A harmonized public resource of deeply sequenced diverse human genomes

Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.

Root pressure-volume curve traits capture rootstock drought tolerance

BACKGROUND AND AIMS

Living root tissues significantly constrain plant water uptake under drought, but we lack functional traits to feasibly screen diverse plants for variation in the drought responses of these tissues. Water stress causes roots to lose volume and turgor, which are crucial to root structure, hydraulics and growth. Thus, we hypothesized that root pressure-volume (p-v) curve traits, which quantify the effects of water potential on bulk root turgor and volume, would capture differences in rootstock drought tolerance.

METHODS

We used a greenhouse experiment to evaluate relationships between root p-v curve traits and gas exchange, whole-plant hydraulic conductance and biomass under drought for eight grapevine rootstocks that varied widely in drought performance in field trials (101-14, 110R, 420A, 5C, 140-Ru, 1103P, Ramsey and Riparia Gloire), grafted to the same scion variety (Vitis vinifera 'Chardonnay').

KEY RESULTS

The traits varied significantly across rootstocks, and droughted vines significantly reduced root turgor loss point (πtlp), osmotic potential at full hydration (πo) and capacitance (C), indicating that roots became less susceptible to turgor loss and volumetric shrinkage. Rootstocks that retained a greater root volume (i.e. a lower C) also maintained more gas exchange under drought. The rootstocks that previous field trials have classified as drought tolerant exhibited significantly lower πtlp, πo and C values in well-watered conditions, but significantly higher πo and πtlp values under water stress, than the varieties classified as drought sensitive.

CONCLUSIONS

These findings suggest that acclimation in root p-v curve traits improves gas exchange in persistently dry conditions, potentially through impacts on root hydraulics or root to shoot chemical signalling. However, retaining turgor and volume in previously unstressed roots, as these roots deplete wet soil to moderately negative water potentials, could be more important to drought performance in the deep, highly heterogenous rooting zones which grapevines develop under field conditions.

GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts

Summary

We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic hosts. This pipeline is available in the Genome Analysis Toolkit (GATK) as a suite of configurable tools that can report the microbial composition of DNA or RNA short-read sequencing samples and identify unknown sequences for downstream assembly of novel organisms. GATK PathSeq enables sample analysis in minutes at low cost. In addition, these tools are built with the GATK engine and Apache Spark framework, providing robust, rapid parallelization of read quality filtering, host subtraction and microbial alignment in workstation, cluster and cloud environments.

Availability and implementation

These tools are available as a part of the GATK at https://github.com/broadinstitute/gatk.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genetic characterization of Vitis germplasm collected from the southwestern US and Mexico to expedite Pierce's disease-resistance breeding

Pierce's disease (PD) limits the cultivation of Vitis vinifera grape cultivars in California, across the southern United States and into South America. Resistance has been well characterized in V. arizonica, and one resistance locus has been identified (PdR1). However, resistance is poorly characterized in most other grape species. We tested a wide range of Vitis species from the southwestern United States for resistance to PD and used nuclear and chloroplast markers to phenotypically and genetically select a diverse set of resistant accessions. Chloroplast SSR markers identified 11 maternal lineage lines within the set of 17 (14 new and three previously identified) PD resistant accessions. A total of 19 breeding populations (F1 and pseudo-BC1) were developed with the 14 PD resistant accessions, and a total of 705 seedlings were analyzed for PD resistance. Using a limited mapping approach, 12 SSR markers, linked to the PdR1 locus, were used to genotype the breeding populations and phenotypic data were analyzed. Nine accessions had a major resistance quantitative trait locus (QTL) within the genomic region containing PdR1. The phenotypic data for these three resistant accessions, ANU67, b41-13, and T03-16, did not associate with PdR1 linked markers, indicating that their resistance is located in other regions of the genome. These three accessions were identified as candidates for use in the development of framework maps with larger populations capable of detecting additional and unique loci for PD resistance breeding and the stacking of PD resistance genes.

Not quite type 1 or type 2, what now? Review of monogenic, mitochondrial, and syndromic diabetes

Diabetes mellitus is a heterogeneous group of conditions defined by resultant chronic hyperglycemia. Given the increasing prevalence of diabetes mellitus and the increasing understanding of genetic etiologies, we present a broad review of rare genetic forms of diabetes that have differing diagnostic and/or treatment implications from type 1 and type 2 diabetes. Advances in understanding the genotype-phenotype associations in these rare forms of diabetes offer clinically available examples of evolving precision medicine where defining the correct genetic etiology can radically alter treatment approaches. In this review, we focus on forms of monogenic diabetes, mitochondrial diabetes, and syndromic diabetes.

Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue

Ectopic heartbeats can trigger reentrant arrhythmias, leading to ventricular fibrillation and sudden cardiac death. Such events have been attributed to perturbed Ca²⁺ handling in cardiac myocytes leading to spontaneous Ca²⁺ release and delayed afterdepolarizations (DADs). However, the ways in which perturbation of specific molecular mechanisms alters the probability of ectopic beats is not understood. We present a multiscale model of cardiac tissue incorporating a biophysically detailed three-dimensional model of the ventricular myocyte. This model reproduces realistic Ca²⁺ waves and DADs driven by stochastic Ca²⁺ release channel (RyR) gating and is used to study mechanisms of DAD variability. In agreement with previous experimental and modeling studies, key factors influencing the distribution of DAD amplitude and timing include cytosolic and sarcoplasmic reticulum Ca²⁺ concentrations, inwardly rectifying potassium current (I_K1) density, and gap junction conductance. The cardiac tissue model is used to investigate how random RyR gating gives rise to probabilistic triggered activity in a one-dimensional myocyte tissue model. A novel spatial-average filtering method for estimating the probability of extreme (i.e. rare, high-amplitude) stochastic events from a limited set of spontaneous Ca²⁺ release profiles is presented. These events occur when randomly organized clusters of cells exhibit synchronized, high amplitude Ca²⁺ release flux. It is shown how reduced I_K1 density and gap junction coupling, as observed in heart failure, increase the probability of extreme DADs by multiple orders of magnitude. This method enables prediction of arrhythmia likelihood and its modulation by alterations of other cellular mechanisms.

Arrhythmias are electrical abnormalities of the heart that can degenerate into fibrillation, thus preventing normal heartbeats and leading to sudden cardiac death. The mechanisms leading to ventricular arrhythmias and the unexpected nature of sudden cardiac death are not fully understood. One hypothesis is that a group of cardiac myocytes, which generate contraction, spontaneously depolarize at precisely the same moment to excite the surrounding tissue. In individual myocytes, such misfires, known as delayed afterdepolarizations, are driven by random ion channel gating and thus stochastic in nature. While incidental afterdepolarizations in a large number of myocytes is highly improbable on any given beat, it may be feasible over a long time frame, thus explaining the unpredictability of arrhythmias. We developed a detailed model spanning the molecular, cellular, and tissue scales that realistically reproduces the mechanisms underlying this hypothesis. An efficient method is presented for estimating the probability of extremely rare delayed afterdepolarizations in tissue from a limited set of simulations. Furthermore, we demonstrate how altered tissue and ion channel properties in heart disease increase the risk of arrhythmia. This approach can be used generally to probe the effects of specific molecular mechanisms on the likelihood of rare delayed afterdepolarizations.

The Unilateral Swollen Lower Limb: Etiology, Investigation, and Management

The swollen lower limb, a common finding in routine clinical practice, is clinically challenging. The cause underlying this problem is often multifactorial, and its management may involve different specialties. It is important, though difficult, to avoid unnecessary and expensive investigations. The aim of this article is to provide an overview of the management of this problem by addressing the common causes, methods of assessment, diagnosis, and therapeutic options.

Superresolution modeling of calcium release in the heart

Stable calcium-induced calcium release (CICR) is critical for maintaining normal cellular contraction during cardiac excitation-contraction coupling. The fundamental element of CICR in the heart is the calcium (Ca²⁺) spark, which arises from a cluster of ryanodine receptors (RyR). Opening of these RyR clusters is triggered to produce a local, regenerative release of Ca²⁺ from the sarcoplasmic reticulum (SR). The Ca²⁺ leak out of the SR is an important process for cellular Ca²⁺ management, and it is critically influenced by spark fidelity, i.e., the probability that a spontaneous RyR opening triggers a Ca²⁺ spark. Here, we present a detailed, three-dimensional model of a cardiac Ca²⁺ release unit that incorporates diffusion, intracellular buffering systems, and stochastically gated ion channels. The model exhibits realistic Ca²⁺ sparks and robust Ca²⁺ spark termination across a wide range of geometries and conditions. Furthermore, the model captures the details of Ca²⁺ spark and nonspark-based SR Ca²⁺ leak, and it produces normal excitation-contraction coupling gain. We show that SR luminal Ca²⁺-dependent regulation of the RyR is not critical for spark termination, but it can explain the exponential rise in the SR Ca²⁺ leak-load relationship demonstrated in previous experimental work. Perturbations to subspace dimensions, which have been observed in experimental models of disease, strongly alter Ca²⁺ spark dynamics. In addition, we find that the structure of RyR clusters also influences Ca²⁺ release properties due to variations in inter-RyR coupling via local subspace Ca²⁺ concentration ([Ca²⁺]_ss). These results are illustrated for RyR clusters based on super-resolution stimulated emission depletion microscopy. Finally, we present a believed-novel approach by which the spark fidelity of a RyR cluster can be predicted from structural information of the cluster using the maximum eigenvalue of its adjacency matrix. These results provide critical insights into CICR dynamics in heart, under normal and pathological conditions.

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models

We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources for execution. We also present tools for simulating models encoded in the SBML and CellML model description languages, thus demonstrating how Galaxy's reproducible research features can be leveraged by existing technologies. Finally, we demonstrate how the Galaxy workflow editor can be used to compose integrative models from constituent submodules. This work represents an important novel approach, to our knowledge, to making computational simulations more accessible to the broader scientific community.

Real-time detection of an extreme scattering event: Constraints on Galactic plasma lenses

Extreme scattering events (ESEs) are distinctive fluctuations in the brightness of astronomical radio sources caused by occulting plasma lenses in the interstellar medium. The inferred plasma pressures of the lenses are ~10(3) times the ambient pressure, challenging our understanding of gas conditions in the Milky Way. Using a new survey technique, we discovered an ESE while it was in progress. Here we report radio and optical follow-up observations. Modeling of the radio data demonstrates that the lensing structure is a density enhancement and the lens is diverging, ruling out one of two competing physical models. Our technique will uncover many more ESEs, addressing a long-standing mystery of the small-scale gas structure of our Galaxy.

Modeling calcium regulation of contraction, energetics, signaling, and transcription in the cardiac myocyte

Calcium (Ca(2+)) plays many important regulatory roles in cardiac muscle cells. In the initial phase of the action potential, influx of Ca(2+) through sarcolemmal voltage-gated L-type Ca(2+) channels (LCCs) acts as a feed-forward signal that triggers a large release of Ca(2+) from the junctional sarcoplasmic reticulum (SR). This Ca(2+) drives heart muscle contraction and pumping of blood in a process known as excitation-contraction coupling (ECC). Triggered and released Ca(2+) also feed back to inactivate LCCs, attenuating the triggered Ca(2+) signal once release has been achieved. The process of ECC consumes large amounts of ATP. It is now clear that in a process known as excitation-energetics coupling, Ca(2+) signals exert beat-to-beat regulation of mitochondrial ATP production that closely couples energy production with demand. This occurs through transport of Ca(2+) into mitochondria, where it regulates enzymes of the tricarboxylic acid cycle. In excitation-signaling coupling, Ca(2+) activates a number of signaling pathways in a feed-forward manner. Through effects on their target proteins, these interconnected pathways regulate Ca(2+) signals in complex ways to control electrical excitability and contractility of heart muscle. In a process known as excitation-transcription coupling, Ca(2+) acting primarily through signal transduction pathways also regulates the process of gene transcription. Because of these diverse and complex roles, experimentally based mechanistic computational models are proving to be very useful for understanding Ca(2+) signaling in the cardiac myocyte.

On the Adjacency Matrix of RyR2 Cluster Structures

In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2). Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1) of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED) microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.

Coenzyme Q10 and immunity: A case report and new implications for treatment of recurrent infections in metabolic diseases

Coenzyme Q10 (CoQ10) deficiency can manifest diversely, from isolated myopathy to multisystem involvement. Immune dysregulation has not been reported as a feature of the disease. We report a four-year old girl with failure to thrive, recurrent infections, developmental delay with hypotonia, and CoQ10 deficiency with impaired immune function, which improved after CoQ10 and immunoglobulin replacement therapy. Immune dysfunction in CoQ10 deficiency should be considered and treated appropriately.

Genetic dissection of agronomic traits within a segregating population of breeding table grapes

Grapes (Vitis vinifera) are of great economic importance worldwide. We genetically dissected a table grape breeding population, using hidden Markov models (HMM) applied to quantitative trait locus (QTL) analyses. We evaluated and dissected the following traits: total number of clusters, leaf score, peduncle length, cluster length, number of berries, weight of 10 berries, average seed number, nature of seeds, berry skin color, soluble solids, titratable acidity, and berry anthocyanin. A consensus map was developed with 255 SSR molecular markers, ordered into 19 linkage groups. The observed length of this map was 1871.4 cM, with 89.7% coverage. QTL were identified using interval mapping with HMM. The number of QTL detected for each trait varied between 1 and 8, reflecting the quantitative nature of these traits. The percentage of variation explained by these QTL was small, varying between 1.56 and 11.98%. We found QTL across linkage groups 2, 7, 12, 13, and 14 for berry anthocyanin.

Soil Temperature Effects on the Interaction of Grape Rootstocks and Plant-parasitic Nematodes

Resistance to Meloidogyne spp. in commonly used resistant grape rootstocks is slightly compromised at soil temperatures above 27°C. Newly released UCD-GRN series rootstocks, which have broad nematode resistance, exhibit trace infections by Meloidogyne spp. at elevated temperature. Pathotypes of M. incognita and M. arenaria that are virulent on 'Harmony' rootstock, as well as M. incognita Race 3, which is avirulent on 'Harmony', failed to produce egg masses on the UCD-GRN series rootstocks and other resistant selections at 24°C. At 27°C and above, there was increased nematode galling and egg mass production; at 30°C, egg mass production levels of M. incognita Race 3 on 'Harmony' were up to 12% of that on susceptible 'Colombard' while reproduction of the virulent pathotypes on the UCD-GRN series was less than 5% of that on 'Colombard'. Resistance of several of the parental genotypes of the UCD-GRN rootstock series was slightly compromised at soil temperatures of 30°C and above; however, others maintained their resistance to even the virulent M. arenaria pathotype A at high temperatures. Effects of high temperature on resistance to Xiphinema index could not be assessed because of temperature sensitivity of the nematodes while resistance to Mesocriconema xenoplax was not compromised at high soil temperature. Resistance to Meloidogyne spp. in the UCD-GRN series rootstocks was not compromised when plants and nematodes were subjected to cyclical high and low temperature conditions, indicating that once initiated, the resistance mechanism is not reversed.

Resistance of Grape Rootstocks to Plant-parasitic Nematodes

Candidate grape rootstocks were selected through a rigorous screening program initiated with important sources of resistance to Meloidogyne pathotypes and to Xiphinema index in Muscadinia rotundifolia and Vitis species native to North America. Based on their rooting capability and horticultural characteristics, 200 candidates were selected from 5,000 progeny of multiple crosses between commercial grape rootstocks and wild grape species that exhibited resistance to nematodes. After a 15-year screening process, 13 selections emerged with either almost complete or complete combined resistance to M. incognita Race 3, M. incognita pathotype Harmony C, M. arenaria pathotype Harmony A, and X. index, important nematode pests of grapevines. Durability of this broad resistance was tested by challenging the selections with the target nematodes in combination and with the target nematodes in combinations with species not included in the screening process. Durability of resistance of the candidate rootstocks was also tested by exposure to the nematode communities of infested field soils from different locations. Breadth of resistance was determined on the basis of their host status to non-target nematodes, including Mesocriconema xenoplax, Pratylenchus vulnus, Tylenchulus semipenetrans and Paratylenchus hamatus. After a total of 204 separate trials, the rootstocks were released to the grape industry as UCD GRN1, UCD GRN2, UCD GRN3, UCD GRN4, and UCD GRN5. We provide a compilation of current knowledge of the host status of these five newly released rootstocks and of 27 other rootstock cultivars to plant-parasitic nematodes.

Direct measurement of group delay dispersion in metamagnetics for ultrafast pulse shaping

In this paper, we explore the use of magnetic resonant metamaterials, so called metamagnetics, as dispersive elements for optical pulse shaping. We measure both positive and negative group delay dispersion (GDD) values in a metamagnetic material using the multiphoton interference phase scan (MIIPS) technique and show pulse temporal profiles numerically. The results are compared with finite element models. These GDD properties of metamagnetics, along with previously shown tunability and loss control with gain media, enable their use in ultrashort pulse optical applications.

A framework genetic map of Muscadinia rotundifolia

This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n = 20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879 cM on 18 chromosomes. The average distance between the markers was 4.1 cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841 cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088 cM, which represented 66 % of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.

Balloon-expandable stent deformation during deployment into the iliac artery: a procedural complication managed conservatively

The management of aortoiliac insufficiency has been improved considerably since the introduction of balloon-expandable stents in 1991. Although numerous studies have shown the safety and efficacy of balloon-expandable iliac artery stent placement, the procedure is not without potential complication. We report here a very unusual case of iliac artery stenting being complicated by deformation and elongation of the stent following balloon rupture at initial deployment with retention of the distal balloon marker and our successful approach to subsequent management with combined acetylsalicylic acid and clopidogrel. In conclusion, this conservative approach may be an alternative treatment of a partially deployed aortoiliac stent with a retained foreign body when further intervention is considered to be of high risk.

Evaluation of genetic dissimilarity in a segregating wine grape population

This study examined the genetic diversity present in a population obtained by crossing two very distinctive varieties of wine grapes (142 progeny from a Riesling x Cabernet Sauvignon cross, including both parents, created at the University of California). The following list of morphological characters were evaluated and found to segregate in this population: cluster weight, cluster length, presence or absence of cluster wings, cluster wing length, number of berries, cluster density (CD), and berry weight. The following juice parameters were also measured: °Brix, pH, total phenolics, and titratable acidity. Genetic diversity within this population was estimated through multivariate methods that utilized the Gower index of dissimilarity and UPGMA clustering. The correlations between traits and relative contribution of each variable were also compared. Eleven groups of progeny were distinguished into categories with low, intermediate and high values for cluster weight and cluster density, and low and high values for total phenolics. An inverse correlation was detected between the variables related to production and those related to the quality of the fruit. Principal components analysis demonstrated that all variables examined in this study are important for the correct discrimination of optimal genotypes in this population. These statistical tools can be used to select individuals with the greatest potential for producing high-quality wines.

Fine-scale genetic mapping of two Pierce's disease resistance loci and a major segregation distortion region on chromosome 14 of grape

A refined genetic map of chromosome 14, which contains the Pierce's disease (PD) resistance locus, was created from three grape mapping populations. The source of PD resistance in these populations was b43-17, a male form of Vitis arizonica Engelm. that is homozygous resistant. The resistance locus segregated as a single dominant gene and mapped as PdR1a in the F1 selection F8909-17 (9621 population) and as PdR1b in a sibling F1 selection F8909-08 (04190 population). These two full sibs inherited either allele of the Pierce's disease resistance locus from the b43-17 parent, which is homozygous at that locus. The 9621 population consisted of 425 progeny and PdR1a mapped between markers VvCh14-56/VvCh14-02 and UDV095 within a 0.6 cM genetic distance. The 04190 population consisted of 361 progeny and PdR1b mapped between markers VvCh14-02 and UDV095/VvCh14-10 within a 0.4 cM distance. Many of the markers present on chromosome 14 were distorted with an excess of female alleles in the 04190 and 04373 population (developed from a cross of V. vinifera L. F2-35 x b43-17) indicating that potential gametophytic factors are present in this region. Common markers from this region within the 9621 population were not distorted except Scu15. When these markers were compared to V. vinifera-based maps of chromosome 14 they were also distorted suggesting the involvement of gametophytic factors, and prompting the identification of this region as Vitis-segregation distortion region 1 (V-SDR1). The refined genetic maps developed from this study can be used to identify and clone genes that confer resistance to Pierce's disease.

Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross

Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4-8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F(1) progeny from a cross of D8909-15 x F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population.

Femtosecond micromachining in transparent bulk materials using an anamorphic lens

A unique anamorphic lens design was applied to a circular 780nm femtosecond laser pulse to transform it into an elliptically shaped beam at focus. This lens was developed to give an alternative method of micromachining bulk transparent materials. The challenge for femtosecond laser processing is to control the nonlinear affect of self-focusing, which can occur when using a fast f-number lens. Once the focused spot is dominated by self-focusing the predicted focused beam becomes a filament inside the bulk, which is an undesirable effect. The anamorphic lens resolves this self-focusing by increasing the numerical aperture (NA) and employing an elliptical beam shape. The anamorphic lens was designed to furnish a 2.5mum by 190mum line at focus. Provided the pulse energy is high enough, transparent bulk material will be damaged with a single femtosecond laser pulse. Damage in this text refers to visual change in the index of refraction as observed under an optical microscope. Using this elliptical shape (or line), grating structures were micro-machined on the surface of SiC bulk transparent substrate. SiC was chosen because it is known for its micromachining difficulty and its crystalline structure. From the lack of self-focusing and using energy that is just above the damage threshold the focused line beam generated from the anamorphic lens grating structures produced a line shape nearly identical to the geometrical approximation. In this paper we discuss a new method of writing gratings (or other types of structures) in bulk transparent materials using a single femtosecond laser pulse. We will investigate the grating structures visually (inspected under an optical microscope) and also by use of an atomic force microscopy (AFM). In addition, we test the grating diffraction efficiency (DE) as a function of grating spacing, d.

Visual documentation of ovine pituitary gland development with magnetic resonance imaging following zeranol treatment

The objective of the current study was to determine whether magnetic resonance imaging (MRI) could be successfully utilized to document the effect of an oestrogenic anabolic agent on pituitary gland growth. The experimental animals consisted of two 1/2 sibling Suffolk wethers (castrated rams), which received either no implant (control, n = 1) or a 24 mg zeranol implant at day 0 and day 42 (zeranol; n = 1). Animals were anaesthetized with propofol and supported with oxygen during the MRI procedure. A mobile MRI unit with a 0.5 tesla (T), superconducting magnet was used to obtain 3 mm thick, non-contrast enhanced, T1-weighted (TR 500-600, TE25) sagittal, transverse and dorsal images of the pituitary gland. Sagittal images were recorded only when the mesencephalic aqueduct and infundibulum were distinctly visible in the same image. Pituitary glands were imaged at 14-day intervals for 70 days to determine if and when the anabolic effects of zeranol on pituitary gland growth could be visualized using MRI techniques. Three separate measurements of the pituitary gland dimensions made with the on-screen cursor were averaged to calculate pituitary gland dimensions and volume. A computer-assisted image analysis system and laser film images were used to determine pituitary gland area. Increases in pituitary gland volume for control and zeranol-treated animals were evident within 14 days, and by the end of the 70-day study, the increase in pituitary volume for the zeranol-treated animal was three times greater than that of the control animal. Overall, our results indicate that MRI technology can be successfully used to document the development of the pituitary gland in vivo. Application of knowledge gained from this novel approach to study the growth, development and function of endocrine glands over time, and within the same animal, will enhance human and animal endocrine diagnostic procedures.

Refined mapping of the Pierce's disease resistance locus, PdR1, and Sex on an extended genetic map of Vitis rupestris x V. arizonica

A framework genetic map based on genomic DNA-derived SSR, EST-derived SSR, EST-STS and EST-RFLP markers was developed using 181 genotypes generated from D8909-15 (female) x F8909-17 (male), the '9621' population. Both parents are half siblings with a common female parent, Vitis rupestris 'A. de Serres', and different male parents (forms of V. arizonica). A total of 542 markers were tested, and 237 of them were polymorphic for the female and male parents. The female map was developed with 159 mapped markers covering 865.0 cM with an average marker distance of 5.4 cM in 18 linkage groups. The male map was constructed with 158 mapped molecular markers covering 1055.0 cM with an average distance of 6.7 cM in 19 linkage groups. The consensus '9621' map covered 1154.0 cM with 210 mapped molecular markers in 19 linkage groups, with average distance of 5.5 cM. Ninety-four of the 210 markers on the consensus map were new. The 'Sex' expression locus segregated as single major gene was mapped to linkage group 2 on the consensus and the male map. PdR1, a major gene for resistance to Pierce's disease, caused by the bacterium Xylella fastidiosa, was mapped to the linkage group 14 between markers VMCNg3h8 and VVIN64, located 4.3 and 2.7 cM away from PdR1, respectively. Differences in segregation distortion of markers were also compared between parents, and three clusters of skewed markers were observed on linkage groups 6, 7 and 14.

Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) x Riparia Gloire (Vitis riparia)

The first genetic linkage map of grape derived from rootstock parents was constructed using 188 progeny from a cross of Ramsey (Vitis champinii) x Riparia Gloire (V. riparia). Of 354 simple sequence repeat markers tested, 205 were polymorphic for at least one parent, and 57.6% were fully informative. Maps of Ramsey, Riparia Gloire, and the F1 population were created using JoinMap software, following a pseudotestcross strategy. The set of 205 SSRs allowed for the identification of all 19 Vitis linkage groups (2n=38), with a total combined map length of 1,304.7 cM, averaging 6.8 cM between markers. The maternal map consists of 172 markers aligned into 19 linkage groups (1,244.9 cM) while 126 markers on the paternal map cover 18 linkage groups (1,095.5 cM). The expected genome coverage is over 92%. Segregation distortion occurred in the Ramsey, Riparia Gloire, and consensus maps for 10, 13, and 16% of the markers, respectively. These distorted markers clustered primarily on the linkage groups 3, 5, 14 and 17. No genome-wide difference in recombination rate was observed between Ramsey and Riparia Gloire based on 315 common marker intervals. Fifty-four new Vitis-EST-derived SSR markers were mapped, and were distributed evenly across the genome on 16 of the 19 linkage groups. These dense linkage maps of two phenotypically diverse North American Vitis species are valuable tools for studying the genetics of many rootstock traits including nematode resistance, lime and salt tolerance, and ability to induce vigor.

Identification and molecular mapping of PdR1, a primary resistance gene to Pierce's disease in Vitis

A major quantitative trait locus (QTL) controlling resistance to Pierce's disease (PD) of grape, caused by the bacterium Xylella fastidiosa (Xf), was identified on a Vitis linkage map and denoted as 'Pierce's disease resistance 1' (PdR1). Placement of the locus was accomplished by evaluating a family of full-sib progeny from a cross of two PD-resistant interspecific hybrids with resistance inherited from Vitis arizonica. Resistance was measured under greenhouse conditions by direct quantification of Xf numbers in stem tissues as well as by evaluation of disease symptoms based on leaf scorch and a cane maturation index (CMI). A large QTL (LOD 17.2) accounting for 72% of the phenotypic variance in bacterial numbers was localized to linkage group 14 of the male parent F8909-17. The approximate 95% confidence interval around the QTL peak extended 5.7 cM when using composite interval mapping. The other disease evaluation methods (leaf scorch and CMI, respectively) placed the resistance QTL to the same region on linkage group 14, although at wider 95% confidence intervals (6.0 and 7.5 cM), lower peak LOD scores (11.9 and 7.7) and accounting for less phenotypic variance (59 and 42%). This is the first report of an Xf resistance QTL mapped in any crop species. The relevance of the markers located in the region spanning the QTL will be discussed, addressing their usefulness for the development of PD-resistant grape cultivars.

The continued value of central histopathological review of testicular tumours

AIMS

Central histopathological review of testicular tumours prior to definitive treatment can have an important impact on patient management. This study was designed to assess the continued value of central review in the light of increasing subspecialization and increased numbers of consultant histopathologists.

MATERIALS AND RESULTS

The original and review reports of 291 testicular cancer specimens from 1998 to 2002 were analysed, looking particularly at major diagnosis, vascular invasion and the tumour elements within non-seminomatous germ cell tumours (NSGCT). When a diagnosis was altered any effect on subsequent patient management was assessed. There was a discrepancy in tumour type in 11 cases (4%) compared with 6% in 1992-1997. The commonest change was from seminoma to NSGCT or combined germ cell tumour (5/11). There was also diagnostic difficulty with spermatocytic seminoma (3/11). The clinical management of all 11 cases was influenced as a result of the review diagnosis. Discrepancies in vascular invasion were noted in 13 of the 126 NSGCTs (10%) compared with 20% in 1992-1997. Differences in NSGCT tumour elements, though clinically less important, were frequent in both groups.

CONCLUSIONS

There continues to be a small number of significant and clinically important errors identified following central histopathological review of testicular tumours. This study highlights the value of central review and supports its continued practice in the management of testicular tumours.

Inheritance of resistance to Xylella fastidiosa within a Vitis rupestris x Vitis arizonica hybrid population

The inheritance of resistance to Xylella fastidiosa (Xf), the bacterium which causes Pierce's disease (PD) in grapevines, was evaluated within a factorial mating design consisting of 16 full-sib families with resistance derived from Vitis arizonica interspecific hybrids. Measurements of disease progression under greenhouse conditions were based on quantitative assessment of Xf populations in stem tissues and on three phenotypic scores: leaf scorch, a cane maturation index (CMI) and an index that incorporated shoot stunting into the cane maturation index (CMSSI). Measurement of bacterial populations yielded the highest broad-sense heritability for resistance on a genotype mean basis (0.97), indicating that this measure of resistance was the least effected by environmental variation. Narrow-sense heritability of PD resistance was moderately high and measured 0.52, 0.60, 0.63 and 0.37 for Xf populations, CMI scores, CMSSI scores and leaf scorch values, respectively. Complex segregation analysis using the computer program Statistical Analysis for Genetic Epidemiology (SAGE: ) strongly indicated the existence of a major gene for PD resistance, which accounted for 91% of the total genetic variance. Conversion of the quantitative data into qualitative resistance levels and evaluation via a chi-square analysis showed that 15 of the 16 families segregated in accordance with a single gene hypothesis with a dominant allele controlling PD resistance. These data indicate that the trait should be relatively easy to pass on from parents to progeny in a breeding program for the development of PD-resistant grape cultivars, particularly when selection is based on cane maturation scores or stem Xf populations.

Vitis Resistance to Pierce's Disease Is Characterized by Differential Xylella fastidiosa Populations in Stems and Leaves

ABSTRACT The pattern of Xylella fastidiosa infection in resistant and susceptible grapevines representing a diverse selection of Vitis spp. was characterized through measurements of X. fastidiosa bacterial movement and accumulation in artificially inoculated greenhouse-grown grapevines. A double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) was optimized for quantification of X. fastidiosa populations and tested on known amounts of X. fastidiosa added to grape tissue extracts. Predicted versus known X. fastidiosa concentrations proved to be highly correlated (R(2) = 0.99). Populations of X. fastidiosa in stem internode, stem node, petiole, and leaf blade samples from the genotypes in this study were measured at 12 weeks postinoculation using the optimized ELISA procedure. Samples from each plant part were taken at eight positions along the inoculated shoots. Systemic infection was detected in both susceptible and resistant genotypes. Resistant genotypes were characterized by significant differences in X. fastidiosa populations between stem internodes and leaves (1.0 x 10(6) and 1.1 x 10(7) cells/g of sample, respectively). In contrast, the susceptible genotypes were characterized by high mean X. fastidiosa populations in both stems and leaves (5.6 x 10(7) and 4.8 x 10(7) cells/g, respectively) the latter of which were not significantly different from the resistant genotypes. A high correlation (R(2) = 0.97) between stem X. fastidiosa numbers to previously characterized field Pierce's disease (PD) performance indicates that the quantitative ELISA measurements of X. fastidiosa in greenhouse-grown grapevines should be a useful tool for predicting PD resistance under field conditions.

Development and Comparison of Symptom Indices for Quantifying Grapevine Resistance to Pierce's Disease

ABSTRACT Symptoms of Pierce's disease (PD) were assessed under greenhouse conditions on field-resistant and field-susceptible grapevines in order to characterize the PD resistance phenotype in the genus Vitis. A cane maturation index (CMI) was developed to quantify the green-islands symptom, which was measured at 12 weeks post-bacterial inoculation, along with leaf scorch and percentage of xylem vessels blocked by occlusions. Canes of resistant genotypes matured normally and had a significantly lower CMI score of 0.9 (on a 0-to-6 scale) compared with 5.1 for the susceptible genotypes. The CMI scoring method had a high correlation (R(2) = 0.91) with previously characterized field performance, whereas leaf scorch had only a moderate correlation (R(2) = 0.51) with field performance. Average scorched area on leaves of the susceptible and resistant genotypes was 80 and 48%, respectively, demonstrating that leaf scorch can be extensive in resistant genotypes under the presented screening conditions, and suggesting that systemic infection can occur in all evaluated genotypes. Occlusions within both stem and petiole vessels were composed principally of tyloses and were significantly higher in petioles than in stems of either resistant or susceptible backgrounds. Susceptible genotypes displayed a higher level of stem tylose occlusions relative to resistant genotypes, but correlation to field performance was low (R(2) = 0.13). Ease of use and high correlation to field performance makes CMI scoring a better choice for PD resistance evaluations relative to other phenotypic symptom assessments.

A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica

A genetic linkage map of grape was constructed, utilizing 116 progeny derived from a cross of two Vitis rupestris x V. arizonica interspecific hybrids, using the pseudo-testcross strategy. A total of 475 DNA markers-410 amplified fragment length polymorphism, 24 inter-simple sequence repeat, 32 random amplified polymorphic DNA, and nine simple sequence repeat markers-were used to construct the parental maps. Markers segregating 1:1 were used to construct parental framework maps with confidence levels >90% with the Plant Genome Research Initiative mapping program. In the maternal (D8909-15) map, 105 framework markers and 55 accessory markers were ordered in 17 linkage groups (756 cM). The paternal (F8909-17) map had 111 framework markers and 33 accessory markers ordered in 19 linkage groups (1,082 cM). One hundred eighty-one markers segregating 3:1 were used to connect the two parental maps' parents. This moderately dense map will be useful for the initial mapping of genes and/or QTL for resistance to the dagger nematode, Xiphinema index, and Xylella fastidiosa, the bacterial causal agent of Pierce's disease.

Size of hippocampal pyramidal neurons in schizophrenia

BACKGROUND

Meta-analyses of hippocampal size have indicated that this structure is smaller in schizophrenia. This could reflect a reduction in the size of constituent neurons or a reduced number of neurons.

AIMS

To measure the size of hippocampal pyramidal neurons in the brains of people with and without schizophrenia.

METHOD

Pyramidal neuron size in hippocampal subfields was estimated stereologically from sections taken at 5 mm intervals throughout the whole length of right and left hippocampi from the brains of 13 people with schizophrenia and 16 controls. Results were assessed using repeated-measures analysis of covariance looking for a main effect of diagnosis and gender, and interactions of these with side.

RESULTS

We were unable to detect significant differences related to diagnosis, gender or side for any hippocampal subfield for this series of cases.

CONCLUSIONS

For this series of brains, hippocampal cell size is unchanged in schizophrenia.

Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

A postmortem study of the mediodorsal nucleus of the thalamus in schizophrenia

Four studies have reported that the mediodorsal nucleus of the thalamus (MD) is smaller and contains fewer neurons in schizophrenia. The MD is a key node in a circuit proposed to be dysfunctional in the disorder. However, one study did not find a MD volume loss in schizophrenia, and all the studies to date are relatively small. Given the importance of establishing unequivocally the presence of MD pathology, we have carried out a study of the volume and number of neurons in the left and right MD in 21 patients with schizophrenia and 27 healthy comparison subjects. We also measured the size of MD neurons, and estimated total thalamic volume. We found no difference in the volume of the MD, the number of MD neurons, or the size of MD neurons in either hemisphere in schizophrenia. Neither was total thalamic volume altered. There are no obvious methodological or clinical factors to explain our failure to replicate the finding of MD involvement in schizophrenia. Hence our negative observations, in the largest sample yet investigated, cast doubt on the robustness and/or the generalisability of MD neuropathology in schizophrenia.

Larval debridement therapy: a cost-effective alternative to hydrogel in necrotic venous ulcers: a randomized trial

Background

Evidence for the effectiveness of larval debridement therapy (LDT) in necrotic wounds has hitherto been the anecdotal results of enthusiasts. The aim of this study was to compare the cost and effectiveness of LDT with standard hydrogel treatment of necrotic venous ulcers.

Methods

Patients with sloughy venous ulcers were randomized to either standard hydrogel dressings (Intrasite gel) (group 1) or LDT (group 2). All patients were reviewed every 72 h until effective debridement had occurred, for a maximum of 1 month. The outcome measure used for effectiveness was whether or not desloughing occurred and time to deslough. The measures of cost were the cost of nursing time, dressing costs, and costs of larvae and hydrogel required to achieve healing in 1 month's treatment.

Results

Twelve patients were randomized. Ulcers in all patients receiving LDT (group 2) desloughed within two applications of larva therapy. All of these patients were treated subsequently with four-layer bandaging and all healed within 4 months. Ulcers in only two patients in group 1 desloughed completely within 1 month. One of the patients in whom hydrogel had failed at 1 month was changed to LDT and the ulcer desloughed with one application. Taking into account the cost of a vial of larvae (£58), the overall median cost of treatment in group 1 was greater than that in group 2 (£136·23 (range 63·89–319·30) versus £78·64 (range 73·49–£92·36)).

Conclusion

LDT is more effective and significantly less expensive than hydrogel in the debridement of sloughy venous ulcers. While a larger randomized controlled study should be performed to confirm these observations, LDT appears to be a cost-effective alternative to hydrogel.

Ecological and genetic aspects of grape phylloxera Daktulosphaira vitifoliae (Hemiptera: Phylloxeridae) performance on rootstock hosts

Performance and genetic variability of clonal lineages derived from one Californian and one German population of grape phylloxera, Daktulosphaira vitifoliae Fitch were studied on their natal grape rootstock host and on three novel hosts over four generations in an aseptic dual culture system. The ability of D. vitifoliae to adapt to new hosts was measured by changes in fitness (rm) over four generations. The performance of a given clonal lineage changed over successive generations, depending upon the host plant and the phylloxera group. Analysis of amplified fragment length polymorphism-polymerase chain reaction (AFLP-PCR) banding patterns from 40 individual parthenogenetic D. vitifoliae revealed equal levels of genetic variation both among the four clonal lineages analysed and within the different generations of one lineage. Analysis of molecular variance (AMOVA) showed no significant differences between the D. vitifoliae lineages reared on different host plants, nor was a correlation between host performance and genotype found.

A Technique for Screening Grape Germplasm for Resistance to Meloidogyne incognita

A technique to evaluate the root-knot nematode resistance of grape seedlings was developed. Seedlings of rootstock crosses and nematode-susceptible Vitis vinifera cvs. Colombard and Carignane were inoculated with Meloidogyne incognita juveniles. Reproduction of nematodes on individual plants was measured by counting the number of egg masses stained with eosin and the number of eggs present. Egg mass counts were highly correlated with egg counts. Resistant and susceptible cultivars could be clearly distinguished by the number of egg masses produced on vegetatively propagated cuttings. It is concluded that egg mass counting can substitute for the more laborious and time-consuming methods of counting nematode eggs or juveniles in the evaluation of root-knot nematode resistance in Vitis.

Synthesis of a novel C-10 spiro-epoxide of paclitaxel

New analogues of paclitaxel (1a, active constituent of Taxol) were synthesized containing an epoxide at the C-10 position. The introduction of the epoxide was carried out by selective removal of the C10-acetate followed by protection of the C2'- and C7-hydroxyl groups. After oxidation to yield a ketone at the C10-position, this intermediate was reacted with dimethylsulfonium ylide. Deprotection and further manipulations provide the C10-spiro epoxide of paclitaxel (1b) and the corresponding C7-MOM ether (1c).

Simple sequence repeat analysis of a clonally propagated species: a tool for managing a grape germplasm collection

The USDA germplasm repositories help to preserve the genetic variability of important crop species by collecting and maintaining representative cultivars and related germplasm. Simple sequence repeat markers with high allelic diversity were used to type 41 grapevines from 40 accessions. All vines were either seedless table grape cultivars or cultivars with names similar to table grape cultivars. The proportion of shared alleles was selected as the most appropriate statistical measure of genetic distance for this population. In conjunction with morphological traits, known synonyms were confirmed and a previously unknown synonym was discovered. An alleged synonym in the literature was disproved by the DNA data. The data were consistent with known parentage, where such data were available. Two mislabeled vines in the USDA collection were identified. UPGMA grouped the cultivars loosely into three groups: a group of nine mostly Middle Eastern cultivars, a group of 22 accessions mostly from Russia and Afghanistan that were morphologically similar to 'Thompson Seedless', and a third very loose group of 11 accessions consisting mostly of eastern European wine grape cultivars. The limitations and usefulness of this type of analysis are discussed.

Schizophrenia and the frontal lobes: post-mortem stereological study of tissue volume

BACKGROUND

It has been suggested that there is frontal lobe involvement in schizophrenia, and that it may be lateralised and gender-specific.

AIMS

To clarify the structure of the frontal lobes in schizophrenia in a post-mortem series.

METHOD

The volume of white matter and cortical components of the frontal lobes was measured in brains of controls and patients with schizophrenia using planimetry and the Cavalieri principle. The components measured were: superior frontal gyrus, middle frontal gyrus, a composite of inferior frontal gyrus and orbito-frontal cortex, as well as total frontal lobe cortex and white matter. In addition, the anterior cingulate gyrus was measured.

RESULTS

No diagnosis, gender, diagnosis x side, diagnosis x gender or diagnosis x gender x side interactions were observed in the volume of any of the components, the grey matter as a whole or the white matter. No evidence for volumetric inter-group differences was found for the anterior cingulate gyrus.

CONCLUSIONS

Such structural abnormalities as are present in the frontal lobes are more subtle than straightforward alterations in tissue volume; they may include changes in shape and the pattern of gyral folding.

Seasonal capacity of attached and detached vineyard roots to support grape phylloxera (Homoptera: Phylloxeridae)

Field experiments were conducted to evaluate population densities and survival, developmental rate, and fecundity of grape phylloxera, Daktulosphaira vitifoliae (Fitch), as influenced by root attachment or detachment from mature, field-grown, Vitis vinifera L. grapevines through the growing season. Experiments were performed using artificial infestations of California biotype A grape phylloxera. Thirty-day bioassays on attached- and detached-roots were repeated monthly from May to September in 1997 (cultivar 'Carignane') and April to September in 1998 (cultivar 'Thompson Seedless'). The bioassays showed that attached roots had lower population densities than detached roots in all months of both years. Densities varied by month, tending to be higher in spring than in summer. Of the population parameters studied, survival was most influenced by attachment condition, being higher on detached than on attached roots by up to 25-fold. These results imply the importance of vine-related mortality factors to grape phylloxera population density. Influence of root attachment condition on developmental rate and fecundity was not uniform across bioassay months for either year; however, in the four out of 21 assays where there was a significant difference it favored detached roots by twofold. Fruit harvest resulted in higher survival in the July assay but not for assays in August and September; however, neither developmental rate nor fecundity was affected by harvest in any ofthe assays. We conclude that mortality rather than nutritional factors are most limiting for field populations on susceptible vines. This work suggests that detachment of roots as occurs with root girdling by root pathogens may increase grape phylloxera populations on infested, susceptible vines. These results imply that excised root bioassays over-estimate grape phylloxera virulence and underestimate rootstock resistance.

Biology and management of grape phylloxera

Grape phylloxera, Daktulosphaira vitifoliae (Homoptera: Phylloxeridae), is a worldwide pest of grapevines. Its life cycle has sexual and asexual portions with forms that feed from leaf and root galls. Not all forms occur throughout the insect's range. Root forms predominate on Vitis vinifera cultivars; leaf forms predominate on other Vitis species characteristic of the American native range. Other conditions influence expression of the life cycle. Hosts and conditions similarly affect life table performance. Damage to grapevines is by secondary soilborne pathogens attacking the feeding site and by physiological interaction of the insect with the grapevine, though the latter has not been well studied. Resistant rootstocks derived from native American Vitis are the primary control tool. The insect varies genetically and relative to performance on hosts. Use of insecticides is limited in effect, and other control methods are not proven. More research on the biology, ecology, and management of phylloxera is needed.

A two-component pericyclic reaction for synthesis of substituted benzofurans and aryl-quaternary carbon bonds

The reaction shown is presumed to be a new [3,3]-sigmatropic rearrangement involving an O-arylsulfoxonium species or related sulfurane. It allows a sulfoxide and a phenol to be joined and rearranged in one operation at or below room temperature, coupling an aromatic to a quaternary carbon and creating benzofurans or articulated dihydrobenzofurans in a number of examples.