Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.

Homogeneity of the geochemical reference material BRP-1 (paranábasin basalt) and assessment of minimum mass

Reference materials (RM) are required for quantitative analyses and their successful use is associated with the degree of homogeneity, and the traceability and confidence limits of the values established by characterisation. During the production of a RM, the chemical characterisation can only commence after it has been demonstrated that the material has the required level of homogeneity. Here we describe the preparation of BRP-1, a proposed geochemical reference material, and the results of the tests to evaluate its degree of homogeneity between and within bottles. BRP-1 is the first of two geochemical RM being produced by Brazilian institutions in collaboration with the United States Geological Survey (USGS) and the International Association of Geoanalysts (IAG). Two test portions of twenty bottles of BRP-1 were analysed by wavelength dispersive-XRF spectrometry and major, minor and eighteen trace elements were determined. The results show that for most of the investigated elements, the units of BRP-1 were homogeneous at conditions approximately three times more rigorous than those strived for by the test of sufficient homogeneity. Furthermore, the within bottle homogeneity of BRP-1 was evaluated using small beam (1 mm(2)) synchrotron radiation XRF spectrometry and, for comparison, the USGS reference materials BCR-2 and GSP-2 were also evaluated. From our data, it has been possible to assign representative minimum masses for some major constituents (1 mg) and for some trace elements (1-13 mg), except Zr in GSP-2, for which test portions of 74 mg are recommended.

Multifunctional current reference generation strategy for grid-tied power electronic converter

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Studies on the Helminth Fauna of Alaska. XIII. Disease in the Sea Otter, with Special Reference to Helminth Parasites

During the spring of 1951, the U. S. Fish and Wildlife Service undertook the removal of sea otter, Enhydra lutris (L)., from the Aleutian Island of Amchitka, for the purpose of restocking range from which the animals have long been exterminated. The decision to undertake this activity was influenced by the nature of military operations planned for the island later the same year. The capture and removal of the otter were under the supervision of Mr. Robert D. Jones, Biologist, U. S. Fish and Wildlife Service. Heavy losses among the animals shortly after capture made the venture unsuccessful. Many deaths were concurrent among animals in the wild state. The writer was asked to investigate the causes of disease in the sea otter, and it is the purpose of this paper to report the results of these investigation, with special reference to helminth parasites.

What Business Reference Librarians Need to Know about Intellectual Property: Presentations sponsored by the Patent and Trademark Depository Library Association (PTDLA) at the American Library Association Annual Conference, New Orleans, June 25, 2006

Presentations sponsored by the Patent and Trademark Depository Library Association (PTDLA) at the American Library Association Annual Conference, New Orleans, June 25, 2006 Speaker #1: Nan Myers Associate Professor; Government Documents, Patents and Trademarks Librarian Wichita State University, Wichita, KS Title: Intellectual Property Roundup: Copyright, Trademarks, Trade Secrets, and Patents Abstract: This presentation provides a capsule overview of the distinctive coverage of the four types of intellectual property – What they are, why they are important, how to get them, what they cost, how long they last. Emphasis will be on what questions patrons ask most, along with the answers! Includes coverage of the mission of Patent & Trademark Depository Libraries (PTDLs) and other sources of business information outside of libraries, such as Small Business Development Centers. Speaker #2: Jan Comfort Government Information Reference Librarian Clemson University, Clemson, SC Title: Patents as a Source of Competitive Intelligence Information Abstract: Large corporations often have R&D departments, or large numbers of staff whose jobs are to monitor the activities of their competitors. This presentation will review strategies that small business owners can employ to do their own competitive intelligence analysis. The focus will be on features of the patent database that is available free of charge on the USPTO website, as well as commercial databases available at many public and academic libraries across the country. Speaker #3: Virginia Baldwin Professor; Engineering Librarian University of Nebraska-Lincoln, Lincoln, NE Title: Mining Online Patent Data for Business Information Abstract: The United States Patent and Trademark Office (USPTO) website and websites of international databases contains information about granted patents and patent applications and the technologies they represent. Statistical information about patents, their technologies, geographical information, and patenting entities are compiled and available as reports on the USPTO website. Other valuable information from these websites can be obtained using data mining techniques. This presentation will provide the keys to opening these resources and obtaining valuable data. Speaker #4: Donna Hopkins Engineering Librarian Renssalaer Polytechnic Institute, Troy, NY Title: Searching the USPTO Trademark Database for Wordmarks and Logos Abstract: This presentation provides an overview of wordmark searching in www.uspto.gov, followed by a review of the techniques of searching for non-word US trademarks using codes from the Design Search Code Manual. These codes are used in an electronic search, either on the uspto website or on CASSIS DVDs. The search is sometimes supplemented by consulting the Official Gazette. A specific example of using a section of the codes for searching is included. Similar searches on the Madrid Express database of WIPO, using the Vienna Classification, will also be briefly described.

Spatial reference of black capuchin monkeys in Brazilian Atlantic Forest: egocentric or allocentric?

Wild primates occupy large home ranges and travel long distances to reach goals. However, how primates are able to remember goal locations and travel efficiently is unclear. Few studies present consistent results regarding what reference system primates use to navigate, and what kind of spatial information they recognize. We analysed the pattern of navigation of one wild group of black capuchin monkeys, Cebus nigritus, at Atlantic Forest for 100 days in Carlos Botelho State Park (PECB), Brazil. We tested predictions based on the alternative hypotheses that black capuchin monkeys navigate using a sequence of landmarks as an egocentric reference system or an allocentric reference system, or both, depending on availability of food resources. The group location was recorded using a GPS device collecting coordinates at 5 min intervals, and route maps were generated using ArcView v9.3.1. The study group travelled through habitual routes during less than 30% of our study sample, and revisited resources from different starting points, using different paths and routes, even when prominent landmarks near feeding locations were not visible. The study group used habitual routes more frequently when high-quality foods were scarce, and navigated using different paths when revisiting food sources. Results support the hypothesis that black capuchin monkeys at PECB navigate using both egocentric and allocentric systems of reference, depending on the quality and distribution of the food resource they find. (C) 2010 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Longitudinal reference ranges for fetal ultrasound biometry in twin pregnancies

OBJECTIVE: The purpose of this study was to establish longitudinal reference ranges for fetal ultrasound biometry measurements and growth parameters in twin pregnancies. METHOD: A total of 200 uncomplicated twin pregnancies before 21 weeks of gestation were recruited for this prospective, longitudinal study. Women who abandoned follow-up, pregnancies with unknown outcomes or pregnancies with complications were excluded. Ultrasound scans were performed every three weeks, and biparietal and occipitofrontal diameters, head and abdominal circumferences, and femur diaphysis length measurements were obtained for each fetus at each visit. Estimated fetal weight, biparietal/occipitofrontal diameter, head circumference/abdominal circumference, and femur diaphysis length/abdominal circumference ratios were also calculated. Multilevel regression analysis was performed on normalized data. RESULTS: A total of 807 ultrasound examinations were performed in 125 twin pregnancies between 14 and 38 weeks of gestation (6.5 +/- 1.4 scans/pregnancy). Regression analysis demonstrated significant correlations for all variables with gestational age, namely log of the biparietal diameter (r = 0.98), log of the occipitofrontal diameter (r = 0.98), log of the head circumference (r = 0.99), log of the abdominal circumference (r = 0.98), square root of the femur length (r = 0.99), log of the estimated fetal weight (r = 0.99), biparietal/occipitofrontal ratio (r = -0.11), head/abdomen circumference ratio (r = -0.56), and log of the femur length/abdominal circumference ratio (r = 0.61). Values corresponding to the 10th, 50th, and 90th percentiles for estimated fetal weight at 28, 32, and 36 weeks, respectively, were as follows: 937, 1,096, 1,284 g; 1,462, 1,720, 2,025 g; and 2,020, 2,399, 2,849 g. CONCLUSION: In twin pregnancies, fetal ultrasound biometry measurements and growth parameters show a significant correlation with gestational age.

Hematologic Reference Values for Clinically Healthy Captive Golden Conures (Guaruba guarouba)

Golden conures or ararajubas (Guaruba guarouba) are endangered parrots endemic to the Brazilian Amazon forest. Body mass, blood cell counts, and total plasma protein were determined for 70 clinically healthy golden conures captive at zoologic parks and private breeder facilities in Brazil. Hematologic results (mean +/- SD) were: Erythrocytes 3.6 +/- 0.5 x 10(6) cells/mm(3), hemoglobin 12.8 +/- 1.4 g/dl, packed cell volume 46 +/- 3.8%, mean corpuscular volume 132 +/- 20 fl, mean corpuscular hemoglobin (MCH) 36 +/- 5.7 pg, mean corpuscular hemoglobin concentration (MCHC) 28 +/- 3.5%, thrombocytes 26.3 +/- 9.3 x 10(3) cells/mm(3), leukocytes 11.9 +/- 4.5 x 10(3) cells/mm(3), heterophils 6284 +/- 2715 cells/mm(3), lymphocytes 5473 +/- 2408 cells/mm(3), monocytes 113 +/- 162 cells/mm(3), eosinophils 10 +/- 42 cells/mm(3), basophils 27 +/- 64 cells/mm(3). Body mass was 254 +/- 24.9 g and total plasma protein (TPP) was 3.54 +/- 0.58 g/dl. No statistical differences were observed between genders within age groups. Differences between juveniles (J) and adults (A) were identified for TPP < A), MCH (J > A), and MCHC (J > A). These results provide reliable reference values for the clinical interpretation of hematologic results for the species. Hematology may be an important tool for population health investigations on free-ranging golden conure populations and will also be essential to survey the health of release candidates in future reintroduction programs.

rpb2 is a reliable reference gene for quantitative gene expression analysis in the dermatophyte Trichophyton rubrum

The selection of reference genes used for data normalization to quantify gene expression by real-time PCR amplifications (qRT-PCR) is crucial for the accuracy of this technique. In spite of this, little information regarding such genes for qRT-PCR is available for gene expression analyses in pathogenic fungi. Thus, we investigated the suitability of eight candidate reference genes in isolates of the human dermatophyte Trichophyton rubrum subjected to several environmental challenges, such as drug exposure, interaction with human nail and skin, and heat stress. The stability of these genes was determined by geNorm, NormFinder and Best-Keeper programs. The gene with the most stable expression in the majority of the conditions tested was rpb2 (DNA-dependent RNA polymerase II), which was validated in three T. rubrum strains. Moreover, the combination of rpb2 and chs1 (chitin synthase) genes provided for the most reliable qRT-PCR data normalization in T. rubrum under a broad range of biological conditions. To the best of our knowledge this is the first report on the selection of reference genes for qRT-PCR data normalization in dermatophytes and the results of these studies should permit further analysis of gene expression under several experimental conditions, with improved accuracy and reliability.

Reference model for implementing an MRP system in a highly diverse component and seasonal lean production environment

Companies are currently choosing to integrate logics and systems to achieve better solutions. These combinations also include companies striving to join the logic of material requirement planning (MRP) system with the systems of lean production. The purpose of this article was to design an MRP as part of the implementation of an enterprise resource planning (ERP) in a company that produces agricultural implements, which has used the lean production system since 1998. This proposal is based on the innovation theory, theory networks, lean production systems, ERP systems and the hybrid production systems, which use both components and MRP systems, as concepts of lean production systems. The analytical approach of innovation networks enables verification of the links and relationships among the companies and departments of the same corporation. The analysis begins with the MRP implementation project carried out in a Brazilian metallurgical company and follows through the operationalisation of the MRP project, until its production stabilisation. The main point is that the MRP system should help the company's operations with regard to its effective agility to respond in time to demand fluctuations, facilitating the creation process and controlling the branch offices in other countries that use components produced in the matrix, hence ensuring more accurate estimates of stockpiles. Consequently, it presents the enterprise knowledge development organisational modelling methodology in order to represent further models (goals, actors and resources, business rules, business process and concepts) that should be included in this MRP implementation process for the new configuration of the production system.

Pimavanserin, a selective serotonin (5-HT)2A-inverse agonist, enhances the efficacy and safety of risperidone, 2 mg/day, but does not enhance efficacy of haloperidol, 2 mg/day: Comparison with reference dose risperidone, 6 mg/day

Most atypical antipsychotic drugs (APDs), e. g. risperidone (RIS), produce more extensive blockade of brain serotonin (5-HT)(2A) than dopamine (DA) D-2 receptors. This distinguishes them from typical APDs, e.g. haloperidol (HAL). Our objective was to test the hypothesis that augmentation of low doses of RIS or HAL (2 mg/day) with pimavanserin (PIM), a selective 5-HT2A inverse agonist, to enhance 5-HT2A receptor blockade, can achieve efficacy comparable to RIS, 6 mg/day, but with lesser side effects. In a multi-center, randomized, double-blind, 6 week trial, 423 patients with chronic schizophrenia experiencing a recent exacerbation of psychotic symptoms were randomized to RIS2mg + placebo (RIS2PBO), RIS2mg + PIM20mg (RIS2PIM), RIS6mg + PBO (RIS6PBO), HAL2mg + PBO (HAL2PBO), or HAL2mg + PIM20mg (HAL2PIM). Improvement in psychopathology was measured by the PANSS and CGI-S. The reduction in PANSS Total Score with RIS2PIM at endpoint was significantly greater than RIS2PBO: -23.0 vs. -16.3 (p = 0.007), and not significantly different from the RIS6PBO group: -23.2 points. The percentage of patients with >= 20% improvement at day 15 in the RIS2PIM group was 62.3%, significantly greater than the RIS6PBO (42.1%; p = 0.01) and the RIS2PBO groups (37.7%; p = 0.002). Weight gain and hyperprolactinemia were greater in the RIS6PBO group than the RIS2PIM group but there was no difference in extrapyramidal side effects (EPS). HAL2PBO and HAL2PIM were not significantly different from each other in efficacy but HAL2PIM had less EPS at end point. Both HAL groups and RIS6PBO showed equal improvement in psychopathology at endpoint, indicating HAL 2 mg/day is effective to treat an acute exacerbation in chronic schizophrenia patients. In conclusion, a sub-effective RIS dose combined with PIM to enhance 5-HT2A receptor blockade provided faster onset of action, and at endpoint, equal efficacy and better safety, compared to standard dose RIS. These results support the conclusion that 5-HT2A receptor blockade is a key component of the action of some atypical APDs and can reduce EPS due to a typical APD. (C) 2012 Elsevier B.V. All rights reserved.

Nutrient reference concentrations and trophic state boundaries in subtropical reservoirs

Nutrient criteria as reference concentrations and trophic state boundaries are necessary for water management worldwide because anthropogenic eutrophication is a threat to the water uses. We compiled data on total phosphorus (TP), nitrogen (TN) and chlorophyll a (Chl a) from 17 subtropical reservoirs monitored from 2005-2009 in the Sao Paulo State (Brazil) to calculate reference concentrations through the trisection method (United States Environmental Protection Agency). By dividing our dataset into thirds we presented trophic state boundaries and frequency curves for the nutrient levels in water bodies with different enrichment conditions. TP and TN baseline concentrations (0.010 mg/L and 0.350 mg/L, respectively) were bracketed by ranges for temperate reservoirs available in the literature. We propose trophic state boundaries (upper limits for the oligotrophic category: 0.010 mg TP/L, 0.460 mg TN/L and 1.7 mu g Chl a/L; for the mesotrophic: 0.030 mg TP/L, 0.820 mg TN/L and 9.0 mu g Chl a/L). Through an example with a different dataset (from the Itupararanga Reservoir, Brazil), we encouraged the use of frequency curves to compare data from individual monitoring efforts with the expected concentrations in oligotrophic, mesotrophic and eutrophic regional systems. Such analysis might help designing recovery programs to reach targeted concentrations and mitigate the undesirable eutrophication symptoms in subtropical freshwaters.

17 beta-Estradiol replacement in young, adult and middle-aged female ovariectomized rats promotes improvement of spatial reference memory and an antidepressant effect and alters monoamines and BDNF levels in memory- and depression-related brain areas

Clinical and experimental evidence suggest that estrogens have a major impact on cognition, presenting neurotrophic and neuroprotective actions in regions involved in such function. In opposite, some studies indicate that certain hormone therapy regimens may provoke detrimental effects over female cognitive and neurological function. Therefore, we decided to investigate how estrogen treatment would influence cognition and depression in different ages. For that matter, this study assessed the effects of chronic 17 beta-estradiol treatment over cognition and depressive-like behaviors of young (3 months old), adult (7 months old) and middle-aged (12 months old) reproductive female Wistar rats. These functions were also correlated with alterations in the serotonergic system, as well as hippocampal BDNF. 17 beta-Estradiol treatment did not influence animals' locomotor activity and exploratory behavior, but it was able to improve the performance of adult and middle-aged rats in the Morris water maze, the latter being more responsive to the treatment. Young and adult rats displayed decreased immobility time in the forced swimming test, suggesting an effect of 17 beta-estradiol also over such depressive-like behavior. This same test revealed increased swimming behavior, triggered by serotonergic pathway, in adult rats. Neurochemical evaluations indicated that 17 beta-estradiol treatment was able to increase serotonin turnover rate in the hippocampus of adult rats. Interestingly, estrogen treatment increased BDNF levels from animals of all ages. These findings support the notion that the beneficial effects of 17 beta-estradiol over spatial reference memory and depressive-like behavior are evident only when hormone therapy occurs at early ages and early stages of hormonal decline. (C) 2011 Elsevier B.V. All rights reserved.

Perfomance of methods for estimating reference evapotranspiration in the municipalities of Frederico Westphalen and Palmeira das Missoes, State of Rio Grande do Sul, Brazil

The estimation of reference evapotranspiration (ETo), used in water balance, allows to determine soil water content, assisting on irrigation management. The present study aimed to compare simple ETo estimating methods with the Penman-Monteith (FAO), in the folowing time scales: daily, 5, 10, 15 and 30 days and monthly in the counties of Frederico Westphalen and Palmeira das Missoes, in the Rio Grande do Sul state, Brazil. The methods tested had their efficiency improved by increasing the time scale of analysis, keeping the same performance for both locations. The highest and lowest ETo values occurred in December and June, respectively. Most methods underestimated ETo. For any of the time scales Makking and Radiaton FAO24 methods can replace the Penman-Monteith for estimating ETo.

Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses

Selection of reference genes is an essential consideration to increase the precision and quality of relative expression analysis by the quantitative RT-PCR method. The stability of eight expressed sequence tags was evaluated to define potential reference genes to study the differential expression of common bean target genes under biotic (incompatible interaction between common bean and fungus Colletotrichum lindemuthianum) and abiotic (drought; salinity; cold temperature) stresses. The efficiency of amplification curves and quantification cycle (C (q)) were determined using LinRegPCR software. The stability of the candidate reference genes was obtained using geNorm and NormFinder software, whereas the normalization of differential expression of target genes [beta-1,3-glucanase 1 (BG1) gene for biotic stress and dehydration responsive element binding (DREB) gene for abiotic stress] was defined by REST software. High stability was obtained for insulin degrading enzyme (IDE), actin-11 (Act11), unknown 1 (Ukn1) and unknown 2 (Ukn2) genes during biotic stress, and for SKP1/ASK-interacting protein 16 (Skip16), Act11, Tubulin beta-8 (beta-Tub8) and Unk1 genes under abiotic stresses. However, IDE and Act11 were indicated as the best combination of reference genes for biotic stress analysis, whereas the Skip16 and Act11 genes were the best combination to study abiotic stress. These genes should be useful in the normalization of gene expression by RT-PCR analysis in common bean, the most important edible legume.