Showing papers by "Virginia Tech published in 2011"

Genome sequence and analysis of the tuber crop potato.

Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

Piezoelectric Energy Harvesting

Abstract: About the Authors. Preface. 1. Introduction to Piezoelectric Energy Harvesting. 1.1 Vibration-Based Energy Harvesting Using Piezoelectric Transduction. 1.2 An Examples of a Piezoelectric Energy Harvesting System. 1.3 Mathematical Modeling of Piezoelectric Energy Harvesters. 1.4 Summary of the Theory of Linear Piezoelectricity. 1.5 Outline of the Book. 2. Base Excitation Problem for Cantilevered Structures and Correction of the Lumped-Parameter Electromechanical Model. 2.1 Base Excitation Problem for the Transverse Vibrations. 2.2 Correction of the Lumped-Parameter Base Excitation Model for Transverse Vibrations. 2.3 Experimental Case Studies for Validation of the Correction Factor. 2.4 Base Excitation Problem for Longitudinal Vibrations and Correction of its Lumped-Parameter Model. 2.5 Correction Factor in the Electromechanically Coupled Lumped-Parameter Equations and a Theoretical Case Study. 2.6 Summary. 2.7 Chapter Notes. 3. Analytical Distributed-Parameter Electromechanical Modeling of Cantilevered Piezoelectric Energy Harvesters. 3.1 Fundamentals of the Electromechanically Coupled Distributed-Parameter Model. 3.2 Series Connection of the Piezoceramic Layers. 3.3 Parallel Connection of Piezoceramic Layers. 3.4 Equivalent Representation of the Series and the Parallel Connection Cases. 3.5 Single-Mode Electromechanical Equations for Modal Excitations. 3.6 Multi-mode and Single-Mode Electromechanical FRFs. 3.7 Theoretical Case Study. 3.8 Summary. 3.9 Chapter Notes. 4. Experimental Validation of the Analytical Solution for Bimorph Configurations. 4.1 PZT-5H Bimorph Cantilever without a Tip Mass. 4.2 PZT-5H Bimorph Cantilever with a Tip Mass. 4.3 PZT-5A Bimorph Cantilever. 4.4 Summary. 4.5 Chapter Notes. 5. Dimensionless Equations, Asymptotic Analyses, and Closed-Form Relations for Parameter Identification and Optimization. 5.1 Dimensionless Representation of the Single-Mode Electromechanical FRFs. 5.2 Asymptotic Analyses and Resonance Frequencies. 5.3 Identification of Mechanical Damping. 5.4 Identification of the Optimum Electrical Load for Resonance Excitation. 5.5 Intersection of the Voltage Asymptotes and a Simple Technique for the Experimental Identification of the Optimum Load Resistance. 5.6 Vibration Attenuation Amplification from the Short-Circuit to Open-Circuit Conditions. 5.7 Experimental Validation for a PZT-5H Bimorph Cantilever. 5.8 Summary. 5.9 Chapter Notes. 6. Approximate Analytical Distributed-Parameter Electromechanical Modeling of Cantilevered Piezoelectric Energy Harvesters. 6.1 Unimorph Piezoelectric Energy Harvester Configuration. 6.2 Electromechanical Euler-Bernoulli Model with Axial Deformations. 6.3 Electromechanical Rayleigh Model with Axial Deformations. 6.4 Electromechanical Timoshenko Model with Axial Deformations. 6.5 Modeling of Symmetric Configurations. 6.6 Presence of a Tip Mass in the Euler-Bernoulli, Rayleigh, and Timoshenko Models. 6.7 Comments on the Kinematically Admissible Trial Functions. 6.8 Experimental Validation of the Assumed-Modes Solution for a Bimorph Cantilever. 6.9 Experimental Validation for a Two-Segment Cantilever. 6.10 Summary. 6.11 Chapter Notes. 7. Modeling of Piezoelectric Energy Harvesting for Various Forms of Dynamic Loading. 7.1 Governing Electromechanical Equations. 7.2 Periodic Excitation. 7.3 White Noise Excitation. 7.4 Excitation Due to Moving Loads. 7.5 Local Strain Fluctuations on Large Structures. 7.6 Numerical Solution for General Transient Excitation. 7.7 Case Studies. 7.8 Summary. 7.9 Chapter Notes. 8. Modeling and Exploiting Mechanical Nonlinearities in Piezoelectric Energy Harvesting. 8.1 Perturbation Solution of the Piezoelectric Energy Harvesting Problem: the Method of Multiple Scales. 8.2 Monostable Duffing Oscillator with Piezoelectric Coupling. 8.3 Bistable Duffing Oscillator with Piezoelectric Coupling: the Piezomagnetoelastic Energy Harvester. 8.4 Experimental Performance Results of the Bistable Peizomagnetoelastic Energy Harvester. 8.5 A Bistable Plate for Piezoelectric Energy Harvesting. 8.6 Summary. 8.7 Chapter Notes. 9. Piezoelectric Energy Harvesting from Aeroelastic Vibrations. 9.1 A Lumped-Parameter Piezoaeroelastic Energy Harvester Model for Harmonic Response. 9.2 Experimental Validations of the Lumped-Parameter Model at the Flutter Boundary. 9.3 Utilization of System Nonlinearities in Piezoaeroelastic Energy Harvesting. 9.4 A Distributed-Parameter Piezoaeroelastic Model for Harmonic Response: Assumed-Modes Formulation. 9.5 Time-Domain and Frequency-Domain Piezoaeroelastic Formulations with Finite-Element Modeling. 9.6 Theoretical Case Study for Airflow Excitation of a Cantilevered Plate. 9.7 Summary. 9.8 Chapter Notes. 10. Effects of Material Constants and Mechanical Damping on Power Generation. 10.1 Effective Parameters of Various Soft Ceramics and Single Crystals. 10.2 Theoretical Case Study for Performance Comparison of Soft Ceramics and Single Crystals. 10.3 Effective Parameters of Typical Soft and Hard Ceramics and Single Crystals. 10.4 Theoretical Case Study for Performance Comparison of Soft and Hard Ceramics and Single Crystals. 10.5 Experimental Demonstration for PZT-5A and PZT-5H Cantilevers. 10.6 Summary. 10.7 Chapter Notes. 11. A Brief Review of the Literature of Piezoelectric Energy Harvesting Circuits. 11.1 AC-DC Rectification and Analysis of the Rectified Output. 11.2 Two-Stage Energy Harvesting Circuits: DC-DC Conversion for Impedance Matching. 11.3 Synchronized Switching on Inductor for Piezoelectric Energy Harvesting. 11.4 Summary. 11.5 Chapter Notes. Appendix A. Piezoelectric Constitutive Equations. Appendix B. Modeling of the Excitation Force in Support Motion Problems of Beams and Bars. Appendix C. Modal Analysis of a Uniform Cantilever with a Tip Mass. Appendix D. Strain Nodes of a Uniform Thin Beam for Cantilevered and Other Boundary Conditions. Appendix E. Numerical Data for PZT-5A and PZT-5H Piezoceramics. Appendix F. Constitutive Equations for an Isotropic Substructure. Appendix G. Essential Boundary Conditions for Cantilevered Beams. Appendix H. Electromechanical Lagrange Equations Based on the Extended Hamilton s Principle. Index.

The genome of woodland strawberry ( Fragaria vesca )

Abstract: The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.

A Review of Morphing Aircraft

Abstract: Aircraft wings are a compromise that allows the aircraft to fly at a range of flight conditions, but the performance at each condition is sub-optimal. The ability of a wing surface to change its geometry during flight has interested researchers and designers over the years as this reduces the design compromises required. Morphing is the short form for metamorphose; however, there is neither an exact definition nor an agreement between the researchers about the type or the extent of the geometrical changes necessary to qualify an aircraft for the title ‘shape morphing.’ Geometrical parameters that can be affected by morphing solutions can be categorized into: planform alteration (span, sweep, and chord), out-of-plane transformation (twist, dihedral/gull, and span-wise bending), and airfoil adjustment (camber and thickness). Changing the wing shape or geometry is not new. Historically, morphing solutions always led to penalties in terms of cost, complexity, or weight, although in certain circumstances, thes...

The family of terpene synthases in plants: A mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

Abstract: Summary Some plant terpenes such as sterols and carotenes are part of primary metabolism and found essentially in all plants. However, the majority of the terpenes found in plants are classified as ‘secondary’ compounds, those chemicals whose synthesis has evolved in plants as a result of selection for increased fitness via better adaptation to the local ecological niche of each species. Thousands of such terpenes have been found in the plant kingdom, but each species is capable of synthesizing only a small fraction of this total. In plants, a family of terpene synthases (TPSs) is responsible for the synthesis of the various terpene molecules from two isomeric 5-carbon precursor ‘building blocks’, leading to 5-carbon isoprene, 10-carbon monoterpenes, 15-carbon sesquiterpenes and 20-carbon diterpenes. The bryophyte Physcomitrella patens has a single TPS gene, copalyl synthase/kaurene synthase (CPS/KS), encoding a bifunctional enzyme producing ent-kaurene, which is a precursor of gibberellins. The genome of the lycophyte Selaginella moellendorffii contains 18 TPS genes, and the genomes of some model angiosperms and gymnosperms contain 40–152 TPS genes, not all of them functional and most of the functional ones having lost activity in either the CPS- or KS-type domains. TPS genes are generally divided into seven clades, with some plant lineages having a majority of their TPS genes in one or two clades, indicating lineage-specific expansion of specific types of genes. Evolutionary plasticity is evident in the TPS family, with closely related enzymes differing in their product profiles, subcellular localization, or the in planta substrates they use.

Determination of antineutrino spectra from nuclear reactors

Abstract: In this paper we study the effect of well-known higher-order corrections to the allowed $\ensuremath{\beta}$-decay spectrum on the determination of antineutrino spectra resulting from the decays of fission fragments. In particular, we try to estimate the associated theory errors and find that induced currents like weak magnetism may ultimately limit our ability to improve the current accuracy and under certain circumstance could even greatly increase the theoretical errors. We also perform a critical evaluation of the errors associated with our method to extract the antineutrino spectrum using synthetic $\ensuremath{\beta}$ spectra. It turns out that a fit using only virtual $\ensuremath{\beta}$ branches with a judicious choice of the effective nuclear charge provides results with a minimal bias. We apply this method to actual data for ${}^{235}$U, ${}^{239}$Pu, and ${}^{241}$Pu and confirm, within errors, recent results, which indicate a net $3%$ upward shift in energy-averaged antineutrino fluxes. However, we also find significant shape differences which can, in principle, be tested by high-statistics antineutrino data samples.

A Pedagogical Framework for Mobile Learning: Categorizing Educational Applications of Mobile Technologies into Four Types.

Abstract: Instructional designers and educators recognize the potential of mobile technologies as a learning tool for students and have incorporated them into the distance learning environment. However, little research has been done to categorize the numerous examples of mobile learning in the context of distance education, and few instructional design guidelines based on a solid theoretical framework for mobile learning exist. In this paper I compare mobile learning (m-learning) with electronic learning (e-learning) and ubiquitous learning (u-learning) and describe the technological attributes and pedagogical affordances of mobile learning presented in previous studies. I modify transactional distance (TD) theory and adopt it as a relevant theoretical framework for mobile learning in distance education. Furthermore, I attempt to position previous studies into four types of mobile learning: 1) high transactional distance socialized m-learning, 2) high transactional distance individualized m-learning, 3) low transactional distance socialized m-learning, and 4) low transactional distance individualized m-learning. As a result, this paper can be used by instructional designers of open and distance learning to learn about the concepts of mobile learning and how mobile technologies can be incorporated into their teaching and learning more effectively.

Bicycling renaissance in North America? An update and re-appraisal of cycling trends and policies

Abstract: This paper reviews trends in cycling levels, safety, and policies in Canada and the USA over the past two decades. We analyze aggregate data for the two countries as well as city-specific case study data for nine large cities (Chicago, Minneapolis, Montreal, New York, Portland, San Francisco, Toronto, Vancouver, and Washington). Cycling levels have increased in both the USA and Canada, while cyclist fatalities have fallen. There is much spatial variation and socioeconomic inequality in cycling rates. The bike share of work commuters is more than twice as high in Canada as in the USA, and is higher in the western parts of both countries. Cycling is concentrated in central cities, especially near universities and in gentrified neighborhoods near the city center. Almost all the growth in cycling in the USA has been among men between 25-64 years old, while cycling rates have remained steady among women and fallen sharply for children. Cycling rates have risen much faster in the nine case study cities than in their countries as a whole, at least doubling in all the cities since 1990. They have implemented a wide range of infrastructure and programs to promote cycling and increase cycling safety: expanded and improved bike lanes and paths, traffic calming, parking, bike-transit integration, bike sharing, training programs, and promotional events. We describe the specific accomplishments of the nine case study cities, focusing on each city's innovations and lessons for other cities trying to increase cycling. Portland's comprehensive package of cycling policies has succeeded in raising cycling levels 6-fold and provides an example that other North American cities can follow.

Angiosperm phylogeny: 17 genes, 640 taxa

Abstract: PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

Review: Regional land subsidence accompanying groundwater extraction

Abstract: The extraction of groundwater can generate land subsidence by causing the compaction of susceptible aquifer systems, typically unconsolidated alluvial or basin-fill aquifer systems comprising aquifers and aquitards. Various ground-based and remotely sensed methods are used to measure and map subsidence. Many areas of subsidence caused by groundwater pumping have been identified and monitored, and corrective measures to slow or halt subsidence have been devised. Two principal means are used to mitigate subsidence caused by groundwater withdrawal—reduction of groundwater withdrawal, and artificial recharge. Analysis and simulation of aquifer-system compaction follow from the basic relations between head, stress, compressibility, and groundwater flow and are addressed primarily using two approaches—one based on conventional groundwater flow theory and one based on linear poroelasticity theory. Research and development to improve the assessment and analysis of aquifer-system compaction, the accompanying subsidence and potential ground ruptures are needed in the topic areas of the hydromechanical behavior of aquitards, the role of horizontal deformation, the application of differential synthetic aperture radar interferometry, and the regional-scale simulation of coupled groundwater flow and aquifer-system deformation to support resource management and hazard mitigation measures.

Nitrous oxide emission from denitrification in stream and river networks

Abstract: Nitrous oxide (N2O) is a potent greenhouse gas that contributes to climate change and stratospheric ozone destruction. Anthropogenic nitrogen (N) loading to river networks is a potentially important source of N2O via microbial denitrification that converts N to N2O and dinitrogen (N2). The fraction of denitrified N that escapes as N2O rather than N2 (i.e., the N2O yield) is an important determinant of how much N2O is produced by river networks, but little is known about the N2O yield in flowing waters. Here, we present the results of whole-stream 15N-tracer additions conducted in 72 headwater streams draining multiple land-use types across the United States. We found that stream denitrification produces N2O at rates that increase with stream water nitrate (NO3−) concentrations, but that <1% of denitrified N is converted to N2O. Unlike some previous studies, we found no relationship between the N2O yield and stream water NO3−. We suggest that increased stream NO3− loading stimulates denitrification and concomitant N2O production, but does not increase the N2O yield. In our study, most streams were sources of N2O to the atmosphere and the highest emission rates were observed in streams draining urban basins. Using a global river network model, we estimate that microbial N transformations (e.g., denitrification and nitrification) convert at least 0.68 Tg·y−1 of anthropogenic N inputs to N2O in river networks, equivalent to 10% of the global anthropogenic N2O emission rate. This estimate of stream and river N2O emissions is three times greater than estimated by the Intergovernmental Panel on Climate Change.

Hydrodeoxygenation of guaiacol as model compound for pyrolysis oil on transition metal phosphide hydroprocessing catalysts

Abstract: The gas phase hydrodeoxygenation (HDO) of guaiacol, as a model compound for pyrolysis oil, was tested on a series of novel hydroprocessing catalysts – transition metal phosphides which included Ni2P/SiO2, Fe2P/SiO2, MoP/SiO2, Co2P/SiO2 and WP/SiO2. The turnover frequency based on active sites titrated by the chemisorption of CO followed the order: Ni2P > Co2P > Fe2P, WP, MoP. The major products from hydrodeoxygenation of guaiacol for the most active phosphides were benzene and phenol, with a small amount of methoxybenzene formed. Kinetic studies revealed the formation of reaction intermediates such as catechol and cresol at short contact times. A commercial catalyst 5% Pd/Al2O3 was more active than the metal phosphides at lower contact time but produced only catechol. A commercial CoMoS/Al2O3 deactivated quickly and showed little activity for the HDO of guaiacol at these conditions. Thus, transition metal phosphides are promising materials for catalytic HDO of biofuels.

The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Abstract: Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.

Graphene-based electrochemical energy conversion and storage: fuel cells, supercapacitors and lithium ion batteries.

Abstract: Graphene has attracted extensive research interest due to its strictly 2-dimensional (2D) structure, which results in its unique electronic, thermal, mechanical, and chemical properties and potential technical applications. These remarkable characteristics of graphene, along with the inherent benefits of a carbon material, make it a promising candidate for application in electrochemical energy devices. This article reviews the methods of graphene preparation, introduces the unique electrochemical behavior of graphene, and summarizes the recent research and development on graphene-based fuel cells, supercapacitors and lithium ion batteries. In addition, promising areas are identified for the future development of graphene-based materials in electrochemical energy conversion and storage systems.

Morphological classification of plant cell deaths.

Abstract: Programmed cell death (PCD) is an integral part of plant development and of responses to abiotic stress or pathogens. Although the morphology of plant PCD is, in some cases, well characterised and molecular mechanisms controlling plant PCD are beginning to emerge, there is still confusion about the classification of PCD in plants. Here we suggest a classification based on morphological criteria. According to this classification, the use of the term 'apoptosis' is not justified in plants, but at least two classes of PCD can be distinguished: vacuolar cell death and necrosis. During vacuolar cell death, the cell contents are removed by a combination of autophagy-like process and release of hydrolases from collapsed lytic vacuoles. Necrosis is characterised by early rupture of the plasma membrane, shrinkage of the protoplast and absence of vacuolar cell death features. Vacuolar cell death is common during tissue and organ formation and elimination, whereas necrosis is typically found under abiotic stress. Some examples of plant PCD cannot be ascribed to either major class and are therefore classified as separate modalities. These are PCD associated with the hypersensitive response to biotrophic pathogens, which can express features of both necrosis and vacuolar cell death, PCD in starchy cereal endosperm and during self-incompatibility. The present classification is not static, but will be subject to further revision, especially when specific biochemical pathways are better defined.

The ALPS project release 2.0: open source software for strongly correlated systems

Abstract: We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. The code development is centered on common XML and HDF5 data formats, libraries to simplify and speed up code development, common evaluation and plotting tools, and simulation programs. The programs enable non-experts to start carrying out serial or parallel numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), the density matrix renormalization group (DMRG) both in a static version and a dynamic time-evolving block decimation (TEBD) code, and quantum Monte Carlo solvers for dynamical mean field theory (DMFT). The ALPS libraries provide a powerful framework for programmers to develop their own applications, which, for instance, greatly simplify the steps of porting a serial code onto a parallel, distributed memory machine. Major changes in release 2.0 include the use of HDF5 for binary data, evaluation tools in Python, support for the Windows operating system, the use of CMake as build system and binary installation packages for Mac OS X and Windows, and integration with the VisTrails workflow provenance tool. The software is available from our web server at http://alps.comp-phys.org/.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Abstract: Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

Abstract: The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Bacterial cellulose-based materials and medical devices: current state and perspectives.

Abstract: Bacterial cellulose (BC) is a unique and promising material for use as implants and scaffolds in tissue engineering. It is composed of a pure cellulose nanofiber mesh spun by bacteria. It is remarkable for its strength and its ability to be engineered structurally and chemically at nano-, micro-, and macroscales. Its high water content and purity make the material biocompatible for multiple medical applications. Its biocompatibility, mechanical strength, chemical and morphologic controllability make it a natural choice for use in the body in biomedical devices with broader application than has yet been utilized. This paper reviews the current state of understanding of bacterial cellulose, known methods for controlling its physical and chemical structure (e.g., porosity, fiber alignment, etc.), biomedical applications for which it is currently being used, or investigated for use, challenges yet to be overcome, and future possibilities for BC.

Modern Natural Products Drug Discovery and its Relevance to Biodiversity Conservation

Abstract: Natural products continue to provide a diverse and unique source of bioactive lead compounds for drug discovery, but maintaining their continued eminence as source compounds is challenging in the face of the changing face of the pharmaceutical industry and the changing nature of biodiversity prospecting brought about by the Convention on Biological Diversity. This review provides an overview of some of these challenges and suggests ways in which they can be addressed so that natural products research can remain a viable and productive route to drug discovery. Results from International Cooperative Biodiversity Groups (ICBGs) working in Madagascar, Panama, and Suriname are used as examples of what can be achieved when biodiversity conservation is linked to drug discovery.