bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos
Authors: Jaensch Steffen , Decker Markus , Hyman Anthony A. , Myers Eugene W.
Published: June 2010

Motivation: The centrosome is a dynamic structure in animal cells that serves as a microtubule organizing center during mitosis and also regulates cell-cycle progression and sets polarity cues. Automated and reliable tracking of centrosomes is essential for genetic screens that study the process of centrosome assembly and maturation in the nematode Caenorhabditis elegans.

Results: We have developed a fully automatic system for tracking and measuring fluorescently labeled centrosomes in 3D time-lapse images of early C.elegans embryos. Using a spinning disc microscope, we monitor the centrosome cycle in living embryos from the 1- up to the 16-cell stage at imaging intervals between 30 and 50 s. After establishing the centrosome trajectories with a novel method involving two layers of inference, we also automatically detect the nuclear envelope breakdown in each cell division and recognize the identities of the centrosomes based on the invariant cell lineage of C.elegans. To date, we have tracked centrosomes in over 500 wild type and mutant embryos with almost no manual correction required.

Availability: The centrosome tracking software along with test data is freely available at http://publications.mpi-cbg.de/itemPublication.html?documentId=4082

Contact:  jaensch@mpi-cbg.de
A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images
Authors: Lin Yu-Shi , Lin Chung-Chih , Tsai Yuh-Show , Ku Tien-Chuan , Huang Yi-Hung , Hsu Chun-Nan
Published: June 2010

Motivation: High-throughput image-based assay technologies can rapidly produce a large number of cell images for drug screening, but data analysis is still a major bottleneck that limits their utility. Quantifying a wide variety of morphological differences observed in cell images under different drug influences is still a challenging task because the result can be highly sensitive to sampling and noise.

Results: We propose a graph-based approach to cell image analysis. We define graph transition energy to quantify morphological differences between image sets. A spectral graph theoretic regularization is applied to transform the feature space based on training examples of extremely different images to calibrate the quantification. Calibration is essential for a practical quantification method because we need to measure the confidence of the quantification. We applied our method to quantify the degree of partial fragmentation of mitochondria in collections of fluorescent cell images. We show that with transformation, the quantification can be more accurate and sensitive than that without transformation. We also show that our method outperforms competing methods, including neighbourhood component analysis and the multi-variate drug profiling method by Loo et al. We illustrate its utility with a study of Annonaceous acetogenins, a family of compounds with drug potential. Our result reveals that squamocin induces more fragmented mitochondria than muricin A.

Availability: Mitochondrial cell images, their corresponding feature sets (SSLF and WSLF) and the source code of our proposed method are available at http://aiia.iis.sinica.edu.tw/.

Contact:  chunnan@iis.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures
Authors: Saha Mitul , Levitt Michael , Chiu Wah
Published: June 2010

We present a new, first-of-its-kind, fully automated computational tool MOTIF-EM for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.) that remain conformationally conserved. As a by-product, regions in structures that are not conserved are revealed: this can indicate local molecular flexibility related to biological activity. MOTIF-EM takes cryoEM volumetric maps as inputs. The technique used by MOTIF-EM to detect conserved sub-structures is inspired by a recent breakthrough in 2D object recognition. The technique works by constructing rotationally invariant, low-dimensional representations of local regions in the input cryoEM maps. Correspondences are established between the reduced representations (by comparing them using a simple metric) across the input maps. The correspondences are clustered using hash tables and graph theory is used to retrieve conserved structural domains or motifs. MOTIF-EM has been used to extract conserved domains occurring in large macromolecular assembly maps, including as those of viruses P22 and epsilon 15, Ribosome 70S, GroEL, that remain structurally conserved in different functional states. Our method can also been used to build atomic models for some maps. We also used MOTIF-EM to identify the conserved folds shared among dsDNA bacteriophages HK97, Epsilon 15, and ô29, though they have low-sequence similarity.

Contact:  mitul@cs.stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution
Authors: Kumar Anoop , Cowen Lenore
Published: June 2010

Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related, has been profile hidden Markov models. However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in β-sheets. We thus explore methods for incorporating pairwise dependencies into these models.

Results: We consider the remote homology detection problem for β-structural motifs. In particular, we ask if a statistical model trained on members of only one family in a SCOP β-structural superfamily, can recognize members of other families in that superfamily. We show that HMMs trained with our pairwise model of simulated evolution achieve nearly a median 5% improvement in AUC for β-structural motif recognition as compared to ordinary HMMs.

Availability: All datasets and HMMs are available at: http://bcb.cs.tufts.edu/pairwise/

Contact:  anoop.kumar@tufts.edu; lenore.cowen@tufts.edu
Model-based detection of alternative splicing signals
Authors: Barash Yoseph , Blencowe Benjamin J. , Frey Brendan J.
Published: June 2010

Motivation: Transcripts from ∼95% of human multi-exon genes are subject to alternative splicing (AS). The growing interest in AS is propelled by its prominent contribution to transcriptome and proteome complexity and the role of aberrant AS in numerous diseases. Recent technological advances enable thousands of exons to be simultaneously profiled across diverse cell types and cellular conditions, but require accurate identification of condition-specific splicing changes. It is necessary to accurately identify such splicing changes to elucidate the underlying regulatory programs or link the splicing changes to specific diseases.

Results: We present a probabilistic model tailored for high-throughput AS data, where observed isoform levels are explained as combinations of condition-specific AS signals. According to our formulation, given an AS dataset our tasks are to detect common signals in the data and identify the exons relevant to each signal. Our model can incorporate prior knowledge about underlying AS signals, measurement quality and gene expression level effects. Using a large-scale multi-tissue AS dataset, we demonstrate the advantage of our method over standard alternative approaches. In addition, we describe newly found tissue-specific AS signals which were verified experimentally, and discuss associated regulatory features.

Contact:  yoseph@psi.utoronto.ca; frey@psi.utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps
Authors: Zhang Shihua , Vasishtan Daven , Xu Min , Topf Maya , Alber Frank
Published: June 2010

Motivation: Single-particle cryo electron microscopy (cryoEM) typically produces density maps of macromolecular assemblies at intermediate to low resolution (∼5–30 Å). By fitting high-resolution structures of assembly components into these maps, pseudo-atomic models can be obtained. Optimizing the quality-of-fit of all components simultaneously is challenging due to the large search space that makes the exhaustive search over all possible component configurations computationally unfeasible.

Results: We developed an efficient mathematical programming algorithm that simultaneously fits all component structures into an assembly density map. The fitting is formulated as a point set matching problem involving several point sets that represent component and assembly densities at a reduced complexity level. In contrast to other point matching algorithms, our algorithm is able to match multiple point sets simultaneously and not only based on their geometrical equivalence, but also based on the similarity of the density in the immediate point neighborhood. In addition, we present an efficient refinement method based on the Iterative Closest Point registration algorithm. The integer quadratic programming method generates an assembly configuration in a few seconds. This efficiency allows the generation of an ensemble of candidate solutions that can be assessed by an independent scoring function. We benchmarked the method using simulated density maps of 11 protein assemblies at 20 Å, and an experimental cryoEM map at 23.5 Å resolution. Our method was able to generate assembly structures with root-mean-square errors <6.5 Å, which have been further reduced to <1.8 Å by the local refinement procedure.

Availability: The program is available upon request as a Matlab code package.

Contact:  alber@usc.edu and m.topf@cryst.bbk.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping
Authors: Bercovici Sivan , Meek Christopher , Wexler Ydo , Geiger Dan
Published: June 2010

Motivation: Association analysis is the method of choice for studying complex multifactorial diseases. The premise of this method is that affected persons contain some common genomic regions with similar SNP alleles and such areas will be found in this analysis. An important disadvantage of GWA studies is that it does not distinguish between genomic areas that are inherited from a common ancestor [identical by descent (IBD)] and areas that are identical merely by state [identical by state (IBS)]. Clearly, areas that can be marked with higher probability as IBD and have the same correlation with the disease status of identical areas that are more probably only IBS, are better candidates to be causative, and yet this distinction is not encoded in standard association analysis.

Results: We develop a factorial hidden Markov model-based algorithm for computing genome-wide IBD sharing. The algorithm accepts as input SNP data of measured individuals and estimates the probability of IBD at each locus for every pair of individuals. For two g-degree relatives, when g≥8, the computation yields a precision of IBD tagging of over 50% higher than previous methods for 95% recall. Our algorithm uses a first-order Markovian model for the linkage disequilibrium process and employs a reduction of the state space of the inheritance vector from being exponential in g to quadratic. The higher accuracy along with the reduced time complexity marks our method as a feasible means for IBD mapping in practical scenarios.

Availability: A software implementation, called IBDMAP, is freely available at http://bioinfo.cs.technion.ac.il/IBDmap.

Contact:  sberco@gmail.com
Discovering transcriptional modules by Bayesian data integration
Authors: Savage Richard S. , Ghahramani Zoubin , Griffin Jim E. , de la Cruz Bernard J. , Wild David L.
Published: June 2010

Motivation: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets.

Results: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs.

Availability: If interested in the code for the work presented in this article, please contact the authors.

Contact:  d.l.wild@warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inferring combinatorial association logic networks in multimodal genome-wide screens
Authors: de Ridder Jeroen , Gerrits Alice , Bot Jan , de Haan Gerald , Reinders Marcel , Wessels Lodewyk
Published: June 2010

Motivation: We propose an efficient method to infer combinatorial association logic networks from multiple genome-wide measurements from the same sample. We demonstrate our method on a genetical genomics dataset, in which we search for Boolean combinations of multiple genetic loci that associate with transcript levels.

Results: Our method provably finds the global solution and is very efficient with runtimes of up to four orders of magnitude faster than the exhaustive search. This enables permutation procedures for determining accurate false positive rates and allows selection of the most parsimonious model. When applied to transcript levels measured in myeloid cells from 24 genotyped recombinant inbred mouse strains, we discovered that nine gene clusters are putatively modulated by a logical combination of trait loci rather than a single locus. A literature survey supports and further elucidates one of these findings. Due to our approach, optimal solutions for multi-locus logic models and accurate estimates of the associated false discovery rates become feasible. Our algorithm, therefore, offers a valuable alternative to approaches employing complex, albeit suboptimal optimization strategies to identify complex models.

Availability: The MATLAB code of the prototype implementation is available on: http://bioinformatics.tudelft.nl/ or http://bioinformatics.nki.nl/

Contact:  m.j.t.reinders@tudelft.nl; l.wessels@nki.nl
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
Authors: Hormozdiari Fereydoun , Hajirasouliha Iman , Dao Phuong , Hach Faraz , Yorukoglu Deniz , Alkan Can , Eichler Evan E. , Sahinalp S. Cenk
Published: June 2010

Recent years have witnessed an increase in research activity for the detection of structural variants (SVs) and their association to human disease. The advent of next-generation sequencing technologies make it possible to extend the scope of structural variation studies to a point previously unimaginable as exemplified by the 1000 Genomes Project. Although various computational methods have been described for the detection of SVs, no such algorithm is yet fully capable of discovering transposon insertions, a very important class of SVs to the study of human evolution and disease. In this article, we provide a complete and novel formulation to discover both loci and classes of transposons inserted into genomes sequenced with high-throughput sequencing technologies. In addition, we also present ‘conflict resolution’ improvements to our earlier combinatorial SV detection algorithm (VariationHunter) by taking the diploid nature of the human genome into consideration. We test our algorithms with simulated data from the Venter genome (HuRef) and are able to discover >85% of transposon insertion events with precision of >90%. We also demonstrate that our conflict resolution algorithm (denoted as VariationHunter-CR) outperforms current state of the art (such as original VariationHunter, BreakDancer and MoDIL) algorithms when tested on the genome of the Yoruba African individual (NA18507).

Availability: The implementation of algorithm is available at http://compbio.cs.sfu.ca/strvar.htm.

Contact:  eee@gs.washington.edu; cenk@cs.sfu.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Authors: Coelho Luis Pedro , Peng Tao , Murphy Robert F.
Published: June 2010

Motivation: Proteins exhibit complex subcellular distributions, which may include localizing in more than one organelle and varying in location depending on the cell physiology. Estimating the amount of protein distributed in each subcellular location is essential for quantitative understanding and modeling of protein dynamics and how they affect cell behaviors. We have previously described automated methods using fluorescent microscope images to determine the fractions of protein fluorescence in various subcellular locations when the basic locations in which a protein can be present are known. As this set of basic locations may be unknown (especially for studies on a proteome-wide scale), we here describe unsupervised methods to identify the fundamental patterns from images of mixed patterns and estimate the fractional composition of them.

Methods: We developed two approaches to the problem, both based on identifying types of objects present in images and representing patterns by frequencies of those object types. One is a basis pursuit method (which is based on a linear mixture model), and the other is based on latent Dirichlet allocation (LDA). For testing both approaches, we used images previously acquired for testing supervised unmixing methods. These images were of cells labeled with various combinations of two organelle-specific probes that had the same fluorescent properties to simulate mixed patterns of subcellular location.

Results: We achieved 0.80 and 0.91 correlation between estimated and underlying fractions of the two probes (fundamental patterns) with basis pursuit and LDA approaches, respectively, indicating that our methods can unmix the complex subcellular distribution with reasonably high accuracy.

Availability:  http://murphylab.web.cmu.edu/software

Contact:  murphy@cmu.edu
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals
Authors: Li Xin , Yin Xiaolin , Li Jing
Published: June 2010

Motivation: Inference of identical-by-descent (IBD) probabilities is the key in family-based linkage analysis. Using high-density single nucleotide polymorphism (SNP) markers, one can almost always infer haplotype configurations of each member in a family given all individuals being typed. Consequently, the IBD status can be obtained directly from haplotype configurations. However, in reality, many family members are not typed due to practical reasons. The problem of IBD/haplotype inference is much harder when treating untyped individuals as missing.

Results: We present a novel hidden Markov model (HMM) approach to infer the IBD status in a pedigree with many untyped members using high-density SNP markers. We introduce the concept of inheritance-generating function, defined for any pair of alleles in a descent graph based on a pedigree structure. We derive a recursive formula for efficient calculation of the inheritance-generating function. By aggregating all possible inheritance patterns via an explicit representation of the number and lengths of all possible paths between two alleles, the inheritance-generating function provides a convenient way to theoretically derive the transition probabilities of the HMM. We further extend the basic HMM to incorporate population linkage disequilibrium (LD). Pedigree-wise IBD sharing can be constructed based on pair-wise IBD relationships. Compared with traditional approaches for linkage analysis, our new model can efficiently infer IBD status without enumerating all possible genotypes and transmission patterns of untyped members in a family. Our approach can be reliably applied on large pedigrees with many untyped members, and the inferred IBD status can be used for non-parametric genome-wide linkage analysis.

Availability: The algorithm is implemented in Matlab and is freely available upon request.

Contact:  jingli@cwru.edu

Supplementary information:  Supplementary data are available on Bioinformatics online.
Leaf Blight Disease on the Invasive GrassMicrostegium vimineumCaused by aBipolarissp.
Authors: Kleczewski Nathan M. , Flory S. Luke
Published: June 2010

In 2009, a previously undescribed disease was found on the nonnative invasive annual grass Microstegium vimineum (Japanese stiltgrass). Diseased plants exhibited foliar lesions, wilting, and in some cases, death of entire plants. We identified the causal agent as a Bipolaris sp. similar to B. zeicola. We observed spores and associated structures characteristic of Bipolaris spp. growing from leaf lesions on field collected plants. Pure cultures of the fungus were made and spore suspensions were applied to laboratory-reared M. vimineum seedlings in growth chamber and greenhouse experiments. Initial symptoms appeared on seedlings in the growth chamber experiment within 72 h of inoculation, and seedlings exhibited characteristic lesions within 10 days. The fungus was reisolated from lesions, and the internal transcribed spacer (ITS) region was sequenced to confirm its identity. In the greenhouse experiment, inoculated plants displayed characteristic lesions, and relatively greater spore loads increased disease incidence. Disease reduced seed head production by 40% compared to controls. This is the first report of a Bipolaris sp. causing disease on invasive M. vimineum. Following further analysis, including assays with co-occurring native species, this Bipolaris sp. may be considered as a biocontrol agent for invasive M. vimineum.
Epidemiology of Diseases Caused byXylella fastidiosain California: Evaluation of Alfalfa as a Source of Vectors and Inocula
Authors: Sisterson Mark S. , Thammiraju Shyamala R. , Lynn-Patterson Kris , Groves Russell L. , Daane Kent M.
Published: June 2010

Pierce's disease and almond leaf scorch disease have been chronic problems for California grape and almond growers, respectively. Both diseases are caused by the xylem-limited, bacterial pathogen Xylella fastidiosa, which is transmitted by xylem-feeding insects. We evaluated the potential for alfalfa to serve as a source of vectors and inocula in California. Analysis of Geographic Information Systems maps on the distribution and abundance of grape, almond, and alfalfa plantings determined that 94,521 ha of almond and grape were planted within 1.6 km of an alfalfa field. Seasonal trends of X. fastidiosa detection were monitored outdoors and in the greenhouse in five needle-inoculated alfalfa cultivars (CUF101, Moapa69, WL342, WL530HQ, and WL625HQ) over 2 years. Results suggest that cool winter temperatures reduced X. fastidiosa populations to undetectable levels but did not eliminate infections. Sampling of alfalfa fields to assess incidence of X. fastidiosa corroborated this result, with positive samples detected in summer only. Incidence of X. fastidiosa in alfalfa during summer was low, with only 6 positive samples out of 1,156 samples collected over 3 years. Insect trapping in alfalfa fields over 3 years found that the green sharpshooter (Draeculacephala minerva) was the most abundant vector. Within alfalfa fields, green sharpshooter abundance was highest in weedy areas, suggesting a preference for weeds over alfalfa. These results confirm that weedy alfalfa fields can serve as an important source of vectors. Incidence of X. fastidiosa in alfalfa was low, possibly due to preference of vectors for weeds over alfalfa.
Efficacy of Brassicaceous Seed Meal Formulations for the Control of Apple Replant Disease in Conventional and Organic Production Systems
Authors: Mazzola Mark , Brown Jack
Published: June 2010

The efficacy of brassicaceous seed meals for the control of apple replant disease and the effects of such treatments on the causal pathogen complex were examined in conventional and organic production systems. When used in conjunction with a postplant application of mefenoxam, Brassica juncea and Sinapis alba seed meal soil amendments were as effective as preplant fumigation of soil with 1,3-dichloropropene-chloropicrin in terms of disease control, tree growth, and overall fruit yields of Gala/M26. Brassica napus seed meal amendment–mefenoxam soil drench also enhanced yields in a manner comparable to preplant fumigation, but vegetative growth was intermediate between the control and fumigation treatments. When applied alone, seed meal amendments failed to enhance tree growth or control disease to the level attained in response to soil fumigation. Postplant mefenoxam treatments revealed that failure of seed meal amendments to enhance tree growth and yield when used independently was due, at least in part, to increased apple root infection by Pythium spp. in B. napus and S. alba seed meal–amended soils, and by Phytophthora cambivora in B. juncea–amended soil. As mefenoxam treatment is not compatible with organic cropping systems, a seed meal blend was formulated which, based upon biological activity, was predicted to suppress known components of the target pathogen complex without need of additional treatment. Gala/M26 trees planted in soils treated with a 1:1 ratio of B. juncea:B. napus seed meal blend performed as well in terms of disease control and vegetative growth as trees cultivated in fumigated soil at an organic-certified orchard. Because these trials utilized the highly susceptible rootstock M26, the results demonstrate that these amendments are a viable alternative to soil fumigation for the control of apple replant disease in both conventional and organic systems.
First Report of Shallot latent virus in Garlic in Argentina
Authors: Torrico A. K. , Cafrune E. E. , Conci V. C.
Published: June 2010

Because of exclusively agamic propagation, garlic is commonly infected with a virus complex mainly composed of species within the genera Potyvirus, Allexivirus, and Carlavirus. This virus complex causes leaf striping that ranges from various shades of green to yellow and results in yield losses (2,4). Onion yellow dwarf virus, Leek yellow stripe virus (potyviruses), Garlic virus A, Garlic virus C (allexiviruses), and Garlic common latent virus (carlavirus) have been detected in Argentina previously (1,2). Recently, Shallot latent virus (SLV; another carlavirus) was detected in 25 of 30 garlic plants (cv. Morado) growing in four different fields near Córdoba, Argentina by double-antibody sandwich (DAS)-ELISA using BIOREBA (Reinach, Switzerland) antibodies. To confirm the presence of the virus, DAS-ELISA-positive plants were also analyzed by one-step reverse transcription (RT)-PCR using the Access RT-PCR system (Promega, Madison, WI) with specific primers reported by Tsuneyoshi et al. (3). RNA extractions were performed from 100 mg of leaves with the Qiagen RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Primers used were Car-V1 (5′-AAACCTTTTGGTTCACTTTAGG-3′); Car-V2 (5′-AGGTGCATTGTTATCATTACTGG-3′); and Car-Cp3 (5′-GCGTGCTATATTTAAGTTGCATAC-3′). Primer pairs Car-V1/Car-Cp3 and Car-V2/Car-Cp3 were used for the amplification of the coat protein (CP) gene of SLV and an isolate of SLV formerly known as Garlic latent virus, respectively. Fragments of 992 bp and 1,079 bp were amplified with these primer pairs, respectively. The RT-PCR products were cloned with the TOPO TA Cloning Kit in the 3.9-kb pCR-TOPO vector (Qiagen). The nucleotide sequences of both fragments were determined and were found to be identical (GenBank No. GU355922) showing 94.2% nt sequence identity with the CP gene of an isolate of SLV from Indonesian garlic (GenBank No. AB004686) formerly referred to as Garlic latent virus (3). Consequently, the Argentinean virus is now considered a garlic isolate of SLV.

References: (1) E. Cafrune et al. Plant Dis. 90:898, 2006. (2) V. C. Conci. Virus y Fitoplasmas de Ajo. Page 267 in: 50 Temas Sobre Producción de Ajo. Vol. 3. J. L. Burba, ed. Ediciones INTA, Mendoza, Argentina. 1997. (3) T. Tsuneyoshi et al. Arch. Virol. 143:1093, 1998. (4) D. G. A. Walkey and D. N. Antill. J. Hortic. Sci. 64:53, 1989.
Zoospore Density-Dependent Behaviors of Phytophthora nicotianae Are Autoregulated by Extracellular Products
Authors: Kong Ping , Hong Chuanxue
Published: June 2010

Phytophthora species are destructive fungus-like plant pathogens that use asexual single-celled flagellate zoospores for dispersal and plant infection. Many of the zoospore behaviors are density-dependent although the underlying mechanisms are poorly understood. Here, we use P. nicotianae as a model and demonstrate autoregulation of some zoospore behaviors using signal molecules that zoospores release into the environment. Specifically, zoospore aggregation, plant targeting, and infection required or were enhanced by threshold concentrations of these signal molecules. Below the threshold concentration, zoospores did not aggregate and move toward a cauline leaf of Arabidopsis thaliana (Col-0) and failed to individually attack annual vinca (Catharanthus roseus cv. Little Bright Eye). These processes were reversed when supplemented with zoospore-free fluid (ZFF) prepared from a zoospore suspension above threshold densities but not with calcium chloride at a concentration equivalent to extracellular Ca2+ in ZFF. These results suggest that Ca2+ is not a primary signal molecule regulating these communal behaviors. Zoospores coordinated their communal behaviors by releasing, detecting, and responding to signal molecules. This chemical communication mechanism raises the possibility that Phytophthora plant infection may not depend solely on zoospore number in the real world. Single zoospore infection may take place if it is signaled by a common molecule available in the environment which contributes to the destructiveness of these plant pathogens.
Survival of Secondary Sporidia of Floret-Infecting Tilletia Species: Implications for Epidemiology
Authors: Goates Blair J.
Published: June 2010

Secondary sporidia of Tilletia horrida, T. indica, and T. walkeri initiate local infection of rice, wheat, and ryegrass florets, respectively, leading to disease in seed. Secondary sporidia are considered to be fragile and short lived. To examine this, secondary sporidia from agar cultures of these species were naturally discharged onto petri dish lids and were air-dried and maintained in the laboratory at 10 to 20% relative humidity (RH) at 20 to 22°C, and at 40 to 50% RH at 18°C. Lids were periodically inverted over fresh agar to determine viability of dried sporidia. Sporidia held 31 to 49 days at 10 to 20% RH and 56 to 88 days at 40 to 50% RH regenerated rapidly. Commonly, 18 h after lids with dried sporidia were inverted over agar, newly produced secondary sporidia had discharged onto the agar and produced extensive hyphal growth. There was no difference in the viability of sporidia that were initially dried rapidly or dried slowly over 10 h. Sporidia of T. horrida or T. indica dried on petri dish lids placed in the lower canopy of barley or wheat fields in Idaho and Arizona during early flag leaf to soft dough stages and held until crops were near or beyond maturity regenerated rapidly despite temperatures up to 46°C and several days of RH < 20%. These results suggest that sporidia produced well prior to susceptible growth stages of the host can lay dormant in very dry field environments and then rapidly regenerate under humid rainy conditions associated with the diseases.
Efficiency of Adaptive Cluster Sampling for Estimating Plant Disease Incidence
Authors: Ojiambo P. S. , Scherm H.
Published: June 2010

Conventional sampling designs such as simple random sampling (SRS) tend to be inefficient when assessing rare and highly clustered populations because most of the time is spent evaluating empty quadrats, leading to high error variances and high cost. In previous studies with rare plant and animal populations, adaptive cluster sampling, where sampling occurs preferentially in the neighborhood of quadrats in which the species of interest is detected during the sampling bout, has been shown to estimate population parameters with greater precision at an effort comparable to SRS. Here, we use computer simulations to evaluate the efficiency of adaptive cluster sampling for estimating low levels of disease incidence (0.1, 0.5, 1.0, and 5.0%) at various levels of aggregation of infected plants having variance-to-mean ratios (V/M) of ≈1, 3, 5, and 10. For each simulation, an initial sample size of 50, 100, and 150 quadrats was evaluated, and the condition to adapt neighborhood sampling (CA), i.e., the minimum number of infected plants per quadrat that triggers a switch from random sampling to sampling in neighboring quadrats, was varied from 1 to 4 (corresponding to 7.7 to 30.8% incidence of infected plants per quadrat). The simulations showed that cluster sampling was consistently more precise than SRS at a field-level disease incidence of 0.1 and 0.5%, especially when diseased plants were highly aggregated (V/M = 5 or 10) and when the most liberal condition to adapt (CA = 1) was used. One drawback of adaptive cluster sampling is that the final sample size is unknown at the beginning of the sampling bout because it depends on how often neighborhood sampling is triggered. In our simulations, the final sample size was close to the initial sample size for disease incidence up to 1.0%, especially when a more conservative condition to adapt (CA > 1) was used. For these conditions, the effect of disease aggregation was minor. In summary, both precision and the sample size required with adaptive cluster sampling responded similarly to disease incidence and aggregation, i.e., both were most favorable at the lowest disease incidence with the highest levels of clustering. However, whereas relative precision was optimized with the most liberal condition to adapt, the ratio of final to initial sample size was best for more conservative CA values, indicating a tradeoff. In our simulations, precision and final sample size were both simultaneously favorable for disease incidence of up to 1.0%, but only when infected plants were most aggregated (V/M = 10).
Temperature, Moisture, and Fungicide Effects in Managing Rhizoctonia Root and Crown Rot of Sugar Beet
Authors: Bolton Melvin D. , Panella Lee , Campbell Larry , Khan Mohamed F. R.
Published: June 2010

Rhizoctonia solani AG-2-2 is the causal agent of Rhizoctonia root and crown rot in sugar beet; however, recent increases in disease incidence and severity were grounds to reevaluate this pathosystem. To assess the capacity at which other anastomosis groups (AGs) are able to infect sugar beet, 15 AGs and intraspecific groups (ISGs) were tested for pathogenicity on resistant (‘FC708 CMS’) and susceptible (‘Monohikari’) seedlings and 10-week-old plants. Several AGs and ISGs were pathogenic on seedlings regardless of host resistance but only AG-2-2 IIIB and AG-2-2 IV caused significant disease on 10-week-old plants. Because fungicides need to be applied prior to infection for effective disease control, temperature and moisture parameters were assessed to identify potential thresholds that limit infection. Root and leaf disease indices were used to evaluate disease progression of AG-2-2 IIIB- and AG-2-2 IV-inoculated plants in controlled climate conditions of 7 to 22 growing degree days (GDDs) per day. Root disease ratings were positively correlated with increasing temperature of both ISGs, with maximum disease symptoms occurring at 22 GDDs/day. No disease symptoms were evident from either ISG at 10 GDDs/day but disease symptoms did occur in plants grown in growth chambers set to 11 GDDs/day. Using growth chambers adjusted to 22 GDDs/day, disease was evaluated at 25, 50, 75, and 100% moisture-holding capacity (MHC). Disease symptoms for each ISG were highest in soils with 75 and 100% MHC but disease still occurred at 25% MHC. Isolates were tested for their ability to cause disease at 1, 4, and 8 cm from the plant hypocotyl. Only AG-2-2 IIIB was able to cause disease symptoms at 8 cm during the evaluation period. In all experiments, isolates of AG-2-2 IIIB were found to be more aggressive than AG-2-2 IV. Using environmental parameters that we identified as the most conducive to disease development, azoxystrobin, prothioconazole, pyraclostrobin, difenoconazole/propiconazole, flutolanil, polyoxin D, and a water control were evaluated for their ability to suppress disease development by AG-2-2 IIIB and AG-2-2 IV 17 days after planting. Flutolanil, polyoxin-D, and azoxystrobin provided the highest level of disease suppression. Because R. solani AG-2-2 IIIB and AG-2-2 IV are affected by temperature and moisture, growers may be able to evaluate environmental parameters for optimization of fungicide application.
The potential of Raman spectroscopy for the analysis of diagenetically transformed carotenoids
Authors: Marshall Craig P. , Olcott Marshall Alison
Published: June 2010

Recently, carotenoids have received much attention as target compounds for astrobiological prospecting principally because they are a group of molecules that display unique diagnostic Raman spectra that can be assigned to organic material of unequivocal biological origin. However, no work has been performed on assessing the potential of Raman spectroscopic detection of carotenoids from fossilized microbes. Here, we report the first Raman spectra acquired from ‘perhydro’ derivatives of β-carotene and lycopene formed by hydrogenation of the polyene chain during diagenesis, resulting in much less specific fossil hydrocarbons such as β-carotane and lycopane, respectively. We propose here that diagenetically altered carotenoids formed by hydrogenation reactions during the fossilization processes also provide unique diagnostic spectra that can be interpreted as a biological signature.
Using portable Raman spectrometers for the identification of organic compounds at low temperatures and high altitudes: exobiological applications
Authors: Jehlička J. , Edwards H. G. M. , Culka A.
Published: June 2010

Organic minerals, organic acids and NH-containing organic molecules represent important target molecules for astrobiology. Here, we present the results of the evaluation of a portable hand-held Raman spectrometer to detect these organic compounds outdoors under field conditions. These measurements were carried out during the February–March 2009 winter period in Austrian Alpine sites at temperatures ranging between −5 and −25°C. The compounds investigated were detected under field conditions and their main Raman spectral features were observed unambiguously at their correct reference wavenumber positions. The results obtained demonstrate that a miniaturized Raman spectrometer equipped with 785 nm excitation could be applied with advantage as a key instrument for investigating the presence of organic minerals, organic acids and nitrogen-containing organic compounds outdoors under terrestrial low-temperature conditions. Within the payload designed by ESA and NASA for several missions focusing on Mars, Titan, Europa and other extraterrestrial bodies, Raman spectroscopy can be proposed as an important non-destructive analytical tool for thein situidentification of organic compounds relevant to life detection on planetary and moon surfaces or near subsurfaces.
Raman spectroscopy of volcanic lavas and inclusions of relevance to astrobiological exploration
Authors: Jorge-Villar Susana E. , Edwards Howell G. M.
Published: June 2010

Volcanic eruptions and lava flows comprise one of the most highly stressed terrestrial environments for the survival of biological organisms; the destruction of botanical and biological colonies by molten lava, pyroclastic flows, lahars, poisonous gas emissions and the deposition of highly toxic materials from fumaroles is the normal expectation from such events. However, the role of lichens and cyanobacteria in the earlier colonization of volcanic lava outcrops has now been recognized. In this paper, we build upon earlier Raman spectroscopic studies on extremophilic colonies in old lava flows to assess the potential of finding evidence of biological colonization in more recent lava deposits that would inform, first, the new colonization of these rocks and also provide evidence for the relict presence of biological colonies that existed before the volcanism occurred and were engulfed by the lava. In this research, samples were collected from a recent expedition to the active volcano at Kilauea, Hawaii, which comprises very recent lava flows, active fumaroles and volcanic rocks that had broken through to the ocean and had engulfed a coral reef. The Raman spectra indicated that biological and geobiological signatures could be identified in the presence of geological matrices, which is encouraging for the planned exploration of Mars, where it is believed that there is evidence of an active volcanism that perhaps could have preserved traces of biological activity that once existed on the planet’s surface, especially in sites near the old Martian oceans.
Micro-Raman spectroscopic study of extremely large atmospheric ice conglomerations (megacryometeors)
Authors: Rull F. , Delgado A. , Martínez-Frías J.
Published: June 2010

For the first time, micro-Raman spectroscopy has been applied to the structural study of four megacryometeors (extremely large atmospheric ice conglomerations that fall in general under blue-sky atmospheric conditions) that fell in Spain. The Raman spectra taken on the megacryometeor cores have been compared with those obtained from an
in situ
and online study performed on the crystallization process of water in the laboratory. A detailed comparison of the band profiles obtained made it possible to place the formation of the megacryometeors within a particular range of temperatures (−10 to −20°C), which in turn can be related with the altitude of formation in the atmosphere. These results have also been compared with isotope concentrations (δ
18
O and δD) previously obtained in these cores. The two sets of results show a close correlation.
Protein overexpression and gene amplification of epidermal growth factor receptor in adult testicular germ cell tumors: Potential role in tumor progression
Authors: Miyai Kosuke , Yamamoto Sohei , Asano Tomohiko , Tamai Seiichi , Matsubara Osamu , Tsuda Hitoshi
Published: June 2010

Little is known about the pathologic significance of epidermal growth factor receptor (EGFR) expression in malignant testicular germ cell tumors (TGCTs) in adults. From the primary tumor sites of a cohort of 110 TGCT cases, we obtained 209 histologically distinct components: 53 intratubular germ cell neoplasia unclassified (IGCNU) lesions, 83 seminomas (66 pure‐form seminomas and 17 seminoma components in the mixed‐form with nonseminomatous TGCTs), 27 embryonal carcinomas, eight choriocarcinomas, 18 yolk sac tumors, and 20 immature teratomas. Samples were analyzed for expression of EGFR protein and EGFR gene amplification by immunohistochemistry and fluorescence in situ hybridization (FISH), respectively. Overexpression of the EGFR protein was detected in 28% of seminomas (27% in the pure‐form and 29% in the mixed‐form), 11% of embryonal carcinomas, 88% of choriocarcinomas, 44% of yolk sac tumors, and none of the IGCNU lesions or immature teratomas. A higher copy number (≥4 copies per cell) and amplification of the EGFR gene were detected in 20% and 10% of seminomas, 13% and 0% of embryonal carcinomas, 71% and 60% of choriocarcinomas, 15% and 8% of yolk sac tumors, and none of the IGCNU lesions or immature teratomas, respectively. Both higher copy number and amplification of the EGFR gene were positively correlated with immunohistochemical overexpression of EGFR protein (each P < 0.0001). These results suggest that overexpression of EGFR protein and increased copy number or amplification of the EGFR gene occur relatively frequently in primary TGCTs, and may play roles in the formation of invasive cancer and in the progression, especially morphological evolution, of tumors. (Cancer Sci 2010)
Expression of platelet‐derived growth factor (PDGF)‐B and PDGF‐receptor β is associated with lymphatic metastasis in human gastric carcinoma
Authors: Kodama Michiyo , Kitadai Yasuhiko , Sumida Tomonori , Ohnishi Mayu , Ohara Eiji , Tanaka Miwako , Shinagawa Kei , Tanaka Shinji , Yasui Wataru , Chayama Kazuaki
Published: June 2010

Recent study of murine fibrosarcoma has revealed that platelet‐derived growth factor (PDGF) plays a direct role in promoting lymphangiogenesis and metastatic spread to lymph nodes. Thus, we investigated the relation between PDGF and PDGF receptor (PDGF‐R) expression and lymphatic metastasis in human gastric carcinoma. We examined PDGF‐B and PDGF‐Rβ expression in four human gastric carcinoma cell lines (TMK‐1, MKN‐1, MKN‐45, and KKLS) and in 38 surgical specimens of gastric carcinoma. PDGF‐B and PDGF‐Rβ expression was examined by immunofluorescence in surgical specimens and in human gastric carcinoma cells (TMK‐1) implanted orthotopically in nude mice. Groups of mice (n = 10, each) received saline (control) or PDGF‐R tyrosine kinase inhibitor imatinib. PDGF‐B and PDGF‐Rβ mRNA expression was significantly higher in patients with lymph node metastasis than in those without and was also significantly higher in diffuse‐type carcinoma than in intestinal‐type carcinoma. In surgical specimens, tumor cells expressed PDGF‐B, but PDGF‐Rβ was expressed predominantly by stromal cells. Under culture conditions, expression of PDGF‐B mRNA was found in all of the gastric cell lines, albeit at different levels. In orthotopic TMK‐1 tumors, cancer cells expressed PDGF‐B but not PDGF‐Rβ. PDGF‐Rβ was expressed by stromal cells, including lymphatic endothelial cells. Four weeks of treatment with imatinib significantly decreased the area of lymphatic vessels. Our data indicate that secretion of PDGF‐B by gastric carcinoma cells and expression of PDGF‐Rβ by tumor‐associated stromal cells are associated with lymphatic metastasis. Blockade of PDGF‐R signaling pathways may inhibit lymph node metastasis of gastric carcinoma. (Cancer Sci2010)
Requiring suspended drunk drivers to install alcohol interlocks to reinstate their licenses: effective?
Authors: Voas Robert B. , Tippetts S. Scott , Fisher Deborah , Grosz Milton
Published: June 2010

Aims  To evaluate a new method being used by some states for motivating interlock installation by requiring it as a prerequisite to reinstatement of the driver's license.

Design  The driving records of Florida DWI offenders convicted between July 2002 and June 2008 were analyzed to determine the proportion of offenders subject to the interlock requirement who installed interlocks.

Setting  Most driving‐while‐impaired (DWI) offenders succeed in avoiding state laws requiring the installation of a vehicle alcohol interlock.

Participants  A total of 82 318 Florida DWI offenders.

Findings  Due to long periods of complete suspension when no driving was permitted and the failure to complete all the requirements imposed by the court, only 21 377 of the 82 318 offenders studied qualified for reinstatement, but 93% of those who qualified did install interlocks to be reinstated.

Conclusions  Because of the lengthy license suspensions and other barriers that the offenders face in qualifying for reinstatement, it is not clear that requiring a period on the interlock as a prerequisite to reinstating will greatly increase the current installment rate.