The Economics of Spruce Budworm Outbreaks in the Lake States: An Overview

Economic effects of spruce budworm outbreaks in the Lake States were examined. The recent outbreak caused spruce and fir mortality on 420 thousand ha (I.OS million acres) of commercial forest land in the Lake States. Two models of Lake States spruce-fir markets were developed. A Static Economic Model established the nature of the Lake States spruce-fir market and a Comparative Static Model examined changes brought about by spruce budworm outbreaks. Outbreaks result in short-run supply shifts which probably decrease total revenue to stumpage owners but do not affect demand. The magnitude of long-run impacts were dependent on developing Lake States markets and forest management techniques. Further research is necessary on the value of short-run losses to stumpage owners so that the costs of forest management can be compared with outbreak losses. Long-run shifts in demand can be facilitated by attracting new industry to the area, developing new markets for the spruce-fir resource, and demonstrating that the spruce-fir resource can provide a continuous fiber source in the future. These shifts would provide the price incentives that land managers require to undertake intensive forest management. Research on the development of new markets for the spruce-fir resource is needed. As markets develop, the long-run impacts become less severe. Technology transfer programs already exist to aid land managers in developing management strategies to increase yields of spruce-fir and minimize outbreak impact

Structural aspects of molecular recognition in the immune system. Part II: Pattern recognition receptors (IUPAC Technical Report)

The vertebrate immune system uses pattern recognition receptors (PRRs) to detect a large variety of molecular signatures (pathogen-associated molecular patterns, PAMPs) from a broad range of different invading pathogens. The PAMPs range in size from relatively small molecules, to others of intermediate size such as bacterial lipopolysaccharide, lipopeptides, and oligosaccharides, to macromolecules such as viral DNA, RNA, and pathogen-derived proteins such as flagellin. Underlying this functional diversity of PRRs is a surprisingly small number of structurally distinct protein folds that include leucine-rich repeats in Toll-like receptors (TLRs) and NOD-like receptors (NLRs), the DExH box helicase domain in RIG-like receptors (RLRs), and C-type lectin domains (CTLDs) in the C-type lectins. Following PAMP recognition by the PRRs, downstream signaling pathways activate the innate immune system to respond to invading pathogenic organisms. The resulting stimulatory response is also vital for a balanced adaptive immune response to the pathogen, mediated by circulating antibodies and/or cytotoxic T cells. However, an aberrant stimulation of the innate immune system can also lead to excessive inflammatory and toxic stress responses. Exciting opportunities are now arising for the design of small synthetic molecules that bind to PRRs and influence downstream signaling pathways. Such molecules can be useful tools to modulate immune responses, for example, as adjuvants to stimulate adaptive immune responses to a vaccine, or as therapeutic agents to dampen aberrant immune responses, such as inflammation. The design of agonists or antagonists of PRRs can now benefit from a surge in knowledge of the 3D structures of PRRs, many in complexes with their natural ligands. This review article describes recent progress in structural studies of PRRs (TLRs, NLRs, CTLs, and RLRs), which is required for an understanding of how they specifically recognize structurally diverse "foreign” PAMPs amongst a background of other "self” molecules, sometimes closely related in structure, that are present in the human bod

Reflection high-energy electron diffraction patterns of CrSi_2 films on (111) silicon

Highly oriented films of the semiconducting transition metal silicide, CrSi2, were grown on (111) silicon substrates, with the matching crystallographic faces being CrSi_2(001)/Si(111). Reflection high‐energy electron diffraction (RHEED) yielded symmetric patterns of sharp streaks. The expected streak spacings for different incident RHEED beam directions were calculated from the reciprocal net of the CrSi_2(001) face and shown to match the observed spacings. The predominant azimuthal orientation of the films was thus determined to be CrSi_2〈210〉∥Si〈110〉. This highly desirable heteroepitaxial relationship may be described with a common unit mesh of 51 Å^2 and a mismatch of −0.3%. RHEED also revealed the presence of limited film regions of a competing azimuthal orientation, CrSi_2〈110〉∥Si〈110〉. A new common unit mesh for this competing orientation is suggested; it possesses an area of 612 Å^2 and a mismatch of −1.2%

Aeroelastic analysis of wings using the Euler equations with a deforming mesh

Modifications to the CFL3D three dimensional unsteady Euler/Navier-Stokes code for the aeroelastic analysis of wings are described. The modifications involve including a deforming mesh capability which can move the mesh to continuously conform to the instantaneous shape of the aeroelastically deforming wing, and including the structural equations of motion for their simultaneous time-integration with the governing flow equations. Calculations were performed using the Euler equations to verify the modifications to the code and as a first step toward aeroelastic analysis using the Navier-Stokes equations. Results are presented for the NACA 0012 airfoil and a 45 deg sweptback wing to demonstrate applications of CFL3D for generalized force computations and aeroelastic analysis. Comparisons are made with published Euler results for the NACA 0012 airfoil and with experimental flutter data for the 45 deg sweptback wing to assess the accuracy of the present capability. These comparisons show good agreement and, thus, the CFL3D code may be used with confidence for aeroelastic analysis of wings

Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits.

Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material

Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein

The pharmacological disruption of the interaction between the HIV Tat protein and its cognate transactivation response RNA (TAR) would generate novel anti-viral drugs with a low susceptibility to drug resistance, but efforts to discover ligands with sufficient potency to warrant pharmaceutical development have been unsuccessful. We have previously described a family of structurally constrained β-hairpin peptides that potently inhibits viral growth in HIV-infected cells. The nuclear magnetic resonance (NMR) structure of an inhibitory complex revealed that the peptide makes intimate contacts with the 3-nt bulge and the upper helix of the RNA hairpin, but that a single residue contacts the apical loop where recruitment of the essential cellular co-factor cyclin T1 occurs. Attempting to extend the peptide to form more interactions with the RNA loop, we examined a library of longer peptides and achieved >6-fold improvement in affinity. The structure of TAR bound to one of the extended peptides reveals that the peptide slides down the major groove of the RNA, relative to our design, in order to maintain critical interactions with TAR. These conserved contacts involve three amino acid side chains and identify critical interaction points required for potent and specific binding to TAR RNA. They constitute a template of essential interactions required for inhibition of this RN

Synthesis and antimicrobial activity against Pseudomonas aeruginosa of macrocyclic β-hairpin peptidomimetic antibiotics containing N-methylated amino acids

Antimicrobial resistance among Gram-negative bacteria is a growing problem, fueled by the paucity of new antibiotics that target these microorganisms. One novel family of macrocyclic β-hairpin-shaped peptidomimetics was recently shown to act specifically against Pseudomonas spp. by a novel mechanism of action, targeting the outer membrane protein LptD, which mediates lipopolysaccharide transport to the cell surface during outer membrane biogenesis. Here we explore the mode of binding of one of these β-hairpin peptidomimetics to LptD in Pseudomonas aeruginosa, by examining the effects on antimicrobial activity following N-methylation of individual peptide bonds. An N-methyl scan of the cyclic peptide revealed that residues on both sides of the β-hairpin structure at a non-hydrogen bonding position likely mediate hydrogen-bonding interactions with the target LptD. Structural analyses by NMR spectroscopy further reinforce the conclusion that the folded β-hairpin structure of the peptidomimetic is critical for binding to the target LptD. Finally, new NMe analogues with potent activity have been identified, which opens new avenues for optimization in this family of antimicrobial peptides

Report on the Southern Ocean Continuous Plankton Recorder (SO-CPR) Standards Workshop 2016: SCAR SO-CPR Database Expert Group

2016年12月12−16日にオーストラリア南極局にて「南極研究科学委員会（以下SCAR）連続プランクトン採集器（以下CPR）データベース専門家グループワークショップ2016」を開催した．南大洋CPR観測プロジェクトを主導する日本，オーストラリア，ニュージーランドの実務担当者の間で，観測データの品質管理，種同定やデータ分析手法の再確認，および今後の活動についての詳細な討議を行った．前半はこれまでのプロジェクト活動を総括し，各国のマネージメントの状況を確認し，さらには将来的な観測計画を議論した．後半は動物プランクトンの種同定リストの更新のため，具体的な分類カテゴリーの種同定を実施した．特に有孔虫とオキアミ類の幼生期について，確認を行った．まとめられた種同定基準を用いて新たなマニュアル作成を開始することになった．今後，2年に一度を目途にプロジェクト参加国の技術者を集めたワークショップを開催し，各国間で統一された試料処理およびデータ管理を維持していくことを目指すこととなった．The“Southern Ocean Continuous Plankton Recorder (SO-CPR) Survey Standards Workshop”was held at the Australian Antarctic Division on 12−16December 2016. The purposes of the workshop were to confirm that consistent and high standards of species identification, methodology, and data quality were being maintained amongst the main analysts in the SO-CPR Survey, and to discuss future training methods, including a SO-CPR manual that will include a counting rule book, and a future road map for the SO-CPR program. During the workshop we discussed a range of topics including: taxonomic resolution issues (particularly for Foraminifera and euphausiid larval identification and staging); laboratory methods (preservation and storage, with emphasis on maintaining correct pH); shipboard techniques; training methods; data handling (metadata, database, data sharing); gap analysis (spatial, temporal, data, quantitative); and future workshops/conferences, including comprehensive training workshops for emerging SO-CPR survey partners (India). We agreed that there should be a larger workshop every two years to ensure that the high standards of the SO-CPR program are maintained

How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape

The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used 13C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loo

Spectroscopy of Nine Cataclysmic Variable Stars

We present optical spectroscopy of nine cataclysmic binary stars, mostly dwarf novae, obtained primarily to determine orbital periods Porb. The stars and their periods are LX And, 0.1509743(5) d; CZ Aql, 0.2005(6) d; LU Cam, 0.1499686(4) d; GZ Cnc, 0.0881(4) d; V632 Cyg, 0.06377(8) d; V1006 Cyg, 0.09903(9) d; BF Eri, 0.2708804(4) d; BI Ori, 0.1915(5) d; and FO Per, for which Porb is either 0.1467(4) or 0.1719(5) d. Several of the stars proved to be especially interesting. In BF Eri, we detect the absorption spectrum of a secondary star of spectral type K3 +- 1 subclass, which leads to a distance estimate of approximately 1 kpc. However, BF Eri has a large proper motion (100 mas/yr), and we have a preliminary parallax measurement that confirms the large proper motion and yields only an upper limit for the parallax. BF Eri's space velocity is evidently large, and it appears to belong to the halo population. In CZ Aql, the emission lines have strong wings that move with large velocity amplitude, suggesting a magnetically-channeled accretion flow. The orbital period of V1006 Cyg places it squarely within the 2- to 3-hour "gap" in the distribution of cataclysmic binary orbital periods.Comment: 31 pages, 5 postscript and one PNG figure. Accepted for PAS