bluuebunny/crossref_metadata_2025 huggingface dataset:
A label-free optical detection method for biosensors and microfluidics
Authors: Shan Xiaonan , Foley Kyle J. , Tao Nongjian
Published: April 2008

A label-free detection method is developed for biosensors and for microfluidic applications. Multiple optical modes, including a conventional surface plasmon resonance (SPR) mode and many bulk modes, are created in a microfluidic channel with metallic coatings on top and bottom. The bulk modes are bulk sensitive and detect analytes in the channel with 20 times higher sensitivity than the SPR, which is particularly suitable for microfluidic devices. The method can be operated either in the SPR mode for detection of molecular binding on a surface or in one of the bulk optical modes for monitoring analytes in the channel.
Analytic perturbation solution to the capacitance system of a hyberboloidal tip and a rough surface
Authors: Shen Yongxing , Barnett David M. , Pinsky Peter M.
Published: April 2008

The capacitance system of a hyperboloidal tip and a rough surface is usually encountered in analyzing electrostatic force microscopy images. In this letter, a perturbation approach has been applied to solve for the electric potential of this system, in which the rough surface is treated as perturbation from a flat one. For the first-variation solution, the boundary value problem is represented in the prolate-spheroidal coordinate system and solved in terms of a generalized Fourier series involving conical functions. Based on this solution, the tip-surface Coulombic interaction can be computed. Sample calculations have been applied to sinusoidal surface profiles.
Ballistic rectification in a Z-shaped graphene nanoribbon junction
Authors: Wang Z. F. , Li Qunxiang , Shi Q. W. , Wang Xiaoping , Hou J. G. , Zheng Huaixiu , Chen Jie
Published: April 2008

In this paper, we focus on a graphene heterojunction device: a Z-shaped graphene nanoribbon, which consists of two armchair leads and a zigzag junction. Based on the Landauer–Büttiker formula and the tight binding model, we found that the rectifying behavior can be achieved by applying an external gate voltage in the heterjunction region. We also found that the rectification effect is independent of junction width and length, it is an intrinsic property of the Z-junction graphene nanoribbon. This platform can be used to design and study functional graphene nanoscale devices.
Direct observation of three-photon resonance in water-soluble ZnS quantum dots
Authors: He Jun , Scholes Gregory D. , Ang Yu Long , Ji Wei , Beh Cyrus W. J. , Chin Wee Shong
Published: April 2008

We report on large three-photon absorption (3PA) in thioglycol-capped ZnS semiconductor quantum dots (QDs) at different wavelengths with femtosecond Z-scan technique. Both the intrinsic 3PA coefficients and cross sections of the 1.3nm sized ZnS QDs in aqueous solution are nearly one order of magnitude greater than that of ZnS bulk crystal. The 3PA resonance in ZnS QDs is observed at the lowest excitonic transition of 1S(e)-1S3∕2(h).
Ordered n-type ZnO nanorod arrays
Authors: Zhou Huijuan , Fallert Johannes , Sartor Janos , Dietz Roman J. B. , Klingshirn Claus , Kalt Heinz , Weissenberger Daniel , Gerthsen Dagmar , Zeng Haibo , Cai Weiping
Published: April 2008

Using indium as catalyst for growth and simultaneously as doping source, ordered arrays of n-type ZnO single crystal nanorods have been perpendicularly grown on p-GaN∕Al2O3 substrates with a vapor phase transport growth method. The low temperature photoluminescence measurements of the n-ZnO nanorods show dominant In-related neutral donor bound exciton emission in the ultraviolet region. Electrical transport measurements performed on single n-ZnO nanorods yield resistances of about 50–200kΩ and a typical specific resistivity of 2.0×10−2Ωcm. The resistivity is one order of magnitude reduced by introducing In compared to the nominally undoped ZnO nanorods.
Fast reverse osmosis using boron nitride and carbon nanotubes
Authors: Suk M. E. , Raghunathan A. V. , Aluru N. R.
Published: April 2008

We investigate reverse osmosis through commonly used polymeric and advanced inorganic nanotube based semipermeable membranes by performing nonequilibrium molecular dynamics simulations. Simulations indicate that there is a significantly higher water flux through boron-nitride nanotube (BNNT) and carbon nanotube (CNT) compared to a polymethyl methacrylate (PMMA) pore, and a slightly higher water flux through BNNT as compared to CNT. The calculated permeation coefficient is in reasonable agreement with the theoretical single-file “hopping” model. Potential of mean force analysis indicates that the irregular nature of PMMA pore surface can cause significant localized energy barriers inside the pore, thereby reducing the water flux.
Cross-sectional insight in the water evolution and transport in polymer electrolyte fuel cells
Authors: Hartnig Christoph , Manke Ingo , Kuhn Robert , Kardjilov Nikolay , Banhart John , Lehnert Werner
Published: April 2008

The evolution of liquid water and its transport through the porous gas diffusion media in an operating fuel cell were investigated applying an experimental setup for high spatial resolution of 3μm. Fundamental aspects of cluster formation in hydrophobic/hydrophilic porous materials as well as processes of multiphase flow are addressed. The obtained water distributions provide a detailed insight in the membrane electrode assembly and the porous electrode with regard on the existence and transport of liquid water. In addition, the results approve transport theories used within the framework of percolation theory and demonstrate the need for adapted modeling approaches.
High-performance n-type carbon nanotube field-effect transistors with estimated sub-10-ps gate delay
Authors: Zhang Z. Y. , Wang S. , Ding L. , Liang X. L. , Xu H. L. , Shen J. , Chen Q. , Cui R. L. , Li Y. , Peng L.-M.
Published: April 2008

High-performance top-gated n-type single-walled carbon nanotube (CNT) field-effect transistors (FETs) have been fabricated using scandium contacts and HfO2 gate oxide and are benchmarked against the state-of-the-art n-type Si metal-oxide semiconductor FETs. Two key device metrics, the intrinsic gate-delay (CV∕I) and energy-delay product (CV∕I⋅CV2) per unit width, of the n-type CNT FETs are found to show significant improvement over the Si devices. In particular, the gate-delay time is estimated to be 2.1ps for an n-type CNT FET which is based on a CNT with a diameter of 1.1nm and a channel length of 220nm.
Light exhibits a spin hall effect
Authors: Day Charles
Published: April 2008

Whenever a linearly polarized beam of light refracts, it splits into two parallel, almost overlapping beams of opposite circular polarization.
A muscle’s mechanical advantage is not constant
Authors: Miller Johanna
Published: April 2008

Experiments and simulations reveal that the velocity amplification in a turkey’s calf muscle depends on the force that the muscle opposes.
A bubble chamber brings new capabilities to the search for WIMPs
Authors: Schwarzschild Bertram
Published: April 2008

In the quest to learn what dark matter is made of, bubble chambers can render the enormous background of keV electrons invisible.
New European agency introduces internationally competitive funding for basic research
Authors: Feder Toni
Published: April 2008

Some 300 young researchers are receiving roughly €1 million apiece in a new strategy to strengthen Europe’s research base through broader competition.
Medieval dynamics
Authors: Sylla Edith Dudley
Published: April 2008

Thomas Bradwardine’s 14th-century dynamical law may not be well known today, but it greatly influenced European scholars through the late Middle Ages and into the Renaissance.
Shining a light on dental composite restoratives
Authors: Stansbury Jeffrey W. , Bowman Christopher N. , Newman Sheldon M.
Published: April 2008

Dental fillings made from light-activated, polymer-based composites obviate some of the safety concerns associated with the metal amalgams they are replacing. They look better too.
DNA surface hybridization regimes
Authors: Gong Ping , Levicky Rastislav
Published: April 2008

Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and interpret genomic information. Although hybridization is fairly well understood in bulk solution, the greater complexity of an interfacial environment presents new challenges to a fundamental understanding, and hence application, of these assays. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer, which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. This study finds that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes that maps specific behaviors to experimental ranges of ionic strength and probe coverage.
Oxygen-regulated isoforms of cytochrome
c
oxidase have differential effects on its nitric oxide production and on hypoxic signaling
Authors: Castello Pablo R. , Woo Dong Kyun , Ball Kerri , Wojcik Jay , Liu Laura , Poyton Robert O.
Published: April 2008

Recently, it has been reported that mitochondria possess a novel pathway for nitric oxide (NO) synthesis. This pathway is induced when cells experience hypoxia, is nitrite (NO
2
−
)-dependent, is independent of NO synthases, and is catalyzed by cytochrome
c
oxidase (Cco). It has been proposed that this mitochondrially produced NO is a component of hypoxic signaling and the induction of nuclear hypoxic genes. In this study, we examine the NO
2
−
-dependent NO production in yeast engineered to contain alternative isoforms, Va or Vb, of Cco subunit V. Previous studies have shown that these isoforms have differential effects on oxygen reduction by Cco, and that their genes (
COX5a
and
COX5b
, respectively) are inversely regulated by oxygen. Here, we find that the Vb isozyme has a higher turnover rate for NO production than the Va isozyme and that the Vb isozyme produces NO at much higher oxygen concentrations than the Va isozyme. We have also found that the hypoxic genes
CYC7
and
OLE1
are induced to higher levels in a strain carrying the Vb isozyme than in a strain carrying the Va isozyme. Together, these results demonstrate that the subunit V isoforms have differential effects on NO
2
−
-dependent NO production by Cco and provide further support for a role of Cco in hypoxic signaling. These findings also suggest a positive feedback mechanism in which mitochondrially produced NO induces expression of
COX5b
, whose protein product then functions to enhance the ability of Cco to produce NO in hypoxic/anoxic cells.
The lattice as allosteric effector: Structural studies of αβ- and γ-tubulin clarify the role of GTP in microtubule assembly
Authors: Rice Luke M. , Montabana Elizabeth A. , Agard David A.
Published: April 2008

GTP-dependent microtubule polymerization dynamics are required for cell division and are accompanied by domain rearrangements in the polymerizing subunit, αβ-tubulin. Two opposing models describe the role of GTP and its relationship to conformational change in αβ-tubulin. The allosteric model posits that unpolymerized αβ-tubulin adopts a more polymerization-competent conformation upon GTP binding. The lattice model posits that conformational changes occur only upon recruitment into the growing lattice. Published data support a lattice model, but are largely indirect and so the allosteric model has prevailed. We present two independent solution probes of the conformation of αβ-tubulin, the 2.3 Å crystal structure of γ-tubulin bound to GDP, and kinetic simulations to interpret the functional consequences of the structural data. These results (with our previous γ-tubulin:GTPγS structure) support the lattice model by demonstrating that major domain rearrangements do not occur in eukaryotic tubulins in response to GTP binding, and that the unpolymerized conformation of αβ-tubulin differs significantly from the polymerized one. Thus, geometric constraints of lateral self-assembly must drive αβ-tubulin conformational changes, whereas GTP plays a secondary role to tune the strength of longitudinal contacts within the microtubule lattice. αβ-Tubulin behaves like a bent spring, resisting straightening until forced to do so by GTP-mediated interactions with the growing microtubule. Kinetic simulations demonstrate that resistance to straightening opposes microtubule initiation by specifically destabilizing early assembly intermediates that are especially sensitive to the strength of lateral interactions. These data provide new insights into the molecular origins of dynamic microtubule behavior.
Prediction of the translocon-mediated membrane insertion free energies of protein sequences
Authors: Park Yungki , Helms Volkhard
Published: April 2008

Motivation: Helical membrane proteins (HMPs) play crucial roles in a variety of cellular processes. Unlike water-soluble proteins, HMPs need not only to fold but also get inserted into the membrane to be fully functional. This process of membrane insertion is mediated by the translocon complex. Thus, it is of great interest to develop computational methods for predicting the translocon-mediated membrane insertion free energies of protein sequences.

Result: We have developed Membrane Insertion (MINS), a novel sequence-based computational method for predicting the membrane insertion free energies of protein sequences. A benchmark test gives a correlation coefficient of 0.74 between predicted and observed free energies for 357 known cases, which corresponds to a mean unsigned error of 0.41 kcal/mol. These results are significantly better than those obtained by traditional hydropathy analysis. Moreover, the ability of MINS to reasonably predict membrane insertion free energies of protein sequences allows for effective identification of transmembrane (TM) segments. Subsequently, MINS was applied to predict the membrane insertion free energies of 316 TM segments found in known structures. An in-depth analysis of the predicted free energies reveals a number of interesting findings about the biogenesis and structural stability of HMPs.

Availability: A web server for MINS is available at http://service.bioinformatik.uni-saarland.de/mins

Contact:  volkhard.helms@bioinformatik.uni-saarland.de

Supplementary information: Supplementary data are available at Bioinformatic online.
MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins
Authors: Hennig Janosch , Hennig Klaus D. M. , Sunnerhagen Maria
Published: April 2008

Summary: In structural biology and -genomics, nuclear magnetic resonance (NMR) spectroscopy and crystallography are the methods of choice, but sample requirements can be hard to fulfil. Valuable structural information can also be obtained by using a combination of limited proteolysis and mass spectrometry, providing not only knowledge of how to improve sample conditions for crystallization trials or NMR spectrosopy by gaining insight into subdomain identities but also probing tertiary and quaternary structure, folding and stability, ligand binding, protein interactions and the location of post-translational modifications. For high-throughput studies and larger proteins, however, this experimentally fast and easy approach produces considerable amounts of data, which until now has made the evaluation exceedingly laborious if at all manually possible. MTMDAT, equipped with a browser-like graphical user interface, accelerates this evaluation manifold by automated peak picking, assignment, data processing and visualization.

Availability: MTMDAT can be downloaded from the following page: http://www.cms.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat by clicking on the corresponding links (windows- or unix-based) together with the manual and example files. The program is free for academic/non-commercial purposes only.

Contact:  janhe@ifm.liu.se
Envisioning Difference in Le Clézio's
Onitsha
Authors: Yillah Dauda
Published: April 2008

Le Clézio's
Onitsha
was published in 1991 and is to date the most important fictional piece the author has devoted to his childhood experience of colonial black Africa (British-ruled Nigeria of the late 1940s). I approach the work as an instance of postcolonial discursive practice and focus specifically on the nature and function of the cross-cultural perspective it offers. I grant that any attempt to describe a culture other than one's own inevitably involves using one's cultural reference to describe that culture. I further grant that the unavoidable use of one's cultural lens to relate to another culture rules out the possibility of there being a one-to-one relationship between what one writes about the other culture and what that culture is in its complexity. I claim none the less that the attempt at crossing boundaries — even from a culture that has stood in a position of antagonism and domination in relation to another — is not always to be seen as a cultural self-serving and self-aggrandizing venture. The attempt may well be for all its imperfections a necessary exercise in cultural self-questioning and a welcome threshold of engaging with or indeed opening up to difference. This is perhaps particularly so when one considers that
Onitsha
was written and published some three decades or so after the achievement of independence in black Africa.
Representing Place in Corrozet's
Antiquitez de Paris
Authors: Hodges Elisabeth
Published: April 2008

This article investigates how the French Renaissance guidebook creates a legible sense of place. In part a response to the developing marketplace for printed texts in the capital, the genre was developed by Gilles Corrozet between 1530 and 1550. A hybrid text, part urban history, part folkloric national memoir, the guidebook narrates the history of the city through an examination of its antiquities and origin stories. For Corrozet, place was a means to understand and negotiate relations between history, the self and space at an historical moment when the book, like the map, functioned as a material signifier for the exploration and the representation of the self and the world. While Corrozet's guidebooks locate the experience of given places within an historical trajectory, the portability of these books, produced mostly in handheld format, reveals another of the guidebook's functions as it traces a traveller's itinerary, a journey that provides the book's spatial plan. As a portable ‘lieu de mémoire’, it guides the reader to experience place and landscape as a continuum between the book and its object, and also participates in a larger historical and political demography by aligning writings on cities with an emerging politics of centralization.
Plant Receptor-Like Serine Threonine Kinases: Roles in Signaling and Plant Defense
Authors: Afzal Ahmed J. , Wood Andrew J. , Lightfoot David A.
Published: April 2008

Plants are hosts to a wide array of pathogens from all kingdoms of life. In the absence of an active immune system or combinatorial diversifications that lead to recombination-driven somatic gene flexibility, plants have evolved different strategies to combat both individual pathogen strains and changing pathogen populations. The receptor-like kinase (RLK) gene-family expansion in plants was hypothesized to have allowed accelerated evolution among domains implicated in signal reception, typically a leucine-rich repeat (LRR). Under that model, the gene-family expansion represents a plant-specific adaptation that leads to the production of numerous and variable cell surface and cytoplasmic receptors. More recently, it has emerged that the LRR domains of RLK interact with a diverse group of proteins leading to combinatorial variations in signal response specificity. Therefore, the RLK appear to play a central role in signaling during pathogen recognition, the subsequent activation of plant defense mechanisms, and developmental control. The future challenges will include determinations of RLK modes of action, the basis of recognition and specificity, which cellular responses each receptor mediates, and how both receptor and kinase domain interactions fit into the defense signaling cascades. These challenges will be complicated by the limited information that may be derived from the primary sequence of the LRR domain. The review focuses upon implications derived from recent studies of the secondary and tertiary structures of several plant RLK that change understanding of plant receptor function and signaling. In addition, the biological functions of plant and animal RLK-containing receptors were reviewed and commonalities among their signaling mechanisms identified. Further elucidated were the genomic and structural organizations of RLK gene families, with special emphasis on RLK implicated in resistance to disease and development.
A Putative MAP Kinase Kinase Kinase,MCK1, Is Required for Cell Wall Integrity and Pathogenicity of the Rice Blast Fungus,Magnaporthe oryzae
Authors: Jeon Junhyun , Goh Jaeduk , Yoo Sungyong , Chi Myoung-Hwan , Choi Jaehyuk , Rho Hee-Sool , Park Jongsun , Han Seong-Sook , Kim Byeong Ryun , Park Sook-Young , Kim Soonok , Lee Yong-Hwan
Published: April 2008

Insertional mutagenesis of Magnaporthe oryzae led to the identification of MCK1, a pathogenicity gene predicted to encode mitogen-activated protein kinase kinase kinase (MAPKKK) homologous to BCK1 in Saccharomyces cerevisiae. Targeted disruption of MCK1 resulted in the fungus undergoing autolysis and showing hypersensitivity to cell-wall-degrading enzyme. The mck1 produced significantly reduced numbers of conidia and developed appressoria in a slightly retarded manner compared with the wild type. Appressorium of the mck1 mutant was unable to penetrate into plant tissues, thereby rendering the mutant nonpathogenic. Cytorrhysis assay and monitoring of lipid mobilization suggested that the appressorial wall was altered, presumably affecting the level of turgor pressure within appressorium. Furthermore, the mck1 mutant failed to grow inside plant tissue. Complementation of the mutated gene restored its ability to cause disease symptoms, demonstrating that MCK1 is required for fungal pathogenicity. Taken together, our results suggest that MCK1 is an MAPKKK involved in maintaining cell wall integrity of M. oryzae, and that remodeling of the cell wall in response to host environments is essential for fungal pathogenesis.
An Oleic Acid–Mediated Pathway Induces Constitutive Defense Signaling and Enhanced Resistance to Multiple Pathogens in Soybean
Authors: Kachroo Aardra , Fu Da-Qi , Havens Wendy , Navarre DuRoy , Kachroo Pradeep , Ghabrial Said A.
Published: April 2008

Stearoyl-acyl carrier protein-desaturase (SACPD)-catalyzed synthesis of oleic acid (18:1) is an essential step in fatty acid biosynthesis. Arabidopsis mutants (ssi2) with reduced SACPD activity accumulate salicylic acid (SA) and exhibit enhanced resistance to multiple pathogens. We show that reduced levels of 18:1 induce similar defense-related phenotypes in soybean. A Bean pod mottle virus (BPMV)-based vector was employed to effectively silence soybean SACPDs. The silenced plants contained reduced 18:1 and increased stearic acid, developed spontaneous cell death lesions, increased SA accumulation, and constitutively expressed pathogenesis-related genes. These plants also expressed elevated levels of resistance-like genes and showed resistance to bacterial and oomycete pathogens. Exogenous application of glycerol induced similar phenotypes, mimicking the effect of silencing SACPDs in healthy soybean plants. Overexpression of a soybean SACPD increased 18:1 levels in ssi2 but not in wild-type Arabidopsis plants, suggesting that the soybean enzyme was under feedback regulation similar to that of the Arabidopsis isozymes. These results suggest that soybean and Arabidopsis respond similarly to 18:1-derived cues by inducing a novel broad-spectrum resistance-conferring pathway, even though they differ significantly in their lipid biosynthetic pathways. We also demonstrate the efficacy of BPMV-induced gene silencing as a tool for functional studies in soybean.
Silencing a Candidate Nematode Effector Gene Corresponding to the Tomato Resistance Gene Mi-1 Leads to Acquisition of Virulence
Authors: Gleason Cynthia A. , Liu Qingli L. , Williamson Valerie M.
Published: April 2008

The Mi-1 gene in tomato confers effective resistance against several species of root-knot nematode, including Meloidogyne javanica. A strain of M. javanica that can reproduce on tomato with Mi-1 was obtained from a culture of an avirulent strain after greenhouse selection. DNA blots and amplified fragment length polymorphism (AFLP) analysis indicated that the two nematode strains are closely related. Expression patterns visualized as cDNA AFLPs were nearly identical except for a cDNA fragment, Cg-1, that was present in the avirulent strain but not in the virulent strain. DNA blots showed that Cg-1 corresponds to a member of a small gene family with one or more copies missing in the virulent strain compared with the avirulent strain. Except for the presence of a histone stem loop near the 3′ end of the transcript, Cg-1 shows no similarity to other sequences in GenBank. The longest open reading frame is 32 amino acids and initiates at the fourth AUG in the predicted transcript. When nematode juveniles of the Mi-1-avirulent strain were soaked in dsRNA corresponding to part of the predicted Cg-1 transcript, they produced progeny that were virulent on tomato carrying the Mi-1 gene, strongly suggesting that Cg-1 is required in the nematode for Mi-1-mediated resistance.
NTH201, a Novel Class II KNOTTED1-Like Protein, Facilitates the Cell-to-Cell Movement of Tobacco mosaic virus in Tobacco
Authors: Yoshii Atsushi , Shimizu Takumi , Yoshida Akiko , Hamada Koji , Sakurai Keitaro , Yamaji Yasuyuki , Suzuki Masashi , Namba Shigetou , Hibi Tadaaki
Published: April 2008

NTH201, a novel class II KNOTTED1-like protein gene, was cloned from tobacco (Nicotiana tabacum cv. Xanthi) and its role in Tobacco mosaic virus (TMV) infection was analyzed. Virus-induced gene silencing of NTH201 caused a delay in viral RNA accumulation as well as virus spread in infected tobacco plants. Overexpression of the gene in a transgenic tobacco plant (N. tabacum cv. Xanthi nc) infected by TMV showed larger local lesions than those of the nontransgenic plant. NTH201 exhibited no intercellular trafficking ability but did exhibit colocalization with movement protein (MP) at the plasmodesmata. When NTH201-overexpressing tobacco BY-2 cultured cells were infected with TMV, the accumulation of MP but not of viral genomic and subgenomic RNA clearly was accelerated compared with those in nontransgenic cells at an early infection period. The formation of virus replication complexes (VRC) also was accelerated in these transgenic cells. Conversely, NTH201-silenced cells showed less MP accumulations and fewer VRC formations than did nontransgenic cells. These results suggested that NTH201 might indirectly facilitate MP accumulation and VRC formation in TMV-infected cells, leading to rapid viral cell-to-cell movement in plants at an early infection stage.
Multiple Activities Associated with the Capsid Protein of Satellite Panicum Mosaic Virus Are Controlled Separately by the N- and C-Terminal Regions
Authors: Qi Dong , Scholthof Karen-Beth G.
Published: April 2008

The 17-kDa capsid protein (CP) of satellite panicum mosaic virus (SPMV) contains a distinct N-terminal arginine-rich motif (N-ARM) which is required for SPMV virion assembly and the activity of SPMV CP to promote systemic accumulation of its cognate RNA. The present study indicates that SPMV CP also is involved in SPMV RNA accumulation in inoculated leaves and that this activity is also dependent on a functional N-ARM. In addition, deletions of a C-terminal region abolish virion assembly and impair SPMV RNA accumulation in both inoculated and systemic leaves. Unlike the N-ARM mutations, substantial deletions of the SPMV CP C-terminus do not affect SPMV RNA binding activity. Interestingly, SPMV CP also binds Panicum mosaic virus genomic RNA via N-ARM-mediated CP:RNA interactions. Mutations of the N-ARM and the C-terminal regions significantly reduce SPMV CP titers and result in symptom attenuation. In contrast, virions were not associated per se with symptom exacerbation or successful SPMV RNA accumulation. The results show the existence of a correlation between N- and C-termini-mediated contributions for CP accumulation, symptom induction, defective-interfering RNA accumulation, and temperature sensitivity of SPMV RNA maintenance. The data provide further evidence that SPMV CP has multiple roles during infection, which might involve the formation of nonvirion CP:RNA complexes whose stability is controlled in a biologically relevant manner by the N- and C-termini of the CP.
Genome Organization and Evolution of theAVR-PitaAvirulence Gene Family in theMagnaporthe griseaSpecies Complex
Authors: Khang Chang Hyun , Park Sook-Young , Lee Yong-Hwan , Valent Barbara , Kang Seogchan
Published: April 2008

The avirulence (AVR) gene AVR-Pita in Magnaporthe oryzae prevents the fungus from infecting rice cultivars containing the resistance gene Pi-ta. A survey of isolates of the M. grisea species complex from diverse hosts showed that AVR-Pita is a member of a gene family, which led us to rename it to AVR-Pita1. Avirulence function, distribution, and genomic context of two other members, named AVR-Pita2 and AVR-Pita3, were characterized. AVR-Pita2, but not AVR-Pita3, was functional as an AVR gene corresponding to Pi-ta. The AVR-Pita1 and AVR-Pita2 genes were present in isolates of both M. oryzae and M. grisea, whereas the AVR-Pita3 gene was present only in isolates of M. oryzae. Orthologues of members of the AVR-Pita family could not be found in any fungal species sequenced to date, suggesting that the gene family may be unique to the M. grisea species complex. The genomic context of its members was analyzed in eight strains. The AVR-Pita1 and AVR-Pita2 genes in some isolates appeared to be located near telomeres and flanked by diverse repetitive DNA elements, suggesting that frequent deletion or amplification of these genes within the M. grisea species complex might have resulted from recombination mediated by repetitive DNA elements.
Nucleic Acid–Based Pathogen Detection in Applied Plant Pathology
Authors: Vincelli Paul , Tisserat Ned
Published: April 2008

Nucleic acid–based (NA-based) detection techniques are becoming fundamental for the applied plant pathologist. Their speed, sensitivity, specificity, versatility have resulted in the use of these tools to address an increasing number of applied questions and hypotheses. In order to use based detection techniques to best advantage, it is important to recognize only their advantages but also their limitations, such as the possibility particular NA-based tests may not have complete specificity for the of interest and only for that organism. The distinction between detection and disease diagnosis must also be recognized, and we believe NA-based tools are techniques for the former and not the latter. Several pathogen detection technologies are also discussed.
Lima Bean Downy Mildew Epiphytotics Caused by New Physiological Races of Phytophthora phaseoli
Authors: Davidson C. R. , Evans T. A. , Mulrooney R. P. , Gregory N. F. , Carroll R. B. , O'Neill N. R.
Published: April 2008

Before 1995, race D of Phytophthora phaseoli, the causal agent of downy mildew on lima bean (Phaseolus lunatus), was the prevalent physiological race in the mid-Atlantic region of the United States. Since 1995, however, new physiological races of P. phaseoli have been responsible for downy mildew outbreaks in previously resistant cultivars in this region. Cultivar differential testing of 180 isolates of P. phaseoli collected between 1994 and 2005 from Delaware and the eastern shore of Maryland has confirmed the presence of two new physiological races. The detection of race E in 1995 and race F only 5 years later in 2000, plus the lack of resistant cultivars to manage the epiphytotics in lima bean, have led to millions of dollars of crop losses. Intra- and interspecific genetic variation of Phytophthora spp. and isolates were assessed using amplified fragment length polymorphism DNA fingerprinting. Primer groups EcoRI+AG and MseI+C distinguished P. phaseoli and P. capsici from P. infestans but did not distinguish among different races of P. phaseoli.
An Internal Reaction Control for Routine Detection of Clavibacter michiganensis subsp. sepedonicus Using a Real-Time TaqMan PCR-Based Assay
Authors: Smith Donna S. , De Boer Solke H. , Gourley Jane
Published: April 2008

An internal reaction control was integrated into a TaqMan polymerase chain reaction (PCR) assay for the detection of Clavibacter michiganensis subsp. sepedonicus, the causal organism of bacterial ring rot of potato. The reaction control, cloned into plasmid pCmsC4, consisted of a sequence unrelated to C. michiganensis subsp. sepedonicus flanked by the primer sequences used in the TaqMan PCR, thus eliminating the need for multiplexing. Inclusion of the reaction control plasmid in the TaqMan assay had no effect on either the limit of detection or the specificity of the method. Addition of SYBR Green permitted melt analysis of PCR products. The 242-bp reaction control amplicon, with a melt temperature of approximately 94.5°C, could easily be distinguished from the 152-bp primary diagnostic target amplicon, which had a melt temperature of about 85.5°C. Electrophoretic analysis showed that appearance of either melt peak correlated well with the presence of the appropriate amplicon. Two different substances, guanidine-HCl and humic acid, inhibited the amplification of the reaction control at concentrations lower than those that inhibited the primary diagnostic target, demonstrating the reaction control's effectiveness in detecting inhibition or reaction failure. Using the reaction control plasmid, a quantitative threshold for inhibitor detection was established. This permitted the validation of negative results, and thus facilitated the use of TaqMan real-time PCR in the routine testing of diagnostic samples for C. michiganensis subsp. sepedonicus.
Screening Two Lycopersicon peruvianum Collections for Resistance to Tomato spotted wilt virus
Authors: Gordillo Luis F. , Stevens Mikel R. , Millard Mark A. , Geary Brad
Published: April 2008

The United States Department of Agriculture (USDA) Research Service and the Tomato Genetics Resource Center (TGRC) Lycopersicon peruvianum germplasm collections (16,335 plants from 285 accessions) were screened with the Tomato spotted wilt virus (TSWV) isolates TSWV6 from Hawaii, and Anwa-1 from Western Australia. Using TSWV6 to screen for resistance, 10,634 L. peruvianum plants from 280 accessions were screened for resistance, resulting in 168 (60%) accessions with 1,437 (14%) plants indicating resistance, with all 1,404 89S (Sw-5+/Sw-5+) and 1,456 89R (Sw-5/Sw-5) controls infected. When using Anwa-1 for screening, 864 (15%) of 5,701 L. peruvianum plants were uninfected from 106 of the 181 accessions tested, and 472 (95%) of the 495 89S and 421 (73%) of the 574 89R controls were infected. Of the 172 accessions tested with both isolates, 54 were resistant to one isolate but not the other. Additionally, more accessions from the USDA than from the TGRC collection indicated resistance. TSWV-resistant accessions were somewhat equally distributed throughout the L. peruvianum geographic range, with an observation that northern Chile and southern Peru seemed to have an unusually high portion of accession indicating resistance. The value of Sw-5 is discussed in relationship to potential additional sources of TSWV resistance.
Reaction of a Bean Germplasm Collection Against Five Races of Colletotrichum lindemuthianum Identified in Northern Spain and Implications for Breeding
Authors: Ferreira Juan José , Campa Ana , Pérez-Vega Elena , Giraldez Ramón
Published: April 2008

Anthracnose, caused by Colletotrichum lindemuthianum, is one of the most serious diseases of common bean (Phaseolus vulgaris). The pathogenic variability of this fungus in northern Spain and the response of a bean germplasm collection maintained at Servicio Regional de Investigación y Desarrollo Agroalimentario (Villaviciosa, Asturias, Spain) were screened in order to identify potential resistance sources. Races 3, 6, 19, 38, and 102 were identified from 55 isolates collected in this area, race 38 being the most common one. In all, 246 landraces and 42 lines derived from breeding programs were evaluated in search of resistant lines. No local accession showed adequate resistance to the five races. However, three local accessions were resistant to four races and presented intermediate or mixed reactions against the fifth one: accession V225, with a large great northern seed phenotype (R3R6I38R102R19); accession V369, with a great northern seed phenotype (R3R6R38R102R/S19); and accession V309, with a navy seed phenotype (R3R6R38R/S102R19). The results revealed a wide variation in the resistance spectra or resistance combinations, although not all the possible resistance spectra were present in the evaluated accessions. Among the breeding lines, nine materials were resistant to five races and three lines (A252, A321, and A493) were selected as resistance sources to transfer genetic resistance to Andecha bean cultivar. The results indicated that lines A252 and A321 have two dominant and independent genes involved in the resistance to race 38 whereas line A493 has a single locus.
Association of Olpidium bornovanus and Melon necrotic spot virus with Vine Decline of Melon in Guatemala
Authors: de Cara M. , López V. , Córdoba M. C. , Santos M. , Jordá C. , Tello J. C.
Published: April 2008

Thirty-one soil samples from 14 different fields of Guatemala melon with vine decline symptoms were analyzed for the presence of organisms associated with the disease. With a soil-dilution plating method, only Macrophomina phaseolina was detected in five samples. With a melon bait plant technique, Olpidium bornovanus, often together with Melon necrotic spot virus (MNSV), was found in nearly all the samples, corresponding with all the fields studied. Other pathogens that were detected less frequently included Pythium aphanidermatum, Monosporascus cannonballus, and Rhizoctonia solani. Consequently, O. bornovanus and MNSV were uniquely associated with disease occurrence and thus are the most probable cause of melon vine decline in the fields studied.
Isolation of Streptomycin-Resistant Isolates of Erwinia amylovora in New York
Authors: Russo Nicole L. , Burr Thomas J. , Breth Deborah I. , Aldwinckle Herb S.
Published: April 2008

Streptomycin is currently the only antibiotic registered for the control of fire blight, a devastating disease of apple (Malus), pear (Pyrus), and other rosaceous plants caused by the bacterium Erwinia amylovora. Resistance of E. amylovora to streptomycin was first identified in California pear orchards in 1971 and is currently endemic in many parts of the United States. The Northeast remains the only major U.S. apple-growing region without streptomycin-resistant isolates of E. amylovora. In 2002, during a routine survey for streptomycin resistance, isolates from two neighboring orchards in Wayne County, NY were found to be highly resistant to streptomycin at a concentration of 100 μg/ml. This constitutes the first authenticated report of streptomycin resistance in New York State. Infected trees were shipped at the same time from a single nursery in Michigan. Resistance was caused by the acquisition of the strA-strB gene pair, inserted into the ubiquitous nontransmissible E. amylovora plasmid pEA29. Previously, streptomycin-resistant E. amylovora populations from Michigan were described with a similar mechanism of resistance, although the strA-strB genes are not unique to Michigan. These findings illustrate how unintentional movement of nursery material could undermine efforts to prevent the spread of antibiotic-resistant E. amylovora.
Characterization of a Strain of Turnip vein-clearing virus Causing Red Ringspot of Penstemon
Authors: Lockhart Benham E. , Swenson Axelina S. , Olszewski Neil E. , Voth Peter
Published: April 2008

A disease of penstemon (Penstemon digitalis) occurring in commercial nurseries in Minnesota in 2004 to 2006 and characterized by red foliar ringspots, leaf deformation, and plant stunting was found to be caused by a strain of Turnip vein-clearing virus (TVCV) that was named Penstemon ringspot virus (PenRSV). This is the first report of a viral disease of penstemon. The genome organization of PenRSV was similar to that of the crucifer-infecting tobamoviruses. The nucleotide sequence of PenRSV was almost identical (99%) to that of TVCV, but the two viruses differed importantly in host range and symptoms induced. The only sequence difference between PenRSV and TVCV occurred at the 3′ end of open reading frame I, where the amino acid sequence FRDSNL in TVCV is replaced by FRGQQL in PenRSV. The experimental host range of PenRSV included species in the families Brassicaceae (Cruciferae), Cactaceae, Cucurbitaceae, Leguminosae, Malvaceae, and Solanaceae. This virus poses a potential threat to commercial nursery and bedding plant production because of its wide host range and because it will escape detection by immunoenzymatic screening procedures for tobamoviruses based on use of antibodies to Tobacco mosaic virus (TMV).
Survival, Dispersal, and Primary Infection Site for Cercospora beticola in Sugar Beet
Authors: Khan J. , Rio L. E. del , Nelson R. , Rivera-Varas V. , Secor G. A. , Khan M. F. R.
Published: April 2008

Cercospora beticola survives as stromata in infected crop residue. Spores produced on these survival structures serve as primary inoculum during the next cropping season. This study was conducted to determine how long C. beticola can survive at different soil depths, the mechanism of inoculum dispersal, and the primary infection site in sugar beet. Longevity of C. beticola was studied over a 3-year period under field conditions at Fargo, ND. C. beticola-infected leaves were placed at depths of 0, 10, and 20 cm and retrieved after 10, 22, and 34 months. Survival of C. beticola inoculum declined with time and soil depth. Inoculum left on the soil surface, 0 cm in depth, survived the longest (22 months) compared with that buried at 10 cm (10 months) and 20 cm (10 months). C. beticola dispersal from the primary source of inoculum was studied in the field for three growing seasons. Sugar beet plants were surrounded with plastic cages with and without ground cover, or exposed with and without ground cover. Significantly higher disease severity was observed on exposed plants than caged plants with or without ground cover, suggesting that wind was the major dispersal factor for C. beticola inoculum. The primary infection site by C. beticola was determined in a greenhouse study. Leaves, roots, and stems of healthy sugar beet plants were inoculated with C. beticola. Cercospora leaf spot symptoms were observed only on plants that were leaf inoculated, suggesting that the leaf was the primary infection site for C. beticola.
An Immunocapture RT-PCR Procedure Using Apple stem grooving virus Antibodies Facilitates Analysis of Citrus tatter leaf virus from the Original Meyer Lemon Host
Authors: Hilf Mark E.
Published: April 2008

A magnetic bead-based immunocapture system using polyclonal antiserum against Apple stem grooving virus (ASGV) successfully facilitated polymerase chain reaction (PCR) amplification of sequences from three Citrus tatter leaf virus (CTLV) isolates originally isolated from the citrus host Meyer lemon. Primers designed from a pairwise alignment of genomic sequences of CTLV isolates from lily and from kumquat amplified two nonoverlapping genomic regions of 625 and 1,165 bp (approximately 28% of the CTLV genome) which were cloned and sequenced. Despite being propagated separately in the glasshouse for more than 40 years, the CTLV sequences from separate Meyer lemon sources were identical but had only approximately 80% nucleotide identity with the homologous regions of CTLV genomes of isolates from lily and kumquat. Neighbor-joining phylogenetic analysis indicated the CTLV isolates from Meyer lemon were distinct from but more closely related to CTLV from kumquat than from lily, and these CTLV sequences showed equivalent genetic distances from two ASGV isolates.
Novel Sources of Resistance to Fusarium Stalk Rot of Maize in Tropical Africa
Authors: Afolabi C. G. , Ojiambo P. S. , Ekpo E. J. A. , Menkir A. , Bandyopadhyay R.
Published: April 2008

Fusarium stalk rot is one of the most widespread and destructive diseases of maize, and deployment of resistant genotypes is one of the most effective strategies for controlling the disease. Fifty inbred lines and four checks from the breeding program of the International Institute of Tropical Agriculture were evaluated in field trials at Ikenne and Ibadan, Nigeria in 2003 and 2004 to identify new sources of resistance to stalk rot caused by Fusarium verticillioides. Evaluations were conducted under artificial inoculation and natural infection at Ibadan and Ikenne, respectively. Disease severity was recorded using a severity scale (SS) and direct estimation of stalk discoloration (SD). The two methods of disease assessment were compared and combined to classify genotypes into resistance groups using results from rank-sum analysis. In 2003, disease severity ranged from SS = 1 to 5 and SD = 1.3 to 33.8% at both locations. Both SS and SD were significantly (P < 0.01) higher in 2003 than in 2004 at the two locations. In both years, inbred lines significantly differed in SS (P < 0.02) and SD (P < 0.04) at Ibadan. Similarly, inbred lines significantly differed in SS (P < 0.04) and SD (P < 0.04) when genotypes were evaluated at Ikenne. Disease assessments based on SS and SD were significantly correlated (0.68 < r < 0.95, P < 0.01) in both years. Based on the results from rank-sum analysis, inbred lines were separated into highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible groups. At Ibadan, 6 (11.1%) and 8 (14.8%) were identified as highly resistant and resistant, respectively, whereas 11 (20.4%) were identified as resistant at Ikenne. Inbred lines 02C14609, 02C14643, 02C14654, and 02C14678 were consistently classified as either highly resistant or resistant to stalk rot across locations and years while the check genotypes were classified either as susceptible or moderately susceptible to stalk rot. These four inbred lines identified to have high levels of disease resistance may be used for breeding maize with resistance to Fusarium stalk rot.