Research Progress Report, No. 17

Legumes are notable for their ability to convert atmospheric dinitrogen into forms of nitrogen which are usable by plants. This is done in association with bacteria (called Rhizobium) which inhabit nodules of the plant roots. This process is called nitrogen-fixation. Legumes are important as forage and food crops due to their high protein content. Some are also useful for soil conservation purposes. There was no information on nitrogen fixation by legume crops in Alaska. This research was initiated to determine how much nitrogen different types of legumes can fix in interior Alaska

MP 2012-02

Final report to BP.The Prudhoe Bay oil fields, Alaska were discovered in 1968, and commercial production commenced in 1977 with the completion of the Trans-Alaska Pipeline. Oil production has been declining since 1989, although additional exploratory drilling continues. Support facilities for oil production are built on permafrost soils that surface-thaw in summer to form extensive wetlands composed of moist meadows, sedge marshes, moist sedge-dwarf shrub tundra, grass marshes, small ponds and lakes (Walker and Acevedo 1987). To prevent thawing and subsidence of subsurface, ice-rich soils, gravel pads, 2m (6 ft) or more thickness have been built to support drilling sites as well as roads, airstrips and building pads (Kidd et al. 2006). As well sites are decommissioned, the gravel is wholly or partially removed resulting in the need for site rehabilitation and/or restoration to support wetland plants and, in some instances, enhance wildlife habitat (McKendrick 1991, Jorgenson and Joyce 1994, Kidd et al. 2004, 2006). Since the 1970s, methods to revegetate arctic wetlands have included a variety of planting techniques, seed treatments, seeding with native and non-native species (mostly grasses), and fertilizer applications (Chapin and Chapin 1980; Bishop and Chapin 1989, Jorgenson 1988, Kidd and Rossow 1998, Kidd et al. 2004, 2006, Maslen and Kershaw 1989, McKendrick 1987, 1991, 2000, McKendrick et al. 1980, McKendrick and Mitchell 1978, Mitchell et al. 1974). Treatments also have included sprigging and plug transplantation (Kidd et al. 2004, 2006), surface manipulation (Streever et al. 2003), as well as natural re-colonization (Ebersole 1987, Schwarzenbach 1996). These methods have been partially successful. The gravelly soils often are dry, nutrient-poor, and have a higher pH and lower organic matter content than surrounding soils, so natural recolonization does not occur readily (Bishop and Chapin 1989, Jorgenson and Joyce 1994). Methods such as sprigging and plug transplanting are slow, labor intensive and expensive compared to direct seeding. Fertilization, especially with phosphorus, is recommended for long-term survival of plants grown on gravelly sandy soils (BP Exploration and McKendrick 2004). Two common species in the arctic coastal wetlands are water sedge, Carex aquatilis Wahlenb. and cotton sedge, Eriophorum angustifolium Honck. Carex aquatilis in particular forms large populations that spread vegetatively by rhizomes and often dominate these wetland environments (Shaver and Billings 1975). Despite their abundance, these species have not been considered for revegetation because of poor seed germination and inadequate information on seed development and viability (Dr. William Streever, BP Alaska, pers. comm.). Both Carex and Eriophorum in arctic environments produce abundant seeds, but seed viability and germination often is low and highly variable among years and locations (Archibold 1984, Billings and Mooney 1968, Ebersole 1989, Gartner et al. 1983). Germination recommendations for both species vary by location and have included an array of pretreatments such as light, alternating temperatures, cold stratification, scarification, and high and low temperature dry storage (Amen 1966, Billings and Mooney 1960, Bliss 1958, Hunt and Moore 2003, Johnson et al. 1965, Phillips 1954 and Steinfeld 2001). The purpose of this project was to explore methods of seed germination of Carex aquatilis and Eriophorum angustifolium, to learn the conditions for germination and dormancy control mechanisms, and identify seed treatments that might enhance germination for eventual use in direct-seeding or plug production for arctic wetland revegetation

MP 2009-09

As the price of traditional fossil fuels escalates, there is increasing interest in using renewable resources, such as biomass, to meet our energy needs. Biomass resources are of particular interest to communities in interior Alaska, where they are abundant (Fresco, 2006). Biomass has the potential to partially replace heating oil, in addition to being a possible source for electric power generation (Crimp and Adamian, 2000; Nicholls and Crimp, 2002; Fresco, 2006). The communities of Tanana and Dot Lake have already installed small Garn boilers to provide space heating for homes and businesses (Alaska Energy Authority, 2009). A village-sized combined heat and power (CHP) demonstration project has been proposed in North Pole. In addition, several Fairbanks area organizations are interested in using biomass as a fuel source. For example, the Fairbanks North Star Borough is interested in using biomass to supplement coal in a proposed coal-to-liquids project, the Cold Climate Housing Research Center is planning to test a small biomass fired CHP unit, and the University of Alaska is planning an upgrade to its existing coal-fired power plant that could permit co-firing with biomass fuels. The challenge for all of these projects is in ensuring that biomass can be harvested on both an economically and ecologically sustainable basis

No-till Forage Establishment in Alaska

We assessed the effectiveness of no-till forage establishment at six Alaska locations: Anchor Point, Sterling, Point MacKenzie, Palmer, Delta Junction, and Fairbanks. Directly seeding grass into established grass stands generally did not improve forage yields or quality. Seeding rate had little effect on establishment of newly seeded forages in no-till. Grass yields were depressed when companion crop yields were high, and they typically did not recover in subsequent years. Red clover established well, producing high yields of good quality forage under no-till at Point MacKenzie, but established poorly at Anchor Point and Delta Junction. These results indicated that no-till seeding of most forage crops into declining grass stands is not likely to be successful in Alaska with current available technology

Harvest and Nitrogen Management of Three Perennial Grasses as Biomass Feedstock in Subarctic Alaska

High energy costs in high-latitude regions have generated interest in the feasibility of bioenergy cropping. The goal of this study was to determine the N response and best harvest regime for biomass production of three perennial, cool-season grass species—tufted hairgrass (Deschampsia caespitosa (L.) P. Beauv.), slender wheatgrass (Elymus trachy­caulus (Link) Gould ex Shinners), and smooth bromegrass (Bromus inermis Leyss)—at two locations in central Alaska. Maximum dry matter yields were 11.3 Mg ha-1 for smooth bromegrass, 8.1 Mg ha-1 for tufted hairgrass, and 8.0 Mg ha-1 for slender wheatgrass, but yields varied greatly among years. We found a linear N response in most cases, with highest yields at the 100 kg N ha-1 application rate. Yields for the double-harvest regime usually did not vary significantly from those of the fall harvest, but spring harvest sometimes reduced yields dramatically. Biomass in the spring harvest was usually dry enough not to require additional drying for storage. Results of this study indicate it may be possible to produce grass biomass yields high enough for use as bioenergy feedstocks in central Alaska, but questions remain about the best management practices and the economics of growing bioenergy crops in Alaska.Les coûts élevés de l’énergie en haute latitude incitent les gens à se pencher sur la faisabilité d’entreprendre des cultures bioénergétiques. L’objectif de cette étude consistait à déterminer la réponse à l’azote et le meilleur régime d’exploitation pour la bioproduction de trois espèces de graminées vivaces en saison fraîche, soit la deschampsie cespiteuse (Deschampsia caespitosa (L.) P. Beauv.), l’élyme à chaumes rudes (Elymus trachycaulus (Link) Gould ex Shinners) et le brome inerme (Bromus inermis Leyss), à deux endroits du centre de l’Alaska. Le rendement maximum de matière sèche était de 11,3 tm ha-1 dans le cas du brome inerme, de 8,1 tm ha-1 dans le cas de la deschampsie cespiteuse et de 8,0 tm ha-1 dans le cas de l’élyme à chaumes rudes, bien que les rendements aient connu d’importantes variations d’une année à l’autre. Nous avons trouvé une réponse linéaire à l’azote dans la plupart des cas, les rendements les plus élevés étant ceux de la dose d’application de 100 kg N ha-1. Le rendement du régime à double récolte ne variait généralement pas beaucoup du régime à récolte d’automne, bien que les récoltes du printemps donnaient parfois un rendement considérablement réduit. De manière générale, la biomasse de la récolte du printemps était suffisamment sèche pour ne pas avoir besoin d’être asséchée davantage avant d’être stockée. Les résultats de cette étude indiquent qu’il peut être possible de produire des rendements en biomasse suffisamment élevés à partir de graminées pour être utilisés comme charge bioénergétique dans le centre de l’Alaska, mais cela dit, il y a toujours lieu de répondre aux questions portant sur les pratiques de gestion exemplaires et le caractère économique des productions bioéner­gétiques en Alaska

Hyperautofluorescent Dots are Characteristic in Ceramide Kinase Like-associated Retinal Degeneration.

There is a lack of studies which seek to discern disease expression in patients with mutations that alter retinal ceramide metabolism, specifically in the ceramide kinase like (CERKL) gene. This cross-sectional case series reports a novel phenotypic manifestation of CERKL-associated retinopathy. Four unrelated patients with homozygous CERKL mutations underwent a complete ocular exam, spectral-domain optical coherence tomography, short-wavelength fundus autofluorescence (SW-AF), quantitative autofluorescence (qAF), and full-field electroretinogram (ffERG). Decreased visual acuity and early-onset maculopathy were present in all patients. All four patients had extensive hyperautofluorescent foci surrounding an area of central atrophy on SW-AF imaging, which has not been previously characterized. An abnormal spatial distribution of qAF signal was seen in one patient, and abnormally elevated qA

Electroretinography Reveals Difference in Cone Function between Syndromic and Nonsyndromic USH2A Patients

Usher syndrome is an inherited and irreversible disease that manifests as retinitis pigmentosa (RP) and bilateral neurosensory hearing loss. Mutations in Usherin 2A (USH2A) are not only a frequent cause of Usher syndrome, but also nonsyndromic RP. Although gene-and cell-based therapies are on the horizon for RP and Usher syndrome, studies characterizing natural disease are lacking. In this retrospective analysis, retinal function of USH2A patients was quantified with electroretinography. Both groups had markedly reduced rod and cone responses, but nonsyndromic USH2A patients had 30 Hz-flicker electroretinogram amplitudes that were significantly higher than syndromic patients, suggesting superior residual cone function. There was a tendency for Usher syndrome patients to have a higher distribution of severe mutations, and alleles in this group had a higher odds of containing nonsense or frame-shift mutations. These data suggest that the previously reported severe visual phenotype seen in syndromic USH2A patients could relate to a greater extent of cone dysfunction. Additionally, a genetic threshold may exist where mutation burden relates to visual phenotype and the presence of hearing deficits. The auditory phenotype and allelic hierarchy observed among patients should be considered in prospective studies of disease progression and during enrollment for future clinical trials.National Institute of HealthNational Cancer InstituteResearch to Prevent Blindness (RPB)RPB, New York, NY, USARPBInternational Council of Ophthalmology - Retina Research FoundationNIHTistou and Charlotte Kerstan FoundationSchneeweiss Stem Cell Fund, New York StateFoundation Fighting Blindness New York Regional Research CenterCrowley Family FundGebroe Family FoundationColumbia Univ, Dept Ophthalmol, Med Ctr, Jonas Childrens Vis Care, New York, NY 10027 USAColumbia Univ, Dept Ophthalmol, Med Ctr, Bernard & Shirlee Brown Glaucoma Lab, New York, NY 10027 USANew York Presbyterian Hosp, Edward S Harkness Eye Inst, New York, NY 10034 USASuny Downstate Med Ctr, Brooklyn, NY 11203 USAUniv Fed Espirito Santo, Dept Ophthalmol, Vitoria, BrazilUniv Fed Sao Paulo, Dept Ophthalmol, Sao Paulo, BrazilColumbia Univ, Dept Biostat, New York, NY USAUniv Montreal, Dept Ophthalmol, Montreal, PQ, CanadaShanghai Jiao Tong Univ, Sch Med, Xin Hua Hosp, Dept Ophthalmol, Shanghai, Peoples R ChinaColumbia Univ, Inst Human Nutr, Dept Pathol & Cell Biol, Stem Cell Initiat CSCI,Coll Phys & Surg, New York, NY 10032 USAStanford Univ, Dept Ophthalmol, Om Lab, Byers Eye Inst, Palo Alto, CA 94304 USAUniv Fed Sao Paulo, Dept Ophthalmol, Sao Paulo, BrazilWeb of Scienc

Retrospective Analysis of Structural Disease Progression in Retinitis Pigmentosa Utilizing Multimodal Imaging

In this report, we assess the natural progression rate of retinitis pigmentosa (RP) over an average of three years using spectral-domain optical coherence tomography (SD-OCT) and short wavelength fundus autofluorescence (SW-AF). Measurement of the ellipsoid zone (EZ) line width and hyperautofluorescent ring diameters was performed in 81 patients with RP in a retrospective, longitudinal fashion. Rate of structural disease progression, symmetry between eyes, and test-retest variability were quantified. We observed on average, EZ-line widths decreased by 140 mu m (5.2%, p < 0.001) per year, and average horizontal and vertical hyperautofluorescent ring diameters decreased by 149 mu m (3.6%, p < 0.001) and 120 mu m (3.9%, p < 0.001) per year, respectively. The 95th percentile of this cohort had differences in progression slopes between eyes that were less than 154 mu m, 118 mu m, and 132 mu m for EZ-line width and horizontal and vertical ring diameters, respectively. For all measures except horizontal ring diameter, progression rates were significantly slower at end-stage disease. From our data, we observed a statistically significant progression rate in EZ line width and SW-AF ring diameters over time, verifying the utility of these measurements for disease monitoring purposes. Additionally, calculated differences in progression slopes between eyes may prove useful for investigators evaluating the efficacy of unilateral treatments for RP in clinical trials.National Institutes of HealthNational Cancer Institute CoreResearch to Prevent Blindness (RPB) Physician-Scientist AwardRPB medical student eye research fellowshipICO-Retina Research Foundation Helmerich Fellowships - Retina Research FoundationICO FoundationNIHTistou and Charlotte Kerstan FoundationSchneeweiss Stem Cell Fund, New York StateFoundation Fighting Blindness New York Regional Research CenterJoel Hoffman FundProfessor Gertrude Rothschild Stem Cell FoundationGebroe Family FoundationColumbia Univ, Dept Ophthalmol, Jonas Childrens Vis Care & Bernard & Shirlee Brow, New York, NY 10027 USANew York Presbyterian Hosp, Edward S Harkness Eye Inst, New York, NY USAUniv Fed Espirito Santo, Dept Ophthalmol, Vitoria, BrazilUniv Fed Sao Paulo, Dept Ophthalmol, Sao Paulo, BrazilSuny Downstate Med Ctr, Brooklyn, NY 11203 USAColumbia Univ, Dept Biostat, New York, NY USAUniv Montreal, Dept Ophthalmol, Montreal, PQ, CanadaStanford Univ, Dept Ophthalmol, Byers Eye Inst, Om Lab, Palo Alto, CA 94304 USAColumbia Univ, Inst Human Nutr, Dept Pathol & Cell Biol, Coll Phys & Surg, New York, NY 10032 USAUniv Fed Sao Paulo, Dept Ophthalmol, Sao Paulo, BrazilWeb of Scienc

Patterns and Intensities of Near-Infrared and Short-Wavelength Fundus Autofluorescence in Choroideremia Probands and Carriers

PURPOSE. To ascertain cellular constituents within islands of preserved retina in choroideremia (CHM) by multimodal imaging. METHODS. CHM probands (16) and female carriers (9) of CHM were studied. Near-infrared autofluorescence (NIR-AF; 787-nm excitation; emission, > 830 nm), short-wavelength autofluorescence (SW-AF; 488-nm excitation, 500-to 680-nm emission), and spectral-domain optical coherence tomography (SD-OCT) images were acquired with a confocal scanning laser ophthalmoscope. SW-AF intensities were measured by quantitative fundus autofluorescence (qAF), and NIR-AF intensity profiles were analyzed. Retinal thicknesses and visual acuity were measured. RESULTS. In 19 of 31 eyes of affected males, islands of preserved NIR-AF signal were also visible as fluorescence signal in SW-AF images. Notable in 12 eyes were areas of speckled SW-AF that was hypoautofluorescent in the NIR-AF image. Islands of preserved NIR-AF and SW-AF signal were often associated with the presence of visible but thinned outer nuclear layer and discontinuous interdigitation zone, ellipsoid zone, and external limiting membrane. NIR-AF profiles revealed that even in areas of preserved retina, the NIR-AF signal from retinal pigment epithelium (RPE) melanin is greatly reduced. qAF was reduced overall. The fundus of carriers was characterized by a mosaicism in which patches of reduced NIR-AF colocalized with reduced SW-AF. CONCLUSIONS. In CHM-affected males, the presence of RPE was indicated by an NIR-AF signal and the absence of hypertransmission of OCT signal into the choroid. RPE preservation was associated with better visual acuity. In carriers, patches of reduced SW-AF colocalized with decreased NIR-AF and qAF was severely reduced.Peer reviewe

Computer-aided assessment of diagnostic images for epidemiological research

<p>Abstract</p> <p>Background</p> <p>Diagnostic images are often assessed for clinical outcomes using subjective methods, which are limited by the skill of the reviewer. Computer-aided diagnosis (CAD) algorithms that assist reviewers in their decisions concerning outcomes have been developed to increase sensitivity and specificity in the clinical setting. However, these systems have not been well utilized in research settings to improve the measurement of clinical endpoints. Reductions in bias through their use could have important implications for etiologic research.</p> <p>Methods</p> <p>Using the example of cortical cataract detection, we developed an algorithm for assisting a reviewer in evaluating digital images for the presence and severity of lesions. Available image processing and statistical methods that were easily implementable were used as the basis for the CAD algorithm. The performance of the system was compared to the subjective assessment of five reviewers using 60 simulated images. Cortical cataract severity scores from 0 to 16 were assigned to the images by the reviewers and the CAD system, with each image assessed twice to obtain a measure of variability. Image characteristics that affected reviewer bias were also assessed by systematically varying the appearance of the simulated images.</p> <p>Results</p> <p>The algorithm yielded severity scores with smaller bias on images where cataract severity was mild to moderate (approximately ≤ 6/16^<it>ths</it>). On high severity images, the bias of the CAD system exceeded that of the reviewers. The variability of the CAD system was zero on repeated images but ranged from 0.48 to 1.22 for the reviewers. The direction and magnitude of the bias exhibited by the reviewers was a function of the number of cataract opacities, the shape and the contrast of the lesions in the simulated images.</p> <p>Conclusion</p> <p>CAD systems are feasible to implement with available software and can be valuable when medical images contain exposure or outcome information for etiologic research. Our results indicate that such systems have the potential to decrease bias and discriminate very small changes in disease severity. Simulated images are a tool that can be used to assess performance of a CAD system when a gold standard is not available.</p