24 research outputs found
Market and non-market benefits in government-assisted reforestation in the Queensland wet tropics
No full textAltered expression of the core circadian clock component PERIOD2 contributes to osteoarthritis-like changes in chondrocyte activity
No full textIn osteoarthritis, chondrocytes undergo a phenotype shift characterised by reduced expression of SOX9 (sry-box 9) and increased production of cartilage-degrading enzymes, e.g. MMP13 (matrix metalloproteinase 13) and ADAMTS5 (a disintegrin and metalloproteinase with thrombospondin motifs 5). The chondrocyte clock is also altered. Specifically, the peak level of PER2 is elevated, but peak level of BMAL1 reduced in osteoarthritic chondrocytes. The purpose of this study was to determine whether increased PER2 expression causes disease-associated changes in chondrocyte activity and to identify whether known risk factors for osteoarthritis induce changes in PER2 and BMAL1 expression. Primary human chondrocytes isolated from macroscopically normal cartilage were serum-starved overnight then re-fed with serum-replete media with/without interleukin 1β (IL-1β) (10 ng/mL), hydrogen peroxide (100 µM) or basic calcium phosphate (BCP) crystals (50 µg/mL). Peak level of BMAL1 was lower, whereas PER2 levels remained elevated for longer, in chondrocytes treated with IL-1β, hydrogen peroxide or BCP crystals compared to untreated cells. Levels of SOX9 were lower, whereas levels of ADAMTS5 and MMP13 were higher, in chondrocytes exposed to any of the three treatments compared to untreated cells. Knockdown of PER2 using siRNA partially abrogated the effects of each treatment on chondrocyte phenotype marker expression. Similarly, in chondrocytes isolated from osteoarthritic cartilage PER2 knockdown was associated with increased SOX9, reduced ADAMTS5 and reduced RNA and protein levels of MMP13 indicating partial mitigation of the osteoarthritic phenotype. Conversely, further ablation of BMAL1 expression in osteoarthritic chondrocytes resulted in a further reduction in SOX9 and increase in MMP13 expression. Overexpression of PER2 in the H5 chondrocyte cell line led to increased ADAMTS5 and MMP13 and decreased SOX9 expression. Localised inflammation, oxidative stress and BCP crystal deposition in osteoarthritic joints may contribute to disease pathology by inducing changes in the chondrocyte circadian clock.</p
Geographically conserved spatially derived nucleotide diversity for full-length AMA1.
No full textNei’s nucleotide diversity calculation for geographic area or countries from Asia-Pacific and African regions for AMA1 with incorporation of protein structural information using 15°A window. Structure was coloured according to nucleotide diversity mapped to each residue. Sample size for each respective population are as follows: Malawi (n = 139), Ghana (n = 243), Cambodia (n = 433), and PNG (n = 112). Similar to selection pressure (determined by D*), silent face of AMA1 has low nucleotide diversity. (TIFF)</p
Relative solvent accessibility of polymorphic versus conserved residues.
No full textRelative solvent accessibility (RSA) was calculated for all residues for 23 antigens. RSA was calculated using neural network based NetSurfP1.1 program or DSSP program respectively based on the presence of known PDB or homology-modelled structures [30,31]. Polymorphic residues from more than 1000 sequences regardless of minor allele frequency (MAF) were included in the analysis. Box and whisker plots show the median (blue line), and interquartile range (blue box) of RSA values for each residue from respective group. The violin plot (which uses Kernel Density Estimation to compute an empirical probability distribution) shows a smooth distribution of RSA values for most of the calculated group. RSA scores for individual antigens as well as for the combination of all antigens were calculated. Only significant p-values are shown.</p
Polymorphism and selection of full-length rh5 in the context linear sequence level for different populations.
No full textThe sliding window analyses (a window size of 50 bp and a step size of 5 bp) calculated for segregation sites (S, yellow lines), nucleotide diversity (π, blue lines) and Tajima’s D (D, red lines) for each geographic area or country. The results were plotted together and scaled to Tajima’s D values. Nucleotide positions based on coding region are shown in the x-axis. The significant values for Tajima’s D was determined based on sample size. (TIFF)</p
Distribution of haplotype diversity, nucleotide diversity, and Tajima’s D values amongst countries for each antigen.
No full textThe lines from ridgeline plots indicate the range and distribution of respective diversity parameters for each antigen across different parasite populations (countries). Tramp, and cyrpa were conserved across all populations, whilst trap, ama1, eba175, and celtos were diverse and showed evidence of diversifying selection across all parasite populations.</p
Geographically variable spatially derived nucleotide diversity for MSP1-19.
No full textNei’s nucleotide diversity calculation for geographic area or countries from Asia-Pacific and African regions for MSP1-19 with incorporation of protein structural information using 15°A window. Structure was coloured according to nucleotide diversity mapped to each residue. Sample size for each respective population are as follows: Malawi (n = 101), Ghana (n = 183), Cambodia (n = 270), and PNG(n = 72). (TIFF)</p
Geographically varied selection pressure for SERA5.
No full textTajima’s D (D*) calculation for geographic area or countries from Asia-Pacific and African regions for SERA5 (C-terminal) with incorporation of protein structural information using 15°A window. The structured region of SERA5 based on experimentally defined structure PDB code: 2WBF was used. The structure was coloured according to D* scores mapped to each residue with undefined D* were shown in grey. Only Malawi (n = 106), and PNG (n = 108) populations were shown. (TIFF)</p
F<sub>ws</sub> output from moimix R-package for each country.
No full textFws > 0.90 assumed as MOI 1 isolates are highlighted in red, and 0.90 ≥ Fws > 0.80 assumed as MOI 2 isolates are highlighted in blue. Samples with Fws below 0.80 are excluded from the analysis. (TIFF)</p
Antigens displaying geographically conserved balancing selection at functionally important interfaces. Antigens were not normalised based on their sizes.
No full texta. Spatially derived Tajima’s D (D*) score calculation for TRAP (Ectodomain) with incorporation of protein structural information using a 15Å window. TRAP (ectodomain) (PDB Code: 4HQF.A) was used. The structure was coloured according to D* scores mapped to each residue, and undefined D* are shown in white. Residues S123, R130 and R140 are involved in mediating heparin binding. Sample sizes: Malawi (n = 133), Ghana (n = 238), Cambodia (n = 430), and PNG (n = 112). b. Spatially derived Tajima’s D (D*) calculations for AMA1 with incorporation of protein structural information using 15 Å window. The manually modelled structure of AMA1 was used based on published results [27]. The structure was coloured according to D* scores mapped to each residue with undefined D* scores were shown in white. The DI, DII, DIII, and surface exposed c1L loop are indicated. Sample sizes: Malawi (n = 139), Ghana (n = 243), Cambodia (n = 433), and PNG (n = 112). c. Polymorphism and evidence of selection for ripr. Tajima’s D statistic calculated for disordered regions of RIPR in samples from Cambodia, PNG, Malawi, and Ghana. Tajima’s D is calculated with a sliding window approach (a window size of 50 bp and a step size of 5 bp). Nucleotide positions based on coding region are shown in the x-axis. Sample size for each respective population are as follows: Malawi (n = 137), Ghana (n = 246), Cambodia (n = 428), and PNG (n = 111).</p
