op=view_citation&hl=en&user=WsrNo_MAAAAJ&citation_for_view=WsrNo_MAAAAJ:2osOgNQ5qMEC Collaborator (and former BBSRC postdoc) Dr Michael Doube at RVC received a Wellcome Trust grant (£160k) for 3 years' Research Software Engineer effort to turn BoneJ into BoneJ2 software, leveraging ImageJ2's new technologies and engineering the code properly with more tests, more modularity and more reusability. Richard Domander, a Finnish software engineer, joined Doube's group at RVC in October 2015 (he's currently in Madison, Wisconsin getting trained up by the ImageJ2 core team). http://www.wellcome.ac.uk/Funding/Biomedical-science/Funding-schemes/Biomedical-resource-and-technology-development-grants/index.htm for the funding scheme for that Wellcome award. 
URL http://www.bonej.org
 
Description New collaboration with Anjali Goswami (UCL) 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution co-I role on grant: co-supervising PhD student Marcela Randau (UCL) and postdoc Andrew Cuff (UCL-RVC).
Collaborator Contribution PI role on grant.
Impact Leverhulme project grant (as co-I; with Anjali Goswami, UCL) "Walking the cat back" £226,493; 2014-2017.
Start Year 2014
 
Description New collaborations with Andrew Pitsillides (RVC) - and Alan Boyde (QMUL) 
Organisation Royal Veterinary College (RVC)
Country United Kingdom 
Sector Academic/University 
PI Contribution New collaborations with RVC and Queen Mary Univ. London on 2011 Science paper, to conduct elephant foot bone imaging and histology; ongoing.
Start Year 2011
 
Description Paid consultant on cat anatomy: Weta Digital (filmmaker) 
Organisation Weta Digital
Country New Zealand 
Sector Private 
PI Contribution Provided CT scan data for cat species for use in major motion picture production, creation of digital character(s).
Collaborator Contribution £500 contribution to our research funds in return for this assistance with CT data.
Impact enhanced CGI character in Weta Digital film
Start Year 2012
 
Title BoneJ software 
Description bone measurement software 
Type Of Technology Software 
Year Produced 2010 
Open Source License? Yes  
Impact >8000 users and >160 citations of original paper by Doube et al in Bone; widely used methodology. 
URL http://www.bonej.org
 
Description BBC TV appearance 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact PI Hutchinson was a featured consultant on this BBC TV documentary, shown studying how elephants move (BBSRC funded research work) and how this relates to interpreting fossil organisms (NERC funded research work). The programme was a massive success internationally (reportedly breaking BBC documentary records), with millions of viewers (8.5M in the UK on the first night alone) and ongoing discussions as well as likely lead-ins to future documentary programme involvement by Hutchinson's team.
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/programmes/p03dwy5z
 
Description BBSRC Impact Summary released 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact BBSRC worked with our team to release a 3-page report (pdf below) on the impact of our project, as a public example of the broader applications of the research that it is funding.
Year(s) Of Engagement Activity 2016
URL http://www.bbsrc.ac.uk/documents/1701-bone-biology-software-pdf/
 
Description Charles Darwin BSF award lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The lecture theatre was fully booked (250 attendees) for the highly interactive presentation (incorporating the Be The Dinosaur simulation), with many visitors staying on to ask questions and examine specimens, plus subsequent discussion via Twitter.

All feedback responses rated the event 'good' or 'excellent, with a good level of understanding regarding overall research results
Year(s) Of Engagement Activity 2012
URL http://www.britishscienceassociation.org/sites/default/files/root/festival/BSFprog12%20lr%202.pdf
 
Description Misc. TV documentary involvement 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Prof. Hutchinson's research was featured in the 2011 "Dino Gangs" documentary on the Discovery Channel, which aired worldwide, with the work on theropod growth and speed also referenced in the accompanying book. Other programmes covering the team's work include "Evolutions" (National Geographic, 2008), "Raw Anatomy" (National Geographic Channel, 2009) and 'How to build a Dinosaur" (BBC4, 2011), featuring our NERC-funded research.

Very broad viewership and more informed, entertained public. More requests for documentary involvement- Prof. Hutchinson is now contacted several times a month with TV documentary requests/advice.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012,2013,2014
 
Description NatGeo TV appearance: giant rhinoceroses 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Featured appearance in "Top 10 Biggest Beasts Ever" documentary on NatGeo TV, focusing on interpreting the anatomy and behaviour of giant extinct rhinoceroses (relevant to NERC and BBSRC grant research).
Year(s) Of Engagement Activity 2015
URL http://natgeotv.com/uk/top-10-biggest-beasts-ever
 
Description RVC Open Day bones demonstration 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact RVC Hawkshead campus open day event, where our research team presented a publically accessible stand showing different kinds of animal bones and how these relate to biomechanics, behaviour, welfare, evolution and other topics of general interest as well as direct connection to our BBSRC- and NERC-funded research. Visitors were streaming through the stand (hosted by 5 postgrad researchers) for >6 hours and had many interactions with those hosting the stands to answer their questions about relevant topics and about our research.
Year(s) Of Engagement Activity 2015
 
Description Royal College of Veterinary Surgeons, Share Jones Lecture in Veterinary Anatomy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact An audience of about 100 listened to the latest research results from Dr. Hutchinson's team, which stimulated questions and discussion afterwards.

Further invitations for speaking engagements by Prof. Hutchinson have stemmed from this.
Year(s) Of Engagement Activity 2011
URL http://www.rcvs.org.uk/news-and-events/news/share-jones-lecture-2011-big-and-nimble/
 
Description Science Blog 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Anatomy blog: sharing the latest scientific research and insights from Prof. Hutchinson's team, with a strong focus on RCUK-funded research. Highly visual and stimulating discussion. As of submission in 2016, total 354,000 views, 3239 followers, 1855 comments, 161 posts.

255,944 all-time views (average 250/day) as of 14/10/2014; 1,529 comments, 750 Subscribers, 642 shares; with additional viewers (53,412) and subscribers (92) at associated Youtube Channel: https://www.youtube.com/user/Whatsinjohnsfreezer
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
URL http://whatsinjohnsfreezer.com/
 
Description Twitter: Science Communication 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Persistent, daily public engagement by Prof. Hutchinson on his personal account, which regularly addresses scientific research that his team is conducting, including RCUK-funded research. Averages ~250,000 impressions/month; as of submission in 2016 is 27,500 tweets total, 4778 followers, 1652 photos and videos.

>19,000 tweets, >3,000 followers, Klout score ~63 as of 14 October 2014-- indicates strong engagement in science communication. Twitter Analytics indicate 224.9K impressions (views) and thousands of engagements (clicks, favourites, retweets, replies etc.) during a representative month.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
URL https://twitter.com/JohnRHutchinson