HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B.

Science.gov (United States)

Collin, Vanessa; Flamand, Louis

2017-06-26

Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B genome in every cell, are referred to as having inherited chromosomally-integrated HHV-6A/B (iciHHV-6) and represent approximately 1% of the world's population. Interestingly, HHV-6A/B integrate their genomes in a specific region of the chromosomes known as telomeres. Telomeres are located at chromosomes' ends and play essential roles in chromosomal stability and the long-term proliferative potential of cells. Considering that the integrated HHV-6A/B genome is mostly intact without any gross rearrangements or deletions, integration is likely used for viral maintenance into host cells. Knowing the roles played by telomeres in cellular homeostasis, viral integration in such structure is not likely to be without consequences. At present, the mechanisms and factors involved in HHV-6A/B integration remain poorly defined. In this review, we detail the potential biological and medical impacts of HHV-6A/B integration as well as the possible chromosomal integration and viral excision processes.

Secondary metabolites from Nepeta juncea | Jamila | African Journal ...

African Journals Online (AJOL)

The study of the phytochemical investigation on the chemical constituents of the whole plant of Nepeta juncea belonging to the family Lamiaceae resulted in the isolation and characterization of 11 compounds. Nine of these compounds were identified as ursolic acid, oleanolic acid, β-sitosterol, stigmasterol, stigmasterol ...

Uptake and localisation of lead in the root system of Brassica juncea

International Nuclear Information System (INIS)

Meyers, Donald E.R.; Auchterlonie, Graeme J.; Webb, Richard I.; Wood, Barry

2008-01-01

The uptake and distribution of Pb sequestered by hydroponically grown (14 days growth) Brassica juncea (3 days exposure; Pb activities 3.2, 32 and 217 μM) was investigated. Lead uptake was restricted largely to root tissue. Examination using scanning transmission electron microscopy-energy dispersive spectroscopy revealed substantial and predominantly intracellular uptake at the root tip. Endocytosis of Pb at the plasma membrane was not observed. A membrane transport protein may therefore be involved. In contrast, endocytosis of Pb into a subset of vacuoles was observed, resulting in the formation of dense Pb aggregates. Sparse and predominantly extracellular uptake occurred at some distance from the root tip. X-ray photoelectron spectroscopy confirmed that the Pb concentration was greater in root tips. Heavy metal rhizofiltration using B. juncea might therefore be improved by breeding plants with profusely branching roots. Uptake enhancement using genetic engineering techniques would benefit from investigation of plasma membrane transport mechanisms. - The sites of Pb sequestration within the root system of hydroponically grown Brassica juncea were identified

Overexpression of NPR1 in Brassica juncea Confers Broad Spectrum Resistance to Fungal Pathogens

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Sajad Ali

2017-10-01

Full Text Available Brassica juncea (Indian mustard is a commercially important oil seed crop, which is highly affected by many biotic stresses. Among them, Alternaria leaf blight and powdery mildew are the most devastating diseases leading to huge yield losses in B. juncea around the world. In this regard, genetic engineering is a promising tool that may possibly allow us to enhance the B. juncea disease resistance against these pathogens. NPR1 (non-expressor of pathogen-related gene 1 is a bonafide receptor of salicylic acid (SA which modulates multiple immune responses in plants especially activation of induced and systemic acquired resistance (SAR. Here, we report the isolation and characterization of new NPR1 homolog (BjNPR1 from B. juncea. The phylogenetic tree constructed based on the deduced sequence of BjNPR1 with homologs from other species revealed that BjNPR1 grouped together with other known NPR1 proteins of Cruciferae family, and was nearest to B. napus. Furthermore, expression analysis showed that BjNPR1 was upregulated after SA treatment and fungal infection but not by jasmonic acid or abscisic acid. To understand the defensive role of this gene, we generated B. juncea transgenic lines overexpressing BjNPR1, and further confirmed by PCR and Southern blotting. The transgenic lines showed no phenotypic abnormalities, and constitutive expression of BjNPR1 activates defense signaling pathways by priming the expression of antifungal PR genes. Moreover, BjNPR1 transgenic lines showed enhanced resistance to Alternaria brassicae and Erysiphe cruciferarum as there was delay in symptoms and reduced disease severity than non-transgenic plants. In addition, the rate of disease spreading to uninfected or distal parts was also delayed in transgenic plants thus suggesting the activation of SAR. Altogether, the present study suggests that BjNPR1 is involved in broad spectrum of disease resistance against fungal pathogens.

The chemical toxicity of cesium in Indian mustard (Brassica juncea L.) seedlings

International Nuclear Information System (INIS)

Lai, Jin-long; Tao, Zong-ya; Fu, Qian; Han, Na; Wu, Guo; Zhang, Hong; Lu, Hong; Luo, Xue-gang

2016-01-01

To distinguish between the radiological and chemical effects of radiocesium, we study the chemical toxicity of cesium in the seedlings of Indian mustard (Brassica juncea L.). In this study, the experiment was designed in two factors and five levels random block design to investigate the interaction effects of Cs and K. Results showed that excessive Cs was one of the main factors influence the growth of Brassica juncea seedlings. And the toxicity of Cs in Brassica juncea is likely to be caused by Cs interacts with K-binding sites in essential K-dependent protein, either competes with K for essential biochemical functions, causing intracellular metabolic disturbance. To test the hypothesis that the toxicity of Cs might cause intracellular metabolic disturbance, next-generation sequencing (NGS)-based Illumina paired-end Solexa sequencing platform was employed to analysis the changes in gene expression, and understand the key genes in B. juncea seedlings responding to the toxicity of Cs. Based on the assembled de novo transcriptome, 2032 DEGs that play significant roles in the response to the toxicity of Cs were identified. Further analysis showed that excessive Cs is disturbance the auxin signal transduction pathway, and inhibited the indoleacetic acid-induced protein (AUX/IAA) genes expression eventually lead the seedlings growth and development be inhibited. The results suggest that disturbances to tryptophan metabolism might be linked to changes in growth. - Highlights: • Analyze the chemical toxicity of cesium in seedlings of Indian mustard. • Distinguish between the radiological and chemical effects of radiocesium. • 2032 DEGs that play significant roles in the response to Cs toxicity were identified. • Excessive Cs is disturbance the auxin signal transduction pathway.

Feeding behaviour of generalist pests on Brassica juncea: implication for manipulation of glucosinolate biosynthesis pathway for enhanced resistance.

Science.gov (United States)

Kumar, Pawan; Augustine, Rehna; Singh, Amarjeet Kumar; Bisht, Naveen C

2017-10-01

Differential accumulation of plant defence metabolites has been suggested to have important ecological consequence in the context of plant-insect interactions. Feeding of generalist pests on Brassica juncea showed a distinct pattern with selective exclusion of leaf margins which are high in glucosinolates. Molecular basis of this differential accumulation of glucosinolates could be explained based on differential expression profile of BjuMYB28 homologues, the major biosynthetic regulators of aliphatic glucosinolates, as evident from quantitative real-time PCR and promoter:GUS fusion studies in allotetraploid B. juncea. Constitutive overexpression of selected BjuMYB28 homologues enhanced accumulation of aliphatic glucosinolates in B. juncea. Performance of two generalist pests, Helicoverpa armigera and Spodoptera litura larvae, on transgenic B. juncea plants were poor compared to wild-type plants in a no-choice experiment. Correlation coefficient analysis suggested that weight gain of H. armigera larvae was negatively correlated with gluconapin (GNA) and glucobrassicanapin (GBN), whereas that of S. litura larvae was negatively correlated with GNA, GBN and sinigrin (SIN). Our study explains the significance and possible molecular basis of differential distribution of glucosinolates in B. juncea leaves and shows the potential of overexpressing BjuMYB28 for enhanced resistance of Brassica crops against the tested generalist pests. © 2017 John Wiley & Sons Ltd.

Salicylic acid-mediated establishment of the compatibility between Alternaria brassicicola and Brassica juncea is mitigated by abscisic acid in Sinapis alba.

Science.gov (United States)

Mazumder, Mrinmoy; Das, Srirupa; Saha, Upala; Chatterjee, Madhuvanti; Bannerjee, Kaushik; Basu, Debabrata

2013-09-01

This work addresses the changes in the phytohormonal signature in the recognition of the necrotrophic fungal pathogen Alternaria brassicicola by susceptible Brassica juncea and resistant Sinapis alba. Although B. juncea, S. alba and Arabidopsis all belong to the same family, Brassicaceae, the phytohormonal response of susceptible B. juncea towards this pathogen is unique because the latter two species express non-host resistance. The differential expression of the PR1 gene and the increased level of salicylic acid (SA) indicated that an SA-mediated biotrophic mode of defence response was triggered in B. juncea upon challenge with the pathogen. Compared to B. juncea, resistant S. alba initiated enhanced abscisic acid (ABA) and jasmonic acid (JA) responses following challenge with this pathogen, as revealed by monitoring the expression of ABA-related genes along with the concentration of ABA and JA. Furthermore, these results were verified by the exogenous application of ABA on B. juncea leaves prior to challenge with A. brassicicola, which resulted in a delayed disease progression, followed by the inhibition of the pathogen-mediated increase in SA response and enhanced JA levels. Therefore, it seems that A. brassicicola is steering the defence response towards a biotrophic mode by mounting an SA response in susceptible B. juncea, whereas the enhanced ABA response of S. alba not only counteracts the SA response but also restores the necrotrophic mode of resistance by enhancing JA biosynthesis. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Pulmonary and hepatic lesions caused by the dehydropyrrolizidine alkaloid-producing plants Crotalaria juncea and Crotalaria retusa in donkeys

Science.gov (United States)

The effects and susceptibility of donkeys to Crotalaria juncea and Crotalaria retusa poisoning were determined at high and low doses. Seeds of C. juncea conaining 0.074% of dehyrdropyrrolizidine alkaloids (DHPAs) were administered to three donkeys at 0.3, 0.6 and 1 g/kg body weight daily for 365 day...

Effects of derived meals from juncea (Brassica juncea, yellow and black seeded canola (Brassica napus and multicarbohydrase enzymes supplementation on apparent metabolizable energy in broiler chickens

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Balachandar Jayaraman

2016-09-01

Full Text Available Two experiments were conducted to determine the nitrogen-corrected apparent metabolizable energy (AMEn of differently processed meals from Juncea (Brassica juncea, yellow and black seeded canola (Brassica napus, with or without supplementation of multi-carbohydrase enzymes (Enz in diets for broiler chickens. The first experiment was a 3 × 2 × 2 factorial arrangement with the main factors being seed type (yellow [Yellow] or black [B1] canola seeds and Juncea seeds, processed at two temperatures (high temperature desolventized-toasted [HTDT] at 95°C or low temperature desolventized-toasted [LTDT] at 57°C, with or without Enz. In Exp. 1, a total of 384 one-day-old male broiler chicks were randomly assigned to 64 battery cages, with 6 birds/cage. The second experiment was a 2 × 2 × 2 factorial arrangement with the main factors being seed type (Yellow or black [B2], seed source (Scott, Saskatchewan or Truro, Nova Scotia and Enz (with or without supplementation. A total of 264 one-day-old male broiler chicks were randomly assigned to 44 battery cages, with 6 birds per cage. In Exp. 1 and 2, all birds were fed a common starter diet from 1 to 14 days of age. From d 15 to 21, the birds were fed one of the test treatments, a basal grower diet or the basal grower diet replaced with 30% test ingredient with celite (0.8% added as an inert marker. Excreta was collected on d 20 and 21. In Exp. 1, there were no interactions (P > 0.05 among seed type, processing temperature and Enz. Processing temperature and dietary Enz did not affect (P > 0.05 AMEn of different canola meals. The AMEn of prepress solvent extracted canola and juncea meals (PSEM from Yellow (11.2 MJ/kg was higher (P  0.05 among seed color, location and Enz. Supplementation of dietary Enz did not affect (P > 0.05 AMEn of different cold press canola meals. The AMEn of cold press canola meals (CPM from Yellow (14.7 MJ/kg was higher (P < 0.05 compared with B2 (12.2�

Phosphate-assisted phytoremediation of arsenic by Brassica napus and Brassica juncea: Morphological and physiological response.

Science.gov (United States)

Niazi, Nabeel Khan; Bibi, Irshad; Fatimah, Ayesha; Shahid, Muhammad; Javed, Muhammad Tariq; Wang, Hailong; Ok, Yong Sik; Bashir, Safdar; Murtaza, Behzad; Saqib, Zulfiqar Ahmad; Shakoor, Muhammad Bilal

2017-07-03

In this study, we examined the potential role of phosphate (P; 0, 50, 100 mg kg -1 ) on growth, gas exchange attributes, and photosynthetic pigments of Brassica napus and Brassica juncea under arsenic (As) stress (0, 25, 50, 75 mg kg -1 ) in a pot experiment. Results revealed that phosphate supplementation (P100) to As-stressed plants significantly increased shoot As concentration, dry biomass yield, and As uptake, in addition to the improved morphological and gas exchange attributes and photosynthetic pigments over P0. However, phosphate-assisted increase in As uptake was substantially (up to two times) greater for B. napus, notably due to higher shoot As concentration and dry biomass yield, compared to B. juncea at the P100 level. While phosphate addition in soil (P100) led to enhanced shoot As concentration in B. juncea, it reduced shoot dry biomass, primarily after 50 and 75 mg kg -1 As treatments. The translocation factor and bioconcentration factor values of B. napus were higher than B. juncea for all As levels in the presence of phosphate. This study demonstrates that phosphate supplementation has a potential to improve As phytoextraction efficiency, predominantly for B. napus, by minimizing As-induced damage to plant growth, as well as by improving the physiological and photosynthetic attributes.

Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species.

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Payal Bansal

Full Text Available Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA and B. nigra (2n = 16; BB. Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11 and the corresponding progenitor genotypes of B. rapa (10×10 and B. nigra (9×9 were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47 of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis.

Resynthesized Brassica juncea lines with novel organellar genome ...

Indian Academy of Sciences (India)

To obtain shoot cultures, shoot apices were ... and culture, plant regeneration and hardening etc. are as described ... Hence two other media were tested for plant regeneration. .... genomes exert a strong influence on reorganization of nuclear.

Biofumigation with Brassica juncea, Raphanus sativus and Eruca sativa for the management of field populations of the potato cyst nematode Globodera pallida.

Science.gov (United States)

Ngala, Bruno M; Haydock, Patrick P J; Woods, Simon; Back, Matthew A

2015-05-01

The viability of potato cyst nematode (PCN) populations (Globodera pallida) was evaluated in three field experiments using Brassica juncea, Raphanus sativus and Eruca sativa amendments. These species were summer cultivated and autumn incorporated in experiment 1; in experiment 2, overwintered brassicaceous cover crops were spring incorporated. Experiment 3 involved determination of effects of metconazole application on biomass/glucosinolate production by B. juncea and R. sativus and on PCN pre- and post-incorporation. Glucosinolate contents were determined before incorporation. Following cover crop incorporation, field plots were planted with susceptible potatoes to evaluate the biofumigation effects on PCN reproduction. In experiment 1, PCN population post-potato harvest was reduced (P = 0.03) in B. juncea-treated plots, while R. sativus prevented further multiplication, but in experiment 2 there were no significant effects on PCN reproduction. In experiment 3, B. juncea or R. sativus either untreated or treated with metconazole reduced PCN populations. Glucosinolate concentrations varied significantly between different plant regions and cultivation seasons. Metconazole application increased the sinigrin concentration in B. juncea tissues. Glucosinolate concentrations correlated positively with PCN mortality for summer-cultivated brassicaceous plants. The results demonstrated that B. juncea and R. sativus green manures can play an important role in PCN management, particularly if included in an integrated pest management scheme. © 2014 Society of Chemical Industry.

Remediation of cadmium by Indian mustard (Brassica juncea L. from cadmium contaminated soil: a phytoextraction study

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Rajeev Kumar Bhadkariya

2014-05-01

Full Text Available Cadmium is a toxic metal for living organisms and an environmental contaminant. Soils in many parts of the world are slightly too moderately contaminated by Cd due to long term use and disposal of Cd-contaminated wastes. Cost effective technologies are needed to remove cadmium from the contaminated sites. Soil phytoextraction is engineering based, low cost and socially accepted developing technology that uses plants to clean up contaminants in soils. This technology can be adopted as a remediation of cadmium from Cd-contaminated soils with the help of Brassica juncea plant. The objective of this work was to evaluate the cadmium (Cd accumulate and the tolerance of Brassica juncea. The Cd accumulates in all parts of plants (roots, stems and leaves. It was found that accumulating efficiency increased with the increase in the concentration of applied cadmium metal solution. Maximum accumulation of cadmium was found in roots than stem and leaves. Phytoextraction coefficient and translocation factor were highest to show the validity of the Brassica juncea species for hyperaccumulation of the Cd metal. These results suggested that Brassica juncea has a high ability to tolerate and accumulate Cd, so it might be a promising plant to be used for phytoextraction of Cd contaminated soil. DOI: http://dx.doi.org/10.3126/ije.v3i2.10533 International Journal of the Environment Vol.3(2 2014: 229-237

PEMANFAATAN LIMBAH KOTORAN SAPI DAN JERAMI KACANG TANAH SEBAGAI BOKASHI CAIR BAGI PERTUMBUHAN TANAMAN SAWI (Brassica juncea L.

Directory of Open Access Journals (Sweden)

Artiana Artiana

2016-12-01

Full Text Available Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.. Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control using Bokashi solid. This research was conducted with four replications. Bokashi liquid nutrient content of C of 0,1045%, 0,0461% of N, P and K amounted to 0.0172% at 0.2500%. The content of nutrient dense Bokashi C of 6,0874%, 2,0169% of N, P and K amounted to 0,0218% at 5,7802%. Bokashi dosing different liquid to the growth of mustard (Brassica juncea L. significant effect on the growth of mustard, but still lower than the solid Bokashi. Dose liquid Bokashi most optimal for growing mustard (Brassica juncea L. is at 375 ml.

Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

Science.gov (United States)

Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

2016-01-01

Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.

Origins and diversity of rush Skeletonweed (Chondrilla juncea) from three continents

Science.gov (United States)

J. Gaskin; C. L. Kinter; M. Schwarzlander; G. P. Markin; S. Novak; J. F. Smith

2013-01-01

Rush skeletonweed (Chondrilla juncea L.) is an invasive apomictic perennial plant in Australia, South- and North America, accidentally introduced from Eurasia, which shows differential resistance/tolerance to some herbicides and classical biological control agents. Rush skeletonweed biotypes have been locally described using morphology, phenology, isozyme patterns, and...

Selenite resistant rhizobacteria stimulate SeO(3) (2-) phytoextraction by Brassica juncea in bioaugmented water-filtering artificial beds.

Science.gov (United States)

Lampis, Silvia; Ferrari, Anita; Cunha-Queda, A Cristina F; Alvarenga, Paula; Di Gregorio, Simona; Vallini, Giovanni

2009-09-01

Selenium is a trace metalloid of global environmental concern. The boundary among its essentiality, deficiency, and toxicity is narrow and mainly depends on the chemical forms and concentrations in which this element occurs. Different plant species-including Brassica juncea-have been shown to play a significant role in Se removal from soil as well as water bodies. Furthermore, the interactions between such plants, showing natural capabilities of metal uptake and their rhizospheric microbial communities, might be exploited to increase both Se scavenging and vegetable biomass production in order to improve the whole phytoextraction efficiency. The aim of the present study was to evaluate the capability of selenite removal of B. juncea grown in hydroponic conditions on artificially spiked effluents. To optimize phytoextraction efficiency, interactions between B. juncea and rhizobacteria were designedly elicited. Firstly, B. juncea was grown on water-filtering agriperlite beds in the presence of three different selenite concentrations, namely, 0.2, 1.0, and 2.0 mM. Plant growth was measured after 3 and 6 weeks of incubation in order to establish the selenite concentration at which the best plant biomass production could be obtained. Afterwards, water-filtering agriperlite beds were inoculated either with a selenium-acclimated microbial community deriving from the rhizosphere of B. juncea grown, erstwhile, in a selenite-amended soil or with axenic cultures of two bacterial strains, vicelike Bacillus mycoides SeITE01 and Stenotrophomonas maltophilia SeITE02, previously isolated and described for their high resistance to selenite. These latter were seeded separately or as a dual consortium. Selenite was amended at a final concentration of 1.0 mM. Total Se content in plant tissues (both shoots and roots), plant biomass production, and persistence of bioaugmented microbial inocula during the experimental time were monitored. Moreover, parameters such as bioconcentration

Brassinosteroids Denigrate the Seasonal Stress through Antioxidant Defense System in Seedlings of Brassica juncea L.

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Sandeep Kumar

2014-05-01

Full Text Available The present work has been undertaken to study the effect of exogenously application of 24-epiBL and 28-homoBL on soluble protein, proline contents and antioxidant defense system of Brassica juncea L. RLM 619 under the influence of seasonal stress. It was observed that 24-epiBL and 28-homoBL treatment enhance the soluble protein, dry weight and shoot length of B. juncea seedlings under seasonal stress. If seeds treated with the different concentrations (10-6, 10-8 and 10-10 M of 24-epiBL and 28-homoBL revealed batter growth, protein and proline contents as compare to untreated seedlings. Similarly the activities of antioxidant enzymes SOD, CAT, APOX, DHAR, PPO and Auxinases were enhanced by the application of different concentration of both brassinosteroids, whereas MDA content was decrease with both brassinosteroids treatments. Then we have concluded that both brassinolides have the seasonal stress ameliorative properties in B. juncea seedlings grown under the influence of seasonal stress. This study culminates to the role of brassinolides as an anti-stress property for protection of plant from various types of stresses.

De novo transcriptome profiling of cold-stressed siliques during pod filling stages of Indian mustard (Brassica juncea L.

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Somya eSinha

2015-10-01

Full Text Available Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h or long (12 h durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina’s NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering of these differentially expressed transcripts along with Spearman correlation analysis identified two major clusters representing early (5-15 DAP and late stages (20-30 DAP of silique development. Detailed analysis led to the discovery of two gene expression clusters whose transcripts were inducible at both durations of the cold stress irrespective of the developmental stages. We further explored the expression patterns of gene families encoding for transcription factors (TFs, transcription regulators (TRs and kinases, and found that cold stress induced protein kinases specifically during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold

PCIB an antiauxin enhances microspore embryogenisis in microspore culture of Brassica juncea

NARCIS (Netherlands)

Agarwal, P.K.; Agarwal, P.; Custers, J.B.M.; Liu, C.M.; Bhojwani, S.S.

2006-01-01

An efficient protocol to improve microspore embryogenesis is established in an important oleiferous crop, Brassica juncea (Indian mustard). Colchicine was used for enhancing microspore embryogenesis and also to obtain doubled haploid embryos. Colchicine at high concentrations (>10 mg l¿1), for 24

Role of Streptomyces pactum in phytoremediation of trace elements by Brassica juncea in mine polluted soils.

Science.gov (United States)

Ali, Amjad; Guo, Di; Mahar, Amanullah; Wang, Zhen; Muhammad, Dost; Li, Ronghua; Wang, Ping; Shen, Feng; Xue, Quanhong; Zhang, Zengqiang

2017-10-01

The industrial expansion, smelting, mining and agricultural practices have increased the release of toxic trace elements (TEs) in the environment and threaten living organisms. The microbe-assisted phytoremediation is environmentally safe and provide an effective approach to remediate TEs contaminated soils. A pot experiment was conducted to test the potential of an Actinomycete, subspecies Streptomyces pactum (Act12) along with medical stone compost (MSC) by growing Brassica juncea in smelter and mines polluted soils of Feng County (FC) and Tongguan (TG, China), respectively. Results showed that Zn (7, 28%), Pb (54, 21%), Cd (16, 17%) and Cu (8, 10%) uptake in shoot and root of Brassica juncea was pronounced in FC soil. Meanwhile, the Zn (40, 14%) and Pb (82, 15%) uptake in the shoot and root were also increased in TG soil. Shoot Cd uptake remained below detection, while Cu decreased by 52% in TG soil. The Cd and Cu root uptake were increased by 17% and 33%, respectively. Results showed that TEs uptake in shoot increased with increasing Act12 dose. Shoot/root dry biomass, chlorophyll and carotenoid content in Brassica juncea were significantly influenced by the application of Act12 in FC and TG soil. The antioxidant enzymatic activities (POD, PAL, PPO and CAT) in Brassica juncea implicated enhancement in the plant defense mechanism against the TEs induced stress in contaminated soils. The extraction potential of Brasssica was further evaluated by TF (translocation factor) and MEA (metal extraction amount). Based on our findings, further investigation of Act12 assisted phytoremediation of TEs in the smelter and mines polluted soil and hyperaccumulator species are suggested for future studies. Copyright © 2017. Published by Elsevier Inc.

PEMANFAATAN LIMBAH KOTORAN SAPI DAN JERAMI KACANG TANAH SEBAGAI BOKASHI CAIR BAGI PERTUMBUHAN TANAMAN SAWI (Brassica juncea L.)

OpenAIRE

Artiana Artiana; Lilis Hartati; Abrani Sulaiman; Jamzuri Hadie

2016-01-01

Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.)". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.). Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control...

Pemanfaatan Limbah Kotoran Sapi Dan Jerami Kacang Tanah Sebagai Bokashi Cair Bagi Pertumbuhan Tanaman Sawi (Brassica Juncea L.)

OpenAIRE

Artiana Artiana; Lilis Hartati; Abrani Sulaiman; Jamzuri Hadie

2016-01-01

Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.)". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.). Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control...

Variabilidade espacial de atributos de solo e de Crotalaria juncea L. em área severamente erodida

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A. A. C. Salviano

1998-03-01

Full Text Available O trabalho foi desenvolvido numa área de produção comercial de cana-de-açúcar, situada no município de Piracicaba (SP, numa associação de Podzólico Vermelho-Amarelo + solo litólico, no período de novembro de 1994 a março de 1995. Essa área vem sendo explorada com cana-de-açúcar há, aproximadamente, 30 anos e apresentava diversos sulcos de erosão. O objetivo deste trabalho foi caracterizar a variabilidade espacial de atributos de crotalária juncea (Crotalaria juncea L. e de solo em uma área sob condições de erosão severa. A área foi arada e gradeada com incorporação de 4 t ha-1 de calcário, antes da semeadura a lanço de 30 kg ha-1 de semente de crotalária juncea. Uma parcela de 50 x 70 m foi amostrada de acordo com uma malha de 5 por 5 m, totalizando 140 pontos. Foram avaliados atributos químicos do solo superficial (0,00-0,20 m e subsuperficial (0,20-0,40 m, sua granulometria e a espessura de solo remanescente (ES - definida como a camada do solo acima do horizonte C, além da produtividade de matéria seca (MS e altura da crotalária juncea (ALTPL. Os valores de atributos maiores ou menores que quatro desvios-padrões da média foram descartados. A colheita da parte aérea da crotalária foi realizada no início de sua floração, em miniparcelas de 2 x 2,5 m, e calculada a matéria seca. A dependência espacial dos atributos estudados foi avaliada por semivariogramas escalonados. Esses apresentaram dependência espacial, com exceção do P (0,00-0,20 m e K nas duas camadas. Os atributos puderam ser agrupados em três categorias homogêneas quanto ao alcance do semivariograma: atributos químicos do solo (12 a 32 m < componentes de planta (25 a 32 m < frações granulométricas (32 a 42 m. Os atributos que melhor explicaram a produtividade da crotalária juncea foram H + Al, valor T e saturação por bases.

Radiation induced pseudoisochromosomes in sunn hemp (Crotalaria juncea L.)

International Nuclear Information System (INIS)

Gupta, P.K.; Gupta, Rani

1978-01-01

In a population of sunn hemp (C. juncea), irradiated with gamma rays (30 Kr), a single plant was found to exhibit the presence of two ring univalents in 75.5% pollen mother cells. This was interpreted as a result of an interchange between the opposite arms of two homologous chromosomes giving rise to pseudoisochromosomes. In few other cells, four univalents and a single quadrivalent were also observed, thus indicating that two other interchanges involved very small segments, one of them between homologous chromosomes and the other between non-homologous chromosomes. (auth.)

Radiation induced pseudoisochromosomes in sunn hemp (Crotalaria juncea L. )

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Gupta, P K; Gupta, R [Meerut Univ. (India). Inst. of Advanced Studies

1978-01-01

In a population of sunn hemp (C. juncea), irradiated with gamma rays (30 Kr), a single plant was found to exhibit the presence of two ring univalents in 75.5% pollen mother cells. This was interpreted as a result of an interchange between the opposite arms of two homologous chromosomes giving rise to pseudoisochromosomes. In few other cells, four univalents and a single quadrivalent were also observed, thus indicating that two other interchanges involved very small segments, one of them between homologous chromosomes and the other between non-homologous chromosomes.

Does salt stress constrain spatial distribution of dune building grasses Ammophila arenaria and Elytrichia juncea on the beach?

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van Puijenbroek, Marinka E B; Teichmann, Corry; Meijdam, Noortje; Oliveras, Imma; Berendse, Frank; Limpens, Juul

2017-09-01

Rising sea levels threaten coastal safety by increasing the risk of flooding. Coastal dunes provide a natural form of coastal protection. Understanding drivers that constrain early development of dunes is necessary to assess whether dune development may keep pace with sea-level rise. In this study, we explored to what extent salt stress experienced by dune building plant species constrains their spatial distribution at the Dutch sandy coast. We conducted a field transplantation experiment and a glasshouse experiment with two dune building grasses Ammophila arenaria and Elytrigia juncea . In the field, we measured salinity and monitored growth of transplanted grasses in four vegetation zones: (I) nonvegetated beach, (II) E. juncea occurring, (III) both species co-occurring, and (IV) A. arenaria dominant. In the glasshouse, we subjected the two species to six soil salinity treatments, with and without salt spray. We monitored biomass, photosynthesis, leaf sodium, and nutrient concentrations over a growing season. The vegetation zones were weakly associated with summer soil salinity; zone I and II were significantly more saline than zones III and IV. Ammophila arenaria performed equally (zone II) or better (zones III, IV) than E. juncea , suggesting soil salinity did not limit species performance. Both species showed severe winter mortality. In the glasshouse, A. arenaria biomass decreased linearly with soil salinity, presumably as a result of osmotic stress. Elytrigia juncea showed a nonlinear response to soil salinity with an optimum at 0.75% soil salinity. Our findings suggest that soil salinity stress either takes place in winter, or that development of vegetated dunes is less sensitive to soil salinity than hitherto expected.

PEMANFAATAN PESTISIDA NABATI PADA PENGENDALIAN HAMA PLUTELLA XYLOSTELLA TANAMAN SAWI (Brassica juncea L. MENUJU PERTANIAN RAMAH LINGKUNGAN

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suhartini suhartini

2017-05-01

ABSTRACT The use of chemical pesticides has many negative impacts on the environment, it is necessary for the use of biological pesticide towards sustainable agriculture or environmentally friendly agriculture. In the village were encountered many types of leaves that can be used as a biological pesticide, and therefore this study aims to determine the effectiveness of pesticide plant extracts of the leaves of some plants covering the leaves of tobacco, elephantopus, yellow wood and green betel on mortality of Plutella xylostella pests in plants mustard greens (Brassica juncea L, heavy wet mustard and mustard leaf damage    This study uses a completely randomized design with the treatment of various crops as a pesticide vegetable. The treatments used 6 kinds (degree ie negative control (P0, the leaves of tobacco (P1, the leaves of elephantopus (P2, the leaves of yellow wood (P3, the leaves of greens betel (P4 and chemical pesticides as a positive control (P5 with each grade of 10 %. Parameters measured were mortality pests, heavy wet mustard greens and mustard greens leaf damage rate. The analysis was performed by one-way ANOVA.    The results showed that the extract from the leaves of tobacco (Nicotiana tabacum, the leaves of elephantopus, the leaves of yellow wood (Arcangelisia flava L. and the leaves of green betel (Piper betle Linn. With a 10 percent concentration of the extract on a variety of  leaves are not yet significant effect on mortality pests Plutella xylostella, heavy wet of mustard greens (brassica juncea l. and severity of leaf mustard greens (brassica juncea l.. The leaf extract the most influence on mortality Plutella xylostella sequential is an extract of the leaves tobacco, the leaves of greens betel, the leaves of yellow wood and the leaves of elephantopus. While the effect on weight of wet mustard greens (Brassica juncea l. in order are as follows: the leaves of yellow wood, the leaves of green betel, the leaves of elephantopus, and the

Fontes e níveis de salinidade na germinação de sementes de Crotalaria juncea L. Sources and levels of salinity on germination of Crotalaria juncea L. seeds

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Anísio da Silva Nunes

2009-06-01

Full Text Available Objetivou-se avaliar o efeito dos sais cloreto de cálcio (CaCl2, cloreto de sódio (NaCl e cloreto de potássio (KCl na germinação de Crotalaria juncea L. As sementes foram acondicionadas em caixas tipo gerbox, forradas com duas folhas de papel-filtro e umedecidas com as soluções-teste. Em cada tratamento foram utilizadas 200 sementes, dispostas em quatro repetições de 50 sementes. A indução do estresse salino foi realizada com soluções de NaCl, CaCl2 e KCl com potenciais osmóticos de 0; -0,4; -0,8; -1,2;-1,6 e -2,0 MPa. Foram realizadas avaliações de porcentagem de germinação, fitotoxicidade, tamanho de plântulas, matéria seca e IVG. O delineamento experimental utilizado foi o inteiramente casualizado, em esquema fatorial (3x5+1, composto pelas três fontes salinas em cinco doses e uma solução- teste. O aumento da concentração de KCl provocou toxicidade, prejudicando o IVG, a porcentagem de germinação e o crescimento de plântulas de C. juncea, enquanto as concentrações de NaCl e o CaCl2 não interferiram significativamente na germinação das sementes e no vigor de plântulas.This study was carried out in order to evaluate the effect of calcium chloride (CaCl2, sodium chloride (NaCl, and potassium chloride (KCl salts on germination of Crotalaria juncea L. seeds. The seeds were placed in gerbox boxes lined with two filter paper sheets and wet with test-solution. In each treatment, 200 seeds were used, distributed in four replicates of 50 seeds. The induction of the salt stress was done with solutions of NaCl, CaCl2 and KCl with osmotic potential of 0, -0.4, -0.8, -1.2, -1.6, and -2.0 MPa. Germination percentage, phytotoxicity, seedling size, mass of dry matter, and IVG were assessed. The experimental design was completely randomized, in a (3x5+1 factorial structure, composed of three salt sources in five levels and a test-solution. The increasing concentration of KCl caused toxicity, hindering the IVG, the germination

Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii.

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Zhang, J; Liu, X; Li, X-J

2015-01-16

The phages of Acinetobacter baumannii has drawn increasing attention because of the multi-drug resistance of A. baumanni. The aim of this study was to sequence Acinetobacter baumannii phage AB3 and conduct bioinformatic analysis to lay a foundation for genome remodeling and phage therapy. We isolated and sequenced A. baumannii phage AB3 and attempted to annotate and analyze its genome. The results showed that the genome is a double-stranded DNA with a total length of 31,185 base pairs (bp) and 97 open reading frames greater than 100 bp. The genome includes 28 predicted genes, of which 24 are homologous to phage AB1. The entire coding sequence is located on the negative strand, representing 90.8% of the total length. The G+C mol% was 39.18%, without areas of high G+C content over 200 bp in length. No GC island, tRNA gene, or repeated sequence was identified. Gene lengths were 120-3099 bp, with an average of 1011 bp. Six genes were found to be greater than 2000 bp in length. Genomic alignment and phylogenetic analysis of the RNA polymerase gene showed that similar to phage AB1, phage AB3 is a phiKMV-like virus in the T7 phage family.

Genome sequence of Prevotella intermedia SUNY aB G8-9K-3, a biofilm forming strain with drug-resistance.

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Moon, Ji-Hoi; Kim, Minjung; Lee, Jae-Hyung

Prevotella intermedia has long been known to be as the principal etiologic agent of periodontal diseases and associated with various systemic diseases. Previous studies showed that the intra-species difference exists in capacity of biofilm formation, antibiotic resistance, and serological reaction among P. intermedia strains. Here we report the genome sequence of P. intermedia SUNY aB G8-9K-3 (designated ATCC49046) that displays a relatively high antimicrobial resistant and biofilm-forming capacity. Genome sequencing information provides important clues in understanding the genetic bases of phenotypic differences among P. intermedia strains. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Potential for rhizofiltration of uranium using hairy root cultures of Brassica juncea and Chenopodium amaranticolor

International Nuclear Information System (INIS)

Eapen, Susan; Suseelan, K.N.; Tivarekar, Suchita; Kotwal, S.A.; Mitra, R.

2003-01-01

Hairy root cultures of Brassica juncea and Chenopodium amaranticolor were developed by genetic transformation using Agrobacterium rhizogenes. The stable, transformed root systems demonstrated a high growth rate of 1.5-3. g/g dry weight/day in Murashige and Skoog medium. In the present study, hairy root system was used for removal of uranium from the solution of concentration up to 5000 μM. The results indicated that the hairy roots could remove uranium from the aqueous solution within a short period of incubation. B. juncea could take up 20-23% of uranium from the solution containing up to 5000 μM, when calculated on g/g dry weight basis. C. amaranticolor showed a slow and steady trend in taking up uranium, with 13 uptake from the solution of 5000 μM concentration. Root growth was not affected up to 500 μM of uranium nitrate over a period of 10 days

Castasterone confers copper stress tolerance by regulating antioxidant enzyme responses, antioxidants, and amino acid balance in B. juncea seedlings.

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Yadav, Poonam; Kaur, Ravdeep; Kanwar, Mukesh Kumar; Sharma, Anket; Verma, Vinod; Sirhindi, Geetika; Bhardwaj, Renu

2018-01-01

The aim of the present study was to explore the effect of exogenous application of castasterone (CS) on physiologic and biochemical responses in Brassica juncea seedlings under copper (Cu) stress. Seeds were pre-soaked in different concentrations of CS and grown for 7 days under various levels of Cu. The exposure of B. juncea to higher levels of Cu led to decrease of morphologic parameters, with partial recovery of length and fresh weight in the CS pre-treated seedlings. Metal content was high in both roots and shoots under Cu exposure while the CS pre-treatment reduced the metal uptake. Accumulation of hydrogen peroxide (H 2 O 2 ) and superoxide anion radical (O 2 - ) were chosen as stress biomarker and higher levels of H 2 O 2 (88.89%) and O 2 - (62.11%) showed the oxidative stress in metal treated B. juncea seedlings, however, CS pre-treatment reduced ROS accumulation in Cu-exposed seedlings. The Cu exposures lead to enhance the plant's enzymatic and non-enzymatic antioxidant system. It was observed that enzymatic activities of ascorbate peroxidase (APOX), dehydroascorbate reductase (DHAR), and glutathione reductase (GR), glutathione perxoidase (GPOX) and gultrathione-s-transferase increased while activity of monodehydroascorbate reductase (MDHAR) decreased under Cu stress. The pre-treatment with CS positively affected the activities of enzymes. RT-PCR analysis showed that mRNA transcript levels were correlated with total enzymatic activity of DHAR, GR, GST and GSH. Increase in the gene expression of DHAR (1.85 folds), GR (3.24 folds), GST-1 (2.00 folds) and GSH-S (3.18 folds) was noticed with CS pre-treatment. Overall, the present study shows that Cu exposure induced severe oxidative stress in B. juncea plants and exogenous application of CS improved antioxidative defense system by modulating the ascorbate-glutathione cycle and amino acid metabolism. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome analysis of Brassica juncea var. tumida Tsen responses to Plasmodiophora brassicae primed by the biocontrol strain Zhihengliuella aestuarii.

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Luo, Yuanli; Dong, Daiwen; Su, Yu; Wang, Xuyi; Peng, Yumei; Peng, Jiang; Zhou, Changyong

2018-05-01

Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P. brassicae (P), one inoculated with P. brassica and the biocontrol agent Z. aestuarii at the same time (P + B), and the other was the control (H), in which P. brassicae was replaced by sterile water. A total of 19.94 Gb was generated by Illumina HiSeq sequencing. The sequence data were de novo assembled, and 107,617 unigenes were obtained. In total, 5629 differentially expressed genes between biocontrol-treated (P + B) and infected (P) samples were assigned to 126 KEGG pathways. Using multiple testing corrections, 20 pathways were significantly enriched with Qvalue ≤ 0.05. The resistance-related genes, involved in the production of pathogenesis-related proteins, pathogen-associated molecular pattern-triggered immunity, and effector-triggered immunity signaling pathways, calcium influx, salicylic acid pathway, reactive oxygen intermediates, and mitogen-activated protein kinase cascades, and cell wall modification, were obtained. The various defense responses induced by the biocontrol strain combatted the P. brassicae infection. The genes and pathways involved in plant resistance were induced by a biocontrol strain. The transcriptome data explained the molecular mechanism of the potential biocontrol strain against P. brassicae. The data will also serve as an important public information platform to study B. juncea var. tumida Tsen and will be useful for breeding mustard plants resistant to P. brassicae.

Isolation of phytase-producing bacteria from Himalayan soils and their effect on growth and phosphorus uptake of Indian mustard (Brassica juncea).

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Kumar, Vinod; Singh, Prashant; Jorquera, Milko A; Sangwan, Punesh; Kumar, Piyush; Verma, A K; Agrawal, Sanjeev

2013-08-01

Phytase-producing bacteria (PPB) is being investigated as plant growth promoting rhizobacteria (PGPR) to improve the phosphorus (P) nutrition and growth of plants grown in soil with high phytate content. Phytate is dominant organic P forms in many soils and must be hydrolyzed to be available for plants. Indian mustard (Brassica juncea) is a plant with economic importance in agriculture and phytoremediation, therefore biotechnological tools to improve growth and environmental stress tolerance are needed. In this study, we isolated and characterized PPB from Himalayan soils and evaluated their effect on growth and P uptake by B. juncea under greenhouse conditions. Sixty five PPB were isolated and based on phytate hydrolysis, three efficient PPB were chosen and identified as Acromobacter sp. PB-01, Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13. Selected PPB showed ability to grow at wide range of pH, temperature and salt concentrations as well as to harbour diverse PGPR activities, such as: solubilization of insoluble Ca-phosphate (193-642 μg ml(-1)), production of phytohormone indole acetic acid (5-39 μg ml(-1)) and siderophore. Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 showed 50 and 70 % inhibition of phytopathogen Rhizoctonia solani, respectively. Greenhouse potting assay also showed that the bacterization of B. juncea seeds with Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 significantly increased the biomass and P content in 30 days old seedlings. This study reveals the potential of PPB as PGPR to improve the growth of B. juncea.

Changes in the glucosinolate-myrosinase defense system in Brassica juncea cotyledons during seedling development.

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Wallace, S K; Eigenbrode, Sanford D

2002-02-01

Optimal defense theory (ODT) predicts that plant defenses will be allocated to plant organs and tissues in proportion to their relative fitness values and susceptibilities to attack. This study was designed to test ODT predictions on the myrosinase-glucosinolate defense system in Brassica juncea by examining the relationships between the fitness value of B. juncea cotyledons and the levels and effectiveness of cotyledon defenses. Specifically, we estimated fitness value of cotyledons during plant development by measuring plant growth and seed production after cotyledon damage or removal at successive seedling ages. Cotyledon removal within five days of emergence had a significant impact on growth and seed production, but cotyledon removal at later stages did not. Consistent with ODT, glucosinolate and myrosinase levels in cotyledons also declined with seedling age, as did relative defenses against a generalist herbivore, Spodoptera eridania, as estimated by bioassay. Declines in glucosinolates were as predicted by a passive, allometric dilution model based on cotyledon expansion. Declines in myrosinase activity were significantly more gradual than predicted by allometric dilution, suggesting active retention of myrosinase activity as young cotyledons expand.

Genetic Variability in Glucosinolates in Seed of Brassica juncea: Interest in Mustard Condiment

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Othmane Merah

2015-01-01

Full Text Available Brassica juncea is mostly used for oil production which implies selection of genotypes with low glucosinolates level and high oil content. In contrast, condiment production needs varieties with high level in some glucosinolates including sinigrin. The genetic variability was studied mostly by molecular tools. The objectives were almost the decrease of glucosinolates level in order to use the oilcake for animal feed. The aim of this work is to study the genetic variability for different glucosinolates and their relationships with agronomical traits within a large collection of Brassica juncea genotypes for condiment uses. A collection of 190 genotypes from different origins was studied in Dijon (France. Oil content and total glucosinolates, and sinigrin and gluconapin levels were measured. Flowering and maturation durations, seed yield, and yield components were also measured. Large variability was observed between genotypes for the measured traits within the studied collection. Total glucosinolates varied twofold between extreme genotypes. Values of sinigrin content varied from 0 to more than 134 µmol·g−1. Correlations between glucosinolates traits and both phenological and agronomical characters are presented and discussed for their potential for industrial condiment uses.

Development of transgenic Brassica juncea lines for reduced seed sinapine content by perturbing phenylpropanoid pathway genes.

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Sachin Kajla

Full Text Available Sinapine is a major anti-nutritive compound that accumulates in the seeds of Brassica species. When ingested, sinapine imparts gritty flavuor in meat and milk of animals and fishy odor to eggs of brown egg layers, thereby compromising the potential use of the valuable protein rich seed meal. Sinapine content in Brassica juncea germplasm ranges from 6.7 to 15.1 mg/g of dry seed weight (DSW which is significantly higher than the prescribed permissible level of 3.0 mg/g of DSW. Due to limited natural genetic variability, conventional plant breeding approach for reducing the sinapine content has largely been unsuccessful. Hence, transgenic approach for gene silencing was adopted by targeting two genes-SGT and SCT, encoding enzymes UDP- glucose: sinapate glucosyltransferase and sinapoylglucose: choline sinapoyltransferase, respectively, involved in the final two steps of sinapine biosynthetic pathway. These two genes were isolated from B. juncea and eight silencing constructs were developed using three different RNA silencing approaches viz. antisense RNA, RNAi and artificial microRNA. Transgenics in B. juncea were developed following Agrobacterium-mediated transformation. From a total of 1232 independent T0 transgenic events obtained using eight silencing constructs, 25 homozygous lines showing single gene inheritance were identified in the T2 generation. Reduction of seed sinapine content in these lines ranged from 15.8% to 67.2%; the line with maximum reduction had sinapine content of 3.79 mg/g of DSW. The study also revealed that RNAi method was more efficient than the other two methods used in this study.

Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

Science.gov (United States)

2011-01-01

Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): An apomictic invader on three continents

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Assessing the propagule pressure and geographic origins of invasive populations using molecular markers provides insights into the invasion process. Rush skeletonweed (Chondrilla juncea) is an apomictic perennial plant that is invasive in Australia, Argentina, Canada and the USA. Invasive biotypes...

Cell Culture Systems To Study Human Herpesvirus 6A/B Chromosomal Integration.

Science.gov (United States)

Gravel, Annie; Dubuc, Isabelle; Wallaschek, Nina; Gilbert-Girard, Shella; Collin, Vanessa; Hall-Sedlak, Ruth; Jerome, Keith R; Mori, Yasuko; Carbonneau, Julie; Boivin, Guy; Kaufer, Benedikt B; Flamand, Louis

2017-07-15

Human herpesviruses 6A/B (HHV-6A/B) can integrate their viral genomes in the telomeres of human chromosomes. The viral and cellular factors contributing to HHV-6A/B integration remain largely unknown, mostly due to the lack of efficient and reproducible cell culture models to study HHV-6A/B integration. In this study, we characterized the HHV-6A/B integration efficiencies in several human cell lines using two different approaches. First, after a short-term infection (5 h), cells were processed for single-cell cloning and analyzed for chromosomally integrated HHV-6A/B (ciHHV-6A/B). Second, cells were infected with HHV-6A/B and allowed to grow in bulk for 4 weeks or longer and then analyzed for the presence of ciHHV-6. Using quantitative PCR (qPCR), droplet digital PCR, and fluorescent in situ hybridization, we could demonstrate that HHV-6A/B integrated in most human cell lines tested, including telomerase-positive (HeLa, MCF-7, HCT-116, and HEK293T) and telomerase-negative cell lines (U2OS and GM847). Our results also indicate that inhibition of DNA replication, using phosphonoacetic acid, did not affect HHV-6A/B integration. Certain clones harboring ciHHV-6A/B spontaneously express viral genes and proteins. Treatment of cells with phorbol ester or histone deacetylase inhibitors triggered the expression of many viral genes, including U39 , U90 , and U100 , without the production of infectious virus, suggesting that the tested stimuli were not sufficient to trigger full reactivation. In summary, both integration models yielded comparable results and should enable the identification of viral and cellular factors contributing to HHV-6A/B integration and the screening of drugs influencing viral gene expression, as well as the release of infectious HHV-6A/B from the integrated state. IMPORTANCE The analysis and understanding of HHV-6A/B genome integration into host DNA is currently limited due to the lack of reproducible and efficient viral integration systems. In the

Identification and comprehensive evaluation of reference genes for RT-qPCR analysis of host gene-expression in Brassica juncea-aphid interaction using microarray data.

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Ram, Chet; Koramutla, Murali Krishna; Bhattacharya, Ramcharan

2017-07-01

Brassica juncea is a chief oil yielding crop in many parts of the world including India. With advancement of molecular techniques, RT-qPCR based study of gene-expression has become an integral part of experimentations in crop breeding. In RT-qPCR, use of appropriate reference gene(s) is pivotal. The virtue of the reference genes, being constant in expression throughout the experimental treatments, needs to be validated case by case. Appropriate reference gene(s) for normalization of gene-expression data in B. juncea during the biotic stress of aphid infestation is not known. In the present investigation, 11 reference genes identified from microarray database of Arabidopsis-aphid interaction at a cut off FDR ≤0.1, along with two known reference genes of B. juncea, were analyzed for their expression stability upon aphid infestation. These included 6 frequently used and 5 newly identified reference genes. Ranking orders of the reference genes in terms of expression stability were calculated using advanced statistical approaches such as geNorm, NormFinder, delta Ct and BestKeeper. The analysis suggested CAC, TUA and DUF179 as the most suitable reference genes. Further, normalization of the gene-expression data of STP4 and PR1 by the most and the least stable reference gene, respectively has demonstrated importance and applicability of the recommended reference genes in aphid infested samples of B. juncea. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

BjuB.CYP79F1 Regulates Synthesis of Propyl Fraction of Aliphatic Glucosinolates in Oilseed Mustard Brassica juncea: Functional Validation through Genetic and Transgenic Approaches.

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Manisha Sharma

Full Text Available Among the different types of methionine-derived aliphatic glucosinolates (GS, sinigrin (2-propenyl, the final product in 3C GS biosynthetic pathway is considered very important as it has many pharmacological and therapeutic properties. In Brassica species, the candidate gene regulating synthesis of 3C GS remains ambiguous. Earlier reports of GSL-PRO, an ortholog of Arabidopsis thaliana gene At1g18500 as a probable candidate gene responsible for 3C GS biosynthesis in B. napus and B. oleracea could not be validated in B. juncea through genetic analysis. In this communication, we report the isolation and characterization of the gene CYP79F1, an ortholog of A. thaliana gene At1g16410 that is involved in the first step of core GS biosynthesis. The gene CYP79F1 in B. juncea showed presence-absence polymorphism between lines Varuna that synthesizes sinigrin and Heera virtually free from sinigrin. Using this presence-absence polymorphism, CYP79F1 was mapped to the previously mapped 3C GS QTL region (J16Gsl4 in the LG B4 of B. juncea. In Heera, the gene was observed to be truncated due to an insertion of a ~4.7 kb TE like element leading to the loss of function of the gene. Functional validation of the gene was carried out through both genetic and transgenic approaches. An F2 population segregating only for the gene CYP79F1 and the sinigrin phenotype showed perfect co-segregation. Finally, genetic transformation of a B. juncea line (QTL-NIL J16Gsl4 having high seed GS but lacking sinigrin with the wild type CYP79F1 showed the synthesis of sinigrin validating the role of CYP79F1 in regulating the synthesis of 3C GS in B. juncea.

Assessment of the root system of Brassica juncea (L.) czern. and Bidens pilosa L. exposed to lead polluted soils using rhizobox systems.

Science.gov (United States)

Graziani, Natalia Soledad; Salazar, María Julieta; Pignata, María Luisa; Rodriguez, Judith Hebelen

2016-01-01

The purpose of this study was to compare the behavior of the root system of one of the most frequently cited species in phytoremediation Indian mustard [Brassica juncea (L.) Czern.] and a representative perennial herb (Bidens pilosa L.) native of Argentina, for different concentrations of lead in soils through chemical and visualization techniques of the rhizosphere. Lead polluted soils from the vicinity of a lead recycling plant in the locality of Bouwer, were used in juxtaposed rhizobox systems planted with seedlings of B. juncea and B. pilosa with homogeneous and heterogeneous soil treatments. Root development, pH changes in the rhizosphere, dry weight biomass, lead content of root and aerial parts and potential extraction of lead by rhizosphere exudates were determined. In both species lead was mainly accumulated in roots. However, although B. juncea accumulated more lead than B. pilosa at elevated concentrations in soils, the latter achieved greater root and aerial development. No changes in the pH of the rhizosphere associated to lead were observed, despite different extractive potentials of lead in the exudates of the species analyzed. Our results indicated that Indian mustard did not behave as a hyperaccumulator in the conditions of the present study.

Factors affecting emission of AITC and subsequent disease control efficacy of Brassica juncea seed meal soil amendment

Science.gov (United States)

Soil physical conditions demonstrably affected allyl isothiocyanate (AITC) emitted from Brassica juncea cv Pacific Gold seed meal (SM) amended soil. The AITC concentration detected increased with an increase in temperature from 10 oC to 30 oC. AITC concentration also increased with an increase in so...

Nitrogen-15 labeling of Crotalaria juncea green manure

International Nuclear Information System (INIS)

Ambrosano, Edmilson Jose; Rossetto, Raffaella; Trivelin, Paulo Cesar Ocheuze; Muraoka, Takashi; Bendassolli, Jose Albertino; Cantarella, Heitor; Ambrosano, Glaucia Maria Bovi; Tamiso, Luciano Grassi; Vieira, Felipe de Campos; Prada Neto, Ithamar

2003-01-01

Most studies dealing with the utilization of 15 N labeled plant material do not present details about the labeling technique. This is especially relevant for legume species since biological nitrogen fixation difficult plant enrichment. A technique was developed for labeling leguminous plant tissue with 15 N to obtain labeled material for nitrogen dynamics studies. Sun hemp (Crotalaria juncea L.) was grown on a Paleudalf, under field conditions. An amount of 58.32 g of urea with 70.57± 0.04 atom % 15 N was sprayed three times on plants grown on eight 6-m2-plots. The labelled material presented 2.412 atom % 15 N in a total dry matter equivalent to 9 Mg ha -1 This degree of enrichment enables the use of the green manure in pot or field experiments requiring 15 N-labeled material. (author)

Nitrogen-15 labeling of Crotalaria juncea green manure Marcação do adubo verde Crotalaria juncea com 15N

Directory of Open Access Journals (Sweden)

Edmilson José Ambrosano

2003-02-01

Full Text Available Most studies dealing with the utilization of 15N labeled plant material do not present details about the labeling technique. This is especially relevant for legume species since biological nitrogen fixation difficults plant enrichment. A technique was developed for labeling leguminous plant tissue with 15N to obtain labeled material for nitrogen dynamics studies. Sun hemp (Crotalaria juncea L. was grown on a Paleudalf, under field conditions. An amount of 58.32 g of urea with 70.57 ± 0.04 atom % 15N was sprayed three times on plants grown on eight 6-m²-plots. The labelled material presented 2.412 atom % 15N in a total dry matter equivalent to 9 Mg ha-1 This degree of enrichment enables the use of the green manure in pot or field experiments requiring 15N-labeled material.A grande maioria dos estudos com a utilização de material vegetal marcado com o isótopo 15N não apresentam detalhes tão importantes sobre como foram obtidos esses materiais. Em se tratando de marcação de leguminosas as dificuldades em se obter material marcado com 15N são ainda maiores pelo fato de serem plantas fixadoras de nitrogênio. Isso posto foi estabelecida uma técnica de marcação de leguminosas com nitrogênio (15N, com o objetivo de obter material vegetal marcado isotopicamente para estudos de dinâmica do nitrogênio. Cultivou-se a leguminosa crotalária júncea (Crotalaria juncea L., em Argissolo Vermelho Amarelo distrófico, em campo. Ao se aplicarem via foliar 58,32 gramas de uréia em oito canteiros experimentais, (uréia com 70,57 ± 0,04% de átomos de 15N parceladas em três vezes, obteve-se material vegetal marcado seco que continha 2,412 % em átomos de 15N em uma massa seca equivalente a 9 Mg ha-1. Essa marcação permite o uso dessa massa vegetal em estudos de dinâmica de nitrogênio.

Morphological and genetic characterization of a new cytoplasmic male sterility system (oxa CMS) in stem mustard (Brassica juncea).

Science.gov (United States)

Heng, Shuangping; Liu, Sansan; Xia, Chunxiu; Tang, HongYu; Xie, Fei; Fu, Tingdong; Wan, Zhengjie

2018-01-01

KEY MESSAGE: oxa CMS is a new cytoplasmic male sterility type in Brassica juncea. oxa CMS is a cytoplasmic male sterility (CMS) line that has been widely used in the production and cultivation of stem mustard in the southwestern China. In this study, different CMS-type specific mitochondrial markers were used to confirm that oxa CMS is distinct from the pol CMS, ogu CMS, nap CMS, hau CMS, tour CMS, Moricandia arvensis CMS, orf220-type CMS, etc., that have been previously reported in Brassica crops. Pollen grains of the oxa CMS line are sterile with a self-fertility rate of almost 0% and the sterility strain rate and sterility degree of oxa CMS is 100% due to a specific flower structure and flowering habit. Scanning electron microscopy revealed that most pollen grains in mature anthers of the oxa CMS line are empty, flat and deflated. Semi-thin section further showed that the abortive stage of anther development in oxa CMS is initiated at the late uninucleate stage. Abnormally vacuolated microspores caused male sterility in the oxa CMS line. This cytological study combined with marker-assisted selection showed that oxa CMS is a novel CMS type in stem mustard (Brassica juncea). Interestingly, the abortive stage of oxa CMS is later than those in other CMS types reported in Brassica crops, and there is no negative effect on the oxa CMS line growth period. This study demonstrated that this novel oxa CMS has a unique flower structure with sterile pollen grains at the late uninucleate stage. Our results may help to uncover the mechanism of oxa CMS in Brassica juncea.

Comparison of the karyotypes ofPsathyrostachys juncea andP. huashanica (Poaceae) studied by banding techniques

DEFF Research Database (Denmark)

Linde-Laursen, Ib; Bothmer, R. von

1986-01-01

. The patterns of both taxa are polymorphic, supporting that both taxa are outbreeders. The karyotypic characters suggest that P. juncea is more closely related to P. fragilis than either is to P. huashanica. N-banding stains weakly. Silver nitrate staining demonstrates that nucleolus organizers of both species...... have different nucleolus forming capacities. The presence of micronucleoli suggests that both species have an extra unidentified chromosome with nucleolus forming capacity....

Agrobacterium mediated transformation of brassica juncea (l.) czern with chitinase gene conferring resistance against fungal infections

International Nuclear Information System (INIS)

Ahmad, B.; Ambreen, S.; Khan, I.

2015-01-01

Brassica juncea (Czern and Coss., L.) is an important oilseed crop. Since it is attacked by several bacterial and fungal diseases, therefore, we developed an easy and simple protocol for the regeneration and transformation of B. juncea variety RAYA ANMOL to give rise to transgenic plants conferring resistance against various fungal diseases. The transformation was carried out using Agrobacterium with Chitinase gene. This gene was isolated from Streptomyces griseus HUT6037. We used two types of explants for transformation i.e. hypocotyls and cotyledons. Only hypocotyls explants showed good results regarding callus initiation. Different hormonal concentrations were applied i.e. BAP 2, 4 and 6 mgL-1 and NAA 0.1, 0.2 and 0.3 mgL-1. However, high transformation efficiency was observed by supplementing the medium with combination of 2 mgL-1 BAP and 0.2 mgL-1 for initiation of callus. Similarly 10 mgL-1 kanamycin and 200 mgL-1 cefotaxime also proved successful for the selection of transformed callus. In order to confirm the presence of transgenic callus Polymerase chain reaction was performed using specific primers for Chitinase gene. (author)

Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L

International Nuclear Information System (INIS)

Schneider, Thorsten; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schuessler, Arthur

1999-01-01

Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants

Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L.

Science.gov (United States)

Schneider, Thorsten; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schüßler, Arthur

1999-10-01

Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants.

Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L

Energy Technology Data Exchange (ETDEWEB)

Schneider, Thorsten E-mail: thorsten.schneider@mpi-hd.mpg.de; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schuessler, Arthur

1999-09-02

Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants.

Uptake of heavy metals and As by Brassica juncea grown in a contaminated soil in Aznalcollar (Spain): The effect of soil amendments

Energy Technology Data Exchange (ETDEWEB)

Clemente, Rafael [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain); Walker, David J. [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain); Bernal, M. Pilar [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain)]. E-mail: pbernal@cebas.csic.es

2005-11-15

Two crops of Brassica juncea (L.) Czern. were grown in a field experiment, at the site affected by the toxic spillage of acidic, metal-rich waste in Aznalcollar (Seville, Spain), to study its metal accumulation and the feasibility of its use for metal phytoextraction. The effects of organic soil amendments (cow manure and mature compost) and lime on biomass production and plant survival were also assessed; plots without organic amendment and without lime were used as controls. Plots, with or without organic amendment, having pH<5 were limed for the second crop. Soil acidification conditioned plant growth and metal accumulation. The addition of lime and the organic amendments achieved higher plant biomass production, although effects concerning metal bioavailability and accumulation were masked somewhat by pH variability with time and between and within plots. Tissue metal concentrations of B. juncea were elevated for Zn, Cu and Pb, especially in leaves of plants from plots with low pH values (maxima of 2029, 71 and 55 {mu}g g{sup -1}, respectively). The total uptake of heavy metals in the plants was relatively low, emphasising the problems faced when attempting to employ phytoextraction for clean-up of pluri-contaminated sites. - Although organic amendments improved soil conditions and plant growth, the phytoextraction capacity of Brassica juncea (cv. Z1) is too low for efficient soil remediation.

Effects of phosphate and thiosulphate on arsenic accumulation in Brassica juncea plants grown in soil and in hydroponic culture

Science.gov (United States)

Pezzarossa, Beatrice; Petruzzelli, Gianniantonio; Grifoni, Martina; Rosellini, Irene; Malagoli, Mario; Schiavon, Michela

2013-04-01

Arsenic is recognised as a toxic metalloid and a strong pollutant in soils of many countries. Thus, the reclamation of contaminated areas is fundamental in order to protect both human health and agricultural production. This study is focused on the assisted phytoextraction, a technology for reclaiming polluted soils that takes advantage of the capability of some plants to extract inorganic elements from soils with the aid of additive agents. The nutrients phosphorus, as phosphate, and sulphur, as thiosulphate, can compete with the form more oxidised of arsenic, both in soil and plant. This study examined the capability of thiosulphate (Th) and phosphate (Ph) to promote the release of As from soil surfaces in order to improve the phytoavailability and thus the absorption of As by Brassica juncea plants. In the first experiment B. juncea plants were grown on a soil that had been sampled from an industrial area strongly contaminated by As (790 mg As kg-1 soil). The second experiment was carried out in hydroponics where As has been added at a concentration (100 microM) similar to the As available concentration measured in soil. In both trials ammonium thiosulphate (at the concentration of 0.27 M in soil, and 400 microM in hydroponics) and potassium hydrogen phosphate (at the concentration of 0.05 M in soil, and 112 microM in hydroponics) were added. The biomass of B. juncea was determined and the accumulation of P, S and As in root and in the above-ground tissues have been analyzed. Our results showed that thiosulphate and phosphate acted either as nutrients and detoxifying agents, due to the stimulation of plant defensive systems, and influenced either the biomass production and the As accumulation in plant tissues. In the plants grown in soil, As accumulated at higher levels in the above-ground part than in the roots and the addition of Th induced a higher biomass production and a higher total As accumulation (concentration x biomass) in the above-ground tissues

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Energy Technology Data Exchange (ETDEWEB)

McMurdie, Paul J.; Behrens, Sebastien F.; Muller, Jochen A.; Goke, Jonathan; Ritalahti, Kirsti M.; Wagner, Ryan; Goltsman, Eugene; Lapidus, Alla; Holmes, Susan; Loffler, Frank E.; Spormann, Alfred M.

2009-06-30

Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.

Growth of Crotalaria juncea L. supplied with mineral nitrogen

Directory of Open Access Journals (Sweden)

Elenira Henrique Miranda Mendonça

2005-03-01

Full Text Available Plants of Crotalaria juncea inoculated with Rhizobium were treated with nutrient solution containing 10 or 20mg of either N/NO3 or N/NH4.plant-1.week-1 . The control plants received nutrient solution without N. An investigation was conducted on the effect of these sources of N on growth and nitrogen fixation of plants with 30, 60 and 90 days after sowing (DAS. Those that received mineral N presented higher growth than -N plants, but the presence of nodules occurred in all the treatments. Plants treated with NH4 presented higher N content until 60 days. The highest concentrations of leghemoglobin and protein in nodules were found at 30 DAS and there was no difference in leghemoglobin content between treatments for any age and in protein from 60 DAS. Nitrogenase activity did not vary from 60 to 90 days, with the exception of plants that received 20mg N/NO3, where it was higher at 60 daysPlantas de Crotalaria juncea inoculadas com Rhizobium foram tratadas com solução nutritiva contendo 10 ou 20mg de N/NO3 ou N/NH4.planta-1 .semana-1. As plantas controle receberam solução nutritiva sem N. Foi verificado o efeito destas fontes de N no crescimento e fixação de nitrogênio em plantas com 30, 60 e 90 dias após a semeadura (DAS. Aquelas que receberam N mineral apresentaram maior crescimento que plantas -N, mas a presença de nódulos ocorreu em todos os tratamentos. Plantas tratadas com NH4 apresentaram maior conteúdo de N até os 60 dias. As maiores concentrações de leghemoglobina e proteínas em nódulos foram verificadas aos 30 DAS e não houve diferença no conteúdo de leghemoglobina entre os tratamentos, em nenhuma das idades e em proteínas a partir de 60 DAS. A atividade da nitrogenase não variou dos 60 aos 90 dias, com exceção de plantas que receberam 20mg N/NO3, nas quais esta foi maior aos 60 dias.

Production of transgenic brassica juncea with the synthetic chitinase gene (nic) conferring resistance to alternaria brassicicola

International Nuclear Information System (INIS)

Munir, I.; Hussan, W.; Kazi, M.; Mian, A.

2016-01-01

Brassica juncea is an important oil seed crop throughout the world. The demand and cultivation of oil seed crops has gained importance due to rapid increase in world population and industrialization. Fungal diseases pose a great threat to Brassica productivity worldwide. Absence of resistance genes against fungal infection within crossable germplasms of this crop necessitates deployment of genetic engineering approaches to produce transgenic plants with resistance against fungal infections. In the current study, hypocotyls and cotyledons of Brassica juncea, used as explants, were transformed with Agrobacterium tumefacien strain EHA101 harboring binary vector pEKB/NIC containing synthetic chitinase gene (NIC), an antifungal gene under the control of cauliflower mosaic virus promoter (CaMV35S). Bar genes and nptII gene were used as selectable markers. Presence of chitinase gene in trangenic lines was confirmed by PCR and southern blotting analysis. Effect of the extracted proteins from non-transgenic and transgenic lines was observed on the growth of Alternaria brassicicola, a common disease causing pathogen in brassica crop. In comparison to non-transgenic control lines, the leaf tissue extracts of the transgenic lines showed considerable resistance and antifungal activity against A. brassicicola. The antifungal activity in transgenic lines was observed as corresponding to the transgene copy number. (author)

Resultados experimentais com a cultura da Crotalaria juncea L. L., como planta produtora de celulose para papel Results from field trials with Crotalaria juncea L. as fiber plant for paper pulp

Directory of Open Access Journals (Sweden)

Júlio César Medina

1961-01-01

Full Text Available São apresentados e discutidos os resultados de vários experimentos de campo realizados na Estação Experimental de Tatuí, do Instituto Agronômico, com a Crotalaria juncea L. como planta produtora de celulose para papel. Êsses resultados permitem fazer recomendações úteis sôbre o melhoramento técnico da cultura e da produção, no concernente às questões de variedades, espaçamento, densidade de semeação, época de semeação e época de colheita dos caules.This paper reports the results obtained in sunn hemp (Crotalaria juncea L. field trials carried out at the Tatui Experiment Station, São Paulo State. The trials were designed to study the effect of varieties, spacing x rate of seeding, time of sowing and time of harvesting on sunn hemp fiber production as a raw material for paper pulp. From the results achieved in these trials, the following recommendations can be made for growing sunn hemp as a fiber plant for paper pulp in the State of São Paulo. VARIETY: to use the common variety that is normally sowed for green manuring. TIME OF SOWING: to sow the seeds during october. RATE OF SEED SOWING AND SPACING: to sow the seeds at the rate of 100 lbs/ acre in rows spaced 8 inches apart. TIME OF HARVESTING: to harvest the stalks for mechanical fiber extraction when the seed pods are in the mature stage.

Uptake of heavy metals and As by Brassica juncea grown in a contaminated soil in Aznalcollar (Spain): The effect of soil amendments

International Nuclear Information System (INIS)

Clemente, Rafael; Walker, David J.; Bernal, M. Pilar

2005-01-01

Two crops of Brassica juncea (L.) Czern. were grown in a field experiment, at the site affected by the toxic spillage of acidic, metal-rich waste in Aznalcollar (Seville, Spain), to study its metal accumulation and the feasibility of its use for metal phytoextraction. The effects of organic soil amendments (cow manure and mature compost) and lime on biomass production and plant survival were also assessed; plots without organic amendment and without lime were used as controls. Plots, with or without organic amendment, having pH -1 , respectively). The total uptake of heavy metals in the plants was relatively low, emphasising the problems faced when attempting to employ phytoextraction for clean-up of pluri-contaminated sites. - Although organic amendments improved soil conditions and plant growth, the phytoextraction capacity of Brassica juncea (cv. Z1) is too low for efficient soil remediation

Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

Science.gov (United States)

Goel, Parul; Bhuria, Monika; Kaushal, Mamta

2016-01-01

In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8) in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2) in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen. PMID:27637072

Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

Directory of Open Access Journals (Sweden)

Parul Goel

Full Text Available In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C and Nitrogen (N are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N, C source alone (+Suc-N, with N and C source (+Suc+N or without N and C source (-Suc-N. Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8 in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2 in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen.

Path and ridge regression analysis of seed yield and seed yield components of Russian wildrye (Psathyrostachys juncea Nevski) under field conditions

DEFF Research Database (Denmark)

Wang, Quanzhen; Zhang, Tiejun; Cui, Jian

2011-01-01

The correlations among seed yield components, and their direct and indirect effects on the seed yield (Z) of Russina wildrye (Psathyrostachys juncea Nevski) were investigated. The seed yield components: fertile tillers m-2 (Y1), spikelets per fertile tillers (Y2), florets per spikelet- (Y3), seed...

Atmospheric H2S and SO2 as sulfur source for Brassica juncea and Brassica rapa: Impact on the glucosinolate composition

NARCIS (Netherlands)

Aghajanzadeh, T.; Kopriva, S; Hawkesford, M.J.; Koprivova, A.; De Kok, L.J.

2015-01-01

The impact of sulfate deprivation and atmospheric H2S and SO2 nutrition on the content and composition of glucosinolates was studied in Brassica juncea and Brasscia rapa. Both species contained a number of aliphatic and indolic glucosinolates. The total glucosinolate content was more than 5.5-fold

The effects of seed size on hybrids formed between oilseed rape (Brassica napus and wild brown mustard (B. juncea.

Directory of Open Access Journals (Sweden)

Yong-Bo Liu

Full Text Available Seed size has significant implications in ecology, because of its effects on plant fitness. The hybrid seeds that result from crosses between crops and their wild relatives are often small, and the consequences of this have been poorly investigated. Here we report on plant performance of hybrid and its parental transgenic oilseed rape (Brassica napus and wild B. juncea, all grown from seeds sorted into three seed-size categories.Three seed-size categories were sorted by seed diameter for transgenic B. napus, wild B. juncea and their transgenic and non-transgenic hybrids. The seeds were sown in a field at various plant densities. Globally, small-seeded plants had delayed flowering, lower biomass, fewer flowers and seeds, and a lower thousand-seed weight. The seed-size effect varied among plant types but was not affected by plant density. There was no negative effect of seed size in hybrids, but it was correlated with reduced growth for both parents.Our results imply that the risk of further gene flow would probably not be mitigated by the small size of transgenic hybrid seeds. No fitness cost was detected to be associated with the Bt-transgene in this study.

[Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

Science.gov (United States)

Katsy, E I; Petrova, L P

2015-12-01

Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

Transgenic Brassica juncea plants expressing MsrA1, a synthetic cationic antimicrobial peptide, exhibit resistance to fungal phytopathogens.

Science.gov (United States)

Rustagi, Anjana; Kumar, Deepak; Shekhar, Shashi; Yusuf, Mohd Aslam; Misra, Santosh; Sarin, Neera Bhalla

2014-06-01

Cationic antimicrobial peptides (CAPs) have shown potential against broad spectrum of phytopathogens. Synthetic versions with desirable properties have been modeled on these natural peptides. MsrA1 is a synthetic chimera of cecropin A and melittin CAPs with antimicrobial properties. We generated transgenic Brassica juncea plants expressing the msrA1 gene aimed at conferring fungal resistance. Five independent transgenic lines were evaluated for resistance to Alternaria brassicae and Sclerotinia sclerotiorum, two of the most devastating pathogens of B. juncea crops. In vitro assays showed inhibition by MsrA1 of Alternaria hyphae growth by 44-62 %. As assessed by the number and size of lesions and time taken for complete leaf necrosis, the Alternaria infection was delayed and restricted in the transgenic plants with the protection varying from 69 to 85 % in different transgenic lines. In case of S. sclerotiorum infection, the lesions were more severe and spread profusely in untransformed control compared with transgenic plants. The sclerotia formed in the stem of untransformed control plants were significantly more in number and larger in size than those present in the transgenic plants where disease protection of 56-71.5 % was obtained. We discuss the potential of engineering broad spectrum biotic stress tolerance by transgenic expression of CAPs in crop plants.

First generation annotations for the fathead minnow (Pimephales promelas) genome

Science.gov (United States)

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula.

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Daejin Hyung

Full Text Available Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from relatively simple model system to other less studied, but related, genomes. The information of abiotic stress (ABS-responsive genes in Arabidopsis was identified and translated into the legume model system, Medicago truncatula. Various data resources, such as TAIR/AtGI DB, expression profiles and literatures, were used to build a genome-wide list of ABS genes. tBlastX/BlastP similarity search tools and manual inspection of alignments were used to identify orthologous genes between the two genomes. A total of 1,377 genes were finally collected and classified into 18 functional criteria of gene ontology (GO. The data analysis according to the expression cues showed that there was substantial level of interaction among three major types (i.e., drought, salinity and cold stress of abiotic stresses. In an attempt to translate the ABS genes between these two species, genomic locations for each gene were mapped using an in-house-developed comparative analysis platform. The comparative analysis revealed that fragmental colinearity, represented by only 37 synteny blocks, existed between Arabidopsis and M. truncatula. Based on the combination of E-value and alignment remarks, estimated translation rate was 60.2% for this cross-family translation. As a prelude of the functional comparative genomic approaches, in-silico gene network/interactome analyses were conducted to predict key components in the ABS responses, and one of the sub-networks was integrated with corresponding comparative map. The results demonstrated that core members of the sub-network were well aligned with previously reported ABS regulatory networks. Taken together, the results indicate that network-based integrative approaches of comparative and functional genomics are important to interpret and translate genomic information for complex traits such as abiotic stresses.

Atmospheric H2S and SO2 as sulfur sources for Brassica juncea and Brassica rapa: Regulation of sulfur uptake and assimilation

NARCIS (Netherlands)

Aghajanzadeh, T.; Hawkesford, M.J.; De Kok, L.J.

2016-01-01

Brassica juncea and Brassica rapa were able to utilize foliarly absorbed H2S and SO2 as sulfur source for growth and resulted in a decreased sink capacity of the shoot for sulfur supplied by the root and subsequently in a partial decrease in sulfate uptake capacity of the roots. Sulfate-deprived

SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

Science.gov (United States)

Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

2018-01-01

Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa , while lowest cross-transferability (91.93%) was obtained for Eruca sativa . The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea / B. nigra/B. rapa and B. carinata/B. napus/B. oleracea . C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

ParABS Systems of the Four Replicons of Burkholderia cenocepacia: New Chromosome Centromeres Confer Partition Specificity†

Science.gov (United States)

Dubarry, Nelly; Pasta, Franck; Lane, David

2006-01-01

Most bacterial chromosomes carry an analogue of the parABS systems that govern plasmid partition, but their role in chromosome partition is ambiguous. parABS systems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterized parABS systems in Burkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A single parAB locus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. The parS sites on the smaller chromosomes and the plasmid are similar to the “universal” parS of the main chromosome but with a sequence specific to their replicon. In an Escherichia coli plasmid stabilization test, each parAB exhibits partition activity only with the parS of its own replicon. Hence, parABS function is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation of parS sites and a promoter internal to their parAB operons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation. PMID:16452432

Genomic selection for the improvement of antibody response to Newcastle disease and avian influenza virus in chickens.

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Tianfei Liu

Full Text Available Newcastle disease (ND and avian influenza (AI are the most feared diseases in the poultry industry worldwide. They can cause flock mortality up to 100%, resulting in a catastrophic economic loss. This is the first study to investigate the feasibility of genomic selection for antibody response to Newcastle disease virus (Ab-NDV and antibody response to Avian Influenza virus (Ab-AIV in chickens. The data were collected from a crossbred population. Breeding values for Ab-NDV and Ab-AIV were estimated using a pedigree-based best linear unbiased prediction model (BLUP and a genomic best linear unbiased prediction model (GBLUP. Single-trait and multiple-trait analyses were implemented. According to the analysis using the pedigree-based model, the heritability for Ab-NDV estimated from the single-trait and multiple-trait models was 0.478 and 0.487, respectively. The heritability for Ab-AIV estimated from the two models was 0.301 and 0.291, respectively. The estimated genetic correlation between the two traits was 0.438. A four-fold cross-validation was used to assess the accuracy of the estimated breeding values (EBV in the two validation scenarios. In the family sample scenario each half-sib family is randomly allocated to one of four subsets and in the random sample scenario the individuals are randomly divided into four subsets. In the family sample scenario, compared with the pedigree-based model, the accuracy of the genomic prediction increased from 0.086 to 0.237 for Ab-NDV and from 0.080 to 0.347 for Ab-AIV. In the random sample scenario, the accuracy was improved from 0.389 to 0.427 for Ab-NDV and from 0.281 to 0.367 for Ab-AIV. The multiple-trait GBLUP model led to a slightly higher accuracy of genomic prediction for both traits. These results indicate that genomic selection for antibody response to ND and AI in chickens is promising.

Clinical significance of combined detection of multiple serum antibodies (AsAb, EmAb, AcAb, AoAb, ToxAb) in infertile women

International Nuclear Information System (INIS)

Chen Jing; Jiang Li; Lu Ya

2005-01-01

Objective: To determine the clinical significance of combined detection of multiple serum antibodies in infertile women. Methods; Serum multiple antibodies were examined in 120 infertile women, including 88 failed to get pregnancy and 32 with repeated spontaneous abortion. The antibodies tested were: (1) anti-sperm antibody (AsAb) (2) endometrial antibody (EmAb) (3) anti-cardiophospholipid antibody (AcAb) (4) Anti-ovarian antibody (AoAb) and Toxoplasmosis antibody (ToxAb). Results: In 48 of the infertile women, none of the five antibodies were positive (40% of 120). The rest were: one antibody positive--38/120 or 31.6%; two antibodies positive--31/120 or 25.83%, three and four antibodies positive--4/120 or 3.33%. None of the women were positive with all five antibodies. Conclusion: Immune factor was the chief cause of infertility in women. (authors)

evaluation of best planting time of mustard (brassica juncea) strains in southern punjab

International Nuclear Information System (INIS)

Aslam, M.; Hussain, G.; Hussain, M.

2008-01-01

The study was conducted to find out the proper planting time of newly evolved mustard (Brassica juncea) strains at Regional Agriculture Research Institute, Bahawalpur during the year 2000-2002. The study included 4 planting dates from 1st October to November 15th and three strains i.e. BRS-2 and BRS-10 and KH- 74 along with check RL-18. The 1st fortnight of October proved to be the best sowing time. KH-74 and BRS-2 gave significantly higher yield in wide range of sown period i.e. 1st October to 15th November. The highest grain yield of 2435 and 2341 Kgs, ha were obtained when crop was planted on 1st October and 15th October respectively. (author)

Sulfur utilization by rice and Crotalaria juncea from sulfate - 34S applied to the soil

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Trivelin Paulo Cesar Ocheuze

2002-01-01

Full Text Available In tropical soils with intensive agriculture an increasing sulfur deficiency has been verified in several crops. The low available S in these soils is caused by the continuous use of concentrated NPK fertilizers. The objective of this work was to evaluate the utilization by rice (Oriza sativa L. and crotalaria juncea (Crotalaria juncea L. of sulfur applied to the soil, under greenhouse conditions. Pots with 3 kg of an Argisol (Paleudalf were used to test the isotopic technique with the stable isotope 34S, adding a solution of sodium sulfate labeled with 34S (14.30 ± 0.05 atom % of 34S to the soil (70 mg SO4-S per kg-1 of soil 18 days after sowing both species. The shoots of the crotalaria and rice were harvested, respectively on the 72nd and 122nd days after S fertilization. The concentration and the amount of sulfur in the crotalaria were higher than in rice, due to the higher legume requirement for this nutrient. The sulfur requirement and the short time interval between fertilization and harvest of the crotalaria resulted in a small amount of native SO4-S mineralized in the soil and a small quantity of 34SO4 immobilized by soil microorganisms. Thus, the percentage of sulfur in the crotalaria derived from the fertilizer (Sdff was higher than in the rice (%Sdff crotalaria = 91.3 ± 3.5%; %Sdff rice = 66.3 ± 0.8%. The expressive values of %Sdff indicate a low rate of mineralization of SO4-S probably as a consequence of the low available sulfur content in the soil.

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

DEFF Research Database (Denmark)

Wasmund, Kenneth; Cooper, Myriel; Schreiber, Lars

2016-01-01

The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affilia......The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene...... that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding...... dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many...

Pre-sowing Seed Treatment with 24-Epibrassinolide Ameliorates Pesticide Stress in Brassica juncea L. through the Modulation of Stress Markers

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Parvaiz Ahmad

2016-11-01

Full Text Available The present experiment was designed to assess the effects of seed soaking with 24-epibrassinolide (EBR on the physiology of Brassica juncea L. seedlings grown under imidacloprid (IMI toxicity. Application of EBR increased the length of seedlings, dry weight, and pigment contents, polyphenols, total phenols and organic acids under IMI toxicity. The expression of genes coding key enzymes of pigment, phenols, polyphenols and organic acid biosynthetic pathways was also studied including CHLASE (chlorophyllase, PSY (phytoene synthase, CHS (chalcone synthase and PAL (phenylalanine ammonialyase, CS (citrate synthase, SUCLG1 (succinyl Co-A ligase,, SDH (succinate dehydrogenase, FH (fumarate hydratase, MS (malate synthase. Multiple linear regression analysis revealed that IMI application regressed negatively on seedling length, dry weight and total chlorophyll content. However, EBR seed treatment regressed positively on all of the parameters studied. Moreover, interaction between IMI and EBR showed positive regression for growth parameters, content of pigments, total polyphenol, total phenol and malate, and expression of PSY and PAL. Negative interactions were noticed for the contents of fumarate, succinate and citrate, and expression of CHS and all genes studied related to organic acid metabolism. In conclusion, EBR enhanced the growth and contents of all studied metabolites by regulating the gene expression of B. juncea seedlings under IMI stress.

The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

Science.gov (United States)

Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

2014-01-01

Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

Insecticidal, food utilisation and biochemical effect of essential oils extracted from seeds of Brassica juncea (Czern. against Spodoptera litura (Lepidoptera: Noctuidae (Fabricius

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Shallina Gupta

2017-09-01

Full Text Available The glucosinolate rich hot and cold hexane extracts of Brassica juncea had a negative effect on the development of Spodoptera litura larvae when they were fed on different concentrations of the extracts. Both larval growth index and pupal growth index declined with treatment. However the hot extract with 3-butenyl isothiocyanate as the predominant compound had a more deleterious effect as at 3125ppm the larvae were unable to complete their development. The nutritional indices too were more adversely affected with hot extract as compared to cold extract. The RGR, RCR, ECI and ECD declined significantly with increase in concentration of the hot hexane extract. The activity of antioxidant enzymes, SOD and catalase decreased while that of phosphatases, GSTs, phenol oxidases increased during the initial treatment duration but decreased on prolonged treatment of the larvae with LC50 concentration of hot extract. A similar trend was observed for glutathione and lipid peroxides but a decrease in ascorbate content was observed as compared to control. The findings reveal a toxic effect of 3-butenylisothiocyanate rich hot hexane extract of B. juncea on S. litura larvae.

Effects of inoculation of plant growth-promoting rhizobacteria on metal uptake by Brassica juncea

International Nuclear Information System (INIS)

Wu, S.C.; Cheung, K.C.; Luo, Y.M.; Wong, M.H.

2006-01-01

A greenhouse study was carried out with Brassica juncea to critically evaluate effects of bacterial inoculation on the uptake of heavy metals from Pb-Zn mine tailings by plants. Application of plant growth-promoting rhizobacteria, including nitrogen-fixing bacteria and phosphate and potassium solubilizers, might play an important role in the further development of phytoremediation techniques. The presence of these beneficial bacteria stimulated plant growth and protected the plant from metal toxicity. Inoculation with rhizobacteria had little influence on the metal concentrations in plant tissues, but produced a much larger above-ground biomass and altered metal bioavailability in the soil. As a consequence, higher efficiency of phytoextraction was obtained compared with control treatments. - Rhizobacteria promoted growth above normal biomass, but did not influence plant metal concentrations

Effects of inoculation of plant growth-promoting rhizobacteria on metal uptake by Brassica juncea

Energy Technology Data Exchange (ETDEWEB)

Wu, S.C. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Cheung, K.C. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Luo, Y.M. [Institute of Soil Science, Chinese Academy of Sciences, Nanjing (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Wong, M.H. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China) and Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China)]. E-mail: mhwong@hkbu.edu.hk

2006-03-15

A greenhouse study was carried out with Brassica juncea to critically evaluate effects of bacterial inoculation on the uptake of heavy metals from Pb-Zn mine tailings by plants. Application of plant growth-promoting rhizobacteria, including nitrogen-fixing bacteria and phosphate and potassium solubilizers, might play an important role in the further development of phytoremediation techniques. The presence of these beneficial bacteria stimulated plant growth and protected the plant from metal toxicity. Inoculation with rhizobacteria had little influence on the metal concentrations in plant tissues, but produced a much larger above-ground biomass and altered metal bioavailability in the soil. As a consequence, higher efficiency of phytoextraction was obtained compared with control treatments. - Rhizobacteria promoted growth above normal biomass, but did not influence plant metal concentrations.

Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

Science.gov (United States)

Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

2012-01-01

Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and “fixed heterosis” in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

The K Domain Mediates Homologous and Heterologous Interactions Between FLC and SVP Proteins of Brassica juncea

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Ma Guanpeng

2015-07-01

Full Text Available The transcription factors FLOWERING LOCUS C (FLC and SHORT VEGETATIVE PHASE (SVP can interact to form homologous and heterologous protein complexes that regulate flowering time in Brassica juncea Coss. (Mustard.Previous studies showed that protein interactions were mediated by the K domain, which contains the subdomains K1, K2 and K3. However, it remains unknown how the subdomains mediate the interactions between FLC and SVP. In the present study, we constructed several mutants of subdomains K1–K3 and investigated the mechanisms involved in the heterologous interaction of BjFLC/BjSVP and in the homologous interaction of BjFLC/BjFLC or BjSVP/BjSVP. Yeast two-hybrid and β-Galactosidase activity assays showed that the 19 amino acids of the K1 subdomain in BjSVP and the 17 amino acids of the K1 subdomain in BjFLC were functional subdomains that interact with each other to mediate hetero-dimerization. The heterologous interaction was enhanced by the K2 subdomain of BjSVP protein, but weakened by its interhelical domain L2. The heterologous interaction was also enhanced by the K2 subdomain of BjFLC protein, but weakened by its K3 subdomain. The homologous interaction of BjSVP was mediated by the full K-domain. However, the homologous interaction of BjFLC was regulated only by its K1 and weakened by its K2 and K3 subdomains. The results provided new insights into the interactions between FLC and SVP, which will be valuable for further studies on the molecular regulation mechanisms of the regulation of flowering time in B. juncea and other Brassicaceae.

Ploidy and genome composition of Musa germplasm at the ...

African Journals Online (AJOL)

GRACE

2006-07-03

Jul 3, 2006 ... Musa spp (bananas and plantains) constitute a hybrid-polyploid complex and are classified according to different genome compositions such as AA, BB, AB, AAA, AAB, ABB, AAAA, ABBB, AAAB and. AABB. Knowledge of ploidy and exact genome compositions of the parental material is essential for.

PirAB protein from Xenorhabdus nematophila HB310 exhibits a binary toxin with insecticidal activity and cytotoxicity in Galleria mellonella.

Science.gov (United States)

Yang, Qing; Zhang, Jie; Li, Tianhui; Liu, Shen; Song, Ping; Nangong, Ziyan; Wang, Qinying

2017-09-01

PirAB (Photorhabdus insect-related proteins, PirAB) toxin was initially found in the Photorhabdus luminescens TT01 strain and has been shown to be a binary toxin with high insecticidal activity. Based on GenBank data, this gene was also found in the Xenorhabdus nematophila genome sequence. The predicted amino acid sequence of pirA and pirB in the genome of X. nematophila showed 51% and 50% identity with those gene sequences from P. luminescens. The purpose of this experiment is to identify the relevant information for this toxin gene in X. nematophila. The pirA, pirB and pirAB genes of X. nematophila HB310 were cloned and expressed in Escherichia coli BL21 (DE3) using the pET-28a vector. A PirAB-fusion protein (PirAB-F) was constructed by linking the pirA and pirB genes with the flexible linker (Gly) 4 DNA encoding sequence and then efficiently expressed in E. coli. The hemocoel and oral insecticidal activities of the recombinant proteins were analyzed against the larvae of Galleria mellonella. The results show that PirA/B alone, PirA/B mixture, co-expressed PirAB protein, and PirAB-F all had no oral insecticidal activity against the second-instar larvae of G. mellonella. Only PirA/B mixture and co-expressed PirAB protein had hemocoel insecticidal activity against G. mellonella fifth-instar larvae, with an LD 50 of 2.718μg/larva or 1.566μg/larva, respectively. Therefore, we confirmed that PirAB protein of X. nematophila HB310 is a binary insecticidal toxin. The successful expression and purification of PirAB laid a foundation for further studies on the function, insecticidal mechanism and expression regulation of the binary toxin. Copyright © 2017 Elsevier Inc. All rights reserved.

Breeding strategy for the improvement of mustard (Brassica Juncea Coss.)

International Nuclear Information System (INIS)

Nayar, G.G.

1980-01-01

Mutants having desirable agronomic characters were obtained in the high yielding, recommended mustard (B. juncea) varieties Rai 5, RL 9 and Varuna (T 59). Following hybridizations between induced mutants or mutants with other promising varieties, recombinants having superior agronomic traits have been developed. The parent varieties are characterised by open pod arrangement and blackish brown seeds. The mutants and the recombinants have desirable agronomic characters like compact plant type, appressed pods with less shattering nature, yellow seeds, higher oil content and lighter coloured oil. Among the 12 new strains developed at this centre, five have been tested at various locations in the country. At many places, TM-(Trombay Mustard-) cultures outyielded or were at par with the local check varieties. TM-2-11 (Appressed pod mutant) and TM-4 (Yellow bold seeded Mutant) have also been included in the Initial Evaluation Trial of the All India Co-ordinated Research Project in Oilseeds (AICORPO) improvement. Reports so far received from various locations in the country indicate that TM-strains, being relatively early cultures, are suited more for states of Rajasthan, Gujarat, U.P. and Bihar. (author)

Discrimination between Native and Tn6010-Associated oqxAB in Klebsiella spp., Raoultella spp., and other Enterobacteriaceae by Using a Two-Step Strategy

DEFF Research Database (Denmark)

Guillard, Thomas; Lebreil, Anne-Laure; Hansen, Lars Hestbjerg

2015-01-01

ABSTRACT We developed a two-step PCR-based strategy to detect genes encoding OqxAB, allowing a specific assignment of Tn6010-associated oqxAB in Enterobacteriaceae. Chromosomal location in this setup was confirmed by hybridization with I-CeuI-restricted genomes. This approach led us to find...

Seed Coat Microsculpturing Is Related to Genomic Components in Wild Brassica juncea and Sinapis arvensis

OpenAIRE

Wang, Ying-hao; Wei, Wei; Kang, Ding-ming; Ma, Ke-ping

2013-01-01

It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM) is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relatio...

Genome size variation in the genus Avena.

Science.gov (United States)

Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

2016-03-01

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

Science.gov (United States)

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers

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Vinu V.

2013-12-01

Full Text Available Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

A novel Pseudomonas aeruginosa bacteriophage, Ab31, a chimera formed from temperate phage PAJU2 and P. putida lytic phage AF: characteristics and mechanism of bacterial resistance.

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Libera Latino

Full Text Available A novel temperate bacteriophage of Pseudomonas aeruginosa, phage vB_PaeP_Tr60_Ab31 (alias Ab31 is described. Its genome is composed of structural genes related to those of lytic P. putida phage AF, and regulatory genes similar to those of temperate phage PAJU2. The virion structure resembles that of phage AF and other lytic Podoviridae (S. enterica Epsilon 15 and E. coli phiv10 with similar tail spikes. Ab31 was able to infect P. aeruginosa strain PA14 and two genetically related strains called Tr60 and Tr162, out of 35 diverse strains from cystic fibrosis patients. Analysis of resistant host variants revealed different phenotypes, including induction of pigment and alginate overproduction. Whole genome sequencing of resistant variants highlighted the existence of a large deletion of 234 kbp in two strains, encompassing a cluster of genes required for the production of CupA fimbriae. Stable lysogens formed by Ab31 in strain Tr60, permitted the identification of the insertion site. During colonization of the lung in cystic fibrosis patients, P. aeruginosa adapts by modifying its genome. We suggest that bacteriophages such as Ab31 may play an important role in this adaptation by selecting for bacterial characteristics that favor persistence of bacteria in the lung.

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

Science.gov (United States)

2013-01-01

Background Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors. Conclusions Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease. PMID:24330828

Isolation and Characterization of a Virulent Bacteriophage AB1 of Acinetobacter baumannii

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Jia Shiru

2010-04-01

Full Text Available Abstract Background Acinetobacter baumannii is an emerging nosocomial pathogen worldwide with increasing prevalence of multi-drug and pan-drug resistance. A. baumannii exists widely in natural environment, especially in health care settings, and has been shown difficult to be eradicated. Bacteriophages are often considered alternative agent for controlling bacterial infection and contamination. In this study, we described the isolation and characterization of one virulent bacteriophage AB1 capable of specifically infecting A. baumannii. Results A virulent bacteriophage AB1, specific for infecting a clinical strain A. baumannii KD311, was first isolated from marine sediment sample. Restriction analysis indicated that phage AB1 was a dsDNA virus with an approximate genome size of 45.2 kb to 46.9 kb. Transmission electron microscopy showed that phage AB1 had an icosahedral head with a non-contractile tail and collar or whisker structures, and might be tentatively classified as a member of the Siphoviridae family. Proteomic pattern of phage AB1, generated by SDS-PAGE using purified phage particles, revealed five major bands and six minor bands with molecular weight ranging from 14 to 80 kilo-dalton. Also determined was the adsorption rate of phage AB1 to the host bacterium, which was significantly enhanced by addition of 10 mM CaCl2. In a single step growth test, phage AB1 was shown having a latent period of 18 minutes and a burst size of 409. Moreover, pH and thermal stability of phage AB1 were also investigated. At the optimal pH 6.0, 73.2% of phages survived after 60 min incubation at 50°C. When phage AB1 was used to infect four additional clinical isolates of A. baumannii, one clinical isolate of Stenotrophomonas maltophilia, and Pseudomonas aeruginosa lab strains PAK and PAO1, none of the tested strains was found susceptible, indicating a relatively narrow host range for phage AB1. Conclusion Phage AB1 was capable of eliciting efficient lysis

Evaluation of candidate reference genes for gene expression normalization in Brassica juncea using real time quantitative RT-PCR.

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Ruby Chandna

Full Text Available The real time quantitative reverse transcription PCR (qRT-PCR is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes, ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes, in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization.

Kajian Hubungan Populasi Tanaman dengan Neraca Unsur Hara Nitrogen dan Fosfor pada Sistem Vertikultur Sawi Hijau (Brassica juncea L dan Kangkung (Ipomea reptana

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I MADE PURNA WIDANA

2016-05-01

Full Text Available Analysis of Relationship Between Crop Density and The Balancing of Both Soil Nitrogenand Phosporus in Verticulture System of Mustard Green (Brassica juncea L and Kale(Ipomea reptana. The relationship between crops density and the balancing of both soilnitrogen and phosphorus in verticulture system remained to be important issue. A glasshouseexperiment had carried out from October 2014 to March 2015 in order to determine (1 theoptimum population density of both mustard greens (Brassica juncea L and kale (Ipomeareptana, (2 soil total-N or available-P balance, and (3 the relatiohships between plantspopulations and soil nutrients balance. A split plot experiment under complete block designwas applied to examine the effect of the main plot (crops type i.e. mustard green and kale andsub plot (crops population i.e 10, 15, 20,25, and 30 crops per planting container 0,12 m2 insize. The results showed that no optimal crops population density had achieved. Themaximum crops population was 30 for both mustard greens and kale. The soil total-N balancewas negative while these was positive for soil available-P balance of P and N negative. Alogarithmic relationships was calculated between soil total-N balance with mustard green,while linier patterns were significant for soil-N balance with kale and available-P balancewith both mustard greens and kale.

SUSTAINABILITY EFFECTS OF Crotalaria juncea L. AND Crotalaria spectabilis ROTH ON SOIL FERTILITY AND SOIL CONSERVATION

Science.gov (United States)

László, Márton, ,, Dr.

2010-05-01

Sustainable agriculture is defined as the successful management of resources for agriculture to satisfy changing human needs while maintaining or enhancing the quality of the environment and conserving natural resources. A sustained increase of agricultural production becomes a great possibility for international community. In this process a green manure crops application for example crotalaria get a new chance for improvement process on soil fertility and soil conservation. Field experiment was carried out on a calcareous chernozem soil (Experiment station Nagyhörcsök of RISSAC-HAS) in partly of experiment series (3 years) at Hungary in 1998. The soil with about 20% clay, 3% humus, 5% CaCO3 in its ploughed layer. To ensure a sufficient macro and micronutrient supply in the whole experiment, 100 kg N, 100 kg P2O5 and 100 kg K2O were given hectare. The Crotalaria juncea L. and Crotalaria spectabilis ROTH were applied with 2 replications. Each plot has an area of 45 m2 with 230-230 individual plants. In vegetation grown period were measured green and dry matter yield. The soil and plant samples were analysed for the macro and microelements contents. The main results achieved in 1998 are summarized as follows: 1. The green matter yield at before flowering reached 63.8 t ha-1 in case of Crotalaria juncea L. 2. Total dry matter yield at harvest (without roots) fluctuated between 9.6 and 17.0 t ha-1, depending on the crotalaria species. 3. The average of element concentration (including stems, leaves of Crotalaria juncea L. and Crotalaria spectabilis ROTH) before flowering reached to 3.2 % N, 2.3 % Ca, 1.3 % K, 0.39 % Mg, 0.22 % P and 0.24 % S. The content of Al and Fe total 14 - 25, while that of Sr, Mn, Na, B and Ba 2 - 6 ppm in dry matter. The Zn, Cu, Mo, Cr, Se, Ni, As, Pb, Cd and Co concentration did not reach here the value of 1 ppm. 4. The average of biological activated element uptake (including stems, leaves of Crotalaria juncea L. and Crotalaria spectabilis

Mercury-induced oxidative stress in Indian mustard (Brassica juncea L.).

Science.gov (United States)

Shiyab, Safwan; Chen, Jian; Han, Fengxiang X; Monts, David L; Matta, Fank B; Gu, Mengmeng; Su, Yi; Masad, Motasim A

2009-10-01

Mercury, a potent neurotoxin, is released to the environment in significant amounts by both natural processes and anthropogenic activities. No natural hyperaccumulator plant has been reported for mercury phytoremediation. Few studies have been conducted on the physiological responses of Indian mustard, a higher biomass plant with faster growth rates, to mercury pollution. This study investigated the phytotoxicity of mercury to Indian mustard (Brassica juncea L.) and mercury-induced oxidative stress in order to examine the potential application of Indian mustard to mercury phytoremediation. Two common cultivars (Florida Broadleaf and Longstanding) of Indian mustard were grown hydroponically in a mercury-spiked solution. Plant uptake, antioxidative enzymes, peroxides, and lipid peroxidation under mercury stress were investigated. Antioxidant enzymes (catalase, CAT; peroxidase, POD; and superoxide dismutase, SOD) were the most sensitive indices of mercury-induced oxidative response of Indian mustard plants. Indian mustard effectively generated an enzymatic antioxidant defense system (especially CAT) to scavenge H(2)O(2), resulting in lower H(2)O(2) in shoots with higher mercury concentrations. These two cultivars of Indian mustard demonstrated an efficient metabolic defense and adaptation system to mercury-induced oxidative stress. A majority of Hg was accumulated in the roots and low translocations of Hg from roots to shoots were found in two cultivars of Indian mustard. Thus Indian mustard might be a potential candidate plant for phytofiltration/phytostabilization of mercury contaminated waters and wastewater.

Isolation and characterization of useful mutants induced by gamma irradiation in 'Kranti' indian mustard (Brassica juncea)

International Nuclear Information System (INIS)

Rai, B.; Kumar, H.

1998-01-01

Genetic variability was induced, in the 'Kranti' Indian mustard [Brassica/juncea (L.) Czemj. & Cosson]. utilizing 30,40 and 50 kr doses of gamma-ray Irradiation. 'In M 3 generation, compared with the econtrol, substantial decrease was observed in the mean value of various quantitative characters in the mutagen-treated populations. More variation was induced at 30 kr compared with that at 40 or 50 kr dose. Four mutants were identified ar 30 kr dose, which besides being early in maturity, gave better yield also-compared with the control. The better seed yield of the transmutated plants was due either to increase in seed weight or to increase in number of siliquae/plant

Physiological and Biochemical Changes in Brassica juncea Plants under Cd-Induced Stress

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Dhriti Kapoor

2014-01-01

Full Text Available Plants of Brassica juncea L. var. RLC-1 were exposed for 30 days to different concentrations (0, 0.2, 0.4, and 0.6 mM of cadmium (Cd to analyze the Cd uptake, H2O2 content, hormonal profiling, level of photosynthetic pigments (chlorophyll, carotenoid, and flavonoid, gaseous exchange parameters (photosynthetic rate, vapour pressure deficit, intercellular CO2 concentration, and intrinsic mesophyll rate, antioxidative enzymes (superoxide dismutase, polyphenol oxidase, glutathione-S transferase, and glutathione peroxidase, antioxidant assays (DPPH, ABTS, and total phenolic content, and polyphenols. Results of the present study revealed the increased H2O2 content and Cd uptake with increasing metal doses. UPLC analysis of plants showed the presence of various polyphenols. Gaseous exchange measurements were done by infrared gas analyzer (IRGA, which was negatively affected by metal treatment. In addition, LC/MS study showed the variation in the expression of plant hormones. Level of photosynthetic pigments and activities of antioxidative enzymes were altered significantly in response to metal treatment. In conclusion, the antioxidative defence system of plants got activated due to heavy metal stress, which protects the plants by scavenging free radicals.

Clinical significance of determination of serum leptin and AsAb, EmAb levels in infertile women

International Nuclear Information System (INIS)

Luo Jian; Zhou Minglian; Sun Gang; He Haoming

2010-01-01

Objective: To study the clinical significance of determination of serum leptin, AsAb, and EmAb levels in infertile women. Methods: Serum leptin (with RIA) and AsAb, EmAb (with ELISA) levels were detected in 32 infertile women and 35 controls. Results: Serum leptin levels in infertile women were significantly lower than those in controls (P<0.01). Serum AsAb and EmAb were both positive in 25 of the 32 infertile women (78.1%) and EmAb (one of two Abs) was positive in the rest 7 women (21.9%). These positive rates were also significantly higher than the respective ones in the controls (both P<0.01). Conclusion: Lower serum leptin level with highly positive AsAb and EmAb might be the chief cause of infertility in women. (authors)

Efek Paparan Musik dan Noise pada Karakteristik Morfologi dan Produktivitas Tanaman Sawi Hijau (Brassica Juncea

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Joko Prasetyo

2014-04-01

Full Text Available The objective of present study was to investigate the effect of various sounds on the green mustard’s (Brassica Juncea morphology characteristic and productivity. The plant has been subjected to three various sound, namely classical music (rhythmic violin music, machine and traffic noise, and mixed sound (classical music and traffic noise with 70-75 dB sound pressure level, from germination to harvest for three hours (7-10 am. each day. Six parameters, i.e. germination, plant height, leaf width, leaf lenght, total plant lenght, and fresh weight, related with growth and productivity of plant were been monitored on regular basis.The results showed classical music improves germination up to 15% for 36 hours, plant height 13,5%, leaf width 14,8%, leaf length 14,2%, and wet weight 57,1%. In general, exposure to classical music gives the best results on the morphological characteristics and productivity of green mustard.

24-Epibrassinolide Restores the Synthesis of Proteins and Amino Acids in Brassica juncea L. Leaves Under Imidacloprid Stress

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Sharma Anket

2017-12-01

Full Text Available Pesticides are applied to protect crops from a variety of insect pests but their application cause toxicity to plants that results, among others, in reduction of protein as well as amino acid contents. The present study is aimed at observing the effect of seed pre-soaking with 24-epibrassinolide (EBL on the protein and amino acid content in the leaves of Brassica juncea L. grown in soil that is amended with pesticide im-idacloprid (IMI. Soil amendment with IMI resulted in a decrease in the contents in leaves of total proteins and 21 amino acids studied. Seed soaking with 100 nM of EBL resulted in the recovery of total protein as well as amino acid contents in leaves, when compared with plants grown in only IMI amended soils.

Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: II - disponibilidade de N, P e K no solo ao longo do ciclo de cultivo Organic fertilization of potato with manure and, or, Crotalaria juncea: II - soil N, P, and K availability throughout the growing season

OpenAIRE

Tácio Oliveira da Silva; Rômulo Simões Cezar Menezes

2007-01-01

Os solos do Agreste paraibano têm baixa fertilidade e a prática usual de adubação é a incorporação de esterco na época do plantio. Entretanto, dependendo da qualidade do esterco, essa prática pode causar a imobilização de nutrientes do solo durante os primeiros meses de cultivo. É possível que o cultivo e incorporação de Crotalaria juncea, combinado com o esterco, possa promover mineralização mais sincronizada com a demanda de nutrientes pelas plantas. No presente estudo, realizado em 2003, f...

Effect of unlabelled monoclonal antibody (MoAb) on biodistribution of /sup 111/Indium labelled (MoAb)

Energy Technology Data Exchange (ETDEWEB)

Lamki, L M; Murray, J L; Rosenblum, M G; Patt, Y Z; Babaian, Richard; Unger, M W

1988-08-01

We have evaluated immunoscintigraphy in cancer patients using four /sup 111/In-labelled murine monoclonal antibodies (MoAb): 96.5 (anti-P97 of melanoma), ZME-018 (anti-high molecular weight antibody of melanoma), ZCE-025 (anti-CEA for colon cancer) and PAY-276 (anti-prostatic acid phosphatase for prostatic cancer). The effect of increasing the doses of unlabelled MoAb (co-infused with 1 mg labelled MoAb) on the relative body distribution of each labelled MoAb was assessed. Localization in the liver decreased significantly in all cases, with increasing MoAb dose, except for ZME-018. Localization in other organs increased significantly as the liver activity decreased. The spleen activity, however, fell in the case of MoAb ZME-018. Blood-pool activity increased with MoAb dose in all four MoAbs. These findings correlated with the rise in the detection rate of metastases, the plasma half-life, and other pharmacokinetic parameters. However, the dose level at which this correlation occurred varied with each antibody. These data demonstrate the co-infusion of unlabelled MoAb with /sup 111/In-labelled MoAb could alter the organ distribution, pharmacokinetics and tumour uptake in a favourable manner, though the degree to which this occurs depends on the antibody in question.

The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30

DEFF Research Database (Denmark)

Kruse, Thomas; Biedenkopf, Nadine; Hertz, Emil Peter Thrane

2018-01-01

Transcription of the Ebola virus genome depends on the viral transcription factor VP30 in its unphosphorylated form, but the underlying molecular mechanism of VP30 dephosphorylation is unknown. Here we show that the Ebola virus nucleoprotein (NP) recruits the host PP2A-B56 protein phosphatase......A-B56 and show that it suppresses Ebola virus transcription and infection. This work dissects the molecular mechanism of VP30 dephosphorylation by PP2A-B56, and it pinpoints this phosphatase as a potential target for therapeutic intervention....

Homology of ab1 and ab3 monoclonal antibodies that neutralize Semliki Forest virus

NARCIS (Netherlands)

Fernandez, IM; Bos, NA; Harmsen, M; Verheul, AFM; Snippe, H; Kraaijeveld, CA

2001-01-01

A noninternal image monoclonal antiidiotypic antibody (ab2 mAb), designated 1,13A321, that had proved its efficacy as vaccine against infection with Semliki Forest virus (SFV) in BALB/c mice, was used as immunogen to generate a panel of SFV-neutralizing monoclonal anti-anti-idiotypic antibodies (ab3

Diode laser surgery. Ab interno and ab externo versus conventional surgery in rabbits.

Science.gov (United States)

Karp, C L; Higginbotham, E J; Edward, D P; Musch, D C

1993-10-01

Fibroblastic proliferation of subconjunctival tissues remains a primary mechanism of failure in filtration surgery. Minimizing the surgical manipulation of episcleral tissues may reduce scarring. Laser sclerostomy surgery involves minimal tissue dissection, and is gaining attention as a method of potentially improving filter duration in high-risk cases. Twenty-five New Zealand rabbits underwent filtration surgery in one eye, and the fellow eye remained as the unoperated control. Ten rabbits underwent ab externo diode laser sclerostomy surgery, ten underwent ab interno diode sclerostomy surgery, and five had posterior sclerostomy procedures. Filtration failure was defined as a less-than-4-mmHg intraocular pressure (IOP) difference between the operative and control eyes. The mean time to failure for the ab externo, ab interno, and conventional posterior sclerostomy techniques measured 17.4 +/- 11.5, 13.1 +/- 6.7, and 6.0 +/- 3.1 days, respectively. In a comparison of the laser-treated groups with the conventional procedure, the time to failure was significantly longer (P = 0.02) for the ab externo filter. The mean ab interno sclerostomy duration was longer than the posterior lip procedure, but this difference was not statistically significant (P = 0.15). The overall level of IOP reduction was similar in the three groups. These data suggest that diode laser sclerostomy is a feasible technique in rabbits, and the ab externo approach resulted in longer filter duration than the conventional posterior lip procedure in this model.

Mitochondrial nad2 gene is co-transcripted with CMS-associated orfB gene in cytoplasmic male-sterile stem mustard (Brassica juncea).

Science.gov (United States)

Yang, Jing-Hua; Zhang, Ming-Fang; Yu, Jing-Quan

2009-02-01

The transcriptional patterns of mitochondrial respiratory related genes were investigated in cytoplasmic male-sterile and fertile maintainer lines of stem mustard, Brassica juncea. There were numerous differences in nad2 (subunit 2 of NADH dehydrogenase) between stem mustard CMS and its maintainer line. One novel open reading frame, hereafter named orfB gene, was located at the downstream of mitochondrial nad2 gene in the CMS. The novel orfB gene had high similarity with YMF19 family protein, orfB in Raphanus sativus, Helianthus annuus, Nicotiana tabacum and Beta vulgaris, orfB-CMS in Daucus carota, atp8 gene in Arabidopsis thaliana, 5' flanking of orf224 in B. napus (nap CMS) and 5' flanking of orf220 gene in CMS Brassica juncea. Three copies probed by specific fragment (amplified by primers of nad2F and nad2R from CMS) were found in the CMS line following Southern blotting digested with HindIII, but only a single copy in its maintainer line. Meanwhile, two transcripts were shown in the CMS line following Northern blotting while only one transcript was detected in the maintainer line, which were probed by specific fragment (amplified by primers of nad2F and nad2R from CMS). Meanwhile, the expression of nad2 gene was reduced in CMS bud compared to that in its maintainer line. We thus suggested that nad2 gene may be co-transcripted with CMS-associated orfB gene in the CMS. In addition, the specific fragment that was amplified by primers of nad2F and nad2R just spanned partial sequences of nad2 gene and orfB gene. Such alterations in the nad2 gene would impact the activity of NADH dehydrogenase, and subsequently signaling, inducing the expression of nuclear genes involved in male sterility in this type of cytoplasmic male sterility.

Pulmonary and hepatic lesions caused by the dehydropyrrolizidine alkaloid-producing plants Crotalaria juncea and Crotalaria retusa in donkeys.

Science.gov (United States)

Pessoa, C R M; Pessoa, A F A; Maia, L A; Medeiros, R M T; Colegate, S M; Barros, S S; Soares, M P; Borges, A S; Riet-Correa, F

2013-09-01

The effects and susceptibility of donkeys to Crotalaria juncea and Crotalaria retusa poisoning were determined at high and low doses. Seeds of C. juncea containing 0.074% of dehydropyrrolizidine alkaloids (DHPAs) (isohemijunceines 0.05%, trichodesmine 0.016%, and junceine 0.008%) were administered to three donkeys at 0.3, 0.6 and 1 g/kg body weight (g/kg) daily for 365 days. No clinical signs were observed and, on liver and lung biopsies, the only lesion was a mild liver megalocytosis in the donkeys ingesting 0.6 and 1 g/kg/day. Two other donkeys that received daily doses of 3 and 5 g seed/kg showed initial respiratory signs 70 and 40 days after the start of the administration, respectively. The donkeys were euthanized following severe respiratory signs and the main lung lesions were proliferation of Clara cells and interstitial fibrosis. Three donkeys ingested seeds of C. retusa containing 5.99% of monocrotaline at daily doses of 0.025, 0.05 and 0.1 g/kg for 365 days. No clinical signs were observed and, on liver and lung biopsies, the only lesion was moderate liver megalocytosis in each of the three donkeys. One donkey that received a single dose of 5 g/kg of C. retusa seeds and another that received 1 g/kg daily for 7 days both showed severe clinical signs and died with diffuse centrilobular liver necrosis. No lung lesions were observed. Another donkey that received a single dose of 2.5 g/kg of C. retusa seeds showed no clinical signs. The hepatic and pneumotoxic effects observed are consistent with an etiology involving DHPAs. Furthermore, the occurrence of lung or liver lesions correlates with the type of DHPAs contained in the seeds. Similarly as has been reported for horses, the data herein suggest that in donkeys some DHPAs are metabolized in the liver causing liver disease, whereas others are metabolized in the lung by Clara cells causing lung disease. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metal accumulation, growth, antioxidants and oil yield of Brassica juncea L. exposed to different metals.

Science.gov (United States)

Sinha, Sarita; Sinam, Geetgovind; Mishra, Rohit Kumar; Mallick, Shekhar

2010-09-01

In agricultural fields, heavy metal contamination is responsible for limiting the crop productivity and quality. This study reports that the plants of Brassica juncea L. cv. Pusa bold grown on contaminated substrates [Cu, Cr(VI), As(III), As(V)] under simulated field conditions have shown translocation of metals to the upper part and its sequestration in the leaves without significantly affecting on oil yield, except for Cr and higher concentration of As(V), compared to control. Decrease in the oil content in As(V) treated plants was observed in a dose dependent manner; however, maximum decrease was recorded in Cr treated plants. Among all the metal treatments, Cr was the most toxic as evident from the decrease in oil content, growth parameters and antioxidants. The accumulation of metals was below the detection limit in the seeds grown on 10 and 30 mg kg(-1) As(III) and Cr(VI); 10 mg kg(-1) As(V)) and thus can be recommended only for oil cultivation. Copyright (c) 2010 Elsevier Inc. All rights reserved.

A cysteine protease (cathepsin Z) from disk abalone, Haliotis discus discus: Genomic characterization and transcriptional profiling during bacterial infections.

Science.gov (United States)

Godahewa, G I; Perera, N C N; Lee, Sukkyoung; Kim, Myoung-Jin; Lee, Jehee

2017-09-05

Cathepsin Z (CTSZ) is lysosomal cysteine protease of the papain superfamily. It participates in the host immune defense via phagocytosis, signal transduction, cell-cell communication, proliferation, and migration of immune cells such as monocytes, macrophages, and dendritic cells. Hence, CTSZ is also acknowledged as an acute-phase protein in host immunity. In this study, we sought to identify the CTSZ homolog from disk abalone (AbCTSZ) and characterize it at the molecular, genomic, and transcriptional levels. AbCTSZ encodes a protein with 318 amino acids and a molecular mass of 36kDa. The structure of AbCTSZ reveals amino acid sequences that are characteristic of the signal sequence, pro-peptide, peptidase-C1 papain family cysteine protease domain, mini-loop, HIP motif, N-linked glycosylation sites, active sites, and conserved Cys residues. A pairwise comparison revealed that AbCTSZ shared the highest amino acid homology with its molluscan counterpart from Crassostrea gigas. A multiple alignment analysis revealed the conservation of functionally crucial elements of AbCTSZ, and a phylogenetic study further confirmed a proximal evolutionary relationship with its invertebrate counterparts. Further, an analysis of AbCTSZ genomic structure revealed seven exons separated by six introns, which differs from that of its vertebrate counterparts. Quantitative real time PCR (qPCR) detected the transcripts of AbCTSZ in early developmental stages and in eight different tissues. Higher levels of AbCTSZ transcripts were found in trochophore, gill, and hemocytes, highlighting its importance in the early development and immunity of disk abalone. In addition, we found that viable bacteria (Vibrio parahaemolyticus and Listeria monocytogenes) and bacterial lipopolysaccharides significantly modulated AbCTSZ transcription. Collectively, these lines of evidences suggest that AbCTSZ plays an indispensable role in the innate immunity of disk abalone. Copyright © 2017. Published by Elsevier

Ab initio pseudopotential theory

International Nuclear Information System (INIS)

Yin, M.T.; Cohen, M.L.

1982-01-01

The ab initio norm-conserving pseudopotential is generated from a reference atomic configuration in which the pseudoatomic eigenvalues and wave functions outside the core region agree with the corresponding ab initio all-electron results within the density-functional formalism. This paper explains why such pseudopotentials accurately reproduce the all-electron results in both atoms and in multiatomic systems. In particular, a theorem is derived to demonstrate the energy- and perturbation-independent properties of ab initio pseudopotentials

The influence of different hydroponic conditions on thorium uptake by Brassica juncea var. foliosa.

Science.gov (United States)

Wang, Dingna; Zhou, Sai; Liu, Li; Du, Liang; Wang, Jianmei; Huang, Zhenling; Ma, Lijian; Ding, Songdong; Zhang, Dong; Wang, Ruibing; Jin, Yongdong; Xia, Chuanqin

2015-05-01

The effects of different hydroponic conditions (such as concentration of thorium (Th), pH, carbonate, phosphate, organic acids, and cations) on thorium uptake by Brassica juncea var. foliosa were evaluated. The results showed that acidic cultivation solutions enhanced thorium accumulation in the plants. Phosphate and carbonate inhibited thorium accumulation in plants, possibly due to the formation of Th(HPO4)(2+), Th(HPO4)2, or Th(OH)3CO3 (-) with Th(4+), which was disadvantageous for thorium uptake in the plants. Organic aids (citric acid, oxalic acid, lactic acid) inhibited thorium accumulation in roots and increased thorium content in the shoots, which suggested that the thorium-organic complexes did not remain in the roots and were beneficial for thorium transfer from the roots to the shoots. Among three cations (such as calcium ion (Ca(2+)), ferrous ion (Fe(2+)), and zinc ion (Zn(2+))) in hydroponic media, Zn(2+) had no significant influence on thorium accumulation in the roots, Fe(2+) inhibited thorium accumulation in the roots, and Ca(2+) was found to facilitate thorium accumulation in the roots to a certain extent. This research will help to further understand the mechanism of thorium uptake in plants.

Biosorption of Acid Blue 290 (AB 290) and Acid Blue 324 (AB 324) dyes on Spirogyra rhizopus

International Nuclear Information System (INIS)

Ozer, Ayla; Akkaya, Goenuel; Turabik, Meral

2006-01-01

In this study, the biosorption of Acid Blue 290 and Acid Blue 324 on Spirogyra rhizopus, a green algae growing on fresh water, was studied with respect to initial pH, temperature, initial dye concentration and biosorbent concentration. The optimum initial pH and temperature values for AB 290 and AB 324 biosorption were found to be 2.0, 30 deg. C and 3.0, 25 deg. C, respectively. It was observed that the adsorbed AB 290 and AB 324 amounts increased with increasing the initial dye concentration up to 1500 and 750 mg/L, respectively. The Langmuir, Freundlich, Redlich-Peterson and Koble-Corrigan isotherm models were applied to the experimental equilibrium data and the isotherm constants were determined by using Polymath 4.1 software. The monolayer coverage capacities of S. rhizopus for AB 290 and AB 324 dyes were found as 1356.6 mg/g and 367.0 mg/g, respectively. The intraparticle diffusion model and the pseudo-second order kinetic model were applied to the experimental data in order to describe the removal mechanism of these acidic dyes by S. rhizopus. The pseudo-second order kinetic model described very well the biosorption kinetics of AB 290 and AB 324 dyes. Thermodynamic studies showed that the biosorption of AB 290 and AB 324 on S. rhizopus was exothermic in nature

Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6.

Science.gov (United States)

Fukami, Josiane; Abrantes, Julia Laura Fernandes; Del Cerro, Pablo; Nogueira, Marco Antonio; Ollero, Francisco Javier; Megías, Manuel; Hungria, Mariangela

2018-01-01

Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

Genome analysis methods: Arabidopsis lyrata [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

Lifescience Database Archive (English)

Full Text Available (http://genome.imim.es/software/geneid/) applying dicot and A. thaliana specific matrices 32,670 (v1.0) JGI; http://www.phytozome.net/alyrata v1.0 v1.0 10.1038/ng.807 21478890 ... ...8.3x Arachne 1,309 ... Fgenesh package of ab initio and homology-based gene predictors, EuGene12, and GeneID13

[A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

Science.gov (United States)

Guliy, O I; Karavaeva, O A; Velikov, V A; Sokolov, O I; Pavily, S A; Larionova, O S; Burov, A M; Ignatov, O V

2016-01-01

The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed.

Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

Science.gov (United States)

Knotts, Greg

2009-11-01

This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

nGASP - the nematode genome annotation assessment project

Energy Technology Data Exchange (ETDEWEB)

Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

2008-12-19

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

Comparative Genomic Analysis of Neutrophilic Iron(II Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer

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Shaomei He

2017-08-01

Full Text Available Extracellular electron transfer (EET is recognized as a key biochemical process in circumneutral pH Fe(II-oxidizing bacteria (FeOB. In this study, we searched for candidate EET genes in 73 neutrophilic FeOB genomes, among which 43 genomes are complete or close-to-complete and the rest have estimated genome completeness ranging from 5 to 91%. These neutrophilic FeOB span members of the microaerophilic, anaerobic phototrophic, and anaerobic nitrate-reducing FeOB groups. We found that many microaerophilic and several anaerobic FeOB possess homologs of Cyc2, an outer membrane cytochrome c originally identified in Acidithiobacillus ferrooxidans. The “porin-cytochrome c complex” (PCC gene clusters homologous to MtoAB/PioAB are present in eight FeOB, accounting for 19% of complete and close-to-complete genomes examined, whereas PCC genes homologous to OmbB-OmaB-OmcB in Geobacter sulfurreducens are absent. Further, we discovered gene clusters that may potentially encode two novel PCC types. First, a cluster (tentatively named “PCC3” encodes a porin, an extracellular and a periplasmic cytochrome c with remarkably large numbers of heme-binding motifs. Second, a cluster (tentatively named “PCC4” encodes a porin and three periplasmic multiheme cytochromes c. A conserved inner membrane protein (IMP encoded in PCC3 and PCC4 gene clusters might be responsible for translocating electrons across the inner membrane. Other bacteria possessing PCC3 and PCC4 are mostly Proteobacteria isolated from environments with a potential niche for Fe(II oxidation. In addition to cytochrome c, multicopper oxidase (MCO genes potentially involved in Fe(II oxidation were also identified. Notably, candidate EET genes were not found in some FeOB, especially the anaerobic ones, probably suggesting EET genes or Fe(II oxidation mechanisms are different from the searched models. Overall, based on current EET models, the search extends our understanding of bacterial EET and

Development of an efficient regeneration protocol for three genotypes of brassica juncea

International Nuclear Information System (INIS)

Bano, R.; Khan, M.H.; Rashid, H.

2010-01-01

Two phytohormones, auxins (Naphthalene acetic acid and Indole acetic acid) and cytokinins (Benzyl aminopurine and Kinetin) with concentrations were used to develop an efficient regeneration protocol for 3 genotypes of Brassica juncea (UCD-635, RL-18 and NIFA RAYE). The explants were cultured on MS-medium supplemented with BAP 1.0 mgL/sup -1//NAA 0.1 mgL-1, BAP 2.0 mg L/sup -1//NAA 0.2 mg L/sup -1/, BAP 3.0 mgL/sup -1/ NAA 0.3 mg L-1 and Kinetin 1.0 mg L/sup -1/ IAA 0.1 mg L/sup -1/, Kinetin 2.0 mg L/sup -1//IAA 0.2 mg L/sup -1/, Kinetin 3.0mg L-1/IAA 0.3 mg L/sup -1/. Maximum callus production (65.55) was observed on MS medium containing with BAP 2.0 mgL-1/NAA 0.2 mg L/sup -1/. Maximum shooting (22.31) was observed BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/ and KIN 3.0 mg L-1/IAA 0.3 mg L/sup -1/. Regeneration efficiency was found maximum (7.13) with BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/. The three genotypes were found significantly different at p greater or equal to 0.05 in shoots production and regeneration efficiency. (author)

AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

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Shankavaram Uma

2006-04-01

Full Text Available Abstract Background Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. Description AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60 and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different

AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

Science.gov (United States)

Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

2006-04-06

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that

Preliminary Phytochemical and Biological activities on Russelia juncea Zucc

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Maryam Bibi

2017-12-01

Full Text Available To probe the ethnomedicinal claims of Russelia juncea Zucc. (Plantaginaceae as prescribed traditionally in the folklore history of medicines. Methods: The dichloromethane and methanol extracts of aerial parts and roots were examined for antimicrobial, antioxidant, antiglycation, insecticidal, leishmanicidal, cytotoxic and phytotoxic activities. Different phytochemical tests were also performed to confirm the presence of various groups of secondary metabolites such as alkaloids, glycosides, saponins, tannins, flavonoids and terpenoids. Results: Phytochemical screening of this plant confirmed the presence of alkaloids, saponins, tannins, flavonoids and terpenoids. Antibacterial activity was only shown by RJRD with 80% inhibition at the concentration of 150µg/ml against Shigella flexneri. Among the tested samples, RJAM and RJRM displayed significant radical scavenging activity up to 93% and 89% with IC50 values of 184.75 ± 4.05µM and 263.01 ± 9.36µM. The significant antiglycation potential was exhibited by RJAD, RJAM and RJRM with 55.35%, 62.25% and 59.22% inhibition and IC50 values of 0.84 ± 0.08mg/ml, 1.37 ± 0.15mg/ml and 1.52 ± 0.10mg/ml respectively. Moderate leishmanicidal activity was exposed by RJAD and RJRM with IC50 values of 73.04 ± 1.05µg/ml and 77.66 ± 0.23µg/ml while RJAM was found to be more potent and exposed significant leishmanicidal activity having IC50 of 48 ± 0.39µg/ml. However, prominent cytotoxic activity was displayed by RJRM with 66.08% inhibition and IC50 of 31.20 ± 3µg/ml. Non-significant antifungal, insecticidal and phytotoxic activities were demonstrated by all the tested samples. Conclusion: All the above contributions give serious attentiveness to scientists to isolate and purify the biologically active phytoconstituents by using advanced scientific methodologies that serve as lead compounds in the synthesis of new therapeutic agents of desired interest in the world of drug discovery.

Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

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José Cuenca

Full Text Available Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR to map a genome region linked to Alternaria brown spot (ABS resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

Science.gov (United States)

Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

2013-01-01

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

Science.gov (United States)

Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

2009-07-23

Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

Ab initio study of the isomerism of (LiAB)2 salt dimers with 24 valence electrons (AB- = NO-, PO-, NS-, PS-)

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

2000-01-01

The nonempiric calculations of the potential energies surfaces in the vicinity of the key structures of the loose dimer molecules of the (LiNO) 2 , (LiPO) 2 , (LiNS) 2 and (LiPS) 2 lithium salts with 24 valence electrons are accomplished within the frames of the MP2/6-31G * //HF/6-31g * + ZPE(HF/6-31G * and MP4SDTQ/6-31G * //MP2/6-31G * + ZPE(MP2/6-31G * ) approximation. The equilibrium geometrical parameters, relative energies and isomer decay energies, frequencies and IR-intensities of normal vibrations are determined. The geometrical deformations and shifts of vibrational frequencies of the cis- and trans-dianions under the effect of cations by different ways of their coordination as well as tendencies of the molecular properties behaviour in various series of dimers (LiAB) 2 are analyzed. The results obtained are compared with the data of previous calculations of the LiAB salts monomeric molecules, the Li 2 AB + ions with 12 valence electrons and the (LiAB) 2 dimers with 20 valence electrons [ru

Topsoil drying combined with increased sulfur supply leads to enhanced aliphatic glucosinolates in Brassica juncea leaves and roots.

Science.gov (United States)

Tong, Yu; Gabriel-Neumann, Elke; Ngwene, Benard; Krumbein, Angelika; George, Eckhard; Platz, Stefanie; Rohn, Sascha; Schreiner, Monika

2014-01-01

The decrease of water availability is leading to an urgent demand to reduce the plants' water supply. This study evaluates the effect of topsoil drying, combined with varying sulfur (S) supply on glucosinolates in Brassica juncea in order to reveal whether a partial root drying may already lead to a drought-induced glucosinolate increase promoted by an enhanced S supply. Without decreasing biomass, topsoil drying initiated an increase in aliphatic glucosinolates in leaves and in topsoil dried roots supported by increased S supply. Simultaneously, abscisic acid was determined, particularly in dehydrated roots, associated with an increased abscisic acid concentration in leaves under topsoil drying. This indicates that the dehydrated roots were the direct interface for the plants' stress response and that the drought-induced accumulation of aliphatic glucosinolates is related to abscisic acid formation. Indole and aromatic glucosinolates decreased, suggesting that these glucosinolates are less involved in the plants' response to drought. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ab initio vel ex eventu

Science.gov (United States)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

Contribution of EmrAB efflux pumps to colistin resistance in Acinetobacter baumannii.

Science.gov (United States)

Lin, Ming-Feng; Lin, Yun-You; Lan, Chung-Yu

2017-02-01

Efflux pumps play an important role in antimicrobial resistance for Acinetobacter baumannii. However, the function of the Emr pump system and the relationship between Emr and drug resistance has not been characterized in A. baumannii. In this study, four possible groups of emr-like genes were found by searching a genome database. Among them, A1S_1772 (emrB) and A1S_1773 (emrA) were demonstrated to be co-transcribed as a single operon. Moreover, during osmotic stress, A1S_1772 showed the largest change in gene expression compared to the other emrB-like genes, and deletion of A1S_1772 (AB ΔemrB) significantly slowed cell growth in 20% sucrose. Using a phenotypic microarray analysis, the AB ΔemrB mutant was more susceptible to colistin and nafcillin, paromomycin, spiramycin, and D,L-serine hydroxmate than the wild type. The spot assay, time kill assay and minimal inhibition concentration determination also indicated that the wild type could tolerate colistin better than the AB ΔemrB mutant. Finally, the increased expression levels of all emrB-like genes, including A1S_0775, A1S_0909, A1S_1772, and A1S_1799, in colistin resistance-induced A. baumannii further supported the possible involvement of the emrB genes in A. baumannii colistin resistance. Together, the Emr pump systems in A. baumannii contribute to adaptation to osmotic stress and resistance to colistin.

SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data

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Songbo eHuang

2011-07-01

Full Text Available RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.

Study on Exothermic Oxidation of Acrylonitrile-butadiene-styrene (ABS Resin Powder with Application to ABS Processing Safety

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Jenq-Renn Chen

2010-08-01

Full Text Available Oxidative degradation of commercial grade ABS (Acrylonitrile-butadiene-styrene resin powders was studied by thermal analysis. The instabilities of ABS containing different polybutadiene (PB contents with respect to temperature were studied by Differential Scanning Calorimeter (DSC. Thermograms of isothermal test and dynamic scanning were performed. Three exothermic peaks were observed and related to auto-oxidation, degradation and oxidative decomposition, respectively. Onset temperature of the auto-oxidation was determined to be around 193 °C. However, threshold temperature of oxidation was found to be as low as 140 °C by DSC isothermal testing. Another scan of the powder after degeneration in air showed an onset temperature of 127 °C. Reactive hazards of ABS powders were verified to be the exothermic oxidation of unsaturated PB domains, not the SAN (poly(styrene-acrylonitrile matrix. Heat of oxidation was first determined to be 2,800 ± 40 J per gram of ABS or 4,720 ± 20 J per gram of PB. Thermal hazards of processing ABS powder are assessed by adiabatic temperature rise at process conditions. IR spectroscopy associated with heat of oxidation verified the oxidative mechanism, and these evidences excluded the heat source from the degradation of SAN. A specially prepared powder of ABS without adding anti-oxidant was analyzed by DSC for comparing the exothermic behaviors. Exothermic onset temperatures were determined to be 120 °C and 80 °C by dynamic scanning and isothermal test, respectively. The assessment successfully explained fires and explosions in an ABS powder dryer and an ABS extruder.

Two duplicated chicken-type lysozyme genes in disc abalone Haliotis discus discus: molecular aspects in relevance to structure, genomic organization, mRNA expression and bacteriolytic function.

Science.gov (United States)

Umasuthan, Navaneethaiyer; Bathige, S D N K; Kasthuri, Saranya Revathy; Wan, Qiang; Whang, Ilson; Lee, Jehee

2013-08-01

Lysozymes are crucial antibacterial proteins that are associated with catalytic cleavage of peptidoglycan and subsequent bacteriolysis. The present study describes the identification of two lysozyme genes from disc abalone Haliotis discus discus and their characterization at sequence-, genomic-, transcriptional- and functional-levels. Two cDNAs and BAC clones bearing lysozyme genes were isolated from abalone transcriptome and BAC genomic libraries, respectively and sequences were determined. Corresponding deduced amino acid sequences harbored a chicken-type lysozyme (LysC) family profile and exhibited conserved characteristics of LysC family members including active residues (Glu and Asp) and GS(S/T)DYGIFQINS motif suggested that they are LysC counterparts in disc abalone and designated as abLysC1 and abLysC2. While abLysC1 represented the homolog recently reported in Ezo abalone [1], abLysC2 shared significant identity with LysC homologs. Unlike other vertebrate LysCs, coding sequence of abLysCs were distributed within five exons interrupted by four introns. Both abLysCs revealed a broader mRNA distribution with highest levels in mantle (abLysC1) and hepatopancreas (abLysC2) suggesting their likely main role in defense and digestion, respectively. Investigation of temporal transcriptional profiles post-LPS and -pathogen challenges revealed induced-responses of abLysCs in gills and hemocytes. The in vitro muramidase activity of purified recombinant (r) abLysCs proteins was evaluated, and findings indicated that they are active in acidic pH range (3.5-6.5) and over a broad temperature range (20-60 °C) and influenced by ionic strength. When the antibacterial spectra of (r)abLysCs were examined, they displayed differential activities against both Gram positive and Gram negative strains providing evidence for their involvement in bacteriolytic function in abalone physiology. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

Science.gov (United States)

Aversano, Riccardo; Contaldi, Felice; Ercolano, Maria Raffaella; Grosso, Valentina; Iorizzo, Massimo; Tatino, Filippo; Xumerle, Luciano; Dal Molin, Alessandra; Avanzato, Carla; Ferrarini, Alberto; Delledonne, Massimo; Sanseverino, Walter; Cigliano, Riccardo Aiese; Capella-Gutierrez, Salvador; Gabaldón, Toni; Frusciante, Luigi; Bradeen, James M.; Carputo, Domenico

2015-01-01

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes. PMID:25873387

Solvent (acetone-butanol: ab) production

Science.gov (United States)

This article describes production of butanol [acetone-butanol-ethanol, (also called AB or ABE or solvent)] by fermentation using both traditional and current technologies. AB production from agricultural commodities, such as corn and molasses, was an important historical fermentation. Unfortunately,...

The 2-alkyl-2H-indazole regioisomers of synthetic cannabinoids AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA are possible manufacturing impurities with cannabimimetic activities

OpenAIRE

Longworth, Mitchell; Banister, Samuel D.; Mack, James B. C.; Glass, Michelle; Connor, Mark; Kassiou, Michael

2016-01-01

Indazole-derived synthetic cannabinoids (SCs) featuring an alkyl substituent at the 1-position and l-valinamide at the 3-carboxamide position (e.g., AB-CHMINACA) have been identified by forensic chemists around the world, and are associated with serious adverse health effects. Regioisomerism is possible for indazole SCs, with the 2-alkyl-2H-indazole regioisomer of AB-CHMINACA recently identified in SC products in Japan. It is unknown whether this regiosiomer represents a manufacturing impurit...

Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

Science.gov (United States)

Behzad, Somayeh

2016-09-01

Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

Field Trial Performance of Herculex XTRA (Cry34Ab1/Cry35Ab1) and SmartStax (Cry34Ab1/Cry35Ab1 + Cry3Bb1) Hybrids and Soil Insecticides Against Western and Northern Corn Rootworms (Coleoptera: Chrysomelidae).

Science.gov (United States)

Johnson, K D; Campbell, L A; Lepping, M D; Rule, D M

2017-06-01

Western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), and northern corn rootworm, Diabrotica barberi Smith and Lawrence (Coleoptera: Chrysomelidae), are important insect pests in corn, Zea mays L. For more than a decade, growers have been using transgenic plants expressing proteins from the bacterium Bacillus thuringiensis (Bt) to protect corn roots from feeding. In 2011, western corn rootworm populations were reported to have developed resistance to Bt hybrids expressing Cry3Bb1 and later found to be cross-resistant to hybrids expressing mCry3A and eCry3.1Ab. The identification of resistance to Cry3 (Cry3Bb1, mCry3A, and eCry3.1Ab) hybrids led to concerns about durability and efficacy of products with single traits and of products containing a pyramid of a Cry3 protein and the binary Bt proteins Cry34Ab1 and Cry35Ab1. From 2012 to 2014, 43 field trials were conducted across the central United States to estimate root protection provided by plants expressing Cry34Ab1/Cry35Ab1 alone (Herculex RW) or pyramided with Cry3Bb1 (SmartStax). These technologies were evaluated with and without soil-applied insecticides to determine if additional management measures provided benefit where Cry3 performance was reduced. Trials were categorized for analysis based on rootworm damage levels on Cry3-expressing hybrids and rootworm feeding pressure within each trial. Across scenarios, Cry34Ab1/Cry35Ab1 hybrids provided excellent root protection. Pyramided traits provided greater root and yield protection than non-Bt plus a soil-applied insecticide, and only in trials where larval feeding pressure exceeded two nodes of damage did Cry34Ab1/Cry35Ab1 single-trait hybrids and pyramided hybrids show greater root protection from the addition of soil-applied insecticides. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Complete genome sequence and phylogenetic analyses of an aquabirnavirus isolated from a diseased marbled eel culture in Taiwan.

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Wen, Chiu-Ming

2017-08-01

An aquabirnavirus was isolated from diseased marbled eels (Anguilla marmorata; MEIPNV1310) with gill haemorrhages and associated mortality. Its genome segment sequences were obtained through next-generation sequencing and compared with published aquabirnavirus sequences. The results indicated that the genome sequence of MEIPNV1310 contains segment A (3099 nucleotides) and segment B (2789 nucleotides). Phylogenetic analysis showed that MEIPNV1310 is closely related to the infectious pancreatic necrosis Ab strain within genogroup II. This genome sequence is beneficial for studying the geographic distribution and evolution of aquabirnaviruses.

Cyclin dependent kinase inhibitor 2A/B gene deletions are markers of poor prognosis in Indian children with acute lymphoblastic leukemia.

Science.gov (United States)

Agarwal, Manisha; Bakhshi, Sameer; Dwivedi, Sadanand N; Kabra, Madhulika; Shukla, Rashmi; Seth, Rachna

2018-06-01

Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study. Genomic DNA from pretreatment bone marrow/peripheral blood samples of these children was investigated for copy number alterations in CDKN2A/B genes using multiplex ligation dependent probe amplification assay. Immunophenotype subtyping and cytogenetic and molecular analysis of ALL was performed at start of induction chemotherapy in all children. Children were monitored for response to prednisolone (Day 8), complete morphological remission, and minimal residual disease at the end of induction. The minimum postinduction follow-up period was 6 months. CDKN2A/B deletions were seen in 19.8% (18/91) of B lineage acute lymphoblastic leukemia (B-ALL) and 38.5% (5/13) of T lineage acute lymphoblastic leukemia (T-ALL). Monoallelic CDKN2A/B deletions were found in 61.1% of total deletions in B-ALL while all the children with T-ALL harbored biallelic deletions. The prevalence of CDKN2A/B gene deletions was found to be significantly higher in older children (P = 0.002), in those with higher leukocyte count (P = 0.037), and in National Cancer Institute high risk group patients (P = 0.001) in the B-ALL subgroup. Hazard ratio was significantly high for children with CDKN2A/B deletions in total cohort (P = 0.004). Children with CDKN2A/B deletion had significantly lesser event free survival (P = 0.03). CDKN2A/B deletions were significantly more prevalent in T-ALL subgroup and were found to have higher hazard ratio and lesser event free survival in total cohort in our study. © 2018 Wiley Periodicals, Inc.

A continuous culture system of direct somatic embryogenesis in microspore-derived embryos of Brassica juncea.

Science.gov (United States)

Prabhudesai, V; Bhaskaran, S

1993-03-01

An efficient culture system has been developed for repeated cycles of somatic embryogenesis in microspore-derived embryos of Brassica juncea without a callus phase. Haploid embryos produced through anther culture showed a high propensity for direct production of somatic embryos in response to 2 mgL(-1) BA and 0.1 mgL(-1) NAA. The embryogenic cultures which comprised the elongated embryonal axis of microspore-derived embryos when explanted and grown on the medium of same composition produced a large number of secondary embryos. These somatic embryos in turn underwent axis elongation and produced more somatic embryos when explanted and cultured. This cycle of repetitive somatic embryogenesis continued with undiminished vigour passage after passage and was monitored for more than a year. Somatic embryos from any passage when isolated at cotyledonary stage and grown on auxin-free medium for 5 days and then on a medium containing NAA (0.1 mgL(-1)), developed into complete plants with a profuse root system and were easily established in the soil. The cytology of the root tips of these plants confirmed their haploid nature. The total absence of callus phase makes the system ideal for continuous cloning of androgenic lines, Agrobacterium-mediated transformation and mutation induction studies.

Biorefinery process for protein extraction from oriental mustard (Brassica juncea (L.) Czern.) using ethanol stillage.

Science.gov (United States)

Ratanapariyanuch, Kornsulee; Tyler, Robert T; Shim, Youn Young; Reaney, Martin Jt

2012-01-12

Large volumes of treated process water are required for protein extraction. Evaporation of this water contributes greatly to the energy consumed in enriching protein products. Thin stillage remaining from ethanol production is available in large volumes and may be suitable for extracting protein rich materials. In this work protein was extracted from ground defatted oriental mustard (Brassica juncea (L.) Czern.) meal using thin stillage. Protein extraction efficiency was studied at pHs between 7.6 and 10.4 and salt concentrations between 3.4 × 10-2 and 1.2 M. The optimum extraction efficiency was pH 10.0 and 1.0 M NaCl. Napin and cruciferin were the most prevalent proteins in the isolate. The isolate exhibited high in vitro digestibility (74.9 ± 0.80%) and lysine content (5.2 ± 0.2 g/100 g of protein). No differences in the efficiency of extraction, SDS-PAGE profile, digestibility, lysine availability, or amino acid composition were observed between protein extracted with thin stillage and that extracted with NaCl solution. The use of thin stillage, in lieu of water, for protein extraction would decrease the energy requirements and waste disposal costs of the protein isolation and biofuel production processes.

14CO2 fixation and allocation of 14C into major biochemical fractions in different parts of Indian mustard (Brassica juncea)

International Nuclear Information System (INIS)

Subrahmanyam, D.; Rathore, V.S.

1993-01-01

14CO2 fixation and transport of 14C-photosynthates amongst different parts of Indian mustard (Brassica juncea) and the incorporation of 14C into major chemical fractions in different plant parts was studied at ripening stage. Stem and pod together contributed 70 % of the total 14C fixed by the plant. In all plant parts neutral saccharide fraction contained maximum radioactivity immediately after exposing plants to 14CO2. After 24 h, the radioactivity in this fraction declined considerably due to translocation or conversion into other fractions. Concomitantly radioactivity in lipids and pigments, residue and starch fractions increased after 24 h. The 14C allocation patterns in stem and leaves were similar. However, in pods very high radioactivity was recovered from amino and organic acid fractions indicating the presence of active phosphoenolpyruvate carboxylase in pod walls

Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

Science.gov (United States)

Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

2016-01-01

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

Identification of Clusters that Condition Resistance to Anthracnose in the Common Bean Differential Cultivars AB136 and MDRK.

Science.gov (United States)

Campa, Ana; Trabanco, Noemí; Ferreira, Juan José

2017-12-01

The correct identification of the anthracnose resistance systems present in the common bean cultivars AB136 and MDRK is important because both are included in the set of 12 differential cultivars proposed for use in classifying the races of the anthracnose causal agent, Colletrotrichum lindemuthianum. In this work, the responses against seven C. lindemuthianum races were analyzed in a recombinant inbred line population derived from the cross AB136 × MDRK. A genetic linkage map of 100 molecular markers distributed across the 11 bean chromosomes was developed in this population to locate the gene or genes conferring resistance against each race, based on linkage analyses and χ 2 tests of independence. The identified anthracnose resistance genes were organized in clusters. Two clusters were found in AB136: one located on linkage group Pv07, which corresponds to the anthracnose resistance cluster Co-5, and the other located at the end of linkage group Pv11, which corresponds to the Co-2 cluster. The presence of resistance genes at the Co-5 cluster in AB136 was validated through an allelism test conducted in the F 2 population TU × AB136. The presence of resistance genes at the Co-2 cluster in AB136 was validated through genetic dissection using the F 2:3 population ABM3 × MDRK, in which it was directly mapped to a genomic position between 46.01 and 47.77 Mb of chromosome Pv11. In MDRK, two independent clusters were identified: one located on linkage group Pv01, corresponding to the Co-1 cluster, and the second located on LG Pv04, corresponding to the Co-3 cluster. This report enhances the understanding of the race-specific Phaseolus vulgaris-C. lindemuthianum interactions and will be useful in breeding programs.

Simulation and Robust Contol of Antilock Braking System ABS

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David Jordan DELICHRISTOV

2009-06-01

Full Text Available This paper deals with simulation and robust control of Antilock Braking System ABS. The briefly are described the main parts of ABS hydraulic system and control algorithm of ABS. Hydraulic system described here is BOSCH ABS 5.x series. The goal of ABS system is vehicle stability and vehicle steering response when braking. If during the braking occurred slip at one or more wheels from any reason, ABS evaluates this by “brake slip” controller. At this moment ABS is trying to use maximal limits of adhesion between tire and road. It means that is necessary control the differences between braking torque and friction torque , which reacts to the wheel via friction reaction tire-road surface. This is realized through the solenoid valves, which are controls (triggered by on the base of PID controller described further in chapter 4. Presented concept is more or less standard for most of the existing ABS systems. The issue should be applied concept of robust ABS control algorithm, which is specific for every type of ABS.

SdAb heterodimer formation using leucine zippers

Science.gov (United States)

Goldman, Ellen R.; Anderson, George P.; Brozozog-Lee, P. Audrey; Zabetakis, Dan

2013-05-01

Single domain antibodies (sdAb) are variable domains cloned from camel, llama, or shark heavy chain only antibodies, and are among the smallest known naturally derived antigen binding fragments. SdAb derived from immunized llamas are able to bind antigens with high affinity, and most are capable of refolding after heat or chemical denaturation to bind antigen again. We hypothesized that the ability to produce heterodimeric sdAb would enable reagents with the robust characteristics of component sdAb, but with dramatically improved overall affinity through increased avidity. Previously we had constructed multimeric sdAb by genetically linking sdAb that bind non-overlapping epitopes on the toxin, ricin. In this work we explored a more flexible approach; the construction of multivalent binding reagents using multimerization domains. We expressed anti-ricin sdAb that recognize different epitopes on the toxin as fusions with differently charged leucine zippers. When the initially produced homodimers are mixed the leucine zipper domains will pair to produce heterodimers. We used fluorescence resonance energy transfer to confirm heterodimer formation. Surface plasmon resonance, circular dichroism, enzyme linked immunosorbent assays, and fluid array assays were used to characterize the multimer constructs, and evaluate their utility in toxin detection.

AB/sub 5/-catalyzed hydrogen evolution cathodes

Energy Technology Data Exchange (ETDEWEB)

Hall, D E; Sawada, T; Shepard, V R; Tsujikawa, Y

1984-01-01

The AB/sub 5/ metal compounds are highly efficient hydrogen evolution electrocatalysts in alkaline electrolyte. Three types of AB/sub 5/-catalyzed cathode structures were made, using the hydride-forming AB/sub 5/ compounds in particulate form. Plastic-bonded cathodes containing >90 w/o AB/sub 5/ (finished-weight basis) were the most efficient, giving hydrogen evolution overpotentials (/eta/ /SUB H2/ ) of about 0.05 V at 200 mA cm/sup -2/. However, they tended to swell and shed material during electrolysis. Pressed, sintered cathodes containing 40-70 w/o catalyst in a nickel binder gave /eta/ /SUB H2/ about0.08 V; catalyst retention was excellent. Porous, sintered cathode coatings were made with 30-70 w/o AB/sub 5/ catalyst loadings. Their overpotentials were similar to those of the pressed, sintered cathodes. However, at catalyst loadings below about 40 w/o, high overpotentials characteristic of the nickel binder were observed. The structural and electrochemical properties of the three AB/sub 5/-catalyzed cathodes are discussed.

Deterioração de sementes de Crotalaria juncea e suas conseqüências em laboratório e campo Deterioration of Crotalaria juncea seeds and its consequences under laboratory and field conditions

Directory of Open Access Journals (Sweden)

Jocely Andreuccetti Maeda

1986-01-01

Full Text Available Sementes de Crotalaria juncea L. com conteúdos de umidade de 6,3 e 11,1%, foram armazenadas por 84 meses em condições ambientes e às temperaturas controladas de 20 e 30°C, e testadas periodicamente no laboratório quanto a germinação e vigor (índice de velocidade de germinação e no campo quanto a emergência, altura da planta, produção de massa seca (massa vegetal na maturação e de sementes. Até aos 30 meses, não se observaram diferenças significativas de germinação entre as sementes nas diversas condições, apresentando todas porcentagens acima de 90. Dos 30 meses em diante, as sementes armazenadas nas condições de maior umidade e temperatura exibiram maior velocidade de deterioração, notadamente as mantidas com 11,1% de umidade a 30°C, que mostraram germinação e vigor praticamente nulos a partir dos 66 meses. As sementes com 6,3% de umidade mantiveram germinação acima de 90% até aos 84 meses, independente da temperatura. Do quarto ano de plantio em diante, as sementes armazenadas com 11,1% de umidade a 30°C se destacaram negativamente das demais quanto a "stand", produção de massa seca e de sementes. Das condições estudadas, as mais adequadas para a preservação da longevidade das sementes foram a secagem a 6,3% de umidade e manutenção a 20 ou 30°C, tendo as sementes assim armazenadas apresentado, ao final dos sete anos, satisfatórios níveis de germinação e vigor e bom comportamento no campo.Crotalaria juncea L. seeds with 6.3% and 11.1% moisture contents were stored for 84 months under room temperature and controlled conditions (at 20°C and 30°C. The seeds were tested periodically, in the laboratory for germination and vigor (germination speed index and in the field, for emergence, plant height, green matter production (at time of maturation and grain yield. No significant differences among the seeds were observed up to 30 months of storage, under the several conditions, all presenting above 90

Impact of Indian Mustard (Brassica juncea and Flax (Linum usitatissimum Seed Meal Applications on Soil Carbon, Nitrogen, and Microbial Dynamics

Directory of Open Access Journals (Sweden)

Autumn S. Wang

2012-01-01

Full Text Available There is a critical need to investigate how land application of dedicated biofuel oilseed meals affects soil ecosystems. In this study, mustard (Brassica juncea and flax (Linum usitatissimum seed meals and sorghum-sudangrass (Sorghum bicolor were added to soil at levels of 0, 1, 2.5, and 5% (w/w. Both the type of amendment and application rate affected soil organic C, total C & N, and C & N mineralization. Mustard meal amendment initially inhibited C mineralization as compared to flax, but >50% of mustard and flax organic C was mineralized within 51 d. Nitrogen mineralization was similar for flax and mustard, except for the 2.5% rate for which a lower proportion of mustard N was converted to nitrate. The mustard meal greatly impacted microbial community composition, appearing to select for specific fungal populations. The potential varying impacts of different oilseed meals on soil ecosystems should be considered when developing recommendations for land application.

Preparation, biodistribution, and dosimetry of 188Re-Labeled MoAb ior cea1 and its f(ab')2 fragments by avidin-biotin strategy

International Nuclear Information System (INIS)

Ferro-Flores, Guillermina; Pimentel-Gonzalez, Gilmara; Gonzalez-Zavala, Maria Antonia; Murphy, Consuelo Arteaga de; Melendez-Alafort, Laura; Tendilla, Jose I.; Croft, Barbara Y.

1999-01-01

The biotinylated monoclonal antibody (MoAb) ior cea1 and its F(ab') 2 fragments were labeled with Re-188 by combination of avidin-biotin strategy. 188 Re-MoAb, 188 Re-MoAb-biotin, 188 Re-F(ab') 2 , and 188 Re-F(ab') 2 -biotin preparations were produced for these studies with specific activities of 1.30±0.18 GBq/mg and from instant freeze-dried kit formulations using ethane-1-hydroxy-1,1-diphosphonic acid (EHDP) as a weak competing ligand. There were no significant differences (p>0.05) between the biodistribution in mice of biotinylated and unbiotinylated 188 Re-labeled immunoconjugates. When avidin was injected as a chase after injection of 188 Re-MoAb-biotin or 188 Re-F(ab') 2 -biotin, the blood radioactivity level decreased approximately 75% (cumulated activity) and the effective dose decreased almost 25% with respect to that of the radioimmunoconjugates in which the chase effect was not used. Our results suggest that 188 Re-labeled biotinylated MoAb ior cea1 and its F(ab') 2 fragments prepared by this method are stable complexes in vivo

PENGARUH MEDIA TANAM DAN NUTRISI TERHADAP PERTUMBUHAN DAN HASIL TANAMAN PAKCHOI (Brassica juncea L. DENGAN SISTEM HIDROPONIK

Directory of Open Access Journals (Sweden)

Balia Perwitasari

2012-03-01

Full Text Available Pakchoi (Brassica juncea L.. is one kind of a vegetable crop that has high economic value and high nutrition. The technology of hydroponic is one of alternative cultivation using other media than soil substrates and nutrients. The purpose of this research is to determine the effect of media composition and nutrition on growth and yield of  pakchoi crops and find out which treatment is best for plant growth and yield of pakchoi. Researchcarried outinthe gardenexperiment ina plastichouse, Faculty ofAgriculture, University ofTrunojoyoMadura, at an altitude of±5 mabove sea level, temperature29ºC, and± 75% RH. The research was conductedin December2011 toFebruary2012.The analysis was usednonfaktorialRAL. Treatmentwithcomposemediatypes(raw rice husk, rice huskcharcoal, sand andnutrients(no nutrients, premiumnutrition, nutritiongoodplant. There are ninetreatment, threereplicationsandthreesamples ofthe plant, furthertestswere analyzed byDMRT5%. Results showedthe treatmentcompositionandnutrientmediaprovidesignificantly differentresultsatdifferent ages ofobservationson eachvariableobservation. The besttreatmentcompositioncontained in thehusk charcoalandnutrientmediagoodplant(M2N2. Evidenced by theaverage ofthe highestresultson the length ofthe plant(29.38cm, number of leaves(22.22 strands, leaf area(3226.79 cm2, wetweight(242.19 g and dry weight(13, 27g totalplantpakchoiat age4 MST.

The complete mitochondrial genome of Ambastaia sidthimunki (Cypriniformes: Cobitidae).

Science.gov (United States)

Yu, Peng; Wei, Min; Yang, Qichao; Yang, Yingming; Wan, Quan

2016-09-01

Ambastaia sidthimunki is a beautiful small-sized fish and it was categorized as Endangered B2ab (iii,v) in the IUCN Red List. In this study, we reported the complete mitochondrial genome of the A. sidthimunki. The mitochondrial genome sequence was a circular molecule with 16,574 bp in length, and it contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 26.94% for C, 15.55% for G, 31.84% for A and 25.67% for T, with an AT content of 57.51%. This research contributes new molecular data for the conservation of this Endangered species.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

Science.gov (United States)

Cabal, Adriana; Jun, Se-Ran; Jenjaroenpun, Piroon; Wanchai, Visanu; Nookaew, Intawat; Wongsurawat, Thidathip; Burgess, Mary J; Kothari, Atul; Wassenaar, Trudy M; Ussery, David W

2018-02-14

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same

The intensity of tyrosine nitration is associated with selenite and selenate toxicity in Brassica juncea L.

Science.gov (United States)

Molnár, Árpád; Feigl, Gábor; Trifán, Vanda; Ördög, Attila; Szőllősi, Réka; Erdei, László; Kolbert, Zsuzsanna

2018-01-01

Selenium phytotoxicity involves processes like reactive nitrogen species overproduction and nitrosative protein modifications. This study evaluates the toxicity of two selenium forms (selenite and selenate at 0µM, 20µM, 50µM and 100µM concentrations) and its correlation with protein tyrosine nitration in the organs of hydroponically grown Indian mustard (Brassica juncea L.). Selenate treatment resulted in large selenium accumulation in both Brassica organs, while selenite showed slight root-to-shoot translocation resulting in a much lower selenium accumulation in the shoot. Shoot and root growth inhibition and cell viability loss revealed that Brassica tolerates selenate better than selenite. Results also show that relative high amounts of selenium are able to accumulate in Brassica leaves without obvious visible symptoms such as chlorosis or necrosis. The more severe phytotoxicity of selenite was accompanied by more intense protein tyrosine nitration as well as alterations in nitration pattern suggesting a correlation between the degree of Se forms-induced toxicities and nitroproteome size, composition in Brassica organs. These results imply the possibility of considering protein tyrosine nitration as novel biomarker of selenium phytotoxicity, which could help the evaluation of asymptomatic selenium stress of plants. Copyright © 2017 Elsevier Inc. All rights reserved.

Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki.

Directory of Open Access Journals (Sweden)

Dann Turner

Full Text Available Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA under the accession number LN890663.

First insight into the genome of an uncultivated crenarchaeote from soil

DEFF Research Database (Denmark)

Quaiser, Achim; Ochsenreiter, Torsten; Klenk, Hans-Peter

2002-01-01

RNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ......Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study...... we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we...

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae.

Science.gov (United States)

Nam, Bo-Hye; Kwak, Woori; Kim, Young-Ok; Kim, Dong-Gyun; Kong, Hee Jeong; Kim, Woo-Jin; Kang, Jeong-Ha; Park, Jung Youn; An, Cheul Min; Moon, Ji-Young; Park, Choul Ji; Yu, Jae Woong; Yoon, Joon; Seo, Minseok; Kim, Kwondo; Kim, Duk Kyung; Lee, SaetByeol; Sung, Samsun; Lee, Chul; Shin, Younhee; Jung, Myunghee; Kang, Byeong-Chul; Shin, Ga-Hee; Ka, Sojeong; Caetano-Anolles, Kelsey; Cho, Seoae; Kim, Heebal

2017-05-01

Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [ 1 ]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H . discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H . discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H . discus hannai , with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution. © The Authors 2017. Published by Oxford University Press.

[Phylogenetic analysis of genomes of Vibrio cholerae strains isolated on the territory of Rostov region].

Science.gov (United States)

Kuleshov, K V; Markelov, M L; Dedkov, V G; Vodop'ianov, A S; Kermanov, A V; Pisanov, R V; Kruglikov, V D; Mazrukho, A B; Maleev, V V; Shipulin, G A

2013-01-01

Determination of origin of 2 Vibrio cholerae strains isolated on the territory of Rostov region by using full genome sequencing data. Toxigenic strain 2011 EL- 301 V. cholerae 01 El Tor Inaba No. 301 (ctxAB+, tcpA+) and nontoxigenic strain V. cholerae O1 Ogawa P- 18785 (ctxAB-, tcpA+) were studied. Sequencing was carried out on the MiSeq platform. Phylogenetic analysis of the genomes obtained was carried out based on comparison of conservative part of the studied and 54 previously sequenced genomes. 2011EL-301 strain genome was presented by 164 contigs with an average coverage of 100, N50 parameter was 132 kb, for strain P- 18785 - 159 contigs with a coverage of69, N50 - 83 kb. The contigs obtained for strain 2011 EL-301 were deposited in DDBJ/EMBL/GenBank databases with access code AJFN02000000, for strain P-18785 - ANHS00000000. 716 protein-coding orthologous genes were detected. Based on phylogenetic analysis strain P- 18785 belongs to PG-1 subgroup (a group of predecessor strains of the 7th pandemic). Strain 2011EL-301 belongs to groups of strains of the 7th pandemic and is included into the cluster with later isolates that are associated with cases of cholera in South Africa and cases of import of cholera to the USA from Pakistan. The data obtained allows to establish phylogenetic connections with V cholerae strains isolated earlier.

Genetics Home Reference: GM2-gangliosidosis, AB variant

Science.gov (United States)

... Resources Genetic Testing (1 link) Genetic Testing Registry: Tay-Sachs disease, variant AB General Information from MedlinePlus (5 links) ... AB variant Activator Deficiency/GM2 Gangliosidosis Activator-deficient Tay-Sachs disease GM2 Activator Deficiency Disease GM2 gangliosidosis, type AB ...

Nitrogen availability regulates proline and ethylene production and alleviates salinity stress in mustard (Brassica juncea).

Science.gov (United States)

Iqbal, Noushina; Umar, Shahid; Khan, Nafees A

2015-04-15

Proline content and ethylene production have been shown to be involved in salt tolerance mechanisms in plants. To assess the role of nitrogen (N) in the protection of photosynthesis under salt stress, the effect of N (0, 5, 10, 20 mM) on proline and ethylene was studied in mustard (Brassica juncea). Sufficient N (10 mM) optimized proline production under non-saline conditions through an increase in proline-metabolizing enzymes, leading to osmotic balance and protection of photosynthesis through optimal ethylene production. Excess N (20 mM), in the absence of salt stress, inhibited photosynthesis and caused higher ethylene evolution but lower proline production compared to sufficient N. In contrast, under salt stress with an increased demand for N, excess N optimized ethylene production, which regulates the proline content resulting in recovered photosynthesis. The effect of excess N on photosynthesis under salt stress was further substantiated by the application of the ethylene biosynthesis inhibitor, 1-aminoethoxy vinylglycine (AVG), which inhibited proline production and photosynthesis. Without salt stress, AVG promoted photosynthesis in plants receiving excess N by inhibiting stress ethylene production. The results suggest that a regulatory interaction exists between ethylene, proline and N for salt tolerance. Nitrogen differentially regulates proline production and ethylene formation to alleviate the adverse effect of salinity on photosynthesis in mustard. Copyright © 2015 Elsevier GmbH. All rights reserved.

Phytoextraction based on Indian mustard (Brassica juncea arawali planted on spiked soil by aliquot amount of Lead and Nickel

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Leela Kaur

2015-12-01

Full Text Available Phytoextraction is one of the mechanisms of phytoremediation for removal of heavy metals from contaminated soils. The objective of the present study was to investigate the effect of metal chelants, ethelyne diamine tetraacetic acid (EDTA and salicylic acid (SA, on the accumulation of lead and nickel by Indian mustard (Brassica juncea arawali plants in contaminated soil. Plants were treated with Pb and Ni, each at concentrations of 800 mg/l. EDTA and SA were amended at 0.1 M and 1.0 mM respectively. Plants were harvested and oven-dried. Pb and Ni content were estimated using ICP-OES (Varian Vista-MPX CCD Simultaneous ICP-OES. The samples thus prepared were investigated for metals distribution and morphology in different tissues (root, stem and leaf using energy dispersive X-ray analysis (EDAX spectrometer attached to the scanning electron microscope (SEM. Metal distribution study in different tissues (root, stem, leaf was done by SEM/EDS. The results showed that EDTA increased Pb and Ni uptake as compared to SA.

PHYSIOLOGICAL REACTION OF THE SPECIES BRASSICA JUNCEA (L. CZERN. ON SALINIZED SOILS AMELIORATED WITH ZEOLITIC TUFF, PEAT AND PERLITE

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Maria Cătălina PASTIA

2017-12-01

Full Text Available The physiological reaction of saline stress which Brassica juncea (L. Czern. plants undergo shows a greater growth and fresh substance gain process on previously cultivated soils that were fined with 20% zeolitic tuff and 5.09 g of neutral peat than the ones that had a substrate which hasn’t been cultivated on before that was fined with 5% zeolitic tuff and 1.39 g of perlite. The dry substance values obtained present a positive correlation with the values of fresh substance. Analysis of stomatal conductance enhances the hydric stress of plants which respond to saline stress with osmotic adjustment, accumulating high quantities of water comparing to the witness plant, which induces lower values of stomatal conductance and implicitly values are decreasing for photosynthesis, determining a low productivity. Higher values of stomatal conductance are reached at plants grown on previously cultivated soils fined with 20% zeolitic tuff and peat, and also at the ones grown on uncultivated soils fined with peat (29.45, respectively 30.05 mmol/m2/s.

Expression of Cry1Ab and Cry2Ab by a polycistronic transgene with a self-cleavage peptide in rice.

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Qichao Zhao

Full Text Available Insect resistance to Bacillus thuringiensis (Bt crystal protein is a major threat to the long-term use of transgenic Bt crops. Gene stacking is a readily deployable strategy to delay the development of insect resistance while it may also broaden insecticidal spectrum. Here, we report the creation of transgenic rice expressing discrete Cry1Ab and Cry2Ab simultaneously from a single expression cassette using 2A self-cleaving peptides, which are autonomous elements from virus guiding the polycistronic viral gene expression in eukaryotes. The synthetic coding sequences of Cry1Ab and Cry2Ab, linked by the coding sequence of a 2A peptide from either foot and mouth disease virus or porcine teschovirus-1, regardless of order, were all expressed as discrete Cry1Ab and Cry2Ab at high levels in the transgenic rice. Insect bioassays demonstrated that the transgenic plants were highly resistant to lepidopteran pests. This study suggested that 2A peptide can be utilized to express multiple Bt genes at high levels in transgenic crops.

Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: II - disponibilidade de N, P e K no solo ao longo do ciclo de cultivo

OpenAIRE

Silva, Tácio Oliveira da; Menezes, Rômulo Simões Cezar

2007-01-01

Os solos do Agreste paraibano têm baixa fertilidade e a prática usual de adubação é a incorporação de esterco na época do plantio. Entretanto, dependendo da qualidade do esterco, essa prática pode causar a imobilização de nutrientes do solo durante os primeiros meses de cultivo. É possível que o cultivo e incorporação de Crotalaria juncea, combinado com o esterco, possa promover mineralização mais sincronizada com a demanda de nutrientes pelas plantas. No presente estudo, realizado em 2003, f...

The food-borne pathogen Campylobacter jejuni depends on the AddAB DNA repair system to defend against bile in the intestinal environment.

Science.gov (United States)

Gourley, Christopher R; Negretti, Nicholas M; Konkel, Michael E

2017-10-31

Accurate repair of DNA damage is crucial to ensure genome stability and cell survival of all organisms. Bile functions as a defensive barrier against intestinal colonization by pathogenic microbes. Campylobacter jejuni, a leading bacterial cause of foodborne illness, possess strategies to mitigate the toxic components of bile. We recently found that growth of C. jejuni in medium with deoxycholate, a component of bile, caused DNA damage consistent with the exposure to reactive oxygen species. We hypothesized that C. jejuni must repair DNA damage caused by reactive oxygen species to restore chromosomal integrity. Our efforts focused on determining the importance of the putative AddAB DNA repair proteins. A C. jejuni addAB mutant demonstrated enhanced sensitivity to deoxycholate and was impaired in DNA double strand break repair. Complementation of the addAB mutant restored resistance to deoxycholate, as well as function of the DNA double strand break repair system. The importance of these findings translated to the natural host, where the AddAB system was found to be required for efficient C. jejuni colonization of the chicken intestine. This research provides new insight into the molecular mechanism utilized by C. jejuni, and possibly other intestinal pathogens, to survive in the presence of bile.

Collective rotation from ab initio theory

International Nuclear Information System (INIS)

Caprio, M.A.; Maris, P.; Vary, J.P.; Smith, R.

2015-01-01

Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7–9 Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction. (author)

Effect of monoclonal antibodies (MoAb) to class I and class II HLA antigens on lectin- and MoAb OKT3-induced lymphocyte proliferation.

Science.gov (United States)

Akiyama, Y; Zicht, R; Ferrone, S; Bonnard, G D; Herberman, R B

1985-04-01

We have examined the effect of several monoclonal antibodies (MoAb) to monomorphic determinants of class II HLA antigens, and MoAb to monomorphic determinants of class I HLA antigens and to beta-2-microglobulin (beta 2-mu) on lectin- and MoAb OKT3-induced proliferation of human peripheral blood mononuclear cells (PBMNC) and cultured T cells (CTC). Some, but not all, anti-class II HLA MoAb inhibited the proliferative response of PBMNC to MoAb OKT3 and pokeweed mitogen (PWM). The degree of inhibitory effect varied considerably. This effect was not limited to anti-class II HLA MoAb since anti-class I HLA MoAb and anti-beta 2-mu MoAb also inhibited MoAb OKT3- or PWM-induced proliferative responses. In contrast, the response of PBMNC to phytohemagglutinin (PHA) and concanavalin A (Con A) was not blocked by any anti-class II HLA MoAb. However, some anti-class II HLA MoAb also inhibited the proliferative response of CTC plus allogeneic peripheral blood adherent accessory cells (AC) to PHA or Con A as well as to MoAb OKT3 or PWM. This may be attributable to the substantially greater class II HLA antigen expression by CTC than by fresh lymphocytes. Pretreatment of either CTC or AC with anti-class II HLA MoAb inhibited OKT3-induced proliferation. In contrast, pretreatment of CTC, but not AC, with anti-class I HLA MoAb inhibited the proliferative response of CTC to OKT3. Pretreatment of CTC with anti-class I HLA MoAb inhibited PHA-, Con A and PWM-induced proliferation, to a greater degree than the anti-class II HLA MoAb. It appears as if lymphocyte activation by different mitogens exhibits variable requirements for the presence of cells expressing major histocompatibility determinants. Binding of Ab to membrane markers may interfere with lymphocyte-AC cooperation, perhaps by inhibiting binding of mitogens to their receptors or by interfering with lymphocyte and AC function. We also have examined the role of class II HLA antigens on CTC by depleting class II HLA-positive cells

Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs.

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Marnie L Fusco

2015-06-01

Full Text Available The filoviruses, which include the marburg- and ebolaviruses, have caused multiple outbreaks among humans this decade. Antibodies against the filovirus surface glycoprotein (GP have been shown to provide life-saving therapy in nonhuman primates, but such antibodies are generally virus-specific. Many monoclonal antibodies (mAbs have been described against Ebola virus. In contrast, relatively few have been described against Marburg virus. Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston, but these epitopes are masked differently by the mucin-like domains themselves. The most efficacious mAbs in this panel were found to recognize a novel "wing" feature on the GP2 subunit that is unique to Marburg and does not exist in Ebola. Two of these anti-wing antibodies confer 90 and 100% protection, respectively, one hour post-exposure in mice challenged with MARV.

Ab initio study of isomerism in molecular ions Li2AB+ with 10 valence electrons

International Nuclear Information System (INIS)

Charkin, O.P.; Mak-Ki, M.L.; Shlojer, P.R.

1997-01-01

Ab initio calculations of surfaces of Li 2 AB + molecular ion potential energy with biatomic anions AB - with 10 valence electrons have been made in the framework of approximations MP2/6-31G 1 /HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/631G*//MP2/6-31G*+ZPE(MP2/6-31G*). Influence of electron correlation on the accuracy of calculations of their structural and vibrational characteristics is studied. The following most favourable structures have been found: linear for Li 2 BO + , Li 2 CN + , and bent one for Li 2 BS + , with cations coordinated at different anion atoms; onium one for AlOLi 2 + , AlSLi 2 + , SiNLi 2 + and SiPLi 2 + with both cations at electronegative atom of anion

Genome-wide identification of significant aberrations in cancer genome.

Science.gov (United States)

Yuan, Xiguo; Yu, Guoqiang; Hou, Xuchu; Shih, Ie-Ming; Clarke, Robert; Zhang, Junying; Hoffman, Eric P; Wang, Roger R; Zhang, Zhen; Wang, Yue

2012-07-27

Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1) exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2) performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3) iteratively detecting Significant Copy Number Aberrations (SCAs) and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS) on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma). When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC) or tumor suppressor genes (e.g., CDKN2A/B). Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes. Open-source and platform-independent SAIC software is

AP calculus AB & BC crash course

CERN Document Server

Rosebush, J

2012-01-01

AP Calculus AB & BC Crash Course - Gets You a Higher Advanced Placement Score in Less Time Crash Course is perfect for the time-crunched student, the last-minute studier, or anyone who wants a refresher on the subject. AP Calculus AB & BC Crash Course gives you: Targeted, Focused Review - Study Only What You Need to Know Crash Course is based on an in-depth analysis of the AP Calculus AB & BC course description outline and actual AP test questions. It covers only the information tested on the exams, so you can make the most of your valuable study time. Written by experienced math teachers, our

Modeling of truck's braking dynamics with ABS

Directory of Open Access Journals (Sweden)

Maxym DYACHUK

2014-09-01

Full Text Available In the article some questions of ABS simulation on the basis of plane vehicle's dynamics and automatic modeling are considered. The author's algorithm of ABS modulators control is presented.

Effects of Nitrogen and Desferal Treatments on CROTALARIA's (Crotalaria juncea Roth) Biomass Production

Science.gov (United States)

László Phd, M., ,, Dr.

2009-04-01

Presently sustainable agriculture is vital to achieving food security poverty alleviation and environmental protection because land degradation and desertification has occurred in all the world over cutting across a broad spectrum of contrasts in climate, ecosystem types, land uses and socio/economic settings. For this reason improving integrated soil fertility management is appreciationed and has become a major issue of concern on the development plant nutrition and plant production agendas. On plant nutrition level mineral macronutrients so nitrogen and chelating agents of different microelements so Desferal- deferoxamin-methansulfonic are essential for plant growth and development. Crotalari juncea L. is a well-known nutrient indicator fodder and green manure crop with a high yield potential. Field experiment was carried out on a chernozem meadow soil (Kunság- region of Hungary, Kunmadaras) in partly of experiment series (6 years) in 2001. The ploughed layer of region soils contained with about 2.6-3.4% humus and 40-42% clay, had a humus stability index of 0.9-2.5 by Márton (1997), pH (H2O) of 6.5-7.7, pH (KCl) of 5.3-6.8, y1 of 6.7-13.3. The topsoil was poorly supplied with all five macronutrients (N-NO3 1 mg 100 g-1, AL-soluble P2O5 14 mg 100 g-1, AL-K2O 36 mg 100 g-1, Ca 330 mg 100 g-1, Mg 43 mg 100 g-1) and with all four micronutrients (0.5m HNO3 soluble Cu 1 mg kg-1, Zn 1 mg kg-1, Mn 9 mg kg-1, Fe 80 mg kg-1) according to soil analysis. The groundwater depth was 2-3 m. Nitrogen x Desferal (Novartis Pharma AG Basie, Switzerland, Suiza 500mg) x Genotype (Brazíl-EMBRAPA/CNPH, Brazilia-DF, India-University of Agricultural Sciences, Bangalore) x Time experiment involved 4Nx2Dx2Gx3T=48 treatments in 3 replications giving a total of 144 plots. The N levels were 0, 100, 200 and 300 kg ha-1 year-1, and desferal levels 0 and 20 kg ha-1 year-1 with a 100 kg ha-1 year-1 P2O5 and 120 kg ha-1 year-1 K2O basic fertilisation. The plot size had an area of 4x2=8 m2 with

Effects of phosphate and thiosulphate on arsenic accumulation in the species Brassica juncea.

Science.gov (United States)

Grifoni, Martina; Schiavon, Michela; Pezzarossa, Beatrice; Petruzzelli, Gianniantonio; Malagoli, Mario

2015-02-01

Arsenic (As) is recognized as a toxic pollutant in soils of many countries. Since phosphorus (P) and sulphur (S) can influence arsenic mobility and bioavailability, as well as the plant tolerance to As, phytoremediation techniques employed to clean-up As-contaminated areas should consider the interaction between As and these two nutrients. In this study, the bioavailability and accumulation of arsenate in the species Brassica juncea were compared between soil system and hydroponics in relation to P and S concentration of the growth substrate. In one case, plants were grown in pots filled with soil containing 878 mg As kg(-1). The addition of P to soil resulted in increased As desorption and significantly higher As accumulation in plants, with no effect on growth. The absence of toxic effects on plants was likely due to high S in soil, which could efficiently mitigate metal toxicity. In the hydroponic experiment, plants were grown with different combinations of As (0 or 100 μM) and P (56 or 112 μM). S at 400 μM was also added to the nutrient solution of control (-As) and As-treated plants, either individually or in combination with P. The addition of P reduced As uptake by plants, while high S resulted in higher As accumulation and lower P content. These results suggest that S can influence the interaction between P and As for the uptake by plants. The combined increase of P and S in the nutrient solution did not lead to higher accumulation of As, but enhanced As translocation from the root to the shoot. This aspect is of relevance for the phytoremediation of As-contaminated sites.

Bacteriophage Prevalence in the Genus Azospirillum and Analysis of the First Genome Sequence of an Azospirillum brasilense Integrative Phage▿

Science.gov (United States)

Boyer, Mickaël; Haurat, Jacqueline; Samain, Sylvie; Segurens, Béatrice; Gavory, Frédérick; González, Víctor; Mavingui, Patrick; Rohr, René; Bally, René; Wisniewski-Dyé, Florence

2008-01-01

The prevalence of bacteriophages was investigated in 24 strains of four species of plant growth-promoting rhizobacteria belonging to the genus Azospirillum. Upon induction by mitomycin C, the release of phage particles was observed in 11 strains from three species. Transmission electron microscopy revealed two distinct sizes of particles, depending on the identity of the Azospirillum species, typical of the Siphoviridae family. Pulsed-field gel electrophoresis and hybridization experiments carried out on phage-encapsidated DNAs revealed that all phages isolated from A. lipoferum and A. doebereinerae strains had a size of about 10 kb whereas all phages isolated from A. brasilense strains displayed genome sizes ranging from 62 to 65 kb. Strong DNA hybridizing signals were shown for most phages hosted by the same species whereas no homology was found between phages harbored by different species. Moreover, the complete sequence of the A. brasilense Cd bacteriophage (ΦAb-Cd) genome was determined as a double-stranded DNA circular molecule of 62,337 pb that encodes 95 predicted proteins. Only 14 of the predicted proteins could be assigned functions, some of which were involved in DNA processing, phage morphogenesis, and bacterial lysis. In addition, the ΦAb-Cd complete genome was mapped as a prophage on a 570-kb replicon of strain A. brasilense Cd, and a region of 27.3 kb of ΦAb-Cd was found to be duplicated on the 130-kb pRhico plasmid previously sequenced from A. brasilense Sp7, the parental strain of A. brasilense Cd. PMID:18065619

Bacteriophage prevalence in the genus Azospirillum and analysis of the first genome sequence of an Azospirillum brasilense integrative phage.

Science.gov (United States)

Boyer, Mickaël; Haurat, Jacqueline; Samain, Sylvie; Segurens, Béatrice; Gavory, Frédérick; González, Víctor; Mavingui, Patrick; Rohr, René; Bally, René; Wisniewski-Dyé, Florence

2008-02-01

The prevalence of bacteriophages was investigated in 24 strains of four species of plant growth-promoting rhizobacteria belonging to the genus Azospirillum. Upon induction by mitomycin C, the release of phage particles was observed in 11 strains from three species. Transmission electron microscopy revealed two distinct sizes of particles, depending on the identity of the Azospirillum species, typical of the Siphoviridae family. Pulsed-field gel electrophoresis and hybridization experiments carried out on phage-encapsidated DNAs revealed that all phages isolated from A. lipoferum and A. doebereinerae strains had a size of about 10 kb whereas all phages isolated from A. brasilense strains displayed genome sizes ranging from 62 to 65 kb. Strong DNA hybridizing signals were shown for most phages hosted by the same species whereas no homology was found between phages harbored by different species. Moreover, the complete sequence of the A. brasilense Cd bacteriophage (phiAb-Cd) genome was determined as a double-stranded DNA circular molecule of 62,337 pb that encodes 95 predicted proteins. Only 14 of the predicted proteins could be assigned functions, some of which were involved in DNA processing, phage morphogenesis, and bacterial lysis. In addition, the phiAb-Cd complete genome was mapped as a prophage on a 570-kb replicon of strain A. brasilense Cd, and a region of 27.3 kb of phiAb-Cd was found to be duplicated on the 130-kb pRhico plasmid previously sequenced from A. brasilense Sp7, the parental strain of A. brasilense Cd.

Ab initio study of isomerism of Li2AB2 molecules and Li2AB2+ ions with 16 valent electrons

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

2000-01-01

In the framework of MP2(6-31*//HF/6-31G + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations ab initio calculations of surfaces of potential energy of molecules of lithium salts of Li 2 AB 2 (Li 2 BeO 2 , L 2 MgO 2 , Li 2 BeS 2 , Li 2 MgS 2 , Li 2 CN 2 , Li 2 SiN 2 , Li 2 CP 2 ) type and ions of Li 2 AB 2 + (Li 2 BO 2 + , Li 2 AlO 2 + , Li 2 BS 2 + , Li 2 AlS 2 + , Li 2 N 3 + , Li 2 PN 2 + , Li 2 P 3 + ) type with 16 valent electrons are done. For oxide and nitride systems global minimum corresponds to symmetric linear structure D ∞h and for their sulfide and phosphorus analogues curved plane or unplane (C 2 ) structure with bond angle φ(LBA)=90-110 Deg are preferable. Equilibrium geometric parameters, relative energies and energies of isomer decomposition, frequencies and IR-intensities of normal vibrations are determined [ru

The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data.

Science.gov (United States)

Greiner, Stephan; Wang, Xi; Herrmann, Reinhold G; Rauwolf, Uwe; Mayer, Klaus; Haberer, Georg; Meurer, Jörg

2008-09-01

A unique combination of genetic features and a rich stock of information make the flowering plant genus Oenothera an appealing model to explore the molecular basis of speciation processes including nucleus-organelle coevolution. From representative species, we have recently reported complete nucleotide sequences of the 5 basic and genetically distinguishable plastid chromosomes of subsection Oenothera (I-V). In nature, Oenothera plastid genomes are associated with 6 distinct, either homozygous or heterozygous, diploid nuclear genotypes of the 3 basic genomes A, B, or C. Artificially produced plastome-genome combinations that do not occur naturally often display interspecific plastome-genome incompatibility (PGI). In this study, we compare formal genetic data available from all 30 plastome-genome combinations with sequence differences between the plastomes to uncover potential determinants for interspecific PGI. Consistent with an active role in speciation, a remarkable number of genes have high Ka/Ks ratios. Different from the Solanacean cybrid model Atropa/tobacco, RNA editing seems not to be relevant for PGIs in Oenothera. However, predominantly sequence polymorphisms in intergenic segments are proposed as possible sources for PGI. A single locus, the bidirectional promoter region between psbB and clpP, is suggested to contribute to compartmental PGI in the interspecific AB hybrid containing plastome I (AB-I), consistent with its perturbed photosystem II activity.

Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

Science.gov (United States)

Knotts, Greg

2009-01-01

This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

Cloning and characterization of a mitochondrial glyoxalase II from Brassica juncea that is upregulated by NaCl, Zn, and ABA

International Nuclear Information System (INIS)

Saxena, Mukesh; Bisht, Rekha; Roy, Suchandra Deb; Sopory, S.K.; Bhalla-Sarin, Neera

2005-01-01

A cDNA (1061 bp) Bj glyII was cloned from a mannitol induced library of Brassica juncea. It encoded a protein of 335 amino acids with a molecular weight of 36.52 kDa. The deduced amino acid sequence of the clone showed 92% and 56% identity with Pennisetum and rice glyoxalase II, respectively, and 30% identity was observed with the human glyoxalase II. Search for the identical residues revealed the presence of highly conserved THHHXDH domain which is involved in zinc binding. p-NN and pSORT analysis of this sequence revealed a N-terminal mitochondrial target peptide. The cDNA was cloned in pMAL and a fusion protein with MBP (78 kDa) was expressed in Escherichia coli. The recombinant protein was purified approximately sixfold by affinity purification on amylose column and showed its pH optima at 7.0. The K m was determined to be 120 μM using S-D-lactoylglutathione as substrate. The expression of Bj glyII under various abiotic stress conditions showed that it is upregulated by salinity, heavy metal stress, and ABA

Genome Sequence of Enterococcus faecium Strain ICIS 96 Demonstrating Intermicrobial Antagonism Associated with Bacteriocin Production.

Science.gov (United States)

Pashkova, Tatiana M; Vasilchenko, Alexey S; Khlopko, Yuriy A; Kochkina, Elena E; Kartashova, Olga L; Sycheva, Maria V

2018-03-08

We report here the complete genome sequence of Enterococcus faecium strain ICIS 96, which was isolated from the feces of a horse. Bacteriological characterization of strain ICIS 96 revealed the absence of pathogenicity factors, while its spectrum of antagonistic activity was found to be broad, having activities associated with both Gram-positive and Gram-negative bacteria. Analysis of the E. faecium ICIS 96 genome revealed five genes associated with antimicrobial activity (enterocin [ent] A, ent B, lactobin A/cerein 7b, and ent L50 A/B). No genes that correlate with human pathogenicity were identified. Copyright © 2018 Pashkova et al.

TITRATION METHOD OF AB0 ANTIBODIES WITH THE USE OF MODERN GEL TECHNOLOGY IN AB0-INCOMPATIBLE TRANSPLANTATION

Directory of Open Access Journals (Sweden)

A. K. Porunova

2014-01-01

Full Text Available It is shown that developed method of titrating AB0 antibodies allows defi ning the titer of the investigational antibodies more precisely on 1–3 dilution of serum compared to the prototype method (titration method of antibodiesin saline medium on the plane. It is more obvious as it excludes hardly interpretable results due to the possibility of conducting visual assessment of agglutination reaction in the gel card thick column and requires less time foranalysis. The results can be saved for comparison with the results of further research. That is not possible under prototype titration method. Aim: our aim is to create a laboratory technique that can accurately, reliably and clearly produce titration of AB0 system antibodies, including in patients with low initial concentration of agglutinins in the blood; a technique more economical in terms of spending serum and that takes less time.Materials and methods: those modes were empirically chosen which allow titration of AB0 system agglutinins using gel technology based micro typing; to titer group antibodies 1640 serum assays of recipients in AB0-incompatibletransplantation were analyzed.The result of the use of specially developed method in organ transplantation from incompatible blood donors consists in enhancing accuracy, sensitivity of natural, complete and incomplete AB0 system immune antibodies titration, in its clarity, using of blood micro-doses for earlier detection of sensitizing of the patient, which is especially important in Pediatrics. Conclusion: the developed procedure of AB0-antibodies’ titration using modern gel technology makes possible a more precise monitoring of the titer of antibodies that is necessary to predict the graft rejection risk, to select the Protocol of preoperative preparation and postoperative management of patients, to assess the effectiveness of therapy in patients for whom it is diffi cult to fi nd a compatible blood type donor, and for whom today AB

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Energy Technology Data Exchange (ETDEWEB)

Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

2010-05-26

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

Influence of indian mustard (Brassica juncea) on rhizosphere soil solution chemistry in long-term contaminated soils: a rhizobox study.

Science.gov (United States)

Kim, Kwon-Rae; Owens, Gary; Kwon, Soon-lk

2010-01-01

This study investigated the influence of Indian mustard (Brassica juncea) root exudation on soil solution properties (pH, dissolved organic carbon (DOC), metal solubility) in the rhizosphere using a rhizobox. Measurement was conducted following the cultivation of Indian mustard in the rhizobox filled four different types of heavy metal contaminated soils (two alkaline soils and two acidic soils). The growth of Indian mustard resulted in a significant increase (by 0.6 pH units) in rhizosphere soil solution pH of acidic soils and only a slight increase (soil solution varied considerably amongst different soils, resulting in significant changes to soil solution metals in the rhizosphere. For example, the soil solution Cd, Cu, Pb, and Zn concentrations increased in the rhizosphere of alkaline soils compared to bulk soil following plant cultivation. In contrast, the soluble concentrations of Cd, Pb, and Zn in acidic soils decreased in rhizosphere soil when compared to bulk soils. Besides the influence of pH and DOC on metal solubility, the increase of heavy metal concentration having high stability constant such as Cu and Pb resulted in a release of Cd and Zn from solid phase to liquid phase.

Improved radioimaging and tumor localization with monoclonal F(ab')2

International Nuclear Information System (INIS)

Wahl, R.L.; Parker, C.W.; Philpott, G.W.

1983-01-01

Monoclonal anti-tumor antibodies have great promise for radioimmunodetection and localization of tumors. Fab and F(ab')2 fragments, which lack the Fc fragment of antibody (Ab), are cleared more rapidly from the circulation and may have less nonspecific tissue binding than intact Ab. In radioimaging studies using a murine monoclonal antibody to carcinoembryonic antigen in a human colon carcinoma xenografted into hamsters, F(ab')2 fragments were shown superior to Fab fragments and intact antibody for scintiscanning. In double-label experiments with anti-CEA antibody and control monoclonal IgG, F(ab')2 fragments were found to give better and more rapid specific tumor localization than intact antibody or Fab fragments. F(ab')2 fragments offer significant promise for tumor imaging and possibly therapy

Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.

Science.gov (United States)

Mao, Yuejian; Chen, Meng; Horvath, Philippe

2015-07-30

Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol% and 2,797 predicted coding sequences (CDSs). Copyright © 2015 Mao et al.

Crotalaria (Crotalaria juncea L.) Heavy Metal Uptake in Eastern Hungary

Science.gov (United States)

László Phd, M., ,, Dr.

2009-04-01

Summary: Soil condition, plant production and ecological protection are most important parts of the sustainable agricultural activity on all over the world nowadays. Soils, their fertility, their content of different macro-, mezo-, micro-, trace elements have almost always dictated the spread of agricultural farmlands, including the plant production-, yield harvest levels and yield element contents possible. The success of agriculturists in the 20th and 21th century, particularly in the Europe has relied on inproved soil fertility managements, appropriate crop production and environmental protection. We can test and improve the situations by using different plant species (Crotalaria juncea L.) x macro nutrients (nitrogen) x chelating agents (Desferal as deferoxamine-mesilate: C25H48N6O8-CH4O3S) methods. Crotalaria has a very potential and important role in soil fertility as a green manure crop in the design of plant rotation to field plant production, in the animal foraging as a fodder-crop with a high protein content (30%) and in the pytoremediation possibilities. Field experiment was carried out on a calcareous chernozem meadow soil (Kunság-region of Hungary, Kunmadaras) in partly of crotalaria experiment series (5 years) in 2001. The agrochemical parameters of the ploughed layer of the region soils were as follows: humus 2.5-3.0%, pH (H2O) 7.7, pH (KCl) 7.0, LE (Lakanen & Erviö 1971 [3])-P2O5 183-218 mg kg-1, LE-K2O 82-115 mg kg-1, LE-Ca 1.3%, LE-Mg 56-60 mg kg-1, LE-Mn 45 mg kg-1 according to soil analysis. Nitrogen (N) x Desferal ("D"-Novartis Pharma AG Basie [7], Switzerland, Suiza 500 mg) x Genotype ("G"-India-University of Agricultural Sciences, Bangalore) x Time (T) experiment involved The N levels were 0, 100, 200 and 300 kg ha-1 year-1, and Desferal 0 and 20 kg ha-1 year-1. The plot size had an area of 4x2=8 m2. Experimental datas were estimated by MANOVA of SPSS. The main results can be summarised as follows: a., At harvest, total air dry phytomass

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.

Science.gov (United States)

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-08-04

Experimental structure determination remains difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average Cα root-mean-square deviation 2.4 Å in the TM regions. The new hybrid protocol was applied to model all 1,026 GPCRs in the human genome, where 923 have a high confidence score and are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin, and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of TM proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development and Application of Loop-Mediated Isothermal Amplification Assays for Rapid Visual Detection of cry2Ab and cry3A Genes in Genetically-Modified Crops

Directory of Open Access Journals (Sweden)

Feiwu Li

2014-08-01

Full Text Available The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops.

Science.gov (United States)

Li, Feiwu; Yan, Wei; Long, Likun; Qi, Xing; Li, Congcong; Zhang, Shihong

2014-08-27

The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

Science.gov (United States)

Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

2014-01-01

Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

Heavy Metal Contents and Physical Parameters of Aegiceras corniculatum, Brassica juncea, and Litchi chinensis Honeys from Bangladesh

Directory of Open Access Journals (Sweden)

Nandita Sarker

2015-01-01

Full Text Available The present study was undertaken to determine the heavy metal levels and the physicochemical parameters (pH, electrical conductivity (EC, and ash, moisture, and total sugar content of honeys from Bangladesh. Three different floral honeys were investigated, namely, khalsi (Aegiceras corniculatum, mustard (Brassica juncea, and litchi (Litchi chinensis honeys. The heavy metals in the honeys were determined by using a High Temperature Dry Oxidation method followed by Atomic Absorption Spectroscopy. The mean pH, EC, and ash, moisture, and total sugar contents of the investigated honeys were 3.6, 0.51 mS/cm, 0.18%, 18.83%, and 68.30%, respectively. Iron was the most abundant among all the investigated heavy metals, ranging from 13.51 to 15.44 mg/kg. The mean concentrations of Mn and Zn in the investigated honeys were 0.28 mg/kg and 2.99 mg/kg, respectively. Cd was below the detection limit, and lead was found in some honey samples, but their contents were below the recommended Maximum Acceptable Level. Cr was also found in all of the samples, but its concentration was within the limit. The physicochemical analysis of the honey samples yielded levels within the limits set by the international honey legislation, indicating that the honey samples were of good quality and had acceptable values for maturity, purity, and freshness.

Genomic Insights into the Sulfur Metabolism of Phototrophic Green Sulfur Bacteria

DEFF Research Database (Denmark)

Frigaard, Niels-Ulrik; Bryant, Donald A.

2008-01-01

Green sulfur bacteria (GSB) utilize various combinations of sulfide, elemental sulfur, thiosulfate, ferrous iron, and hydrogen for anaerobic photoautotrophic growth. Genome sequence data is currently available for 12 strains of GSB. We present here a genome-based survey of the distribution...... and phylogenies of genes involved in oxidation of sulfur compounds in these strains. Sulfide:quinone reductase, encoded by sqr, is the only known sulfur-oxidizing enzyme found in all strains. All sulfide-utilizing strains contain the dissimilatory sulfite reductase dsrABCEFHLNMKJOPT genes, which appear...... to be involved in elemental sulfur utilization. All thiosulfate-utilizing strains have an identical sox gene cluster (soxJXYZAKBW). The soxCD genes found in certain other thiosulfate-utilizing organisms like Paracoccus pantotrophus are absent from GSB. Genes encoding flavocytochrome c (fccAB), adenosine-5...

Ab initio model of porous periclase

International Nuclear Information System (INIS)

Drummond, Neil D.; Swift, Damian C.; Ackland, Graeme J.

2004-01-01

A two-phase equilibrium equation of state (EOS) for periclase (MgO) was constructed using ab initio quantum mechanics, including a rigorous calculation of quasiharmonic phonon modes. Much of the shock wave data reported for periclase is on porous material. We compared the theoretical EOS with porous data using a simple 'snowplough' treatment and also a model using finite equilibration rates suitable for continuum mechanics simulations. (This model has been applied previously to various heterogeneous explosives as well as other porous materials.) The results were consistent and matched the data well at pressures above the regime affected by strength - and ramp-wave formation - during compaction. Ab initio predictions of the response of porous material have been cited recently as a novel and advanced capability; we feel that this is a fairly routine extension to established ab initio techniques

Pattern of callose deposition during the course of meiotic diplospory in Chondrilla juncea (Asteraceae, Cichorioideae).

Science.gov (United States)

Musiał, Krystyna; Kościńska-Pająk, Maria

2017-07-01

Total absence of callose in the ovules of diplosporous species has been previously suggested. This paper is the first description of callose events in the ovules of Chondrilla juncea, which exhibits meiotic diplospory of the Taraxacum type. We found the presence of callose in the megasporocyte wall and stated that the pattern of callose deposition is dynamically changing during megasporogenesis. At the premeiotic stage, no callose was observed in the ovules. Callose appeared at the micropylar pole of the cell entering prophase of the first meioticdivision restitution but did not surround the megasporocyte. After the formation of a restitution nucleus, a conspicuous callose micropylar cap and dispersed deposits of callose were detected in the megasporocyte wall. During the formation of a diplodyad, the micropylar callose cap decreased and the walls of a newly formed megaspores showed scattered distribution of callose. Within the older diplodyad, callose was mainly accumulated in the wall between megaspores, as well as in the wall of the micropylar cell; however, a dotted fluorescence of callose was also visible in the wall of the chalazal megaspore. Gradual degradation of callose in the wall of the chalazal cell and intense callose accumulation in the wall of the micropylar cell were related to the selection of the functional megaspore. Thus, our findings may suggest that callose fulfills a similar role both during megasporogenesis in sexual angiosperms and in the course of meiotic diplospory in apomicts and seems to form a regulatory interface between reproductive and somatic cells.

Genome-wide identification of significant aberrations in cancer genome

Directory of Open Access Journals (Sweden)

Yuan Xiguo

2012-07-01

Full Text Available Abstract Background Somatic Copy Number Alterations (CNAs in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC, a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1 exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2 performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3 iteratively detecting Significant Copy Number Aberrations (SCAs and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. Results We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma. When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC or tumor suppressor genes (e.g., CDKN2A/B. Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Conclusions Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes

Development of Anti-lock Braking System (ABS) for Vehicles Braking

OpenAIRE

Minh Vu Trieu; Oamen Godwin; Vassiljeva Kristina; Teder Leo

2016-01-01

This paper develops a real laboratory of anti-lock braking system (ABS) for vehicle and conducts real experiments to verify the ability of this ABS to prevent the vehicle wheel from being locked while braking. Two controllers of PID and fuzzy logic are tested for analysis and comparison. This ABS laboratory is designed for bachelor and master students to simulate and analyze performances of ABS with different control techniques on various roads and load conditions. Thi...

[Kidney allotransplantation from the AB0-incompatible donors].

Science.gov (United States)

Goriaĭnov, V A; Kaabak, M M; Babenko, N N; Shishlo, L A; Morozova, M M; Ragimov, A A; Dazhkova, N G; Salimov, E L

2013-01-01

The experience of 28 kidney allotransplantations from the AB0-incompatible donors was analyzed. The comparative group consisted of 38 patients, who received the AB0-compatible organ. The results were assessed using the following parameters: renal function, morphology of the biopsy samples of the transplanted kidney and actuary survival of the recipients with functioning transplants in both groups. The comparative analysis showed no significant difference between the two groups, giving the right to consider the kidney allotransplantation from the AB0-incompatible donors safe and effective.

An ab initio molecular

Indian Academy of Sciences (India)

mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

Ab initio derivation of model energy density functionals

International Nuclear Information System (INIS)

Dobaczewski, Jacek

2016-01-01

I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results. (letter)

ParABS system in chromosome partitioning in the bacterium Myxococcus xanthus.

Directory of Open Access Journals (Sweden)

Antonio A Iniesta

Full Text Available Chromosome segregation is an essential cellular function in eukaryotic and prokaryotic cells. The ParABS system is a fundamental player for a mitosis-like process in chromosome partitioning in many bacterial species. This work shows that the social bacterium Myxococcus xanthus also uses the ParABS system for chromosome segregation. Its large prokaryotic genome of 9.1 Mb contains 22 parS sequences near the origin of replication, and it is shown here that M. xanthus ParB binds preferentially to a consensus parS sequence in vitro. ParB and ParA are essential for cell viability in M. xanthus as in Caulobacter crescentus, but unlike in many other bacteria. Absence of ParB results in anucleate cells, chromosome segregation defects and loss of viability. Analysis of ParA subcellular localization shows that it clusters at the poles in all cells, and in some, in the DNA-free cell division plane between two chromosomal DNA masses. This ParA localization pattern depends on ParB but not on FtsZ. ParB inhibits the nonspecific interaction of ParA with DNA, and ParA colocalizes with chromosomal DNA only when ParB is depleted. The subcellular localization of ParB suggests a single ParB-parS complex localized at the edge of the nucleoid, next to a polar ParA cluster, with a second ParB-parS complex migrating after the replication of parS takes place to the opposite nucleoid edge, next to the other polar ParA cluster.

Cloning, purification and preliminary crystallographic studies of the 2AB protein from hepatitis A virus

International Nuclear Information System (INIS)

Garriga, Damià; Vives-Adrián, Laia; Buxaderas, Mònica; Ferreira-da-Silva, Frederico; Almeida, Bruno; Macedo-Ribeiro, Sandra; Pereira, Pedro José Barbosa; Verdaguer, Núria

2011-01-01

The 2AB protein derived from the nonstructural P2 region of hepatitis A virus has been cloned, purified and crystallized. The preliminary characterization of native and selenomethionine-derivative crystals is reported. The Picornaviridae family contains a large number of human pathogens such as rhinovirus, poliovirus and hepatitis A virus (HAV). Hepatitis A is an infectious disease that causes liver inflammation. It is highly endemic in developing countries with poor sanitation, where infections often occur in children. As in other picornaviruses, the genome of HAV contains one open reading frame encoding a single polyprotein that is subsequently processed by viral proteinases to originate mature viral proteins during and after the translation process. In the polyprotein, the N-terminal P1 region generates the four capsid proteins, while the C-terminal P2 and P3 regions contain the enzymes, precursors and accessory proteins essential for polyprotein processing and virus replication. Here, the first crystals of protein 2AB of HAV are reported. The crystals belonged to space group P4 1 or P4 3 , with unit-cell parameters a = b = 90.42, c = 73.43 Å, and contained two molecules in the asymmetric unit. Native and selenomethionine-derivative crystals diffracted to 2.7 and 3.2 Å resolution, respectively

Ab initio study of isomerism in molecular Li2AB+ ions with 12 and 14 valence electrons

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; Mak-Ki, M.L.; Shlojer, P.R.

1997-01-01

Ab initio calculations of potential energy surfaces (PES) of molecular ions Li 2 AB + with 12 and 14 valence electrons have been made in the framework of approximations MP2/6-31G*//HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/6-31*//MP2/6-31G*+ZPE(MP2/6-31G*). The following most favourable structures have been found: a double-terminal linear for LiNO + (a triplet); a plane bicyclic one for Li 2 OF + , Li 2 SCl + , Li 2 NO + (a singlet) and Li 2 PS + (a singlet), where both cations are coordinated to A-B bond; rectangular (T-shaped) for Li 2 OCl + and SFLi + , as well as for LiNS + and POLi 2 + ions in singlet and triplet states; in the form of a half-opened butterfly for Li 2 PS + (a triplet) and Li 2 SCl +

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

Science.gov (United States)

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin.

Science.gov (United States)

Makitrynskyy, Roman; Ostash, Bohdan; Tsypik, Olga; Rebets, Yuriy; Doud, Emma; Meredith, Timothy; Luzhetskyy, Andriy; Bechthold, Andreas; Walker, Suzanne; Fedorenko, Victor

2013-10-23

Unlike the majority of actinomycete secondary metabolic pathways, the biosynthesis of peptidoglycan glycosyltransferase inhibitor moenomycin in Streptomyces ghanaensis does not involve any cluster-situated regulators (CSRs). This raises questions about the regulatory signals that initiate and sustain moenomycin production. We now show that three pleiotropic regulatory genes for Streptomyces morphogenesis and antibiotic production-bldA, adpA and absB-exert multi-layered control over moenomycin biosynthesis in native and heterologous producers. The bldA gene for tRNA(Leu)UAA is required for the translation of rare UUA codons within two key moenomycin biosynthetic genes (moe), moeO5 and moeE5. It also indirectly influences moenomycin production by controlling the translation of the UUA-containing adpA and, probably, other as-yet-unknown repressor gene(s). AdpA binds key moe promoters and activates them. Furthermore, AdpA interacts with the bldA promoter, thus impacting translation of bldA-dependent mRNAs-that of adpA and several moe genes. Both adpA expression and moenomycin production are increased in an absB-deficient background, most probably because AbsB normally limits adpA mRNA abundance through ribonucleolytic cleavage. Our work highlights an underappreciated strategy for secondary metabolism regulation, in which the interaction between structural genes and pleiotropic regulators is not mediated by CSRs. This strategy might be relevant for a growing number of CSR-free gene clusters unearthed during actinomycete genome mining.

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

Science.gov (United States)

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Development of Anti-lock Braking System (ABS) for Vehicles Braking

Science.gov (United States)

Minh, Vu Trieu; Oamen, Godwin; Vassiljeva, Kristina; Teder, Leo

2016-11-01

This paper develops a real laboratory of anti-lock braking system (ABS) for vehicle and conducts real experiments to verify the ability of this ABS to prevent the vehicle wheel from being locked while braking. Two controllers of PID and fuzzy logic are tested for analysis and comparison. This ABS laboratory is designed for bachelor and master students to simulate and analyze performances of ABS with different control techniques on various roads and load conditions. This paper provides educational theories and practices on the design of control for system dynamics.

[VDRL and FTA-ABS reactivity in cerebrospinal fluid: our experience].

Science.gov (United States)

García-Rodríguez, J A; Martín-Sánchez, A M; Canut, A; García-García, L; Cacho, J

1990-01-01

The reactivity of 194 samples of CSF against VDRL and FTA-ABS was studied in patients attending the Clinical Hospital in Salamanca over a five years period. This laboratory was asked to rule out an etiology of syphilis. Twelve samples of CSF proved to be reactive (6.2%) against VDRL and/or FTA-ABS. Seven of these corresponded to six adults diagnosed as suffering from neurosyphilis and one to an infant with early congenital syphilis without neurological alterations; these had in common the presence of active syphilis and a reactive FTA-ABS in serum. In the CSF of the six cases of neurosyphilis, VDRL was reactive in two patients (33.3%) and FTA-ABS in five (83.3%). One minimally reactive VDRL and four FTA-ABS were detected in the remaining five patients, with no known previous history of syphilis, that were suffering from different neurological alterations and that had a nonreactive FTA-ABS in serum. The results obtained in this study point to inappropriate use in CSF of VDRL and FTA-ABS to exclude neurosyphilis in our hospital since only 3.6% of the CSF studied corresponded to patients diagnosed as suffering from neurosyphilis and also to the need for improving the criteria for patient selection.

Pathogens present on vegetative organs and seeds of white mustard (Sinapis alba L. and chinese mustad (Brassica juncea L.

Directory of Open Access Journals (Sweden)

Barbara Majchrzak

2013-12-01

Full Text Available The research was conducted in the years 1999-2001. The aim of the research was to determine the health condition of overground parts and seeds of white niuslard (Sinapis alba L. cv. Metex and chinese mustard (Brassica juncea L. cv. Małopolska. In all the years of the research alternaria blight was found on the leaves of white mustard which injury index ranged from 5,6% in 2001 to 17,6% in 200O. The most dangerous disease of chinese mustard also was alternaria blight and its symptoms were found on leaves and siliques. The strongest infection of leaves was in 2000 (50% and the weakest in 2001 (6,7%. In all the years of the research siliques were rather weak infected (50-8,89%. Besides powdery mildew was found on chinese mustard which injury index ranged from 0,3% in 1999 to 32,3% in 2000. Intensity of diseases was affected generally by the weather conditions. From the seeds of white mustard and chinese mustard were isolated respectively 263 and 137 colonies. Alternaria alternata was the most numerous species which makes respectively 60,9% and 42,3% isolates. Among the fungi pathogenic for white and chinese mustard were also isolated: A. brassicae, Botrytis cinerea and Rhizoctonia solami.

Comportamento mecânico e termo-mecânico de blendas poliméricas PBT/ABS Mechanical and thermo-mechanical behavior of PBT/ABS polymer blends

Directory of Open Access Journals (Sweden)

Luís Antonio S. Ferreira

1997-03-01

Full Text Available RESUMO: Blendas de poli(tereftalato de butileno (PBT e copolímero ABS foram estudadas usando-se três tipos diferentes de ABS. As blendas foram caracterizadas mecanicamente através de ensaios de tração e de impacto, e termo-mecanicamente através da determinação da temperatura de deflexão térmica (HDT. Uma influência mais pronunciada foi observada para a variação da composição química do ABS, em relação às diferentes composições de fase, onde blendas com ABS de maior proporção de acrilonitrila mostraram melhor comportamento. Foi observado que baixos níveis de ABS nas blendas proporcionam principalmente um aumento pronunciado da HDT e sem variação da resistência ao impacto, em relação ao PBT puro. Por outro lado, baixos níveis de PBT nas blendas não alteram as propriedades em relação ao ABS puro, com exceção da resistência ao impacto, que mostrou uma redução significativa.ABSTRACT: Polymer blends of poly(butylene terephthalate, PBT, and three grades of Acrylonitrile-Butadiene-Styrene copolymer, ABS, were studied. Polymer blends were characterized by impact resistance, tensile strength and heat deflection temperature tests. It was observed a stronger influence of the chemical composition of the ABS resin on the blends properties, mainly for the blends with higher ABS content which show better properties, than the phase composition of the ABS. It was observed that low levels of ABS in the blends promote mainly a high increase in HDT at the same level of impact resistance, as compared to neat PBT. On the other hand, low levels of PBT in the blend basically keep all the properties at the same level except the impact resistance which shows a significant decrease.

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

Science.gov (United States)

Ghai, Rohit; Mehrshad, Maliheh; Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco

2017-01-01

Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.

Workshop on automated beam steering and shaping (ABS). Proceedings

Energy Technology Data Exchange (ETDEWEB)

Lindroos, M [ed.

1999-09-10

A workshop on Automated Beam Steering and Shaping (ABS) was held at CERN in December 1998. This was the first workshop dedicated to this subject. The workshop had two major goals: to review the present status of ABS algorithms and systems around the world and to create a worldwide ABS community. These proceedings contain summary reports from all sessions, contributions from several presentations held at the workshop, and a complete set of abstracts for all presentations. (orig.)

Workshop on automated beam steering and shaping (ABS). Proceedings

International Nuclear Information System (INIS)

Lindroos, M.

1999-01-01

A workshop on Automated Beam Steering and Shaping (ABS) was held at CERN in December 1998. This was the first workshop dedicated to this subject. The workshop had two major goals: to review the present status of ABS algorithms and systems around the world and to create a worldwide ABS community. These proceedings contain summary reports from all sessions, contributions from several presentations held at the workshop, and a complete set of abstracts for all presentations. (orig.)

Speed-up of ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo simulations by using an auxiliary potential energy surface

International Nuclear Information System (INIS)

Nakayama, Akira; Taketsugu, Tetsuya; Shiga, Motoyuki

2009-01-01

Efficiency of the ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo methods is enhanced by employing an auxiliary potential energy surface that is used to update the system configuration via molecular dynamics scheme. As a simple illustration of this method, a dual-level approach is introduced where potential energy gradients are evaluated by computationally less expensive ab initio electronic structure methods. (author)

Ab initio valence calculations in chemistry

CERN Document Server

Cook, D B

1974-01-01

Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): an apomictic invader on three continents.

Science.gov (United States)

Gaskin, John F; Schwarzländer, Mark; Kinter, C Lynn; Smith, James F; Novak, Stephen J

2013-09-01

Assessing propagule pressure and geographic origins of invasive species provides insight into the invasion process. Rush skeletonweed (Chondrilla juncea; Asteraceae) is an apomictic, perennial plant that is invasive in Australia, South America (Argentina), and North America (Canada and the United States). This study comprehensively compares propagule pressure and geographic structure of genotypes to improve our understanding of a clonal invasion and enhance management strategies. • We analyzed 1056 native range plants from Eurasia and 1156 plants from three invaded continents using amplified fragment length polymorphism (AFLP) techniques. We used measures of diversity (Simpson's D) and evenness (E), analysis of molecular variance, and Mantel tests to compare invasions, and genotype similarity to determine origins of invasive genotypes. • We found 682 unique genotypes in the native range, but only 13 in the invaded regions. Each invaded region contained distinct AFLP genotypes, suggesting independent introduction events, probably with different geographic origins. Relatively low propagule pressure was associated with each introduction around the globe, but levels of among-population variation differed. We found exact AFLP genotype matches between the native and invaded ranges for five of the 13 invasive genotypes. • Invasion dynamics can vary across invaded ranges within a species. Intensive sampling for molecular analyses can provide insight for understanding intraspecific invasion dynamics, which can hold significance for the management of plant species, especially by finding origins and distributions of invasive genotypes for classical biological control efforts.

Characterization and Testing the Efficiency of Acinetobacter baumannii Phage vB-GEC_Ab-M-G7 as an Antibacterial Agent

Directory of Open Access Journals (Sweden)

Ia Kusradze

2016-10-01

Full Text Available Acinetobacter baumannii is a gram-negative, non-motile bacterium that, due to its multidrug resistance, has become a major nosocomial pathogen .The increasing number of multidrug resistant (MDR strains has renewed interest in phage therapy. The aim of our study was to assess the effectiveness of phage administration in Acinetobacter baumannii wound infections in an animal model to demonstrate phage therapy as non-toxic, safe and alternative antibacterial remedy. Using classical methods for the study of bacteriophage properties, we characterized phage vB-GEC_Ab-M-G7 as a dsDNA myovirus with a 90kb genome size. Important characteristics of vB-GEC_Ab-M-G7include a short latent period and large burst size, wide host range, resistance to chloroform and thermal and pH stability. In a rat wound model, phage application effectively decreased the number of bacteria isolated from the wounds of successfully treated animals. This study highlights the effectiveness of the phage therapy and provides further insight into treating infections caused by MDR strains using phage administration.

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering.

Science.gov (United States)

Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M Teresa; Buchholz, Frank

2016-07-22

Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets.

Comparative uptake of plutonium from soils by Brassica juncea and Helianthus annuus

International Nuclear Information System (INIS)

Lee, J.H.; Hossner, L.R.; Attrep, M.; Kung, K.S.

2002-01-01

Extractability of Pu from soils was most affected by pH and amounts of clay, salts, and carbonates. - Plutonium uptake by Brassica juncea (Indian mustard) and Helianthus annuus (sunflower) from soils with varying chemical composition and contaminated with Pu complexes (Pu-nitrate [ 239 Pu(NO 3 ) 4 ], Pu-citrate [ 239 Pu(C 6 H 5 O 7 ) + ], and Pu-diethylenetriaminepentaacetic acid (Pu-DTPA [ 239 Pu-C 14 H 23 O 10 N 3 ]) was investigated. Sequential extraction of soils incubated with applied Pu was used to determine the distribution of Pu in the various soil fractions. The initial Pu activity levels in soils were 44.40-231.25 Bq g -1 as Pu-nitrate , Pu-citrate, or Pu-DTPA. A difference in Pu uptake between treatments of Pu-nitrate and Pu-citrate without chelating agent was observed only with Indian mustard in acidic Crowley soil. The uptake of Pu by plants was increased with increasing DTPA rates, however, the Pu concentration of plants was not proportionally increased with increasing application rate of Pu to soil. Plutonium uptake from Pu-DTPA was significantly higher from the acid Crowley soil than from the calcareous Weswood soil. The uptake of Pu from the soils was higher in Indian mustard than in sunflower. Sequential extraction of Pu showed that the ion-exchangeable Pu fraction in soils was dramatically increased with DTPA treatment and decreased with time of incubation. Extractability of Pu in all fractions was not different when Pu-nitrate and Pu-citrate were applied to the same soil. More Pu was associated with the residual Pu fraction without DTPA application. Consistent trends with time of incubation for other fractions were not apparent. The ion-exchangeable fraction, assumed as plant-available Pu, was significantly higher in acid soil compared with calcareous soil with or without DTPA treatment. When the calcareous soil was treated with DTPA, the ion-exchangeable Pu was comparatively less influenced. This fraction in the soil was more affected with time

Bicanonical ab Initio Molecular Dynamics for Open Systems.

Science.gov (United States)

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

12 CFR Appendixes A-B to Part 41 - [Reserved

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 1 2010-01-01 2010-01-01 false [Reserved] A Appendixes A-B to Part 41 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY FAIR CREDIT REPORTING Appendixes A-B to Part 41 [Reserved] ...

ABS, MBS and CDO compared : An empirical analysis

NARCIS (Netherlands)

Vink, D.; Thibeault, A.

2008-01-01

The capital market in which the asset-backed securities are issued and traded is composed of three main categories: ABS, MBS and CDOs. We were able to examine a total number of 3,951 loans (worth €730.25 billion) of which 1,129 (worth €208.94 billion) have been classified as ABS. MBS issues

Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

International Nuclear Information System (INIS)

Ree, F.H.; Winter, N.W.

1980-01-01

Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

Ab-initio ZORA calculations

NARCIS (Netherlands)

Faas, S.; Snijders, Jaap; van Lenthe, J.H.; HernandezLaguna, A; Maruani, J; McWeeny, R; Wilson, S

2000-01-01

In this paper we present the first application of the ZORA (Zeroth Order Regular Approximation of the Dirac Fock equation) formalism in Ab Initio electronic structure calculations. The ZORA method, which has been tested previously in the context of Density Functional Theory, has been implemented in

AB Manpower Plan 2007

CERN Document Server

Myers, Stephen

2007-01-01

The present exercise is not as such a "manpower plan" but a purely budgetary comparison of known plus requested resources with the known commitments over the period 2007-2012. From a purely budgetary point of view, AB will have the capacity to maintain all those recently hired staff who fulfill the criteria for long term employment at CERN. Following this budgetary exercise, AB proposes to perform a CERN-wide staff work plan so as to compare the manpower available to the quantity of work to be done in the totality of the work-packages. If there is a significant mismatch between these two quantities then we propose the following measures which would create personnel economies and allow us to redress the mismatch by increased recruitment: a new job severance scheme; CERN restructuring; use of the new CERN-ITER agreement; more flexibility in transfers from Materials to Personnel budgets. Failing this a re-examination of possible closure of lower priority facilities may be needed.

Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection.

OpenAIRE

Tweedy, J; Spyrou, MA; Pearson, M; Lassner, D; Kuhl, U; Gompels, UA

2016-01-01

Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated "CiHHV-6A/B". These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, imp...

Report on enrichment work at AB Atomenergi, 1965-1978

International Nuclear Information System (INIS)

Maartensson, M.

1978-11-01

A review of the Rand D performed at AB Atomenergi (now Studsvik Energiteknik AB) in the field of enrichment during the period 1965-1978. The report also describes the international development, and discusses the possibilities for continued Swedish efforts in this area. (L.E.)

A Kine-chemical Investigation of the AB Dor Moving Group "Stream"

Science.gov (United States)

Barenfeld, Scott A.; Bubar, Eric J.; Mamajek, Eric E.; Young, Patrick A.

2013-03-01

The AB Dor Moving Group consists of a "nucleus" of ~10 stars at d ~= 20 pc, along with dozens of purported "stream" members distributed across the sky. We perform a chemical and kinematic analysis of a subsample of AB Dor stream stars to test whether they constitute a physical stellar group. We use the NEMO Galactic kinematic code to investigate the orbits of the stream members, and perform a chemical abundance analysis using high resolution spectra taken with the Magellan Clay 6.5 m telescope. Using a χ2 test with the measured abundances for 10 different elements, we find that only half of the purported AB Dor stream members could possibly constitute a statistically chemically homogeneous sample. Some stream members with three-dimensional velocities were hundreds of parsecs from the AB Dor nucleus ~108 yr ago, and hence were unlikely to share a common origin. We conclude that the published lists of AB Dor moving group stream members are unlikely to represent the dispersed remnant of a single star formation episode. A subsample of the stream stars appears to be both statistically chemically homogeneous and in the vicinity of the AB Dor nucleus at birth. Their mean metallicity is [Fe/H] = 0.02 ± 0.02 dex, which we consider representative for the AB Dor group. Finally, we report a strong lower limit on the age of the AB Dor nucleus of >110 Myr based on the pre-main sequence contraction times for K-type members which have reached the main sequence.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Science.gov (United States)

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and

Non-catalytic Roles for XPG with BRCA1 and BRCA2 in Homologous Recombination and Genome Stability

DEFF Research Database (Denmark)

Trego, Kelly S.; Groesser, Torsten; Davalos, Albert R.

2016-01-01

XPG is a structure-specific endonuclease required for nucleotide excision repair, and incision-defective XPG mutations cause the skin cancer-prone syndrome xeroderma pigmentosum. Truncating mutations instead cause the neurodevelopmental progeroid disorder Cockayne syndrome, but little is known ab......-phosphorylation and persistent chromatin binding. These unexpected findings establish XPG as an HRR protein with important roles in genome stability and suggest how XPG defects produce severe clinical consequences including cancer and accelerated aging....... about how XPG loss results in this devastating disease. We identify XPG as a partner of BRCA1 and BRCA2 in maintaining genomic stability through homologous recombination (HRR). XPG depletion causes DNA double-strand breaks, chromosomal abnormalities, cell-cycle delays, defective HRR, inability...

Differential screening of phage-ab libraries by oligonucleotide microarray technology.

Directory of Open Access Journals (Sweden)

Paolo Monaci

Full Text Available A novel and efficient tagArray technology was developed that allows rapid identification of antibodies which bind to receptors with a specific expression profile, in the absence of biological information. This method is based on the cloning of a specific, short nucleotide sequence (tag in the phagemid coding for each phage-displayed antibody fragment (phage-Ab present in a library. In order to set up and validate the method we identified about 10,000 different phage-Abs binding to receptors expressed in their native form on the cell surface (10 k Membranome collection and tagged each individual phage-Ab. The frequency of each phage-Ab in a given population can at this point be inferred by measuring the frequency of its associated tag sequence through standard DNA hybridization methods. Using tiny amounts of biological samples we identified phage-Abs binding to receptors preferentially expressed on primary tumor cells rather than on cells obtained from matched normal tissues. These antibodies inhibited cell proliferation in vitro and tumor development in vivo, thus representing therapeutic lead candidates.

Helicase properties of the Escherichia coli UvrAb protein complex

International Nuclear Information System (INIS)

Oh, E.Y.; Grossman, L.

1987-01-01

The Escherichia coli UvrA protein has an associated ATPase activity with a turnover number affected by the presence of UvrB protein as well as by DNA. Specifically, the structure of DNA significantly influences the turnover rate of the UvrAB ATPase activity. Double-stranded DNA maximally activates the turnover rate 10-fold whereas single-stranded DNA maximally activates the turnover rate 20-fold, suggesting that the mode of interaction of UvrAB protein with different DNAs is distinctive. We have previously shown that the UvrAB protein complex, driven by the binding energy of ATP, can locally unwind supercoiled DNA. The nature of the DNA unwinding activity and single-stranded DNA activation of ATPase activity suggest potential helicase activity. In the presence of a number of helicase substrates, the UvrAB complex, indeed, manifests a strand-displacement activity-unwinding short duplexes and D-loop DNA, thereby generating component DNA structures. The energy for the activity is derived from ATP or dATP hydrolysis. Unlike the E. coli DnaB, the UvrAB helicase is sensitive to UV-induced photoproducts

AB toxins: a paradigm switch from deadly to desirable.

Science.gov (United States)

Odumosu, Oludare; Nicholas, Dequina; Yano, Hiroshi; Langridge, William

2010-07-01

To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.

AB Toxins: A Paradigm Switch from Deadly to Desirable

Directory of Open Access Journals (Sweden)

Oludare Odumosu

2010-06-01

Full Text Available To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.

Ab interno trabeculectomy: patient selection and perspectives

Science.gov (United States)

Vinod, Kateki; Gedde, Steven J

2016-01-01

Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

Kinesin-2 KIF3AB exhibits novel ATPase characteristics.

Science.gov (United States)

Albracht, Clayton D; Rank, Katherine C; Obrzut, Steven; Rayment, Ivan; Gilbert, Susan P

2014-10-03

KIF3AB is an N-terminal processive kinesin-2 family member best known for its role in intraflagellar transport. There has been significant interest in KIF3AB in defining the key principles that underlie the processivity of KIF3AB in comparison with homodimeric processive kinesins. To define the ATPase mechanism and coordination of KIF3A and KIF3B stepping, a presteady-state kinetic analysis was pursued. For these studies, a truncated murine KIF3AB was generated. The results presented show that microtubule association was fast at 5.7 μm(-1) s(-1), followed by rate-limiting ADP release at 12.8 s(-1). ATP binding at 7.5 μm(-1) s(-1) was followed by an ATP-promoted isomerization at 84 s(-1) to form the intermediate poised for ATP hydrolysis, which then occurred at 33 s(-1). ATP hydrolysis was required for dissociation of the microtubule·KIF3AB complex, which was observed at 22 s(-1). The dissociation step showed an apparent affinity for ATP that was very weak (K½,ATP at 133 μm). Moreover, the linear fit of the initial ATP concentration dependence of the dissociation kinetics revealed an apparent second-order rate constant at 0.09 μm(-1) s(-1), which is inconsistent with fast ATP binding at 7.5 μm(-1) s(-1) and a Kd ,ATP at 6.1 μm. These results suggest that ATP binding per se cannot account for the apparent weak K½,ATP at 133 μm. The steady-state ATPase Km ,ATP, as well as the dissociation kinetics, reveal an unusual property of KIF3AB that is not yet well understood and also suggests that the mechanochemistry of KIF3AB is tuned somewhat differently from homodimeric processive kinesins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Time course of physiological, biochemical, and gene expression changes under short-term salt stress in Brassica juncea L.

Directory of Open Access Journals (Sweden)

Manish Pandey

2017-06-01

Full Text Available Salinity-imposed limitations on plant growth are manifested through osmotic and ionic imbalances. However, because salinity-induced responses vary considerably among crop plants, monitoring of such responses at an early stage has relevance. In this study, physiological (seed germination, seed vigor index, root length, shoot length, fresh weight, dry weight and biochemical attributes (osmoprotectants, K+/Na+ ratio were analyzed for a time-course assessment of salt responses in Indian mustard (Brassica juncea L. with an emphasis on early monitoring. The results showed strong correlations for total soluble sugars at germination phase (24 h, proline content in the seedling establishment phase (48 h and various physiological parameters including seed vigor index (R2 = 0.901, shoot length (R2 = 0.982, and fresh weight (R2 = 0.980 at 72 h (adaptation under stress. In addition, transcriptional changes were observed under NaCl treatment for key genes belonging to the family of selective ion transporters (NHX, HKT and abscisic acid synthesis (AAO-3. The status of mitochondrial respiration was also examined as a probe for salinity tolerance at an early stage. The results suggested that although all the analyzed parameters showed correlations (negative or positive with salt stress magnitude, their critical response times differed, with most of the studied biochemical, physiological, or molecular markers providing valuable information only after radicle emergence, whereas mitochondrial respiration via alternative oxidase was useful for the early detection of salt responses.

Effect of sunn hemp (Crotalaria juncea L.) cutting date and planting density on weed suppression in Georgia, USA.

Science.gov (United States)

Morris, J Bradley; Chase, Carlene; Treadwell, Danielle; Koenig, Rosie; Cho, Alyssa; Morales-Payan, Jose Pable; Murphy, Tim; Antonious, George F

2015-01-01

A field study was conducted in 2008 and 2009 at the USDA, ARS, Plant Genetic Resources Conservation Unit in Griffin, GA, to investigate weed suppression by sunn hemp (Crotalaria juncea L). The objectives were to (1) evaluate the effects of apical meristem removal (AMR) at three dates [5, 6, and 7 wks after planting (WAP) on May 14, 2008 and May 21, 2009] and (2) assess the impact of seeding rates (11, 28, and 45 kg ha(-1)) on weed biomass reduction. Weed species were identified at 4, 8, and 12 wks after sunn hemp planting. Sunn hemp cutting date had no significant effect on weed suppression in 2008 but significant differences for grass weeds at 4, 8, and 12 WAP and for yellow nutsedge at 8 and 12 WAP did occur when compared to the control in 2009. In comparison to the sunn hemp-free control plot in 2009, all three seeding rates had reduced grass weed dry weights at 4, 8, and 12 WAP. The total mass of yellow nutsedge when grown with sunn hemp was reduced compared to the total mass of yellow nutsedge grown in the weedy check for all seeding rates at 8 and 12 WAP. Lower grass weed biomass was observed by 12 WAP for cutting dates and seeding rates during 2008 and 2009. Sunn hemp cutting date and seeding rate reduced branch numbers in both years. The reduction in sunn hemp seeding rates revealed a decrease in weed populations.

ABS 3D printed solutions for cryogenic applications

Science.gov (United States)

Bartolomé, E.; Bozzo, B.; Sevilla, P.; Martínez-Pasarell, O.; Puig, T.; Granados, X.

2017-03-01

3D printing has become a common, inexpensive and rapid prototyping technique, enabling the ad hoc fabrication of complex shapes. In this paper, we demonstrate that 3D printed objects in ABS can be used at cryogenic temperatures, offering flexible solutions in different fields. Firstly, a thermo-mechanical characterization of ABS 3D printed specimens at 77 K is reported, which allowed us to delimit the type of cryogenic uses where 3D printed pieces may be implemented. Secondly, we present three different examples where ABS 3D printed objects working at low temperatures have provided specific solutions: (i) SQUID inserts for angular magnetometry (low temperature material characterization field); (ii) a cage support for a metamaterial ;magnetic concentrator; (superconductivity application), and (iii) dedicated tools for cryopreservation in assisted reproductive techniques (medicine field).

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

Directory of Open Access Journals (Sweden)

Yang Yi-Fan

2007-03-01

Full Text Available Abstract Background Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. Results This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs and Translation Initiation Sites (TISs. The former is based on a linguistic "Entropy Density Profile" (EDP model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. Conclusion Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.

Identification of Bacillus thuringiensis Cry1AbMod binding-proteins from Spodoptera frugiperda.

Science.gov (United States)

Martínez de Castro, Diana L; García-Gómez, Blanca I; Gómez, Isabel; Bravo, Alejandra; Soberón, Mario

2017-12-01

Bacillus thuringiensis Cry toxins are currently used for pest control in transgenic crops but evolution of resistance by the insect pests threatens the use of this technology. The Cry1AbMod toxin was engineered to lack the alpha helix-1 of the parental Cry1Ab toxin and was shown to counter resistance to Cry1Ab and Cry1Ac toxins in different insect species including the fall armyworm Spodoptera frugiperda. In addition, Cry1AbMod showed enhanced toxicity to Cry1Ab-susceptible S. frugiperda populations. To gain insights into the mechanisms of this Cry1AbMod-enhanced toxicity, we isolated the Cry1AbMod toxin binding proteins from S. frugiperda brush border membrane vesicles (BBMV), which were identified by pull-down assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS results indicated that Cry1AbMod toxin could bind to four classes of aminopeptidase (N1, N3, N4 y N5) and actin, with the highest amino acid sequence coverage acquired for APN 1 and APN4. In addition to these proteins, we found other proteins not previously described as Cry toxin binding proteins. This is the first report that suggests the interaction between Cry1AbMod and APN in S. frugiperda. Copyright © 2017 Elsevier Inc. All rights reserved.

Radioimmunoimaging using F(ab')2 fragment of monoclonal antibodies against human alpha-fetoprotein

International Nuclear Information System (INIS)

Sakahara, Harumi; Endo, Keigo; Nakashima, Tetsuo; Koizumi, Mitsuru; Ohta, Hitoya; Torizuka, Kanji; Okada, Kenichiro; Yoshida, Osamu; Nishi, Shinzo.

1985-01-01

Using monoclonal antibodies against human α-fetoprotein (AFP), radioiodinated F(ab') 2 fragments were compared with whole IgG as a radiotracer for radioimmunoimaging of cancer. F(ab') 2 fragments were obtained by pepsin digestion of whole IgG (IgGl). IgG and F(ab') 2 were labeled with 125 I or 131 I by the chloramine-T method with almost full retention of antibody activity. F(ab') 2 fragments were cleared more rapidly from the circulation in normal mice with a half life of 6.3 hours than whole IgG with a half life of 5.5 days. Radioactivity of F(ab') 2 in various organs also decreased faster than IgG. In nude mice transplanted with AFP-producing human testicular tumor, F(ab') 2 fragments demonstrated superior scintigrams to whole IgG at 2 days after the injection, because of the fast disappearance of background radioactivity. Although absolute accumulation of 131 I labeled F(ab') 2 in the tumor was less than that of 131 I labeled IgG, tumor to other organ ratios were much higher with F(ab') 2 than those of IgG. The tumor to blood ratio of 131 I labeled F(ab') 2 was 1.04 at day 2, whereas tumor to blood ratio of 131 I labeled IgG was 0.55 at day 2 and 0.92 at day 4, respectively. These results indicated that for the radiolabeling of monoclonal antibodies, F(ab') 2 fragments would be superior to whole IgG in the radioimmunoimaging of cancer. (author)

CRY 1AB trangenic cowpea obtained by nodal electroporation ...

African Journals Online (AJOL)

Electroporation-mediated genetic transformation was used to introduce Cry 1 Ab insecticidal gene into cowpea. Nodal buds were electroporated in planta with a plasmid carrying the Cry 1Ab and antibiotic resistance npt II genes driven by a 35S CaMV promoter. T1 seeds derived from electroporated branches were selected ...

Electronic brakes. From ABS to brake-by-wire. 2. ed.; Elektronische Bremssysteme. Vom ABS zum Brake-by-Wire

Energy Technology Data Exchange (ETDEWEB)

Reichel, H.R.

2003-07-01

The book reports trends in vehicle brakes from 1968 to 1998. This was the age of the electronic revolution. The book presents conventional brakes, antiblocking systems (ABS), antislip systems (ASS), brake assistants (BAS), dynamic control systems, and brake-by-wire systems. [German] Das Buch berichtet ueber Entwicklungen an Fahrzeugbremsanlagen in der Zeitspanne von 1968 bis etwa 1998. Diese Zeit war gepraegt vom Vordringen der Elektronik in die Bremsen, was fuer Hersteller und Kunden eine Revolution bedeutete. Behandelt sind: (a) Konventionelle Bremsanlagen, (b) Antiblockiersysteme (ABS), (c) Anti-Schlupf-regelungen (ASR), (d) Bremsassistenten (BAS), (e) Fahrdynamikregelungen (FDR, ESP), (f) Brake-by-Wire (orig.)

First draft genome sequencing of indole acetic acid producing and plant growth promoting fungus Preussia sp. BSL10.

Science.gov (United States)

Khan, Abdul Latif; Asaf, Sajjad; Khan, Abdur Rahim; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Lee, In-Jung

2016-05-10

Preussia sp. BSL10, family Sporormiaceae, was actively producing phytohormone (indole-3-acetic acid) and extra-cellular enzymes (phosphatases and glucosidases). The fungus was also promoting the growth of arid-land tree-Boswellia sacra. Looking at such prospects of this fungus, we sequenced its draft genome for the first time. The Illumina based sequence analysis reveals an approximate genome size of 31.4Mbp for Preussia sp. BSL10. Based on ab initio gene prediction, total 32,312 coding sequences were annotated consisting of 11,967 coding genes, pseudogenes, and 221 tRNA genes. Furthermore, 321 carbohydrate-active enzymes were predicted and classified into many functional families. Copyright © 2016 Elsevier B.V. All rights reserved.

Pengaruh bahan pengisi serat kaca terhadap sifat fisik dan kristalinitas polipaduan PC/ABS

Directory of Open Access Journals (Sweden)

Dwi Wahini Nurhajati

2017-06-01

Full Text Available This research aimed to determine the effects of the addition of glass fibers on the physical and crystallinity properties of PC/ABS polyblends. The ratio of PC/ABS used in this research was 75/25, while the addition of glass fibers ranged from 0; 5; 10; to 15 phr (based on the weight of PC/ABS. Polyblends of PC/ABS/glass fibers were prepared in a twin screw extruder. The test results showed that density and tensile strength of PC/ABS polyblends increased with an increase in the glass fiber content. The presence of glass fibers decreased MFI and impact strength of these PC/ABS polyblends. The functional groups were determined by the fourier transform infrared (FTIR spectrophotometer while crystallinity was examined using X-ray diffractometer (XRD.

Importance of radioimmunoassays (HBsAg, HBsAb and HBcAb) for reducing the risk of hepatitis B transfer by blood

International Nuclear Information System (INIS)

Novak, J.; Kselikova, M.

1979-01-01

The principles are reported of the radioimmunoanalytical assay of the hepatitis B surface antigen, antibodies against this antigen which constitute immunologically indirect evidence, and antibodies against the nucleus of Dane's particles, which is circumstantial immunological evidence. The results obtained by radioimmunoassay are compared with those obtained by enzyme immunoassay. The results are presented obtained during the investigations of a total of 79 individuals, blood donors, health workers, and haemodialytic patients. In the whole group the hepatitis B surface antigen was proved by radioimmunoassay in 54%, by enzyme immunoassay in 47%; the antibody against the hepatitis B surface antigen in 19%; the antibody against the nucleus of the hepatitis B virus showed the largest proportion 75%. In 6.3% radioimmunoassay showed symptoms all three of hepatitis B, i.e., the surface antigen, the antibody against it, and the antibody against the hepatitis B virus nucleus; the correlation of the three symptoms is shown. The presence of HBsAg, HBsAb, and HBcAb is believed to be a contraindication of blood taking for routine purposes; the disappearance of HBsAg for a longer time may justify the re-inclusion among blood donors; the presence of HBsAb and HBcAb does not preclude the preparation of the plasma from such blood for the production of a specific anti-HBs immunoglobulin. (author)

Genomic characterization and expression profiles upon bacterial infection of a novel cystatin B homologue from disk abalone (Haliotis discus discus).

Science.gov (United States)

Premachandra, H K A; Wan, Qiang; Elvitigala, Don Anushka Sandaruwan; De Zoysa, Mahanama; Choi, Cheol Young; Whang, Ilson; Lee, Jehee

2012-12-01

Cystatins are a large family of cysteine proteinase inhibitors which are involved in diverse biological and pathological processes. In the present study, we identified a gene related to cystatin superfamily, AbCyt B, from disk abalone Haliotis discus discus by expressed sequence tag (EST) analysis and BAC library screening. The complete cDNA sequence of AbCyt B is comprised of 1967 nucleotides with a 306 bp open reading frame (ORF) encoding for 101 amino acids. The amino acid sequence consists of a single cystatin-like domain, which has a cysteine proteinase inhibitor signature, a conserved Gly in N-terminal region, QVVAG motif and a variant of PW motif. No signal peptide, disulfide bonds or carbohydrate side chains were identified. Analysis of deduced amino acid sequence revealed that AbCyt B shares up to 44.7% identity and 65.7% similarity with the cystatin B genes from other organisms. The genomic sequence of AbCyt B is approximately 8.4 Kb, consisting of three exons and two introns. Phylogenetic tree analysis showed that AbCyt B was closely related to the cystatin B from pacific oyster (Crassostrea gigas) under the family 1.Functional analysis of recombinant AbCyt B protein exhibited inhibitory activity against the papain, with almost 84% inhibition at a concentration of 3.5 μmol/L. In tissue expression analysis, AbCyt B transcripts were expressed abundantly in the hemocyte, gill, mantle, and digestive tract, while weakly in muscle, testis, and hepatopancreas. After the immune challenge with Vibrio parahemolyticus, the AbCyt B showed significant (P<0.05) up-regulation of relative mRNA expression in gill and hemocytes at 24 and 6 h of post infection, respectively. These results collectively suggest that AbCyst B is a potent inhibitor of cysteine proteinases and is also potentially involved in immune responses against invading bacterial pathogens in abalone. Copyright © 2012 Elsevier Ltd. All rights reserved.

Polyvalent horse F(Ab`) 2 snake antivenom: Development of ...

African Journals Online (AJOL)

F(ab´)2 fragments were further purified by Q-Fast Flow chromatography, concentrated by molecular ultrafiltration and sterilized by filtration through 0.22 m membranes. The resulting F(ab´)2 preparations were rich in intact L and in pieces of H IgG(T) chains, as demonstrated by electrophoresis and Western blot and exhibited ...

ABS, MBS and CDO pricing comparisons : An empirical analysis

NARCIS (Netherlands)

Vink, D.; Thibeault, A.

2008-01-01

The capital market in which asset-backed securities are issued and traded is composed of three main categories: ABS, MBS and CDOs. The authors examined a total of 3,466 loans (worth €548.51 billion) of which 1,102 (worth €163.90 billion) have been classified as ABS. MBS issues represent 1,782 issues

40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PROCEDURES AND REQUIREMENTS FOR PLANT-INCORPORATED PROTECTANTS...

A technique developed for labeling the green manures (sunnhemp and velvet bean) with {sup 15} N for nitrogen dynamic studies; Tecnica para marcacao dos adubos verdes crotalaria juncea e mucuna-preta com {sup 15} N para estudos de dinamica do nitrogenio

Energy Technology Data Exchange (ETDEWEB)

Ambrosano, Edmilson Jose [Instituto Agronomico de Campinas, SP (Brazil). Secao de Leguminosas; Trivelin, Paulo Cesar Ocheuze; Muruoka, Takashi [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

1997-07-01

A technique was developed for labeling the leguminous plant tissue with nitrogen ({sup 15} N) to obtain labelled material for nitrogen dynamic studies. Sunnhemp (crotalaria juncea L.) and velvet beans (Mucuna aterrima, sinonimia Stizolobium aterrimum Piper and Tracy) were grown in pots containing 10 kg of a Red Yellow Podzolic soil, under greenhouse conditions. The rate of 1.2 of nitrogen (ammonium sulphate with 11.37 atom % {sup 15} N) per pot was applied three times. The labelled dried plant material showed 3.177 and 4.337 of atom % {sup 15} N, respectively for velvet beans and sunnhemp. (author)

Radiator-induced erythema ab igne in 8-year-old girl.

Science.gov (United States)

Brzezinski, Piotr; Ismail, Samir; Chiriac, Anca

2014-04-01

The cutaneous lesion of erythema ab Igne are characterized by a reticulate erythema, hyperpigmentation, fine scaling, epidermal atrophy and telangiectasias, and reticulated erythema. We report a case of erythema ab igne on the hands of a 8-year-old girl, induced by classic homemade radiator.

Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms.

Science.gov (United States)

Plácido, Alexandra; Coelho, Andreia; Abreu Nascimento, Lucas; Gomes Vasconcelos, Andreanne; Fátima Barroso, Maria; Ramos-Jesus, Joilson; Costa, Vladimir; das Chagas Alves Lima, Francisco; Delerue-Matos, Cristina; Martins Ramos, Ricardo; Marani, Mariela M; Roberto de Souza de Almeida Leite, José

2017-07-01

Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody-peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248-1257. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Physical and Mechanical Characteristics of Kevlar Fiber-Reinforced PC/ABS Composites

Directory of Open Access Journals (Sweden)

Kuljira Sujirote

2012-01-01

Full Text Available In this research, the composites between polycarbonate (PC and acrylonitrile-butadiene-styrene (ABS alloy and Kevlar fiber were prepared. The flexural and tensile properties of PC/ABS alloy and its composites were determined using a universal testing machine. The synergistic behavior of flexural modulus was observed for all regions of PC contents, while the synergism of flexural strength and tensile strength were found in some PC contents. It was found that the optimum weight ratio of PC:ABS was 60:40. In the Kevlar Fiber-reinforced PC/ABS composite system at PC:ABS of 60:40, both flexural modulus and strength were increased with matrix contents. Additionally, the flexural strength drastically increased with the matrix content and then reached the maximum value of 167 MPa at the matrix content of 33.4 wt%. The results from peel test, water contact measurement, and scanning electron microscopy (SEM reveal that the interfacial adhesion between the Kevlar fiber and the polymer matrix could be improved by increasing the PC content in the matrix.

Ultra-low-power, class-AB, CMOS four-quadrant current multiplier

NARCIS (Netherlands)

Sawigun, C.; Serdijn, W.A.

2009-01-01

A class-AB four-quadrant current multiplier constituted by a class-AB current amplifier and a current splitter which can handle input signals in excess of ten times the bias current is presented. The proposed circuit operation is based on the exponential characteristic of BJTs or subthreshold

Stacking stability of MoS2 bilayer: An ab initio study

International Nuclear Information System (INIS)

Tao Peng; Guo Huai-Hong; Yang Teng; Zhang Zhi-Dong

2014-01-01

The study of the stacking stability of bilayer MoS 2 is essential since a bilayer has exhibited advantages over single layer MoS 2 in many aspects for nanoelectronic applications. We explored the relative stability, optimal sliding path between different stacking orders of bilayer MoS 2 , and (especially) the effect of inter-layer stress, by combining first-principles density functional total energy calculations and the climbing-image nudge-elastic-band (CI-NEB) method. Among five typical stacking orders, which can be categorized into two kinds (I: AA, AB and II: AA', AB', A'B), we found that stacking orders with Mo and S superposing from both layers, such as AA' and AB, is more stable than the others. With smaller computational efforts than potential energy profile searching, we can study the effect of inter-layer stress on the stacking stability. Under isobaric condition, the sliding barrier increases by a few eV/(ucGPa) from AA' to AB', compared to 0.1 eV/(ucGPa) from AB to [AB]. Moreover, we found that interlayer compressive stress can help enhance the transport properties of AA'. This study can help understand why inter-layer stress by dielectric gating materials can be an effective means to improving MoS 2 on nanoelectronic applications. (condensed matter: structural, mechanical, and thermal properties)

Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection.

Science.gov (United States)

Tweedy, Joshua; Spyrou, Maria Alexandra; Pearson, Max; Lassner, Dirk; Kuhl, Uwe; Gompels, Ursula A

2016-01-15

Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated "CiHHV-6A/B". These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, implying functional non-defective genomes. To further define the relationship between HHV-6A and CiHHV-6A we used next-generation sequencing to characterize genomes from three CiHHV-6A cardiac patients. Comparisons to known exogenous HHV-6A showed CiHHV-6A genomes formed a separate clade; including all 85 non-interrupted genes and necessary cis-acting signals for reactivation as infectious virus. Greater single nucleotide polymorphism (SNP) density was defined in 16 genes and the direct repeats (DR) terminal regions. Using these SNPs, deep sequencing analyses demonstrated superinfection with exogenous HHV-6A in two of the CiHHV-6A patients with recurrent cardiac disease. Characterisation of the integration sites in twelve patients identified the human chromosome 17p subtelomere as a prevalent site, which had specific repeat structures and phylogenetically related CiHHV-6A coding sequences indicating common ancestral origins. Overall CiHHV-6A genomes were similar, but distinct from known exogenous HHV-6A virus, and have the capacity to reactivate as emerging virus infections.

Genome Sequence of the Lager-Brewing Yeast Saccharomyces sp. Strain M14, Used in the High-Gravity Brewing Industry in China.

Science.gov (United States)

Liu, Chunfeng; Li, Qi; Niu, Chengtuo; Zheng, Feiyun; Li, Yongxian; Zhao, Yun; Yin, Xiangsheng

2017-10-26

Lager-brewing yeasts are mainly used for the production of lager beers. Illumina and PacBio-based sequence analyses revealed an approximate genome size of 22.8 Mb, with a GC content of 38.98%, for the Chinese lager-brewing yeast Saccharomyces sp. strain M14. Based on ab initio prediction, 9,970 coding genes were annotated. Copyright © 2017 Liu et al.

Production and characterization of monoclonal antibodies (mAbs) against human serum albumin (HSA) for the development of an immunoaffinity system with oriented anti-HSA mAbs as immobilized ligand.

Science.gov (United States)

Rajak, Poonam; Vijayalakshmi, M A; Jayaprakash, N S

2013-05-05

Proteins present in human serum are of immense importance in the field of biomarker discovery. But, the presence of high-abundant proteins like albumin makes the analysis more challenging because of masking effect on low-abundant proteins. Therefore, removal of albumin using highly specific monoclonal antibodies (mAbs) can potentiate the discovery of low-abundant proteins. In the present study, mAbs against human serum albumin (HSA) were developed and integrated in to an immunoaffinity based system for specific removal of albumin from the serum. Hybridomas were obtained by fusion of Sp2/0 mouse myeloma cells with spleen cells from the mouse immunized with HSA. Five clones (AHSA1-5) producing mAbs specific to HSA were established and characterized by enzyme linked immunosorbent assay (ELISA) and immunoblotting for specificity, sensitivity and affinity in terms of antigen binding. The mAbs were able to bind to both native albumin as well as its glycated isoform. Reactivity of mAbs with different mammalian sera was tested. The affinity constant of the mAbs ranged from 10(8) to 10(9)M(-1). An approach based on oriented immobilization was followed to immobilize purified anti-HSA mAbs on hydrazine activated agarose gel and the dynamic binding capacity of the column was determined. Copyright © 2013 Elsevier B.V. All rights reserved.

Ab initio study of ortho-meta-isomerism of Li4AB3+ ions of nitrite and phosphite oxo- and thiosalts (A=N, P; B=O, S)

International Nuclear Information System (INIS)

Charkin, O.D.; MakKi, M.L.; Charkin, O.P.

2000-01-01

In the framework of MP2(6-31*//HF/6-31G + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations ab initio calculations of surfaces of potential energy of Li 4 NO 3 + , Li 4 PO 3 + , Li 4 NS 3 + , LiPS 3 + ions and Li 3 NO 3 , Li 3 PO 3 , Li 3 NS 3 , Li 3 PS 3 molecules of lithium oxo-and thiosalts with 26 valent electrons. Several low-level energy local minimums are determined for each of these ions including (Li + ) 4 ·AB 3 3- ortho-structure of C 3V symmetry with pyramidal three-charge AB 3 3- anion and totality of meta-structures of L + ·AB 2 - ·BL 3 + ion type and AB 2 - ·BL 4 2+ ion pair of C 2V and C s symmetry with onium OLi 3 + , OLi 4 2+ cations or their thio-analogues. Equilibrium geometric parameters and relative energy of isomers, energy of different channels of decomposition, frequencies and IR-intensities of normal vibrations, characteristics of electron density distribution are determined [ru

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Effect of gamma irradiation on nutritional components and Cry1Ab protein in the transgenic rice with a synthetic cry1Ab gene from Bacillus thuringiensis

International Nuclear Information System (INIS)

Wu Dianxing; Ye Qingfu; Wang Zhonghua; Xia Yingwu

2004-01-01

The effects of gamma irradiation on the transgenic rice containing a synthetic cry1Ab gene from Bacillus thuringiensis were investigated. There was almost no difference in the content of the major nutritional components, i.e. crude protein, crude lipid, eight essential amino acids and total ash between the irradiated grains and the non-irradiated transgenic rice. However, the amounts of Cry1Ab protein and apparent amylose in the irradiated transgenic rice were reduced significantly by the doses higher than 200 Gy. In vivo observation showed that Cry1Ab protein contents also decreased in the fresh leaf tissues of survival seedlings after irradiation with 200 Gy or higher doses and showed inhibition of seedling growth. The results indicate that gamma irradiation might improve the quality of transgenic rice due to removal of the toxic Cry1Ab protein

Ab Initio Calculation of Hyperfine Interaction Parameters: Recent Evolutions, Recent Examples

International Nuclear Information System (INIS)

Cottenier, Stefaan; Vanhoof, Veerle; Torumba, Doru; Bellini, Valerio; Cakmak, Mehmet; Rots, Michel

2004-01-01

For some years already, ab initio calculations based on Density Functional Theory (DFT) belong to the toolbox of the field of hyperfine interaction studies. In this paper, the standard ab initio approach is schematically sketched. New features, methods and possibilities that broke through during the past few years are listed, and their relation to the standard approach is explained. All this is illustrated by some highlights of recent ab initio work done by the Nuclear Condensed Matter Group at the K.U.Leuven.

Extraction of Proteins with ABS

NARCIS (Netherlands)

Desai, R.K.; Streefland, M.; Wijffels, R.H.; Eppink, M.H.M.

2016-01-01

Over the past years, there has been an increasing trend in research on the extraction and purification of proteins using aqueous biphasic systems (ABS) formed by polymers, e.g., polyethylene glycol (PEG). In general, when dealing with protein purification processes, it is essential to maintain their

Impact of mixed low-molecular-weight organic acids on uranium accumulation and distribution in a variant of mustard (Brassica juncea var. tumida)

International Nuclear Information System (INIS)

Fangfang Qi; Dingna Wang; Lijian Ma; Yongdong Jin; Liang Du; Dong Zhang; Chuanqin Xia; Sichuan University, Chengdu

2014-01-01

The impact of a mixture of low-molecular-weight organic acids (LMWOAs) composed of CA/MA/OA/LA with a molar ratio of 2.5:2.31:1.15:0.044 on uranium (U) accumulation and distribution in mustard (Brassica juncea var. tumida) was studied in this paper in order to understand the mechanism of rhizosphere-exudation assisted phytoremediation by hydroponic and pot culture experiments. The impact of the mixture of LWMOAs (Mix) on U accumulation showed that in hydroponic conditions Mix could enhance U translocation from root-to-shoot in mustard, but inhibit U uptake in root. In pot experiments, Mix enhanced both root and shoot U accumulation in mustard. The time-dependent kinetics of U uptake in mustard on Mix treatment showed that U content in plant shoots and roots increased with time increasing, and the steady state conditions were obtained at the 8th and 5th day with the U content of 1,528 and 2,300 mg/kg, respectively. Transmission electron microscope and energy dispersive X-ray spectrometry analysis for mustard roots showed that U was mainly observed on cell membrane of mustard roots on Mix treatment. This study would provide new insights for the mixture of LWMOAs-assisted phytoremediation of U-contaminated soil. (author)

Comparative Study of Electroless Copper Film on Different Self-Assembled Monolayers Modified ABS Substrate

Directory of Open Access Journals (Sweden)

Jiushuai Xu

2014-04-01

Full Text Available Copper films were grown on (3-Mercaptopropyltrimethoxysilane (MPTMS, (3-Aminopropyltriethoxysilane (APTES and 6-(3-(triethoxysilylpropylamino-1,3,5- triazine-2,4-dithiol monosodium (TES self-assembled monolayers (SAMs modified acrylonitrile-butadiene-styrene (ABS substrate via electroless copper plating. The copper films were examined using scanning electron microscopy (SEM and X-ray diffraction (XRD. Their individual deposition rate and contact angle were also investigated to compare the properties of SAMs and electroless copper films. The results indicated that the formation of copper nuclei on the TES-SAMs modified ABS substrate was faster than those on the MPTMS-SAMs and APTES-SAMs modified ABS substrate. SEM images revealed that the copper film on TES-SAM modified ABS substrate was smooth and uniform, and the density of copper nuclei was much higher. Compared with that of TES-SAMs modified resin, the coverage of copper nuclei on MPTMS and APTES modified ABS substrate was very limited and the copper particle size was too big. The adhesion property test demonstrated that all the SAMs enhanced the interfacial interaction between copper plating and ABS substrate. XRD analysis showed that the copper film deposited on SAM-modified ABS substrate had a structure with Cu(111 preferred orientation, and the copper film deposited on TES-SAMs modified ABS substrate is better than that deposited on MPTMS-SAMs or APTES-SAMs modified ABS resins in electromigrtion resistance.

A Case of Laptop Computer-Induced Erythema Ab Igne

Directory of Open Access Journals (Sweden)

Nurettin Özgür Doğan

2014-12-01

Full Text Available Erythema ab igne, also known as toasted skin syndrome, is a skin reaction characterized by reticulate erythema, brown pigmentation, and telangiectasia. In some cases, epidermal atrophy and scaling are also identified. The condition is usually caused by prolonged exposure to a source of heat or infrared radiation. Here, we report a case of erythema ab igne associated with laptop computer use.

Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

Energy Technology Data Exchange (ETDEWEB)

Bernard, St

1998-12-31

The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

Energy Technology Data Exchange (ETDEWEB)

Bernard, St

1999-12-31

The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

Science.gov (United States)

2012-01-01

Background Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event. Results We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp. Conclusions The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future. PMID:22424280

Modeling Disordered Materials with a High Throughput ab-initio Approach

Science.gov (United States)

2015-11-13

Modeling Disordered Materials with a High Throughput ab - initio Approach Kesong Yang,1 Corey Oses,2 and Stefano Curtarolo3, 4 1Department of...J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54, 11169–11186 (1996

Embedded atom approach for gold–silicon system from ab initio

Indian Academy of Sciences (India)

In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...

Ab initio potential for solids

DEFF Research Database (Denmark)

Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel

1992-01-01

. At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...

Diffusion of hydrogen interstitials in Zr based AB2 and mischmetal based AB5 alloys

International Nuclear Information System (INIS)

Mani, N; Ravi, N; Ramaprabhu, S

2005-01-01

The Zr based AB 2 alloys ZrMnFe 0.5 Ni 0.5 , ZrMnFe 0.5 Co 0.5 and mischmetal (Mm) based AB 5 alloy MmNi 3.5 Al 0.5 Fe 0.5 Co 0.5 have been prepared and characterized by means of powder x-ray diffractograms. The hydrogen absorption kinetics of these alloys have been studied in the temperature and pressure ranges 450-650 0 C and 10-100 mbar respectively with a maximum H to host alloy formula unit ratio of 0.01, using a pressure reduction technique. The diffusion coefficient of the hydrogen interstitials has been determined from hydrogen absorption kinetics experiments. The dependence of the diffusion coefficient on the alloy content has been discussed. For Mm based MmNi 3.5 Al 0.5 Fe 0.5 Co 0.5 alloy, the diffusion coefficient is about an order of magnitude higher than that of the Zr based alloys

Student Measurements of STFA 10AB (Theta Tauri)

Science.gov (United States)

Gillette, Sean; Estrada, Chris; Estrada, Reed; Aguilera, Sophia; Chavez, Valerie; Givens, Jalynn; Lindorfer, Sarah; Michels, Kaylie; Mobley, Makenzie; Reder, Gabriel; Renteria, Kayla; Shattles, Jenna; Wilkin, Aiden; Woodbury, Maisy; Rhoades, Breauna; Rhoades, Mark

2017-04-01

Eighth grade students at Vanguard Preparatory School measured the double star STFA 10AB using a 22-inch Newtonian Alt/Az telescope and a Celestron Micro Guide eyepiece. Bellatrix was used as the calibration star. The calculated means of multiple observations of STFA 10AB resulted in a separation of 45.18,” a scale constant of 7.88 arcseconds per division, and position angle of 257.9°. These measurements were compared to the most recent values in the Washington Double Star Catalog.

Numerical evaluation of ABS parts fabricated by fused deposition modeling and vapor smoothing

Directory of Open Access Journals (Sweden)

Sung-Uk Zhang

2017-12-01

Full Text Available The automotive industry has focused to use polymer materials in order to increase energy efficiency. So, the industry pays attention to use 3D printing technologies using several polymers. Among several 3D printer technologies, fused deposition modeling (FDM is one of the popular 3D printing technologies due to an inexpensive extrusion machine and multi-material printing. FDM could use thermoplastics such as ABS, PLA, ULTEM so on. However, it has a problem related to the post-processing because FDM has relatively poor layer resolution. In this study, the mechanical properties of ABS parts fabricated by FDM were measured. The ABS parts were divided into one with vapor smoothing process and the other without the vapor smoothing process which is one of the post-processing methods. Using dynamic mechanical analysis (DMA and dilatometer, temperature-dependent storage modulus and CTE for ABS specimens were measured. Based on the measured thermo-mechanical properties of ABS parts, finite element analysis was performed for an automotive bumper made of ABS. Moreover, response surface methodology was applied to study relationships among design parameters of thickness of the bumper, ambient temperature, and application of the vapor smoothing process. In result, a design guideline for a ABS product could be provided without time-consuming experiments

Influence of Cellulose on the Mechanical and Thermal Stability of ABS Plastic Composites

Directory of Open Access Journals (Sweden)

K. Crews

2016-01-01

Full Text Available Microcrystalline cellulose was explored as possible biodegradable fillers in the fabrication of ABS plastic composites. TGA indicates that upon inclusion of cellulose microcrystals the thermal stability of the ABS plastics was improved significantly when compared to the neat ABS plastic counterparts. Furthermore, inclusion of extracted cellulose from plant biomass showed a higher thermal stability with maximum decomposition temperatures around 131.95°C and 124.19°C for cellulose from cotton and Hibiscus sabdariffa, respectively, when compared to that of the purchased cellulose. In addition, TMA revealed that the average CTE value for the neat ABS and 1 : 1 ratio of cellulose to ABS fabricated in this study was significantly lower than the reported CTE (ca. 73.8 μm/m°C.

Multicapillary SDS-gel electrophoresis for the analysis of fluorescently labeled mAb preparations: a high throughput quality control process for the production of QuantiPlasma and PlasmaScan mAb libraries.

Science.gov (United States)

Székely, Andrea; Szekrényes, Akos; Kerékgyártó, Márta; Balogh, Attila; Kádas, János; Lázár, József; Guttman, András; Kurucz, István; Takács, László

2014-08-01

Molecular heterogeneity of mAb preparations is the result of various co- and post-translational modifications and to contaminants related to the production process. Changes in molecular composition results in alterations of functional performance, therefore quality control and validation of therapeutic or diagnostic protein products is essential. A special case is the consistent production of mAb libraries (QuantiPlasma™ and PlasmaScan™) for proteome profiling, quality control of which represents a challenge because of high number of mAbs (>1000). Here, we devise a generally applicable multicapillary SDS-gel electrophoresis process for the analysis of fluorescently labeled mAb preparations for the high throughput quality control of mAbs of the QuantiPlasma™ and PlasmaScan™ libraries. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sorbitol crystallization-induced aggregation in frozen mAb formulations.

Science.gov (United States)

Piedmonte, Deirdre Murphy; Hair, Alison; Baker, Priti; Brych, Lejla; Nagapudi, Karthik; Lin, Hong; Cao, Wenjin; Hershenson, Susan; Ratnaswamy, Gayathri

2015-02-01

Sorbitol crystallization-induced aggregation of mAbs in the frozen state was evaluated. The effect of protein aggregation resulting from sorbitol crystallization was measured as a function of formulation variables such as protein concentration and pH. Long-term studies were performed on both IgG1 and IgG2 mAbs over the protein concentration range of 0.1-120 mg/mL. Protein aggregation was measured by size-exclusion HPLC (SE-HPLC) and further characterized by capillary-electrophoresis SDS. Sorbitol crystallization was monitored and characterized by subambient differential scanning calorimetry and X-ray diffraction. Aggregation due to sorbitol crystallization is inversely proportional to both protein concentration and formulation pH. At high protein concentrations, sorbitol crystallization was suppressed, and minimal aggregation by SE-HPLC resulted, presumably because of self-stabilization of the mAbs. The glass transition temperature (Tg ') and fragility index measurements were made to assess the influence of molecular mobility on the crystallization of sorbitol. Tg ' increased with increasing protein concentration for both mAbs. The fragility index decreased with increasing protein concentration, suggesting that it is increasingly difficult for sorbitol to crystallize at high protein concentrations. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Ab interno trabeculectomy: ultrastructural evidence and early tissue response in a human eye.

Science.gov (United States)

Ferrari, Ettore; Ortolani, Fulvia; Petrelli, Lucia; Contin, Magali; Pognuz, Derri Roman; Marchini, Maurizio; Bandello, Francesco

2007-10-01

To report the results of ultrastructural analysis of the postoperative effects of ab interno trabeculectomy in a human eye. Department of Ophthalmology, Palmanova Hospital, Palmanova, Udine, Italy. A 60-year-old woman with cataract and glaucoma had enucleation for a choroidal melanoma 10 days after ab interno trabeculectomy combined with phacoemulsification. A second ab interno trabeculectomy was performed after enucleation to evaluate the outcomes of the previous trabeculectomy. Light and transmission electron microscopy analyses were performed on samples excised from areas (1) not subjected to a procedure (control samples), (2) that had ab interno trabeculectomy before enucleation, and (3) that had ab interno trabeculectomy immediately after enucleation. Control samples showed normal trabecular features. Semithin sections of all ab interno trabeculectomy samples showed full-thickness removal of trabeculum segments, with Schlemm's canal lumen opening into the anterior chamber and apparent preservation of the adjacent structures. On ultrathin sections of samples that had ab interno trabeculectomy before enucleation, the endothelium lining the outer wall of Schlemm's canal and other angle components showed intact ultrastructural features. In trabecular beams that were not removed, the extracellular matrix appeared to have maintained its fine texture and was free of activated fibroblasts or leucocyte infiltrates. Observations confirm that ab interno trabeculectomy causes direct communication between Schlemm's canal lumen and the anterior chamber in vivo and immediately after enucleation during the early postoperative period. The absence of an evident inflammatory reaction in the examined case should be considered with caution because of possible tumor-induced immune suppression.

Rescue of failed filtering blebs with ab interno trephination.

Science.gov (United States)

Shihadeh, Wisam A; Ritch, Robert; Liebmann, Jeffrey M

2006-06-01

We evaluated the effectiveness of ab interno automated trephination as a technique for rescuing failed mature filtering blebs. A retrospective chart review of 40 failed blebs of 38 patients who had a posttrephination follow-up period of at least 3 months was done. With success defined as intraocular pressure (IOP) control with other modalities of management. Complications were few. We believe that ab interno trephination is an excellent option for rescuing selected failed filtering blebs.

Transport of Cd and Zn to seeds of Indian mustard (Brassica juncea) during specific stages of plant growth and development.

Science.gov (United States)

Sankaran, Renuka P; Ebbs, Stephen D

2008-01-01

The accumulation of excess Cd in the seeds of cereal and other crops compromises their commercial value and presents a potential risk to human health. Indian mustard [Brassica juncea (L.) Czern.] is a moderate accumulator of heavy metals such as Cd and Zn, and the seeds are consumed throughout the world, particularly in the Indian subcontinent. The study here examined the transport of Cd into Indian mustard plants and to seeds as a function of external Cd and the stage of the life cycle (vegetative growth, flowering and seed set) to identify critical developmental windows where transport from roots to seeds was the greatest. Plants were also treated simultaneously with Zn to determine if Zn fertilization mitigated the transport of Cd to seeds. Plants treated with Cd during the seed set accumulated the highest concentrations of Cd, exceeding 8 mg kg(-1) dry weight in some instances. Cadmium accumulated during vegetative growth was not highly redistributed to seeds. No effects of Zn were observed with regard to Cd redistribution to seeds. This may be because of the relatively small Zn : Cd ratios tested. However, the results suggest that if Zn fertilization is to be used to reduce the Cd accumulation in seeds of this species, that plants should be treated during the seed set stage. As the seeds of Indian mustard consistently accumulated Cd to concentrations that exceed acceptable limits for food crops, additional study of Cd redistribution in this species is warranted.

Gas atomization of Cu-modified AB5 metal hydride alloys

International Nuclear Information System (INIS)

Young, K.; Ouchi, T.; Banik, A.; Koch, J.; Fetcenko, M.A.; Bendersky, L.A.; Wang, K.; Vaudin, M.

2011-01-01

Research highlights: → The gas atomization process together with a hydrogen annealing process was demonstrated on AB5 alloys. → The method was found to be effective in restoring the original cycle life sacrificed by the incorporation of copper in the alloy formula as a means of improving the low temperature performance of AB 5 alloys. → The new process also improves high rate, low temperature, and charge retention performances for both Cu-free and Cu-containing AB 5 alloys. - Abstract: Gas atomization together with a hydrogen annealing process has been proposed as a method to achieve improved low-temperature performance of AB 5 alloy electrodes in Ni/MH batteries and restore the original cycle life which was sacrificed by the incorporation of copper in the alloy formula. While the gas atomization process reduces the lattice constant aspect ratio c/a of the Cu-containing alloys, the addition of a hydrogen annealing step recovers this property, although it is still inferior to the conventionally prepared annealed Cu-free alloy. This observation correlates very well with the cycle life performance. In addition to extending the cycle life of the Cu-containing metal hydride electrode, processing by gas atomization with additional hydrogen annealing improves high-rate, low-temperature, and charge retention performances for both Cu-free and Cu-containing AB 5 alloys. The degradation mechanisms of alloys made by different processes through cycling are also discussed.

Phytoextraction and accumulation of mercury in three plant species: Indian mustard (Brassica juncea), beard grass (Polypogon monospeliensis), and Chinese brake fern (Pteris vittata).

Science.gov (United States)

Su, Yi; Han, Fengxiang X; Chen, Jian; Sridhar, B B Maruthi; Monts, David L

2008-01-01

The objective of this research was to screen and search for suitable plant species to phytoextract mercury-contaminated soil. Our effort focused on using some of the known metal-accumulating wild-type plants since no natural plant species with mercury-hyperaccumulat ing properties has yet been identified. Three plant species were evaluated for their uptake efficiency for mercury: Indian mustard (Brassica juncea), beard grass (Polypogon monospeliensis), and Chinese brake fern (Pteris vittata). Four sets of experiments were conducted to evaluate the phytoremediation potential of these three plant species: a pot study with potting mix where mercury was provided daily as HgCl2 solution; experiments with freshly mercury-spiked soil; and a study with aged soils contaminated with different mercury sources (HgCl2, Hg(NO3)2, and HgS). Homemade sunlit chambers were also used to study foliar uptake of Hg from ambient air. Among the three plant species, Chinese brake fern showed the least stress symptoms resulting from mercury exposure and had the highest mercury accumulation. Our results indicate that Chinese brake fern may be a potential candidate for mercury phytoextraction. We found that mercury contamination is biologically available for plant uptake and accumulation, even if the original and predominating mercury form is HgS, and also after multiple phytoremediation cycles.

Thyroglobulin (Tg) Testing Revisited: Tg Assays, TgAb Assays, and Correlation of Results With Clinical Outcomes.

Science.gov (United States)

Netzel, Brian C; Grebe, Stefan K G; Carranza Leon, B Gisella; Castro, M Regina; Clark, Penelope M; Hoofnagle, Andrew N; Spencer, Carole A; Turcu, Adina F; Algeciras-Schimnich, Alicia

2015-08-01

Measurement of thyroglobulin (Tg) by mass spectrometry (Tg-MS) is emerging as a tool for accurate Tg quantification in patients with anti-Tg autoantibodies (TgAbs). The objective of the study was to perform analytical and clinical evaluations of two Tg-MS assays in comparison with immunometric Tg assays (Tg-IAs) and Tg RIAs (Tg-RIAs) in a cohort of thyroid cancer patients. A total of 589 samples from 495 patients, 243 TgAb-/252 TgAb+, were tested by Beckman, Roche, Siemens-Immulite, and Thermo-Brahms Tg and TgAb assays, two Tg-RIAs, and two Tg-MS assays. The frequency of TgAb+ was 58%, 41%, 27%, and 39% for Roche, Beckman, Siemens-Immulite, and Thermo-Brahms, respectively. In TgAb- samples, clinical sensitivities and specificities of 100% and 74%-100%, respectively, were observed across all assays. In TgAb+ samples, all Tg-IAs demonstrated assay-dependent Tg underestimation, ranging from 41% to 86%. In TgAb+ samples, the use of a common cutoff (0.5 ng/mL) for the Tg-MS, three Tg-IAs, and the USC-RIA improved the sensitivity for the Tg-MSs and Tg-RIAs when compared with the Tg-IAs. In up to 20% of TgAb+ cases, Tg-IAs failed to detect Tg that was detectable by Tg-MS. In Tg-RIAs false-high biases were observed in TgAb+ samples containing low Tg concentrations. Tg-IAs remain the method of choice for Tg quantitation in TgAb- patients. In TgAb+ patients with undetectable Tg by immunometric assay, the Tg-MS will detect Tg in up to 20% additional cases. The Tg-RIA will detect Tg in approximately 35% cases, but a significant proportion of these will be clinical false-positive results. The undetectable Tg-MS seen in approximately 40% of TgAb+ cases in patients with disease need further evaluation.

Alleviation of cadmium toxicity in Brassica juncea L. (Czern. & Coss. by calcium application involves various physiological and biochemical strategies.

Directory of Open Access Journals (Sweden)

Parvaiz Ahmad

Full Text Available Calcium (Ca plays important role in plant development and response to various environmental stresses. However, its involvement in mitigation of heavy metal stress in plants remains elusive. In this study, we examined the effect of Ca (50 mM in controlling cadmium (Cd uptake in mustard (Brassica juncea L. plants exposed to toxic levels of Cd (200 mg L(-1 and 300 mg L(-1. The Cd treatment showed substantial decrease in plant height, root length, dry weight, pigments and protein content. Application of Ca improved the growth and biomass yield of the Cd-stressed mustard seedlings. More importantly, the oil content of mustard seeds of Cd-stressed plants was also enhanced with Ca treatment. Proline was significantly increased in mustard plants under Cd stress, and exogenously sprayed Ca was found to have a positive impact on proline content in Cd-stressed plants. Different concentrations of Cd increased lipid peroxidation but the application of Ca minimized it to appreciable level in Cd-treated plants. Excessive Cd treatment enhanced the activities of antioxidant enzymes superoxide dismutase, ascorbate peroxidase and glutathione reductase, which were further enhanced by the addition of Ca. Additionally, Cd stress caused reduced uptake of essential elements and increased Cd accumulation in roots and shoots. However, application of Ca enhanced the concentration of essential elements and decreased Cd accumulation in Cd-stressed plants. Our results indicated that application of Ca enables mustard plant to withstand the deleterious effect of Cd, resulting in improved growth and seed quality of mustard plants.

Characterization of virulence factor regulation by SrrAB, a two-component system in Staphylococcus aureus.

Science.gov (United States)

Pragman, Alexa A; Yarwood, Jeremy M; Tripp, Timothy J; Schlievert, Patrick M

2004-04-01

Workers in our laboratory have previously identified the staphylococcal respiratory response AB (SrrAB), a Staphylococcus aureus two-component system that acts in the global regulation of virulence factors. This system down-regulates production of agr RNAIII, protein A, and toxic shock syndrome toxin 1 (TSST-1), particularly under low-oxygen conditions. In this study we investigated the localization and membrane orientation of SrrA and SrrB, transcription of the srrAB operon, the DNA-binding properties of SrrA, and the effect of SrrAB expression on S. aureus virulence. We found that SrrA is localized to the S. aureus cytoplasm, while SrrB is localized to the membrane and is properly oriented to function as a histidine kinase. srrAB has one transcriptional start site which results in either an srrA transcript or a full-length srrAB transcript; srrB must be cotranscribed with srrA. Gel shift assays of the agr P2, agr P3, protein A (spa), TSST-1 (tst), and srr promoters revealed SrrA binding at each of these promoters. Analysis of SrrAB-overexpressing strains by using the rabbit model of bacterial endocarditis demonstrated that overexpression of SrrAB decreased the virulence of the organisms compared to the virulence of isogenic strains that do not overexpress SrrAB. We concluded that SrrAB is properly localized and oriented to function as a two-component system. Overexpression of SrrAB, which represses agr RNAIII, TSST-1, and protein A in vitro, decreases virulence in the rabbit endocarditis model. Repression of these virulence factors is likely due to a direct interaction between SrrA and the agr, tst, and spa promoters.

Effects of 4WD and ABS of safe driving on slippery roads; Tei {mu} ji ni okeru 4WD to ABS no koka to unten sosa hoho

Energy Technology Data Exchange (ETDEWEB)

Kojima, Y [National Research Inst. of Police Science, Tokyo (Japan); Takigami, K; Asano, K [Japan Safe Driving Center, Tokyo (Japan); Nagai, M [Tokyo University of Agriculture and Technology, Tokyo (Japan)

1997-10-01

Effects of 4WD and ABS on safe driving were examined by brake, obstacle avoidance, acceleration, cornering and lane-changing tests on slippery road. The braking operations, used in these tests, are full, intermitted and modulated brakings. As the results of discussion, the major findings are (1) ABS is effective to shorten the stopping distance and to increase the ability of obstacle avoidance in many cases, (2) `Modulated Braking (without wheel locks)` has the same function as ABS, and (3) 4WD is effective to increase the stability while accelerating, cornering and lane-changing. 5 refs., 6 figs.

Inhibition of cholera toxin and other AB toxins by polyphenolic compounds

Science.gov (United States)

All AB-type protein toxins have intracellular targets despite an initial extracellular location. These toxins use different methods to reach the cytosol and have different effects on the target cell. Broad-spectrum inhibitors against AB toxins are therefore hard to develop because the toxins use dif...

Summation of Parquet diagrams as an ab initio method in nuclear structure calculations

International Nuclear Information System (INIS)

Bergli, Elise; Hjorth-Jensen, Morten

2011-01-01

Research highlights: → We present a Green's function based approach for doing ab initio nuclear structure calculations. → In particular the sum the subset of so-called Parquet diagrams. → Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. → This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.

PirAB Toxin from Photorhabdus asymbiotica as a Larvicide against Dengue Vectors▿

OpenAIRE

Ahantarig, Arunee; Chantawat, Nantarat; Waterfield, Nicholas R.; ffrench-Constant, Richard; Kittayapong, Pattamaporn

2009-01-01

We have evaluated Photorhabdus insect-related protein (Pir) from Photorhabdus asymbiotica against dengue vectors. PirAB shows larvicidal activity against both Aedes aegypti and Aedes albopictus larvae but did not affect the Mesocyclops thermocyclopoides predator. PirAB expressed the strongest toxicity compared to PirA, PirB, or the mixture of PirA plus PirB. Whether the presence of an enterobacterial repetitive intergenic consensus sequence in PirAB, but not in PirA, PirB, or the mixture of P...

Standardiserat arbete i produktionssystemet hos Inission Munkfors AB

OpenAIRE

Jonas, Arnesson

2014-01-01

Sammanfattning Denna rapport behandlar införandet av standardiserat arbete i produktionssystemet hos företaget Inission Munkfors AB. Arbetet har utförts i kursen Examensarbete för högskoleingenjörsexamen i maskinteknik (MSGC17), som ges vid Fakulteten för hälsa, natur & teknikvetenskap på Karlstads universitet.Företaget Inission Munkfors AB har som mål att från år 2012 till år 2017 kunna fördubbla omsättningen och halvera ledtiden, med samma personalstyrka som år 2012 (75st anställda). De...

Neutron Reflection Study of Surface Adsorption of Fc, Fab, and the Whole mAb.

Science.gov (United States)

Li, Zongyi; Li, Ruiheng; Smith, Charles; Pan, Fang; Campana, Mario; Webster, John R P; van der Walle, Christopher F; Uddin, Shahid; Bishop, Steve M; Narwal, Rojaramani; Warwicker, Jim; Lu, Jian Ren

2017-07-12

Characterizing the influence of fragment crystallization (Fc) and antigen-binding fragment (Fab) on monoclonal antibody (mAb) adsorption at the air/water interface is an important step to understanding liquid mAb drug product stability during manufacture, shipping, and storage. Here, neutron reflection is used to study the air/water adsorption of a mAb and its Fc and Fab fragments. By varying the isotopic contrast, the adsorbed amount, thickness, orientation, and immersion of the adsorbed layers could be determined unambiguously. While Fc adsorption reached saturation within the hour, its surface adsorbed amount showed little variation with bulk concentration. In contrast, Fab adsorption was slower and the adsorbed amount was concentration dependent. The much higher Fc adsorption, as compared to Fab, was linked to its lower surface charge. Time and concentration dependence of mAb adsorption was dominated by Fab behavior, although both Fab and Fc behaviors contributed to the amount of mAb adsorbed. Changing the pH from 5.5 to 8.8 did not much perturb the adsorbed amount of Fc, Fab, or mAb. However, a small decrease in adsorption was observed for the Fc over pH 8-8.8 and vice versa for the Fab and mAb, consistent with a dominant Fab behavior. As bulk concentration increased from 5 to 50 ppm, the thicknesses of the Fc layers were almost constant at 40 Å, while Fab and mAb layers increased from 45 to 50 Å. These results imply that the adsorbed mAb, Fc, and Fab all retained their globular structures and were oriented with their short axial lengths perpendicular to the interface.

The combined benefits of motorcycle antilock braking systems (ABS) in preventing crashes and reducing crash severity.

Science.gov (United States)

Rizzi, Matteo; Kullgren, Anders; Tingvall, Claes

2016-01-01

Several studies have reported the benefits of motorcycle antilock braking systems (ABS) in reducing injury crashes, due to improved stability and braking performance. Both aspects may prevent crashes but may also reduce the crash severity when a collision occurs. However, it is still unknown to what extent the reductions in injury crashes with ABS may be due to a combination of these mechanisms. Swedish hospital and police reports (2003-2012) were used. The risk for permanent medical impairment (RPMI) was calculated, showing the risk of at least 1 or 10% permanent medical impairment. In total, 165 crashes involving ABS-equipped motorcycles were compared with 500 crashes with similar motorcycles without ABS. The analysis was performed in 3 steps. First, the reduction in emergency care visits with ABS was calculated using an induced exposure approach. Secondly, the injury mitigating effects of ABS were investigated. The mean RPMI 1+ and RPMI 10+ were analyzed for different crash types. The distributions of impairing injuries (PMI 1+) and severely impairing injuries (PMI 10+) were also analyzed. In the third step, the total reduction of PMI 1+ and PMI 10+ injured motorcyclists was calculated by combining the reductions found in the previous steps. An additional analysis of combined braking systems (CBS) together with ABS was also performed. The results showed that emergency care visits were reduced by 47% with ABS. In the second step, it was found that the mean RPMI 1+ and RPMI 10+ with ABS were 15 and 37% lower, respectively. Finally, the third step showed that the total reductions in terms of crash avoidance and mitigation of PMI 1+ and PMI 10+ injured motorcyclists with ABS were 67 and 55%, respectively. However, PMI 1+ and PMI 10+ leg injuries were not reduced by ABS to the same extent. Indications were found suggesting that the benefits of ABS together with CBS may be greater than ABS alone. This article indicated that motorcycle ABS reduced impairing injuries

Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles.

Science.gov (United States)

Longkumer, Toshisangba; Kamireddy, Swetha; Muthyala, Venkateswar Reddy; Akbarpasha, Shaikh; Pitchika, Gopi Krishna; Kodetham, Gopinath; Ayaluru, Murali; Siddavattam, Dayananda

2013-01-01

While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002.

Report on the Personnel Dosimetry at AB Atomenergi during 1965

Energy Technology Data Exchange (ETDEWEB)

Edvardsson, K A

1966-10-15

This report presents the results of the personnel dosimetry at AB Atomenergi during 1965. No doses exceeding the recommendations of ICRP were reported. For AB Atomenergi the average external total body dose during the year was 60 mrem which corresponds to 89.4 manrem. 31200 gamma films and 5850 neutron films were evaluated. 2067 urine analyses and 692 measurements of body activity were made.

Report on the Personnel Dosimetry at AB Atomenergi during 1965

International Nuclear Information System (INIS)

Edvardsson, K.A.

1966-10-01

This report presents the results of the personnel dosimetry at AB Atomenergi during 1965. No doses exceeding the recommendations of ICRP were reported. For AB Atomenergi the average external total body dose during the year was 60 mrem which corresponds to 89.4 manrem. 31200 gamma films and 5850 neutron films were evaluated. 2067 urine analyses and 692 measurements of body activity were made

Radiolabeled F(ab')2-cetuximab for theranostic purposes in colorectal and skin tumor-bearing mice models.

Science.gov (United States)

Bellaye, P-S; Moreau, M; Raguin, O; Oudot, A; Bernhard, C; Vrigneaud, J-M; Dumont, L; Vandroux, D; Denat, F; Cochet, A; Brunotte, F; Collin, B

2018-05-17

This study aimed to investigate theranostic strategies in colorectal and skin cancer based on fragments of cetuximab, an anti-EGFR mAb, labeled with radionuclide with imaging and therapeutic properties, 111 In and 177 Lu, respectively. We designed F(ab') 2 -fragments of cetuximab radiolabeled with 111 In and 177 Lu. 111 In-F(ab') 2 -cetuximab tumor targeting and biodistribution were evaluated by SPECT in BalbC nude mice bearing primary colorectal tumors. The efficacy of 111 In-F(ab') 2 -cetuximab to assess therapy efficacy was performed on BalbC nude mice bearing colorectal tumors receiving 17-DMAG, an HSP90 inhibitor. Therapeutic efficacy of the radioimmunotherapy based on 177 Lu-F(ab') 2 -cetuximab was evaluated in SWISS nude mice bearing A431 tumors. Radiolabeling procedure did not change F(ab') 2 -cetuximab and cetuximab immunoreactivity nor affinity for HER1 in vitro. 111 In-DOTAGA-F(ab') 2 -cetuximab exhibited a peak tumor uptake at 24 h post-injection and showed a high tumor specificity determined by a significant decrease in tumor uptake after the addition of an excess of unlabeled-DOTAGA-F(ab') 2 -cetuximab. SPECT imaging of 111 In-DOTAGA-F(ab') 2 -cetuximab allowed an accurate evaluation of tumor growth and successfully predicted the decrease in tumor growth induced by 17-DMAG. Finally, 177 Lu-DOTAGA-F(ab') 2 -cetuximab radioimmunotherapy showed a significant reduction of tumor growth at 4 and 8 MBq doses. 111 In-DOTAGA-F(ab') 2 -cetuximab is a reliable and stable tool for specific in vivo tumor targeting and is suitable for therapy efficacy assessment. 177 Lu-DOTAGA-F(ab') 2 -cetuximab is an interesting theranostic tool allowing therapy and imaging.

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

2010-03-22

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

Bacteria–zinc co-localization implicates enhanced synthesis of cysteine-rich peptides in zinc detoxification when Brassica juncea is inoculated with Rhizobium leguminosarum

Science.gov (United States)

Adediran, Gbotemi A; Ngwenya, Bryne T; Mosselmans, J Frederick W; Heal, Kate V

2016-01-01

Some plant growth promoting bacteria (PGPB) are enigmatic in enhancing plant growth in the face of increased metal accumulation in plants. Since most PGPB colonize the plant root epidermis, we hypothesized that PGPB confer tolerance to metals through changes in speciation at the root epidermis. We employed a novel combination of fluorophore-based confocal laser scanning microscopic imaging and synchrotron based microscopic X-ray fluorescence mapping with X-ray absorption spectroscopy to characterize bacterial localization, zinc (Zn) distribution and speciation in the roots of Brassica juncea grown in Zn contaminated media (400 mg kg−1 Zn) with the endophytic Pseudomonas brassicacearum and rhizospheric Rhizobium leguminosarum. PGPB enhanced epidermal Zn sequestration relative to PGBP-free controls while the extent of endophytic accumulation depended on the colonization mode of each PGBP. Increased root accumulation of Zn and increased tolerance to Zn was associated predominantly with R. leguminosarum and was likely due to the coordination of Zn with cysteine-rich peptides in the root endodermis, suggesting enhanced synthesis of phytochelatins or glutathione. Our mechanistic model of enhanced Zn accumulation and detoxification in plants inoculated with R. leguminosarum has particular relevance to PGPB enhanced phytoremediation of soils contaminated through mining and oxidation of sulphur-bearing Zn minerals or engineered nanomaterials such as ZnS. PMID:26263508

YaxAB, a Yersinia enterocolitica Pore-Forming Toxin Regulated by RovA

Science.gov (United States)

Wagner, Nikki J.; Lin, Carolina P.; Borst, Luke B.

2013-01-01

The transcriptional regulator RovA positively regulates transcription of the Yersinia enterocolitica virulence gene inv. Invasin, encoded by inv, is important for establishment of Y. enterocolitica infection. However, a rovA mutant is more attenuated for virulence than an inv mutant, implying that RovA regulates additional virulence genes. When the Y. enterocolitica RovA regulon was defined by microarray analysis, YE1984 and YE1985 were among the genes identified as being upregulated by RovA. Since these genes are homologous to Xenorhabdus nematophila cytotoxin genes xaxA and xaxB, we named them yaxA and yaxB, respectively. In this work, we demonstrate the effects of YaxAB on the course of infection in the murine model. While a yaxAB mutant (ΔyaxAB) is capable of colonizing mice at the same level as the wild type, it slightly delays the course of infection and results in differing pathology in the spleen. Further, we found that yaxAB encode a probable cytotoxin capable of lysing mammalian cells, that both YaxA and YaxB are required for cytotoxic activity, and that the two proteins associate. YaxAB-mediated cell death occurs via osmotic lysis through the formation of distinct membrane pores. In silico tertiary structural analysis identified predicted structural homology between YaxA and proteins in pore-forming toxin complexes from Bacillus cereus (HBL-B) and Escherichia coli (HlyE). Thus, it appears that YaxAB function as virulence factors by inducing cell lysis through the formation of pores in the host cell membrane. This characterization of YaxAB supports the hypothesis that RovA regulates expression of multiple virulence factors in Y. enterocolitica. PMID:24002058

Monte Carlo simulation of AB-copolymers with saturating bonds

CERN Document Server

Chertovich, A V; Khokhlov, A R; Bohr, J

2003-01-01

Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A-and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending on the nature of a particular AB-sequence: statistical random sequence, diblock sequence and 'random-complementary' sequence (one-half of such an AB-sequence is random with Bernoulli statistics while the other half is complementary to the first one). The properties of random-complementary sequences are closer to those of diblock sequences than to the properties of random sequences. The model (although quite rough) is expected to represent some basic features of real RNA molecules, i.e. the formation of secondary structure of RNA due to hydrogen bonding of corresponding bases and stacking interactions of the base pairs in helixes. We introduce the notation of RNA-like copolymers and discuss in what sense the sequences studie...

Imam et Mahdi : Ibn Abî Mahallî

Directory of Open Access Journals (Sweden)

Mercedes García-Arenal

2009-05-01

Full Text Available Ibn Abî Mahallî (m. 1613 est le dernier mahdi maghrébin à avoir pris le pouvoir. Je fais usage dans cet article, de trois types de sources : les œuvres d'Ibn Abî Mahallî lui-même, les sources arabes contemporaines et postérieures, soutenant toujours le pouvoir dynastique régnant et, troisièmement, les documents d'archive européens écrits par des observateurs et des voyageurs contemporains. Cette variété de sources permet de tracer le spectre qui va depuis les attentes et les croyances populaires des adeptes, jusqu'à la personne et à l'élaboration doctrinale d'Ibn Abî Mahallî. J'ai donc tenté de percevoir quelles parties ou aspects d'une pensée individuelle arrivent à acquérir, et de quelle manière, une légitimité publique, en se transformant en même temps.

Studies on the runaway reaction of ABS polymerization process

International Nuclear Information System (INIS)

Hu, K.-H.; Kao, C.-S.; Duh, Y.-S.

2008-01-01

Taiwan has the largest acrylonitrile-butadiene-styrene (ABS) copolymer production in the world. Preventing on unexpected exothermic reactions and related emergency relief hazard is essential in the safety control of ABS emulsion polymerization. A VSP2 (Vent Sizing Package 2) apparatus is capable of studying both normal and abnormal conditions (e.g., cooling failure, mischarge, etc.) of industrial process. In this study, the scenarios were verified from the following abnormal conditions: loss of cooling, double charge of initiator, overcharge of monomer, without charge of solvent, and external fire. An external fire with constant heating will promote higher self-heat rate and this is recommended as the worst case scenario of emulsion polymerization on butadiene. Cooling failure coupled with bulk system of reactant was determined to be the credible worst case in ABS emulsion polymerization. Finally, the emergency vent sizing based on thermokinetics from VSP associated with DIERS methodology were used for evaluating the vent sizing and compared to that of the industrial plants

The NISTmAb Reference Material 8671 lifecycle management and quality plan.

Science.gov (United States)

Schiel, John E; Turner, Abigail

2018-03-01

Comprehensive analysis of monoclonal antibody therapeutics involves an ever expanding cadre of technologies. Lifecycle-appropriate application of current and emerging techniques requires rigorous testing followed by discussion between industry and regulators in a pre-competitive space, an effort that may be facilitated by a widely available test metric. Biopharmaceutical quality materials, however, are often difficult to access and/or are protected by intellectual property rights. The NISTmAb, humanized IgG1κ Reference Material 8671 (RM 8671), has been established with the intent of filling that void. The NISTmAb embodies the quality and characteristics of a typical biopharmaceutical product, is widely available to the biopharmaceutical community, and is an open innovation tool for development and dissemination of results. The NISTmAb lifecyle management plan described herein provides a hierarchical strategy for maintenance of quality over time through rigorous method qualification detailed in additional submissions in the current publication series. The NISTmAb RM 8671 is a representative monoclonal antibody material and provides a means to continually evaluate current best practices, promote innovative approaches, and inform regulatory paradigms as technology advances. Graphical abstract The NISTmAb Reference Material (RM) 8671 is intended to be an industry standard monoclonal antibody for pre-competitive harmonization of best practices and designing next generation characterization technologies for identity, quality, and stability testing.

Explicit and Implicit Subject Bias in the "ABS Journal Quality Guide"

Science.gov (United States)

Hoepner, Andreas G. F.; Unerman, Jeffrey

2012-01-01

This paper addresses issues raised in two recent papers published in this journal about the UK "Association of Business Schools' Journal Quality Guide (ABS Guide)". While much of the debate about journal rankings in general, and the "ABS Guide" in particular, has focused on the construction, power and (mis)use of these…

The melt rheological behavior of AB, ABA, BAB, and (AB)n block copolymers with monodisperse aramide segments

NARCIS (Netherlands)

Araichimani, A.; Dullaert, Konraad; Gaymans, R.J.

2009-01-01

The melt rheological behavior of segmented block copolymers with high melting diamide (A) hard segments (HS) and polyether (B) soft segments was studied. The block copolymers can be classified as B (monoblock), AB (diblock), ABA (triblock, diamide end segment), BAB (triblock, diamide mid-segment)

Preparation of a pure 99mTc-F(ab')2 radioimmunoconjugate by direct labeling methods

International Nuclear Information System (INIS)

Griffiths, G.L.; Jones, A.L.; Hansen, H.J.; Goldenberg, D.M.

1994-01-01

Intact IgG and Fab' can be labeled directly with 99m Tc to give quantitative incorporation of radioactivity into the protein. With F(ab') 2 the reductive conditions yield a mixture of 99m Tc-F(ab') 2 and 99m Tc-Fab'. We now report a direct labeling method to produce only 99m Tc-F(ab') 2 in quantitative yield and contaminated with 99m Tc-Fab'. The properties, stability and biodistribution of the 99m Tc-F(ab') 2 have been compared to 99m Tc-Fab'. This new technology will allow us to compare technetium direct-labeled IgG, F(ab') 2 and Fab' derivatives of the same antibody for radioimmunodetection. (author)

Towards hydrogen metallization: an Ab initio approach

International Nuclear Information System (INIS)

Bernard, St.

1998-01-01

The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H 2 ) 2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

Many-body optimization using an ab initio monte carlo method.

Science.gov (United States)

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Report on the Personnel Dosimetry at AB Atomenergi during 1964

International Nuclear Information System (INIS)

Edvardsson, K.A.; Hagsgaard, S.

1966-01-01

This report presents the results of the personnel dosimetry at AB Atomenergi during 1964. No doses exceeding the recommendations of ICRP were reported. The sum of the reported external total body doses during the year was for AB Atomenergi 51.5 manrem which, distributed over the whole company personnel, corresponds to an average dose of about 35 mrem per year and person or less than 1 % of the maximum permissible dose. 31,400 gamma films and 5,800 neutron films were evaluated. The films were changed every month. Urine analyses numbered 2,731 and whole body measurements 485. A comparison is made between dose distributions at AB Atomenergi and at institutions in other countries. The fraction of all personnel carrying dosimeters and exposed to more than a nominal dose seems generally to have been less than 10-20 %

Report on the Personnel Dosimetry at AB Atomenergi during 1964

Energy Technology Data Exchange (ETDEWEB)

Edvardsson, K A; Hagsgaard, S

1966-01-15

This report presents the results of the personnel dosimetry at AB Atomenergi during 1964. No doses exceeding the recommendations of ICRP were reported. The sum of the reported external total body doses during the year was for AB Atomenergi 51.5 manrem which, distributed over the whole company personnel, corresponds to an average dose of about 35 mrem per year and person or less than 1 % of the maximum permissible dose. 31,400 gamma films and 5,800 neutron films were evaluated. The films were changed every month. Urine analyses numbered 2,731 and whole body measurements 485. A comparison is made between dose distributions at AB Atomenergi and at institutions in other countries. The fraction of all personnel carrying dosimeters and exposed to more than a nominal dose seems generally to have been less than 10-20 %.

The preparation of F(ab')2 fragment and it's application in tumor radioimmunoimaging

International Nuclear Information System (INIS)

Yang Ziyi

1991-01-01

Monoclonal antibody against lung cancer was digested into F(ab') 2 fragment by pepsin and papain digestion. The yields of pure F(ab') 2 were 32.3 ± 5.5% and 52.3 ± 12.0% respectively. The immunoreactivity of F(ab') 2 was based on the ELISA assay and the cell binding studies was retained well. In the localization experiments, radioiodinated F(ab') 2 was injected intraperitoneally into the nude mice bearing human xenografts of lung cancer. The highest radioactivity in tumors, 1.37% of injected dose per gram, was reached on the first day after injection; its T/NT ratios were higher than those of the intact IgG in all tissues except kidney. The localization index (LI) in tumors was 4.95, while the average LI value of normal tissues was 1.25. After the injection of 131 I-F(ab') 2 intraperitoneally into lung tumor-bearing nude mice, photo scintigraphy was performed at intervals of 12 hrs. The xenografts were visualized distinctly during 36 ∼ 48 hr, and the nonspecific background was very low at 48 hr

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Study on the relationship between changes of serum true insulin (Tl) C-peptide, GAD-Ab, INS-Ab contents and age, course of disease, degree of obesity in patients with DM2

International Nuclear Information System (INIS)

Du Tongxin; Wang Zizheng; Cao Jiwei; Wu Jindan; Tao Xiaojun

2009-01-01

Objective: To study the changes of serum TI, C-peptide, GAD-Ab and INS-Ab in different groups of patients with DM2 (age,course of disease and degree of obesity). Methods: Serum C-peptide(with CLIA), INS-Ab(with RIA) and TI, GAD-Ab(with ELISA) contents were measured in altogether 428 patients with DM2. Relationship between changes of the above parameters and different groups of patients was studide in accordance with age, course of disease and degree of obesity respectively. Results: 1)Relationship among different age groups:(below 50, n=86, 51-70, n=216, over 71 n=126). The serum levels of the 4 parameters were significantly higher in all age group than those in the controls(n=40). Among the various age groups, the levels of all parameters were significantly lower in age group below 50 than the levels,in the other 2 groups with the only exception of INS-Ab, which was not significantly different from that in age group 51-70.The levels were significantly different between age-group 51-70 and age groups over 70, with the only exception of GAD-Ab, which was about the same in the two age-groups. 2)Relationship between changes of serum levels and course of disease(below 5yrs n=157, 6-10yrs n=168,over 1yrs,n=103). The serum levels in patients with disease less than 5years were significantly lower than those in other groups with the exception of GAD-Ab, which was not significantly different from that in patients with disease 6-10 years. 3) Relationship among different degree of obesity(non-obese, BMI BMI≥25, n=202, super-obese BMI≥32 n=50): The serum levels of all the parameters were significantly lower in the non-obese subjects than those in the other two groups.The levels in the super-obese group were also significantly higher than those in the obese group (P<0.01, P<0.05). Conclusion: Serum levels of the 4 parameters (TI, C-peptide, GAD-Ab, INS-Ab)were significantly increased in patients with DM2, especially in the older patients with prolonged course of disease as

Effect of earthworms on growth, photosynthetic efficiency and metal uptake in Brassica juncea L. plants grown in cadmium-polluted soils.

Science.gov (United States)

Kaur, Parminder; Bali, Shagun; Sharma, Anket; Vig, Adarsh Pal; Bhardwaj, Renu

2017-05-01

The present study has been carried out to examine the role of earthworms in phytoremediation of Cd and its effect on growth, pigment content, expression of genes coding key enzymes of pigments, photosynthetic efficiency and osmoprotectants in Brassica juncea L. plants grown under cadmium (Cd) metal stress. The effect of different Cd concentrations (0.50, 0.75, 1.0, 1.25 mM) was studied in 30 and 60-day-old plants grown in soils containing earthworms. It was observed that earthworm inoculation showed stimulatory effect on phytoremediation capacity and Cd uptake has increased by 49% (in 30-day-old plants) and 35% (in 60-day-old plants) in shoots and 13.3% (in 30-day-old plants) and 10% (in 60-day-old plants) in roots in 30 and 60-day-old plants in Cd (1.25 mM) treatments. Plant growth parameters such as root and shoot length, relative water content and tolerance index were found to increase in the presence of earthworms. Recovery in photosynthetic pigments (chlorophyll and carotenoid) and gas exchange parameters, i.e. net photosynthetic rate (P n ), stomatal conductance (G s ), intercellular CO 2 concentration (C i ) and transpiration rate (E t ), was observed after earthworm's supplementation. Modulation in expression of key enzymes for pigment synthesis, i.e. chlorophyllase, phytoene synthase, chalcone synthase and phenylalanine ammonia lyase, was also observed. The results of our study revealed that earthworms help to mitigate the toxic effects produced by Cd on plant growth and photosynthetic efficiency along with enhanced phytoremediation capacity when co-inoculated with Cd in soil.

Production and characterization of anti-human IgG F(ab')2 antibody fragment.

Science.gov (United States)

Valedkarimi, Zahra; Nasiri, Hadi; Aghebati-Maleki, Leili; Abdolalizadeh, Jalal; Esparvarinha, Mojghan; Majidi, Jafar

2018-04-10

In present study an optimized protocol for the separation of antibodies into antigen-binding fragments F(ab')2 using pepsin digestion was investigated. The production of these fragments is a consequential step in the development of medical research, treatment and diagnosis. For production of polyclonal antibody rabbit received antigen in four steps. The rabbit serum at 1/128000 dilution showed high absorbance in reaction with human IgG at the designed ELISA method. Rabbit IgG was purified by Ion-Exchange Chromatography (IEC) method. Purity was assessed by SDS-PAGE method. In non-reduced condition only one band was seen in about 150 kDa MW position and in reduced form, two bands were seen in 50 and 25 kDa MW positions. Rabbit IgG was digested by pepsin enzyme. The antibody fragments solution was applied to Gel filtration column to isolate the F(ab')2. Non-reduced SDS-PAGE for determining the purity of F(ab')2 fragment resulted in one band in 100 kDa corresponds to F(ab')2 fragment and a band in 150 kDa MW position corresponds to undigested IgG antibodies. The activities of FITC conjugated F(ab')2 fragment and commercial ones were compared using flowcytometry method. The activity results implied that the FITC conjugated- anti human F(ab')2 fragment worked as efficiently as the commercial one.

Susceptibility of different subsets of immature thymocytes to apoptosis induced by anti-TCRmAb

International Nuclear Information System (INIS)

Li Hongmei; Zhong Renqian; Yu Jiaping; Kong Xiantao; Chen Weifeng

2003-01-01

To analysis the susceptibility of different subsets of immature mice thymocytes to apoptosis induced by anti-TCRmAbs in vitro apoptosis was induced in unfractionated mice thymocytes by anti-TCRmAb. In Vivo apoptosis was induced in BALB/c mice by anti-TCR mAb, and thymocytes were examined by FACS. Results showed that CD4 + CD8 + DP thymocytes and CD4 - CD8 + CD3 - thymocytes were equally sensitive to apoptosis after treatment with the anti-TCR mAb. In sharp contrast, the early migrants or precursor containing thymocytes which are CD4 - CD8 - CD3 - TN have a lower spontaneous apoptosis rate and were relatively resistant to the anti-TCR mAb. The findings showed a breakpoint in thymocyte sensitivity to apoptosis which occurs after the onset of CD4 - CD8 + CD3 expression, suggesting that susceptibility of thymocytes to apoptosis is developmentally regulated

Structural insights and ab initio sequencing within the DING proteins family

International Nuclear Information System (INIS)

Elias, Mikael; Liebschner, Dorothee; Gotthard, Guillaume; Chabriere, Eric

2011-01-01

DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated

Structural insights and ab initio sequencing within the DING proteins family

Energy Technology Data Exchange (ETDEWEB)

Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

2011-01-01

DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

Performance of the BioPlex 2200 HIV Ag-Ab assay for identifying acute HIV infection.

Science.gov (United States)

Eshleman, Susan H; Piwowar-Manning, Estelle; Sivay, Mariya V; Debevec, Barbara; Veater, Stephanie; McKinstry, Laura; Bekker, Linda-Gail; Mannheimer, Sharon; Grant, Robert M; Chesney, Margaret A; Coates, Thomas J; Koblin, Beryl A; Fogel, Jessica M

Assays that detect HIV antigen (Ag) and antibody (Ab) can be used to screen for HIV infection. To compare the performance of the BioPlex 2200 HIV Ag-Ab assay and two other Ag/Ab combination assays for detection of acute HIV infection. Samples were obtained from 24 individuals (18 from the US, 6 from South Africa); these individuals were classified as having acute infection based on the following criteria: positive qualitative RNA assay; two negative rapid tests; negative discriminatory test. The samples were tested with the BioPlex assay, the ARCHITECT HIV Ag/Ab Combo test, the Bio-Rad GS HIV Combo Ag-Ab EIA test, and a viral load assay. Twelve (50.0%) of 24 samples had RNA detected only ( > 40 to 13,476 copies/mL). Ten (43.5%) samples had reactive results with all three Ag/Ab assays, one sample was reactive with the ARCHITECT and Bio-Rad assays, and one sample was reactive with the Bio-Rad and BioPlex assays. The 11 samples that were reactive with the BioPlex assay had viral loads from 83,010 to >750,000 copies/mL; 9/11 samples were classified as Ag positive/Ab negative by the BioPlex assay. Detection of acute HIV infection was similar for the BioPlex assay and two other Ag/Ab assays. All three tests were less sensitive than a qualitative RNA assay and only detected HIV Ag when the viral load was high. The BioPlex assay detected acute infection in about half of the cases, and identified most of those infections as Ag positive/Ab negative. Copyright © 2018 Elsevier B.V. All rights reserved.

Study of lamellar structure and crystallization behavior of poly(butylene terephthalate (PBT) in PBT/ABS and PBT/ABS/MMA-GMA blends using DSC, SAXS and DMTA

International Nuclear Information System (INIS)

Mantovani, Gerson L.; Pessan, Luiz A.; Hage, Elias; Torriani, Iris L.

2001-01-01

The effects of processing conditions and blend composition in the crystallization behaviour and lamellar structure of poly(butylene terephthalate) (PBT) in blends with acrylonitrile-butadiene-styrene copolymer (ABS) were studied. Differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS) and dynamic mechanical thermal analysis (DMTA) were used to observe those effects. Addition of reactive acrylic compatibilizer to the PBT/ABS blends has promoted an increase in the heat of crystallization of the related blends. The Long Period (L), obtained from the peak in the Lorentz-corrected SAXS pattern, was used to observe the effect in the lamellar structure of PBT phase in the blends. The results were in good agreement with the calculated values from de correlation function and the values of L do not show a significant dependence with the PBT mass fraction, either in the binary blends (PBT/ABS) or in the compatibilized blends. A slight but clear increase of the long period (from 3 to 5 angstrom) is noted for the systems injection molded at 240 deg C when compared to the ones molded at 260 deg C, although PBT crystallinity in the blends does not change significantly with blend composition or processing conditions. DMTA curves show a slight shift in the temperature of the tan δ main peaks for both PBT and ABS phases in the compatibilized blends, thereby indicating changes in the degree of miscibility or interaction between phases of those blends. Changes in the compatibilized blends miscibility may be responsible by the effects in the crystallization behaviour and lamellar structure of the PBT/ABS blends. (author)

Study of lamellar structure and crystallization behavior of poly(butylene terephthalate (PBT) in PBT/ABS and PBT/ABS/MMA-GMA blends using DSC, SAXS and DMTA

Energy Technology Data Exchange (ETDEWEB)

Mantovani, Gerson L.; Pessan, Luiz A.; Hage, Elias [Sao Carlos Univ., SP (Brazil). Dept. de Engenharia de Materiais]. E-mail: elias@power.ufscar.br; Plivelic, Tomas S. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil); Torriani, Iris L. [Universidade Estadual de Campinas, SP (Brazil). Inst. de Fisica Gleb Wataghin

2001-07-01

The effects of processing conditions and blend composition in the crystallization behaviour and lamellar structure of poly(butylene terephthalate) (PBT) in blends with acrylonitrile-butadiene-styrene copolymer (ABS) were studied. Differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS) and dynamic mechanical thermal analysis (DMTA) were used to observe those effects. Addition of reactive acrylic compatibilizer to the PBT/ABS blends has promoted an increase in the heat of crystallization of the related blends. The Long Period (L), obtained from the peak in the Lorentz-corrected SAXS pattern, was used to observe the effect in the lamellar structure of PBT phase in the blends. The results were in good agreement with the calculated values from de correlation function and the values of L do not show a significant dependence with the PBT mass fraction, either in the binary blends (PBT/ABS) or in the compatibilized blends. A slight but clear increase of the long period (from 3 to 5 angstrom) is noted for the systems injection molded at 240 deg C when compared to the ones molded at 260 deg C, although PBT crystallinity in the blends does not change significantly with blend composition or processing conditions. DMTA curves show a slight shift in the temperature of the tan {delta} main peaks for both PBT and ABS phases in the compatibilized blends, thereby indicating changes in the degree of miscibility or interaction between phases of those blends. Changes in the compatibilized blends miscibility may be responsible by the effects in the crystallization behaviour and lamellar structure of the PBT/ABS blends. (author)

Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

Directory of Open Access Journals (Sweden)

Rodrigo Pessôa

Full Text Available BACKGROUND: Here, we report on the partial and full-length genomic (FLG variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs, 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP and 7 adult T-cell leukemia/lymphoma (ATLL patients, using an Illumina paired-end protocol. METHODS: Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. RESULTS: A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14 and FLG (n = 76 data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5% individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA and that 4 individuals (4.5% were infected with the Japanese sub-subtypes (aB. A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. CONCLUSIONS: This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data

Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

Science.gov (United States)

Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Nukui, Youko; Pereira, Juliana; Casseb, Jorge; Kasseb, Jorge; de Oliveira, Augusto César Penalva; Segurado, Aluisio Cotrim; Sanabani, Sabri Saeed

2014-01-01

Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the

An ab initio and TD DFT

Indian Academy of Sciences (India)

The photophysical behaviour of N-(2-hydroxy benzylidene) aniline or most commonly known as salicylideneaniline (SA) has been investigated using the ab initio and DFT levels of theory. The quantum chemical calculations show that the optimized non planar enol (1) form of the SA molecule is the most stable conformer ...

Application of bokashi and sunn hemp (Crotalaria juncea L. to improve inorganic fertilizer efficiency on maize (Zea mays L.

Directory of Open Access Journals (Sweden)

A.I. Yuliana

2015-10-01

Full Text Available A field experiment was conducted lo learn about the effect of Bokashi and Sunn hemp (Crotalaria juncea L. on maize production and inorganic fertilizer use efficiency on maize. The experiment was conducted in Jatikerto, Malang; at the altitude of 303 m above sea level, in Alfisol soil type, the average daily temperature ranges 21-33oC, from June to October 2013. The experiment was conducted as factorial, designed in a randomized block design (RBD. The first factor was dose of inorganic fertilizer (100% ; 75% and 50% of recommendation dose. The second factor was the organic fertilizer (Without organic fertilizer20 t Bokashi/ ha, 20 t Sunn hemp/ha, 10 t Bokashi/ha + 10 t Sunn hemp/ha. The results showed that application of 20 t Bokashi/ha, 20 t Sunn hemp/ha, and combination of 10 t Bokashi/ha + 10 t Sunn hemp/ha, along with the application of inorganic fertilizer by dose of 100% increased the yields of maize for about 41.8%; 47.6% and 54.7% (10.73 t/ha; 11.17 t/ha, and 11.71 t/ha, respectively. The yield and nutrient use efficiency in the treatment dose of 100% inorganic fertilizer did not have any significant difference from the application of 20 t Bokashi /ha, 20 t Sunn hemp/ha, and 10 t Bokashi/ha + 10 t Sunn hemp/ha along with doses of inorganic fertilization 75% and 50%. Therefore, the organic fertilizer of 20 t Bokashi/ ha, 20 t Sunn hemp/ha, and combination of 10 t Bokashi/ha + 10 t Sunn hemp/ha could reduce the need of inorganic fertilizer for about 50%.

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of the Staphylococcus aureus vfrAB operon, a novel virulence factor regulatory locus.

Science.gov (United States)

Bose, Jeffrey L; Daly, Seth M; Hall, Pamela R; Bayles, Kenneth W

2014-05-01

During a screen of the Nebraska Transposon Mutant Library, we identified 71 mutations in the Staphylococcus aureus genome that altered hemolysis on blood agar medium. Although many of these mutations disrupted genes known to affect the production of alpha-hemolysin, two of them were associated with an apparent operon, designated vfrAB, that had not been characterized previously. Interestingly, a ΔvfrB mutant exhibited only minor effects on the transcription of the hla gene, encoding alpha-hemolysin, when grown in broth, as well as on RNAIII, a posttranscriptional regulatory RNA important for alpha-hemolysin translation, suggesting that VfrB may function at the posttranscriptional level. Indeed, a ΔvfrB mutant had increased aur and sspAB protease expression under these conditions. However, disruption of the known secreted proteases in the ΔvfrB mutant did not restore hemolytic activity in the ΔvfrB mutant on blood agar. Further analysis revealed that, in contrast to the minor effects of VfrB on hla transcription when strains were cultured in liquid media, the level of hla transcription was decreased 50-fold in the absence of VfrB on solid media. These results demonstrate that while VfrB represses protease expression when strains are grown in broth, hla regulation is highly responsive to factors associated with growth on solid media. Intriguingly, the ΔvfrB mutant displayed increased pathogenesis in a model of S. aureus dermonecrosis, further highlighting the complexity of VfrB-dependent virulence regulation. The results of this study describe a phenotype associated with a class of highly conserved yet uncharacterized proteins found in Gram-positive bacteria, and they shed new light on the regulation of virulence factors necessary for S. aureus pathogenesis.

Effectiveness of motorcycle antilock braking systems (ABS) in reducing crashes, the first cross-national study.

Science.gov (United States)

Rizzi, Matteo; Strandroth, Johan; Kullgren, Anders; Tingvall, Claes; Fildes, Brian

2015-01-01

This study set out to evaluate the effectiveness of motorcycle antilock braking systems (ABS) in reducing real-life crashes. Since the European Parliament has voted on legislation making ABS mandatory on all new motorcycles over 125 cc from 2016, the fitment rate in Europe is likely to increase in the coming years. Though previous research has focused on mostly large displacement motorcycles, this study used police reports from Spain (2006-2009), Italy (2009), and Sweden (2003-2012) in order to analyze a wide range of motorcycles, including scooters, and compare countries with different motorcycling habits. The statistical analysis used odds ratio calculations with an induced exposure approach. Previous research found that head-on crashes were the least ABS-affected crash type and was therefore used as the nonsensitive crash type for ABS in these calculations. The same motorcycle models, with and without ABS, were compared and the calculations were carried out for each country separately. Crashes involving only scooters were further analyzed. The effectiveness of motorcycle ABS in reducing injury crashes ranged from 24% (95% confidence interval [CI], 12-36) in Italy to 29% (95% CI, 20-38) in Spain, and 34% (95% CI, 16-52) in Sweden. The reductions in severe and fatal crashes were even greater, at 34% (95% CI, 24-44) in Spain and 42% (95% CI, 23-61) in Sweden. The overall reductions of crashes involving ABS-equipped scooters (at least 250 cc) were 27% (95% CI, 12-42) in Italy and 22% (95% CI, 2-42) in Spain. ABS on scooters with at least a 250 cc engine reduced severe and fatal crashes by 31% (95% CI, 12-50), based on Spanish data alone. At this stage, there is more than sufficient scientific-based evidence to support the implementation of ABS on all motorcycles, even light ones. Further research should aim at understanding the injury mitigating effects of motorcycle ABS, possibly in combination with combined braking systems.

Perspective: Ab initio force field methods derived from quantum mechanics

Science.gov (United States)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Training in AB Department 2004/2005

CERN Document Server

Schinzel, Josi; CERN. Geneva. AB Department

2006-01-01

This note provides an overview of the training attended by members of the AB Department during the years 2004 and 2005, giving a break-down of the different courses and costs as well as training directions. It describes the organisation of training in the department, and evolution in training directions and planning.

A/B Testing in Improving Conversion on a Website : Case: Sanoma Entertainment Oy

OpenAIRE

Arento, Thomas

2010-01-01

The purpose of this thesis is to study marketing possibilities of improved conversion rates on websites. The study was made for Sanoma Entertainment Oy’s Gaming & Online unit. The main objective was to explore A/B testing as a tool to improve conversion rates by increasing click-through rates. The secondary objective was to test Google Website Optimizer as an A/B testing tool in comparison to current methods of A/B testing in Sanoma Entertainment Oy. The results of this study will be used as ...

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

Science.gov (United States)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

Clinical significance of detection of GAD-Ab, ICA and IAA in patients with diabetes mellitus

International Nuclear Information System (INIS)

Zhou Jinhong; Liu Zhenzong; Wang Huimin

2006-01-01

To explore value of combined detection of glutamic acid decarboxylase antibody(GAD-Ab), islet cell antibody (ICA) and insulin autoantibody (IAA) in patients with diabetes mellitus (DM). Serum GAD-Ab, ICA and IAA were detected by chemiluminescent immunoassay and RIA in 46 of type 1 diabetes mellitus (1 DM), 78 of 2 DM respectively, and in 50 nondiabetic subjects as control group, and analysed according to the positive rates of different groups. Results showed that the positive rate of GAD-Ab was 67.39%, ICA 39.73%, IAA 23.91% in 1 DM,and that of GAD-Ab was 8.97%, ICA 15.39%, IAA 10.26% in 2 DM respectively. The positive rate of combined detection of GAD-Ab, ICA and IAA was 91.30% in patients with 1 DM, and 29.49% which was higher than that in control group (P<0.01). The detection of serum GAD-Ab,ICA and IAA might be regarded as clinical significance for classification, treatment and predict prognosis of DM. (authors)

Unique synergism in flame retardancy in ABS based composites through blending PVDF and halloysite nanotubes

Science.gov (United States)

Remanan, Sanjay; Sharma, Maya; Jayashree, Priyadarshini; Parameswaranpillai, Jyotishkumar; Fabian, Thomas; Shih, Julie; Shankarappa, Prasad; Nuggehalli, Bharath; Bose, Suryasarathi

2017-06-01

This study demonstrates flame retardant materials designed using bi-phasic polymer blends of acrylonitrile butadiene styrene (ABS) and polyvinylidene fluoride (PVDF) containing halloysite nanotubes (HNTs) and Cloisite 30B nanoclay. The prepared blends with and without nanoparticles were extensively characterized. The nanoparticles were added in different weight concentrations to improve the flame retardancy. It was observed that prepared ABS/PVDF blends showed better flame retardancy than ABS based composites. The flame resistance was further improved by the addition of nanoparticles in the blends. The microscale combustion calorimetry (MCC) test showed better flame resistance in ABS/PVDF blends filled with 5 wt% HNTs than other composites. The total heat release of ABS/PVDF blend filled with 5 wt% HNTs decreased by 31% and also the heat of combustion decreased by 26% as compared to neat ABS. When compared with nanoparticles, the addition of PVDF reduced the peak heat release rate (PHRR) and increased the char residue more effectively. A synergistic improvement was observed from both PVDF and HNTs on the flame resistance properties.

Use of laser-induced breakdown spectroscopy for the determination of polycarbonate (PC) and acrylonitrile-butadiene-styrene (ABS) concentrations in PC/ABS plastics from e-waste.

Science.gov (United States)

Costa, Vinicius Câmara; Aquino, Francisco Wendel Batista; Paranhos, Caio Marcio; Pereira-Filho, Edenir Rodrigues

2017-12-01

Due to the continual increase in waste generated from electronic devices, the management of plastics, which represents between 10 and 30% by weight of waste electrical and electronic equipment (WEEE or e-waste), becomes indispensable in terms of environmental and economic impacts. Considering the importance of acrylonitrile-butadiene-styrene (ABS), polycarbonate (PC), and their blends in the electronics and other industries, this study presents a new application of laser-induced breakdown spectroscopy (LIBS) for the fast and direct determination of PC and ABS concentrations in blends of these plastics obtained from samples of e-waste. From the LIBS spectra acquired for the PC/ABS blend, multivariate calibration models were built using partial least squares (PLS) regression. In general, it was possible to infer that the relative errors between the theoretical or reference and predicted values for the spiked samples were lower than 10%. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metode Abû Dâwud Dalam Menulis Al-Sunan

OpenAIRE

Ma'sum, Ma'sum

2011-01-01

In this paper the author will reveal one of the prominent figures who have long been through the mill of hadith more over the quality of his knowledge in this field does not need to worry about, Abû Dâwud made a large contribution which includes hadith of the prophet in the his book. This study on the book of hadith methodology writing is owned by Abû Dâwud hadith have found some result of hadîth da‘îf that contained therein. the indication of hadîth da‘îf loading (also mawdû‘ according to Ib...

Metode Abû Dâwud dalam Menulis al-Sunan

OpenAIRE

Ma'sum Ma'sum

2015-01-01

In this paper the author will reveal one of the prominent figures who have long been through the mill of hadith more over the quality of his knowledge in this field does not need to worry about, Abû Dâwud made a large contribution which includes hadith of the prophet in the his book. This study on the book of hadith methodology writing is owned by Abû Dâwud hadith have found some result of hadîth da‘îf that contained therein. the indication of hadîth da‘îf loading (also mawdû‘ according to Ib...

Cry1Ab protein from Bt transgenic rice does not residue in rhizosphere soil

International Nuclear Information System (INIS)

Wang Haiyan; Ye Qingfu; Wang Wei; Wu Licheng; Wu Weixiang

2006-01-01

Expression of Cry1Ab protein in Bt transgenic rice (KMD) and its residue in the rhizosphere soil during the whole growth in field, as well as degradation of the protein from KMD straw in five soils under laboratory incubation were studied. The residue of Cry1Ab protein in KMD rhizosphere soil was undetectable (below the limit of 0.5 ng/g air-dried soil). The Cry1Ab protein contents in the shoot and root of KMD were 3.23-8.22 and 0.68-0.89 μg/g (fresh weight), respectively. The half-lives of the Cry1Ab protein in the soils amended with KMD straw (4%, w/w) ranged from 11.5 to 34.3 d. The residence time of the protein varied significantly in a Fluvio-marine yellow loamy soil amended with KMD straw at the rate of 3, 4 and 7%, with half-lives of 9.9, 13.8 and 18 d, respectively. In addition, an extraction method for Cry1Ab protein in soil was developed, with extraction efficiencies of 46.4-82.3%. - Cry1Ab protein was not detected in the rhizosphere soil of field-grown Bt transgenic rice

URHEILUN SPONSOROINTI JA LUMILAUTAILU : FOREX Bank Ab:n mahdollisuudet lumilautailun sponsorointiin

OpenAIRE

Autio, Suvi

2011-01-01

FOREX Bank Ab on Pohjoismaiden suurin valuutanvaihtoon erikoistunut yritys. FOREXin liikeideana on tarjota maasta lähteville ja maahan saapuville matkailijoille valuuttaa joustaviin kellonaikoihin, keskeisillä paikoilla, sekä kilpailukykyisillä kursseilla ja toimitusmaksuilla. Opinnäytetyön aiheena oli urheilun sponsorointi ja lumilautailu. Opinnäytetyön tarkoituksena oli selvittää FOREX Bank Ab:n sponsoroinnin nykytilaa ja lumilautailun sopivuutta FOREXin sponsorointikohteeksi. Teoriaosu...

Genome Maps, a new generation genome browser.

Science.gov (United States)

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Energy conservation campaign at Sandvik AB in Sandviken

Energy Technology Data Exchange (ETDEWEB)

Larsson, Rune

1979-07-01

Sandvik AB's performed an analysis showing oil consumption for steam production was increasing considerably. Energy conservation measures were implemented to decrease the oil consumption and to make lasting changes.

Popular Herbig AE star AB Aur

International Nuclear Information System (INIS)

Shevchenko, V.S.

1987-01-01

The variability of AB Aur emission line H α , H β , H γ profiles, equivalent widths (EW λ ) and relative intensity have been observed on the photoelectric scanner. During the 20 d observation period EW λ H α ranged from 23.20 to 35.35 A. Mean EW λ H α is 27.25 A, daily average deviation is 3.60 ± 0.07 A. The minimum time of variability is 1 h . The chromospheric lines near-infrared triplet Ca II and KCaII and emission lines H β -H13, P12-P20, 0I 8446.5 A and the variability of other lines have been studied on the photographic and image-tube spectra. The intensity of these lines and EW λ changed 2-4 times during an interval from 1 h to several years. The AB Aur variability nature of emission lines made it possible to assume that the ''deep chromosphere'' is not a centre-symmetrical or axisymmetrical formation but is a conglomerate of different density and speed gas condensations

Ab initio calculations of 3H(d,n)4He fusion

International Nuclear Information System (INIS)

Navratil, Petr; Quaglioni, Sofia

2012-01-01

We build a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the ab initio no-core shell model. In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. We will present the first results of the d- 3 H and d- 3 He fusion calculation obtained within our ab initio approach. We will also discuss our d- 4 He, 3 H- 4 He and 3 H- 3 H scattering calculations and the outline of the extension of the formalism to include three-cluster final states with the goal to calculate the 3 H( 3 H,2n) 4 He cross section

Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

Energy Technology Data Exchange (ETDEWEB)

Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)

2014-09-28

We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

International Nuclear Information System (INIS)

Draayer, Jerry P.

2014-01-01

We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

Effects of goat manure liquid fertilizer combined with AB-MIX on foliage vegetables growth in hydroponic

Science.gov (United States)

Sunaryo, Y.; Purnomo, D.; Darini, M. T.; Cahyani, V. R.

2018-03-01

Hydroponic as one of the protected cultivation practices is very important to be developed in Indonesia due to not only the reduction of arable agricultural lands in lines with increasing of residential demand and other public facilities but also due to the negative influences of climate change as well global warming to plant growth. The effects of liquid fertilizer made from goat manure (LFGM) in combination with AB-Mix on three kinds of foliage vegetable growth was examined in hydroponics. The research was conducted by 3 x 4 factorial experiment and arranged in Completely Randomized Design with 3 replications. The first factor was foliage vegetable consisting of 3 levels: Mustard Green, Lettuce, and Red Spinach. The second factor was the mixture composition of nutrient solution consisting of 4 levels: LFGM + AB-Mix (v/v: 1:1), LFGM + AB-Mix (v/v: 1:3), LFGM + AB-Mix (v/v: 3:1), and A/B mix as control. Results indicated that the application of LFGM + AB-Mix (v/v: 1:3) resulted in similar plant growth as control (AB-Mix application), and also resulted in the highest chlorophyll content of Mustard green.

Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

Ab Initio Calculations Of Light-Ion Reactions

International Nuclear Information System (INIS)

Navratil, P.; Quaglioni, S.; Roth, R.; Horiuchi, W.

2012-01-01

The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

Science.gov (United States)

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

Labelling of MoAb with 153SmH1ETA: Preliminary results

International Nuclear Information System (INIS)

Ferro-Flores, G.; De, F.; Ramirez, M.; Pedraza-Lopez, M.; Tendilla, J.I.; Melendez-Alafort, L.; Murphy, C.A.

2001-01-01

A method to label MoAb with Sm-153 using 1,5,9,13-tetraazacyclohexadecane N,N',N'',N''' tetraacetic acid (H 4 ETA) as a bifunctional chelator was developed. H 4 ETA and SmH 1 ETA were synthesized in our laboratory and characterized by IR spectroscopy, TGA (thermogravimetric analysis), SEM (Scattering Electronic Microscopy), EDAX (Elemental Dispersion Analysis by X-rays) and EPR (Electron Paramagnetic Resonance) at 6 K. The 153 SmH 1 ETAMoAb was prepared by a simple incubation of the MoAb ior cea1, and the 153 SmH 1 ETA complex at neutral pH and at room temperature for 24 h. The specific activity of the labelled antibody was 111 MBq/mg (3 mCi/mg). Sm-153(III) is commercially available with specific activities up to 318.2 GBq/mg. Therefore, under the conditions described above 153 SmH 1 ETA labelled MoAb could be obtained with specific activity up to 1.14 GBq/mg (30.7 mCi/mg). (author)

Espécies vegetais para cobertura do solo: influência sobre plantas daninhas e a produtividade do algodoeiro em sistema plantio direto

Directory of Open Access Journals (Sweden)

Alexandre Cunha de Barcellos Ferreira

2010-12-01

Full Text Available Este trabalho objetivou avaliar a produção, a persistência e os efeitos de coberturas vegetais sobre as plantas daninhas e a produtividade do algodoeiro em sistema plantio direto. Os tratamentos consistiram das espécies de cobertura: milheto (Pennisetum glaucum (L. R. Brown, Brachiaria ruziziensis Germain & Evrard, sorgo forrageiro (Sorghum bicolor L. Moench, capim-pé-de-galinha (Eleusine coracana L. Gaerth, Crotalaria juncea L., Crotalaria spectabilis Roth, aveia-preta (Avena strigosa Schreb., nabo forrageiro (Raphanus sativus L., P. glaucum + C. juncea, P. glaucum + C. spectabilis, B. ruziziensis + C. juncea, B. ruziziensis + C. spectabilis, S. bicolor + C. juncea, S. bicolor + C. spectabilis, E. coracana + C. juncea, E. coracana + C. spectabilis, A. strigosa + R. sativus, P. glaucum + R. sativus e pousio. As espécies foram semeadas no final do verão, após a colheita de soja, e o algodoeiro BRS 269-Buriti, nove meses após. O delineamento experimental foi em blocos ao acaso, com quatro repetições. As espécies B. ruziziensis, B. ruziziensis + C. juncea, B. ruziziensis + C. spectabilis e P. glaucum + R. sativus produziram mais de 6,8 t ha-1 de biomassa seca. A palhada produzida pela B. ruziziensis garantiu boa cobertura do solo durante o ciclo do algodoeiro. A biomassa seca de B. ruziziensis, B. ruziziensis + C. juncea e B. ruziziensis + C. spectabilis reduziu a infestação de plantas daninhas até a época de semeadura do algodão e durante os estádios iniciais de seu desenvolvimento. Palhas de R. sativus e A. strigosa, solteiras e consorciadas, interferiram negativamente na produtividade do algodoeiro.

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

The mechanochemical cycle of mammalian kinesin-2 KIF3A/B under load

Science.gov (United States)

Andreasson, Johan O.L.; Shastry, Shankar; Hancock, William O.; Block, Steven M.

2015-01-01

Summary The response of motor proteins to external loads underlies their ability to work in teams and determines the net speed and directionality of cargo transport. The mammalian kinesin-2, KIF3A/B, is a heterotrimeric motor involved in intraflagellar transport and vesicle motility in neurons. Bidirectional cargo transport is known to result from the opposing activities of KIF3A/B and dynein bound to the same cargo, but the load-dependent properties of kinesin-2 are poorly understood. We used a feedback-controlled optical trap to probe the velocity, run length and unbinding kinetics of mouse KIF3A/B under various loads and nucleotide conditions. The kinesin-2 motor velocity is less sensitive than kinesin-1 to external forces, but its processivity diminishes steeply with load, and the motor was observed occasionally to slip and reattach. Each motor domain was characterized by studying homodimeric constructs, and a global fit to the data resulted in a comprehensive pathway that quantifies the principal force-dependent kinetic transitions. The properties of the KIF3A/B heterodimer are intermediate between the two homodimers, and the distinct load-dependent behavior is attributable to the properties of the motor domains, and not to the neck-linkers or the coiled-coil stalk. We conclude that the force-dependent movement of KIF3A/B differs significantly from conventional kinesin-1. Against opposing dynein forces, KIF3A/B motors are predicted to rapidly unbind and rebind, resulting in qualitatively different transport behavior from kinesin-1. PMID:25866395

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

2004-01-01

SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

Studies of the distribution of intrathecally injected 125I-tetanus antitoxin-F(ab')2

International Nuclear Information System (INIS)

Hanauske, A.R.

1981-01-01

Overall F(ab') 2 and antitetanus-f(ab') 2 - fragments were labelled with 125 I and injected i.th. into normal juvenile cats and adult rats. One group of rats was normal; in the other, unilateral local tetanus had been induced by injection of tetanus toxin into a M. gastrocnemius. The animals were sacrificed 24 h after the i.th. injection, and tissue samples were taken for histoautoradiography. 125 I-antitetanus-F(ab') 2 permeated into the extracellular space of the spinal cord, roots, and ganglia but not into the neuronal intracellular space. 125 I-overall-F(ab') showed identical permeation behaviour. 125 I-antitetanus-F(ab') 2 reacted with tetanus toxin issuing from the motoneurons after i.th. injection, forming an immunocomplex around the motorneurons. The immunocomplex was not formed around pseudo-unipolar ganglian cells in the spinal ganglia even though some of the ganglian cells contained tetanus toxin, and 125 I-antitetanus-F(ab') 2 was present in the extracellular space. As an explanation, it was suggested that tetanus toxin does not permeate into the extracellular space through the membrane of the pseudo-unipolar ganglian cells so that immune reactions will not occur. These findings help to explain the widely divergent results of tetanus therapy by means of i.th. injection of tetanus antitoxin. Recommendations for future therapy measures are derived from the findings. (orig./MG) [de

Cationization increases brain distribution of an amyloid-beta protofibril selective F(ab')2 fragment

OpenAIRE

Syvänen, Stina; Edén, Desireé; Sehlin, Dag

2017-01-01

Antibodies and fragments thereof are, because of high selectivity for their targets, considered as potential therapeutics and biomarkers for several neurological disorders. However, due to their large molecular size, antibodies/fragments do not easily penetrate into the brain. The aim of the present study was to improve the brain distribution via adsorptive-mediated transcytosis of an amyloid-beta (A beta) protofibril selective F(ab')2 fragment (F(ab')2-h158). F(ab')2-h158 was cationized to d...

High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

Science.gov (United States)

Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

2012-01-01

Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

Dynamics of immature mAb glycoform secretion during CHO cell culture

DEFF Research Database (Denmark)

Jimenez del Val, Ioscani; Fan, Yuzhou; Weilguny, Dietmar

2016-01-01

Ensuring consistent glycosylation-associated quality of therapeutic monoclonal antibodies (mAbs) has become a priority in pharmaceutical bioprocessing given that the distribution and composition of the carbohydrates (glycans) bound to these molecules determines their therapeutic efficacy and immu......Ensuring consistent glycosylation-associated quality of therapeutic monoclonal antibodies (mAbs) has become a priority in pharmaceutical bioprocessing given that the distribution and composition of the carbohydrates (glycans) bound to these molecules determines their therapeutic efficacy...

AB Levitator and Electricity Storage

OpenAIRE

Bolonkin, Alexander

2007-01-01

The author researched this new idea - support of flight by any aerial vehicles at significant altitude solely by the magnetic field of the planet. It is shown that current technology allows humans to create a light propulsion (AB engine) which does not depend on air, water or ground terrain. Simultaniosly, this revolutionary thruster is a device for the storage of electricity which is extracted and is replenished (during braking) from/into the storage with 100 percent efficiency. The relative...

Report on the Personnel Dosimetry at AB Atomenergi during 1962

International Nuclear Information System (INIS)

Edvardsson, K.A.; Hagsgaard, S.

1963-12-01

This report presents the results of the personnel dosimetry at AB Atomenergi during 1962. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses (≥ 100 mrem/quarter) is for the whole of AB Atomenergi during this year 74. 2 manrem corresponding to about 50 mrem/year and person or 1 % of the maximum permissible dose. 32500 gamma films and 6200 neutron films have been evaluated. The total number of urine analyses is 2700 and of whole body measurements 10

Report on the Personnel Dosimetry at AB Atomenergi during 1962

Energy Technology Data Exchange (ETDEWEB)

Edvardsson, K A; Hagsgaard, S

1964-07-15

This report presents the results of the personnel dosimetry at AB Atomenergi during 1963. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses during the year is for AB Atomenergi 64.2 manrem which, distributed over the whole company personnel, corresponds to about 40 mrem per year and person or about 1 % of the maximum permissible dose. 37800 gamma films and 6700 neutron films have been evaluated. The total number of urine analyses is 3603 and of whole body measurements 211.

Report on the Personnel Dosimetry at AB Atomenergi during 1962

Energy Technology Data Exchange (ETDEWEB)

Edvardsson, K A; Hagsgaard, S

1963-12-15

This report presents the results of the personnel dosimetry at AB Atomenergi during 1962. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses ({>=} 100 mrem/quarter) is for the whole of AB Atomenergi during this year 74. 2 manrem corresponding to about 50 mrem/year and person or 1 % of the maximum permissible dose. 32500 gamma films and 6200 neutron films have been evaluated. The total number of urine analyses is 2700 and of whole body measurements 10.

Use of ab initio quantum chemical methods in battery technology

Energy Technology Data Exchange (ETDEWEB)

Deiss, E [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1997-06-01

Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

Phosphoric acid doped AB-PBI membranes and its applications in high temperature PEMFC

DEFF Research Database (Denmark)

He, Ronghuan; Qingfeng, Li; Bjerrum, Niels

2005-01-01

Poly(2,5-benzimidazole) (ab-PBI) was prepared from 3，4-diaminobenzoic acid via a polymerisation reaction. The obtained polymer exhibits excellent thermal stability in a temperature range ….. The membrane of ab-PBI when doped with phosphoric acid at room temperaturepresents high proton conductivity...

Remodeling of the AB site of rat parvalbumin and oncomodulin into a canonical EF-hand

DEFF Research Database (Denmark)

Cox, J A; Durussel, I; Scott, D J

1999-01-01

-residue canonical loop. To create an optical conformational probe we also expressed the homologs with a F102W replacement. Unexpectedly, in none of the proteins did the mutation reactivate the AB site. The AB-remodeled parvalbumins bind two Ca2+ ions with strong positive cooperativity (nH = 2......Parvalbumin (PV) and the homologous protein oncomodulin (OM) contain three EF-hand motifs, but the first site (AB) cannot bind Ca2+. Here we aimed to recreate the putative ancestral proteins [D19-28E]PV and [D19-28E]OM by replacing the 10-residue-long nonfunctional loop in the AB site by a 12...... conformations. The AB-remodeled oncomodulins also bind two Ca2+ with [Ca2+]0.5 = 43 microM and nH = 1.45. Mg2+ does not affect Ca2+ binding. Again the Ca2+ forms display two-thirds of the alpha-helical content in the wild-type, while their core is still strongly hydrophobic as monitored by Trp and Tyr...

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

Directory of Open Access Journals (Sweden)

Barloy-Hubler Frédérique

2008-12-01

Full Text Available Abstract Background Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. Description In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. Conclusion OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software

EST Table: AB046365 [KAIKOcDNA[Archive

Lifescience Database Archive (English)

Full Text Available 1073 aa FBpp0259641|DyakGE14631-PA 10/08/27 47 %/329 aa W03F8.5#CE34386#WBGene00002247#locus:lam- 1#laminin#...AB046365 10/09/29 97 %/1069 aa dbj|BAB21565.1| laminin [Bombyx mori] 10/08/27 40 %/

Personality at Work: A Study of Type A-B

Directory of Open Access Journals (Sweden)

Amber Raza

2007-10-01

Full Text Available The objective of this study was to measure the impact of stressors on personality types in Call Centers. Based on literature survey five potential workplace stressors were identified, namely (1 Task Demands, (2 Role Demands, (3 Interpersonal Demands, (4 Organizational Structure and (5 Organizational Leadership. Based on the literature survey, a relationship model was developed that was inclusive of the above stressors, and three personality types, which were Type A, Type AB and Type B.The sample size for the study was 100. The subjects were supervisors and agents drawn non-randomly from various Call Centers of Karachi. All the subjects completed a questionnaire comprised of 27 questions based on occupational stress index (Srivasta and Singh 1981 and AB Personality Continuum (National Institute of Safety and Health 1975. The three personality types A, B & AB all go through stress, however it is the Type A, which thrives on stress. The sources of stress measured in the study were Task Demand, Role Demand, Interpersonal Demands, Organizational Structure and Organizational Leadership.The stressor that most contributed to the Personality type A’s stress in the study was Interpersonal Demand (0.38, which is justified by the literature review as Personality type A are not team players and prefer to work alone.Whereas Personality type B was stressed because of Role Demand (0.38 which is also proved by the literature review as personality type B are laid back and do not take there roles seriously. Hence it can be concluded that it type A tends to cope well with stress as compared to type AB and type B. The performance of the respondents can be made better if the supervisors are aware of the personality types and thereby motivate them according.

Comparison of F(ab')2 versus Fab antivenom for pit viper envenomation: a prospective, blinded, multicenter, randomized clinical trial.

Science.gov (United States)

Bush, Sean P; Ruha, Anne-Michelle; Seifert, Steven A; Morgan, David L; Lewis, Brandon J; Arnold, Thomas C; Clark, Richard F; Meggs, William J; Toschlog, Eric A; Borron, Stephen W; Figge, Gary R; Sollee, Dawn R; Shirazi, Farshad M; Wolk, Robert; de Chazal, Ives; Quan, Dan; García-Ubbelohde, Walter; Alagón, Alejandro; Gerkin, Richard D; Boyer, Leslie V

2015-01-01

Crotalidae Polyvalent Immune Fab (Ovine) has been the only antivenom commercially available in the US since 2007 for treatment of Crotalinae envenomation. Late coagulopathy can occur or recur after clearance of Fab antivenom, often after hospital discharge, lasting in some cases more than 2 weeks. There have been serious, even fatal, bleeding complications associated with recurrence phenomena. Frequent follow-up is required, and additional intervention or hospitalization is often necessary. F(ab')2 immunoglobulin derivatives have longer plasma half life than do Fab. We hypothesized that F(ab')2 antivenom would be superior to Fab in the prevention of late coagulopathy following treatment of patients with Crotalinae envenomation. We conducted a prospective, double-blind, randomized clinical trial, comparing late coagulopathy in snakebitten patients treated with F(ab')2 with maintenance doses [F(ab')2/F(ab')2], or F(ab')2 with placebo maintenance doses [F(ab')2/placebo], versus Fab with maintenance doses [Fab/Fab]. The primary efficacy endpoint was coagulopathy (platelet count Fab/Fab cohort experienced late coagulopathy versus 4/39 (10.3%, p < 0.05) in the F(ab')2/F(ab')2 cohort and 2/38 (5.3%, p < 0.05) in the F(ab')2/placebo cohort. The lowest heterologous protein exposure was with F(ab')2/placebo. No serious adverse events were related to study drug. In each study arm, one patient experienced an acute serum reaction and one experienced serum sickness. In this study, management of coagulopathic Crotalinae envenomation with longer-half-life F(ab')2 antivenom, with or without maintenance dosing, reduced the risk of subacute coagulopathy and bleeding following treatment of envenomation.

Pressure tracking control of vehicle ABS using piezo valve modulator

Science.gov (United States)

Jeon, Juncheol; Choi, Seung-Bok

2011-03-01

This paper presents a wheel slip control for the ABS(anti-lock brake system) of a passenger vehicle using a controllable piezo valve modulator. The ABS is designed to optimize for braking effectiveness and good steerability. As a first step, the principal design parameters of the piezo valve and pressure modulator are appropriately determined by considering the braking pressure variation during the ABS operation. The proposed piezo valve consists of a flapper, pneumatic circuit and a piezostack actuator. In order to get wide control range of the pressure, the pressure modulator is desired. The modulator consists of a dual-type cylinder filled with different substances (fluid and gas) and a piston rod moving vertical axis to transmit the force. Subsequently, a quarter car wheel slip model is formulated and integrated with the governing equation of the piezo valve modulator. A sliding mode controller to achieve the desired slip rate is then designed and implemented. Braking control performances such as brake pressure and slip rate are evaluated via computer simulations.

Ab initio nuclear structure - the large sparse matrix eigenvalue problem

Energy Technology Data Exchange (ETDEWEB)

Vary, James P; Maris, Pieter [Department of Physics, Iowa State University, Ames, IA, 50011 (United States); Ng, Esmond; Yang, Chao [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sosonkina, Masha, E-mail: jvary@iastate.ed [Scalable Computing Laboratory, Ames Laboratory, Iowa State University, Ames, IA, 50011 (United States)

2009-07-01

The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10{sup 10} and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

Ab initio nuclear structure - the large sparse matrix eigenvalue problem

International Nuclear Information System (INIS)

Vary, James P; Maris, Pieter; Ng, Esmond; Yang, Chao; Sosonkina, Masha

2009-01-01

The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10 10 and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

Ab-initio calculations of superconducting properties of YBa2Cu3O7

International Nuclear Information System (INIS)

Zhao, G.L.; Bagayoko, D.

1999-01-01

The authors present ab-initio calculations for the electronic structure and superconducting properties of YBa 2 Cu 3 O 7 (YBCO). The electronic structure was calculated using a self-consistent ab-initio LCAO method. They solved the anisotropic Eliashberg gap equation numerically. The strong coupling of the high energy optical phonons around 60--73 meV, with the electrons at the Fermi surface, leads to a high Tc in YBCO. The calculated Tc is about 89 K for μ* = 0.1. The good agreement of the calculated results with experimental measurements and the ab-initio nature of the calculations support the scenario of an anisotropic s-wave superconductor for YBCO

On the impact of `smart tyres' on existing ABS/EBD control systems

Science.gov (United States)

Cheli, Federico; Leo, Elisbetta; Melzi, Stefano; Sabbioni, Edoardo

2010-12-01

The paper focuses on the possibility of enhancing the performances of the ABS (Antilock Braking System)/EBD (electronic braking distribution) control system by using the additional information provided by 'smart tyres' (i.e. tyres with embedded sensors and digital-computing capability). In particular, on the basis of previous works [Braghin et al., Future car active controls through the measurement of contact forces and patch features, Veh. Syst. Dyn. 44 (2006), pp. 3-13], the authors assumed that these components should be able to provide estimates for the normal loads acting on the four wheels and for the tyre-road friction coefficient. The benefits produced by the introduction of these additional channels into the existing ABS/EBD control logic were evaluated through simulations carried out with a validated 14 degrees of freedom (dofs) vehicle + ABS/EBD control logic numerical model. The performance of the ABS control system was evaluated through a series of braking manoeuvres on straight track focusing the attention on μ -jump conditions, while the performance of the EBD control system was assessed by means of braking manoeuvres carried out considering several weight distributions.

RssAB signaling coordinates early development of surface multicellularity in Serratia marcescens.

Directory of Open Access Journals (Sweden)

Yu-Huan Tsai

Full Text Available Bacteria can coordinate several multicellular behaviors in response to environmental changes. Among these, swarming and biofilm formation have attracted significant attention for their correlation with bacterial pathogenicity. However, little is known about when and where the signaling occurs to trigger either swarming or biofilm formation. We have previously identified an RssAB two-component system involved in the regulation of swarming motility and biofilm formation in Serratia marcescens. Here we monitored the RssAB signaling status within single cells by tracing the location of the translational fusion protein EGFP-RssB following development of swarming or biofilm formation. RssAB signaling is specifically activated before surface migration in swarming development and during the early stage of biofilm formation. The activation results in the release of RssB from its cognate inner membrane sensor kinase, RssA, to the cytoplasm where the downstream gene promoters are located. Such dynamic localization of RssB requires phosphorylation of this regulator. By revealing the temporal activation of RssAB signaling following development of surface multicellular behavior, our findings contribute to an improved understanding of how bacteria coordinate their lifestyle on a surface.

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Tratamento químico superficial e metalização de ABS, PVC e blendas de PVC/ABS

Directory of Open Access Journals (Sweden)

Ana Paula Kurek

2015-04-01

Full Text Available Visando à substituição do ABS em peças cromadas, amostras de PVC e blendas de PVC/ABS, na razão mássica de 20/80, 40/60 e 60/40, foram submetidas ao pré-tratamento em solução sulfocrômica sob diferentes condições de concentração, tempo e temperatura e sendo em seguida cromadas. As modificações na superfície das peças após o condicionamento foram analisadas por microscopia eletrônica de varredura, microscopia de força atômica e rugosidade. A qualidade da deposição metálica foi avaliada por inspeção visual e teste de adesão. Os resultados mostraram que, aumentando a concentração de PVC nas peças necessitou-se de condições operacionais mais agressivas, tais como maiores temperaturas de banho, tempo de imersão e concentração de solução sulfocrômica para que ocorresse a adesão da camada metálica. De todas as condições testadas com a solução condicionante sulfocrômica no tratamento das peças de PVC e blendas PVC/ABS de 20/80 e 40/60, a concentração de 350 g/L de ácido crômico e 400 g/L de ácido sulfúrico, temperatura de 70°C e tempo de imersão de 15 minutos, ocasionou deposição do metal em toda a superfície das peças, as quais foram aprovadas nos testes de adesão e corrosão.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

National Research Council Canada - National Science Library

Rogal, Jutta; Reuter, Karsten

2006-01-01

.... These techniques are referred to as first-principles (or in latin: ab initio) to indicate that they do not rely on empirical or fitted parameters, which then makes them applicable for a wide range of realistic conditions...

Growth and "1"3"7Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain

International Nuclear Information System (INIS)

Djedidi, Salem; Kojima, Katsuhiro; Ohkama-Ohtsu, Naoko; Bellingrath-Kimura, Sonoko Dorothea; Yokoyama, Tadashi

2016-01-01

Fifty six local Japanese cultivars of Brassica rapa (40 cultivars), Brassica juncea (10 cultivars) and Brassica napus (6 cultivars) were assessed for variability in growth and "1"3"7Cs uptake and accumulation in association with a Bacillus pumilus strain. Field trial was conducted at a contaminated farmland in Nihonmatsu city, in Fukushima prefecture. Inoculation resulted in different responses of the cultivars in terms of growth and radiocesium uptake and accumulation. B. pumilus induced a significant increase in shoot dry weight in 12 cultivars that reached up to 40% in one B. rapa and three B. juncea cultivars. Differences in radiocesium uptake were observed between the cultivars of each Brassica species. Generally, inoculation resulted in a significant increase in "1"3"7Cs uptake in 22 cultivars, while in seven cultivars it was significantly decreased. Regardless of plant cultivar and bacterial inoculation, the transfer of "1"3"7Cs to the plant shoots (TF) varied by a factor of up to 5 and it ranged from to 0.011 to 0.054. Five inoculated cultivars, showed enhanced shoot dry weights and decreased "1"3"7Cs accumulations, among which two B. rapa cultivars named Bitamina and Nozawana had a significantly decreased "1"3"7Cs accumulation in their shoots. Such cultivars could be utilized to minimize the entry of radiocesium into the food chain; however, verifying the consistency of their radiocesium accumulation in other soils is strongly required. Moreover, the variations in growth and radiocesium accumulation, as influenced by Bacillus inoculation, could help selecting well grown inoculated Brassica cultivars with low radiocesium accumulation in their shoots. - Highlights: • Out of 56 Brassica cultivars, inoculation significantly increased shoot dry weight in 12 cultivars. • Inoculation triggered a significant increase and decrease in "1"3"7Cs uptake, respectively in 22 and 7 cultivars. • Five cultivars had an enhanced shoot dry weight and decreased "1"3"7Cs

Inheritance Patterns, Dominance and Cross-Resistance of Cry1Ab- and Cry1Ac-Selected Ostrinia furnacalis (Guenée

Directory of Open Access Journals (Sweden)

Tiantao Zhang

2014-09-01

Full Text Available Two colonies of Asian corn borer, Ostrinia furnacalis (Guenée, artificially selected from a Bt-susceptible colony (ACB-BtS for resistance to Cry1Ab (ACB-AbR and Cry1Ac (ACB-AcR toxins, were used to analyze inheritance patterns of resistance to Cry1 toxins. ACB-AbR and ACB-AcR evolved significant levels of resistance, with resistance ratios (RR of 39-fold and 78.8-fold to Cry1Ab and Cry1Ac, respectively. The susceptibility of ACB-AbR larvae to Cry1Ac and Cry1F toxins, which had not previously been exposed, were significantly reduced, being >113-fold and 48-fold, respectively. Similarly, susceptibility of ACB-AcR larvae to Cry1Ab and Cry1F were also significantly reduced (RR > nine-fold, RR > 18-fold, respectively, indicating cross-resistance among Cry1Ab, Cry1Ac, and Cry1F toxins. However, ACB-AbR and ACB-AcR larvae were equally susceptible to Cry1Ie as were ACB-BtS larvae, indicating no cross-resistance between Cry1Ie and Cry1Ab or Cry1Ac toxins; this may provide considerable benefits in preventing or delaying the evolution of resistance in ACB to Cry1Ab and Cry1Ac toxins. Backcrossing studies indicated that resistance to Cry1Ab toxin was polygenic in ACB-AbR, but monogenic in ACB-AcR, whilst resistance to Cry1Ac toxin was primarily monogenic in both ACB-AbR and ACB-AcR, but polygenic as resistance increased.

Formation of reflective and conductive silver film on ABS surface via covalent grafting and solution spray

Energy Technology Data Exchange (ETDEWEB)

Chen, Dexin; Zhang, Yan [School of Mechanical and Automotive Engineering, South China University of Technology, 381 Wushan, Guangzhou 510640 (China); Bessho, Takeshi [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan); Kudo, Takahiro; Sang, Jing; Hirahara, Hidetoshi; Mori, Kunio [Faculty of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan); Kang, Zhixin, E-mail: zxkang@scut.edu.cn [School of Mechanical and Automotive Engineering, South China University of Technology, 381 Wushan, Guangzhou 510640 (China)

2015-09-15

Highlights: • A pure and homogenous silver film was deposited by spray-style plating technique. • The mechanism of covalent bonding between coating and substrate was studied. • The silver coating is highly reflective and conductive. • UV light was used to activate the ABS surface with triazine azide derivative. - Abstract: Conductive and reflective silver layers on acrylonitrile butadiene styrene (ABS) plastics have been prepared by photo grafting of triazine azides upon ultraviolet activation, self-assembling of triazine dithiols and silver electroless plating by solution spray based on silver mirror reaction. The as-prepared silver film exhibited excellent adhesion with ABS owing to covalent bonds between coating and substrate, and the detailed bonding mechanism have been investigated by X-ray photoelectron spectroscopy (XPS). X-ray diffraction (XRD) result revealed that silver film on ABS was pure and with a nanocrystalline structure. Atomic force microscope (AFM) analysis demonstrated that massive silver particles with sizes varying from 80 to 120 nm were deposited on ABS and formed a homogenous and smooth coating, resulting in highly reflective surface. Furthermore, silver maintained its unique conductivity even as film on ABS surface in term of four-point probe method.

Formation of reflective and conductive silver film on ABS surface via covalent grafting and solution spray

International Nuclear Information System (INIS)

Chen, Dexin; Zhang, Yan; Bessho, Takeshi; Kudo, Takahiro; Sang, Jing; Hirahara, Hidetoshi; Mori, Kunio; Kang, Zhixin

2015-01-01

Highlights: • A pure and homogenous silver film was deposited by spray-style plating technique. • The mechanism of covalent bonding between coating and substrate was studied. • The silver coating is highly reflective and conductive. • UV light was used to activate the ABS surface with triazine azide derivative. - Abstract: Conductive and reflective silver layers on acrylonitrile butadiene styrene (ABS) plastics have been prepared by photo grafting of triazine azides upon ultraviolet activation, self-assembling of triazine dithiols and silver electroless plating by solution spray based on silver mirror reaction. The as-prepared silver film exhibited excellent adhesion with ABS owing to covalent bonds between coating and substrate, and the detailed bonding mechanism have been investigated by X-ray photoelectron spectroscopy (XPS). X-ray diffraction (XRD) result revealed that silver film on ABS was pure and with a nanocrystalline structure. Atomic force microscope (AFM) analysis demonstrated that massive silver particles with sizes varying from 80 to 120 nm were deposited on ABS and formed a homogenous and smooth coating, resulting in highly reflective surface. Furthermore, silver maintained its unique conductivity even as film on ABS surface in term of four-point probe method

Evaluation of a fully automated treponemal test and comparison with conventional VDRL and FTA-ABS tests.

Science.gov (United States)

Park, Yongjung; Park, Younhee; Joo, Shin Young; Park, Myoung Hee; Kim, Hyon-Suk

2011-11-01

We evaluated analytic performances of an automated treponemal test and compared this test with the Venereal Disease Research Laboratory test (VDRL) and fluorescent treponemal antibody absorption test (FTA-ABS). Precision performance of the Architect Syphilis TP assay (TP; Abbott Japan, Tokyo, Japan) was assessed, and 150 serum samples were assayed with the TP before and after heat inactivation to estimate the effect of heat inactivation. A total of 616 specimens were tested with the FTA-ABS and TP, and 400 were examined with the VDRL. The TP showed good precision performance with total imprecision of less than a 10% coefficient of variation. An excellent linear relationship between results before and after heat inactivation was observed (R(2) = 0.9961). The FTA-ABS and TP agreed well with a κ coefficient of 0.981. The concordance rate between the FTA-ABS and TP was the highest (99.0%), followed by the rates between FTA-ABS and VDRL (85.0%) and between TP and VDRL (83.8%). The automated TP assay may be adequate for screening for syphilis in a large volume of samples and can be an alternative to FTA-ABS.

AP calculus AB/BC

CERN Document Server

Schwartz, Stu

2013-01-01

All Access for the AP® Calculus AB & BC Exams Book + Web + Mobile Everything you need to prepare for the Advanced Placement® exam, in a study system built around you! There are many different ways to prepare for an Advanced Placement® exam. What's best for you depends on how much time you have to study and how comfortable you are with the subject matter. To score your highest, you need a system that can be customized to fit you: your schedule, your learning style, and your current level of knowledge. This book, and the free online tools that come with it, will help you personalize your AP® Cal

Combined glaucoma and cataract surgery: Comparison of viscocanalostomy, endocyclophotocoagulation, and ab interno trabeculectomy.

Science.gov (United States)

Moghimi, Sasan; Hamzeh, Nikoo; Mohammadi, Massood; Khatibi, Nassim; Bowd, Christopher; Weinreb, Robert N

2018-05-01

To compare outcomes of phacoemulsification combined with viscocanalostomy, endocyclophotocoagulation (ECP), or ab interno trabulectomy for intraocular pressure (IOP) control and safety in eyes with open-angle glaucoma and visually significant cataract. Farabi Eye Hospital, Tehran, Iran. Retrospective case series. Medical records of patients who had combined surgery and were followed for at least 1 year were reviewed. Complete success, postoperative IOP, number of medications at each visit, and complications were evaluated and compared before and after adjustments for confounders. Forty-six eyes had combined phacoviscocanalostomy, 35 had phaco-ECP, and 28 eyes phaco-ab interno trabulectomy. The groups were matched for baseline IOP (P = .24). At the final follow-up (mean 17.2 months ± 5.5 [SD]), the phacoviscocanalostomy group had the lowest mean IOP (13.5 ± 4.7 mm Hg, 29% decrease) (P = .01). There was no significant difference in the final IOP between phaco-ECP and phaco-ab interno trabulectomy (16.4 ± 3.9 mm Hg, 20% decrease versus 15.8 ± 4.2 mm Hg, 15% decrease) (P = .88). The reduction in the number of medications was greater with phacoviscocanalostomy (77%) than with phaco-ECP (40%) and phaco-ab interno trabulectomy (44%) (P = .01). Phacoemulsification-ab interno trabulectomy had the fewest complications. Intraocular pressure spikes were more frequent in the phaco-ECP group (20%) than in the other groups (4%) (P = .05). All procedures significantly lowered IOP. Phacoemulsification-ab interno trabulectomy resulted in fewest complications and phacoviscocanalostomy led to the largest IOP drop and largest reduction of medications. Copyright © 2018 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Field-evolved resistance to Cry1Ab maize by Spodoptera frugiperda in Brazil.

Science.gov (United States)

Omoto, Celso; Bernardi, Oderlei; Salmeron, Eloisa; Sorgatto, Rodrigo J; Dourado, Patrick M; Crivellari, Augusto; Carvalho, Renato A; Willse, Alan; Martinelli, Samuel; Head, Graham P

2016-09-01

The first Bt maize in Brazil was launched in 2008 and contained the MON 810 event, which expresses Cry1Ab protein. Although the Cry1Ab dose in MON 810 is not high against fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), MON 810 provided commercial levels of control. To support insect resistance management in Brazil, the baseline and ongoing susceptibility of FAW was examined using protein bioassays, and the level of control and life history parameters of FAW were evaluated on MON 810 maize. Baseline diet overlay assays with Cry1Ab (16 µg cm(-2) ) caused 76.3% mortality to field FAW populations sampled in 2009. Moderate mortality (48.8%) and significant growth inhibition (88.4%) were verified in leaf-disc bioassays. In greenhouse trials, MON 810 had significantly less damage than non-Bt maize. The surviving FAW larvae on MON 810 (22.4%) had a 5.5 day increase in life cycle time and a 24% reduction in population growth rate. Resistance monitoring (2010-2015) showed a significant reduction in Cry1Ab susceptibility of FAW over time. Additionally, a significant reduction in the field efficacy of MON 810 maize against FAW was observed in different regions from crop season 2009 to 2013. The decrease in susceptibility to Cry1Ab was expected, but the specific contributions to this resistance by MON 810 maize cannot be distinguished from cross-resistance to Cry1Ab caused by exposure to Cry1F maize. Technologies combining multiple novel insecticidal traits with no cross-resistance to the current Cry1 proteins and high activity against the same target pests should be pursued in Brazil and similar environments. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Synthesis of an A'B' Precursor to Angelmicin B: Product Diversification in the Suárez Lactol Fragmentation.

Science.gov (United States)

Li, Jialiang; Todaro, Louis; Mootoo, David R

2011-11-01

We describe a synthetic strategy for the angelimicin family of anthraquinoid natural products that involves converting a central highly oxygenated decalin intermediate to the AB and A'B' subunits. Herein, we report the synthesis of the bicyclic A'B' subunit that complements our earlier route to the tricyclic AB framework. The differentiating tact in the two syntheses focused on controlling the Suárez radical fragmentation of lactol precursors by modulating the substrate's structural rigidity. A more flexible lactol gave the tricyclic AB framework, whereas a more rigid substrate led to the bicyclic A'B' precursor, presumably through divergent pathways from the radical produced in the initial fragmentation step. These results establish a versatile advanced synthetic precursor for the angelimicins, and on a more general note, illustrate strategies for applying the Suárez fragmentation to diverse and complex molecular frameworks.

The B-subdomain of the Xenopus laevis XFIN KRAB-AB domain is responsible for its weaker transcriptional repressor activity compared to human ZNF10/Kox1.

Science.gov (United States)

Born, Nadine; Thiesen, Hans-Jürgen; Lorenz, Peter

2014-01-01

The Krüppel-associated box (KRAB) domain interacts with the nuclear hub protein TRIM28 to initiate or mediate chromatin-dependent processes like transcriptional repression, imprinting or suppression of endogenous retroviruses. The prototype KRAB domain initially identified in ZNF10/KOX1 encompasses two subdomains A and B that are found in hundreds of zinc finger transcription factors studied in human and murine genomes. Here we demonstrate for the first time transcriptional repressor activity of an amphibian KRAB domain. After sequence correction, the updated KRAB-AB domain of zinc finger protein XFIN from the frog Xenopus laevis was found to confer transcriptional repression in reporter assays in Xenopus laevis A6 kidney cells as well as in human HeLa, but not in the minnow Pimephales promelas fish cell line EPC. Binding of the XFIN KRAB-AB domain to human TRIM28 was demonstrated in a classical co-immunoprecipitation approach and visualized in a single-cell compartmentalization assay. XFIN-AB displayed reduced potency in repression as well as lower strength of interaction with TRIM28 compared to ZNF10 KRAB-AB. KRAB-B subdomain swapping between the two KRAB domains indicated that it was mainly the KRAB-B subdomain of XFIN that was responsible for its lower capacity in repression and binding to human TRIM28. In EPC fish cells, ZNF10 and XFIN KRAB repressor activity could be partially restored to low levels by adding exogenous human TRIM28. In contrast to XFIN, we did not find any transcriptional repression activity for the KRAB-like domain of human PRDM9 in HeLa cells. PRDM9 is thought to harbor an evolutionary older domain related to KRAB whose homologs even occur in invertebrates. Our results support the notion that functional bona fide KRAB domains which confer transcriptional repression and interact with TRIM28 most likely co-evolved together with TRIM28 at the beginning of tetrapode evolution.

AB INITIO calculations of magneto-optical effects

Czech Academy of Sciences Publication Activity Database

Kuneš, Jan; Oppeneer, P. M.

2002-01-01

Roč. 2, - (2002), s. 141-146 ISSN 1346-7948 R&D Projects: GA AV ČR IAA1010214 Institutional research plan: CEZ:AV0Z1010914 Keywords : electronic structure * ab initio calculation * polar magneto-optical Kerr effect * transitiom metal * uranium intermetallics * CrO 2 Subject RIV: BM - Solid Matter Physics ; Magnetism

Evaluation of tumor targeting with radiolabeled F(ab2 fragment of a humanized monoclonal antibody

Directory of Open Access Journals (Sweden)

"Babaei MH

2002-08-01

Full Text Available Humanized monoclonal antibody U36 and its F(ab'2 fragment, radio labeled with 125I, were tested for tumor localization in nude mice bearing a squamous cell carcinoma xenograft line derived from a head and neck carcinoma. Monoclonal antibody IgG or F(ab'2 fragment were injected in parallel and at days 1, 2 and 3, mice were dissected for determination of isotope biodistribution. IgG as well as F(ab'2 showed highly specific localization in tumor tissue. The mean tumor uptake (n=3 is expressed as the percentage of the injected dose per gram of tumor tissue (%ID/g. %ID/g of IgG was 11.7% at day 1 and decreased to 10.9% at day 3 whereas %ID/g of F(ab'2 was 2.9% at day 1 and decreased on following days. Tumor to blood ratios (T/B at day 1 were 0.86 for IgG and 1.32 for F(ab'2 and reached a maximum at day 3 with values of 4.41 and 1.84 respectively. These findings suggest that the superior tumor to non-tumor ratios in the day of 1 render the F(ab'2 fragment more qualified for specific targeting radioisotopes to tumor xenografts in this exprimental setting.

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Ab initio investigation of isomerism in not rigid dimer molecules of (LiAB)2 salts with 20 valent electrons (AB-=BO-, AlO-, BS-, AlS-, CN-, CP-, SiN-, SiP-)

International Nuclear Information System (INIS)

Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.; Shlojer, P.R.

1999-01-01

Ab initio calculations of potential energy surfaces in neighborhood of key structures of non rigid dimer molecules of lithium salts of (LiAB) 2 type - (LiBO) 2 , (LiAlO) 2 , (LiBS) 2 , (LiAlS) 2 , (LiCN) 2 , (LiSiN) 2 , (LiCP) 2 , (LiSiP) 2 - with 20 valent electrons are done in the framework of MP2/6-31G8//HF/6-31G* + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations. Totality of low-lying isomers containing four- and six-membered cycles with lithium bridges is localized. It is shown that for all cycles not rigidity to high deformation of angles in the case of low energy changes is characterized. Equilibrium geometrical parameters, relative energy and energy of isomer decomposition, frequency and intensities of normal vibrations are determined [ru

Leonid Apananski müüs AB Grupi maa oma firmale / Silva Männik

Index Scriptorium Estoniae

Männik, Silva, 1974-

1999-01-01

Ilmunud ka: Den za Dnjom Nov/26 lk. 8. Apananski müüs AB Kindlustuse Grupile kuulunud Maakri tänava kinnistu. Skeem: AB Grupist on välja viidud ligikaudu 70 milj. krooni. Ilmunud ka: Den za Dnjom 23. nov. lk. 3

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

Science.gov (United States)

Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

2016-01-01

Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

Discovery and annotation of small proteins using genomics, proteomics and computational approaches

Energy Technology Data Exchange (ETDEWEB)

Yang, Xiaohan; Tschaplinski, Timothy J.; Hurst, Gregory B.; Jawdy, Sara; Abraham, Paul E.; Lankford, Patricia K.; Adams, Rachel M.; Shah, Manesh B.; Hettich, Robert L.; Lindquist, Erika; Kalluri, Udaya C.; Gunter, Lee E.; Pennacchio, Christa; Tuskan, Gerald A.

2011-03-02

Small proteins (10 200 amino acids aa in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained 2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10 200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) codingpotential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

Augmented wave ab initio EFG calculations: some methodological warnings

International Nuclear Information System (INIS)

Errico, Leonardo A.; Renteria, Mario; Petrilli, Helena M.

2007-01-01

We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO 2 . The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects

Augmented wave ab initio EFG calculations: some methodological warnings

Energy Technology Data Exchange (ETDEWEB)

Errico, Leonardo A. [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Renteria, Mario [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Petrilli, Helena M. [Instituto de Fisica-DFMT, Universidade de Sao Paulo, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: hmpetril@macbeth.if.usp.br

2007-02-01

We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO{sub 2}. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.

Data characteristics and preliminary results from the atacama b-mode search (ABS)

Science.gov (United States)

Visnjic, Catherine

The Atacama B-Mode Search (ABS) is a 145 GHz polarimeter located at a high altitude site on Cerro Toco, in the Andes of northern Chile. Having deployed in early 2012, it is currently in its second year of operation, observing the polarization of the Cosmic Microwave Background (CMB). It seeks to probe the as yet undetected odd-parity B-modes of the polarization, which would have been created by the primordial gravitational wave background (GWB) predicted by theories of inflation. The magnitude of the B-mode signal is characterized by the tensor-to-scalar ratio, r. ABS features 60 cm cryogenic reflectors in the crossed-Dragone configuration, and a warm, continuously rotating sapphire half-wave plate to modulate the polarization of incoming radiation. The focal plane consists of 480 antenna-coupled transition edge sensor bolometers, arranged in orthogonal pairs for polarization sensitivity, and coupled to feedhorns in a hexagonal array. In this thesis we describe the ABS instrument in the state in which it is now operating, outline the first season of observations, and characterize the data obtained. Focusing on observations of the primary CMB field during a one month reference period, we detail the algorithms currently used to select the data suitable for making maps. This is the first pass at data cuts and provides a conservative estimate for the sensitivity of ABS to the polarization modes in the sky. We project that with one year total observation time of the primary CMB field, ABS should be able to detect the B-mode signal at roughly the level of r = 0.03.

Combined clear corneal phacoemulsification and ab interno trabeculectomy: three-year case series.

Science.gov (United States)

Ferrari, Ettore; Bandello, Francesco; Roman-Pognuz, Derri; Menchini, Francesca

2005-09-01

To evaluate the efficacy and safety of a novel surgical approach, ab interno trabeculectomy, in a combined procedure (clear corneal phacoemulsification + ab interno trabeculectomy) for the management of concurrent cataract and glaucoma with prognostic factors for filtration failure. Department of Ophthalmology, Palmanova Hospital, Udine, Italy. A prospective noncomparative case series of 11 eyes of 11 consecutive cataract patients with medically uncontrolled primary open-angle glaucoma or pseudoexfoliation glaucoma was performed. Each patient had phacoemulsification + intraocular lens implantation + ab interno trabeculectomy, which consisted of a gonioscopically controlled ab interno removal of a quadrant (3 clock hours) of the trabecular meshwork. The main outcome measures were intraocular pressure (IOP), the number of antiglaucomatous medications used, and complications. Ten patients completed a 3-year follow-up. One patient had further surgery because of poor IOP control; in this case, the last valid observation was carried forward for IOP calculation. Mean preoperative IOP and IOPs measured 1, 3, 6, 12, 24, and 36 months after surgery were 25.0, 15.8, 15.4, 15.4, 15.2, 15.0, and 15.3 (-38.56%) mm Hg respectively. The number of medications averaged 2.4 before surgery and dropped to 0.8 at the end of follow-up. No major complications occurred during the follow-up period. The new surgical procedure combining phacoemulsification with ab interno trabeculectomy can induce a clinically relevant decrease in IOP in eyes with cataract and glaucoma with poor prognosis for filtering surgery. However, a randomized controlled clinical trial with a more extended follow-up and a larger series of patients is needed to ascertain the actual effectiveness and safety of this procedure.

The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

International Nuclear Information System (INIS)

Perron, A.; Turchi, P.E.A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.

2015-01-01

Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies

The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

Energy Technology Data Exchange (ETDEWEB)

Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)

2015-03-15

Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.

Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.

Science.gov (United States)

Liu, Maoyan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

2016-03-01

The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

Ab initio lattice dynamics of metal surfaces

International Nuclear Information System (INIS)

Heid, R.; Bohnen, K.-P.

2003-01-01

Dynamical properties of atoms on surfaces depend sensitively on their bonding environment and thus provide valuable insight into the local geometry and chemical binding at the boundary of a solid. Density-functional theory provides a unified approach to the calculation of structural and dynamical properties from first principles. Its high accuracy and predictive power for lattice dynamical properties of semiconductor surfaces has been demonstrated in a previous article by Fritsch and Schroeder (Phys. Rep. 309 (1999) 209). In this report, we review the state-of-the-art of these ab initio approaches to surface dynamical properties of metal surfaces. We give a brief introduction to the conceptual framework with focus on recent advances in computational procedures for the ab initio linear-response approach, which have been a prerequisite for an efficient treatment of surface dynamics of noble and transition metals. The discussed applications to clean and adsorbate-covered surfaces demonstrate the high accuracy and reliability of this approach in predicting detailed microscopic properties of the phonon dynamics for a wide range of metallic surfaces

Focused Wind Mass Accretion in Mira AB

Science.gov (United States)

Karovska, Margarita; de Val-Borro, M.; Hack, W.; Raymond, J.; Sasselov, D.; Lee, N. P.

2011-05-01

At a distance of about only 100pc, Mira AB is the nearest symbiotic system containing an Asymptotic Giant Branch (AGB) star (Mira A), and a compact accreting companion (Mira B) at about 0.5" from Mira A. Symbiotic systems are interacting binaries with a key evolutionary importance as potential progenitors of a fraction of asymmetric Planetary Nebulae, and SN type Ia, cosmological distance indicators. The region of interaction has been studied using high-angular resolution, multiwavelength observations ranging from radio to X-ray wavelengths. Our results, including high-angular resolution Chandra imaging, show a "bridge" between Mira A and Mira B, indicating gravitational focusing of the Mira A wind, whereby components exchange matter directly in addition to the wind accretion. We carried out a study using 2-D hydrodynamical models of focused wind mass accretion to determine the region of wind acceleration and the characteristics of the accretion in Mira AB. We highlight some of our results and discuss the impact on our understanding of accretion processes in symbiotic systems and other detached and semidetached interacting systems.

Ab initio transport across bismuth selenide surface barriers

KAUST Repository

Narayan, Awadhesh; Rungger, Ivan; Droghetti, Andrea; Sanvito, Stefano

2014-01-01

© 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results

Brassica juncea nitric oxide synthase like activity is stimulated by PKC activators and calcium suggesting modulation by PKC-like kinase.

Science.gov (United States)

Talwar, Pooja Saigal; Gupta, Ravi; Maurya, Arun Kumar; Deswal, Renu

2012-11-01

Nitric oxide (NO) is an important signaling molecule having varied physiological and regulatory roles in biological systems. The fact that nitric oxide synthase (NOS) is responsible for NO generation in animals, prompted major search for a similar enzyme in plants. Arginine dependent NOS like activity (BjNOSla) was detected in Brassica juncea seedlings using oxyhemoglobin and citrulline assays. BjNOSla showed 25% activation by NADPH (0.4 mM) and 40% by calcium (0.4 mM) but the activity was flavin mononucleotide (FMN), flavin dinucleotide (FAD) and calmodulin (CaM) independent. Pharmacological approach using mammalian NOS inhibitors, NBT (300 μM) and l-NAME (5 mM), showed significant inhibition (100% and 67% respectively) supporting that the BjNOSla operates via the oxidative pathway. Most of the BjNOSla activity (80%) was confined to shoot while root showed only 20% activity. Localization studies by NADPH-diaphorase and DAF-2DA staining showed the presence of BjNOSla in guard cells. Kinetic analysis showed positive cooperativity with calcium as reflected by a decreased K(m) (∼13%) and almost two fold increase in V(max). PMA (438 nM), a kinase activator, activated BjNOSla ∼1.9 fold while its inactive analog 4αPDD was ineffective. Calcium and PMA activated the enzyme to ∼3 folds. Interestingly, 1,2-DG6 (2.5 μM) and PS (1 μM) with calcium activated the enzyme activity to ∼7 fold. A significant inhibition of BjNOSla by PKC inhibitors-staurosporine (∼90%) and calphostin-C (∼40%), further supports involvement of PKC-like kinase. The activity was also enhanced by abiotic stress conditions (7-46%). All these findings suggest that BjNOSla generates NO via oxidative pathway and is probably regulated by phosphorylation. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Thiourea, a ROS scavenger, regulates source-to-sink relationship to enhance crop yield and oil content in Brassica juncea (L..

Directory of Open Access Journals (Sweden)

Manish Pandey

Full Text Available In the present agricultural scenario, the major thrust is to increase crop productivity so as to ensure sustainability. In an earlier study, foliar application of thiourea (TU; a non physiological thiol based ROS scavenger has been demonstrated to enhance the stress tolerance and yield of different crops under field condition. Towards this endeavor, present work deals with the effect of TU on photosynthetic efficiency and source-to-sink relationship of Indian mustard (Brassica juncea for understanding its mode of action. The application of TU increased the efficiency of both PSI and PSII photosystems and vegetative growth of plant. The comparative analysis of sucrose to starch ratio and expression level of sugar transporters confirmed the higher source and sink strength in response to TU treatment. The biochemical evidence in support of this was derived from higher activities of sucrose phosphate synthase and fructose-1,6-bis-phosphatase at source; and sucrose synthase and different classes of invertases at both source and sink. This indicated an overall increase in photoassimilate level at sink. An additional contribution through pod photosynthesis was confirmed through the analysis of phosphoenol pyruvate carboxylase enzyme activity and level of organic acids. The increased photoassimilate level was also co-ordinated with acetyl coA carboxylase mediated oil biosynthesis. All these changes were ultimately reflected in the form of 10 and 20% increase in total yield and oil content, respectively under TU treatment as compared to control. Additionally, no change was observed in oil composition of seeds derived from TU treated plants. The study thus signifies the co-ordinated regulation of key steps of photosynthesis and source-to-sink relationship through the external application of TU resulting in increased crop yield and oil content.

Synergistic action of tropospheric ozone and carbon dioxide on yield and nutritional quality of Indian mustard (Brassica juncea (L.) Czern.).

Science.gov (United States)

Singh, Satyavan; Bhatia, Arti; Tomer, Ritu; Kumar, Vinod; Singh, B; Singh, S D

2013-08-01

Field experiments were conducted in open top chamber during rabi seasons of 2009-10 and 2010-11 at the research farm of the Indian Agricultural Research Institute, New Delhi to study the effect of tropospheric ozone (O3) and carbon dioxide (CO2) interaction on yield and nutritional quality of Indian mustard (Brassica juncea (L.) Czern.). Mustard plants were grown from emergence to maturity under different treatments: charcoal-filtered air (CF, 80-85 % less O3 than ambient O3 and ambient CO2), nonfiltered air (NF, 5-10 % less O3 than ambient O3 and ambient CO2 ), nonfiltered air with elevated carbon dioxide (NF + CO2, NF air and 550 ± 50 ppm CO2), elevated ozone (EO, NF air and 25-35 ppb elevated O3), elevated ozone along with elevated carbon dioxide (EO + CO2, NF air, 25-35 ppb O3 and 550 ± 50 ppm CO2), and ambient chamber less control (AC, ambient O3 and CO2). Elevated O3 exposure led to reduced photosynthesis and leaf area index resulting in decreased seed yield of mustard. Elevated ozone significantly decreased the oil and micronutrient content in mustard. Thirteen to 17 ppm hour O3 exposure (accumulated over threshold of 40 ppm, AOT 40) reduced the oil content by 18-20 %. Elevated CO2 (500 ± 50 ppm) along with EO was able to counter the decline in oil content in the seed, and it increased by 11 to 13 % over EO alone. Elevated CO2, however, decreased protein, calcium, zinc, iron, magnesium, and sulfur content in seed as compared to the nonfiltered control, whereas removal of O3 from air in the charcoal-filtered treatment resulted in a significant increase in the same.

Phage-Mediated Competitive Chemiluminescent Immunoassay for Detecting Cry1Ab Toxin by Using an Anti-Idiotypic Camel Nanobody.

Science.gov (United States)

Qiu, Yulou; Li, Pan; Dong, Sa; Zhang, Xiaoshuai; Yang, Qianru; Wang, Yulong; Ge, Jing; Hammock, Bruce D; Zhang, Cunzheng; Liu, Xianjin

2018-01-31

Cry toxins have been widely used in genetically modified organisms for pest control, raising public concern regarding their effects on the natural environment and food safety. In this work, a phage-mediated competitive chemiluminescent immunoassay (c-CLIA) was developed for determination of Cry1Ab toxin using anti-idiotypic camel nanobodies. By extracting RNA from camels' peripheral blood lymphocytes, a naive phage-displayed nanobody library was established. Using anti-Cry1Ab toxin monoclonal antibodies (mAbs) against the library for anti-idiotypic antibody screening, four anti-idiotypic nanobodies were selected and confirmed to be specific for anti-Cry1Ab mAb binding. Thereafter, a c-CLIA was developed for detection of Cry1Ab toxin based on anti-idiotypic camel nanobodies and employed for sample testing. The results revealed a half-inhibition concentration of developed assay to be 42.68 ± 2.54 ng/mL, in the linear range of 10.49-307.1 ng/mL. The established method is highly specific for Cry1Ab recognition, with negligible cross-reactivity for other Cry toxins. For spiked cereal samples, the recoveries of Cry1Ab toxin ranged from 77.4% to 127%, with coefficient of variation of less than 9%. This study demonstrated that the competitive format based on phage-displayed anti-idiotypic nanobodies can provide an alternative strategy for Cry toxin detection.

Avaliação da degradação térmica e fotooxidativa do ABS Automotivo Thermal degradation and Photo-oxidation of the ABS used for automotive applications

Directory of Open Access Journals (Sweden)

Elisabete M. S. Sanchez

1999-12-01

Full Text Available A degradação do ABS foi avaliada após envelhecimento térmico (ASTM D794 e fotooxidativo (ASTM G53 e G24. Essas condições foram escolhidas na tentativa de simular as condições a que esse polímero é submetido durante seu ciclo de vida como componente automobilístico. As mudanças ocorridas no ABS envelhecido pelos três métodos, em diferentes tempos, foram caracterizadas por ensaios mecânicos de tração e impacto, pelo índice de fluidez, pelo índice de carbonilas (FT-IR, pelo índice de amarelecimento e por fotografias ampliadas das fraturas de impacto. Os resultados mostraram que cada técnica utilizada fornece uma resposta característica em função do método de envelhecimento utilizado. A aplicação de técnicas de análise multivariada aos resultados permitiu uma visualização da degradação do material em função das técnicas de envelhecimento.The ABS degradation was investigated after thermal- (80°C and photo-oxidative ageing (ASTM G53 and G24. These conditions were selected to simulate a car interior and the ABS lifetime weatherability. ABS changes were characterised by mechanical properties, melt flow index, carbonyl index (FT-IR, yellowing index and macro-photography of impact fracture. The results showed that each technique gives a characteristically answer for the ageing method. The multivariate analysis provided the degradation view as a function of the ageing method.

Time-resolved photoelectron spectroscopy and ab initio multiple spawning studies of hexamethylcyclopentadiene

DEFF Research Database (Denmark)

Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

2014-01-01

Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.......Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....

Ab Initio Molecular Dynamics Simulations of Furfural at the Liquid-Solid Interface

OpenAIRE

Sanwu Wang; Hongli Dang; Wenhua Xue; Darwin Shields; Xin Liu; Friederike C. Jentoft; Daniel E. Resasco

2013-01-01

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurati...

Geographic isolates of Lymantria dispar multiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains.

Science.gov (United States)

Harrison, Robert L; Rowley, Daniel L; Keena, Melody A

2016-06-01

Isolates of the baculovirus species Lymantria dispar multiple nucleopolyhedrovirus have been formulated and applied to suppress outbreaks of the gypsy moth, L. dispar. To evaluate the genetic diversity in this species at the genomic level, the genomes of three isolates from Massachusetts, USA (LdMNPV-Ab-a624), Spain (LdMNPV-3054), and Japan (LdMNPV-3041) were sequenced and compared with four previously determined LdMNPV genome sequences. The LdMNPV genome sequences were collinear and contained the same homologous repeats (hrs) and clusters of baculovirus repeat orf (bro) gene family members in the same relative positions in their genomes, although sequence identities in these regions were low. Of 146 non-bro ORFs annotated in the genome of the representative isolate LdMNPV 5-6, 135 ORFs were found in every other LdMNPV genome, including the 37 core genes of Baculoviridae and other genes conserved in genus Alphabaculovirus. Phylogenetic inference with an alignment of the core gene nucleotide sequences grouped isolates 3041 (Japan) and 2161 (Korea) separately from a cluster containing isolates from Europe, North America, and Russia. To examine phenotypic diversity, bioassays were carried out with a selection of isolates against neonate larvae from three European gypsy moth (Lymantria dispar dispar) and three Asian gypsy moth (Lymantria dispar asiatica and Lymantria dispar japonica) colonies. LdMNPV isolates 2161 (Korea), 3029 (Russia), and 3041 (Japan) exhibited a greater degree of pathogenicity against all L. dispar strains than LdMNPV from a sample of Gypchek. This study provides additional information on the genetic diversity of LdMNPV isolates and their activity against the Asian gypsy moth, a potential invasive pest of North American trees and forests. Published by Elsevier Inc.

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Atomic carbon chains as spin-transmitters: An ab initio transport study

DEFF Research Database (Denmark)

Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

2010-01-01

An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin...

Mercury genomics in the Arctic Ocean

Science.gov (United States)

Bowman, K.; Lamborg, C. H.; Collins, E.; Hammerschmidt, C. R.; Agather, A. M.

2017-12-01

Methyl-mercury production in the ocean is likely dependent on microbial activity, however, methylation pathways remain elusive. In the Arctic, high concentrations of methyl-mercury are found in top predator marine mammals and seabirds. As a result of seafood consumption, pregnant women and women of child-bearing age in the Arctic often have blood Hg concentrations that exceed U.S. and Canadian safety guidelines. To understand the chemical cycling of mercury in the Arctic Ocean we participated in the 2015 U.S. GEOTRACES Arctic expedition (GN01) to measure Hg speciation in the water column of the Bering Sea, Makarov basin, and Canada basin between Dutch Harbor, Alaska and the North Pole. At select stations, seawater was filtered through 0.22 µm Sterivex filters and genomic DNA was collected using a phenol-chloroform extraction. Broad-range degenerate PCR primers were used to detect the presence of hgcAB, and clade-specific degenerate quantitative PCR primers were used to determine the abundance of hgcA. Metagenomic sequencing was done at three stations to identify taxonomic and functional groups, and to search for hgcA-like genes that the PCR primers may have missed.

Genotyping of Helicobacter pylori Strains Isolated from Patients with Gastric Ulcer and Non Ulcer Disease using RFLP-PCR of ureAB, vacA , cagA Genes

Directory of Open Access Journals (Sweden)

Sh. Farshad

2008-10-01

Full Text Available Introduction & Objective: Different studies show that the reasons for clinically diverse outcomes of infections caused by H. pylori may include host and environmental factors as well as differences in the prevalence or expression of bacterial virulence factors. The aim of this study was to study the distribution of different genotypes of major virulence factors cagA, vacA and ureAB among H. pylori strains isolated from patients with gastric ulcer (ulcerative disease and patients with gastritis (non ulcerative disease.Materials & Methods: In this cross sectional study 65 H. pylori strains, 30 from patients with gastric ulcer and 35 from patients with non ulcerative gastritis disease were investigated by RFLP-PCR.Results: The prevalence of vacA-positive strains in ulcerative patients was significantly more than that in non ulcerative patients (P0.05.Conclusion: It seems that in the patients under our study the presence of cagA gene may not necessarily be a risk factor for ulcer disease, while a homologous genotype of vacA appears to be associated with an increase risk of ulcer development. Lastly, despite the existence of a high degree of genomic variability within ureAB, conserved DNA banding profiles are distributed in our areas.

Ab initio study of alanine polypeptide chain twisting

DEFF Research Database (Denmark)

Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

2006-01-01

chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

Ab initio simulation of dislocation cores in metals

International Nuclear Information System (INIS)

Ventelon, L.

2008-01-01

In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

GenColors-based comparative genome databases for small eukaryotic genomes.

Science.gov (United States)

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

Science.gov (United States)

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

A New Algorithm for ABS/GPS Integration Based on Fuzzy-Logic in Vehicle Navigation System

Directory of Open Access Journals (Sweden)

Ali Amin Zadeh

2011-10-01

Full Text Available GPS based vehicle navigation systems have difficulties in tracking vehicles in urban canyons due to poor satellite availability. ABS (Antilock Brake System Navigation System consists of self-contained optical encoders mounted on vehicle wheels that can continuously provide accurate short-term positioning information. In this paper, a new concept regarding GPS/ABS integration, based on Fuzzy Logic is presented. The proposed algorithm is used to identify GPS position accuracy based on environment and vehicle dynamic knowledge. The GPS is used as reference during the time it is in a good condition and replaced by ABS positioning system when GPS information is unreliable. We compare our proposed algorithm with other common algorithm in real environment. Our results show that the proposed algorithm can significantly improve the stability and reliability of ABS/GPS navigation system.

Comparative study of intact A7 MoAc and F(ab')2 fragments for radioimmunoimaging of human colon cancer in nude mice

International Nuclear Information System (INIS)

Kojima, Shuji; Suzuki, Naomi; Shimura, Noriko; Kubodera, Akiko; Kubota, Kazuhiko; Yamaguchi, Toshiharu; Takahashi, Toshio; Oyamada, Hiyoshimaru

1993-01-01

Differences of pharmacokinetics and tumor imaging ability between intact monoclonal antibody A7 (A7 MoAb) and F(ab) 2 fragments were studied in human colon cancer (LS-174T)-bearing nude mice. The authors examined the yield and the immunoreactivity of F(ab) 2 fragments after treatment with ficin as a function of time. The yield of F(ab) 2 fragments reached about 50% after ficin treatment for 8 h, and the F(ab) 2 retained about 80% of the immunoreactivity of the corresponding MoAb. Longer digestion with ficin produced smaller fragments (less than 92 kDa) with a lower yield and most of the immunoreactivity was lost. In pharmacokinetics studies, the F(ab') 2 was preferentially taken up by the tumor, cleared more rapidly from the blood circulation and seemed to have less non-specific tissue binding than intact A7 MoAb. The tumor image obtained at an early time using 131 I-F(ab') 2 was much superior in quality to that with intact 131 I-A7 MoAb. The use of F(ab') 2 fragments may be effective for tumor diagnosis and therapy. (author)

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Rodent malaria parasites : genome organization & comparative genomics

NARCIS (Netherlands)

Kooij, Taco W.A.

2006-01-01

The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

Stellar Origin of 15N-rich Presolar SiC Grains of Type AB: Supernovae with Explosive Hydrogen Burning

International Nuclear Information System (INIS)

Liu, Nan; Nittler, Larry R.; Alexander, Conel M. O’D.; Wang, Jianhua; Pignatari, Marco

2017-01-01

We report C, N, and Si isotopic data for 59 highly 13 C-enriched presolar submicron- to micron-sized SiC grains from the Murchison meteorite, including eight putative nova grains (PNGs) and 29 15 N-rich ( 14 N/ 15 N ≤ solar) AB grains, and their Mg–Al, S, and Ca–Ti isotope data when available. These 37 grains are enriched in 13 C, 15 N, and 26 Al with the PNGs showing more extreme enhancements. The 15 N-rich AB grains show systematically higher 26 Al and 30 Si excesses than the 14 N-rich AB grains. Thus, we propose to divide the AB grains into groups 1 ( 14 N/ 15 N < solar) and 2 ( 14 N/ 15 N ≥ solar). For the first time, we have obtained both S and Ti isotopic data for five AB1 grains and one PNG and found 32 S and/or 50 Ti enhancements. Interestingly, one AB1 grain had the largest 32 S and 50 Ti excesses, strongly suggesting a neutron-capture nucleosynthetic origin of the 32 S excess and thus the initial presence of radiogenic 32 Si ( t 1/2 = 153 years). More importantly, we found that the 15 N and 26 Al excesses of AB1 grains form a trend that extends to the region in the N–Al isotope plot occupied by C2 grains, strongly indicating a common stellar origin for both AB1 and C2 grains. Comparison of supernova models with the AB1 and C2 grain data indicates that these grains came from supernovae that experienced H ingestion into the He/C zones of their progenitors.

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Use of an anti-platelet monoclonal antibody F (ab')2 fragment for imaging thrombus

International Nuclear Information System (INIS)

Loutfi, I.; Stuttle, A.W.J.; Peters, A.M.; George, P.; Lavender, J.P.; Lumley, P.

1990-01-01

Ten patients with suspected thrombus have been studied using 111 In-labelled F (ab')2 fragments of P256, a monoclonal antibody which recognizes an epitope on the platelet membrane glycoprotein IIb/IIIa complex. The F (ab')2 fragment was radiolabelled with 111 In via diethylenetri-aminepentamacetic acid to give a specific activity of up to 190 MBq (5mCi) mg - 1 without impairment of immunoreactivity. In vitro platelet aggregation studies showed that the F (ab')2 fragment caused less platelet aggregation than the whole antibody on a molar ratio and was without significant effect upon the sensitivity of platelets to a range of aggregating agents. Platalets were labelled in ten patients by intravenous injection of approximately 100 μg P256 F (ab')2. Of the ten patients studies, six showed localization of activity consistent with platelet accumulation. Localization was clearly seen when associated with thrombus of the lower limbs (three patients: deep vein thrombosis; one patient: aortofemoral graft), and was apparent although less marked in two other cases, one of aortic aneurysm and one of carotid stenosis. Use of radiolabelled P256 F (ab')2 offers a means of non-invasive detection of thrombus which, from in vitro studies, would appear to have less direct effect of platelet behaviour than the whole antibody. (author). 9 refs. 8 figs. 1 tab

Preparation and characterization of ABS/anhydrous cobalt chloride composites

Science.gov (United States)

Shao, Chengli; Shang, Peng; Mao, Yapeng; Li, Qiuying; Wu, Chifei

2018-01-01

Anhydrous cobalt chloride (CoCl2) particles filled acrylonitrile-butadiene-styrene (ABS) composites were successfully prepared and investigated. A strong interfacial interaction between CoCl2 particles and ABS matrix was generated by heat pressing at 190 °C for 15 min. SEM results demonstrated that the particles were dispersed uniformly in the matrix. Fourier transform infrared, x-ray photoelectron spectroscopy and electron spin resonance were used for the investigation of the coordination reaction. The interfacial interaction resulted from a solid-state coordination reaction between nitrile groups (-CN) and cobalt ions (Co2+), leading to an increase in mechanical properties and glass transition temperature. Moreover, heat deflection temperatures were measured and proved to achieve an improvement of 30.6 °C when the CoCl2 content was 7 wt%.

Stellar Origin of 15N-rich Presolar SiC Grains of Type AB: Supernovae with Explosive Hydrogen Burning

Science.gov (United States)

Liu, Nan; Nittler, Larry R.; Pignatari, Marco; O'D. Alexander, Conel M.; Wang, Jianhua

2017-06-01

We report C, N, and Si isotopic data for 59 highly 13C-enriched presolar submicron- to micron-sized SiC grains from the Murchison meteorite, including eight putative nova grains (PNGs) and 29 15N-rich (14N/15N ≤ solar) AB grains, and their Mg-Al, S, and Ca-Ti isotope data when available. These 37 grains are enriched in 13C, 15N, and 26Al with the PNGs showing more extreme enhancements. The 15N-rich AB grains show systematically higher 26Al and 30Si excesses than the 14N-rich AB grains. Thus, we propose to divide the AB grains into groups 1 (14N/15N PNG and found 32S and/or 50Ti enhancements. Interestingly, one AB1 grain had the largest 32S and 50Ti excesses, strongly suggesting a neutron-capture nucleosynthetic origin of the 32S excess and thus the initial presence of radiogenic 32Si (t 1/2 = 153 years). More importantly, we found that the 15N and 26Al excesses of AB1 grains form a trend that extends to the region in the N-Al isotope plot occupied by C2 grains, strongly indicating a common stellar origin for both AB1 and C2 grains. Comparison of supernova models with the AB1 and C2 grain data indicates that these grains came from supernovae that experienced H ingestion into the He/C zones of their progenitors.

Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries

International Nuclear Information System (INIS)

Draayer, J P; Dytrych, T; Launey, K D; Dreyfuss, A C; Langr, D

2015-01-01

An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si

Realization of prediction of materials properties by ab initio ...

Indian Academy of Sciences (India)

Unknown

alization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube ... micro-clusters to estimate absolute highest occupied mo- .... To analyse the observed properties theoretically,.

Attack modes and defence reactions in pathosystems involving Sclerotinia sclerotiorum, Brassica carinata, B. juncea and B. napus.

Science.gov (United States)

Uloth, Margaret B; Clode, Peta L; You, Ming Pei; Barbetti, Martin J

2016-01-01

Sclerotinia stem rot (SSR, Sclerotinia sclerotiorum) is a damaging disease of oilseed brassicas world-wide. Host resistance is urgently needed to achieve control, yet the factors that contribute to stem resistance are not well understood. This study investigated the mechanisms of resistance to SSR. Stems of 5-week-old Brassica carinata, B. juncea and B. napus of known resistance were infected via filter paper discs impregnated with S. sclerotiorum mycelium under controlled conditions. Transverse sections of the stem and portions of the stem surface were examined using optical and scanning electron microscopy. The association of anatomical features with the severity of disease (measured by mean lesion length) was determined. Several distinct resistance mechanisms were recorded for the first time in these Brassica-pathogen interactions, including hypersensitive reactions and lignification within the stem cortex, endodermis and in tissues surrounding the lesions. Genotypes showing a strong lignification response 72 h post-infection (hpi) tended to have smaller lesions. Extensive vascular invasion by S. sclerotiorum was observed only in susceptible genotypes, especially in the vascular fibres and xylem. Mean lesion length was negatively correlated with the number of cell layers in the cortex, suggesting progress of S. sclerotiorum is impeded by more cell layers. Hyphae in the centre of lesions became highly vacuolate 72 hpi, reflecting an ageing process in S. sclerotiorum hyphal networks that was independent of host resistance. The infection process of S. sclerotiorum was analogous in B. carinata and B. napus. Infection cushions of the highly virulent isolate of S. sclerotiorum MBRS-1 were grouped together in dense parallel bundles, while hyphae in the infection cushions of a less aggressive isolate WW-3 were more diffuse, and this was unaffected by host genotype. A variety of mechanisms contribute to host resistance against S. sclerotiorum across the three

(4)He Thermophysical Properties: New Ab Initio Calculations.

Science.gov (United States)

Hurly, John J; Mehl, James B

2007-01-01

Since 2000, atomic physicists have reduced the uncertainty of the helium-helium "ab initio" potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ 07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of (4)He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ 07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties.

4He Thermophysical Properties: New Ab Initio Calculations

Science.gov (United States)

Hurly, John J.; Mehl, James B.

2007-01-01

Since 2000, atomic physicists have reduced the uncertainty of the helium-helium “ab initio” potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of 4He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties. PMID:27110456

Experimental study of biotin-avidin pretargeting technique for anti-CEA McAb radioimmunoimaging

International Nuclear Information System (INIS)

Sun Jianzhong; Zhu Chengmo; Guan Liang; Li Biao; Zhang Jixian; Shi Ailan; Zhang Suyin

1996-01-01

Biotin-avidin pretargeting technique was used in promoting the diagnostic efficacy of anti-CEA McAb radioimmunoimaging. CEA McAb was conjugated with biotin McAb (B-McAb), streptavidin (SA) was labeled with 131 I ( 131 I-SA) and DTPA-biotin with 111 In( 111 In-DTPA-B). Experimental human colonic tumor bearing nude mice were used. Two step method: B-McAb was preinjected, followed by 131 I SA 48h later, 24, 48, 96 and 120 h postinjection, γ-imaging and biodistribution were studied. Three step method: B-McAb was preinjected, followed by cold SA 24h later and 111 In-DTPA-B another 24h later. 2,6,24 and 48h postinjection, γ-imaging and biodistribution were also studied. Two step method: T/NT of all organs in experimental group was significantly increased compared with controls. The blood T/NT in experimental group and control group at 24 and 120h was 1.11:0.42 and 8.58:3.51, respectively. Tumor % ID/g in all organs slightly decreased compared with direct group. In γ-imaging radioactivity has been accumulated in tumor site as early as 24h, while only slightly visualized or non-visualized in controls. Three step method: in experimental group the blood T/NT reached 4.19 at 2 h, whereas all was < 1.37 at each phase of controls, the T/NT of all organs was also higher in experimental grouped than in controls. The tumor % ID/g in experimental group was 9.72% at 2h and 3.65% at 48h whereas % ID/g in controls in all phases was <3.07. The tumor clearly visualized at 2h and clearer at 48h in γ-imaging. In controls, the tumor was slightly visualized also to early stage, but faded away later on. Biotin-avidin pretargeting technique can elevate the T/NT ratio and decrease the blood background. Early imaging was obtained with better imaging quality

Immunogenicity and therapeutic effects of recombinant Ag85AB fusion protein vaccines in mice infected with Mycobacterium tuberculosis.

Science.gov (United States)

Liang, Yan; Zhang, Junxian; Yang, Yourong; Bai, Xuejuan; Yu, Qi; Li, Ning; Hou, Ying; Shi, Yingchang; Wang, Lan; Wu, Xueqiong

2017-07-13

The immune function of tuberculosis (TB) patients is disordered. By using immune regulators to assist chemotherapy for TB the curative effect might be improved. In this study, a vaccine containing Mycobacterium tuberculosis (M. tuberculosis) recombinant Ag85AB fusion protein (rAg85AB) was constructed and evaluated. The mice were immunized intramuscularly three times at two-week intervals with Ag85AB fusion protein combined with Corynebacterium parvum adjuvant (rAg85AB+CP). In comparison to control mice that received either CP alone or saline, the mice that received rAg85AB+CP had significantly higher number of T cells secreting IFN-γ and higher levels of specific antibodies of IgG, IgG1 and IgG2a isotypes in sera. The specific antibodies also had higher ratios of IgG2a to IgG1, indicating a predominant Th1 immune response. To test for immunotherapy of TB, M. tuberculosis infected mice were given three intramuscular doses of 20μg, 40μg or 60μg of rAg85AB in rAg85AB+CP, or phosphate-buffered saline (PBS), or CP or Mycobacterium phlei (M. Phlei) F.U.36. Compared with the PBS group, 20µg, 40µg and 60µg rAg85AB+CP and M. phlei F.U.36 groups reduced the pulmonary bacterial loads by 0.13, 0.15, 0.42 and 0.40 log 10 , and the liver bacterial loads by 0.64, 0.64, 0.53 and 0.61 log 10 , respectively. Pathological changes of lungs were less, and the lesions were limited to a certain extent in 40µg and 60µg rAg85AB+CP and M. phlei F.U.36 groups. These results showed that rAg85AB+CP had immunotherapeutic effect on TB, significantly increasing the cellular immune response, and inhibiting the growth of M. tuberculosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen

LENUS (Irish Health Repository)

O'Toole, Paul W

2010-03-10

Abstract Background Helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. H. mustelae remains the only helicobacter other than H. pylori that causes gastric ulceration and cancer in its natural host. To improve understanding of H. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. Results The H. mustelae genome lacks orthologs of major H. pylori virulence factors including CagA, VacA, BabA, SabA and OipA. However, it encodes ten autotransporter surface proteins, seven of which were detected in the expressed proteome, and which, except for the Hsr protein, are of unknown function. There are 26 putative outer membrane proteins in H. mustelae, some of which are most similar to the Hof proteins of H. pylori. Although homologs of putative virulence determinants of H. pylori (NapA, plasminogen adhesin, collagenase) and Campylobacter jejuni (CiaB, Peb4a) are present in the H. mustelae genome, it also includes a distinct complement of virulence-related genes including a haemagglutinin\\/haemolysin protein, and a glycosyl transferase for producing blood group A\\/B on its lipopolysaccharide. The most highly expressed 264 proteins in the cytosolic proteome included many corresponding proteins from H. pylori, but the rank profile in H. mustelae was distinctive. Of 27 genes shown to be essential for H. pylori colonization of the gerbil, all but three had orthologs in H. mustelae, identifying a shared set of core proteins for gastric persistence. Conclusions The determination of the genome sequence and expressed proteome of the ulcerogenic species H mustelae provides a comparative model for H. pylori to investigate bacterial gastric carcinogenesis in mammals, and to suggest ways whereby cag minus H. pylori strains might cause ulceration and cancer. The genome sequence was

AB0-incompatible living donor kidney transplantation: the long-term outcomes

Directory of Open Access Journals (Sweden)

Ya. G. Moysyuk

2017-01-01

Full Text Available Background: AB0-incompatible kidney transplantation is one of the ways to effectively expand the pool of living donors. In Russia, this technology has been used for more than 10 years, but until now there have been no reports on its long-term results. Aim: To evaluate the short- and long-term outcomes of the living-related AB0-incompatible kidney transplantations. Materials and methods: We analyzed the results of 49 consecutive AB0-incompatible kidney transplantations, performed from 2011 to 2017. Preoperative management of recipients included administration of rituximab and intravenous immunoglobulin, plasmapheresis and/or selective immunoadsorption, and combination of tacrolimus, mycophenolates and steroids. The target of anti-A/B antibody levels were is 1:8. All patients received standard immunosuppression after transplantation. Results: At baseline, median anti-A/B titer was 1:16 (1:2 to 1:1024 for IgM and 1:4 (0 to 1:512 for IgG. Median rituximab dose was 286 mg/m2 (range, from 94 to 396. To achieve target antibody levels, up to 10 plasmapheresis and/or immunoadsorption sessions (median, 2 were required. There were no deaths during the follow-up. Five grafts were lost, one of them due to hyperacute rejection. The incidence of biopsy-proven rejection was 6%. One-, three and six-year graft survival was 94%, 90% and 80%, respectively. Conclusion: Kidney transplantation across the AB0-incompatibility barrier is a  safe, successful and reasonable option to reduce the organ shortage. 

Baseline sensitivity of lepidopteran corn pests in India to Cry1Ab insecticidal protein of Bacillus thuringiensis.

Science.gov (United States)

Jalali, Sushil K; Lalitha, Yadavalli; Kamath, Subray P; Mohan, Komarlingam S; Head, Graham P

2010-08-01

Genetically engineered corn (Bt corn) expressing Bacillus thuringiensis Berliner insecticidal protein Cry1Ab is a biotechnological option being considered for management of lepidopteran corn pests in India. As a resistance management practice it was essential to determine the sensitivity of multiple populations of the stalk borer Chilo partellus (Swinhoe), pink borer Sesamia inferens (Walker) and the cob borer Helicoverpa armigera (Hübner) to Cry1Ab protein through bioassays. The insect populations were collected during growing seasons of Rabi 2005 (October 2005 to February 2006) and Kharif 2006 (May to September 2006). Multiple populations of the three lepidopteran corn pests were found to be susceptible to Cry1Ab. Median lethal concentrations (LC(50)) ranged between 0.008 and 0.068 microg Cry1Ab mL(-1) diet for 18 populations of C. partellus (across two seasons), between 0.12 and 1.99 microg mL(-1) for seven populations of H. armigera and between 0.46 and 0.56 microg mL(-1) for two populations of S. inferens. Dose-response concentrations for lethality and growth inhibition have been determined to mark baseline sensitivity of multiple populations of key lepidopteran corn pests in India to Cry1Ab protein. These benchmark values will be referenced while monitoring resistance to Cry1Ab should Bt corn hybrids expressing Cry1Ab be approved for commercial cultivation in India. Copyright (c) 2010 Society of Chemical Industry.

New species of Maerua (Capparaceae) from Angola

NARCIS (Netherlands)

Abreu, J.A.; Martins, E.S.; Catarino, L.

2014-01-01

Genus Maerua has around 60 species represented on the African continent, of which three have been reported for Angola. Two new species of Maerua (Capparaceae) from Angola are here described. Both are closely similar to M. juncea subsp. juncea, being distinguished by floral traits such as the

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

Science.gov (United States)

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations

International Nuclear Information System (INIS)

Laskowski, R; Blaha, P

2008-01-01

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-p x,y of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed σ-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system

Genomics Portals: integrative web-platform for mining genomics data.

Science.gov (United States)

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

i-Genome: A database to summarize oligonucleotide data in genomes

Directory of Open Access Journals (Sweden)

Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.