A Genetic Approach to Tuning Compact Trie Clustering

The Compact Trie method for document clustering is sensitive to the kind oftext it is applied to, but contains various parameters that may be tuned foradaptation to specific applications. We implement a genetic algorithm foroptimizing these parameters and apply it to a corpus of texts to demonstratethe feasibility of using genetic algorithms for tuning

Sequence mining and transcript profiling to explore cyst nematode parasitism

<p>Abstract</p> <p>Background</p> <p>Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants.</p> <p>Results</p> <p>We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, <it>Heterodera glycines</it>, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean Genome Array GeneChip, which contains probeset sequences for 6,860 genes derived from preparasitic and parasitic <it>H. glycines </it>life stages. Targeting the identification of additional <it>H. glycines </it>parasitism-associated genes, we isolated 633 genes encoding secretory proteins using algorithms to predict secretory signal peptides. Furthermore, because some of the known <it>H. glycines </it>parasitism proteins have strongest similarity to proteins of plants and microbes, we searched for predicted protein sequences that showed their highest similarities to plant or microbial proteins and identified 156 <it>H. glycines </it>genes, some of which also contained a signal peptide. Analyses of the expression profiles of these genes allowed the formulation of hypotheses about potential roles in parasitism. This is the first study combining sequence analyses of a substantial EST dataset with microarray expression data of all major life stages (except adult males) for the identification and characterization of putative parasitism-associated proteins in any parasitic nematode.</p> <p>Conclusion</p> <p>We have established an expression atlas for all known <it>H. glycines </it>parasitism genes. Furthermore, in an effort to identify additional <it>H. glycines </it>genes with putative functions in parasitism, we have reduced the currently known 6,860 <it>H. glycines </it>genes to a pool of 788 most promising candidate genes (including known parasitism genes) and documented their expression profiles. Using our approach to pre-select genes likely involved in parasitism now allows detailed functional analyses in a manner not feasible for larger numbers of genes. The generation of the candidate pool described here is an important enabling advance because it will significantly facilitate the unraveling of fascinating plant-animal interactions and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the exploration of true parasitism genes verified from the gene pool delineated here will identify weaknesses in the nematode life cycle that can be exploited by novel anti-nematode efforts.</p

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

The generation and analysis of over 20,000 ESTs allowed the identification and expression profiling of 6,860 predicted genes in the nematode Heterodera glycines. This revealed that gene expression patterns in the dauer stage of Caenorhabditis elegans are not conserved in H. glycines

Relationship Between Climatic Factors and Distribution of Pratylenchus spp. in the Dryland Wheat-Production Areas of Eastern Washington

Field surveys were conducted by collecting soil samples to estimate nematode densities in soil from winter wheat, spring wheat, spring barley, and spring legumes (lentil, chickpea, and pea) fields during 2010 and 2011. Pratylenchus spp. were observed in 60% of sampled fields. However, nematodes were detected in nearly all of the survey fields in high numbers where crops were grown every year. To identify climatic variables associated with density of Pratylenchus spp. in soil, correlation and regression analyses were performed using climate data of survey sites from 1979 to 2010. Fifty-seven climate variables were significantly correlated with densities of Pratylenchus spp. All precipitation variables were significantly positively correlated with nematode abundance. Summer maximum air temperature was negatively correlated and winter minimum air temperature was positively correlated with nematode densities. In addition, both years’ nematode densities were significantly correlated with cropping intensity. Five multivariate regression models for 2010 and seven models for 2011 nematode abundance levels were developed. The majority of the climate variables selected in the models were related to precipitation. Knowledge of root-lesion nematode distribution in the dryland region of eastern Washington and associated climate variables may be helpful to determine risk and apply management practices to minimize crop damage

Effective and specific in planta RNAi in cyst nematodes: expression interference of four parasitism genes reduces parasitic success

Cyst nematodes are highly evolved sedentary plant endoparasites that use parasitism proteins injected through the stylet into host tissues to successfully parasitize plants. These secretory proteins likely are essential for parasitism as they are involved in a variety of parasitic events leading to the establishment of specialized feeding cells required by the nematode to obtain nourishment. With the advent of RNA interference (RNAi) technology and the demonstration of host-induced gene silencing in parasites, a new strategy to control pests and pathogens has become available, particularly in root-knot nematodes. Plant host-induced silencing of cyst nematode genes so far has had only limited success but similarly should disrupt the parasitic cycle and render the host plant resistant. Additional in planta RNAi data for cyst nematodes are being provided by targeting four parasitism genes through host-induced RNAi gene silencing in transgenic Arabidopsis thaliana, which is a host for the sugar beet cyst nematode Heterodera schachtii. Here it is reported that mRNA abundances of targeted nematode genes were specifically reduced in nematodes feeding on plants expressing corresponding RNAi constructs. Furthermore, this host-induced RNAi of all four nematode parasitism genes led to a reduction in the number of mature nematode females. Although no complete resistance was observed, the reduction of developing females ranged from 23% to 64% in different RNAi lines. These observations demonstrate the relevance of the targeted parasitism genes during the nematode life cycle and, potentially more importantly, suggest that a viable level of resistance in crop plants may be accomplished in the future using this technology against cyst nematodes

Nematode effector proteins: an emerging paradigm of parasitism

Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda

The plant apoplasm is an important recipient compartment for nematode secreted proteins

Similarly to microbial pathogens, plant-parasitic nematodes secrete into their host plants proteins that are essential to establish a functional interaction. Identifying the destination of nematode secreted proteins within plant cell compartment(s) will provide compelling clues on their molecular functions. Here the fine localization of five nematode secreted proteins was analysed throughout parasitism in Arabidopsis thaliana. An immunocytochemical method was developed that preserves both the host and the pathogen tissues, allowing the localization of nematode secreted proteins within both organisms. One secreted protein from the amphids and three secreted proteins from the subventral oesophageal glands involved in protein degradation and cell wall modification were secreted in the apoplasm during intercellular migration and to a lower extent by early sedentary stages during giant cell formation. Conversely, another protein produced by both subventral and dorsal oesophageal glands in parasitic stages accumulated profusely at the cell wall of young and mature giant cells. In addition, secretion of cell wall-modifying proteins by the vulva of adult females suggested a role in egg laying. The study shows that the plant apoplasm acts as an important destination compartment for proteins secreted during migration and during sedentary stages of the nematode

MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors

There is increasing evidence that oncogenic transformation modifies the metabolic program of cells. A common alteration is the upregulation of glycolysis, and efforts to target glycolytic enzymes for anticancer therapy are under way. Here, we performed a genome-wide haploid genetic screen to identify resistance mechanisms to 3-bromopyruvate (3-BrPA), a drug candidate that inhibits glycolysis in a poorly understood fashion. We identified the SLC16A1 gene product, MCT1, as the main determinant of 3-BrPA sensitivity. MCT1 is necessary and sufficient for 3-BrPA uptake by cancer cells. Additionally, SLC16A1 mRNA levels are the best predictor of 3-BrPA sensitivity and are most elevated in glycolytic cancer cells. Furthermore, forced MCT1 expression in 3-BrPA–resistant cancer cells sensitizes tumor xenografts to 3-BrPA treatment in vivo. Our results identify a potential biomarker for 3-BrPA sensitivity and provide proof of concept that the selectivity of cancer-expressed transporters can be exploited for delivering toxic molecules to tumors.National Institutes of Health (U.S.) (NIH CA103866)Jane Coffin Childs Memorial Fund for Medical Research (Fellowship)National Science Foundation (U.S.) (Fellowship)Howard Hughes Medical Institute (Investigator

Descent toward the icehouse: Eocene sea surface cooling inferred from GDGT distributions

The TEX86 proxy, based on the distribution of marine isoprenoidal glycerol dialkyl glycerol tetraether lipids (GDGTs), is increasingly used to reconstruct sea surface temperature (SST) during the Eocene epoch (56.0–33.9 Ma). Here we compile published TEX86 records, critically reevaluate them in light of new understandings in TEX86 palaeothermometry, and supplement them with new data in order to evaluate long-term temperature trends in the Eocene. We investigate the effect of archaea other than marine Thaumarchaeota upon TEX86 values using the branched-to-isoprenoid tetraether index (BIT), the abundance of GDGT-0 relative to crenarchaeol (%GDGT-0), and the Methane Index (MI). We also introduce a new ratio, % GDGTRS, which may help identify Red Sea-type GDGT distributions in the geological record. Using the offset between TEX86H and TEX86L(ΔH-L) and the ratio between GDGT-2 and GDGT-3 ([2]/[3]), we evaluate different TEX86 calibrations and present the first integrated SST compilation for the Eocene (55 to 34 Ma). Although the available data are still sparse some geographic trends can now be resolved. In the high latitudes (>55°), there was substantial cooling during the Eocene (~6°C). Our compiled record also indicates tropical cooling of ~2.5°C during the same interval. Using an ensemble of climate model simulations that span the Eocene, our results indicate that only a small percentage (~10%) of the reconstructed temperature change can be ascribed to ocean gateway reorganization or paleogeographic change. Collectively, this indicates that atmospheric carbon dioxide (pCO2) was the likely driver of surface water cooling during the descent toward the icehouse

Diagnosis and treatment of urticaria and angioedema: a worldwide perspective

Urticaria and angioedema are common clinical conditions representing a major concern for physicians and patients alike. The World Allergy Organization (WAO), recognizing the importance of these diseases, has contributed to previous guidelines for the diagnosis and management of urticaria. The Scientific and Clinical Issues Council of WAO proposed the development of this global Position Paper to further enhance the clinical management of these disorders through the participation of renowned experts from all WAO regions of the world. Sections on definition and classification, prevalence, etiology and pathogenesis, diagnosis, treatment, and prognosis are based on the best scientific evidence presently available. Additional sections devoted to urticaria and angioedema in children and pregnant women, quality of life and patient-reported outcomes, and physical urticarias have been incorporated into this document. It is expected that this article will supplement recent international guidelines with the contribution of an expert panel designated by the WAO, increasing awareness of the importance of urticaria and angioedema in medical practice and will become a useful source of information for optimum patient management worldwide