Latitudinal patterns of amino acid cycling and plant N uptake among North American forest ecosystems

Thesis (Ph.D.) University of Alaska Fairbanks, 2008Interest in the role of organic nitrogen (N) to the N economy of forest ecosystems is gaining momentum as ecologists revise the traditional paradigm in N cycling to emphasize the importance of depolymerization of soil organic matter (SOM) in controlling the bioavailability of N in forest soils. Still, there has yet to be a coordinated effort aimed at developing general patterns for soil organic N cycling across ecosystems that vary in climate, SOM quality, plant taxa, or dominant mycorrhizal association: ectomycorrhizae (EM) vs. arbuscular mycorrhizae (AM). In this study, experimental additions of 13C15N-glycine and 15NH4+ were traced in situ through fine root and soil N pools for six North American forest ecosystems in an effort to define patterns of plant and microbial N utilization among divergent forest types. Recovery of 15N in extractable soil pools varied by N form, forest type, and sampling period. At all sites, immobilization by the soil microbial biomass represented the largest short-term (<24 h) biotic sink for NH4+ and amino acid-N, but differences in microbial turnover of the two N forms were linked to cross-ecosystem differences in SOM quality, particularly the availability of labile carbon (C). At the conclusion of the experiment, microbial N turnover had transferred the majority of immobilized 15N to non-extractable soil N pools. By comparison, fine root uptake of NH4+ and glycine-N was low (<10% total tracer recovery), but 15N enrichment of this pool was still increasing at the final sampling period. Since there was no significant loss of 15N tracer within the bulk soil after 14 days for any forest type except sugar maple, it suggests plants have the capacity to capitalize on multiple N turnover events and thus represent an important long-term sink for ecosystem N. Plants in all stands had some capacity to absorb glycine intact, but plant N preference again varied by forest type. Relative uptake of amino acid-N versus inorganic N was lowest in tulip poplar and highest in red pine and balsam poplar, while white oak, sugar maple, and white spruce stands were statistically near unity with respect to the two N forms. However, N uptake ratios were threefold higher in EM-dominated stands than in AM-dominated stands indicating mycorrhizal association in part mediated plant N preference. Thus, amino acids represent an important component of the N economies of a broad spectrum of forest ecosystems, but their relevance to plant nutrition likely varies as a function of microbial demand for C as well as N

Clinical Trial of the Virtual Integration Environment to Treat Phantom Limb Pain With Upper Extremity Amputation

Background: Phantom limb pain (PLP) is commonly seen following upper extremity (UE) amputation. Use of both mirror therapy, which utilizes limb reflection in a mirror, and virtual reality therapy, which utilizes computer limb simulation, has been used to relieve PLP. We explored whether the Virtual Integration Environment (VIE), a virtual reality UE simulator, could be used as a therapy device to effectively treat PLP in individuals with UE amputation.Methods: Participants with UE amputation and PLP were recruited at Walter Reed National Military Medical Center (WRNMMC) and instructed to follow the limb movements of a virtual avatar within the VIE system across a series of study sessions. At the end of each session, participants drove virtual avatar limb movements during a period of “free-play” utilizing surface electromyography recordings collected from their residual limbs. PLP and phantom limb sensations were assessed at baseline and following each session using the Visual Analog Scale (VAS) and Short Form McGill Pain Questionnaire (SF-MPQ), respectively. In addition, both measures were used to assess residual limb pain (RLP) at baseline and at each study session. In total, 14 male, active duty military personnel were recruited for the study.Results: Of the 14 individuals recruited to the study, nine reported PLP at the time of screening. Eight of these individuals completed the study, while one withdrew after three sessions and thus is not included in the final analysis. Five of these eight individuals noted RLP at baseline. Participants completed an average of 18, 30-min sessions with the VIE leading to a significant reduction in PLP in seven of the eight (88%) affected limbs and a reduction in RLP in four of the five (80%) affected limbs. The same user reported an increase in PLP and RLP across sessions. All participants who denied RLP at baseline (n = 3) continued to deny RLP at each study session.Conclusions: Success with the VIE system confirms its application as a non-invasive and low-cost therapy option for PLP and phantom limb symptoms for individuals with upper limb loss

Virtual Integration Environment as an Advanced Prosthetic Limb Training Platform

Background: Despite advances in prosthetic development and neurorehabilitation, individuals with upper extremity (UE) loss continue to face functional and psychosocial challenges following amputation. Recent advanced myoelectric prostheses offer intuitive control over multiple, simultaneous degrees of motion and promise sensory feedback integration, but require complex training to effectively manipulate. We explored whether a virtual reality simulator could be used to teach dexterous prosthetic control paradigms to individuals with UE loss.Methods: Thirteen active-duty military personnel with UE loss (14 limbs) completed twenty, 30-min passive motor training sessions over 1–2 months. Participants were asked to follow the motions of a virtual avatar using residual and phantom limbs, and electrical activity from the residual limb was recorded using surface electromyography. Eight participants (nine limbs), also completed twenty, 30-min active motor training sessions. Participants controlled a virtual avatar through three motion sets of increasing complexity (Basic, Advanced, and Digit) and were scored on how accurately they performed requested motions. Score trajectory was assessed as a function of time using longitudinal mixed effects linear regression.Results: Mean classification accuracy for passive motor training was 43.8 ± 10.7% (14 limbs, 277 passive sessions). In active motor sessions, &gt;95% classification accuracy (which we used as the threshold for prosthetic acceptance) was achieved by all participants for Basic sets and by 50% of participants in Advanced and Digit sets. Significant improvement in active motor scores over time was observed in Basic and Advanced sets (per additional session: β-coefficient 0.125, p = 0.022; β-coefficient 0.45, p = 0.001, respectively), and trended toward significance for Digit sets (β-coefficient 0.594, p = 0.077).Conclusions: These results offer robust evidence that a virtual reality training platform can be used to quickly and efficiently train individuals with UE loss to operate advanced prosthetic control paradigms. Participants can be trained to generate muscle contraction patterns in residual limbs that are interpreted with high accuracy by computer software as distinct active motion commands. These results support the potential viability of advanced myoelectric prostheses relying on pattern recognition feedback or similar controls systems

HLA-DM Mediates Epitope Selection by a “Compare-Exchange” Mechanism when a Potential Peptide Pool Is Available

BACKGROUND: HLA-DM (DM) mediates exchange of peptides bound to MHC class II (MHCII) during the epitope selection process. Although DM has been shown to have two activities, peptide release and MHC class II refolding, a clear characterization of the mechanism by which DM facilitates peptide exchange has remained elusive. METHODOLOGY/PRINCIPAL FINDINGS: We have previously demonstrated that peptide binding to and dissociation from MHCII in the absence of DM are cooperative processes, likely related to conformational changes in the peptide-MHCII complex. Here we show that DM promotes peptide release by a non-cooperative process, whereas it enhances cooperative folding of the exchange peptide. Through electron paramagnetic resonance (EPR) and fluorescence polarization (FP) we show that DM releases prebound peptide very poorly in the absence of a candidate peptide for the exchange process. The affinity and concentration of the candidate peptide are also important for the release of the prebound peptide. Increased fluorescence energy transfer between the prebound and exchange peptides in the presence of DM is evidence for a tetramolecular complex which resolves in favor of the peptide that has superior folding properties. CONCLUSION/SIGNIFICANCE: This study shows that both the peptide releasing activity on loaded MHCII and the facilitating of MHCII binding by a candidate exchange peptide are integral to DM mediated epitope selection. The exchange process is initiated only in the presence of candidate peptides, avoiding possible release of a prebound peptide and loss of a potential epitope. In a tetramolecular transitional complex, the candidate peptides are checked for their ability to replace the pre-bound peptide with a geometry that allows the rebinding of the original peptide. Thus, DM promotes a "compare-exchange" sorting algorithm on an available peptide pool. Such a "third party"-mediated mechanism may be generally applicable for diverse ligand recognition in other biological systems

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Appendix C. Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.

Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations

Appendix A. Site coordinates, sampling information, and F:P ratios across sites.

Site coordinates, sampling information, and F:P ratios across sites

Supplement 1. Three files containing BLAST identifications for fungal OTUs and abundances across samples.

<h2>File List</h2><div> <p><a href="Blast_IDs.csv">Blast_IDs.csv</a> (MD5: 62e5100c20160c284f4d0c0d7e966652)</p> <p><a href="OTU_by_site_matrix.csv">OTU_by_site_matrix.csv</a> (MD5: fd8cb6e0180fda1c17b283fb1bb9de0e)</p> <p><a href="Phyla_Guild_Assignments.csv">Phyla_Guild_Assignments.csv</a> (MD5: 835a54ac9732fb782bc6756fd8e10fa6)</p> </div><h2>Description</h2><div> <p>Blast_IDs is a comma-delimited spreadsheet with a row for each OTU encountered in this study. The columns are as follows: Rank = the relative abundance of that OTU across the entire dataset. Rank #1 was the most abundant OTU (in terms of number of clone sequences falling into that OTU). Operational Taxonomic Unit = the code assigned to that OTU when the sequences were clustered using Cap3. Representative Clone = the code for the original clone sequence that was chosen to represent that OTU. Best Match GenBank Accession = the accession number for the sequence in GenBank with the highest bit score when the OTU representative sequence was blasted against our in-house database. Best Match Description = edited text from the title of the top GenBank blast hit meant to convey the putative identity. Percent Identity = the percent of identical bases over the region of the query and hit that were sufficiently similar to be aligned by BLAST. Length of Overlap = the length of the region that was sufficiently similar to be aligned by BLAST. Bit Score = the quality of the match assigned by BLAST. Quality of Top Match = the taxonomic level to which the query sequence could be identified based on a set of rules involving percent identity combined with overlap length, as described in the text of the article.</p> <p>OTU_by_site_matrix is a comma-delimited spreadsheet providing OUT abundances. Counts of clones belonging to a particular OTU in each sample (site × year × horizon combination) are given. Each row represents one OTU. The site is designated by the first number (e.g., '109'), the horizon by M = mineral and O = organic and the sampling year by 4 = 2004 and 5 = 2005. The first column gives the OTU designation, the second column gives the rank of that OTU and subsequent columns give the clone counts in each sample. The last column provides a cumulative total clone count for each OTU. </p> <p>Phyla_Guild_Assignments is a comma-delimited spreadsheet showing the guilds that were assigned to particular fungal OTUs. The first five columns are identical to those described above for the file Blast_IDs. The next columns, labeled “Phylum or Subphylum” and “Order” give the corresponding GenBank taxonomy designations for the top BLAST match. The last column, labeled “Guild”, provides our best estimate of the trophic guild to which the OTU belongs. ECM = ectomycorrhizal; sap = saprotrophic (typically wood or litter decay); lichen = lichen; ?? = unknown. We only attempted to define guild for a subset of well-defined OTUs.</p> </div