ORCID Profile
0000-0001-6390-6094
Current Organisation
James Cook University
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Publisher: Wiley
Date: 22-04-2011
Publisher: Oxford University Press (OUP)
Date: 06-05-2021
Abstract: Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic ersity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of ergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population sub ision limits local adaptation and therefore also the likelihood of parallel evolution.
Publisher: Wiley
Date: 19-10-2023
DOI: 10.1111/MEC.17163
Publisher: Akademiai Kiado Zrt.
Date: 08-01-2020
Abstract: In iduals who meet criteria for compulsive buying–shopping disorder (i.e., acquiring problems only) or hoarding disorder (i.e., acquiring and discarding problems) may acquire possessions to compensate for unmet belonging needs, but may do so in different ways. Those with compulsive buying–shopping disorder may acquire objects that they believe will relieve the distress associated with unmet belonging needs (e.g., objects that distract or comfort), whereas those with hoarding disorder may acquire objects that they believe achieve belonging needs (e.g., objects that have interpersonal connotations). Accordingly, this study examined whether a belongingness threat would drive in iduals who excessively acquire possessions to choose a human-like object (person-shaped tea holder) or a comfort item (box of chamomile tea). One hundred seventy-five participants (57 self-reported excessive acquiring only 118 self-reported excessive acquiring and difficulty discarding) recalled a time when they either felt supported or unsupported by a significant other before choosing an object to take home with them. Participants rated how anthropomorphic and comforting the objects were as well as how attached they became to their chosen object. Unsupported in iduals were more likely to acquire the comfort item than supported in iduals however, in iduals with both acquiring and discarding problems were more likely to acquire the human-like item than those with an acquiring problem only. Comfort and anthropomorphism ratings predicted object choice and attachment. The current findings extend the Compensatory Consumer Behavior Model to include what factors determine strategy choice and object attachment.
Publisher: Wiley
Date: 15-07-2022
DOI: 10.1111/EVO.14559
Abstract: The European whitefish (Coregonus lavaretus) species complex is a classic ex le of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three ergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric ergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
Publisher: Cambridge University Press (CUP)
Date: 2015
DOI: 10.1017/S1755267215000548
Abstract: Genetically verified catch data from fishers in eastern Indonesia provide new distribution records for the fossil shark Hemipristis elongata in the Halmahera, Seram and Arafura seas. Previously only recorded from the island of Java, this study reports a range extension for this species of & km across the Indonesian archipelago, suggesting that fossil sharks are subjected to fishing pressure over a much larger geographic area than implied by previous species records. We recommend a review of the current species assessment to reflect the reported range extension and inform management of this fishery-targeted shark.
Publisher: Wiley
Date: 07-09-2020
DOI: 10.1111/MEC.15584
Publisher: Cold Spring Harbor Laboratory
Date: 26-01-2021
DOI: 10.1101/2021.01.26.428263
Abstract: Population genetic theory predicts that small effective population sizes ( N e ) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e. parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically co-distributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius ). We found that P. pungitius harbours less genetic ersity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2996 vs. 379 SNPs located within 26 vs nine genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius , respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of ergence, suggestive of selection on ancient haplotypes. In contrast, regions involved in freshwater adaptation in P. pungitius were younger, and often associated with reduced ersity. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population sub ision limits local adaptation and therefore also the likelihood of parallel evolution.
Publisher: Elsevier BV
Date: 09-2013
Publisher: Cold Spring Harbor Laboratory
Date: 12-09-2021
DOI: 10.1101/2021.09.11.459905
Abstract: The European whitefish ( Coregonus lavaretus ) species complex is a classic ex le of recent adaptive radiation. Here we examine a whitefish population introduced to northern Finnish Lake Tsahkal in late 1960’s, where three ergent morphs ( viz . littoral, pelagic and profundal feeders) were found ten generations after. Using demographic modelling based on genomic data we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid symmetric speciation scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping three quantitative trait loci associated with gonad weight variation, a proxy for sexual maturity and spawning time, were identified. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
Publisher: Wiley
Date: 21-01-2019
DOI: 10.1111/EVA.12738
Publisher: Proceedings of the National Academy of Sciences
Date: 22-05-2017
Abstract: Divergent selection can lead to the evolution of distinct species, a process known as ecological speciation. Evidence for ecological speciation in the marine environment is scarce, and the few known ex les have happened within a time frame of hundreds of thousands to millions of years. We present evidence that European flounders in the Baltic Sea exhibiting different breeding behaviors are a species pair arising from a recent event of ecological speciation. The two lineages erged within less than 3,000 generations. This is the fastest event of speciation ever reported for any marine vertebrate. Extraordinarily rapid speciation driven by natural selection can therefore happen even in the marine environment.
Publisher: Frontiers Media SA
Date: 03-03-2015
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.YMPEV.2019.106646
Abstract: Incomplete lineage sorting (ILS) can lead to biased ergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated ergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study. Both the updated calibrations and the application of the MSC model influenced ergence time estimates, sometimes significantly. The new ergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, since the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in ergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around ergence time estimates.
Publisher: Elsevier BV
Date: 03-2023
Publisher: Wiley
Date: 30-07-2022
DOI: 10.1111/IBI.13117
Abstract: We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black‐billed Gull Chroicocephalus bulleri and the Red‐billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 s led Black‐billed Gulls possessed mtDNA typical of Red‐billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red‐billed Gulls s led from different colonies possessed Black‐billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red‐billed Gulls and Black‐billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black‐billed Gulls, effectively diluting the Red‐billed Gull nuclear DNA contribution. Divergence of Red‐billed Gulls and Black‐billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re‐established following a period of strict isolation. The ability of Black‐billed and Red‐billed Gulls to successfully interbreed shows that despite significant differentiation ( F ST 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one‐way transfer of Red‐billed Gull mtDNA into Black‐billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red‐billed Gull population. The high incidence of introgression in Black‐billed Gulls conflicts with field observations that interbreeding is extremely rare.
Publisher: Cambridge University Press (CUP)
Date: 2015
DOI: 10.1017/S1755267215000354
Abstract: The threatened grey nurse shark ( Carcharias taurus ) is reported for the first time from oceanic coral reefs in the Timor Sea. Generally known from temperate and subtropical coastal reef habitats, this species was encountered by Indonesian traditional fishers on oceanic coral reefs in an area of the Australian Exclusive Economic Zone known as the 1974 MoU Box, some 200 km from the Australian mainland. The presence of C. taurus on these remote tropical reefs bears important management implications, including the species’ protected status in Australian waters and the challenges of regulating catches in areas permitted for traditional Indonesian fishing.
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.MARGEN.2009.11.001
Abstract: Lactate dehydrogenase-B (ldh-b) encodes a metabolic enzyme (LDH-B) which plays an important role in maintaining aerobic performance and in thermal acclimation and/or adaptation of fish. As the first step in understanding the effect this enzyme has on the ability of tropical coral reef fishes to cope with thermal stress, we characterized both coding and non-coding regions of ldh-b in two congeneric perciformes, Plectropomus leopardus and Plectropomus laevis. Ldh-b was 4666 and 4539bp in length in P. leopardus and P. laevis, respectively, with coding regions comprising 1005bp in both species. We report a high level of sequence homology between the coding regions of ldh-b in these two species, with 98.1% identity of nucleotides corresponding to 100% amino acid identity between the deduced protein sequences. Comparison between non-coding (intron) regions of both species revealed the presence of several indels, despite the high level of homology observed (95.9% identity of intron nucleotides). Potential regulatory motifs and elements, including twenty-six simple sequence repeat motifs (mono-, di-, tri- and tetranucleotide) and twenty-three putative microRNA elements are identified within the introns of both species, further supporting recent demonstrations that such short motifs and elements exhibit widespread positioning throughout non-coding regions of the genome. This novel characterization of ldh-b in these two coral reef fishes allows for a wide range of future studies (e.g. analytical comparisons of ldh-b and LDH-B among different fish genera from different thermal environments and habitats).
Publisher: Inter-Research Science Center
Date: 08-03-2012
DOI: 10.3354/MEPS09557
Publisher: Inter-Research Science Center
Date: 02-10-2013
DOI: 10.3354/MEPS10465
Publisher: Springer Science and Business Media LLC
Date: 16-03-2022
Publisher: Cambridge University Press
Date: 22-12-2014
Publisher: Springer Science and Business Media LLC
Date: 22-04-2021
Publisher: Springer Science and Business Media LLC
Date: 12-03-2021
Publisher: Wiley
Date: 09-12-2021
DOI: 10.1111/MEC.16295
Abstract: The three‐spined stickleback ( Gasterosteus aculeatus ) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G . aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b‐RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average F ST ≈ 0.45), of low genetic ersity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine–freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.
Publisher: Frontiers Media SA
Date: 11-07-2018
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.BIOMATERIALS.2018.10.025
Abstract: Stem cell spheroids have been studied extensively in organoid culture and therapeutic transplantation. Herein, hydrogels with an embossed surface (HES) were developed as an all-in-one platform that can enable the rapid formation and culture of a large quantity of size-controllable stem cell spheroids. The embossed structure on the hydrogel was adjustable according to the grit designation of the sandpaper. Human adipose-derived stem cells (hADSCs) were rapidly assembled into spheroids on the hydrogel, with their size distribution precisely controlled from 95 ± 6 μm to 181 ± 15 μm depending on surface roughness. The hADSC spheroids prepared from the HES demonstrated expression of stemness markers and differentiation capacity. In addition, HES-based spheroids showed significantly greater VEGF secretion than spheroids grown on a commercially available low-attachment culture plate. Exploiting those advantages, the HES-based spheroids were used for 3D bioprinting, and the spheroids within the 3D-printed construct showed improved retention and VEGF secretion compared to the same 3D structure containing single cell suspension. Collectively, HES would offer a useful platform for mass fabrication and culture of stem cell spheroids with controlled sizes for a variety of biomedical applications.
Publisher: Oxford University Press (OUP)
Date: 24-02-2021
Abstract: Testing among competing demographic models of ergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic ergence scenarios, failure to account for population size (Ne) changes in daughter and ancestral populations leads to strong biases in ergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Schopthalmus maximus) by testing 16 Isolation with Migration (IM) and 16 Secondary Contact (SC) scenarios, modelling changes in Ne as well as the effects of linked selection and barrier loci. Failure to account for changes in Ne resulted in selecting SC models with long periods of isolation and ergence times preceding the formation of the Baltic Sea. In contrast, models accounting for Ne changes suggest recent (& kya) ergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For ex le, in the turbots data islands of differentiation show signatures of recent selective sweeps, rather than old ergence resisting secondary introgression. The results have broad implications for the study of population ergence by high-lighting the potential effects of unmodeleld changes in Ne on demographic inference. Tested models should aim at representing realistic ergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modelling.
Publisher: Cold Spring Harbor Laboratory
Date: 26-10-2021
DOI: 10.1101/2021.10.25.465682
Abstract: The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult-disperser species, and when distribution-wide s ling is difficult. Here, we developed a two-step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos , a reef-associated shark distributed across the tropical Indo-Pacific. In the first step, we developed a seascape genomic approach based on isolation-by-resistance models involving circuit theory applied to 515 shark s les, genotyped for 4,491 nuclear single-nucleotide polymorphisms, to explore which parameters drive their population genetic differentiation. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global-scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.
Publisher: Cold Spring Harbor Laboratory
Date: 05-06-2020
DOI: 10.1101/2020.06.03.128298
Abstract: Testing among competing demographic models of ergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic ergence scenarios, failure to account for population size ( N e ) changes in daughter and ancestral populations leads to strong biases in ergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots ( Schopthalmus maximus ) by testing 16 Isolation with Migration (IM) and 16 Secondary Contact (SC) scenarios, modelling changes in N e as well as the effects of linked selection and barrier loci. Failure to account for changes in N e resulted in selecting SC models with long periods of isolation and ergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N e changes suggest recent ( kya) ergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For ex le, in the turbots data islands of differentiation show signatures of recent selective sweeps, rather than old ergence resisting secondary introgression. The results have broad implications for the study of population ergence by high-lighting the potential effects of unmodeleld changes in N e on demographic inference. Tested models should aim at representing realistic ergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modelling.
Publisher: Wiley
Date: 09-2019
DOI: 10.1111/MEC.15204
Abstract: Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.
Publisher: Routledge
Date: 05-06-2014
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/PC14909
Abstract: The grey nurse shark (Carcharius taurus) is listed as threatened throughout much of its global distribution, and as critically endangered in eastern Australia. Captive breeding programs have thus far been largely unsuccessful and little is known of its mating system in this context. Here we carry out a paternity analysis to determine if the mating system in captivity is characterised by multiple mating, and whether poor offspring survival is associated with a particular male. Tissue s les from grey nurse sharks were collected from three potential sires, the two dams and nine pups housed at Manly SEA LIFE Sanctuary in eastern Australia. Each in idual was genotyped at seven microsatellite markers and three cases of multiple paternity were inferred. No paternal link to stillborn (5), or scoliotic (2) pups was indicated. For the first time, we show the natural wild phenomenon of multiple paternity occurring in a captive environment.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2015
DOI: 10.1038/SREP13229
Abstract: Grey reef sharks ( Carcharhinus amblyrhynchos ) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200 km latitudinal gradient, comparing empirical data with models simulating different levels of migration. The empirical data did not reveal any genetic structuring along the entire latitudinal gradient s led, suggesting regular widespread dispersal and gene flow of the species throughout most of the GBR. Our simulated datasets indicate that even with substantial migrations (up to 25% of in iduals migrating between neighboring reefs) both large scale genetic structure and genotypic spatial autocorrelation at the reef scale were maintained. We suggest that present migration rates therefore exceed this level. These findings have important implications regarding the effectiveness of networks of spatially discontinuous Marine Protected Areas to protect reef sharks.
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4CC00933A
Abstract: Polymorphic metal-organic framework (MOF) materials offer a platform for small-scale separation of complex mixtures of polycyclic aromatic hydrocarbons (PAHs) and polar compounds. Retention factors show dependence on both analyte dimensions and polarity, suggesting mixed-mode separation, allowing complete resolution of some analytes from multi-component mixtures.
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.ACTBIO.2017.07.040
Abstract: Scaffold-free harvest of microtissue with a defined structure has received a great deal of interest in cell-based assay and regenerative medicine. In this study, we developed thermally expandable hydrogels with spatially controlled cell adhesive patterns for rapid harvest of geometrically controlled microtissue. We patterned polydopamine (PD) on to the hydrogel via microcontact printing (μCP), in linear shapes with widths of 50, 100 and 200μm. The hydrogels facilitated formation of spatially controlled strip-like microtissue of human dermal fibroblasts (HDFBs). It was possible to harvest and translocate microtissues with controlled widths of 61.4±14.7, 104.3±15.6, and 186.6±22.3μm from the hydrogel to glass substrates by conformal contact upon expansion of the hydrogel in response to a temperature change from 37 to 4°C, preserving high viability, extracellular matrix, and junction proteins. Microtissues were readily translocated in vivo to the subcutaneous tissue of mouse. The microtissues were further utilized as a simple assay model for monitoring of contraction in response to ROCK1 inhibitor. Collectively, micro-sized patterning of PD on the thermally expandable hydrogels via μCP holds promise for the development of microtissue harvesting systems that can be employed to ex vivo tissue assay and cell-based therapy. Harvest of artificial tissue with controlled cellular arrangement independently from external materials has been widely studied in cell-based assay and regenerative medicine. In this study, we developed scaffold-free harvest system of microtissues with anisotropic arrangement and controlled width by exploiting thermally expandable hydrogels with cell-adhesive patterns of polydopamine formed by simple microcontact printing. Cultured strips of human dermal fibroblasts on the hydrogels were rapidly delivered to various targets ranging from flat coverglass to mice subcutaneous tissue by thermal expansion of the hydrogel at 4°C for 10min. These were further utilized as a drug screening model responding to ROCK1 inhibitor, which imply its versatile applicability.
Publisher: Cold Spring Harbor Laboratory
Date: 31-10-2019
DOI: 10.1101/826412
Abstract: An important model system for the study of genomic mechanisms underlying parallel ecological adaptation in the wild is the three-spined stickleback ( Gasterosteus aculeatus ), which has repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies have identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes, but these are typically based on limited geographic s ling and are biased towards studies in the Eastern Pacific. We analysed population genomic data from marine and freshwater ecotypes of three-spined sticklebacks with from a comprehensive global collection of marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Our findings highlight that most signatures of parallel evolution were unique to the Eastern Pacific. Trans-oceanic marine and freshwater differentiation was only found in a very limited number of genomic regions, including three chromosomal inversions. Using both simulations and empirical data, we demonstrate that this is likely due to both the stochastic loss of freshwater-adapted alleles during founder events during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which have reduced the amount of standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the existence of highly elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is also consistent with a secondary contact scenario between marine and freshwater populations that have evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies focused on Eastern Pacific populations have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.
Publisher: Oxford University Press (OUP)
Date: 21-08-2019
Abstract: Recent years have brought the realization that evolutionary changes driven by selection can occur in ecological time scales. However, recent evolutionary events can be hard to detect and may easily go unnoticed. For harvested species, such cryptic ersity may lead to suboptimal management. These points are illustrated by the two flounder species in the Baltic Sea. Although early ecological studies identified two ecotypes of European flounder (Platichthys flesus) based on spawning differences, genomic studies only recently demonstrated that they were reproductively isolated species, P. flesus and P. solemdali, separated through rapid ecologically driven speciation. These morphologically indistinguishable species are harvested within a mixed-stock fishery. In the northern Baltic Sea flounder landings have declined since the mid-1980s, with a drop in the Gulf of Finland (GoF) being particularly dramatic (∼90%). Genetic analyses of historical otolith s les from GoF catches have revealed that back in 1983 the fishery unknowingly targeted primarily P. flesus, whereas thereafter almost exclusively P. solemdali. Hence, the case of two flounder species illustrates (i) how ecological studies stimulated genetic investigations leading to discovery of ecological speciation and (ii) how cryptic species turnover discovered with genetic tools in turn improved ecological understanding with benefits to management and conservation.
Publisher: Springer Science and Business Media LLC
Date: 19-04-2017
DOI: 10.1038/HDY.2017.21
Publisher: Springer Science and Business Media LLC
Date: 03-05-2013
DOI: 10.1038/SREP01769
Publisher: Wiley
Date: 28-06-2022
DOI: 10.1111/DOM.14779
Abstract: To test the hypothesis that the reduction in urinary kidney injury molecule‐1 (KIM‐1) observed with the sodium‐glucose cotransporter‐2 (SGLT2) inhibitor canagliflozin is mediated through its effects on urine albumin to creatinine ratio (UACR) and monocyte chemoattractant protein‐1 (MCP‐1) by assessing the proportion of the effect of canagliflozin on KIM‐1 that is mediated through its effects on MCP‐1 and UACR in patients with type 2 diabetes and albuminuric kidney disease. We measured KIM‐1 and MCP‐1 levels in urine s les from the CANVAS trial at baseline and Week 52 with the Mesoscale QuickPlex SQ 120 platform. KIM‐1 and MCP‐1 were standardized by urinary creatinine (Cr). The proportion of the effect of canagliflozin that is mediated through UACR and MCP‐1/Cr on KIM‐1/Cr was estimated with G‐computation. In total, 763 patients with micro‐ or macroalbuminuria (17.6% of the total cohort) were included. Baseline characteristics were well balanced between the canagliflozin and placebo group. At Year 1, canagliflozin compared to placebo reduced UACR, MCP‐1/Cr and KIM‐1/Cr by 40.4% (95% CI 31.0, 48.4), 18.1% (95% CI 8.9, 26.4) and 30.9% (95% CI 23.0, 38.0), respectively. The proportion of the effect of canagliflozin on KIM‐1/Cr mediated by its effect on UACR and in turn on MCP‐1/Cr was 15.2% (95% CI 9.4, 24.5). Canagliflozin reduces urinary KIM‐1, suggesting decreased tubular damage. This effect was partly mediated through a reduction in MCP‐1, indicative of reduced tubular inflammation, which was in turn mediated by a reduction in UACR. This post hoc analysis suggests that urinary albumin leakage may lead to tubular inflammation and induction of injury, and provide mechanistic insight for how canagliflozin may ameliorate tubular damage, but further research is required to confirm these findings.
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.HAL.2017.04.006
Abstract: Increases in reported incidence of ciguatera fish poisoning (hereafter ciguatera) have been linked to warmer sea temperatures that are known to trigger coral bleaching events. The drivers that trigger blooms of ciguatera-causing dinoflagellates on the Great Barrier Reef (GBR) are poorly understood. This study investigated the effects of increased temperatures and lowered salinities, often associated with environmental disturbance events, on the population growth of two strains of the potentially ciguatera-causing dinoflagellate, Gambierdiscus carpenteri (NQAIF116 and NQAIF380). Both strains were isolated from the central GBR with NQAIF116 being an inshore strain and NQAIF380 an isolate from a stable environment of a large coral reef aquarium exhibit in ReefHQ, Townsville, Australia. Species of Gambierdiscus are often found as part of a mixed assemblage of benthic toxic dinoflagellates on macroalgal substrates. The effect of assemblage structure of dinoflagellates on the growth of Gambierdiscus populations has, however, not been explored. The study, therefore investigated the growth of G. carpenteri within mixed assemblages of benthic dinoflagellates. Population growth was monitored over a period of 28days under three salinities (16, 26 and 36) and three temperature (24, 28 and 34°C) conditions in a fully crossed experimental design. Temperature and salinity had a significant effect on population growth. Strain NQAIF380 exhibited significantly higher growth at 28°C compared to strain NQAIF116, which had highest growth at 24°C. When strain NQAIF116 was co-cultured with the benthic dinoflagellates, Prorocentrum lima and Ostreopsis sp., inhibitory effects on population growth were observed at a salinity of 36. In contrast, growth stimulation of G. carpenteri (strain NQAIF116) was observed at a salinity of 26 and particularly at 16 when co-cultured with Ostreopsis-dominated assemblages. Range expansion of ciguatera-causing dinoflagellates could lead to higher frequency of reported ciguatera illness in populated temperate Australian regions, outside the tropical range of the GBR. Therefore, the findings on salinity and temperature tolerance of two strains of G. carpenteri indicates potential adaptability to different local environmental conditions. These are baseline data for future investigations into the potential southward range expansion of ciguatera-causing dinoflagellates originating from the GBR.
Publisher: Wiley
Date: 06-02-2023
DOI: 10.1111/DOM.14978
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2023
DOI: 10.1101/2023.03.17.533073
Abstract: Understanding what determines species and population differences in levels of genetic ersity has important implications for our understanding of evolution, as well as for the conservation and management of wild populations. Previous comparative studies have emphasized the roles of linked selection, life-history trait variation and genomic properties, rather than pure demography, as important determinants of genetic ersity. However, these findings are based on coarse estimates across a range of highly erged taxa, and it is unclear how well they represent the processes within in idual species. We assessed genome-wide genetic ersity ( π ) in 45 nine-spined stickleback ( Pungitius pungitius ) populations and found that π varied 15-fold among populations ( π min ≈0.00015, π max ≈0.0023) whereas estimates of recent effective population sizes varied 122-fold. Analysis of inbreeding coefficients (F ROH ) estimated from runs of homozygosity revealed strong negative association between π and F ROH . Genetic ersity was also negatively correlated with mean body size and longevity, but these associations were not statistically significant after controlling for demographic effects (F ROH ). The results give strong support for the view that populations’ demographic features, rather than life history differences, are the chief determinants of genetic ersity in the wild.
Publisher: Springer Science and Business Media LLC
Date: 03-04-2014
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.BIOMATERIALS.2019.119534
Abstract: 3D culture of stem cells can improve therapeutic effects. However, there is limited research on how to deliver cultured stem cell spheroids to the desired target. Here, we developed lotus seedpod-inspired hydrogel (LoSH) containing microwells for culture and delivery of stem cell spheroids. Human adipose-derived stem cells (hADSCs) inside the square microwells (200 or 400 μm in width with various depths) spontaneously formed spheroids with high viability (94.08 ± 1.56%), and fibronectins conjugated to the hydrogel successfully gripped the spheroids, similar to the funiculus gripping seeds in the lotus seedpod. The spheroids slightly bound to the LoSH surface at 37 °C were detached by the expansion of LoSH at lower temperature of 4 °C. After spheroid formation, LoSH was placed on the target substrate upside-down, expanded at 4 °C for 10 min, and removed from the target. As a result, the spheroids within the microwell were successfully transferred to the target substrate with high transfer efficiency (93.78 ± 2.30%). A delivery of spheroids from LoSH to full-thickness murine skin wound with chimney model showed significant enhancement of the number of SMA-positive vessels at day 21 compared to the group received the same number of spheroids by injection. Together, our findings demonstrate LoSH as a one-step platform that can culture and deliver spheroids to a large target area, which will be useful for various biomedical applications.
Publisher: Public Library of Science (PLoS)
Date: 23-10-2013
Publisher: Elsevier BV
Date: 10-2014
Publisher: American Diabetes Association
Date: 22-09-2022
DOI: 10.2337/DC22-0866
Abstract: The inflammatory cytokine interleukin-6 (IL-6) is associated with cardiovascular (CV) and kidney outcomes in various populations. However, data in patients with type 2 diabetes are limited. We assessed the association of IL-6 with CV and kidney outcomes in the Canagliflozin Cardiovascular Assessment Study (CANVAS) and determined the effect of canagliflozin on IL-6. Patients with type 2 diabetes at high CV risk were randomly assigned to canagliflozin or placebo. Plasma IL-6 was measured at baseline and years 1, 3, and 6. The composite CV outcome was nonfatal myocardial infarction, nonfatal stroke, or CV death the composite kidney outcome was sustained ≥40% estimated glomerular filtration rate decline, end-stage kidney disease, or kidney-related death. Multivariable-adjusted Cox proportional hazards regression was used to estimate the associations between IL-6 and the outcomes. The effect of canagliflozin on IL-6 over time was assessed with a repeated-measures mixed-effects model. The geometric mean IL-6 at baseline, available in 3,503 (80.2%) participants, was 1.7 pg/mL. Each doubling of baseline IL-6 was associated with 14% (95% CI 4, 24) and 21% (95% CI 1, 45) increased risk of CV and kidney outcomes, respectively. Over 6 years, IL-6 increased by 5.8% (95% CI 3.4, 8.3) in the placebo group. Canagliflozin modestly attenuated the IL-6 increase (absolute percentage difference vs. placebo 4.4% [95% CI 1.3, 9.9 P = 0.01]). At year 1, each 25% lower level of IL-6 compared with baseline was associated with 7% (95% CI 1, 22) and 14% (95% CI 5, 22) lower risks for the CV and kidney outcome, respectively. In patients with type 2 diabetes at high CV risk, baseline IL-6 and its 1-year change were associated with CV and kidney outcomes. The effect of IL-6–lowering therapy on CV, kidney, and safety outcomes remains to be tested.
Publisher: Springer Science and Business Media LLC
Date: 11-11-2019
Publisher: Wiley
Date: 28-03-2022
DOI: 10.1111/ECOG.06158
Abstract: The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult‐disperser species, and when distribution‐wide s ling is difficult. Here, we developed a two‐step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos , a reef‐associated shark distributed across the tropical Indo‐Pacific. In the first step, we developed a seascape genomic approach based on isolation‐by‐resistance models involving circuit theory applied to 515 shark s les, genotyped for 4991 nuclear single‐nucleotide polymorphisms. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global‐scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.
Publisher: Springer Science and Business Media LLC
Date: 22-06-2020
DOI: 10.1038/S41559-020-1222-6
Abstract: The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic s ling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global s les of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine-freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.
Location: Australia
Start Date: 2017
End Date: 2017
Funder: Suomen Kulttuurirahasto
View Funded ActivityStart Date: 2022
End Date: 2025
Funder: Agencia Estatal de Investigación
View Funded Activity