Biology subjects

Bradford, M.

Publications and source records attributed to Bradford, M..

6 recordsLinked to original sources

bioRxiv2025

Optimal TELSAM-Target Protein Linker Character is TargetProtein-Dependent

Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukaemia protein (TELSAM) to a protein of interest has been shown to significantly enhance crystallization propensity. TELSAM is a pH-dependent, polymer-forming protein crystallization chaperone which, when covalently fused to a protein of interest, forms a stable, well-ordered crystal lattice. However, despite its success, a challenge persists in that crystal quality and diffraction limits appear to be heavily dependent on the choice of linker between TELSAM and the protein of interest, with identification of a functional linker relying on trial-and-error methods. Likewise, previous studies revealed that the 10xHis tag at the TELSAM N-terminus can either facilitate or hinder the ordered crystallization of target proteins attached via flexible or semi-flexible linkers. To address these challenges, we designed multiple constructs with several types of linkers--rigid (helical fusion), semi-flexible (Pro-Alan), and flexible (poly-Gly)--of varying lengths to fuse a designed ankyrin repeat protein (DARPin) to the TELSAM C-terminus. Semi-flexible and flexible linker constructs were made with and without the 10xHis tag. Our findings indicate that short semi-flexible and rigid linkers consistently yield large crystals within 24 hours with a DARPin target protein, but that flexible linkers perform best with a TNK1 UBA domain target protein. Removing the 10xHis tag enhanced crystallization rates, improved crystal morphology, and increased the crystallization propensity of semi-flexible and flexible linker constructs. While removing the His tag did not have a significant effect on crystal size, it improved the diffraction limits and crystal quality of the 1TEL-PA-DARPin construct. These results suggest that the ideal linker selection primarily depends on the properties of the target protein. Our data support the recommendation to use a short yet flexible or semi-flexible linker between TELSAM and the target protein to facilitate protein crystallization and high-resolution structure determination. SynopsisIn this study, we examine the effect of short to medium-length flexible, semi-flexible, and rigid linkers on the crystallization of a DARPin fused to the 1TEL protein crystallization chaperone, demonstrating that while rigid linkers impair crystallization and reduce diffraction quality, the ideal linker character remain target-protein dependent. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672704v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@b90d1org.highwire.dtl.DTLVardef@1508e7dorg.highwire.dtl.DTLVardef@1baf0d1org.highwire.dtl.DTLVardef@1843df_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Local controls modify the effects of timber harvesting on surface soil carbon and nitrogen dynamics

Managing for structural complexity to enhance forest ecosystem health and resiliency is increasingly incorporated in silvicultural treatments. High spatial variability in stands managed for structural complexity could obscure the effects of forest management on surface soils. Yet few studies have assessed how within-stand variation in forest structure and other local controls influence surface soil organic matter dynamics over time following timber harvests. We used a stratified random sampling design to capture variation in stand age, legacy structure, soil type, and topography in a second-growth, oak-hardwood forest in the northeastern U.S. We compared surface soil carbon and nitrogen content and availability in 15 harvested stands managed to promote tree regeneration (n = 144 plots) and five unharvested controls (n = 48 plots). We also examined changes over time since harvest in just the harvested stands using a 22-year chronosequence. Forest management strongly influenced surface soil carbon and nitrogen dynamics. The timber harvests had lower soil carbon and nitrogen, microbial biomass, and carbon mineralization but higher nitrogen mineralization. These differences were more pronounced in the drier, less fertile soil type than in more moist, fertile soils. Across the 22-year chronosequence, topography, soil type, and downed woody material density dictated the direction of changes in surface soil carbon and nitrogen over time. Soil carbon and nitrogen accrued over time at drier, higher elevation ([~]300 m) sites and under higher densities of fine woody material but declined at lower elevations ([~]180 m) and under lower fine woody material. Proximity to legacy trees was associated with higher soil carbon and nitrogen concentrations and availability. Our findings underscore the importance of silvicultural practices that retain structural legacies and downed woody material in shaping surface soil carbon and nitrogen dynamics over time. Our results also highlight how accounting for spatial variation in local controls on soil carbon and nitrogen, such as topography, can improve detection of changes from forest management practices that increase spatial heterogeneity within stands, such as irregular shelterwood and seed tree regeneration methods.

ecology↗

bioRxiv2023

A Method for Sampling the Living Wood Microbiome

Efforts to characterize microbial life across diverse environments have progressed tremendously, yet the microbiome of Earths largest biomass reservoir--the wood of living trees--has been largely unexplored. Current understanding of the tree microbiome is largely confined to roots and leaves, with little attention given to the endophytic microbiome of wood, even though emergent studies have indicated this zone as a niche for unique taxa, of consequence for ecosystem health and global biogeochemical cycles. The lack of investigation derives partly from the physical recalcitrance of wood, which presents challenges during sampling, homogenization, and the extraction of nucleic acids. In response to these issues, we present an optimized method for processing wood for use in microbial analyses, from sampling through to downstream analyses. Using methane-cycling taxa as model endophytes, we assess losses in recovery during our method, and determine a limit-of-detection of approximately 500 cells per 100 mg of (dry) wood. For all six species evaluated--which represented several diverse taxa of hardwoods and softwoods--PCR inhibition proved minimal, and we expect this method to be applicable for a majority of tree species. The methods presented herein can facilitate future investigation into the wood microbiome and global microbial ecology of methane cycling.

ecology↗

bioRxiv2021

Tropical tree growth sensitivity to climate is driven by species intrinsic growth rate and leaf traits

A better understanding of how climate affects growth in tree species is essential for improved predictions of forest dynamics under climate change. Long-term climate averages (mean climate) and short-term deviations from these averages (anomalies) both influence tree growth, but the rarity of long-term data integrating climatic gradients with tree censuses has so far limited our understanding of their respective role, especially in tropical systems. Here, we combined 49 years of growth data for 509 tree species across 23 tropical rainforest plots along a climatic gradient to examine how tree growth responds to both climate means and anomalies, and how species functional traits mediate these tree growth responses to climate. We showed that short-term, anomalous increases in atmospheric evaporative demand and solar radiation consistently reduced tree growth. Drier forests and fast-growing species were more sensitive to water stress anomalies. In addition, species traits related to water use and photosynthesis partly explained differences in growth sensitivity to both long-term and short-term climate variations. Our study demonstrates that both climate means and anomalies shape tree growth in tropical forests, and that species traits can be leveraged to understand these demographic responses to climate change, offering a promising way forward to forecast tropical forest dynamics under different climate trajectories.

ecology↗

bioRxiv2018

The importance of large-diameter trees in the wet tropical rainforests of Australia

Large trees are keystone structures in many terrestrial ecosystems. They contribute disproportionately to reproduction, recruitment and succession, and influence the structure, dynamics, and diversity of forests. Recently, researchers have become concerned about evidence showing rapid declines in large, old trees in a range of ecosystems across the globe. We used [≥]10cm diameter at breast height (DBH) stem inventory data from 20, 0.5 ha forest plots spanning the wet tropical rainforest of Queensland, Australia to examine the contribution of large-diameter trees to above ground biomass (AGB), richness, dominance, mortality and recruitment. We show consistencies with tropical rainforest globally in that large-diameter trees ([≥]70 cm DBH) contribute much of the biomass (33%) from few trees (2.4% of stems [≥]10cm DBH) with the density of the largest trees explaining much of the variation (62%) in AGB across plots. Measurement of AGB in the largest 5% of trees allows plot biomass to be predicted with ~85% precision. In contrast to rainforest in Africa and America, we show that a high proportion of species are capable of reaching a large-diameter in Australian wet tropical rainforest resulting in weak biomass hyperdominance (~10% of species account for 50% of the biomass) and high potential resilience to regional disturbances and global environmental change. We show that the high AGB in Australian tropical forests is driven primarily by the relatively high density of large trees coupled with contributions from significantly higher densities of medium size trees. Australian wet tropical rainforests are well positioned to maintain the current densities of large-diameter trees and high AGB into the future due to the species richness of large trees and a high density of replacement smaller trees.

ecology↗

bioRxiv2017

Transparency in Authors’ Contributions and Responsibilities to Promote Integrity in Scientific Publication

In keeping with the growing movement in scientific publishing toward transparency in data and methods, we argue that the names of authors accompanying journal articles should provide insight into who is responsible for which contributions, a process should exist to confirm that the list is complete, clearly articulated standards should establish whether and when the contributions of an individual justify authorship credit, and those involved in the generation of scientific knowledge should follow these best practices.\n\nTo accomplish these goals, we recommend that journals adopt common and transparent standards for authorship, outline responsibilities for corresponding authors, adopt the CRediT (Contributor Roles Taxonomy)1 methodology for attributing contributions, include this information in article metadata, and encourage authors to use the digital persistent identifier ORCID.2 Furthermore, we suggest that research institutions have regular open conversations on authorship criteria and ethics and that funding agencies adopt ORCID and accept CRediT. Scientific societies should further authorship transparency by promoting these recommendations through their meetings and publications programs.

scientific communication and education↗