Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes
- Sloan, Shelly, Jenvey, C. J., Piedrafita, David, Preston, Sarah, Stear, Michael
- Authors: Sloan, Shelly , Jenvey, C. J. , Piedrafita, David , Preston, Sarah , Stear, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: Bmc Biotechnology Vol. 21, no. 1 (May 17 2021), p.
- Full Text:
- Reviewed:
- Authors: Sloan, Shelly , Jenvey, C. J. , Piedrafita, David , Preston, Sarah , Stear, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: Bmc Biotechnology Vol. 21, no. 1 (May 17 2021), p.
- Full Text:
- Reviewed:
Differential associations of hypoxia, sleep fragmentation, and depressive symptoms with cognitive dysfunction in obstructive sleep apnea
- Alomri, Ridwan, Kennedy, Gerard, Wali, Siraj, Ahejaili, Faris, Robinson, Stephen
- Authors: Alomri, Ridwan , Kennedy, Gerard , Wali, Siraj , Ahejaili, Faris , Robinson, Stephen
- Date: 2021
- Type: Text , Journal article
- Relation: Sleep Vol. 44, no. 4 (2021), p.
- Full Text:
- Reviewed:
- Description: Obstructive sleep apnea (OSA) is characterized by recurrent episodes of partial or complete cessation of breathing during sleep and increased effort to breathe. This study examined patients who underwent overnight polysomnographic studies in a major sleep laboratory in Saudi Arabia. The study aimed to determine the extent to which intermittent hypoxia, sleep disruption, and depressive symptoms are independently associated with cognitive impairments in OSA. In the sample of 90 participants, 14 had no OSA, 30 mild OSA, 23 moderate OSA, and 23 severe OSA. The findings revealed that hypoxia and sleep fragmentation are independently associated with impairments of sustained attention and reaction time (RT). Sleep fragmentation, but not hypoxia, was independently associated with impairments in visuospatial deficits. Depressive symptoms were independently associated with impairments in the domains of sustained attention, RT, visuospatial ability, and semantic and episodic autobiographical memories. Since the depressive symptoms are independent of hypoxia and sleep fragmentation, effective reversal of cognitive impairment in OSA may require treatment interventions that target each of these factors. © Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.
- Authors: Alomri, Ridwan , Kennedy, Gerard , Wali, Siraj , Ahejaili, Faris , Robinson, Stephen
- Date: 2021
- Type: Text , Journal article
- Relation: Sleep Vol. 44, no. 4 (2021), p.
- Full Text:
- Reviewed:
- Description: Obstructive sleep apnea (OSA) is characterized by recurrent episodes of partial or complete cessation of breathing during sleep and increased effort to breathe. This study examined patients who underwent overnight polysomnographic studies in a major sleep laboratory in Saudi Arabia. The study aimed to determine the extent to which intermittent hypoxia, sleep disruption, and depressive symptoms are independently associated with cognitive impairments in OSA. In the sample of 90 participants, 14 had no OSA, 30 mild OSA, 23 moderate OSA, and 23 severe OSA. The findings revealed that hypoxia and sleep fragmentation are independently associated with impairments of sustained attention and reaction time (RT). Sleep fragmentation, but not hypoxia, was independently associated with impairments in visuospatial deficits. Depressive symptoms were independently associated with impairments in the domains of sustained attention, RT, visuospatial ability, and semantic and episodic autobiographical memories. Since the depressive symptoms are independent of hypoxia and sleep fragmentation, effective reversal of cognitive impairment in OSA may require treatment interventions that target each of these factors. © Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.
Historical reports of quolls in Victoria’s south-west
- Authors: Wallis, Robert
- Date: 2021
- Type: Text , Journal article
- Relation: Victorian Naturalist Vol. 138, no. 3 (2021), p. 78-84
- Full Text:
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- Description: The Eastern Quoll Dasyurus viverrinus is now extinct on mainland Australia, but was once common in southwestern Victoria. It was persecuted by landholders for its predation of poultry, but also suffered dramatic declines in population through an unknown disease from about 140 years ago. Eastern Quolls were also considered significant predators of young European Rabbits Oryctolagus cuniculus. The Spot-tailed Quoll D. maculatus was historically widespread though uncommon in south-western Victoria, but now is confined there to only a couple of sites. © 2021, Field Naturalists Club of Victoria. All rights reserved.
- Authors: Wallis, Robert
- Date: 2021
- Type: Text , Journal article
- Relation: Victorian Naturalist Vol. 138, no. 3 (2021), p. 78-84
- Full Text:
- Reviewed:
- Description: The Eastern Quoll Dasyurus viverrinus is now extinct on mainland Australia, but was once common in southwestern Victoria. It was persecuted by landholders for its predation of poultry, but also suffered dramatic declines in population through an unknown disease from about 140 years ago. Eastern Quolls were also considered significant predators of young European Rabbits Oryctolagus cuniculus. The Spot-tailed Quoll D. maculatus was historically widespread though uncommon in south-western Victoria, but now is confined there to only a couple of sites. © 2021, Field Naturalists Club of Victoria. All rights reserved.
Insights from long-term shorebird monitoring for tracking change in ecological character of Australasian Ramsar sites
- Hansen, Birgita, Szabo, Judit, Fuller, Richard, Clemens, Robert, Rogers, Danny, Milton, David
- Authors: Hansen, Birgita , Szabo, Judit , Fuller, Richard , Clemens, Robert , Rogers, Danny , Milton, David
- Date: 2021
- Type: Text , Journal article
- Relation: Biological Conservation Vol. 260, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The Ramsar Convention is the centrepiece of international efforts for wetland conservation, aiming to maintain the ecological character of wetlands through holistic ecosystem management. Here, we review studies on shorebird populations at individual Australasian Ramsar sites and compare these against original listings under Criterion 6 to determine if there have been potential changes in ecological character. One to 12 migratory shorebird species have declined at four New Zealand and 18 Australian Ramsar sites over a 12 to 36-year period, resulting in 22 species (at 13 sites) no longer reaching Criterion 6 thresholds for Ramsar designation. In addition, 10 species at six Australian sites had exceeded the Limits of Acceptable Change. Despite these concerning results, there were remarkably few published site-based determinations of listed shorebird species' trends (and even fewer that were ≤5 years old). This is especially surprising since shorebird populations are regularly monitored at 27 out of 35 Australasian Ramsar sites (listed on the basis of one or more shorebird species). Thus, despite the volume of data available for analysis, long-term shorebird monitoring provides only limited insights about Ramsar ecological character. The value of these data would be greatly enhanced through complementary monitoring of other ecological characters at sites, particularly where shorebird populations provide early warning signs of potential deterioration. The main impediment to achieving a good understanding of how Ramsar sites are changing in Australasia appears to be a lack of analysis and centralised system for data and analytics, rather than a lack of monitoring data. © 2021 Elsevier Ltd
- Authors: Hansen, Birgita , Szabo, Judit , Fuller, Richard , Clemens, Robert , Rogers, Danny , Milton, David
- Date: 2021
- Type: Text , Journal article
- Relation: Biological Conservation Vol. 260, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The Ramsar Convention is the centrepiece of international efforts for wetland conservation, aiming to maintain the ecological character of wetlands through holistic ecosystem management. Here, we review studies on shorebird populations at individual Australasian Ramsar sites and compare these against original listings under Criterion 6 to determine if there have been potential changes in ecological character. One to 12 migratory shorebird species have declined at four New Zealand and 18 Australian Ramsar sites over a 12 to 36-year period, resulting in 22 species (at 13 sites) no longer reaching Criterion 6 thresholds for Ramsar designation. In addition, 10 species at six Australian sites had exceeded the Limits of Acceptable Change. Despite these concerning results, there were remarkably few published site-based determinations of listed shorebird species' trends (and even fewer that were ≤5 years old). This is especially surprising since shorebird populations are regularly monitored at 27 out of 35 Australasian Ramsar sites (listed on the basis of one or more shorebird species). Thus, despite the volume of data available for analysis, long-term shorebird monitoring provides only limited insights about Ramsar ecological character. The value of these data would be greatly enhanced through complementary monitoring of other ecological characters at sites, particularly where shorebird populations provide early warning signs of potential deterioration. The main impediment to achieving a good understanding of how Ramsar sites are changing in Australasia appears to be a lack of analysis and centralised system for data and analytics, rather than a lack of monitoring data. © 2021 Elsevier Ltd
Lack of effectiveness of 13-valent pneumococcal conjugate vaccination against pneumococcal carriage density in Papua New Guinean infants
- Britton, Kathryn, Pickering, Janessa, Pomat, William, de Gier, Camilla, Greenhill, Andrew
- Authors: Britton, Kathryn , Pickering, Janessa , Pomat, William , de Gier, Camilla , Greenhill, Andrew
- Date: 2021
- Type: Text , Journal article
- Relation: Vaccine Vol. 39, no. 38 (2021), p. 5401-5409
- Full Text:
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- Description: Background: Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. Methods: Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. Results: Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log10 genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. Conclusion: PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered. © 2021 The Authors. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Andrew Greenhill" is provided in this record**
- Authors: Britton, Kathryn , Pickering, Janessa , Pomat, William , de Gier, Camilla , Greenhill, Andrew
- Date: 2021
- Type: Text , Journal article
- Relation: Vaccine Vol. 39, no. 38 (2021), p. 5401-5409
- Full Text:
- Reviewed:
- Description: Background: Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. Methods: Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. Results: Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log10 genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. Conclusion: PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered. © 2021 The Authors. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Andrew Greenhill" is provided in this record**
Outfoxing the fox : effect of prey odor on fox behavior in a pastoral landscape
- Andrewartha, Tim, Evans, Maldwyn, Batson, William, Manning, Adrian, Barton, Philip
- Authors: Andrewartha, Tim , Evans, Maldwyn , Batson, William , Manning, Adrian , Barton, Philip
- Date: 2021
- Type: Text , Journal article
- Relation: Conservation Science and Practice Vol. 3, no. 12 (2021), p.
- Full Text:
- Reviewed:
- Description: Invasive mammalian predators have had a devastating effect on native species globally. The European red fox (Vulpes vulpes) is one such species where it has been introduced in Australia. A novel but unexplored tactic to reduce the impact of mammalian predators is the use of unrewarded prey odors to undermine the effectiveness of olfactory hunting behavior. To test the viability of unrewarded prey odors in an applied setting we investigated how foxes responded to the odors of three different prey species. We used the odors of two locally extinct native Australian marsupials; the eastern quoll (a smaller carnivore) and eastern bettong (a fungivore), and the European rabbit, an introduced herbivore. Conducting our research over a period of 3 weeks in a pastoral environment in South-eastern Australia, we used video observations of foxes' behaviors, as they encountered the different odors. We found a reduction in the number of fox visits to bettong odors in the third week. In contrast, we observed a sustained number of visits to rabbit odors. Foxes also spent more time investigating rabbit odors and displayed longer durations of vigilance behavior at quoll odors. Our results support the hypothesis that the exposure of wild foxes to unrewarded odors of novel prey species can reduce their interest in these odors, which might translate to a reduction in predation pressure. Our results also suggest, however, that olfactory pre-exposure may not be as effective at reducing fox interest in a competitor species' odor. © 2021 The Authors. Conservation Science and Practice published by Wiley Periodicals LLC. on behalf of Society for Conservation Biology
- Authors: Andrewartha, Tim , Evans, Maldwyn , Batson, William , Manning, Adrian , Barton, Philip
- Date: 2021
- Type: Text , Journal article
- Relation: Conservation Science and Practice Vol. 3, no. 12 (2021), p.
- Full Text:
- Reviewed:
- Description: Invasive mammalian predators have had a devastating effect on native species globally. The European red fox (Vulpes vulpes) is one such species where it has been introduced in Australia. A novel but unexplored tactic to reduce the impact of mammalian predators is the use of unrewarded prey odors to undermine the effectiveness of olfactory hunting behavior. To test the viability of unrewarded prey odors in an applied setting we investigated how foxes responded to the odors of three different prey species. We used the odors of two locally extinct native Australian marsupials; the eastern quoll (a smaller carnivore) and eastern bettong (a fungivore), and the European rabbit, an introduced herbivore. Conducting our research over a period of 3 weeks in a pastoral environment in South-eastern Australia, we used video observations of foxes' behaviors, as they encountered the different odors. We found a reduction in the number of fox visits to bettong odors in the third week. In contrast, we observed a sustained number of visits to rabbit odors. Foxes also spent more time investigating rabbit odors and displayed longer durations of vigilance behavior at quoll odors. Our results support the hypothesis that the exposure of wild foxes to unrewarded odors of novel prey species can reduce their interest in these odors, which might translate to a reduction in predation pressure. Our results also suggest, however, that olfactory pre-exposure may not be as effective at reducing fox interest in a competitor species' odor. © 2021 The Authors. Conservation Science and Practice published by Wiley Periodicals LLC. on behalf of Society for Conservation Biology
Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial
- Zilko, Joseph, Harley, Dan, Hansen, Birgita, Pavlova, Alexandra, Sunnucks, Paul
- Authors: Zilko, Joseph , Harley, Dan , Hansen, Birgita , Pavlova, Alexandra , Sunnucks, Paul
- Date: 2020
- Type: Text , Journal article
- Relation: Molecular Ecology Vol. 29, no. 16 (2020), p. 2978-2993
- Full Text:
- Reviewed:
- Description: Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III, to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179–237 per trait), and computed revised coefficients, FHby group and F^IIIby group, adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FHby group) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population. © 2020 John Wiley & Sons Ltd
- Authors: Zilko, Joseph , Harley, Dan , Hansen, Birgita , Pavlova, Alexandra , Sunnucks, Paul
- Date: 2020
- Type: Text , Journal article
- Relation: Molecular Ecology Vol. 29, no. 16 (2020), p. 2978-2993
- Full Text:
- Reviewed:
- Description: Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III, to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179–237 per trait), and computed revised coefficients, FHby group and F^IIIby group, adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FHby group) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population. © 2020 John Wiley & Sons Ltd
Blood and saliva-derived exomes from healthy Caucasian subjects do not display overt evidence of somatic mosaicism
- Hall, Nathan, Mamrot, Jared, Frampton, Chris, Read, Prue, Steele, Edward, Bischoff, Robert, Lindley, Robyn
- Authors: Hall, Nathan , Mamrot, Jared , Frampton, Chris , Read, Prue , Steele, Edward , Bischoff, Robert , Lindley, Robyn
- Date: 2020
- Type: Text , Journal article
- Relation: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis Vol. 821, no. (2020), p.
- Full Text:
- Reviewed:
- Description: Somatic mosaicism is a normal occurrence during development in the tissues and organs. As part of establishing a “healthy population “(HP) background or base-line, we investigated whether such mosaicism can be routinely detected in the circulating DNA secured from a rigorously designed healthy human liquid biopsy clinical trial (saliva, blood). We deployed next generation (NG) whole exome sequencing (WES) at median exome coverage rates of 97.2 % (-to-30x) and 70.0 % (-to-100x). We found that somatic mosaicism is not detectable by such standard bulk WES sequencing assays in saliva and blood DNA in 24 normal healthy Caucasians of both sexes from 18 to 60 years of age. We conclude that for circulating DNA using standard WES no novel somatic mutational variants can be detected in protein-coding regions of normal healthy subjects. This implies that the extent within normal tissues of somatic mosaicism must be at a lower level, below the detection threshold, for these circulating DNA WES read depths. © 2020 The Author(s)
- Authors: Hall, Nathan , Mamrot, Jared , Frampton, Chris , Read, Prue , Steele, Edward , Bischoff, Robert , Lindley, Robyn
- Date: 2020
- Type: Text , Journal article
- Relation: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis Vol. 821, no. (2020), p.
- Full Text:
- Reviewed:
- Description: Somatic mosaicism is a normal occurrence during development in the tissues and organs. As part of establishing a “healthy population “(HP) background or base-line, we investigated whether such mosaicism can be routinely detected in the circulating DNA secured from a rigorously designed healthy human liquid biopsy clinical trial (saliva, blood). We deployed next generation (NG) whole exome sequencing (WES) at median exome coverage rates of 97.2 % (-to-30x) and 70.0 % (-to-100x). We found that somatic mosaicism is not detectable by such standard bulk WES sequencing assays in saliva and blood DNA in 24 normal healthy Caucasians of both sexes from 18 to 60 years of age. We conclude that for circulating DNA using standard WES no novel somatic mutational variants can be detected in protein-coding regions of normal healthy subjects. This implies that the extent within normal tissues of somatic mosaicism must be at a lower level, below the detection threshold, for these circulating DNA WES read depths. © 2020 The Author(s)
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals
- Surendran, Praveen, Feofanova, Elena, Lahrouchi, Najim, Ntalla, Ionna, Karthikeyan, Savita, Cook, James, Chen, Lingyan, Mifsud, Borbala, Yao, Chen, Kraja, Aldi, Cartwright, James, Hellwege, Jacklyn, Giri, Ayush, Tragante, Vinicius, Thorleifsson, Gudmar, Liu, Dajiang, Prins, Bram, Stewart, Isobel, Cabrera, Claude, Eales, James, Akbarov, Artur, Auer, Paul, Charchar, Fadi, Howson, Joanna, LifeLines Cohort, Study, Epic, C. V. D., Epic InterAct, Understanding Society Scientific, Group, Million Veteran, Program
- Authors: Surendran, Praveen , Feofanova, Elena , Lahrouchi, Najim , Ntalla, Ionna , Karthikeyan, Savita , Cook, James , Chen, Lingyan , Mifsud, Borbala , Yao, Chen , Kraja, Aldi , Cartwright, James , Hellwege, Jacklyn , Giri, Ayush , Tragante, Vinicius , Thorleifsson, Gudmar , Liu, Dajiang , Prins, Bram , Stewart, Isobel , Cabrera, Claude , Eales, James , Akbarov, Artur , Auer, Paul , Charchar, Fadi , Howson, Joanna , LifeLines Cohort, Study , Epic, C. V. D. , Epic InterAct , Understanding Society Scientific, Group , Million Veteran, Program
- Date: 2020
- Type: Text , Journal article
- Relation: Nature Genetics Vol. 52, no. 12 (2020), p. 1314-1332
- Full Text:
- Reviewed:
- Description: Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency ≤ 0.01) variant BP associations (P < 5 × 10−8), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were ~8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. There are 286 authors of this articles not all are listed in this record.
- Authors: Surendran, Praveen , Feofanova, Elena , Lahrouchi, Najim , Ntalla, Ionna , Karthikeyan, Savita , Cook, James , Chen, Lingyan , Mifsud, Borbala , Yao, Chen , Kraja, Aldi , Cartwright, James , Hellwege, Jacklyn , Giri, Ayush , Tragante, Vinicius , Thorleifsson, Gudmar , Liu, Dajiang , Prins, Bram , Stewart, Isobel , Cabrera, Claude , Eales, James , Akbarov, Artur , Auer, Paul , Charchar, Fadi , Howson, Joanna , LifeLines Cohort, Study , Epic, C. V. D. , Epic InterAct , Understanding Society Scientific, Group , Million Veteran, Program
- Date: 2020
- Type: Text , Journal article
- Relation: Nature Genetics Vol. 52, no. 12 (2020), p. 1314-1332
- Full Text:
- Reviewed:
- Description: Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency ≤ 0.01) variant BP associations (P < 5 × 10−8), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were ~8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. There are 286 authors of this articles not all are listed in this record.
Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea
- Jonduo, Marinjho, Wawae, Lorry, Masiria, Geraldine, Suda, Wataru, Hattori, Masahira, Takayasu, Lena, Abdad, Mohammad, Greenhill, Andrew, Horwood, Paul, Pomat, William, Umezaki, Masahiro
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
- Full Text:
- Reviewed:
- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
- Full Text:
- Reviewed:
- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
Quantifying shifts in topic popularity over 44 years of austral ecology
- Westgate, Martin, Barton, Philip, Lindenmayer, David, Andrew, Nigel
- Authors: Westgate, Martin , Barton, Philip , Lindenmayer, David , Andrew, Nigel
- Date: 2020
- Type: Text , Journal article
- Relation: Austral Ecology Vol. 45, no. 6 (2020), p. 663-671
- Full Text:
- Reviewed:
- Description: The Ecological Society of Australia was founded in 1959, and the society’s journal was first published in 1976. To examine how research published in the society’s journal has changed over this time, we used text mining to quantify themes and trends in the body of work published by the Australian Journal of Ecology and Austral Ecology from 1976 to 2019. We used topic models to identify 30 ‘topics’ within 2778 full-text articles in 246 issues of the journal, followed by mixed modelling to identify topics with above-average or below-average popularity in terms of the number of publications or citations that they contain. We found high inter-decadal turnover in research topics, with an early emphasis on highly specific ecosystems or processes giving way to a modern emphasis on community, spatial and fire ecology, invasive species and statistical modelling. Despite an early focus on Australian research, papers discussing South American ecosystems are now among the fastest-growing and most frequently cited topics in the journal. Topics that were growing fastest in publication rates were not always the same as those with high citation rates. Our results provide a systematic breakdown of the topics that Austral Ecology authors and editors have chosen to research, publish and cite through time, providing a valuable window into the historical and emerging foci of the journal. © 2020 Ecological Society of Australia
- Authors: Westgate, Martin , Barton, Philip , Lindenmayer, David , Andrew, Nigel
- Date: 2020
- Type: Text , Journal article
- Relation: Austral Ecology Vol. 45, no. 6 (2020), p. 663-671
- Full Text:
- Reviewed:
- Description: The Ecological Society of Australia was founded in 1959, and the society’s journal was first published in 1976. To examine how research published in the society’s journal has changed over this time, we used text mining to quantify themes and trends in the body of work published by the Australian Journal of Ecology and Austral Ecology from 1976 to 2019. We used topic models to identify 30 ‘topics’ within 2778 full-text articles in 246 issues of the journal, followed by mixed modelling to identify topics with above-average or below-average popularity in terms of the number of publications or citations that they contain. We found high inter-decadal turnover in research topics, with an early emphasis on highly specific ecosystems or processes giving way to a modern emphasis on community, spatial and fire ecology, invasive species and statistical modelling. Despite an early focus on Australian research, papers discussing South American ecosystems are now among the fastest-growing and most frequently cited topics in the journal. Topics that were growing fastest in publication rates were not always the same as those with high citation rates. Our results provide a systematic breakdown of the topics that Austral Ecology authors and editors have chosen to research, publish and cite through time, providing a valuable window into the historical and emerging foci of the journal. © 2020 Ecological Society of Australia
Regulation of the rabbit's once-daily pattern of nursing : A circadian or hourglass-dependent process?
- Apel, Sabine, Hudson, Robyn, Coleman, Grahame, Rodel, Heiko, Kennedy, Gerard
- Authors: Apel, Sabine , Hudson, Robyn , Coleman, Grahame , Rodel, Heiko , Kennedy, Gerard
- Date: 2020
- Type: Text , Journal article
- Relation: Chronobiology International Vol. 37, no. 8 (2020), p. 1151-1162
- Full Text:
- Reviewed:
- Description: The European rabbitOryctolagus cuniculushas an unusual pattern of nursing behavior. After giving birth in a nursery burrow (or laboratory nest box), the mother immediately leaves the young and only returns to nurse for a few minutes once approximately every 24 h. It has been assumed this schedule, like a variety of other functions in the rabbit, is under circadian control. This assumption has been largely based on findings from mothers only permitted restricted access to their young once every 24 h. However, in nature and in the laboratory, mothers with free access to young show nursing visits with a periodicity shorter than 24 h, that does not correspond to other behavioral and physiological rhythms entrained to the prevailing 24 h light/dark (LD) cycle. To investigate how this unusual, apparently non-circadian pattern might be regulated, we conducted two experiments using female Dutch-belted rabbits housed individually in cages designed to automatically register feeding activity and nest box visits. In Experiment 1 we recorded the behavior of 17 mothers with free access to their young under five different LD cycles with long photo and short scotoperiods, spanning the limits of entrainment of the rabbit's circadian system. Whereas feeding rhythms were entrained by LD cycles within the rabbit's circadian range of entrainment, nursing visits showed a consistently shorter periodicity regardless of the LD regimen, largely independent of the circadian system. In Experiment 2 we tested further 12 mothers under more conventional LD 16:8 cycles but "trained" by having access to the nest box restricted to 1 h at the same time each day for the first 7 d of nursing. Mothers were then allowed free access either when their young were left in the box (n= 6), or when the litter had been permanently removed (n= 6). Mothers with pups still present returned to nurse them on the following days according to a similarly advancing pattern to the mothers of Experiment 1 despite the previous 7 d of "training" to an experimentally enforced 24 h nursing schedule as commonly used in previous studies of rabbit maternal behavior. Mothers whose pups had been removed entered the box repeatedly several times on the first day of unrestricted access, but on subsequent days did so only rarely, and at times of day apparently unrelated to the previously scheduled access. We conclude that the pattern of the rabbit's once-daily nursing visits has a periodicity largely independent of the circadian system, and that this is reset at each nursing. When nursing fails to occur nest box visits cease abruptly, with mothers making few or no subsequent visits. Together, these findings suggest that the rabbit's once-daily pattern of nursing is regulated by an hourglass-type process with a period less than 24 h that is reset at each nursing, rather than by a circadian oscillator. Such a mechanism might be particularly adaptive for rhythms of short duration that should end abruptly with a sudden change in context such as death or weaning of the young.
- Description: This work was supported by the Australian Federal Government via a Postgraduate PhD Scholarship for Sabibe Apel [APA SA 1].
- Authors: Apel, Sabine , Hudson, Robyn , Coleman, Grahame , Rodel, Heiko , Kennedy, Gerard
- Date: 2020
- Type: Text , Journal article
- Relation: Chronobiology International Vol. 37, no. 8 (2020), p. 1151-1162
- Full Text:
- Reviewed:
- Description: The European rabbitOryctolagus cuniculushas an unusual pattern of nursing behavior. After giving birth in a nursery burrow (or laboratory nest box), the mother immediately leaves the young and only returns to nurse for a few minutes once approximately every 24 h. It has been assumed this schedule, like a variety of other functions in the rabbit, is under circadian control. This assumption has been largely based on findings from mothers only permitted restricted access to their young once every 24 h. However, in nature and in the laboratory, mothers with free access to young show nursing visits with a periodicity shorter than 24 h, that does not correspond to other behavioral and physiological rhythms entrained to the prevailing 24 h light/dark (LD) cycle. To investigate how this unusual, apparently non-circadian pattern might be regulated, we conducted two experiments using female Dutch-belted rabbits housed individually in cages designed to automatically register feeding activity and nest box visits. In Experiment 1 we recorded the behavior of 17 mothers with free access to their young under five different LD cycles with long photo and short scotoperiods, spanning the limits of entrainment of the rabbit's circadian system. Whereas feeding rhythms were entrained by LD cycles within the rabbit's circadian range of entrainment, nursing visits showed a consistently shorter periodicity regardless of the LD regimen, largely independent of the circadian system. In Experiment 2 we tested further 12 mothers under more conventional LD 16:8 cycles but "trained" by having access to the nest box restricted to 1 h at the same time each day for the first 7 d of nursing. Mothers were then allowed free access either when their young were left in the box (n= 6), or when the litter had been permanently removed (n= 6). Mothers with pups still present returned to nurse them on the following days according to a similarly advancing pattern to the mothers of Experiment 1 despite the previous 7 d of "training" to an experimentally enforced 24 h nursing schedule as commonly used in previous studies of rabbit maternal behavior. Mothers whose pups had been removed entered the box repeatedly several times on the first day of unrestricted access, but on subsequent days did so only rarely, and at times of day apparently unrelated to the previously scheduled access. We conclude that the pattern of the rabbit's once-daily nursing visits has a periodicity largely independent of the circadian system, and that this is reset at each nursing. When nursing fails to occur nest box visits cease abruptly, with mothers making few or no subsequent visits. Together, these findings suggest that the rabbit's once-daily pattern of nursing is regulated by an hourglass-type process with a period less than 24 h that is reset at each nursing, rather than by a circadian oscillator. Such a mechanism might be particularly adaptive for rhythms of short duration that should end abruptly with a sudden change in context such as death or weaning of the young.
- Description: This work was supported by the Australian Federal Government via a Postgraduate PhD Scholarship for Sabibe Apel [APA SA 1].
Soil reconstruction after mining fails to restore soil function in an Australian arid woodland
- Duncan, Corrine, Good, Megan, Sluiter, Ian, Cook, Simon, Schultz, Nick
- Authors: Duncan, Corrine , Good, Megan , Sluiter, Ian , Cook, Simon , Schultz, Nick
- Date: 2020
- Type: Text , Journal article
- Relation: Restoration Ecology Vol. 28, no. S1 (2020), p. A35-A43
- Full Text:
- Reviewed:
- Description: The biogeochemical properties of soils drive ecosystem function and vegetation dynamics, and hence soil restoration after mining should aim to reinstate the soil properties and hydrological dynamics of remnant ecosystems. The aim of this study is to assess soil structure in two vegetation types in an arid ecosystem, and to understand how these soil properties compare to a reconstructed soil profile after mining. In an arid ecosystem in southeast Australia, soil samples were collected at five depths (to 105 cm) from remnant woodland and shrubland sites, and sites either disturbed or totally reconstructed after mining. We assessed soil physico-chemical properties and microbial activity. Soils in the remnant arid ecosystem had coarse-textured topsoils that overlay clay horizons, which allows water to infiltrate and avoid evaporation, but also slows drainage to deeper horizons. Conversely, reconstructed soils had high sand content at subsoil horizons and high bulk density and compaction at surface layers (0–20 cm). Reconstructed soils had topsoils with higher pH and electrical conductivity. The reconstructed soils did not show increased microbial activity with time since restoration. Overall, the reconstructed soil horizons were not organized in a way that allowed rainfall infiltration and water storage, as is imperative to arid-zone ecosystem function. Future restoration efforts in arid ecosystems should focus on increasing sand content of soils near the surface, to reduce evaporative water loss and improve soil quality and plant health. © 2020 Society for Ecological Restoration
- Authors: Duncan, Corrine , Good, Megan , Sluiter, Ian , Cook, Simon , Schultz, Nick
- Date: 2020
- Type: Text , Journal article
- Relation: Restoration Ecology Vol. 28, no. S1 (2020), p. A35-A43
- Full Text:
- Reviewed:
- Description: The biogeochemical properties of soils drive ecosystem function and vegetation dynamics, and hence soil restoration after mining should aim to reinstate the soil properties and hydrological dynamics of remnant ecosystems. The aim of this study is to assess soil structure in two vegetation types in an arid ecosystem, and to understand how these soil properties compare to a reconstructed soil profile after mining. In an arid ecosystem in southeast Australia, soil samples were collected at five depths (to 105 cm) from remnant woodland and shrubland sites, and sites either disturbed or totally reconstructed after mining. We assessed soil physico-chemical properties and microbial activity. Soils in the remnant arid ecosystem had coarse-textured topsoils that overlay clay horizons, which allows water to infiltrate and avoid evaporation, but also slows drainage to deeper horizons. Conversely, reconstructed soils had high sand content at subsoil horizons and high bulk density and compaction at surface layers (0–20 cm). Reconstructed soils had topsoils with higher pH and electrical conductivity. The reconstructed soils did not show increased microbial activity with time since restoration. Overall, the reconstructed soil horizons were not organized in a way that allowed rainfall infiltration and water storage, as is imperative to arid-zone ecosystem function. Future restoration efforts in arid ecosystems should focus on increasing sand content of soils near the surface, to reduce evaporative water loss and improve soil quality and plant health. © 2020 Society for Ecological Restoration
The oligomeric assembly of galectin-11 is critical for anti-parasitic activity in sheep (Ovis aries)
- Sakthivel, Dhanasekaran, Preston, Sarah, Gasser, Robin, Meeusen, Els, Piedrafita, David
- Authors: Sakthivel, Dhanasekaran , Preston, Sarah , Gasser, Robin , Meeusen, Els , Piedrafita, David
- Date: 2020
- Type: Text , Journal article
- Relation: Communications Biology Vol. 3, no. 1 (2020), p.
- Full Text:
- Reviewed:
- Description: Galectins are a family of glycan-binding molecules with a characteristic affinity for ß-D-glycosides that mediate a variety of important cellular functions, including immune and inflammatory responses. Galectin-11 (LGALS-11) has been recently identified as a mediator induced specifically in animals against gastrointestinal nematodes and can interfere with parasite growth and development. Here, we report that at least two natural genetic variants of LGALS-11 exist in sheep, and demonstrate fundamental differences in anti-parasitic activity, correlated with their ability to dimerise. This study improves our understanding of the role of galectins in the host immune and inflammatory responses against parasitic nematodes and provides a basis for genetic studies toward selective breeding of animals for resistance to parasites. © 2020, The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Dhanasekaran Sakthivel, Sarah Preston, Robin Gasser, Els Meeusen, David Piedrafita” is provided in this record**
The oligomeric assembly of galectin-11 is critical for anti-parasitic activity in sheep (Ovis aries)
- Authors: Sakthivel, Dhanasekaran , Preston, Sarah , Gasser, Robin , Meeusen, Els , Piedrafita, David
- Date: 2020
- Type: Text , Journal article
- Relation: Communications Biology Vol. 3, no. 1 (2020), p.
- Full Text:
- Reviewed:
- Description: Galectins are a family of glycan-binding molecules with a characteristic affinity for ß-D-glycosides that mediate a variety of important cellular functions, including immune and inflammatory responses. Galectin-11 (LGALS-11) has been recently identified as a mediator induced specifically in animals against gastrointestinal nematodes and can interfere with parasite growth and development. Here, we report that at least two natural genetic variants of LGALS-11 exist in sheep, and demonstrate fundamental differences in anti-parasitic activity, correlated with their ability to dimerise. This study improves our understanding of the role of galectins in the host immune and inflammatory responses against parasitic nematodes and provides a basis for genetic studies toward selective breeding of animals for resistance to parasites. © 2020, The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Dhanasekaran Sakthivel, Sarah Preston, Robin Gasser, Els Meeusen, David Piedrafita” is provided in this record**
Animal movements in fire-prone landscapes
- Nimmo, Dale, Avitabile, Sarah, Banks, Sam, Bird, Rebecca, Callister, Kate, Clarke, Michael, Dickman, Chris, Doherty, Tim, Driscoll, Don, Greenville, Aaron, Haslem, Angie, Kelly, Luke, Kenny, Sally, Lahoz-Monfort, Jose, Lee, Connie, Leonard, Steven, Moore, Harry, Newsome, Thomas, Parr, Catherine, Ritchie, Euan, Schneider, Kathryn, Turner, James, Watson, Simon, Westbrooke, Martin, Wouters, Mike, White, Matthew, Bennett, Andrew
- Authors: Nimmo, Dale , Avitabile, Sarah , Banks, Sam , Bird, Rebecca , Callister, Kate , Clarke, Michael , Dickman, Chris , Doherty, Tim , Driscoll, Don , Greenville, Aaron , Haslem, Angie , Kelly, Luke , Kenny, Sally , Lahoz-Monfort, Jose , Lee, Connie , Leonard, Steven , Moore, Harry , Newsome, Thomas , Parr, Catherine , Ritchie, Euan , Schneider, Kathryn , Turner, James , Watson, Simon , Westbrooke, Martin , Wouters, Mike , White, Matthew , Bennett, Andrew
- Date: 2019
- Type: Text , Journal article , Review
- Relation: Biological Reviews Vol. 94, no. 3 (2019), p. 981-998
- Full Text:
- Reviewed:
- Description: Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire-prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer-term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire-prone ecosystems.
- Authors: Nimmo, Dale , Avitabile, Sarah , Banks, Sam , Bird, Rebecca , Callister, Kate , Clarke, Michael , Dickman, Chris , Doherty, Tim , Driscoll, Don , Greenville, Aaron , Haslem, Angie , Kelly, Luke , Kenny, Sally , Lahoz-Monfort, Jose , Lee, Connie , Leonard, Steven , Moore, Harry , Newsome, Thomas , Parr, Catherine , Ritchie, Euan , Schneider, Kathryn , Turner, James , Watson, Simon , Westbrooke, Martin , Wouters, Mike , White, Matthew , Bennett, Andrew
- Date: 2019
- Type: Text , Journal article , Review
- Relation: Biological Reviews Vol. 94, no. 3 (2019), p. 981-998
- Full Text:
- Reviewed:
- Description: Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire-prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer-term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire-prone ecosystems.
DRfit : A Java tool for the analysis of discrete data from multi-well plate assays
- Hofmann, Andreas, Preston, Sarah, Cross, Megan, Herath, Dilrukshi, Simon, Anne, Gasser, Robin
- Authors: Hofmann, Andreas , Preston, Sarah , Cross, Megan , Herath, Dilrukshi , Simon, Anne , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 20, no. (2019), p. 1-6
- Full Text:
- Reviewed:
- Description: Background: Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results: We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions: DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.
- Authors: Hofmann, Andreas , Preston, Sarah , Cross, Megan , Herath, Dilrukshi , Simon, Anne , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 20, no. (2019), p. 1-6
- Full Text:
- Reviewed:
- Description: Background: Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results: We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions: DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.
Reverse engineering genetic networks using nonlinear saturation kinetics
- Youseph, Ahammed, Chetty, Madhu, Karmakar, Gour
- Authors: Youseph, Ahammed , Chetty, Madhu , Karmakar, Gour
- Date: 2019
- Type: Text , Journal article
- Relation: BioSystems Vol. 182, no. (2019), p. 30-41
- Full Text:
- Reviewed:
- Description: A gene regulatory network (GRN) represents a set of genes along with their regulatory interactions. Cellular behavior is driven by genetic level interactions. Dynamics of such systems show nonlinear saturation kinetics which can be best modeled by Michaelis-Menten (MM) and Hill equations. Although MM equation is being widely used for modeling biochemical processes, it has been applied rarely for reverse engineering GRNs. In this paper, we develop a complete framework for a novel model for GRN inference using MM kinetics. A set of coupled equations is first proposed for modeling GRNs. In the coupled model, Michaelis-Menten constant associated with regulation by a gene is made invariant irrespective of the gene being regulated. The parameter estimation of the proposed model is carried out using an evolutionary optimization method, namely, trigonometric differential evolution (TDE). Subsequently, the model is further improved and the regulations of different genes by a given gene are made distinct by allowing varying values of Michaelis-Menten constants for each regulation. Apart from making the model more relevant biologically, the improvement results in a decoupled GRN model with fast estimation of model parameters. Further, to enhance exploitation of the search, we propose a local search algorithm based on hill climbing heuristics. A novel mutation operation is also proposed to avoid population stagnation and premature convergence. Real life benchmark data sets generated in vivo are used for validating the proposed model. Further, we also analyze realistic in silico datasets generated using GeneNetweaver. The comparison of the performance of proposed model with other existing methods shows the potential of the proposed model.
- Authors: Youseph, Ahammed , Chetty, Madhu , Karmakar, Gour
- Date: 2019
- Type: Text , Journal article
- Relation: BioSystems Vol. 182, no. (2019), p. 30-41
- Full Text:
- Reviewed:
- Description: A gene regulatory network (GRN) represents a set of genes along with their regulatory interactions. Cellular behavior is driven by genetic level interactions. Dynamics of such systems show nonlinear saturation kinetics which can be best modeled by Michaelis-Menten (MM) and Hill equations. Although MM equation is being widely used for modeling biochemical processes, it has been applied rarely for reverse engineering GRNs. In this paper, we develop a complete framework for a novel model for GRN inference using MM kinetics. A set of coupled equations is first proposed for modeling GRNs. In the coupled model, Michaelis-Menten constant associated with regulation by a gene is made invariant irrespective of the gene being regulated. The parameter estimation of the proposed model is carried out using an evolutionary optimization method, namely, trigonometric differential evolution (TDE). Subsequently, the model is further improved and the regulations of different genes by a given gene are made distinct by allowing varying values of Michaelis-Menten constants for each regulation. Apart from making the model more relevant biologically, the improvement results in a decoupled GRN model with fast estimation of model parameters. Further, to enhance exploitation of the search, we propose a local search algorithm based on hill climbing heuristics. A novel mutation operation is also proposed to avoid population stagnation and premature convergence. Real life benchmark data sets generated in vivo are used for validating the proposed model. Further, we also analyze realistic in silico datasets generated using GeneNetweaver. The comparison of the performance of proposed model with other existing methods shows the potential of the proposed model.
Safety and immunogenicity of pneumococcal conjugate vaccines in a high-risk population : A randomized controlled trial of 10-valent and 13-valent pneumococcal conjugate vaccine in Papua New Guinean infants
- Pomat, William, Van Den Biggelaar, Anita, Wana, Sandra, Francis, Jacinta, Solomon, Vela, Greenhill, Andrew, Ford, Rebecca, Orami, Tilda, Passey, Megan, Jacoby, Peter, Kirkham, Lea-Ann, Lehmann, Deborah, Richmond, Peter
- Authors: Pomat, William , Van Den Biggelaar, Anita , Wana, Sandra , Francis, Jacinta , Solomon, Vela , Greenhill, Andrew , Ford, Rebecca , Orami, Tilda , Passey, Megan , Jacoby, Peter , Kirkham, Lea-Ann , Lehmann, Deborah , Richmond, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Clinical Infectious Diseases Vol. 68, no. 9 (2019), p. 1472-1481
- Full Text:
- Reviewed:
- Description: Background. There are little data on the immunogenicity of PCV10 and PCV13 in the same high-risk population. Methods. PCV10 and PCV13 were studied head-to-head in a randomized controlled trial in Papua New Guinea in which 262 infants received 3 doses of PCV10 or PCV13 at 1, 2, and 3 months of age. Serotype-specific immunoglobulin G (IgG) concentrations, and pneumococcal and nontypeable Haemophilus influenzae (NTHi) carriage were assessed prevaccination and at 4 and 9 months of age. Infants were followed up for safety until 9 months of age. Results. One month after the third dose of PCV10 or PCV13, 80% of infants had IgG concentrations ≥0.35µg/mL for vaccine serotypes, and 6 months postvaccination IgG concentrations ≥0.35 µg/mL were maintained for 8/10 shared PCV serotypes in > 75% of children vaccinated with either PCV10 or PCV13. Children carried a total of 65 different pneumococcal serotypes (plus nonserotypeable). At 4 months of age, 92% (95% confidence interval [CI] 85–96) of children vaccinated with PCV10 and 81% (95% CI 72–88) vaccinated with PCV13 were pneumococcal carriers (P = .023), whereas no differences were seen at 9 months of age, or for NTHi carriage. Both vaccines were well tolerated and not associated with serious adverse events. Conclusions. Infant vaccination with 3 doses of PCV10 or PCV13 is safe and immunogenic in a highly endemic setting; however, to significantly reduce pneumococcal disease in these settings, PCVs with broader serotype coverage and potency to reduce pneumococcal carriage are needed. Clinical Trials Registration. NCT01619462.
- Authors: Pomat, William , Van Den Biggelaar, Anita , Wana, Sandra , Francis, Jacinta , Solomon, Vela , Greenhill, Andrew , Ford, Rebecca , Orami, Tilda , Passey, Megan , Jacoby, Peter , Kirkham, Lea-Ann , Lehmann, Deborah , Richmond, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Clinical Infectious Diseases Vol. 68, no. 9 (2019), p. 1472-1481
- Full Text:
- Reviewed:
- Description: Background. There are little data on the immunogenicity of PCV10 and PCV13 in the same high-risk population. Methods. PCV10 and PCV13 were studied head-to-head in a randomized controlled trial in Papua New Guinea in which 262 infants received 3 doses of PCV10 or PCV13 at 1, 2, and 3 months of age. Serotype-specific immunoglobulin G (IgG) concentrations, and pneumococcal and nontypeable Haemophilus influenzae (NTHi) carriage were assessed prevaccination and at 4 and 9 months of age. Infants were followed up for safety until 9 months of age. Results. One month after the third dose of PCV10 or PCV13, 80% of infants had IgG concentrations ≥0.35µg/mL for vaccine serotypes, and 6 months postvaccination IgG concentrations ≥0.35 µg/mL were maintained for 8/10 shared PCV serotypes in > 75% of children vaccinated with either PCV10 or PCV13. Children carried a total of 65 different pneumococcal serotypes (plus nonserotypeable). At 4 months of age, 92% (95% confidence interval [CI] 85–96) of children vaccinated with PCV10 and 81% (95% CI 72–88) vaccinated with PCV13 were pneumococcal carriers (P = .023), whereas no differences were seen at 9 months of age, or for NTHi carriage. Both vaccines were well tolerated and not associated with serious adverse events. Conclusions. Infant vaccination with 3 doses of PCV10 or PCV13 is safe and immunogenic in a highly endemic setting; however, to significantly reduce pneumococcal disease in these settings, PCVs with broader serotype coverage and potency to reduce pneumococcal carriage are needed. Clinical Trials Registration. NCT01619462.
The conservation significance of the biota of barrow island, western australia
- Lynch, A. Jasmyn, Beeton, Robert, Greenslade, Penelope
- Authors: Lynch, A. Jasmyn , Beeton, Robert , Greenslade, Penelope
- Date: 2019
- Type: Text , Journal article
- Relation: Journal of the Royal Society of Western Australia Vol. 102, no. (2019), p. 98-133
- Full Text:
- Reviewed:
- Description: Offshore islands are often important in conservation because of the presence of locally endemic species and for acting as refuges for native wildlife from the impacts of invasive species and inappropriate development. Barrow Island, a small, semi-arid island off the Pilbara coast of northwestern Australia, has maintained the integrity of its terrestrial and aquatic biota despite sporadic incursions by invasive species and the operation of commercial oil extraction and liquified natural gas processing for over 50 years. We collate information from a wide range of sources to provide a framework to inform the ongoing management of the terrestrial and aquatic fauna and flora species that have conservation significance on the island. These include endemic flora and fauna; species listed as threatened by state, national and international authorities; species that are rare or extinct in other parts of their original range; species of biogeographic significance; and migratory birds and marine fauna of national and international significance. In addition, Barrow Island has been of value in acting as a source area for translocations of vulnerable and endangered mammal species that have been eradicated in other parts of their range. The many species with conservation significance and their use in successful translocation programs demonstrates the island’s national and international importance for conservation. In addition, Barrow Island provides exemplary opportunities for research on effective co-management of development and conservation, on mitigation and prevention of the invasion and impacts of exotic species, and on the influence of historical biogeographic processes on the distributions and evolution of biota. © Royal Society of Western Australia 2019.
- Authors: Lynch, A. Jasmyn , Beeton, Robert , Greenslade, Penelope
- Date: 2019
- Type: Text , Journal article
- Relation: Journal of the Royal Society of Western Australia Vol. 102, no. (2019), p. 98-133
- Full Text:
- Reviewed:
- Description: Offshore islands are often important in conservation because of the presence of locally endemic species and for acting as refuges for native wildlife from the impacts of invasive species and inappropriate development. Barrow Island, a small, semi-arid island off the Pilbara coast of northwestern Australia, has maintained the integrity of its terrestrial and aquatic biota despite sporadic incursions by invasive species and the operation of commercial oil extraction and liquified natural gas processing for over 50 years. We collate information from a wide range of sources to provide a framework to inform the ongoing management of the terrestrial and aquatic fauna and flora species that have conservation significance on the island. These include endemic flora and fauna; species listed as threatened by state, national and international authorities; species that are rare or extinct in other parts of their original range; species of biogeographic significance; and migratory birds and marine fauna of national and international significance. In addition, Barrow Island has been of value in acting as a source area for translocations of vulnerable and endangered mammal species that have been eradicated in other parts of their range. The many species with conservation significance and their use in successful translocation programs demonstrates the island’s national and international importance for conservation. In addition, Barrow Island provides exemplary opportunities for research on effective co-management of development and conservation, on mitigation and prevention of the invasion and impacts of exotic species, and on the influence of historical biogeographic processes on the distributions and evolution of biota. © Royal Society of Western Australia 2019.
Timing of snowmelt affects species composition via plant strategy filtering
- Good, Megan, Morgan, John, Venn, Susanna, Green, Peter
- Authors: Good, Megan , Morgan, John , Venn, Susanna , Green, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Basic and Applied Ecology Vol. 35, no. (2019), p. 54-62
- Full Text:
- Reviewed:
- Description: Plant strategy schemes aim to classify plants according to measurable traits and group species according to their shared evolutionary responses to selective pressures. In this way, it becomes possible to make meaningful comparisons among ecosystems and communities and to predict how plant communities might respond to changes in their environment. Here, we classified common alpine plants which occur in snowpatches (Early and Late snowmelt sites) and in adjacent vegetation (Snow-free sites which melt early in the growing season) using Grime's CSR plant strategy scheme. Alpine plant communities are largely driven by environmental filters associated with a relatively constant gradient of snowmelt timing. Since snow persistence influences the abiotic environment and plant assemblages alike, we hypothesised that these patterns would be reflected in community CSR scores. Weighted community CSR scores were clustered towards the stress-tolerator (S) corner of the triangular CSR space, and Snow-free communities were significantly more stress-tolerant than Early and Late snowmelt communities. This suggests that snowpatch communities are functionally distinct from surrounding vegetation when considering the major axes of plant variation identified by CSR theory. These results lend further support to the importance of the timing of snowmelt as a key filter, influencing how species and plant strategy types distribute themselves across the alpine landscape.
- Authors: Good, Megan , Morgan, John , Venn, Susanna , Green, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Basic and Applied Ecology Vol. 35, no. (2019), p. 54-62
- Full Text:
- Reviewed:
- Description: Plant strategy schemes aim to classify plants according to measurable traits and group species according to their shared evolutionary responses to selective pressures. In this way, it becomes possible to make meaningful comparisons among ecosystems and communities and to predict how plant communities might respond to changes in their environment. Here, we classified common alpine plants which occur in snowpatches (Early and Late snowmelt sites) and in adjacent vegetation (Snow-free sites which melt early in the growing season) using Grime's CSR plant strategy scheme. Alpine plant communities are largely driven by environmental filters associated with a relatively constant gradient of snowmelt timing. Since snow persistence influences the abiotic environment and plant assemblages alike, we hypothesised that these patterns would be reflected in community CSR scores. Weighted community CSR scores were clustered towards the stress-tolerator (S) corner of the triangular CSR space, and Snow-free communities were significantly more stress-tolerant than Early and Late snowmelt communities. This suggests that snowpatch communities are functionally distinct from surrounding vegetation when considering the major axes of plant variation identified by CSR theory. These results lend further support to the importance of the timing of snowmelt as a key filter, influencing how species and plant strategy types distribute themselves across the alpine landscape.