173 Works

Different genes are recruited during convergent evolution of pregnancy and the placenta

Charles Foster, James Van Dyke, Michael Thompson, Nicholas Smith, Colin Simpfendorfer, Christopher Murphy & Camilla Whittington
The repeated evolution of the same traits in distantly related groups (convergent evolution) raises a key question in evolutionary biology: do the same genes underpin convergent phenotypes? Here, we explore one such trait, viviparity (live birth), which, qualitative studies suggest, may indeed have evolved via genetic convergence. There are 150 independent origins of live birth in vertebrates, providing a uniquely powerful system to test the mechanisms underpinning convergence in morphology, physiology, and/or gene recruitment during...

Caecal dysfunction and neuro-immune alterations in a preclinical model of autism

Chalystha Yie Qin Lee, Gayathri K Balasuriya, Madushani Herath, Ashley Franks & Elisa Hill-Yardin
Autism Spectrum Disorder (ASD; autism) is commonly presented with gastrointestinal (GI) illness in addition to core diagnostic behavioural traits. Important for GI homeostasis is the appendix, or the caecum in mice, which functions as a key site for fermentation and a microbial reservoir. Even so, the role of the appendix and caecum in autism-associated GI symptoms remains uninvestigated. Here, we studied mice with an autism-associated missense mutation in the post-synaptic protein neuroligin-3 (NL3R451C), which impacts...

Additional file 1 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 1. Complete analysis ready dataset containing all protein identifications associated with the manuscript.

Additional file 4 of Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex

Zsofia I. Laszlo, Nicole Hindley, Anna Sanchez Avila, Rachel A. Kline, Samantha L. Eaton, Douglas J. Lamont, Colin Smith, Tara L. Spires-Jones, Thomas M. Wishart & Christopher M. Henstridge
Additional file 4. Supplementary Table 2, primary antibody information.

Additional file 6 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 6: List of protein tertiary structures from Venturia inaequalis with a confident AlphaFold2 prediction and list of predicted SCOPe folds.

Methods for synthesis when meta-analysis is not used: Data dictionary

Miranda Cumpston, Sue Brennan, Joanne McKenzie & Rebecca Ryan
This data dictionary describes the coding system applied to the data extracted from systematic reviews included in the paper:
Cumpston MS, Brennan SE, Ryan R, McKenzie JE. 2022. Methods for synthesis when meta-analysis is not used: a survey of current practice in systematic reviews of public health and health systems interventions.
Associated files: 1. Methods for synthesis when meta-analysis is not used: data file: Cumpston_et_al_2022_other_synthesis_methods.xlsx (https://doi.org/10.26180/20785396) 2. Methods for synthesis when meta-analysis is...

cellCounts

Yang Liao, Dinesh Raghu, Bhupinder Pal, Lisa Mielke & Wei Shi
This page includes the data and code necessary to reproduce the results of the following paper: Yang Liao, Dinesh Raghu, Bhupinder Pal, Lisa Mielke and Wei Shi. cellCounts: fast and accurate quantification of 10x Chromium single-cell RNA sequencing data. Under review. A Linux computer running an operating system of CentOS 7 (or later) or Ubuntu 20.04 (or later) is recommended for running this analysis. The computer should have >2 TB of disk space and >64...

Moving from a project to a supported service: knowledge transfer and sustainability

Rachel Salby
Example of dataset not yet published

Synthesis methods data dictionary

Miranda Cumpston, Sue Brennan, Joanne McKenzie & Rebecca Ryan
This data dictionary describes the coding system applied to the data extracted from systematic reviews included in the paper:
Cumpston MS, Brennan SE, Ryan R, McKenzie JE. 2023. Statistical synthesis methods other than meta-analysis are commonly used but seldom specified: survey of systematic reviews of interventions
Associated files: 1. Synthesis methods data file: Cumpston_et_al_2023_other_synthesis_methods.xlsx (https://doi.org/10.26180/20785396) 2. Synthesis methods Stata code: Cumpston_et_al_2023_other_synthesis_methods.do (https://doi.org/10.26180/20786251) 3. Study protocol: Cumpston MS, McKenzie JE, Thomas J and Brennan...

Synthesis methods Stata code: Cumpston_et_al_2023_other_synthesis_methods.do

Miranda Cumpston, Sue Brennan, Rebecca Ryan & Joanne McKenzie
This Stata .do file provides the code used to analyse the data extracted and coded from systematic reviews included in the paper: Cumpston MS, Brennan SE, Ryan R, McKenzie JE. 2023. Statistical synthesis methods other than meta-analysis are commonly used, but are seldom specified: a survey of systematic reviews of interventions Input file: Synthesis methods data file: Cumpston_et_al_2023_other_synthesis_methods.xlsx (https://doi.org/10.26180/20785396) Associated file: Synthesis methods data dictionary (https://doi.org/10.26180/20785948) Study protocol: Cumpston MS, McKenzie JE, Thomas J and...

Synthesis methods data file: Cumpston_et_al_2022_other_synthesis_methods.xlsx

Miranda Cumpston, Sue Brennan, Joanne McKenzie & Rebecca Ryan
This file includes the data extracted and coded from systematic reviews included in the paper: "Cumpston MS, Brennan SE, Ryan R, McKenzie JE. 2022. Statistical synthesis methods other than meta-analysis are commonly used, but are seldom specified: a survey of systematic reviews of interventions"
Associated files: 1. Synthesis methods data dictionary (https://doi.org/10.26180/20785948) 2. Synthesis methods Stata code: Cumpston_et_al_2022_other_synthesis_methods 220902.do (https://doi.org/10.26180/20786251) 3. Study protocol: Cumpston MS, McKenzie JE, Thomas J and Brennan SE. The use...

Data from: Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

Carmen Amador, Ben J. Hayes & Hans D. Daetwyler
Critically endangered breeds and populations are often crossed with more common breeds or subspecies. This results in genetic admixture that can be undesirable when it challenges the genetic integrity of wild and domestic populations, causing a loss in special characteristics or unique genetic material and ultimately extinction. Here, we present two genomic selection strategies, using genome-wide DNA markers, to recover the genomic content of the original endangered population from admixtures. Each strategy relies on the...

Data from: Current and projected global distribution of Phytophthora cinnamomi, one of the world’s worst plant pathogens

Treena Burgess, John K. Scott, Keith L. McDougall, Michael J. C. Stukely, Colin Crane, William A. Dunstan, Frances Brigg, Vera Andjic, Diane White, Tim Rudman, Frans Arentz, Noboru Ota, Giles E. St.J. Hardy, Treena I. Burgess & Giles E. St. J. Hardy
Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a CLIMEX model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on...

Data from: Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii

Cecilia Villacorta-Rath, Irina Ilyushkina, Jan M. Strugnell, Bridget S. Green, Nicholas P. Murphy, Stephen R. Doyle, Nathan E. Hall, Andrew J. Robinson & James J. Bell
Recent advances in next-generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction site-associated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total...

Data from: Genetic rescue increases fitness and aids rapid recovery of an endangered marsupial population

Andrew R. Weeks, Dean Heinze, Louise Perrin, Jakub Stoklosa, Ary A. Hoffmann, Anthony Van Rooyen, Tom Kelly & Ian Mansergh
Genetic rescue has now been attempted in several threatened species, but the contribution of genetics per se to any increase in population health can be hard to identify. Rescue is expected to be particularly useful when individuals are introduced into small isolated populations with low levels of genetic variation. Here we consider such a situation by documenting genetic rescue in the mountain pygmy possum, Burramys parvus. Rapid population recovery occurred in the target population after...

Experimental evidence for ecological cascades following threatened mammal reintroduction: Arachnids at Scotia Sanctuary, NSW, Australia

Heloise Gibb
Please see the abstract from the Ecology paper: Gibb, Heloise, Silvey, C.J., Robinson, C., L’Hotellier, F.A. & Eldridge, D.J. (accepted August 2020) Experimental evidence for ecological cascades following threatened mammal reintroduction. This dataset includes: foraging pits, scorpion burrows and spider abundances from mensurative, exclusion and disturbance experiments at Scotia Sanctuary.

Data from: The cascading pathogenic consequences of Sarcoptes scabiei infection that manifest in host disease

Alynn M. Martin, Tamieka A. Fraser, John A. Lesku, Kellie Simpson, Georgia L. Roberts, Jillian Garvey, Adam Polkinghorne, Christopher P. Burridge & Scott Carver
Sarcoptic mange, caused by the parasitic mite Sarcoptes scabiei, causes a substantive burden of disease to humans, domestic animals, and wildlife, globally. There are many effects of S. scabiei infection, culminating in the disease which hosts suffer. However, major knowledge gaps remain on the pathogenic impacts of this infection. Here, we focus on the bare-nosed wombat host (Vombatus ursinus) to investigate the effects of mange on: (i) host heat loss and thermoregulation, (ii) field metabolic...

How does prescribed fire shape bird and plant communities in a temperate dry forest ecosystem?

Frederick Rainsford
To mitigate the impact of severe wildfire on human society and the environment, prescribed fire is widely used in forest ecosystems to reduce fuel loads and limit fire spread. To avoid detrimental effects on conservation values, it is imperative to understand how prescribed fire affects taxa having a range of different adaptations to disturbance. Such studies will have greatest benefit if they extend beyond short-term impacts of burning. We used a field study to examine...

Data from: Elevated [CO2] mitigates the effect of surface drought by stimulating root growth to access sub-soil water

Shihab Uddin, Markus Löw, Shahnaj Parvin, Glenn J. Fitzgerald, Sabine Tausz-Posch, Roger Armstrong, Garry O’Leary & Michael Tausz
Through stimulation of root growth, increasing atmospheric CO2 concentration ([CO2]) may facilitate access of crops to sub-soil water, which could potentially prolong physiological activity in dryland environments, particularly because crops are more water use efficient under elevated [CO2] (e[CO2]). This study investigated the effect of drought in shallow soil versus sub-soil on agronomic and physiological responses of wheat to e[CO2] in a glasshouse experiment. Wheat (Triticum aestivum L. cv. Yitpi) was grown in split-columns with...

Data from: Population genetic signatures of a climate change driven marine range extension

Jorge E. Ramos, Gretta T. Pecl, Natalie A. Moltschaniwskyj, Jayson M. Semmens, Carla A. Souza & Jan M. Strugnell
Shifts in species distribution, or ‘range shifts’, are one of the most commonly documented responses to ocean warming, with important consequences for the function and structure of ecosystems, and for socio-economic activities. Understanding the genetic signatures of range shifts can help build our knowledge of the capacity of species to establish and persist in colonised areas. Here, seven microsatellite loci were used to examine the population connectivity, genetic structure and diversity of Octopus tetricus, which...

Changes in participant behaviour and attitudes are associated with knowledge and skills gained by using a turtle conservation citizen science app

Claudia Santori, Ryan J. Keith, Camilla M. Whittington, Mike B. Thompson, James U. Van Dyke & Ricky-John Spencer
Citizen science has become a popular way to collect biodiversity data and engage the wider public in scientific research. It has the potential to improve the knowledge and skills of participants, and positively change their behaviour and attitude towards the environment. Citizen science outcomes are particularly valuable for wildlife conservation, as they could help alleviate human impacts on the environment. We used an online questionnaire to investigate the consequences of participating in an Australian turtle...

Data from: Compact cities or sprawling suburbs? optimising the distribution of people in cities to maximise species diversity

Andrew Geschke, Simon James, Andrew F. Bennett & Dale G. Nimmo
1. Conservation of biodiversity in urban environments depends on the responses of species to the intensity of urban development. ‘Land sharing’ and ‘land sparing’ represent alternate ends of a gradient that conceptualises a trade-off between the human population and biodiversity. We used a linear optimisation procedure to 1) identify the optimal allocation of land for people and nature, 2) assess whether the optimal allocation is more similar to land sparing or land sharing, and 3)...

Data from: Restoration potential of threatened ecosystem engineers increases with aridity: broad scale effects on soil nutrients and function

Orsi Decker, David J. Eldridge & Heloise Gibb
Species extinctions alter ecosystem services, and the magnitude of this impact is likely to change across environmental gradients. In Australia, soil-disturbing mammals that are now considered ecologically extinct are thought to be important ecosystem engineers. Previous studies have demonstrated microsite-level impacts of reintroduced soil-disturbing mammals on soil functions, but effects are yet to be tested across larger scales. Further, it is unclear how impacts vary across environmental gradients and if the restoration potential of reintroductions...

Data from: Maternal effects obscure condition-dependent sex allocation in changing environments

Amy Edwards, Elissa Cameron, Erik Wapstra & Joanne McEvoy
Climate change increases environmental fluctuations which thereby impact population demography. Species with temperature-dependent sex determination may experience more extreme sex ratio skews, but this has not been considered in species with chromosomally-determined sex. However, anticipatory maternal effects cause lifelong physiological changes impacting sex ratios. Here we show, in mice, that more sons were born to mothers in good condition when their breeding environment matched their gestational environment, consistent with theoretical predictions, but mothers in mismatched...

Influential factors for access to and participation in rehabilitation for people with lower limb amputation in East, South, and Southeast Asian developing countries: a scoping review

Md Shapin Ibne Sayeed, Jodi Oakman, Michael P. Dillon & Rwth Stuckey
To explore factors impacting access to and participation in rehabilitation for people with lower limb amputation (LLA) in East, South, and Southeast Asian developing countries. A scoping review was undertaken following the PRISMA-ScR guidelines. Five electronic databases (PsycINFO (Ovid), Medline (Ovid), CINAHL (EBSCO), AMED, and Proquest Social Sciences) were searched for articles from January 1980 till March 2020. Two authors independently assessed articles for inclusion. Included articles were classified according to the Health Care Delivery...

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