Fish assemblage change following the structural restoration of a degraded stream

Decades of anthropogenic pressure have harmed riverscapes throughout North America by degrading habitats and water quality and can result in the extirpation of sensitive aquatic taxa. Local stream restoration projects have increased in frequency, but monitoring is still infrequent. In 2010, Kickapoo Creek in East Central Illinois was subjected to a stream restoration project that included implementation of artificial riffles, riprap, scouring keys, and riparian vegetation. We monitored the restoration efforts for 6years after the restoration through annual sampling efforts at restored and reference sites to determine changes in habitat and fish assemblage using standard habitat sampling and electrofishing techniques. We observed distinct temporal and spatial shifts in physico-chemical parameters along with changes in fish community structure. Although biotic integrity remained moderately low in reference assemblages, restored reaches showed 3-year delay in response to restoration, with biotic integrity positively linked to additional instream habitat and altered channel morphology. Larger substrate sizes, submerged terrestrial vegetation, and newly formed scour pools along with reduced siltation were found in the restored sites, in contrast to the reference sites. These changes resulted in increased species diversity, reduced number of opportunistic species and consequently an overall increase in health of fish communities. We also observed recruitment of habitat specialists and increase in species with reproductive strategies that rely on complex substrates. The results of this study highlight some of the complex dynamics driving reach-scale restoration projects. We demonstrate the usefulness of structural restoration as a management tool to increase biotic integrity through long-term alteration of critical habitat. The delay in the response of species to the restoration efforts emphasizes the need for long-term continuous temporal and spatial monitoring

Habitat Associations of Fish Species of Greatest Conservation Need at Multiple Spatial Scales in Wadeable Iowa Streams

Fish and habitat data were collected from 84 wadeable stream reaches in the Mississippi River drainage of Iowa to predict the occurrences of seven fish species of greatest conservation need and to identify the relative importance of habitat variables measured at small (e.g., depth, velocity, and substrate) and large (e.g., stream order, elevation, and gradient) scales in terms of their influence on species occurrences. Multiple logistic regression analysis was used to predict fish species occurrences, starting with all possible combinations of variables (5 large-scale variables, 13 small-scale variables, and all 18 variables) but limiting the final models to a maximum of five variables. Akaike’s information criterion was used to rank candidate models, weight model parameters, and calculate model-averaged predictions. On average, the correct classification rate (CCR = 80%) and Cohen’s kappa (κ = 0.59) were greatest for multiple-scale models (i.e., those including both large-scale and small-scale variables), intermediate for small-scale models (CCR = 75%; κ = 0.49), and lowest for large-scale models (CCR = 73%; κ = 0.44). The occurrence of each species was associated with a unique combination of large-scale and small-scale variables. Our results support the necessity of understanding factors that constrain the distribution of fishes across spatial scales to ensure that management decisions and actions occur at the appropriate scale

Growth, Fecundity, and Diets of Newly Established Silver Carp in the Middle Mississippi River

The silver carp Hypophthalmichthys molitrix has spread throughout the Mississippi River drainage. During 2003, we determined its population status and potential impact in the middle Mississippi River (MMR), the conduit between the lower Mississippi River and the upper Mississippi, Missouri, and Illinois rivers. We quantified growth, age structure, fecundity, and diets of silver carp sampled with trammel nets and AC electrofishing in main-channel areas. Mean length at age in the MMR exceeded that of populations in Asia by as much as 26%. Individuals were typically more than 1 year old and 230 mm total length, suggesting that small, young fish were absent. Individuals in this population matured earlier (age 2) than in the species\u27 native range. Regardless of phytoplankton variation (using chlorophyll a as a surrogate) and zooplankton concentration at MMR sites, phytoplankton was consistently most abundant in diets. Silver carp are finding suitable resources within the MMR, allowing individuals to grow rapidly during early life, persist as adults, and successfully disperse upstream

Growth Rate Responses of Missouri and Lower Yellowstone River Fishes to a Latitudinal Gradient

Notropis atherinoides, freshwater drums Aplodinotus grunniens, river carpsuckers Carpiodes carpio and saugers Stizostedion canadense collected in 1996-1998 from nine river sections of the Missouri and lower Yellowstone rivers at two life-stages (young-of-the-year and age 1+ years) were significantly different among sections. However, they showed no river-wide latitudinal trend except for age 1+ years emerald shiners that did show a weak negative relation between growth and both latitude and length of growing season. The results suggest growth rates of fishes along the Missouri River system are complex and could be of significance in the management and conservation of fish communities in this altered system

Habitat, Fish Species, and Fish Assemblage Associations of the Topeka Shiner in West-Central Iowa

Our goal was to identify habitat, fish species, and fish assemblages associated with the occurrence of Topeka Shiners Notropis topeka in stream and off-channel habitat (OCH) of west-central Iowa. Fish assemblages and habitat characteristics were estimated in 67 stream and 27OCHsites during 2010–2011. Topeka Shiners were sampled in 52% of OCH sites, but in only 9% of stream sites, which supports the hypothesis that OCH is an important component of their life history. Fish assemblages containing Topeka Shiners were different from those that did not contain Topeka Shiners in OCH sites, but this was not evident in stream sites. Results from logistic regression models suggested that Topeka Shiner presence was associated with increased submerged vegetation and abundance of Fathead Minnow Pimephales promelas. Contrary to the findings of other studies, the abundance of large piscivorous fishes was not associated with the occurrence of Topeka Shiners. Our results provide new information about the biology and life history of the Topeka Shiner that will guide habitat restoration and other recovery efforts

Cross-Sample Validation Provides Enhanced Proteome Coverage in Rat Vocal Fold Mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high Mr ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high Mr glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories

Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

<p>Abstract</p> <p>Background</p> <p>The barley-<it>Puccinia hordei </it>(barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL) for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs) have been developed that combine two QTL, <it>Rphq</it>2 and <it>Rphq</it>3, the largest effects detected in a recombinant-inbred-line (RIL) population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown.</p> <p>Results</p> <p>An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi) with <it>Puccinia hordei</it>. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at <it>Rphq</it>2 and <it>Rphq</it>3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (<it>HvERF4</it>) was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that <it>Rphq</it>2 or <it>Rphq</it>3 contains a <it>trans</it>-eQTL that modulates expression of <it>HvERF4</it>. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s) contained within <it>Rphq</it>2 or <it>Rphq</it>3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of <it>Ph</it>-responsive genes and that hormone-related signalling pathways are actively involved in response to <it>Puccinia hordei</it>.</p> <p>Conclusions</p> <p>Differential gene expression between QTL-NILs identifies genes predominantly located within the target region(s) providing both transcriptional and positional candidate genes for the QTL. Genetically mapping the differentially expressed genes relative to the QTL has the potential to discover <it>trans</it>-eQTL mediated regulatory relays initiated from genes within the QTL regions.</p

Plasma-liquid interactions: a review and roadmap

Plasma-liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas

A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map

Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively