| 1. |
- Rich, Rebecca L., et al.
(author)
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A global benchmark study using affinity-based biosensors
- 2009
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Journal article (peer-reviewed)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 2. |
- Bainbridge, Matthew N, et al.
(author)
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Germline mutations in shelterin complex genes are associated with familial glioma
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 107:1
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Journal article (peer-reviewed)abstract
- Gliomas are the most common brain tumor, with several histological subtypes of various malignancy grade. The genetic contribution to familial glioma is not well understood. Using whole exome sequencing of 90 individuals from 55 families, we identified two families with mutations in POT1 (p.G95C, p.E450X), a member of the telomere shelterin complex, shared by both affected individuals in each family and predicted to impact DNA binding and TPP1 binding, respectively. Validation in a separate cohort of 264 individuals from 246 families identified an additional mutation in POT1 (p.D617Efs), also predicted to disrupt TPP1 binding. All families with POT1 mutations had affected members with oligodendroglioma, a specific subtype of glioma more sensitive to irradiation. These findings are important for understanding the origin of glioma and could have importance for the future diagnostics and treatment of glioma.
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| 3. |
- Chatzopoulos, Paschalis, et al.
(author)
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Height-diameter allometry for a dominant palm to improve understanding of carbon and forest dynamics in forests of Puerto Rico
- 2024
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In: Biotropica. - : John Wiley & Sons. - 0006-3606 .- 1744-7429. ; 56:2
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Journal article (peer-reviewed)abstract
- Tropical forests play a major role in the global carbon cycle but their diversity and structural complexity challenge our ability to accurately estimate carbon stocks and dynamics. Palms, in particular, are prominent components of many tropical forests that have unique anatomical, physiological, and allometric differences from dicot trees, which impede accurate estimates of their aboveground biomass (AGB) and population dynamics. We focused on improving height estimates and, ultimately, AGB estimates for a highly abundant palm in Puerto Rico, Prestoea acuminata. Based on field measurements of 1003 individuals, we found a strong relationship between stem height and diameter. We also found some evidence that height–diameter allometry of P. acuminata is mediated by various sources of environmental heterogeneity including slope and neighborhood crowding. We then examined variability in AGB estimates derived from three models developed to estimate palm AGB. Finally, we applied our novel height:diameter allometric model to hindcast dynamics of P. acuminata in the Luquillo Forest Dynamics Plot during a 27-year period (1989–2016) of post-hurricane recovery. Overall, our study provides improved estimates of AGB in wet forests of Puerto Rico and will facilitate novel insights to the dynamics of palms in tropical forests.
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| 4. |
- Hall, Jazlynn, et al.
(author)
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Hurricane-Induced Rainfall is a Stronger Predictor of Tropical Forest Damage in Puerto Rico Than Maximum Wind Speeds
- 2020
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)abstract
- Projected increases in cyclonic storm intensity under a warming climate will have profound effects on forests, potentially changing these ecosystems from carbon sinks to sources. Forecasting storm impacts on these ecosystems requires consideration of risk factors associated with storm meteorology, landscape structure, and forest attributes. Here we evaluate risk factors associated with damage severity caused by Hurricanes Maria and Irma across Puerto Rican forests. Using field and remote sensing data, total forest aboveground biomass (AGB) lost to the storms was estimated at 10.44 (+/- 2.33) Tg, ca. 23% of island-wide pre-hurricane forest AGB. Storm-related rainfall was a stronger predictor of forest damage than maximum wind speeds. Soil water storage capacity was also an important risk factor, corroborating the influence of rainfall on forest damage. Expected increases of 20% in hurricane-associated rainfall in the North Atlantic highlight the need to consider how such shifts, together with high speed winds, will affect terrestrial ecosystems.
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| 5. |
- Hülsmann, Lisa, et al.
(author)
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Latitudinal patterns in stabilizing density dependence of forest communities
- 2024
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In: Nature. - 0028-0836 .- 1476-4687. ; 627, s. 564-571
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Journal article (peer-reviewed)abstract
- Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10–12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizingCNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.
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| 6. |
- Ibanez, Thomas, et al.
(author)
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Damage to tropical forests caused by cyclones is driven by wind speed but mediated by topographical exposure and tree characteristics
- 2024
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In: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 30:5
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Journal article (peer-reviewed)abstract
- Each year, an average of 45 tropical cyclones affect coastal areas and potentially impact forests. The proportion of the most intense cyclones has increased over the past four decades and is predicted to continue to do so. Yet, it remains uncertain how topographical exposure and tree characteristics can mediate the damage caused by increasing wind speed. Here, we compiled empirical data on the damage caused by 11 cyclones occurring over the past 40 years, from 74 forest plots representing tropical regions worldwide, encompassing field data for 22,176 trees and 815 species. We reconstructed the wind structure of those tropical cyclones to estimate the maximum sustained wind speed (MSW) and wind direction at the studied plots. Then, we used a causal inference framework combined with Bayesian generalised linear mixed models to understand and quantify the causal effects of MSW, topographical exposure to wind (EXP), tree size (DBH) and species wood density (ρ) on the proportion of damaged trees at the community level, and on the probability of snapping or uprooting at the tree level. The probability of snapping or uprooting at the tree level and, hence, the proportion of damaged trees at the community level, increased with increasing MSW, and with increasing EXP accentuating the damaging effects of cyclones, in particular at higher wind speeds. Higher ρ decreased the probability of snapping and to a lesser extent of uprooting. Larger trees tended to have lower probabilities of snapping but increased probabilities of uprooting. Importantly, the effect of ρ decreasing the probabilities of snapping was more marked for smaller than larger trees and was further accentuated at higher MSW. Our work emphasises how local topography, tree size and species wood density together mediate cyclone damage to tropical forests, facilitating better predictions of the impacts of such disturbances in an increasingly windier world.
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| 7. |
- Lasky, Jesse R., et al.
(author)
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Ontogenetic shifts in trait-mediated mechanisms of plant community assembly
- 2015
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In: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 96
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Journal article (peer-reviewed)abstract
- Identifying the processes that maintain highly diverse plant communities remains a central goal in ecology. Species variation in growth and survival rates across ontogeny, represented by tree size classes, and life history stage-specific niche partitioning, are potentially important mechanisms for promoting forest diversity. However, the role of ontogeny in mediating competitive dynamics and promoting functional diversity is not well understood, particular in high-diversity systems such as tropical forests. The interaction between interspecific functional trait variation and ontogenetic shifts in competitive dynamics may yield insights into the ecophysiological mechanisms promoting community diversity. We investigated how functional trait (seed size, maximum height, SLA, leaf N and wood density) associations with growth and survival and response to competing neighbors, differ among seedlings and two size classes of trees in a subtropical rainforest in Puerto Rico. We used a hierarchical Bayes model of diameter growth and survival to infer trait relationships with ontogenetic change in competitive dynamics. Traits were more strongly associated with average growth and survival than with neighborhood interactions, and were highly consistent across ontogeny for most traits. The associations between trait values and tree responses to crowding by neighbors showed significant shifts as trees grew. Large trees exhibited greater growth as the difference in species trait values among neighbors increased, suggesting trait-associated niche partitioning was important for the largest size class. Our results identify potential axes of niche partitioning and performance-equalizing functional tradeoffs across ontogeny, promoting species coexistence in this diverse forest community.
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| 8. |
- Leite, Melina de Souza, et al.
(author)
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Major axes of variation in tree demography across global forests
- 2024
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In: Ecography. - 0906-7590 .- 1600-0587.
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Journal article (peer-reviewed)abstract
- The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatio-temporal patterns in tree population dynamics. While previous research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach to overcome these limitations is to group mechanisms according to their shared effects on the variability of tree vital rates and quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions – categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28–33% of demographic variance alone, and 14–17% in interaction with space, totalling 40–43%. Our results support the hypothesis that the range of vital rates is similar across global forests. However, the average variability among species declined with species richness, indicating that diverse forests featured smaller interspecific differences in vital rates. Moreover, decomposing the variance in vital rates into the proposed OPs showed the importance of unexplained variability, which includes individual variation, in tree demography. A focus on how demographic variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.
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| 9. |
- Liu, Yanhong, et al.
(author)
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Insight in glioma susceptibility through an analysis of 6p22.3, 12p13.33-12.1, 17q22-23.2 and 18q23 SNP genotypes in familial and non-familial glioma
- 2012
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In: Human Genetics. - : Springer Science and Business Media LLC. - 0340-6717 .- 1432-1203. ; 131:9, s. 1507-1517
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Journal article (peer-reviewed)abstract
- The risk of glioma has consistently been shown to be increased twofold in relatives of patients with primary brain tumors (PBT). A recent genome-wide linkage study of glioma families provided evidence for a disease locus on 17q12-21.32, with the possibility of four additional risk loci at 6p22.3, 12p13.33-12.1, 17q22-23.2, and 18q23. To identify the underlying genetic variants responsible for the linkage signals, we compared the genotype frequencies of 5,122 SNPs mapping to these five regions in 88 glioma cases with and 1,100 cases without a family history of PBT (discovery study). An additional series of 84 familial and 903 non-familial cases were used to replicate associations. In the discovery study, 12 SNPs showed significant associations with family history of PBT (P < 0.001). In the replication study, two of the 12 SNPs were confirmed: 12p13.33-12.1 PRMT8 rs17780102 (P = 0.031) and 17q12-21.32 SPOP rs650461 (P = 0.025). In the combined analysis of discovery and replication studies, the strongest associations were attained at four SNPs: 12p13.33-12.1 PRMT8 rs17780102 (P = 0.0001), SOX5 rs7305773 (P = 0.0001) and STKY1 rs2418087 (P = 0.0003), and 17q12-21.32 SPOP rs6504618 (P = 0.0006). Further, a significant gene-dosage effect was found for increased risk of family history of PBT with these four SNPs in the combined data set (P (trend) <1.0 × 10(-8)). The results support the linkage finding that some loci in the 12p13.33-12.1 and 17q12-q21.32 may contribute to gliomagenesis and suggest potential target genes underscoring linkage signals.
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| 10. |
- Medina-Vega, José A., et al.
(author)
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Tropical tree ectomycorrhiza are distributed independently of soil nutrients
- 2024
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In: Nature Ecology and Evolution. - 2397-334X. ; 8, s. 400-410
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Journal article (peer-reviewed)abstract
- Mycorrhizae, a form of plant–fungal symbioses, mediate vegetation impacts on ecosystem functioning. Climatic effects on decomposition and soil quality are suggested to drive mycorrhizal distributions, with arbuscular mycorrhizal plants prevailing in low-latitude/high-soil-quality areas and ectomycorrhizal (EcM) plants in high-latitude/low-soil-quality areas. However, these generalizations, based on coarse-resolution data, obscure finer-scale variations and result in high uncertainties in the predicted distributions of mycorrhizal types and their drivers. Using data from 31 lowland tropical forests, both at a coarse scale (mean-plot-level data) and fine scale (20 × 20 metres from a subset of 16 sites), we demonstrate that the distribution and abundance of EcM-associated trees are independent of soil quality. Resource exchange differences among mycorrhizal partners, stemming from diverse evolutionary origins of mycorrhizal fungi, may decouple soil fertility from the advantage provided by mycorrhizal associations. Additionally, distinct historical biogeographies and diversification patterns have led to differences in forest composition and nutrient-acquisition strategies across three major tropical regions. Notably, Africa and Asia’s lowland tropical forests have abundant EcM trees, whereas they are relatively scarce in lowland neotropical forests. A greater understanding of the functional biology of mycorrhizal symbiosis is required, especially in the lowland tropics, to overcome biases from assuming similarity to temperate and boreal regions.
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