ARTICLE Watershed-scale effectiveness of floodplain habitat restoration for juvenile coho salmon in the Chilliwack River, British Columbia

Abstract: Although billions of dollars have been spent restoring degraded watersheds worldwide, watershed-scale studies evaluating their effectiveness are rare. To mitigate damage from past logging activities, the floodplain of the upper Chilliwack River watershed (ϳ600 km 2 ) was extensively restored from 1996 to 2000 through off-channel habitat restoration. The contribution of restored habitat to watershed-scale production of wild coho (Oncorhynchus kisutch) smolts was estimated through an extensive mark-recapture program in 2002. 27%-34% of the production of the estimated 247 200 out-migrating coho smolts could be attributed to the 157 000 m 2 of newly created habitat. Area-based habitat models from the literature performed reasonably well in predicting smolt production from restored habitat, providing an acceptable first-order approach for evaluating production benefits of restoration. The costs of smolt production integrated over 30 years ranged from US$0.69-US$10.05 per smolt, falling within the range of hatchery production costs reported elsewhere (typical cost of ϳUS1.00 per smolt) at the most cost-effective restoration sites. This study demonstrates that large-scale habitat restoration can effectively enhance fish production at a watershed scale, at a cost that may be comparable to hatchery smolt production. Résumé : Bien que des milliards de dollars aient été dépensés à restaurer des bassins versants dégradés dans le monde entier, les études à l'échelle du bassin versant qui s'intéressent à l'efficacité de ces actions sont rares. Afin d'atténuer les dommages causés par les activités de coupe de bois passées, la plaine inondable du bassin versant du cours supérieur de la rivière Chilliwack (ϳ600 km 2 ) a fait l'objet d'une vaste restauration de 1996 à 2000 reposant sur la restauration d'habitats à l'extérieur du chenal. La contribution des habitats restaurés à la production de saumoneaux sauvages de saumons cohos (Oncorhynchus kisutch) à l'échelle du bassin versant a été estimée dans le cadre d'un vaste programme de marquage-recapture en 2002. De 27 % à 34 % de la production d'un total estimé de 247 200 saumoneaux cohos ayant migré vers la mer peut être attribuée aux 157 000 m 2 de nouveaux habitats créés. Les modèles d'habitat reposant sur la superficie recensés dans la littérature prédisent raisonnablement bien la production de saumoneaux d'habitats restaurés, fournissant une approche de premier ordre acceptable pour évaluer les avantages de la restauration en ce qui concerne la production. Les coûts de la production de saumoneaux intégrés sur 30 ans allaient de 0,69 US à 10,05 US par saumoneau, soit dans la fourchette des coûts de production en écloserie rapportés dans d'autres ouvrages (coût typique de 1,00 US par saumoneau) pour les sites restaurés les plus efficaces en terme de coûts. L'étude démontre que la restauration d'habitats à grande échelle peut accroître efficacement la production de poissons à l'échelle du bassin versant à un coût qui pourrait se comparer à la production de saumoneaux en écloserie. [Traduit par la Rédaction

Understanding light quanta: First quantization of the free electromagnetic field

The quantization of the electromagnetic field in vacuum is presented without reference to lagrangean quantum field theory. The equal time commutators of the fields are calculated from basic principles. A physical discussion of the commutators suggest that the electromagnetic fields are macroscopic emergent properties of more fundamental physical system: the photons

Ambient pH and the response to chemical alarm cues in juvenile Atlantic salmon (Salmo salar): mechanisms of reduced behavioral responses.

Even at sublethal concentrations, various anthropogenic pollutants may disrupt the transfer of chemosensory information, often inducing maladaptive behavioral responses. Recent studies of freshwater prey fishes have shown impaired abilities to respond to damage-released chemical alarm cues from conspecifics under weakly acidic conditions (pH ; 6.0). Several factors acting individually or collectively may account for such chemosensory impairment. By itself, acidification may chemically disrupt the alarm cues and affect fish olfactory functions. Alternatively, differences in local environmental conditions may affect biochemical composition, quantity of chemical alarm cues produced by epidermal tissue, or both, leading to variations in alarm response. Our goal was to assess whether the ability to produce and detect onspecific chemical alarm cues is similar in individuals reared under neutral versus acidic conditions. We conducted two experiments in which we measured the behavioral response of wild juvenile Atlantic salmon Salmo salar exposed to chemical alarm cues. In particular, we looked for differences in the ability of individual fish to (1) produce alarm cues capable of eliciting consistent antipredator behavior in conspecifics and (2) detect alarm cues upon the fish’s introduction into a stream with a pH differing from that of the stream of origin; the latter experiment involved reciprocal transplant of fish between neutral (pH range ; 7.0–7.3) and acidic (pH range ; 5.9–6.3) sites. Our results demonstrate that the ability to produce and respond to chemical alarm cues is maintained in Atlantic salmon reared under acidic conditions and did not differ from that of fish reared under neutral conditions. Overall, these data suggest that no permanent olfactory damage occurred under reduced pH and, likewise, no significant difference in functional alarm cue production existed between Atlantic salmon reared under neutral and acidic conditions. Short-term reduction in olfactory sensitivity and degradation of the chemical alarm cues under acidic conditions are the likely mechanisms affecting detection of these important chemicals by prey fish

The influence of temperature and habitat on the distribution of chiselmouth, Acrocheilus alutaceus, in British Columbia

Synopsis We intensively sampled fish in rivers and streams within a single major drainage basin (the Blackwater River) and across major drainages in British Columbia to assess the factors influencing distribution of chiselmouth, Acrocheilus alutaceus, and to develop models for predicting chislemouth presence. Chiselmouth were typically absent from sites with maximum temperatures below 20 • C or 2100 annual degree days, both within a single drainage and between larger drainages. Indices of stream size (bankfull channel width and basin area) were the most significant predictors of chiselmouth presence within the Blackwater drainage (p = 0.016 and p = 0.032, respectively), and inclusion of thermal variables only marginally increased classification success. In contrast, bankfull channel width and basin area were poor predictors of chiselmouth presence in mainstem habitat within larger drainage basins throughout British Columbia. Inclusion of thermal variables (particularly degree days > 12 • C) doubled correct classification rates of chiselmouth presence across larger drainage basins. These habitat associations suggest that water temperature is the primary constraint on presence of chiselmouth populations in larger drainages across a landscape, while selection of different habitat types (mainstem habitat over smaller tributaries) determines distribution within any given basin

Stochastic semiclassical cosmological models

We consider the classical stochastic fluctuations of spacetime geometry induced by quantum fluctuations of massless non-conformal matter fields in the Early Universe. To this end, we supplement the stress-energy tensor of these fields with a stochastic part, which is computed along the lines of the Feynman-Vernon and Schwinger-Keldysh techniques; the Einstein equation is therefore upgraded to a so called Einstein-Langevin equation. We consider in some detail the conformal fluctuations of flat spacetime and the fluctuations of the scale factor in a simple cosmological modelintroduced by Hartle, which consists of a spatially flat isotropic cosmology driven by radiation and dust.Comment: 29 pages, no figures, ReVTeX fil

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Genotype–phenotype correlations in individuals with pathogenic RERE variants

Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype–phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7

Genotype–phenotype correlations in individuals with pathogenic RERE variants

Heterozygous variants in the arginine‐glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin‐1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss‐of‐function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine‐rich region in the Atrophin‐1 domain. We have also identified a recurrent two‐amino‐acid duplication in this region that is associated with the development of a CHARGE syndrome‐like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype–phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7.We describe nine unrelated individuals who carry partial deletions or putatively deleterious sequence variants in RERE. An analysis of clinical and molecular data from individuals with mutations affecting RERE suggests the existence of novel genotype‐phenotype correlations and demonstrates that a high percentage of RERE pathogenic variants affect a histidine‐rich region in the Atrophin‐1 domain. We have also identified a recurrent two‐amino‐acid duplication in this region that is associated with the development of a CHARGE syndrome‐like phenotype.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143789/1/humu23400_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143789/2/humu23400.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143789/3/humu23400-sup-0001-SuppMat.pd