bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes
Authors: Fredlake Christopher P. , Hert Daniel G. , Kan Cheuk-Wai , Chiesl Thomas N. , Root Brian E. , Forster Ryan E. , Barron Annelise E.
Published: January 2008

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the
de novo
sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require ≈70 min to deliver ≈650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered “hybrid” mechanism of DNA electromigration, in which DNA molecules alternate rapidly between reptating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.
A crop population perspective on maize seed systems in Mexico
Authors: Dyer George A. , Taylor J. Edward
Published: January 2008

Improvement of local germplasm through artificial selection is regarded as the main force behind maize evolution and diversity in Mexico, the crop's center of origin. This perspective neglects the larger social context of maize evolution. Using a theoretical approach and Mexico-wide data, we show that farmer-led evolution of maize is largely driven by a technological diffusion and appropriation process that selectively integrates nonlocal germplasm into local seed stocks. Our approach construes farmer practices as events in the life history of seed to build a demographic model. The model shows how random and systematic differences in management combine to structure maize seed populations into subpopulations that can spread or become extinct, in some cases independently of visible agronomic advantages. The process involves continuous population bottlenecks that can lead to diversity loss. Nonlocal germplasm thus might play a critical role in maintaining diversity in individual localities. Empirical estimates show that introduction of nonlocal seed in Central and Southeastern Mexico is rarer than previously thought; prompt replacement further prevents new seed from spreading. Yet introduced seed perceived as valuable diffuses rapidly, contributing variation in the form of type diversity or through introgression into local seed. Maize seed dynamics and evolution are thus part of a complex social process driven by farmers' desire to appropriate the value in maize farming, not always achieved by preserving or improving local seed stocks.
Learning-related long-term potentiation of inhibitory synapses in the cerebellar cortex
Authors: Scelfo Bibiana , Sacchetti Benedetto , Strata Piergiorgio
Published: January 2008

Despite the widespread distribution of inhibitory synapses throughout the central nervous system, plasticity of inhibitory synapses related to associative learning has never been reported. In the cerebellum, the neural correlate of fear memory is provided by a long-term potentiation (LTP) of the excitatory synapse between the parallel fibers (PFs) and the Purkinje cell (PC). In this article, we provide evidence that inhibitory synapses in the cerebellar cortex also are affected by fear conditioning. Whole-cell patch-clamp recordings of spontaneous and miniature GABAergic events onto the PC show that the frequency but not the amplitude of these events is significantly greater up to 24 h after the conditioning. Adequate levels of excitation and inhibition are required to maintain the temporal fidelity of a neuronal network. Such fidelity can be evaluated by determining the time window for multiple input coincidence detection. We found that, after fear learning, PCs are able to integrate excitatory inputs with greater probability within short delays, but the width of the whole window is unchanged. Therefore, excitatory LTP provides a more effective detection, and inhibitory potentiation serves to maintain the time resolution of the system.
High-frequency
HTR3B
variant associated with major depression dramatically augments the signaling of the human 5-HT
3AB
receptor
Authors: Krzywkowski Karen , Davies Paul A. , Feinberg-Zadek Paula L. , Bräuner-Osborne Hans , Jensen Anders A.
Published: January 2008

The 5-hydroxytryptamine-3 (5-HT
3
) receptor mediates the fast excitatory neurotransmission of serotonin and is known to mediate the nausea/emesis induced by radio/chemotherapy and anesthetics. A polymorphism encoding the variation Y129S in the 5-HT
3B
subunit exists in high frequency in the general population and has been shown to be inversely correlated to the incidence of major depression in women. We show that 5-HT
3AB
(Y129S) receptors exhibit a substantially increased maximal response to serotonin compared with WT receptors in two fluorescence-based cellular assays. In electrophysiological recordings, the deactivation and desensitization kinetics of the 5-HT
3AB
(Y129S) receptor are 20- and 10-fold slower, respectively, than those of the WT receptor. Single-channel measurements reveal a 7-fold-increased mean open time of 5-HT
3AB
(Y129S) receptors compared with WT receptors. The augmented signaling displayed by 5-HT
3AB
(Y129S) receptors may confer protection against the development of depression. The variant also may influence the development and/or treatment of nausea and other disorders involving 5-HT
3
receptors. Thus, the impact of the high-frequency variant 5-HT
3B
(Y129S) on 5-HT
3AB
receptor signaling calls for a search for additional phenotypes, and the variant may thus aid in establishing the role of the 5-HT
3AB
receptor in pathophysiology.
Activation of the hypoxia-inducible factor-1α pathway accelerates bone regeneration
Authors: Wan Chao , Gilbert Shawn R. , Wang Ying , Cao Xuemei , Shen Xing , Ramaswamy Girish , Jacobsen Kimberly A. , Alaql Zainab S. , Eberhardt Alan W. , Gerstenfeld Louis C. , Einhorn Thomas A. , Deng Lianfu , Clemens Thomas L.
Published: January 2008

The hypoxia-inducible factor-1α (HIF-1α) pathway is the central regulator of adaptive responses to low oxygen availability and is required for normal skeletal development. Here, we demonstrate that the HIF-1α pathway is activated during bone repair and can be manipulated genetically and pharmacologically to improve skeletal healing. Mice lacking
pVHL
in osteoblasts with constitutive HIF-1α activation in osteoblasts had markedly increased vascularity and produced more bone in response to distraction osteogenesis, whereas mice lacking
HIF-1
α in osteoblasts had impaired angiogenesis and bone healing. The increased vascularity and bone regeneration in the pVHL mutants were VEGF dependent and eliminated by concomitant administration of VEGF receptor antibodies. Small-molecule inhibitors of HIF prolyl hydroxylation stabilized HIF/VEGF production and increased angiogenesis
in vitro
. One of these molecules (DFO) administered
in vivo
into the distraction gap increased angiogenesis and markedly improved bone regeneration. These results identify the HIF-1α pathway as a critical mediator of neoangiogenesis required for skeletal regeneration and suggest the application of HIF activators as therapies to improve bone healing.
Respiratory metabolism of illuminated leaves depends on CO
2
and O
2
conditions
Authors: Tcherkez Guillaume , Bligny Richard , Gout Elizabeth , Mahé Aline , Hodges Michael , Cornic Gabriel
Published: January 2008

Day respiration is the process by which nonphotorespiratory CO
2
is produced by illuminated leaves. The biological function of day respiratory metabolism is a major conundrum of plant photosynthesis research: because the rate of CO
2
evolution is partly inhibited in the light, it is viewed as either detrimental to plant carbon balance or necessary for photosynthesis operation (e.g., in providing cytoplasmic ATP for sucrose synthesis). Systematic variations in the rate of day respiration under contrasting environmental conditions have been used to elucidate the metabolic rationale of respiration in the light. Using isotopic techniques, we show that both glycolysis and the tricarboxylic acid cycle activities are inversely related to the ambient CO
2
/O
2
ratio: day respiratory metabolism is enhanced under high photorespiratory (low CO
2
) conditions. Such a relationship also correlates with the dihydroxyacetone phosphate/Glc-6-P ratio, suggesting that photosynthetic products exert a control on day respiration. Thus, day respiration is normally inhibited by phosphoryl (ATP/ADP) and reductive (NADH/NAD) poise but is up-regulated by photorespiration. Such an effect may be related to the need for NH
2
transfers during the recovery of photorespiratory cycle intermediates.
Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide
Authors: Kudo Norio , Kumagai Keigo , Tomishige Nario , Yamaji Toshiyuki , Wakatsuki Soichi , Nishijima Masahiro , Hanada Kentaro , Kato Ryuichi
Published: January 2008

In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic 68-kDa protein with a C-terminal steroidogenic acute regulatory protein-related lipid transfer (START) domain. The CERT START domain efficiently transfers natural
d
-erythro-C
16
-ceramide, but not lipids with longer (C
20
) amide-acyl chains. The molecular mechanisms of ceramide specificity, both stereo-specific recognition and length limit, are not well understood. Here we report the crystal structures of the CERT START domain in its apo-form and in complex with ceramides having different acyl chain lengths. In these complex structures, one ceramide molecule is buried in a long amphiphilic cavity. At the far end of the cavity, the amide and hydroxyl groups of ceramide form a hydrogen bond network with specific amino acid residues that play key roles in stereo-specific ceramide recognition. At the head of the ceramide molecule, there is no extra space to accommodate additional bulky groups. The two aliphatic chains of ceramide are surrounded by the hydrophobic wall of the cavity, whose size and shape dictate the length limit for cognate ceramides. Furthermore, local high-crystallographic
B
-factors suggest that the α-3 and the Ω1 loop might work as a gate to incorporate the ceramide into the cavity. Thus, the structures demonstrate the structural basis for the mechanism by which CERT can distinguish ceramide from other lipid types yet still recognize multiple species of ceramides.
Differential response of the plant
Medicago truncatula
to its symbiont
Sinorhizobium meliloti
or an exopolysaccharide-deficient mutant
Authors: Jones Kathryn M. , Sharopova Natalya , Lohar Dasharath P. , Zhang Jennifer Q. , VandenBosch Kathryn A. , Walker Graham C.
Published: January 2008

Sinorhizobium meliloti
forms symbiotic, nitrogen-fixing nodules on the roots of
Medicago truncatula
. The bacteria invade and colonize the roots through structures called infection threads.
S. meliloti
unable to produce the exopolysaccharide succinoglycan are unable to establish a symbiosis because they are defective in initiating the production of infection threads and in invading the plant. Here, we use microarrays representing 16,000
M. truncatula
genes to compare the differential transcriptional responses of this host plant to wild-type and succinoglycan-deficient
S. meliloti
at the early time point of 3 days postinoculation. This report describes an early divergence in global plant gene expression responses caused by a rhizobial defect in succinoglycan production, rather than in Nod factor production. The microarray data show that
M. truncatula
inoculated with wild-type, succinoglycan-producing
S. meliloti
more strongly express genes encoding translation components, protein degradation machinery, and some nodulins than plants inoculated with succinoglycan-deficient bacteria. This finding is consistent with wild-type-inoculated plants having received a signal, distinct from the well characterized Nod factor, to alter their metabolic activity and prepare for invasion. In contrast,
M. truncatula
inoculated with succinoglycan-deficient
S. meliloti
more strongly express an unexpectedly large number of genes in two categories: plant defense responses and unknown functions. One model consistent with our results is that appropriate symbiotically active exopolysaccharides act as signals to plant hosts to initiate infection thread formation and that, in the absence of this signal, plants terminate the infection process, perhaps via a defense response.
Water shrews detect movement, shape, and smell to find prey underwater
Authors: Catania Kenneth C. , Hare James F. , Campbell Kevin L.
Published: January 2008

American water shrews (Sorex palustris) are aggressive predators that feed on a variety of terrestrial and aquatic prey. They often forage at night, diving into streams and ponds in search of food. We investigated how shrews locate submerged prey using high-speed videography, infrared lighting, and stimuli designed to mimic prey. Shrews attacked brief water movements, indicating motion is an important cue used to detect active or escaping prey. They also bit, retrieved, and attempted to eat model fish made of silicone in preference to other silicone objects showing that tactile cues are important in the absence of movement. In addition, water shrews preferentially sniffed model prey fish and crickets underwater by exhaling and reinhaling air through the nostrils, suggesting olfaction plays an important role in aquatic foraging. The possibility of echolocation, sonar, or electroreception was investigated by testing for ultrasonic and audible calls above and below water and by presenting electric fields to foraging shrews. We found no evidence for these abilities. We conclude that water shrews detect motion, shape, and smell to find prey underwater. The short latency of attacks to water movements suggests shrews may use a flush-pursuit strategy to capture some prey.
Eoxins are proinflammatory arachidonic acid metabolites produced via the 15-lipoxygenase-1 pathway in human eosinophils and mast cells
Authors: Feltenmark Stina , Gautam Narinder , Brunnström Åsa , Griffiths William , Backman Linda , Edenius Charlotte , Lindbom Lennart , Björkholm Magnus , Claesson Hans-Erik
Published: January 2008

Human eosinophils contain abundant amounts of 15-lipoxygenase (LO)-1. The biological role of 15-LO-1 in humans, however, is unclear. Incubation of eosinophils with arachidonic acid led to formation of a product with a UV absorbance maximum at 282 nm and shorter retention time than leukotriene (LT)C4in reverse-phase HPLC. Analysis with positive-ion electrospray tandem MS identified this eosinophil metabolite as 14,15-LTC4. This metabolite could be metabolized to 14,15-LTD4and 14,15-LTE4in eosinophils. Because eosinophils are such an abundant source of these metabolites and to avoid confusion with 5-LO-derived LTs, we suggest the names eoxin (EX)C4, -D4, and -E4instead of 14,15-LTC4, -D4, and -E4, respectively. Cord blood-derived mast cells and surgically removed nasal polyps from allergic subjects also produced EXC4. Incubation of eosinophils with arachidonic acid favored the production of EXC4, whereas challenge with calcium ionophore led to exclusive formation of LTC4. Eosinophils produced EXC4after challenge with the proinflammatory agents LTC4, prostaglandin D2, and IL-5, demonstrating that EXC4can be synthesized from the endogenous pool of arachidonic acid. EXs induced increased permeability of endothelial cell monolayerin vitro, indicating that EXs can modulate and enhance vascular permeability, a hallmark of inflammation. In this model system, EXs were 100 times more potent than histamine and almost as potent as LTC4and LTD4. Taken together, this article describes the formation of proinflammatory EXs, in particular in human eosinophils but also in human mast cells and nasal polyps.
Opioid neuropeptide genotypes in relation to heroin abuse: Dopamine tone contributes to reversed mesolimbic proenkephalin expression
Authors: Nikoshkov Andrej , Drakenberg Katarina , Wang Xinyu , Horvath Monika Cs. , Keller Eva , Hurd Yasmin L.
Published: January 2008

Striatal enkephalin and dynorphin opioid systems mediate reward and negative affect, respectively, relevant to addiction disorders. We examined polymorphisms of proenkephalin (PENK) and prodynorphin (PDYN) genes in relation to heroin abuse and gene expression in the human striatum and the relevance of genetic dopaminergic tone, critical for drug reward and striatal function. Heroin abuse was significantly associated withPENKpolymorphic 3′ UTR dinucleotide (CA) repeats; 79% of subjects homozygous for the 79-bp allele were heroin abusers. Such individuals tended to express higher PENK mRNA than the 81-bp homozygotes, but PENK levels within the nucleus accumbens (NAc) shell were most strongly correlated to catecholamine-O-methyltransferase (COMT) genotype. Control Met/Met individuals expressed lower PENK mRNA than Val carriers, a pattern reversed in heroin users. Up-regulation of NAc PENK in Met/Met heroin abusers was accompanied by impaired tyrosine hydroxylase (TH) mRNA expression in mesolimbic dopamine neurons. In contrast toPENK, no association was detected betweenPDYNgenotype (68-bp repeat element containing one to four copies of AP-1 binding sites in the promoter region) and heroin abuse, although there was a clear functional association with striatal PDYN mRNA expression: an increased number of inducible repeats (three and four) correlated with higher PDYN levels than adult or fetal subjects with noninducible (one and two) alleles. Moreover, PDYN expression was not related toCOMTgenotype. Altogether, the data suggest that dysfunction of the opioid reward system is significantly linked to opiate abuse vulnerability and that heroin use alters the apparent influence of heritable dopamine tone on mesolimbic PENK and TH function.
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
Authors: Sakarya Onur , Kosik Kenneth S. , Oakley Todd H.
Published: January 2008

Motivation: Gene duplications and losses (GDLs) are important events in genome evolution. They result in expansion or contraction of gene families, with a likely role in phenotypic evolution. As more genomes become available and their annotations are improved, software programs capable of rapidly and accurately identifying the content of ancestral genomes and the timings of GDLs become necessary to understand the unique evolution of each lineage.

Results: We report EvolMAP, a new algorithm and software that utilizes a species tree-based gene clustering method to join all-to-all symmetrical similarity comparisons of multiple gene sets in order to infer the gene composition of multiple ancestral genomes. The algorithm further uses Dollo parsimony-based comparison of the inferred ancestral genes to pinpoint the timings of GDLs onto evolutionary intervals marked by speciation events. Using EvolMAP, first we analyzed the expansion of four families of G-protein coupled receptors (GPCRs) within animal lineages. Additional to demonstrating the unique expansion tree for each family, results also show that the ancestral eumetazoan genome contained many fewer GPCRs than modern animals, and these families expanded through concurrent lineage-specific duplications. Second, we analyzed the history of GDLs in mammalian genomes by comparing seven proteomes. In agreement with previous studies, we report that the mammalian gene family sizes have changed drastically through their evolution. Interestingly, although we identified a potential source of duplication for 75% of the gained genes, remaining 25% did not have clear-cut sources, revealing thousands of genes that have likely gained their distinct sequence identities within the descent of mammals.

Availability: Query server, source code and executable are available at http://kosik-web.mcdb.ucsb.edu/evolmap/index.htm

Contact:  kosik@lifesci.ucsb.edu, oakley@lifesci.ucsb.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
The ModFOLD server for the quality assessment of protein structural models
Authors: McGuffin Liam J.
Published: January 2008

Summary: The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.

Availability:  http://www.biocentre.rdg.ac.uk/bioinformatics/ModFOLD/

Contact:  l.j.mcguffin@reading.ac.uk
High Temperatures Activate Local Viral Multiplication and Cell-to-Cell Movement ofMelon necrotic spot virusbut Restrict Expression of Systemic Symptoms
Authors: Kido K. , Tanaka C. , Mochizuki T. , Kubota K. , Ohki T. , Ohnishi J. , Knight L. M. , Tsuda S.
Published: January 2008

The infection of melon plants by Melon necrotic spot virus (MNSV) and the development of necrotic disease symptoms are a seasonal occurrence in Japan, which take place between winter and early summer, but not during mid-summer. In this paper we investigate the effect of three different temperatures (15, 20, and 25°C) on the local and systemic expression of MNSV in melon plants. Previously, the incidence of plants expressing systemic symptoms caused by MNSV and other viruses was found to be greater at temperatures less than 20°C. In this study, our temperature-shift experiments support previous studies that found the expression of systemic symptoms increases as temperature falls from 25 to 20°C and decreases as temperature rises from 20 to 25°C. However, MNSV replication in melon cells and local viral movement within leaves following the inoculation of melon protoplasts or cotyledons were more frequent at 25°C than at 15 or 20°C.
Colonization ofPythium oligandrumin the Tomato Rhizosphere for Biological Control of Bacterial Wilt Disease Analyzed by Real-Time PCR and Confocal Laser-Scanning Microscopy
Authors: Takenaka Shigehito , Sekiguchi Hiroyuki , Nakaho Kazuhiro , Tojo Motoaki , Masunaka Akira , Takahashi Hideki
Published: January 2008

It recently has been reported that the non-plant-pathogenic oomycete Pythium oligandrum suppresses bacterial wilt caused by Ralstonia solanacearum in tomato. As one approach to determine disease-suppressive mechanisms of action, we analyzed the colonization of P. oligandrum in rhizospheres of tomato using real-time polymerase chain reaction (PCR) and confocal laser-scanning microscopy. The real-time PCR specifically quantified P. oligandrum in the tomato rhizosphere that is reliable over a range of 0.1 pg to 1 ng of P. oligandrum DNA from 25 mg dry weight of soil. Rhizosphere populations of P. oligandrum from tomato grown for 3 weeks in both unsterilized and sterilized field soils similarly increased with the initial application of at least 5 × 105oospores per plant. Confocal microscopic observation also showed that hyphal development was frequent on the root surface and some hyphae penetrated into root epidermis. However, rhizosphere population dynamics after transplanting into sterilized soil showed that the P. oligandrum population decreased with time after transplanting, particularly at the root tips, indicating that this biocontrol fungus is rhizosphere competent but does not actively spread along roots. Protection over the long term from root-infecting pathogens does not seem to involve direct competition. However, sparse rhizosphere colonization of P. oligandrum reduced the bacterial wilt as well as more extensive colonization, which did not reduce the rhizosphere population of R. solanacearum. These results suggest that competition for infection sites and nutrients in rhizosphere is not the primary biocontrol mechanism of bacterial wilt by P. oligandrum.
Identification of Quantitative Trait Loci for Resistance Against Verticillium longisporum in Oilseed Rape (Brassica napus)
Authors: Rygulla W. , Snowdon R. J. , Friedt W. , Happstadius I. , Cheung W. Y. , Chen D.
Published: January 2008

Verticillium longisporum is one of the major pathogens of oilseed rape (Brassica napus; genome AACC, 2n = 38) in Europe. Current European cultivars possess only a low level of resistance against V. longisporum, meaning that heavy infection can cause major yield losses. The aim of this study was to identify quantitative trait loci (QTL) for resistance against V. longisporum as a starting point for marker-assisted breeding of resistant cultivars. Resistance QTL were localized in a segregating oilseed rape population of 163 doubled haploid (DH) lines derived by microspore culture from the F1 of a cross between two B. napus breeding lines, one of which exhibited V. longisporum resistance derived by pedigree selection from a resynthesized B. napus genotype. A genetic map was constructed comprising 165 restriction fragment length polymorphism, 94 amplified fragment length polymorphism and 45 simple sequence repeats (SSR) markers covering a total of 1,739 cM on 19 linkage groups. Seedlings of the DH lines and parents were inoculated with V. longisporum isolates in four greenhouse experiments performed in Sweden during autumn 1999. In three of the experiments the DH lines were inoculated with a mixture of five isolates, while in the fourth experiment only one of the isolates was used. The intention was to simulate four different environments with variable disease pressure, while still maintaining uniform conditions in each environment to enable reliable disease scoring. The disease index (DI) was calculated by scoring symptoms on a total of 21 inoculated plants per line in comparison to 21 noninoculated plants per line. Using the composite interval mapping procedure a total of four different chromosome regions could be identified that showed significant QTL for resistance in more than one environment. Two major QTL regions were identified on the C-genome linkage groups N14 and N15, respectively; each of these QTL consistently exhibited significant effects on resistance in multiple environments. The presence of flanking markers for the respective QTL was associated with a significant reduction in DI in the inoculated DH lines.
The Basic Reproduction Number of Plant Pathogens: Matrix Approaches to Complex Dynamics
Authors: van den Bosch F. , McRoberts N. , van den Berg F. , Madden L. V.
Published: January 2008

The basic reproduction number, R0, is defined as the total number of infections arising from one newly infected individual introduced into a healthy (disease-free) host population. R0 is widely used in ecology and animal and human epidemiology, but has received far less attention in the plant pathology literature. Although the calculation of R0 in simple systems is straightforward, the calculation in complex situations is challenging. A very generic framework exists in the mathematical and biomathematical literature, which is difficult to interpret and apply in specific cases. In this paper we describe a special case of this general framework involving the use of matrix population models. Leading by example, we explain the existing mathematical literature on this subject in such a way that plant pathologists can apply the method for a wide range of pathosystems.
Hydrodynamic aspects of fish olfaction
Authors: Cox Jonathan P.L
Published: January 2008

Flow into and around the olfactory chamber of a fish determines how odorant from the fish's immediate environment is transported to the sensory surface (olfactory epithelium) lining the chamber. Diffusion times in water are long, even over comparatively short distances (millimetres). Therefore, transport from the external environment to the olfactory epithelium must be controlled by processes that rely on convection (i.e. the bulk flow of fluid). These include the beating of cilia lining the olfactory chamber and the relatively inexpensive pumping action of accessory sacs. Flow through the chamber may also be induced by an external flow. Flow over the olfactory epithelium appears to be laminar. Odorant transfer to the olfactory epithelium may be facilitated in several ways: if the olfactory organs are mounted on stalks that penetrate the boundary layer; by the steep velocity gradients generated by beating cilia; by devices that deflect flow into the olfactory chamber; by parallel arrays of olfactory lamellae; by mechanical agitation of the chamber (or olfactory stalks); and by vortices. Overall, however, our knowledge of the hydrodynamics of fish olfaction is far from complete. Several areas of future research are outlined.
Assistants to enlightenment: William Lewis, Alexander Chisholm and invisible technicians in the Industrial Revolution
Authors: Stewart Larry
Published: January 2008

Artisans, assistants and technicians in laboratories remain largely anonymous amid the rapidly expanding experimental practice of the eighteenth century. Where their activities can be traced, it is apparent that the binary conceptions of scholar and craftsman, of philosopher and practitioner, hardly held during the first industrial revolution. Who actually did the work in the early-modern laboratory remains an important issue. In the case explored in this article, William Lewis, chemical lecturer, and Josiah Wedgwood, pottery manufacturer, both employed the skill and expertise of Alexander Chisholm. Chisholm moved among industrial innovators, gathering the knowledge of workmen, and promoted the experimental method ultimately employed in the Wedgwood manufactory.
Coimmunopurification of Phosphorylated Bacterial- and Plant-Type Phosphoenolpyruvate Carboxylases with the Plastidial Pyruvate Dehydrogenase Complex from Developing Castor Oil Seeds
Authors: Uhrig R. Glen , O'Leary Brendan , Spang H. Elizabeth , MacDonald Justin A. , She Yi-Min , Plaxton William C.
Published: January 2008

The phosphoenolpyruvate carboxylase (PEPC) interactome of developing castor oil seed (COS; Ricinus communis) endosperm was assessed using coimmunopurification (co-IP) followed by proteomic analysis. Earlier studies suggested that immunologically unrelated 107-kD plant-type PEPCs (p107/PTPC) and 118-kD bacterial-type PEPCs (p118/BTPC) are subunits of an unusual 910-kD hetero-octameric class 2 PEPC complex of developing COS. The current results confirm that a tight physical interaction occurs between p118 and p107 because p118 quantitatively coimmunopurified with p107 following elution of COS extracts through an anti-p107-IgG immunoaffinity column. No PEPC activity or immunoreactive PEPC polypeptides were detected in the corresponding flow-through fractions. Although BTPCs lack the N-terminal phosphorylation motif characteristic of PTPCs, Pro-Q Diamond phosphoprotein staining, immunoblotting with phospho-serine (Ser)/threonine Akt substrate IgG, and phosphate-affinity PAGE established that coimmunopurified p118 was multiphosphorylated at unique Ser and/or threonine residues. Tandem mass spectrometric analysis of an endoproteinase Lys-C p118 peptide digest demonstrated that Ser-425 is subject to in vivo proline-directed phosphorylation. The co-IP of p118 with p107 did not appear to be influenced by their phosphorylation status. Because p118 phosphorylation was unchanged 48 h following elimination of photosynthate supply due to COS depodding, the signaling mechanisms responsible for photosynthate-dependent p107 phosphorylation differ from those controlling p118's in vivo phosphorylation. A 110-kD PTPC coimmunopurified with p118 and p107 when depodded COS was used. The plastidial pyruvate dehydrogenase complex (PDCpl) was identified as a novel PEPC interactor. Thus, a putative metabolon involving PEPC and PDCpl could function to channel carbon from phosphoenolpyruvate to acetyl-coenzyme A and/or to recycle CO2 from PDCpl to PEPC.
Characterization of Pea Aphid Resistance in Medicago truncatula
Authors: Gao Ling-Ling , Klingler John P. , Anderson Jonathan P. , Edwards Owain R. , Singh Karam B.
Published: January 2008

To achieve a thorough understanding of plant-aphid interactions, it is necessary to investigate in detail both the plant and insect side of the interaction. The pea aphid (PA; Acyrthosiphon pisum) has been selected by an international consortium as the model species for genetics and genomics studies, and the model legume Medicago truncatula is a host of this aphid. In this study, we identified resistance to PA in a M. truncatula line, ‘Jester’, with well-characterized resistance to a closely related aphid, the bluegreen aphid (BGA; Acyrthosiphon kondoi). The biology of resistance to the two aphid species shared similarity, with resistance in both cases occurring at the level of the phloem, requiring an intact plant and involving a combination of antixenosis, antibiosis, and plant tolerance. In addition, PA resistance cosegregated in ‘Jester’ with a single dominant gene for BGA resistance. These results raised the possibility that both resistances may be mediated by the same mechanism. This was not supported by the results of gene induction studies, and resistance induced by BGA had no effect on PA feeding. Moreover, different genetic backgrounds containing a BGA resistance gene from the same resistance donor differ in resistance to PA. These results suggest that distinct mechanisms are involved in resistance to these two aphid species. Resistance to PA and BGA in the same genetic background in M. truncatula makes this plant an attractive model for the study of both plant and aphid components of resistant and susceptible plant-aphid interactions.
Modulation of the Hormone Setting byRhodococcus fasciansResults in EctopicKNOXActivation in Arabidopsis
Authors: Depuydt Stephen , Doležal Karel , Van Lijsebettens Mieke , Moritz Thomas , Holsters Marcelle , Vereecke Danny
Published: January 2008

The biotrophic actinomycete Rhodococcus fascians has a profound impact on plant development and a common aspect of the symptomatology is the deformation of infected leaves. In Arabidopsis (Arabidopsis thaliana), the serrated leaf margins formed upon infection resemble the leaf phenotype of transgenic plants with ectopic expression of KNOTTED-like homeobox (KNOX) genes. Through transcript profiling, we demonstrate that class-I KNOX genes are transcribed in symptomatic leaves. Functional analysis revealed that BREVIPEDICELLUS/KNOTTED-LIKE1 and mainly SHOOT MERISTEMLESS were essential for the observed leaf dissection. However, these results also positioned the KNOX genes downstream in the signaling cascade triggered by R. fascians infection. The much faster activation of ARABIDOPSIS RESPONSE REGULATOR5 and the establishment of homeostatic and feedback mechanisms to control cytokinin (CK) levels support the overrepresentation of this hormone in infected plants due to the secretion by the pathogen, thereby placing the CK response high up in the cascade. Hormone measurements show a net decrease of tested CKs, indicating either that secretion by the bacterium and degradation by the plant are in balance, or, as suggested by the strong reaction of 35S:CKX plants, that other CKs are at play. At early time points of the interaction, activation of gibberellin 2-oxidase presumably installs a local hormonal setting favorable for meristematic activity that provokes leaf serrations. The results are discussed in the context of symptom development, evasion of plant defense, and the establishment of a specific niche by R. fascians.
Tris(Bipyridine) Ruthenium(II): An Efficient Detector of Excited Species Generated by Chemiluminescent Processes*
Authors: Grijalba Mercedes Toledo , Nantes Lseli Lourenço , Cilento Giuseppe , Quina Frank H.
Published: January 2008

In systems that are known to generate electronically excited species, the tris(bipyridine) ruthenium(II) cation, Ru(bpy)32+, ion is found to be an efficient, chemically stable, emissive energy acceptor for probing excited state formation. The chemiexcitation system employed was the thermolysis of tetramethyldioxetane. The system employed for enzymatic generation of excited species was the horseradish peroxidase‐catalyzed oxidation of appropriate substrates such as isobutyraldehyde, phenylacetal‐dehyde and indoleacetic acid. The versatility of the Ru(bpy)32+ ion is exemplified by its capacity to detect excited state formation in both chemical and enzymatic systems and in homogeneous and microheterogeneous media. The long wavelength emission and chemical stability of Ru(bpy)32+ facilitate quantitative studies of the sensi‐tization process. Possible routes leading to excitation of the Ru(bpy)32+ ion by the chemi‐ or enzyme‐generated excited species include electronic energy transfer and electron transfer‐induced luminescence.
Primary Quantum Yield and Volume Change of Phytochrome‐A Phototransformation Determined by Laser‐Induced Optoacoustic Spectroscopy*
Authors: Gensch Thomas , Churio M. Sandra , Braslavsky Silvia E. , Schaffner Kurt
Published: January 2008

The primary quantum yield, Φ1700, for the photoconver‐sion of the red‐absorbing form of phytochrome, Pr, to the set of primary intermediates, Ii700, was redetermined by laser‐induced optoacoustic spectroscopy at very low excitation laser fluences. The Ii700 value obtained is in the range of ΦPfr reported for the complete phototransformation Pr→ Pfr (J. M. Kelly and C. Lagarias, 1985, Biochemistry24, 4003–6010). An energy level of ca 150 kJ/ mol was found for the intermediates Ii700, i.e. ca 85% of the 0–0 level of Pr. Furthermore, a molecular expansion of 7 mL/mol (equivalent to 11 Å3/molecule) was determined for the Pr→ Ii700 transformation. It reflects the protein reorganization induced by the geometrical pho‐toisomerization of the chromophore, which results in changes of bonding interactions, in particular between the chromophore and its protein surrounding.
Determining Counterion Exchange Selectivities at Micelle Surfaces from Fluorescence Decay Measurements*
Authors: Okano Laura T. , Alonso Elena O. , Waissbluth L. Oscar L. , Quina Frank H.
Published: January 2008

A method for determining counterion exchange selectivities at the surface of ionic micelles from time‐resolved fluorescence quenching measurements is developed. This method is employed to determine selectivity coefficients for thiosulfate/chloride exchange at the surface of cati‐onic hexadecyltrimethylammonium chloride micelles (KTS/CI, = 1.1 ± 0.4) and for copper (II)/sodium exchange at the surface of anionic sodium dodecyl sulfate micelles (KCu/Na= 1.3 ± 0.3). In both cases, the selectivity coefficients are found to be independent of detergent and added salt concentration.
Formation of Nitrosyl Hemoglobin and Nitrotyrosine during Murine Leishmaniasis*
Authors: Giorgio Selma , Linares Edlaine , Capurro Margareth de L. , de Bianchi Antonio G. , Augusto Ohara
Published: January 2008

Peroxynitrite, the potent oxidant formed by the fast reaction between nitric oxide and superoxide anion, has been suggested to be the reactive intermediate responsible for some of the pathologies associated with an overproduction of nitric oxide. In this report, we demonstrate that both nitric oxide and peroxynitrite are formed during infection of the susceptible mouse strain, BALBk, with Leishmania amazonensis. Nitric oxide was detected as the nitrosyl hemoglobin complex by EPR analysis of blood drawn from mice at35, 64 and 148 days of infection. The levels of nitrosyl hemoglobin complex increased with disease evolution, which in the murine model used is characterized by skin lesions, ulceration and visceral‐ization of the parasites. Peroxynitrite formation was inferred from immunoreaction of homogenates obtained from footpad lesions in the late stages of the infection with anti‐nitrotyrosine antibody; homogenates from parasites drawn from the lesions were also immunoreactive, although to a lesser extent. Analysis of protein homogenates by gel electrophoresis and western blots suggests that peroxynitrite may degrade proteins in vivo, in addition to nitrating them. The results demonstrate that peroxynitrite is formed during murine leishmaniasis and may play a role in the aggravation of the disease.
Effect of Anions from the Hofmeister Series and Urea on the Binding of the Charged and Uncharged Forms of the Local Anesthetic Tetracaine to Zwitterionic Micelles*
Authors: Ferreira Graziela S. S. , Périgo Daniel M. , Politi Mario J. , Schreier Shirley
Published: January 2008

It is widely known that ions in the aqueous phase affect the binding of charged solutes to membranes. Here we report the effect of ions and urea on the interaction of both the charged and uncharged forms of the local anesthetic tetracaine (TTC, an aminoester derivative of ben‐zoic acid) to zwitterionic micelles. Binding was monitored by the increase in TTC fluorescence. Shifts in the emission wavelength maximum (δmax) indicated that the anesthetic was located in an environment of lower polarity. The neutral form of TTC bound to micelles to a larger extent than the protonated form, in agreement with results found for lipid bilayers (Boulanger, Leitch, Schreier and Smith, Can. J. Biochem. 58, 986–995, 1980). When ions from the Hofmeister series and urea were compared in their ability to affect the partitioning of the anesthetic, binding of both the charged and uncharged forms was found to increase upon addition of SO42– and CI− but was seen to decrease in the presence of SCN−, CIO4−‐ and urea. Solubility measurements revealed that the solubility of uncharged TTC increases in solutions containing the additives in the following order: SO42– < CI− < CIO4−‐ < dilute buffer < SCN− < urea. Spin label EPR spectra indicated that, except for CIO4−‐, the ions had little effect on micellar structure. Static light scattering measurements corroborated this result indicating a large increase in micellar molecular weight in the presence of CIO4−‐ and lesser increases for CI.‐ and SCN−. The results show that, besides affecting the binding of ionic species through an electrostatic mechanism, ions also act by altering water structure and, as a consequence, the water solubility and the tendency to partition into the less polar micellar environment of polar charged or uncharged small organic solutes such as the benzoic acid ester derivative. Moreover, evidence suggests that the ions bind directly to the zwitterionic polar groups of the micelles, leading to changes in structure and size.
Preparation and Evaluation of Arylazide‐Substituted Pyridine Adenine Dinucleotides for Photoaffinity Labeling Experiments
Authors: Liu Wenqiu , Gaines Michelle , Bao Rong , Clifford Jacquelynn , Li Yuzhou
Published: January 2008

Two pyridine‐modified NAD’analogs, 3–(3‐azido benzo‐yl) pyridine adenine dinucleotide 1 and N‐(3‐azido‐5‐car‐boxyl) phenyl nicotinamide adenine dinucleotide 2 have been prepared and evaluated for photoaffinity labeling experiments. The syntheses were accomplished via a mammalian NADase‐catalyzed base exchange reaction. The new NAD+ analogs retained the carbonyl or carhox‐amido functional group at the 3 position of the pyridine ring. The analog 1 is the first pyridine‐modified azido derivative of NAD+ that has shown coenzyme activity in a stereospecific hydride transfer reaction catalyzed by a dehydrogenase. Both NAD+ analogs have shown potential for the study of active sites of NAD+‐utilizing enzymes.
Accelerated Degradation of the D2 Protein of Photosystem II Under Ultraviolet Radiation
Authors: Jansen Marcel A. K. , Greenberg Bruce M. , Edelman Marvin , Mattoo Autar K. , Gaba Victor
Published: January 2008

The D2 protein of photosystem II is relatively stable in vivo under photosynthetic active radiation, but its degradation accelerates under UVB radiation. Little is known about accelerated D2 protein degradation. We characterized wavelength dependence and sensitivity toward photosystem II inhibitors. The in vivo D2 degradation spectrum resembles the pattern for the rapidly turning over D1 protein of photosystem II, with rates being maximal in the UVB region. We propose that D2 degradation, like D1 degradation, is activated by distinct photosensitizers in the UVB and visible regions of the spectrum. In both wavelength regions, photosystem II inhibitors that are known to be targeted to the D1 protein affect D2 degradation. This suggests that degradation of the two proteins is coupled, D2 degradation being influenced by events occurring at the QB niche on the D1 protein.
UVB Induces IL‐12 Transcription in Human Keratinocytes in vivo and in vitro
Authors: Enk Claes D. , Mahanty Siddhartha , Blauvelt Andrew , Katz Stephen I.
Published: January 2008

Human epidermal cells produce a wide range of cytokines, including those characteristic of Th2‐like responses such as interleukin (IL)‐4 and IL‐10. As well, keratinocytes have recently been shown to produce Th1‐like cytokines such as IL‐12. Exposure to UVB has profound effects on the skin and systemic immune system, which is in part mediated by secretion of tumor necrosis factor (TNF)‐α by epidermal cells. Because IL‐12 induces production of TNF‐α by certain cells of the immune system, we sought to determine whether UVB is an inducer of IL‐12 gene expression in epidermal cells. Human epidermal cells were exposed to UVB radiation in vivo, isolated by suction blister technique and trypsinization and transcription of the IL‐12 p35 and p40 chains was examined by RT‐PCR. We found the p35 chain of IL‐12 to be constitutively expressed and the p40 chain inducible by UVB irradiation. Because epidermis consists of a heterogenous cell population with distinct cytokine repertoires, we sought to determine the cellular source of the IL‐12 message after UVB exposure. After depleting UVB‐exposed epidermal cells for DR+ cells, no reduction in the IL‐12 activity was detected, suggesting that keratinocytes are a source of IL‐12 transcripts in UVB‐exposed human epidermis. This was supported by the up‐regulation of IL‐12 p40 transcripts in UV‐irradiated cultured keratinocytes that were devoid of DR+ cells. Up‐regulation of IL‐12 p40 gene expression by UVB as demonstrated here, taken together with the finding that keratinocytes also up‐regulate IL‐10 transcription, suggests that there is a complex interplay between Th1‐and Th2‐like epidermisderived cytokines following exposure to UVB.