Martin Simard

Argonaute proteins: key players in RNA silencing.

During the past decade, small non-coding RNAs have rapidly emerged as important contributors to gene regulation. To carry out their biological functions, these small RNAs require a unique class of proteins called Argonautes. The discovery and our comprehension of this highly conserved protein family is closely linked to the study of RNA-based gene silencing mechanisms. With their functional domains, Argonaute proteins can bind small non-coding RNAs and control protein synthesis, affect messenger RNA stability and even participate in the production of a new class of small RNAs, Piwi-interacting RNAs.

Do mountain pine beetle outbreaks change the probability of active crown fire in lodgepole pine forests

Disturbance interactions have received growing interest in ecological research in the last decade. Fire and bark beetle outbreaks have recently increased in severity and extent across western North America, raising concerns about their possible interactions. Although it is often presumed that bark beetle outbreaks increase probability of active crown fire by producing high loads of surface and canopy dead fuels, empirical data are scarce and results are ambivalent. We combined field measurements and modeling to address the following question: How do fuel characteristics, microclimate, and potential fire behavior change with time since a severe mountain pine beetle outbreak in Pinus contorta forests of Greater Yellowstone (Wyoming, USA)? We measured surface and canopy fuels, and soil surface temperature in a time-since-beetle-outbreak chronosequence (n = 35 sites) from undisturbed to 36 years post-outbreak, including stands in red- and gray-needle stages (respectively, 1–2 and 3–5 years post-outbreak). Fie...

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

Secondary Endogenous Small and Interfering In many eukaryotes, Piwi proteins bind small noncoding Piwi-interacting RNAs (piRNAs) that function to silence transposons in the germ line and protect the germ line from transposable element–driven recombination and mutation. Bagijn et al. (p. 574, published online 14 June; see the Perspective by Xiol and Pillai) show that in the nematode, Caenorhabditis elegans, a messenger RNA (mRNA) that contains a piRNA target sequence gives rise to a second, downstream class of small RNAs known as secondary endogenous small interfering RNAs, or endo siRNAs. These endo siRNAs map to the vicinity of the piRNA complementary sequence in the mRNA target and depend on both Piwi and on factors involved in the related RNA interference pathway for their genesis, but not on the Piwi slicer activity. Mapping the endo siRNAs reveals that piRNAs can target imperfectly matched targets and that piRNAs target a subset of both transposons and endogenous genes for silencing. Piwi-bound piwi-interacting RNAs recruit endogenous small interfering RNAs to silence mobile genetic elements. Piwi-interacting RNAs (piRNAs) are small RNAs required to maintain germline integrity and fertility, but their mechanism of action is poorly understood. Here we demonstrate that Caenorhabditis elegans piRNAs silence transcripts in trans through imperfectly complementary sites. Target silencing is independent of Piwi endonuclease activity or “slicing.” Instead, piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes and tend to overlap the start and end of transposons in sense and antisense, respectively. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNA interference in C. elegans.

FOREST PRODUCTIVITY DECLINE CAUSED BY SUCCESSIONAL PALUDIFICATION OF BOREAL SOILS

Long-term forest productivity decline in boreal forests has been extensively studied in the last decades, yet its causes are still unclear. Soil conditions associated with soil organic matter accumulation are thought to be responsible for site productivity decline. The objectives of this study were to determine if paludification of boreal soils resulted in reduced forest productivity, and to identify changes in the physical and chemical properties of soils associated with reduction in productivity. We used a chronosequence of 23 black spruce stands ranging in postfire age from 50 to 2350 years and calculated three different stand productivity indices, including site index. We assessed changes in forest productivity with time using two complementary approaches: (1) by comparing productivity among the chronosequence stands and (2) by comparing the productivity of successive cohorts of trees within the same stands to determine the influence of time independently of other site factors. Charcoal stratigraphy indicates that the forest stands differ in their fire history and originated either from high- or low-severity soil burns. Both chronosequence and cohort approaches demonstrate declines in black spruce productivity of 50-80% with increased paludification, particularly during the first centuries after fire. Paludification alters bryophyte abundance and succession, increases soil moisture, reduces soil temperature and nutrient availability, and alters the vertical distribution of roots. Low-severity soil burns significantly accelerate rates of paludification and productivity decline compared with high-severity fires and ultimately reduce nutrient content in black spruce needles. The two combined approaches indicate that paludification can be driven by forest succession only, independently of site factors such as position on slope. This successional paludification contrasts with edaphic paludification, where topography and drainage primarily control the extent and rate of paludification. At the landscape scale, the fire regime (frequency and severity) controls paludification and forest productivity through its effect on soil organic layers. Implications for global carbon budgets and sustainable forestry are discussed.

Fire severity and long-term ecosystem biomass dynamics in coniferous boreal forests of eastern Canada

The objective of this study was to characterize the effects of soil burn severity and initial tree composition on long-term forest floor dynamics and ecosystem biomass partitioning within the Picea mariana [Mill.] BSP-feathermoss bioclimatic domain of northwestern Quebec. Changes in forest floor organic matter and ecosystem biomass partitioning were evaluated along a 2,355-year chronosequence of extant stands. Dendroecological and paleoecological methods were used to determine the time since the last fire, the soil burn severity of the last fire (high vs. low severity), and the post-fire tree composition of each stand (P. mariana vs. Pinus banksiana Lamb). In this paper, soil burn severity refers to the thickness of the organic matter layer accumulated above the mineral soil that was not burned by the last fire. In stands originating from high severity fires, the post-fire dominance by Pinus banksiana or P. mariana had little effect on the change in forest floor thickness and tree biomass. In contrast, stands established after low severity fires accumulated during the first century after fire 73% thicker forest floors and produced 50% less tree biomass than stands established after high severity fires. Standing tree biomass increased until approximately 100 years after high severity fires, and then decreased at a logarithmic rate in the millennial absence of fire. Forest floor thickness also showed a rapid initial accumulation rate, and continued to increase in the millennial absence of fire at a much slower rate. However, because forest floor density increased through time, the overall rate of increase in forest floor biomass (58 g m−2 y−1) remained constant for numerous centuries after fire (700 years). Although young stands (< 200 years) have more than 60% of ecosystem biomass locked-up in living biomass, older stands (> 200 years) sequester the majority (> 80%) of it in their forest floor. The results from this study illustrate that, under similar edaphic conditions, a single gradient related to time since disturbance is insufficient to account for the full spectrum of ecosystem biomass dynamics occurring in eastern boreal forests and highlights the importance of considering soil burn severity. Although fire severity induces diverging ecosystem biomass dynamics in the short term, the extended absence of fire brings about a convergence in terms of ecosystem biomass accumulation and partitioning.

Effects of fire severity and initial tree composition on stand structural development in the coniferous boreal forest of northwestern Québec, Canada

ABSTRACT The effects of fire severity and initial post-fire tree composition on long-term stand structural development were investigated in the Picea mariana–feathermoss bioclimatic domain of northwestern Québec. Paleoecological methods were used to categorize the severity of the last fire (high or low) and initial tree composition (Picea mariana versus Pinus banksiana). Changes in stand structure were evaluated by quantifying stand structural attributes along three chronosequences. Except for accelerating stand break-up, the post-fire presence of P. banksiana (which is eventually replaced by P. mariana) had little effect on stand structural development. Fire severity had significant effects on the evolution of stand structural attributes, with low severity fires being particularly detrimental for stand productivity. Stands colonizing low severity fires were characterized by low post-fire tree recruitment and growth and remained open throughout succession. In contrast, after high severity fires, dense productive stands were rapidly established regardless of tree composition and gradually became open as succession proceeded. These results suggest that in the prolonged absence of fire, the different stand structural development pathways gradually converge regardless of fire severity or initial composition. We argue that stand structural diversity within the coniferous boreal forest is a result of the severity of the last fire and of processes operating at the stand scale in the absence of fire.

Effects of fire severity and initial tree composition on understorey vegetation dynamics in a boreal landscape inferred from chronosequence and paleoecological data

Abstract Question and Location: How does soil burn severity and early post-fire tree composition affect long-term understorey vegetation dynamics in the coniferous forests of eastern Canada? Method: Vegetation dynamics were assessed using paleoecological methods and a chronosequence analysis of extant stands. The relation between environmental factors and succession was evaluated using ordination techniques on the chronosequence data. Understorey succession was studied by regression analysis on the chronosequence data and through within-site Markovian transition probabilities between successive 1-cm layers of plant macroremains from soil organic matter profiles. Results: Initial tree composition (Picea mariana and Pinus banksiana) had little effect on understorey composition. Soil burn severity (measured as the thickness of the residual forest floor humus) significantly affected temporal changes in understorey species. Following fires of high severity, stands underwent a gradual paludification with a net increase in Sphagnum and ericaceous shrubs (Ledum groenlandicum), and a decrease in feathermosses. Paludification was accelerated after low severity fires, which led to the dominance of Sphagnum less than 200 years after fire, and of L. groenlandicum shortly after fire. In situ paleoecological work confirmed results obtained with the chrono-sequence analysis. Conclusions: One vegetation gradient related to time after disturbance is insufficient to account for the full complexity of long-term changes in understorey composition following fire. Current forestry practices that protect the forest floor humus may induce a premature paludification. Abbreviations: AMS = Accelerated mass spectrometry; GCC = Global climate change; HS = High severity; LS = Low severity; TSF = Time since last fire. Nomenclature: Marie-Victorin (1995) and Montgomery (1977) for vascular plants; Anderson et al. (1990) for bryophytes and Lévesque et al. (1988) for macrofossils.

The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans

Despite the importance of microRNAs (miRNAs) in gene regulation, it is unclear how the miRNA–Argonaute complex—or miRNA‐induced silencing complex (miRISC)—can regulate the translation of their targets in such diverse ways. We demonstrate here a direct interaction between the miRISC and the ribosome by showing that a constituent of the eukaryotic 40S subunit, receptor for activated C‐kinase (RACK1), is important for miRNA‐mediated gene regulation in animals. In vivo studies demonstrate that RACK1 interacts with components of the miRISC in nematodes and mammals. In both systems, the alteration of RACK1 expression alters miRNA function and impairs the association of the miRNA complex with the translating ribosomes. Our data indicate that RACK1 can contribute to the recruitment of miRISC to the site of translation, and support a post‐initiation mode of miRNA‐mediated gene repression.

SRp30c Is a Repressor of 3′ Splice Site Utilization

ABSTRACT Several intron elements influence exon 7B skipping in the mammalian hnRNP A1 pre-mRNA. We have shown previously that the 38-nucleotide CE9 element located in the intron separating alternative exon 7B from exon 8 can repress the use of a downstream 3′ splice site. The ability of CE9 to act on heterologous substrates, combined with the results of competition and gel shift assays, indicates that the activity of CE9 is mediated by a trans-acting factor. UV cross-linking analysis revealed the specific association of a 25-kDa nuclear protein with CE9. Using RNA affinity chromatography, we isolated a 25-kDa protein that binds to CE9 RNA. This protein corresponds to SRp30c. Consistent with a role for SRp30c in the activity of CE9, recombinant SRp30c interacts specifically with CE9 and can promote splicing repression in vitro in a CE9-dependent manner. The closest homologue of SRp30c, ASF/SF2, does not bind to CE9 and does not repress splicing even when the intronic SRp30c binding sites are replaced with high-affinity ASF/SF2 binding sites. Only the first 7 nucleotides of CE9 are sufficient for binding to SRp30c, and mutations that abolish binding also prevent repression. Our results indicate that SRp30c can function as a repressor of 3′ splice site utilization and suggest that the SRp30c-CE9 interaction may contribute to the control of hnRNP A1 alternative splicing.

Bark beetle effects on fuel profiles across a range of stand structures in Douglas-fir forests of Greater Yellowstone

Consequences of bark beetle outbreaks for forest wildfire potential are receiving heightened attention, but little research has considered ecosystems with mixed-severity fire regimes. Such forests are widespread, variable in stand structure, and often fuel limited, suggesting that beetle outbreaks could substantially alter fire potentials. We studied canopy and surface fuels in interior Douglas-fir (Pseudotsuga menziesii v. glauca) forests in Greater Yellowstone, Wyoming, USA, to determine how fuel characteristics varied with time since outbreak of the Douglas-fir beetle (Dendroctonus pseudotsugae). We sampled five stands in each of four outbreak stages, validated for pre-outbreak similarity: green (undisturbed), red (1-3 yr), gray (4-14 yr), and silver (25-30 yr). General linear models were used to compare variation in fuel profiles associated with outbreak to variation associated with the range of stand structures (dense mesic forest to open xeric parkland) characteristic of interior Douglas-fir forest. Beetle outbreak killed 38-83% of basal area within stands, generating a mix of live trees and snags over several years. Canopy fuel load and bulk density began declining in the red stage via needle drop and decreased by approximately 50% by the silver stage. The dead portion of available canopy fuels peaked in the red stage at 41%. After accounting for background variation, there was little effect of beetle outbreak on surface fuels, with differences mainly in herbaceous biomass (50% greater in red stands) and coarse woody fuels (doubled in silver stands). Within-stand spatial heterogeneity of fuels increased with time since outbreak, and surface-to-crown continuity decreased and remained low because of slow/sparse regeneration. Collectively, results suggest reduced fire potentials in post-outbreak stands, particularly for crown fire after the red stage, although abundant coarse fuels in silver stands may increase burn residence time and heat release. Outbreak effects on fuels were comparable to background variation in stand structure. The net effect of beetle outbreak was to shift the structure of mnsic closed-canopy stands toward that of parklands, and to shift xeric parklands toward very sparse woodlands. This study highlights the importance of evaluating outbreak effects in the context of the wide structural variation inherent to many forest types in the absence of beetle disturbance.