- Rodriguez, Blanca Morales, Khouzami, Lara, Decostre, Valérie, Varnous, Shaida, Pekovic-Vaughan, Vanja, Hutchison, Christopher, Pecker, Françoise, Bonne, Gisèle, Muchir, Antoine
- Authors: Rodriguez, Blanca Morales , Khouzami, Lara , Decostre, Valérie , Varnous, Shaida , Pekovic-Vaughan, Vanja , Hutchison, Christopher , Pecker, Françoise , Bonne, Gisèle , Muchir, Antoine
- Date: 2018
- Type: Text , Journal article
- Relation: Human Molecular Genetics Vol. 27, no. 19 (2018), p. 3353-3360
- Full Text: false
- Reviewed:
- Description: Cardiomyopathy caused by lamin A/C gene (LMNA) mutations (hereafter referred as LMNA cardiomyopathy) is an anatomic and pathologic condition associated with muscular and electrical dysfunction of the heart, often leading to heart failure-related disability. There is currently no specific therapy available for patients that target the molecular pathophysiology of LMNA cardiomyopathy. We showed here an increase in oxidative stress levels in the hearts of mice carrying LMNA mutation, associated with a decrease of the key cellular antioxidant glutathione (GHS). Oral administration of N-acetyl cysteine, a GHS precursor, led to a marked improvement of GHS content, a decrease in oxidative stress markers including protein carbonyls and an improvement of left ventricular structure and function in a model of LMNA cardiomyopathy. Collectively, our novel results provide therapeutic insights into LMNA cardiomyopathy.
Netflix and chill? What sex differences can tell us about mate preferences in (hypothetical) booty-call relationships
- March, Evita, Van Doorn, George, Grieve, Rachel
- Authors: March, Evita , Van Doorn, George , Grieve, Rachel
- Date: 2018
- Type: Text , Journal article
- Relation: Evolutionary Psychology Vol. 16, no. 4 (2018), p. 1-10
- Full Text:
- Reviewed:
- Description: The booty-call relationship is defined by both sexual characteristics and emotional involvement. In the current study, men’s and women’s preferences for a booty-call mate were explored. Men and women were predicted to exhibit different mate preferences depending on whether they considered a booty-call relationship a short- or long-term relationship. Participants (N = 559, 74% women) completed an anonymous online questionnaire, designing their ideal booty-call mate using the mate dollars paradigm. Both sexes considered the physical attractiveness and kindness of a booty-call mate a necessity, expressing both short- and long-term mate preferences. The current study highlights the need to explore mate preferences outside the dichotomy of short- and long-term relationships, providing evidence of a compromise relationship.
- Authors: March, Evita , Van Doorn, George , Grieve, Rachel
- Date: 2018
- Type: Text , Journal article
- Relation: Evolutionary Psychology Vol. 16, no. 4 (2018), p. 1-10
- Full Text:
- Reviewed:
- Description: The booty-call relationship is defined by both sexual characteristics and emotional involvement. In the current study, men’s and women’s preferences for a booty-call mate were explored. Men and women were predicted to exhibit different mate preferences depending on whether they considered a booty-call relationship a short- or long-term relationship. Participants (N = 559, 74% women) completed an anonymous online questionnaire, designing their ideal booty-call mate using the mate dollars paradigm. Both sexes considered the physical attractiveness and kindness of a booty-call mate a necessity, expressing both short- and long-term mate preferences. The current study highlights the need to explore mate preferences outside the dichotomy of short- and long-term relationships, providing evidence of a compromise relationship.
Proteomic identification of galectin-11 and 14 ligands from Haemonchus contortus
- Sakthivel, Dhanasekaran, Swan, Jaclyn, Preston, Sarah, Shakif-Azam, MD, Faou, Pierre, Jiao, Yaqing, Downs, Rachael, Rajapaksha, Harinda, Gasser, Robin, Piedrafita, David, Beddoe, Travis
- Authors: Sakthivel, Dhanasekaran , Swan, Jaclyn , Preston, Sarah , Shakif-Azam, MD , Faou, Pierre , Jiao, Yaqing , Downs, Rachael , Rajapaksha, Harinda , Gasser, Robin , Piedrafita, David , Beddoe, Travis
- Date: 2018
- Type: Text , Journal article
- Relation: Peerj Vol. 6, no. 3 (2018), p. 1-19
- Full Text:
- Reviewed:
- Description: Haemonchus contortus is the most pathogenic nematode of small ruminants. Infection in sheep and goats results in anaemia that decreases animal productivity and can ultimately cause death. The involvement of ruminant-specific galectin-11 (LGALS-11) and galectin-14 (LGALS-14) has been postulated to play important roles in protective immune responses against parasitic infection; however, their ligands are unknown. In the current study, LGALS-11 and LGALS-14 ligands in H. contortus were identified from larval (L4) and adult parasitic stages extracts using immobilised LGALS-11 and LGALS-14 affinity column chromatography and mass spectrometry. Both LGALS-11 and LGALS-14 bound more putative protein targets in the adult stage of H. contortus (43 proteins) when compared to the larval stage (two proteins). Of the 43 proteins identified in the adult stage, 34 and 35 proteins were bound by LGALS-11 and LGALS-14, respectively, with 26 proteins binding to both galectins. Interestingly, hematophagous stage-specific sperm-coating protein and zinc metalloprotease (M13), which are known vaccine candidates, were identified as putative ligands of both LGALS-11 and LGALS- 14. The identification of glycoproteins of H. contortus by LGALS-11 and LGALS-14 provide new insights into host-parasite interactions and the potential for developing new interventions.
- Authors: Sakthivel, Dhanasekaran , Swan, Jaclyn , Preston, Sarah , Shakif-Azam, MD , Faou, Pierre , Jiao, Yaqing , Downs, Rachael , Rajapaksha, Harinda , Gasser, Robin , Piedrafita, David , Beddoe, Travis
- Date: 2018
- Type: Text , Journal article
- Relation: Peerj Vol. 6, no. 3 (2018), p. 1-19
- Full Text:
- Reviewed:
- Description: Haemonchus contortus is the most pathogenic nematode of small ruminants. Infection in sheep and goats results in anaemia that decreases animal productivity and can ultimately cause death. The involvement of ruminant-specific galectin-11 (LGALS-11) and galectin-14 (LGALS-14) has been postulated to play important roles in protective immune responses against parasitic infection; however, their ligands are unknown. In the current study, LGALS-11 and LGALS-14 ligands in H. contortus were identified from larval (L4) and adult parasitic stages extracts using immobilised LGALS-11 and LGALS-14 affinity column chromatography and mass spectrometry. Both LGALS-11 and LGALS-14 bound more putative protein targets in the adult stage of H. contortus (43 proteins) when compared to the larval stage (two proteins). Of the 43 proteins identified in the adult stage, 34 and 35 proteins were bound by LGALS-11 and LGALS-14, respectively, with 26 proteins binding to both galectins. Interestingly, hematophagous stage-specific sperm-coating protein and zinc metalloprotease (M13), which are known vaccine candidates, were identified as putative ligands of both LGALS-11 and LGALS- 14. The identification of glycoproteins of H. contortus by LGALS-11 and LGALS-14 provide new insights into host-parasite interactions and the potential for developing new interventions.
Using non-invasive sampling methods to determine the prevalence and distribution of Chlamydia pecorum and koala retrovirus in a remnant koala population with conservation importance
- Wedrowicz, Faye, Mosse, Jennifer, Wright, Wendy, Hogan, Fiona
- Authors: Wedrowicz, Faye , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
- Date: 2018
- Type: Text , Journal article
- Relation: Wildlife Research Vol. 45, no. 4 (2018), p. 366-380
- Full Text:
- Reviewed:
- Description: Context Pathogenic infections are an important consideration for the conservation of native species, but obtaining such data from wild populations can be expensive and difficult. Two pathogens have been implicated in the decline of some koala (Phascolarctos cinereus) populations: Urogenital infection with Chlamydia pecorum and koala retrovirus subgroup A (KoRV-A). Pathogen data for a wild koala population of conservation importance in South Gippsland, Victoria are essentially absent. Aims This study uses non-invasive sampling of koala scats to provide prevalence and genotype data for C. pecorum and KoRV-A in the South Gippsland koala population, and compares pathogen prevalence between wild koalas and koalas in rescue shelters. Methods C. pecorum and KoRV-A provirus were detected by PCR of DNA isolated from scats collected in the field. Pathogen genetic variation was investigated using DNA sequencing of the C. pecorum ompA and KoRV-A env genes. Key results C. pecorum and KoRV-A were detected in 61% and 27% of wild South Gippsland individuals tested, respectively. KoRV-A infection tended to be higher in shelter koalas compared with wild koalas. In contrast with other Victorian koala populations sampled, greater pathogen diversity was present in South Gippsland. Conclusions In the South Gippsland koala population, C. pecorum is widespread and common whereas KoRV appears less prevalent than previously thought. Further work exploring the dynamics of these pathogens in South Gippsland koalas is warranted and may help inform future conservation strategies for this important population. Implications Non-invasive genetic sampling from scats is a powerful method for obtaining data regarding pathogen prevalence and diversity in wildlife. The use of non-invasive methods for the study of pathogens may help fill research gaps in a way that would be difficult or expensive to achieve using traditional methods.
- Authors: Wedrowicz, Faye , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
- Date: 2018
- Type: Text , Journal article
- Relation: Wildlife Research Vol. 45, no. 4 (2018), p. 366-380
- Full Text:
- Reviewed:
- Description: Context Pathogenic infections are an important consideration for the conservation of native species, but obtaining such data from wild populations can be expensive and difficult. Two pathogens have been implicated in the decline of some koala (Phascolarctos cinereus) populations: Urogenital infection with Chlamydia pecorum and koala retrovirus subgroup A (KoRV-A). Pathogen data for a wild koala population of conservation importance in South Gippsland, Victoria are essentially absent. Aims This study uses non-invasive sampling of koala scats to provide prevalence and genotype data for C. pecorum and KoRV-A in the South Gippsland koala population, and compares pathogen prevalence between wild koalas and koalas in rescue shelters. Methods C. pecorum and KoRV-A provirus were detected by PCR of DNA isolated from scats collected in the field. Pathogen genetic variation was investigated using DNA sequencing of the C. pecorum ompA and KoRV-A env genes. Key results C. pecorum and KoRV-A were detected in 61% and 27% of wild South Gippsland individuals tested, respectively. KoRV-A infection tended to be higher in shelter koalas compared with wild koalas. In contrast with other Victorian koala populations sampled, greater pathogen diversity was present in South Gippsland. Conclusions In the South Gippsland koala population, C. pecorum is widespread and common whereas KoRV appears less prevalent than previously thought. Further work exploring the dynamics of these pathogens in South Gippsland koalas is warranted and may help inform future conservation strategies for this important population. Implications Non-invasive genetic sampling from scats is a powerful method for obtaining data regarding pathogen prevalence and diversity in wildlife. The use of non-invasive methods for the study of pathogens may help fill research gaps in a way that would be difficult or expensive to achieve using traditional methods.
Vertebrate trace fossils from the Late Pleistocene of Kangaroo Island, South Australia
- Camens, Aaron, Carey, Stephen, Arnold, Lee
- Authors: Camens, Aaron , Carey, Stephen , Arnold, Lee
- Date: 2018
- Type: Text , Journal article
- Relation: Ichnos: an International Journal of Plant and Animal Vol. 25, no. 2-3 (2018), p. 232-251
- Full Text: false
- Reviewed:
- Description: It is rapidly becoming apparent that the Late Pleistocene vertebrate trace fossil record of southern Australia is much more comprehensive than previously understood, and complements the skeletal fossil record with regard to the distribution of taxa in coastal environments and the palaeobiology of both extinct and extant organisms. We surveyed the majority of prospective Bridgewater Formation outcrops on Kangaroo Island in South Australia and discovered a trace fossil site preserving hundreds of individual traces. A minimum of ten different reptile, bird, and mammal taxa, as well as invertebrates, are represented at the site. Single-grain optically stimulated luminescence dating indicates that the dune in which the traces imprinted was deposited at the beginning of Marine Isotope Stage 5e (135.4 ± 5.9 ka). The traces were made by several extinct taxa including large quadrupeds (most probably diprotodontids), short-faced (sthenurine) kangaroos, and thylacines, as well as extant taxa including possums, the Tasmanian Devil, goannas, shorebirds, and a variety of kangaroos. This site demonstrates that, even though vertebrate trace fossil sites do not often allow the same level of taxonomic differentiation as skeletal fossil deposits, they can nevertheless provide important information about taxon distribution and behavior that can be correlated and contrasted with skeletal fossil assemblages. © 2018 Informa UK Limited, trading as Taylor & Francis Group.
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.
Emerging threats and persistent conservation challenges for freshwater biodiversity
- Reid, Andrea, Carlson, Andrew, Creed, Irena, Eliason, Erika, Gell, Peter, Johnson, Pieter, Kidd, Karen, MacCormack, Tyson, Olden, Julian, Ormerod, Steve, Smol, John, Taylor, William, Tockner, Klement, Vermaire, Jesse, Dudgeon, David, Cooke, Steven
- Authors: Reid, Andrea , Carlson, Andrew , Creed, Irena , Eliason, Erika , Gell, Peter , Johnson, Pieter , Kidd, Karen , MacCormack, Tyson , Olden, Julian , Ormerod, Steve , Smol, John , Taylor, William , Tockner, Klement , Vermaire, Jesse , Dudgeon, David , Cooke, Steven
- Date: 2019
- Type: Text , Journal article
- Relation: Biological Reviews Vol. 94, no. 3 (2019), p. 849-873
- Full Text: false
- Reviewed:
- Description: In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.
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.
- Young, Barnaby, Sadarangani, Sapna, Haur, Sen, Yung, Chee, Barr, Ian, Connolly, John, Chen, Mark, Wilder-Smith, Annelies
- Authors: Young, Barnaby , Sadarangani, Sapna , Haur, Sen , Yung, Chee , Barr, Ian , Connolly, John , Chen, Mark , Wilder-Smith, Annelies
- Date: 2019
- Type: Text , Journal article
- Relation: Clinical Infectious Diseases Vol. 69, no. 1 (2019), p. 121-129
- Full Text: false
- Reviewed:
- Description: Background. Antibody titres and vaccine effectiveness decline within 6 months after influenza vaccination in older adults. Biannual vaccination may be necessary to provide year-round protection in the tropics, where influenza circulates throughout the year. Methods. Tropical Influenza Control Strategies (TROPICS1) was a single-center, 1:1 randomized, observer-blinded, active-comparator- controlled, superiority study in 200 community-resident adults aged ≥65 years. Participants received a standard-dose trivalent inactivated influenza vaccination (IIV3) at enrollment, and either tetanus-diphtheria-pertussis vaccination or IIV3 6 months later. The primary outcome was the proportion of participants with haemagglutination-inhibition (HI) geometric mean titre (GMT) ≥1:40 1 month after the second vaccination (month 7). Secondary outcomes included GMTs to month 12, the incidence of influenza- like illness (ILI), and adverse reactions after vaccination. Results. At month 7, the proportion of participants with an HI tire ≥1:40 against A/H1N1 increased by 21.4% (95% confidence interval [CI] 8.6-33.4) in the semiannual vaccination group. This proportion was not significantly higher for A/H3N2 (4.3, 95% CI -1.1-10.8) or B (2.1, 95% CI -2.0-7.3). Semiannual vaccination significantly increased GMTs against A/H1N1 and A/H3N2, but not B, at month 7. Participants receiving a repeat vaccination of IIV3 reported a significantly lower incidence of ILI in the 6 months after the second vaccination (relative vaccine effectiveness 57.1%, 95% CI 0.6-81.5). The frequency of adverse events was similar after the first and second influenza vaccinations. Conclusions. Semiannual influenza vaccination in older residents of tropical countries has the potential to improve serological measures of protection against infection. Alternative vaccination strategies should also be studied.
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.
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.
GCNA interacts with spartan and topoisomerase II to regulate genome stability
- Dokshin, Gregoriy, Davis, Gregory, Sawle, Ashley, Eldridge, Matthew, Nicholls, Peter, Gourley, Taylin, Romer, Katherine, Molesworth, Luke, Tatnell, Hannah, Ozturk, Ahmet, de Rooij, Dirk, Hannon, Gregory, Page, David, Mello, Craig, Carmell, Michelle
- Authors: Dokshin, Gregoriy , Davis, Gregory , Sawle, Ashley , Eldridge, Matthew , Nicholls, Peter , Gourley, Taylin , Romer, Katherine , Molesworth, Luke , Tatnell, Hannah , Ozturk, Ahmet , de Rooij, Dirk , Hannon, Gregory , Page, David , Mello, Craig , Carmell, Michelle
- Date: 2020
- Type: Text , Journal article
- Relation: Developmental Cell Vol. 52, no. 1 (2020), p. 53-68.e6
- Full Text: false
- Reviewed:
- Description: GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs. DNA topoisomerases help unwind DNA but occasionally get trapped, resulting in DNA-protein crosslinks (DPCs). DPCs damage DNA and threaten genomic integrity. Dokshin et al. find that GCNA protein family complements standard DPC processing machinery in resolving topoisomerase II DPCs to ensure heritable genome stability and germline immortality. © 2019 Elsevier Inc.
- Description: We thank S. Cheloufi, D. Bellott, D. Durning, L. Okumura, L. Teitz, and members of the Page and Mello labs for advice and discussion. We thank E. Spooner for mass spectrometry and K. Igarashi for technical assistance. We thank P. Boag and R. Pocock for access to microscopes and technical advice. Some strains provided by the CGC were supported by NIH ( P40 OD010440 ) and the International C. elegans Gene Knockout Consortium . This work was supported by the Life Sciences Research Foundation to M.A.C.; American Cancer Society 129916-PF16-232-RMC to G.A.D.; and NIH grants (R37 GM058800 and P01 HD078253 ) to C.C.M. G.J.H. is supported by Cancer Research UK and by a Royal Society Wolfson Research Professorship. D.C.P. and C.C.M. are Howard Hughes Medical Institute Investigators.
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.
- Brown, Geoff, Robertson, Peter, Fanson, Ben
- Authors: Brown, Geoff , Robertson, Peter , Fanson, Ben
- Date: 2020
- Type: Text , Journal article
- Relation: Austral Ecology Vol. 45, no. 2 (2020), p. 206-214
- Full Text: false
- Reviewed:
- Description: Threatened species that exist in small isolated populations are vulnerable to extinction processes, so effectively monitoring the trajectory of such populations will help determine the most appropriate management actions to combat extinction threats. In this study, we aimed to track the population status of the fossorial heath skink Liopholis multiscutata that is listed as threatened in Victoria, south-eastern Australia, and exists there as a few small and highly disjunct populations, by using an appropriate surrogate population monitoring metric. This secretive lizard is a habitat specialist, is highly localised in Victoria and lives in warrens in semi-arid heathland or mallee on large dunes. Survey data, which included every warren and their constituent burrows, as well as an assessment of whether each burrow was ‘active’, were collected for the four known Victorian populations in 2007 and annually during 2014–2018 inclusive. We compared five population indices per monitoring site: number of active warrens (NAW), number of active burrows (NAB), population area for 80% of active warrens (PA80), percentage of warrens that were active (PAW) and average number of active burrows per active warren. The heath skink currently occurs in small populations (8–46 active warrens) and these populations have typically declined over recent years. NAW was the most robust metric; NAB and PA80 did not reveal strong temporal trends. PAW indicated that inactive warrens and burrows persist less than a year and hence may provide information about recent (within months) population changes. It is imperative to establish a material link between the effective monitoring of small, vulnerable populations and the implementation of management actions that benefit such populations. Here, NAW could be used as a long-term monitoring tool to provide an estimate of the minimum population size of the heath skink at a site. Its use would also ensure continuity in monitoring approaches for the Victorian populations. © 2019 Ecological Society of Australia
Influence of elements of climate change on the growth and fecundity of Datura stramonium
- Chadha, Aakansha, Florentine, Singarayer, Javaid, Muhammad, Welgama, Amali, Turville, Christopher
- Authors: Chadha, Aakansha , Florentine, Singarayer , Javaid, Muhammad , Welgama, Amali , Turville, Christopher
- Date: 2020
- Type: Text , Journal article
- Relation: Environmental Science and Pollution Research Vol. 27, no. 28 (2020), p. 35859-35869
- Full Text: false
- Reviewed:
- Description: In this study, the performance of Datura stramonium, an invasive weed of soybean and solanaceous crops, was examined under different elements of climate change. Experiments conducted in CO2 chambers at ambient CO2 (400 ppm) and elevated CO2 (700 ppm) levels under both well-watered and drought conditions exhibited the fertilization effect of elevated CO2. This was, however, limited by drought. Clearly, growth of D. stramonium will be significantly enhanced by enriched atmospheric CO2 concentration under well-watered conditions, producing taller plants with greater biomass and higher seed output. Glasshouse experiments were conducted to evaluate the effect of different soil moisture regimes (100%, 75%, 50% and 25% water-holding capacity (WHC)) on the growth and fecundity of D. stramonium. Plants grown in 75% WHC had the highest plant height (15.24 cm) and shoot diameter (4.25 mm). The lowest leaf area (305.91 mm2), fresh weight (14.48 g) and dry weight (4.45 g) were observed in 25% WHC conditions. The ability of D. stramonium plants to grow and complete their life cycle with high seed output, even under limited water availability, shows the weedy nature of this species which is well adapted to survive future inhospitable climatic conditions. Radiant heat treatment on the plants indicated that temperatures of 120 °C and above for more than 180 s were enough to kill the plants, suggesting that thermal weeding or wildfires will be adequate to act as a circuit breaker on the D. stramonium invasion cycle, thus allowing other control measures to be engaged for greater control. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.