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1. Climates of Warm Earth-like Planets I: 3-D Model Simulations

Author

Way, M. J., Del Genio, A. D., Aleinov, I., Clune, T. L., Kelley, M., and Kiang, N. Y.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

We present a large ensemble of simulations of an Earth-like world with increasing insolation and rotation rate. Unlike previous work utilizing idealized aquaplanet configurations we focus our simulations on modern Earth-like topography. The orbital period is the same as modern Earth, but with zero obliquity and eccentricity. The atmosphere is 1 bar N$_{2}$-dominated with CO$_{2}$=400 ppmv and CH$_{4}$=1 ppmv. The simulations include two types of oceans; one without ocean heat transport (OHT) between grid cells as has been commonly used in the exoplanet literature, while the other is a fully coupled dynamic bathtub type ocean. The dynamical regime transitions that occur as day length increases induce climate feedbacks producing cooler temperatures, first via the reduction of water vapor with increasing rotation period despite decreasing shortwave cooling by clouds, and then via decreasing water vapor and increasing shortwave cloud cooling, except at the highest insolations. Simulations without OHT are more sensitive to insolation changes for fast rotations while slower rotations are relatively insensitive to ocean choice. OHT runs with faster rotations tend to be similar with gyres transporting heat poleward making them warmer than those without OHT. For slower rotations OHT is directed equator-ward and no high latitude gyres are apparent. Uncertainties in cloud parameterization preclude a precise determination of habitability but do not affect robust aspects of exoplanet climate sensitivity. This is the first paper in a series that will investigate aspects of habitability in the simulations presented herein. The datasets from this study are opensource and publicly available., Comment: 27 pages ApJS accepted. Expanded Introduction and several additional figures

Published
2018
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2. Exploring the Inner Edge of the Habitable Zone with Fully Coupled Oceans

Author

Way, M. J., Del Genio, A. D., Kelley, M., Aleinov, I., and Clune, T.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Rotation in planetary atmospheres plays an important role in regulating atmospheric and oceanic heat flow, cloud formation and precipitation. Using the Goddard Institute for Space Studies (GISS) three dimension General Circulation Model (3D-GCM) we investigate how the effects of varying rotation rate and increasing the incident stellar flux on a planet set bounds on a planet's habitable zone with its parent star. From ensemble climate simulations we identify which factors are the primary controllers of uncertainty in setting these bounds. This is shown in particular for fully coupled ocean (FCO) runs -- some of the first that have been utilized in this context. Results with a Slab Ocean (SO) of 100m mixed layer depth are compared with a similar study by Yang et al. 2014, which demonstrates consistency across models. However, there are clear differences for rotations rates of 1-16x present Earth sidereal day lengths between the 100m SO and FCO models, which points to the necessity of using FCOs whenever possible. The latter was recently demonstrated quite clearly by Hu & Yang 2014 in their aquaworld study with a FCO when compared with similar mixed layer ocean studies and by Cullum et al. 2014. We also show how these results have implications for Venus in the early history of our Solar System since even at this time Venus received more solar flux than Earth does today while it may still have had a slow retrograde rotation. The Venus runs utilize a 2.9Gya solar spectrum generated with the code of Claire et al. 2012, a modern Venus topography with an ocean filling the lowlands (giving an equivalent depth of 310 meters if spread across the entire surface), atmosphere of 1 bar N2, CO2=0.4mb, CH4=0.001mb and present day orbital parameters, radius, & gravity. We demonstrate that ancient Venus could have had quite moderate surface temperatures given these assumptions., Comment: 4 pages, 15 figures, to be published in Comparative Climatology of Terrestrial Planets II, NASA Conference Proceeding technical No. TBD. Updated Figure 1 (2016/12) and associated text

Published
2015

3. Molecular characterisation of the Australian and New Zealand livestock Chlamydia pecorum strains confirms novel but clonal ST23 in association with ovine foetal loss.

Author

Jelocnik, M, White, RT, Clune, T, O'Connell, J, Foxwell, J, Hair, S, Besier, S, Tom, L, Phillips, N, Robbins, A, Bogema, D, Vaz, PK, Legione, AR, Jenkins, C, Jacobson, C, Jelocnik, M, White, RT, Clune, T, O'Connell, J, Foxwell, J, Hair, S, Besier, S, Tom, L, Phillips, N, Robbins, A, Bogema, D, Vaz, PK, Legione, AR, Jenkins, C, and Jacobson, C

Abstract

Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on C. pecorum strains associated with reproductive disease, although whole genome sequencing (WGS) of one abortigenic ST23 C. pecorum strain identified unique features, including a deletion in the CDS1 locus of the chlamydial plasmid. We applied WGS on two ST23 strains detected in aborted and stillborn lambs from Australia and used phylogenetic and comparative analyses to compare these to the other available C. pecorum genomes. To re-evaluate the genetic diversity of contemporary strains, we applied C. pecorum genotyping, and chlamydial plasmid sequencing to a range of C. pecorum positive samples and isolates from ewes, aborted foetuses and stillborn lambs, cattle and a goat from diverse geographical regions across Australia and New Zealand.The two new C. pecorum genomes are nearly identical to the genome of the Australian abortigenic strain including the unique deletion in the chlamydial plasmid. Genotyping revealed that these novel C. pecorum ST23 strains are widespread and associated with sheep abortions on Australian and New Zealand farms. In addition, a goat C. pecorum strain (denoted ST 304) from New Zealand was also characterised. This study expands the C. pecorum genome catalogue and describes a comprehensive molecular characterisation of the novel livestock ST23 strains associated with foetal and lamb mortality.

Published
2023

4. THE EARTH SYSTEM PREDICTION SUITE : Toward a Coordinated U.S. Modeling Capability

Author

Theurich, Gerhard, DeLuca, C., Campbell, T., Liu, F., Saint, K., Vertenstein, M., Chen, J., Oehmke, R., Doyle, J., Whitcomb, T., Wallcraft, A., Iredell, M., Black, T., da Silva, A. M., Clune, T., Ferraro, R., Li, P., Kelley, M., Aleinov, I., Balaji, V., Zadeh, N., Jacob, R., Kirtman, B., Giraldo, F., McCarren, D., Sandgathe, S., Peckham, S., and Dunlap, R.

Published
2016

5. Water banking in aquifers as a tool for drought resilience in the Murray-Darling Basin.

Author

Page, D.W., Gonzalez, D., Clune, T., Colton, Y., and Bonnett, G.D.

Subjects
GROUNDWATER recharge, AQUIFERS, DROUGHT management, WATER table, WATER rights, WATER supply
Abstract

Water banking in aquifers is an internationally proven, low-cost solution that could improve drought resilience across the Murray Darling Basin. While significant potential for water banking through managed aquifer recharge (MAR) or conjunctive use of surface and groundwater resources has been identified in the Murray Darling Basin Plan, there is a need to establish clear policy and institutional foundations to incentivise adoption. To provide appropriate incentives for schemes, the legal status of rights to recharge, store and recover water, and the rules and costs which apply to groundwater extraction need to be clear and transparent. This paper aims to clarify principles and frameworks to secure water rights for recharge, storage, and recovery within the sustainable limits of water resources currently set under law. The current Basin Plan supports water banking, and banking would be complementary with objective and outcomes sought by future Basin Plans. Existing water accounting systems would need to accommodate this new capacity. Institutional arrangements and financial structures of water banking in the USA provide guidance for Australia. Demonstration sites would enable concurrent policy development and institutional set-up and provide critical experience to serve as models for wider adoption as part of future Murray Darling Basin plans. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Toxoplasma gondii is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: A prospective cohort study

Author

Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Bruce, M., Beetson, S., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., Jacobson, C., Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Bruce, M., Beetson, S., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., and Jacobson, C.

Abstract

Background Toxoplasma gondii causes reproductive losses in sheep worldwide, including Australia. The reproductive performance of primiparous ewes is typically lower than for mature, multiparous ewes, and younger ewes are more likely to be immunologically naïve and therefore more susceptible to reproductive disease if T. gondii infection occurs during pregnancy. The aim of this study was to assess the impact of infection with T. gondii on the reproductive performance of primiparous ewes in southern Australia using a prospective cohort study. This will inform the need for targeted control strategies for T. gondii in Australian sheep. Results Toxoplasma gondii seropositivity using indirect ELISA was detected at 16/28 farms located across southern Australia. Apparent seropositivity to T. gondii was lower in primiparous ewes (1.1, 95% confidence interval (CI) 0.6, 1.8) compared to mature, multiparous ewes (8.1, 95% CI 6.0, 10.5; P < 0.001). Toxoplasma gondii seroconversion during the gestation and lambing period was confirmed for 11/1097 (1.0, 95% CI 0.5, 1.7) of pregnant primiparous ewes that failed to raise a lamb, and 1/161 (0.6, 95% CI 0.1, 2.9) primiparous ewes with confirmed mid-pregnancy abortion. Conclusions Low frequency of detection of T. gondii seroconversion during gestation and low frequency of seropositivity to T. gondii suggests that toxoplasmosis was not an important contributor to reproductive losses in primiparous ewes on farms located over a wide geographical area in southern Australia.

Published
2022

8. Abortion and Lamb Mortality between Pregnancy Scanning and Lamb Marking for Maiden Ewes in Southern Australia

Author

Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Campbell, AJD, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, Kearney, G, Jacobson, C, Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Campbell, AJD, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, Kearney, G, and Jacobson, C

Abstract

The contribution of abortions to the overall mortality of lambs born to maiden (primiparous) ewes in Australia remains unclear. This cohort study aimed to quantify abortion and lamb mortality for ewe lambs and maiden Merino two-tooth ewes. Lamb mortality from pregnancy scanning to marking were determined for 19 ewe lamb and 11 Merino two-tooth ewe flocks across southern Australia. Average lamb mortality from scanning to marking was 35.8% (range 14.3-71.1%) for the ewe lambs and 29.4% (range 19.7-52.7%) for the two-tooth ewes. Mid-pregnancy abortion was detected in 5.7% of ewes (range 0-50%) in the ewe lamb flocks and 0.9% of ewes (range 0-4.4%) in the two-tooth ewe flocks. Mid-pregnancy abortion affecting ≥2% of ewes was observed in 6/19 ewe lamb flocks and 2/11 two-tooth ewe flocks. Lamb mortality from birth to marking represented the greatest contributor to foetal and lamb mortality after scanning, but mid-pregnancy abortion was an important contributor to lamb mortality in some ewe lamb flocks. Variability between the flocks indicates scope to improve the overall reproductive performance for maiden ewes by reducing foetal and lamb losses. Addressing mid-pregnancy abortion may improve the reproductive performance in some flocks.

Published
2022

9. Seropositivity to Coxiella burnetii in primiparous and multiparous ewes from southern Australia: A cross-sectional study

Author

Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Bruce, M, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, Jacobson, C, Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Bruce, M, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, and Jacobson, C

Abstract

The role of infectious diseases including coxiellosis in causing poorer reproductive performance of primiparous ewes are not well studied. The aims of this study were to determine if natural exposure to Coxiella burnetii is widespread in breeding ewes and whether seropositivity is associated with poor reproductive performance of primiparous ewes. Seropositivity to Coxiella burnetii was 0.08% (CI95% 0.01, 0.36) in primiparous ewes and 0.36% (CI95% 0.07, 1.14) in mature ewes. Coxiella burnetii was not detected in aborted or stillborn lambs using qPCR. These findings suggest C. burnetii infection was unlikely to be an important contributor to abortion and perinatal mortalities observed for primiparous ewe flocks, and exposure to C. burnetii was not widespread in ewes on farms located over wide geographical region of southern Australia. Whilst ewes on these farms were not an important reservoir for C. burnetii, sporadic zoonotic transmission from sheep is reported and has public health implications.

Published
2022

10. Toxoplasma gondii is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: a prospective cohort study

Author

Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Bruce, M, Beetson, S, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, Jacobson, C, Clune, T, Lockwood, A, Hancock, S, Thompson, AN, Bruce, M, Beetson, S, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, and Jacobson, C

Abstract

BACKGROUND: Toxoplasma gondii causes reproductive losses in sheep worldwide, including Australia. The reproductive performance of primiparous ewes is typically lower than for mature, multiparous ewes, and younger ewes are more likely to be immunologically naïve and therefore more susceptible to reproductive disease if T. gondii infection occurs during pregnancy. The aim of this study was to assess the impact of infection with T. gondii on the reproductive performance of primiparous ewes in southern Australia using a prospective cohort study. This will inform the need for targeted control strategies for T. gondii in Australian sheep. RESULTS: Toxoplasma gondii seropositivity using indirect ELISA was detected at 16/28 farms located across southern Australia. Apparent seropositivity to T. gondii was lower in primiparous ewes (1.1, 95% confidence interval (CI) 0.6, 1.8) compared to mature, multiparous ewes (8.1, 95% CI 6.0, 10.5; P < 0.001). Toxoplasma gondii seroconversion during the gestation and lambing period was confirmed for 11/1097 (1.0, 95% CI 0.5, 1.7) of pregnant primiparous ewes that failed to raise a lamb, and 1/161 (0.6, 95% CI 0.1, 2.9) primiparous ewes with confirmed mid-pregnancy abortion. CONCLUSIONS: Low frequency of detection of T. gondii seroconversion during gestation and low frequency of seropositivity to T. gondii suggests that toxoplasmosis was not an important contributor to reproductive losses in primiparous ewes on farms located over a wide geographical area in southern Australia.

Published
2022

11. Seropositivity to Campylobacter and association with abortion and lamb mortality in maiden ewes from Western Australia, South Australia and Victoria

Author

Clune, T., Bruce, M., Glanville, E., Campbell, A.J.D., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Brookes, D., Trengove, C., O'Handley, R., Jacobson, C., Clune, T., Bruce, M., Glanville, E., Campbell, A.J.D., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Brookes, D., Trengove, C., O'Handley, R., and Jacobson, C.

Abstract

This case-control study investigated associations between Campylobacter fetus or Campylobacter jejuni titre and reproductive outcomes in 22 flocks of Merino and non-Merino maiden ewes aged 1–2 years old. Campylobacter titres were also determined for multiparous ewes aged 3 years or older on the same farms. C. fetus ‘positivity’ (titre ≥1:80) was detected for 12% (57/462; 95% confidence interval [95% CI] 9.6 to 15.6) of maiden ewes and 31% (65/210; 95% CI 25.0 to 37.4) of mature ewes. The odds for failing to rear a lamb in C. fetus-‘exposed’ maiden ewes (titre ≥1:10) was 2.01 times that of seronegative ewes (95% CI 1.09 to 3.77; P = 0.027), but there was no association between C. fetus-‘positivity’ (titre ≥1:80) and failure to rise (OR 1.69; 95% CI 0.77 to 3.76; P = 0.191). C. fetus abortions were confirmed with microbial culture in one maiden ewe flock. In this flock, C. fetus titres fluctuated and often waned by lamb marking, highlighting the value of necropsies during abortion investigations. C. jejuni-‘positivity’ (titre ≥1:80) was detected for 44% (204/462; 95% CI 39.7 to 48.7) maiden ewes, but odds of failing to rear were decreased for C. jejuni-‘positive’ ewes (OR 0.52; 95% CI 0.32 to 0.83; P = 0.007). The association between Campylobacter serology and the reproductive outcome was inconsistent in these flocks. Serology should be considered in the context of other risk factors and used in conjunction with other strategies to investigate the impact of Campylobacter exposure on ewe reproductive performance such as monitoring for abortions and lamb necropsies to determine aetiological diagnosis, and vaccination trials.

Published
2022

12. Seropositivity to Coxiella burnetii in primiparous and multiparous ewes from southern Australia: A cross-sectional study

Author

Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Bruce, M., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., Jacobson, C., Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Bruce, M., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., and Jacobson, C.

Abstract

The role of infectious diseases including coxiellosis in causing poorer reproductive performance of primiparous ewes are not well studied. The aims of this study were to determine if natural exposure to Coxiella burnetii is widespread in breeding ewes and whether seropositivity is associated with poor reproductive performance of primiparous ewes. Seropositivity to Coxiella burnetii was 0.08% (CI95% 0.01, 0.36) in primiparous ewes and 0.36% (CI95% 0.07, 1.14) in mature ewes. Coxiella burnetii was not detected in aborted or stillborn lambs using qPCR. These findings suggest C. burnetii infection was unlikely to be an important contributor to abortion and perinatal mortalities observed for primiparous ewe flocks, and exposure to C. burnetii was not widespread in ewes on farms located over wide geographical region of southern Australia. Whilst ewes on these farms were not an important reservoir for C. burnetii, sporadic zoonotic transmission from sheep is reported and has public health implications.

Published
2022

13. Seropositivity to Campylobacter and association with abortion and lamb mortality in maiden ewes from Western Australia, South Australia and Victoria

Author

Clune, T, Bruce, M, Glanville, E, Campbell, AJD, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Brookes, D, Trengove, C, O'Handley, R, Jacobson, C, Clune, T, Bruce, M, Glanville, E, Campbell, AJD, Lockwood, A, Hancock, S, Thompson, AN, Beetson, S, Brookes, D, Trengove, C, O'Handley, R, and Jacobson, C

Abstract

This case-control study investigated associations between Campylobacter fetus or Campylobacter jejuni titre and reproductive outcomes in 22 flocks of Merino and non-Merino maiden ewes aged 1-2 years old. Campylobacter titres were also determined for multiparous ewes aged 3 years or older on the same farms. C. fetus 'positivity' (titre ≥1:80) was detected for 12% (57/462; 95% confidence interval [95% CI] 9.6 to 15.6) of maiden ewes and 31% (65/210; 95% CI 25.0 to 37.4) of mature ewes. The odds for failing to rear a lamb in C. fetus-'exposed' maiden ewes (titre ≥1:10) was 2.01 times that of seronegative ewes (95% CI 1.09 to 3.77; P = 0.027), but there was no association between C. fetus-'positivity' (titre ≥1:80) and failure to rise (OR 1.69; 95% CI 0.77 to 3.76; P = 0.191). C. fetus abortions were confirmed with microbial culture in one maiden ewe flock. In this flock, C. fetus titres fluctuated and often waned by lamb marking, highlighting the value of necropsies during abortion investigations. C. jejuni-'positivity' (titre ≥1:80) was detected for 44% (204/462; 95% CI 39.7 to 48.7) maiden ewes, but odds of failing to rear were decreased for C. jejuni-'positive' ewes (OR 0.52; 95% CI 0.32 to 0.83; P = 0.007). The association between Campylobacter serology and the reproductive outcome was inconsistent in these flocks. Serology should be considered in the context of other risk factors and used in conjunction with other strategies to investigate the impact of Campylobacter exposure on ewe reproductive performance such as monitoring for abortions and lamb necropsies to determine aetiological diagnosis, and vaccination trials.

Published
2022

15. A Quantum Annealing Computer Team Addresses Climate Change Predictability

Author

Halem, M, LeMoigne, J, Dorband, J, Lomonaco, S, Yesha, Ya, Simpson, D, Clune, T, Pelissier, C, Nearing, G, Gentine, P, Fang, B, Shehab, A, Radov, Asen, Tikak, N, Prouty, Roy, and Harrison, Kenneth

Subjects
Astronautics (General)
Abstract

The near confluence of the successful launch of the Orbiting Carbon Observatory2 on July 2, 2014 and the acceptance on August 20, 2015 by Google, NASA Ames Research Center and USRA of a 1152 qubit D-Wave 2X Quantum Annealing Computer (QAC), offered an exceptional opportunity to explore the potential of this technology to address the scientific prediction of global annual carbon uptake by land surface processes. At UMBC,we have collected and processed 20 months of global Level 2 light CO2 data as well as fluorescence data. In addition we have collected ARM data at 2sites in the US and Ameriflux data at more than 20 stations. J. Dorband has developed and implemented a multi-hidden layer Boltzmann Machine (BM) algorithm on the QAC. Employing the BM, we are calculating CO2 fluxes by training collocated OCO-2 level 2 CO2 data with ARM ground station tower data to infer to infer measured CO2 flux data. We generate CO2 fluxes with a regression analysis using these BM derived weights on the level 2 CO2 data for three Ameriflux sites distinct from the ARM stations. P. Gentine has negotiated for the access of K34 Ameriflux data in the Amazon and is applying a neural net to infer the CO2 fluxes. N. Talik validated the accuracy of the BM performance on the QAC against a restricted BM implementation on the IBM Softlayer Cloud with the Nvidia co-processors utilizing the same data sets. G. Nearing and K. Harrison have extended the GSFC LIS model with the NCAR Noah photosynthetic parameterization and have run a 10 year global prediction of the net ecosystem exchange. C. Pellisier is preparing a BM implementation of the Kalman filter data assimilation of CO2 fluxes. At UMBC, R. Prouty is conducting OSSE experiments with the LISNoah model on the IBM iDataPlex to simulate the impact of CO2 fluxes to improve the prediction of global annual carbon uptake. J. LeMoigne and D. Simpson have developed a neural net image registration system that will be used for MODIS ENVI and will be converted to a BM algorithm implementation on the QAC. The first integer adder has been implemented on the D-Wave 2X by A. Shehab that will perform HAAR wavelets for image compression of MODIS scenes. Finally, based on the next generations of QACs, we are preparing a 5-year performance road map on the scalability of the current QAC algorithms.

Published
2016

16. Exploring the Inner Edge of the Habitable Zone with Fully Coupled Oceans

Author

Way, M.J, Del Genio, A.D, Kelley, M, Aleinov, I, and Clune, T

Subjects
Lunar And Planetary Science And Exploration
Abstract

The role of rotation in planetary atmospheres plays an important role in regulating atmospheric and oceanic heat flow, cloud formation and precipitation. Using the Goddard Institute for Space Studies (GISS) three dimension General Circulation Model (3D-GCM) we demonstrate how varying rotation rate and increasing the incident solar flux on a planet are related to each other and may allow the inner edge of the habitable zone to be much closer than many previous habitable zone studies have indicated. This is shown in particular for fully coupled ocean runs -- some of the first that have been utilized in this context. Results with a 100m mixed layer depth and our fully coupled ocean runs are compared with those of Yang et al. 2014, which demonstrates consistency across models. However, there are clear differences for rotations rates of 1-16x present earth day lengths between the mixed layer and fully couple ocean models, which points to the necessity of using fully coupled oceans whenever possible. The latter was recently demonstrated quite clearly by Hu & Yang 2014 in their aquaworld study with a fully coupled ocean when compared with similar mixed layer ocean studies and by Cullum et al. 2014. Atmospheric constituent amounts were also varied alongside adjustments to cloud parameterizations (results not shown here). While the latter have an effect on what a planet's global mean temperature is once the oceans reach equilibrium they do not qualitatively change the overall relationship between the globally averaged surface temperature and incident solar flux for rotation rates ranging from 1 to 256 times the present Earth day length. At the same time this study demonstrates that given the lack of knowledge about the atmospheric constituents and clouds on exoplanets there is still a large uncertainty as to where a planet will sit in a given star's habitable zone.

Published
2015

17. GEOS-5 Chemistry Transport Model User's Guide

Author

Kouatchou, J, Molod, A, Nielsen, J. E, Auer, B, Putman, W, and Clune, T

Subjects
Earth Resources And Remote Sensing, Geophysics, Computer Programming And Software
Abstract

The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.

Published
2015

18. Neospora caninum is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: evidence from a cross-sectional study

Author

Clune, T, Lockwood, A, Hancock, S, Bruce, M, Thompson, AN, Beetson, S, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, Jacobson, C, Clune, T, Lockwood, A, Hancock, S, Bruce, M, Thompson, AN, Beetson, S, Campbell, AJ, Glanville, E, Brookes, D, Trengove, C, O'Handley, R, and Jacobson, C

Abstract

Neospora caninum has been implicated as a sporadic cause of abortion and perinatal deaths in sheep flocks globally. However, its significance as a reproductive pathogen for sheep in Australia remains unknown. The aims of this study were to (i) determine the seroprevalence of N. caninum in Australian breeding ewes and (ii) examine if natural exposure to N. caninum is associated with poor reproductive performance of primiparous ewes in southern Australia. Thirty flocks of primiparous ewes (aged 1–2 years old at lambing) from 28 farms in three states (Western Australia, South Australia and Victoria) were monitored between mating and lamb marking. Blood samples were also collected from multiparous mature ewes (aged 3 years or older) at each farm. Seroprevalence for anti-N. caninum IgG using indirect ELISA was determined for a subset of primiparous ewes that were predominantly determined to be pregnant and subsequently failed to rear a lamb (n = 1279) and randomly selected mature multiparous ewes with unknown reproductive status (n = 558). Neopsora caninum apparent seroprevalence was 0.16% (95% confidence interval 0.03%, 0.5%) in primiparous ewes, with seropositivity identified in two ewes from farms located in South Australia and Victoria. There was no evidence of seropositivity in mature ewes with apparent seroprevalence 0% (0%, 0.45%). These findings suggest that N. caninum infection was not widespread in primiparous ewes or mature multiparous ewes on these farms, and exposure to N. caninum infection was unlikely to explain abortion and perinatal mortalities observed for primiparous ewes.

Published
2021

19. Neospora caninum is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: Evidence from a cross-sectional study

Author

Clune, T., Lockwood, A., Hancock, S., Bruce, M., Thompson, A.N., Beetson, S., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., Jacobson, C., Clune, T., Lockwood, A., Hancock, S., Bruce, M., Thompson, A.N., Beetson, S., Campbell, A.J., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., and Jacobson, C.

Abstract

Neospora caninum has been implicated as a sporadic cause of abortion and perinatal deaths in sheep flocks globally. However, its significance as a reproductive pathogen for sheep in Australia remains unknown. The aims of this study were to (i) determine the seroprevalence of N. caninum in Australian breeding ewes and (ii) examine if natural exposure to N. caninum is associated with poor reproductive performance of primiparous ewes in southern Australia. Thirty flocks of primiparous ewes (aged 1–2 years old at lambing) from 28 farms in three states (Western Australia, South Australia and Victoria) were monitored between mating and lamb marking. Blood samples were also collected from multiparous mature ewes (aged 3 years or older) at each farm. Seroprevalence for anti-N. caninum IgG using indirect ELISA was determined for a subset of primiparous ewes that were predominantly determined to be pregnant and subsequently failed to rear a lamb (n = 1279) and randomly selected mature multiparous ewes with unknown reproductive status (n = 558). Neopsora caninum apparent seroprevalence was 0.16% (95% confidence interval 0.03%, 0.5%) in primiparous ewes, with seropositivity identified in two ewes from farms located in South Australia and Victoria. There was no evidence of seropositivity in mature ewes with apparent seroprevalence 0% (0%, 0.45%). These findings suggest that N. caninum infection was not widespread in primiparous ewes or mature multiparous ewes on these farms, and exposure to N. caninum infection was unlikely to explain abortion and perinatal mortalities observed for primiparous ewes.

Published
2021

20. Real-time fluorometric isothermal LAMP assay for detection of Chlamydia pecorum in rapidly processed ovine abortion samples: A veterinary practitioner’s perspective

Author

Clune, T., Anstey, S., Kasimov, V., Jacobson, C., Jelocnik, M., Clune, T., Anstey, S., Kasimov, V., Jacobson, C., and Jelocnik, M.

Abstract

Traditional methods of detecting Chlamydia pecorum in tissue samples such as polymerase chain reaction or cell culture are laborious and costly. We evaluated the use of a previously developed C. pecorum LAMP assay using minimally processed ovine samples. Cotyledon (n = 16), foetal liver (n = 22), foetal lung (n = 2), and vaginal (n = 6) swabs, in addition to cotyledon (n = 6) and foetal liver (n = 8) tissue samples, were rapidly processed and used for LAMP testing without DNA extraction. Overall, LAMP test results were highly congruent with the in-house reference qPCR, with 80.43% (37/46; 72.73% positive agreement (PA); 84.75% negative agreement (NA)) overall agreeance for swab samples, and 85.71% (12/14; 80% PA; 88.89% NA) overall agreeance for tissue samples. Out of the 11 total discrepant results, discrepancy was mainly observed in samples (n = 10) with less than 100 copies/µL C. pecorum DNA. While sensitivity could be improved, the simplicity, low cost, and accuracy of detection makes this test amenable for use at point-of-care for detecting C. pecorum in sheep.

Published
2021

21. Chlamydia pecorum detection in aborted and stillborn lambs from Western Australia

Author

Clune, T., Besier, S., Hair, S., Hancock, S., Lockwood, A., Thompson, A., Jelocnik, M., Jacobson, C., Clune, T., Besier, S., Hair, S., Hancock, S., Lockwood, A., Thompson, A., Jelocnik, M., and Jacobson, C.

Abstract

Lamb survival is an important welfare and productivity issue for sheep industries worldwide. Lower lamb survival has been reported for primiparous ewes, but the causes of this are not well studied. The aim of this study was to determine causes of perinatal deaths for lambs born to primiparous ewes in Western Australia, and identify if infectious diseases are implicated. Lamb mortality from birth to marking were determined for 11 primiparous ewe flocks on 10 farms in Western Australia. Lamb mortality from birth to marking averaged 14% for single-born and 26% for multiple-born lambs. Lamb necropsies (n = 298) identified starvation–mismosthering–exposure (34%), dystocia (24%) and stillbirth (15%) as the most common causes of perinatal lamb death. There was no evidence of exotic abortigenic pathogens in aborted and stillborn lambs (n = 35). Chlamydia pecorum was detected by qPCR in 15/35 aborted and stillborn lambs on 5/6 farms. Preliminary molecular characterisation of C. pecorum detected in samples from aborted and stillborn lambs (n = 8) using both Multilocus Sequence Typing and ompA genotyping indicated all strains were genetically identical to previously described pathogenic livestock strains, denoted ST23, and dissimilar to gastrointestinal strains. High frequency of detection of a pathogenic C. pecorum strains ST23 associated with ovine abortion and stillbirth on multiple farms located across a wide geographic area has not been previously reported. Chlamydia pecorum may contribute to reproductive wastage for primiparous sheep in Western Australia. Further investigation to understand C. pecorum epidemiology and impact on sheep reproduction is warranted.

Published
2021

22. Ovine abortion and stillbirth investigations in Australia

Author

Clune, T., Beetson, S., Besier, S., Knowles, G., Paskin, R., Rawlin, G., Suter, R., Jacobson, C., Clune, T., Beetson, S., Besier, S., Knowles, G., Paskin, R., Rawlin, G., Suter, R., and Jacobson, C.

Abstract

Fetal loss and lamb mortality between mid‐pregnancy and weaning are important economic and welfare issues for the Australian sheep industry. The aim of this study was to determine common causes of ovine abortion and stillbirths based on submissions to veterinary laboratories and identify factors that impact the determination of an aetiological diagnosis. Data for 529 investigations on abortion or stillbirth between 2000 and 2018 were retrieved from four state veterinary laboratories in Western Australia, South Australia, Victoria and Tasmania. An aetiological diagnosis was made for 57% of investigations. Investigations that included placental tissue samples were more than twice as likely to have an aetiological diagnosis compared to investigations without placenta (P = 0.017, 95% confidence interval 1.1, 4.5). Of the investigations where an aetiological diagnosis was made, 81% involved infectious abortion, with Campylobacter spp. (32%), Listeria spp. (25%) and Toxoplasma gondii (9%) being the three most common abortigenic pathogens implicated. The remaining 19% of investigations with an aetiological diagnosis included a wide range of infectious and non‐infectious diseases. Diagnoses made varied year to year and between states. No evidence of exotic abortigenic pathogens were reported. Veterinary practitioners can improve the probability of an aetiological diagnosis by emphasising to farmers the importance of collecting any aborted material, especially placenta, and appropriate storage of the tissues until they can be submitted to the laboratory. Some diseases that cause abortion in Australian sheep have zoonotic potential, and veterinary practitioners play an important role in educating clients about appropriate hygiene when handling pregnant and lambing ewes or any aborted material.

Published
2021

23. Chlamydia pecorum–induced arthritis in experimentally and naturally infected sheep

Author

Ostfeld, N., Islam, M.M., Jelocnik, M., Hilbe, M., Sydler, T., Hartnack, S., Jacobson, C., Clune, T., Marsh, I., Sales, N., Polkinghorne, A., Borel, N., Ostfeld, N., Islam, M.M., Jelocnik, M., Hilbe, M., Sydler, T., Hartnack, S., Jacobson, C., Clune, T., Marsh, I., Sales, N., Polkinghorne, A., and Borel, N.

Abstract

Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum.

Published
2021

24. Abortion and lamb mortality between pregnancy scanning and lamb marking for maiden ewes in southern Australia

Author

Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Campbell, A.J.D., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., Kearney, G., Jacobson, C., Clune, T., Lockwood, A., Hancock, S., Thompson, A.N., Beetson, S., Campbell, A.J.D., Glanville, E., Brookes, D., Trengove, C., O’Handley, R., Kearney, G., and Jacobson, C.

Abstract

The contribution of abortions to the overall mortality of lambs born to maiden (primiparous) ewes in Australia remains unclear. This cohort study aimed to quantify abortion and lamb mortality for ewe lambs and maiden Merino two-tooth ewes. Lamb mortality from pregnancy scanning to marking were determined for 19 ewe lamb and 11 Merino two-tooth ewe flocks across southern Australia. Average lamb mortality from scanning to marking was 35.8% (range 14.3–71.1%) for the ewe lambs and 29.4% (range 19.7–52.7%) for the two-tooth ewes. Mid-pregnancy abortion was detected in 5.7% of ewes (range 0–50%) in the ewe lamb flocks and 0.9% of ewes (range 0–4.4%) in the two-tooth ewe flocks. Mid-pregnancy abortion affecting ≥2% of ewes was observed in 6/19 ewe lamb flocks and 2/11 two-tooth ewe flocks. Lamb mortality from birth to marking represented the greatest contributor to foetal and lamb mortality after scanning, but mid-pregnancy abortion was an important contributor to lamb mortality in some ewe lamb flocks. Variability between the flocks indicates scope to improve the overall reproductive performance for maiden ewes by reducing foetal and lamb losses. Addressing mid-pregnancy abortion may improve the reproductive performance in some flocks.

Published
2021

26. Reproductive wastage in young ewes

Author

Clune, T., Lockwood, A., Hancock, S., Beetson, S., Thompson, A., Jacobson, C., Clune, T., Lockwood, A., Hancock, S., Beetson, S., Thompson, A., and Jacobson, C.

Abstract

This article presents the preliminary findings of an ongoing, national project investigating the magnitude, timing and causes of reproductive wastage for maiden ewes.

Published
2019

27. Reproductive wastage in young ewes

Author

Jacobson, C., Clune, T., Lockwood, A., Thompson, A., Beetson, S., Hancock, S., Jacobson, C., Clune, T., Lockwood, A., Thompson, A., Beetson, S., and Hancock, S.

Abstract

This article presents the preliminary findings of an ongoing, national project investigating the magnitude, timing and causes of reproductive wastage for maiden ewes.

Published
2019

28. Ovine abortion and stillbirth investigations in Australia.

Author

Clune, T, Beetson, S, Besier, S, Knowles, G, Paskin, R, Rawlin, G, Suter, R, and Jacobson, C

Subjects
*ABORTION, *STILLBIRTH, *DIAGNOSIS, *EWES, *SHEEP diseases, *SHEEP industry, *NON-communicable diseases, *SHEEP
Abstract

Fetal loss and lamb mortality between mid‐pregnancy and weaning are important economic and welfare issues for the Australian sheep industry. The aim of this study was to determine common causes of ovine abortion and stillbirths based on submissions to veterinary laboratories and identify factors that impact the determination of an aetiological diagnosis. Data for 529 investigations on abortion or stillbirth between 2000 and 2018 were retrieved from four state veterinary laboratories in Western Australia, South Australia, Victoria and Tasmania. An aetiological diagnosis was made for 57% of investigations. Investigations that included placental tissue samples were more than twice as likely to have an aetiological diagnosis compared to investigations without placenta (P = 0.017, 95% confidence interval 1.1, 4.5). Of the investigations where an aetiological diagnosis was made, 81% involved infectious abortion, with Campylobacter spp. (32%), Listeria spp. (25%) and Toxoplasma gondii (9%) being the three most common abortigenic pathogens implicated. The remaining 19% of investigations with an aetiological diagnosis included a wide range of infectious and non‐infectious diseases. Diagnoses made varied year to year and between states. No evidence of exotic abortigenic pathogens were reported. Veterinary practitioners can improve the probability of an aetiological diagnosis by emphasising to farmers the importance of collecting any aborted material, especially placenta, and appropriate storage of the tissues until they can be submitted to the laboratory. Some diseases that cause abortion in Australian sheep have zoonotic potential, and veterinary practitioners play an important role in educating clients about appropriate hygiene when handling pregnant and lambing ewes or any aborted material. [ABSTRACT FROM AUTHOR]

Published
2021
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29. Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) 1.0 : A General Circulation Model for Simulating the Climates of Rocky Planets

Author

Way, Michael J., Aleinov, I., Amundsen, David S., Chandler, M. A., Clune, T. L., Del Genio, A. D., Fujii, Y., Kelley, M., Kiang, N. Y., Sohl, L., Tsigaridis, K., Way, Michael J., Aleinov, I., Amundsen, David S., Chandler, M. A., Clune, T. L., Del Genio, A. D., Fujii, Y., Kelley, M., Kiang, N. Y., Sohl, L., and Tsigaridis, K.

Abstract

Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) is a three-dimensional General Circulation Model (GCM) developed at the NASA Goddard Institute for Space Studies for the modeling of atmospheres of solar system and exoplanetary terrestrial planets. Its parent model, known as ModelE2, is used to simulate modern Earth and near-term paleo-Earth climates. ROCKE-3D is an ongoing effort to expand the capabilities of ModelE2 to handle a broader range of atmospheric conditions, including higher and lower atmospheric pressures, more diverse chemistries and compositions, larger and smaller planet radii and gravity, different rotation rates (from slower to more rapid than modern Earth's, including synchronous rotation), diverse ocean and land distributions and topographies, and potential basic biosphere functions. The first aim of ROCKE-3D is to model planetary atmospheres on terrestrial worlds within the solar system such as paleo-Earth, modern and paleo-Mars, paleo-Venus, and Saturn's moon Titan. By validating the model for a broad range of temperatures, pressures, and atmospheric constituents, we can then further expand its capabilities to those exoplanetary rocky worlds that have been discovered in the past, as well as those to be discovered in the future. We also discuss the current and near-future capabilities of ROCKE-3D as a community model for studying planetary and exoplanetary atmospheres.

Published
2017
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30. Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) 1.0: A General Circulation Model for Simulating the Climates of Rocky Planets

Author

Way, M. J., primary, Aleinov, I., additional, Amundsen, David S., additional, Chandler, M. A., additional, Clune, T. L., additional, Genio, A. D. Del, additional, Fujii, Y., additional, Kelley, M., additional, Kiang, N. Y., additional, Sohl, L., additional, and Tsigaridis, K., additional

Published
2017
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31. The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

Author

Applied Mathematics, Theurich, Gerhard, DeLuca, C., Campbell, T., Liu, F., Saint, K., Vertenstein, M., Chen, J., Oehmke, R., Whitcomb, T., Doyle, J., Wallcraft, A., Iredell, M., Black, T., DaSilva, A., Clune, T., Ferraro, R., Li, P., Kelley, M., Aleinov, I., Balaji, V., Zadeh, N., Jacob, R., Kirtman, B., Giraldo, F., McCarren, D., Sandgathe, S., Peckham, S., Dunlap, R., Applied Mathematics, Theurich, Gerhard, DeLuca, C., Campbell, T., Liu, F., Saint, K., Vertenstein, M., Chen, J., Oehmke, R., Whitcomb, T., Doyle, J., Wallcraft, A., Iredell, M., Black, T., DaSilva, A., Clune, T., Ferraro, R., Li, P., Kelley, M., Aleinov, I., Balaji, V., Zadeh, N., Jacob, R., Kirtman, B., Giraldo, F., McCarren, D., Sandgathe, S., Peckham, S., and Dunlap, R.

Abstract

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users.

Published
2015

32. Future climate change under RCP emission scenarios with GISS ModelE2

Author

Nazarenko, L., primary, Schmidt, G. A., additional, Miller, R. L., additional, Tausnev, N., additional, Kelley, M., additional, Ruedy, R., additional, Russell, G. L., additional, Aleinov, I., additional, Bauer, M., additional, Bauer, S., additional, Bleck, R., additional, Canuto, V., additional, Cheng, Y., additional, Clune, T. L., additional, Del Genio, A. D., additional, Faluvegi, G., additional, Hansen, J. E., additional, Healy, R. J., additional, Kiang, N. Y., additional, Koch, D., additional, Lacis, A. A., additional, LeGrande, A. N., additional, Lerner, J., additional, Lo, K. K., additional, Menon, S., additional, Oinas, V., additional, Perlwitz, J., additional, Puma, M. J., additional, Rind, D., additional, Romanou, A., additional, Sato, M., additional, Shindell, D. T., additional, Sun, S., additional, Tsigaridis, K., additional, Unger, N., additional, Voulgarakis, A., additional, Yao, M.-S., additional, and Zhang, Jinlun, additional

Published
2015
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34. Detection of ovine respiratory syncytial virus in pneumonic lungs from apparently healthy sheep slaughtered at 5 abattoirs in Australia.

Author

Lloyd JB, Clune T, Jacobson C, and Schröder J

Subjects
Humans, Sheep, Animals, Cattle, Abattoirs, Respiratory Syncytial Viruses, Lung, Australia epidemiology, Pneumonia veterinary, Sheep Diseases diagnosis, Sheep Diseases epidemiology, Respiratory Syncytial Virus Infections diagnosis, Respiratory Syncytial Virus Infections epidemiology, Respiratory Syncytial Virus Infections veterinary, Cattle Diseases diagnosis
Abstract

Respiratory disease is one of the main diseases of sheep in many regions globally. Respiratory syncytial virus (RSV) causes severe disease in humans and in calves, but little is known about the role of RSV in sheep. We studied the prevalence of ovine RSV in sheep processed at 5 abattoirs in southern Australia. Bronchial swab samples were collected from 182 consignments of lambs up to 12 months of age and 71 consignments of adult sheep; these were tested for the presence of the virus using a qPCR based on the F gene sequence. Six of the 253 abattoir consignments (2.4%) tested positive for ovine RSV. Four of the positive consignments were lambs and 2 were adult sheep. To our knowledge, this is the first report of the ovine strain of RSV in sheep with pneumonia from Australia. Further research is needed to clarify the role of RSV in pneumonia in sheep., (Copyright and/or publishing rights held by the Canadian Veterinary Medical Association.)

Published
2023

35. Molecular characterisation of the Australian and New Zealand livestock Chlamydia pecorum strains confirms novel but clonal ST23 in association with ovine foetal loss.

Author

Jelocnik M, White RT, Clune T, O'Connell J, Foxwell J, Hair S, Besier S, Tom, Phillips N, Robbins A, Bogema D, Vaz PK, Legione AR, Jenkins C, and Jacobson C

Subjects
Animals, Cattle, Female, Pregnancy, Australia epidemiology, Goats, Livestock, New Zealand epidemiology, Phylogeny, Sheep, Cattle Diseases epidemiology, Chlamydia, Chlamydia Infections epidemiology, Chlamydia Infections veterinary, Goat Diseases, Sheep Diseases epidemiology
Abstract

Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on C. pecorum strains associated with reproductive disease, although whole genome sequencing (WGS) of one abortigenic ST23 C. pecorum strain identified unique features, including a deletion in the CDS1 locus of the chlamydial plasmid. We applied WGS on two ST23 strains detected in aborted and stillborn lambs from Australia and used phylogenetic and comparative analyses to compare these to the other available C. pecorum genomes. To re-evaluate the genetic diversity of contemporary strains, we applied C. pecorum genotyping, and chlamydial plasmid sequencing to a range of C. pecorum positive samples and isolates from ewes, aborted foetuses and stillborn lambs, cattle and a goat from diverse geographical regions across Australia and New Zealand.The two new C. pecorum genomes are nearly identical to the genome of the Australian abortigenic strain including the unique deletion in the chlamydial plasmid. Genotyping revealed that these novel C. pecorum ST23 strains are widespread and associated with sheep abortions on Australian and New Zealand farms. In addition, a goat C. pecorum strain (denoted ST 304) from New Zealand was also characterised. This study expands the C. pecorum genome catalogue and describes a comprehensive molecular characterisation of the novel livestock ST23 strains associated with foetal and lamb mortality., Competing Interests: Declaration of Competing Interest The authors declare that there are no conflicts of interest. The funders had no role in the design of this study, analyses, interpretation of the data, or decision to publish., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Published
2023
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36. Toxoplasma gondii is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: a prospective cohort study.

Author

Clune T, Lockwood A, Hancock S, Thompson AN, Bruce M, Beetson S, Campbell AJ, Glanville E, Brookes D, Trengove C, O'Handley R, and Jacobson C

Subjects
Abortion, Veterinary epidemiology, Animals, Antibodies, Protozoan, Australia epidemiology, Female, Humans, Pregnancy, Prospective Studies, Sheep, Sheep Diseases diagnosis, Toxoplasma, Toxoplasmosis, Animal diagnosis
Abstract

Background: Toxoplasma gondii causes reproductive losses in sheep worldwide, including Australia. The reproductive performance of primiparous ewes is typically lower than for mature, multiparous ewes, and younger ewes are more likely to be immunologically naïve and therefore more susceptible to reproductive disease if T. gondii infection occurs during pregnancy. The aim of this study was to assess the impact of infection with T. gondii on the reproductive performance of primiparous ewes in southern Australia using a prospective cohort study. This will inform the need for targeted control strategies for T. gondii in Australian sheep., Results: Toxoplasma gondii seropositivity using indirect ELISA was detected at 16/28 farms located across southern Australia. Apparent seropositivity to T. gondii was lower in primiparous ewes (1.1, 95% confidence interval (CI) 0.6, 1.8) compared to mature, multiparous ewes (8.1, 95% CI 6.0, 10.5; P < 0.001). Toxoplasma gondii seroconversion during the gestation and lambing period was confirmed for 11/1097 (1.0, 95% CI 0.5, 1.7) of pregnant primiparous ewes that failed to raise a lamb, and 1/161 (0.6, 95% CI 0.1, 2.9) primiparous ewes with confirmed mid-pregnancy abortion., Conclusions: Low frequency of detection of T. gondii seroconversion during gestation and low frequency of seropositivity to T. gondii suggests that toxoplasmosis was not an important contributor to reproductive losses in primiparous ewes on farms located over a wide geographical area in southern Australia., (© 2022. The Author(s).)

Published
2022
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37. Seropositivity to Coxiella burnetii in primiparous and multiparous ewes from southern Australia: A cross-sectional study.

Author

Clune T, Lockwood A, Hancock S, Thompson AN, Beetson S, Bruce M, Campbell AJ, Glanville E, Brookes D, Trengove C, O'Handley R, and Jacobson C

Subjects
Animals, Australia epidemiology, Cross-Sectional Studies, Female, Pregnancy, Seroepidemiologic Studies, Sheep, Coxiella burnetii, Q Fever epidemiology, Q Fever veterinary, Sheep Diseases epidemiology
Abstract

The role of infectious diseases including coxiellosis in causing poorer reproductive performance of primiparous ewes are not well studied. The aims of this study were to determine if natural exposure to Coxiella burnetii is widespread in breeding ewes and whether seropositivity is associated with poor reproductive performance of primiparous ewes. Seropositivity to Coxiella burnetii was 0.08% (CI95% 0.01, 0.36) in primiparous ewes and 0.36% (CI95% 0.07, 1.14) in mature ewes. Coxiella burnetii was not detected in aborted or stillborn lambs using qPCR. These findings suggest C. burnetii infection was unlikely to be an important contributor to abortion and perinatal mortalities observed for primiparous ewe flocks, and exposure to C. burnetii was not widespread in ewes on farms located over wide geographical region of southern Australia. Whilst ewes on these farms were not an important reservoir for C. burnetii, sporadic zoonotic transmission from sheep is reported and has public health implications., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2022
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38. Abortion and Lamb Mortality between Pregnancy Scanning and Lamb Marking for Maiden Ewes in Southern Australia.

Author

Clune T, Lockwood A, Hancock S, Thompson AN, Beetson S, Campbell AJD, Glanville E, Brookes D, Trengove C, O'Handley R, Kearney G, and Jacobson C

Abstract

The contribution of abortions to the overall mortality of lambs born to maiden (primiparous) ewes in Australia remains unclear. This cohort study aimed to quantify abortion and lamb mortality for ewe lambs and maiden Merino two-tooth ewes. Lamb mortality from pregnancy scanning to marking were determined for 19 ewe lamb and 11 Merino two-tooth ewe flocks across southern Australia. Average lamb mortality from scanning to marking was 35.8% (range 14.3-71.1%) for the ewe lambs and 29.4% (range 19.7-52.7%) for the two-tooth ewes. Mid-pregnancy abortion was detected in 5.7% of ewes (range 0-50%) in the ewe lamb flocks and 0.9% of ewes (range 0-4.4%) in the two-tooth ewe flocks. Mid-pregnancy abortion affecting ≥2% of ewes was observed in 6/19 ewe lamb flocks and 2/11 two-tooth ewe flocks. Lamb mortality from birth to marking represented the greatest contributor to foetal and lamb mortality after scanning, but mid-pregnancy abortion was an important contributor to lamb mortality in some ewe lamb flocks. Variability between the flocks indicates scope to improve the overall reproductive performance for maiden ewes by reducing foetal and lamb losses. Addressing mid-pregnancy abortion may improve the reproductive performance in some flocks.

Published
2021
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39. Neospora caninum is not an important contributor to poor reproductive performance of primiparous ewes from southern Australia: evidence from a cross-sectional study.

Author

Clune T, Lockwood A, Hancock S, Bruce M, Thompson AN, Beetson S, Campbell AJ, Glanville E, Brookes D, Trengove C, O'Handley R, and Jacobson C

Subjects
Animals, Antibodies, Protozoan, Australia epidemiology, Cross-Sectional Studies, Female, Pregnancy, Seroepidemiologic Studies, Sheep, South Australia, Coccidiosis epidemiology, Coccidiosis veterinary, Neospora
Abstract

Neospora caninum has been implicated as a sporadic cause of abortion and perinatal deaths in sheep flocks globally. However, its significance as a reproductive pathogen for sheep in Australia remains unknown. The aims of this study were to (i) determine the seroprevalence of N. caninum in Australian breeding ewes and (ii) examine if natural exposure to N. caninum is associated with poor reproductive performance of primiparous ewes in southern Australia. Thirty flocks of primiparous ewes (aged 1-2 years old at lambing) from 28 farms in three states (Western Australia, South Australia and Victoria) were monitored between mating and lamb marking. Blood samples were also collected from multiparous mature ewes (aged 3 years or older) at each farm. Seroprevalence for anti-N. caninum IgG using indirect ELISA was determined for a subset of primiparous ewes that were predominantly determined to be pregnant and subsequently failed to rear a lamb (n = 1279) and randomly selected mature multiparous ewes with unknown reproductive status (n = 558). Neopsora caninum apparent seroprevalence was 0.16% (95% confidence interval 0.03%, 0.5%) in primiparous ewes, with seropositivity identified in two ewes from farms located in South Australia and Victoria. There was no evidence of seropositivity in mature ewes with apparent seroprevalence 0% (0%, 0.45%). These findings suggest that N. caninum infection was not widespread in primiparous ewes or mature multiparous ewes on these farms, and exposure to N. caninum infection was unlikely to explain abortion and perinatal mortalities observed for primiparous ewes., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Published
2021
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40. Real-Time Fluorometric Isothermal LAMP Assay for Detection of Chlamydia pecorum in Rapidly Processed Ovine Abortion Samples: A Veterinary Practitioner's Perspective.

Author

Clune T, Anstey S, Kasimov V, Jacobson C, and Jelocnik M

Abstract

Traditional methods of detecting Chlamydia pecorum in tissue samples such as polymerase chain reaction or cell culture are laborious and costly. We evaluated the use of a previously developed C. pecorum LAMP assay using minimally processed ovine samples. Cotyledon ( n = 16), foetal liver ( n = 22), foetal lung ( n = 2), and vaginal ( n = 6) swabs, in addition to cotyledon ( n = 6) and foetal liver ( n = 8) tissue samples, were rapidly processed and used for LAMP testing without DNA extraction. Overall, LAMP test results were highly congruent with the in-house reference qPCR, with 80.43% (37/46; 72.73% positive agreement (PA); 84.75% negative agreement (NA)) overall agreeance for swab samples, and 85.71% (12/14; 80% PA; 88.89% NA) overall agreeance for tissue samples. Out of the 11 total discrepant results, discrepancy was mainly observed in samples ( n = 10) with less than 100 copies/µL C. pecorum DNA. While sensitivity could be improved, the simplicity, low cost, and accuracy of detection makes this test amenable for use at point-of-care for detecting C. pecorum in sheep.

Published
2021
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41. Chlamydia pecorum detection in aborted and stillborn lambs from Western Australia.

Author

Clune T, Besier S, Hair S, Hancock S, Lockwood A, Thompson A, Jelocnik M, and Jacobson C

Subjects
Abortion, Veterinary microbiology, Animals, Chlamydia Infections epidemiology, Chlamydia Infections microbiology, Female, Incidence, Male, Prevalence, Sheep, Sheep Diseases microbiology, Sheep, Domestic, Stillbirth epidemiology, Western Australia epidemiology, Abortion, Veterinary epidemiology, Chlamydia isolation & purification, Chlamydia Infections veterinary, Sheep Diseases epidemiology, Stillbirth veterinary
Abstract

Lamb survival is an important welfare and productivity issue for sheep industries worldwide. Lower lamb survival has been reported for primiparous ewes, but the causes of this are not well studied. The aim of this study was to determine causes of perinatal deaths for lambs born to primiparous ewes in Western Australia, and identify if infectious diseases are implicated. Lamb mortality from birth to marking were determined for 11 primiparous ewe flocks on 10 farms in Western Australia. Lamb mortality from birth to marking averaged 14% for single-born and 26% for multiple-born lambs. Lamb necropsies (n = 298) identified starvation-mismosthering-exposure (34%), dystocia (24%) and stillbirth (15%) as the most common causes of perinatal lamb death. There was no evidence of exotic abortigenic pathogens in aborted and stillborn lambs (n = 35). Chlamydia pecorum was detected by qPCR in 15/35 aborted and stillborn lambs on 5/6 farms. Preliminary molecular characterisation of C. pecorum detected in samples from aborted and stillborn lambs (n = 8) using both Multilocus Sequence Typing and ompA genotyping indicated all strains were genetically identical to previously described pathogenic livestock strains, denoted ST23, and dissimilar to gastrointestinal strains. High frequency of detection of a pathogenic C. pecorum strains ST23 associated with ovine abortion and stillbirth on multiple farms located across a wide geographic area has not been previously reported. Chlamydia pecorum may contribute to reproductive wastage for primiparous sheep in Western Australia. Further investigation to understand C. pecorum epidemiology and impact on sheep reproduction is warranted.

Published
2021
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42. Chlamydia pecorum -Induced Arthritis in Experimentally and Naturally Infected Sheep.

Author

Ostfeld N, Islam MM, Jelocnik M, Hilbe M, Sydler T, Hartnack S, Jacobson C, Clune T, Marsh I, Sales N, Polkinghorne A, and Borel N

Subjects
Animals, Cattle, Sheep, Sheep, Domestic, Swine, Arthritis, Infectious veterinary, Cattle Diseases, Chlamydia, Chlamydia Infections veterinary, Phascolarctidae, Sheep Diseases, Swine Diseases
Abstract

Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum .

Published
2021
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43. Was Venus the First Habitable World of our Solar System?

Author

Way MJ, Del Genio AD, Kiang NY, Sohl LE, Grinspoon DH, Aleinov I, Kelley M, and Clune T

Abstract

Present-day Venus is an inhospitable place with surface temperatures approaching 750K and an atmosphere 90 times as thick as Earth's. Billions of years ago the picture may have been very different. We have created a suite of 3-D climate simulations using topographic data from the Magellan mission, solar spectral irradiance estimates for 2.9 and 0.715 Gya, present-day Venus orbital parameters, an ocean volume consistent with current theory, and an atmospheric composition estimated for early Venus. Using these parameters we find that such a world could have had moderate temperatures if Venus had a rotation period slower than ~16 Earth days, despite an incident solar flux 46-70% higher than Earth receives. At its current rotation period, Venus's climate could have remained habitable until at least 715 million years ago. These results demonstrate the role rotation and topography play in understanding the climatic history of Venus-like exoplanets discovered in the present epoch.

Published
2016
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