The Engineering of Peatland Form and Function by Beaver (Castor spp.)

Northern peatlands are significant contributors to global biogeochemical cycles. In Canada alone, peatlands cover over a tenth of the land surface and store over half of the country’s terrestrial carbon. Their ability to function as a carbon sink is inextricably linked to hydrological conditions defined by an intricate web of feedbacks from numerous autogenic (internal) and allogenic (external) drivers. Research over the last forty years has been focused on understanding the importance of each driver, as such knowledge is necessary to foresee how these landscapes might respond climate change. However, one external driver - the activity of beaver (Castor canadensis in North America and C. fiber in Eurasia) - has received little attention, even though beaver have inhabited northern peatlands for many thousands of years. Identified as a keystone species and ecosystem engineer, beaver can alter the physical, hydrological, and biogeochemical function of landscapes on a scale comparable to that of humans. Thus, the primary goal of this dissertation was to enhance our understanding of how beaver activity alters peatland function and transforms these landscapes over time. To achieve this goal, the associated impacts of beaver activity were studied over numerous scales, mostly in the montane peatlands of Alberta, Canada, via the collection and analyses of field data comprised of different physiographic, hydrological and soil variables. It was found that the activities of beaver have profound impacts on peatland landscapes. Beaver activity changes the physical appearance of peatlands, with the construction of berm-like dams that persist for long periods even after dams breach and/or are abandoned. Peat, excavated from the surrounding area, was a primary dam building material, and dams often extended far beyond the stream channel and inundated large surface areas. Peat excavation added complexity to the pond shape and bathymetry, but despite the physical complexity of beaver ponds, it was found that relationships between quickly measured field attributes allows for reliable estimates of surface water storage in these features. In addition to storing large volumes of surface water, Beaver dams/ponds had significant impacts on hydrological processes in the peatlands studied. Just as in mineral soil environments, beaver ponds acted as sinks for mineral and organic sediments. Furthermore, a multi-year study in a Rocky Mountain fen, showed that the beaver dams connected the peatland to the stream, thereby raising and stabilizing shallow ground water tables within 150-m proximity. Such findings have implications for peat formation in affected areas because plant community and carbon sequestration are tightly linked to water table behavior. Beaver ponds also had significant impacts on underlying soils. Regional sampling of peatland beaver meadows found they were depleted in organic matter. Deeper inspection of this phenomenon through multi-proxy analysis and paleo-reconstruction of peat cores revealed that beaver-meadow soils accumulated the least amount of peat over time compared to areas unaffected by beaver. This phenomenon is likely a result of sediment deposition, which increases the bulk density of peat bulk volumes and may enhance turnover and decomposition when ponds wash out. Unlike beaver ponds built in mineral soil environments, the peatland beaver ponds studied here were not associated with an accumulation of organic matter. Overall, this research shows that beaver activity can alter the appearance of peatlands and exert control over processes fundamental to their function as a carbon sink. This activity leaves a legacy beyond cyclic pond creation and abandonment that contributes to the spatial complexity of the landscape. Beavers deserve greater inclusion in peatland conceptual models and further research is needed in the peatlands beavers are known to inhabit

Rapid surface-water volume estimations in beaver ponds

Beaver ponds are surface-water features that are transient through space and time. Such qualities complicate the inclusion of beaver ponds in local and regional water balances, and in hydrological models, as reliable estimates of surface-water storage are difficult to acquire without time- and labour-intensive topographic surveys. A simpler approach to overcome this challenge is needed, given the abundance of the beaver ponds in North America, Eurasia, and southern South America. We investigated whether simple morphometric characteristics derived from readily available aerial imagery or quickly measured field attributes of beaver ponds can be used to approximate surface-water storage among the range of environmental settings in which beaver ponds are found. Studied were a total of 40 beaver ponds from four different sites in North and South America. The simplified volume–area–depth (V–A–h) approach, originally developed for prairie potholes, was tested. With only two measurements of pond depth and corresponding surface area, this method estimated surface-water storage in beaver ponds within 5%on average. Beaver pond morphometry was characterized by a median basin coefficient of 0.91, and dam length and pond surface area were strongly correlated with beaver pond storage capacity, regardless of geographic setting. These attributes provide a means for coarsely estimating surface-water storage capacity in beaver ponds. Overall, this research demonstrates that reliable estimates of surface-water storage in beaver ponds only requires simple measurements derived from aerial imagery and/or brief visits to the field. Future research efforts should be directed at incorporating these simple methods into both broader beaver-related tools and catchment-scale hydrological models

Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes

Deletions of chromosome 8p are a recurrent event in B-cell non-Hodgkin lymphoma (B-NHL), suggesting the presence of a tumor suppressor gene. We have characterized these deletions using comparative genomic hybridization to microarrays, fluorescence in situ hybridization (FISH) mapping, DNA sequencing, and functional studies. A minimal deleted region (MDR) of 600 kb was defined in chromosome 8p21.3, with one mantle cell lymphoma cell line (Z138) exhibiting monoallelic deletion of 650 kb. The MDR extended from bacterial artificial chromosome (BAC) clones RP11-382J24 and RP11-109B10 and included the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor gene loci. Sequence analysis of the individual expressed genes within the MDR and DNA sequencing of the entire MDR in Z138 did not reveal any mutation. Gene expression analysis and quantitative reverse transcriptase-polymerase chain reaction (QRT-PCR) showed down-regulation of TRAIL-R1 and TRAIL-R2 receptor genes as a consistent event in B-NHL with 8p21.3 loss. Epigenetic inactivation was excluded via promoter methylation analysis. In vitro studies showed that TRAIL-induced apoptosis was dependent on TRAIL-R1 and/or -R2 dosage in most tumors. Resistance to apoptosis of cell lines with 8p21.3 deletion was reversed by restoration of TRAIL-R1 or TRAIL-R2 expression by gene transfection. Our data suggest that TRAIL-R1 and TRAIL-R2 act as dosage-dependent tumor suppressor genes whose monoallelic deletion can impair TRAIL-induced apoptosis in B-cell lymphoma

Homozygous deletions localize novel tumor suppressor genes in B-cell lymphomas

Integrative genomic and gene-expression analyses have identified amplified oncogenes in B-cell non-Hodgkin lymphoma (B-NHL), but the capability of such technologies to localize tumor suppressor genes within homozygous deletions remains unexplored. Array-based comparative genomic hybridization (CGH) and gene-expression microarray analysis of 48 cell lines derived from patients with different B-NHLs delineated 20 homozygous deletions at 7 chromosome areas, all of which contained tumor suppressor gene targets. Further investigation revealed that only a fraction of primary biopsies presented inactivation of these genes by point mutation or intragenic deletion, but instead some of them were frequently silenced by epigenetic mechanisms. Notably, the pattern of genetic and epigenetic inactivation differed among B-NHL subtypes. Thus, the P53-inducible PIG7/LITAF was silenced by homozygous deletion in primary mediastinal B-cell lymphoma and by promoter hypermethylation in germinal center lymphoma, the proapoptotic BIM gene presented homozygous deletion in mantle cell lymphoma and promoter hypermethylation in Burkitt lymphoma, the proapoptotic BH3-only NOXA was mutated and preferentially silenced in diffuse large B-cell lymphoma, and INK4c/P18 was silenced by biallelic mutation in mantle-cell lymphoma. Our microarray strategy has identified novel candidate tumor suppressor genes inactivated by genetic and epigenetic mechanisms that substantially vary among the B-NHL subtypes

Fill‐and‐spill: a process description of runoff generation at the scale of the beholder

Descriptions of runoff generation processes continue to grow, helping to reveal complexities and hydrologic behavior across a wide range of environments and scales. But to date, there has been little grouping of these process facts. Here, we discuss how the “fill-and-spill” concept can provide a framework to group event-based runoff generation processes. The fill-and-spill concept describes where vertical and lateral additions of water to a landscape unit are placed into storage (the fill)—and only when this storage reaches a critical level (the spill), and other storages are filled and become connected, does a previously infeasible (but subsequently important) outflow pathway become activated. We show that fill-and-spill can be observed at a range of scales and propose that future fieldwork should first define the scale of interest and then evaluate what is filling-and-spilling at that scale. Such an approach may be helpful for those instrumenting and modeling new hillslopes or catchments because it provides a structured way to develop perceptual models for runoff generation and to group behaviors at different sites and scales

Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase

Hydrolytic deamination of 5-methylcytosine leads to the formation of G/T mismatches. We have shown previously that these G/T mispairs are corrected to G/C pairs by a mismatch-specific thymine-DNA glycosylase, TDG, which we subsequently purified from human cells. Here we describe the cloning of the human cDNA encoding TDG. We have identified two distinct cDNA species that differ by 100 nucleotides at the 3'-untranslated region. These cDNAs contain a 410-amino acid open reading frame that encodes a 46-kDa polypeptide. The G/T glycosylase, expressed both in vitro and in Escherichia coli, migrated in denaturing polyacrylamide gels with an apparent size of 60 kDa. The substrate specificity of the recombinant protein corresponded to that of the cellular enzyme, and polyclonal antisera raised against the recombinant protein neutralized both activities. We therefore conclude that the cDNA described below encodes human TDG. Data base searches identified a serendipitously cloned mouse cDNA sequence that could be shown to encode the murine TDG homologue. No common amino acid sequence motifs between the G/T-specific enzyme and other DNA glycosylases could be found, suggesting that TDG belongs to a new class of base-excision repair enzymes

Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes

Deletions of chromosome 8p are a recurrent event in B-cell non-Hodgkin lymphoma (B-NHL), suggesting the presence of a tumor suppressor gene. We have characterized these deletions using comparative genomic hybridization to microarrays, fluorescence in situ hybridization (FISH) mapping, DNA sequencing, and functional studies. A minimal deleted region (MDR) of 600 kb was defined in chromosome 8p21.3, with one mantle cell lymphoma cell line (Z138) exhibiting monoallelic deletion of 650 kb. The MDR extended from bacterial artificial chromosome (BAC) clones RP11-382J24 and RP11-109B10 and included the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor gene loci. Sequence analysis of the individual expressed genes within the MDR and DNA sequencing of the entire MDR in Z138 did not reveal any mutation. Gene expression analysis and quantitative reverse transcriptase-polymerase chain reaction (QRT-PCR) showed down-regulation of TRAIL-R1 and TRAIL-R2 receptor genes as a consistent event in B-NHL with 8p21.3 loss. Epigenetic inactivation was excluded via promoter methylation analysis. In vitro studies showed that TRAIL-induced apoptosis was dependent on TRAIL-R1 and/or -R2 dosage in most tumors. Resistance to apoptosis of cell lines with 8p21.3 deletion was reversed by restoration of TRAIL-R1 or TRAIL-R2 expression by gene transfection. Our data suggest that TRAIL-R1 and TRAIL-R2 act as dosage-dependent tumor suppressor genes whose monoallelic deletion can impair TRAIL-induced apoptosis in B-cell lymphoma

Homozygous deletions localize novel tumor suppressor genes in B-cell lymphomas

Integrative genomic and gene-expression analyses have identified amplified oncogenes in B-cell non-Hodgkin lymphoma (B-NHL), but the capability of such technologies to localize tumor suppressor genes within homozygous deletions remains unexplored. Array-based comparative genomic hybridization (CGH) and gene-expression microarray analysis of 48 cell lines derived from patients with different B-NHLs delineated 20 homozygous deletions at 7 chromosome areas, all of which contained tumor suppressor gene targets. Further investigation revealed that only a fraction of primary biopsies presented inactivation of these genes by point mutation or intragenic deletion, but instead some of them were frequently silenced by epigenetic mechanisms. Notably, the pattern of genetic and epigenetic inactivation differed among B-NHL subtypes. Thus, the P53-inducible PIG7/LITAF was silenced by homozygous deletion in primary mediastinal B-cell lymphoma and by promoter hypermethylation in germinal center lymphoma, the proapoptotic BIM gene presented homozygous deletion in mantle cell lymphoma and promoter hypermethylation in Burkitt lymphoma, the proapoptotic BH3-only NOXA was mutated and preferentially silenced in diffuse large B-cell lymphoma, and INK4c/P18 was silenced by biallelic mutation in mantle-cell lymphoma. Our microarray strategy has identified novel candidate tumor suppressor genes inactivated by genetic and epigenetic mechanisms that substantially vary among the B-NHL subtypes