WorldWideScience

Sample records for range gene suitable

  1. Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

    Directory of Open Access Journals (Sweden)

    Turner Renee J

    2009-08-01

    Full Text Available Abstract Background Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization. Methods Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT, 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms. Results Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder. Conclusion The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.

  2. In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

    Directory of Open Access Journals (Sweden)

    Kristiansen Glen

    2007-06-01

    Full Text Available Abstract Background Housekeeping genes are commonly used as endogenous reference genes for the relative quantification of target genes in gene expression studies. No conclusive systematic study comparing the suitability of different candidate reference genes in clear cell renal cell carcinoma has been published to date. To remedy this situation, 10 housekeeping genes for normalizing purposes of RT-PCR measurements already recommended in various studies were examined with regard to their usefulness as reference genes. Results The expression of the potential reference genes was examined in matched malignant and non-malignant tissue specimens from 25 patients with clear cell renal cell carcinoma. Quality assessment of isolated RNA performed with a 2100 Agilent Bioanalyzer showed a mean RNA integrity number of 8.7 for all samples. The between-run variations related to the crossing points of PCR reactions of a control material ranged from 0.17% to 0.38%. The expression of all genes did not depend on age, sex, and tumour stage. Except the genes TATA box binding protein (TBP and peptidylprolyl isomerase A (PPIA, all genes showed significant differences in expression between malignant and non-malignant pairs. The expression stability of the candidate reference genes was additionally controlled using the software programs geNorm and NormFinder. TBP and PPIA were validated as suitable reference genes by normalizing the target gene ADAM9 using these two most stably expressed genes in comparison with up- and down-regulated housekeeping genes of the panel. Conclusion Our study demonstrated the suitability of the two housekeeping genes PPIA and TBP as endogenous reference genes when comparing malignant tissue samples with adjacent normal tissue samples from clear cell renal cell carcinoma. Both genes are recommended as reference genes for relative gene quantification in gene profiling studies either as single gene or preferably in combination.

  3. A Fixed-Frequency Bidirectional Resonant DC-DC Converter Suitable for Wide Voltage Gain Range

    DEFF Research Database (Denmark)

    Shen, Yanfeng; Wang, Huai; Al-Durra, Ahmed;

    2017-01-01

    This paper proposes a new bidirectional resonant dc-dc converter suitable for wide voltage gain range applications (e.g., energy storage systems). The proposed converter overcomes the narrow voltage gain range of conventional resonant DC-DC converters, and meanwhile achieves high efficiency...... and characteristics of the proposed converter are analyzed. Finally, a 1-kW converter prototype is built and the experimental results verify the theoretical analyses....

  4. Identification of suitable grapevine reference genes for qRT-PCR derived from heterologous species.

    Science.gov (United States)

    Tashiro, Rebecca M; Philips, Joshua G; Winefield, Christopher S

    2016-02-01

    Identification and validation of suitable reference genes that exhibit robust transcriptional stability across many sample types is an absolute requirement of all qRT-PCR experiments. Often, however, only small numbers of reference genes, validated across limited sample types, are available for non-model species. This points to a clear need to assess and validate a wider range of potential reference genes than is currently available. We therefore looked to test and validate a large number of potential reference genes across a wide range of tissue types and treatments to determine the applicability of these reference genes for use in grapevine and other non-model plant species. Potential reference genes were selected based on stability of gene transcription in the model plant species Arabidopsis or due to their common use in the grapevine community. The selected reference genes were analyzed across two datasets consisting of a range of either 'Sauvignon blanc' or 'Pinot noir' tissues. A total of 11 potential reference genes were screened across the two datasets. Gene stability was analyzed by GeNorm, a widely used Excel application, or an ANOVA-based method developed in red clover. Both analysis methods showed that all 11 potential reference genes are stably expressed in the datasets tested, but the rankings of gene stability differed based on the datasets and analysis method used. Furthermore, the transcript stability of these genes, initially identified in Arabidopsis and now validated in grapevine, suggests applicability across a wide range of non-model plant species in addition to their utility in grapevine.

  5. Assessing range-wide habitat suitability for the Lesser Prairie-Chicken

    Directory of Open Access Journals (Sweden)

    Catherine S. Jarnevich

    2016-06-01

    Full Text Available Population declines of many wildlife species have been linked to habitat loss incurred through land-use change. Incorporation of conservation planning into development planning may mitigate these impacts. The threatened Lesser Prairie-Chicken (Tympanuchus pallidicinctus is experiencing loss of native habitat and high levels of energy development across its multijurisdictional range. Our goal was to explore relationships of the species occurrence with landscape characteristics and anthropogenic effects influencing its distribution through evaluation of habitat suitability associated with one particular habitat usage, lekking. Lekking has been relatively well-surveyed, though not consistently, in all jurisdictions. All five states in which Lesser Prairie-Chickens occur cooperated in development of a Maxent habitat suitability model. We created two models, one with state as a factor and one without state. When state was included it was the most important predictor, followed by percent of land cover consisting of known or suspected used vegetation classes within a 5000 m area around a lek. Without state, land cover was the most important predictor of relative habitat suitability for leks. Among the anthropogenic predictors, landscape condition, a measure of human impact integrated across several factors, was most important, ranking third in importance without state. These results quantify the relative suitability of the landscape within the current occupied range of Lesser Prairie-Chickens. These models, combined with other landscape information, form the basis of a habitat assessment tool that can be used to guide siting of development projects and targeting of areas for conservation.

  6. Assessing range-wide habitat suitability for the Lesser Prairie-Chicken

    Science.gov (United States)

    Jarnevich, Catherine S.; Holcombe, Tracy R.; Grisham, Blake A.; Timmer, Jennifer M.; Boal, Clint W.; Butler, Matthew; Pitman, James C.; Kyle, Sean; Klute, David; Beauprez, Grant M.; Janus, Allan; Van Pelt, William E.

    2016-01-01

    Population declines of many wildlife species have been linked to habitat loss incurred through land-use change. Incorporation of conservation planning into development planning may mitigate these impacts. The threatened Lesser Prairie-Chicken (Tympanuchus pallidicinctus) is experiencing loss of native habitat and high levels of energy development across its multijurisdictional range. Our goal was to explore relationships of the species occurrence with landscape characteristics and anthropogenic effects influencing its distribution through evaluation of habitat suitability associated with one particular habitat usage, lekking. Lekking has been relatively well-surveyed, though not consistently, in all jurisdictions. All five states in which Lesser Prairie-Chickens occur cooperated in development of a Maxent habitat suitability model. We created two models, one with state as a factor and one without state. When state was included it was the most important predictor, followed by percent of land cover consisting of known or suspected used vegetation classes within a 5000 m area around a lek. Without state, land cover was the most important predictor of relative habitat suitability for leks. Among the anthropogenic predictors, landscape condition, a measure of human impact integrated across several factors, was most important, ranking third in importance without state. These results quantify the relative suitability of the landscape within the current occupied range of Lesser Prairie-Chickens. These models, combined with other landscape information, form the basis of a habitat assessment tool that can be used to guide siting of development projects and targeting of areas for conservation.

  7. Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

    Science.gov (United States)

    Froese, Jens G; Smith, Carl S; Durr, Peter A; McAlpine, Clive A; van Klinken, Rieks D

    2017-01-01

    Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

  8. Experimental method for determination of a suitable temperature range for glasses used in precision molding

    Science.gov (United States)

    Ma, Tao; Chen, Fan; Yu, Jingchi

    2010-10-01

    Viscosity of glass is one of its important technological properties. It is usually adopted as a mark in controlling and evaluating the workability of glass. The viscous features in a glass forming process are strongly relevant to the temperature distribution. Appropriate procedure setting and controlling of temperature is an essential issue for precision glass molding. But the characteristic viscosity of glass is difficult to be observed directly in a practical lens molding. It's not convenient to set up the molding conditions caused by the differences between theoretical data and actual system. The purpose of this experimental study is intended to provide a simple and reliable method for determination of suitable temperature intervals of glasses used in the precision molding fabrication which meets the requirements of process tolerances in the industrial productions. The average glass deforming force and center thickness of molded lens are taken as the two conditions of determination principle for molding temperature ranges. The average force should not less than the minimum value of measurement accuracy and the lens thickness should reach the design target in these temperature ranges. These two conditions are easy to be measured and fit for application in the engineering. The molding temperature ranges of several kinds of glass were obtained in this project. One of them is Schott optical glass P-LASF51 which is selected for evaluating and validating this method. Its suitable molding temperature range is from 590 to 614 . The results of molding experiments demonstrate the method is effective and feasible.

  9. Reference Genes in the Pathosystem Phakopsora pachyrhizi/ Soybean Suitable for Normalization in Transcript Profiling

    Directory of Open Access Journals (Sweden)

    Daniela Hirschburger

    2015-09-01

    Full Text Available Phakopsora pachyrhizi is a devastating pathogen on soybean, endangering soybean production worldwide. Use of Host Induced Gene Silencing (HIGS and the study of effector proteins could provide novel strategies for pathogen control. For both approaches quantification of transcript abundance by RT-qPCR is essential. Suitable stable reference genes for normalization are indispensable to obtain accurate RT-qPCR results. According to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE guidelines and using algorithms geNorm and NormFinder we tested candidate reference genes from P. pachyrhizi and Glycine max for their suitability in normalization of transcript levels throughout the infection process. For P. pachyrhizi we recommend a combination of CytB and PDK or GAPDH for in planta experiments. Gene expression during in vitro stages and over the whole infection process was found to be highly unstable. Here, RPS14 and UbcE2 are ranked best by geNorm and NormFinder. Alternatively CytB that has the smallest Cq range (Cq: quantification cycle could be used. We recommend specification of gene expression relative to the germ tube stage rather than to the resting urediospore stage. For studies omitting the resting spore and the appressorium stages a combination of Elf3 and RPS9, or PKD and GAPDH should be used. For normalization of soybean genes during rust infection Ukn2 and cons7 are recommended.

  10. High Resolution Habitat Suitability Modelling For Restricted-Range Hawaiian Alpine Arthropod Species

    Science.gov (United States)

    Stephenson, N. M.

    2016-12-01

    Mapping potentially suitable habitat is critical for effective species conservation and management but can be challenging in areas exhibiting complex heterogeneity. An approach that combines non-intrusive spatial data collection techniques and field data can lead to a better understanding of landscapes and species distributions. Nysius wekiuicola, commonly known as the wēkiu bug, is the most studied arthropod species endemic to the Maunakea summit in Hawai`i, yet details about its geographic distribution and habitat use remain poorly understood. To predict the geographic distribution of N. wekiuicola, MaxEnt habitat suitability models were generated from a diverse set of input variables, including fifteen years of species occurrence data, high resolution digital elevation models, surface mineralogy maps derived from hyperspectral remote sensing, and climate data. Model results indicate that elevation (78.2 percent), and the presence of nanocrystalline hematite surface minerals (13.7 percent) had the highest influence, with lesser contributions from aspect, slope, and other surface mineral classes. Climatic variables were not included in the final analysis due to auto-correlation and coarse spatial resolution. Biotic factors relating to predation and competition also likely dictate wēkiu bug capture patterns and influence our results. The wēkiu bug range and habitat suitability models generated as a result of this study will be directly incorporated into management and restoration goals for the summit region and can also be adapted for other arthropod species present, leading to a more holistic understanding of metacommunity dynamics. Key words: Microhabitat, Structure from Motion, Lidar, MaxEnt, Habitat Suitability

  11. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits.

    Science.gov (United States)

    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits.

  12. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits

    Science.gov (United States)

    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits. PMID:27536316

  13. Identification of housekeeping genes suitable for gene expression analysis in Jian carp (Cyprinus carpio var. jian).

    Science.gov (United States)

    Tang, Yong-kai; Yu, Ju-hua; Xu, Pao; Li, Jian-lin; Li, Hong-xia; Ren, Hong-tao

    2012-10-01

    Jian carp (Cyprinus carpio var. jian) is an important economic fish species cultured in China. In this report, we performed a systematic analysis to identify an appropriate housekeeping (HK) gene for the study of gene expression in Jian carp. For this purpose, partial DNA sequences of four potential candidate genes (elongation factor 1 alpha (EF-1α), glyceraldehyde-3-phosphate (GAPDH), beta-actin (ACTB), and 18S ribosomal RNA (18S rRNA) were isolated, and their expression levels were studied using RNA extracted from nine tissues (forebrain, hypothalamus, liver, fore-intestine, hind-intestine, ovary, muscle, heart, kidney) in juvenile and adult Jian carp. Gene expression levels were quantified by quantitative real time RT-PCR (qRT-PCR), and expression stability was evaluated by comparing the coefficients of variation (CV) of the Ct values. The results showed that EF-1α was the most suitable HK gene in all tissues of juvenile and adult Jian carp. However, at distinct juvenile and adult developmental stages, there was not a single optimal gene for normalization of expression levels in all tissues. EF-1α was the most stable gene only in forebrain, hypothalamus, liver, heart, and kidney. These results provide data that can be expected to aid gene expression analysis in Jian carp research, but underline the importance of identifying the optimal HK gene for each new experimental paradigm.

  14. Identification of suitable reference genes for gene expression studies of shoulder instability.

    Directory of Open Access Journals (Sweden)

    Mariana Ferreira Leal

    Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

  15. Validation of suitable reference genes for quantitative gene expression analysis in Panax ginseng

    Directory of Open Access Journals (Sweden)

    Meizhen eWang

    2016-01-01

    Full Text Available Reverse transcription-qPCR (RT-qPCR has become a popular method for gene expression studies. Its results require data normalization by housekeeping genes. No single gene is proved to be stably expressed under all experimental conditions. Therefore, systematic evaluation of reference genes is necessary. With the aim to identify optimum reference genes for RT-qPCR analysis of gene expression in different tissues of Panax ginseng and the seedlings grown under heat stress, we investigated the expression stability of eight candidate reference genes, including elongation factor 1-beta (EF1-β, elongation factor 1-gamma (EF1-γ, eukaryotic translation initiation factor 3G (IF3G, eukaryotic translation initiation factor 3B (IF3B, actin (ACT, actin11 (ACT11, glyceraldehyde-3-phosphate dehydrogenase (GAPDH and cyclophilin ABH-like protein (CYC, using four widely used computational programs: geNorm, Normfinder, BestKeeper, and the comparative ΔCt method. The results were then integrated using the web-based tool RefFinder. As a result, EF1-γ, IF3G and EF1-β were the three most stable genes in different tissues of P. ginseng, while IF3G, ACT11 and GAPDH were the top three-ranked genes in seedlings treated with heat. Using three better reference genes alone or in combination as internal control, we examined the expression profiles of MAR, a multiple function-associated mRNA-like non-coding RNA (mlncRNA in P. ginseng. Taken together, we recommended EF1-γ/IF3G and IF3G/ACT11 as the suitable pair of reference genes for RT-qPCR analysis of gene expression in different tissues of P. ginseng and the seedlings grown under heat stress, respectively. The results serve as a foundation for future studies on P. ginseng functional genomics.

  16. Suitability of commonly used housekeeping genes in gene expression studies for space radiation research

    Science.gov (United States)

    Arenz, A.; Stojicic, N.; Lau, P.; Hellweg, C. E.; Baumstark-Khan, C.

    Research on the effects of ionizing radiation exposure involves the use of real-time reverse transcription polymerase chain reaction (qRT-PCR) for measuring changes in gene expression. Several variables need to be controlled for gene expression analysis, such as different amounts of starting material between the samples, variations in enzymatic efficiencies of the reverse transcription step, and differences in RNA integrity. Normalization of the obtained data to an invariant endogenous control gene (reference gene) is the elementary step in relative quantification strategy. There is a strong correlation between the quality of the normalized data and the stability of the reference gene itself. This is especially relevant when the samples have been obtained after exposure to radiation qualities inducing different amounts and kinds of damage, leading to effects on cell cycle delays or even on cell cycle blocks. In order to determine suitable reference genes as internal controls in qRT-PCR assays after exposure to ionizing radiation, we studied the gene expression levels of nine commonly used reference genes which are constitutively expressed in A549 lung cancer cells. Expression levels obtained for ACTB, B2M, GAPDH, PBGD, 18S rRNA, G6PDH, HPRT, UBC, TFRC and SDHA were determined after exposure to 2 and 6 Gy X-radiation. Gene expression data for Growth arrest and damage-inducible gene 45 (GADD45α) and Cyclin-dependent kinase inhibitor 1A (CDKN1A/p21CIP1) were selected to elucidate the influence of normalization by using appropriate and inappropriate internal control genes. According to these results, we strongly recommend the use of a panel of reference genes instead of only one.

  17. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs

    Directory of Open Access Journals (Sweden)

    Guanglin Niu

    2016-12-01

    Full Text Available The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods. We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.

  18. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs.

    Science.gov (United States)

    Niu, Guanglin; Yang, Yalan; Zhang, YuanYuan; Hua, Chaoju; Wang, Zishuai; Tang, Zhonglin; Li, Kui

    2016-01-01

    The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.

  19. Screening for the Most Suitable Reference Genes for Gene Expression Studies in Equine Milk Somatic Cells.

    Directory of Open Access Journals (Sweden)

    Jakub Cieslak

    Full Text Available Apart from the well-known role of somatic cell count as a parameter reflecting the inflammatory status of the mammary gland, the composition of cells isolated from milk is considered as a valuable material for gene expression studies in mammals. Due to its unique composition, in recent years an increasing interest in mare's milk consumption has been observed. Thus, investigating the genetic background of horse's milk variability presents and interesting study model. Relying on 39 milk samples collected from mares representing three breeds (Polish Primitive Horse, Polish Cold-blooded Horse, Polish Warmblood Horse we aimed to investigate the utility of equine milk somatic cells as a source of mRNA and to screen the best reference genes for RT-qPCR using geNorm and NormFinder algorithms. The results showed that despite relatively low somatic cell counts in mare's milk, the amount and the quality of the extracted RNA are sufficient for gene expression studies. The analysis of the utility of 7 potential reference genes for RT-qPCR experiments for the normalization of equine milk somatic cells revealed some differences between the outcomes of the applied algorithms, although in both cases the KRT8 and TOP2B genes were pointed as the most stable. Analysis by geNorm showed that the combination of 4 reference genes (ACTB, GAPDH, TOP2B and KRT8 is required for apropriate RT-qPCR experiments normalization, whereas NormFinder algorithm pointed the combination of KRT8 and RPS9 genes as the most suitable. The trial study of the relative transcript abundance of the beta-casein gene with the use of various types and numbers of internal control genes confirmed once again that the selection of proper reference gene combinations is crucial for the final results of each real-time PCR experiment.

  20. Environmental predictors of habitat suitability and biogeographical range of Franciscana dolphins (Pontoporia blainvillei

    Directory of Open Access Journals (Sweden)

    Jonatan J. Gomez

    2015-01-01

    Full Text Available The aim of this study was to use species distribution models to estimate the effects of environmental variables on the habitat suitability of river dolphins Pontoporia blainvillei (franciscanas along their overall biogeographical distribution. Based on the literature, we selected six environmental variables to be included in the models; four climatic factors (surface sea temperature, salinity, turbidity and productivity and two biotic factors (prey availability and fishing effort. We determined that the biographic range is under the following limits: temperature less than 19°C, a salinity of 36 psu and a minimal probability of the occurrence of fish C. guatucupa of 0.297. In the discussion, we postulate hypotheses on the behavioural and physiological mechanisms that cause these associations between environmental predictors and Franciscanas distribution. There was a good fit between the distribution predicted by the species distribution model and the one proposed by the experts of the International Union for Conservation of Nature; however, our analysis failed to highlight the fundamental role of bycatch as the main threat to this dolphin species.

  1. RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes

    Directory of Open Access Journals (Sweden)

    Yiwei Chen

    2013-01-01

    Full Text Available We developed a single vector recombinant adeno-associated viral (rAAV expression system for spatial and reversible control of polycistronic gene expression. Our approach (i integrates the advantages of the tetracycline (Tet-controlled transcriptional silencer tTSKid and the self-cleaving 2A peptide bridge, (ii combines essential regulatory components as an autoregulatory loop, (iii simplifies the gene delivery scheme, and (iv regulates multiple genes in a synchronized manner. Controlled by an upstream Tet-responsive element (TRE, both the ubiquitous chicken β-actin promoter (CAG and the neuron-specific synapsin-1 promoter (Syn could regulate expression of tTSKid together with two 2A-linked reporter genes. Transduction in vitro exhibited maximally 50-fold regulation by doxycycline (Dox. Determined by gene delivery method as well as promoter, highly specific tissues were transduced in vivo. Bioluminescence imaging (BLI visualized reversible “ON/OFF” gene switches over repeated “Doxy-Cycling” in living mice. Thus, the reversible rAAV-mediated N-cistronic gene expression system, termed RANGE, may serve as a versatile tool to achieve reversible polycistronic gene regulation for the study of gene function as well as gene therapy.

  2. RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes.

    Science.gov (United States)

    Chen, Yiwei; Cao, Liji; Luo, Chonglin; Ditzel, Désirée Aw; Peter, Jörg; Sprengel, Rolf

    2013-04-09

    We developed a single vector recombinant adeno-associated viral (rAAV) expression system for spatial and reversible control of polycistronic gene expression. Our approach (i) integrates the advantages of the tetracycline (Tet)-controlled transcriptional silencer tTS(Kid) and the self-cleaving 2A peptide bridge, (ii) combines essential regulatory components as an autoregulatory loop, (iii) simplifies the gene delivery scheme, and (iv) regulates multiple genes in a synchronized manner. Controlled by an upstream Tet-responsive element (TRE), both the ubiquitous chicken β-actin promoter (CAG) and the neuron-specific synapsin-1 promoter (Syn) could regulate expression of tTS(Kid) together with two 2A-linked reporter genes. Transduction in vitro exhibited maximally 50-fold regulation by doxycycline (Dox). Determined by gene delivery method as well as promoter, highly specific tissues were transduced in vivo. Bioluminescence imaging (BLI) visualized reversible "ON/OFF" gene switches over repeated "Doxy-Cycling" in living mice. Thus, the reversible rAAV-mediated N-cistronic gene expression system, termed RANGE, may serve as a versatile tool to achieve reversible polycistronic gene regulation for the study of gene function as well as gene therapy.Molecular Therapy - Nucleic Acids (2013) 2, e85; doi:10.1038/mtna.2013.15; published online 9 April 2013.

  3. Evaluating suitable internal control genes for transcriptional studies in heat-stressed mammary explants of buffaloes.

    Science.gov (United States)

    Sodhi, M; Kishore, A; Khate, K; Kapila, N; Mishra, B P; Kataria, R S; Mohanty, A K; Varshney, N; Mukesh, M

    2013-04-01

    It is now a well-accepted notion that each new experimental design requires proper evaluation of internal control genes (ICGs) for accurate normalization of expression data. In riverine buffaloes, till date no appropriate ICG has been reported for studying transcriptional response under any of the physiological stressful condition. The objective here was to test 16 well-known reference genes from different functional categories that could serve as suitable ICG during heat stress studies in buffalo mammary tissue. Briefly, the mammary explants were exposed to 45°C for 1 h and subsequently allowed to recover at 37°C for different time points (2-24 h). Three software programs, geNorm, Normfinder and BestKeeper, were used to measure gene transcript stability. RPL22 was excluded because of weak amplification and unacceptable PCR efficiency. Except GAPDH, all other genes showed expression stability within the acceptable range (<1.5). RPL4, B2M, RPS23 and EEF1A1 genes were found to be most stably expressed while GAPDH and ACTB showed least stability. The BestKeeper analysis identified high correlation for RPL4 (r=0.953) and EEF1A1 (r=0.914) with BestKeeper index. Based on the present findings, it could be suggested that geometric average of RPL4, B2M, RPS23 and EEF1A1 would provide accurate normalization to transcriptional data of buffalo mammary explant in response to heat stress. © 2012 Blackwell Verlag GmbH.

  4. Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum for abiotic stresses and hormone stimuli

    Directory of Open Access Journals (Sweden)

    Meng-Yao Li

    2016-09-01

    Full Text Available Parsley is one of the most important vegetable in Apiaceae family and widely used in food industry, medicinal and cosmetic. The recent studies in parsley are mainly focus on chemical composition, further research involving the analysis of the gene functions and expressions will be required. qPCR is a powerful method for detecting very low quantities of target transcript levels and widely used for gene expression studies. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, three software geNorm, NormFinder, and BestKeeper were used to evaluate the expression stabilities of eight candidate reference genes (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB under various conditions including abiotic stresses (heat, cold, salt, and drought and hormone stimuli treatments (GA, SA, MeJA, and ABA. The results showed that EF-1α and TUB were identified as the most stable genes for abiotic stresses, while EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes across all the tested samples, while UBC was the least stable one. The expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study provides a guideline for selection the suitable reference genes in gene expression in parsley.

  5. Defining suitable reference genes for RT-qPCR analysis on intestinal epithelial cells.

    Science.gov (United States)

    Sirakov, Maria; Borra, Marco; Cambuli, Francesca Maria; Plateroti, Michelina

    2013-07-01

    The study of the mammalian intestinal epithelium concerns several aspects of cellular and molecular biology. In fact, most of these studies aim to define molecular components or mechanisms related with the control of stemness and the balance between cell proliferation and differentiation in physiopathological conditions. It is worth mentioning that real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) approaches are commonly used, but only a few studies are available regarding suitable reference genes to normalize gene expression data. The present study was designed to validate potential reference genes in freshly isolated proliferating or differentiated epithelial cells from the mouse intestine. We also extended our analysis to the IEC6 intestinal epithelial cells, as a promising model to study intestinal physiopathology in vitro. The stability of six potential reference genes (Hprt1, Ppia, Gapdh, Rplp0, Ppib, and Vil1) has been tested both in epithelial cells isolated from the mouse intestine and in the IEC6 cell line. The software programs-geNorm and Normfinder-were used to obtain an estimation of the expression stability of each gene and, by comparing the results, to identify the most suitable genes for RT-qPCR data normalization. These multiple approaches allowed us to select different suitable reference genes for the correct quantification of mRNAs depending on the differentiated or proliferative nature of the cells.

  6. Anticipating knowledge to inform species management: predicting spatially explicit habitat suitability of a colonial vulture spreading its range.

    Directory of Open Access Journals (Sweden)

    Patricia Mateo-Tomás

    Full Text Available BACKGROUND: The knowledge of both potential distribution and habitat suitability is fundamental in spreading species to inform in advance management and conservation planning. After a severe decline in the past decades, the griffon vulture (Gyps fulvus is now spreading its breeding range towards the northwest in Spain and Europe. Because of its key ecological function, anticipated spatial knowledge is required to inform appropriately both vulture and ecosystem management. METHODOLOGY/FINDINGS: Here we used maximum entropy (Maxent models to determine the habitat suitability of potential and current breeding distribution of the griffon vulture using presence-only data (N = 124 colonies in north-western Spain. The most relevant ecological factors shaping this habitat suitability were also identified. The resulting model had a high predictive performance and was able to predict species' historical distribution. 7.5% (approximately 1,850 km(2 of the study area resulted to be suitable breeding habitat, most of which (approximately 70% is already occupied by the species. Cliff availability and livestock density, especially of sheep and goats, around 10 km of the colonies were the fundamental factors determining breeding habitat suitability for this species. CONCLUSIONS/SIGNIFICANCE: Griffon vultures could still spread 50-60 km towards the west, increasing their breeding range in 1,782 km(2. According to our results, 7.22% of the area suitable for griffon vulture will be affected by wind farms, so our results could help to better plan wind farm locations. The approach here developed could be useful to inform management of reintroductions and recovery programmes currently being implemented for both the griffon vulture and other threatened vulture species.

  7. Selection of suitable endogenous reference genes for relative copy number detection in sugarcane.

    Science.gov (United States)

    Xue, Bantong; Guo, Jinlong; Que, Youxiong; Fu, Zhiwei; Wu, Luguang; Xu, Liping

    2014-05-19

    Transgene copy number has a great impact on the expression level and stability of exogenous gene in transgenic plants. Proper selection of endogenous reference genes is necessary for detection of genetic components in genetically modification (GM) crops by quantitative real-time PCR (qPCR) or by qualitative PCR approach, especially in sugarcane with polyploid and aneuploid genomic structure. qPCR technique has been widely accepted as an accurate, time-saving method on determination of copy numbers in transgenic plants and on detection of genetically modified plants to meet the regulatory and legislative requirement. In this study, to find a suitable endogenous reference gene and its real-time PCR assay for sugarcane (Saccharum spp. hybrids) DNA content quantification, we evaluated a set of potential "single copy" genes including P4H, APRT, ENOL, CYC, TST and PRR, through qualitative PCR and absolute quantitative PCR. Based on copy number comparisons among different sugarcane genotypes, including five S. officinarum, one S. spontaneum and two S. spp. hybrids, these endogenous genes fell into three groups: ENOL-3--high copy number group, TST-1 and PRR-1--medium copy number group, P4H-1, APRT-2 and CYC-2--low copy number group. Among these tested genes, P4H, APRT and CYC were the most stable, while ENOL and TST were the least stable across different sugarcane genotypes. Therefore, three primer pairs of P4H-3, APRT-2 and CYC-2 were then selected as the suitable reference gene primer pairs for sugarcane. The test of multi-target reference genes revealed that the APRT gene was a specific amplicon, suggesting this gene is the most suitable to be used as an endogenous reference target for sugarcane DNA content quantification. These results should be helpful for establishing accurate and reliable qualitative and quantitative PCR analysis of GM sugarcane.

  8. Selection of Suitable Endogenous Reference Genes for Relative Copy Number Detection in Sugarcane

    Directory of Open Access Journals (Sweden)

    Bantong Xue

    2014-05-01

    Full Text Available Transgene copy number has a great impact on the expression level and stability of exogenous gene in transgenic plants. Proper selection of endogenous reference genes is necessary for detection of genetic components in genetically modification (GM crops by quantitative real-time PCR (qPCR or by qualitative PCR approach, especially in sugarcane with polyploid and aneuploid genomic structure. qPCR technique has been widely accepted as an accurate, time-saving method on determination of copy numbers in transgenic plants and on detection of genetically modified plants to meet the regulatory and legislative requirement. In this study, to find a suitable endogenous reference gene and its real-time PCR assay for sugarcane (Saccharum spp. hybrids DNA content quantification, we evaluated a set of potential “single copy” genes including P4H, APRT, ENOL, CYC, TST and PRR, through qualitative PCR and absolute quantitative PCR. Based on copy number comparisons among different sugarcane genotypes, including five S. officinarum, one S. spontaneum and two S. spp. hybrids, these endogenous genes fell into three groups: ENOL-3—high copy number group, TST-1 and PRR-1—medium copy number group, P4H-1, APRT-2 and CYC-2—low copy number group. Among these tested genes, P4H, APRT and CYC were the most stable, while ENOL and TST were the least stable across different sugarcane genotypes. Therefore, three primer pairs of P4H-3, APRT-2 and CYC-2 were then selected as the suitable reference gene primer pairs for sugarcane. The test of multi-target reference genes revealed that the APRT gene was a specific amplicon, suggesting this gene is the most suitable to be used as an endogenous reference target for sugarcane DNA content quantification. These results should be helpful for establishing accurate and reliable qualitative and quantitative PCR analysis of GM sugarcane.

  9. Validation of Suitable Reference Genes for Expression Normalization in Echinococcus spp. Larval Stages

    Science.gov (United States)

    Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

    2014-01-01

    In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

  10. Selection of suitable reference genes for quantitative gene expression studies in milk somatic cells of lactating cows (Bos indicus).

    Science.gov (United States)

    Varshney, N; Mohanty, A K; Kumar, S; Kaushik, J K; Dang, A K; Mukesh, M; Mishra, B P; Kataria, R; Kimothi, S P; Mukhopadhyay, T K; Malakar, D; Prakash, B S; Grover, S; Batish, V K

    2012-06-01

    We assessed the suitability of 9 internal control genes (ICG) in milk somatic cells of lactating cows to find suitable reference genes for use in quantitative PCR (qPCR). Eighteen multiparous lactating Sahiwal cows were used, 6 in each of 3 lactation stages: early (25 ± 5 d in milk), mid (160 ± 15 d in milk), and late (275 ± 25 d in milk) lactation. Nine candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), protein phosphatase 1 regulatory subunit 11 (PPP1R11), β-actin (ACTB), β-2 microglobulin (B2M), 40S ribosomal protein S15a (RPS15A), ubiquitously expressed transcript (UXT), mitochondrial GTPase 1 (MTG1), 18S rRNA (RN18S1), and ubiquitin (UBC)] were evaluated. Three genes, β-casein (CSN2), lactoferrin (LTF), and cathelicidin (CAMP) were chosen as target genes. Very high amplification was observed in 7 ICG and very low level amplification was observed in 2 ICG (UXT and MTG1). Thus, UXT and MTG1 were excluded from further analysis. The qPCR data were analyzed by 2 software packages, geNorm and NormFinder, to determine suitable reference genes, based on their stability and expression. Overall, PPP1R11, ACTB, UBC, and GAPDH were stably expressed among all candidate reference genes. Therefore, these genes could be used as ICG for normalization of qPCR data in milk somatic cells through lactation.

  11. A “twisted” microfluidic mixer suitable for a wide range of flow rate applications

    Science.gov (United States)

    Sivashankar, Shilpa; Agambayev, Sumeyra; Mashraei, Yousof; Li, Er Qiang; Thoroddsen, Sigurdur T.; Salama, Khaled Nabil

    2016-01-01

    This paper proposes a new “twisted” 3D microfluidic mixer fabricated by a laser writing/microfabrication technique. Effective and efficient mixing using the twisted micromixers can be obtained by combining two general chaotic mixing mechanisms: splitting/recombining and chaotic advection. The lamination of mixer units provides the splitting and recombination mechanism when the quadrant of circles is arranged in a two-layered serial arrangement of mixing units. The overall 3D path of the microchannel introduces the advection. An experimental investigation using chemical solutions revealed that these novel 3D passive microfluidic mixers were stable and could be operated at a wide range of flow rates. This micromixer finds application in the manipulation of tiny volumes of liquids that are crucial in diagnostics. The mixing performance was evaluated by dye visualization, and using a pH test that determined the chemical reaction of the solutions. A comparison of the tornado-mixer with this twisted micromixer was made to evaluate the efficiency of mixing. The efficiency of mixing was calculated within the channel by acquiring intensities using ImageJ software. Results suggested that efficient mixing can be obtained when more than 3 units were consecutively placed. The geometry of the device, which has a length of 30 mm, enables the device to be integrated with micro total analysis systems and other lab-on-chip devices. PMID:27453767

  12. A "twisted" microfluidic mixer suitable for a wide range of flow rate applications.

    Science.gov (United States)

    Sivashankar, Shilpa; Agambayev, Sumeyra; Mashraei, Yousof; Li, Er Qiang; Thoroddsen, Sigurdur T; Salama, Khaled Nabil

    2016-05-01

    This paper proposes a new "twisted" 3D microfluidic mixer fabricated by a laser writing/microfabrication technique. Effective and efficient mixing using the twisted micromixers can be obtained by combining two general chaotic mixing mechanisms: splitting/recombining and chaotic advection. The lamination of mixer units provides the splitting and recombination mechanism when the quadrant of circles is arranged in a two-layered serial arrangement of mixing units. The overall 3D path of the microchannel introduces the advection. An experimental investigation using chemical solutions revealed that these novel 3D passive microfluidic mixers were stable and could be operated at a wide range of flow rates. This micromixer finds application in the manipulation of tiny volumes of liquids that are crucial in diagnostics. The mixing performance was evaluated by dye visualization, and using a pH test that determined the chemical reaction of the solutions. A comparison of the tornado-mixer with this twisted micromixer was made to evaluate the efficiency of mixing. The efficiency of mixing was calculated within the channel by acquiring intensities using ImageJ software. Results suggested that efficient mixing can be obtained when more than 3 units were consecutively placed. The geometry of the device, which has a length of 30 mm, enables the device to be integrated with micro total analysis systems and other lab-on-chip devices.

  13. A “twisted” microfluidic mixer suitable for a wide range of flow rate applications

    KAUST Repository

    Sivashankar, Shilpa

    2016-06-27

    This paper proposes a new “twisted” 3D microfluidic mixer fabricated by a laser writing/microfabrication technique. Effective and efficient mixing using the twisted micromixers can be obtained by combining two general chaotic mixing mechanisms: splitting/recombining and chaotic advection. The lamination of mixer units provides the splitting and recombination mechanism when the quadrant of circles is arranged in a two-layered serial arrangement of mixing units. The overall 3D path of the microchannel introduces the advection. An experimental investigation using chemical solutions revealed that these novel 3D passive microfluidic mixers were stable and could be operated at a wide range of flow rates. This micromixer finds application in the manipulation of tiny volumes of liquids that are crucial in diagnostics. The mixing performance was evaluated by dye visualization, and using a pH test that determined the chemical reaction of the solutions. A comparison of the tornado-mixer with this twisted micromixer was made to evaluate the efficiency of mixing. The efficiency of mixing was calculated within the channel by acquiring intensities using ImageJ software. Results suggested that efficient mixing can be obtained when more than 3 units were consecutively placed. The geometry of the device, which has a length of 30 mm, enables the device to be integrated with micro total analysis systems and other lab-on-chip devices.

  14. Suitable environmental ranges for potential coral reef habitats in the tropical ocean.

    Science.gov (United States)

    Guan, Yi; Hohn, Sönke; Merico, Agostino

    2015-01-01

    Coral reefs are found within a limited range of environmental conditions or tolerance limits. Estimating these limits is a critical prerequisite for understanding the impacts of climate change on the biogeography of coral reefs. Here we used the diagnostic model ReefHab to determine the current environmental tolerance limits for coral reefs and the global distribution of potential coral reef habitats as a function of six factors: temperature, salinity, nitrate, phosphate, aragonite saturation state, and light. To determine these tolerance limits, we extracted maximum and minimum values of all environmental variables in corresponding locations where coral reefs are present. We found that the global, annually averaged tolerance limits for coral reefs are 21.7-29.6 °C for temperature, 28.7-40.4 psu for salinity, 4.51 μmol L-1 for nitrate, 0.63 μmol L-1 for phosphate, and 2.82 for aragonite saturation state. The averaged minimum light intensity in coral reefs is 450 μmol photons m-2 s-1. The global area of potential reef habitats calculated by the model is 330.5 × 103 km2. Compared with previous studies, the tolerance limits for temperature, salinity, and nutrients have not changed much, whereas the minimum value of aragonite saturation in coral reef waters has decreased from 3.28 to 2.82. The potential reef habitat area calculated with ReefHab is about 121×103 km2 larger than the area estimated from the charted reefs, suggesting that the growth potential of coral reefs is higher than currently observed.

  15. Himalayan ibex (Capra ibex sibirica habitat suitability and range resource dynamics in the Central Karakorum National Park, Pakistan

    Directory of Open Access Journals (Sweden)

    Garee Khan

    2016-07-01

    Full Text Available The study investigates Himalayan ibex (Capra ibex sibirica and their range resource condition within the preferred habitat in the Central Karakoram National Park, Pakistan. We apply ecological niche factor analysis (ENFA using 110 ibex sighting data and 6 key biophysical variables describing the habitat conditions and produce habitat suitability and maps with GIS and statistical tool (BioMapper. The modeling results of specialization factor shows some limitation for ibex over the use of slope, elevation, vegetation types and ruggedness. The habitat area selection for the ibex is adjusted to the ibex friendly habitat available conditions. The model results predicted suitable habitat for ibex in certain places, where field observation was never recorded. The range resource dynamics depict a large area that comes under the alpine meadows has the highest seasonal productivity, assessed by remote sensing based fortnightly vegetation condition data of the last 11 years. These meadows are showing browning trend over the years, attributable to grazing practices or climate conditions. At lower elevation, there are limited areas with suitable dry steppes, which may cause stress on ibex, especially during winter.

  16. Identification of suitable reference genes in bone marrow stromal cells from osteoarthritic donors.

    Science.gov (United States)

    Schildberg, Theresa; Rauh, Juliane; Bretschneider, Henriette; Stiehler, Maik

    2013-11-01

    Bone marrow stromal cells (BMSCs) are key cellular components for musculoskeletal tissue engineering strategies. Furthermore, recent data suggest that BMSCs are involved in the development of Osteoarthritis (OA) being a frequently occurring degenerative joint disease. Reliable reference genes for the molecular evaluation of BMSCs derived from donors exhibiting OA as a primary co-morbidity have not been reported on yet. Hence, the aim of the study was to identify reference genes suitable for comparative gene expression analyses using OA-BMSCs. Passage 1 bone marrow derived BMSCs were isolated from n=13 patients with advanced stage idiopathic hip osteoarthritis and n=15 age-matched healthy donors. The expression of 31 putative reference genes was analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using a commercially available TaqMan(®) assay. Calculating the coefficient of variation (CV), mRNA expression stability was determined and afterwards validated using geNorm and NormFinder algorithms. Importin 8 (IPO8), TATA box binding protein (TBP), and cancer susceptibility candidate 3 (CASC3) were identified as the most stable reference genes. Notably, commonly used reference genes, e.g. beta-actin (ACTB) and beta-2-microglobulin (B2M) were among the most unstable genes. For normalization of gene expression data of OA-BMSCs the combined use of IPO8, TBP, and CASC3 gene is recommended.

  17. Identification of housekeeping genes suitable for gene expression analysis in the pearl mussel, Hyriopsis cumingii, during biomineralization.

    Science.gov (United States)

    Bai, Zhiyi; Lin, Jingyun; Ma, Keyi; Wang, Guiling; Niu, Donghong; Li, Jiale

    2014-08-01

    Quantitative real-time polymerase chain reaction is a sensitive technique for quantifying gene expression levels. One or more appropriate reference genes must be selected to accurately compare mRNA transcript levels across different samples and tissues. The freshwater pearl, Hyriopsis cumingii (Lea), is an important economic species cultured in China. To date, no reference genes for gene expression analysis in this species have been validated. This study aimed to compare the relative expression of seven housekeeping genes across different tissue types and in the mantle or pearl sac during three biomineralization processes: seasonal shell growth, shell healing and pearl-sac formation in H. cumingii. Three programs evaluated the expression stabilities of the seven genes: BestKeeper, geNorm and NormFinder. The beta actin gene (ACTB), commonly used as a housekeeping gene in many studies, was the least stable. The expressions of Ubiquitin (Ubi) and Ribosomal protein L18 (Rpl18) and Elongation factor 1-alpha (EF1α) were more stable than the remaining four genes. Therefore, we suggest that Ubi, Rpl18 and EF1α are suitable reference genes. The three selected reference genes are expected to facilitate analysis of gene expressions during shell or pearl formation in H. cumingii.

  18. Mesenchymal stromal cells retrovirally transduced with prodrug-converting genes are suitable vehicles for cancer gene therapy.

    Science.gov (United States)

    Ďuriniková, E; Kučerová, L; Matúšková, M

    2014-01-01

    Mesenchymal stem/stromal cells (MSC) possess a set of several fairly unique properties which make them ideally suitable both for cellular therapies and regenerative medicine. These include: relative ease of isolation, the ability to differentiate along mesenchymal and non-mesenchymal lineages in vitro and the ability to be extensively expanded in culture without a loss of differentiative capacity. MSC are not only hypoimmunogenic, but they mediate immunosuppression upon transplantation, and possess pronounced anti-inflammatory properties. They are able to home to damaged tissues, tumors, and metastases following systemic administration. The ability of homing holds big promise for tumor-targeted delivery of therapeutic agents. Viruses are naturally evolved vehicles efficiently transferring their genes into host cells. This ability made them suitable for engineering vector systems for the delivery of genes of interest. MSC can be retrovirally transduced with genes encoding prodrug-converting genes (suicide genes), which are not toxic per se, but catalyze the formation of highly toxic metabolites following the application of a nontoxic prodrug. The homing ability of MSC holds advantages compared to virus vehicles which display many shortcomings in effective delivery of the therapeutic agents. Gene therapies mediated by viruses are limited by their restricted ability to track cancer cells infiltrating into the surrounding tissue, and by their low migratory capacity towards tumor. Thus combination of cellular therapy and gene delivery is an attractive option - it protects the vector from immune surveillance, and supports targeted delivery of a therapeutic gene/protein to the tumor site.

  19. Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress.

    Science.gov (United States)

    Cui, Bintao; Smooker, Peter M; Rouch, Duncan A; Deighton, Margaret A

    2016-08-01

    Accurate and reproducible measurement of gene transcription requires appropriate reference genes, which are stably expressed under different experimental conditions to provide normalization. Staphylococcus capitis is a human pathogen that produces biofilm under stress, such as imposed by antimicrobial agents. In this study, a set of five commonly used staphylococcal reference genes (gyrB, sodA, recA, tuf and rpoB) were systematically evaluated in two clinical isolates of Staphylococcus capitis (S. capitis subspecies urealyticus and capitis, respectively) under erythromycin stress in mid-log and stationary phases. Two public software programs (geNorm and NormFinder) and two manual calculation methods, reference residue normalization (RRN) and relative quantitative (RQ), were applied. The potential reference genes selected by the four algorithms were further validated by comparing the expression of a well-studied biofilm gene (icaA) with phenotypic biofilm formation in S. capitis under four different experimental conditions. The four methods differed considerably in their ability to predict the most suitable reference gene or gene combination for comparing icaA expression under different conditions. Under the conditions used here, the RQ method provided better selection of reference genes than the other three algorithms; however, this finding needs to be confirmed with a larger number of isolates. This study reinforces the need to assess the stability of reference genes for analysis of target gene expression under different conditions and the use of more than one algorithm in such studies. Although this work was conducted using a specific human pathogen, it emphasizes the importance of selecting suitable reference genes for accurate normalization of gene expression more generally.

  20. Suitability of endogenous reference genes for gene expression studies with human intraocular endothelial cells

    Directory of Open Access Journals (Sweden)

    Wei Ruoxin

    2013-02-01

    Full Text Available Abstract Background The use of quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR has become widely applied as a method to measure transcript abundance. In order to be reflective of biological processes during health and disease this method is dependent on normalisation of data against stable endogenous controls. However, these genes can vary in their stability in different cell types. The importance of reference gene validation for a particular cell type is now well recognised and is an important step in any gene expression study. Results Cultured primary human choroidal and retinal endothelial cells were treated with the immunostimulant polyinosinic: polycytidylic acid or untreated. qRT-PCR was used to quantify the expression levels of 10 commonly used endogenous control genes, TBP, HPRT1, GAPDH, GUSB, PPIA, RPLP0, B2M, 18S rRNA, PGK1 and ACTB. Three different mathematical algorithms, GeNorm, NormFinder, and BestKeeper were used to analyse gene stability to give the most representative validation. In choroidal endothelial cells the most stable genes were ranked as HPRT1 and GUSB by GeNorm and NormFinder and HPRT1 and PPIA by BestKeeper. In retinal endothelial cells the most stable genes ranked were TBP and PGK1 by GeNorm and NormFinder and HPRT1 by BestKeeper. The least stable gene for both cell types was 18S with all 3 algorithms. Conclusions We have identified the most stable endogenous control genes in intraocular endothelial cells. It is suggested future qRT-PCR studies using these cells would benefit from adopting the genes identified in this study as the most appropriate endogenous control genes.

  1. Identification of Suitable Reference Genes for Peripheral Blood Mononuclear Cell Subset Studies in Multiple Sclerosis

    DEFF Research Database (Denmark)

    Oturai, D B; Søndergaard, H B; Börnsen, L;

    2016-01-01

    Quantitative real-time PCR (qPCR) involves the need of a proper standard for normalizing the gene expression data. Different studies have shown the validity of reference genes to vary greatly depending on tissue, cell subsets and experimental context. This study aimed at the identification...... of suitable reference genes for qPCR studies using different peripheral blood cell subsets (whole blood (WB) cells, peripheral blood mononuclear cells (PBMCs) and PBMC subsets (CD4(+) T cells, CD8(+) T cells, NK cells, monocytes, B cells and dendritic cells) from healthy controls (HC), patients with relapsing...... stable combination for analyses of cell subsets between HC and RRMS patients, while the combination of UBC and YWHAZ was superior for analysis of cell subsets between HC, RRMS and RRMS-IFN-β groups. GAPDH was generally unsuitable for blood cell subset studies in multiple sclerosis. In conclusion, we...

  2. Identification of suitable reference genes for gene expression studies using quantitative polymerase chain reaction in lung cancer in vitro.

    Science.gov (United States)

    Ali, Hassan; Du, Zhenwu; Li, Xiuying; Yang, Qiwei; Zhang, Yu Cheng; Wu, Mei; Li, Yi; Zhang, Guizhen

    2015-05-01

    The present study aimed to examine 10 housekeeping genes (HKGs), including 18s ribosomal RNA (18S), glyceraldehyde‑3‑phosphate dehydrogenase (GAPDH), ribosomal protein large P0 (RPLP0), β‑actin (ACTB), peptidylprolyl isomerase A (PPIA), phosphoglycerate kinase‑1 (PGK1), β‑2‑microglobulin (B2M), ribosomal protein LI3a (RPL13A), hypoxanthine phosphoribosyl transferase‑1 (HPRT1) and TATA box binding protein (TBP) in order to identify the most stable and suitable reference genes for use in expression studies in non‑small cell lung cancer. The mRNA expression encoding the panel of the 10 HKGs was determined using reverse transcription‑quantitative PCR (RT‑qPCR) in human lung cancer cell lines. Three software programs, BestKeeper, NormFinder and geNorm, were used to ascertain the most suitable reference genes to normalize the RNA input. The present study examined three lung cancer cell lines (A549, NCI‑H446 and NCI‑H460). The analysis of the experimental data using BestKeeper software revealed that all 10 HKGs were stable, with GADPH, followed by 18S being the most stable genes and PPIA and HPRT1 being the least stable genes. The NormFinder software results demonstrated that PPIA followed by ACTB were the most stable and B2M and RPLP0 were the least stable. The geNorm software results revealed that ACTB and PGK1, followed by PPIA were the most stable genes and B2M and RPLP0 were identified as the least stable genes. Due to discrepancies in the ranking orders of the reference genes obtained by different analyzing software programs, it was not possible to determine a single universal reference gene. The suitability of selected reference genes requires unconditional validation prior to each study. Based on the three analyzing programs, ACTB, PPIA and PGK1 were the most stable reference genes in lung cancer cell lines.

  3. Biofouling community composition across a range of environmental conditions and geographical locations suitable for floating marine renewable energy generation.

    Science.gov (United States)

    Macleod, Adrian K; Stanley, Michele S; Day, John G; Cook, Elizabeth J

    2016-01-01

    Knowledge of biofouling typical of marine structures is essential for engineers to define appropriate loading criteria in addition to informing other stakeholders about the ecological implications of creating novel artificial environments. There is a lack of information regarding biofouling community composition (including weight and density characteristics) on floating structures associated with future marine renewable energy generation technologies. A network of navigation buoys were identified across a range of geographical areas, environmental conditions (tidal flow speed, temperature and salinity), and deployment durations suitable for future developments. Despite the perceived importance of environmental and temporal factors, geographical location explained the greatest proportion of the observed variation in community composition, emphasising the importance of considering geography when assessing the impact of biofouling on device functioning and associated ecology. The principal taxa associated with variation in biofouling community composition were mussels (Mytilus edulis), which were also important when determining loading criteria.

  4. Evaluation of suitable reference genes for gene expression studies in porcine PBMCs in response to LPS and LTA

    Directory of Open Access Journals (Sweden)

    Cinar Mehmet Ulas

    2013-02-01

    -positive bacteria. In case of PBMCs without any stimulation, PPIA, BLM and GAPDH could be suggested as suitable reference genes.

  5. Evaluation of suitable reference genes for gene expression studies in porcine alveolar macrophages in response to LPS and LTA

    Directory of Open Access Journals (Sweden)

    Cinar Mehmet

    2012-02-01

    Full Text Available Abstract Background To obtain reliable quantitative real-time PCR data, normalization relative to stable housekeeping genes (HKGs is required. However, in practice, expression levels of 'typical' housekeeping genes have been found to vary between tissues and under different experimental conditions. To date, validation studies of reference genes in pigs are relatively rare and have never been performed in porcine alveolar macrophages (AMs. In this study, expression stability of putative housekeeping genes were identified in the porcine AMs in response to the stimulation with two pathogen-associated molecular patterns (PAMPs lipopolysaccharide (LPS and lipoteichoic acid (LTA. Three different algorithms (geNorm, Normfinder and BestKeeper were applied to assess the stability of HKGs. Results The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ was determined by qRT-PCR in AMs that were stimulated by LPS and LTA in vitro. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (P SDHA, B2M and RPL4 showed a high expression stability in the irrespective to the stimulation group, while SDHA, YWHAZ and RPL4 showed high stability in non-stimulated control group. In all cases, GAPDH showed the least stability in geNorm. NormFinder revealed that SDHA was the most stable gene in all the groups. Moreover, geNorm software suggested that the geometric mean of the three most stable genes would be the suitable combination for accurate normalization of gene expression study. Conclusions There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms. In conclusion, the geometric mean of the SDHA, YWHAZ and RPL4 seemed to be the most appropriate combination of HKGs for accurate normalization of gene expression data in porcine AMs without knowing the type of bacterial pathogenic status of

  6. Employing Range Separation on the meta-GGA Rung: New Functional Suitable for Both Covalent and Noncovalent Interactions

    CERN Document Server

    Modrzejewski, Marcin; Chalasinski, Grzegorz; Szczesniak, Malgorzata M

    2016-01-01

    We devise a scheme for converting an existing exchange functional into its range-separated hybrid variant. The underlying exchange hole of the Becke-Roussel type has the exact second-order expansion in the interelectron distance. The short-range part of the resulting range-separated exchange energy depends on the kinetic energy density and the Laplacian even if the base functional lacks the dependence on these variables. The most successful practical realization of the scheme, named LC-PBETPSS, combines the range-separated PBE exchange lifted to the hybrid meta-GGA rung and the TPSS correlation. The value of the range-separation parameter is estimated theoretically and confirmed by empirical optimization. The D3 dispersion correction is recommended for all energy computations employing the presented functional. Numerical tests show remarkably robust performance of the method for noncovalent interaction energies, barrier heights, main-group thermochemistry, and excitation energies.

  7. Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Three Types of Rat Adipose Tissue.

    Science.gov (United States)

    Zhang, Wan-Xia; Fan, Jie; Ma, Jing; Rao, Yi-Song; Zhang, Li; Yan, You-E

    2016-06-22

    Quantitative real-time PCR (qRT-PCR) is the most classical technique in the field of gene expression study. This method requires an appropriate reference gene to normalize mRNA levels. In this study, the expression stability of four frequently-used reference genes in epididymal white adipose tissue (eWAT), inguinal beige adipose tissue (iBeAT) and brown adipose tissue (BAT) from obese and lean rats were evaluated by geNorm, NormFinder and BestKeeper. Based on the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, the two most stable reference genes were recommended in each type of adipose tissue. Two target genes were applied to test the stability of the reference genes. The geNorm and NormFinder results revealed that GAPDH and 36B4 exhibited the highest expression stabilities in eWAT, while 36B4 and β-actin had the highest expression stabilities in iBeAT and BAT. According to the results of the BestKeeper analysis, 36B4 was the most stable gene in eWAT, iBeAT and BAT, in terms of the coefficient of variance. In terms of the coefficient of correlation, GAPDH, 36B4 and β-actin were the most stable genes in eWAT, iBeAT and BAT, respectively. Additionally, expected results and statistical significance were obtained using a combination of two suitable reference genes for data normalization. In conclusion, 36B4 and GAPDH, in combination, are the best reference genes for eWAT, while 36B4 and β-actin are two most suitable reference genes for both iBeAT and BAT. We recommend using these reference genes accordingly.

  8. Identification of reference genes suitable for normalization of RT-qPCR expression data in Saccharomyces cerevisiae during alcoholic fermentation.

    Science.gov (United States)

    Vaudano, Enrico; Noti, Olta; Costantini, Antonella; Garcia-Moruno, Emilia

    2011-08-01

    Expression data from RT-qPCR (reverse transcription quantitative PCR) needs to be normalized to account for experimental variability among samples caused by differential yields of the transcripts in RNA extraction or in the reverse transcription. The most common method is to normalize against one or more reference genes (RG). We have selected RGs suitable for normalization of RT-qPCR raw data in Saccharomyces cerevisiae during alcoholic fermentation. The RGs were evaluated by three different statistical methods. The suitability of the selected RG sets was compared with ACT1, a commonly used non-validated single RG, by normalizing the expression of two target genes. Expression profiles of the target genes revealed the risk of misleading interpretation of expression data due to an unreliable RG.

  9. Quantitative comparison of suitability of various beams for range monitoring with induced beta+ activity in hadron therapy.

    Science.gov (United States)

    Inaniwa, Taku; Tomitani, Takehiro; Kohno, Toshiyuki; Kanai, Tatsuaki

    2005-03-21

    In radiation therapy with hadron beams, it is important to evaluate the range of incident ions and the deposited dose distribution in a patient body for the effective utilization of such properties as the dose concentration and the biological effect around the Bragg peak. However, there is some ambiguity in determining this range because of a conversion error from the x-ray CT number to the charged particle range. This is because the CT number is related to x-ray absorption coefficients, while the ion range is determined by the electron density of the substance. Using positron emitters produced in the patient body through fragmentation reactions during the irradiation has been proposed to overcome this problem. The activity distribution in the patient body can be deduced by detecting pairs of annihilation gamma rays emitted from the positron emitters, and information about the range of incident ions can be obtained. In this paper, we propose a quantitative comparison method to evaluate the mean range of incident ions and monitor the activity distribution related to the deposited dose distribution. The effectiveness of the method was demonstrated by evaluating the range of incident ions using the maximum likelihood estimation (MLE) method and Fisher's information was calculated under realistic conditions for irradiations with several kinds of ions. From the calculated Fisher's information, we compared the relative advantages of initial beams to determine the range of incident ions. The (16)O irradiation gave the most information among the stable heavy ions when we measured the induced activity for 500 s and 60 s just after the irradiation. Therefore, under these conditions, we concluded that the (16)O beam was the optimum beam to monitor the activity distribution and to evaluate the range. On the other hand, if the positron emitters were injected directly as a therapeutic beam, the (15)O irradiation gave the most information. Although the relative advantages of

  10. Selection of Suitable Reference Genes for Quantitative Real-time PCR in Sapium sebiferum

    Directory of Open Access Journals (Sweden)

    Xue Chen

    2017-05-01

    Full Text Available Chinese tallow (Sapium sebiferum L. is a promising landscape and bioenergy plant. Measuring gene expression by quantitative real-time polymerase chain reaction (qRT-PCR can provide valuable information on gene function. Stably expressed reference genes for normalization are a prerequisite for ensuring the accuracy of the target gene expression level among different samples. However, the reference genes in Chinese tallow have not been systematically validated. In this study, 12 candidate reference genes (18S, GAPDH, UBQ, RPS15, SAND, TIP41, 60S, ACT7, PDF2, APT, TBP, and TUB were investigated with qRT-PCR in 18 samples, including those from different tissues, from plants treated with sucrose and cold stresses. The data were calculated with four common algorithms, geNorm, BestKeeper, NormFinder, and the delta cycle threshold (ΔCt. TIP41 and GAPDH were the most stable for the tissue-specific experiment, GAPDH and 60S for cold treatment, and GAPDH and UBQ for sucrose stresses, while the least stable genes were 60S, TIP41, and 18S respectively. The comprehensive results showed APT, GAPDH, and UBQ to be the top-ranked stable genes across all the samples. The stability of 60S was the lowest during all experiments. These selected reference genes were further validated by comparing the expression profiles of the chalcone synthase gene in Chinese tallow in different samples. The results will help to improve the accuracy of gene expression studies in Chinese tallow.

  11. A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies.

    Science.gov (United States)

    Faccioli, Primetta; Ciceri, Gian Paolo; Provero, Paolo; Stanca, Antonio Michele; Morcia, Caterina; Terzi, Valeria

    2007-03-01

    Traditionally housekeeping genes have been employed as endogenous reference (internal control) genes for normalization in gene expression studies. Since the utilization of single housekeepers cannot assure an unbiased result, new normalization methods involving multiple housekeeping genes and normalizing using their mean expression have been recently proposed. Moreover, since a gold standard gene suitable for every experimental condition does not exist, it is also necessary to validate the expression stability of every putative control gene on the specific requirements of the planned experiment. As a consequence, finding a good set of reference genes is for sure a non-trivial problem requiring quite a lot of lab-based experimental testing. In this work we identified novel candidate barley reference genes suitable for normalization in gene expression studies. An advanced web search approach aimed to collect, from publicly available web resources, the most interesting information regarding the expression profiling of candidate housekeepers on a specific experimental basis has been set up and applied, as an example, on stress conditions. A complementary lab-based analysis has been carried out to verify the expression profile of the selected genes in different tissues and during heat shock response. This combined dry/wet approach can be applied to any species and physiological condition of interest and can be considered very helpful to identify putative reference genes to be shortlisted every time a new experimental design has to be set up.

  12. Selection of suitable reference genes for quantitative real-time PCR in apoptosis-induced MCF-7 breast cancer cells.

    Science.gov (United States)

    Ferreira, Eloise; Cronjé, Marianne J

    2012-02-01

    Apoptosis is induced in MCF-7 breast cancer cells following treatment with salicylic acid (20 mM), either in the presence or absence of a heat shock (42°C for 30 min). In order to study the alterations of apoptotic genes with quantitative real-time PCR (qPCR), suitable genes with unchanged expression following the treatments is required for normalizing the gene expression levels. In this study, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin (ACTB), Histone H2A (HIST), constitutively expressed heat shock protein 70 (HSC70) and tyrosine 3-monooxygenase/trytophan 5 monooxygenase activation protein, 14-3-3 (YWHAZ) were evaluated as appropriate reference genes. Analysis of gene expression data with one-way ANOVA, geNorm and NormFinder identified HIST and YWHAZ as the least affected during the induction of apoptosis by the different treatments, and is the most suitable gene-pair for normalization during qPCR analysis in MCF-7 breast cancer cells undergoing apoptosis following treatment with SA and/or HS.

  13. Renal tissue thawed for 30 minutes is still suitable for gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Yi Ma

    Full Text Available Some biosamples obtained from biobanks may go through thawing before processing. We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis. A time course study with four time points was conducted to investigate the expression profiling on 10 thawed normal mice renal tissue samples through Affymetrix GeneChip mouse gene 2.0 st array. Microarray results were validated by quantitative real time polymerase chain reactions (qPCR on 6 candidate reference genes and 11 target genes. Additionally, we used geNorm plus and NormFinder to identify the most stably expressed reference genes over time. The results showed RNA degraded more after longer incubation at room temperature. However, microarray results showed only 240 genes (0.91% altered significantly in response to thawing at room temperature. The signal of majority altered probe sets decreased with thawing time, and the crossing point (Cp values of all candidate reference genes correlated positively with the thawing time (p<0.05. The combination of B2M, ACTB and PPIA was identified as the best choice for qPCR normalization. We found most target genes were stable by using this normalization method. However, serious gene quantification errors were resulted from improper reference genes. In conclusion, thirty minutes of thawing at room temperature has a limited impact on microarray and qPCR analysis, gene expression variations due to RNA degradation in early period after thawing can be largely reduced by proper normalization.

  14. Selection of suitable reference genes for RT-qPCR analyses in cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Filipe Pinto

    Full Text Available Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works.

  15. Selection of Suitable Reference Genes for Analysis of Salivary Transcriptome in Non-Syndromic Autistic Male Children

    Directory of Open Access Journals (Sweden)

    Yasin Panahi

    2016-10-01

    Full Text Available Childhood autism is a severe form of complex genetically heterogeneous and behaviorally defined set of neurodevelopmental diseases, collectively termed as autism spectrum disorders (ASD. Reverse transcriptase quantitative real-time PCR (RT-qPCR is a highly sensitive technique for transcriptome analysis, and it has been frequently used in ASD gene expression studies. However, normalization to stably expressed reference gene(s is necessary to validate any alteration reported at the mRNA level for target genes. The main goal of the present study was to find the most stable reference genes in the salivary transcriptome for RT-qPCR analysis in non-syndromic male childhood autism. Saliva samples were obtained from nine drug naïve non-syndromic male children with autism and also sex-, age-, and location-matched healthy controls using the RNA-stabilizer kit from DNA Genotek. A systematic two-phased measurement of whole saliva mRNA levels for eight common housekeeping genes (HKGs was carried out by RT-qPCR, and the stability of expression for each candidate gene was analyzed using two specialized algorithms, geNorm and NormFinder, in parallel. Our analysis shows that while the frequently used HKG ACTB is not a suitable reference gene, the combination of GAPDH and YWHAZ could be recommended for normalization of RT-qPCR analysis of salivary transcriptome in non-syndromic autistic male children.

  16. Selection of Suitable Reference Genes for Analysis of Salivary Transcriptome in Non-Syndromic Autistic Male Children.

    Science.gov (United States)

    Panahi, Yasin; Salasar Moghaddam, Fahimeh; Ghasemi, Zahra; Hadi Jafari, Mandana; Shervin Badv, Reza; Eskandari, Mohamad Reza; Pedram, Mehrdad

    2016-10-12

    Childhood autism is a severe form of complex genetically heterogeneous and behaviorally defined set of neurodevelopmental diseases, collectively termed as autism spectrum disorders (ASD). Reverse transcriptase quantitative real-time PCR (RT-qPCR) is a highly sensitive technique for transcriptome analysis, and it has been frequently used in ASD gene expression studies. However, normalization to stably expressed reference gene(s) is necessary to validate any alteration reported at the mRNA level for target genes. The main goal of the present study was to find the most stable reference genes in the salivary transcriptome for RT-qPCR analysis in non-syndromic male childhood autism. Saliva samples were obtained from nine drug naïve non-syndromic male children with autism and also sex-, age-, and location-matched healthy controls using the RNA-stabilizer kit from DNA Genotek. A systematic two-phased measurement of whole saliva mRNA levels for eight common housekeeping genes (HKGs) was carried out by RT-qPCR, and the stability of expression for each candidate gene was analyzed using two specialized algorithms, geNorm and NormFinder, in parallel. Our analysis shows that while the frequently used HKG ACTB is not a suitable reference gene, the combination of GAPDH and YWHAZ could be recommended for normalization of RT-qPCR analysis of salivary transcriptome in non-syndromic autistic male children.

  17. Integrase minus lentiviral vector: A suitable vector for β-thalassemia gene targeting

    OpenAIRE

    Davoud Nouri Inanlou; Bagher Yakhchali; Hossein Khanahmad; Mossa Gardaneh; Hesam Movassagh; Tooraj Farazmandfar; Aida Feiz Barazandeh; Sirous Zeinali

    2009-01-01

    "nβ-Thalassemia is a congenital disorder caused by mutation in β-globin gene. The current therapies to treat β-thalassemia have many complications and limitations necessitating development of new curative methods. Recently, a great attention has been paid to gene therapy of β-thalassemia using lentiviral vectors. Although insertion of transgene into these vectors direct regulated expression of β-globin at therapeutic levels, lentiviruses unfav...

  18. In search of a suitable reference gene for normalization of gene expression in MDV-infected chicken cells

    Science.gov (United States)

    Marek’s disease (MD) is a contagious lymphoproliferative disease of domestic chickens caused by a highly cell-associated alpha-herpesvirus, MD virus (MDV). The choice of an appropriate housekeeping gene as an endogenous reference gene is an essential requirement for relative quantification of gene ...

  19. Screening suitable reference genes for normalization in reverse transcription quantitative real-time PCR analysis in melon.

    Directory of Open Access Journals (Sweden)

    Qiusheng Kong

    Full Text Available Melon (Cucumis melo. L is not only an economically important cucurbitaceous crop but also an attractive model for studying many biological characteristics. Screening appropriate reference genes is essential to reverse transcription quantitative real-time PCR (RT-qPCR, which is key to many studies involving gene expression analysis. In this study, 14 candidate reference genes were selected, and the variations in their expression in roots and leaves of plants subjected to biotic stress, abiotic stress, and plant growth regulator treatment were assessed by RT-qPCR. The stability of the expression of the selected genes was determined and ranked using geNorm and NormFinder. geNorm identified the two most stable genes for each set of conditions: CmADP and CmUBIep across all samples, CmUBIep and CmRPL in roots, CmRAN and CmACT in leaves, CmADP and CmRPL under abiotic stress conditions, CmTUA and CmACT under biotic stress conditions, and CmRAN and CmACT under plant growth regulator treatments. NormFinder determined CmRPL to be the best reference gene in roots and under biotic stress conditions and CmADP under the other experimental conditions. CmUBC2 and CmPP2A were not found to be suitable under many experimental conditions. The catalase family genes CmCAT1, CmCAT2, and CmCAT3 were identified in melon genome and used as target genes to validate the reliability of identified reference genes. The catalase family genes showed the most upregulation 3 days after inoculation with Fusarium wilt in roots, after which they were downregulated. Their levels of expression were significantly overestimated when the unsuitable reference gene was used for normalization. These results not only provide guidelines for the selection of reference genes for gene expression analyses in melons but may also provide valuable information for studying the functions of catalase family genes in stress responses.

  20. Identification and evaluation of suitable reference genes for gene expression studies in the whitefly Bemisia tabaci (Asia I) by reverse transcription quantitative realtime PCR.

    Science.gov (United States)

    Collins, Carl; Patel, Mitulkumar V; Colvin, John; Bailey, David; Seal, Susan

    2014-05-02

    This study presents a reliable method for performing reverse transcription quantitative realtime PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1α (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and α-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data pre- sented here will assist future transcript profiling studies in whiteflies.

  1. Identification and Evaluation of Suitable Reference Genes for Gene Expression Studies in the Whitefly Bemisia tabaci (Asia I) by Reverse Transcription Quantitative Real-Time PCR

    Science.gov (United States)

    Collins, Carl; Patel, Mitulkumar V.; Colvin, John; Bailey, David; Seal, Susan

    2014-01-01

    This study presents a reliable method for performing reverse transcription quantitative real-time PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1α (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and α-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data presented here will assist future transcript profiling studies in whiteflies. PMID:25373210

  2. Identification of Suitable Reference Genes for Investigating Gene Expression in Anterior Cruciate Ligament Injury by Using Reverse Transcription-Quantitative PCR.

    Directory of Open Access Journals (Sweden)

    Mariana Ferreira Leal

    Full Text Available The anterior cruciate ligament (ACL is one of the most frequently injured structures during high-impact sporting activities. Gene expression analysis may be a useful tool for understanding ACL tears and healing failure. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR has emerged as an effective method for such studies. However, this technique requires the use of suitable reference genes for data normalization. Here, we evaluated the suitability of six reference genes (18S, ACTB, B2M, GAPDH, HPRT1, and TBP by using ACL samples of 39 individuals with ACL tears (20 with isolated ACL tears and 19 with ACL tear and combined meniscal injury and of 13 controls. The stability of the candidate reference genes was determined by using the NormFinder, geNorm, BestKeeper DataAssist, and RefFinder software packages and the comparative ΔCt method. ACTB was the best single reference gene and ACTB+TBP was the best gene pair. The GenEx software showed that the accumulated standard deviation is reduced when a larger number of reference genes is used for gene expression normalization. However, the use of a single reference gene may not be suitable. To identify the optimal combination of reference genes, we evaluated the expression of FN1 and PLOD1. We observed that at least 3 reference genes should be used. ACTB+HPRT1+18S is the best trio for the analyses involving isolated ACL tears and controls. Conversely, ACTB+TBP+18S is the best trio for the analyses involving (1 injured ACL tears and controls, and (2 ACL tears of patients with meniscal tears and controls. Therefore, if the gene expression study aims to compare non-injured ACL, isolated ACL tears and ACL tears from patients with meniscal tear as three independent groups ACTB+TBP+18S+HPRT1 should be used. In conclusion, 3 or more genes should be used as reference genes for analysis of ACL samples of individuals with and without ACL tears.

  3. Identification of Suitable Reference Genes for Investigating Gene Expression in Anterior Cruciate Ligament Injury by Using Reverse Transcription-Quantitative PCR.

    Science.gov (United States)

    Leal, Mariana Ferreira; Astur, Diego Costa; Debieux, Pedro; Arliani, Gustavo Gonçalves; Silveira Franciozi, Carlos Eduardo; Loyola, Leonor Casilla; Andreoli, Carlos Vicente; Smith, Marília Cardoso; Pochini, Alberto de Castro; Ejnisman, Benno; Cohen, Moises

    2015-01-01

    The anterior cruciate ligament (ACL) is one of the most frequently injured structures during high-impact sporting activities. Gene expression analysis may be a useful tool for understanding ACL tears and healing failure. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has emerged as an effective method for such studies. However, this technique requires the use of suitable reference genes for data normalization. Here, we evaluated the suitability of six reference genes (18S, ACTB, B2M, GAPDH, HPRT1, and TBP) by using ACL samples of 39 individuals with ACL tears (20 with isolated ACL tears and 19 with ACL tear and combined meniscal injury) and of 13 controls. The stability of the candidate reference genes was determined by using the NormFinder, geNorm, BestKeeper DataAssist, and RefFinder software packages and the comparative ΔCt method. ACTB was the best single reference gene and ACTB+TBP was the best gene pair. The GenEx software showed that the accumulated standard deviation is reduced when a larger number of reference genes is used for gene expression normalization. However, the use of a single reference gene may not be suitable. To identify the optimal combination of reference genes, we evaluated the expression of FN1 and PLOD1. We observed that at least 3 reference genes should be used. ACTB+HPRT1+18S is the best trio for the analyses involving isolated ACL tears and controls. Conversely, ACTB+TBP+18S is the best trio for the analyses involving (1) injured ACL tears and controls, and (2) ACL tears of patients with meniscal tears and controls. Therefore, if the gene expression study aims to compare non-injured ACL, isolated ACL tears and ACL tears from patients with meniscal tear as three independent groups ACTB+TBP+18S+HPRT1 should be used. In conclusion, 3 or more genes should be used as reference genes for analysis of ACL samples of individuals with and without ACL tears.

  4. Identification of suitable reference genes for quantitative RT-PCR during 3T3-L1 adipocyte differentiation.

    Science.gov (United States)

    Zhang, Juan; Tang, Hongju; Zhang, Yuqing; Deng, Ruyuan; Shao, Li; Liu, Yun; Li, Fengying; Wang, Xiao; Zhou, Libin

    2014-05-01

    Quantitative reverse transcription PCR (qRT-PCR) is becoming increasingly important in the effort to gain insight into the molecular mechanisms underlying adipogenesis. However, the expression profile of a target gene may be misinterpreted due to the unstable expression of the reference genes under different experimental conditions. Therefore, in this study, we investigated the expression stability of 10 commonly used reference genes during 3T3-L1 adipocyte differentiation. The mRNA expression levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and transferrin receptor (TFRC) significantly increased during the course of 3T3-L1 adipocyte differentiation, which was decreased by berberine, an inhibitor of adipogenesis. Three popular algorithms, GeNorm, NormFinder and BestKeeper, identified 18 ribosomal RNA and hydroxymethylbilane synthase (HMBS) as the most stable reference genes, while GAPDH and TFRC were the least stable ones. Peptidylprolyl isomerase A [PIPA (cyclophilin A)], ribosomal protein, large, P0 (36-B4), beta-2-microglobulin (B2M), α1-tubulin, hypoxanthine-guanine phosphoribosyltransferase (HPRT) and β-actin showed relatively stable expression levels. The choice of reference genes with various expression stabilities exerted a profound influence on the expression profiles of 2 target genes, peroxisome proliferator-activated receptor (PPAR)γ2 and C/EBPα. In addition, western blot analysis revealed that the increased protein expression of GAPDH was markedly inhibited by berberine during adipocyte differentiation. This study highlights the importance of selecting suitable reference genes for qRT-PCR studies of gene expression during the process of adipogenesis.

  5. Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers

    Directory of Open Access Journals (Sweden)

    Wilson Gareth A

    2012-07-01

    Full Text Available Abstract Background Methylated DNA immunoprecipitation (MeDIP is a popular enrichment based method and can be combined with sequencing (termed MeDIP-seq to interrogate the methylation status of cytosines across entire genomes. However, quality control and analysis of MeDIP-seq data have remained to be a challenge. Results We report genome-wide DNA methylation profiles of wild type (wt and mutant mouse cells, comprising 3 biological replicates of Thymine DNA glycosylase (Tdg knockout (KO embryonic stem cells (ESCs, in vitro differentiated neural precursor cells (NPCs and embryonic fibroblasts (MEFs. The resulting 18 methylomes were analysed with MeDUSA (Methylated DNA Utility for Sequence Analysis, a novel MeDIP-seq computational analysis pipeline for the identification of differentially methylated regions (DMRs. The observed increase of hypermethylation in MEF promoter-associated CpG islands supports a previously proposed role for Tdg in the protection of regulatory regions from epigenetic silencing. Further analysis of genes and regions associated with the DMRs by gene ontology, pathway, and ChIP analyses revealed further insights into Tdg function, including an association of TDG with low-methylated distal regulatory regions. Conclusions We demonstrate that MeDUSA is able to detect both large-scale changes between cells from different stages of differentiation and also small but significant changes between the methylomes of cells that only differ in the KO of a single gene. These changes were validated utilising publicly available datasets and confirm TDG's function in the protection of regulatory regions from epigenetic silencing.

  6. A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens.

    Science.gov (United States)

    Babion, Iris; Snoek, Barbara C; van de Wiel, Mark A; Wilting, Saskia M; Steenbergen, Renske D M

    2017-09-01

    miRNAs represent an emerging class of promising biomarkers for cancer diagnostics. To perform reliable miRNA expression analysis using quantitative PCR, adequate data normalization is essential to remove nonbiological, technical variations. Ideal reference genes should be biologically stable and reduce technical variability of miRNA expression analysis. Herein is a new strategy for the identification and evaluation of reference genes that can be applied for miRNA-based diagnostic tests without entailing excessive additional experiments. We analyzed the expression of 11 carefully selected candidate reference genes in different types of cervical specimens [ie, tissues, scrapes, and self-collected cervicovaginal specimens (self-samples)]. To identify the biologically most stable reference genes, three commonly used algorithms (GeNorm, NormFinder, and BestKeeper) were combined. Signal-to-noise ratios and P values between control and disease groups were calculated to validate the reduction in technical variability on expression analysis of two marker miRNAs. miR-423 was identified as a suitable reference gene for all sample types, to be used in combination with RNU24 in cervical tissues, RNU43 in scrapes, and miR-30b in self-samples. These findings demonstrate that the choice of reference genes may differ between different types of specimens, even when originating from the same anatomical source. More important, it is shown that adequate normalization increases the signal-to-noise ratio, which is not observed when normalizing to commonly used reference genes. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. Suitable hardness range of soccer turf; Soccer kyogi ni tekishita tennenshiba kyogijo field men no katasa han'i no kento

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, H. [Kajima Corp., Tokyo (Japan); Ono, H. [Tokyo Institute of Technology, Tokyo (Japan)

    1999-09-30

    In the CIV measurement most spread at present as a means for measuring hardness of the field surface of a natural turf ground, it was elucidated that the ideal range by the official evaluation standard is greatly different from the distribution of measurement results in five large domestic fields. Consequently, in order to examine the validity of the official evaluation standard, measurement was done on various kinds of test surface mainly of natural turf by means of the 'measuring apparatus for hardness of sport surface', an already established technology in evaluating hardness of the surface of athletic facilities, with comparison made with measurement results by an existing evaluation technology such as CIV. Consequently, a range harder than one in the official standard was considered as suitable for soccer. In addition, it revealed that the CIV measurement had a possibility of causing a difference from human sense by the degree of hardness on the field. (translated by NEDO)

  8. Toward a suitable structural analysis of gene delivery carrier based on polycationic carbohydrates by electron transfer dissociation tandem mass spectrometry.

    Science.gov (United States)

    Przybylski, Cédric; Benito, Juan M; Bonnet, Véronique; Mellet, Carmen Ortiz; García Fernández, José M

    2016-12-15

    Polycationic carbohydrates represent an attractive class of biomolecules for several applications and particularly as non viral gene delivery vectors. In this case, the establishment of structure-biological activity relationship requires sensitive and accurate characterization tools to both control and achieve fine structural deciphering. Electrospray-tandem mass spectrometry (ESI-MS/MS) appears as a suitable approach to address these questions. In the study herein, we have investigated the usefulness of electron transfer dissociation (ETD) to get structural data about five polycationic carbohydrates demonstrated as promising gene delivery agents. A particular attention was paid to determine the influence of charge states as well as both fluoranthene reaction time and supplementary activation (SA) on production of charge reduced species, fragmentation yield, varying from 2 to 62%, as well as to obtain the most higher both diversity and intensity of fragments, according to charge states and targeted compounds. ETD fragmentation appeared to be mainly directed toward pending group rather than carbohydrate cyclic scaffold leading to a partial sequencing for building blocks when amino groups are close to carbohydrate core, but allowing to complete structural deciphering of some of them, such as those including dithioureidocysteaminyl group which was not possible with CID only. Such findings clearly highlight the potential to help the rational choice of the suitable analytical conditions, according to the nature of the gene delivery molecules exhibiting polycationic features. Moreover, our ETD-MS/MS approach open the way to a fine sequencing/identification of grafted groups carried on various sets of oligo-/polysaccharides in various fields such as glycobiology or nanomaterials, even with unknown or questionable extraction, synthesis or modification steps.

  9. Defining suitable reference genes for RT-qPCR analysis on human sertoli cells after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure.

    Science.gov (United States)

    Ribeiro, Mariana Antunes; dos Reis, Mariana Bisarro; de Moraes, Leonardo Nazário; Briton-Jones, Christine; Rainho, Cláudia Aparecida; Scarano, Wellerson Rodrigo

    2014-11-01

    Quantitative real-time RT-PCR (qPCR) has proven to be a valuable molecular technique to quantify gene expression. There are few studies in the literature that describe suitable reference genes to normalize gene expression data. Studies of transcriptionally disruptive toxins, like tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. The present study was designed to validate potential reference genes in human Sertoli cells after exposure to TCDD. 32 candidate reference genes were analyzed to determine their applicability. geNorm and NormFinder softwares were used to obtain an estimation of the expression stability of the 32 genes and to identify the most suitable genes for qPCR data normalization.

  10. A plant virus evolved by acquiring multiple nonconserved genes to extend its host range

    Science.gov (United States)

    Tatineni, Satyanarayana; Robertson, Cecile J.; Garnsey, Stephen M.; Dawson, William O.

    2011-01-01

    Viruses have evolved as combinations of genes whose products interact with cellular components to produce progeny virus throughout the plants. Some viral genes, particularly those that are involved in replication and assembly, tend to be relatively conserved, whereas other genes that have evolved for interactions with the specific host for movement and to counter host–defense systems tend to be less conserved. Closteroviridae encode 1–5 nonconserved ORFs. Citrus tristeza virus (CTV), a Closterovirus, possesses nonconserved p33, p18, and p13 genes that are expendable for systemic infection of the two laboratory hosts, Citrus macrophylla and Mexican lime. In this study, we show that the extended host range of CTV requires these nonconserved genes. The p33 gene was required to systemically infect sour orange and lemon trees, whereas either the p33 or the p18 gene was sufficient for systemic infection of grapefruit trees and the p33 or the p13 gene was sufficient for systemic infection of calamondin plants. Thus, these three genes are required for systemic infection of the full host range of CTV, but different genes were specific for different hosts. Remarkably, either of two genes was sufficient for infection of some citrus hybrids. These findings suggest that CTV acquired multiple nonconserved genes (p33, p18, and p13) and, as a result, gained the ability to interact with multiple hosts, thus extending its host range during the course of evolution. These results greatly extend the complexity of known virus–plant interactions. PMID:21987809

  11. Identification of Suitable Reference Genes for mRNA Studies in Bone Marrow in a Mouse Model of Hematopoietic Stem Cell Transplantation.

    Science.gov (United States)

    Li, H; Chen, C; Yao, H; Li, X; Yang, N; Qiao, J; Xu, K; Zeng, L

    2016-10-01

    Bone marrow micro-environment changes during hematopoietic stem cell transplantation (HSCT) with subsequent alteration of genes expression. Quantitative polymerase chain reaction (q-PCR) is a reliable and reproducible technique for the analysis of gene expression. To obtain more accurate results, it is essential to find a reference during HSCT. However, which gene is suitable during HSCT remains unclear. This study aimed to identify suitable reference genes for mRNA studies in bone marrow after HSCT. C57BL/6 mice were treated with either total body irradiation (group T) or busulfan/cyclophosphamide (BU/CY) (group B) followed by infusion of bone marrow cells. Normal mice without treatments were served as a control. All samples (group T + group B + control) were defined as group G. On days 7, 14, and 21 after transplantation, transcription levels of 7 candidate genes, ACTB, B2M, GAPDH, HMBS, HPRT, SDHA, and YWHAZ, in bone marrow cells were measured by use of real-time quantitative PCR. The expression stability of these 7 candidate reference genes were analyzed by 2 statistical software programs, GeNorm and NormFinder. Our results showed that ACTB displayed the highest expression in group G, with lowest expression of PSDHA in group T and HPRT in groups B and G. Analysis of expression stability by use of GeNorm or NormFinder demonstrated that expression of B2M in bone marrow were much more stable during HSCT, compared with other candidate genes including commonly used reference genes GAPDH and ACTB. ACTB could be used as a suitable reference gene for mRNA studies in bone marrow after HSCT. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Discussion on Suitable Range of Gestational Weight Gain%孕期体质量增长适宜范围的探讨

    Institute of Scientific and Technical Information of China (English)

    黄菊芳; 黄晓玲; 杨春芬

    2013-01-01

    evaluated .[Results] The un-derweight women accounted 25 .15% ,and normal weight women accounted 65 .92% ,and overweight women accounted 8 .93% .There were significant differences in pregnancy outcome and cesarean section rate among different groups( P <0 .05) .The range of gestational weight gain with the lowest rate of adverse pregnancy outcome in underweight group ,normal weight group and overweight group were 16~20kg ,14~18kg and 12~16kg ,respectively( P <0 .05) .[Conclusion]The high BMI before pregnancy and gestational weight gain too much are closely associated with adverse pregnancy outcome and cesarean section .The average gestational weight gain is higher in all study groups .It is extremely important to enhance health education ,rational diet and proper exercise and control the gestational weight gain in a suitable range so as to improve pregnancy out-comes and reduce pregnant complications is extremely important .The recommending optimal range of gesta-tional weight gain in underweight group ,normal weight group and overweight group are 16~20kg ,14~18kg and 12~16kg ,respectively .

  13. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence.

    Science.gov (United States)

    Gholami, Khadijeh; Loh, Su Yi; Salleh, Naguib; Lam, Sau Kuen; Hoe, See Ziau

    2017-01-01

    Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies.

  14. Isolation and selection of suitable reference genes for real-time PCR analyses in the skeletal muscle of the fine flounder in response to nutritional status: assessment and normalization of gene expression of growth-related genes.

    Science.gov (United States)

    Fuentes, Eduardo N; Safian, Diego; Valdés, Juan Antonio; Molina, Alfredo

    2013-08-01

    In the present study, different reference genes were isolated, and their stability in the skeletal muscle of fine flounder subjected to different nutritional states was assessed using geNorm and NormFinder. The combinations between 18S and ActB; Fau and 18S; and Fau and Tubb were chosen as the most stable gene combinations in feeding, long-term fasting and refeeding, and short-term refeeding conditions, respectively. In all periods, ActB was identified as the single least stable gene. Subsequently, the expression of the myosin heavy chain (MYH) and the insulin-like growth factor-I receptor (IGF-IR) was assessed. A large variation in MYH and IGF-IR expression was found depending on the reference gene that was chosen for normalizing the expression of both genes. Using the most stable reference genes, mRNA levels of MYH decreased and IGF-IR increased during fasting, with both returning to basal levels during refeeding. However, the drop in mRNA levels for IGF-IR occurred during short-term refeeding, in contrast with the observed events in the expression of MYH, which occurred during long-term refeeding. The present study highlights the vast differences incurred when using unsuitable versus suitable reference genes for normalizing gene expression, pointing out that normalization without proper validation could result in a bias of gene expression.

  15. Evaluation of suitable reference genes for quantitative RT-PCR during development and abiotic stress in Panonychus citri (McGregor) (Acari: Tetranychidae).

    Science.gov (United States)

    Niu, Jin-Zhi; Dou, Wei; Ding, Tian-Bo; Yang, Li-Hong; Shen, Guang-Mao; Wang, Jin-Jun

    2012-05-01

    Quantitative real time reverse transcriptase polymerase chain reaction (RT-qPCR) is preferred for gene expression analysis in living organisms. Currently, it is a valuable tool for biological and ecological studies as it provides a relatively straightforward way to assess the relevance of transcriptional regulation under developmental and stress tolerance conditions. However, studies have shown that some commonly used reference genes varied among different experimental treatments, thus, systematic evaluation of reference genes is critical for gene expression profiling, which is often neglected in gene expression studies of arthropods. The aim of this study is to identify the suitable reference genes for RT-qPCR experiments involving various developmental stages and/or under abiotic stresses in citrus red mite Panonychus citri, a key pest in citrus orchards worldwide. GeNorm, NormFinder, and Bestkeeper software analysis indicates that elongation factor-1 alpha (ELF1A), RNA polymerase II largest subunit, alpha tublin, and glyceraldhyde-3-phosphate dehydrogenase (GAPDH) are the most stable reference genes in various developmental stages, meanwhile, ELF1A and GAPDH were the most stable reference genes under various abiotic stresses. Furthermore, this study will serve as a resource to screen reference genes for gene expression studies in any other spider mite species.

  16. Validation of suitable reference genes for expression studies in different pilocarpine-induced models of mesial temporal lobe epilepsy.

    Directory of Open Access Journals (Sweden)

    Thalita Ewellyn Batista Sales Marques

    Full Text Available It is well recognized that the reference gene in a RT-qPCR should be properly validated to ensure that gene expression is unaffected by the experimental condition. We investigated eight potential reference genes in two different pilocarpine PILO-models of mesial temporal lobe epilepsy (MTLE performing a stability expression analysis using geNorm, NormFinder and BestKepeer softwares. Then, as a validation strategy, we conducted a relative expression analysis of the Gfap gene. Our results indicate that in the systemic PILO-model Actb, Gapdh, Rplp1, Tubb2a and Polr1a mRNAs were highly stable in hippocampus of rats from all experimental and control groups, whereas Gusb revealed to be the most variable one. In fact, we observed that using Gusb for normalization, the relative mRNA levels of the Gfap gene differed from those obtained with stable genes. On the contrary, in the intrahippocampal PILO-model, all softwares included Gusb as a stable gene, whereas B2m was indicated as the worst candidate gene. The results obtained for the other reference genes were comparable to those observed for the systemic Pilo-model. The validation of these data by the analysis of the relative expression of Gfap showed that the upregulation of the Gfap gene in the hippocampus of rats sacrificed 24 hours after status epilepticus (SE was undetected only when B2m was used as the normalizer. These findings emphasize that a gene that is stable in one pathology model may not be stable in a different experimental condition related to the same pathology and therefore, the choice of reference genes depends on study design.

  17. Suitable internal control genes for qRT-PCR normalization in cotton fiber development and somatic embryogenesis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The mechanisms of cotton fiber development and somatic embryogenesis have been explored systematically with microarray and suppression subtractive hybridization. Real-time RT-PCR provides the simultaneous measurement of gene expression in many different samples, with which the data from microarray or others can be confirmed in detail. To achieve accurate and reliable gene expression results, normalization of real-time PCR data against one or several internal control genes is required, which should not fluctuate in different tissues during various stages of development. We assessed the gene expression of 7 frequently used housekeeping genes, including 18S rRNA, Histone3, UBQ7, Actin, Cyclophilin, Gbpolyubiquitin-1 and Gbpolyubiquitin-2, in a diverse set of 21 cotton samples. For fiber developmental series the expression of all housekeeping genes had the same down tendency after 17 DPA. But the expression of the AGP gene (arabinogalactan protein) that has high expression level at the later fiber development stage was up-regulated from 15 to 27 DPA. So the relative absolute quantification should be an efficient and convenient method for the fiber developmental series. The expression of nonfiber tissues series varied not so much against the fiber developmental series. And three best control genes Histone3, UBQ7 and Gbpolyubiquitin-1 have to be used in a combinated way to get better normalization.

  18. Verification of suitable and reliable reference genes for quantitative real-time PCR during adipogenic differentiation in porcine intramuscular stromal-vascular cells.

    Science.gov (United States)

    Li, X; Huang, K; Chen, F; Li, W; Sun, S; Shi, X-E; Yang, G

    2016-06-01

    Intramuscular fat (IMF) is an important trait influencing meat quality, and intramuscular stromal-vascular cell (MSVC) differentiation is a key factor affecting IMF deposition. Quantitative real-time PCR (qPCR) is often used to screen the differentially expressed genes during differentiation of MSVCs, where proper reference genes are essential. In this study, we assessed 31 of previously reported reference genes for their expression suitability in porcine MSVCs derived form longissimus dorsi with qPCR. The expression stability of these genes was evaluated using NormFinder, geNorm and BestKeeper algorithms. NormFinder and geNorm uncovered ACTB, ALDOA and RPS18 as the most three stable genes. BestKeeper identified RPL13A, SSU72 and DAK as the most three stable genes. GAPDH was found to be the least stable gene by all of the three software packages, indicating it is not an appropriate reference gene in qPCR assay. These results might be helpful for further studies in pigs that explore the molecular mechanism underlying IMF deposition.

  19. Light water reactor fuel element suitable for thorium employment in a discrete seed and blanket configuration with the aim to attain conversion ratios above the range of one

    Energy Technology Data Exchange (ETDEWEB)

    Hrovat, M.F.; Grosse, K.H.; Seemann, R. [ALD Vacuum Technologies GmbH, Hanau (Germany)

    2008-07-01

    The thorium resources in the world are relatively large. According to the IAEA-NEA-publication ''Red Book'' they amount to 4.5 10E6 metric tons and are about 4 times greater than the resources of Uranium. The fuel element described in this paper could be used in light water reactor (LWR) preferably in pressurized water reactor (PWR). The seed (feed) rods contain uranium 235 as fissionable material and the blanket (breed) rods contain thorium and uranium. The thorium in the blanket rods is converted to fissionable U-233 by irradiation with thermal neutrons. The U-233 produced is a valuable fissionable material and is characterized by high revalues, where t is defined as the number of fission neutrons per absorption in fissile materials. By optimized configuration and loading of the seed- and blanket rods the thorium is converted to U-233 and the U-238 is converted to fissionable Plutonium isotopes. Consequently more fissionable material is generated than is used. The fuel cycle is also flexible. Thus U-235, Pu-239 or weapons-grade Plutonium can be used.Based on knowledge obtained in the development of fuel elements for material test reactors (MTR), high temperature reactors (HTR) and light water reactors (LWR), a new design of fuel element suitable for thorium employment in PWR is described.

  20. The suitable dose range for the calibration of EBT2 film by the PDD method with a comparison of two curve fitting algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Liyun, E-mail: cliyun2000@gmail.com [Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, Taiwan (China); Ho, Sheng-Yow [Department of Radiation Oncology, Chi Mei Medical Center, Liouying, Tainan, Taiwan (China); Lee, Tsair-Fwu [Medical Physics and Informatics Laboratory, Department of Electronics Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan (China); Yeh, Shyh-An [Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, Taiwan (China); Department of Radiation Oncology, E-Da Hospital, Kaohsiung, Taiwan (China); Ding, Hueisch-Jy [Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, Taiwan (China); Chen, Pang-Yu, E-mail: pangyuchen@yahoo.com.tw [Department of Radiation Oncology, Sinlau Christian Hospital, Tainan, Taiwan (China)

    2015-03-21

    EBT2 film is a convenient dosimetry quality-assurance (QA) tool with high 2D dosimetry resolution and a self-development property for use in verifications of radiation therapy treatment planning and special projects; however, the user will suffer from a relatively higher degree of uncertainty (more than ±6% by Hartmann et al. [29]), and the trouble of cutting one piece of film into small pieces and then reintegrating them each time. To prevent this tedious cutting work, and save calibration time and budget, a dose range analysis is presented in this study for EBT2 film calibration using the Percentage–Depth–Dose (PDD) method. Different combinations of the three dose ranges, 9–26 cGy, 33–97 cGy and 109–320 cGy, with two types of curve fitting algorithms, film pixel values and net optical densities converting into doses, were tested and compared. With the lowest error and acceptable inaccuracy of less than 3 cGy for the clinical dose range (9–320 cGy), a single film calibrated by the net optical density algorithm with the dose range 109–320 cGy was suggested for routine calibration.

  1. Gene expression under thermal stress varies across a geographical range expansion front.

    Science.gov (United States)

    Lancaster, Lesley T; Dudaniec, Rachael Y; Chauhan, Pallavi; Wellenreuther, Maren; Svensson, Erik I; Hansson, Bengt

    2016-03-01

    Many ectothermic species are currently expanding their distributions polewards due to anthropogenic global warming. Molecular genetic mechanisms facilitating range expansion under these conditions are largely unknown, but understanding these could help mitigate expanding pests and disease vectors, or help explain why some species fail to track changing climates. Here, using RNA-seq data, we examine genomewide changes in gene expression under heat and cold stress in the range-expanding damselfly Ischnura elegans in northern Europe. We find that both the number of genes involved and levels of gene expression under heat stress have become attenuated during the expansion, consistent with a previously reported release from selection on heat tolerances as species move polewards. Genes upregulated under cold stress differed between core and edge populations, corroborating previously reported rapid adaptation to cooler climates at the expansion front. Expression of sixty-nine genes exhibited a region x treatment effect; these were primarily upregulated in response to heat stress in core populations but in response to cold stress at the range edge, suggesting that some cellular responses originally adapted to heat stress may switch to cold-stress functionality upon encountering novel thermal selection regimes during range expansion. Transcriptional responses to thermal stress involving heat-shock and neural function genes were largely geographically conserved, while retrotransposon, regulatory, muscle function and defence gene expression patterns were more variable. Flexible mechanisms of cold-stress response and the ability of some genes to shift their function between heat and cold stress might be key mechanisms facilitating rapid poleward expansion in insects.

  2. Identification of adeno-associated viral vectors suitable for intestinal gene delivery and modulation of experimental colitis.

    Science.gov (United States)

    Polyak, Steven; Mach, Annette; Porvasnik, Stacy; Dixon, Lisa; Conlon, Thomas; Erger, Kirsten E; Acosta, Andres; Wright, Amy J; Campbell-Thompson, Martha; Zolotukhin, Irene; Wasserfall, Clive; Mah, Cathryn

    2012-02-01

    Effective gene transfer with sustained gene expression is an important adjunct to the study of intestinal inflammation and future therapy in inflammatory bowel disease. Recombinant adeno-associated virus (AAV) vectors are ideal for gene transfer and long-term transgene expression. The purpose of our study was to identify optimal AAV pseudotypes for transduction of the epithelium in the small intestine and colon, which could be used for studies in experimental colitis. The tropism and transduction efficiencies of AAV pseudotypes 1-10 were examined in murine small intestine and colon 8 wk after administration by real-time PCR and immunohistochemistry. The clinical and histopathological effects of IL-10-mediated intestinal transduction delivered by AAVrh10 were examined in the murine IL-10⁻/⁻ enterocolitis model. Serum IL-10 levels and IL-10 expression were followed by ELISA and real-time PCR, respectively. AAV pseudotypes 4, 7, 8, 9, and 10 demonstrated optimal intestinal transduction. Transgene expression was sustained 8 wk after administration and was frequently observed in enteroendocrine cells. Long-term IL-10 gene expression and serum IL-10 levels were observed following AAV transduction in an IL-10-/- model of enterocolitis. Animals treated with AAVrh10-IL-10 had lower disease activity index scores, higher colon weight-to-length ratios, and lower microscopic inflammation scores. This study identifies novel AAV pseudotypes with small intestine and colon tropism and sustained transgene expression capable of modulating mucosal inflammation in a murine model of enterocolitis.

  3. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

    Directory of Open Access Journals (Sweden)

    Jing Cai

    Full Text Available Quantitative real-time PCR (qPCR is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD, an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA and nonparametric (Kruskal-Wallis tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

  4. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

    Science.gov (United States)

    Cai, Jing; Li, Tao; Huang, Bangxing; Cheng, Henghui; Ding, Hui; Dong, Weihong; Xiao, Man; Liu, Ling; Wang, Zehua

    2014-01-01

    Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

  5. Development of a gene silencing DNA vector derived from a broad host range geminivirus

    Directory of Open Access Journals (Sweden)

    Hancock Leandria C

    2009-07-01

    Full Text Available Abstract Background Gene silencing is proving to be a powerful tool for genetic, developmental, and physiological analyses. The use of viral induced gene silencing (VIGS offers advantages to transgenic approaches as it can be potentially applied to non-model systems for which transgenic techniques are not readily available. However, many VIGS vectors are derived from Gemini viruses that have limited host ranges. We present a new, unipartite vector that is derived from a curtovirus that has a broad host range and will be amenable to use in many non-model systems. Results The construction of a gene silencing vector derived from the geminivirus Beet curly top virus (BCTV, named pWSRi, is reported. Two versions of the vector have been developed to allow application by biolistic techniques or by agro-infiltration. We demonstrate its ability to silence nuclear genes including ribulose bisphosphate carboxylase small subunit (rbcS, transketolase, the sulfur allele of magnesium chelatase (ChlI, and two homeotic transcription factors in spinach or tomato by generating gene-specific knock-down phenotypes. Onset of phenotypes occurred 3 to 12 weeks post-inoculation, depending on the target gene, in organs that developed after the application. The vector lacks movement genes and we found no evidence for significant spread from the site of inoculation. However, viral amplification in inoculated tissue was detected and is necessary for systemic silencing, suggesting that signals generated from active viral replicons are efficiently transported within the plant. Conclusion The unique properties of the pWSRi vector, the ability to silence genes in meristem tissue, the separation of virus and silencing phenotypes, and the broad natural host range of BCTV, suggest that it will have wide utility.

  6. Selection of suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using quantitative real-time polymerase chain reaction

    DEFF Research Database (Denmark)

    Zornhagen, K. W.; Kristensen, A. T.; Hansen, Anders Elias;

    2015-01-01

    Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive technique for quantifying gene expression. Stably expressed reference genes are necessary for normalization of RT-qPCR data. Only a few articles have been published on reference genes in canine tumours...

  7. Universal primers suitable to assess population dynamics reveal apparent mutually exclusive transcription of the Babesia bovis ves1alpha gene.

    Science.gov (United States)

    Zupańska, Agata K; Drummond, Paul B; Swetnam, Daniele M; Al-Khedery, Basima; Allred, David R

    2009-07-01

    Babesia bovis is an intraerythrocytic hemoparasite of widespread distribution, which adversely affects livestock production in many regions of the world. This parasite establishes persistent infections of long duration, at least in part through rapid antigenic variation of the VESA1 protein on the infected-erythrocyte surface. To understand the dynamics of in vivo antigenic variation among the parasite population it is necessary to have sensitive and broadly applicable tools enabling monitoring of variation events in parasite antigen genes. To address this need for B. bovis, "universal" primers for the polymerase chain reaction have been designed for the ves1alpha gene, spanning from exon 2 to near the 3' end of cysteine-lysine-rich domain (CKRD) sequences in exon 3. These primers robustly amplified this segment, with minimal bias, from essentially the entire repertoire of full-length ves1alpha sequences in the B. bovis Mexico isolate genome, and are equivalently present in other isolates. On purified genomic DNA, this primer set can achieve a sensitivity of 10 genome equivalents or less. When applied to the amplification of cDNA derived from the B. bovis C9.1 clonal line evidence consistent with mutually exclusive transcription of the ves1alpha gene was obtained, concomitant with detection of numerous mutational events among members of the parasite population. These characteristics of the primers will facilitate the application of polymerase chain reaction-based methodologies to the study of B. bovis population and antigenic switching dynamics.

  8. Provide a suitable range to include the thermal creeping effect on slip velocity and temperature jump of an air flow in a nanochannel by lattice Boltzmann method

    Science.gov (United States)

    Karimipour, Arash

    2017-01-01

    The thermal creeping effect on slip velocity of air forced convection through a nanochannel is studied for the first time by using a lattice Boltzmann method. The nanochannel side walls are kept hot while the cold inlet air streams along them. The computations are presented for the wide range of Reynolds number, Knudsen number and Eckert number while slip velocity and temperature jump effects are involved. Moreover appropriate validations are performed versus previous works concerned the micro-nanoflows. The achieved results are shown as the velocity and temperature profiles at different cross sections, streamlines and isotherms and also the values of slip velocity and temperature jump along the nanochannel walls. The ability of the lattice Boltzmann method to simulate the thermal creeping effects on hydrodynamic and thermal domains of flow is shown at this study; so that its effects should be involved at lower values of Eckert number and higher values of Reynolds number especially at entrance region where the most temperature gradient exists.

  9. EF1α and RPL13a represent normalization genes suitable for RT-qPCR analysis of bone marrow derived mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    Curtis Kevin M

    2010-08-01

    Full Text Available Abstract Background RT-qPCR analysis is a widely used method for the analysis of mRNA expression throughout the field of mesenchymal stromal cell (MSC research. Comparison between MSC studies, both in vitro and in vivo, are challenging due to the varied methods of RT-qPCR data normalization and analysis. Therefore, this study focuses on putative housekeeping genes for the normalization of RT-qPCR data between heterogeneous commercially available human MSC, compared with more homogeneous populations of MSC such as MIAMI and RS-1 cells. Results Eight genes including; ACTB, B2M, EF1α, GAPDH, RPL13a, YWHAZ, UBC and HPRT1 were tested as possible housekeeping genes based on their expression level and variability. EF1α and RPL13a were validated for RT-qPCR analysis of MIAMI cells during expansion in varied oxygen tensions, endothelial differentiation, neural precursor enrichment, and during the comparison with RS-1 cells and commercially available MSC. RPL13a and YWHAZ were validated as normalization genes for the cross-species analysis of MIAMI cells in an animal model of focal ischemia. GAPDH, which is one of the most common housekeeping genes used for the normalization of RT-qPCR data in the field of MSC research, was found to have the highest variability and deemed not suitable for normalization of RT-qPCR data. Conclusions In order to make comparisons between heterogeneous MSC populations, as well as adult stem cell like MSC which are used in different laboratories throughout the world, it is important to have a standardized, reproducible set of housekeeping genes for RT-qPCR analysis. In this study we demonstrate that EF1α, RPL13a and YWHAZ are suitable genes for the RT-qPCR analysis and comparison of several sources of human MSC during in vitro characterization and differentiation as well as in an ex vivo animal model of global cerebral ischemia. This will allow for the comparative RT-qPCR analysis of multiple MSC populations with the goal of

  10. Genome organization and long-range regulation of gene expression by enhancers.

    Science.gov (United States)

    Smallwood, Andrea; Ren, Bing

    2013-06-01

    It is now well accepted that cell-type specific gene regulation is under the purview of enhancers. Great strides have been made recently to characterize and identify enhancers both genetically and epigenetically for multiple cell types and species, but efforts have just begun to link enhancers to their target promoters. Mapping these interactions and understanding how the 3D landscape of the genome constrains such interactions is fundamental to our understanding of mammalian gene regulation. Here, we review recent progress in mapping long-range regulatory interactions in mammalian genomes, focusing on transcriptional enhancers and chromatin organization principles. Copyright © 2013. Published by Elsevier Ltd.

  11. A modified protocol for RNA extraction from different peach tissues suitable for gene isolation and real-time PCR analysis.

    Science.gov (United States)

    Tong, Zhaoguo; Qu, Shenchun; Zhang, Jiyu; Wang, Fei; Tao, Jianmin; Gao, Zhihong; Zhang, Zhen

    2012-03-01

    RNA extraction is the first step in the study of gene isolation and expression. However, it is difficult to extract high quantity and quality RNA from tissues containing large quantities of polysaccharides and polyphenols. Peach (Prunus persica), in addition to containing high levels of polysaccharides and polyphenols, is a challenging starting material for RNA isolation using a single method because of different amounts of those substances in diverse tissues. Based on three reported methods, we developed a modified RNA isolation protocol to solve this problem, leading to high quality and quantity of total RNA from peach mesocarp tissues of fruits which were sampled from all developmental stages and different storage periods, as well as from other tissues including flowers, leaves, stems, and roots. With our modified method, 28-650 μg of total RNA was routinely obtained from per gram of fresh material, gave at least a 1.16-fold improvement by compared with those isolated by other seven methods. The RNA extracts were successfully used in downstream applications such as RT-PCR, RACE, and real-time PCR.

  12. Gene expression profiling in the Cynomolgus macaque Macaca fascicularis shows variation within the normal birth range

    Directory of Open Access Journals (Sweden)

    Vickers Mark H

    2011-10-01

    Full Text Available Abstract Background Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevance to humans are largely unknown. Importantly, emerging evidence suggests that these effects operate within the normal range of birth weights and involve mechanisms of developmental palsticity rather than pathology. Method To explore this further, we utilised a non-human primate model Macaca fascicularis (Cynomolgus macaque which shares with humans the same progressive history of the metabolic syndrome. Using microarray we compared tissues from neonates in the average birth weight (50-75th centile to those of lower birth weight (5-25th centile and studied the effect of different growth trajectories within the normal range on gene expression levels in the umbilical cord, neonatal liver and skeletal muscle. Results We identified 1973 genes which were differentially expressed in the three tissue types between average and low birth weight animals (P Conclusion These differences in gene expression levels between animals in the upper and lower percentiles of the normal birth weight range may point towards early life metabolic adaptations that in later life result in differences in disease risk.

  13. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito.

    Science.gov (United States)

    Medley, Kim A; Jenkins, David G; Hoffman, Eric A

    2015-01-01

    Human-aided transport is responsible for many contemporary species introductions, yet the contribution of human-aided transport to dispersal within non-native regions is less clear. Understanding dispersal dynamics for invasive species can streamline mitigation efforts by targeting routes that contribute disproportionally to spread. Because of its limited natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes albopictus) has been attributed to human-aided transport, but until now, the relative roles of human-aided and natural movement have not been rigorously evaluated. Here, we use landscape genetics and information-theoretic model selection to evaluate 52 models representing 9240 pairwise dispersal paths among sites across the US range for Ae. albopictus and show that recent gene flow reflects a combination of natural and human-aided dispersal. Highways and water availability facilitate dispersal at a broad spatial scale, but gene flow is hindered by forests at the current distributional limit (range edge) and by agriculture among sites within the mosquito's native climatic niche (range core). Our results show that highways are important to genetic structure between range-edge and range-core pairs, suggesting a role for human-aided mosquito transport to the range edge. In contrast, natural dispersal is dominant at smaller spatial scales, reflecting a shifting dominance to natural movement two decades after introduction. These conclusions highlight the importance of (i) early intervention for species introductions, particularly those with readily dispersed dormant stages and short generation times, and (ii) strict monitoring of commercial shipments for transported immature stages of Ae. albopictus, particularly towards the northern edge of the US range.

  14. Hypervariable pili and flagella genes provide suitable new targets for DNA high-resolution melt-based genotyping of dairy Geobacillus spp.

    Science.gov (United States)

    Chauhan, Kanika; Seale, R Brent; Deeth, Hilton C; Turner, Mark S

    2014-10-01

    Although nonpathogenic in nature, spores of Geobacillus are able to attach to surfaces, germinate, and form biofilms, allowing rapid multiplication and persistence within milk powder processing plants, causing final product contamination, and eventually leading to a loss of revenue in terms of downgraded product quality. As a result, Geobacillus spp. have been found to be common contaminants of milk powder worldwide. Genotyping methods can help in gaining insight into the ecology and transmission of these thermophilic bacteria within and between dairy processing plants. The objective of this study was to use the assembled draft genomes of two Geobacillus spp. to identify and test new hypervariable genotyping targets for differentiating closely related dairy Geobacillus isolates. The two Geobacillus spp. strains obtained from high spore count powders were obtained in 2010 (isolate 7E) and in 1995 (isolate 126) and were previously shown to be of same genotype based on a variable number tandem repeat genotyping method. Significant nucleotide sequence variation was found in genes encoding pili and flagella, which were further investigated as suitable loci for a new high-resolution melt analysis (HRMA)-based genotyping method. Three genes encoding pulG (containing prepilin-type N-terminal cleavage domain), pilT (pili retraction protein), and fliW (flagellar assembly protein) were selected as targets for the new pili/flagella gene (PilFla) HRMA genotyping method. The three-gene-based PilFla-HRMA genotyping method differentiated 35 milk powder Geobacillus spp. isolates into 19 different genotype groups (D = 0.93), which compared favorably to the previous method (which used four variable number tandem repeat loci) that generated 16 different genotype groups (D = 0.90). In conclusion, through comparative genomics of two closely related dairy Geobacillus strains, we have identified new hypervariable regions that prove to be useful targets for highly discriminatory genotyping.

  15. Broad-Host Range Vector-Particle: Gene Transfer Particles From Thermal Vents

    Science.gov (United States)

    Chiura, H. X.; Nakamura, K.; Fukazawa, Y.; Nakata, D.; Tomaru, A.; Okita, N.; Hoaki, T.

    2002-12-01

    Viruses or virus-like particles (VLPs) are common in aquatic ecosystems, however, VLP-host interactions and its commitments to gene transfer in the environment is yet unclear. We have proposed that at least some of the widely distributed VLPs could be general gene transfer agents among a wide range of microbial host cells, and might function as a universal vector (1-4). To elucidate such a broad host range gene transfer mediated by "VLP", the sampling site was extended to the hyper hydrothermal vent, and boring cores. VLP (v) and cell (b) abundances per ml water samples from drilling holes of Suiyo seamount were: APSK04 (28°34.303'N, 140°38.618'E, 1385 m deep, 21°C, b = 8.26 *E^{6}, v = 6.03 x 10^{6}); APSK07 (28°34.299'N, 140°38.690'E, 1386 m deep, 250.5°C, b = 5.33 \\times 104, v = 2.52 \\times 104); a natural vent near APSK05 (28°34.322'N, 140°38.594'E, 1382 m deep, 304.7°C, b = 3.23 x 10^{4}, v = 1.85 x 10^{4}). A boring core sample was obtained from APSK06 (28°34.313'N, 140°38.617', 1386 m deep), from which a hyper thermophilic Archaean, Thermococcus kodakaraensis was successfully cultivated in sulphur supplemented medium between 70 and 90°C. VLP production was observed from T. kodakaraensis, whose VLP (v) and cell (b) abundances per ml at 480 h culture at 70°C were: b = 3.61 *E^{9}, v = 3.46 *E^{9}. Transduction experiment at multiplicity of infection of ca 0.2 using particles from APSK07 and T. kodakaraensis showed a plate efficiency on recipient Escherichia coli AB1157 by ca 72 % and ca 89 % regardless of UV treatment of the particle. Gene transfer frequency of APSK07 particle was (x 10^{-5} cfu/particle) between 2.4 and 0.92, and that of T. kodakaraensis particle was between x 10^{-4} and x 10^{-5}$ cfu/particle. These findings suggest the non-specific gene transfer by such particles may be a ubiquitous event in the natural environment. Such gene transfer particles may have mediated gene flux among phylogenetically diverse microbial

  16. Effect of Drought on Herbivore-Induced Plant Gene Expression: Population Comparison for Range Limit Inferences

    Directory of Open Access Journals (Sweden)

    Gunbharpur Singh Gill

    2016-03-01

    Full Text Available Low elevation “trailing edge” range margin populations typically face increases in both abiotic and biotic stressors that may contribute to range limit development. We hypothesize that selection may act on ABA and JA signaling pathways for more stable expression needed for range expansion, but that antagonistic crosstalk prevents their simultaneous co-option. To test this hypothesis, we compared high and low elevation populations of Boechera stricta that have diverged with respect to constitutive levels of glucosinolate defenses and root:shoot ratios; neither population has high levels of both traits. If constraints imposed by antagonistic signaling underlie this divergence, one would predict that high constitutive levels of traits would coincide with lower plasticity. To test this prediction, we compared the genetically diverged populations in a double challenge drought-herbivory growth chamber experiment. Although a glucosinolate defense response to the generalist insect herbivore Spodoptera exigua was attenuated under drought conditions, the plastic defense response did not differ significantly between populations. Similarly, although several potential drought tolerance traits were measured, only stomatal aperture behavior, as measured by carbon isotope ratios, was less plastic as predicted in the high elevation population. However, RNAseq results on a small subset of plants indicated differential expression of relevant genes between populations as predicted. We suggest that the ambiguity in our results stems from a weaker link between the pathways and the functional traits compared to transcripts.

  17. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

    Science.gov (United States)

    Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

    2011-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

  18. Genetic analysis of the PKHD1 gene with long-rang PCR sequencing.

    Science.gov (United States)

    Tong, Yong-Qing; Liu, Bei; Fu, Chao-Hong; Zheng, Hong-Yun; Gu, Jian; Liu, Hang; Luo, Hong-Bo; Li, Yan

    2016-10-01

    PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease (ARPKD). However, it is inconvenient to detect the mutations by common polymerase chain reaction (PCR) because the open reading frame of PKHD1 is very long. Recently, long-range (LR) PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.

  19. Construction of a host range-expanded hybrid baculovirus of BmNPV and AcNPV,and knockout of cysteinase gene for more efficient expression

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    AcNPV(Autographa californica nuclear polyhedrosis virus)and BmNPV(Bombyx mori nuclear polyhedrosis virus)are two principal insect-baculovirus expression systems,each having different characteristics.AcNPV has a wider host range and can infect a series of cell lines thus making it suitable for cell suspension culture expression,but the small size of the host insect,A.californica,makes AcNPV less suitable for large scale protein synthesis.In contrast,BmNPV can only infect the silkworm,Bornbyx rnori,which is well-known for its easy rearing and large size.These characteristics make the BmNPV system especially suitable for large-scale industrial expression.To utilize the advantages of both AcNPV and BmNPV,we tried to expand their host range through homologous recombination and successfully constructed a hybrid baculovirus of AcNPV and BmNPV,designated as HyNPV.The hybrid baculovirus can infect the hosts of both AcNPV and BmNPV.Taking the human basic fibroblast growth factor(Bfgf)gene as an application example,we constructed a recombinant,HyNPV-Bfgf.This construct is able to express the Bfgf protein both in silkworm larvae and in common-use cell lines,sf21,sf9 and High-five.Moreover,to reduce the loss of recombinant protein due to degradation by proteases that are simultaneously expressed by the baculovirus,we knocked out the cysteinase gene coding for one of the most important baculovirus proteases.This knockout mutation improves the production efficiency of the Bfgf recombinant protein.

  20. Molecular karyotype and chromosomal localization of genes encoding ß-tubulin, cysteine proteinase, hsp 70 and actin in Trypanosoma rangeli

    Directory of Open Access Journals (Sweden)

    CB Toaldo

    2001-01-01

    Full Text Available The molecular karyotype of nine Trypanosoma rangeli strains was analyzed by contour-clamped homogeneous electric field electrophoresis, followed by the chromosomal localization of ß-tubulin, cysteine proteinase, 70 kDa heat shock protein (hsp 70 and actin genes. The T. rangeli strains were isolated from either insects or mammals from El Salvador, Honduras, Venezuela, Colombia, Panama and southern Brazil. Also, T. cruzi CL-Brener clone was included for comparison. Despite the great similarity observed among strains from Brazil, the molecular karyotype of all T. rangeli strains analyzed revealed extensive chromosome polymorphism. In addition, it was possible to distinguish T. rangeli from T. cruzi by the chromosomal DNA electrophoresis pattern. The localization of ß-tubulin genes revealed differences among T. rangeli strains and confirmed the similarity between the isolates from Brazil. Hybridization assays using probes directed to the cysteine proteinase, hsp 70 and actin genes discriminated T. rangeli from T. cruzi, proving that these genes are useful molecular markers for the differential diagnosis between these two species. Numerical analysis based on the molecular karyotype data revealed a high degree of polymorphism among T. rangeli strains isolated from southern Brazil and strains isolated from Central and the northern South America. The T. cruzi reference strain was not clustered with any T. rangeli strain.

  1. Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes

    Science.gov (United States)

    Garner, Emily; Wallace, Joshua S.; Argoty, Gustavo Arango; Wilkinson, Caitlin; Fahrenfeld, Nicole; Heath, Lenwood S.; Zhang, Liqing; Arabi, Mazdak; Aga, Diana S.; Pruden, Amy

    2016-12-01

    Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery. With 277 ARG subtypes identified across samples, total bulk water ARGs decreased following the flood but recovered to near pre-flood abundances by ten months post-flood at both a pristine site and at a site historically heavily influenced by wastewater treatment plants and animal feeding operations. Network analysis of de novo assembled sequencing reads into 52,556 scaffolds identified ARGs likely located on mobile genetic elements, with up to 11 ARGs per plasmid-associated scaffold. Bulk water bacterial phylogeny correlated with ARG profiles while sediment phylogeny varied along the river’s anthropogenic gradient. This rare flood afforded the opportunity to gain deeper insight into factors influencing the spread of ARGs in watersheds.

  2. RPL13A and EEF1A1 Are Suitable Reference Genes for qPCR during Adipocyte Differentiation of Vascular Stromal Cells from Patients with Different BMI and HOMA-IR

    Science.gov (United States)

    Gentile, Adriana-Mariel; Lhamyani, Said; Coín-Aragüez, Leticia; Oliva-Olivera, Wilfredo; Zayed, Hatem; Vega-Rioja, Antonio; Monteseirin, Javier; Romero-Zerbo, Silvana-Yanina; Tinahones, Francisco-José; Bermúdez-Silva, Francisco-Javier; El Bekay, Rajaa

    2016-01-01

    Real-time or quantitative PCR (qPCR) is a useful technique that requires reliable reference genes for data normalization in gene expression analysis. Adipogenesis is among the biological processes suitable for this technique. The selection of adequate reference genes is essential for qPCR gene expression analysis of human Vascular Stromal Cells (hVSCs) during their differentiation into adipocytes. To the best of our knowledge, there are no studies validating reference genes for the analyses of visceral and subcutaneous adipose tissue hVSCs from subjects with different Body Mass Index (BMI) and Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) index. The present study was undertaken to analyze this question. We first analyzed the stability of expression of five potential reference genes: CYC, GAPDH, RPL13A, EEF1A1, and 18S ribosomal RNA, during in vitro adipogenic differentiation, in samples from these types of patients. The expression of RPL13A and EEF1A1 was not affected by differentiation, thus being these genes the most stable candidates, while CYC, GAPDH, and 18S were not suitable for this sort of analysis. This work highlights that RPL13A and EEF1A1 are good candidates as reference genes for qPCR analysis of hVSCs differentiation into adipocytes from subjects with different BMI and HOMA-IR. PMID:27304673

  3. Evaluation of the suitability of six host genes as internal control in real-time RT-PCR assays in chicken embryo cell cultures infected with infectious bursal disease virus

    DEFF Research Database (Denmark)

    Li, Yiping; Bang, Dang Duong; Handberg, Kurt

    2005-01-01

    -time RT-PCR is needed to a suitable internal control. We thus investigated the expression pattern of six chicken genes, including P-actin, 28S rRNA, 18S rRNA, glyceral dehyde-3-phosphate dehydrogenase (GAPDH), TATA box-binding protein (TBP) and beta-2-microglobulin, in chicken embryo (CE) cell cultures...... and GAPDH had a lower expression level in CE cell cultures. Also, beta-actin showed no significant variation in both normalized and non-normalized assays and virus dose-independent of inoculation, while other genes did. beta-Actin was further successfully used as an internal control to quantitate Bursine-2...... virus-specific RNA load in CE cell cultures. Thus, beta-actin was suggested as a suitable internal control in studying gene expression as well as virus-specific RNA load in CE cell after IBDV infection....

  4. Range of retinal diseases potentially treatable by AAV-vectored gene therapy.

    Science.gov (United States)

    Hauswirth, William W; Li, Quihong; Raisler, Brian; Timmers, Adrian M; Berns, Kenneth I; Flannery, John G; LaVail, Matthew M; Lewin, Alfred S

    2004-01-01

    Viable strategies for retinal gene therapy must be designed to cope with the genetic nature of the disease and/or the primary pathologic process responsible for retinal malfunction. For dominant gene defects the aim must be to destroy the presumably toxic gene product, for recessive gene defects the direct approach aims to provide a wild-type copy of the gene to the affected retinal cell type, and for diseases of either complex or unknown genetic origin, more general cell survival strategies that deal with preserving affected retinal cells are often the best and only option. Hence examples of each type of therapy will be briefly discussed in several animal models, including ribozyme therapy for autosomal dominant retinitis pigmentosa in the transgenic P23H opsin rat, beta-PDE gene augmentation therapy for autosomal recessive retinitis pigmentosa in the rd mouse, glial cell-derived neurotrophic factor (GDNF) gene therapy for autosomal dominant RP in the transgenic S334ter opsin rat and pigment epithelial cell-derived neurotrophic factor (PEDF) gene therapy for neovascular retinal disease in rodents. Each employs a recombinant AAV vectored passenger gene controlled by one of several promoters supporting either photoreceptor-specific expression or more general retinal cell expression depending on the therapeutic requirements.

  5. Study on Suitable Range Indices of Major Chemical Components in Enshi Flue-cured Tobacco Region%恩施烟区烤烟主要化学成分适宜指标研究

    Institute of Scientific and Technical Information of China (English)

    申国明; 时鹏; 向德恩; 刘光亮; 高林; 王瑞; 向必坤; 陈红华; 高欣欣

    2011-01-01

    对恩施烟区2008和2009年烤烟中部烟叶主要化学成分进行了分析,发现烤烟质量适宜范围指标年度间整体上相差不大,建议质量指标平均范围为:还原糖27.20%~30.54%,总糖32.03%~36.30%,总植物碱2.20%~2.76%,总氮1.66%~1.99%,两糖差3.73%~6.88%,还原糖碱比10.29~13.35,总糖碱比12.12~15.88,两糖比0.81~0.89,总糖氮比16.46~21.48,还原糖氮比14.09~17.93;与贵州、山东和云南省中部烟叶相比,恩施烟区中部烟叶化学成分及比值处于中等水平,且还原糖、总糖、总植物碱含量及两糖差、还原糖碱比和两糖比均接近于云南省烟叶.整体上,恩施烟区烤烟中部烟叶化学成分及比值比较协调,满足优质烟叶的要求.%We analyzed the main chemical components in middle leaves of the flue-cured tobacco in Enshi of the year 2008 and 2009. The results showed that the differences of quality suitable range index was little between 2008 and 2009. The average quality suitable range index are as follow: reducing sugar 27.20%-30.54%, total sugar 32.03%-36.30%, totalalkaloids 2.20%-2.76%, total nitrogen 1.66%-1.99%, the difference between the total sugar and reducing sugar 3.73%-6.88%, the ratio of reducing sugar to total alkaloids 10.29-13.35, the ratio of total sugar to total alkaloids 12.12-15.88, the ratio of reducing sugar to total sugar 0.81-0.89, the ratio of total sugar to total nitrogen 16.46-21.48, and the ratio of reducing sugar to total nitrogen 14.09-17.93. Compared with Guizhou, Shandong and Yunnan province, the chemical components and ratios in Enshi were at middle level, and the reducing sugar, total sugar, total alkaloids, the difference between the total sugar and reducing sugar, the ratio of reducing sugar to total alkaloids and the ratio of reducing sugar to total sugar were closed to Yunnan province. The chemical components and ratios of the flue-cured tobacco middle leaves in Enshi were harmonious, which

  6. Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment.

    Science.gov (United States)

    Rowe, Will; Verner-Jeffreys, David W; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan J; Pearce, Gareth P

    2016-01-01

    The aquatic environment has been implicated as a reservoir for antimicrobial resistance genes (ARGs). In order to identify sources that are contributing to these gene reservoirs, it is crucial to assess effluents that are entering the aquatic environment. Here we describe a metagenomic assessment for two types of effluent entering a river catchment. We investigated the diversity and abundance of resistance genes, mobile genetic elements (MGEs) and pathogenic bacteria. Findings were normalised to a background sample of river source water. Our results show that effluent contributed an array of genes to the river catchment, the most abundant being tetracycline resistance genes tetC and tetW from farm effluents and the sulfonamide resistance gene sul2 from wastewater treatment plant (WWTP) effluents. In nine separate samples taken across 3 years, we found 53 different genes conferring resistance to seven classes of antimicrobial. Compared to the background sample taken up river from effluent entry, the average abundance of genes was three times greater in the farm effluent and two times greater in the WWTP effluent. We conclude that effluents disperse ARGs, MGEs and pathogenic bacteria within a river catchment, thereby contributing to environmental reservoirs of ARGs.

  7. Solanum venturii, a suitable model system for virus-induced gene silencing studies in potato reveals StMKK6 as an important player in plant immunity

    NARCIS (Netherlands)

    Dobnik, David; Lazar, Ana; Stare, Tjaša; Gruden, Kristina; Vleeshouwers, Vivianne G.A.A.; Žel, Jana

    2016-01-01

    Background: Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole plant. Potato (Solanum tuberosum) is one of the most important food crops,

  8. 75 FR 68222 - Suitability

    Science.gov (United States)

    2010-11-05

    ...; ] OFFICE OF PERSONNEL MANAGEMENT 5 CFR PART 731 RIN 3206-AL90 Suitability AGENCY: U.S. Office of Personnel... possible, of security and suitability standards. Public Trust Positions Public trust positions are those...) for a new public trust reinvestigation. Likewise, a suitability investigation based on a change...

  9. Distribution of Microbial Arsenic Reduction, Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations

    OpenAIRE

    Escudero, Lorena V.; Casamayor, Emilio O.; Guillermo Chong; Carles Pedrós-Alió; Cecilia Demergasso

    2013-01-01

    The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared onl...

  10. Escherichia coli Vertebral Osteomyelitis Diagnosed According to Broad-range 16S rRNA Gene Polymerase Chain Reaction (PCR).

    Science.gov (United States)

    Shibata, Satoshi; Tanizaki, Ryutaro; Watanabe, Koji; Makabe, Kenta; Shoda, Naoki; Kutsuna, Satoshi; Nagamatsu, Maki; Oka, Shinichi; Ohmagari, Norio

    2015-01-01

    Identifying the causative agent of pyogenic osteomyelitis is often challenging, especially when antibiotics are administered before a biopsy. We herein present a case of osteomyelitis in the cervical vertebrae presenting with progressive paralytic symptoms, in which we successfully identified Escherichia coli from a biopsy specimen using broad-range 16S rRNA gene polymerase chain reaction (PCR) even though sensitive antibiotics had been used for more than 50 days before the biopsy. Broad-range 16S rRNA gene PCR is a useful diagnostic method, especially when prebiopsy antibiotics are unavoidably used for a clinically unstable state.

  11. High Efficiency Control Strategy for Isolated Full-Bridge-Boost Converter Suitable for Wide Input Voltage Range%宽输入电压范围下隔离型全桥Boost变换器的高效率控制

    Institute of Scientific and Technical Information of China (English)

    姚川; 阮新波; 王学华

    2012-01-01

    A family of isolated Buck-Boost converters is proposed to be suitable for the application,where the input voltage range is wide and galvanic isolation is required in this paper.Full-Bridge(FB)-Boost converter is analyzed as one of the typical topologies.Considering the duty cycle loss,an improved two-edge modulation strategy based on phase-shift control is proposed to minimize the inductor current ripple over the input voltage range.In order to achieve the reliability and efficiency of this converter,a 3-mode dual-frequency control scheme is proposed.Under the 3-mode dual-frequency control scheme,the input voltage is divided into three regions,i.e.the low,medium and high voltage rang,and corresponding operating modes are Boost,FB-Boost and FB modes respectively.As the inductor current ripple in FB-Boost mode is much smaller,the switching frequency of the boost cell in this mode can be lowered to reduce the switching loss and further improve the efficiency.To verify the effectiveness of the design and control,a 250~500V input,360V output and 6kW rated power prototype is fabricated.High efficiency can be achieved all over the input voltage range,and the highest efficiency is 97.2%.%本文提出了一族隔离型的Buck-Boost变换器以适应宽输入电压范围并要求隔离的应用场合,以全桥(Full-Bridge,FB)Boost变换器作为其典型电路之一在文中展开分析。考虑占空比的丢失,提出了基于移相控制的双沿调制策略以减小整个输入电压范围内的电感电流脉动。为实现变换器可靠高效的工作,提出了三模式双频控制策略。三模式双频控制策略下,输入电压被分为低、中、高三个电压区间,分别对应于FB-Boost变换器的Boost、FB-Boost和FB三个工作模式。由于FB-Boost模式下电感电流脉动较小,可以降低该模式下Boost单元的开关频率以减小开关损耗,进一步提高效率。为验证设计和控制策略的有效

  12. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression.

    Directory of Open Access Journals (Sweden)

    Yichi Xu

    2016-05-01

    Full Text Available Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chromosome architecture. We focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor in circadian rhythm. Using circular chromosome conformation capture sequencing, we systematically examined the interacting loci of a Bmal1-bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions are largely stable in the circadian cycle and cohesin binding sites are enriched in the interactome. Global analysis showed that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites are associated with high circadian rhythmicity of transcription. A model integrating the effects of cohesin and CTCF markedly improved the mechanistic understanding of circadian gene expression. Further experiments in cohesin knockout cells demonstrated that cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. This study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.

  13. Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations.

    Science.gov (United States)

    Escudero, Lorena V; Casamayor, Emilio O; Chong, Guillermo; Pedrós-Alió, Carles; Demergasso, Cecilia

    2013-01-01

    The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

  14. Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations.

    Directory of Open Access Journals (Sweden)

    Lorena V Escudero

    Full Text Available The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V to As (III in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V as electron acceptor, was found in all the systems studied. The As (III oxidation gene aioA and the As (III transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

  15. Myxoma virus M063R is a host range gene essential for virus replication in rabbit cells.

    Science.gov (United States)

    Barrett, John W; Shun Chang, Chew; Wang, Gen; Werden, Steven J; Shao, Zhuhong; Barrett, Catherine; Gao, Xiujuan; Belsito, Tara A; Villenevue, Danielle; McFadden, Grant

    2007-04-25

    The myxoma virus M063R gene product exhibits some sequence similarity to the poxvirus host range gene, C7L, of vaccinia virus. To address the potential host range function of the M063R gene product in rabbits, a deletion mutant of myxoma virus (vMyx63KO) was generated and characterized. vMyx63KO replicated to normal titre levels and produced foci that were indistinguishable from those produced by MV in vitro in a monkey kidney cell line (BGMK) that are permissive for wild type MV. However, vMyx63KO failed to replicate in all rabbit cell lines tested, including both primary and established cells lines, as well as cells derived from a variety of tissues. M063R expression was not required for myxoma virus binding, entry or early gene expression, whereas DNA replication was aborted and late genes were not expressed in vMyx63KO infected rabbit cells. Thus, the replication block for vMyx63KO in rabbit cells preceded the stage of late gene expression and DNA replication. Finally, an in vivo pathogenesis study indicated that vMyx63KO failed to cause any signs of classic myxomatosis in infected rabbits, but functioned as a non-replicating vaccine and provided protection for subsequent challenge by wild type myxoma virus. Altogether, these observations demonstrate that M063R plays a critical role in determining the host specificity of myxoma virus in rabbit cells.

  16. Cross-study homogeneity of psoriasis gene expression in skin across a large expression range.

    Directory of Open Access Journals (Sweden)

    Jeannette Bigler

    Full Text Available BACKGROUND: In psoriasis, only limited overlap between sets of genes identified as differentially expressed (psoriatic lesional vs. psoriatic non-lesional was found using statistical and fold-change cut-offs. To provide a framework for utilizing prior psoriasis data sets we sought to understand the consistency of those sets. METHODOLOGY/PRINCIPAL FINDINGS: Microarray expression profiling and qRT-PCR were used to characterize gene expression in PP and PN skin from psoriasis patients. cDNA (three new data sets and cRNA hybridization (four existing data sets data were compared using a common analysis pipeline. Agreement between data sets was assessed using varying qualitative and quantitative cut-offs to generate a DEG list in a source data set and then using other data sets to validate the list. Concordance increased from 67% across all probe sets to over 99% across more than 10,000 probe sets when statistical filters were employed. The fold-change behavior of individual genes tended to be consistent across the multiple data sets. We found that genes with 10-fold changes in either direction such as CHRM3, IL12B and IFNG. CONCLUSIONS/SIGNIFICANCE: Gene expression changes in psoriatic lesions were consistent across different studies, despite differences in patient selection, sample handling, and microarray platforms but between-study comparisons showed stronger agreement within than between platforms. We could use cut-offs as low as log10(ratio = 0.1 (fold-change = 1.26, generating larger gene lists that validate on independent data sets. The reproducibility of PP signatures across data sets suggests that different sample sets can be productively compared.

  17. Shorebird Habitat Suitability Indicies

    Data.gov (United States)

    Arctic Landscape Conservation Cooperative — This dataset consists of predicted habitat suitability indices and species richness for eight shorebird species (Black-bellied Plover [Pluvialis squatarola],...

  18. 76 FR 69601 - Suitability

    Science.gov (United States)

    2011-11-09

    ... RIN 3206-AL90 Suitability AGENCY: U.S. Office of Personnel Management. ACTION: Final rule. SUMMARY... reinvestigation) as determined by the Director of the Office of Personnel Management, to ensure their suitability... public trust positions with a frequency as determined by the Director of the Office of...

  19. Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene.

    Science.gov (United States)

    Baines, John F; Parsch, John; Stephan, Wolfgang

    2004-01-01

    Recent advances in experimental analyses of the evolution of RNA secondary structures suggest a more complex scenario than that typically considered by Kimura's classical model of compensatory evolution. In this study, we examine one such case in more detail. Previous experimental analysis of long-range compensatory interactions between the two ends of Drosophila Adh mRNA failed to fit the classical model of compensatory evolution. To further investigate and verify long-range pairing in Drosophila Adh with respect to models of compensatory evolution and its potential functional role, we introduced site-directed mutations in the Drosophila melanogaster Adh gene. We explore two alternative hypotheses for why previous analysis of long-range compensatory interactions failed to fit the classical model. Specifically, we investigate whether the disruption of a conserved short-range pairing within Adh exon 2 has an effect on Adh expression or if there is a dual functional role of a conserved sequence in the 3'-UTR in both long-range pairing and the negative regulation of Adh expression. We find that a classical result was not observed due to the pleiotropic effect of changing a nucleotide involved in both long-range base pairing and the negative regulation of gene expression. PMID:15020421

  20. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation

    Directory of Open Access Journals (Sweden)

    Charlotte Proudhon

    2016-06-01

    Full Text Available V(DJ recombination relies on the presence of proximal enhancers that activate the antigen receptor (AgR loci in a lineage- and stage-specific manner. Unexpectedly, we find that both active and inactive AgR enhancers cooperate to disseminate their effects in a localized and long-range manner. Here, we demonstrate the importance of short-range contacts between active enhancers that constitute an Igk super-enhancer in B cells. Deletion of one element reduces the interaction frequency between other enhancers in the hub, which compromises the transcriptional output of each component. Furthermore, we establish that, in T cells, long-range contact and cooperation between the inactive Igk enhancer MiEκ and the active Tcrb enhancer Eβ alters enrichment of CBFβ binding in a manner that impacts Tcrb recombination. These findings underline the complexities of enhancer regulation and point to a role for localized and long-range enhancer-sharing between active and inactive elements in lineage- and stage-specific control.

  1. Identification from diverse mammalian poxviruses of host-range regulatory genes functioning equivalently to vaccinia virus C7L.

    Science.gov (United States)

    Meng, Xiangzhi; Chao, Jie; Xiang, Yan

    2008-03-15

    Vaccinia virus (VACV) C7L is a host-range gene that regulates cellular tropism of VACV. Distantly related C7L homologues are encoded by nearly all mammalian poxviruses, but whether they are host-range genes functioning similar to VACV C7L has not been determined. Here, we used VACV as a model system to analyze five different C7L homologues from diverse mammalian poxviruses for their abilities to regulate poxvirus cellular tropism. Three C7L homologues (myxoma virus M63R, M64R and cowpox virus 020), when expressed with an epitope tag and from a VACV mutant lacking the host-range genes K1L and C7L (vK1L-C7L-), failed to support productive viral replication in human and murine cells. In nonpermissive cells, these viruses did not synthesize viral late proteins, expressed a reduced level of the early protein E3L, and were defective at suppressing cellular PKR activation. In contrast, two other C7L homologues, myxoma virus (MYXV) M62R and yaba-like disease virus (YLDV) 67R, when expressed with an epitope tag and from vK1L(-)C7L(-), supported normal viral replication in human and murine cells and restored the ability of the virus to suppress PKR activation. Furthermore, M62R rescued the defect of vK1L(-)C7L(-) at replicating and disseminating in mice following intranasal inoculation. These results show that MYXV M62R and YLDV 67R function equivalently to C7L at supporting VACV replication in mammalian hosts and suggest that a C7L-like host-range gene is essential for the replication of many mammalian poxviruses in mammalian hosts.

  2. Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species.

    Science.gov (United States)

    Nouripour-Sisakht, Sadegh; Ahmadi, Bahram; Makimura, Koichi; Hoog, Sybren de; Umeda, Yoshiko; Alshahni, Mohamed Mahdi; Mirhendi, Hossein

    2017-04-21

    We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides. The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.

  3. Evolution of Compatibility Range in the Rice-Magnaporthe oryzae System: An Uneven Distribution of R Genes Between Rice Subspecies.

    Science.gov (United States)

    Gallet, Romain; Fontaine, Colin; Bonnot, François; Milazzo, Joëlle; Tertois, Christophe; Adreit, Henri; Ravigné, Virginie; Fournier, Elisabeth; Tharreau, Didier

    2016-04-01

    Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

  4. Intrathecal long-term gene expression by self-complementary adeno-associated virus type 1 suitable for chronic pain studies in rats

    Directory of Open Access Journals (Sweden)

    Janssen William GM

    2006-01-01

    Full Text Available Abstract Background Intrathecal (IT gene transfer is an attractive approach for targeting spinal mechanisms of nociception but the duration of gene expression achieved by reported methods is short (up to two weeks impairing their utility in the chronic pain setting. The overall goal of this study was to develop IT gene transfer yielding true long-term transgene expression defined as ≥ 3 mo following a single vector administration. We defined "IT" administration as atraumatic injection into the lumbar cerebrospinal fluid (CSF modeling a lumbar puncture. Our studies focused on recombinant adeno-associated virus (rAAV, one of the most promising vector types for clinical use. Results Conventional single stranded rAAV2 vectors performed poorly after IT delivery in rats. Pseudotyping of rAAV with capsids of serotypes 1, 3, and 5 was tested alone or in combination with a modification of the inverted terminal repeat. The former alters vector tropism and the latter allows packaging of self-complementary rAAV (sc-rAAV vectors. Combining both types of modification led to the identification of sc-rAAV2/l as a vector that performed superiorly in the IT space. IT delivery of 3 × 10e9 sc-rAAV2/l particles per animal led to stable expression of enhanced green fluorescent protein (EGFP for ≥ 3 mo detectable by Western blotting, quantitative PCR, and in a blinded study by confocal microscopy. Expression was strongest in the cauda equina and the lower sections of the spinal cord and only minimal in the forebrain. Microscopic examination of the SC fixed in situ with intact nerve roots and meninges revealed strong EGFP fluorescence in the nerve roots. Conclusion sc-rAAVl mediates stable IT transgene expression for ≥ 3 mo. Our findings support the underlying hypothesis that IT target cells for gene transfer lack the machinery for efficient conversion of the single-stranded rAAV genome into double-stranded DNA and favor uptake of serotype 1 vectors over 2

  5. A suitable duplex PCR for ovine embryo sex and genotype of PrnP gene determination for MOET-based selection programmes.

    Science.gov (United States)

    Dervishi, E; Sánchez, P; Alabart, J L; Cocero, M J; Folch, J; Calvo, J H

    2011-12-01

    The objective of this study was to test the suitability of a duplex PCR assay for sex and scrapie resistance genotype determination in fresh embryos. Duplex PCR amplified a repetitive and specific fragment of Y chromosome, used for sex diagnosis, and a PrnP fragment. PrnP codons 134 and 156, and codon 171 were genotyped by restriction fragment length polymorphisms and allele-specific PCR, respectively, after re-amplification of PrnP fragment. The specificity of the method was first assessed by testing 359 blood samples from Rasa Aragonesa sheep breed (161 males and 198 females). No amplification failures and total agreement between genotypic and phenotypic sex were found. In the same way, PrnP genotype determination by duplex PCR assay was in agreement with the PrnP animal's genotype established by sequencing. Finally, 73 samples of 1-10 cells from compact morulae were aspirated through the zona pellucida and genotyped for sex and PrnP. The efficiency was 96% when three or more cells were sampled. These results confirm that the duplex PCR assay reported in this work can be used for rapid sex determination in ovine embryos, with a high efficiency and accuracy (96%) when three or more cells are sampled, allowing sexed fresh embryos of known PrnP genotype to be transferred in multiple ovulation and embryo transfer programmes.

  6. Adaptive gene amplification as an intermediate step in the expansion of virus host range.

    Directory of Open Access Journals (Sweden)

    Greg Brennan

    2014-03-01

    Full Text Available The majority of recently emerging infectious diseases in humans is due to cross-species pathogen transmissions from animals. To establish a productive infection in new host species, viruses must overcome barriers to replication mediated by diverse and rapidly evolving host restriction factors such as protein kinase R (PKR. Many viral antagonists of these restriction factors are species specific. For example, the rhesus cytomegalovirus PKR antagonist, RhTRS1, inhibits PKR in some African green monkey (AGM cells, but does not inhibit human or rhesus macaque PKR. To model the evolutionary changes necessary for cross-species transmission, we generated a recombinant vaccinia virus that expresses RhTRS1 in a strain that lacks PKR inhibitors E3L and K3L (VVΔEΔK+RhTRS1. Serially passaging VVΔEΔK+RhTRS1 in minimally-permissive AGM cells increased viral replication 10- to 100-fold. Notably, adaptation in these AGM cells also improved virus replication 1000- to 10,000-fold in human and rhesus cells. Genetic analyses including deep sequencing revealed amplification of the rhtrs1 locus in the adapted viruses. Supplying additional rhtrs1 in trans confirmed that amplification alone was sufficient to improve VVΔEΔK+RhTRS1 replication. Viruses with amplified rhtrs1 completely blocked AGM PKR, but only partially blocked human PKR, consistent with the replication properties of these viruses in AGM and human cells. Finally, in contrast to AGM-adapted viruses, which could be serially propagated in human cells, VVΔEΔK+RhTRS1 yielded no progeny virus after only three passages in human cells. Thus, rhtrs1 amplification in a minimally permissive intermediate host was a necessary step, enabling expansion of the virus range to previously nonpermissive hosts. These data support the hypothesis that amplification of a weak viral antagonist may be a general evolutionary mechanism to permit replication in otherwise resistant host species, providing a molecular foothold

  7. Optimisation of a 96-well electroporation assay for postnatal rat CNS neurons suitable for cost-effective medium-throughput screening of genes that promote neurite outgrowth

    Directory of Open Access Journals (Sweden)

    Thomas eHutson

    2011-12-01

    Full Text Available Following an injury, central nervous system (CNS neurons show a very limited regenerative response which results in their failure to successfully form functional connections with their original target. This is due in part to the reduced intrinsic growth state of CNS neurons, which is characterised by their failure to express key regeneration-associated genes (RAGs and by the presence of growth inhibitory molecules in CNS environment that form a molecular and physical barrier to regeneration. Here we have optimised a 96-well electroporation and neurite outgrowth assay for postnatal rat cerebellar granule neurons cultured upon an inhibitory cellular substrate expressing myelin-associated glycoprotein or a mixture of growth-inhibitory chondroitin sulphate proteoglycans. Optimal electroporation parameters resulted in 25% transfection efficiency and 50% viability for postnatal rat cerebellar granule neurons (CGNs. The neurite outgrowth of transduced neurons was quantitatively measured using a semi-automated image capture and analysis system. The neurite outgrowth was significantly reduced by the inhibitory substrates which we demonstrated could be partially reversed using a Rho Kinase inhibitor. We are now using this assay to screen large sets of RAGs for their ability to increase neurite outgrowth on a variety of growth inhibitory and permissive substrates.

  8. ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi.

    Science.gov (United States)

    Bödeker, Inga T M; Nygren, Cajsa M R; Taylor, Andy F S; Olson, Ake; Lindahl, Björn D

    2009-12-01

    Fungal peroxidases (ClassII) have a key role in degrading recalcitrant polyphenolic compounds in boreal forest wood, litter and humus. To date, their occurrence and activity have mainly been studied in a small number of white-rot wood decomposers. However, peroxidase activity is commonly measured in boreal forest humus and mineral soils, in which ectomycorrhizal fungi predominate. Here, we used degenerate PCR primers to investigate whether peroxidase-encoding genes are present in the genomes of a wide phylogenetic range of ectomycorrhizal taxa. Cloning and sequencing of PCR products showed that ectomycorrhizal fungi from several different genera possess peroxidase genes. The new sequences represent four major homobasidiomycete lineages, but the majority is derived from Cortinarius, Russula and Lactarius. These genera are ecologically important, but consist mainly of non-culturable species from which little ecophysiological information is available. The amplified sequences contain conserved active sites, both for folding and substrate oxidation. In some Cortinarius spp., there is evidence for gene duplications during the evolution of the genus. ClassII peroxidases seem to be an ancient and a common feature of most homobasidiomycetes, including ectomycorrhizal fungi. Production of extracellular peroxidases may provide ectomycorrhizal fungi with access to nitrogen sequestered in complex polyphenolic sources.

  9. Terrain correlation suitability

    Science.gov (United States)

    Tang, Wang; McClintock, Robert L.

    1994-07-01

    Terrain-aided navigation (TAN), also referred to as terrain correlation, is a technique that has proven to be highly successful as a navigational aid for autonomous, unmanned guided missiles. Qualitatively speaking, the effectiveness of terrain correlation is a function of signal- to-noise (S/N) ratio. The signal is equivalent to terrain roughness, while the noise is the combination of reference map errors, radar altimeter errors, and INS altitude errors. However, it is not practical to use only a single parameter, such as S/N, to define the suitability of terrain correlation. This paper discusses the shortcomings of the conventional single-parameter approach to the terrain contour matching algorithm (TERCOM) used in cruise missile guidance systems scene selection. A more comprehensive technique is then presented that analyzes the terrain correlation suitability based on a Monte Carlo simulation technique. A figure-of-merit (FOM) for terrain correlation suitability, computed from sample statistics, is introduced and simulation results are provided to illustrate the feasibility of using a multi-parameter FOM technique. The preliminary results indicate that the proposed approach could provide a cost effective enhancement to the TAN-based mission planning process.

  10. A suitable streptomycin-resistant mutant for constructing unmarked in-frame gene deletions using rpsL as a counter-selection marker.

    Directory of Open Access Journals (Sweden)

    Yu-Kuo Tsai

    Full Text Available The streptomycin counter-selection system is a useful tool for constructing unmarked in-frame gene deletions, which is a fundamental approach to study bacteria and their pathogenicity at the molecular level. A prerequisite for this system is acquiring a streptomycin-resistant strain due to rpsL mutations, which encodes the ribosomal protein S12. However, in this study no streptomycin resistance was found to be caused by rpsL mutations in all 127 clinical strains of Klebsiella pneumoniae isolated from liver abscess patients. By screening 107 spontaneous mutants of streptomycin resistance from a clinical strain of K. pneumoniae, nucleotide substitution or insertion located within the rpsL was detected in each of these strains. Thirteen different mutants with varied S12 proteins were obtained, including nine streptomycin-dependent mutants. The virulence of all four streptomycin-resistant mutants was further evaluated. Compared with the parental strain, the K42N, K42T and K87R mutants showed a reduction in growth rate, and the K42N and K42T mutants became susceptible to normal human serum. In the mice LD50 (the bacterial dose that caused 50% death assay, the K42N and K42T mutants were ∼ 1,000-fold less lethal (∼ 2 × 10(5 CFU and the K87R mutant was ∼ 50-fold less lethal (∼ 1 × 10(4 CFU than the parental strain (∼ 2 × 10(2 CFU. A K42R mutant showed non-observable effects on the above assays, while this mutant exhibited a small cost (P < 0.01 in an in vitro growth competition experiment. In summary, most of the K. pneumoniae strains with streptomycin resistance caused by rpsL mutations are less virulent than their parental strain in the absence of streptomycin. The K42R mutant showed similar pathogenicity to its parental strain and should be one of the best choices when using rpsL as a counter-selection marker.

  11. Acidic pH shock induces the expressions of a wide range of stress-response genes

    Directory of Open Access Journals (Sweden)

    Hong Soon-Kwang

    2008-12-01

    Full Text Available Abstract Background Environmental signals usually enhance secondary metabolite production in Streptomycetes by initiating complex signal transduction system. It is known that different sigma factors respond to different types of stresses, respectively in Streptomyces strains, which have a number of unique signal transduction mechanisms depending on the types of environmental shock. In this study, we wanted to know how a pH shock would affect the expression of various sigma factors and shock-related proteins in S. coelicolor A3(2. Results According to the results of transcriptional and proteomic analyses, the major number of sigma factor genes were upregulated by an acidic pH shock. Well-studied sigma factor genes of sigH (heat shock, sigR (oxidative stress, sigB (osmotic shock, and hrdD that play a major role in the secondary metabolism, were all strongly upregulated by the pH shock. A number of heat shock proteins including the DnaK family and chaperones such as GroEL2 were also observed to be upregulated by the pH shock, while their repressor of hspR was strongly downregulated. Oxidative stress-related proteins such as thioredoxin, catalase, superoxide dismutase, peroxidase, and osmotic shock-related protein such as vesicle synthases were also upregulated in overall. Conclusion From these observations, an acidic pH shock was considered to be one of the strongest stresses to influence a wide range of sigma factors and shock-related proteins including general stress response proteins. The upregulation of the sigma factors and shock proteins already found to be related to actinorhodin biosynthesis was considered to have contributed to enhanced actinorhodin productivity by mediating the pH shock signal to regulators or biosynthesis genes for actinorhodin production.

  12. Domestic dog origin of canine distemper virus in free-ranging wolves in Portugal as revealed by hemagglutinin gene characterization.

    Science.gov (United States)

    Müller, Alexandra; Silva, Eliane; Santos, Nuno; Thompson, Gertrude

    2011-07-01

    Serologic evidence for canine distemper virus (CDV) has been described in grey wolves but, to our knowledge, virus strains circulating in wolves have not been characterized genetically. The emergence of CDV in several non-dog hosts has been associated with amino acid substitutions at sites 530 and 549 of the hemagglutinin (H) protein. We sequenced the H gene of wild-type canine distemper virus obtained from two free-ranging Iberian wolves (Canis lupus signatus) and from one domestic dog (Canis familiaris). More differences were found between the two wolf sequences than between one of the wolves (wolf 75) and the dog. The latter two had a very high nucleotide similarity resulting in identical H gene amino acid sequences. Possible explanations include geographic and especially temporal proximity of the CDV obtained from wolf 75 and the domestic dog, taken in 2007-2008, as opposed to that from wolf 3 taken more distantly in 1998. Analysis of the deduced amino acids of the viral hemagglutinin revealed a glycine (G) and a tyrosine (Y) at amino acid positions 530 and 549, respectively, of the partial signaling lymphocytic activation molecule (SLAM)-receptor binding region which is typically found in viral strains obtained from domestic dogs. This suggests that the CDV found in these wolves resulted from transmission events from local domestic dogs rather than from wildlife species.

  13. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  14. LysM domains mediate lipochitin-oligosaccharide recognition and Nfr genes extend the symbiotic host range.

    Science.gov (United States)

    Radutoiu, Simona; Madsen, Lene H; Madsen, Esben B; Jurkiewicz, Anna; Fukai, Eigo; Quistgaard, Esben M H; Albrektsen, Anita S; James, Euan K; Thirup, Søren; Stougaard, Jens

    2007-09-05

    Legume-Rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. Individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. We show here that expression of Lotus japonicus Nfr1 and Nfr5 Nod-factor receptor genes in Medicago truncatula and L. filicaulis, extends their host range to include bacterial strains, Mesorhizobium loti or DZL, normally infecting L. japonicus. As a result, the symbiotic program is induced, nodules develop and infection threads are formed. Using L. japonicus mutants and domain swaps between L. japonicus and L. filicaulis NFR1 and NFR5, we further demonstrate that LysM domains of the NFR1 and NFR5 receptors mediate perception of the bacterial Nod-factor signal and that recognition depends on the structure of the lipochitin-oligosaccharide Nod-factor. We show that a single amino-acid variation in the LysM2 domain of NFR5 changes recognition of the Nod-factor synthesized by the DZL strain and suggests a possible binding site for bacterial lipochitin-oligosaccharide signal molecules.

  15. Independent gene phylogenies and morphology demonstrate a malagasy origin for a wide-ranging group of swallowtail butterflies.

    Science.gov (United States)

    Zakharov, Evgueni V; Smith, Campbell R; Lees, David C; Cameron, Alison; Vane-Wright, Richard I; Sperling, Felix A H

    2004-12-01

    Madagascar is home to numerous endemic species and lineages, but the processes that have contributed to its endangered diversity are still poorly understood. Evidence is accumulating to demonstrate the importance of Tertiary dispersal across varying distances of oceanic barriers, supplementing vicariance relationships dating back to the Cretaceous, but these hypotheses remain tentative in the absence of well-supported phylogenies. In the Papilio demoleus group of swallowtail butterflies, three of the five recognized species are restricted to Madagascar, whereas the remaining two species range across the Afrotropical zone and southern Asia plus Australia. We reconstructed phylogenetic relationships for all species in the P. demoleus group, as well as 11 outgroup Papilio species, using 60 morphological characters and about 4 kb of nucleotide sequences from two mitochondrial (cytochrome oxidase I and II) and two nuclear (wg and EF-1alpha) genes. Of the three endemic Malagasy species, the two that are formally listed as endangered or at risk represented the most basal divergences in the group, while the more common third endemic was clearly related to African P. demodocus. The fifth species, P. demoleus, showed little differentiation across southern Asia, but showed divergence from its subspecies sthenelus in Australia. Dispersal-vicariance analysis using cladograms derived from morphology and three independent genes indicated a Malagasy diversification of lime swallowtails in the middle Miocene. Thus, diversification processes on the island of Madagascar may have contributed to the origin of common butterflies that now occur throughout much of the Old World tropical and subtemperate regions. An alternative hypothesis, that Madagascar is a refuge for ancient lineages resulting from successive colonizations from Africa, is less parsimonious and does not explain the relatively low continental diversity of the group.

  16. nodSU, two new nod genes of the broad host range Rhizobium strain NGR234 encode host-specific nodulation of the tropical tree Leucaena leucocephala.

    Science.gov (United States)

    Lewin, A; Cervantes, E; Chee-Hoong, W; Broughton, W J

    1990-01-01

    Rhizobium species strain NGR234 nodulates at least 35 diverse genera of legumes as well as the nonlegume Parasponia andersonii. Most nodulation genes are located on the 500-kilobase pair symbiotic plasmid, pNGR234a. Previously, three plasmid-borne host range determinants (HsnI, HsnII, and HsnIII) were identified by their ability to extend the nodulation capacity of heterologous rhizobia to include Vigna unguiculata. In this study, we show that HsnII contains two new nod-box linked hsn genes, nodS and nodU.nodS controls nodulation of the tropical tree Leucaena leucocephala, while the nodSU genes regulate nodulation of the pasture legume Desmodium intortum and the grain legume V. unguiculata. Regulation of the nod-box upstream of nodSU by the flavonoid naringenin was shown using a fusion with a promoterless lacZ gene. Determination of the nucleotide sequence of the nodS gene did not reveal homology with any gene in the EMBL library, although Bradyrhizobium japonicum USDA110 contains both nodS and nodU (M. Göttfert, S. Hitz, and H. Hennecke, Molecular Plant-Microbe Interactions 3:308-316, 1990). We suggest that broad host range in NGR234 is controlled in part by a nodD gene which interacts with a wide range of flavonoids, and in part by host-specific nod genes such as nodS.

  17. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

    Science.gov (United States)

    Medvedovic, Jasna; Ebert, Anja; Tagoh, Hiromi; Tamir, Ido M; Schwickert, Tanja A; Novatchkova, Maria; Sun, Qiong; Huis In 't Veld, Pim J; Guo, Chunguang; Yoon, Hye Suk; Denizot, Yves; Holwerda, Sjoerd J B; de Laat, Wouter; Cogné, Michel; Shi, Yang; Alt, Frederick W; Busslinger, Meinrad

    2013-08-22

    The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.

  18. Construction of an extended range whole-cell tetracycline biosensor by use of the tet(M) resistance gene

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Hansen, Lars Hestbjerg; Sørensen, Søren Johannes

    2005-01-01

    An extended range whole-cell tetracycline biosensor strain was constructed by insertion of the tet(M) gene, encoding tetracycline resistance by ribosomal protection, into plasmid pTGFP2, which contains a transcriptional fusion between a tetracycline regulated promoter and the green fluorescent pr...

  19. Selection of the suitable reference genes for gene expression analysis of human peripheral blood from patients with colorectal cancer%结直肠癌患者外周血基因表达分析中参照基因的选择

    Institute of Scientific and Technical Information of China (English)

    杜玉珍; 彭伟; 高锋

    2011-01-01

    Objective To select the suitable endogenous reference genes in peripheral blood from patients with colorectal cancer for gene expression analysis.Methods The expressions of candidate reference genes ( ACTB,GAPDH, GUSB, UBC, B2M, PBGD and 18S rRNA) were determined in peripheral blood of 8 healthy subjects and 8 patients with colorectal cancer by real-time relative quantitative reverse transcription polymerase chain reaction ( RTPCR) dilution method.The stability of candidate reference genes was analyzed by geNorm and NormFinder software programs and t test.The suitable reference genes were analyzed.Results By geNorm software, ACTB, GAPDH and GUSB were identified as the stable and reliable reference genes.By NormFinder algorithms, GAPDH was the stable reference gene, which was followed by B2M, ACTB and GUSB.The candidate reference genes were GAPDH and B2M.All candidate reference genes showed statistical significance in the expression between the patients and the healthy subjects except ACTB, GUSB and UBC.Conclusions The housekeeping genes of ACTB and GUSB are the suitable reference genes in peripheral blood from patients with colorectal cancer for expression analysis, while PBGD and 18S rRNA are not reliable.%目的 筛选结直肠癌患者全血样本的合适内参照基因.方法 以ACTB、GAPDH、GUSB、UBC、B2M、PBGD和18S rRNA为候选基因,用实时相对定量逆转录聚合酶链反应(RT-PCR)稀释法检测其在8例结直肠癌患者和8名健康人全血中的表达水平,再用geNorm和NormFinder程序及两样本均数t检验评价候选参照基因的稳定性,探寻应用于结直肠癌患者全血基因表达检测的合适参照基因.结果 geNorm评估发现,最适合的参照基因是ACTB、GAPDH和GUSB;NormFinder计算结果 认为GAPDH稳定性最好,B2M、ACTB和GUSB次之,推荐的参照基因组合是GAPDH和B2M;候选基因表达水平的组间比较(结直肠癌组和健康组)发现,除ACTB、GUSB和UBC之外,其他候选参照基因

  20. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci.

    Science.gov (United States)

    Martin, Paul; McGovern, Amanda; Orozco, Gisela; Duffus, Kate; Yarwood, Annie; Schoenfelder, Stefan; Cooper, Nicholas J; Barton, Anne; Wallace, Chris; Fraser, Peter; Worthington, Jane; Eyre, Steve

    2015-11-30

    Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions. We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1).

  1. Rock suitability classification RSC 2012

    Energy Technology Data Exchange (ETDEWEB)

    McEwen, T. (ed.) [McEwen Consulting, Leicester (United Kingdom); Kapyaho, A. [Geological Survey of Finland, Espoo (Finland); Hella, P. [Saanio and Riekkola, Helsinki (Finland); Aro, S.; Kosunen, P.; Mattila, J.; Pere, T.

    2012-12-15

    This report presents Posiva's Rock Suitability Classification (RSC) system, developed for locating suitable rock volumes for repository design and construction. The RSC system comprises both the revised rock suitability criteria and the procedure for the suitability classification during the construction of the repository. The aim of the classification is to avoid such features of the host rock that may be detrimental to the favourable conditions within the repository, either initially or in the long term. This report also discusses the implications of applying the RSC system for the fulfilment of the regulatory requirements concerning the host rock as a natural barrier and the site's overall suitability for hosting a final repository of spent nuclear fuel.

  2. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

    Science.gov (United States)

    Martin, Paul; McGovern, Amanda; Orozco, Gisela; Duffus, Kate; Yarwood, Annie; Schoenfelder, Stefan; Cooper, Nicholas J.; Barton, Anne; Wallace, Chris; Fraser, Peter; Worthington, Jane; Eyre, Steve

    2015-01-01

    Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions. We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1). PMID:26616563

  3. Unraveling the effects of selection and demography on immune gene variation in free-ranging plains zebra (Equus quagga populations.

    Directory of Open Access Journals (Sweden)

    Pauline L Kamath

    Full Text Available Demography, migration and natural selection are predominant processes affecting the distribution of genetic variation among natural populations. Many studies use neutral genetic markers to make inferences about population history. However, the investigation of functional coding loci, which directly reflect fitness, is critical to our understanding of species' ecology and evolution. Immune genes, such as those of the Major Histocompatibility Complex (MHC, play an important role in pathogen recognition and provide a potent model system for studying selection. We contrasted diversity patterns of neutral data with MHC loci, ELA-DRA and -DQA, in two southern African plains zebra (Equus quagga populations: Etosha National Park, Namibia, and Kruger National Park, South Africa. Results from neutrality tests, along with observations of elevated diversity and low differentiation across populations, supported previous genus-level evidence for balancing selection at these loci. Despite being low, MHC divergence across populations was significant and may be attributed to drift effects typical of geographically separated populations experiencing little to no gene flow, or alternatively to shifting allele frequency distributions driven by spatially variable and fluctuating pathogen communities. At the DRA, zebra exhibited geographic differentiation concordant with microsatellites and reduced levels of diversity in Etosha due to highly skewed allele frequencies that could not be explained by demography, suggestive of spatially heterogeneous selection and local adaptation. This study highlights the complexity in which selection affects immune gene diversity and warrants the need for further research on the ecological mechanisms shaping patterns of adaptive variation among natural populations.

  4. SATB1 Mediates Long-Range Chromatin Interactions: A Dual Regulator of Anti-Apoptotic BCL2 and Pro-Apoptotic NOXA Genes.

    Science.gov (United States)

    Yang, Yin; Wang, Zongdan; Sun, Luan; Shao, Lipei; Yang, Nan; Yu, Dawei; Zhang, Xin; Han, Xiao; Sun, Yujie

    2015-01-01

    Aberrant expression of special AT-rich binding protein 1 (SATB1), a global genomic organizer, has been associated with various cancers, which raises the question of how higher-order chromatin structure contributes to carcinogenesis. Disruption of apoptosis is one of the hallmarks of cancer. We previously demonstrated that SATB1 mediated specific long-range chromosomal interactions between the mbr enhancer located within 3'-UTR of the BCL2 gene and the promoter to regulate BCL2 expression during early apoptosis. In the present study, we used chromosome conformation capture (3C) assays and molecular analyses to further investigate the function of the SATB1-mediated higher-order chromatin structure in co-regulation of the anti-apoptotic BCL2 gene and the pro-apoptotic NOXA gene located 3.4Mb downstream on Chromosome 18. We demonstrated that the mbr enhancer spatially juxtaposed the promoters of BCL2 and NOXA genes through SATB1-mediated chromatin-loop in Jurkat cells. Decreased SATB1 levels switched the mbr-BCL2 loop to mbr-NOXA loop, and thus changed expression of these two genes. The SATB1-mediated dynamic switch of the chromatin loop structures was essential for the cooperative expression of the BCL2 and NOXA genes in apoptosis. Notably, the role of SATB1 was specific, since inhibition of SATB1 degradation by caspase-6 inhibitor or caspase-6-resistant SATB1 mutant reversed expression of BCL-2 and NOXA in response to apoptotic stimulation. This study reveals the critical role of SATB1-organized higher-order chromatin structure in regulating the dynamic equilibrium of apoptosis-controlling genes with antagonistic functions and suggests that aberrant SATB1 expression might contribute to cancer development by disrupting the co-regulated genes in apoptosis pathways.

  5. FTO gene associated fatness in relation to body fat distribution and metabolic traits throughout a broad range of fatness

    DEFF Research Database (Denmark)

    Kring, Sofia I I; Holst, Claus; Zimmermann, Esther

    2008-01-01

    A common single nucleotide polymorphism (SNP) of FTO (rs9939609, T/A) is associated with total body fatness. We investigated the association of this SNP with abdominal and peripheral fatness and obesity-related metabolic traits in middle-aged men through a broad range of fatness present already i...

  6. FTO gene associated fatness in relation to body fat distribution and metabolic traits throughout a broad range of fatness

    DEFF Research Database (Denmark)

    Kring, Sofia I I; Holst, Claus; Zimmermann, Esther;

    2008-01-01

    A common single nucleotide polymorphism (SNP) of FTO (rs9939609, T/A) is associated with total body fatness. We investigated the association of this SNP with abdominal and peripheral fatness and obesity-related metabolic traits in middle-aged men through a broad range of fatness present already...

  7. LysM domains mediate lipochitin-oligosaccharide recognition and Nfr genes extend the symbiotic host range

    DEFF Research Database (Denmark)

    Radutoiu, Simona; Madsen, Lene H; Madsen, Esben B

    2007-01-01

    Legume-Rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. Individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. We show here that expression of Lotus japonicus Nfr1...

  8. Characterisation of single nucleotide polymorphisms identified in the bovine lactoferrin gene sequences across a range of dairy cow breeds.

    Science.gov (United States)

    O'Halloran, F; Bahar, B; Buckley, F; O'Sullivan, O; Sweeney, T; Giblin, L

    2009-01-01

    The lactoferrin gene sequences of 70 unrelated dairy cows representing six different dairy breeds were investigated for single nucleotide polymorphisms to establish a baseline of polymorphisms that exist within the Irish bovine population. Twenty-nine polymorphisms were identified within a 2.2kb regulatory region. Nineteen novel polymorphisms were identified and some of these were found within transcription factor binding sites, including GATA-1 and SPI transcription factor sites. Forty-seven polymorphisms were identified within exon sequences with unique polymorphisms that were associated with amino acid substitutions. These included a T/A SNP, identified in a Holstein Friesian animal, which resulted in a valine to aspartic acid substitution (Val89Asp) in the mature lactoferrin protein. Other SNPs of interest were associated with amino acid substitutions in the lactoferricin B peptide sequence and an A/G SNP, identified in a Jersey animal, was associated with a tyrosine to cysteine change (Tyr181Cys). The polymorphisms identified in the promoter region may have implications relating to lactoferrin expression levels in cows and those identified in the coding sequence indicate the existence of protein variants in the Irish bovine population. The data presented in this study emphasises the potential for lactoferrin to serve as a candidate gene to select for mastitis resistance with the aim of improving animal health.

  9. Gene therapy via inducible nitric oxide synthase: a tool for the treatment of a diverse range of pathological conditions.

    Science.gov (United States)

    McCarthy, Helen O; Coulter, Jonathan A; Robson, Tracy; Hirst, David G

    2008-08-01

    Nitric oxide (NO(.)) is a reactive nitrogen radical produced by the NO synthase (NOS) enzymes; it affects a plethora of downstream physiological and pathological processes. The past two decades have seen an explosion in the understanding of the role of NO(.) biology, highlighting various protective and damaging modes of action. Much of the controversy surrounding the role of NO(.) relates to the differing concentrations generated by the three isoforms of NOS. Both calcium-dependent isoforms of the enzyme (endothelial and neuronal NOS) generate low-nanomolar/picomolar concentrations of NO(.). By contrast, the calcium-independent isoform (inducible NOS (iNOS)) generates high concentrations of NO(.), 2-3 orders of magnitude greater. This review summarizes the current literature in relation to iNOS gene therapy for the therapeutic benefit of various pathological conditions, including various states of vascular disease, wound healing, erectile dysfunction, renal dysfunction and oncology. The available data provide convincing evidence that manipulation of endogenous NO(.) using iNOS gene therapy can provide the basis for future clinical trials.

  10. Global habitat suitability models of terrestrial mammals

    Science.gov (United States)

    Rondinini, Carlo; Di Marco, Moreno; Chiozza, Federica; Santulli, Giulia; Baisero, Daniele; Visconti, Piero; Hoffmann, Michael; Schipper, Jan; Stuart, Simon N.; Tognelli, Marcelo F.; Amori, Giovanni; Falcucci, Alessandra; Maiorano, Luigi; Boitani, Luigi

    2011-01-01

    Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals. PMID:21844042

  11. SMC6 is an essential gene in mice, but a hypomorphic mutant in the ATPase domain has a mild phenotype with a range of subtle abnormalities.

    Science.gov (United States)

    Ju, Limei; Wing, Jonathan; Taylor, Elaine; Brandt, Renata; Slijepcevic, Predrag; Horsch, Marion; Rathkolb, Birgit; Rácz, Ildikó; Becker, Lore; Hans, Wolfgang; Adler, Thure; Beckers, Johannes; Rozman, Jan; Klingenspor, Martin; Wolf, Eckhard; Zimmer, Andreas; Klopstock, Thomas; Busch, Dirk H; Gailus-Durner, Valérie; Fuchs, Helmut; de Angelis, Martin Hrabě; van der Horst, Gilbertus; Lehmann, Alan R

    2013-05-01

    Smc5-6 is a highly conserved protein complex related to cohesin and condensin involved in the structural maintenance of chromosomes. In yeasts the Smc5-6 complex is essential for proliferation and is involved in DNA repair and homologous recombination. siRNA depletion of genes involved in the Smc5-6 complex in cultured mammalian cells results in sensitivity to some DNA damaging agents. In order to gain further insight into its role in mammals we have generated mice mutated in the Smc6 gene. A complete knockout resulted in early embryonic lethality, demonstrating that this gene is essential in mammals. However, mutation of the highly conserved serine-994 to alanine in the ATP hydrolysis motif in the SMC6 C-terminal domain, resulted in mice with a surprisingly mild phenotype. With the neo gene selection marker in the intron following the mutation, resulting in reduced expression of the SMC6 gene, the mice were reduced in size, but fertile and had normal lifespans. When the neo gene was removed, the mice had normal size, but detailed phenotypic analysis revealed minor abnormalities in glucose tolerance, haematopoiesis, nociception and global gene expression patterns. Embryonic fibroblasts derived from the ser994 mutant mice were not sensitive to killing by a range of DNA damaging agents, but they were sensitive to the induction of sister chromatid exchanges induced by ultraviolet light or mitomycin C. They also accumulated more oxidative damage than wild-type cells. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Resonance enhancement by suitably chosen frequency detuning

    CERN Document Server

    Dutykh, Denys

    2014-01-01

    In this Letter we report new effects of resonance detuning on various dynamical parameters of a generic 3-wave system. Namely, for suitably chosen values of detuning the variation range of amplitudes can be significantly wider than for exact resonance. Moreover, the range of energy variation is not symmetric with respect to the sign of the detuning. Finally, the period of the energy oscillation exhibits non-monotonic dependency on the magnitude of detuning. These results have important theoretical implications where nonlinear resonance analysis is involved, such as geophysics, plasma physics, fluid dynamics. Numerous practical applications are envisageable e.g. in energy harvesting systems.

  13. Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids

    Institute of Scientific and Technical Information of China (English)

    GUO Haitao; XU Xudong

    2004-01-01

    Gloeobacter violaceus, a cyanobacterium lack of thylakoids, is refractory to genetic manipulations because its cells are enveloped by a thick gelatinous sheath and in colonial form.In this study, a large number of single cells were obtained by repeated pumping with a syringe with the gelatinous sheath removed.And an exogenous broad host range plasmid pKT210 was conjugatively transferred into G.violaceus.Analyses with dot-blot hybridization and restriction mapping showed that the exogenous plasmid pKT210 had been introduced into G.violaceus and stably maintained with no alteration in its structure.pKT210 extracted from G.violaceus exconjugants could be transformed into the mcr- mrr- E.coli strain DH10B but not the mcr+ mrr+ strain DH5α, which suggests that a methylase system may be present in G.violaceus.

  14. Environmental Suitability for Leasing Property

    Science.gov (United States)

    This is a Memorandum of Understanding between the U.S. Environmental Protection Agency and the U.S. Department of Defense, regarding the procedures to determine environmental suitability for leasing property available as a result of a base closure or realignment.

  15. FTO gene associated fatness in relation to body fat distribution and metabolic traits throughout a broad range of fatness.

    Directory of Open Access Journals (Sweden)

    Sofia I I Kring

    Full Text Available BACKGROUND: A common single nucleotide polymorphism (SNP of FTO (rs9939609, T/A is associated with total body fatness. We investigated the association of this SNP with abdominal and peripheral fatness and obesity-related metabolic traits in middle-aged men through a broad range of fatness present already in adolescence. METHODOLOGY/PRINCIPAL FINDINGS: Obese young Danish men (n = 753, BMI > or = 31.0 kg/m(2 and a randomly selected group (n = 879 from the same population were examined in three surveys (mean age 35, 46 and 49 years, respectively. The traits included anthropometrics, body composition, oral glucose tolerance test, blood lipids, blood pressure, fibrinogen and aspartate aminotransferase. Logistic regression analysis was used to assess the age-adjusted association between the phenotypes and the odds ratios for the FTO rs9939609 (TT and TA genotype versus the AA genotype, for anthropometrics and body composition estimated per unit z-score. BMI was strongly associated with the AA genotype in all three surveys: OR = 1.17, p = 1.1*10(-6, OR = 1.20, p = 1.7*10(-7, OR = 1.17, p = 3.4*10(-3, respectively. Fat body mass index was also associated with the AA genotype (OR = 1.21, p = 4.6*10(-7 and OR = 1.21, p = 1.0*10(-3. Increased abdominal fatness was associated with the AA genotype when measured as waist circumference (OR = 1.21, p = 2.2*10(-6 and OR = 1.19, p = 5.9*10(-3, sagittal abdominal diameter (OR = 1.17, p = 1.3*10(-4 and OR = 1.18, p = 0.011 and intra-abdominal adipose tissue (OR = 1.21, p = 0.005. Increased peripheral fatness measured as hip circumference (OR = 1.19, p = 1.3*10(-5 and OR = 1.18, p = 0.004 and lower body fat mass (OR = 1.26, p = 0.002 was associated with the AA genotype. The AA genotype was significantly associated with decreased Stumvoll insulin sensitivity index (OR = 0.93, p = 0.02 and with decreased non-fasting plasma HDL-cholesterol (OR = 0.57, p = 0.037, but not with any other of the metabolic traits. However

  16. A Broad Range of Dose Optima Achieve High-level, Long-term Gene Expression After Hydrodynamic Delivery of Sleeping Beauty Transposons Using Hyperactive SB100x Transposase

    Science.gov (United States)

    Podetz-Pedersen, Kelly M; Olson, Erik R; Somia, Nikunj V; Russell, Stephen J; McIvor, R Scott

    2016-01-01

    The Sleeping Beauty (SB) transposon system has been shown to enable long-term gene expression by integrating new sequences into host cell chromosomes. We found that the recently reported SB100x hyperactive transposase conferred a surprisingly high level of long-term expression after hydrodynamic delivery of luciferase-encoding reporter transposons in the mouse. We conducted dose-ranging studies to determine the effect of varying the amount of SB100x transposase-encoding plasmid (pCMV-SB100x) at a set dose of luciferase transposon and of varying the amount of transposon-encoding DNA at a set dose of pCMV-SB100x in hydrodynamically injected mice. Animals were immunosuppressed using cyclophosphamide in order to prevent an antiluciferase immune response. At a set dose of transposon DNA (25 µg), we observed a broad range of pCMV-SB100x doses (0.1–2.5 µg) conferring optimal levels of long-term expression (>1011 photons/second/cm2). At a fixed dose of 0.5 μg of pCMV-SB100x, maximal long-term luciferase expression (>1010 photons/second/cm2) was achieved at a transposon dose of 5–125 μg. We also found that in the linear range of transposon doses (100 ng), co-delivering the CMV-SB100x sequence on the same plasmid was less effective in achieving long-term expression than delivery on separate plasmids. These results show marked flexibility in the doses of SB transposon plus pCMV-SB100x that achieve maximal SB-mediated gene transfer efficiency and long-term gene expression after hydrodynamic DNA delivery to mouse liver. PMID:26784638

  17. Ecological variables governing habitat suitability and the distribution ...

    African Journals Online (AJOL)

    Ecological variables governing habitat suitability and the distribution of the endangered ... This cryptic species is not evenly distributed throughout its restricted range and ... A multiple logistic regression model highlighted the importance of soil ...

  18. Baculovirus Host-Range

    Institute of Scientific and Technical Information of China (English)

    Suzanne M. Thiem; Xiao-Wen Cheng

    2009-01-01

    Baculoviruses are used as microbial insecticides, protein expression vectors, epitope display platforms, and most recently as vectors for gene therapy. Understanding the mechanisms that control baculovirus host-range and tissue tropisms are important for assessing their safety and for improving their properties for these biotechnology applications. In the past two decades some progress has been made and several baculovirus genes that influence host-range have been identified. Despite this progress, our understanding of the underlying mechanisms that restrict baculovirus host-range is still limited. Here we review what is currently known about baculovirus genes that influence virus host-range.

  19. Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions.

    Science.gov (United States)

    Volis, S; Ormanbekova, D; Shulgina, I

    2016-04-01

    Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.

  20. Long-range enhancer associated with chromatin looping allows AP-1 regulation of the peptidylarginine deiminase 3 gene in differentiated keratinocyte.

    Directory of Open Access Journals (Sweden)

    Stéphane Chavanas

    Full Text Available Transcription control at a distance is a critical mechanism, particularly for contiguous genes. The peptidylarginine deiminases (PADs catalyse the conversion of protein-bound arginine into citrulline (deimination, a critical reaction in the pathophysiology of multiple sclerosis, Alzheimer's disease and rheumatoid arthritis, and in the metabolism of the major epidermal barrier protein filaggrin, a strong predisposing factor for atopic dermatitis. PADs are encoded by 5 clustered PADI genes (1p35-6. Unclear are the mechanisms controlling the expression of the gene PADI3 encoding the PAD3 isoform, a strong candidate for the deimination of filaggrin in the terminally differentiating epidermal keratinocyte. We describe the first PAD Intergenic Enhancer (PIE, an evolutionary conserved non coding segment located 86-kb from the PADI3 promoter. PIE is a strong enhancer of the PADI3 promoter in Ca2+-differentiated epidermal keratinocytes, and requires bound AP-1 factors, namely c-Jun and c-Fos. As compared to proliferative keratinocytes, calcium stimulation specifically associates with increased local DNase I hypersensitivity around PIE, and increased physical proximity of PIE and PADI3 as assessed by Chromosome Conformation Capture. The specific AP-1 inhibitor nordihydroguaiaretic acid suppresses the calcium-induced increase of PADI3 mRNA levels in keratinocytes. Our findings pave the way to the exploration of deimination control during tumorigenesis and wound healing, two conditions for which AP-1 factors are critical, and disclose that long-range transcription control has a role in the regulation of the gene PADI3. Since invalidation of distant regulators causes a variety of human diseases, PIE results to be a plausible candidate in association studies on deimination-related disorders or atopic disease.

  1. Genetic variation in codons 167, 198 and 200 of the beta-tubulin gene in whipworms (Trichuris spp.) from a range of domestic animals and wildlife.

    Science.gov (United States)

    Hansen, Tina V A; Nejsum, Peter; Olsen, Annette; Thamsborg, Stig Milan

    2013-03-31

    A recurrent problem in the control of whipworm (Trichuris spp.) infections in many animal species and man is the relatively low efficacy of treatment with a single application of benzimidazoles (BZs). The presence of single nucleotide polymorphisms (SNPs) in codons 167, 198 and 200 in the beta-tubulin gene has been associated with BZ anthelmintic resistance in intestinal nematodes of veterinary importance. We hypothesized that the low susceptibility to BZ could be related to a natural tolerance or induced resistance caused by BZ-resistant associated SNPs. The aim of the present study was therefore to investigate the presence of these SNPs in the beta-tubulin gene of Trichuris spp. obtained from a range of animals. DNA was extracted from a total of 121 Trichuris spp. adult whipworm specimens obtained from 6 different host species. The number of worms from each host was pig: 31, deer: 21, sheep: 18, mouse: 17, dog: 19 and Arabian camels: 14. A pooled sample of Trichuris eggs from 3 moose was also used. In order to amplify the beta-tubulin fragments which covered codons 167, 198 and 200 of the gene, degenerate primers were designed. The sequences obtained were used to design species specific primers and used to amplify a ~476 bp fragment of the beta-tubulin gene. The PCR products were sequenced, analysed and evaluated. We did not identify SNPs in codons 167, 198 or 200 that led to amino acid substitutions in any of the studied Trichuris spp., but genetic variation expected to be related to species differences was observed. The cluster analysis showed close evolutionary relationship between Trichuris spp. from ruminants and between mouse and dog whereas the pig-derived worms, T. suis, clustered with T. trichiura obtained from Genbank.

  2. Fine mapping of the gene Rvi18 (V25) for broad-spectrum resistance to apple scab, and development of a linked SSR marker suitable for marker-assisted breeding

    NARCIS (Netherlands)

    Soriano, J.M.; Madduri, M.; Schaart, J.; Burgh, van der A.M.; Kaauwen, van M.P.W.; Tomic, L.; Groenwold, R.; Velasco, R.; Weg, van de W.E.; Schouten, H.J.

    2014-01-01

    Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most devastating diseases for the apple growing industry in temperate zones with humid springs and summers. Breeding programs around the world have identified several sources of resistance, of which the Rvi6 (Vf) gene from

  3. Identification of process suitable diluent

    Energy Technology Data Exchange (ETDEWEB)

    Dean R. Peterman

    2014-01-01

    The Sigma Team for Minor Actinide Separation (STMAS) was formed within the USDOE Fuel Cycle Research and Development (FCRD) program in order to develop more efficient methods for the separation of americium and other minor actinides (MA) from used nuclear fuel. The development of processes for MA separations is driven by the potential benefits; reduced long-term radiotoxicty of waste placed in a geologic repository, reduced timeframe of waste storage, reduced repository heat load, the possibility of increased repository capacity, and increased utilization of energy potential of used nuclear fuel. The research conducted within the STMAS framework is focused upon the realization of significant simplifications to aqueous recycle processes proposed for MA separations. This report describes the research efforts focused upon the identification of a process suitable diluent for a flowsheet concept for the separation of MA which is based upon the dithiophosphinic acid (DPAH) extractants previously developed at the Idaho National Laboratory (INL).

  4. Suitable footwear for enhanced safety

    CERN Multimedia

    2004-01-01

    Safety shoes are the theme of a new safety campaign. Always remember that accidents can happen - even to your feet! When entering hazardous areas such as underground halls, work sites, experiment assembly sites, workshops etc., sandals, ordinary shoes or similar light footwear should not be worn. Whatever the risks to which you may be exposed, always think safety and wear suitable footwear, i.e. safety shoes, which have non-slip soles and steel reinforcements to protect your feet from being crushed, fractured or pierced. Is it serious, Doctor? "Some traumas resulting from foot-related accidents - open fractures for instance - can be quite serious," explains CERN Works Doctor Véronique Fassnacht. "But the most common injuries are sprained ankles sustained during simple falls caused by differences in floor-levels (e.g. false floors). Fractures, bruising, surface wounds or deep wounds caused by objects falling onto the top of the foot are also quite common." ...

  5. C7L family of poxvirus host range genes inhibits antiviral activities induced by type I interferons and interferon regulatory factor 1.

    Science.gov (United States)

    Meng, Xiangzhi; Schoggins, John; Rose, Lloyd; Cao, Jingxin; Ploss, Alexander; Rice, Charles M; Xiang, Yan

    2012-04-01

    Vaccinia virus (VACV) K1L and C7L function equivalently in many mammalian cells to support VACV replication and antagonize antiviral activities induced by type I interferons (IFNs). While K1L is limited to orthopoxviruses, genes that are homologous to C7L are found in diverse mammalian poxviruses. In this study, we showed that the C7L homologues from sheeppox virus and swinepox virus could rescue the replication defect of a VACV mutant deleted of both K1L and C7L (vK1L(-)C7L(-)). Interestingly, the sheeppox virus C7L homologue could rescue the replication of vK1L(-)C7L(-) in human HeLa cells but not in murine 3T3 and LA-4 cells, in contrast to all other C7L homologues. Replacing amino acids 134 and 135 of the sheeppox virus C7L homologue, however, made it functional in the two murine cell lines, suggesting that these two residues are critical for antagonizing a putative host restriction factor which has some subtle sequence variation in human and murine cells. Furthermore, the C7L family of host range genes from diverse mammalian poxviruses were all capable of antagonizing type I IFN-induced antiviral activities against VACV. Screening of a library of more than 350 IFN-stimulated genes (ISGs) identified interferon-regulated factor 1 (IRF1) as an inhibitor of vK1L(-)C7L(-) but not wild-type VACV. Expression of either K1L or C7L, however, rendered vK1L(-)C7L(-) resistant to IRF1-induced antiviral activities. Altogether, our data show that K1L and C7L antagonize IRF1-induced antiviral activities and that the host modulation function of C7L is evolutionally conserved in all poxviruses that can readily replicate in tissue-cultured mammalian cells.

  6. Construction and use of a broad-host-range plasmid expressing the lamB gene for utilization of bacteriophage lambda vectors in the marine bacterium Vibrio harveyi.

    Science.gov (United States)

    Jasiecki, J; Czy, A; Gabig, M; Wegrzyn, G

    2001-07-01

    The remarkable success of Escherichia coli as a model organism in molecular genetics was dependent, among other things, on its susceptibility to genetic manipulation. Many versatile and sophisticated genetic tools for molecular biology studies are derived from bacteriophage lambda. However, this bacteriophage is specific for E. coli, and thus lambda-based techniques have been restricted to this bacterium. Plasmids expressing the E. coli gene coding for bacteriophage lambda receptor were reported previously, and introduction of such plasmids into cells of some other bacteria made them sensitive to phage lambda infection. However, we found that these systems were not efficient for Vibrio harveyi, one of the most frequently investigated species of marine bacteria. Here we describe construction of a broad-host-range plasmid expressing the lamB gene. Introduction of this plasmid to V. harveyi cells and expression of lamB made this strain susceptible to bacteriophage lambda adsorption and lambda DNA injection. Foreign genetic material could be introduced into cells of this strain using a cosmid vector.

  7. Detection of genomic variations in BRCA1 and BRCA2 genes by long-range PCR and next-generation sequencing.

    Science.gov (United States)

    Hernan, Imma; Borràs, Emma; de Sousa Dias, Miguel; Gamundi, María José; Mañé, Begoña; Llort, Gemma; Agúndez, José A G; Blanca, Miguel; Carballo, Miguel

    2012-01-01

    Advances in sequencing technologies, such as next-generation sequencing (NGS), represent an opportunity to perform genetic testing in a clinical scenario. In this study, we developed and tested a method for the detection of mutations in the large BRCA1 and BRCA2 tumor suppressor genes, using long-range PCR (LR-PCR) and NGS, in samples from individuals with a personal and/or family history of breast and/or ovarian cancer. Eleven LR-PCR fragments, between 3000 and 15,300 bp, containing all coding exons and flanking splice junctions of BRCA1 and BRCA2, were obtained from DNA samples of five individuals carrying mutations in either BRCA1 or BRCA2. Libraries for NGS were prepared using an enzymatic (Nextera technology) method. We analyzed five individual samples in parallel by NGS and obtained complete coverage of all LR-PCR fragments, with an average coding sequence depth for each nucleotide of >30 reads, running from ×7 (in exon 22 of BRCA1) to >×150. We detected and confirmed 100% of the mutations that predispose to the risk of cancer, together with other genomic variations in BRCA1 and BRCA2. Our approach demonstrates that genomic LR-PCR, together with NGS, using the GS Junior 454 System platform, is an effective method for patient sample analysis of BRCA1 and BRCA2 genes. In addition, this method could be performed in regular molecular genetics laboratories.

  8. Coupling of pollination services and coffee suitability under climate change.

    Science.gov (United States)

    Imbach, Pablo; Fung, Emily; Hannah, Lee; Navarro-Racines, Carlos E; Roubik, David W; Ricketts, Taylor H; Harvey, Celia A; Donatti, Camila I; Läderach, Peter; Locatelli, Bruno; Roehrdanz, Patrick R

    2017-09-26

    Climate change will cause geographic range shifts for pollinators and major crops, with global implications for food security and rural livelihoods. However, little is known about the potential for coupled impacts of climate change on pollinators and crops. Coffee production exemplifies this issue, because large losses in areas suitable for coffee production have been projected due to climate change and because coffee production is dependent on bee pollination. We modeled the potential distributions of coffee and coffee pollinators under current and future climates in Latin America to understand whether future coffee-suitable areas will also be suitable for pollinators. Our results suggest that coffee-suitable areas will be reduced 73-88% by 2050 across warming scenarios, a decline 46-76% greater than estimated by global assessments. Mean bee richness will decline 8-18% within future coffee-suitable areas, but all are predicted to contain at least 5 bee species, and 46-59% of future coffee-suitable areas will contain 10 or more species. In our models, coffee suitability and bee richness each increase (i.e., positive coupling) in 10-22% of future coffee-suitable areas. Diminished coffee suitability and bee richness (i.e., negative coupling), however, occur in 34-51% of other areas. Finally, in 31-33% of the future coffee distribution areas, bee richness decreases and coffee suitability increases. Assessing coupled effects of climate change on crop suitability and pollination can help target appropriate management practices, including forest conservation, shade adjustment, crop rotation, or status quo, in different regions.

  9. Synthesis of poly(ethylene glycol)-g-chitosan-g-poly(ethylene imine) co-polymer and in vitro study of its suitability as a gene-delivery vector.

    Science.gov (United States)

    Zhang, Wei; Pan, Shirong; Wen, Yuting; Luo, Xin; Zhang, Xuan

    2010-01-01

    There are two main hindrances for the application of chitosan (CS) as a gene-delivery vector: poor water solubility and low transfection efficiency. To address these problems, we modified chitosan with poly(ethylene glycol) (PEG) and poly(ethylene imine) (PEI). As previously described, PEG was grafted onto CS by a reaction between the activated PEG and CS amine. This increased the solubility of CS in neutral or basic solution. Then, monomers of PEI (i.e., aziridine) were polymerized on the CS chain of the PEG(40k)-CS(50k) co-polymer obtained in the previous step. The resulting PEG-CS-PEI (PCP) co-polymer was characterized by (1)H-NMR, (13)C-NMR and gel-permeation chromatography (GPC). It was found in the preliminary experiments that, amongst the series of PEG-CS-PEI co-polymers with various PEI molecular weights, PEG(40k)-CS(50k)-PEI(20k) was the most efficient one; therefore, it was chosen for the study. The PCP co-polymer showed lower cytotoxicity compared to PEI (25k) by MTT assay. Particle size and zeta potential of PCP/DNA complexes were measured by dynamic light scattering (DLS) and were shown to be predominantly affected by N/P ratios. PCP/DNA complexes at N/P ratio 20 were observed under a transmission electron microscope (TEM) as spherical particles with a mean diameter of about 50 nm. Plasmid DNA could be efficiently protected by PCP co-polymer from DNase I. The in vitro gene-transfection efficiency of PCP/pEGFP was higher than that of PEI(25k)/pEGFP and was markedly facilitated by serum.

  10. Phylogeography of the olive sea snake, Aipysurus laevis (Hydrophiinae) indicates Pleistocene range expansion around northern Australia but low contemporary gene flow.

    Science.gov (United States)

    Lukoschek, V; Waycott, M; Marsh, H

    2007-08-01

    Pleistocene sea-level fluctuations profoundly changed landmass configurations around northern Australia. The cyclic emergence of the Torres Strait land bridge and concomitant shifts in the distribution of shallow-water marine habitats repeatedly sundered east and west coast populations. These biogeographical perturbations invoke three possible scenarios regarding the directions of interglacial range expansion: west to east, east to west, or bidirectional. We evaluated these scenarios for the olive sea snake, Aipysurus laevis, by exploring its genetic structure around northern Australia based on 354 individuals from 14 locations in three regions (Western Australia, WA; Gulf of Carpentaria, GoC; Great Barrier Reef, GBR). A 726-bp fragment of the mitochondrial DNA ND4 region revealed 41 variable sites and 38 haplotypes, with no shared haplotypes among the three regions. Population genetic structure was strong overall, phiST=0.78, PSea. Levels of contemporary female-mediated gene flow varied within regions and reflected potential connectivity among populations afforded by the different regional habitat types.

  11. 45 CFR 12a.4 - Suitability determination.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Suitability determination. 12a.4 Section 12a.4... PROPERTY TO ASSIST THE HOMELESS § 12a.4 Suitability determination. (a) Suitability determination. Within 30... determination to the landholding agency. Properties that are under lease, contract, license, or agreement by...

  12. 24 CFR 581.4 - Suitability determination.

    Science.gov (United States)

    2010-04-01

    ... reviewed for suitability. HUD will maintain a written public record of the following: (1) The suitability... 24 Housing and Urban Development 3 2010-04-01 2010-04-01 false Suitability determination. 581.4... (Continued) OFFICE OF ASSISTANT SECRETARY FOR COMMUNITY PLANNING AND DEVELOPMENT, DEPARTMENT OF HOUSING...

  13. Habitat Suitability Index Models: Mink

    Science.gov (United States)

    Allen, Arthur W.

    1983-01-01

    The mink (Mustela vison) is a predatory, semiaquatic mammal that is generally associated with stream and river banks, lake shores, fresh and saltwater marshes, and marine shore habitats (Gerell 1970).  Mink are chiefly nocturnal and remain active throughout the year (Marshall 1936); Gerell 1969; Burgess 1978).  The species is adaptable in its use of habitat, modifying daily habits according to environmental conditions, particularly prey availability (Wise et al. 1981; Linn and Birds 1981; Birks and Linn 1982).  The species is tolerant of human activity and will inhabit suboptimum habitats as long as an adequate food source is available; however, mink will be more mobile and change home ranges more frequently under such conditions (Linn pers. comm.).

  14. Superconducting materials suitable for magnets

    CERN Document Server

    CERN. Geneva. Audiovisual Unit

    2002-01-01

    The range of materials available for superconducting magnets is steadily expanding, even as the choice of material becomes potentially more complex. When virtually all magnets were cooled by helium at ~2-5 K it was easy to separate the domain of Nb-Ti from those of Nb3Sn applications and very little surprise that more than 90% of all magnets are still made from Nb-Ti. But the development of useful conductors of the Bi-Sr-Ca-Cu-O and YBa2Cu3Ox high temperature superconductors, coupled to the recent discovery of the 39 K superconductor MgB2 and the developing availability of cryocoolers suggests that new classes of higher temperature, medium field magnets based on other than Nb-based conductors could become available in the next 5-10 years. My talks will discuss the essential physics and materials science of these 5 classes of material - Nb-Ti, Nb3Sn, MgB2, Bi-Sr-Ca-Cu-O and YBa2Cu3Ox - in the context of those aspects of their science, properties and fabrication properties, which circumscribe their applications...

  15. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

    Directory of Open Access Journals (Sweden)

    Schaefer H Martin

    2011-06-01

    Full Text Available Abstract Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.

  16. Disruption of M-T5, a novel myxoma virus gene member of poxvirus host range superfamily, results in dramatic attenuation of myxomatosis in infected European rabbits.

    Science.gov (United States)

    Mossman, K; Lee, S F; Barry, M; Boshkov, L; McFadden, G

    1996-07-01

    Myxoma virus is a pathogenic poxvirus that induces a lethal myxomatosis disease profile in European rabbits, which is characterized by fulminating lesions at the primary site of inoculation, rapid dissemination to secondary internal organs and peripheral external sites, and supervening gram-negative bacterial infection. Here we describe the role of a novel myxoma virus protein encoded by the M-T5 open reading frame during pathogenesis. The myxoma virus M-T5 protein possesses no significant sequence homology to nonviral proteins but is a member of a larger poxviral superfamily designated host range proteins. An M-T5- mutant virus was constructed by disruption of both copies of the M-T5 gene followed by insertion of the selectable marker p7.5Ecogpt. Although the M-T5- deletion mutant replicated with wild-type kinetics in rabbit fibroblasts, infection of a rabbit CD4+ T-cell line (RL5) with the myxoma virus M-T5- mutant virus resulted in the rapid and complete cessation of both host and viral protein synthesis, accompanied by the manifestation of all the classical features of programmed cell death. Infection of primary rabbit peripheral mononuclear cells with the myxoma virus M-T5-mutant virus resulted in the apoptotic death of nonadherent lymphocytes but not adherent monocytes. Within the European rabbit, disruption of the M-T5 open reading frame caused a dramatic attenuation of the rapidly lethal myxomatosis infection, and none of the infected rabbits displayed any of the characteristic features of myxomatosis. The two most significant histological observations in rabbits infected with the M-T5-mutant virus were (i) the lack of progression of the infection past the primary site of inoculation, coupled with the establishment of a rapid and effective inflammatory reaction, and (ii) the inability of the virus to initiate a cellular reaction within secondary immune organs. We conclude that M-T5 functions as a critical virulence factor by allowing productive infection of

  17. Doping Asymmetry Problem in ZnO: Current Status and Outlook. A Review of Experimental and Theoretical Efforts Focused on Achieving P-Type ZnO Suitable for Light-Emitting Optoelectronic Devices for the Blue/Ultraviolet Spectral Range

    Science.gov (United States)

    2009-04-24

    Richmond VA 23284 USA. (e-mail: hmorkoc@vcu.edu). Donald Silversmith is with the Air Force Office of Scientific Research, Arlington, VA 22203 USA (e...for light-emitting optoelectronic devices for the blue/ultraviolet spectral range. Vitaliy Avrutin, Donald Silversmith , Fellow, IEEE, and Hadis Morkoç

  18. How to Evaluate the Rice Cultivation Suitability?

    Institute of Scientific and Technical Information of China (English)

    Wenxi; LI; Yueping; ZHANG; Changsong; WANG; Wei; MAO; Tianwen; HANG; Ming; CHEN; Bingning; ZHANG

    2013-01-01

    To rationally allocate farmland resources,and scientifically make farming industrial planning,we take Yizheng City in Jiangsu Province as the research object,and select 13 indicators.Based on Farmland Resources Management Information System in Yizheng City,we establish AHP model,and membership function model,for the evaluation of farmland suitability of rice.The results show that the farmland area in the highly suitable areas accounts for 10.2%of the total farmland area;the farmland area in the suitable areas accounts for 56.08%of the total farmland area;the farmland area in the marginally suitable areas accounts for 25.50%of the total farmland area;the farmland area in the unsuitable areas accounts for 8.22%of the total farmland area.There is significant positive correlation between the actual yield of rice surveyed and suitability index obtained through evaluation(R2=0.1964,319 samples);the actual yield of rice in the highly suitable areas is higher than in the marginally suitable areas and suitable areas,and the rice yield is the lowest in the unsuitable areas.

  19. LAND SUITABILITY SCENARIOS FOR ARID COASTAL PLAINS USING GIS MODELING: SOUTHWESTERN SINAI COASTAL PLAIN, EGYPT

    Directory of Open Access Journals (Sweden)

    Ahmed Mohamed Wahid

    2009-12-01

    Full Text Available Site selection analysis was carried out to find the best suitable lands for development activities in an example of promising coastal plains, southwestern Sinai, Egypt. Two GIS models were developed to represent two scenarios of land use suitability in the study area using GIS Multi Criteria Analysis Modeling. The factors contributed in the analysis are the Topography, Land cover, Existing Land use, Flash flood index, Drainage lines and Water points. The first scenario was to classify the area according to various gradual ranges of suitability. According to this scenario, the area is classified into five classes of suitability. The percentage of suitability values are 51.16, 6.13, 22.32, 18.49 and 1.89% for unsuitable, least suitable, low suitable, suitable and high suitable, respectively. The second scenario is developed for a particular kind of land use planning; tourism and recreation projects. The suitability map of this scenario was classified into five values. Unsuitable areas represent 51.18% of the study area, least suitable 16.67%, low suitable 22.85%, suitable 8.61%, and high suitable 0.68%. The best area for locating development projects is the area surrounding El-Tor City and close to the coast. This area could be an urban extension of El-Tor City with more economical and environmental management.

  20. LAND SUITABILITY SCENARIOS FOR ARID COASTAL PLAINS USING GIS MODELING: SOUTHWESTERN SINAI COASTAL PLAIN, EGYPT

    Directory of Open Access Journals (Sweden)

    Ahmed Wahid

    2009-01-01

    Full Text Available Site selection analysis was carried out to find the best suitable lands for development activities in an example of promising coastal plains, southwestern Sinai, Egypt. Two GIS models were developed to represent two scenarios of land use suitability in the study area using GIS Multi Criteria Analysis Modeling. The factors contributed in the analysis are the Topography, Land cover, Existing Land use, Flash flood index, Drainage lines and Water points. The first scenario was to classify the area according to various gradual ranges of suitability. According to this scenario, the area is classified into five classes of suitability. The percentage of suitability values are 51.16, 6.13, 22.32, 18.49 and 1.89% for unsuitable, least suitable, low suitable, suitable and high suitable, respectively. The second scenario is developed for a particular kind of land use planning; tourism and recreation projects. The suitability map of this scenario was classified into five values. Unsuitable areas represent 51.18% of the study area, least suitable 16.67%, low suitable 22.85%, suitable 8.61%, and high suitable 0.68%. The best area for locating development projects is the area surrounding El-Tor City and close to the coast. This area could be an urban extension of El-Tor City with more economical and environmental management.

  1. Range Tracing

    OpenAIRE

    Jenke, Philipp; Huhle, Benjamin

    2010-01-01

    In this report, we tackle the problem of merging an arbitrary number of range scans (depth images) into a single surface mesh. The mesh-based representation is superior to point-based approaches since it contains important connectivity information. Most previous mesh-based merge methods, however, lose surface details by using simplifying intermediate surface representations (e.g.\\ implicit functions). Such details are essential for further processing steps, especially for feature-preserving r...

  2. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences.

    Science.gov (United States)

    Bhatia, Shipra; Kleinjan, Dirk A

    2014-07-01

    The precise control of gene expression programs is crucial for the establishment of the diverse gene activity patterns required for the correct development, patterning and differentiation of the myriad of cell types within an organism. The crucial importance of non-coding regions of the genome in the control of gene regulation is well established and depends on a diverse group of sequence fragments called cis-regulatory elements that reside in these regions. Advances in novel genome-wide techniques have greatly increased the ability to identify potential regulatory elements. In contrast, their functional characterisation and the determination of their diverse modes of action remain a major bottleneck. Greater knowledge of gene expression control is of major importance for human health as disruption of gene regulation has become recognised as a significant cause of human disease. Appreciation of the role of cis-regulatory polymorphism in natural variation and susceptibility to common disease is also growing. While novel techniques such as GWAS and NGS provide the ability to collect large genomic datasets, the challenge for the twenty-first century will be to extract the relevant sequences and how to investigate the functional consequences of disease-associated changes. Here, we review how studies of transcriptional control at selected paradigm disease gene loci have revealed general principles of cis-regulatory logic and regulatory genome organisation, yet also demonstrate how the variety of mechanisms can combine to result in unique phenotypic outcomes. Integration of these principles with the emerging wealth of genome-wide data will provide enhanced insight into the workings of our regulatory genome.

  3. Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India.

    Science.gov (United States)

    Bera, Bidhan Ch; Shanmugasundaram, K; Barua, Sanjay; Anand, Taruna; Riyesh, T; Vaid, Rajesh K; Virmani, Nitin; Bansal, Manish; Shukla, Brihaspati N; Malik, Praveen; Singh, Raj K

    2012-12-01

    Buffalopox virus (BPXV), a close variant of vaccinia virus (VACV) has emerged as a zoonotic pathogen. The host tropism of poxviruses is governed by host-range genes. Among the host-range genes: E3L, K3L, and C7L are essential for virus replication by preventing interferon resistance, whereas B5R is essential for spread of the virus and evasion from the host's immune response as in VACV. We report sequence analysis of host-range genes: E3L, K3L, C7L, and membrane protein gene (B5R) of BPXVs from buffalo, cattle, and human from recent outbreaks in India-their phylogenetic relationship with reference strain (BP4) and other Orthopoxviruses. BPXVs revealed a sequence homology with VACVs including zoonotic Brazilian VACV-like viruses. The aa sequences of E3L and K3L genes were 100 % similar in buffalo, cattle, and human isolates. However, four significant point mutations (I11K; N12K and S36F in C7L gene and D249G in B5R gene) were observed specific to buffalo isolate only. This signifies that different strains of BPXV were circulated during the outbreak. The mutations in C7L and B5R could play an important role in adaptation of BPXV in human and cattle which needs further functional studies. The strain of BPXV isolated from buffalo may not be adopted in human and cow. Various point mutations were observed in the host-range genes of reference strain (BPXV-BP4) which may be due to several passages of virus in cell culture. The phylogeny constructed based on concatenated gene sequences revealed that BPXVs are not as closely related to vaccine strain (Lister and Lister-derived strain-LC16m8), as hypothesized earlier, rather they are more closely related to reference strain (BPXV-BP4) and other vaccinia and vaccinia-like viruses such as Passatempo and Aracatuba viruses. The availability of information regarding host tropism determinants would allow us to understand molecular mechanism of species tropism of poxviruses which would be useful in unveiling new strategies to

  4. Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Fei Wang

    Full Text Available This study set out to identify and characterize transcription factors regulating photosynthesis in rice. Screening populations of rice T-DNA activation lines led to the identification of a T-DNA mutant with an increase in intrinsic water use efficiency (iWUE under well-watered conditions. Flanking sequence analysis showed that the T-DNA construct was located upstream of LOC_Os07g38240 (OsSAP16 encoding for a stress-associated protein (SAP. A second mutant identified with activation in the same gene exhibited the same phenotype; expression of OsSAP16 was shown to be enhanced in both lines. There were no differences in stomatal development or morphology in either of these mutants, although overexpression of OsSAP16 reduced stomatal conductance. This phenotype limited CO2 uptake and the rate of photosynthesis, which resulted in the accumulation of less biomass in the two mutants. Whole transcriptome analysis showed that overexpression of OsSAP16 led to global changes in gene expression consistent with the function of zinc-finger transcription factors. These results show that the gene is involved in modulating the response of rice to drought stress through regulation of the expression of a set of stress-associated genes.

  5. Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.).

    Science.gov (United States)

    Wang, Fei; Coe, Robert A; Karki, Shanta; Wanchana, Samart; Thakur, Vivek; Henry, Amelia; Lin, Hsiang-Chun; Huang, Jianliang; Peng, Shaobing; Quick, William Paul

    2016-01-01

    This study set out to identify and characterize transcription factors regulating photosynthesis in rice. Screening populations of rice T-DNA activation lines led to the identification of a T-DNA mutant with an increase in intrinsic water use efficiency (iWUE) under well-watered conditions. Flanking sequence analysis showed that the T-DNA construct was located upstream of LOC_Os07g38240 (OsSAP16) encoding for a stress-associated protein (SAP). A second mutant identified with activation in the same gene exhibited the same phenotype; expression of OsSAP16 was shown to be enhanced in both lines. There were no differences in stomatal development or morphology in either of these mutants, although overexpression of OsSAP16 reduced stomatal conductance. This phenotype limited CO2 uptake and the rate of photosynthesis, which resulted in the accumulation of less biomass in the two mutants. Whole transcriptome analysis showed that overexpression of OsSAP16 led to global changes in gene expression consistent with the function of zinc-finger transcription factors. These results show that the gene is involved in modulating the response of rice to drought stress through regulation of the expression of a set of stress-associated genes.

  6. Land Suitability Assessmemtin Continental Grits of

    African Journals Online (AJOL)

    use types (LUTs). using a qualitative physical land evaluation methodology. The results indicated that the ..... Suggested land characteristics and scores for suitability evaluation for cereals ..... the FAO framework: an example from Zambia.

  7. Suitable long tendon technologies and practices

    CSIR Research Space (South Africa)

    Altounyan, P

    2001-10-01

    Full Text Available effective long tendon support systems suitable in South African coalmines. Appropriate test procedures for the evaluation of the performance of long tendon systems were also determined and are detailed in this report....

  8. Modulation of gene expression made easy

    DEFF Research Database (Denmark)

    Solem, Christian; Jensen, Peter Ruhdal

    2002-01-01

    A new approach for modulating gene expression, based on randomization of promoter (spacer) sequences, was developed. The method was applied to chromosomal genes in Lactococcus lactis and shown to generate libraries of clones with broad ranges of expression levels of target genes. In one example...... beta-glucuronidase, resulting in an operon structure in which both genes are transcribed from a common promoter. We show that there is a linear correlation between the expressions of the two genes, which facilitates screening for mutants with suitable enzyme activities. In a second example, we show......, overexpression was achieved by introducing an additional gene copy into a phage attachment site on the chromosome. This resulted in a series of strains with phosphofructokinase activities from 1.4 to 11 times the wild-type activity level. In this example, the pfk gene was cloned upstream of a gusA gene encoding...

  9. Pdx1 and BETA2/NeuroD1 participate in a transcriptional complex that mediates short-range DNA looping at the insulin gene.

    Science.gov (United States)

    Babu, Daniella A; Chakrabarti, Swarup K; Garmey, James C; Mirmira, Raghavendra G

    2008-03-28

    The activity of the insulin gene, Ins, in islet beta cells is thought to arise in part from the synergistic action of the transcription factors Pdx1 and BETA2/NeuroD1. We asked how the binding of these factors to A and E elements many tens or hundreds of base pairs upstream of the start site could influence activity of transcriptional machinery. We therefore tested the hypothesis that the complex of Pdx1 and BETA2/NeuroD1 maintains a DNA conformation such that distal regions of the gene are brought into proximity of the promoter and coding region. We show by coimmunoprecipitation that Pdx1 and BETA2/NeuroD1 exist within a complex and that the two physically interact with one another in this complex as assessed by fluorescence resonance energy transfer. Consistent with this interaction, we found that the two factors simultaneously occupy the same fragment of the Ins gene in beta cell lines using the chromatin immunoprecipitation/re-chromatin immunoprecipitation assay. Using a modification of the chromosome conformation capture assay in vitro and in beta cells, we observed that Pdx1 and BETA2/NeuroD1 mediate looping of a segment of Ins that brings EcoRI sites located at -623 and +761 bp (relative to the transcriptional start site) in proximity to one another. This looping appears to be dependent in vitro upon an intact A3 binding element, but not upon the E2 element. Based on our findings, we propose a model whereby Pdx1 and BETA2/NeuroD1 physically interact to form a nucleoprotein complex on the Ins gene that mediates formation of a short DNA loop. Our results suggest that such short loop conformations may be a general mechanism to permit interactions between transcription factors and basal transcriptional machinery.

  10. Suitability of Missions for the Air Force Reserve Components

    Science.gov (United States)

    2014-01-01

    capacity for out-of-the-ordinary or intermittent surges—e.g., for satellite constellation changes, resolution of anomalies, or system transitions...xiv Table S.2. Suitability of Space Missions for Assignment to the RC Launch Range Test Satellite Ops Warning Depl Control In-Place Control...one-third of the combined units’ crews. If it were reconfigured as an equipped RC unit, it would take one-third of the host unit’s aircraft with it

  11. Suitability of different β-galactosidases as reporter enzymes in Bacillus subtilis.

    Science.gov (United States)

    Welsch, Norma; Homuth, Georg; Schweder, Thomas

    2012-01-01

    The suitability of three β-galactosidases as reporter enzymes for promoter expression analyses was investigated in Bacillus subtilis with respect to various temperature conditions during cultivation and assay procedures. Starting from the hypothesis that proteins derived from diverse habitats have different advantages as reporters at different growth temperatures, the beta-galactosidases from the thermophilic organism Bacillus stearothermophilus, from the mesophilic bacterium Escherichia coli and from the psychrophilic organism Pseudoalteromonas haloplanktis TAE79 were analysed under control of the constitutive B. subtilis lepA promoter. Subsequent expression of the β-galactosidase genes and determination of specific activities was performed at different cultivation and assay temperatures using B. subtilis as host. Surprisingly, the obtained results demonstrated that the highest activities over a broad cultivation temperature range were obtained using the β-galactosidase from the mesophilic bacterium E. coli whereas the enzymes from the thermophilic and psychrophilic bacteria revealed a more restricted usability in terms of cultivation temperature.

  12. Strong decline of gene diversity in local populations of the highly endangered Common hamster (Cricetus cricetus) in the western part of its European range

    NARCIS (Netherlands)

    Haye, la M.J.J.; Neumann, K.; Koelewijn, H.P.

    2012-01-01

    The Common hamster (Cricetus cricetus) has declined by more than 99% in the westernmost part of its range in Belgium, the Netherlands and the adjacent German federal state of North Rhine-Westphalia (BNN region) during recent decades. Various conservation schemes are ongoing to support the remaining

  13. [Ecology suitability study of Ephedra intermedia].

    Science.gov (United States)

    Ma, Xiao-Hui; Lu, You-Yuan; Huang, De-Dong; Zhu, Tian-Tian; Lv, Pei-Lin; Jin, Ling

    2017-06-01

    The study aims at predicting ecological suitability of Ephedra intermedia in China by using maximum entropy Maxent model combined with GIS, and finding the main ecological factors affecting the distribution of E. intermedia suitability in appropriate growth area. Thirty-eight collected samples of E. intermedia and E. intermedia and 116 distribution information from CVH information using ArcGIS technology were analyzed. MaxEnt model was applied to forecast the E. intermedia in our country's ecology. E. intermedia MaxEnt ROC curve model training data and testing data sets the AUC value was 0.986 and 0.958, respectively, which were greater than 0.9, tending to be 1.The calculated E. intermedia habitat suitability by the model showed a high accuracy and credibility, which indicated that MaxEnt model could well predict the potential distribution area of E. intermedia in China. Copyright© by the Chinese Pharmaceutical Association.

  14. A simple index of habitat suitability for Cape mountain zebras

    Directory of Open Access Journals (Sweden)

    P. Novellie

    1993-09-01

    Full Text Available An index of habitat suitability for Cape mountain zebras was calculated using two parameters: acceptability indices for different grass species, and the aerial cover of the grass species in the habitat. The index was tested by calculating its value for a range of different habitat patches and comparing this with the frequency of use of the patches by zebras. The close relationship between the index and the observed frequency of use verified that the index could be used as a guide to habitat suitability. Two methods were used to determine the frequency of use of the patches: counts of faecal pellet groups and frequency of sightings. Both methods yielded similar results but the pellet group counts were less time- consuming and expensive. It is recommended that the index of habitat suitability be used (i as a parameter for monitoring of long-term changes in habitat suitability in the Mountain Zebra National Park and (ii as a guide for selecting appropriate areas to re- introduce mountain zebras.

  15. From Suitable Weak Solutions to Entropy Viscosity

    KAUST Repository

    Guermond, Jean-Luc

    2010-12-16

    This paper focuses on the notion of suitable weak solutions for the three-dimensional incompressible Navier-Stokes equations and discusses the relevance of this notion to Computational Fluid Dynamics. The purpose of the paper is twofold (i) to recall basic mathematical properties of the three-dimensional incompressible Navier-Stokes equations and to show how they might relate to LES (ii) to introduce an entropy viscosity technique based on the notion of suitable weak solution and to illustrate numerically this concept. © 2010 Springer Science+Business Media, LLC.

  16. lpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria Dickeya dadantii.

    Directory of Open Access Journals (Sweden)

    Florence Hommais

    Full Text Available BACKGROUND: Quantitative RT-PCR is the method of choice for studying, with both sensitivity and accuracy, the expression of genes. A reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression. Here, we propose a set of reference genes, of the phytopathogenic bacteria Dickeya dadantii and Pectobacterium atrosepticum, which are stable in a wide range of growth conditions. RESULTS: We extracted, from a D. dadantii micro-array transcript profile dataset comprising thirty-two different growth conditions, an initial set of 49 expressed genes with very low variation in gene expression. Out of these, we retained 10 genes representing different functional categories, different levels of expression (low, medium, and high and with no systematic variation in expression correlating with growth conditions. We measured the expression of these reference gene candidates using quantitative RT-PCR in 50 different experimental conditions, mimicking the environment encountered by the bacteria in their host and directly during the infection process in planta. The two most stable genes (ABF-0017965 (lpxC and ABF-0020529 (yafS were successfully used for normalization of RT-qPCR data. Finally, we demonstrated that the ortholog of lpxC and yafS in Pectobacterium atrosepticum also showed stable expression in diverse growth conditions. CONCLUSIONS: We have identified at least two genes, lpxC (ABF-0017965 and yafS (ABF-0020509, whose expressions are stable in a wide range of growth conditions and during infection. Thus, these genes are considered suitable for use as reference genes for the normalization of real-time RT-qPCR data of the two main pectinolytic phytopathogenic bacteria D. dadantii and P. atrosepticum and, probably, of other Enterobacteriaceae. Moreover, we defined general criteria to select good reference genes in bacteria.

  17. Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes.

    Science.gov (United States)

    Cocho, Germinal; Miramontes, Pedro; Mansilla, Ricardo; Li, Wentian

    2014-12-01

    We examine the relationship between exponential correlation functions and Markov models in a bacterial genome in detail. Despite the well known fact that Markov models generate sequences with correlation function that decays exponentially, simply constructed Markov models based on nearest-neighbor dimer (first-order), trimer (second-order), up to hexamer (fifth-order), and treating the DNA sequence as being homogeneous all fail to predict the value of exponential decay rate. Even reading-frame-specific Markov models (both first- and fifth-order) could not explain the fact that the exponential decay is very slow. Starting with the in-phase coding-DNA-sequence (CDS), we investigated correlation within a fixed-codon-position subsequence, and in artificially constructed sequences by packing CDSs with out-of-phase spacers, as well as altering CDS length distribution by imposing an upper limit. From these targeted analyses, we conclude that the correlation in the bacterial genomic sequence is mainly due to a mixing of heterogeneous statistics at different codon positions, and the decay of correlation is due to the possible out-of-phase between neighboring CDSs. There are also small contributions to the correlation from bases at the same codon position, as well as by non-coding sequences. These show that the seemingly simple exponential correlation functions in bacterial genome hide a complexity in correlation structure which is not suitable for a modeling by Markov chain in a homogeneous sequence. Other results include: use of the (absolute value) second largest eigenvalue to represent the 16 correlation functions and the prediction of a 10-11 base periodicity from the hexamer frequencies.

  18. Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene is Associated with Changes in Flowering Time across a Range of Populations

    DEFF Research Database (Denmark)

    Skøt, Leif; Sanderson, Ruth; Thomas, Ann

    2011-01-01

    The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial...... ryegrass (Lolium perenne) ortholog of FT, designated LpFT3, was assessed in a diverse collection of nine European germplasm populations, which together constituted an association panel of 864 plants. Sequencing and genotyping of a series of amplicons derived from the nine populations, containing...... or structured association with further correction using genomic control indicated significant associations between LpFT3 and variation in flowering time. These associations were corroborated in a validation population segregating for the same major alleles. The most "diagnostic" region of genomic variation...

  19. Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif

    Directory of Open Access Journals (Sweden)

    Chang Jan-Gowth

    2011-10-01

    Full Text Available Abstract Background Multiple acyl-coenzyme A dehydrogenase deficiency (MADD is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (ETFDH gene, encoding electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO have been reported to be the major causes of riboflavin-responsive MADD. To date, no studies have been performed to explore the functional impact of these mutations or their mechanism of disrupting enzyme activity. Results High resolution melting (HRM analysis and sequencing of the entire ETFDH gene revealed a novel mutation (p.Phe128Ser and the hotspot mutation (p.Ala84Thr from a patient with MADD. According to the predicted 3D structure of ETF:QO, the two mutations are located within the flavin adenine dinucleotide (FAD binding domain; however, the two residues do not have direct interactions with the FAD ligand. Using molecular dynamics (MD simulations and normal mode analysis (NMA, we found that the p.Ala84Thr and p.Phe128Ser mutations are most likely to alter the protein structure near the FAD binding site as well as disrupt the stability of the FAD binding required for the activation of ETF:QO. Intriguingly, NMA revealed that several reported disease-causing mutations in the ETF:QO protein show highly correlated motions with the FAD-binding site. Conclusions Based on the present findings, we conclude that the changes made to the amino acids in ETF:QO are likely to influence the FAD-binding stability.

  20. Spring Season Habitat Suitability Index raster

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This raster represents a continuous surface of sage-grouse habitat suitability index (HSI, created using ArcGIS 10.2.2) values for Nevada during spring, which is a...

  1. Web page classification on child suitability

    NARCIS (Netherlands)

    Eickhoff, C.; Serdyukov, P.; Vries, A.P. de

    2010-01-01

    Children spend significant amounts of time on the Internet. Recent studies showed, that during these periods they are often not under adult supervision. This work presents an automatic approach to identifying suitable web pages for children based on topical and non-topical web page aspects. We discu

  2. Suitability of Ostrich eggshell for radiocarbon dating

    CSIR Research Space (South Africa)

    Vogel, JC

    2001-01-01

    Full Text Available Ostrich eggshell from archaeological sites remains largely free of more recent carbon contamination and as such is suitable material for radiocarbon dating. The carbonate fraction of the shell does, however, display an initial deficit in C14, which...

  3. Suitable scale of Weigan River plain oasis

    Institute of Scientific and Technical Information of China (English)

    HU ShunJun; SONG YuDong; TIAN ChangYan; LI YueTan; LI XiuCang; CHEN XiaoBing

    2007-01-01

    Desert coexists with oasis in long time, and the existence and development of oasis system demand better oasis vegetation ecological system. Oasis scale of arid zone plain encircling water should be determined in case of desertification caused by land over-reclamation under the circumstance of water resources shortage. Steady oasis with virtuous circle must have appropriate land use structure for agriculture, forestry and graziery. The study on the suitable scale and developmental space of oasis will provide theoretical and applicable foundation for effective construction of oases. By analyzing the hydrothermal, water and soil balance, an optimal mathematical model has been established. Based on hydrometeorology data collected for years in Weigan River plain, and by the principle of water balance,a calculation has been made of the water resources for evapotranspiration and the optimal acreage of oasis and cultivated land, which shows that the water resources for evapotranspiration in the Weigan River plain oasis is 22.32×108 m3 and the optimal oasis acreage under the condition of conventional irrigation mode is 3716.06 km2, in which the suitable cultivated land acreage is 1564.79 km2. Under the condition of water-saving irrigation, the suitable oasis acreage is 5515.49 km2, in which the suitable cultivated land acreage is 2322.31 km2. The oasis area had reached 4123 km2, and the cultivated land acreage had reached 1507 km2 after the Agriculture Irrigation Drainage Water Project of World Bank Loan in Weigan River basin was finished in 1997. The oasis and cultivated land acreage will be more suitable, and the oasis scale can be enlarged moderately by means of water saving irrigation.

  4. Range-Wide Meta-Analysis of Red-Cockaded Woodpecker Foraging Habitat Suitability

    Science.gov (United States)

    2013-12-31

    34o V* • " 0"""° K* „ 0 (d) (h) O O O D >° fee 7 -i 1 r— o m omo so 20 40 60 80 100 120 140...TWo—H •oo,AA6u«B»5 I 8—8- vomKt » omo --nmm ODOO mo mooo oa> ( D00«BOOO^ £ 0 oo 0 O ^O ° O » oT>eo ooo o ^ o O O 000...o oo o o o < o o o o o • mm o m omo a>o 0 50 100 150 200 250 300 350 Acres with Rscore >=4 Figure S3. Relationship

  5. Climate suitability and human influences combined explain the range expansion of an invasive horticultural plant

    Science.gov (United States)

    Carolyn M. Beans; Francis F. Kilkenny; Laura F. Galloway

    2012-01-01

    Ecological niche models are commonly used to identify regions at risk of species invasions. Relying on climate alone may limit a model's success when additional variables contribute to invasion. While a climate-based model may predict the future spread of an invasive plant, we hypothesized that a model that combined climate with human influences would most...

  6. Prion protein gene heterogeneity in free-ranging white-tailed deer within the chronic wasting disease affected region of Wisconsin.

    Science.gov (United States)

    Johnson, Chad; Johnson, Jody; Clayton, Murray; McKenzie, Debbie; Aiken, Judd

    2003-07-01

    Chronic wasting disease (CWD) was first identified in Wisconsin (USA) in whitetailed deer (Odocoileus virginianus) in February 2002. To determine if prion protein gene (Prnp) allelic variability was associated with CWD in white-tailed deer from Wisconsin, we sequenced Prnp from 26 CWD-positive and 100 CWD-negative deer. Sequence analysis of Prnp suggests that at least 86-96% of the white-tailed deer in this region have Prnp allelic combinations that will support CWD infection. Four Prnp alleles were identified in the deer population, one of which, resulting in a glutamine to histidine change at codon 95, has not been previously reported. The predominant allele in the population encodes for glutamine at codon 95, glycine at codon 96, and serine at codon 138 (QGS). Less abundant alleles encoded QSS, QGN, and HGS at the three variable positions. Comparison of CWD-positive with CWD-negative deer suggested a trend towards an over-representation of the QGS allele and an under-representation of the QSS allele.

  7. Increase in quantity and quality of suitable areas for invasive species as climate changes.

    Science.gov (United States)

    Bertelsmeier, Cleo; Luque, Gloria M; Courchamp, Franck

    2013-12-01

    As climatically suitable range projections become increasingly used to assess distributions of species, we recommend systematic assessments of the quality of habitat in addition to the classical binary classification of habitat. We devised a method to assess occurrence probability, captured by a climatic suitability index, through which we could determine variations in the quality of potential habitat. This relative risk assessment circumvents the use of an arbitrary suitability threshold. We illustrated our method with 2 case studies on invasive ant species. We estimated invasion potential of the destroyer ant (Monomorium destructor) and the European fire ant (Myrmica rubra) on a global scale currently and by 2080 with climate change. We found that 21.1% of the world's landmass currently has a suitable climate for the destroyer ant and 16% has a suitable climate for European fire ant. Our climatic suitability index showed that both ant species would benefit from climate change, but in different ways. The size of the potential distribution increased by 35.8% for the destroyer ant. Meanwhile, the total area of potential distribution remained the same for the European fire ant (>0.05%), but the level of climatic suitability within this range increased greatly and led to an improvement in habitat quality (i.e., of invasive species' establishment likelihood). Either through quantity or quality of suitable areas, both invasive ant species are likely to increase the extent of their invasion in the future, following global climate change. Our results show that species may increase their range if either more areas become suitable or if the available areas present improved suitability. Studies in which an arbitrary suitability threshold was used may overlook changes in area quality within climatically suitable areas and as a result reach incorrect predictions. Incremento de la Cantidad y Calidad de Áreas Idóneas para Especies Invasoras a Medida que Cambia el Clima.

  8. Immunochemical characterization of and isolation of the gene for a Borrelia burgdorferi immunodominant 60-kilodalton antigen common to a wide range of bacteria

    DEFF Research Database (Denmark)

    Hansen, K; Bangsborg, Jette Marie; Fjordvang, H

    1988-01-01

    By crossed immunoelectrophoresis and Western blotting (immunoblotting), it was shown that Borrelia burgdorferi expresses the 60-kilodalton Common Antigen (CA) that is cross-reactive with an equivalent antigen in a wide range of remotely related bacteria. B. burgdorferi CA is strongly immunogenic....... A B. burgdorferi genomic library was constructed by using a plasmid cloning system. Escherichia coli recombinants were screened for expression of immunodominant B. burgdorferi antigens. One of the recombinant clones expressed the 60-kilodalton CA of B. burgdorferi. The DNA region encoding B....... burgdorferi CA was localized on a 2.3-kilobase fragment of the plasmid pKH1. CA may have pathogenetic implications in Lyme borreliosis, since the CA of mycobacteria recently has been shown to play a role in the etiology of experimental autoimmune arthritis. The extensive cross-reactivity of this antigen may...

  9. Long-range gene flow and the effects of climatic and ecological factors on genetic structuring in a large, solitary carnivore: the Eurasian lynx.

    Directory of Open Access Journals (Sweden)

    Mirosław Ratkiewicz

    Full Text Available Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers was found in lynx from Norway and Białowieża Primeval Forest (BPF, which coincided with a recent demographic bottleneck (Norway or high habitat fragmentation (BPF. The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and

  10. Mitochondrial data are not suitable for resolving placental mammal phylogeny.

    Science.gov (United States)

    Morgan, Claire C; Creevey, Christopher J; O'Connell, Mary J

    2014-12-01

    Mitochondrial data have traditionally been used in reconstructing a variety of species phylogenies. The low rates of recombination and thorough characterization of mitochondrial data across vertebrate species make it a particularly attractive phylogenetic marker. The relatively low number of fully sequenced mammal genomes and the lack of extensive sampling within Superorders have posed a serious problem for reaching agreement on the placement mammal species. The use of mitochondrial data sequences from large numbers of mammals could serve to circumvent the taxon-sampling deficit. Here we assess the suitability of mitochondrial data as a phylogenetic marker in mammal phylogenetics. MtDNA datasets of mammal origin have been filtered as follows: (i) we have sampled sparsely across the phylogenetic tree, (ii) we have constrained our sampling to genes with high taxon coverage, (iii) we have categorised rates across sites in a phylogeny independent manner and have removed fast evolving sites, and (iv), we have sampled from very shallow divergence times to reduce phylogenetic conflict. However, topologies obtained using these filters are not consistent with previous studies and are discordant across different genes. Individual mitochondrial genes, and indeed all mitochondrial genes analysed as a supermatrix, resulted in poor resolution of the species phylogeny. Overall, our study highlights the limitations of mitochondrial data, not only for resolving deep divergences and but also for shallow divergences in the mammal phylogeny.

  11. Mapping global environmental suitability for Zika virus.

    Science.gov (United States)

    Messina, Jane P; Kraemer, Moritz Ug; Brady, Oliver J; Pigott, David M; Shearer, Freya M; Weiss, Daniel J; Golding, Nick; Ruktanonchai, Corrine W; Gething, Peter W; Cohn, Emily; Brownstein, John S; Khan, Kamran; Tatem, Andrew J; Jaenisch, Thomas; Murray, Christopher Jl; Marinho, Fatima; Scott, Thomas W; Hay, Simon I

    2016-04-19

    Zika virus was discovered in Uganda in 1947 and is transmitted by Aedes mosquitoes, which also act as vectors for dengue and chikungunya viruses throughout much of the tropical world. In 2007, an outbreak in the Federated States of Micronesia sparked public health concern. In 2013, the virus began to spread across other parts of Oceania and in 2015, a large outbreak in Latin America began in Brazil. Possible associations with microcephaly and Guillain-Barré syndrome observed in this outbreak have raised concerns about continued global spread of Zika virus, prompting its declaration as a Public Health Emergency of International Concern by the World Health Organization. We conducted species distribution modelling to map environmental suitability for Zika. We show a large portion of tropical and sub-tropical regions globally have suitable environmental conditions with over 2.17 billion people inhabiting these areas.

  12. A semiotic approach to suitability for psychotherapy.

    Science.gov (United States)

    Meltzer, J D

    1978-11-01

    At the beginning of my career as a psychotherapist I interviewed a number of patients in an effort to find one who seemed to be a good prospect for long-term psychotherapy. While interviewing with this purpose in mind, I was struck by the fact that a number of the people I spoke with gave me a sense of being extremely suitable for this sort of therapy, but that others seemed quite unsuitable. An informal survey among my peers as well as among more senior therapists revealed that they were not unfamiliar with the phenomenon. The present empirical study of the semiotic aspects of suitability for psychotherapy grew out of this early experience.

  13. Habitat Suitability Index Models: Eastern wild turkey

    Science.gov (United States)

    Schroeder, Richard L.

    1985-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the eastern wild turkey (Meleagris gallopavo sylvestris). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  14. Habitat Suitability Index Models: Swamp rabbit

    Science.gov (United States)

    Allen, Arthur W.

    1985-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the swamp rabbit (Sylvilagus aquaticus). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  15. Research on Items Suitable for Online Auction

    Institute of Scientific and Technical Information of China (English)

    LUO Zhanghua; LIU Lu; WU Lihua

    2004-01-01

    Based on the classification to the attribute information of auctioned commodity, the valuation signal of auctioned commodity is categorized into two groups: codable valuation signal and un-codable valuation signal. A valuation signal model is developed and used to reason under the environment of common valuation auction. The results show that the value of commodity auctioned online tends to be lower and the commodity with bigger factor that can be described online is more suitable for online auction.

  16. Localization of the human RNA polymerase I transcription factor gene (UBTF) to the D17S183 locus on chromosome 17q21 and construction of a long-range restriction map of the region

    Energy Technology Data Exchange (ETDEWEB)

    Jones, K.A.; Black, D.M.; Griffiths, B.L.; Solomon, E. [Somatic Cell Genetics Lab., London (United Kingdom)

    1995-12-10

    Human upstream binding factor (hUBF) is a sequence-specific DNA-binding protein that is essential for the activation of human 18s and 28s rRNA gene transcription. We have isolated and localized the gene (UBTF) encoding hUBF to the D17S183 locus on chromosome 17q21 by analyzing a cosmid from the region and carrying out Southern analysis on a previously constructed chromosome 17 somatic cell hybrid mapping panel using a probe from the hUBF cDNA. Confirmation of its location at this region was obtained from the results of pulsed-field gel electrophoresis analysis of genomic DNA using the hUBF cDNA and other probes from the region. These data also enabled the construction of a long-range restriction map of the region. 13 refs., 2 figs., 1 tab.

  17. Niche suitability affects development: skull asymmetry increases in less suitable areas.

    Directory of Open Access Journals (Sweden)

    Renan Maestri

    Full Text Available For conservation purposes, it is important to take into account the suitability of a species to particular habitats; this information may predict the long-term survival of a species. In this sense, morphological measures of developmental stress, such as fluctuating asymmetry, can be proxies for an individual's performance in different regions. In this study, we conducted tests to determine whether areas with different levels of suitability for a species (generated by ecological niche models were congruent with morphological markers that reflect environmental stress and morphological variance. We generated a Maxent niche model and compared the suitability assessments of several areas with the skull morphology data (fluctuating asymmetry and morphological disparity of populations of the Atlantic forest endemic to Brazil rodent Akodon cursor. Our analyses showed a significant negative relationship between suitability levels and fluctuating asymmetry levels, which indicates that in less suitable areas, the individuals experience numerous disturbances during skull ontogeny. We have not found an association between morphological variance and environmental suitability. As expected, these results suggest that in environments with a lower suitability, developmental stress is increased. Such information is helpful in the understanding of the species evolution and in the selection of priority areas for the conservation of species.

  18. Comparison of Prime Movers Suitable for USMC Expeditionary Power Sources

    Energy Technology Data Exchange (ETDEWEB)

    Theiss, T J; Conklin, J. C.; Thomas, John F.; Armstrong, T. R.

    2000-04-18

    This report documents the results of the ORNL investigation into prime movers that would be desirable for the construction of a power system suitable for the United States Marine Corps (USMC) expeditionary forces under Operational Maneuvers From The Sea (OMFTS) doctrine. Discrete power levels of {approx}1, 5, 15, and 30 kW are considered. The only requirement is that the prime mover consumes diesel fuel. A brief description is given for the prime movers to describe their basic scientific foundations and relative advantages and disadvantages. A list of key attributes developed by ORNL has been weighted by the USMC to indicate the level of importance. A total of 14 different prime movers were scored by ORNL personnel in four size ranges (1,5, 15, & 30 kW) for their relative strength in each attribute area. The resulting weighted analysis was used to indicate which prime movers are likely to be suitable for USMC needs. No single engine or prime mover emerged as the clear-cut favorite but several engines scored as well or better than the diesel engine. At the higher load levels (15 & 30 kW), the results indicate that the open Brayton (gas turbine) is a relatively mature technology and likely a suitable choice to meet USMC needs. At the lower power levels, the situation is more difficult and the market alone is not likely to provide an optimum solution in the time frame desired (2010). Several prime movers should be considered for future developments and may be satisfactory; specifically, the Atkinson cycle, the open Brayton cycle (gas turbine), the 2-stroke diesel. The rotary diesel and the solid oxide fuel cell should be backup candidates. Of all these prime movers, the Atkinson cycle may well be the most suitable for this application but is an immature technology. Additional demonstrations of this engine will be conducted at ORNL. If this analysis is positive, then the performance of a generator set using this engine, the open Brayton and the 2-stroke diesel should

  19. Habitat Suitability Index Models: Red king crab

    Science.gov (United States)

    Jewett, Stephen C.; Onuf, Christopher P.

    1988-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for evaluating habitat of different life stages of red king crab (Paralithodes camtschatica). A model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) and 1.0 (optimum habitat) in Alaskan coastal waters, especially in the Gulf of Alaska and the southeastern Bering Sea. HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  20. Spatial Experiment Technologies Suitable for Unreturnable Bioreactor

    Science.gov (United States)

    Zhang, Tao; Zheng, Weibo; Tong, Guanghui

    2016-07-01

    The system composition and main function of the bioreactor piggybacked on TZ cargo transport spacecraft are introduced briefly in the paper.The spatial experiment technologies which are suitable for unreturnable bioreactor are described in detail,including multi-channel liquid transportion and management,multi-type animal cells circuit testing,dynamic targets microscopic observation in situ etc..The feasibility and effectiveness of these technologies which will be used in space experiment in bioreactor are verified in tests and experiments on the ground.

  1. Understanding Peripheral Bat Populations Using Maximum-Entropy Suitability Modeling

    Science.gov (United States)

    Barnhart, Paul R.; Gillam, Erin H.

    2016-01-01

    Individuals along the periphery of a species distribution regularly encounter more challenging environmental and climatic conditions than conspecifics near the center of the distribution. Due to these potential constraints, individuals in peripheral margins are expected to change their habitat and behavioral characteristics. Managers typically rely on species distribution maps when developing adequate management practices. However, these range maps are often too simplistic and do not provide adequate information as to what fine-scale biotic and abiotic factors are driving a species occurrence. In the last decade, habitat suitability modelling has become widely used as a substitute for simplistic distribution mapping which allows regional managers the ability to fine-tune management resources. The objectives of this study were to use maximum-entropy modeling to produce habitat suitability models for seven species that have a peripheral margin intersecting the state of North Dakota, according to current IUCN distributions, and determine the vegetative and climatic characteristics driving these models. Mistnetting resulted in the documentation of five species outside the IUCN distribution in North Dakota, indicating that current range maps for North Dakota, and potentially the northern Great Plains, are in need of update. Maximum-entropy modeling showed that temperature and not precipitation were the variables most important for model production. This fine-scale result highlights the importance of habitat suitability modelling as this information cannot be extracted from distribution maps. Our results provide baseline information needed for future research about how and why individuals residing in the peripheral margins of a species’ distribution may show marked differences in habitat use as a result of urban expansion, habitat loss, and climate change compared to more centralized populations. PMID:27935936

  2. Suitability of Alternative Lubricants for Automotive Gear Applications

    Directory of Open Access Journals (Sweden)

    Amit Suhane

    2014-03-01

    Full Text Available Rising environmental concerns due to the problems associated with conventional mineral lubricants has renewed interest in usage of alternative resources. Various attempts have been made to explore the possibilities of utilizing vegetable oils for range of applications. Properties like excellent viscosity features, higher biodegradability, lower toxicity, better renewability & natural lubricity etc shows its potential as lubricants inspite of certain technical problems. Critical issues like lower oxidation stability , poor cold temperature properties affects the performance of vegetable oils and restricts its application to limited range . Gear oils are the hidden workhorses of automotive applications. This article highlights the suitability of various vegetable oils for lubricant formulation as an alternative in automotive gearing applications.

  3. Mid-Atlantic elasmobranchs: Suitable metal scouts?

    Science.gov (United States)

    Torres, Paulo; Tristão da Cunha, Regina; Rodrigues, Armindo Dos Santos

    2017-04-15

    Heavy metals are a hazard to marine fauna and human health. In this study we assess stable isotopes and metal content in Prionace glauca and Isurus oxyrinchus and analyse these results within and among other species and across regions and geographical areas. Also, we evaluate their suitability, together with Raja clavata and Galeorhinus galeus, as Mid-Atlantic bioindicators. Prionace glauca and I. oxyrinchus shared the same trophic level in a pelagic food web and did not present significant differences between genders or metals, except for As. Arsenic and Hg accumulated while Cd and Pb were not detected. One I. oxyrinchus presented Hg values above regulatory limits. A high Hg exposure was associated with I. oxyrinchus since its maximum weekly intake was exceeded. Elasmobranchs can be used as metal sentinels, each presenting different key features which defines a good marine bioindicator, allowing long-term monitoring at different temporal and spatial scales. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Monazite as a suitable actinide waste form

    Energy Technology Data Exchange (ETDEWEB)

    Schlenz, Hartmut; Heuser, Julia; Schmitz, Stephan; Bosbach, Dirk [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie und Klimaforschung (IEK), Nukleare Entsorgung und Reaktorsicherheit (IEK-6); Neumann, Andreas [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie und Klimaforschung (IEK), Nukleare Entsorgung und Reaktorsicherheit (IEK-6); RWTH Aachen Univ. (Germany). Inst. for Crystallography

    2013-03-01

    The conditioning of radioactive waste from nuclear power plants and in some countries even of weapons plutonium is an important issue for science and society. Therefore the research on appropriate matrices for the immobilization of fission products and actinides is of great interest. Beyond the widely used borosilicate glasses, ceramics are promising materials for the conditioning of actinides like U, Np, Pu, Am, and Cm. Monazite-type ceramics with general composition LnPO{sub 4} (Ln = La to Gd) and solid solutions of monazite with cheralite or huttonite represent important materials in this field. Monazite appears to be a promising candidate material, especially because of its outstanding properties regarding radiation resistance and chemical durability. This article summarizes the most recent results concerning the characterization of monazite and respective solid solutions and the study of their chemical, thermal, physical and structural properties. The aim is to demonstrate the suitability of monazite as a secure and reliable waste form for actinides. (orig.)

  5. The suitability of internal versus external successors

    DEFF Research Database (Denmark)

    Boyd, Britta; Royer, Susanne

    2012-01-01

    of family business succession in order to understand when family successors are preferred because of their family-specific experiential knowledge. A case study analysis from the German-Danish border region explores how a family firm has used internal successors for the last 12 successions. We argue...... that in industries where tacit knowledge forms the basis for competitive advantage, the use of internal successors can help family firms excel after a transition of power has occurred. Theoretical and practical implications are discussed to enhance the long-term perspective for family businesses.......Understanding knowledge transfer in family firm succession is important for the survival of family firms. Previous research has begun to explore the suitability of internal versus external successor in family firms with regard to relevant knowledge types. This paper builds on the contingency model...

  6. Mapping habitat suitability for at-risk plant species and its implications for restoration and reintroduction.

    Science.gov (United States)

    Questad, Erin J; Kellner, James R; Kinney, Kealoha; Cordell, Susan; Asner, Gregory P; Thaxton, Jarrod; Diep, Jennifer; Uowolo, Amanda; Brooks, Sam; Inman-Narahari, Nikhil; Evans, Steven A; Tucker, Brian

    2014-03-01

    The conservation of species at risk of extinction requires data to support decisions at landscape to regional scales. There is a need for information that can assist with locating suitable habitats in fragmented and degraded landscapes to aid the reintroduction of at-risk plant species. In addition, desiccation and water stress can be significant barriers to the success of at-risk plant reintroduction programs. We examine how airborne light detection and ranging (LiDAR) data can be used to model microtopographic features that reduce water stress and increase resource availability, providing information for landscape planning that can increase the success of reintroduction efforts for a dryland landscape in Hawaii. We developed a topographic habitat-suitability model (HSM) from LiDAR data that identifies topographic depressions that are protected from prevailing winds (high-suitability sites) and contrasts them with ridges and other exposed areas (low-suitability sites). We tested in the field whether high-suitability sites had microclimatic conditions that indicated better-quality habitat compared to low-suitability sites, whether plant-response traits indicated better growing conditions in high-suitability sites, whether the locations of individuals of existing at-risk plant species corresponded with our habitat-suitability classes, and whether the survival of planted individuals of a common native species was greater in high-suitability, compared to low-suitability, planting sites. Mean wind speed in a high-suitability field site was over five times lower than in a low-suitability site, and soil moisture and leaf wetness were greater, indicating less stress and greater resource availability in high-suitability areas. Plant height and leaf nutrient content were greater in high-suitability areas. Six at-risk species showed associations with high-suitability areas. The survival of planted individuals was less variable among high-suitability plots. These results

  7. Construction and testing of a novel host-range defective myxoma virus vaccine with the M063 gene inactivated that is non-permissive for replication in rabbit cells.

    Science.gov (United States)

    Adams, Mathew M; van Leeuwen, Barbara H; McFadden, Grant; Kerr, Peter J

    2008-01-01

    Deletion of the M063 gene from myxoma virus produces a virus that is unable to replicate in rabbit cells in vitro or in live rabbits but can be propagated in non-rabbit cell lines. A targeted M063 deletion mutant was constructed in the attenuated Uriarra strain of myxoma virus and the ability of this virus to act as a safe, non-transmissible vaccine against myxomatosis was tested in outbred laboratory rabbits. Immunization with the M063 deletion vaccine provided good short-term protection against lethal challenge with virulent myxoma virus. Long-term protection was similar to reported results with heterologous live virus, with some rabbits protected but others succumbing to challenge. Replication-deficient poxvirus vaccines, like the Modified Vaccinia Virus Ankara (MVA) in man and the myxoma virus vaccine described here in rabbits, are very attractive from a safety perspective. Seasonal boosting would be predicted to provide long-term protection. Targeted host-range gene deletions could have potential for rapid development of poxvirus vaccines in general.

  8. Uncertainty in Various Habitat Suitability Models and Its Impact on Habitat Suitability Estimates for Fish

    Directory of Open Access Journals (Sweden)

    Yu-Pin Lin

    2015-07-01

    Full Text Available Species distribution models (SDMs are extensively used to project habitat suitability of species in stream ecological studies. Owing to complex sources of uncertainty, such models may yield projections with varying degrees of uncertainty. To better understand projected spatial distributions and the variability between habitat suitability projections, this study uses five SDMs that are based on the outputs of a two-dimensional hydraulic model to project the suitability of habitats and to evaluate the degree of variability originating from both differing model types and the split-sample procedure. The habitat suitability index (HSI of each species is based on two stream flow variables, including current velocity (V, water depth (D, as well as the heterogeneity of these flow conditions as quantified by the information entropy of V and D. The six SDM approaches used to project fish abundance, as represented by HSI, included two stochastic models: the generalized linear model (GLM and the generalized additive model (GAM; as well as three machine learning models: the support vector machine (SVM, random forest (RF and the artificial neural network (ANN, and an ensemble model (where the latter is the average of the preceding five models. The target species Sicyopterus japonicas was found to prefer habitats with high current velocities. The relationship between mesohabitat diversity and fish abundance was indicated by the trends in information entropy and weighted usable area (WUA over the study area. This study proposes a method for quantifying habitat suitability, and for assessing the uncertainties in HSI and WUA that are introduced by the various SDMs and samples. This study also demonstrated both the merits of the ensemble modeling approach and the necessity of addressing model uncertainty.

  9. Attainment of Electron Beam Suitable for Medium Energy Electron Cooling

    Energy Technology Data Exchange (ETDEWEB)

    Seletskiy, Sergei M. [Univ. of Rochester, NY (United States)

    2005-01-01

    Electron cooling of charged particle beams is a well-established technique at electron energies of up to 300 keV. However, up to the present time the advance of electron cooling to the MeV-range energies has remained a purely theoretical possibility. The electron cooling project at Fermilab has recently demonstrated the ¯rst cooling of 8.9 GeV/c antiprotons in the Recycler ring, and therefore, has proved the validity of the idea of relativistic electron cool- ing. The Recycler Electron Cooler (REC) is the key component of the Teva- tron Run II luminosity upgrade project. Its performance depends critically on the quality of electron beam. A stable electron beam of 4.3 MeV car- rying 0.5 A of DC current is required. The beam suitable for the Recycler Electron Cooler must have an angular spread not exceeding 200 ¹rad. The full-scale prototype of the REC was designed, built and tested at Fermilab in the Wideband laboratory to study the feasibility of attaining the high-quality electron beam. In this thesis I describe various aspects of development of the Fermilab electron cooling system, and the techniques used to obtain the electron beam suitable for the cooling process. In particular I emphasize those aspects of the work for which I was principally responsible.

  10. Suitability of digital camcorders for virtual reality image data capture

    Science.gov (United States)

    D'Apuzzo, Nicola; Maas, Hans-Gerd

    1998-12-01

    Today's consumer market digital camcorders offer features which make them appear quite interesting devices for virtual reality data capture. The paper compares a digital camcorder with an analogue camcorder and a machine vision type CCD camera and discusses the suitability of these three cameras for virtual reality applications. Besides the discussion of technical features of the cameras, this includes a detailed accuracy test in order to define the range of applications. In combination with the cameras, three different framegrabbers are tested. The geometric accuracy potential of all three cameras turned out to be surprisingly large, and no problems were noticed in the radiometric performance. On the other hand, some disadvantages have to be reported: from the photogrammetrists point of view, the major disadvantage of most camcorders is the missing possibility to synchronize multiple devices, limiting the suitability for 3-D motion data capture. Moreover, the standard video format contains interlacing, which is also undesirable for all applications dealing with moving objects or moving cameras. Further disadvantages are computer interfaces with functionality, which is still suboptimal. While custom-made solutions to these problems are probably rather expensive (and will make potential users turn back to machine vision like equipment), this functionality could probably be included by the manufacturers at almost zero cost.

  11. Predatory aquatic beetles, suitable trace elements bioindicators.

    Science.gov (United States)

    Burghelea, Carmen I; Zaharescu, Dragos G; Hooda, Peter S; Palanca-Soler, Antonio

    2011-05-01

    Predatory aquatic beetles are common colonizers of natural and managed aquatic environments. While as important components of the aquatic food webs they are prone to accumulate trace elements, they have been largely neglected from metal uptake studies. We aim to test the suitability of three dytiscid species, i.e.Hydroglyphus pusillus, Laccophilus minutus and Rhantus suturalis, as trace elements (Al, As, Cd, Co, Cu, Fe, Mn, Mo, Ni, Pb, Se and Zn) bioindicators. The work was carried out in a case area representing rice paddies and control sites (reservoirs) from an arid region known for its land degradation (Monegros, NE Spain). Categorical principal component analysis (CATPCA) was tested as a nonlinear approach to identify significant relationships between metals, species and habitat conditions so as to examine the ability of these species to reflect differences in metal uptake. Except Se and As, the average concentrations of all other elements in the beetles were higher in the rice fields than in the control habitats. The CATPCA determined that H. pusillus had high capacity to accumulate Fe, Ni and Mn regardless of the habitat type, and hence may not be capable of distinguishing habitat conditions with regards to these metals. On the other hand, L. minutus was found less sensitive for Se in non-managed habitats (i.e. reservoirs), while R. suturalis was good in accumulating Al, Mo and Pb in rice fields. The latter seems to be a promising bioindicator of metal enrichment in rice fields. We conclude that predatory aquatic beetles are good candidates for trace elements bioindication in impacted and non-impacted environments and can be used in environmental monitoring studies. CATPCA proved to be a reliable approach to unveil trends in metal accumulation in aquatic invertebrates according to their habitat status.

  12. Comprehensive Suitability Evaluation of Tea Crops Using GIS and a Modified Land Ecological Suitability Evaluation Model

    Institute of Scientific and Technical Information of China (English)

    LI Bo; ZHANG Feng; ZHANG Li-Wen; HUANG Jing-Feng; JIN Zhi-Feng; D. K. GUPTA

    2012-01-01

    Tea (Camellia sinensis) is one of the most valuable cash crops in southern China; however,the planting distribution of tea crops is not optimal and the production and cultivation regions of tea crops are restricted by law and custom.In order to evaluate the suitability of tea crops in Zhejiang Province,the annual mean temperature,the annual accumulated temperature above 10 ℃,the frequency of extremely low temperature below -13 ℃,the mean humidity from April to October,slope,aspect,altitude,soil type,and soil texture were selected from climate,topography,and soil factors as factors for land ecological evaluation by the Delphi method based on the ecological characteristics of tea crops.These nine factors were quantitatively analyzed using a geographic information system (GIS).The grey relational analysis (GRA) was combined with the analytic hierarchy process (AHP) to address the uncertainties during the process of evaluating the traditional land ecological suitability,and a modified land ecological suitability evaluation (LESE) model was built.Based on the land-use map of Zhejiang Province,the regions that were completely unsuitable for tea cultivation in the province were eliminated and then the spatial distribution of the ecological suitability of tea crops was generated using the modified LESE model and GIS.The results demonstrated that the highly,moderately,and non-suitable regions for the cultivation of tea crops in Zhejiang Province were 27552.66,42724.64,and 26507.97 km2,and accounted for 28.47%,44.14%,and 27.39% of the total evaluation area,respectively.Validation of the method showed a high degree of coincidence with the current planting distribution of tea crops in Zhejiang Province.The modified LESE model combined with GIS could be useful in quickly and accurately evaluating the land ecological suitability of tea crops,providing a scientific basis for the rational distribution of tea crops and acting as a reference to land policy makers and land

  13. Suitability Evaluation of Groundwater for Irrigation, Drinking and Industrial Purposes

    Directory of Open Access Journals (Sweden)

    M. A. Hakim

    2009-01-01

    , drinking and industrial purposes. Except for a few cases there was neither chloride toxicity nor sulphate acidity in the area. The content for NO-3 and P was negligible and water samples were 'good' to 'excellent' with respect to boron and SSP. Range of EC (361-802 µS cm-1 and that of SAR (0.23-0.54 indicated that all samples were in 'medium-salinity low-alkali' hazard class. In respect of TDS and RSC values, all samples were of fresh water and suitable class. Among SSP and SAR, TDS and EC were highly correlated. An Arsanic range was far below than recommended upper limit. Conclusion/Recommendations: In respect of all evaluating criteria, groundwater of all the 28 locations can be safely used for long-term irrigation and drinking purposes. All samples were found suitable for drinking and industrial purpose in consideration of Fe concentration. However, none of the water samples was suitable for industrial use, because of higher TDS and pH values exceeding recommendation.

  14. Predicting Suitable field workdays for soil tillage in North Central ...

    African Journals Online (AJOL)

    Oladimeji S. Ife

    A simulation model was developed to predict suitable field workdays for tillage operations in North Central ... KEYWORDS: Suitable field workdays, tillage, agro –meteorology, tractability. 1. ... approach, the calculation of the components.

  15. 10 CFR 963.14 - Preclosure suitability criteria.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Preclosure suitability criteria. 963.14 Section 963.14 Energy DEPARTMENT OF ENERGY YUCCA MOUNTAIN SITE SUITABILITY GUIDELINES Site Suitability Determination...) Ability to preserve the option to retrieve wastes during the preclosure period....

  16. Suitability of Nettle Fiber for Textile Production

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Nettle plants widely exist in China, but up to now there is no research regarding Chinese nettle fiber properties,especially about its spinnability. This paper has studied the properties of Chinese nettle fiber and its spinnability. The research results show that the average length of nettle fiber is about 34 mm, the nettle fiber fineness ranging from 0.589 to 0. 769 tex. Nettle fiber has high breaking strength, low breaking extension and high initial modulus. Both the biochemical method and chemical method can meet the requirement of nettle degumming, with the residual being less than 4%. Nettle fiber can be utilised as textile material and can be spun in rotor-spinning machines after well degummed.

  17. Assessing Land Suitability for Rainwater Harvesting Using Geospatial Techniques: A Case Study of Njoro Catchment, Kenya

    Directory of Open Access Journals (Sweden)

    C. W. Maina

    2016-01-01

    Full Text Available Water demand increases as population increases leading to overexploitation of water resource. Consequently, there is need for improved water resources management complemented with rain water harvesting within the catchments. This study sought to assess land suitability for surface runoff harvesting using geospatial techniques. Land use/land cover maps of the area were derived from Landsat image. Land use and soils data were used in generating curve number map of the catchment. Lineaments greatly affect the storage depending on whether runoff is for surface storage or ground water recharge purposes. As a result, ArcGIS was used in delineating the lineaments from Digital Elevation Model (DEM of the catchment. Further, using weighted overlay the catchment was grouped into categories of restricted, not suitable, moderately suitable, suitable, or highly suitable. The study found that forest, agriculture, and built-up areas occupied about 39.42%, 36.32%, and 1.35% of catchment area, respectively. A large part of catchment was found to have curve number range of 82–89. About 50% of the catchment was found to fall within suitable and highly suitable categories. This implied that a great potential exists for rain water harvesting within the catchment.

  18. New telescope designs suitable for massively-multiplexed spectroscopy

    CERN Document Server

    Pasquini, L; Ellis, R; de Zeeuw, T

    2016-01-01

    We present two novel designs for a telescope suitable for massively-multiplexed spectroscopy. The first is a very wide field Cassegrain telescope optimised for fibre feeding. It provides a Field Of View (FOV) of 2.5 degrees diameter with a 10m primary mirror. It is telecentric and works at F/3, optimal for fibre injection. As an option, a gravity invariant focus for the central 10 arc-minutes can be added, to host, for instance, a giant integral field unit (IFU). It has acceptable performance in the 360-1300 nm wavelength range. The second concept is an innovative five mirror telescope design based on a Three Mirror Anastigmatic (TMA) concept. The design provides a large FOV in a convenient, gravity- invariant focal plane, and is scalable to a range of telescope diameters. As specific example, we present a 10m telescope with a 1.5 degree diameter FOV and a relay system that allows simultaneous spectroscopy with 10,000 mini-IFUs over a square degree, or, alternatively a 17.5 square arcminutes giant IFU, by usi...

  19. Technological suitability of goat milk for processing

    Directory of Open Access Journals (Sweden)

    Romualda Danków

    2011-06-01

    Full Text Available The world population of dairy goats is estimated at 300 million of which approximately 56% is reared in Asia. Goats raised in Europe (about 12 million constitute 4% of the world herd of these animals. The world goat milk production is assessed to be at the level of about 12 million tons and constitutes over 2% of the global milk obtained from different animal species. In many European countries, goat milk as a dairy raw material comes second after cow milk. The goat population in Poland is estimated at 190 000 heads. With regard to the content of basic constituents, goat milk is similar to cow milk, although it differs from it as to the qualitative composition of fat and protein. Species protein structure of goat milk, different from that of cow milk, causes fewer allergic reactions which are observed to occur in the case of intolerance to cow milk proteins. Rennin curd from goat milk is softer and less compact. A wide range of different products is manufactured from goat milk including: liquid milk (pasteurised and UHT, rennin and cottage cheeses, fermented beverages such as yoghurt, kefir, butter milk, cream, condensed milk, powdered milk, rice goats, butter and even chocolates “Goat’s Milk”.

  20. Agronomic Suitability of Bioenergy Crops in Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    Lemus, Rocky; Baldwin, Brian; Lang, David

    2011-10-01

    In Mississippi, some questions need to be answered about bioenergy crops: how much suitable land is available? How much material can that land produce? Which production systems work best in which scenarios? What levels of inputs will be required for productivity and longterm sustainability? How will the crops reach the market? What kinds of infrastructure will be necessary to make that happen? This publication helps answer these questions: • Which areas in the state are best for bioenergy crop production? • How much could these areas produce sustainably? • How can bioenergy crops impact carbon sequestration and carbon credits? âÂÃÃÂ

  1. Reevaluating Suitability Estimates Based on Dynamics of Cropland Expansion in the Brazilian Amazon

    Science.gov (United States)

    Morton, Douglas C.; Noojipady, Praveen; Macedo, Marcia M.; Victoria, Daniel C.; Bolfe, Edson L.

    2016-01-01

    further legal expansion of crop production in Mato Grosso. Dynamics of cropland expansion from more than a decade of satellite observations indicated narrow ranges of suitability criteria, restricting PAC under current policy conditions, and emphasizing the advantages of field-scale information to assess suitability and utilization.

  2. Suitability of Aquatic Plant Fibers for Handmade Papermaking

    Directory of Open Access Journals (Sweden)

    Nordiah Bidin

    2015-01-01

    Full Text Available Increasing concerns for future fiber supplies in pulp and paper industries has shifted interest in nonwood sources from agriculture residues and aquatic plants. Aquatic plants with short growth cycles, in abundance, and with low lignin are a potential fiber source. Five aquatic plant species, Cyperus digitatus, Cyperus halpan, Cyperus rotundus, Scirpus grossus, and Typha angustifolia, were examined for fiber dimensions and chemical composition (cellulose, lignin and compared with other nonwood plants. All aquatic plants possessed short (length, 0.71–0.83 mm and thin (diameter, 9.13–12.11 µm fibers, narrow lumen (diameter, 4.32–7.30 µm, and thin cell wall (thickness, 2.25–2.83 µm compared with most other nonwood plants. Slenderness ratio ranged from 73.77 to 89.34 with Typha angustifolia having the highest ratio. Except for Scirpus grossus, the flexibility coefficient ranged from 52.91 to 58.08. Scirpus grossus has low Runkel ratio, 0.84 ± 0.17. Fiber characteristics, short and thin fibers, Slenderness ratio >60, flexibility coefficient within 50–75, and Runkel ratio 34% is suitable for pulp and papermaking. Lignin content in aquatic plants in the present study ranged 9.54–20.04% and below the wood lignin content of <23–30% encountered in pulp and papermaking. Handmade paper sheets produced for paperboard, craft, and decorative purposes are with permissible tensile strength, breaking length, and low moisture content.

  3. Land-use suitability analysis for urban development in Beijing.

    Science.gov (United States)

    Liu, Renzhi; Zhang, Ke; Zhang, Zhijiao; Borthwick, Alistair G L

    2014-12-01

    Land-use suitability analyses are of considerable use in the planning of mega-cities. An Urban Development Land-use Suitability Mapping (UDLSM) approach has been constructed, based on opportunity and constraint criteria. Two Multi-criteria Evaluation (MCE) methods, the Ideal Point Method (IPM) and Ordered Weighted Averaging (OWA), were used to generate the opportunity map. The protection map was obtained by means of constraint criteria, utilizing the Boolean union operator. A suitability map was then generated by overlaying the opportunity and protection maps. By applying the UDLSM approach to Beijing, its urban development land-use suitability was mapped, and a sensitivity analysis undertaken to examine the robustness of the proposed approach. Indirect validation was achieved by mutual comparisons of suitability maps resulting from the two MCE methods, where the overall agreement of 91% and kappa coefficient of 0.78 indicated that both methods provide very similar spatial land-use suitability distributions. The suitability level decreases from central Beijing to its periphery, and the area classed as suitable amounts to 28% of the total area. Leading attributes of each opportunity factor for suitability were revealed, with 2256 km(2), i.e. 70%, of existing development land being overlaid by suitable areas in Beijing. Conflicting parcels of land were identified by overlaying the resultant map with two previous development blueprints for Beijing. The paper includes several recommendations aimed at improving the long-term urban development plans for Beijing.

  4. Evaluation of Internal Reference Genes for Quantitative Expression Analysis by Real-Time PCR in Ovine Whole Blood

    OpenAIRE

    Pier Luigi Acutis; Maria Caramelli; Antonio Quasso; Dario Ariello; Claudio Bellino; Maria Grazia Maniaci; Paola Modesto; Chiara Campanella; Simone Bertuzzi; Simone Peletto

    2011-01-01

    The use of reference genes is commonly accepted as the most reliable approach to normalize qRT-PCR and to reduce possible errors in the quantification of gene expression. The most suitable reference genes in sheep have been identified for a restricted range of tissues, but no specific data on whole blood are available. The aim of this study was to identify a set of reference genes for normalizing qRT-PCR from ovine whole blood. We designed 11 PCR assays for commonly employed reference genes b...

  5. Maximizing the Range of a Projectile.

    Science.gov (United States)

    Brown, Ronald A.

    1992-01-01

    Discusses solutions to the problem of maximizing the range of a projectile. Presents three references that solve the problem with and without the use of calculus. Offers a fourth solution suitable for introductory physics courses that relies more on trigonometry and the geometry of the problem. (MDH)

  6. Model suitability to assess regional potato yield patterns in northern Ecuador

    NARCIS (Netherlands)

    Soltani Largani, A.; Stoorvogel, J.J.; Veldkamp, A.

    2013-01-01

    A wide range of scenario studies aiming at rural development require regional patterns of crop yield. This study aims to evaluate three different modeling approaches for their suitability to assess regional potato yield patterns. The three model approaches include (1) an empirical model; (2) a proce

  7. Suitability of sorghum grain for the development of the larger grain ...

    African Journals Online (AJOL)

    Suitability of sorghum grain for the development of the larger grain borer ... on sorghum grain, when stored as whole grain or finely ground grain flour. ... In a similar manner, the mean weight of beetles produced ranged from 1.70 to 3.02 mg.

  8. Automatic Range Changer For SWR Meter

    Science.gov (United States)

    Dengler, Robert J.; Siegel, Peter H.

    1990-01-01

    Commercial unit modified for antenna-pattern measurements. Addition of automatic range-changing circuit converts Hewlett-Packard 415E standing-wave-ratio (SWR) meter into radio-frequency detector suitable for computer-controlled measurements of radiation patterns of antennas. Modification gives SWR meter effective dynamic range of at least 40 dB. Includes two digital lines communicating one of four range settings to controlling computer and one digital line to inhibit transfer of data when range being changed. Ideal instrument for use in applications involving computer-controlled monitoring of power when large changes in signal level expected.

  9. Prepare and pursue: Routes to suitable (re-)employment

    OpenAIRE

    Koen, J.

    2013-01-01

    This dissertation shows that there are routes besides job search that can lead to suitable (re-)employment. Employability is - by providing both the resources to engage and persist in proper job search methods and to eventually land suitable reemployment - a more fruitful route when pursuing genuine reemployment success. Moreover, particularly preparation (i.e., career adaptability) is essential for the quality of (re-)employment. Thus, in the pursuit of suitable (re-)employment, employabilit...

  10. Habitat suitability ofScapharca subcrenata (Lischke) in the shallow water of the Xiaoheishan Island

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jian; SONG Jingjing; BAI Qianling; LIU Chengyue; ZHANG Zhipeng; TANG Haitian

    2016-01-01

    The habitat suitability index (HSI) model was used to identify potential sites for sustainable restoration of ark shell,Scapharca subcrenata (Lischke), in the shallow water of Xiaoheishan Island, using a geographic information system framework. The seven input variables of the HSI model were sediment composition, water temperature, salinity, dissolved oxygen, water depth, pH, and ammonia. A non-linear suitability function for each variable factor was used to transform the value into a normalized quality index ranging from 0 (non-suitability) to 1 (best suitability). In present study, the analysis of habitat suitability was conducted for four seasons respectively. The majority of the study area has a high HSI value (>0.6) year round, which implies a strong suitability for restoration, with the optimal habitat located on the eastern side of the island. Correspondence analysis indicated that water temperature was the main factor causing seasonal variation, while sediment composition and water depth were the two major reasons for the differences in sites. The results of this work could provide support for restoration decision making through identification of potential sites for sustainable establishment ofS. subcrenata.

  11. Low Entalpy Geothermal suitability of north Sardinia (Italy)

    Science.gov (United States)

    Cuccuru, Stefano; Oggiano, Giacomo

    2015-04-01

    This note focus on geothermal potentialities of north Sardinia, where several positive thermal anomalies occur along with geolithological and climatic conditions, which make the area specifically suitable for geoexchange. Sardinia consists of a Variscan basement metamorphosed at different grade and further intruded by a late orogenic batholith. Above this basement, since Mesozoic time, a composite sedimentary and volcanic succession occurs, with maximum thickness of 2-3 Km in correspondence of some extensional and strike-slip Cenozoic basins. The volcanic activity consists of a calcalkaline cycle with crustal component, which started in the late Eocene and ended in the Serravallian; another, mantle derived, alkaline-transitional cycle took place during Pliocene and ended in the middle Pleistocene. Several evidences of geothermal circuits occur in northwestern Sardinia, where some springs characterized by anomalous water temperatures and/or chemical-physical features (e.g., high salinity and carbon dioxide content) were known. In addiction those already exploited (e.g., S. Lucia, S. Martino), new springs and boreholes characterized by positive anomalous water temperatures (in the range of 24 and 35 °C) have been highlighted during our recent surveys. These waters are warmer than the homoeothermic level temperature (where no seasonal variations are recorded), which in the area is 15-16 °C. Considering the absence of active volcanism, the anomalous temperatures must be generated by the uprising of deep meteoric water along a plumbing network of crustal faults that bound the extensional as well as the strike slip basins. Rainwater heated for geothermal gradient can upwell rapidly interacting with surface aquifers that, hence, experience heating at different degree. The physical characteristics (i.e., thermal conductivity, open porosity, permeability etc) of the rocks cropping in north Sardinia, regardless the positive thermal anomalies, are profitably suitable for

  12. Selection of reliable reference genes for gene expression studies in peach using real-time PCR

    Directory of Open Access Journals (Sweden)

    Zhou Jun

    2009-07-01

    Full Text Available Abstract Background RT-qPCR is a preferred method for rapid and reliable quantification of gene expression studies. Appropriate application of RT-qPCR in such studies requires the use of reference gene(s as an internal control to normalize mRNA levels between different samples for an exact comparison of gene expression level. However, recent studies have shown that no single reference gene is universal for all experiments. Thus, the identification of high quality reference gene(s is of paramount importance for the interpretation of data generated by RT-qPCR. Only a few studies on reference genes have been done in plants and none in peach (Prunus persica L. Batsch. Therefore, the present study was conducted to identify suitable reference gene(s for normalization of gene expression in peach. Results In this work, eleven reference genes were investigated in different peach samples using RT-qPCR with SYBR green. These genes are: actin 2/7 (ACT, cyclophilin (CYP2, RNA polymerase II (RP II, phospholipase A2 (PLA2, ribosomal protein L13 (RPL13, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 18S ribosomal RNA (18S rRNA, tubblin beta (TUB, tubblin alpha (TUA, translation elongation factor 2 (TEF2 and ubiquitin 10 (UBQ10. All eleven reference genes displayed a wide range of Cq values in all samples, indicating that they expressed variably. The stability of these genes except for RPL13 was determined by three different descriptive statistics, geNorm, NormFinder and BestKeeper, which produced highly comparable results. Conclusion Our study demonstrates that expression stability varied greatly between genes studied in peach. Based on the results from geNorm, NormFinder and BestKeeper analyses, for all the sample pools analyzed, TEF2, UBQ10 and RP II were found to be the most suitable reference genes with a very high statistical reliability, and TEF2 and RP II for the other sample series, while 18S rRNA, RPL13 and PLA2 were unsuitable as internal controls

  13. Gene Therapy

    Science.gov (United States)

    ... or improve your body's ability to fight disease. Gene therapy holds promise for treating a wide range of diseases, such as cancer, cystic fibrosis, heart disease, diabetes, hemophilia and AIDS. Researchers are still studying how and ...

  14. Cervine tibia morphology and mechanical strength: a suitable tibia model?

    Science.gov (United States)

    Throop, Alexander D W; Landauer, Alexander K; Clark, Alexander Martin; Kuxhaus, Laurel

    2015-03-01

    Animal models for orthopaedic implant testing are well-established but morphologically dissimilar to human tibiae; notably, most are shorter. The purpose of this study was to quantitatively evaluate the morphology and mechanical properties of the cervine tibia, particularly with regard to its suitability for testing orthopaedic implants. Two endosteal and eleven periosteal measurements were made on 15 cervine tibiae. The mechanical strength in axial compression and torsion was measured using 11 tibiae. The cervine tibia is morphologically similar to the human tibia and more closely matches the length of the human tibia than current tibia models (ovine, porcine, and caprine). The distal epiphysis dimensions are notably different, but no more so than the current tibia models. The torsional stiffness of the cervine tibia is within the range of previously reported values for human tibiae. Furthermore, in many regions, cervine tibiae are abundant and locally available at a low cost. Given these mechanical and morphological data, coupled with potential cost savings if regionally available, the cervine tibia may be an appropriate model for orthopaedic implant testing.

  15. A new experimental hybrid of cabbage suitable for early production

    Directory of Open Access Journals (Sweden)

    Červenski Janko

    2012-01-01

    Full Text Available The paper analyzes experimental hybrids of early cabbage developed at the Institute of Field and Vegetable Crops in the previous period. The hybrids were tested together for two years and then one (H17 was chosen and submitted to the Variety Commission of the Republic of Serbia. In 2011, the experimental hybrid H17 was officially released as an early cabbage hybrid and registered under the name of NS Mendo F1. The hybrid had been developed by crossing two early lines, one of which was sterile. It is characterized by a short growing season - 65 days from transplanting to harvest. The head weight ranges from 2.5 to 3.5 kg depending on the cultural practice applied. The head is light green in color, sweet-tasting, and suitable for fresh consumption. The hybrid’s traits that contributed significantly to the formation of the first principal component were in fact those that the breeders attach most importance to in their breeding programs. These are the traits that directly influence the market value of a new hybrid and make a given hybrid recognizable on the market. Most notable among such traits are head weight and the weight of the useful part of the head.[Projekat Ministarstva nauke Republike Srbije, br. TR 31030

  16. Deep Eutectic Salt Formulations Suitable as Advanced Heat Transfer Fluids

    Energy Technology Data Exchange (ETDEWEB)

    Raade, Justin; Roark, Thomas; Vaughn, John; Bradshaw, Robert

    2013-07-22

    Concentrating solar power (CSP) facilities are comprised of many miles of fluid-filled pipes arranged in large grids with reflective mirrors used to capture radiation from the sun. Solar radiation heats the fluid which is used to produce steam necessary to power large electricity generation turbines. Currently, organic, oil-based fluid in the pipes has a maximum temperature threshold of 400 °C, allowing for the production of electricity at approximately 15 cents per kilowatt hour. The DOE hopes to foster the development of an advanced heat transfer fluid that can operate within higher temperature ranges. The new heat transfer fluid, when used with other advanced technologies, could significantly decrease solar electricity cost. Lower costs would make solar thermal electricity competitive with gas and coal and would offer a clean, renewable source of energy. Molten salts exhibit many desirable heat transfer qualities within the range of the project objectives. Halotechnics developed advanced heat transfer fluids (HTFs) for application in solar thermal power generation. This project focused on complex mixtures of inorganic salts that exhibited a high thermal stability, a low melting point, and other favorable characteristics. A high-throughput combinatorial research and development program was conducted in order to achieve the project objective. Over 19,000 candidate formulations were screened. The workflow developed to screen various chemical systems to discover salt formulations led to mixtures suitable for use as HTFs in both parabolic trough and heliostat CSP plants. Furthermore, salt mixtures which will not interfere with fertilizer based nitrates were discovered. In addition for use in CSP, the discovered salt mixtures can be applied to electricity storage, heat treatment of alloys and other industrial processes.

  17. Nanosecond x-ray Laue diffraction apparatus suitable for laser shock compression experiments.

    Science.gov (United States)

    Suggit, Matthew; Kimminau, Giles; Hawreliak, James; Remington, Bruce; Park, Nigel; Wark, Justin

    2010-08-01

    We have used nanosecond bursts of x-rays emitted from a laser-produced plasma, comprised of a mixture of mid-Z elements, to produce a quasiwhite-light spectrum suitable for performing Laue diffraction from single crystals. The laser-produced plasma emits x-rays ranging in energy from 3 to in excess of 10 keV, and is sufficiently bright for single shot nanosecond diffraction patterns to be recorded. The geometry is suitable for the study of laser-shocked crystals, and single-shot diffraction patterns from both unshocked and shocked silicon crystals are presented.

  18. Suitable microscopic entropy for the origin of microbial life: microbiological methods are challenges.

    Science.gov (United States)

    Trevors, J T

    2010-12-01

    A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.

  19. 40 CFR 203.5 - Suitable substitute decision.

    Science.gov (United States)

    2010-07-01

    ... PROGRAMS LOW-NOISE-EMISSION PRODUCTS § 203.5 Suitable substitute decision. (a) If the Administrator... decide whether such product is a suitable substitute for any class or model or product being purchased by... substitute for any product or class of products being purchased by the Federal Government for its use, the...

  20. Evaluation of Agricultural Land Suitability: Application of Fuzzy Indicators

    Science.gov (United States)

    The problem of evaluation of agricultural land suitability is considered as a fuzzy modeling task. The application of individual fuzzy indicators provides an opportunity for assessment of lsand suitability of lands as degree or grade of performance when the lands are used for agricultural purposes....

  1. Prepare and pursue: Routes to suitable (re-)employment

    NARCIS (Netherlands)

    Koen, J.

    2013-01-01

    This dissertation shows that there are routes besides job search that can lead to suitable (re-)employment. Employability is - by providing both the resources to engage and persist in proper job search methods and to eventually land suitable reemployment - a more fruitful route when pursuing genuine

  2. 46 CFR 90.10-38 - Specially suitable for vehicles.

    Science.gov (United States)

    2010-10-01

    ... battery cables, must be in accordance with the applicable provisions of 49 CFR 176.905. ... 46 Shipping 4 2010-10-01 2010-10-01 false Specially suitable for vehicles. 90.10-38 Section 90.10... GENERAL PROVISIONS Definition of Terms Used in This Subchapter § 90.10-38 Specially suitable for...

  3. Technical suitability mapping of feedstocks for biological hydrogen production

    NARCIS (Netherlands)

    Panagiotopoulos, I.A.; Karaoglanoglou, L.S.; Koullas, D.P.; Bakker, R.R.; Claassen, P.A.M.; Koukios, E.G.

    2015-01-01

    The objective of this work was to map and compare the technical suitability of different raw materials for biological hydrogen production. Our model was based on hydrogen yield potential, sugar mobilization efficiency, fermentability and coproduct yield and value. The suitability of the studied r

  4. apparel styles suitable for young swazi women with the prevalent ...

    African Journals Online (AJOL)

    user

    women. Thus, this study aimed at assessing apparel styles suitable for young Swazi women with the two most .... sleeve, cuff, pockets, tucks, pleats, creases and ruffles. A style ...... and pants are not suitable for the triangular body shape, and if ...

  5. Gene expression profiling of soft and firm Atlantic salmon fillet.

    Directory of Open Access Journals (Sweden)

    Thomas Larsson

    Full Text Available Texture of salmon fillets is an important quality trait for consumer acceptance as well as for the suitability for processing. In the present work we measured fillet firmness in a population of farmed Atlantic salmon with known pedigree and investigated the relationship between this trait and gene expression. Transcriptomic analyses performed with a 21 K oligonucleotide microarray revealed strong correlations between firmness and a large number of genes. Highly similar expression profiles were observed in several functional groups. Positive regression was found between firmness and genes encoding proteasome components (41 genes and mitochondrial proteins (129 genes, proteins involved in stress responses (12 genes, and lipid metabolism (30 genes. Coefficients of determination (R(2 were in the range of 0.64-0.74. A weaker though highly significant negative regression was seen in sugar metabolism (26 genes, R(2 = 0.66 and myofiber proteins (42 genes, R(2 = 0.54. Among individual genes that showed a strong association with firmness, there were extracellular matrix proteins (negative correlation, immune genes, and intracellular proteases (positive correlation. Several genes can be regarded as candidate markers of flesh quality (coiled-coil transcriptional coactivator b, AMP deaminase 3, and oligopeptide transporter 15 though their functional roles are unclear. To conclude, fillet firmness of Atlantic salmon depends largely on metabolic properties of the skeletal muscle; where aerobic metabolism using lipids as fuel, and the rapid removal of damaged proteins, appear to play a major role.

  6. The readability and suitability of sexual health promotion leaflets.

    Science.gov (United States)

    Corcoran, Nova; Ahmad, Fatuma

    2016-02-01

    To investigate the readability and suitability of sexual health promotion leaflets. Application of SMOG, FRY and SAM tests to assess the readability and suitability of a selection of sexual health leaflets. SMOG and FRY scores illustrate an average reading level of grade 9. SAM scores indicate that 59% of leaflets are superior in design and 41% are average in design. Leaflets generally perform well in the categories of content, literacy demand, typography and layout. They perform poorly in use of graphics, learning stimulation/motivation and cultural appropriateness. Sexual health leaflets have a reading level that is too high. Leaflets perform well on the suitability scores indicating they are reasonably suitable. There are a number of areas where sexual health leaflets could improve their design. Numerous practical techniques are suggested for improving the readability and suitability of sexual health leaflets. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. Climatic niche divergence and habitat suitability of eight alien invasive weeds in China under climate change.

    Science.gov (United States)

    Wan, Ji-Zhong; Wang, Chun-Jing; Tan, Jing-Fang; Yu, Fei-Hai

    2017-03-01

    Testing climatic niche divergence and modeling habitat suitability under conditions of climate change are important for developing strategies to limit the introduction and expansion of alien invasive weeds (AIWs) and providing important ecological and evolutionary insights. We assessed climatic niches in both native and invasive ranges as well as habitat suitability under climate change for eight representative Chinese AIWs from the American continent. We used climatic variables associated with occurrence records and developed ecological niche models with Maxent. Interestingly, the climatic niches of all eight AIWs diverged significantly between the native and invasive ranges (the American continent and China). Furthermore, the AIWs showed larger climatic niche breadths in the invasive ranges than in the native ranges. Our results suggest that climatic niche shifts between native and invasive ranges occurred. Thus, the occurrence records of both native and invasive regions must be considered when modeling and predicting the spatial distributions of AIWs under current and future climate scenarios. Owing to high habitat suitability, AIWs were more likely to expand into regions of low latitude, and future climate change was predicted to result in a shift in the AIWs in Qinghai and Tibet (regions of higher altitude) as well as Heilongjiang, Jilin, Liaoning, Inner Mongolia, and Gansu (regions of higher latitude). Our results suggest that we need measures to prevent and control AIW expansion at the country-wide level.

  8. Are luminescent bacteria suitable for online detection and monitoring of toxic compounds in drinking water and its sources?

    Science.gov (United States)

    Woutersen, Marjolijn; Belkin, Shimshon; Brouwer, Bram; van Wezel, Annemarie P; Heringa, Minne B

    2011-05-01

    Biosensors based on luminescent bacteria may be valuable tools to monitor the chemical quality and safety of surface and drinking water. In this review, an overview is presented of the recombinant strains available that harbour the bacterial luciferase genes luxCDABE, and which may be used in an online biosensor for water quality monitoring. Many bacterial strains have been described for the detection of a broad range of toxicity parameters, including DNA damage, protein damage, membrane damage, oxidative stress, organic pollutants, and heavy metals. Most lux strains have sensitivities with detection limits ranging from milligrams per litre to micrograms per litre, usually with higher sensitivities in compound-specific strains. Although the sensitivity of lux strains can be enhanced by various molecular manipulations, most reported detection thresholds are still too high to detect levels of individual contaminants as they occur nowadays in European drinking waters. However, lux strains sensing specific toxic effects have the advantage of being able to respond to mixtures of contaminants inducing the same effect, and thus could be used as a sensor for the sum effect, including the effect of compounds that are as yet not identified by chemical analysis. An evaluation of the suitability of lux strains for monitoring surface and drinking water is therefore provided.

  9. Reference genes for quantitative gene expression studies in multiple avian species.

    Directory of Open Access Journals (Sweden)

    Philipp Olias

    Full Text Available Quantitative real-time PCR (qPCR rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ on different tissues of the mallard (Anas platyrhynchos, domestic chicken (Gallus gallus domesticus, common crane (Grus grus, white-tailed eagle (Haliaeetus albicilla, domestic turkey (Meleagris gallopavo f. domestica, cockatiel (Nymphicus hollandicus, Humboldt penguin (Sphenicus humboldti, ostrich (Struthio camelus and zebra finch (Taeniopygia guttata, spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

  10. Reference genes for quantitative gene expression studies in multiple avian species.

    Science.gov (United States)

    Olias, Philipp; Adam, Iris; Meyer, Anne; Scharff, Constance; Gruber, Achim D

    2014-01-01

    Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ) on different tissues of the mallard (Anas platyrhynchos), domestic chicken (Gallus gallus domesticus), common crane (Grus grus), white-tailed eagle (Haliaeetus albicilla), domestic turkey (Meleagris gallopavo f. domestica), cockatiel (Nymphicus hollandicus), Humboldt penguin (Sphenicus humboldti), ostrich (Struthio camelus) and zebra finch (Taeniopygia guttata), spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ) that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

  11. Minnesota Pheasant Range

    Data.gov (United States)

    Minnesota Department of Natural Resources — This dataset delineates the spatial range of wild pheasant populations in Minnesota as of 2002 by dividing the MN state boundary into 2 units: pheasant range and...

  12. Towards optimal range medians

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Gfeller, Beat; Jørgensen, Allan Grønlund

    2011-01-01

    that in the cell-probe model, any data structure which supports updates in O(logO(1)n) time must have Ω(log n/loglog n) query time. Our approach naturally generalizes to higher-dimensional range median problems, where element positions and query ranges are multidimensional - it reduces a range median query...... to a logarithmic number of range counting queries....

  13. Aplicación del análisis de rango reescalado R/S para la predicción de genes en el genoma vegetal Rescaled range R/S analysis application for genes prediction in the plant genome

    Directory of Open Access Journals (Sweden)

    Martha Isabel Almanza Pinzón

    2010-10-01

    alcanzaron promedios de sensibilidad y especificidad mayor del 81% y 70%, respectivamente. Este procedimiento podría ser probado en otros genomas y utilizado como criterio para incrementar la eficiencia de la selección en los programas de mejoramiento genético vegetal.Currently gene's prediction problem is one of the main genomic challenges. Prediction allows performing experiments with high probability of interesting genes to be found and compare DNA regions of agronomic importance among genomes; besides, it helps to restrict the searching spaces into the data bases. A statistical procedure based on the R/S analysis and the Hurst coefficient was developed in order to characterize and predict genes and their structural components (exones and intrones in the whole eukaryotic genomes of Arabidopsis thaliana, Oriza sativa and Mus musculus. Python programming language algorithms were developed with the purpose of extract, screen and modeling more than 80% of the registered gene sequences for these genomes in the NCBI Gene Bank data base. The R/S analysis allows to demonstrate that a structural order do exist in the distribution of the nucleotides which are constituting sequences with the memory or long range dependence phenomena predominance. The memory structure varies according to the sequences type and the species genome. The genes and exones sequences from the analyzed plant genomes showed a persistent behavior whereas those from the intrones had an anti-persistent behavior, in comparison with animal genome in which the three type of sequences showed persistent behavior. According to R/S analysis out coming parameters the genome sequences distribution pattern was replicated in a statistically similar manner in each chromosome belonging to one species, constituting fundamental evidences of invariance by scale change; it means each chromosome by itself is a statistical replication to a minor scale of the whole genome. The parameters constituted compact criteria in order to

  14. Tau ranging revisited

    Science.gov (United States)

    Tausworthe, R. C.

    1987-01-01

    It is shown that a ranging receiver with a sufficient and reasonable number of correlators is competitive with the current sequential component ranging system by some 1.5 to 2.5 dB. The optimum transmitter code, the optimum receiver, and a near-maximum-lilelihood range-estimation algorithm are presented.

  15. Investigation into the suitability of capillary tubes for microcrystalline testing.

    Science.gov (United States)

    Elie, Leonie E; Baron, Mark G; Croxton, Ruth S; Elie, Mathieu P

    2013-07-01

    A comparison between microcrystalline tests performed on microscope slides and flat capillary tubes with inner diameters ranging from 0.1 to 0.7 mm was carried out to explore the appropriateness of tubes for rapid testing of suspected drugs of abuse in the laboratory as well as in the field. Tests for mephedrone, cocaine, and phencyclidine were chosen as examples to investigate the handling of the capillary tubes, the influence on crystal habit, size, and the effects on the limit of detection. Image stacking software was used to increase the depth of field of micrographs taken from developed microcrystals greatly enhancing the interpretability even months after carrying out the microcrystalline test. Additionally, the potential of seeding capillary tubes with a reagent was studied. Pre-treatment of tubes would allow microcrystalline tests to be carried out quicker and anywhere without the necessity of taking along expensive and hazardous reagents. The sealing of capillary tubes containing developed microcrystalline tests in order to preserve results for a long period of time was successfully done by applying paraffin wax to the open ends. Finally, it was concluded that capillary tubes are suitable vessels for performing microcrystalline tests. The increased portability of the improved set-up allows tests to be safely executed outside laboratories without impairing the quality of the result. Findings were applied to six legal high samples purchased online between May and August 2011. The active ingredients like MDAI as well as cutting agents like caffeine were successfully identified using the microcrystalline test technique in capillary tubes.

  16. Performance of wastewater treatment plants in Jordan and suitability ...

    African Journals Online (AJOL)

    Performance of wastewater treatment plants in Jordan and suitability for reuse. ... for restricted use. Before reuse, effluent wastewater needs advanced treatment to prevent its impact on human health and the environment. ... Article Metrics.

  17. Site Suitability For Yam, Rice And Cotton Production In Adamawa ...

    African Journals Online (AJOL)

    Site Suitability For Yam, Rice And Cotton Production In Adamawa State Of Nigeria: A Geographic Information System (GIS) ... FUTY Journal of the Environment ... This paper demonstrated the potentials of GIS technique for mapping and ...

  18. Evaluation of the Reclamation Suitability of Industrial and Mining Wasteland

    Institute of Scientific and Technical Information of China (English)

    Gengjie; ZHANG; Zhongke; BAI

    2013-01-01

    To evaluate the reclamation suitability of industrial and mining wasteland is the premise of reclamation. The wasteland was firstly categorized according to land use status and damage types. Then the evaluation process of reclamation suitability was introduced, which involves two steps, the first step was to exclude those unsuitable wasteland by the limits conditions, while the second step was to evaluate the suitability degree of those suitable wasteland. From the perspectives of soil fertility, soil pollution, farmland water conservancy and land damage, twelve evaluation factors, including soil depth, gravel content, bulk density, organic material content, pollution index, gradient, flatness, irrigation and drainage condition, source of borrowed earth, distance from the residential settlement, erosion modulus and damage extent, were selected to establish an index system for evaluating the abandoned industrial and mining land, aiming to provide references for the future reclamation of industrial and mining wasteland.

  19. Hearing aid user guides: suitability for older adults.

    Science.gov (United States)

    Caposecco, Andrea; Hickson, Louise; Meyer, Carly

    2014-02-01

    The aim of this study was to analyse the content, design, and readability of printed hearing aid user guides to determine their suitability for older adults, who are the main users of hearing aids. Hearing aid user guides were assessed using four readability formulae and a standardized tool to assess content and design (SAM - Suitability Assessment of Materials). A sample of 36 hearing aid user guides (four user guides from nine different hearing aid manufacturers) were analysed. Sixty nine percent of user guides were rated 'not suitable' and 31% were rated 'adequate' for their suitability. Many scored poorly for scope, vocabulary, aspects of layout and typography, and learning stimulation and motivation. The mean reading grade level for all user guides was grade 9.6 which is too high for older adults. The content, design, and readability of hearing aid user guides are not optimal for older adults and thus may serve as a barrier to successful hearing aid outcomes for this population.

  20. High Dynamic Range Video

    CERN Document Server

    Myszkowski, Karol

    2008-01-01

    This book presents a complete pipeline forHDR image and video processing fromacquisition, through compression and quality evaluation, to display. At the HDR image and video acquisition stage specialized HDR sensors or multi-exposure techniques suitable for traditional cameras are discussed. Then, we present a practical solution for pixel values calibration in terms of photometric or radiometric quantities, which are required in some technically oriented applications. Also, we cover the problem of efficient image and video compression and encoding either for storage or transmission purposes, in

  1. Open space suitability analysis for emergency shelter after an earthquake

    Directory of Open Access Journals (Sweden)

    J. Anhorn

    2014-06-01

    Full Text Available In an emergency situation shelter space is crucial for people affected by natural hazards. Emergency planners in disaster relief and mass care can greatly benefit from a sound methodology that identifies suitable shelter areas and sites where shelter services need to be improved. A methodology to rank suitability of open spaces for contingency planning and placement of shelter in the immediate aftermath of a disaster is introduced. The Open Space Suitability Index (OSSI uses the combination of two different measures: a qualitative evaluation criterion for the suitability and manageability of open spaces to be used as shelter sites, and a second quantitative criterion using a capacitated accessibility analysis based on network analysis. For the qualitative assessment, implementation issues, environmental considerations, and basic utility supply are the main categories to rank candidate shelter sites. Geographic Information System (GIS is used to reveal spatial patterns of shelter demand. Advantages and limitations of this method are discussed on the basis of a case study in Kathmandu Metropolitan City (KMC. According to the results, out of 410 open spaces under investigation, 12.2% have to be considered not suitable (Category D and E while 10.7% are Category A and 17.6% are Category B. Almost two third (59.5% are fairly suitable (Category C.

  2. [Research on distribution and quality suitability division of Desmodium styracifolium].

    Science.gov (United States)

    Li, Dan; Tang, Xiao-Min; Zhu, Shou-Dong; Yang, Quan; Cheng, Xuan-Xuan; Zhang, Chun-Rong; Pan, Li-Ming; Chen, Duan-Ni

    2017-02-01

    The research on distribution and quality suitability division of Desmodium styracifolium were formulated by Maxent and ArcGIS model based on the content of schaftoside and polysaccharide of D. styracifolium and its field research in the south and southwest areas of China (Guangdong, Guangxi, Hainan and Yunnan), and the most suitable habitats of distribution suitability and quality suitability were screened. The distribution suitability results indicated that average air temperature in April,mean temperature of coldest quarter, soil type, coldness index were found as the four dominant factors contributing to the plant distribution. The quality suitability results indicated that: ①Polysaccharide content and precipitation in April show significant positive correlation;Schaftoside content and mean temperature of April, mean temperature of coldest quarter show significant negative correlation. Schaftoside content shows significant negative correlation with the precipitation in October and November and the sunshine duration in April and May, while there is a significant positive correlation between schaftoside content and precipitation in April and temperature seasonality standard deviation, and a highly significant positive correlation was found between schaftoside content and precipitation in February and March. ②The quality zoning map was drawn depend on general content of polysaccharide and schaftoside as the index of quality. And this research provides scientific location basis for the production regionalization, cultivation bases selection and directive breeding of D. styracifolium. Copyright© by the Chinese Pharmaceutical Association.

  3. Substring Range Reporting

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2011-01-01

    We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results. – We give efficient reductions for each of the above problems...... to a new problem, which we call substring range reporting. Hence, we unify the previous work by showing that we may restrict our attention to a single problem rather than studying each of the above problems individually. – We show how to solve substring range reporting with optimal query time and little...... range reporting are based on a novel combination of suffix trees and range reporting data structures. The reductions are simple and general and may apply to other combinations of string indexing with range reporting....

  4. Central Makran Range, Pakistan

    Science.gov (United States)

    1981-01-01

    A spectacular view of the Makran Range of Pakistan (27.0N, 65.5E) looking north with the Arabian Sea and the city of Karachi in the foreground. In the center, the Indian sub-continent moving slowly north into the Asian continent has caused the folded sedimentary Makran Range to bend from east-west to north-south as well as the uplift forming The Great Himalaya Range and the high Tibetan Plateau to the north.

  5. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Directory of Open Access Journals (Sweden)

    Orien M W Richmond

    Full Text Available Species distribution models (SDMs are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of

  6. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Science.gov (United States)

    Richmond, Orien M W; McEntee, Jay P; Hijmans, Robert J; Brashares, Justin S

    2010-09-22

    Species distribution models (SDMs) are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion) was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of organisms in response

  7. Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions

    OpenAIRE

    DIANESE, E. de C.; Fonseca, M.E.N.; Goldbach, R W; Kormelink, R.J.M.; Inoue-Nagata, A.K.; Resende, MR; BOITEUX, L. S.

    2010-01-01

    The best levels of broad-spectrum Tospovirus resistance reported in tomatoes thus far are conferred by the Sw-5 locus. This locus contains at least five paralogues (denoted Sw-5a through Sw-5e), of which Sw-5b represents the actual resistance gene. Here we evaluated a panel of seven PCR primer pairs matching different sequences within a genomic region spanning the Sw-5a and Sw-5b gene cluster. Primer efficiency evaluation was done employing tomato isolines with and without the Sw-5 locus. One...

  8. 适于烟草脆裂病毒诱导的本氏烟基因沉默分析的对照载体构建%Establishment of a suitable control vector for Tobacco rattle virus-induced gene silencing analysis in Nicotiana benthamiana

    Institute of Scientific and Technical Information of China (English)

    程维舜; 徐秋芳; 黎飞; 徐幼平; 蔡新忠

    2012-01-01

    Effects of the empty pYL156 vector (pYL156∶∶00),the most commonly used control vector for Tobacco rattle virus (TRV)-induced gene silencing analysis on viral symptom development and growth of VIGS-treated tomato and Nicotiana benthamiana plants were investigated.It was shown that VIGS-treatment for pYL156∶∶00 caused severe systemic viral symptoms and obvious growth repression in treated plants.Therefore,pYL156∶∶00 is not a good control vector for TRV-induced gene silencing analysis in these plant species. To set a better control for this analysis, two new constructs,pYL156∶∶NIRi and pYL156∶∶eGFP,were made.They were released by inserting a 253 bp fragment of a Phaseolus vulgaris nitrite reductase gene intron and a 400 bp fragment of the jellyfish GFP coding sequence in pYL156∶∶00,respectively.Effects of the two new control constructs on viral symptom development and growth of VIGS-treated N.benthamiana plants were compared with pYL156∶∶00.The results showed that VIGS-treatment for pYL156∶∶00 caused severe systemic viral symptoms and significant growth repression in treated plants,resulting in death of 26.7% plants.VIGS-treatment for pYL156∶∶NIRi also led to obvious viral symptoms and growth repression,but in a less severe extent than that for pYL156∶∶00, resulting in death of 13.3% plants. However, VIGS-treatment for pYL156∶∶eGFP did not cause any obvious viral symptom and growth repression. Severity of viral symptom and growth repression was well correlated with the accumulation level of TRV virus.These results demonstrate that pYL156∶∶eGFP is an excellent control vector for TRV-induced gene silencing analysis,and provide some insights into the direction to establish an excellent control for VIGS analysis.%对烟草脆裂病毒(Tobacco rattle virus,TRV)诱导的基因沉默分析体系中目前最常用的对照载体——空pYL156载体(pYL156∶∶00)对沉默处理后番茄和本氏烟(Nicotiana benthamiana)

  9. Compact Antenna Range

    Data.gov (United States)

    Federal Laboratory Consortium — Facility consists of a folded compact antenna range including a computer controlled three axis position table, parabolic reflector and RF sources for the measurement...

  10. Laser Range Sensors

    Directory of Open Access Journals (Sweden)

    K.C. Bahuguna

    2007-11-01

    Full Text Available This paper presents the design aspects of laser range finders and proximity sensors being developed at IRDE for different applications. The principle used in most of the laser range finders is pulse echo or time-of-flight measurement. Optical triangulation is used in proximity sensors while techniques like phase detection and interferometry are employed in instruments for surveying and motion controllers where high accuracy is desired. Most of the laser range finders are designed for ranging non-cooperative targets.

  11. Dryden Aeronautical Test Range

    Data.gov (United States)

    Federal Laboratory Consortium — Recently redesignated to honor Dr. Hugh L. Dryden, NASA's Dryden Aeronautical Test Range (DATR) supports aerospace flight research and technology integration, space...

  12. Compact Antenna Range

    Data.gov (United States)

    Federal Laboratory Consortium — Facility consists of a folded compact antenna range including a computer controlled three axis position table, parabolic reflector and RF sources for the measurement...

  13. Modelling agricultural suitability along soil transects under current conditions and improved scenario of soil factors

    Science.gov (United States)

    Abd-Elmabod, Sameh K.; Jordán, Antonio; Fleskens, Luuk; van der Ploeg, Martine; Muñoz-Rojas, Miriam; Anaya-Romero, María; van der Salm, Renée J.; De la Rosa, Diego

    2015-04-01

    Agricultural land suitability analysis and improvement of soils by addressing major limitations may be a strategy for climate change adaptation. This study aims to investigate the influence of topography and variability of soil factors on the suitability of 12 annual, semiannual and perennial Mediterranean crops in the province of Seville (southern Spain). In order to represent the variability in elevation, lithology and soil, two latitudinal and longitudinal (S-N and W-E) soil transects (TA and TB) were considered including 63 representative points at regular 4 km intervals. These points were represented by 41 soil profiles from the SDBm soil database -Seville. Almagra model, a component of the agro-ecological decision support system MicroLEIS, was used to assess soil suitability. Results were grouped into five soil suitability classes: S1-optimum, S2-high, S3-moderate, S4-marginal and S5-not suitable. Each class was divided in subclasses according to the main soil limiting factors: depth (p), texture (t), drainage (d), carbonate content (c), salinity (s), sodium saturation (a), and the degree of development of the soil profile (g). This research also aimed to maximize soil potential by improving limiting factors d, c, s and a after soil restoration. Therefore, management techniques were also considered as possible scenarios in this study. The results of the evaluation showed that soil suitability ranged between S1 and S5p - S5s along of the transects. In the northern extreme of transect TA, high content of gravels and coarse texture are limiting factors (soils are classified as S4t) In contrast, the limiting factor in the eastern extreme of transect TB is the shallow useful depth (S5p subclass). The absence of calcium carbonate becomes a limiting factor in some parts of TA. In contrast, the excessive content of calcium carbonate appeared to be a limiting factor for crops in some intermediate points of TB transect. For both transects, soil salinity is the main

  14. Mapping the potential ranges of major plant invaders in South Africa, Lesotho and Swaziland using climatic suitability

    CSIR Research Space (South Africa)

    Rouget, M

    2004-09-01

    Full Text Available programmes for managing plant invasions in the world. There is, however, no protocol for assessing the likely future spread patterns needed to inform medium- to long-term planning. This paper presents an assessment of the climatic correlates of distribution...

  15. Current progress of polymeric gene vectors

    Institute of Scientific and Technical Information of China (English)

    ZENG Xuan; SUN YunXia; ZHUO RenXi; ZHANG XianZheng

    2011-01-01

    After over 40 years ot progress,gene therapy provides great opportunities for treating diseases from various genetic disorders,infections and cancers.The success of gene therapy largely depends on the availability of suitable gene vectors.As an attractive alternative to virus-based gene therapy,non-viral gene delivery system has been developed and investigated due to their merits including low immunogenecity,convenient operability,and large-scale manufacturability [1].Because polycations can condense with DNA as a result of electrostatic interactions,form nanosize polyplexes,and protect DNA from degradation by DNase,cationic polymer becomes a major type of non-viral gene delivery vectors (Figure 1) [2].A wide range of polymeric vectors have been developed and investigated in the past decade,such as polyethylenimine (PEI)-based vectors,poly(L-lysine) (PLL)-based vectors,dendrimer-based vectors,polypeptide-based vectors,and chitosan-based vectors [3].However,unlike viral vectors that have the ability to infect host cells and overcome cellular barriers through the course of evolution,nonviral gene vectors exhibit Significantly reduced transfection efficiency as they are obstructed by various extra- and intracellular barriers,including serum proteins in blood stream,cell membrane,endosomal compartment and nuclear membrane [4].

  16. Which GHG emission balancing approach is most suitable for cities and regions?

    OpenAIRE

    Trappers, Leen; Versele, Alexis

    2012-01-01

    This paper aims to provide insight on the main GHG balancing principles by analysing both existing guidelines and particular cases. We will explore the main causes and effects of methodological discrepancies by comparing a range of procedural aspects. The main focus lies on the findings from three Belgian GHG inventories, notably those of the cities of Ghent and Seraing and the province of Limburg. By assembling information on suitable GHG accounting principles and calculation methodologies, ...

  17. Modelling Fish Habitat Suitability in the Eastern English Channel. Application to community habitat level

    OpenAIRE

    Vaz, Sandrine; Carpentier, Andre; Loots, Christophe; Koubbi, Philippe

    2004-01-01

    Valuable marine habitats and living resources can be found in the Eastern English Channel and in 2003, a Franco-British Interreg IIIA project, ‘Eastern Channel Habitat Atlas for Marine Resource Management’ (CHARM), was initiated to support decision-making for management of essential fish habitats. Fish habitat corresponds to geographic areas within which ranges of environmental factors define the presence of a particular species. Habitat Suitability index (HSI) modelling was used to relate fi...

  18. Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions

    NARCIS (Netherlands)

    Dianese, E.C.; Fonseca, M.E.N.; Goldbach, R.W.; Kormelink, R.J.M.; Inoue-Nagata, A.K.; Resende, de R.O.; Boiteux, L.S.

    2010-01-01

    The best levels of broad-spectrum Tospovirus resistance reported in tomatoes thus far are conferred by the Sw-5 locus. This locus contains at least five paralogues (denoted Sw-5a through Sw-5e), of which Sw-5b represents the actual resistance gene. Here we evaluated a panel of seven PCR primer pairs

  19. On Range of Skill

    DEFF Research Database (Denmark)

    Hansen, Thomas Dueholm; Miltersen, Peter Bro; Sørensen, Troels Bjerre

    2008-01-01

    size (and doubly exponential in its depth). We also provide techniques that yield concrete bounds for unbalanced game trees and apply these to estimate the Range of Skill of Tic-Tac-Toe and Heads-Up Limit Texas Hold'em Poker. In particular, we show that the Range of Skill of Tic-Tac-Toe is more than...

  20. Substring Range Reporting

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2011-01-01

    to a new problem, which we call substring range reporting. Hence, we unify the previous work by showing that we may restrict our attention to a single problem rather than studying each of the above problems individually. – We show how to solve substring range reporting with optimal query time and little...

  1. Range Selection and Median

    DEFF Research Database (Denmark)

    Jørgensen, Allan Grønlund; Larsen, Kasper Green

    2011-01-01

    Range selection is the problem of preprocessing an input array A of n unique integers, such that given a query (i; j; k), one can report the k'th smallest integer in the subarray A[i];A[i+1]; : : : ;A[j]. In this paper we consider static data structures in the word-RAM for range selection and sev...

  2. Home range and travels

    Science.gov (United States)

    Stickel, L.F.; King, John A.

    1968-01-01

    The concept of home range was expressed by Seton (1909) in the term 'home region,' which Burr (1940, 1943) clarified with a definition of home range and exemplified in a definitive study of Peromyscus in the field. Burt pointed out the ever-changing characteristics of home-range area and the consequent absence of boundaries in the usual sense--a finding verified by investigators thereafter. In the studies summarized in this paper, sizes of home ranges of Peromyscus varied within two magnitudes, approximately from 0.1 acre to ten acres, in 34 studies conducted in a variety of habitats from the seaside dunes of Florida to the Alaskan forests. Variation in sizes of home ranges was correlated with both environmental and physiological factors; with habitat it was conspicuous, both in the same and different regions. Food supply also was related to size of home range, both seasonally and in relation to habitat. Home ranges generally were smallest in winter and largest in spring, at the onset of the breeding season. Activity and size also were affected by changes in weather. Activity was least when temperatures were low and nights were bright. Effects of rainfall were variable. Sizes varied according to sex and age; young mice remained in the parents' range until they approached maturity, when they began to travel more widely. Adult males commonly had larger home ranges than females, although there were a number of exceptions. An inverse relationship between population density and size of home range was shown in several studies and probably is the usual relationship. A basic need for activity and exploration also appeared to influence size of home range. Behavior within the home range was discussed in terms of travel patterns, travels in relation to home sites and refuges, territory, and stability of size of home range. Travels within the home range consisted of repeated use of well-worn trails to sites of food, shelter, and refuge, plus more random exploratory travels

  3. Separation of the bioclimatic spaces of Himalayan tree rhododendron species predicted by ensemble suitability models

    Directory of Open Access Journals (Sweden)

    Sailesh Ranjitkar

    2014-08-01

    Full Text Available The tree rhododendrons include the most widely distributed Himalayan Rhododendron species belonging to the subsection Arborea. Distributions of two members of this sub-species were modelled using bioclimatic data for current conditions (1950–2000. A subset of the least correlated bioclimatic variables was used for ecological niche modelling (ENM. We used an ENM ensemble method in the BiodiversityR R-package to map the suitable climatic space for tree rhododendrons based on 217 point location records. Ensemble bioclimatic models for tree rhododendrons had high predictive power with bioclimatic variables, which also separated the climatic spaces for the two species. Tree rhododendrons were found occurring in a wide range of climate and the distributional limits were associated with isothermality, temperature ranges, temperature of the wettest quarter, and precipitation of the warmest quarter of the year. The most suitable climatic space for tree rhododendrons was predicted to be in western Yunnan, China, with suitability declining towards the west and east. Its occurrence in a wide range of climatic settings with highly dissected habitats speaks to the adaptive capacity of the species, which might open up future options for their conservation planning in regions where they are listed as threatened.

  4. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe.

    Science.gov (United States)

    Martin, Julien; Chamaillé-Jammes, Simon; Nichols, James D; Fritz, Hervé; Hines, James E; Fonnesbeck, Christopher J; MacKenzie, Darryl I; Bailey, Larissa L

    2010-06-01

    The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat-occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological

  5. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe

    Science.gov (United States)

    Martin, Julien; Chamaille-Jammes, Simon; Nichols, James D.; Fritz, Herve; Hines, James E.; Fonnesbeck, Christopher J.; MacKenzie, Darryl I.; Bailey, Larissa L.

    2010-01-01

    The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat–occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological

  6. Land Suitability Assessment for Sugarcane in "Herois de Caxito" (Angola

    Directory of Open Access Journals (Sweden)

    Baert, G.

    2005-01-01

    Full Text Available The suitability of the soils surrounding the sugarcane plantation at "Herois de Caxito" (7068 ha is assessed. The main goal is to identify land suitability for the enlargement of the present plantation, using FAO land evaluation models (modified to suit Herois de Caxito conditions and GIS. Calculations of the radiationthermal production potential (RPP, land production potential (LPP, irrigation suitability index, and evaluation of the irrigation water quality are done. The water-limited production potential (WPP is found equal to the RPP, because water needs were fully met under irrigation. Maps showing the spatial distribution of the LPP and the suitability for irrigation are generated. The matching of irrigation and fertility indices has shown that, about 40% of the soils with good fertility for sugarcane production present low suitability for irrigation, the main limitations being the very fine texture and the drainage. The available surface water at Herois de Caxito (Dande river is of very good quality for irrigation of sugarcane.

  7. Printed health information materials: evaluation of readability and suitability.

    Science.gov (United States)

    Shieh, Carol; Hosei, Barbara

    2008-01-01

    This study examined readability and suitability of printed health information materials colleted from multiple sources. In phase I, nursing students used Simple Measure of Gobbledygook (SMOG; McLaughlin, 1969) to assess the readability of 21 materials collected from the community. In phases II and III, nursing students and registered nurses used SMOG and the Suitability Assessment of Materials (SAM; Doak, Doak, & Root, 1996) to evaluate 15 prenatal materials from a Healthy Start program. SMOG assigns a reading grade level based on the number of words with 3 or more syllables. SAM has 22 items in 6 evaluation areas: content, literacy demand, graphics, layout and typography, learning stimulation and motivation, and cultural appropriateness. Major findings included that 53% to 86% of the printed materials had a reading level at or higher than 9th grade; materials lacked summary, interaction, and modeled behaviors, and registered nurses rated more materials as not suitable and fewer as superior for suitability qualities than students. Improving printed materials to have lower reading levels and better suitability qualities are indicated.

  8. Genes V.

    Energy Technology Data Exchange (ETDEWEB)

    Lewin, B.

    1994-12-31

    This fifth edition book encompasses a wide range of topics covering 1,272 pages. The book is arranged into nine parts with a total of 36 chapters. These nine parts include Introduction; DNA as a Store of Information; Translation; Constructing Cells; Control of Prokaryotypic Gene Expression; Perpetuation of DNA; Organization of the Eukaryotypic Genome; Eukaryotypic Transcription and RNA Processing; The Dynamic Genome; and Genes in Development.

  9. Inversion of spheroid particle size distribution in wider size range and aspect ratio range

    Directory of Open Access Journals (Sweden)

    Tang Hong

    2013-01-01

    Full Text Available The non-spherical particle sizing is very important in the aerosol science, and it can be determined by the light extinction measurement. This paper studies the effect of relationship of the size range and aspect ratio range on the inversion of spheroid particle size distribution by the dependent mode algorithm. The T matrix method and the geometric optics approximation method are used to calculate the extinction efficiency of the spheroids with different size range and aspect ratio range, and the inversion of spheroid particle size distribution in these different ranges is conducted. Numerical simulation indicates that a fairly reasonable representation of the spheroid particle size distribution can be obtained when the size range and aspect ratio range are suitably chosen.

  10. From Points to Forecasts: Predicting Invasive Species Habitat Suitability in the Near Term

    Directory of Open Access Journals (Sweden)

    Tracy R. Holcombe

    2010-05-01

    Full Text Available We used near-term climate scenarios for the continental United States, to model 12 invasive plants species. We created three potential habitat suitability models for each species using maximum entropy modeling: (1 current; (2 2020; and (3 2035. Area under the curve values for the models ranged from 0.92 to 0.70, with 10 of the 12 being above 0.83 suggesting strong and predictable species-environment matching. Change in area between the current potential habitat and 2035 ranged from a potential habitat loss of about 217,000 km2, to a potential habitat gain of about 133,000 km2.

  11. Introgression of Bt Genes in Novel Germplasm and Contribution to Indian Cotton Economy

    Institute of Scientific and Technical Information of China (English)

    VIDYASAGAR Parchuri

    2008-01-01

    @@ Emergence of transgenic Bt-cotton technology has opened up a new chapter in Indian cotton production in 21st century.The crylAc gene of Monsanto derived from American Upland Coker-312 background was not directly suitable for varied cotton growing situations in India.Delivery of Bt-gene technology to Indian farming systems should be superimposed on hybrid technology,fiber quality,and superior agronomic adaptation.Protection offered by this alien Bt-gene against major serious pest Helicoverpa armigera,by preventing annual losses ranging from 15~35 percent,automaticaly contributed to higher yield.

  12. Atlantic Test Range (ATR)

    Data.gov (United States)

    Federal Laboratory Consortium — ATR controls fully-instrumented and integrated test ranges that provide full-service support for cradle-to-grave testing. Airspace and surface target areas are used...

  13. Light Detection And Ranging

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — LiDAR (Light Detection and Ranging) discrete-return point cloud data are available in the American Society for Photogrammetry and Remote Sensing (ASPRS) LAS format....

  14. Range_Extent_15

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The GIS layer "Range_extent_15" is a simple polyline representing the geographic distribution of the southern sea otter (Enhydra lutris nereis) in mainland...

  15. On Range of Skill

    DEFF Research Database (Denmark)

    Hansen, Thomas Dueholm; Miltersen, Peter Bro; Sørensen, Troels Bjerre

    2008-01-01

    is a small number, but only gave heuristic arguments for this. In this paper, we provide the first methods for rigorously estimating the Range of Skill of a given game. We provide some general, asymptotic bounds that imply that the Range of Skill of a perfectly balanced game tree is almost exponential in its...... size (and doubly exponential in its depth). We also provide techniques that yield concrete bounds for unbalanced game trees and apply these to estimate the Range of Skill of Tic-Tac-Toe and Heads-Up Limit Texas Hold'em Poker. In particular, we show that the Range of Skill of Tic-Tac-Toe is more than...

  16. Correlation radio range finder

    Directory of Open Access Journals (Sweden)

    A. Sorochan

    2012-10-01

    Full Text Available In work widely known methods of range measuring are short characterized. The basic attention is given features of signal processing in a correlation method of range measuring. The signal with angular modulation with one-voice-frequency fluctuation is used as a probing signal. The absence of Doppler effect on the formation of the correlation integral, the frequency instability of the transmitter, the phase change on reflection from the target is presented. It is noticed that the result of signal processing in the range measuring instrument is reduced to formation on an exit one-voice-frequency harmonious fluctuation equal to modulating frequency that provides high characteristics of a radio range finder.

  17. Antenna Pattern Range (APR)

    Data.gov (United States)

    Federal Laboratory Consortium — TheAntenna Pattern Range (APR)features a non-metallic arch with a trolley to move the transmit antenna from the horizon to zenith. At the center of the ground plane,...

  18. Light Detection And Ranging

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — LiDAR (Light Detection and Ranging) discrete-return point cloud data are available in the American Society for Photogrammetry and Remote Sensing (ASPRS) LAS format....

  19. Substring Range Reporting

    OpenAIRE

    Bille, Philip; Gørtz, Inge Li

    2011-01-01

    We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results. {itemize} We give efficient reductions for each of the above problems to a new problem, which we call \\emph{substring range reporting}. Hence, we unify the previous work by showing that we may restrict our attention to a single problem rather than studying each of...

  20. Substring Range Reporting

    OpenAIRE

    Bille, Philip; Gørtz, Inge Li

    2011-01-01

    We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results. {itemize} We give efficient reductions for each of the above problems to a new problem, which we call \\emph{substring range reporting}. Hence, we unify the previous work by showing that we may restrict our attention to a single problem rather than studying each of...

  1. Land suitability for waste disposal in metropolitan areas.

    Science.gov (United States)

    Baiocchi, Valerio; Lelo, Keti; Polettini, Alessandra; Pomi, Raffaella

    2014-08-01

    Site selection for waste disposal is a complex task that should meet the requirements of communities and stakeholders. In this article, three decision support methods (Boolean logic, index overlay and fuzzy gamma) are used to perform land suitability analysis for landfill siting. The study was carried out in one of the biggest metropolitan regions of Italy, with the objective of locating suitable areas for waste disposal. Physical and socio-economic information criteria for site selection were decided by a multidisciplinary group of experts, according to state-of-the-art guidelines, national legislation and local normative on waste management. The geographic information systems (GIS) based models used in this study are easy to apply but require adequate selection of criteria and weights and a careful evaluation of the results. The methodology is arranged in three steps, reflecting the criteria defined by national legislation on waste management: definition of factors that exclude location of landfills or waste treatment plants; classification of the remaining areas in terms of suitability for landfilling; and evaluation of suitable sites in relation to preferential siting factors (such as the presence of quarries or dismissed plants). The results showed that more than 80% of the provincial territory falls within constraint areas and the remaining territory is suitable for waste disposal for 0.72% or 1.93%, according to the model. The larger and most suitable sites are located in peripheral areas of the metropolitan system. The proposed approach represents a low-cost and expeditious alternative to support the spatial decision-making process.

  2. Climate Suitability for Stable Malaria Transmission in Zimbabwe Under Different Climate Change Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Ebi, K.L. [Exponent, Inc., 1800 Diagonal Road, Suite 300, Alexandria, VA, 22314 (United States); Hartman, J. [442 Amsterdam Avenue, Apartment 4-C, New York, NY, 10024 (United States); Chan, N. [Exponent, Inc., 149 Commonwealth Drive, Menlo Park, CA, 94025 (United States); Mcconnell, J. [Department of Emergency Medicine, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Mail Code CR114, Portland, OR, 97239 (United States); Schlesinger, M. [University of Illinois at Urbana-Champaign, 105 S. Gregory Street, Urbana, IL, 61801 (United States); Weyant, J. [Stanford University, Stanford, CA, 94305-4023 (United States)

    2005-12-01

    Climate is one factor that determines the potential range of malaria. As such, climate change may work with or against efforts to bring malaria under control. We developed a model of future climate suitability for stable Plasmodium falciparum malaria transmission in Zimbabwe. Current climate suitability for stable malaria transmission was based on the MARA/ARMA model of climatic constraints on the survival and development of the Anopheles vector and the Plasmodium falciparum malaria parasite. We explored potential future geographic distributions of malaria using 16 projections of climate in 2100. The results suggest that, assuming no future human-imposed constraints on malaria transmission, changes in temperature and precipitation could alter the geographic distribution of malaria in Zimbabwe, with previously unsuitable areas of dense human population becoming suitable for transmission. Among all scenarios, the highlands become more suitable for transmission, while the lowveld and areas with low precipitation show varying degrees of change, depending on climate sensitivity and greenhouse gas emission stabilization scenarios, and depending on the general circulation model used. The methods employed can be used within or across other African countries.

  3. Global decline in suitable habitat for Angiostrongylus ( = Parastrongylus) cantonensis: the role of climate change.

    Science.gov (United States)

    York, Emily M; Butler, Christopher J; Lord, Wayne D

    2014-01-01

    Climate change is implicated in the alteration of the ranges of species worldwide. Such shifts in species distributions may introduce parasites/pathogens, hosts, and vectors associated with disease to new areas. The parasite Angiostrongylus ( = Parastrongylus) cantonensis is an invasive species that causes eosinophilic meningitis in humans and neurological abnormalities in domestic/wild animals. Although native to southeastern Asia, A. cantonensis has now been reported from more than 30 countries worldwide. Given the health risks, it is important to describe areas with potentially favorable climate for the establishment of A. cantonensis, as well as areas where this pathogen might become established in the future. We used the program Maxent to develop an ecological niche model for A. cantonensis based on 86 localities obtained from published literature. We then modeled areas of potential A. cantonensis distribution as well as areas projected to have suitable climatic conditions under four Representative Concentration Pathways (RCP) scenarios by the 2050s and the 2070s. The best model contained three bioclimatic variables: mean diurnal temperature range, minimum temperature of coldest month and precipitation of warmest quarter. Potentially suitable habitat for A. cantonensis was located worldwide in tropical and subtropical regions. Under all climate change RCP scenarios, the center of the projected distribution shifted away from the equator at a rate of 68-152 km per decade. However, the extent of areas with highly suitable habitat (>50%) declined by 10.66-15.66% by the 2050s and 13.11-16.11% by the 2070s. These results conflict with previous studies, which have generally found that the prevalence of tropical pathogens will increase during the 21st century. Moreover, it is likely that A. cantonensis will continue to expand its current range in the near future due to introductions and host expansion, whereas climate change will reduce the total geographic area of

  4. A Dynamic Hashing Algorithm Suitable for Embedded System

    Directory of Open Access Journals (Sweden)

    Li Jianwei

    2013-06-01

    Full Text Available With the increasing of the data numbers, the linear hashing will be a lot of overflow blocks result from Data skew and the index size of extendible hash will surge so as to waste too much memory. This lead to the above two Typical Dynamic hashing algorithm don’t suitable for embedded system that need certain real-time requirements and memory resources are very scarce. To solve this problem, this paper was proposed a dynamic hashing algorithm suitable for embedded system combining with the characteristic of extendible hashing and linear hashing.it is no overflow buckets and the index size is proportional to the adjustment number.

  5. Proposal of an Algorithm to Synthesize Music Suitable for Dance

    Science.gov (United States)

    Morioka, Hirofumi; Nakatani, Mie; Nishida, Shogo

    This paper proposes an algorithm for synthesizing music suitable for emotions in moving pictures. Our goal is to support multi-media content creation; web page design, animation films and so on. Here we adopt a human dance as a moving picture to examine the availability of our method. Because we think the dance image has high affinity with music. This algorithm is composed of three modules. The first is the module for computing emotions from an input dance image, the second is for computing emotions from music in the database and the last is for selecting music suitable for input dance via an interface of emotion.

  6. [A suitable location for the placement of miniscrews].

    Science.gov (United States)

    Breuning, K H

    2014-02-01

    Miniscrews form a stable attachment point for anchoring during orthodontic treatment with fixed appliances. An additional advantage of this method of anchoring is that a set of teeth can be moved simultaneously, which means that the time required for treatment can be shortened considerably. Miniscrews can also be used for tooth movements that would otherwise be impossible. In selecting a suitable location for the placement of miniscrews, a number offactors play a role. On the basis of the findings reported in the literature on research, a miniscrew atlas has been developed which can serve as a guideline for the selection of a suitable location for the placement of miniscrews.

  7. Suitability for 3D Printed Parts for Laboratory Use

    Energy Technology Data Exchange (ETDEWEB)

    Zwicker, Andrew P. [PPPL; Bloom, Josh [PPPL; Albertson, Robert [PPPL; Gershman, Sophia [PPPL

    2014-08-01

    3D printing has become popular for a variety of users, from industrial to the home hobbyist, to scientists and engineers interested in producing their own laboratory equipment. In order to determine the suitability of 3D printed parts for our plasma physics laboratory, we measured the accuracy, strength, vacuum compatibility, and electrical properties of pieces printed in plastic. The flexibility of rapidly creating custom parts has led to the 3D printer becoming an invaluable resource in our laboratory and is equally suitable for producing equipment for advanced undergraduate laboratories.

  8. Studies of the Suitability of Fowlpox as Decontamination and Thermal Stability Simulant for Variola Major

    Science.gov (United States)

    2009-01-01

    a decontamination simulant. Inactivation kinetics studies showed that fowlpox behaved similarly to variola major when treated with 0.1% iodine and 5.7...benzalkonium chloride, but differed in its response to 0.05% iodine and 0.3% polyethyleneglycol nonylphenyl ether and 40% ethanol. Thermal inactivation...Another gene shows similar homology to a protein found in yeast, human, tomato and fruit fly. Secondly, the fowlpox genome contains host range genes

  9. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  10. Systematic ranging and late warning asteroid impacts

    CERN Document Server

    Farnocchia, D; Micheli, M

    2015-01-01

    We describe systematic ranging, an orbit determination technique especially suitable to assess the near-term Earth impact hazard posed by newly discovered asteroids. For these late warning cases, the time interval covered by the observations is generally short, perhaps a few hours or even less, which leads to severe degeneracies in the orbit estimation process. The systematic ranging approach gets around these degeneracies by performing a raster scan in the poorly-constrained space of topocentric range and range rate, while the plane of sky position and motion are directly tied to the recorded observations. This scan allows us to identify regions corresponding to collision solutions, as well as potential impact times and locations. From the probability distribution of the observation errors, we obtain a probability distribution in the orbital space and then estimate the probability of an Earth impact. We show how this technique is effective for a number of examples, including 2008 TC3 and 2014 AA, the only tw...

  11. Gene Therapy for the Treatment of Neurological Disorders: Metabolic Disorders.

    Science.gov (United States)

    Gessler, Dominic J; Gao, Guangping

    2016-01-01

    Metabolic disorders comprise a large group of heterogeneous diseases ranging from very prevalent diseases such as diabetes mellitus to rare genetic disorders like Canavan Disease. Whether either of these diseases is amendable by gene therapy depends to a large degree on the knowledge of their pathomechanism, availability of the therapeutic gene, vector selection, and availability of suitable animal models. In this book chapter, we review three metabolic disorders of the central nervous system (CNS; Canavan Disease, Niemann-Pick disease and Phenylketonuria) to give examples for primary and secondary metabolic disorders of the brain and the attempts that have been made to use adeno-associated virus (AAV) based gene therapy for treatment. Finally, we highlight commonalities and obstacles in the development of gene therapy for metabolic disorders of the CNS exemplified by those three diseases.

  12. Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution

    Directory of Open Access Journals (Sweden)

    E-Bin Gao

    2016-09-01

    Full Text Available Cyanophages, a group of viruses specifically infecting cyanobacteria, are genetically diverse and extensively abundant in water environments. As a result of selective pressure, cyanophages often acquire a range of metabolic genes from host genomes. The host-derived genes make a significant contribution to the ecological success of cyanophages. In this review, we summarize the host-derived metabolic genes, as well as their origin and roles in cyanophage evolution and important host metabolic pathways, such as the light-dependent reactions of photosynthesis, the pentose phosphate pathway, nutrient acquisition and nucleotide biosynthesis. We also discuss the suitability of the host-derived metabolic genes as potential diagnostic markers for the detection of genetic diversity of cyanophages in natural environments.

  13. Gene Therapy for the Treatment of Neurological Disorders: Metabolic Disorders

    Science.gov (United States)

    Gessler, Dominic J.; Gao, Guangping

    2016-01-01

    Metabolic disorders comprise a large group of heterogeneous diseases ranging from very prevalent diseases such as diabetes mellitus to rare genetic disorders like Canavan Disease. Whether either of these diseases is amendable by gene therapy depends to a large degree on the knowledge of their pathomechanism, availability of the therapeutic gene, vector selection, and availability of suitable animal models. In this book chapter, we review three metabolic disorders of the central nervous system (CNS; Canavan Disease, Niemann–Pick disease and Phenylketonuria) to give examples for primary and secondary metabolic disorders of the brain and the attempts that have been made to use adeno-associated virus (AAV) based gene therapy for treatment. Finally, we highlight commonalities and obstacles in the development of gene therapy for metabolic disorders of the CNS exemplified by those three diseases. PMID:26611604

  14. Range Information Propagation Transform

    Institute of Scientific and Technical Information of China (English)

    陈向荣; 朱志刚; 等

    1998-01-01

    A novel method of model-based object recognition is presented in this paper.Its novelty stems from the fact that the gray level image captured by a camera is merged with sparse range information in an active manner.By using a projective transform, which is determined by the sparse range data,festures(e.g.edge points)related to a single planar surface patch of figure in the scene can be assignew with their corresponding range values respectively.As a result,the shape of the very planar patch or figure can be recovered and various kinds of description in the Euclidean space can be calculated.Based on these descriptions values,the hypothesis about the identification of the object and its pose in space can be obtained with a high probability of success,and a high efficiency of hypothesis-verification process can be expected.Another advantage of this method is that the edge detection process can be navigated to the proper location hinted by the sparse range image.In consequence edge features can be extracted even in the regions with low contrast.In this paper the principle of range information propagation transform(RIPT)is explained,and some implementation issues,such as the algorithms using calibrated or uncalibrated gray level image for object recognition,are discussed.The preliminary experimental results are presented to indicate the effectiveness and efficiency of the proposed method.

  15. Range Selection and Median

    DEFF Research Database (Denmark)

    Jørgensen, Allan Grønlund; Larsen, Kasper Green

    2011-01-01

    and several natural special cases thereof. The rst special case is known as range median, which arises when k is xed to b(j 􀀀 i + 1)=2c. The second case, denoted prex selection, arises when i is xed to 0. Finally, we also consider the bounded rank prex selection problem and the xed rank range......Range selection is the problem of preprocessing an input array A of n unique integers, such that given a query (i; j; k), one can report the k'th smallest integer in the subarray A[i];A[i+1]; : : : ;A[j]. In this paper we consider static data structures in the word-RAM for range selection...... selection problem. In the former, data structures must support prex selection queries under the assumption that k for some value n given at construction time, while in the latter, data structures must support range selection queries where k is xed beforehand for all queries. We prove cell probe lower bounds...

  16. Reconfigurable laser ranging instrument

    Science.gov (United States)

    Schneiter, John

    1994-03-01

    This paper describes the design and operation of a fast, flexible, non-contact, eye-safe laser ranging instrument useful in a variety of industrial metrology situations, such as in-process machining control and part inspection. The system has variable computer-controlled standoff and depth of field, and can obtain 3-D images of surfaces within a range of from 1.5 ft to almost 10 ft from the final optical element. The minimum depth of field is about 3.5 in. at 1.5 ft and about 26 in. at the far range. The largest depth of field for which useful data are available is about 41 in. Resolution, with appropriate averaging, is about one part in 4000 of the depth of field, which implies a best case resolution for this prototype of 0.00075 in. System flexibility is achieved by computer controlled relative positioning of optical components.

  17. Substring Range Reporting

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2014-01-01

    We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results. We give efficient reductions for each of the above problems...... to a new problem, which we call substring range reporting. Hence, we unify the previous work by showing that we may restrict our attention to a single problem rather than studying each of the above problems individually. We show how to solve substring range reporting with optimal query time and little...... space. Combined with our reductions this leads to significantly improved time-space trade-offs for the above problems. In particular, for each problem we obtain the first solutions with optimal time query and O(nlog O(1) n) space, where n is the length of the indexed string. We show that our techniques...

  18. Selecting Suitable Sites for Wind Energy Development in Ghana*

    African Journals Online (AJOL)

    Michae O. Mensah

    2016-06-01

    Jun 1, 2016 ... Selecting Suitable Sites for Wind Energy Development in Ghana*. D. Sarpong, P. E. .... from observations and computer model-derived were also used for the .... such as forest and game reserves, tourist sites, etc. (iv) Siting in ...

  19. Regional technical innovation suitability and economic growth in China

    NARCIS (Netherlands)

    Zhou, Qing; Zhu, Dan; Ren, Liqin

    2012-01-01

    This paper aims to use quantitative method to analyse the suitability of regional technical innovation and further compare its influence to regional economic growth in China. Based on literature review, the authors develop an evaluation index system containing four aspects (namely, innovators, innov

  20. Site suitability criteria for solidified high level waste repositories

    Energy Technology Data Exchange (ETDEWEB)

    Heckman, R.A.; Holdsworth, T.; Towse, D.F.

    1979-03-07

    Activities devoted to development of regulations, criteria, and standards for storage of solidified high-level radioactive wastes are reported. The work is summarized in sections on site suitability regulations, risk calculations, geological models, aquifer models, human usage model, climatology model, and repository characteristics. Proposed additional analytical work is also summarized. (JRD)

  1. RESISTANCE OF COATED ELECTRODES SUITABLE FOR RENOVATION OF TILLAGE TOOLS

    OpenAIRE

    2013-01-01

    This article deals with the abrasive wear resistance of additional materials. The resistance of individual materials was figured out by determining a proportional wear resistance on a grinding fabric. Results of the experiment confirmed an increase in welds abrasive wear resistance. Chosen coated electrodes are suitable for the renovation of tillage tools of agricultural machines.

  2. Regional technical innovation suitability and economic growth in China

    NARCIS (Netherlands)

    Zhou, Qing; Zhu, Dan; Brouwers-Ren, Liqin

    2012-01-01

    This paper aims to use quantitative method to analyse the suitability of regional technical innovation and further compare its influence to regional economic growth in China. Based on literature review, the authors develop an evaluation index system containing four aspects (namely, innovators,

  3. Emotions and Young Offenders' Suitability for Victim-Offender Mediation.

    Science.gov (United States)

    Vieira, Tracey A.

    Although evidence indicates that Victim-Offender Mediation (VOM) provides an effective alternative to traditional sanctioning for young offenders, research investigating suitable candidates for VOM is lacking. Reintegrative shaming is theorized to be the mechanism underlying successful mediation; however, it is difficult to determine whether shame…

  4. 21 CFR 640.3 - Suitability of donor.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Suitability of donor. 640.3 Section 640.3 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS... determination shall be made on the day of collection from the donor by means of medical history, a test...

  5. Land suitability for establishing rainwater harvesting systems for fighting wildfires

    Science.gov (United States)

    José María León Villalobos; Manuel Anaya Garduño; Enrique Ojeda Trejo; Dante Arturo Rodríguez Trejo; José Luis Oropeza Mota; Jorge Luis García Rodríguez

    2013-01-01

    Rainwater harvesting systems (RHSs) can be used to improve the efficiency of helicopter firefighting operations. To this end, RHSs need to be strategically located in areas with high wildfire occurrence to maximize their usefulness. In this study, spatial analysis was carried out to determine suitable sites for establishing RHSs intended for air attack operations in...

  6. Evaluating timber harvesting impacts on wildlife habitat suitability using FOREX

    Science.gov (United States)

    Chris B. LeDoux

    1997-01-01

    Precommercial, commercial, and final harvesting operations can impact wildlife habitat suitability by altering the vegetation composition on a given site. Harvesting operations remove trees and many times provide the necessary perturbation to trigger successional conditions different from those that existed prior to the harvest. Although these new successional changes...

  7. A land suitability system for spate irrigation schemes in Eritrea

    NARCIS (Netherlands)

    Tesfai, M.H.

    2002-01-01

    Spate irrigation is a system used for wetting land prior to planting. Use is made of seasonal rivers (wadis) producing flash floods in the uplands, which are directed by structures to irrigate fields in the lowlands. A land suitability system for spate irrigation schemes in Eritrea was studied in th

  8. Groundwater Suitability for Irrigation: a Case Study from Debre ...

    African Journals Online (AJOL)

    Bheema

    irrigation water quality, the groundwater is suitable for irrigation with some minor ... specific toxicity effect on vegetables and field crops, however, there are ... alone cannot sustain the practice, the issues like ecological and social are to be taken in to ... particularly for crops that are sensitive to changes in quality (Bohn et al., ...

  9. An Anti-aliasing Algorithm Suitable to Map Publishing Symbol

    Institute of Scientific and Technical Information of China (English)

    DENG Shujun

    2006-01-01

    On the basis of analysis of various algorithms, an anti-aliasing algorithm called brush method was presented, which is suitable to map publishing symbol. After introducing the basic principle and implementation of brush method in detail, the result and efficiency were evaluated through experiments.

  10. Suitability of integrated protection diodes from diverse semiconductor technologies

    NARCIS (Netherlands)

    Wanum, van Maurice; Lebouille, Tom; Visser, Guido; Vliet, van Frank E.

    2009-01-01

    Abstract In this article diodes from three different semiconductor technologies are compared based on their suitability to protect a receiver. The semiconductor materials involved are silicon, gallium arsenide and gallium nitride. The diodes in the diverse semiconductor technologies themselves are c

  11. Suitability of integrated protection diodes from diverse semiconductor technologies

    NARCIS (Netherlands)

    Wanum, M. van; Lebouille, T.T.N.; Visser, G.C.; Vliet, F.E. van

    2009-01-01

    In this article diodes from three different semiconductor technologies are compared based on their suitability to protect a receiver. The semiconductor materials involved are Silicon, Gallium Arsenide and Gallium Nitride. The diodes in the diverse semiconductor technologies themselves are close in p

  12. Analysis of applications suitable for mobile learning of preschool children

    OpenAIRE

    Stoimenovski, Aleksandar; Kraleva, Radoslava; Kralev, Velin

    2016-01-01

    This article considers the use of mobile learning in Bulgarian education by young children. The most used mobile operating systems are analyzed. Also some of the most used existing applications suitable for mobile learning of preschool children are presented and classified. Keywords: Mobile applications for preschool children, mobile learning.

  13. Fuzzy modeling of farmers' knowledge for land suitability classification

    NARCIS (Netherlands)

    Sicat, R.S.; Carranza, E.J.M.; Nidumolu, U.B.

    2005-01-01

    In a case study, we demonstrate fuzzy modeling of farmers' knowledge (FK) for agricultural land suitability classification using GIS. Capture of FK was through rapid rural participatory approach. The farmer respondents consider, in order of decreasing importance, cropping season, soil color, soil te

  14. Analysis of applications suitable for mobile learning of preschool children

    OpenAIRE

    Stoimenovski, Aleksandar; Kraleva, Radoslava; Kralev, Velin

    2016-01-01

    This article considers the use of mobile learning in Bulgarian education by young children. The most used mobile operating systems are analyzed. Also some of the most used existing applications suitable for mobile learning of preschool children are presented and classified. Keywords: Mobile applications for preschool children, mobile learning.

  15. EXPERT MODEL OF LAND SUITABILITY ASSESSMENT FOR CROPS

    Directory of Open Access Journals (Sweden)

    Boris Đurđević

    2010-12-01

    Full Text Available A total of 17404 soil samples (2003rd-2009th year were analysed in the eastern Croatia. The largest number of soil samples belongs to the Osijek-Baranya county, which together with both Eastern sugar beet Factories (Osijek and Županja, conduct the soil fertility control (~4200 samples/yr.. Computer model suitability assessment for crops, supported by GIS, proved to be fast, efficient enough reliable in terms of the number of analyzed soil samples. It allows the visualization of the agricultural area and prediction of its production properties for the purposes of analysis, planning and rationalization of agricultural production. With more precise data about the soil (soil, climate and reliable Digital Soil Map of Croatia, the model could be an acceptable, not only to evaluate the suitability for growing different crops but also their need for fertilizer, necessary machinery, repairs (liming, and other measures of organic matter input. The abovementioned aims to eliminate or reduce effects of limiting factors in primary agricultural production. Assessment of the relative benefits of soil presented by computer model for the crops production and geostatistical method kriging in the Osijek-Baranya county showed: 1 Average soil suitability being 60.06 percent. 2 Kriging predicted that 51751 ha (17.16% are of limited resources (N1 for growing crops whereas a 86142 ha (28.57% of land is limited suitably (S3, b 132789 ha (44.04% are moderately suitable (S2 and c 30772 ha (10.28% are of excellent fertility (S1. A large number of eastern Croatian land data showed that the computer-geostatistical model for determination of soil benefits for growing crops was automated, fast and simple to use and suitable for the implementation of GIS and automatically downloading the necessary benefit indicators from the input base (land, analytical and climate as well as data from the digital soil maps able to: a visualize the suitability for soil tillage, b predict the

  16. Himalayan Mountain Range, India

    Science.gov (United States)

    1981-01-01

    Snow is present the year round in most of the high Himalaya Mountain Range (33.0N, 76.5E). In this view taken at the onset of winter, the continuous snow line can be seen for hundreds of miles along the south face of the range in the Indian states of Punjab and Kashmir. The snow line is at about 12,000 ft. altitude but the deep Cenab River gorge is easily delineated as a break along the south edge of the snow covered mountains. '

  17. Range-Clustering Queries

    OpenAIRE

    Abrahamsen, Mikkel; de Berg, Mark; Buchin, Kevin; Mehr, Mehran; Mehrabi, Ali D.

    2017-01-01

    In a geometric $k$-clustering problem the goal is to partition a set of points in $\\mathbb{R}^d$ into $k$ subsets such that a certain cost function of the clustering is minimized. We present data structures for orthogonal range-clustering queries on a point set $S$: given a query box $Q$ and an integer $k>2$, compute an optimal $k$-clustering for $S\\setminus Q$. We obtain the following results. We present a general method to compute a $(1+\\epsilon)$-approximation to a range-clustering query, ...

  18. Calibration of Short Range 2D Laser Range Finder for 3D SLAM Usage

    Directory of Open Access Journals (Sweden)

    Petr Olivka

    2016-01-01

    Full Text Available The laser range finder is one of the most essential sensors in the field of robotics. The laser range finder provides an accurate range measurement with high angular resolution. However, the short range scanners require an additional calibration to achieve the abovementioned accuracy. The calibration procedure described in this work provides an estimation of the internal parameters of the laser range finder without requiring any special three-dimensional targets. This work presents the use of a short range URG-04LX scanner for mapping purposes and describes its calibration. The precision of the calibration was checked in an environment with known ground truth values and the results were statistically evaluated. The benefits of the calibration are also demonstrated in the practical applications involving the segmentation of the environment. The proposed calibration method is complex and detects all major manufacturing inaccuracies. The procedure is suitable for easy integration into the current manufacturing process.

  19. An overview of the history, applications, advantages, disadvantages and prospects of gene therapy.

    Science.gov (United States)

    Jafarlou, M; Baradaran, B; Saedi, T A; Jafarlou, V; Shanehbandi, D; Maralani, M; Othman, F

    2016-01-01

    Gene therapy has become a significant issue in science-related news. The principal concept of gene therapy is an experimental technique that uses genes to treat or prevent disease. Although gene therapy was originally conceived as a way to treat life-threatening disorders (inborn defects, cancers) refractory to conventional treatment, it is now considered for many non–life-threatening conditions, such as those adversely impacting a patient’s quality of life. An extensive range of efficacious vectors, delivery techniques, and approaches for developing gene-based interventions for diseases have evolved in the last decade. The lack of suitable treatment has become a rational basis for extending the scope of gene therapy. The aim of this review is to investigate the general methods by which genes are transferred and to give an overview to clinical applications. Maximizing the potential benefits of gene therapy requires efficient and sustained therapeutic gene expression in target cells, low toxicity, and a high safety profile. Gene therapy has made substantial progress albeit much slower than was initially predicted. This review also describes the basic science associated with many gene therapy vectors and the present progress of gene therapy carried out for various surface disorders and diseases. The conclusion is that, with increased pathobiological understanding and biotechnological improvements, gene therapy will become a standard part of clinical practice.

  20. Agriculture, forest, and range

    Science.gov (United States)

    1975-01-01

    The findings and recommendations of the panel for developing a satellite remote-sensing global information system in the next decade are reported. User requirements were identified in five categories: (1) cultivated crops, (2) land resources, (3)water resources, (4)forest management, and (5) range management. The benefits from the applications of satellite data are discussed.

  1. Electric vehicles: Driving range

    Science.gov (United States)

    Kempton, Willett

    2016-09-01

    For uptake of electric vehicles to increase, consumers' driving-range needs must be fulfilled. Analysis of the driving patterns of personal vehicles in the US now shows that today's electric vehicles can meet all travel needs on almost 90% of days from a single overnight charge.

  2. LONG RANGE HEALTH PLANNING

    Directory of Open Access Journals (Sweden)

    ST. Motameni

    1974-03-01

    Full Text Available In the past, health planning in Iran has been carried out in the context of short-range economic plans. Although this mechanism has helped a great deal in the achievement of certain health plans however, the said scheme has been short in meeting the health objectives on a comprehensive basis. Most often, the heath programs have lost their values to the priority and cost effectiveness of economic plans. A brief review of heath planning in the past shows that the second development plan has been devoted to the establishment of new hospitals on a scattered pattern. The development of a coordinated hospital and health center system has been accepted and partly implemented during the third plan period. In the fourth plan the whole direction has changed towards the de­velopment of private hospitals on profit making basis, and now the fifth plan calls for the regionalized hospital system. Thus, one can say that the past twenty years have been spent to the experimentation of different schemes with­out a real long-range goal. In the past decade the World Health Organization has ventured in the development of health planning principles, but most of the efforts have been devoted to the short-range planning. The long-range health planning is not only a new look to the prin­ciples of planning, but a thorough examination of the time factor in health planning.

  3. Online Sorted Range Reporting

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Greve, Mark

    2009-01-01

    We study the following one-dimensional range reporting problem: On an arrayA of n elements, support queries that given two indices i ≤ j and an integerk report the k smallest elements in the subarray A[i..j] in sorted order. We present a data structure in the RAM model supporting such queries in ...

  4. Microencapsulation of Bioactive Principles with an Airless Spray-Gun Suitable for Processing High Viscous Solutions

    Directory of Open Access Journals (Sweden)

    Moreno Cocchietto

    2013-11-01

    Full Text Available Purpose: to design, assemble and test a prototype of a novel production plant, suitable for producing microparticles (MPs by processing highly viscous feed solutions (FSs. Methods: the prototype has been built using a commercial air compressor, a piston pump, an airless spray-gun, a customized air-treatment section, a timer, a rotating base, and a filtration section. Preliminary prototype parameter setting was carried out to individuate the best performing nozzle’s dimension, the nebulization timing, and the CaCl2 concentration in the gelation fluid. In addition, prototype throughput (1 L to 5 L and the range of practicable feed solution (FS viscosities were assayed. A set of four batches was prepared in order to characterize the MPs, in terms of mean particle size and distribution, flow properties, swelling, encapsulation efficiency and release. Results: according to a qualitative scoring, the large nozzle was suitable to nebulize FSs at a higher alginate concentration. Conversely, the small nozzle performed better in the processing of FSs with an alginate concentration up to 2% w/v. Only at the highest degree of viscosity, corresponding to 5% w/v of alginate, the FS processing was not technically possible. Among the CaCl2 concentrations considered, 15% w/v was recognized as the most versatile. The prototype appears to be convenient and suitable to grant a high yield starting from 2 L of FS. The flow behavior of the FSs assayed can be satisfactorily described with the Carreau-Yasuda equation and the throughput begins to slightly decrease for FSs at alginate concentrations exceeding 3% w/v. MP morphology was irregular with crumpled shape. The angle of repose indicates a good flowability and the release studies showed gastro-resistance and potential prolonged release applications. Conclusions: the novel prototype of production plant is suitable to process large amounts (2 L or more of FSs, characterized by a high viscosity, to produce MPs

  5. Site Suitability Analysis for Dissemination of Salt-tolerant Rice Varieties in Southern Bangladesh

    Science.gov (United States)

    Sinha, D. D.; Singh, A. N.; Singh, U. S.

    2014-11-01

    Bangladesh shows five classes of salinity. viz., non-saline with some very slight saline soil, very slightly saline with some slight saline soil, slightly saline with some moderately saline soil, strongly saline with some moderately saline soil, and very strongly saline with some strongly saline soil. The soil EC level of different classes range from 2 dSm-1 to >16 dSm-1. The soil map was geo-referenced and digitized using Arc GIS. Salinity tolerance characteristics of the rice varieties were matched with the soil characteristics shown on the map. Three suitability classes were made; soils suitable for salt-tolerant varieties, not suitable for salt-tolerant varieties due to high soil salinity, and suitable for other high yielding varieties due to slight salinity. The mauza (smallest revenue unit) boundary provided by the Bangladesh Agriculture Research Council was also geo-referenced and digitized in the same projection. Overlaying and intersecting the mauza boundary on the soil suitability map provided the suitable and not suitable mauza. A total of 4070 mauzas in the 12 salinity-affected districts were listed and maps showing suitability of mauza prepared. About 0.6 million ha out of total 0.87 million ha salinity affected area were found suitable for growing the salinity-tolerant BRRI dhan-47, Bina dhan-8 and -10 in these districts. The maps and other generated information have helped the Dept. of Agriculture Extension (DAE) of Bangladesh in large scale dissemination of seeds of the salinity-tolerant rice varieties in different districts during the past two years.

  6. Investigation on the suitability of natural sandstone as a gamma dosimeter

    Energy Technology Data Exchange (ETDEWEB)

    Soliman, C. [Physics Department, Faculty of Science, Ain Shams University, Cairo (Egypt)], E-mail: cairosoliman@yahoo.com; Salama, E. [Physics Department, Faculty of Science, Ain Shams University, Cairo (Egypt)

    2009-10-01

    The suitability of sandstone for the gamma radiation dosimetry using thermoluminescence technique is investigated. Its properties are systematically studied utilizing atomic absorption spectrometry, measurements of natural and laboratory-induced blue thermoluminescence emission band, trap depths and storage effects. The emission of the natural blue-band exhibited broad peak at {approx}315 {sup o}C. The thermoluminescence gamma dose response has a linear behavior over the dose range 1-50 Gy followed by sub-linearity at high dose level, with standard deviation in all cases less than {+-}9%. Trapping depths showed a closely spaced set of traps for both the natural and laboratory-induced glow curves. The variation in thermoluminescence signal over 1 week storage period at room temperature was not more than 7%. The thermoluminescence fading effects were explained by the localized transition model. From our results, it is possible to conclude that natural sandstone is a suitable material for accident and industrial dosimetric applications.

  7. Practicability study on the suitability of artificial, neural networks for the approximation of unknown steering torques

    Science.gov (United States)

    Van Ende, K. T. R.; Schaare, D.; Kaste, J.; Küçükay, F.; Henze, R.; Kallmeyer, F. K.

    2016-10-01

    For steer-by-wire systems, the steering feedback must be generated artificially due to the system characteristics. Classical control concepts require operating-point driven optimisations as well as increased calibration efforts in order to adequately simulate the steering torque in all driving states. Artificial neural networks (ANNs) are an innovative control concept; they are capable of learning arbitrary non-linear correlations without complex knowledge of physical dependencies. The present study investigates the suitability of neural networks for approximating unknown steering torques. To ensure robust processing of arbitrary data, network training with a sufficient volume of training data is required, that represents the relation between the input and target values in a wide range. The data were recorded in the course of various test drives. In this research, a variety of network topologies were trained, analysed and evaluated. Though the fundamental suitability of ANNs for the present control task was demonstrated.

  8. Estimating Rooftop Suitability for PV: A Review of Methods, Patents, and Validation Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Melius, J.; Margolis, R.; Ong, S.

    2013-12-01

    A number of methods have been developed using remote sensing data to estimate rooftop area suitable for the installation of photovoltaics (PV) at various geospatial resolutions. This report reviews the literature and patents on methods for estimating rooftop-area appropriate for PV, including constant-value methods, manual selection methods, and GIS-based methods. This report also presents NREL's proposed method for estimating suitable rooftop area for PV using Light Detection and Ranging (LiDAR) data in conjunction with a GIS model to predict areas with appropriate slope, orientation, and sunlight. NREL's method is validated against solar installation data from New Jersey, Colorado, and California to compare modeled results to actual on-the-ground measurements.

  9. Landscape suitability in Botswana for the conservation of its six large African carnivores.

    Directory of Open Access Journals (Sweden)

    Hanlie E K Winterbach

    Full Text Available Wide-ranging large carnivores often range beyond the boundaries of protected areas into human-dominated areas. Mapping out potentially suitable habitats on a country-wide scale and identifying areas with potentially high levels of threats to large carnivore survival is necessary to develop national conservation action plans. We used a novel approach to map and identify these areas in Botswana for its large carnivore guild consisting of lion (Panthera leo, leopard (Panthera pardus, spotted hyaena (Crocuta crocuta, brown hyaena (Hyaena brunnea, cheetah (Acinonyx jubatus and African wild dog (Lycaon pictus. The habitat suitability for large carnivores depends primarily on prey availability, interspecific competition, and conflict with humans. Prey availability is most likely the strongest natural determinant. We used the distribution of biomass of typical wild ungulate species occurring in Botswana which is preyed upon by the six large carnivores to evaluate the potential suitability of the different management zones in the country to sustain large carnivore populations. In areas where a high biomass of large prey species occurred, we assumed interspecific competition between dominant and subordinated competitors to be high. This reduced the suitability of these areas for conservation of subordinate competitors, and vice versa. We used the percentage of prey biomass of the total prey and livestock biomass to identify areas with potentially high levels of conflict in agricultural areas. High to medium biomass of large prey was mostly confined to conservation zones, while small prey biomass was more evenly spread across large parts of the country. This necessitates different conservation strategies for carnivores with a preference for large prey, and those that can persist in the agricultural areas. To ensure connectivity between populations inside Botswana and also with its neighbours, a number of critical areas for priority management actions exist

  10. Future habitat suitability for coral reef ecosystems under global warming and ocean acidification.

    Science.gov (United States)

    Couce, Elena; Ridgwell, Andy; Hendy, Erica J

    2013-12-01

    Rising atmospheric CO2 concentrations are placing spatially divergent stresses on the world's tropical coral reefs through increasing ocean surface temperatures and ocean acidification. We show how these two stressors combine to alter the global habitat suitability for shallow coral reef ecosystems, using statistical Bioclimatic Envelope Models rather than basing projections on any a priori assumptions of physiological tolerances or fixed thresholds. We apply two different modeling approaches (Maximum Entropy and Boosted Regression Trees) with two levels of complexity (one a simplified and reduced environmental variable version of the other). Our models project a marked temperature-driven decline in habitat suitability for many of the most significant and bio-diverse tropical coral regions, particularly in the central Indo-Pacific. This is accompanied by a temperature-driven poleward range expansion of favorable conditions accelerating up to 40-70 km per decade by 2070. We find that ocean acidification is less influential for determining future habitat suitability than warming, and its deleterious effects are centered evenly in both hemispheres between 5° and 20° latitude. Contrary to expectations, the combined impact of ocean surface temperature rise and acidification leads to little, if any, degradation in future habitat suitability across much of the Atlantic and areas currently considered 'marginal' for tropical corals, such as the eastern Equatorial Pacific. These results are consistent with fossil evidence of range expansions during past warm periods. In addition, the simplified models are particularly sensitive to short-term temperature variations and their projections correlate well with reported locations of bleaching events. Our approach offers new insights into the relative impact of two global environmental pressures associated with rising atmospheric CO2 on potential future habitats, but greater understanding of past and current controls on coral

  11. Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems

    Science.gov (United States)

    2012-01-01

    Background Selecting an appropriate classifier for a particular biological application poses a difficult problem for researchers and practitioners alike. In particular, choosing a classifier depends heavily on the features selected. For high-throughput biomedical datasets, feature selection is often a preprocessing step that gives an unfair advantage to the classifiers built with the same modeling assumptions. In this paper, we seek classifiers that are suitable to a particular problem independent of feature selection. We propose a novel measure, called "win percentage", for assessing the suitability of machine classifiers to a particular problem. We define win percentage as the probability a classifier will perform better than its peers on a finite random sample of feature sets, giving each classifier equal opportunity to find suitable features. Results First, we illustrate the difficulty in evaluating classifiers after feature selection. We show that several classifiers can each perform statistically significantly better than their peers given the right feature set among the top 0.001% of all feature sets. We illustrate the utility of win percentage using synthetic data, and evaluate six classifiers in analyzing eight microarray datasets representing three diseases: breast cancer, multiple myeloma, and neuroblastoma. After initially using all Gaussian gene-pairs, we show that precise estimates of win percentage (within 1%) can be achieved using a smaller random sample of all feature pairs. We show that for these data no single classifier can be considered the best without knowing the feature set. Instead, win percentage captures the non-zero probability that each classifier will outperform its peers based on an empirical estimate of performance. Conclusions Fundamentally, we illustrate that the selection of the most suitable classifier (i.e., one that is more likely to perform better than its peers) not only depends on the dataset and application but also on the

  12. ORANGE: RANGE OF BENEFITS

    OpenAIRE

    Parle Milind; Chaturvedi Dev

    2012-01-01

    No wonder that oranges are one of the most popular fruits in the world. Orange (citrus sinensis) is well known for its nutritional and medicinal properties throughout the world. From times immemorial, whole Orange plant including ripe and unripe fruits, juice, orange peels, leaves and flowers are used as a traditional medicine. Citrus sinensis belongs to the family Rutaceae. The fruit is a fleshy, indehiscent, berry that ranges widely in size from 4 cm to 12 cm. The major medicinal proper...

  13. Predicting Software Suitability Using a Bayesian Belief Network

    Science.gov (United States)

    Beaver, Justin M.; Schiavone, Guy A.; Berrios, Joseph S.

    2005-01-01

    The ability to reliably predict the end quality of software under development presents a significant advantage for a development team. It provides an opportunity to address high risk components earlier in the development life cycle, when their impact is minimized. This research proposes a model that captures the evolution of the quality of a software product, and provides reliable forecasts of the end quality of the software being developed in terms of product suitability. Development team skill, software process maturity, and software problem complexity are hypothesized as driving factors of software product quality. The cause-effect relationships between these factors and the elements of software suitability are modeled using Bayesian Belief Networks, a machine learning method. This research presents a Bayesian Network for software quality, and the techniques used to quantify the factors that influence and represent software quality. The developed model is found to be effective in predicting the end product quality of small-scale software development efforts.

  14. Evaluation methods for ceramic suitability of raw clays

    Directory of Open Access Journals (Sweden)

    Hajjaji M.

    2013-09-01

    Full Text Available Ceramic suitability of kaolinitic-illitic and chloritic-illitic raw clays was assessed by methods involving microstructure investigation and ceramic properties measurements, some reported diagrams and response surface methodology (RSM. Results of the former method showed that all clays are suitable for red stoneware tiles. The stoneware manufacturing is facilitated by the marked reduction of porosity due to the flow of melt, mainly originated from the breakdowns of illite. This result was partially supported by the use of a diagram involving the chemical composition of clays as well as by the RSM results. According to the later method, bricks may be manufactured under restricted firing conditions and stoneware tiles could be prepared at temperatures as low as 950°C.

  15. Evaluation of OMV ranging and docking systems

    Science.gov (United States)

    McDonald, M. W.

    1985-01-01

    The Orbital Maneuvering Vehicle (OMV) will serve as a shuttle-based or permanent space station-based vehicle designed to rendezvous and soft dock with various other free-flying space vehicles for purposes of inspection, support, and retrieval. This study is concerned primarily with the eventual need for the OMV to rendezvous and dock softly with the Edwin P. Hubble Space Telescope (ST). Utilizing the available capabilities of the large microwave anechoic chamber facility at Marshall Space Flight Center for simulating docking target vehicle motions in a free-space environment, a program is being devised for benchmark testing of rendezvous and docking sensor systems proposed for use on the OMV. A testing regimen suitable for evaluating the accuracy and tracking agility in sensing range, range rate, and angle information at close ranges (0 R 30m) has been developed.

  16. The Application of BP Networks to Land Suitability Evaluation

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The back propagation (BP) model of artificial neural networks (ANN) has many good qualities comparing with ordinary methods in land suitability evaluation.Through analyzing ordinary methods' limitations,some sticking points of BP model used in land evaluation,such as network structure,learning algorithm,etc.,are discussed in detail,The land evaluation of Qionghai city is used as a case study.Fuzzy comprehensive assessment method was also employed in this evaluation for validating and comparing.

  17. HEALTH SUITABILITY CRITERIA OF FOOD OF ANIMAL ORIGIN

    Directory of Open Access Journals (Sweden)

    Andrej Kirbiš

    2000-06-01

    Full Text Available Criteria of health suitability of food of animal origin are presence of causing agents of zoonosis and alimentary diseases, presence of environmental pollutants and substances, used in the veterinary treatments, radioactive contamination and senzoric changes. Hygienic irrevocability is guaranteed by a conscientious veterinary-sanitary inspection, strict discipline of breeders of slaughter animals and producers of milk but also by well-informed consumers and especially those who are professionally involved in the preparation of food.

  18. ARE QUATERNARY AMMONIUM ANTIBACTERIALS SUITABLE FOR DENTAL COMPOSITE RESINS?

    Directory of Open Access Journals (Sweden)

    Iman MOHAMMADZADEH

    2016-06-01

    Full Text Available The objective of this study was to answer the following question: are quaternary ammonium antibacterials suitable for dental materials? Reviewing the literature on quaternary ammonium compounds evidenced that this type of compounds is soluble in water. Our own findings also showed that they are well soluble in water and that their application as dental composites requires to check their solubility level in water.

  19. Suitability of Sour Crude Processing and Resid Hydrotreating Technologies

    Institute of Scientific and Technical Information of China (English)

    Sun Lili

    2005-01-01

    This article has analyzed the environment and tasks confronting China's petroleum refining industry, and has referred to principles for selecting the resid processing technologies and viability of various combination technologies for resid processing. Taking into account the actual commercial practice of resid hydrogenation units, this article has also discussed methods for processing high-sulfur inferior crudes as well as the suitability of resid hydrogenation technology.

  20. A Suitable Artificial Intelligence Model for Inventory Level Optimization

    Directory of Open Access Journals (Sweden)

    Tereza Sustrova

    2016-05-01

    Full Text Available Purpose of the article: To examine suitable methods of artificial neural networks and their application in business operations, specifically to the supply chain management. The article discusses construction of an artificial neural networks model that can be used to facilitate optimization of inventory level and thus improve the ordering system and inventory management. For the data analysis from the area of wholesale trade with connecting material is used. Methodology/methods: Methods used in the paper consists especially of artificial neural networks and ANN-based modelling. For data analysis and preprocessing, MS Office Excel software is used. As an instrument for neural network forecasting MathWorks MATLAB Neural Network Tool was used. Deductive quantitative methods for research are also used. Scientific aim: The effort is directed at finding whether the method of prediction using artificial neural networks is suitable as a tool for enhancing the ordering system of an enterprise. The research also focuses on finding what architecture of the artificial neural networks model is the most suitable for subsequent prediction. Findings of the research show that artificial neural networks models can be used for inventory management and lot-sizing problem successfully. A network with the TRAINGDX training function and TANSIG transfer function and 6-8-1 architecture can be considered the most suitable for artificial neural network, as it shows the best results for subsequent prediction.. Conclusions resulting from the paper are beneficial for further research. It can be concluded that the created model of artificial neural network can be successfully used for predicting order size and therefore for improving the order cycle of an enterprise.

  1. Suitability Evaluation for Products Generation from Multisource Remote Sensing Data

    Directory of Open Access Journals (Sweden)

    Jining Yan

    2016-12-01

    Full Text Available With the arrival of the big data era in Earth observation, the remote sensing communities have accumulated a large amount of invaluable and irreplaceable data for global monitoring. These massive remote sensing data have enabled large-area and long-term series Earth observation, and have, in particular, made standard, automated product generation more popular. However, there is more than one type of data selection for producing a certain remote sensing product; no single remote sensor can cover such a large area at one time. Therefore, we should automatically select the best data source from redundant multisource remote sensing data, or select substitute data if data is lacking, during the generation of remote sensing products. However, the current data selection strategy mainly adopts the empirical model, and has a lack of theoretical support and quantitative analysis. Hence, comprehensively considering the spectral characteristics of ground objects and spectra differences of each remote sensor, by means of spectrum simulation and correlation analysis, we propose a suitability evaluation model for product generation. The model will enable us to obtain the Production Suitability Index (PSI of each remote sensing data. In order to validate the proposed model, two typical value-added information products, NDVI and NDWI, and two similar or complementary remote sensors, Landsat-OLI and HJ1A-CCD1, were chosen, and the verification experiments were performed. Through qualitative and quantitative analysis, the experimental results were consistent with our model calculation results, and strongly proved the validity of the suitability evaluation model. The proposed production suitability evaluation model could assist with standard, automated, serialized product generation. It will play an important role in one-station, value-added information services during the big data era of Earth observation.

  2. Is the Dragon a Suitable Symbol for China?

    Institute of Scientific and Technical Information of China (English)

    孙梦雨

    2007-01-01

    <正>Recently there has been a heated discussion on whether we should continue to use the dragon as the symbol for our China.Some claim that the dragon is no longer a suitable symbol for China. Whereas others don’t think so. A professor Wu in Shanghai who holds the view that the dragon is no good a symbol gives the following reasons.Firstly,the dragon is an evil

  3. A Network Software Architecture Suitable for Service Customization

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper explores the service customization in the view of network software architectures. The authors first abstract a network system into a framework that consists of several layered basic systems and then propose a component-based network software architecture for one basic system of network software, which is suitable for service customization. The network software architecture is formalized with the theory of Communicating Sequential Process and show its possible applications in areas of personal service environment and service customization.

  4. Publicly Released Prompt Radiation Spectra Suitable for Nuclear Detonation Simulations

    Science.gov (United States)

    2017-03-01

    emission. During the Hiroshima and Nagasaki bombings, the prompt radiation contributed from 40%-70% of the free-in-air dose depending on distance from...intermediate- and low -yield thermonuclear weapons for initial radiation shielding calculations No Gritzner, et al. 1976 (EM-1, Low , Henre...Publicly Released Prompt Radiation Spectra Suitable for Nuclear Detonation Simulations DISTRIBUTION A. Approved for public release; distribution is

  5. Corrosion resistant coatings suitable for elevated temperature application

    Science.gov (United States)

    Chan, Kwai S [San Antonio, TX; Cheruvu, Narayana Sastry [San Antonio, TX; Liang, Wuwei [Austin, TX

    2012-07-31

    The present invention relates to corrosion resistance coatings suitable for elevated temperature applications, which employ compositions of iron (Fe), chromium (Cr), nickel (Ni) and/or aluminum (Al). The compositions may be configured to regulate the diffusion of metals between a coating and a substrate, which may then influence coating performance, via the formation of an inter-diffusion barrier layer. The inter-diffusion barrier layer may comprise a face-centered cubic phase.

  6. Shifting suitability for malaria vectors across Africa with warming climates

    Directory of Open Access Journals (Sweden)

    Peterson A Townsend

    2009-05-01

    Full Text Available Abstract Background Climates are changing rapidly, producing warm climate conditions globally not previously observed in modern history. Malaria is of great concern as a cause of human mortality and morbidity, particularly across Africa, thanks in large part to the presence there of a particularly competent suite of mosquito vector species. Methods I derive spatially explicit estimates of human populations living in regions newly suitable climatically for populations of two key Anopheles gambiae vector complex species in Africa over the coming 50 years, based on ecological niche model projections over two global climate models, two scenarios of climate change, and detailed spatial summaries of human population distributions. Results For both species, under all scenarios, given the changing spatial distribution of appropriate conditions and the current population distribution, the models predict a reduction of 11.3–30.2% in the percentage of the overall population living in areas climatically suitable for these vector species in coming decades, but reductions and increases are focused in different regions: malaria vector suitability is likely to decrease in West Africa, but increase in eastern and southern Africa. Conclusion Climate change effects on African malaria vectors shift their distributional potential from west to east and south, which has implications for overall numbers of people exposed to these vector species. Although the total is reduced, malaria is likely to pose novel public health problems in areas where it has not previously been common.

  7. Monocular visual ranging

    Science.gov (United States)

    Witus, Gary; Hunt, Shawn

    2008-04-01

    The vision system of a mobile robot for checkpoint and perimeter security inspection performs multiple functions: providing surveillance video, providing high resolution still images, and providing video for semi-autonomous visual navigation. Mid-priced commercial digital cameras support the primary inspection functions. Semi-autonomous visual navigation is a tertiary function whose purpose is to reduce the burden of teleoperation and free the security personnel for their primary functions. Approaches to robot visual navigation require some form of depth perception for speed control to prevent the robot from colliding with objects. In this paper present the initial results of an exploration of the capabilities and limitations of using a single monocular commercial digital camera for depth perception. Our approach combines complementary methods in alternating stationary and moving behaviors. When the platform is stationary, it computes a range image from differential blur in the image stack collected at multiple focus settings. When the robot is moving, it extracts an estimate of range from the camera auto-focus function, and combines this with an estimate derived from angular expansion of a constellation of visual tracking points.

  8. The Uncertainties on the GIS Based Land Suitability Assessment for Urban and Rural Planning

    Science.gov (United States)

    Liu, H.; Zhan, Q.; Zhan, M.

    2017-09-01

    The majority of the research on the uncertainties of spatial data and spatial analysis focuses on some specific data feature or analysis tool. Few have accomplished the uncertainties of the whole process of an application like planning, making the research of uncertainties detached from practical applications. The paper discusses the uncertainties of the geographical information systems (GIS) based land suitability assessment in planning on the basis of literature review. The uncertainties considered range from index system establishment to the classification of the final result. Methods to reduce the uncertainties arise from the discretization of continuous raster data and the index weight determination are summarized. The paper analyzes the merits and demerits of the "Nature Breaks" method which is broadly used by planners. It also explores the other factors which impact the accuracy of the final classification like the selection of class numbers, intervals and the autocorrelation of the spatial data. In the conclusion part, the paper indicates that the adoption of machine learning methods should be modified to integrate the complexity of land suitability assessment. The work contributes to the application of spatial data and spatial analysis uncertainty research on land suitability assessment, and promotes the scientific level of the later planning and decision-making.

  9. THE UNCERTAINTIES ON THE GIS BASED LAND SUITABILITY ASSESSMENT FOR URBAN AND RURAL PLANNING

    Directory of Open Access Journals (Sweden)

    H. Liu

    2017-09-01

    Full Text Available The majority of the research on the uncertainties of spatial data and spatial analysis focuses on some specific data feature or analysis tool. Few have accomplished the uncertainties of the whole process of an application like planning, making the research of uncertainties detached from practical applications. The paper discusses the uncertainties of the geographical information systems (GIS based land suitability assessment in planning on the basis of literature review. The uncertainties considered range from index system establishment to the classification of the final result. Methods to reduce the uncertainties arise from the discretization of continuous raster data and the index weight determination are summarized. The paper analyzes the merits and demerits of the “Nature Breaks” method which is broadly used by planners. It also explores the other factors which impact the accuracy of the final classification like the selection of class numbers, intervals and the autocorrelation of the spatial data. In the conclusion part, the paper indicates that the adoption of machine learning methods should be modified to integrate the complexity of land suitability assessment. The work contributes to the application of spatial data and spatial analysis uncertainty research on land suitability assessment, and promotes the scientific level of the later planning and decision-making.

  10. A GIS – Based Methodology for Land Suitability Evaluation in Veneto (NE Italy

    Directory of Open Access Journals (Sweden)

    Alba Gallo

    2014-12-01

    Full Text Available Since almost ten years, the Soil Science Research Group in Venice is carrying out studies on the characterization of soils in the Veneto region and their suitability for specific uses. Several areas have been investigated with the aim to select the best land use for a sustainable environment. The scenarios taken into consideration range from the Alpine and pre – Alpine region to the alluvial plain. Attention has been focused especially to land suitability for forestry, typical and niche crops, pasture and vineyard. The land evaluation procedure has been applied by a GIS – based methodology. Today, the GIS techniques are essential for the success of a correct and fast work, concerning the interpretation and processing of soil data and its display in form of map. Integrating information with crop and soil requirements, by means of "matching tables", it was possible to edit and manage land suitability maps for specific purposes. The applied methodology proved a useful and effective tool for sustainable land management.

  11. Using RNA-Seq data to select refence genes for normalizing gene expression in apple roots

    Science.gov (United States)

    Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for t...

  12. ORANGE: RANGE OF BENEFITS

    Directory of Open Access Journals (Sweden)

    Parle Milind

    2012-07-01

    Full Text Available No wonder that oranges are one of the most popular fruits in the world. Orange (citrus sinensis is well known for its nutritional and medicinal properties throughout the world. From times immemorial, whole Orange plant including ripe and unripe fruits, juice, orange peels, leaves and flowers are used as a traditional medicine. Citrus sinensis belongs to the family Rutaceae. The fruit is a fleshy, indehiscent, berry that ranges widely in size from 4 cm to 12 cm. The major medicinal properties of orange include anti-bacterial, anti-fungal, anti- diabetic, cardio- protective, anti-cancer, anti-arthritic, anti-inflammatory, anti-oxidant, anti-Tubercular, anti-asthmatic and anti-hypertensive. Phytochemically, whole plant contains limonene, citral, neohesperidin, naringin, rutin, rhamnose, eriocitrin, and vitamin-C. In the present review article, a humble attempt is made to compile all the strange facts available about this tasty fruit.

  13. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  14. [Climatic suitability of single cropping rice planting region in China].

    Science.gov (United States)

    Duan, Ju-Qi; Zhou, Guang-Sheng

    2012-02-01

    To clarify the leading climate factors affecting the distribution of single cropping rice planting region in China at national and annual temporal scales and to reveal the potential distribution and climatic suitability divisions of this planting region in China could not only provide scientific basis for optimizing the allocation of single cropping rice production, modifying planting pattern, and introducing fine varieties, but also ensure the food security of China. In this paper, the potential climate factors affecting the single cropping rice distribution in China at regional and annual scales were selected from related literatures, and the single cropping rice geographic information from the national agro-meteorological observation stations of China Meteorological Administration (CMA), together with the maximum entropy model (MaxEnt) and spatial analyst function of Arc-GIS software, were adopted to clarify the leading climate factors affecting the potential distribution of single cropping rice planting region in China, and to construct a model about the relationships between the potential distribution of the planting region and the climate. The results showed that annual precipitation, moisture index, and days of not less than 18 degrees C stably were the leading climate factors affecting the potential distribution of single cropping rice planting region in China, with their cumulative contribution rate reached 94.5% of all candidate climate factors. The model constructed in this paper could well simulate the potential distribution of single cropping rice planting region in China. According to the appearance frequency, the low, medium and high climatic suitability divisions of single cropping rice planting region in China were clarified, and the climate characteristics of the planting region in each climatic suitability division were analyzed.

  15. Quantitative validation of a habitat suitability index for oyster restoration

    Directory of Open Access Journals (Sweden)

    Seth eTheuerkauf

    2016-05-01

    Full Text Available Habitat suitability index (HSI models provide spatially explicit information on the capacity of a given habitat to support a species of interest, and their prevalence has increased dramatically in recent years. Despite caution that the reliability of HSIs must be validated using independent, quantitative data, most HSIs intended to inform terrestrial and marine species management remain unvalidated. Furthermore, of the eight HSI models developed for eastern oyster (Crassostrea virginica restoration and fishery production, none has been validated. Consequently, we developed, calibrated, and validated an HSI for the eastern oyster to identify optimal habitat for restoration in a tributary of Chesapeake Bay, the Great Wicomico River (GWR. The GWR harbors a high density, restored oyster population, and therefore serves as an excellent model system for assessing the validity of the HSI. The HSI was derived from GIS layers of bottom type, salinity, and water depth (surrogate for dissolved oxygen, and was tested using live adult oyster density data from a survey of high vertical relief reefs (HRR and low vertical relief reefs (LRR in the sanctuary network. Live adult oyster density was a statistically-significant sigmoid function of the HSI, which validates the HSI as a robust predictor of suitable oyster reef habitat for rehabilitation or restoration. In addition, HRR had on average 103-116 more adults m^−2 than LRR at a given level of the HSI. For HRR, HSI values ≥0.3 exceeded the accepted restoration target of 50 live adult oysters m^−2. For LRR, the HSI was generally able to predict live adult oyster densities that meet or exceed the target at HSI values ≥0.3. The HSI indicated that there remain large areas of suitable habitat for restoration in the GWR. This study provides a robust framework for HSI model development and validation, which can be refined and applied to other systems and previously developed HSIs to improve the efficacy of

  16. Climatic Suitability of Growing Summer Squash (Cucurbita pepo L. as a Medicinal Plant in Iran

    Directory of Open Access Journals (Sweden)

    Mohammad BANNAYAN

    2011-05-01

    Full Text Available Diversification of production by including a broader range of plant species, can significantly contribute to improve health and nutrition, livelihoods, household food security and ecological sustainability. Exploring the climate impact on any given crop is one of the first priorities to find new suitable areas for production and management of new crops. Summer squash (Cucurbita pepo L. is an economically valuable plant with various medicinal potentials. In order to investigate summer squash cultivation feasibility under Iran�s climate, three main agricultural regions (Azerbaijan, Khorasan and central part of Iran (Fars and Isfahan were selected. These regions suitability for summer squash cultivation were evaluated by considering three vital climate variables encompass temperature, precipitation, and sunshine hours. These regions show distinct and representative climatic conditions of Iran. Annual and growing season average of maximum, minimum, mean temperature, precipitation, and sunshine hours were calculated (May-September for all locations with 44 years historical weather data (1961-2005 for 8 locations (Oroomieh, Tabriz, Khoy, Mashhad, Sabzevar, Birjand, Shiraz and Isfahan, 39 years (1966-2005 for 2 locations (Kashan and Fassa, 28 years (1977-2005 for 4 locations (Ardebil, Abadeh, Bojnurd and Shargh Isfahan and 20 years (1985-2005 for 9 locations (Mahabad, Sarab, Maragheh, Parsabad, Khalkhal, Ferdous, Ghaen, Kashmar and Sarakhs. Climatic demands of summer squash were determined by four years field studies at four different locations in Iran. Our results showed Azerbaijan region has a suitable condition for this crop cultivation especially from precipitation and temperature perspectives. Central part of Iran and Khorasan were also found as partly suitable locations however as they are near to deserts with hotter and drier climate, there might be some other crops considered as priorities in these areas.

  17. Assessing the Amazon Cloud Suitability for CLARREO's Computational Needs

    Science.gov (United States)

    Goldin, Daniel; Vakhnin, Andrei A.; Currey, Jon C.

    2015-01-01

    In this document we compare the performance of the Amazon Web Services (AWS), also known as Amazon Cloud, with the CLARREO (Climate Absolute Radiance and Refractivity Observatory) cluster and assess its suitability for computational needs of the CLARREO mission. A benchmark executable to process one month and one year of PARASOL (Polarization and Anistropy of Reflectances for Atmospheric Sciences coupled with Observations from a Lidar) data was used. With the optimal AWS configuration, adequate data-processing times, comparable to the CLARREO cluster, were found. The assessment of alternatives to the CLARREO cluster continues and several options, such as a NASA-based cluster, are being considered.

  18. Ammonia as a Suitable Fuel for Fuel Cells

    OpenAIRE

    Lan, Rong; Tao, Shanwen

    2014-01-01

    Ammonia, an important basic chemical, is produced at a scale of 150 million tons per year. Half of hydrogen produced in chemical industry is used for ammonia production. Ammonia containing 17.5 wt% hydrogen is an ideal carbon-free fuel for fuel cells. Compared to hydrogen, ammonia has many advantages. In this mini-review, the suitability of ammonia as fuel for fuel cells, the development of different types of fuel cells using ammonia as the fuel and the potential applications of ammonia fuel ...

  19. Suitability of laboratory animals for screening anti-hyperlipidemic agents.

    Directory of Open Access Journals (Sweden)

    Rajwade N

    1989-07-01

    Full Text Available The present study was undertaken to evaluate and compare the lipid profiles of various laboratory animals to that of human beings. The human subjects and animals included in the study were from three age groups based on key physiological states. A record of the usual dietary constituents and their daily consumption was maintained. The results indicated that the lipid profile of pigs and dogs bears similarity to that of human beings. Results also revealed that lipid profile was labile in the second group of these animals indicating that this age is suitable to bring about the required changes to produce a hyperlipidemic animal.

  20. Ammonia as a suitable fuel for fuel cells

    Directory of Open Access Journals (Sweden)

    Rong eLan

    2014-08-01

    Full Text Available Ammonia, an important basic chemical, is produced at a scale of 150 million tons per year. Half of hydrogen produced in chemical industry is used for ammonia production. Ammonia containing 17.5wt% hydrogen is an ideal carbon-free fuel for fuel cells. Compared to hydrogen, ammonia has many advantages. In this mini-review, the suitability of ammonia as fuel for fuel cells, the development of different types of fuel cells using ammonia as the fuel and the potential applications of ammonia fuel cells are briefly reviewed.

  1. Communication Standards Suitable for MES Systems Designed for SMES

    Directory of Open Access Journals (Sweden)

    Ondřej WINKLER

    2009-06-01

    Full Text Available A MES (Manufacturing Execution System is a system that large companies use to measure or control critical production activities. Individual parts of this system can be used as a model for development of tools suitable for small and medium enterprises (SMEs. It can demonstrate how manufacturing systems works and which communication standards are usable. The communication standards enable data acquisition, data processing, storing and their conversion for any production report. Furthermore, interfaces for web clients allow displaying the raw or transformed data as a text or a graphic chart. The development of tools for an access to the data retrieved from MES software is described in this paper.

  2. Storm surge and tidal range energy

    Science.gov (United States)

    Lewis, Matthew; Angeloudis, Athanasios; Robins, Peter; Evans, Paul; Neill, Simon

    2017-04-01

    The need to reduce carbon-based energy sources whilst increasing renewable energy forms has led to concerns of intermittency within a national electricity supply strategy. The regular rise and fall of the tide makes prediction almost entirely deterministic compared to other stochastic renewable energy forms; therefore, tidal range energy is often stated as a predictable and firm renewable energy source. Storm surge is the term used for the non-astronomical forcing of tidal elevation, and is synonymous with coastal flooding because positive storm surges can elevate water-levels above the height of coastal flood defences. We hypothesis storm surges will affect the reliability of the tidal range energy resource; with negative surge events reducing the tidal range, and conversely, positive surge events increasing the available resource. Moreover, tide-surge interaction, which results in positive storm surges more likely to occur on a flooding tide, will reduce the annual tidal range energy resource estimate. Water-level data (2000-2012) at nine UK tide gauges, where the mean tidal amplitude is above 2.5m and thus suitable for tidal-range energy development (e.g. Bristol Channel), were used to predict tidal range power with a 0D modelling approach. Storm surge affected the annual resource estimate by between -5% to +3%, due to inter-annual variability. Instantaneous power output were significantly affected (Normalised Root Mean Squared Error: 3%-8%, Scatter Index: 15%-41%) with spatial variability and variability due to operational strategy. We therefore find a storm surge affects the theoretical reliability of tidal range power, such that a prediction system may be required for any future electricity generation scenario that includes large amounts of tidal-range energy; however, annual resource estimation from astronomical tides alone appears sufficient for resource estimation. Future work should investigate water-level uncertainties on the reliability and

  3. Gene Cluster Statistics with Gene Families

    Science.gov (United States)

    Durand, Dannie

    2009-01-01

    Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such “gene clusters” is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

  4. Pre-main sequence spectroscopic binaries suitable for VLTI observations

    CERN Document Server

    Guenther, E W; Mundt, R; Covino, E; Alcalá, J M; Cusano, F; Stecklum, B

    2007-01-01

    A severe problem of the research in star-formation is that the masses of young stars are almost always estimated only from evolutionary tracks. Since the tracks published by different groups differ, it is often only possible to give a rough estimate of the masses of young stars. It is thus crucial to test and calibrate the tracks. Up to now, only a few tests of the tracks could be carried out. However, with the VLTI it is now possible to set constrains on the tracks by determining the masses of many young binary stars precisely. In order to use the VLTI efficiently, a first step is to find suitable targets, which is the purpose of this work. Given the distance of nearby star-forming regions, suitable VLTI targets are binaries with orbital periods between at least 50 days, and few years. Although a number of surveys for detecting spectroscopic binaries have been carried out, most of the binaries found so far have periods which are too short. We thus surveyed the Chamaeleon, Corona Australis, Lupus, Sco-Cen, rh...

  5. QFD Based Benchmarking Logic Using TOPSIS and Suitability Index

    Directory of Open Access Journals (Sweden)

    Jaeho Cho

    2015-01-01

    Full Text Available Users’ satisfaction on quality is a key that leads successful completion of the project in relation to decision-making issues in building design solutions. This study proposed QFD (quality function deployment based benchmarking logic of market products for building envelope solutions. Benchmarking logic is composed of QFD-TOPSIS and QFD-SI. QFD-TOPSIS assessment model is able to evaluate users’ preferences on building envelope solutions that are distributed in the market and may allow quick achievement of knowledge. TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution provides performance improvement criteria that help defining users’ target performance criteria. SI (Suitability Index allows analysis on suitability of the building envelope solution based on users’ required performance criteria. In Stage 1 of the case study, QFD-TOPSIS was used to benchmark the performance criteria of market envelope products. In Stage 2, a QFD-SI assessment was performed after setting user performance targets. The results of this study contribute to confirming the feasibility of QFD based benchmarking in the field of Building Envelope Performance Assessment (BEPA.

  6. Thermogravimetric evaluation of the suitability of precursors for MOCVD

    Science.gov (United States)

    Kunte, G. V.; Shivashankar, S. A.; Umarji, A. M.

    2008-02-01

    A method based on the Langmuir equation for the estimation of vapour pressure and enthalpy of sublimation of subliming compounds is described. The variable temperature thermogravimetric/differential thermogravimetric (TG/DTG) curve of benzoic acid is used to arrive at the instrument parameters. Employing these parameters, the vapour pressure-temperature curves are derived for salicylic acid and camphor from their TG/DTG curves. The values match well with vapour pressure data in the literature, obtained by effusion methods. By employing the Clausius-Clapeyron equation, the enthalpy of sublimation could be calculated. Extending the method further, two precursors for metal-organic chemical vapour deposition (MOCVD) of titanium oxide bis-isopropyl bis tert-butyl 2-oxobutanoato titanium, Ti(OiPr)2(tbob)2, and bis-oxo-bis-tertbutyl 2-oxobutanoato titanium, [TiO(tbob)2]2, have been evaluated. The complex Ti(OiPr)2(tbob)2 is found to be a more suitable precursor. This approach can be helpful in quickly screening for the suitability of a compound as a CVD precursor.

  7. Hydrogeochemical quality and suitability studies of groundwater in northern Bangladesh.

    Science.gov (United States)

    Islam, M J; Hakim, M A; Hanafi, M M; Juraimi, Abdul Shukor; Aktar, Sharmin; Siddiqa, Aysha; Rahman, A K M Shajedur; Islam, M Atikul; Halim, M A

    2014-07-01

    Agriculture, rapid urbanization and geochemical processes have direct or indirect effects on the chemical composition of groundwater and aquifer geochemistry. Hydro-chemical investigations, which are significant for assessment of water quality, were carried out to study the sources of dissolved ions in groundwater of Dinajpur district, northern Bangladesh. The groundwater samplish were analyzed for physico-chemical properties like pH, electrical conductance, hardness, alkalinity, total dissolved solids and Ca2+, Mg2+, Na+, K+, CO3(2-), HCO3(-), SO4(2-) and Cl- ions, respectively. Based on the analyses, certain parameters like sodium adsorption ratio, soluble sodium percentage, potential salinity, residual sodium carbonate, Kelly's ratio, permeability index and Gibbs ratio were also calculated. The results showed that the groundwater of study area was fresh, slightly acidic (pH 5.3-6.4) and low in TDS (35-275 mg I(-1)). Ground water of the study area was found suitable for irrigation, drinking and domestic purposes, since most of the parameters analyzed were within the WHO recommended values for drinking water. High concentration of NO3- and Cl- was reported in areas with extensive agriculture and rapid urbanization. Ion-exchange, weathering, oxidation and dissolution of minerals were major geochemical processes governing the groundwater evolution in study area. Gibb's diagram showed that all the samples fell in the rock dominance field. Based on evaluation, it is clear that groundwater quality of the study area was suitable for both domestic and irrigation purposes.

  8. Counter rotating type hydroelectric unit suitable for tidal power station

    Energy Technology Data Exchange (ETDEWEB)

    Kanemoto, T [Faculty of Engineering, Kyushu Institute of Technology, Sensui 1-1, Tobata, Kitakyushu 804-8550 (Japan); Suzuki, T, E-mail: turbo@tobata.isc.kyutech.ac.j [Graduate School of Engineering, Kyushu Institute of Technology, Sensui 1-1, Tobata, Kitakyushu 804-8550 (Japan)

    2010-08-15

    The counter rotating type hydroelectric unit, which is composed of the axial flow type tandem runners and the peculiar generator with double rotational armatures,was proposed to utilize effectively the tidal power. In the unit, the front and the rear runners counter drive the inner and the outer armatures of the generator, respectively. Besides, the flow direction at the rear runner outlet must coincide with the flow direction at the front runner inlet, because the angular momentum through the rear runner must coincides with that through the front runner. That is, the flow runs in the axial direction at the rear runner outlet while the axial inflow at the front runner inlet. Such operations are suitable for working at the seashore with rising and falling tidal flows, and the unit may be able to take place of the traditional bulb type turbines. The tandem runners were operated at the on-cam conditions, in keeping the induced frequency constant. The output and the hydraulic efficiency are affected by the adjustment of the front and the blade setting angles. The both optimum angles giving the maximum output and/or efficiency were presented at the various discharges/heads. To promote more the tidal power generation by this type unit, the runners were also modified so as to be suitable for both rising and falling flows. The hydraulic performances are acceptable while the output is determined mainly by the trailing edge profiles of the runner blades.

  9. Aedes aegypti Global Suitability Maps Using a Water Container Energy Balance Model for Dengue Risk Applications

    Science.gov (United States)

    Steinhoff, D.

    2015-12-01

    Dengue infections are estimated to total nearly 400 million per year worldwide, with both the geographic range and the magnitude of infections having increased in the past 50 years. The primary dengue vector mosquito Aedes aegypti is closely associated with humans. It lives exclusively in urban and semi-urban areas, preferentially bites humans, and spends its developmental stages in artificial water containers. Climate regulates the development of Ae. aegypti immature mosquitoes in artificial containers. Potential containers for Ae. aegypti immature development include, but are not limited to, small sundry items (e.g., bottles, cans, plastic containers), buckets, tires, barrels, tanks, and cisterns. Successful development of immature mosquitoes from eggs to larvae, pupae, and eventually adults is largely dependent on the availability of water and the thermal properties of the water in the containers. Recent work has shown that physics-based approaches toward modeling container water properties are promising for resolving the complexities of container water dynamics and the effects on immature mosquito development. An energy balance container model developed by the author, termed the Water Height And Temperature in Container Habitats Energy Model (WHATCH'EM), solves for water temperature and height for user-specified containers with readily available weather data. Here we use WHATCH'EM with NASA Earth Science products used as input to construct global suitability maps based on established water temperature ranges for immature Ae. aegypti mosquitoes. A proxy for dengue risk is provided from habitat suitability, but also population estimates, as Ae. aegypti is closely associated with human activity. NASA gridded Global Population of the World data is used to mask out rural areas with low dengue risk. Suitability maps are illustrated for a variety of containers (size, material, color) and shading scenarios.

  10. Projections of Suitable Wine Growing Regions and Varieties: Adaptation in Space or Place?

    Science.gov (United States)

    Forrestel, E. J.; Cook, B.; Garcia de Cortazar-Atauri, I.; Nicholas, K. A.; Parker, A.; van Leeuwen, C.; Wolkovich, E. M.

    2015-12-01

    Winegrapes (Vitis vinifera L) are the most valuable horticultural crop in the world with nearly eight million hectares of vineyards in cultivation. Different varieties of winegrapes (e.g., Grenache or Syrah) exhibit an unprecedented amount of phenological and genetic diversity for a cultivated species, which is an important resource to buffer against climate change. Matching phenological strategies of the different winegrape varieties to a particular climate is a fundamental aim for every vineyard manager, especially in the face of significant climatic shifts in many winegrape growing regions. Yet current projections of suitable winegrape growing regions based on future climate scenarios are limited in their utility, as they do not consider the possibility that other varieties better suited to a future climate could be planted within an existing region. For our projections, we built phenological models for the nine most-planted winegrapes globally, which constitutes over 40% of all planted hectares, using a global dataset of budburst, flowering, veraison and maturity. These models were then used to characterize the growing range of 1300 globally planted winegrape varieties. Combing these models with climate projection models under RCP 4.5 and 8.5 emission scenarios we examined future distributions of suitable wine growing regions, as well as the turnover of suitable varieties within existing regions. In some regions of the world, predicted climate change will not significantly alter the varieties that are able to grow, while in others there will need to be shifts in the region itself or in the varieties that are currently planted. Some regions will also see a significant increase in the number and diversity of varieties that can be grown. Our results suggest the need to utilize the full range of winegrape diversity available when considering adaptive strategies in response to changing climates.

  11. Customized rating assessment of climate suitability (CRACS): climate satisfaction evaluation based on subjective perception

    Science.gov (United States)

    Lin, Tzu-Ping; Yang, Shing-Ru; Matzarakis, Andreas

    2015-12-01

    Climate not only influences the behavior of people in urban environments but also affects people's schedules and travel plans. Therefore, providing people with appropriate long-term climate evaluation information is crucial. Therefore, we developed an innovative climate assessment system based on field investigations conducted in three cities located in Northern, Central, and Southern Taiwan. The field investigations included the questionnaire surveys and climate data collection. We first analyzed the relationship between the participants and climate parameters comprising physiologically equivalent temperature, air temperature, humidity, wind speed, solar radiation, cloud cover, and precipitation. Second, we established the neutral value, comfort range, and dissatisfied range of each parameter. Third, after verifying that the subjects' perception toward the climate parameters vary based on individual preferences, we developed the customized rating assessment of climate suitability (CRACS) approach, which featured functions such as personalized and default climate suitability information to be used by users exhibiting varying demands. Finally, we performed calculations using the climate conditions of two cities during the past 10 years to demonstrate the performance of the CRACS approach. The results can be used as a reference when planning activities in the city or when organizing future travel plans. The flexibility of the assessment system enables it to be adjusted for varying regions and usage characteristics.

  12. The suitability evaluation of dredged soil from reservoirs as embankment material.

    Science.gov (United States)

    Park, Jaesung; Son, Younghwan; Noh, Sookack; Bong, Taeho

    2016-12-01

    We assessed the suitability of soil dredged from reservoirs as embankment material and investigated its physical and geochemical properties and strength parameters, as well as its environmental stability. The dredged soil samples were taken from the Ansung, Jechon, and Mulwang Reservoirs in Korea. To evaluate their environmental stability and geochemical properties, we examined their levels of heavy metal contamination, pH, and electrical conductivity. We also conducted X-ray fluorescence and X-ray diffraction analyses. Furthermore, we determined the geotechnical characteristics, such as the compaction characteristics, and permeability coefficient, and we performed consolidated undrained triaxial compression tests to evaluate the recycling potential of dredged soil as embankment material. The concentrations of heavy metals in the sediment samples were lower than those of the standard samples. The pH value of the soil samples ranged from 4.25 to 5.39, and the electrical conductivity ranged between 83.3 and 265.0 μS/cm, indicating suitability for use as construction material with steel and concrete. Based on the values of the mechanical properties of the dredged soil, analysis of slope stability was performed for various cases and water level conditions. Our results indicate that the dredged soil has sufficient stability for substitution of embankment material and also as new embankment material for expansion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Bacillus sphaericus LMG 22257 is physiologically suitable for self-healing concrete.

    Science.gov (United States)

    Wang, Jianyun; Jonkers, Henk M; Boon, Nico; De Belie, Nele

    2017-06-01

    The suitability of using a spore-forming ureolytic strain, Bacillus sphaericus, was evaluated for self-healing of concrete cracks. The main focus was on alkaline tolerance, calcium tolerance, oxygen dependence, and low-temperature adaptability. Experimental results show that B. sphaericus had a good tolerance. It can grow and germinate in a broad range of alkaline pH. The optimal pH range is 7 ∼ 9. High alkaline conditions (pH 10 ∼ 11) slow down but not stop the growth and germination. Oxygen was strictly needed during bacterial growth and germination, but not an essential factor during bacterial urea decomposition. B. sphaericus also had a good Ca tolerance, especially at a high bacterial concentration of 10(8) cells/mL; no significant influence was observed on bacterial ureolytic activity of the presence of 0.9M Ca(2+). Furthermore, at a low temperature (10 °C), bacterial spores germinated and revived ureolytic activity with some retardation. However, this retardation can be counteracted by using a higher bacterial concentration and by supplementing yeast extract. It can be concluded that B. sphaericus is a suitable bacterium for application in bacteria-based self-healing concrete.

  14. Noise modeling for MOAs and ranges

    Science.gov (United States)

    Lucas, Michael J.; Lee, Robert A.

    Whenever there is a reallocation of DOD fixed- or rotary-wing aircraft or a change in the use of the airspace requirements, either an Environmental Assessment or an Environmental Impact Statement must be prepared. These environmental studies require an analysis of the noise impacts resulting from aircraft operations surrounding the airports and under Military Training Routes (MTR's), Military Operating Areas (MOA's), and Ranges. NOISEMAP and ROUTEMAP were developed for the purpose of estimating the noise levels around military airports and under MTR's. Neither of these programs is suitable for estimating noise levels under MOA's or Ranges. MR NMAP is a PC-based computer model that has been developed to calculate the noise levels under MOA's and ranges. The program calculates L(sub dn), CNEL, L(sub eq), SEL, L(sub max), and where appropriate L(sub dnmr). The program output is a tabular form or in graphics suitable for inclusion in reports. The computer program is designed for use by environmental planning personnel who are familiar with MOA and range operations and with noise, but are not necessarily expert. The program will be widely distributed to DOD planners and contractors that have a requirement to make noise estimates. A companion graphical user interface (GUI) computer program called MR OPS has been developed that allows the user to draw the airspace, specify areas of high/medium/low activity, and draw the specific flight tracks for bombing runs and military training routes. MR OPS writes an ASCII file that is read by MR NMAP. Contained in this ASCII file is the operation data and keywords that control the computational features in MR NMAP. MR NMAP is written in FORTRAN; executable versions are available under DOS, Windows, and Windows NT. MR OPS is written in the C programming language and will run under Windows and Windows NT.

  15. Fabrication and functionalization of PCB gold electrodes suitable for DNA-based electrochemical sensing.

    Science.gov (United States)

    Salvo, P; Henry, O Y F; Dhaenens, K; Acero Sanchez, J L; Gielen, A; Werne Solnestam, B; Lundeberg, J; O'Sullivan, C K; Vanfleteren, J

    2014-01-01

    The request of high specificity and selectivity sensors suitable for mass production is a constant demand in medical research. For applications in point-of-care diagnostics and therapy, there is a high demand for low cost and rapid sensing platforms. This paper describes the fabrication and functionalization of gold electrodes arrays for the detection of deoxyribonucleic acid (DNA) in printed circuit board (PCB) technology. The process can be implemented to produce efficiently a large number of biosensors. We report an electrolytic plating procedure to fabricate low-density gold microarrays on PCB suitable for electrochemical DNA detection in research fields such as cancer diagnostics or pharmacogenetics, where biosensors are usually targeted to detect a small number of genes. PCB technology allows producing high precision, fast and low cost microelectrodes. The surface of the microarray is functionalized with self-assembled monolayers of mercaptoundodecanoic acid or thiolated DNA. The PCB microarray is tested by cyclic voltammetry in presence of 5 mM of the redox probe K3Fe(CN6) in 0.1 M KCl. The voltammograms prove the correct immobilization of both the alkanethiol systems. The sensor is tested for detecting relevant markers for breast cancer. Results for 5 nM of the target TACSTD1 against the complementary TACSTD1 and non-complementary GRP, MYC, SCGB2A1, SCGB2A2, TOP2A probes show a remarkable detection limit of 0.05 nM and a high specificity.

  16. A Range-Shift Technique for TOF Range Image Sensors

    Science.gov (United States)

    Sawada, Tomonari; Ito, Kana; Nakayama, Masakatsu; Kawahito, Shoji

    In Time-of-Flight (TOF) range image sensors using periodical pulsed light, there is a trade-off between the maximum range and range resolution. This paper proposes a range-shift technique for improving range resolution of the TOF range image sensor without sacrificing the measurement range. The range-shift operation uses a TOF range imaging pixel with periodical charge draining structure and several time-shifted short pulses. The use of the short pulse can improve the range resolution. The range image using the range-shift technique is synthesized with several sub-frames, each acquires one of the shifted range images. The use of the small duty-ratio pulse leads to reducing the effect of ambient light and improving the range resolution. The range-shift technique is tested with an implemented TOF range image sensor and it is found that the range resolution is improved to 2cm using a 10ns light pulse and 7 overlapped shifted ranges for the measurement range of 0.5m to 4.0m.

  17. Construction of Bacillus thuringiensis Simulant Strains Suitable for Environmental Release.

    Science.gov (United States)

    Park, Sangjin; Kim, Changhwan; Lee, Daesang; Song, Dong Hyun; Cheon, Ki Cheol; Lee, Hong Suk; Kim, Seong Joo; Kim, Jee Cheon; Lee, Sang Yup

    2017-05-01

    For a surrogate bacterium to be used in outdoor studies, it is important to consider environmental and human safety and ease of detection. Recently, Bacillus thuringiensis, a popular bioinsecticide bacterium, has been gaining attention as a surrogate bacterium for use in biodefense. In this study, we constructed simulant strains of B. thuringiensis with enhanced characteristics for environmental studies. Through transposon mutagenesis, pigment genes were inserted into the chromosome, producing yellow-colored colonies for easy detection. To prevent persistence of spores in the environment, a genetic circuit was designed to produce a spore without sporulation capability. Two loxP sites were inserted, one on each side of the spo0A gene, which encodes a sporulation master regulator, and a sporulation-dependent Cre expression cassette was inserted into the chromosome. This genetic circuit successfully deleted spo0A during sporulation, producing spores that lacked the spo0A gene. In addition, two major α/β-type small acid-soluble spore protein (SASP) genes, predicted by synteny analysis, were deleted. The spores of the mutant strain showed increased UV-C sensitivity and quickly lost viability when tested in a solar simulator. When the spores of the mutant strain were administered to the lungs of BALB/c mice, cells were quickly removed from the body, suggesting enhanced in vivo safety. All strains constructed in this study contain no antibiotic resistance markers and all heterologous genes were inserted into the chromosome, which are useful features for simulants to be released into the environment.IMPORTANCEB. thuringiensis has recently been receiving increasing attention as a good spore simulant in biodefense research. However, few studies were done to properly address many important features of B. thuringiensis as a simulant in environmental studies. Since spores can persist in the environment for years after release, environmental contamination is a big problem

  18. Geophysical remote sensing of water reservoirs suitable for desalinization.

    Energy Technology Data Exchange (ETDEWEB)

    Aldridge, David Franklin; Bartel, Lewis Clark; Bonal, Nedra; Engler, Bruce Phillip

    2009-12-01

    In many parts of the United States, as well as other regions of the world, competing demands for fresh water or water suitable for desalination are outstripping sustainable supplies. In these areas, new water supplies are necessary to sustain economic development and agricultural uses, as well as support expanding populations, particularly in the Southwestern United States. Increasing the supply of water will more than likely come through desalinization of water reservoirs that are not suitable for present use. Surface-deployed seismic and electromagnetic (EM) methods have the potential for addressing these critical issues within large volumes of an aquifer at a lower cost than drilling and sampling. However, for detailed analysis of the water quality, some sampling utilizing boreholes would be required with geophysical methods being employed to extrapolate these sampled results to non-sampled regions of the aquifer. The research in this report addresses using seismic and EM methods in two complimentary ways to aid in the identification of water reservoirs that are suitable for desalinization. The first method uses the seismic data to constrain the earth structure so that detailed EM modeling can estimate the pore water conductivity, and hence the salinity. The second method utilizes the coupling of seismic and EM waves through the seismo-electric (conversion of seismic energy to electrical energy) and the electro-seismic (conversion of electrical energy to seismic energy) to estimate the salinity of the target aquifer. Analytic 1D solutions to coupled pressure and electric wave propagation demonstrate the types of waves one expects when using a seismic or electric source. A 2D seismo-electric/electro-seismic is developed to demonstrate the coupled seismic and EM system. For finite-difference modeling, the seismic and EM wave propagation algorithms are on different spatial and temporal scales. We present a method to solve multiple, finite-difference physics

  19. Pastoral suitability driven by future climate change along the Apennines

    Directory of Open Access Journals (Sweden)

    Camilla Dibari

    2015-09-01

    Full Text Available This work aims at evaluating the impacts of climate change on pastoral resources located along the Apennines chain. To this end, random forest machine learning model was first calibrated for the present period and then applied to future conditions, as projected by HadCM3 general circulation model, in order to simulate possible spatial variation/shift of pastoral areas in two time slices (centred on 2050 and 2080 under A2 and B2 SRES scenarios. Pre-existent spatial database, namely Corine land cover map and WorldClim, were integrated and harmonised in a GIS environment in order to extract climate variables (mean seasonal precipitation, mean maximum temperature of the warmest month and minimum temperature of the coldest month and response variables (presence/absence of pastures to be used as model predictors. Random forest model resulted robust and coherent to simulate pastureland suitability under current climatology (classification accuracy error=19%. Accordingly, results indicated that increases in temperatures coupled with decreases in precipitation, as simulated by HadCM3 in the future, would have impacts of great concern on potential pasture distribution. In the specific, an overall decline of pasturelands suitability is predicted by the middle of the century in both A2 (–46% and B2 (–41% along the entire chain. However, despite alarming reductions in pastures suitability along the northern (–69% and –71% under A2 and B2 scenarios, respectively and central Apennines (–90% under both scenarios by the end of the century, expansions are predicted along the southern areas of the chain (+96% and +105% under A2 and B2 scenarios, respectively. This may be probably due to expansions in pastures dominated by xeric and thermophiles species, which will likely benefit from warmer and drier future conditions predicted in the southern zone of the chain by the HadCM3. Hence, the expected climate, coupled with an increasing abandonment of the

  20. A multi-criteria, ecosystem-service value method used to assess catchment suitability for potential wetland reconstruction in Denmark

    DEFF Research Database (Denmark)

    Odgaard, Mette Vestergaard; Turner, Katrine Grace; Bøcher, Peder Klith

    2017-01-01

    were identified with an especially high suitability when optimizing all scenarios. This coincides with a high suitability around peri-urban and urban areas and near natural areas, hence capturing both supply and demand services. Of the 35 identified catchments with potentially high suitability, only 2......Wetlands provide a range of ecosystem services such as drought resistance, flood resistance, nutrient deposition, biodiversity, etc. This study presents a new multi-criteria, ecosystems service value-driven method to drive the optimal placement of restored wetlands in terms of maximizing selected...... ecosystem services which a wetland can provide or affect. We aim to answer two questions: 1) which of the ecosystem services indicators defines the placement of wetlands today? 2) Based on the ecosystem services indicator assessment, what are the recommendations for future selection of catchments...

  1. Environmental Suitability and Distribution of the Caucasian Rock Agama, Paralaudakia caucasia (Sauria:Agamidae) in Western and Central Asia

    Institute of Scientific and Technical Information of China (English)

    Seyyed Saeed HOSSEINIAN YOUSEFKHANI; Gentile Francesco FICETOLA; Nasrullah RASTEGAR-POUYANI; Natalia B ANANJEVA; Eskandar RASTEGAR-POUYANI; Rafaqat MASROOR

    2013-01-01

    Predictive potential distribution modeling is crucial in outlining habitat usage and establishing conservation management priorities. In this paper we provide detailed data on the distribution of the Caucasian rock agama Para-laudakia caucasia, and use species distribution models (MAXENT) to evaluate environmental suitability and potential distribution at a broad spatial scale. Locality data on the distribution of P. caucasia have been gathered over nearly its entire range by various authors from ifeld surveys. The distribution model of P. caucasia showed good performance (AUC=0.887), and predicted high suitability in regions mainly located in Tajikistan, north Pakistan, Afghanistan, southeast Turkmenistan, northeast Iran along the Elburz mountains, Transcaucasus (Azerbajan, Armenia, Georgia), northeastern Turkey and northward along the Caspian Sea coast in Daghestan, Russia. The identiifcation of suitable areas for this species will help to assess conservation status of the species, and to set up management programs.

  2. Dancing girl flap: a new flap suitable for web release.

    Science.gov (United States)

    Shinya, K

    1999-12-01

    To create a deep web, a flap must be designed to have a high elongation effect in one direction along the mid-lateral line of the finger and also to have a shortening effect in the other direction, crossing at a right angle to the mid-lateral line. The dancing girl flap is a modification of a four-flap Z-plasty with two additional Z-plasties. It has a high elongation effect in one direction (>550%) and a shortening effect in the other direction at a right angle (<33%), creating a deep, U-shaped surface. This new flap can be used to release severe scar contracture with a web, and is most suitable for incomplete syndactyly with webs as high as the proximal interphalangeal joint.

  3. A compact electroactive polymer actuator suitable for refreshable Braille display

    Science.gov (United States)

    Ren, Kailiang; Liu, Sheng; Lin, Minren; Wang, Yong; Zhang, Q. M.

    2007-04-01

    The large strain, high elastic modulus, and easy processing of P(VDF-TrFE-CFE) electrostrictive terpolymer make it very attractive to replace low strain piezoceramics and piezopolymers in many applications with much improved performance. In this paper, a compact polymer actuator is developed utilizing the electrostrictive terpolymer, which is suitable for full page Braille Display and graphic display. Key issues related to the reliability of electroactive polymers used in the compact actuators and for the mass fabrication of these polymer actuators are investigated. Making use of a recently developed conductive polymer, a screen printing deposition method was developed which enables direct deposition very thin conductive polymer electrode layer (Braille actuator was designed and fabricated with these terpolymer films wound on a spring core. The test results demonstrate that the EAP Braille actuator meets all the functional requirements of actuators for refreshable full Braille display, which offers compact size, reduced cost and weight.

  4. Suitable Conditions of Reservoir Simulation for Searching Rule Curves

    Science.gov (United States)

    Kangrang, Anongrit; Chaleeraktrakoon, Chavalit

    The objective of this study is to carry out a suitable length of inflow record using in the simulation model. The second objective is to find an effect of initial reservoir capacity of reservoir simulation for searching the optimal rule curves. The reservoir simulation model was connected with genetic algorithms to search the optimal rule curves quickly. The model has been applied to determine the optimal rule curves of the Bhumibol and Sirikit Reservoirs (the Chao Phraya River Basin, Thailand). The optimal rule curves of each condition were used to assess by a Monte Carlo simulation. The results show that the shortest period of dry inflow record using in the simulation model in order to search the optimal rule curves is 10 year. Furthermore, the minimum initial capacity of reservoir for searching optimal rule curves is 10% of full capacity.

  5. Evaluation of colour space transformation suitability to optical temperature measurements

    Science.gov (United States)

    Ziemba, A.; Fornalik-Wajs, E.

    2016-09-01

    All optical measurement methods base on the image analysis and relation between the measured parameter and some image features. In Digital Particle Image Thermometry (DPIT), such relation represents a function between the temperature and particles’ colour (i.a. Thermochromic Liquid Crystals). For the quantitative data acquisition the “colour” information is necessary, therefore the colour spaces based on hue H are used. Due to the big number of numerical operations needed in the analysis, the choice of colour space transformation is significant due to the accuracy and computational time. In this paper commonly applied RGB to HSI colour spaces’ transformations were compared and evaluation of their suitability to temperature measurement was performed. Time of obtaining the final results was considered as the main criterion. Appropriate calculations were conducted and presented.

  6. Forest land suitability in a Mediterranean area under climate change scenarios

    Science.gov (United States)

    Muñoz-Rojas, Miriam; Anaya-Romero, María; Kotb Abd-Elmabod, Sameh; De la Rosa, Diego

    2013-04-01

    As a consequence of the increasing level of atmospheric CO2 and air temperatures, global climate is changing leading to warmer and often drier conditions in many forest ecosystems. The Mediterranean area is particularly vulnerable to climate change as a result of a combination of environmental and human factors. An adequate forest management is associated to improvement of habitat suitability for soil and water quality, climate regulation and other important ecosystem services. The MicroLEIS decision support system (MicroLEIS DSS), through its 12 land evaluation models, is a useful tool to assist decision-makers with specific agro-ecological problems. Among the land evaluation models, Sierra was specifically designed to assess forestry land suitability for restoration of semi-natural habitats in marginal agricultural lands. This model selects up to 22 forest species adapted to Mediterranean conditions based on latitude, longitude, physiographic position, useful depth, texture, drainage, pH, summer and winter temperatures, and precipitation. In this research, Sierra model was applied in 35 benchmark sites representative of the natural regions (NUTS2) of a Mediterranean area (Andalusia, Southern Spain) in current and future climate scenarios for the A1B IPPC SRES (Special Report on Emission Scenarios) and the periods 2040, 2070 and 2100. Data was obtained from SEISnet soil database, CDBm climate database and the future climate change variation values of the State Meteorological Agency. The results showed that Pinus Pinea, Pinus halepensis, Quercus Ilex and Quercus suber are the most suitable forest species in actual and future climate scenarios for the selected marginal lands, according to the tolerance ranges for standard soil and climate variables of the forest species. Various forest species showed a potential aptitude for reforestation in future climate scenarios (i.e. Quercus), whereas others such as Castanea Sativa will not be suitable in the study area in 2070

  7. Spirostomum spp. (Ciliophora, Protista), a suitable system for endocytobiosis research.

    Science.gov (United States)

    Fokin, S I; Schweikert, M; Brümmer, F; Görtz, H-D

    2005-04-01

    Among ciliate genera, only Paramecium and Euplotes species have been studied extensively as host organisms of bacterial endocytobionts. In this article, we show that members of the genus Spirostomum may also serve as a suitable system for endocytobiosis research. Two strains of Spirostomum minus (Heterotrichea, Ciliophora) collected in Germany and Italy, respectively, were found to harbor different types of bacterial infections. Bacteria of various sizes and shapes were observed in the cytoplasm or in the nuclei of the ciliates. The bacteria in the cytoplasm were either surrounded by a peribacterial membrane or lay naked. One of the bacterial species was found in the vicinity of the contractile fibrillar system (myonemes) of the ciliates. In rare cases, another type of bacteria was observed associated with mitochondria. The macronuclei of both the Italian and the German strains were crowded with endocytobionts. The endonuclear bacteria in the two S. minus strains differed with respect to their cytoplasmic structures but they were of similar size and both were rod shaped. According to the results of in situ hybridization, the endonuclear bacteria of the Italian strain belong to the subgroup of alphaproteobacteria, whereas the bacteria associated with the fibrillar system appeared to be gram-positive bacteria with high G+C content. While both the German and the Italian strains were found to permanently maintain their endocytobionts, they were at least partly colonized by different bacteria. This is taken as an indication that geographically separated populations of ciliates may be stably infected by different endocytobionts, possibly due to different ecological conditions. For S. minus and S. ambiguum a total of 7 different bacterial endocytobionts have now been recorded. We recommend the members of the genus Spirostomum as a suitable system for endocytobiosis research.

  8. Wetland suitability and connectivity for trans-Saharan migratory waterbirds.

    Science.gov (United States)

    Merken, Ronny; Deboelpaep, Evelien; Teunen, Joachim; Saura, Santiago; Koedam, Nico

    2015-01-01

    To complete their life cycle waterbirds rely on patchily distributed and often ephemeral wetlands along their migration route in a vast unsuitable matrix. However, further loss and degradation of remaining wetland habitats might lead to a configuration and size of stopovers that is no longer sufficient to ensure long-term survival of waterbird populations. By identifying optimal conservation targets to maintain overall habitat availability en route, we can accommodate an as yet absent functional connectivity component in larger management frameworks for migratory waterbirds, such as the Ramsar Convention and the EU Natura 2000 Network. Using a graph-based habitat availability metric (Equivalent Connected Area) we determine the functional connectivity of wetland networks for seven migratory waterbirds with divergent habitat requirements. Analyses are performed at two spatial extents both spanning the Mediterranean Sea and centered around Greece (Balkan-Cyrenaica and Greece-Cyrenaica). We create species-specific suitable habitat maps and account for human disturbance by species-specific disturbance buffers, based on expert estimates of Flight Initiation Distances. At both spatial extents we quantitatively determine the habitat networks' overall functional connectivity and identify wetland sites that are crucial for maintaining a well-connected network. We show that the wetland networks for both spatial extents are relatively well connected and identify several wetland sites in Greece and Libya as important for maintaining connectivity. The application of disturbance buffers results in wetland site-specific reduction of suitable habitat area (0.90-7.36%) and an overall decrease of the network's connectivity (0.65-6.82%). In addition, we show that the habitat networks of a limited set of species can be combined into a single network which accounts for their autoecological requirements. We conclude that targeted management in few but specific wetland complexes could

  9. Wetland suitability and connectivity for trans-Saharan migratory waterbirds.

    Directory of Open Access Journals (Sweden)

    Ronny Merken

    Full Text Available To complete their life cycle waterbirds rely on patchily distributed and often ephemeral wetlands along their migration route in a vast unsuitable matrix. However, further loss and degradation of remaining wetland habitats might lead to a configuration and size of stopovers that is no longer sufficient to ensure long-term survival of waterbird populations. By identifying optimal conservation targets to maintain overall habitat availability en route, we can accommodate an as yet absent functional connectivity component in larger management frameworks for migratory waterbirds, such as the Ramsar Convention and the EU Natura 2000 Network. Using a graph-based habitat availability metric (Equivalent Connected Area we determine the functional connectivity of wetland networks for seven migratory waterbirds with divergent habitat requirements. Analyses are performed at two spatial extents both spanning the Mediterranean Sea and centered around Greece (Balkan-Cyrenaica and Greece-Cyrenaica. We create species-specific suitable habitat maps and account for human disturbance by species-specific disturbance buffers, based on expert estimates of Flight Initiation Distances. At both spatial extents we quantitatively determine the habitat networks' overall functional connectivity and identify wetland sites that are crucial for maintaining a well-connected network. We show that the wetland networks for both spatial extents are relatively well connected and identify several wetland sites in Greece and Libya as important for maintaining connectivity. The application of disturbance buffers results in wetland site-specific reduction of suitable habitat area (0.90-7.36% and an overall decrease of the network's connectivity (0.65-6.82%. In addition, we show that the habitat networks of a limited set of species can be combined into a single network which accounts for their autoecological requirements. We conclude that targeted management in few but specific wetland

  10. Small Device For Short-Range Antenna Measurements Using Optics

    DEFF Research Database (Denmark)

    Yanakiev, Boyan Radkov; Nielsen, Jesper Ødum; Christensen, Morten

    2011-01-01

    This paper gives a practical solution for implementing an antenna radiation pattern measurement device using optical fibers. It is suitable for anechoic chambers as well as short range channel sounding. The device is optimized for small size and provides a cheap and easy way to make optical antenna...

  11. The long-range electromobility; Die Langstrecken-Elektromobilitaet

    Energy Technology Data Exchange (ETDEWEB)

    Burkert, Andreas

    2013-05-01

    The recent advances in the fuel cell technology prompted the automotive developers to bring to design hybrid electric vehicles with a fuel cell and a lithium-ion battery. Thus, the long-range electric mobility is possible at a short refueling time simultaneously. In addition, the lithium battery is suitable for preconditioning of the hydrogen fuel cell.

  12. Diagnostic Utility of Broad Range Bacterial 16S rRNA Gene PCR with Degradation of Human and Free Bacterial DNA in Bloodstream Infection Is More Sensitive Than an In-House Developed PCR without Degradation of Human and Free Bacterial DNA

    Directory of Open Access Journals (Sweden)

    Petra Rogina

    2014-01-01

    Full Text Available We compared a commercial broad range 16S rRNA gene PCR assay (SepsiTest to an in-house developed assay (IHP. We assessed whether CD64 index, a biomarker of bacterial infection, can be used to exclude patients with a low probability of systemic bacterial infection. From January to March 2010, 23 patients with suspected sepsis were enrolled. CD64 index, procalcitonin, and C-reactive protein were measured on admission. Broad range 16S rRNA gene PCR was performed from whole blood (SepsiTest or blood plasma (IHP and compared to blood culture results. Blood samples spiked with Staphylococcus aureus were used to assess sensitivity of the molecular assays in vitro. CD64 index was lower in patients where possible sepsis was excluded than in patients with microbiologically confirmed sepsis (P=0.004. SepsiTest identified more relevant pathogens than blood cultures (P=0.008; in three patients (13% results from blood culture and SepsiTest were congruent, whereas in four cases (17.4% relevant pathogens were detected by SepsiTest only. In vitro spiking experiments suggested equal sensitivity of SepsiTest and IHP. A diagnostic algorithm using CD64 index as a decision maker to perform SepsiTest shows improved detection of pathogens in patients with suspected blood stream infection and may enable earlier targeted antibiotic therapy.

  13. Suitability Assessment of Printed Dietary Guidelines for Pregnant Women and Parents of Infants and Toddlers From 7 European Countries.

    Science.gov (United States)

    Garnweidner-Holme, Lisa Maria; Dolvik, Stina; Frisvold, Cathrine; Mosdøl, Annhild

    2016-02-01

    To evaluate selected European printed dietary guidelines for pregnant women and parents of infants and toddlers using the suitability assessment of materials (SAM) method. A descriptive study to determine the suitability of 14 printed dietary guidelines from 7 European countries based on deductive quantitative analyses. Materials varied greatly in format and content: 35.7% of materials were rated superior and 64.3% were rated adequate according to the overall SAM score for patient education material. None of the materials were scored not suitable. Among the categories, the highest average scores were for layout and typography and the lowest average scores were for cultural appropriateness and learning stimulation and motivation. Interrater reliability ranged from Cohen's kappa of 0.37 to 0.62 (mean, 0.41), indicating fair to moderate agreement among the 3 investigators. Overall, the suitability of the assessed printed dietary guidelines was adequate. Based on the SAM methodology, printed dietary guidelines may increase in suitability by emphasizing aspects related to health literacy and accommodating the needs of different food cultures within a population. Copyright © 2016 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  14. Regionalization of Habitat Suitability of Masson’s Pine based on geographic information system and Fuzzy Matter-Element Model

    Science.gov (United States)

    Zhou, Xiuteng; Zhao, Manxi; Zhou, Liangyun; Yang, Guang; Huang, Luqi; Yan, Cuiqi; Huang, Quanshu; Ye, Liang; Zhang, Xiaobo; Guo, Lanpin; Ke, Xiao; Guo, Jiao

    2016-01-01

    Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson’s pine (Pinus massoniana Lamb), as well as ensure effective development of Masson’s pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson’s pine needles accounted for only 7.41% of its distribution area. PMID:27694967

  15. Regionalization of Habitat Suitability of Masson’s Pine based on geographic information system and Fuzzy Matter-Element Model

    Science.gov (United States)

    Zhou, Xiuteng; Zhao, Manxi; Zhou, Liangyun; Yang, Guang; Huang, Luqi; Yan, Cuiqi; Huang, Quanshu; Ye, Liang; Zhang, Xiaobo; Guo, Lanpin; Ke, Xiao; Guo, Jiao

    2016-10-01

    Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson’s pine (Pinus massoniana Lamb), as well as ensure effective development of Masson’s pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson’s pine needles accounted for only 7.41% of its distribution area.

  16. Recombinant brewer's yeast strains suitable for accelerated brewing.

    Science.gov (United States)

    Suihko, M L; Blomqvist, K; Penttilä, M; Gisler, R; Knowles, J

    1990-06-01

    Four brewer's yeast strains carrying the alpha-ald gene of Klebsiella terrigena (ex. Aerobacter aerogenes) or of Enterobacter aerogenes on autonomously replicating plasmids were constructed. The alpha-ald genes were linked either to the ADC1 promoter or to the PGK1 promoter of yeast Saccharomyces cerevisiae. In pilot scale brewing (50 l) with three of these recombinant yeasts the formation of diacetyl in beer was so low during fermentation that lagering was not required. All other brewing properties of the strains were unaffected and the quality of finished beers was as good as that of finished beer prepared with the control strain. The total process time of beer production could therefore be reduced to 2 weeks, in contrast to about 5 weeks required in the conventional process.

  17. Recombinant hosts suitable for simultaneous saccharification and fermentation

    Science.gov (United States)

    Ingram, Lonnie O'Neal; Zhou, Shengde

    2007-06-05

    The invention provides recombinant host cells containing at least one heterologous polynucleotide encoding a polysaccharase under the transcriptional control of a surrogate promoter capable of increasing the expression of the polysaccharase. In addition, the invention further provides such hosts with genes encoding secretory protein/s to facilitate the secretion of the expressed polysaccharase. Preferred hosts of the invention are ethanologenic and capable of carrying out simultaneous saccharification fermentation resulting in the production of ethanol from complex cellulose substrates.

  18. Bioclimatic predictions of habitat suitability for the biofuel switchgrass in North America under current and future climate scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Barney, Jacob N.; DiTomaso, Joseph M. [One Shields Ave, Mailstop 4, Department of Plant Sciences, University of California, Davis, CA 95616 (United States)

    2010-01-15

    Dedicated biofuel crops, while providing economic and other benefits, may adversely impact biodiversity directly via land use conversion, or indirectly via creation of novel invasive species. To mitigate negative impacts bioclimatic envelope models (BEM) can be used to estimate the potential distribution and suitable habitat based on the climate and distribution in the native range. We used CLIMEX to evaluate the regions of North America suitable for agronomic production, as well as regions potentially susceptible to an invasion of switchgrass (Panicum virgatum) under both current and future climate scenarios. Model results show that >8.7 million km{sup 2} of North America has suitable to very favorable habitat, most of which occurs east of the Rocky Mountains. The non-native range of western North America is largely unsuitable to switchgrass as a crop or potential weed unless irrigation or permanent water is available. Under both the CGCM2 and HadCM3 climate models and A2 and B2 emissions scenarios, an overall increase in suitable habitat is predicted over the coming century, although the western US remains unsuitable. Our results suggest that much of North America is suitable for switchgrass cultivation, although this is likely to shift north in the coming century. Our results also agree with field collections of switchgrass outside its native range, which indicate that switchgrass is unlikely to establish unless it has access to water throughout the year (e.g., along a stream). Thus, it is the potential invasion of switchgrass into riparian habitats in the West that requires further investigation. (author)

  19. Suitability of black currant (Ribes nigrum L. as bred by NULES of Ukraine to machine harvesting of its berries

    Directory of Open Access Journals (Sweden)

    В. О. Сіленко

    2013-08-01

    Full Text Available In the article the authors show outcome of three years observation of blackcurrant varieties bred by Study Horticulture Department NULES of Ukraine for their suitabi­ lity to machine harvesting. Blackcurrant is the most common berry crop in Ukraine. When establishing intensive industrial plantations the varieties suitable for machine harvesting should be used. During 2006-2008 limited and unlimited traits of varieties bred by NULES of Ukraine suitability to combine harvesting were studied. All parameters of the examined varieties were compared against the requirements of the «ideal variety”. Simultaneous ripening of berries was observed in varieties Dochka Vorskly – 93,6%, Hovtva, Pamyaty Leonida Myhalevskoho – 92,6%. The pick off effort required to collect berries out of their clusters for all varieties but Yarynka was within acceptable range of 67...129 g. By effort applied for berries crush only Yarynka has failed to meet the necessary requirements. All the varie­ ties but Yarynka have been found suitable by growth habit of their bush (upright and semi-spread. Insufficient number fruits (6-7 pc. in clusters for varieties Narodna and Yarynka was noted. Berries weight for all studied varieties ranged within 1.27-1.84 g, their drop-off was 3-8%, duration of harvesting period ranged from 8 to 10 days, so all the parameters of varieties suggested they were suitable for picking berries by berry harvesters. Varieties Dochka Vorskly, Universitetska, Hovtva, Pamyatna, Premiera, Narodna, Leleka and Pamyaty Leonida Myhalevskoho were selected as suitable for combine harvesting by the complex of positive parameters.

  20. Estimating suitable environments for invasive plant species across large landscapes: a remote sensing strategy using Landsat 7 ETM+

    Science.gov (United States)

    Young, Kendal E.; Abbott, Laurie B.; Caldwell, Colleen A.; Schrader, T. Scott

    2013-01-01

    The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive plants in Big Bend National Park, southwest Texas, using a presence-only modeling approach. Giant reed (Arundo donax), Lehmann lovegrass (Eragrostis lehmanniana), horehound (Marrubium vulgare) and buffelgrass (Pennisteum ciliare) were selected for remote sensing spatial analyses. Multiple dates/seasons of imagery were used to account for habitat conditions within the study area and to capture phenological differences among targeted species and the surrounding landscape. Individual species models had high (0.91 to 0.99) discriminative ability to differentiate invasive plant suitable environments from random background locations. Average test area under the receiver operating characteristic curve (AUC) ranged from 0.91 to 0.99, indicating that plant predictive models exhibited high discriminative ability to differentiate suitable environments for invasive plant species from random locations. Omission rates ranged from <1.0 to 18%. We demonstrated that useful models estimating suitable environments for invasive plants may be created with <50 occurrence locations and that reliable modeling using presence-only datasets can be powerful tools for land managers.

  1. Suitable Strategies for the Development of Sahoolan Watery Cave Geotourism

    Directory of Open Access Journals (Sweden)

    H. Nouri

    2013-01-01

    Full Text Available Extended abstract1-IntroductionToday, tourism is one of the largest and most beneficial industries in the world and in many countries it is used as a development strategy. Geotourism or geological tourism is emerging as a new global phenomenon. It is a form of natural area tourism that specifically focuses on geology and landscape. Because of appropriate planning and recognizing advantages and limitations, this kind of tourism can play an important role in the national development and diversification of local economy. There is a wide variety of caves in Iran, including calcareous (karst, salt, ancient and human-made caves which Sahoolan is one of the most important of them. Though Sahoolan has a great range of potentials for geotourism development, geotourism is just emerging and taking its first developmental steps. So these questions arise: What are the potentialities and limitations of Geotourism development in this region? Which strategies are required for developing this type of tourism and following national and regional development?2. Theoretical Bases Geotourism is a new phenomenon in tourism industry. It is defined as tourism activity pertaining to geology and geomorphology, and the natural resources of landscape, landforms, fossil beds, rocks and minerals, with an emphasis on appreciating the processes that are creating and have created such features. Geotourism’s first definition appeared after 1990s. An early definition of geotourism was made by Thomas Hose. He specifically focused on geology and geomorphologic sites. The goal of geotourism is to maintain the character of place. It is not just travelling to undisturbed natural areas or to centers of human activity but travelling to destinations where nature and humans come together to produce a working landscape. The focus is to encourage visitation to an area by visitors who value the same working landscapes valued by the residents. Ideally, geotourism can be beneficial for both

  2. Suitability of Sterillium Gel for surgical hand disinfection.

    Science.gov (United States)

    Kampf, G; Kapella, M

    2003-07-01

    In some countries, alcohol-based hand gels are used for hygienic hand disinfection but their efficacy and suitability for surgical hand disinfection has never been investigated. The efficacy of Sterillium Gel was investigated according to prEN 12791 in two separate experiments. Finger tips of 20 volunteers per experiment were sampled for resident skin bacteria before surgical hand disinfection. In a cross-over design, each volunteer carried out a surgical hand disinfection with the reference alcohol [n-propanol 60%, (v/v)] or Sterillium Gel [ethanol 85% (v/v)] for 3 min. After the product application, one hand was sampled for the immediate effect, the other hand was gloved for 3 h and then sampled for the sustained effect. Samples were analysed for remaining resident bacteria. The mean of the pre-value, the 0 h and 3 h values of the reference disinfection and the test product were calculated. With the reference alcohol, respective mean immediate log10-reduction factors of 2.06+/-0.76 and 2.23+/-1.13 were found in both experiments. The mean sustained effects with the reference alcohol were 2.03+/-1.14 and 1.44+/-0.81. Sterillium Gel achieved respective mean immediate effects of 2.48+/-1.06 and 2.13+/-0.81, the mean sustained effects were 2.77+/-0.95 and 2.18+/-0.72. They proved significantly larger than those obtained with the reference alcohol (PSterillium Gel, therefore, more than fulfils the efficacy requirements for surgical hand disinfection of prEN 12791. In addition, 25 of 26 operating theatre healthcare workers in an orthopaedic hospital found it suitable for surgical hand disinfection after a single use, which included putting on a pair of surgical gloves. Although none of them had ever used an alcohol-based gel before, they had rather been accustomed to alcohol-based liquid products for years. The main reasons given for the positive assessment were better skin feeling after use, smell and easier donning of the surgical gloves. No significant correlation

  3. Ergonomic suitability of educational furniture and possible health implications in a university setting.

    Science.gov (United States)

    Odunaiya, Nse A; Owonuwa, Dolapo D; Oguntibeju, Oluwafemi O

    2014-01-01

    Ergonomically unsuitable school furniture is frequently considered one of the major causes of severe posture problems in adulthood. This study was designed to determine the ergonomic suitability of educational furniture in the lecture theaters at the University of Ibadan to serve as a case study. Sample of convenience was used to select participants for this study. The lecture theaters were selected based on their capacity, design, and dimension. A total of 240 students (120 males and 120 females) participated in this study. The ergonomic suitability of lecture theaters was determined by analyzing the mismatches between student anthropometric dimensions and furniture dimensions, and also by analyzing the design and orientation of the lecture theaters. The data were analyzed using descriptive statistics of mean, standard deviation, range, and median. The results showed that there was a significant difference in height between males and females but no significant difference between other anthropometric variables measured. About 20% of the participants had a fitting seat height, while seat height was unsuitable for the remaining 80.4%. On the other hand, 23.3% had a fitting seat depth, while it was unsuitable for 76.7% of the participants, and 99.6% of the participants had fitting desk clearance but 0.4% found it unsuitable. A total of 25.8% of the participants had a fitting desk height, while 74.2% of the students found it unsuitable. It was concluded that the furniture in the lecture theaters at the university studied was not ergonomically suitable for the students. Hence it is recommended that further studies, including more universities across a wide spectrum of society, should be performed to determine the effect of furniture on student health, and the need to adopt the use of adjustable furniture in lecture theaters to prevent health hazards that may occur secondary to the use of unsuitable furniture.

  4. Modelling the habitat suitability of cetaceans: Example of the sperm whale in the northwestern Mediterranean Sea

    Science.gov (United States)

    Praca, Emilie; Gannier, Alexandre; Das, Krishna; Laran, Sophie

    2009-04-01

    Cetaceans are mobile and spend long periods underwater. Because of this, modelling their habitat could be subject to a serious problem of false absence. Furthermore, extensive surveys at sea are time and money consuming, and presence-absence data are difficult to apply. This study compares the ability of two presence-absence and two presence-only habitat modelling methods and uses the example of the sperm whale ( Physeter macrocephalus) in the northwestern Mediterranean Sea. The data consist of summer visual and acoustical detections of sperm whales, compiled between 1998 and 2005. Habitat maps were computed using topographical and hydrological eco-geographical variables. Four methods were compared: principal component analysis (PCA), ecological niche factor analysis (ENFA), generalized linear model (GLM) and multivariate adaptive regression splines (MARS). The evaluation of the models was achieved by calculating the receiver operating characteristic (ROC) of the models and their respective area under the curve (AUC). Presence-absence methods (GLM, AUC=0.70, and MARS, AUC=0.79) presented better AUC than presence-only methods (PCA, AUC=0.58, and ENFA, AUC=0.66), but this difference was not statistically significant, except between the MARS and the PCA models. The four models showed an influence of both topographical and hydrological factors, but the resulting habitat suitability maps differed. The core habitat on the continental slope was well highlighted by the four models, while GLM and MARS maps also showed a suitable habitat in the offshore waters. Presence-absence methods are therefore recommended for modelling the habitat suitability of cetaceans, as they seem more accurate to highlight complex habitat. However, the use of presence-only techniques, in particular ENFA, could be very useful for a first model of the habitat range or when important surveys at sea are not possible.

  5. The effect of selenium on spoil suitability as root zone material at Navajo Mine, New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Lane, J.R.; Buchanan, B.A. [Buchanan Consultants, Ltd., Farmington, NM (United States); Ramsey, T.C. [BHP-Minerals, Fruitland, NM (United States)

    1995-09-01

    The root zone suitability limits for spoil Se at Navajo Mine in northwest New Mexico are currently 0.8 ppm total Se and 0.15 ppm hot-water soluble Se. These criteria were largely developed by the Office of Surface Mining using data from the Northern Great Plains. Applying these values, approximately 23% of the spoil volume and 47% of the spoil area sampled at Navajo Mine from 1985 to December 1993 were determined to be unsuitable as root zone material. Secondary Se accumulator plants (Atriplex canescens) growing in both undisturbed and reclaimed areas were randomly sampled for selenium from 1985 to December 1993. In most cases the undisturbed soil and reclaimed spoil at these plant sampling sites were sampled for both total and hot-water soluble Se. Selenium values for Atriplex canescens samples collected on the undisturbed sites averaged 0.64 ppm and ranged from 0.20 ppm to 2.5 ppm. Selenium values for the plants growing on spoil ranged from 0.02 ppm to 7.75 ppm and averaged 1.07 ppm. Total and hot-water Se values for spoil averaged 0.66 ppm and 0.06 ppm respectively, and ranged from 0.0 to 14.2 for total Se and 0.0 ppm to 0.72 ppm for hot-water soluble Se. The plant Se values were poorly correlated to both total and hot-water soluble Se values for both soil and spoil. Therefore, predicting suitable guidelines using normal regression techniques was ineffective. Based on background Se levels in native soils, and levels found on reclaimed areas with Atriplex canescens, it is suggested that a total Se level of 2.0 ppm and a hot-water soluble Se level of 0.25 ppm should be used to represent the suitability limits for Se at Navajo Mine. If these Se values are used, it is estimated that less than 1% of the spoil volume would be unsuitable. This volume of spoil seems to be a more accurate estimate of the amount of spoil with unsuitable levels of Se than the estimated 23% using the current guidelines.

  6. Finding Suitable Variability Abstractions for Family-Based Analysis

    DEFF Research Database (Denmark)

    Dimovski, Aleksandar; Brabrand, Claus; Wasowski, Andrzej

    2016-01-01

    For program families (Software Product Lines), specially designed variability-aware static (dataflow) analyses allow analyzing all variants (products) of the family, simultaneously, in a single run without generating any of the variants explicitly. They are also known as lifted or family-based an......For program families (Software Product Lines), specially designed variability-aware static (dataflow) analyses allow analyzing all variants (products) of the family, simultaneously, in a single run without generating any of the variants explicitly. They are also known as lifted or family......) and reduce it to something more tractable. % by manipulating the configuration space of the family. However, the number of possible abstractions is still intractably large to search naively, with most abstractions being too imprecise or too costly. In this work, we propose a technique to efficiently find...... suitable variability abstractions from a large family of abstractions for a variability-aware static analysis. The idea is to use a pre-analysis to estimate the impact of variability-specific parts of the program family on the analysis's precision. Then we use the pre-analysis results to find out when...

  7. Determining Suitable Areas for More Efficient Hazelnut Production

    Science.gov (United States)

    Saralioglu, E.; Yildirim, D.; Gungor, O.

    2016-06-01

    Turkey is the largest hazelnut producer and exporter in the world with approximately 75% worldwide production and 70-75% of world exports, yet according to FAO; annual yield gain rate is significantly lower than Italy and USA. While Turkey produces 0.94 ton/hectare hazelnut, average yield rates for USA, Italy and Spain are 2.6 ton/hectare, 1.68 ton/hectare and 1 ton/hectare, respectively. Hazelnut production in Turkey is primarily concentrated along Black Sea coast centered Giresun and Trabzon provinces. The purpose of this study is to propose a methodology to further improve the efficiency in hazelnut production by determining the most significant geographical criteria and using them for spatial queries and analysis in ArcGIS environment to detect most fertile hazelnut plantation areas. For the study, the Surmene district of Trabzon is selected for pilot region. A thematic map of hazelnut plantation areas created from the classification of WorldView-2 image of the district was used as the base map. Furthermore, a database is created with layers and cost maps using multicriteria decision methods. Detected most suitable areas for hazelnut production area are compared with the present situation. Proposed methodology and the database can be used by officials for better management of hazelnut production in Turkey, therefore in the world.

  8. DETERMINING SUITABLE AREAS FOR MORE EFFICIENT HAZELNUT PRODUCTION

    Directory of Open Access Journals (Sweden)

    E. Saralioglu

    2016-06-01

    Full Text Available Turkey is the largest hazelnut producer and exporter in the world with approximately 75% worldwide production and 70-75% of world exports, yet according to FAO; annual yield gain rate is significantly lower than Italy and USA. While Turkey produces 0.94 ton/hectare hazelnut, average yield rates for USA, Italy and Spain are 2.6 ton/hectare, 1.68 ton/hectare and 1 ton/hectare, respectively. Hazelnut production in Turkey is primarily concentrated along Black Sea coast centered Giresun and Trabzon provinces. The purpose of this study is to propose a methodology to further improve the efficiency in hazelnut production by determining the most significant geographical criteria and using them for spatial queries and analysis in ArcGIS environment to detect most fertile hazelnut plantation areas. For the study, the Surmene district of Trabzon is selected for pilot region. A thematic map of hazelnut plantation areas created from the classification of WorldView-2 image of the district was used as the base map. Furthermore, a database is created with layers and cost maps using multicriteria decision methods. Detected most suitable areas for hazelnut production area are compared with the present situation. Proposed methodology and the database can be used by officials for better management of hazelnut production in Turkey, therefore in the world.

  9. Soil suitability evaluation for crop selection using fuzzy sets methodology

    Directory of Open Access Journals (Sweden)

    Amin SHARIFIFAR

    2016-04-01

    Full Text Available In this study appraisal of four different agricultural land evaluation methods including the so-called Storie method, square root method, maximum limitation method and fuzzy sets method, was done. The study was performed in Bastam region, located in Semnan province at the north east of Iran. Three crops including tomato, wheat and potato were assessed for the purpose of this research. Soil characteristics assessed were rooting depth, CaCo3, organic carboncontent, clay content, pH and slope gradient. Statistical analyses were done at significance levels of α = 0.1 and α = 0.05. Results of regression between land indices, calculated through the four methods, with observed yields of the crops, showed that the regression were significant in fuzzy sets method for all of the assessed crops at p = 0.05 but not significant in maximum limitation method for any of the crops. The Storie and square root methods also showed a significant correlation with wheat yield at p = 0.1. This study was a demonstrative test of fuzzy sets theory in land suitability evaluation for agricultural uses, which revealed that this methodology is the most correct method in given circumstances.

  10. Concrete with carpet recyclates: suitability assessment by surface energy evaluation.

    Science.gov (United States)

    Schmidt, H; Cieślak, M

    2008-01-01

    Worn out textile floor coverings are burdensome wastes that are degraded in landfill sites after a very long period of time. One of the ways to manage this kind of waste may be the use of carpet recyclate (CR) as an additive for concrete reinforcement. Therefore, an attempt was made to predict the effects of recyclate additives on the durability a concrete-carpet mixture by employing the method of assessing surface properties of components in the concrete-carpet recyclates composite. Testing was performed on carpet wastes, containing polyamide (PA) and polypropylene (PP) piles and butadiene-styrene resin with chalk filler (BSC) as back coating, to assess the suitability of CR additive for concrete reinforcement by surface energy evaluation. Based on the measurements of contact angles, the free surface energy of recyclate components was determined. The reversible work of adhesion at the interface between these components in dry and wet states was also calculated. The results show that CR with both PA and PP fibers form a strong and water-resistant bond with concrete.

  11. Suitability of technical materials for machinery subsoilers for soil tillage

    Directory of Open Access Journals (Sweden)

    Radek Bednář

    2013-01-01

    Full Text Available Agricultural soil processing belongs to the basic elements in the process of crop production. Currently classic tillage method is decreasing and the only trend has stated as a shallow plowing. Suitable post harvest soil tillage greatly affects yields in the next cycle. The aim of the study is the analysis of abrasive wear of selected construction materials and their subsequent use for DXRV-HD cultivator. The performed tests are focused on monitoring the mechanical properties of the materials and their use for variable cutting tip of cultivator body. Tested materials are divided into four categories. These materials include tool steel (19436, carbon steel (12050, cast iron with globular graphite and welding material supplied as a functional complex on low carbon steel by the Abraweld company. These materials are tested together with the original part of share cultivator. The present experiment is focused on metallorgraphic, mechanical and abrasive analysis. Structural component of the material is identified by metallographic photos and then compared with the impact strength tested on Charpy hammer. Followed the abrasion resistance according to CSN 01 5084 and the total evaluation of the tested samples are done.

  12. Suitability of various materials for porous filters in diffusion experiments

    Energy Technology Data Exchange (ETDEWEB)

    Aldaba, David; Vidal, Miquel; Rigol, Anna [Univ. de Barcelona (Spain). Dept. de Quimica Analitica; Glaus, Martin; Van Loon, Luc [Paul Scherrer Institut, Villigen PSI (Switzerland). Lab. for Waste Management; Leupin, Olivier [Nagra, Wettingen (Switzerland)

    2014-10-01

    The suitability of different porous materials (stainless steel, VYCOR {sup registered} glass, Al{sub 2}O{sub 3} and PEEK) for use as confining filters in diffusion experiments was evaluated by measuring the effective diffusion coefficients (D{sub e}) of neutral (HTO) and ionic solutes (Na{sup +}, Cs{sup +}, Sr{sup 2+}, Cl{sup -}, SeO{sub 4}{sup 2-}) in the materials in through-diffusion experiments. For stainless steel filters, the D{sub e} values of the target solutes correlated satisfactorily with their bulk diffusion coefficient in water (D{sub w}); thus, the diffusion process in the stainless steel filters was primarily controlled by the diffusivity of the solvated ions. For the remaining materials, the D{sub e} and D{sub w} values were also correlated for the target solutes, and the geometric factors were in the sequence: VYCOR {sup registered} glass < Al{sub 2}O{sub 3} < PEEK. Stainless steel and VYCOR {sup registered} glass were the most appropriate materials because of their high D{sub e} values, but a specific interaction of caesium with VYCOR {sup registered} glass was hypothesised because the D{sub e} values obtained for this solute were slightly higher than expected.

  13. A new FPGA architecture suitable for DSP applications

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liyun; Lai Jinmei; Tong Jiarong; Tang Pushan; Chen Xing; Duan Xueyan; Chen Liguang; Wang Jian; Wang Yuan, E-mail: 071021037@fudan.edu.cn [ASIC and System State Key Laboratory, Fudan University, Shanghai 201203 (China)

    2011-05-15

    A new FPGA architecture suitable for digital signal processing applications is presented. DSP modules can be inserted into FPGA conveniently with the proposed architecture, which is much faster when used in the field of digital signal processing compared with traditional FPGAs. An advanced 2-level MUX (multiplexer) is also proposed. With the added SLEEP MODE PASS to traditional 2-level MUX, static leakage is reduced. Furthermore, buffers are inserted at early returns of long lines. With this kind of buffer, the delay of the long line is improved by 9.8% while the area increases by 4.37%. The layout of this architecture has been taped out in standard 0.13 {mu}m CMOS technology successfully. The die size is 6.3 x 4.5 mm{sup 2} with the QFP208 package. Test results show that performances of presented classical DSP cases are improved by 28.6%-302% compared with traditional FPGAs. (semiconductor integrated circuits)

  14. Site suitability criteria for solidified high level waste repositories

    Energy Technology Data Exchange (ETDEWEB)

    Heckman, R.A.; Holdsworth, T.; Isherwood, D.; Towse, D.F.; Dayem, N.L.

    1979-04-03

    The NRC is developing a framework of regulations, criteria, and standards. Lawrence Livermore Laboratory provides broad technical support to the NRC for developing this regulatory framework, part of which involves site suitability criteria for solidified high-level wastes (SHLW). Both the regulatory framework and the technical base on which it rests have evolved in time. This document is the second report of the technical support project. It was issued as a draft working paper for a programmatic review held at LLL from August 16 to 18, 1977. It was printed and distributed solely as a briefing document on preliminary methodology and initial findings for the purpose of critical review by those in attendance. These briefing documents are being reprinted now in their original formats as UCID-series reports for the sake of the historical record. Analysis results have evolved as both the models and data base have changed. As a result, the methodology, models, and data base in this document are severely outmoded.

  15. Archival bone marrow samples: suitable for multiple biomarker analysis.

    Science.gov (United States)

    Lund, Bendik; Najmi, Laeya A; Wesolowska-Andersen, Agata; Landsem, Veslemøy M; Rasmussen, Kirsten K; Borst, Louise; Gupta, Ramneek; Schmiegelow, Kjeld; Klungland, Helge

    2015-01-01

    AB Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

  16. Host preference and suitability of grasses for Oebalus pugnax

    Science.gov (United States)

    Awuni, GA; Gore, J; Cook, D; Bond, JA; Musser, FR; Adams, CA

    2014-01-01

    The rice stink bug, Oebalus pugnax (Fabricius) (Hemiptera: Pentatomidae: Carpocorini), though graminaceous, discriminates among its numerous host grass species. This could represent a feeding preference, it could be related to host suitability for growth and development. To clarify the role of host grass discrimination, two laboratory studies were conducted: (1) free-choice tests to evaluate preferences of O. pugnax among 11 wild host grass species found in three rice-producing counties of the central Mississippi Delta (MS, USA), and (2) no-choice tests to evaluate the impact of rice (Oryza sativa L.), junglerice [Echinochloa colona (L.) Link], and dallisgrass (Paspalum dilatatum Poir.) (all Poaceae), on the development of O. pugnax from second instar to adult. In the free-choice test, four experiments were conducted, each with four sets of host grass species and observed 1, 2, 4, 8, and 16 h after release in cages. Approximately 4 h was necessary for O. pugnax to settle on preferred host grasses. Oebalus pugnax showed a feeding preference for junglerice over all 10 other grass species. Bahiagrass, Paspalum notatum Flueggé, was the least preferred. The no-choice tests showed significant effect of host grass species on O. pugnax mean development time of nymphal survival to adults. Survival of nymphs was lower and mean development time was longer on dallisgrass compared to rice and junglerice. Knowledge of O. pugnax rate of growth and development on host grasses could be useful in the future development of rice integrated pest management strategies. PMID:25635144

  17. Habitat Suitability Index Models: Gulf of Mexico American Oyster

    Science.gov (United States)

    Cake, Edwin W.

    1983-01-01

    The American or eastern oyster (Crassostrea virrinica [Gmelin]), a bivalve in the family Ostreidae, is an important commercia and recreational species along the Atlantic and Gulf of Mexico coasts of North America and other areas (U.S. Pacific coast and Hawaii) where it has been introduced (Galtsoff 1964). It evolved over the last 25 million years (Miocene and Pliocene epochs) from an ancestral, Atlantic-Pacific species that also gave rise to the Central American oyster of the Pacific coast, Crassostrea corteziensis (Hertlein) (Stenzel 1971). It evolved to fill a eurytopic niche in coastal estuaries where it forms massive reefs in nearshore bays, sounds, lagoons, and river mouths. Its existence depends on suitable substratum (cultch and firm bottom sediments) and acceptable sal-inity conditions. The location and distribution of oyster reefs in a salt marsh-estuari ne ecosystem are not acci denta 1; rather, they result from the interacti on of many bi 01 ogi ca 1, chemica1, geo1ogi ca1, and phys i ca 1 processes (Butler 1954a; Marshall 1954; Bahr and Lanier 1981).

  18. Determination of Selection Method in Genetic Algorithm for Land Suitability

    Directory of Open Access Journals (Sweden)

    Irfianti Asti Dwi

    2016-01-01

    Full Text Available Genetic Algoirthm is one alternative solution in the field of modeling optimization, automatic programming and machine learning. The purpose of the study was to compare some type of selection methods in Genetic Algorithm for land suitability. Contribution of this research applies the best method to develop region based horticultural commodities. This testing is done by comparing the three methods on the method of selection, the Roulette Wheel, Tournament Selection and Stochastic Universal Sampling. Parameters of the locations used in the test scenarios include Temperature = 27°C, Rainfall = 1200 mm, hummidity = 30%, Cluster fruit = 4, Crossover Probabiitiy (Pc = 0.6, Mutation Probabilty (Pm = 0.2 and Epoch = 10. The second test epoch incluides location parameters consist of Temperature = 30°C, Rainfall = 2000 mm, Humidity = 35%, Cluster fruit = 5, Crossover Probability (Pc = 0.7, Mutation Probability (Pm = 0.3 and Epoch 10. The conclusion of this study shows that the Roulette Wheel is the best method because it produces more stable and fitness value than the other two methods.

  19. Which medications are suitable for agonist drug maintenance?

    Science.gov (United States)

    Darke, Shane; Farrell, Michael

    2016-05-01

    We examine the feasibility of agonist maintenance treatment for the major psychoactive drug classes: opioids, nicotine, benzodiazepines, cannabis, psychostimulants and alcohol. Eight clinical criteria for an agonist maintenance drug were assessed for each major drug class. These related to pharmacological aspects of the drug (agonist, pharmacological stability, dose-response, non-toxic) and neurocognitive sequelae (psychiatric, cognitive, craving, salience). Opioids and nicotine met all eight criteria for a maintenance drug. While nicotine has not been promoted widely or used for maintenance, it has the potential to fulfil that role. Cannabis met five criteria and has potential, but long-term data on cognitive impairment are required. Benzodiazepine maintenance would appear an option for the high-dose chaotic abuser, also meeting five criteria, although clinic dosing appears the safest option. Psychostimulants (three of eight criteria) and alcohol (one of eight) appear poor propositions for maintenance, in terms of both their pharmacological and their neurocognitive characteristics. Drug classes have properties that distinguish them in their suitability for maintenance treatment. Some classes not yet used for maintenance (notably nicotine and cannabis) have potential to fulfil such a role. Others, however, by their inherent nature, appear unsuitable for such a treatment regimen. © 2015 Society for the Study of Addiction.

  20. Neuroprotection by Radical Avoidance: Search for Suitable Agents

    Directory of Open Access Journals (Sweden)

    Rüdiger Hardeland

    2009-12-01

    Full Text Available Neurodegeneration is frequently associated with damage by free radicals. However, increases in reactive oxygen and nitrogen species, which may ultimately lead to neuronal cell death, do not necessarily reflect its primary cause, but can be a consequence of otherwise induced cellular dysfunction. Detrimental processes which promote free radical formation are initiated, e.g., by disturbances in calcium homeostasis, mitochondrial malfunction, and an age-related decline in the circadian oscillator system. Free radicals generated at high rates under pathophysiological conditions are insufficiently detoxified by scavengers. Interventions at the primary causes of dysfunction, which avoid secondary rises in radical formation, may be more efficient. The aim of such approaches should be to prevent calcium overload, to reduce mitochondrial electron dissipation, to support electron transport capacity, and to avoid circadian perturbations. l-Theanine and several amphiphilic nitrones are capable of counteracting excitotoxicity and/or mitochondrial radical formation. Resveratrol seems to promote mitochondrial biogenesis. Mitochondrial effects of leptin include attenuation of electron leakage. Melatonin combines all the requirements mentioned, additionally regulates anti- and pro-oxidant enzymes and is, with few exceptions, very well tolerated. In this review, the perspectives, problems and limits of drugs are compared which may be suitable for reducing the formation of free radicals.

  1. THE ROLE OF PEDOLOGICAL INFORMATION IN AGRICULTURAL LAND SUITABILITY ASSESSING

    Directory of Open Access Journals (Sweden)

    D. Dicu

    2012-12-01

    Full Text Available Soil characteristics can exert an influence on the development of root systems, mineral nutrition, providing the required heat treatment and conduct aerohidric main physiological processes, and plants (phytocoenosis, in turn, act both directly and indirectly on the state of soil fertility. In the soil conditions can be defined certain characteristics that may be conducive to land productivity and other properties derived from the first. Attributes such as size and composition of soil, humus content are crucial features, while cationic exchange capacity is determined by the first two and by the mineralogical nature of clay. Similarly, available water capacity can be considered as determined by soil texture and structure. Our research concerns an area of 141,249 ha. (72721ha. in Timis county and 68,528 ha in Arad county, belonging to areas located in Vinga Plain and its connection to the low plains or Lipova hills. The research of ecopedological conditions, data ordering and processing was done according to the Methodology of pedological studies elaboration; (vol I, II, III, developed by ICPA Bucharest in 1987 and the Romanian System of Soil Taxonomy (SRTS-2003. In assessing of land pretability for culture systems are considered soil factors who determine the degree of suitability, soil texture and soil moisture excess. Pretability estimation can be based on the information contained in existing soil studies in the area but also in the field research conducted on soils representative of a particular physical and geographical space.

  2. Treatment of phosphogypsum waste using suitable organic extractants.

    Science.gov (United States)

    El-Didamony, H; Ali, M M; Awwad, N S; Fawzy, M M; Attallah, M F

    Phosphogypsum (PG) is a residue of the phosphate fertilizer industry that has relatively high concentrations of harmful radioactive materials. The reduction in concentration of the radionuclides from PG was investigated. The removal process is based on leaching of radionuclides using suitable organic extractants. The studied radionuclides were (226)Ra, (210)Pb, (238)U and (40)K. The factors affect the leaching process such as type of leaching materials, contact time, concentration of the desired solvent, liquid to solid ratio, and temperature were studied. Based on the experimental results, about 71.1, 76.4, 62.4, and 75.7% of (226)Ra, (210)Pb, (238)U and (40)K respectively were successfully removed from the PG. The reduction in the concentration of radionuclides was accompanied by reduction in the concentration of rare earth elements (∑REE) equals to 69.8%. Using the desired organic extractant under optimum conditions for treatment of the PG waste leads to obtain a decontaminated product that can be safely used in many industrial applications.

  3. An experimental investigation of Fang's Ag superlens suitable for integration

    DEFF Research Database (Denmark)

    Jeppesen, Claus; Nielsen, Rasmus Bundgaard; Xiao, Sanshui

    2009-01-01

    We report on experimental realization of the Fang Ag superlens structure [1] suitable for further processing and integration in bio-chips by replacing PMMA with a highly chemical resistant cyclo-olefin copolymer, mr-I T85 (Micro Resist Technology, Berlin, Germany). The superlens was able to resolve...... processing is needed involving various organic polar solvents, PMMA cannot be used. We propose to use mr-I T85, which is highly chemically resistant to acids and polar solvents. Our superlens stack consists of a quartz/chrome grating mask, a 40 nm layer of mr-I T85, 35 nm Ag, and finally 70 nm...... to the excitation wavelength of the surface plasmons at the mr-I T85/Ag interface. Supporting COMSOL simulations illustrate the field intensity distribution inside the resist as well as the presence of surface plasmons at the mr-I T85/Ag boundary. AFM scans of the exposed structure revealed 80 nm gratings....

  4. A Fast Component-Tree Algorithm for High Dynamic-Range Images and Second Generation Connectivity

    NARCIS (Netherlands)

    Wilkinson, Michael H.F.

    2011-01-01

    Component trees are important data structures for computation of connected attribute filters. Though some of the available algorithms are suitable for high-dynamic range, and in particular floating point data, none are suitable for computation of component trees for so-called second-generation, and

  5. Fiat designs a platform suitable for gasoline, electric or hybrid

    Energy Technology Data Exchange (ETDEWEB)

    Cappelli, P.G.; Bonino, M. [Fiat Auto SpA, Turin (Italy)

    1995-12-31

    With the debate between purpose-built and existing designs, Fiat is working on a strategy to use a common platform for its new generation models which will allow economic concurrent design and development of a small car range featuring thermal, electric and hybrid versions. (Author)

  6. Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana.

    Science.gov (United States)

    Winterbach, Hanlie E K; Winterbach, Christiaan W; Boast, Lorraine K; Klein, Rebecca; Somers, Michael J

    2015-01-01

    Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus), additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs' preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana's agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana's still large and contiguous cheetah population.

  7. Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana

    Directory of Open Access Journals (Sweden)

    Hanlie E.K. Winterbach

    2015-07-01

    Full Text Available Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus, additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population.

  8. Suitability of Smartphone Inertial Sensors for Real-Time Biofeedback Applications

    Directory of Open Access Journals (Sweden)

    Anton Kos

    2016-02-01

    Full Text Available This article studies the suitability of smartphones with built-in inertial sensors for biofeedback applications. Biofeedback systems use various sensors to measure body functions and parameters. These sensor data are analyzed, and the results are communicated back to the user, who then tries to act on the feedback signals. Smartphone inertial sensors can be used to capture body movements in biomechanical biofeedback systems. These sensors exhibit various inaccuracies that induce significant angular and positional errors. We studied deterministic and random errors of smartphone accelerometers and gyroscopes, primarily focusing on their biases. Based on extensive measurements, we determined accelerometer and gyroscope noise models and bias variation ranges. Then, we compiled a table of predicted positional and angular errors under various biofeedback system operation conditions. We suggest several bias compensation options that are suitable for various examples of use in real-time biofeedback applications. Measurements within the developed experimental biofeedback application show that under certain conditions, even uncompensated sensors can be used for real-time biofeedback. For general use, especially for more demanding biofeedback applications, sensor biases should be compensated. We are convinced that real-time biofeedback systems based on smartphone inertial sensors are applicable to many similar examples in sports, healthcare, and other areas.

  9. Suitability of sago starch as a base for dual-modification

    Directory of Open Access Journals (Sweden)

    Saowakon Wattanachant

    2002-07-01

    Full Text Available The quality and physicochemical properties of native sago starch were studied in order to evaluate the suitability of sago starch as a base for dual-modification, hydroxypropylation and crosslinking. The properties of starch derivatives obtained from dual-modification are different depending upon the kind of starch bases used and their basic properties. Therefore, the properties of several starches including waxy maize, waxy barley, tapioca, wheat, corn and rice and properties of their derivatives were investigated comparatively. The data obtained elucidates that the swelling power of a starch base is the most important factor which influences the dual-modification. The native sago starch had higher swelling power and bigger average granule size when compared to that of other starch bases. Its gelatinization temperature was in the same range as that of waxy maize while its pasting characteristic was similar to that of tapioca starch. It can be inferred that sago starch is suitable as a starch base for hydroxypropylation and crosslinking.

  10. The model thin film alumina catalyst support suitable for catalysis-oriented surface science studies

    Energy Technology Data Exchange (ETDEWEB)

    Nartova, Anna V., E-mail: avnartova@gmail.com [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Novosibirsk State University, Pirogova St., 2, Novosibirsk, 630090 (Russian Federation); Bukhtiyarov, Andrey V., E-mail: avb@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Kvon, Ren I., E-mail: kvon@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Bukhtiyarov, Valerii I., E-mail: vib@catalysis.ru [Boreskov Institute of Catalysis SB RAS, Lavrentieva Ave., 5, Novosibirsk, 630090 (Russian Federation); Novosibirsk State University, Pirogova St., 2, Novosibirsk, 630090 (Russian Federation)

    2015-09-15

    Graphical abstract: - Highlights: • New model catalyst on “AlOx-thin film/FeCrAl” support is presented. • Metal substrate minimizes sample charging, allows fast and uniform heating. • Surface is rough to model the catalyst support's morphology. • Planar alumina is stable in air/gases/solutions and similar to γ-Al{sub 2}O{sub 3}. • New model support is suitable for in situ XPS, STM, TPD, TPR, etc. - Abstract: The preparation of thin continuous alumina film at the surface of metal substrate in UHV (ultra high vacuum) conditions is described. The peculiarities of the obtained films studied by XPS (X-ray photoelectron spectroscopy) and STM (scanning tunneling microscopy) are discussed. The long-term durability of the oxide film was tested and proved both under ambient conditions and in acidic aqueous solutions. The stability of the planar alumina samples toward oxidation by oxygen was checked in the wide ranges of gas pressure and sample temperature. The suggested procedure ensures the controlled and reproducible preparation of thin alumina films – model support appropriate for wet chemistry catalyst preparation, suitable for STM and for other Surface Science techniques studies of alumina supported metal catalysts.

  11. Suitable triggering algorithms for detecting strong ground motions using MEMS accelerometers

    Science.gov (United States)

    Jakka, Ravi Sankar; Garg, Siddharth

    2015-03-01

    With the recent development of digital Micro Electro Mechanical System (MEMS) sensors, the cost of monitoring and detecting seismic events in real time can be greatly reduced. Ability of MEMS accelerograph to record a seismic event depends upon the efficiency of triggering algorithm, apart from the sensor's sensitivity. There are several classic triggering algorithms developed to detect seismic events, ranging from basic amplitude threshold to more sophisticated pattern recognition. Algorithms based on STA/LTA are reported to be computationally efficient for real time monitoring. In this paper, we analyzed several STA/LTA algorithms to check their efficiency and suitability using data obtained from the Quake Catcher Network (network of MEMS accelerometer stations). We found that most of the STA/LTA algorithms are suitable for use with MEMS accelerometer data to accurately detect seismic events. However, the efficiency of any particular algorithm is found to be dependent on the parameter set used (i.e., window width of STA, LTA and threshold level).

  12. Suitability of Smartphone Inertial Sensors for Real-Time Biofeedback Applications.

    Science.gov (United States)

    Kos, Anton; Tomažič, Sašo; Umek, Anton

    2016-02-27

    This article studies the suitability of smartphones with built-in inertial sensors for biofeedback applications. Biofeedback systems use various sensors to measure body functions and parameters. These sensor data are analyzed, and the results are communicated back to the user, who then tries to act on the feedback signals. Smartphone inertial sensors can be used to capture body movements in biomechanical biofeedback systems. These sensors exhibit various inaccuracies that induce significant angular and positional errors. We studied deterministic and random errors of smartphone accelerometers and gyroscopes, primarily focusing on their biases. Based on extensive measurements, we determined accelerometer and gyroscope noise models and bias variation ranges. Then, we compiled a table of predicted positional and angular errors under various biofeedback system operation conditions. We suggest several bias compensation options that are suitable for various examples of use in real-time biofeedback applications. Measurements within the developed experimental biofeedback application show that under certain conditions, even uncompensated sensors can be used for real-time biofeedback. For general use, especially for more demanding biofeedback applications, sensor biases should be compensated. We are convinced that real-time biofeedback systems based on smartphone inertial sensors are applicable to many similar examples in sports, healthcare, and other areas.

  13. Assessment of water quality and suitability analysis of River Ganga in Rishikesh, India

    Science.gov (United States)

    Haritash, A. K.; Gaur, Shalini; Garg, Sakshi

    2016-11-01

    The water samples were collected from River Ganga in Rishikesh during December 2008 to assess its suitability for drinking, irrigation, and industrial usages using various indices. Based on the values obtained and suggested designated best use, water in upper segment can be used for drinking but after disinfection (Class A); organized outdoor bathing in middle segment (Class B); and can be used as drinking water source (Class C) in lower segment in Rishikesh. All the parameters were within the specified limits for drinking water quality except E. coli. The indices of suitability for irrigation and industrial application were also evaluated. The irrigation quality ranged from good to excellent at almost all places with the exception of percent sodium. The abundance of major ions followed K+> Ca2+> Cl- > HCO3 - > Na+> Mg2+> CO3 2- trend. The major cations suggested that the water is alkaline (Na + K) than alkaline earth (Ca + Mg) type. The heavy metals (Pb, Cu, Zn, Ni) were found either absent or within the limits specified. There was no specific industrial input of pollutants. Industrial applications of the river water should be limited since the water was found to be aggressive, based on Langelier saturation index (0.3) and Ryznar stability index (8.8), with the problem of heavy to intolerable corrosion. Water quality of Ganga in Rishikesh was good with exception of most probable number (MPN) which needs regular monitoring and measures to control.

  14. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa.

    Directory of Open Access Journals (Sweden)

    Omid Paknia

    Full Text Available The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing "no biogeography."

  15. Assessing the suitability of recycled plastics used as agricultural soil covers: migration study and experimental harvest.

    Science.gov (United States)

    Nerín, C; Batlle, R

    1999-01-01

    The present work is focused on evaluating the suitability of recycling postconsumer agricultural plastic films again for the same use. The criteria to assess the suitability was based on migration study. Both overall and specific migration tests were performed, and the results obtained (ranging from 0.14 to 1.27 mg/dm(2) for overall migration and from not detectable to 6.98 microg/dm(2) for specific migration) show how, from this point of view, the recycled material can be safely proposed to be used again as agricultural soil covers. A theoretical discussion about the migration process is also presented and a simple mathematical model was applied to the data obtained, showing how total migration which is experimentally detected is theoretically predictable. These conclusions found were used to design and develop a controlled crop of tomato by using this recycled film. The use of the recycled plastic in the whole process and the behavior and properties of the pesticides absorbed in the postconsumer film are discussed.

  16. Two dye combinations suitable for two-color/two-dye laser-induced fluorescence thermography for ethanol

    Science.gov (United States)

    Fenner, Andreas; Stephan, Peter

    2017-06-01

    This paper presents two dye combinations suitable for two-color/two-dye laser-induced fluorescence thermography for ethanol. Besides the temperature dependency of the fluorescence, the influences of laser fluence, dye concentration, pressure, dissolved air, and photobleaching are also discussed. The experimental data are compared with models and data available in literature. Based on this, parameter ranges for two-color/two-dye laser-induced fluorescence thermography applications can be determined.

  17. Extraction of DNA from exfoliative cytology specimens and its suitability for analysis by the polymerase chain reaction.

    Science.gov (United States)

    Jackson, D P; Payne, J; Bell, S; Lewis, F A; Taylor, G R; Peel, K R; Sutton, J; Quirke, P

    1990-01-01

    The extraction of DNA from archival exfoliative cytology samples would allow the molecular biological analysis of this readily available material using the polymerase chain reaction (PCR). We have quantitatively and qualitatively studied the extraction of DNA from a variety of cytological preparations. For both fresh and archival cervical smears, overnight incubation with proteinase K produces high yields of high molecular weight DNA, but simply boiling the samples produces DNA suitable for PCR amplification of a single copy gene. Increasing the proteinase K incubation to several days allows the extraction of DNA from fixed and stained archival cytology slides from a variety of sites. The extracted DNA was again suitable for PCR analysis. Fresh and archival cytological material can be utilized for molecular biological study of disease processes using PCR. Archival cytological material is probably the best source of DNA and RNA after stored frozen tissue.

  18. Prospects for altering host range for baculovirus bioinsecticides.

    Science.gov (United States)

    Thiem, S M

    1997-06-01

    Advances in the understanding of baculovirus replication and the identification of genes that affect host range set the stage for constructing recombinant baculoviruses for specific past insects. The modification of baculovirus host specificity has recently been achieved by inserting or deleting genes that affect virus replication or cellular defenses.

  19. Spatio-Temporal Identification of Areas Suitable for West Nile Disease in the Mediterranean Basin and Central Europe

    Science.gov (United States)

    Conte, Annamaria; Candeloro, Luca; Ippoliti, Carla; Monaco, Federica; De Massis, Fabrizio; Bruno, Rossana; Di Sabatino, Daria; Danzetta, Maria Luisa; Benjelloun, Abdennasser; Belkadi, Bouchra; El Harrak, Mehdi; Declich, Silvia; Rizzo, Caterina; Hammami, Salah; Ben Hassine, Thameur; Calistri, Paolo; Savini, Giovanni

    2015-01-01

    West Nile virus (WNV) is a mosquito-transmitted Flavivirus belonging to the Japanese encephalitis antigenic complex of the Flaviviridae family. Its spread in the Mediterranean basin and the Balkans poses a significant risk to human health and forces public health officials to constantly monitor the virus transmission to ensure prompt application of preventive measures. In this context, predictive tools indicating the areas and periods at major risk of WNV transmission are of paramount importance. Spatial analysis approaches, which use environmental and climatic variables to find suitable habitats for WNV spread, can enhance predictive techniques. Using the Mahalanobis Distance statistic, areas ecologically most suitable for sustaining WNV transmission were identified in the Mediterranean basin and Central Europe. About 270 human and equine clinical cases notified in Italy, Greece, Portugal, Morocco, and Tunisia, between 2008 and 2012, have been considered. The environmental variables included in the model were altitude, slope, night time Land Surface Temperature, Normalized Difference Vegetation Index, Enhanced Vegetation Index, and daily temperature range. Seasonality of mosquito population has been modelled and included in the analyses to produce monthly maps of suitable areas for West Nile Disease. Between May and July, the most suitable areas are located in Tunisia, Libya, Egypt, and North Cyprus. Summer/Autumn months, particularly between August and October, characterize the suitability in Italy, France, Spain, the Balkan countries, Morocco, North Tunisia, the Mediterranean coast of Africa, and the Middle East. The persistence of suitable conditions in December is confined to the coastal areas of Morocco, Tunisia, Libya, Egypt, and Israel. PMID:26717483

  20. Spatio-Temporal Identification of Areas Suitable for West Nile Disease in the Mediterranean Basin and Central Europe.

    Directory of Open Access Journals (Sweden)

    Annamaria Conte

    Full Text Available West Nile virus (WNV is a mosquito-transmitted Flavivirus belonging to the Japanese encephalitis antigenic complex of the Flaviviridae family. Its spread in the Mediterranean basin and the Balkans poses a significant risk to human health and forces public health officials to constantly monitor the virus transmission to ensure prompt application of preventive measures. In this context, predictive tools indicating the areas and periods at major risk of WNV transmission are of paramount importance. Spatial analysis approaches, which use environmental and climatic variables to find suitable habitats for WNV spread, can enhance predictive techniques. Using the Mahalanobis Distance statistic, areas ecologically most suitable for sustaining WNV transmission were identified in the Mediterranean basin and Central Europe. About 270 human and equine clinical cases notified in Italy, Greece, Portugal, Morocco, and Tunisia, between 2008 and 2012, have been considered. The environmental variables included in the model were altitude, slope, night time Land Surface Temperature, Normalized Difference Vegetation Index, Enhanced Vegetation Index, and daily temperature range. Seasonality of mosquito population has been modelled and included in the analyses to produce monthly maps of suitable areas for West Nile Disease. Between May and July, the most suitable areas are located in Tunisia, Libya, Egypt, and North Cyprus. Summer/Autumn months, particularly between August and October, characterize the suitability in Italy, France, Spain, the Balkan countries, Morocco, North Tunisia, the Mediterranean coast of Africa, and the Middle East. The persistence of suitable conditions in December is confined to the coastal areas of Morocco, Tunisia, Libya, Egypt, and Israel.

  1. An iterative and targeted sampling design informed by habitat suitability models for detecting focal plant species over extensive areas.

    Science.gov (United States)

    Wang, Ophelia; Zachmann, Luke J; Sesnie, Steven E; Olsson, Aaryn D; Dickson, Brett G

    2014-01-01

    Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods

  2. FORMS OF SUSTAINABLE TOURISM SUITABLE TO APUSENI MOUNTAINS, ROMANIA

    Directory of Open Access Journals (Sweden)

    Bac Dorin Paul

    2015-07-01

    Full Text Available Sustainable tourism is the result of the melange between tourism and sustainable tourism. The concept has evolved during the last decades of the twentieth century, in international conferences, summits etc. organized by the World Tourism Organization, the United Nations and other international organizations where it was defined, characterized and criticized. Unfortunately, the concept was not able to overcome its theoretical conceptualization and it did not reach practitioners of the tourism industry. Sustainable tourism has several forms which are actually practiced by tourists all over the world: ecotourism, backpacking, rural tourism, nature-based tourism, pro-poor tourism, volunteer tourism etc. In the present paper, we have focused on an area in Apuseni Mountains, Romania. We tried to identify the forms of sustainable tourism most suitable for this area considering: natural resources, socio-economical development, protected areas, gastronomic traditions etc. After considering all these we have selected three forms: ecotourism, volunteer tourism and slow tourism, which could have the highest impact in promoting this area, and actually all the Apuseni Mountains as an important destination for sustainable tourism. The arguments for ecotourism are based on the numerous natural tourism resources> caves, gorges, forests and wildlife. Volunteers are needed especially in conservation and English language course. For slow tourism, there are numerous trails for walking and biking. Also there are several foods, mainly based on milk and wild berries that should be promoted and sold under the slow food brand. The shortcomings of the research are the lack of quantitative and qualitative results, as there is no information regarding the number of tourists which visit the area during each year. Also, it is hard to compare the benefits of sustainable tourism with those of mass tourism, due to the lack of references. So it is harder to argue for sustainable

  3. Suitability of marginal biomass-derived biochars for soil amendment.

    Science.gov (United States)

    Buss, Wolfram; Graham, Margaret C; Shepherd, Jessica G; Mašek, Ondřej

    2016-03-15

    The term "marginal biomass" is used here to describe materials of little or no economic value, e.g. plants grown on contaminated land, food waste or demolition wood. In this study 10 marginal biomass-derived feedstocks were converted into 19 biochars at different highest treatment temperatures (HTT) using a continuous screw-pyrolysis unit. The aim was to investigate suitability of the resulting biochars for land application, judged on the basis of potentially toxic element (PTE) concentration, nutrient content and basic biochar properties (pH, EC, ash, fixed carbon). It was shown that under typical biochar production conditions the percentage content of several PTEs (As, Al, Zn) and nutrients (Ca, Mg) were reduced to some extent, but also that biochar can be contaminated by Cr and Ni during the pyrolysis process due to erosion of stainless steel reactor parts (average+82.8% Cr, +226.0% Ni). This can occur to such an extent that the resulting biochar is rendered unsuitable for soil application (maximum addition +22.5 mg Cr kg(-1) biochar and +44.4 mg Ni kg(-1) biochar). Biomass grown on land heavily contaminated with PTEs yielded biochars with PTE concentrations above recommended threshold values for soil amendments. Cd and Zn were of particular concern, exceeding the lowest threshold values by 31-fold and 7-fold respectively, despite some losses into the gas phase. However, thermal conversion of plants from less severely contaminated soils, demolition wood and food waste anaerobic digestate (AD) into biochar proved to be promising for land application. In particular, food waste AD biochar contained very high nutrient concentrations, making it interesting for use as fertiliser.

  4. Groundwater suitability recharge zones modelling - A GIS application

    Science.gov (United States)

    Dabral, S.; Bhatt, B.; Joshi, J. P.; Sharma, N.

    2014-11-01

    Groundwater quality in Gujarat state is highly variable and due to multiplicity of factors viz. influenced by direct sea water encroachment, inherent sediment salinity, water logging, overexploitation leading to overall deterioration in ground water quality, coupled with domestic and industrial pollution etc. The groundwater scenario in the state is not very encouraging due to imbalance between recharge and groundwater exploitation. Further, the demand for water has increased manifold owing to agricultural, industrial and domestic requirement and this has led to water scarcity in many parts of the state, which is likely to become more severe in coming future due to both natural and manmade factors. Therefore, sustainable development of groundwater resource requires precise quantitative assessment based on reasonably valid scientific principles. Hence, delineation of groundwater potential zones (GWPZ), has acquired great significance. The present study focuses on the integrated Geospatial and Multi-Criteria Decision Making (MCDM) techniques to determine the most important contributing factors that affect the groundwater resources and also to delineate the potential zones for groundwater recharge. The multiple thematic layers of influencing parameters viz. geology, geomorphology, soil, slope, drainage density and land use, weightages were assigned to the each factor according to their relative importance as per subject experts opinion owing to the natural setup of the region. The Analytical Hierarchy Process (AHP) was applied to these factors and potential recharge zones were identified. The study area for the assessment of groundwater recharge potential zones is Mahi-Narmada inter-stream region of Gujarat state. The study shows that around 28 % region has the excellent suitability of the ground water recharge.

  5. Ergonomic suitability of kitchen furniture regarding height accessibility.

    Science.gov (United States)

    Hrovatin, Jasna; Prekrat, Silvana; Oblak, Leon; Ravnik, David

    2015-03-01

    It is possible to significantly ease kitchen chores with properly sized and appropriately arranged cupboards. In designing kitchen furniture and the optimal depth and the height of storage capacities, accessibility should be taken into consideration. It is known that the optimal storage zone is between 800 and 1100 mm and that there is reduced visibility and accessibility at the level between 1400 and 1700 mm, which is even more prominent for the elderly. This suggests that wall cabinets are not recommended for the elderly. The aim of this study was to determine to what extent kitchens manufactured by Slovenian furniture manufacturers are suitable for users of different age groups with regard to the accessibility of goods stored in the cupboards. Furthermore, based on the measurement analysis, recommendations are provided for designing kitchen furniture that would meet the needs of the elderly. The study, carried out using a computer simulation model, analyzed the products of three Slovenian kitchen manufacturers. The cross section of accessibility in the wall cabinets was determined for different age groups of men and women. The results show that the efficacy of the volume in wall cabinets higher than 600 mm, in comparison to places where objects are easily reachable, is 30% lower for women, thus indicating the inefficiency of storage space in wall cabinets. In terms of accessibility, existing kitchens are not optimal for the elderly, and a model with a deeper worktop and wall cabinets lowered onto the worktop is proposed. Accessibility in such wall cabinets is increased by up to 70% if the body is moved forward by 30°.

  6. Habitat suitability criteria via parametric distributions: estimation, model selection and uncertainty

    Science.gov (United States)

    Som, Nicholas A.; Goodman, Damon H.; Perry, Russell W.; Hardy, Thomas B.

    2016-01-01

    Previous methods for constructing univariate habitat suitability criteria (HSC) curves have ranged from professional judgement to kernel-smoothed density functions or combinations thereof. We present a new method of generating HSC curves that applies probability density functions as the mathematical representation of the curves. Compared with previous approaches, benefits of our method include (1) estimation of probability density function parameters directly from raw data, (2) quantitative methods for selecting among several candidate probability density functions, and (3) concise methods for expressing estimation uncertainty in the HSC curves. We demonstrate our method with a thorough example using data collected on the depth of water used by juvenile Chinook salmon (Oncorhynchus tschawytscha) in the Klamath River of northern California and southern Oregon. All R code needed to implement our example is provided in the appendix. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  7. Electrospun polycaprolactone matrices with tensile properties suitable for soft tissue engineering.

    Science.gov (United States)

    Elamparithi, Anuradha; Punnoose, Alan M; Kuruvilla, Sarah; Ravi, Maddaly; Rao, Suresh; Paul, Solomon F D

    2016-05-01

    The extracellular environment is a complex network of functional and structural components that impart chemical and mechanical stimuli that affect cellular function and fate. Cell differentiation on three dimensional scaffolds is also determined by the modulus of the substrate. Electrospun PCL nanofibers, which mimic the extra cellular matrix, have been developed with a wide variety of solvents and their combinations. The various studies have revealed that the solvents used influence the physical and mechanical properties, resulting in scaffolds with Young's modulus in the range of 1.8-15.4 MPa, more suitable for engineering of hard tissue like bone. The current study describes the use of benign binary solvent-generated fibrous scaffolds with a Young's modulus of 36.05 ± 13.08 kPa, which is almost 50 times lower than that of scaffolds derived from the commonly used solvents, characterized with myoblast, which can be further explored for applications in muscle and soft tissue engineering.

  8. Smartphone-based distributed data collection enables rapid assessment of shorebird habitat suitability

    Science.gov (United States)

    Thieler, E. Robert; Zeigler, Sara; Winslow, Luke; Hines, Megan K.; Read, Jordan S.; Walker, Jordan I.

    2016-01-01

    Understanding and managing dynamic coastal landscapes for beach-dependent species requires biological and geological data across the range of relevant environments and habitats. It is difficult to acquire such information; data often have limited focus due to resource constraints, are collected by non-specialists, or lack observational uniformity. We developed an open-source smartphone application called iPlover that addresses these difficulties in collecting biogeomorphic information at piping plover (Charadrius melodus) nest sites on coastal beaches. This paper describes iPlover development and evaluates data quality and utility following two years of collection (n = 1799 data points over 1500 km of coast between Maine and North Carolina, USA). We found strong agreement between field user and expert assessments and high model skill when data were used for habitat suitability prediction. Methods used here to develop and deploy a distributed data collection system have broad applicability to interdisciplinary environmental monitoring and modeling.

  9. Determining suitable lego-structures to estimate stability of larger peptide nanostructures using computational methods.

    Science.gov (United States)

    Beke, Tamás; Czajlik, András; Csizmadia, Imre G; Perczel, András

    2006-02-02

    Nanofibers, nanofilms and nanotubes constructed of one to four strands of oligo-alpha- and oligo-beta-peptides were obtained by using carefully selected building units. Lego-type approaches based on thermoneutral isodesmic reactions can be used to reconstruct the total energies of both linear and tubular periodic nanostructures with acceptable accuracy. Total energies of several different nanostructures were accurately determined with errors typically falling in the subchemical range. Thus, attention will be focused on the description of suitable isodesmic reactions that have enabled the determination of the total energy of polypeptides and therefore offer a very fast, efficient and accurate method to obtain energetic information on large and even very large nanosystems.

  10. Essential Bacillus subtilis genes

    DEFF Research Database (Denmark)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

  11. Suitability of ARES for Simulating Tactical Burst EMP Environments.

    Science.gov (United States)

    1980-04-01

    IU- 6 mho/m). It is felt that the above aproach may be overly-restrictive and in this report we adopt a different viewpoint. Rather than...expected effects. Possible methods for simulating direct interaction in ARES will be discussed in Section 4. The range selected in this report represents...the ARES floor (b) Conducting foam (c) Auxiliary pulsers (d) Current injection (e) Direct cable drive None of these methods involve any direct

  12. Assessing Excel VBA Suitability for Monte Carlo Simulation

    OpenAIRE

    2015-01-01

    Monte Carlo (MC) simulation includes a wide range of stochastic techniques used to quantitatively evaluate the behavior of complex systems or processes. Microsoft Excel spreadsheets with Visual Basic for Applications (VBA) software is, arguably, the most commonly employed general purpose tool for MC simulation. Despite the popularity of the Excel in many industries and educational institutions, it has been repeatedly criticized for its flaws and often described as questionable, if not complet...

  13. Severe loss of suitable climatic conditions for marsupial species in Brazil: challenges and opportunities for conservation.

    Directory of Open Access Journals (Sweden)

    Rafael D Loyola

    Full Text Available A wide range of evidences indicate climate change as one the greatest threats to biodiversity in the 21st century. The impacts of these changes, which may have already resulted in several recent species extinction, are species-specific and produce shifts in species phenology, ecological interactions, and geographical distributions. Here we used cutting-edge methods of species distribution models combining thousands of model projections to generate a complete and comprehensive ensemble of forecasts that shows the likely impacts of climate change in the distribution of all 55 marsupial species that occur in Brazil. Consensus projections forecasted range shifts that culminate with high species richness in the southeast of Brazil, both for the current time and for 2050. Most species had a significant range contraction and lost climate space. Turnover rates were relatively high, but vary across the country. We also mapped sites retaining climatic suitability. They can be found in all Brazilian biomes, especially in the pampas region, in the southern part of the Brazilian Atlantic Forest, in the north of the Cerrado and Caatinga, and in the northwest of the Amazon. Our results provide a general overview on the likely effects of global climate change on the distribution of marsupials in the country as well as in the patterns of species richness and turnover found in regional marsupial assemblages.

  14. Suitability of faecal near-infrared reflectance spectroscopy (NIRS) predictions for estimating gross calorific value

    Energy Technology Data Exchange (ETDEWEB)

    De la Roza-Delgado, B.; Modroño, S.; Vicente, F.; Martínez-Fernández, A.; Soldado, A.

    2015-07-01

    A total of 220 faecal pig and poultry samples, collected from different experimental trials were employed with the aim to demonstrate the suitability of Near Infrared Reflectance Spectroscopy (NIRS) technology for estimation of gross calorific value on faeces as output products in energy balances studies. NIR spectra from dried and grounded faeces samples were analyzed using a Foss NIRSystem 6500 instrument, scanning over the wavelength range 400-2500 nm. Validation studies for quantitative analytical models were carried out to estimate the relevance of method performance associated to reference values to obtain an appropriate, accuracy and precision. The results for prediction of gross calorific value (GCV) of NIRS calibrations obtained for individual species showed high correlation coefficients comparing chemical analysis and NIRS predictions, ranged from 0.92 to 0.97 for poultry and pig. For external validation, the ratio between the standard error of cross validation (SECV) and the standard error of prediction (SEP) varied between 0.73 and 0.86 for poultry and pig respectively, indicating a sufficiently precision of calibrations. In addition a global model to estimate GCV in both species was developed and externally validated. It showed correlation coefficients of 0.99 for calibration, 0.98 for cross-validation and 0.97 for external validation. Finally, relative uncertainty was calculated for NIRS developed prediction models with the final value when applying individual NIRS species model of 1.3% and 1.5% for NIRS global prediction. This study suggests that NIRS is a suitable and accurate method for the determination of GCV in faeces, decreasing cost, timeless and for convenient handling of unpleasant samples.. (Author)

  15. New approaches to gene and cell therapy for hemophilia.

    Science.gov (United States)

    Ohmori, T; Mizukami, H; Ozawa, K; Sakata, Y; Nishimura, S

    2015-06-01

    Hemophilia is considered suitable for gene therapy because it is caused by a single gene abnormality, and therapeutic coagulation factor levels may vary across a broad range. Recent success of hemophilia B gene therapy with an adeno-associated virus (AAV) vector in a clinical trial showed the real prospect that, through gene therapy, a cure for hemophilia may become a reality. However, AAV-mediated gene therapy is not applicable to patients with hemophilia A at present, and neutralizing antibodies against AAV reduce the efficacy of AAV-mediated strategies. Because patients that benefit from AAV treatment (hemophilia B without neutralizing antibodies) are estimated to represent only 15% of total patients with hemophilia, the development of basic technologies for hemophilia A and those that result in higher therapeutic effects are critical. In this review, we present an outline of gene therapy methods for hemophilia, including the transition of technical developments thus far and our novel techniques. © 2015 International Society on Thrombosis and Haemostasis.

  16. Extended temperature range rocket injector

    Science.gov (United States)

    Schneider, Steven J. (Inventor)

    1991-01-01

    A rocket injector is provided with multiple sets of manifolds for supplying propellants to injector elements. Sensors transmit the temperatures of the propellants to a suitable controller which is operably connnected to valves between these manifolds and propellant storage tanks. When cryogenic propellant temperatures are sensed, only a portion of the valves are opened to furnish propellants to some of the manifolds. When lower temperatures are sensed, additional valves are opened to furnish propellants to more of the manifolds.

  17. Evaluation of Internal Reference Genes for Quantitative Expression Analysis by Real-Time PCR in Ovine Whole Blood

    Directory of Open Access Journals (Sweden)

    Pier Luigi Acutis

    2011-11-01

    Full Text Available The use of reference genes is commonly accepted as the most reliable approach to normalize qRT-PCR and to reduce possible errors in the quantification of gene expression. The most suitable reference genes in sheep have been identified for a restricted range of tissues, but no specific data on whole blood are available. The aim of this study was to identify a set of reference genes for normalizing qRT-PCR from ovine whole blood. We designed 11 PCR assays for commonly employed reference genes belonging to various functional classes and then determined their expression stability in whole blood samples from control and disease-stressed sheep. SDHA and YWHAZ were considered the most suitable internal controls as they were stably expressed regardless of disease status according to both geNorm and NormFinder software; furthermore, geNorm indicated SDHA/HPRT, YWHAZ/GAPDH and SDHA/YWHAZ as the best reference gene combinations in control, disease-stressed and combined sheep groups, respectively. Our study provides a validated panel of optimal control genes which may be useful for the identification of genes differentially expressed by qRT-PCR in a readily accessible tissue, with potential for discovering new physiological and disease markers and as a tool to improve production traits (e.g., by identifying expression Quantitative Trait Loci. An additional outcome of the study is a set of intron-spanning primer sequences suitable for gene expression experiments employing SYBR Green chemistry on other ovine tissues and cells.

  18. Evaluation of Internal Reference Genes for Quantitative Expression Analysis by Real-Time PCR in Ovine Whole Blood

    Science.gov (United States)

    Peletto, Simone; Bertuzzi, Simone; Campanella, Chiara; Modesto, Paola; Maniaci, Maria Grazia; Bellino, Claudio; Ariello, Dario; Quasso, Antonio; Caramelli, Maria; Acutis, Pier Luigi

    2011-01-01

    The use of reference genes is commonly accepted as the most reliable approach to normalize qRT-PCR and to reduce possible errors in the quantification of gene expression. The most suitable reference genes in sheep have been identified for a restricted range of tissues, but no specific data on whole blood are available. The aim of this study was to identify a set of reference genes for normalizing qRT-PCR from ovine whole blood. We designed 11 PCR assays for commonly employed reference genes belonging to various functional classes and then determined their expression stability in whole blood samples from control and disease-stressed sheep. SDHA and YWHAZ were considered the most suitable internal controls as they were stably expressed regardless of disease status according to both geNorm and NormFinder software; furthermore, geNorm indicated SDHA/HPRT, YWHAZ/GAPDH and SDHA/YWHAZ as the best reference gene combinations in control, disease-stressed and combined sheep groups, respectively. Our study provides a validated panel of optimal control genes which may be useful for the identification of genes differentially expressed by qRT-PCR in a readily accessible tissue, with potential for discovering new physiological and disease markers and as a tool to improve production traits (e.g., by identifying expression Quantitative Trait Loci). An additional outcome of the study is a set of intron-spanning primer sequences suitable for gene expression experiments employing SYBR Green chemistry on other ovine tissues and cells. PMID:22174628

  19. Ranges of control in the transcriptional regulation of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Stoyan Helga

    2009-12-01

    Full Text Available Abstract Background The positioning of genes in the genome is an important evolutionary degree of freedom for organizing gene regulation. Statistical properties of these distributions have been studied particularly in relation to the transcriptional regulatory network. The systematics of gene-gene distances then become important sources of information on the control, which different biological mechanisms exert on gene expression. Results Here we study a set of categories, which has to our knowledge not been analyzed before. We distinguish between genes that do not participate in the transcriptional regulatory network (i.e. that are according to current knowledge not producing transcription factors and do not possess binding sites for transcription factors in their regulatory region, and genes that via transcription factors either are regulated by or regulate other genes. We find that the two types of genes ("isolated" and "regulatory" genes show a clear statistical repulsion and have different ranges of correlations. In particular we find that isolated genes have a preference for shorter intergenic distances. Conclusions These findings support previous evidence from gene expression patterns for two distinct logical types of control, namely digital control (i.e. network-based control mediated by dedicated transcription factors and analog control (i.e. control based on genome structure and mediated by neighborhood on the genome.

  20. Suitability of marginal biomass-derived biochars for soil amendment

    Energy Technology Data Exchange (ETDEWEB)

    Buss, Wolfram [UK Biochar Research Centre, School of Geosciences, University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF (United Kingdom); Graham, Margaret C. [School of Geosciences, University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF (United Kingdom); Shepherd, Jessica G. [UK Biochar Research Centre, School of Geosciences, University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF (United Kingdom); School of Geosciences, University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF (United Kingdom); Mašek, Ondřej, E-mail: ondrej.masek@ed.ac.uk [UK Biochar Research Centre, School of Geosciences, University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF (United Kingdom)

    2016-03-15

    The term “marginal biomass” is used here to describe materials of little or no economic value, e.g. plants grown on contaminated land, food waste or demolition wood. In this study 10 marginal biomass-derived feedstocks were converted into 19 biochars at different highest treatment temperatures (HTT) using a continuous screw-pyrolysis unit. The aim was to investigate suitability of the resulting biochars for land application, judged on the basis of potentially toxic element (PTE) concentration, nutrient content and basic biochar properties (pH, EC, ash, fixed carbon). It was shown that under typical biochar production conditions the percentage content of several PTEs (As, Al, Zn) and nutrients (Ca, Mg) were reduced to some extent, but also that biochar can be contaminated by Cr and Ni during the pyrolysis process due to erosion of stainless steel reactor parts (average + 82.8% Cr, + 226.0% Ni). This can occur to such an extent that the resulting biochar is rendered unsuitable for soil application (maximum addition + 22.5 mg Cr kg{sup −1} biochar and + 44.4 mg Ni kg{sup −1} biochar). Biomass grown on land heavily contaminated with PTEs yielded biochars with PTE concentrations above recommended threshold values for soil amendments. Cd and Zn were of particular concern, exceeding the lowest threshold values by 31-fold and 7-fold respectively, despite some losses into the gas phase. However, thermal conversion of plants from less severely contaminated soils, demolition wood and food waste anaerobic digestate (AD) into biochar proved to be promising for land application. In particular, food waste AD biochar contained very high nutrient concentrations, making it interesting for use as fertiliser. - Highlights: • Marginal biomass feedstocks are materials of little economic value. • Biochar from biomass grown on PTE-rich soils tends to exceed guideline values. • Biochar from biomass with high mineral content can be a beneficial nutrient source. • Cr and Ni