CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

DTM AT 25: ESSAYS ON THEMES AND FUTURE DIRECTIONS

This paper describes the development and evolution of research themes in the Design Theory and Methodology (DTM) conference. Essays containing reflections on the history of DTM, supported by an analysis of session titles and papers winning the ``best paper award'', describe the development of the research themes. A second set of essays describes the evolution of several key research themes. Two broad trends in research themes are evident, with a third one emerging. The topics of the papers in the first decade or so reflect an underlying aim to apply artificial intelligence toward developing systems that could `design'. To do so required understanding how human designers behave, formalizing design processes so that they could be computed, and formalizing representations of design knowledge. The themes in the first DTM conference and the recollections of the DTM founders reflect this underlying aim. The second decade of DTM saw the emergence of product development as an underlying concern and included a growth in a systems view of design. More recently, there appears to be a trend toward design-led innovation, which entails both executing the design process more efficiently and understanding the characteristics of market-leading designs so as to produce engineered products and systems of exceptional levels of quality and customer satisfaction.

A singularly perturbed linear two-point boundary-value problem

We consider the following singularly perturbed linear two-point boundary-value problem:

Ly(x) ≡ Ω(ε)D_xy(x) - A(x,ε)y(x) = f(x,ε) 0≤x≤1 (1a)

By ≡ L(ε)y(0) + R(ε)y(1) = g(ε) ε → 0^+ (1b)

Here Ω(ε) is a diagonal matrix whose first m diagonal elements are 1 and last m elements are ε. Aside from reasonable continuity conditions placed on A, L, R, f, g, we assume the lower right mxm principle submatrix of A has no eigenvalues whose real part is zero. Under these assumptions a constructive technique is used to derive sufficient conditions for the existence of a unique solution of (1). These sufficient conditions are used to define when (1) is a regular problem. It is then shown that as ε → 0^+ the solution of a regular problem exists and converges on every closed subinterval of (0,1) to a solution of the reduced problem. The reduced problem consists of the differential equation obtained by formally setting ε equal to zero in (1a) and initial conditions obtained from the boundary conditions (1b). Several examples of regular problems are also considered.

A similar technique is used to derive the properties of the solution of a particular difference scheme used to approximate (1). Under restrictions on the boundary conditions (1b) it is shown that for the stepsize much larger than ε the solution of the difference scheme, when applied to a regular problem, accurately represents the solution of the reduced problem.

Furthermore, the existence of a similarity transformation which block diagonalizes a matrix is presented as well as exponential bounds on certain fundamental solution matrices associated with the problem (1).

Los inicios de la vascolog��a en Holanda: El Essai de grammaire de la langue basque de Willem J. van Eys (1865, 1867)

Ed. by Xabier Artiagoitia, Patxi Goenaga & Joseba A. Lakarra.

A Detailed Analysis of Transcriptional Regulators Affecting the Saccharomyces cerevisiae Heat-shock Gene SSA1

The yeast Saccharomyces cerevisiae contains a family of hsp70 related genes. One member of this family, SSA1, encodes a 70kD heat-shock protein which in addition to its heat inducible expression has a significant basal level of expression. The first 500 bp upstream of the SSA1 start point of transcription was examined by DNAse I protection analysis. The results reveal the presence of at least 14 factor binding sites throughout the upstream promoter region. The function of these binding sites has been examined using a series of 5' promoter deletions fused to the recorder gene lacZ in a centromere-containing yeast shuttle vector. The following sites have been identified in the promoter and their activity in yeast determined individually with a centromere-based recorder plasmid containing a truncated CYC1 /lacZ fusion: a heat-shock element or HSE which is sufficient to convey heat-shock response on the recorder plasmid; a homology to the SV40 'core' sequence which can repress the GCN4 recognition element (GCRE) and the yAP1 recognition element (ARE), and has been designated a upstream repression element or URE; a 'G'-rich region named G-box which can also convey heatshock response on the recorder plasmid; and a purine-pyrimidine alternating sequence name GT-box which is an activator of transcription. A series of fusion constructs were made to identify a putative silencer-like element upstream of SSA1. This element is position dependent and has been localized to a region containing both an ABF1 binding site and a RAP1 binding site. Five site-specific DNA-binding factors are identified and their purification is presented: the heat-shock transcription factor or HSTF, which recognizes the HSE; the G-box binding factor or GBF; the URE recognition factor or URF; the GT-box binding factor; and the GC-box binding factor or yeast Sp1.

Estudio comparativo de diferentes soluciones de unión en estructuras de madera.

[ES]El encargado como redactor del estudio de este proyecto es el alumno de la Escuela Técnica Superior de Ingeniería de Bilbao, Pello Intxausti Rodriguez. Dicho proyecto, se encargará del análisis de diferentes tipos de juntas de madera laminada disponibles para una misma dificultad. Para ello, se diseñará una cercha tipo Warren (Figura 3) con el fin de hacer un estudio de esfuerzos del sistema y posteriormente se diseñarán distintas uniones para poder adoptar la solución más adecuada. Se empezará por la descripción del conflicto. La situación de la cercha en cuestión, el estudio climatológico y topográfico forman parte de este apartado. Se continuará con el estudio de diferentes soluciones de unión adoptables y la metodolog��a que se va a seguir en el curso del proyecto, con objeto de poder encontrar una solución satisfactoria.

Drawn to the Sea: Charles Bradford Hudson (1865-1939), Artist, Author, Army Officer, with Special Notice of His Work for the United States Fish Commission and Bureau of Fisheries

The biography of Charles Bradford Hudson that follows this preface had its seeds about 1965 when I (VGS) was casually examining the extensive files of original illustrations of fishes stored in the Division of Fishes, National Museum of Natural History, Smithsonian Institution. I happened upon the unpublished illustration of a rainbow trout by Hudson and was greatly impressed with its quality. The thought occurred to me then that the artist must have gone on to do more than just illustrate fishes. During the next 20 years I occasionally pawed through those files, which contained the work of numerous artists, who had worked from 1838 to the present. In 1985, I happened to discuss the files with my supervisor, who urged me to produce a museum exhibit of original fish illustrations. This I did, selecting 200 of the illustrations representing 21 artists, including, of course, Hudson. As part of the text for the exhibit, Drawn from the Sea, Art in the Service of Ichthyology, I prepared short biographies of each of the artists. The exhibit, with an available poster, was shown in the Museum for six months, and a reduced version was exhibited in U.S. and Canadian museums during the next 3 years.

伯胺N_(1923)萃取过渡金属离子机理的研究

伯胺由于其特殊的结构（R-NH_2），使它具有和仲、数胺不相同的一些性质。有较强的和矿物酸HX结合形成RNH_3X的能力，从而以离子交换机理萃取金属离子；也可以-NH_2上的氮、氢原子同以高价存在的过渡金属含氧酸以氢键方式相结合；另外，RNH_2也可通过氮原子以配位键形式与一些属于软酸类的过度金属离子形成配合物。通过伯胺萃取金属离子行为的研究，可发现新的萃取体系，扩大我国自行设计的伯胺N_(1923)萃取剂的应用领域，为金属离子的分离提纯工艺提供基本参数。我们实验室过去曾对伯胺N_(1923)萃取稀土（III）、Fe（III）、Zn （II）、Cd（II）、Ag���I）、Sc（III）等的机理进行了比较系统的研究。本工作是在此基础上，进一步完善及扩大N_(1923)对周期表中各族元素的萃取及应用。为此，我们选择了文献尚未报道的Ti（IV）、HgCl_2、Hg(CH_3COO)_2、Cu(CH_3COO)_2为研究对象，对它们的萃取机理进行了较详细的研究。结果表明，自由的N_(1923)或其盐对上述体系具有良好的萃取性能，并初步讨论了N_(1923)在金属离子萃取分离中的应用。一、伯胺N_(1923)萃取HgCl_2的机理 微量汞的萃取及分离对环境保护具有重要的实际意义。我们的研究结果表明，在pH值为3-4.5范围内，即使Cl~-浓度很低时，伯胺N_(1923)也能几乎定量地萃取HgCl_2，其盐酸盐亦能有效地萃取Hg���II），但两者的萃取机理不同。自由伯胺RNH_2可与HgCl_2形成配合物，其萃取机理为：RHN_(2(0)) + HgCl_2 <-> Hg(RNH_2)Cl_(2(0))对伯胺盐，实验证明其机理主要为加合反应，但当Cl~-浓度较高时，则为阴离子交换反应：加合反应：2RNH_3Cl_((0)) + HgCl_2 <-> (RNH_3Cl)_2HgCl_(2(0))交换反应：2RNH_3Cl_((0)) + HgCl_4~(2-) <-> (RNH_3)_2HgCl_(4(0)) + 2Cl~-通过考察温度对配位萃取反应的影响，求得反应的热效应ΔH = -48.82 KJ/mol，并分析了萃合物的IR、NMR谱。二、伯胺N_(1923)萃取Hg(CH_3COO)_2的机理 与HgCl_2体系相似，自由伯胺或其盐均能萃取Hg(CH_3COO)_2，萃取机理分别为：RNH_(2(0)) + Hg(CH_3CCO)_2 <-> Hg(RNH_2)(CH_3COO)_(2(0)) (CH_3COONH_3R)_(2(0)) + Hg(CH_3COO)_2 <-> (CH_3COONH_3R)_2Hg(CH_3COO)_(2(0))。在不同的萃取剂浓度下，上述反应的表观平衡常数基本不随萃取剂浓度的变化而改变，其对数值分别为：11.85、8.11。三、伯胺N_(1923)萃取Cu(CH_3COO)_2的机理 水相酸度对萃取反应的影响表明，RNH_2在近中性体系中具有很好的萃取性能，而在乙酸浓度较高的条件下，Cu（II）几乎不被RNH_2所萃取。说明自由伯胺能以配位机理的形式萃取Cu(Oh_3coo)_2，经确定，萃取反应式为：2RNH_(2(0)) + Cu(CH_3COO)_2 <-> Cu(RNH_2)_2(CH_3COO)_(2(0))并对该反应的表观平衡常数及热力学函数进行了计算。通过分析萃合物的IR谱，认为Cu(RNH_2)_2(CH_3COO)_2为平面型四配位的配合物。四、(RNH_3)_2SO_4从硫酸溶液中萃取Ti（IV）的研究 在低酸度（pH：0.84）的H_2SO_4溶液中，伯胺N_(1923)对Ti（IV）具有很强的萃取能力。用化学平衡法确定其反应式为：3(RNH_3)_2SO_(4(0)) + Ti(OH)_3~+ + SO_4~(2-) <-> 2(RNH_3)_3Ti(OH_3)(SO_4)_(2(0))我们用正十二胺代替N_(1923)，合成了上述萃合物的模拟物，经元素分析确定了萃合物的分子式：(RNH_3)_3Ti(OH)_3(SO_4)_2。并较详细地分析了萃合物的NMR、IR谱。变温NMR的结果表明，萃合物中存在两种含有活泼氢的基团，用D_2O交换后的NMR的结果亦证明了这一点。从萃合物的IR谱中，可得到SO_4~(2-)是以单齿配位形式同Ti（IV）相结合的信息。这些结果为所提出的萃取机理提供了直接的证据。并求出了上述萃取反应的表观平衡常数，其对数值为10.15，该值基本不随萃取剂浓度的变化而发生改变。反应的热效应ΔH = 66.49 KJ/mol，由计算得出的ΔG���可知，上述萃取反应有很大的向右进行的趋势。五、伯胺N_(1923)在萃取分离中的应用 为了扩大N_(1923)的应用，通过上述研究，我们对其在萃取分离中的应用进行了讨论，认为在以下几方面有可能得到应用：1、从环境废水中除Hg(II)；2、Hg(II)和Zn(II)、Cd(II)在CH_3COOH体系中的分离；3、CH_3COOH体系中Cu(II)、Co(II)、Ni(II)的萃取分离；4、在较高浓度的H_2SO_4体系中，应用(RNH_3)_2SO_4进行了Ti(IV)-Fe(II)的分离。

Characterization and mapping of expressed sequence tags isolated from a subtracted cDNA library of Litopenaeus vannamei injected with white spot syndrome virus

A large number of polymorphic simple sequence repeats (SSRs) or microsatellites are needed to develop a genetic map for shrimp. However, developing an SSR map is very time-consuming, expensive, and most SSRs are not specifically linked to gene loci of immediate interest. We report here on our strategy to develop polymorphic markers using expressed sequence tags (ESTs) by designing primers flanking single or multiple SSRs with three or more repeats. A subtracted cDNA library was prepared using RNA from specific pathogen-free (SPF) Litopenaeus vannamei juveniles (similar to 1 g) collected before (0) and after (48 h) inoculation with the China isolate of white spot syndrome virus (WSSV). A total of 224 clones were sequenced, 194 of which were useful for homology comparisons against annotated genes in NCBI nonredundant (nr) and protein databases, providing 179 sequences encoded by nuclear DNA, 4 mitochondrial DNA, and 11 were similar to portions of WSSV genome. The nuclear sequences clustered in 43 groups, 11 of which were homologous to various ESTs of unknown function, 4 had no homology to any sequence, and 28 showed similarities to known genes of invertebrates and vertebrates, representatives of cellular metabolic processes such as calcium ion balance, cytoskeleton mRNAs, and protein synthesis. A few sequences were homologous to immune system-related (allergens) genes and two were similar to motifs of the sex-lethal gene of Drosophila. A large number of EST sequences were similar to domains of the EF-hand superfamily (Ca2+ binding motif and FRQ protein domain of myosin light chains). Single or multiple SSRs with three or more repeats were found in approximately 61 % of the 179 nuclear sequences. Primer sets were designed from 28 sequences representing 19 known or putative genes and tested for polymorphism (EST-SSR marker) in a small test panel containing 16 individuals. Ten (53%) of the 19 putative or unknown function genes were polymorphic, 4 monomorphic, and 3 either failed to satisfactorily amplify genomic DNA or the allele amplification conditions need to be further optimized. Five polymorphic ESTs were genotyped with the entire reference mapping family, two of them (actin, accession #CX535973 and shrimp allergen arginine kinase, accession #CX535999) did not amplify with all offspring of the IRMF panel suggesting presence of null alleles, and three of them amplified in most of the IRM F offspring and were used for linkage analysis. EF-hand motif of myosin light chain (accession #CX535935) was placed in ShrimpMap's linkage group 7, whereas ribosomal protein S5 (accession #CX535957) and troponin I (accession #CX535976) remained unassigned. Results indicate that (a) a large number of ESTs isolated from this cDNA library are similar to cytoskeleton mRNAs and may reflect a normal pathway of the cellular response after im infection with WSSV, and (b) primers flanking single or multiple SSRs with three or more repeats from shrimp ESTs could be an efficient approach to develop polymorphic markers useful for linkage mapping. Work is underway to map additional SSR-containing ESTs from this and other cDNA libraries as a plausible strategy to increase marker density in ShrimpMap.

Optimized, unequal pulse spacing in multiple echo sequences improves refocusing in magnetic resonance.

A recent quantum computing paper (G. S. Uhrig, Phys. Rev. Lett. 98, 100504 (2007)) analytically derived optimal pulse spacings for a multiple spin echo sequence designed to remove decoherence in a two-level system coupled to a bath. The spacings in what has been called a "Uhrig dynamic decoupling (UDD) sequence" differ dramatically from the conventional, equal pulse spacing of a Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo sequence. The UDD sequence was derived for a model that is unrelated to magnetic resonance, but was recently shown theoretically to be more general. Here we show that the UDD sequence has theoretical advantages for magnetic resonance imaging of structured materials such as tissue, where diffusion in compartmentalized and microstructured environments leads to fluctuating fields on a range of different time scales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T(2)-weighted contrast than do CPMG sequences with the same number of pulses and total delay, with substantial enhancements in most regions. This permits improved characterization of low-frequency spectral density functions in a wide range of applications.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.