Pollinator Interactions with Yellow Starthistle (Centaurea solstitialis) across Urban, Agricultural, and Natural Landscapes

PubMed Central

Leong, Misha; Kremen, Claire; Roderick, George K.

2014-01-01

Pollinator-plant relationships are found to be particularly vulnerable to land use change. Yet despite extensive research in agricultural and natural systems, less attention has focused on these interactions in neighboring urban areas and its impact on pollination services. We investigated pollinator-plant interactions in a peri-urban landscape on the outskirts of the San Francisco Bay Area, California, where urban, agricultural, and natural land use types interface. We made standardized observations of floral visitation and measured seed set of yellow starthistle (Centaurea solstitialis), a common grassland invasive, to test the hypotheses that increasing urbanization decreases 1) rates of bee visitation, 2) viable seed set, and 3) the efficiency of pollination (relationship between bee visitation and seed set). We unexpectedly found that bee visitation was highest in urban and agricultural land use contexts, but in contrast, seed set rates in these human-altered landscapes were lower than in natural sites. An explanation for the discrepancy between floral visitation and seed set is that higher plant diversity in urban and agricultural areas, as a result of more introduced species, decreases pollinator efficiency. If these patterns are consistent across other plant species, the novel plant communities created in these managed landscapes and the generalist bee species that are favored by human-altered environments will reduce pollination services. PMID:24466050

Allele Identification for Transcriptome-Based Population Genomics in the Invasive Plant Centaurea solstitialis

PubMed Central

Dlugosch, Katrina M.; Lai, Zhao; Bonin, Aurélie; Hierro, José; Rieseberg, Loren H.

2013-01-01

Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios. PMID:23390612

Duration of emission of volatile organic compounds from mechanically damaged plant leaves.

PubMed

Smith, Lincoln; Beck, John J

2015-09-01

Classical biological control of invasive alien weeds depends on the use of arthropod herbivores that are sufficiently host specific to avoid risk of injuring nontarget plants. Host plant specificity is usually evaluated by using a combination of behavioral and developmental experiments under choice, no-choice and field conditions. Secondary plant compounds are likely to have an important influence on host plant specificity. However, relatively little is known about the volatile organic compounds (VOCs) that are emitted by target and nontarget plants, and how environmental conditions may affect their emission. Previous studies have shown that mechanical damage of leaves increases the composition and content of VOCs emitted. In this study we measured the VOC emissions of five species of plants in the subtribe Centaureinae (Asteraceae)--Carthamus tinctorius, Centaurea cineraria, Centaurea melitensis, Centaurea rothrockii, and Centaurea solstitialis--that have previously been used in host specificity experiments for a prospective biological control agent of yellow starthistle (C. solstitialis). Leaves of each plant were punctured with a needle and the VOCs were collected by solid-phase microextraction (SPME) periodically over 48 h and analyzed by GC-MS. A total of 49 compounds were detected. Damage caused an immediate increase of 200-600% in the composition of VOCs emitted from each plant species, and the amounts generally remained high for at least 48 h. The results indicate that a very unspecific mechanical damage can cause a prolonged change in the VOC profile of plants. Published by Elsevier GmbH.

The potential medicinal value of plants from Asteraceae family with antioxidant defense enzymes as biological targets.

PubMed

Koc, Suheda; Isgor, Belgin S; Isgor, Yasemin G; Shomali Moghaddam, Naznoosh; Yildirim, Ozlem

2015-05-01

Plants and most of the plant-derived compounds have long been known for their potential pharmaceutical effects. They are well known to play an important role in the treatment of several diseases from diabetes to various types of cancers. Today most of the clinically effective pharmaceuticals are developed from plant-derived ancestors in the history of medicine. The aim of this study was to evaluate the free radical scavenging activity and total phenolic and flavonoid contents of methanol, ethanol, and acetone extracts from flowers and leaves of Onopordum acanthium L., Carduus acanthoides L., Cirsium arvense (L.) Scop., and Centaurea solstitialis L., all from the Asteraceae family, for investigating their potential medicinal values of biological targets that are participating in the antioxidant defense system such as catalase (CAT), glutathione S-transferase (GST), and glutathione peroxidase (GPx). In this study, free radical scavenging activity and total phenolic and flavonoid contents of the plant samples were assayed by DPPH, Folin-Ciocalteu, and aluminum chloride colorimetric methods. Also, the effects of extracts on CAT, GST, and GPx enzyme activities were investigated. The highest phenolic and flavonoid contents were detected in the acetone extract of C. acanthoides flowers, with 90.305 mg GAE/L and 185.43 mg Q/L values, respectively. The highest DPPH radical scavenging was observed with the methanol leaf extracts of C. arvense with an IC50 value of 366 ng/mL. The maximum GPx and GST enzyme inhibition activities were observed with acetone extracts from the flower of C. solstitialis with IC50 values of 79 and 232 ng/mL, respectively.

Dispersal Pathways and Genetic Differentiation among Worldwide Populations of the Invasive Weed Centaurea solstitialis L. (Asteraceae)

PubMed Central

Eriksen, Renée L.; Hierro, José L.; Eren, Özkan; Andonian, Krikor; Török, Katalin; Becerra, Pablo I.; Montesinos, Daniel; Khetsuriani, Liana; Diaconu, Alecu; Kesseli, Rick

2014-01-01

The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments. PMID:25551223

Some popular medicinal plants and diseases of the Upper Palaeolithic in Western Georgia.

PubMed

Martkoplishvili, Inga; Kvavadze, Eliso

2015-05-26

Palynological studies of cultural layers of cave sediments have been used in order to better understand traditional practices. The Upper Palaeolithic in Georgia (36,000-11,000 cal. BP) provides a rich source of such material. However, up to day from such sediments the identification of medicinal plants has hardly been achieved. Large quantities of pollen most notably from entomophilous taxa in fossil spectra can serve as a tool to identify traditionally important species. As these plants are used in modern popular medicine on the territory of Georgia (like Achillea millefolium L., Artemisia annua L., Artemisia absinthium L., Centaurea jacea L., Urtica dioica L.) can be served as an indirect evidence for their medicinal relevance from the Palaeolithic Period up to days. Their modern uses may point that the main diseases during the Upper Palaeolithic were the same as today. The Upper Palaeolithic sediments were studied palynologically come from four caves: Dzudzuana, Satsurblia, Kotias Klde and Bondi. Modern sediments were investigated from 6 caves. Fossil and modern samples were taken according to the standard procedure in palynology. The laboratory treatment was carried out as follows: first, 50g of the sample was boiled in 10% KOH. At the second stage, centrifuging of the material in cadmium liquid was performed. At the final stage, acetolysis treatment was used. Pollen of A. absinthium L. (Asteraceae), A. annua L. (Asteraceae), A. millefolium L. (Asteraceae), C. jacea L. (Asteraceae), and U. dioica L. (Urticaceae) are identified to species level. This species are not edible and are popular in present-day folk medicine. In the Upper Palaeolithic layers, significant amounts of studies species pollen were recorded in the cave, likely due to their flowering branches being brought in by humans for use. Detailed consideration of the pharmacological characteristics of the examined species showed that almost all of them have anti-inflammatory, antibacterial, antimicrobial and antipyretic activity. The fossil pollen complex of medicinal herbs, dominated by A. millefolium and Artemisia (A. annua and A. absinthium), suggests that the ancient population living in the studied caves could have been prone to malaria, rheumatism and gastrointestinal diseases. In the Upper Palaeolithic, the population inhabiting cave sites might have suffered from gout and callouses. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Chromosome numbers of populations of three varieties of Bidens pilosa in Taiwan.

PubMed

Huang, Ya-Lun; Kao, Wen-Yuan

2015-12-01

Hairy beggar-ticks (Bidens pilosa L.) is a common invasive plant in tropical and subtropical regions. The Flora of Taiwan listed three varieties of B. pilosa in Taiwan, var. minor, var. pilosa and var. radiata. Among the three varieties, var. radiata was the most recently, in 1970s, introduced into Taiwan. However, after its introduction into Taiwan, var. radiata has become dominant over the other two varieties and is considered a serious invasive plant in lowland of Taiwan. Our previous study showed that var. radiata is self-incompatible and the other two varieties are self-fertile. Could it be possible that different chromosome numbers contribute to the different breeding systems of these three varieties? In addition, the heterogeneities of traits of var. radiata were found higher than those of var. minor and var. pilosa. Is the phenomenon resulting from the hybridization between var. radiata with other varieties? We counted chromosome numbers of populations of these three varieties distributed in Taiwan and conducted hand pollination treatment between var. radiata (as pollen receiver) and var. minor or var. pilosa (as pollen donor) to provide answer for the aforementioned questions. No difference was found in chromosome numbers among populations of the same variety. Forty-eight chromosomes (2n = 48) were counted for var. radiata while 72 (2n = 72) chromosomes for var. minor and var. pilosa. Therefore, var. radiata is tetraploid and var. minor and var. pilosa are hexaploid. No successful hybridization was found between var. radiata and var. minor or between var. radiata and var. pilosa. This study provided the evidence that the invasive plant (B. pilosa var. radiata) has different chromosome numbers from the other two varieties and is unlikely to hybridize with the other two varieties.

An Evaluation of Voluntary Varicella Vaccination Coverage in Zhejiang Province, East China.

PubMed

Hu, Yu; Chen, Yaping; Zhang, Bing; Li, Qian

2016-06-03

In 2014 a 2-doses varicella vaccine (VarV) schedule was recommended by the Zhejiang Provincial Center for Disease Control and Prevention. We aimed to assess the coverage of the 1st dose of VarV (VarV₁) and the 2nd dose of VarV (VarV₂) among children aged 2-6 years through the Zhejiang Provincial Immunization Information System (ZJIIS) and to explore the determinants associated with the VarV coverage. Children aged 2-6 years (born from 1 January 2009 to 31 December 2013) registered in ZJIIS were enrolled. Anonymized individual records of target children were extracted from the ZJIIS database on 1 January 2016, including their VarV and (measles-containing vaccine) MCV vaccination information. The VarV₁ and VarV₂ coverage rates were evaluated for each birth cohorts. The coverage of VarV also was estimated among strata defined by cities, gender and immigration status. We also evaluated the difference in coverage between VarV and MCV. A total of 3,028,222 children aged 2-6 years were enrolled. The coverage of VarV₁ ranged from 84.8% to 87.9% in the 2009-2013 birth cohorts, while the coverage of VarV₂ increased from 31.8% for the 2009 birth cohort to 48.7% for the 2011 birth cohort. Higher coverage rates for both VarV₁ and VarV₂ were observed among resident children in relevant birth cohorts. The coverage rates of VarV₁ and VarV₂ were lower than those for the 1st and 2nd dose of MCV, which were above 95%. The proportion of children who were vaccinated with VarV₁ at the recommended age increased from 34.6% for the 2009 birth cohort to 75.2% for the 2013 birth cohort, while the proportion of children who were vaccinated with VarV₂ at the recommended age increased from 19.7% for the 2009 birth cohort to 48.7% for the 2011 birth cohort. Our study showed a rapid increasing VarV₂ coverage of children, indicating a growing acceptance of the 2-doses VarV schedule among children's caregivers and physicians after the new recommendation released. We highlighted the necessity for a 2-doses VarV vaccination school-entry requirement to achieve the high coverage of >90% and to eliminate disparities in coverage among sub-populations. We also recommended continuous monitoring of the VarV coverage via ZJIIS over time.

Cytotaxonomic study of the Chilean endemic complex Alstroemeria magnifica Herb. (Alstroemeriaceae).

PubMed

Baeza, Carlos M; Finot, Víctor; Ruiz, Eduardo; Carrasco, Pedro; Novoa, Patricio; Rosas, Marcelo; Toro-Núñez, Oscar

2018-05-14

Alstroemeria L. (Alstroemeriaceae) represents one of the most diverse genera of vascular plants in Chile. It contains approximately 54 taxa, 40 of which are endemic. The "complex" Alstroemeria magnifica is endemic to Chile, and it comprises four varieties: A. magnifica var. magenta, A. magnifica var. magnifica, A. magnifica var. sierrae, and A. magnifica var. tofoensis. It is distributed from Coquimbo to the Valparaíso Region. We analyzed karyotypes of 10 populations along its natural distribution. All the populations presented an asymmetric karyotype, with 2n = 16 chromosomes but with three different karyotypic formulae. Alstroemeria magnifica var. magnifica and A. magnifica var. sierrae presented the same karyotypic fomula, and A. magnifica var. magenta, and A. magnifica var. tofoensis each had a different formula. The scatter plot among CVCL vs. MCA shows different groupings between populations of the four varieties. Based on the results, it is possible to consider raising Alstroemeria magnifica var. magenta to species level (A. magenta) and A. magnifica var. tofoensis to subspecies level (A. magnifica subsp. tofoensis); A. magnifica var. magnifica and A. magnifica var. sierrae should each remain as varieties. Nevertheless, these taxonomic changes should be considered tentative, as additional sources of evidence become available.

Surgery

MedlinePlus

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Understanding Pneumonia

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Oxygen Therapy

MedlinePlus

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Living with Tuberculosis

MedlinePlus

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Learn About Sarcoidosis

MedlinePlus

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How Lungs Work

MedlinePlus

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Understand Your Medication

MedlinePlus

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Learn About Silicosis

MedlinePlus

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Learn About Tuberculosis

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Localization of a variational particle smoother

NASA Astrophysics Data System (ADS)

Morzfeld, M.; Hodyss, D.; Poterjoy, J.

2017-12-01

Given the success of 4D-variational methods (4D-Var) in numerical weather prediction,and recent efforts to merge ensemble Kalman filters with 4D-Var,we consider a method to merge particle methods and 4D-Var.This leads us to revisit variational particle smoothers (varPS).We study the collapse of varPS in high-dimensional problemsand show how it can be prevented by weight-localization.We test varPS on the Lorenz'96 model of dimensionsn=40, n=400, and n=2000.In our numerical experiments, weight localization prevents the collapse of the varPS,and we note that the varPS yields results comparable to ensemble formulations of 4D-variational methods,while it outperforms EnKF with tuned localization and inflation,and the localized standard particle filter.Additional numerical experiments suggest that using localized weights in varPS may not yield significant advantages over unweighted or linearizedsolutions in near-Gaussian problems.

Surface fatigue life of M50NiL and AISI 9310 spur gears and R C bars

NASA Technical Reports Server (NTRS)

Townsend, Dennis P.; Bamberger, Eric N.

1991-01-01

Spur gear endurance tests and rolling element surface fatigue tests were conducted to study vacuum induction melted, vacuum arc remelted (VIM-VAR) M50NiL steel for use as a gear steel in advanced aircraft applications, to determine its endurance characteristics, and to compare the results with those for standard VAR and VIM-VAR AISI 9310 gear material. Tests were conducted with spur gears and rolling contact bars manufactured from VIM-VAR M50NiL and VAR and VIM-VAR AISI 9310. The gear pitch diameter was 8.9 cm. Gear test conditions were an inlet oil temperature of 320 K, and outlet oil temperature of 350 K, a maximum Hertz stress of 1.71 GPa, and a speed of 10000 rpm. Bench rolling element fatigue tests were conducted at ambient temperatures with a bar speed of 12,500 rpm and a maximum Hertz stress of 4.83 GPa. The VIM-VAR M50NiL gears had a surface fatigue life that was 4.5 and 11.5 times that for VIM-VAR and VAR AISI 9310 gears, respectively. The surface fatigue life of the VIM-VAR M50NiL rolling contact bars was 13.2 and 21.6 times that for the VIM-VAR and VAR AISI 9310, respectively. The VIM-VAR M50NiL material was shown to have good resistance to fracture through a fatigue spall and superior fatigue life to both other gears.

What's in a Cigarette?

MedlinePlus

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Managing Your COPD Medications

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Facts about the Common Cold

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Diagnosing and Treating Acute Bronchitis

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Warning Signs of Lung Disease

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Learn about Respiratory Syncytial Virus (RSV)

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Symptoms, Diagnosis and Treatment of Pneumonia

MedlinePlus

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75 FR 78932 - Federal Seed Act Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

....'', ``Broccoli-- Brassica oleracea L. var. botrytis L.'', ``Brussels sprouts--Brassica oleracea L. var. gemmifera...--Vicia faba L. var. faba'', ``Broccoli-- Brassica oleracea L. var. italica Plenck'', ``Brussels sprouts...

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., the preceding twelve months of VAR formula records plus the preceding two months of VAR supporting... request, the preceding two months of VAR formula records and VAR supporting documentation. (3) Facilities... accurately and separately measured, either through the use of a separate storage tank, a separate meter, or...

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the preceding twelve months of VAR formula records plus the preceding two months of VAR supporting... request, the preceding two months of VAR formula records and VAR supporting documentation. (3) Facilities... accurately and separately measured, either through the use of a separate storage tank, a separate meter, or...

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., the preceding twelve months of VAR formula records plus the preceding two months of VAR supporting... request, the preceding two months of VAR formula records and VAR supporting documentation. (3) Facilities... accurately and separately measured, either through the use of a separate storage tank, a separate meter, or...

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., the preceding twelve months of VAR formula records plus the preceding two months of VAR supporting... request, the preceding two months of VAR formula records and VAR supporting documentation. (3) Facilities... accurately and separately measured, either through the use of a separate storage tank, a separate meter, or...

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., the preceding twelve months of VAR formula records plus the preceding two months of VAR supporting... request, the preceding two months of VAR formula records and VAR supporting documentation. (3) Facilities... accurately and separately measured, either through the use of a separate storage tank, a separate meter, or...

Nontuberculous Mycobacterium Infections: Symptoms, Causes & Risk Factors

MedlinePlus

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Murine Model for Preclinical Studies of Var2CSA-Mediated Pathology Associated with Malaria in Pregnancy

PubMed Central

Dechavanne, Sebastien; Sousa, Patrícia M.; Barateiro, André; Cunha, Sónia F.; Nunes-Silva, Sofia; Lima, Flávia A.; Murillo, Oscar; Marinho, Claudio R. F.; Gangnard, Stephane; Srivastava, Anand; Braks, Joanna A.; Janse, Chris J.; Gamain, Benoit; Penha-Gonçalves, Carlos

2016-01-01

Plasmodium falciparum infection during pregnancy leads to abortions, stillbirth, low birth weight, and maternal mortality. Infected erythrocytes (IEs) accumulate in the placenta by adhering to chondroitin sulfate A (CSA) via var2CSA protein exposed on the P. falciparum IE membrane. Plasmodium berghei IE infection in pregnant BALB/c mice is a model for severe placental malaria (PM). Here, we describe a transgenic P. berghei parasite expressing the full-length var2CSA extracellular region (domains DBL1X to DBL6ε) fused to a P. berghei exported protein (EMAP1) and characterize a var2CSA-based mouse model of PM. BALB/c mice were infected at midgestation with different doses of P. berghei-var2CSA (P. berghei-VAR) or P. berghei wild-type IEs. Infection with 104 P. berghei-VAR IEs induced a higher incidence of stillbirth and lower fetal weight than P. berghei. At doses of 105 and 106 IEs, P. berghei-VAR-infected mice showed increased maternal mortality during pregnancy and fetal loss, respectively. Parasite loads in infected placentas were similar between parasite lines despite differences in maternal outcomes. Fetal weight loss normalized for parasitemia was higher in P. berghei-VAR-infected mice than in P. berghei-infected mice. In vitro assays showed that higher numbers of P. berghei-VAR IEs than P. berghei IEs adhered to placental tissue. Immunization of mice with P. berghei-VAR elicited IgG antibodies reactive to DBL1-6 recombinant protein, indicating that the topology of immunogenic epitopes is maintained between DBL1-6–EMAP1 on P. berghei-VAR and recombinant DBL1-6 (recDBL1-6). Our data suggested that impairments in pregnancy caused by P. berghei-VAR infection were attributable to var2CSA expression. This model provides a tool for preclinical evaluation of protection against PM induced by approaches that target var2CSA. PMID:27045035

What is Multidrug and Extensively Drug Resistant TB?

MedlinePlus

... each(function(i){ var city = $(this).find('city').text(); var state = $(this).find('state').text(); var date = $(this).find('date').text(); if ((city != "") && (state != "")){ var citystate = ' | ' + city + ', ' + state; } else ...

Detoxification of Benzoxazolinone Allelochemicals from Wheat by Gaeumannomyces graminis var. tritici, G. graminis var. graminis, G. graminis var. avenae, and Fusarium culmorum

PubMed Central

Friebe, A.; Vilich, V.; Hennig, L.; Kluge, M.; Sicker, D.

1998-01-01

The ability of phytopathogenic fungi to overcome the chemical defense barriers of their host plants is of great importance for fungal pathogenicity. We studied the role of cyclic hydroxamic acids and their related benzoxazolinones in plant interactions with pathogenic fungi. We identified species-dependent differences in the abilities of Gaeumannomyces graminis var. tritici, Gaeumannomyces graminis var. graminis, Gaeumannomyces graminis var. avenae, and Fusarium culmorum to detoxify these allelochemicals of gramineous plants. The G. graminis var. graminis isolate degraded benzoxazolin-2(3H)-one (BOA) and 6-methoxy-benzoxazolin-2(3H)-one (MBOA) more efficiently than did G. graminis var. tritici and G. graminis var. avenae. F. culmorum degraded BOA but not MBOA. N-(2-Hydroxyphenyl)-malonamic acid and N-(2-hydroxy-4-methoxyphenyl)-malonamic acid were the primary G. graminis var. graminis and G. graminis var. tritici metabolites of BOA and MBOA, respectively, as well as of the related cyclic hydroxamic acids. 2-Amino-3H-phenoxazin-3-one was identified as an additional G. graminis var. tritici metabolite of BOA. No metabolite accumulation was detected for G. graminis var. avenae and F. culmorum by high-pressure liquid chromatography. The mycelial growth of the pathogenic fungi was inhibited more by BOA and MBOA than by their related fungal metabolites. The tolerance of Gaeumannomyces spp. for benzoxazolinone compounds is correlated with their detoxification ability. The ability of Gaeumannomyces isolates to cause root rot symptoms in wheat (cultivars Rektor and Astron) parallels their potential to degrade wheat allelochemicals to nontoxic compounds. PMID:9647804

Antigenic variation in malaria: in situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum.

PubMed Central

Scherf, A; Hernandez-Rivas, R; Buffet, P; Bottius, E; Benatar, C; Pouvelle, B; Gysin, J; Lanzer, M

1998-01-01

Members of the Plasmodium falciparum var gene family encode clonally variant adhesins, which play an important role in the pathogenicity of tropical malaria. Here we employ a selective panning protocol to generate isogenic P.falciparum populations with defined adhesive phenotypes for CD36, ICAM-1 and CSA, expressing single and distinct var gene variants. This technique has established the framework for examining var gene expression, its regulation and switching. It was found that var gene switching occurs in situ. Ubiquitous transcription of all var gene variants appears to occur in early ring stages. However, var gene expression is tightly regulated in trophozoites and is exerted through a silencing mechanism. Transcriptional control is mutually exclusive in parasites that express defined adhesive phenotypes. In situ var gene switching is apparently mediated at the level of transcriptional initiation, as demonstrated by nuclear run-on analyses. Our results suggest that an epigenetic mechanism(s) is involved in var gene regulation. PMID:9736619

A comparison between EDA-EnVar and ETKF-EnVar data assimilation techniques using radar observations at convective scales through a case study of Hurricane Ike (2008)

NASA Astrophysics Data System (ADS)

Shen, Feifei; Xu, Dongmei; Xue, Ming; Min, Jinzhong

2017-07-01

This study examines the impacts of assimilating radar radial velocity (Vr) data for the simulation of hurricane Ike (2008) with two different ensemble generation techniques in the framework of the hybrid ensemble-variational (EnVar) data assimilation system of Weather Research and Forecasting model. For the generation of ensemble perturbations we apply two techniques, the ensemble transform Kalman filter (ETKF) and the ensemble of data assimilation (EDA). For the ETKF-EnVar, the forecast ensemble perturbations are updated by the ETKF, while for the EDA-EnVar, the hybrid is employed to update each ensemble member with perturbed observations. The ensemble mean is analyzed by the hybrid method with flow-dependent ensemble covariance for both EnVar. The sensitivity of analyses and forecasts to the two applied ensemble generation techniques is investigated in our current study. It is found that the EnVar system is rather stable with different ensemble update techniques in terms of its skill on improving the analyses and forecasts. The EDA-EnVar-based ensemble perturbations are likely to include slightly less organized spatial structures than those in ETKF-EnVar, and the perturbations of the latter are constructed more dynamically. Detailed diagnostics reveal that both of the EnVar schemes not only produce positive temperature increments around the hurricane center but also systematically adjust the hurricane location with the hurricane-specific error covariance. On average, the analysis and forecast from the ETKF-EnVar have slightly smaller errors than that from the EDA-EnVar in terms of track, intensity, and precipitation forecast. Moreover, ETKF-EnVar yields better forecasts when verified against conventional observations.

IkeNet: Social Network Analysis of E-mail Traffic in the Eisenhower Leadership Development Program

DTIC Science & Technology

2007-11-01

8217Create the recipients TO TempArray = Sphit(strTo,") For Each varArrayltem In TemnpArray hextGuy = Chr(34) & CStr (Trim(varArrayltem)) & Chr(34) MsgBox...34next guy = " & nextGuy ’Set oRecipient = Recipients.Add(nextGuy) Set oRecipient = Recipients.Add( CStr (Trim(varArrayItem))) oRecipient.Type = olTo...TempArray = Split(strAttachments, "" For Each varArrayltern In TempArray .Attachments.Add CStr (Trim(varArrayItem)) Next varArrayltern .Send No return value

Taxonomic study on Japanese Salvia (Lamiaceae): Phylogenetic position of S. akiensis, and polyphyletic nature of S. lutescens var. intermedia.

PubMed

Takano, Atsuko

2017-01-01

Both Salvia akiensis and S. lutescens (Lamiaceae) are endemic to Japan. Salvia akiensis was recently described in 2014 in the Chugoku (= SW Honshu) region, and each four varieties of S. lutescens distributed allopatrically. Among varieties in S. lutescens , var. intermedia show a disjunctive distribution in the Kanto (=E Honshu) and Kinki (= W Honshu) regions. Recent field studies of S. lutescens var. intermedia revealed several morphological differences between the Kanto and Kinki populations. Here, I evaluated these differences among Salvia lutescens var. intermedia and its allies with morphological analysis and molecular phylogenetic analyses of nuclear ribosomal DNA (internal and external transcribed spacer regions) and plastid DNA ( ycf1-rps15 spacer, rbcL , and trnL-F ) sequences. Both morphological analysis and molecular phylogenetic analyses showed that S. lutescens var. intermedia from the Kinki region and var. lutescens were closely related to each other. However, var. intermedia from the Kanto region exhibited an association with S. lutescens var. crenata and var. stolonifera, which also grew in eastern Japan, rather than var. intermedia in the Kinki region. These results indicated that S. lutescens var. intermedia is not a taxon with a disjunctive distribution, but a combination of two or more allopatric taxa. Present study also suggested that S. akiensis was most closely related to S. omerocalyx .

Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development.

PubMed

Naested, Henrik; Holm, Agnethe; Jenkins, Tom; Nielsen, H Bjørn; Harris, Cassandra A; Beale, Michael H; Andersen, Mathias; Mant, Alexandra; Scheller, Henrik; Camara, Bilal; Mattsson, Ole; Mundy, John

2004-09-15

The stable, recessive Arabidopsis variegated 3 (var3) mutant exhibits a variegated phenotype due to somatic areas lacking or containing developmentally retarded chloroplasts and greatly reduced numbers of palisade cells. The VAR3 gene, isolated by transposon tagging, encodes the 85.9 kDa VAR3 protein containing novel repeats and zinc fingers described as protein interaction domains. VAR3 interacts specifically in yeast and in vitro with NCED4, a putative polyene chain or carotenoid dioxygenase, and both VAR3 and NCED4 accumulate in the chloroplast stroma. Metabolic profiling demonstrates that pigment profiles are qualitatively similar in wild type and var3, although var3 accumulates lower levels of chlorophylls and carotenoids. These results indicate that VAR3 is a part of a protein complex required for normal chloroplast and palisade cell development.

Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides)

PubMed Central

Thies, Judy A.; Ariss, Jennifer J.; Kousik, Chandrasekar S.; Hassell, Richard L.; Levi, Amnon

2016-01-01

Southern root-knot nematode (RKN, Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the United States and no resistance is known to exist in commercial watermelon cultivars. Wild watermelon relatives (Citrullus lanatus var. citroides) have been shown in greenhouse studies to possess varying degrees of resistance to RKN species. Experiments were conducted over 2 yr to assess resistance of southern RKN in C. lanatus var. citroides accessions from the U.S. Watermelon Plant Introduction Collection in an artificially infested field site at the U.S. Vegetable Laboratory in Charleston, SC. In the first study (2006), 19 accessions of C. lanatus var. citroides were compared with reference entries of Citrullus colocynthis and C. lanatus var. lanatus. Of the wild watermelon accessions, two entries exhibited significantly less galling than all other entries. Five of the best performing C. lanatus var. citroides accessions were evaluated with and without nematicide at the same field site in 2007. Citrullus lanatus var. citroides accessions performed better than C. lanatus var. lanatus and C. colocynthis. Overall, most entries of C. lanatus var. citroides performed similarly with and without nematicide treatment in regard to root galling, visible egg masses, vine vigor, and root mass. In both years of field evaluations, most C. lanatus var. citroides accessions showed lesser degrees of nematode reproduction and higher vigor and root mass than C. colocynthis and C. lanatus var. lanatus. The results of these two field evaluations suggest that wild watermelon populations may be useful sources of resistance to southern RKN. PMID:27168648

Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides).

PubMed

Thies, Judy A; Ariss, Jennifer J; Kousik, Chandrasekar S; Hassell, Richard L; Levi, Amnon

2016-03-01

Southern root-knot nematode (RKN, Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the United States and no resistance is known to exist in commercial watermelon cultivars. Wild watermelon relatives (Citrullus lanatus var. citroides) have been shown in greenhouse studies to possess varying degrees of resistance to RKN species. Experiments were conducted over 2 yr to assess resistance of southern RKN in C. lanatus var. citroides accessions from the U.S. Watermelon Plant Introduction Collection in an artificially infested field site at the U.S. Vegetable Laboratory in Charleston, SC. In the first study (2006), 19 accessions of C. lanatus var. citroides were compared with reference entries of Citrullus colocynthis and C. lanatus var. lanatus. Of the wild watermelon accessions, two entries exhibited significantly less galling than all other entries. Five of the best performing C. lanatus var. citroides accessions were evaluated with and without nematicide at the same field site in 2007. Citrullus lanatus var. citroides accessions performed better than C. lanatus var. lanatus and C. colocynthis. Overall, most entries of C. lanatus var. citroides performed similarly with and without nematicide treatment in regard to root galling, visible egg masses, vine vigor, and root mass. In both years of field evaluations, most C. lanatus var. citroides accessions showed lesser degrees of nematode reproduction and higher vigor and root mass than C. colocynthis and C. lanatus var. lanatus. The results of these two field evaluations suggest that wild watermelon populations may be useful sources of resistance to southern RKN.

Using ClinVar as a Resource to Support Variant Interpretations

PubMed Central

Harrison, Steven M.; Riggs, Erin R.; Maglott, Donna R.; Lee, Jennifer M.; Azzariti, Danielle R.; Niehaus, Annie; Ramos, Erin M.; Martin, Christa L.; Landrum, Melissa J.; Rehm, Heidi L.

2016-01-01

ClinVar is a freely accessible, public archive of reports of the relationships among genomic variants and phenotypes. To facilitate evaluation of the clinical significance of each variant, ClinVar aggregates submissions of the same variant, displays supporting data from each submission, and determines if the submitted clinical interpretations are conflicting or concordant. The unit describes how to (1) identify sequence and structural variants of interest in ClinVar with by multiple searching approaches, including Variation Viewer and (2) understand the display of submissions to ClinVar and the evidence supporting each interpretation. By following this protocol, ClinVar users will be able to learn how to incorporate the wealth of resources and knowledge in ClinVar into variant curation and interpretation. PMID:27037489

iVAR: a program for imputing missing data in multivariate time series using vector autoregressive models.

PubMed

Liu, Siwei; Molenaar, Peter C M

2014-12-01

This article introduces iVAR, an R program for imputing missing data in multivariate time series on the basis of vector autoregressive (VAR) models. We conducted a simulation study to compare iVAR with three methods for handling missing data: listwise deletion, imputation with sample means and variances, and multiple imputation ignoring time dependency. The results showed that iVAR produces better estimates for the cross-lagged coefficients than do the other three methods. We demonstrate the use of iVAR with an empirical example of time series electrodermal activity data and discuss the advantages and limitations of the program.

Positive Selection of Plasmodium falciparum Parasites With Multiple var2csa-Type PfEMP1 Genes During the Course of Infection in Pregnant Women

PubMed Central

Salanti, Ali; Lavstsen, Thomas; Nielsen, Morten A.; Theander, Thor G.; Leke, Rose G. F.; Lo, Yeung Y.; Bobbili, Naveen; Arnot, David E.; Taylor, Diane W.

2011-01-01

Placental malaria infections are caused by Plasmodium falciparum–infected red blood cells sequestering in the placenta by binding to chondroitin sulfate A, mediated by VAR2CSA, a variant of the PfEMP1 family of adhesion antigens. Recent studies have shown that many P. falciparum genomes have multiple genes coding for different VAR2CSA proteins, and parasites with >1 var2csa gene appear to be more common in pregnant women with placental malaria than in nonpregnant individuals. We present evidence that, in pregnant women, parasites containing multiple var2csa-type genes possess a selective advantage over parasites with a single var2csa gene. Accumulation of parasites with multiple copies of the var2csa gene during the course of pregnancy was also correlated with the development of antibodies involved in blocking VAR2CSA adhesion. The data suggest that multiplicity of var2csa-type genes enables P. falciparum parasites to persist for a longer period of time during placental infections, probably because of their greater capacity for antigenic variation and evasion of variant-specific immune responses. PMID:21592998

AFLP Phylogeny of 36 Erythroxylum species- genetic relationships among Erythroxylum species inferred by AFLP analysis

USDA-ARS?s Scientific Manuscript database

The plant genus Erythroxylum is known for four cultivated taxa, Erythroxylum coca var. coca (Ecc), Erythroxylum coca var. ipadu (Eci), Erythroxylum novogranatense var. novogranatense (Enn) and Erythroxylum novogranatense var. truxillense (Ent) that are cultivated primarily for the illicit extraction...

CRISPR/Cas9 Genome Editing Reveals That the Intron Is Not Essential for var2csa Gene Activation or Silencing in Plasmodium falciparum.

PubMed

Bryant, Jessica M; Regnault, Clément; Scheidig-Benatar, Christine; Baumgarten, Sebastian; Guizetti, Julien; Scherf, Artur

2017-07-11

Plasmodium falciparum relies on monoallelic expression of 1 of 60 var virulence genes for antigenic variation and host immune evasion. Each var gene contains a conserved intron which has been implicated in previous studies in both activation and repression of transcription via several epigenetic mechanisms, including interaction with the var promoter, production of long noncoding RNAs (lncRNAs), and localization to repressive perinuclear sites. However, functional studies have relied primarily on artificial expression constructs. Using the recently developed P. falciparum clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, we directly deleted the var2csa P. falciparum 3D7_1200600 (Pf3D7_1200600) endogenous intron, resulting in an intronless var gene in a natural, marker-free chromosomal context. Deletion of the var2csa intron resulted in an upregulation of transcription of the var2csa gene in ring-stage parasites and subsequent expression of the PfEMP1 protein in late-stage parasites. Intron deletion did not affect the normal temporal regulation and subsequent transcriptional silencing of the var gene in trophozoites but did result in increased rates of var gene switching in some mutant clones. Transcriptional repression of the intronless var2csa gene could be achieved via long-term culture or panning with the CD36 receptor, after which reactivation was possible with chondroitin sulfate A (CSA) panning. These data suggest that the var2csa intron is not required for silencing or activation in ring-stage parasites but point to a subtle role in regulation of switching within the var gene family. IMPORTANCE Plasmodium falciparum is the most virulent species of malaria parasite, causing high rates of morbidity and mortality in those infected. Chronic infection depends on an immune evasion mechanism termed antigenic variation, which in turn relies on monoallelic expression of 1 of ~60 var genes. Understanding antigenic variation and the transcriptional regulation of monoallelic expression is important for developing drugs and/or vaccines. The var gene family encodes the antigenic surface proteins that decorate infected erythrocytes. Until recently, studying the underlying genetic elements that regulate monoallelic expression in P. falciparum was difficult, and most studies relied on artificial systems such as episomal reporter genes. Our study was the first to use CRISPR/Cas9 genome editing for the functional study of an important, conserved genetic element of var genes-the intron-in an endogenous, episome-free manner. Our findings shed light on the role of the var gene intron in transcriptional regulation of monoallelic expression. Copyright © 2017 Bryant et al.

Vector autoregressive model approach for forecasting outflow cash in Central Java

NASA Astrophysics Data System (ADS)

hoyyi, Abdul; Tarno; Maruddani, Di Asih I.; Rahmawati, Rita

2018-05-01

Multivariate time series model is more applied in economic and business problems as well as in other fields. Applications in economic problems one of them is the forecasting of outflow cash. This problem can be viewed globally in the sense that there is no spatial effect between regions, so the model used is the Vector Autoregressive (VAR) model. The data used in this research is data on the money supply in Bank Indonesia Semarang, Solo, Purwokerto and Tegal. The model used in this research is VAR (1), VAR (2) and VAR (3) models. Ordinary Least Square (OLS) is used to estimate parameters. The best model selection criteria use the smallest Akaike Information Criterion (AIC). The result of data analysis shows that the AIC value of VAR (1) model is equal to 42.72292, VAR (2) equals 42.69119 and VAR (3) equals 42.87662. The difference in AIC values is not significant. Based on the smallest AIC value criteria, the best model is the VAR (2) model. This model has satisfied the white noise assumption.

Systematics of Juniperus section Juniperus based on leaf essential oils and random amplified polymorphic DNAs (RAPDs).

PubMed

Adams

2000-07-01

The composition of the leaf essential oils of all the species of Juniperus in sect. Juniperus (=sect. Oxycedrus) are reported and compared (J. brevifolia, J. cedrus, J. communis, J. c. var. saxatilis, J. c. var. oblonga, J. formosana, J. oxycedrus, J. o. subsp. badia, J. o. subsp. macrocarpa, J. o. subsp. transtagana, J. rigida, J. r. subsp. conferta, J. sibirica, J. taxifolia and J. t. var. lutchuensis). In addition, DNA fingerprinting by RAPDs was utilized. Based on these data, several taxa remained at the same taxonomic level: J. brevifolia, J. cedrus, J. communis, J. c. var. saxatilis, J. formosana, J. oxycedrus, J. rigida, J. r. var. conferta, and J. taxifolia. However, several taxa exhibited considerable differentiation that warranted their recognition at the specific level: J. oblonga M.-Bieb. (=J. communis var. oblonga), J. badia H. Gay (=J. oxycedrus subsp. badia), J. macrocarpa Sibth. and Sm. (=J. oxycedrus subsp. macrocarpa), J. navicularis Gand. (=J. oxycedrus subsp. transtagana), J. sibirica Brugsd. (=J. communis var. saxatilis in part), and J. lutchuensis Koidz. (= J. taxifolia var. lutchuensis).

A Two-Dimensional Variational Analysis Method for NSCAT Ambiguity Removal: Methodology, Sensitivity, and Tuning

NASA Technical Reports Server (NTRS)

Hoffman, R. N.; Leidner, S. M.; Henderson, J. M.; Atlas, R.; Ardizzone, J. V.; Bloom, S. C.; Atlas, Robert (Technical Monitor)

2001-01-01

In this study, we apply a two-dimensional variational analysis method (2d-VAR) to select a wind solution from NASA Scatterometer (NSCAT) ambiguous winds. 2d-VAR determines a "best" gridded surface wind analysis by minimizing a cost function. The cost function measures the misfit to the observations, the background, and the filtering and dynamical constraints. The ambiguity closest in direction to the minimizing analysis is selected. 2d-VAR method, sensitivity and numerical behavior are described. 2d-VAR is compared to statistical interpolation (OI) by examining the response of both systems to a single ship observation and to a swath of unique scatterometer winds. 2d-VAR is used with both NSCAT ambiguities and NSCAT backscatter values. Results are roughly comparable. When the background field is poor, 2d-VAR ambiguity removal often selects low probability ambiguities. To avoid this behavior, an initial 2d-VAR analysis, using only the two most likely ambiguities, provides the first guess for an analysis using all the ambiguities or the backscatter data. 2d-VAR and median filter selected ambiguities usually agree. Both methods require horizontal consistency, so disagreements occur in clumps, or as linear features. In these cases, 2d-VAR ambiguities are often more meteorologically reasonable and more consistent with satellite imagery.

[Effect of Water Extracts from Rhizosphere Soil of Cultivated Astragalus membranaceus var. mongholicus on It's Seed Germination and Physiological Characteristics].

PubMed

Lang, Duo-yong; Fu, Xue-yan; Rong, Jia-wang; Zhang, Xin-hui

2015-01-01

To explore the relationship between continuous cropping obstacle and autotoxicity of Astragalus membranaceus var. mongholicus. Distilled water(CK), water extracts of rhizosphere soil(50, 100, 200 and 400 mg/mL) were applied to test their effect on early growth and physiological characteristics of Astragalus membranaceus var. mongholicus. The water extracts from rhizospher soil of cultivated Astragalus membranaceus var. mongholicus significantly increased seedling emergence rate, root length and vigor index of Astragalus membranaceus var. mongholicus seedling when at the concentration of 100 mg/mL or below, however,there was no significant effect at 200 mg/mL or higher. The water extracts from rhizosphere soil of cultivated Astragalus membranaceus var. mongholicus significantly reduced the SOD activity in Astragalus membranaceus var. mongholicus seedling at 400 mg/mL and POD activity at 200 mg/mL and 400 mg/mL,while significantly increased the MDA content. Water extracts from Astragalus membranaceus var. mongholicus rhizosphere soil significantly affected Astragalus membranaceus var. mongholicus germination and seedling growth in a concentration-dependent manner, generally, low concentrations increased the SOD and POD activity which improved seed germination and seedling growth, while high concentrations caused cell membrane damage of the seedling.

Effects of sex, parity, and sequence variation on seroreactivity to candidate pregnancy malaria vaccine antigens.

PubMed

Oleinikov, Andrew V; Rossnagle, Eddie; Francis, Susan; Mutabingwa, Theonest K; Fried, Michal; Duffy, Patrick E

2007-07-01

Plasmodium falciparum-infected erythrocytes adhere to chondroitin sulfate A (CSA) to sequester in the human placenta, and pregnancy malaria (PM) is associated with the development of disease in and the death of both mother and child. A PM vaccine appears to be feasible, because women become protected as they develop antibodies against placental infected erythrocytes (IEs). Two IE surface molecules, VAR1CSA and VAR2CSA, bind CSA in vitro and are potential vaccine candidates. We expressed all domains of VAR1CSA and VAR2CSA as mammalian cell surface proteins, using a novel approach that allows rapid purification, immobilization, and quantification of target antigen. For serum samples from East Africa, we measured reactivity to all domains, and we examined the effects of host sex and parity, as well as the effects of parasite antigenic variation. Serum samples obtained from multigravid women had a higher reactivity to all VAR2CSA domains than did those obtained from primigravid women or from men. Conversely, serum samples obtained from men had consistently higher reactivity to VAR1CSA domains than did those obtained from gravid women. Seroreactivity was strongly influenced by antigenic variation of VAR2CSA Duffy binding-like domains. Women acquire antibodies to VAR2CSA over successive pregnancies, but they lose reactivity to VAR1CSA. Serum reactivity to VAR2CSA is variant specific, and future studies should examine the degree to which functional antibodies, such as binding-inhibition antibodies, are variant specific.

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris.

PubMed

Avril, Marion; Hathaway, Marianne J; Cartwright, Megan M; Gose, Severin O; Narum, David L; Smith, Joseph D

2009-06-29

VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles. VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens. From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes. These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development.

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris

PubMed Central

Avril, Marion; Hathaway, Marianne J; Cartwright, Megan M; Gose, Severin O; Narum, David L; Smith, Joseph D

2009-01-01

Background VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles. Methods VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens. Results From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes. Conclusion These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development. PMID:19563628

Knowledge, Attitude and Practice of Pregnant Women towards Varicella and Their Children’s Varicella Vaccination: Evidence from Three Distrcits in Zhejiang Province, China

PubMed Central

Hu, Yu; Chen, Yaping; Wang, Ying; Liang, Hui

2017-01-01

Background: The objectives of this study were to examine the knowledge, attitudes and practice (KAP) towards varicella and varicella vaccine (VarV) vaccination among pregnant women in three distrcits in Zhejiang Province, China. Methods: From 1 January to 31 March 2014, pregnant women with ≥12 gestational weeks were recruited and received a self-administrated questionnaire. The first dose of VarV (VarV1) vaccination status of children from present pregnancy was extracted at 24 months of age from Zhejiang provincial immunization information system (ZJIIS). Three variables was defined as the main outcomes, which included: (1) knowing about both the availability of VarV and the number of doses required; (2) positive attitude towards the utility of varicella vaccination; (3) the vaccination coverage of VarV1, which meant the proportion of children having received the VarV1. Counts and proportions were used to describe the socio-demographic characteristics of study participants, and their relationship with study outcomes were tested using chi-square tests in univariate analysis and logistic regression in multivariable analysis. Results: A total of 629 pregnant women participated in this study. The majority of the participants (68.0%) answered correctly about the transmission route of varicella. The proportion of participants who heard about varicella vaccination was 76.5% and 66.8% knew that VarV was currently available. Only 13.5% of the participants answered correctly that the complete VarV series needed two doses. Age, immigration status, education level, household income, and number of children of the pregnant women were significant predictors of the KAP regarding the VarV vaccination. Conclusions: The current survey indicated that optimal KAP levels and coverage on VarV vaccination were observed in three districts of Zhejiang Province. Health education programs on varicella and VarV vaccination directed towards both pre-natal and post-natal women are needed, which will result in a better attitude on vaccination of VarV and in a high coverage of VarV. PMID:28946647

Cryptococcosis

MedlinePlus

C. neoformans var. neoformans infection; C. neoformans var. gatti infection; C. neoformans var. grubii infection ... C. neoformans and C. gattii are the fungi that cause this disease. Infection with C. neoformans is ...

The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing.

PubMed

Basquin, Denis; Spierer, Anne; Begeot, Flora; Koryakov, Dmitry E; Todeschini, Anne-Laure; Ronsseray, Stéphane; Vieira, Cristina; Spierer, Pierre; Delattre, Marion

2014-01-01

Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3-7 protein in Drosophila ovaries. We present evidences that Su(var)3-7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3-7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3-7 is required for genome integrity. Females homozygous for Su(var)3-7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3-7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3-7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3-7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3-7 and piwi or aubergine controls important developmental processes independently of transposon silencing.

Antibody levels to recombinant VAR2CSA domains vary with Plasmodium falciparum parasitaemia, gestational age, and gravidity, but do not predict pregnancy outcomes.

PubMed

Fried, Michal; Kurtis, Jonathan D; Swihart, Bruce; Morrison, Robert; Pond-Tor, Sunthorn; Barry, Amadou; Sidibe, Youssoufa; Keita, Sekouba; Mahamar, Almahamoudou; Andemel, Naissem; Attaher, Oumar; Dembele, Adama B; Cisse, Kadidia B; Diarra, Bacary S; Kanoute, Moussa B; Narum, David L; Dicko, Alassane; Duffy, Patrick E

2018-03-09

Maternal malaria is a tropical scourge associated with poor pregnancy outcomes. Women become resistant to Plasmodium falciparum pregnancy malaria as they acquire antibodies to the variant surface antigen VAR2CSA, a leading vaccine candidate. Because malaria infection may increase VAR2CSA antibody levels and thereby confound analyses of immune protection, gravidity-dependent changes in antibody levels during and after infection, and the effect of VAR2CSA antibodies on pregnancy outcomes were evaluated. Pregnant women enrolled in a longitudinal cohort study of mother-infant pairs in Ouelessebougou, Mali provided plasma samples at enrollment, gestational week 30-32, and delivery. Antibody levels to VAR2CSA domains were measured using a multiplex bead-based assay. Antibody levels to VAR2CSA were higher in multigravidae than primigravidae. Malaria infection was associated with increased antibody levels to VAR2CSA domains. In primigravidae but not in secundigravidae or multigravidae, antibodies levels sharply declined after an infection. A relationship between any VAR2CSA antibody specificity and protection from adverse pregnancy outcomes was not detected. During malaria infection, primigravidae acquire short-lived antibodies. The lack of an association between VAR2CSA domain antibody reactivity and improved pregnancy outcomes suggests that the recombinant proteins may not present native epitopes targeted by protective antibodies.

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

PubMed Central

Lai, Zhongwu; Markovets, Aleksandra; Ahdesmaki, Miika; Chapman, Brad; Hofmann, Oliver; McEwen, Robert; Johnson, Justin; Dougherty, Brian; Barrett, J. Carl; Dry, Jonathan R.

2016-01-01

Abstract Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research. PMID:27060149

[Soluble and insoluble dietary fiber in cereals and legumes cultivated in Chile].

PubMed

Pak, N; Ayala, C; Vera, G; Pennacchiotti, I; Araya, H

1990-03-01

Insoluble, soluble and total dietary fiber (DF) were determined in 35 varieties of certified whole seeds (without processing) of cereals (rice, oat, rye, and wheat) and legumes (pea, cowpea, beans, chikpea, lentil and lupine). The enzymatic method of Asp, Johansson and Siljestrom was used, with modifications in relation to time of incubation with alpha amylase, filtration system and volumes of the filtrates. Results were expressed as g/100 g dry weight. Total DF for cereals showed a range from 10.1 (wheat var. Chasqui) to 22.2 (rice var Quella). Rye, var. Tetra Baer and oats var. Pony Baer presented the highest soluble fiber content (3.3 and 3.9, respectively). In legumes, total DF fluctuated between 12.7 (pea, var. yellow) and 36.6 (lupine, var. Multolupa). Bean, var. Pinto INIA and lupine var. Multolupa presented the highest soluble fiber values (5.8 for both). Based on the results of this research work, it might be concluded that great variation exists in regard to the amount of total soluble and insoluble DF in cereals and legumes, a fact which impedes generalization as to its content in each food item.

4D-Var Developement at GMAO

NASA Technical Reports Server (NTRS)

Pelc, Joanna S.; Todling, Ricardo; Akkraoui, Amal El

2014-01-01

The Global Modeling and Assimilation Offce (GMAO) is currently using an IAU-based 3D-Var data assimilation system. GMAO has been experimenting with a 3D-Var-hybrid version of its data assimilation system (DAS) for over a year now, which will soon become operational and it will rapidly progress toward a 4D-EnVar. Concurrently, the machinery to exercise traditional 4DVar is in place and it is desirable to have a comparison of the traditional 4D approach with the other available options, and evaluate their performance in the Goddard Earth Observing System (GEOS) DAS. This work will also explore the possibility for constructing a reduced order model (ROM) to make traditional 4D-Var computationally attractive for increasing model resolutions. Part of the research on ROM will be to search for a suitably acceptable space to carry on the corresponding reduction. This poster illustrates how the IAU-based 4D-Var assimilation compares with our currently used IAU-based 3D-Var.

Isolation of Cryptococcus neoformans var. gattii from Eucalyptus camaldulensis in India.

PubMed Central

Chakrabarti, A; Jatana, M; Kumar, P; Chatha, L; Kaushal, A; Padhye, A A

1997-01-01

Cryptococcus neoformans var. gattii has an ecological association with five Eucalyptus species: E. blakelyi, E. camaldulensis, E. gomphocephala, E. rudis, and E. tereticornis. After human infections due to C. neoformans var. gattii were diagnosed in the states of Punjab, Himachal Pradesh, and Karnataka, India, a study was undertaken to investigate the association of C. neoformans var. gattii with Indian eucalypts, especially in the state of Punjab. A total of 696 specimens collected from E. camaldulensis, E. citriodora and E. tereticornis (hybrid) trees were examined for the presence of C. neoformans var. gattii. Flowers from two trees of E. camaldulensis in the Chak Sarkar forest and one from the village of Periana near the Ferozepur area yielded five isolates of C. neoformans var. gattii. The origin of the trees could be traced to Australia, thus providing evidence that the distribution of E. camaldulensis correlated with the distribution of human cryptococcosis cases caused by C. neoformans var. gattii in northern India. PMID:9399553

Arundina graminifolia var. revoluta (Arethuseae, Orchidaceae) has fern-type rheophyte characteristics in the leaves.

PubMed

Yorifuji, Eri; Ishikawa, Naoko; Okada, Hiroshi; Tsukaya, Hirokazu

2015-03-01

Morphological and molecular variation between Arundina graminifolia var. graminifolia and the dwarf variety, A. graminifolia var. revoluta, was examined to assess the validity of their taxonomic characteristics and genetic background for identification. Morphological analysis in combination with field observations indicated that A. graminifolia var. revoluta is a rheophyte form of A. graminifolia characterized by narrow leaves, whereas the other morphological characteristics described for A. graminifolia var. revoluta, such as smaller flowers and short stems, were not always accompanied by the narrower leaf phenotype. Molecular analysis based on matK sequences indicated that only partial differentiation has occurred between A. graminifolia var. graminifolia and A. graminifolia var. revoluta. Therefore, we should consider the rheophyte form an ecotype rather than a variety. Anatomical observations of the leaves revealed that the rheophyte form of A. graminifolia possessed characteristics of the rheophytes of both ferns and angiosperms, such as narrower palisade tissue cells and thinner spongy tissue cells, as well as fewer cells in the leaf-width direction and fewer mesophyll cell layers.

The Anthelmintic Ingredient Moxidectin Negatively Affects Seed Germination of Three Temperate Grassland Species

PubMed Central

Eichberg, Carsten; Wohde, Manuel; Müller, Kerstin; Rausch, Anja; Scherrmann, Christina; Scheuren, Theresa; Düring, Rolf-Alexander; Donath, Tobias W.

2016-01-01

In animal farming, anthelmintics are regularly applied to control gastrointestinal nematodes. There is plenty of evidence that also non-target organisms, such as dung beetles, are negatively affected by residues of anthelmintics in faeces of domestic ungulates. By contrast, knowledge about possible effects on wild plants is scarce. To bridge this gap of knowledge, we tested for effects of the common anthelmintic formulation Cydectin and its active ingredient moxidectin on seed germination. We conducted a feeding experiment with sheep and germination experiments in a climate chamber. Three wide-spread plant species of temperate grasslands (Centaurea jacea, Galium verum, Plantago lanceolata) were studied. We found significant influences of both, Cydectin and moxidectin, on germination of the tested species. Across species, both formulation and active ingredient solely led to a decrease in germination percentage and synchrony of germination and an increase in mean germination time with the formulation showing a more pronounced response pattern. Our study shows for the first time that anthelmintics have the potential to negatively affect plant regeneration. This has practical implications for nature conservation since our results suggest that treatments of livestock with anthelmintics should be carefully timed to not impede endozoochorous seed exchange between plant populations. PMID:27846249

Anatomy of Subterranean Organs of Medicinally Used Cardueae and Related Species and its Value for Discrimination

PubMed Central

Fritz, Elisabeth; Saukel, Johannes

2011-01-01

Numerous species of the Asteraceae, the composites, are famous for their use in both traditional and conventional medicine. Reliable anatomical descriptions of these plants and of possible adulterations provide a basis for fast identification and cheap purity controls of respective medicinal drugs by means of light microscopy. Nevertheless, detailed comparative studies on root and rhizome anatomy of valuable as well as related inconsiderable composite plants are largely missing yet. The presented study aims to narrow this gap by performing anatomical analyses of roots and rhizomes of 16 species belonging to the tribe Cardueae, of formerly and currently used drugs as well as their near relatives as potential adulterations (Carlina acaulis L., Carlina vulgaris L., Arctium lappa L., Arctium tomentosum Mill., Carduus defloratus L., Carduus personata (L.) Jacq, Cirsium arvense (L.) Scop., Cirsium vulgare (Savi) Ten., Cirsium erisithales (Jacq.) Scop., Onopordum acanthium L., Silybum marianum (L.) Gaertn., Rhaponticum scariosum Lam., Centaurea jacea L., Centaurea scabiosa L., Centaurea cyanus L., Cnicus benedictus L.). A detailed verbal and graphical survey of the analysed anatomical features is provided. Several characters were finally extracted which allow for discrimination of the examined species and may be effectively used for drug quality controls. PMID:21617780

Empirical analysis on future-cash arbitrage risk with portfolio VaR

NASA Astrophysics Data System (ADS)

Chen, Rongda; Li, Cong; Wang, Weijin; Wang, Ze

2014-03-01

This paper constructs the positive arbitrage position by alternating the spot index with Chinese Exchange Traded Fund (ETF) portfolio and estimating the arbitrage-free interval of futures with the latest trade data. Then, an improved Delta-normal method was used, which replaces the simple linear correlation coefficient with tail dependence correlation coefficient, to measure VaR (Value-at-risk) of the arbitrage position. Analysis of VaR implies that the risk of future-cash arbitrage is less than that of investing completely in either futures or spot market. Then according to the compositional VaR and the marginal VaR, we should increase the futures position and decrease the spot position appropriately to minimize the VaR, which can minimize risk subject to certain revenues.

A var gene promoter implicated in severe malaria nucleates silencing and is regulated by 3’ untranslated region and intronic cis-elements

PubMed Central

Muhle, Rebecca A.; Adjalley, Sophie; Falkard, Brie; Nkrumah, Louis J.; Muhle, Michael E.; Fidock, David A.

2009-01-01

Questions surround the mechanism of mutually exclusive expression by which Plasmodium falciparum mediates activation and silencing of var genes. These encode PfEMP1 proteins, which function as cytoadherent and immunomodulatory molecules at the surface of parasitized erythrocytes. Current evidence suggests that promoter silencing by var introns might play a key role in var gene regulation. To evaluate the impact of cis-acting regulatory regions on var silencing, we generated P. falciparum lines in which luciferase was placed under the control of an UpsA var promoter. By utilizing the Bxb1 integrase system, these reporter cassettes were targeted to a genomic region that was not in apposition to var sub-telomeric domains. This eliminated possible effects from surrounding telomeric elements and removed the variability inherent in episomal systems. Studies with highly synchronized parasites revealed that the UpsA element possessed minimal activity in comparison with a heterologous (hrp3) promoter. This may well result from the integrated UpsA promoter being largely silenced by the neighboring cg6 promoter. Our analyses also revealed that the DownsA 3’ untranslated region further decreased the luciferase activity from both cassettes, whereas the var A intron repressed the UpsA promoter specifically. By applying multivariate analysis over the entire cell cycle, we confirmed the significance of these cis-elements and found the parasite stage to be the major factor regulating UpsA promoter activity. Additionally, we observed that the UpsA promoter was capable of nucleating reversible silencing that spread to a downstream promoter. We believe these studies are the first to analyze promoter activity of Group A var genes which have been implicated in severe malaria, and support the model that var introns can further suppress var expression. These data also suggest an important suppressive role for the DownsA terminator. Our findings imply the existence of multiple levels of var gene regulation in addition to intrinsic promoter-dependent silencing. PMID:19463825

Phytochemical characterization of several hawthorn (Crataegus spp.) species sampled from the Eastern Mediterranean region of Turkey.

PubMed

Calişkan, Oğuzhan; Gündüz, Kazim; Serçe, Sedat; Toplu, Celil; Kamiloğlu, Onder; Sengül, Memnune; Ercişli, Sezai

2012-01-01

We evaluated the total phenolic content, antioxidant capacity as well as antioxidant activity of five Crataegus species (A1, A2, Y1, Y2, Y4 accessions of Crataegus aronia var. aronia; B2, B3, B5, B6, B7, B9, Y5 accessions of C. aronia var. dentata; B10 accession of C. aronia var. minuta; Y3 accession of Crataegus orientalis var. orientalis and A3 accession of Crataegus monogyna subsp. azarella). Antioxidant activity and total phenolic content of fruits were determined by β-carotene bleaching and Folin-Ciocalteu assays. Antioxidant capacity was determined by using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. C. monogyna subsp. azarella had the highest total phenol, antioxidant activity and antioxidant capacity of 55.2 mg gallic acid equivalents (GAE)/g dry weight (DW), 81.9% and 31.2%, respectively. C. aronia var. aronia was found to have the lowest total phenolic content (35.7 mg GAE/g DW). The antioxidant activities of fruit extracts increased in the order of C. orientalis var. orientalis < C. aronia var. minuta < C. aronia var. dentata < C. aronia var. aronia < C. monogyna subsp. azarella according to β-carotene/linoleic acid assay. In recent years, C. aronia var. dentata has gained importance as a commercial species in this region. B3 and B7 accessions had fruit weight more than 14 g, and considerable total phenol content, antioxidant activity and antioxidant capacity. This investigation shows the potential value of hawthorn fruit species as a good source of natural antioxidants and that consumption of hawthorn fruit or its products may contribute substantial amounts of antioxidants to the diet.

Phytochemical characterization of several hawthorn (Crataegus spp.) species sampled from the Eastern Mediterranean region of Turkey

PubMed Central

Çalişkan, Oğuzhan; Gündüz, Kazim; Serçe, Sedat; Toplu, Celil; Kamiloğlu, Önder; Şengül, Memnune; Ercişli, Sezai

2012-01-01

Background: We evaluated the total phenolic content, antioxidant capacity as well as antioxidant activity of five Crataegus species (A1, A2, Y1, Y2, Y4 accessions of Crataegus aronia var. aronia; B2, B3, B5, B6, B7, B9, Y5 accessions of C. aronia var. dentata; B10 accession of C. aronia var. minuta; Y3 accession of Crataegus orientalis var. orientalis and A3 accession of Crataegus monogyna subsp. azarella). Materials and Methods: Antioxidant activity and total phenolic content of fruits were determined by β-carotene bleaching and Folin–Ciocalteu assays. Antioxidant capacity was determined by using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Results: C. monogyna subsp. azarella had the highest total phenol, antioxidant activity and antioxidant capacity of 55.2 mg gallic acid equivalents (GAE)/g dry weight (DW), 81.9% and 31.2%, respectively. C. aronia var. aronia was found to have the lowest total phenolic content (35.7 mg GAE/g DW). The antioxidant activities of fruit extracts increased in the order of C. orientalis var. orientalis < C. aronia var. minuta < C. aronia var. dentata < C. aronia var. aronia < C. monogyna subsp. azarella according to β-carotene/linoleic acid assay. In recent years, C. aronia var. dentata has gained importance as a commercial species in this region. B3 and B7 accessions had fruit weight more than 14 g, and considerable total phenol content, antioxidant activity and antioxidant capacity. Conclusion: This investigation shows the potential value of hawthorn fruit species as a good source of natural antioxidants and that consumption of hawthorn fruit or its products may contribute substantial amounts of antioxidants to the diet. PMID:22438658

Comparative Analysis of VaR Estimation of Double Long-Memory GARCH Models: Empirical Analysis of China's Stock Market

NASA Astrophysics Data System (ADS)

Cao, Guangxi; Guo, Jianping; Xu, Lin

GARCH models are widely used to model the volatility of financial assets and measure VaR. Based on the characteristics of long-memory and lepkurtosis and fat tail of stock market return series, we compared the ability of double long-memory GARCH models with skewed student-t-distribution to compute VaR, through the empirical analysis of Shanghai Composite Index (SHCI) and Shenzhen Component Index (SZCI). The results show that the ARFIMA-HYGARCH model performance better than others, and at less than or equal to 2.5 percent of the level of VaR, double long-memory GARCH models have stronger ability to evaluate in-sample VaRs in long position than in short position while there is a diametrically opposite conclusion for ability of out-of-sample VaR forecast.

Influence ofArtemisia princeps var.orientalis components on callus induction and growth.

PubMed

Kil, B S; Yun, K W; Lee, S Y

1992-08-01

An in vitro study was performed to determine the potential application of tissue culture in determining allelopathic potentialof Artemisia princeps var.Orientalis (wormwood). Aqueous extracts and volatile substances ofA. princeps var.Orientalis were tested to determine their effects on callus induction and growth of several tested species. Extracts of 5%A. princeps var.Orientalis caused some reduction in concentration, induction, and growth of callus, although they looked normal, whereas the expiants of most receptor plants did not develop callus at higher concentration. Lettuce andEclipta prostrata were the most sensitive species, andA. princeps var.Orientalis was affected by its own extracts. The growth of calluses in MS 121 medium treated with essential oil ofA. princeps var.Orientalis was inhibited, and the degree of inhibition was proportional to the concentration of the essential oil.

Semi-nonparametric VaR forecasts for hedge funds during the recent crisis

NASA Astrophysics Data System (ADS)

Del Brio, Esther B.; Mora-Valencia, Andrés; Perote, Javier

2014-05-01

The need to provide accurate value-at-risk (VaR) forecasting measures has triggered an important literature in econophysics. Although these accurate VaR models and methodologies are particularly demanded for hedge fund managers, there exist few articles specifically devoted to implement new techniques in hedge fund returns VaR forecasting. This article advances in these issues by comparing the performance of risk measures based on parametric distributions (the normal, Student’s t and skewed-t), semi-nonparametric (SNP) methodologies based on Gram-Charlier (GC) series and the extreme value theory (EVT) approach. Our results show that normal-, Student’s t- and Skewed t- based methodologies fail to forecast hedge fund VaR, whilst SNP and EVT approaches accurately success on it. We extend these results to the multivariate framework by providing an explicit formula for the GC copula and its density that encompasses the Gaussian copula and accounts for non-linear dependences. We show that the VaR obtained by the meta GC accurately captures portfolio risk and outperforms regulatory VaR estimates obtained through the meta Gaussian and Student’s t distributions.

Protective Antibodies against Placental Malaria and Poor Outcomes during Pregnancy, Benin

PubMed Central

Denoeud-Ndam, Lise; Doritchamou, Justin; Viwami, Firmine; Salanti, Ali; Nielsen, Morten A.; Fievet, Nadine; Massougbodji, Achille; Luty, Adrian J.F.; Deloron, Philippe

2015-01-01

Placental malaria is caused by Plasmodium falciparum–infected erythrocytes that bind to placental tissue. Binding is mediated by VAR2CSA, a parasite antigen coded by the var gene, which interacts with chondroitin sulfate A (CSA). Consequences include maternal anemia and fetal growth retardation. Antibody-mediated immunity to placental malaria is acquired during successive pregnancies, but the target of VAR2CSA-specific protective antibodies is unclear. We assessed VAR2CSA-specific antibodies in pregnant women and analyzed their relationships with protection against placental infection, preterm birth, and low birthweight. Antibody responses to the N-terminal region of VAR2CSA during early pregnancy were associated with reduced risks for infections and low birthweight. Among women infected during pregnancy, an increase in CSA binding inhibition was associated with reduced risks for placental infection, preterm birth, and low birthweight. These data suggest that antibodies against VAR2CSA N-terminal region mediate immunity to placental malaria and associated outcomes. Our results validate current vaccine development efforts with VAR2CSA N-terminal constructs. PMID:25898123

Comparative study on the chemical composition, antioxidant properties and hypoglycaemic activities of two Capsicum annuum L. cultivars (Acuminatum small and Cerasiferum).

PubMed

Tundis, Rosa; Loizzo, Monica R; Menichini, Federica; Bonesi, Marco; Conforti, Filomena; Statti, Giancarlo; De Luca, Damiano; de Cindio, Bruno; Menichini, Francesco

2011-09-01

The present study aimed to evaluate for the first time the phenols, flavonoids, carotenoids, capsaicin and dihydrocapsaicin content and the antioxidant and hypoglycemic properties of Capsicum annuum var. acuminatum small and C. annuum var. cerasiferum air-dried fruits. The ethanol extract of C. annuum var. acuminatum small, characterized by the major content of total poliphenols, flavonoids, carotenoids and capsaicinoids, showed the highest radical scavenging activity (IC(50) of 152.9 μg/ml). On the contrary, C. annuum var. cerasiferum showed a significant antioxidant activity evaluated by the β-carotene bleaching test (IC(50) of 3.1 μg/ml). The lipophilic fraction of both C. annuum var. acuminatum and C. annuum var. cerasiferum exhibited an interesting and selective inhibitory activity against α-amylase (IC(50) of 6.9 and 20.1 μg/ml, respectively).

Design of inhibitors of thymidylate kinase from Variola virus as new selective drugs against smallpox.

PubMed

Guimarães, Ana P; de Souza, Felipe R; Oliveira, Aline A; Gonçalves, Arlan S; de Alencastro, Ricardo B; Ramalho, Teodorico C; França, Tanos C C

2015-02-16

Recently we constructed a homology model of the enzyme thymidylate kinase from Variola virus (VarTMPK) and proposed it as a new target to the drug design against smallpox. In the present work, we used the antivirals cidofovir and acyclovir as reference compounds to choose eleven compounds as leads to the drug design of inhibitors for VarTMPK. Docking and molecular dynamics (MD) studies of the interactions of these compounds inside VarTMPK and human TMPK (HssTMPK) suggest that they compete for the binding region of the substrate and were used to propose the structures of ten new inhibitors for VarTMPK. Further docking and MD simulations of these compounds, inside VarTMPK and HssTMPK, suggest that nine among ten are potential selective inhibitors of VarTMPK. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

A new framework for comprehensive, robust, and efficient global sensitivity analysis: 2. Application

NASA Astrophysics Data System (ADS)

Razavi, Saman; Gupta, Hoshin V.

2016-01-01

Based on the theoretical framework for sensitivity analysis called "Variogram Analysis of Response Surfaces" (VARS), developed in the companion paper, we develop and implement a practical "star-based" sampling strategy (called STAR-VARS), for the application of VARS to real-world problems. We also develop a bootstrap approach to provide confidence level estimates for the VARS sensitivity metrics and to evaluate the reliability of inferred factor rankings. The effectiveness, efficiency, and robustness of STAR-VARS are demonstrated via two real-data hydrological case studies (a 5-parameter conceptual rainfall-runoff model and a 45-parameter land surface scheme hydrology model), and a comparison with the "derivative-based" Morris and "variance-based" Sobol approaches are provided. Our results show that STAR-VARS provides reliable and stable assessments of "global" sensitivity across the full range of scales in the factor space, while being 1-2 orders of magnitude more efficient than the Morris or Sobol approaches.

Sex differences in attenuation of nicotine reinstatement after individual and combined treatments of progesterone and varenicline.

PubMed

Swalve, Natashia; Smethells, John R; Carroll, Marilyn E

2016-07-15

Tobacco use is the largest cause of preventable mortality in the western world. Even after treatment, relapse rates for tobacco are high, and more effective pharmacological treatments are needed. Progesterone (PRO), a female hormone used in contraceptives, reduces stimulant use but its effects on tobacco addiction are unknown. Varenicline (VAR) is a commonly used medication that reduces tobacco use. The present study examined sex differences in the individual vs. combined effects of PRO and VAR on reinstatement of nicotine-seeking behavior in a rat model of relapse. Adult female and male Wistar rats self-administered nicotine (NIC, 0.03mg/kg/infusion) for 14days followed by 21days of extinction when no cues or drug were present. Rats were then divided into 4 treatment groups: control (VEH+SAL), PRO alone (PRO+SAL), VAR alone (VEH+VAR) and the combination (PRO+VAR). Reinstatement of nicotine-seeking behavior induced by priming injections of NIC or caffeine (CAF), presentation of cues (CUES), and the combination of drugs and cues (e.g. NIC+CUES, CAF+CUES) were tested after extinction. Male and female rats did not differ in self-administration of nicotine or extinction responding, and both showed elevated levels of responding to the CAF+CUES condition. However, males, but not females, reinstated active lever-pressing to the NIC+CUES condition, and that was attenuated by both VAR and VAR+PRO treatment. Thus, males were more sensitive to NIC+CUE-induced reinstatement than females, and VAR alone and VAR combined with PRO effectively reduced nicotine relapse. Copyright © 2016 Elsevier B.V. All rights reserved.

JIL-1 and Su(var)3-7 Interact Genetically and Counteract Each Other's Effect on Position-Effect Variegation in Drosophila

PubMed Central

Deng, Huai; Cai, Weili; Wang, Chao; Lerach, Stephanie; Delattre, Marion; Girton, Jack; Johansen, Jørgen; Johansen, Kristen M.

2010-01-01

The essential JIL-1 histone H3S10 kinase is a key regulator of chromatin structure that functions to maintain euchromatic domains while counteracting heterochromatization and gene silencing. In the absence of the JIL-1 kinase, two of the major heterochromatin markers H3K9me2 and HP1a spread in tandem to ectopic locations on the chromosome arms. Here we address the role of the third major heterochromatin component, the zinc-finger protein Su(var)3-7. We show that the lethality but not the chromosome morphology defects associated with the null JIL-1 phenotype to a large degree can be rescued by reducing the dose of the Su(var)3-7 gene and that Su(var)3-7 and JIL-1 loss-of-function mutations have an antagonistic and counterbalancing effect on position-effect variegation (PEV). Furthermore, we show that in the absence of JIL-1 kinase activity, Su(var)3-7 gets redistributed and upregulated on the chromosome arms. Reducing the dose of the Su(var)3-7 gene dramatically decreases this redistribution; however, the spreading of H3K9me2 to the chromosome arms was unaffected, strongly indicating that ectopic Su(var)3-9 activity is not a direct cause of lethality. These observations suggest a model where Su(var)3-7 functions as an effector downstream of Su(var)3-9 and H3K9 dimethylation in heterochromatic spreading and gene silencing that is normally counteracted by JIL-1 kinase activity. PMID:20457875

Burkitt lymphoma expresses oncofetal chondroitin sulfate without being a reservoir for placental malaria sequestration.

PubMed

Agerbaek, Mette Ø; Pereira, Marina A; Clausen, Thomas M; Pehrson, Caroline; Oo, Htoo Zarni; Spliid, Charlotte; Rich, Jamie R; Fung, Vincent; Nkrumah, Francis; Neequaye, Janet; Biggar, Robert J; Reynolds, Steven J; Tosato, Giovanna; Pullarkat, Sheeja T; Ayers, Leona W; Theander, Thor G; Daugaard, Mads; Bhatia, Kishor; Nielsen, Morten A; Mbulaiteye, Sam M; Salanti, Ali

2017-04-01

Burkitt lymphoma (BL) is a malignant disease, which is frequently found in areas with holoendemic Plasmodium falciparum malaria. We have previously found that the VAR2CSA protein is present on malaria-infected erythrocytes and facilitates a highly specific binding to the placenta. ofCS is absent in other non-malignant tissues and thus VAR2CSA generally facilitates parasite sequestration and accumulation in pregnant women. In this study, we show that the specific receptor for VAR2CSA, the oncofetal chondroitin sulfate (ofCS), is likewise present in BL tissue and cell lines. We therefore explored whether ofCS in BL could act as anchor site for VAR2CSA-expressing infected erythrocytes. In contrast to the placenta, we found no evidence of in vivo sequestering of infected erythrocytes in the BL tissue. Furthermore, we found VAR2CSA-specific antibody titers in children with endemic BL to be lower than in control children from the same malaria endemic region. The abundant presence of ofCS in BL tissue and the absence of ofCS in non-malignant tissue encouraged us to examine whether recombinant VAR2CSA could be used to target BL. We confirmed the binding of VAR2CSA to BL-derived cells and showed that a VAR2CSA drug conjugate efficiently killed the BL-derived cell lines in vitro. These results identify ofCS as a novel therapeutic BL target and highlight how VAR2CSA could be used as a tool for the discovery of novel approaches for directing BL therapy. © 2016 UICC.

Burkitt lymphoma express oncofetal Chondroitin Sulfate without being a reservoir for placental malaria sequestration

PubMed Central

Agerbæk, Mette Ø.; Pereira, Marina A.; Clausen, Thomas M.; Pehrson, Caroline; Oo, Htoo Zarni; Spliid, Charlotte; Rich, Jamie R.; Fung, Vincent; Nkrumah, Francis; Neequaye, Janet; Biggar, Robert J.; Reynolds, Steven J.; Tosato, Giovanna; Pullarkat, Sheeja T.; Ayers, Leona W.; Theander, Thor G.; Daugaard, Mads; Bhatia, Kishor; Nielsen, Morten A.; Mbulaiteye, Sam M.; Salanti, Ali

2016-01-01

Burkitt lymphoma (BL) is a malignant disease, which is frequently found in areas with holoendemic Plasmodium falciparum malaria. We have previously found that the VAR2CSA protein is present on malaria-infected erythrocytes and facilitates a highly specific binding to the placenta. OfCS is absent from other non-malignant tissues and thus VAR2CSA generally facilitates parasite sequestration and accumulation in pregnant women. In this study, we show that the specific receptor for VAR2CSA, the oncofetal chondroitin sulfate (ofCS), is likewise present in BL tissue and cell lines. We therefore explored whether ofCS in BL could act as anchor-site for VAR2CSA-expressing infected erythrocytes. In contrast to the placenta, we found no evidence of in vivo sequestering of infected erythrocytes in the BL tissue. Furthermore, we found VAR2CSA specific antibody titers in children with endemic BL to be lower than in control children from the same malaria endemic region. The abundant presence of ofCS in BL tissue and the absence of ofCS in non-malignant tissue, encouraged us to examine whether recombinant VAR2CSA could be used to target BL. We confirmed the binding of VAR2CSA to BL-derived cells and showed that a VAR2CSA drug conjugate efficiently killed the BL-derived cell lines in vitro. These results identify ofCS as a novel therapeutic BL target and highlight how VAR2CSA could be used as a tool for the discovery of novel approaches for directing BL therapy. PMID:27997697

A Novel Virus-Like Particle Based Vaccine Platform Displaying the Placental Malaria Antigen VAR2CSA.

PubMed

Thrane, Susan; Janitzek, Christoph M; Agerbæk, Mette Ø; Ditlev, Sisse B; Resende, Mafalda; Nielsen, Morten A; Theander, Thor G; Salanti, Ali; Sander, Adam F

2015-01-01

Placental malaria caused by Plasmodium falciparum is a major cause of mortality and severe morbidity. Clinical testing of a soluble protein-based vaccine containing the parasite ligand, VAR2CSA, has been initiated. VAR2CSA binds to the human receptor chondroitin sulphate A (CSA) and is responsible for sequestration of Plasmodium falciparum infected erythrocytes in the placenta. It is imperative that a vaccine against malaria in pregnancy, if administered to women before they become pregnant, can induce a strong and long lasting immune response. While most soluble protein-based vaccines have failed during clinical testing, virus-like particle (VLP) based vaccines (e.g., the licensed human papillomavirus vaccines) have demonstrated high efficacy, suggesting that the spatial assembly of the vaccine antigen is a critical parameter for inducing an optimal long-lasting protective immune response. We have developed a VLP vaccine display platform by identifying regions of the HPV16 L1 coat protein where a biotin acceptor site (AviTagTM) can be inserted without compromising VLP-assembly. Subsequent biotinylation of Avi-L1 VLPs allow us to anchor monovalent streptavidin (mSA)-fused proteins to the biotin, thereby obtaining a dense and repetitive VLP-display of the vaccine antigen. The mSA-VAR2CSA antigen was delivered on the Avi-L1 VLP platform and tested in C57BL/6 mice in comparison to two soluble protein-based vaccines consisting of naked VAR2CSA and mSA-VAR2CSA. The mSA-VAR2CSA Avi-L1 VLP and soluble mSA-VAR2CSA vaccines induced higher antibody titers than the soluble naked VAR2CSA vaccine after three immunizations. The VAR2CSA Avi-L1 VLP vaccine induced statistically significantly higher endpoint titres compared to the soluble mSA-VAR2CSA vaccine, after 1st and 2nd immunization; however, this difference was not statistically significant after 3rd immunization. Importantly, the VLP-VAR2CSA induced antibodies were functional in inhibiting the binding of parasites to CSA. This study demonstrates that the described Avi-L1 VLP-platform may serve as a versatile system for facilitating optimal VLP-display of large and complex vaccine antigens.

Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae)

PubMed Central

Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

2014-01-01

Abstract Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed. PMID:25009440

Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae).

PubMed

Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

2014-01-01

Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed.

Oil and fatty acid contents in seed of Citrullus lanatus Schrad.

PubMed

Jarret, Robert L; Levy, Irvin J

2012-05-23

Intact seed of 475 genebank accessions of Citrullus ( C. lanatus var. lanatus and C. lanatus var. citroides) were analyzed for percent oil content using TD-NMR. Extracts from whole seed of 96 accessions of C. lanatus (30 var. citroides, 33 var. lanatus, and 33 egusi), C. colocynthis (n = 3), C. ecirrhosus (n = 1), C. rehmii (n = 1), and Benincasa fistulosa (n = 3) were also analyzed for their fatty acids content. Among the materials analyzed, seed oil content varied from 14.8 to 43.5%. Mean seed oil content in egusi types of C. lanatus was significantly higher (mean = 35.6%) than that of either var. lanatus (mean = 23.2%) or var. citroides (mean = 22.6%). Egusi types of C. lanatus had a significantly lower hull/kernel ratio when compared to other C. lanatus var. lanatus or C. lanatus var. citroides. The principal fatty acid in all C. lanatus materials examined was linoleic acid (43.6-73%). High levels of linoleic acid were also present in the materials of C. colocynthis (71%), C. ecirrhosus (62.7%), C. rehmii (75.8%), and B. fistulosa (73.2%), which were included for comparative purposes. Most all samples contained traces (<0.5%) of arachidonic acid. The data presented provide novel information on the range in oil content and variability in the concentrations of individual fatty acids present in a diverse array of C. lanatus, and its related species, germplasm.

A hybrid approach to generating search subspaces in dynamically constrained 4-dimensional data assimilation

NASA Astrophysics Data System (ADS)

Yaremchuk, Max; Martin, Paul; Beattie, Christopher

2017-09-01

Development and maintenance of the linearized and adjoint code for advanced circulation models is a challenging issue, requiring a significant proportion of total effort in operational data assimilation (DA). The ensemble-based DA techniques provide a derivative-free alternative, which appears to be competitive with variational methods in many practical applications. This article proposes a hybrid scheme for generating the search subspaces in the adjoint-free 4-dimensional DA method (a4dVar) that does not use a predefined ensemble. The method resembles 4dVar in that the optimal solution is strongly constrained by model dynamics and search directions are supplied iteratively using information from the current and previous model trajectories generated in the process of optimization. In contrast to 4dVar, which produces a single search direction from exact gradient information, a4dVar employs an ensemble of directions to form a subspace in order to proceed. In the earlier versions of a4dVar, search subspaces were built using the leading EOFs of either the model trajectory or the projections of the model-data misfits onto the range of the background error covariance (BEC) matrix at the current iteration. In the present study, we blend both approaches and explore a hybrid scheme of ensemble generation in order to improve the performance and flexibility of the algorithm. In addition, we introduce balance constraints into the BEC structure and periodically augment the search ensemble with BEC eigenvectors to avoid repeating minimization over already explored subspaces. Performance of the proposed hybrid a4dVar (ha4dVar) method is compared with that of standard 4dVar in a realistic regional configuration assimilating real data into the Navy Coastal Ocean Model (NCOM). It is shown that the ha4dVar converges faster than a4dVar and can be potentially competitive with 4dvar both in terms of the required computational time and the forecast skill.

Efficient transformation and expression of gfp gene in Valsa mali var. mali.

PubMed

Chen, Liang; Sun, Gengwu; Wu, Shujing; Liu, Huixiang; Wang, Hongkai

2015-01-01

Valsa mali var. mali, the causal agent of valsa canker of apple, causes great loss of apple production in apple producing regions. The pathogenic mechanism of the pathogen has not been studied extensively, thus a suitable gene marker for pathogenic invasion analysis and a random insertion of T-DNA for mutants are desirable. In this paper, we reported the construction of a binary vector pKO1-HPH containing a positive selective gene hygromycin phosphotransferase (hph), a reporter gene gfp conferring green fluorescent protein, and an efficient protocol for V. mali var. mali transformation mediated by Agrobacterium tumefaciens. A transformation efficiency up to about 75 transformants per 10(5) conidia was achieved when co-cultivation of V. mali var. mali and A. tumefaciens for 48 h in A. tumefaciens inductive medium agar plates. The insertions of hph gene and gfp gene into V. mali var. mali genome verified by polymerase chain reaction and southern blot analysis showed that 10 randomly-selected transformants exhibited a single, unique hybridization pattern. This is the first report of A. tumefaciens-mediated transformation of V. mali var mali carrying a 'reporter' gfp gene that stably and efficiently expressed in the transformed V. mali var. mali species.

Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa

PubMed Central

2014-01-01

Background Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. Findings Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. Conclusions These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species. PMID:24755442

Fluorescence Spectra of Individual Flowing Airborne Biological Particles Measured in Real Time

DTIC Science & Technology

2001-02-01

and fungal spores ( Aspergillus versicolor, ATCC 9577). B. subtilis var. niger (lyophilized cells) and E. herbicola were grown by streak- ing onto...Excitation Figure 7 shows fluorescence spectra of B. subtilis var. niger vegetative cells and fungal spores ( Aspergillus versicolor), both 5 µm in diameter...µm-diam clusters of B. subtilis var. niger spores, and B. subtilis var. niger vegetative cells ……………………………………… 10 5. Fluorescence spectra of starved

An unusual clinical presentation of tinea faciei caused by Trichophyton mentagrophytes var. erinacei.

PubMed

Lee, Deok-Woo; Yang, Ji-Hye; Choi, Seok-Joo; Won, Chong-Hyun; Chang, Sung-Eun; Lee, Mi-Woo; Choi, Jee-Ho; Moon, Kee-Chan; Kim, Mi-Na

2011-01-01

Trichophyton mentagrophytes var. erinacei, the natural host of which is the hedgehog, has been found to cause highly inflammatory and pruritic eruptions, including tinea manuum, tinea corporis, nail infection, kerion, scalp infection, and tinea barbae. To our knowledge, however, no reports have been made of tinea faciei caused by Trichophyton mentagrophytes var. erinacei in the English language literature. We provide here the case of tinea faciei caused by Trichophyton mentagrophytes var. erinacei. © 2011 Wiley Periodicals, Inc.

Aviation Trainer Technology Test Plan. Volume II. Software Development

DTIC Science & Technology

1991-11-25

feild values in new node *Ieg>X=x newg->X = Y newg->Len =len; newg->Help =help; newg->Ignore = ignore; newg->Format = format; newg->Validation - NULL;I... vector : North long varVFE; /* F-16A velocity vector : East long varVFU; /* F-16A velocity vector : Up */ long varH; /* plane heading */ long varC; /* plane...31\\\\ETH523.sys" parmsdr.args=getds(); parmsdr.non7=OxOO; /*save interrupt vector for future restoration */ cSavvecso; rc=getdso; rc=cInitParameters

Modelling of volatility in monetary transmission mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dobešová, Anna; Klepáč, Václav; Kolman, Pavel

2015-03-10

The aim of this paper is to compare different approaches to modeling of volatility in monetary transmission mechanism. For this purpose we built time-varying parameter VAR (TVP-VAR) model with stochastic volatility and VAR-DCC-GARCH model with conditional variance. The data from three European countries are included in the analysis: the Czech Republic, Germany and Slovakia. Results show that VAR-DCC-GARCH system captures higher volatility of observed variables but main trends and detected breaks are generally identical in both approaches.

Parentage determination of Vanda Miss Joaquim (Orchidaceae) through two chloroplast genes rbcL and matK

PubMed Central

Khew, Gillian Su-Wen; Chia, Tet Fatt

2011-01-01

Background and aims The popular hybrid orchid Vanda Miss Joaquim was made Singapore's national flower in 1981. It was originally described in the Gardeners’ Chronicle in 1893, as a cross between Vanda hookeriana and Vanda teres. However, no record had been kept as to which parent contributed the pollen. This study was conducted using DNA barcoding techniques to determine the pod parent of V. Miss Joaquim, thereby inferring the pollen parent of the hybrid by exclusion. Methodology Two chloroplast genes, matK and rbcL, from five related taxa, V. hookeriana, V. teres var. alba, V. teres var. andersonii, V. teres var. aurorea and V. Miss Joaquim ‘Agnes’, were sequenced. The matK gene from herbarium specimens of V. teres and V. Miss Joaquim, both collected in 1893, was also sequenced. Principal results No sequence variation was found in the 600-bp region of rbcL sequenced. Sequence variation was found in the matK gene of V. hookeriana, V. teres var. alba, V. teres var. aurorea and V. Miss Joaquim ‘Agnes’. Complete sequence identity was established between V. teres var. andersonii and V. Miss Joaquim ‘Agnes’. The matK sequences obtained from the herbarium specimens of V. teres and V. Miss Joaquim were completely identical to the sequences obtained from the fresh samples of V. teres var. andersonii and V. Miss Joaquim ‘Agnes’. Conclusions The pod parent of V. Miss Joaquim ‘Agnes’ is V. teres var. andersonii and, by exclusion, the pollen parent is V. hookeriana. The herbarium and fresh samples of V. teres var. andersonii and V. Miss Joaquim share the same inferred maternity. The matK gene was more informative than rbcL and facilitated differentiation of varieties of V. teres. PMID:22476488

Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

PubMed

Ma, Jun; Kanakala, S; He, Yehua; Zhang, Junli; Zhong, Xiaolan

2015-01-01

Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

Transcriptome Sequence Analysis of an Ornamental Plant, Ananas comosus var. bracteatus, Revealed the Potential Unigenes Involved in Terpenoid and Phenylpropanoid Biosynthesis

PubMed Central

Ma, Jun; Kanakala, S.; He, Yehua; Zhang, Junli; Zhong, Xiaolan

2015-01-01

Background Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. Results The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. Conclusion The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus. PMID:25769053

Evaluation of immunogenicity and safety of VARIVAX™ New Seed Process (NSP) in children.

PubMed

Senders, Shelly D; Bundick, Nickoya D; Li, Jianing; Zecca, Carol; Helmond, Frans A

2018-02-01

Prior to availability of an effective vaccine, an estimated 4 million cases of varicella occurred annually in the United States, resulting in 10,000 hospitalizations and over 100 deaths. With the increased usage of a two-dose varicella vaccine (as recommended by the ACIP), approval of other VZV-containing products and the adoption of varicella vaccination in additional countries, the demand for VZV-containing vaccines has increased. This study (NCT02062502) evaluated the safety, tolerability, and immunogenicity of VARIVAX™ (VAR, varicella vaccine live) manufactured using a new seed manufacturing process (VAR NSP ) compared to the currently licensed VAR. Healthy children 12-23 months were randomized (1:1) into Group 1 (2 doses of VAR NSP given concomitantly with M-M-R™ II, ∼3 months apart) versus  Group 2 (2 doses of VAR given concomitantly with M-M-R™ II, ∼3 months apart).  Serum samples collected prior to vaccination on Day 1 and 6 weeks Postdose 1 were tested for antibody to VZV using a glycoprotein enzyme-linked immunosorbent assay (gpELISA).  Safety was assessed Days 1 to 42 following each vaccination. Six weeks Postdose 1, the response rate (percent of subjects with VZV antibody titer ≥5 gpELISA units/mL) of VAR NSP was non-inferior compared to VAR.  Vaccine-related adverse events (AEs) were comparable with the exception of measles-like rash, where a greater number of rashes were observed with VAR than VAR NSP .  The 2 vaccination groups were comparable with incidence rates of AEs, injection-site AEs, vaccine-related AEs, systemic AEs, and serious AEs. This new process is an important innovation for the extreme demand of sustaining sufficient supplies of varicella vaccine to protect our communities against diseases caused by VZV.

[Study on chemical constituents of volatile oil from rhizomes and leaves of Pileostegia viburnoides var. glabrescens by GC-MS].

PubMed

Zou, Ju-Ying; Chen, Sheng-Huang; Li, Qin-Wen; Chen, Han-Jun; Liu, Bei-Bei; Du, Fan

2012-04-01

To analyze the chemical constituents of volatile oil from the rhizomes and leaves of Pileostegia viburnoides var. glabrescens by GC-MS. The volatile oil was extracted from the rhizomes and leaves of Pileostegia viburnoides var. glabrescens by steam distillation. The constituents of volatile oil were identified by GC-MS technology. 37 compounds were identified from the oil of rhizomes. 36 compounds were identified from the oil of leaves. The rhizomes and leaves volatile oil had 18 compounds in common. This study is the first one to report the volatile components of Pileostegia viburnoides var. glabrescens. It can provide a scientific basis for rational use of the rhizomes and leaves of Pileostegia viburnoides var. glabrescens.

Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia

USDA-ARS?s Scientific Manuscript database

Pityopsis graminifolia (Michx.) Small var. latifolia (Fern.) Semple is an herbaceous perennial that grows in close proximity to the federally endangered species P. ruthii (Small) Small. Twelve polymorphic microsatellite loci were identified from 87 samples of P. graminifolia var. latifolia and addit...

[Genetic variation of some varieties of common juniper Juniperus communis L. inferred from analysis of allozyme loci].

PubMed

Khantemirova, E V; Semerikov, V L

2010-05-01

Using the method of allozyme analysis, genetic variation, diversity, and population structure of Juniperus communis L. var. communis and J. communis L. var. saxatilis Pall. (= J. sibirica Burgsd. = J. nana Wild), growing on the territory of Russia, J. c. var. communis from Sweden, and J. c. var. depressa Pursh from Northern America (Alaska), was investigated. The total level of genetic variation of these varieties was found to be higher than the values obtained for the other conifers. The population samples of J. c. var. depressa from Alaska and J. c. var. saxatilis from Sakhalin were noticeably different from all other populations examined. Between the other samples, no substantial genetic differences were observed. These populations were characterized by weak interpopulation differentiation along with the absence of expressed geographical pattern of the allele frequency spatial distribution. The only exception was the procumbent form of common juniper from the high mountain populations of South and North Ural, which was somewhat different from the others.

Biological activities of organic extracts of four Aureobasidium pullulans varieties isolated from extreme marine and terrestrial habitats.

PubMed

Botić, Tanja; Kralj-Kunčič, Marjetka; Sepčić, Kristina; Batista, Urška; Zalar, Polona; Knez, Željko; Gunde-Cimerman, Nina

2014-01-01

We report on the screening for biological activities of organic extracts from seven strains that represent four varieties of the fungus Aureobasidium pullulans, that is A. pullulans var. melanogenum, A. pullulans var. pullulans, A. pullulans var. subglaciale and A. pullulans var. namibiae. We monitored haemolysis, cytotoxicity, antioxidant capacity and growth inhibition against three bacterial species. The haemolytic activity of A. pullulans var. pullulans EXF-150 strain was due to five different haemolytically active fractions. Extracts from all of the other varieties contained at least one haemolytically active fraction. Short-term exposure of cell lines to these haemolytically active organic extracts resulted in more than 95% cytotoxicity. Strong antioxidant capacity, corresponding to 163.88 μg ascorbic acid equivalent per gram of total solid, was measured in the organic extract of the strain EXF-3382, obtained from A. pullulans var. melanogenum, isolated from the deep sea. Organic extracts from selected varieties of A. pullulans exhibited weak antibacterial activities.

Identification of a Major Dimorphic Region in the Functionally Critical N-Terminal ID1 Domain of VAR2CSA

PubMed Central

Doritchamou, Justin; Sabbagh, Audrey; Jespersen, Jakob S.; Renard, Emmanuelle; Salanti, Ali; Nielsen, Morten A.; Deloron, Philippe; Tuikue Ndam, Nicaise

2015-01-01

The VAR2CSA protein of Plasmodium falciparum is transported to and expressed on the infected erythrocyte surface where it plays a key role in placental malaria (PM). It is the current leading candidate for a vaccine to prevent PM. However, the antigenic polymorphism integral to VAR2CSA poses a challenge for vaccine development. Based on detailed analysis of polymorphisms in the sequence of its ligand-binding N-terminal region, currently the main focus for vaccine development, we assessed var2csa from parasite isolates infecting pregnant women. The results reveal for the first time the presence of a major dimorphic region in the functionally critical N-terminal ID1 domain. Parasite isolates expressing VAR2CSA with particular motifs present within this domain are associated with gravidity- and parasite density-related effects. These observations are of particular interest in guiding efforts with respect to optimization of the VAR2CSA-based vaccines currently under development. PMID:26393516

Effects of seasonal variations on antioxidant activity of pink guava fruits

NASA Astrophysics Data System (ADS)

Ahmad, Haniza; Abdullah, Aminah

2014-09-01

This study aimed to evaluate the effects of seasonal variations during rainy and hot season on antioxidant activity of pink guava fruits in approximately one year duration specifically on November 2012, December 2012, January 2013, March 2013, April 2013, May 2013, July 2013, August 2013 and November 2013. Fruit samples (Sungkai and Semenyih variants) were collected from Sime Darby Beverages plantation located in Sitiawan. The fruits were samples for 9 times from Nov 2012 to Nov 2013 except Feb 2013, Jun 2013, Sept 2013 and Oct 2013. Fruits were peeled, seeded and blended into uniform puree. Samples were then extracted for its antioxidant activity determination using 50% acetone. Antioxidant activity was evaluated using total phenolic compounds (TPC) assay, ferric-reducing antioxidant power assay (FRAP) and 1,1-diphenyl1-2-picrylhydrazyl free radical-scavenging capacity (DPPH). Analysis was conducted using 96-well microplate spectrophotometer UV. The highest TPC result was Semenyih var recorded 2192.80 mg GAE/100g FW whilst Sungkai var 1595.98 mg GAE/100g FW both on July 2013 with rainfall was at the least (45mm) and the lowest for Sungkai var was 792.75 mg GAE/100g FW and 1032.41 mg GAE/100g FW for Semenyih var, both on Nov 2012 with 185mm rainfall. There were significant negative correlation between TPC and rainfall (mm) for both Semenyih var (r = - 0.699, p<0.005, r2 = 0.489) and Sungkai var (r = -0.72, p<0.05, r2 = 0.531). The highest FRAP result (mg TE/100g FW) was 1677.74 for Semenyih var (Aug 2013, rainfall = 160.5mm) and the highest FRAP for Sungkai var was 1104.60 (Jul 2013, rainfall = 45.0mm) whereas the lowest for Semenyih and Sungkai var was 1090.22 (Mar 2013, rainfall = 97.5mm) and 767.88 (Nov 2012, rainfall = 185.50) respectively. There was weak negative correlation between FRAP and rainfall(mm) for both Sungkai var (r = - 0.324, p<0.05, r2 = 0.105) and Semenyih var (r = - 0.362, p<0.05, r2 = 0.132). The highest DPPH for Semenyih var was 88.40% (Aug 2013, rainfall = 160.50mm) whilst Sungkai var was 79.71% (July 2013, rainfall = 45.0mm). There was no significant difference in correlation coefficient of DPPH and rainfall (mm). Meanwhile, there was significant correlation between TPC and FRAP (r = 0.794, p<0.05, r2 = 0.629), TPC and DPPH (r = 0.901,p<0.05, r2= 0.812) and FRAP and DPPH (r = 0.889, p<0.05, r2 = 0.792).

Distribution Management System Volt/VAR Evaluation | Grid Modernization |

Science.gov Websites

NREL Distribution Management System Volt/VAR Evaluation Distribution Management System Volt/VAR Evaluation This project involves building a prototype distribution management system testbed that links a GE Grid Solutions distribution management system to power hardware-in-the-loop testing. This setup is

Ultrastructural Effects of Bacillus thuringiensis var. san diego on Midgut Cells of the Cottonwood Leaf Beetle1

Treesearch

Leah S. Bauer; Stuart H. Pankratz

1992-01-01

Sequential observations of the ultrastructural effects of Bacillus thuringiensis var. san diego were made on midgut epithelial cells of the cottonwood leaf beetle, Chrysomela scripta F. Larvae imbibed a droplet of B. thuringiensis var. san diego containing endotoxin and live...

Antibacterial activity of Mediterranean Oyster mushrooms, species of genus Pleurotus (higher Basidiomycetes).

PubMed

Schillaci, Domenico; Arizza, Vincenzo; Gargano, Maria Letizia; Venturella, Giuseppe

2013-01-01

Extracts of the Mediterranean culinary-medicinal Oyster mushrooms Pleurotus eryngii var. eryngii, P. eryngii var. ferulae, P. eryngii var. elaeoselini, and P. nebrodensis were tested for their in vitro growth inhibitory activity against a group of bacterial reference strains of medical relevance: Staphylococcus aureus ATCC 25923, S. epidermidis RP62A, Pseudomonas aeruginosa ATCC 15442, and Escherichia coli ATCC10536. All of the Pleurotus species analyzed inhibited the tested microorganisms in varying degrees. The data included in this paper for P. nebrodensis and P. eryngii var. elaeoselinii are new reports.

Rolling Contact Fatigue Life and Spall Propagation Characteristics of AISI M50, M50 NiL, and AISI 52100. Part 3. Metallurgical Examination (Preprint)

DTIC Science & Technology

2009-10-01

bearing materials, namely AISI 52100, VIM-VAR M50 , and VIM-VAR M50 NiL steels . While...propagation characteristics of three bearing materials, namely AISI 52100, VIM-VAR M50 , and VIM-VAR M50 NiL steels . While there is substantial prior work...deformation from run in. Residual stress profiles for bearing 075B are shown in Figure 3. The bearing is made from M50 steel and the spall

Antifungal compounds from Zanthoxylum chiloperone var. angustifolium.

PubMed

Thouvenel, Céline; Gantier, Jean-Charles; Duret, Philippe; Fourneau, Christophe; Hocquemiller, Reynald; Ferreira, Maria-Elena; Rojas de Arias, Antonieta; Fournet, Alain

2003-06-01

An alkaloidal extract of the stem barks of Zanthoxylum chiloperone var. angustifolium exhibited antifungal activity against Candida albicans, Aspergillus fumigatus and Trichophyton mentagrophytes var. interdigitale using a TLC bioautographic method. Bioassay-guided fractionation of this extract resulted in the isolation of two active compounds identi fi ed as canthin-6-one and 5-methoxycanthin-6-one. Canthin-6-one exhibited a broad spectrum of activities against Aspergillus fumigatus, A. niger, A. terreus, Candida albicans, C. tropicalis, C. glabrata, Cryptococcus neoformans, Geotrichum candidum, Saccharomyces cerevisiae, Trichosporon beigelii, Trichosporon cutaneum and Trichophyton mentagrophytes var. interdigitale with MICs values between 5.3 and 46 micro mol/L. 5-methoxy-canthin-6-one was active against only Trichophyton mentagrophytes var. interdigitale with a MIC value of 12.3 micro mol/L. Copyright 2003 John Wiley & Sons, Ltd.

Differential recognition of terminal extracellular Plasmodium falciparum VAR2CSA domains by sera from multigravid, malaria-exposed Malian women.

PubMed

Travassos, Mark A; Coulibaly, Drissa; Bailey, Jason A; Niangaly, Amadou; Adams, Matthew; Nyunt, Myaing M; Ouattara, Amed; Lyke, Kirsten E; Laurens, Matthew B; Pablo, Jozelyn; Jasinskas, Algis; Nakajima, Rie; Berry, Andrea A; Takala-Harrison, Shannon; Kone, Abdoulaye K; Kouriba, Bourema; Rowe, J Alexandra; Doumbo, Ogobara K; Thera, Mahamadou A; Laufer, Miriam K; Felgner, Philip L; Plowe, Christopher V

2015-06-01

The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family mediates parasite sequestration in small capillaries through tissue-specific cytoadherence. The best characterized of these proteins is VAR2CSA, which is expressed on the surface of infected erythrocytes that bind to chondroitin sulfate in the placental matrix. Antibodies to VAR2CSA prevent placental cytoadherence and protect against placental malaria. The size and complexity of the VAR2CSA protein pose challenges for vaccine development, but smaller constitutive domains may be suitable for subunit vaccine development. A protein microarray was printed to include five overlapping fragments of the 3D7 VAR2CSA extracellular region. Malian women with a history of at least one pregnancy had antibody recognition of four of these fragments and had stronger reactivity against the two distal fragments than did nulliparous women, children, and men from Mali, suggesting that the C-terminal extracellular VAR2CSA domains are a potential focus of protective immunity. With carefully chosen sera from longitudinal studies of pregnant women, this approach has the potential to identify seroreactive VAR2CSA domains associated with protective immunity against pregnancy-associated malaria. © The American Society of Tropical Medicine and Hygiene.

Data assimilation and prognostic whole ice sheet modelling with the variationally derived, higher order, open source, and fully parallel ice sheet model VarGlaS

NASA Astrophysics Data System (ADS)

Brinkerhoff, D. J.; Johnson, J. V.

2013-07-01

We introduce a novel, higher order, finite element ice sheet model called VarGlaS (Variational Glacier Simulator), which is built on the finite element framework FEniCS. Contrary to standard procedure in ice sheet modelling, VarGlaS formulates ice sheet motion as the minimization of an energy functional, conferring advantages such as a consistent platform for making numerical approximations, a coherent relationship between motion and heat generation, and implicit boundary treatment. VarGlaS also solves the equations of enthalpy rather than temperature, avoiding the solution of a contact problem. Rather than include a lengthy model spin-up procedure, VarGlaS possesses an automated framework for model inversion. These capabilities are brought to bear on several benchmark problems in ice sheet modelling, as well as a 500 yr simulation of the Greenland ice sheet at high resolution. VarGlaS performs well in benchmarking experiments and, given a constant climate and a 100 yr relaxation period, predicts a mass evolution of the Greenland ice sheet that matches present-day observations of mass loss. VarGlaS predicts a thinning in the interior and thickening of the margins of the ice sheet.

Working alliance inventory applied to virtual and augmented reality (WAI-VAR): psychometrics and therapeutic outcomes

PubMed Central

Miragall, Marta; Baños, Rosa M.; Cebolla, Ausiàs; Botella, Cristina

2015-01-01

This study examines the psychometric properties of the Working Alliance Inventory-Short (WAI-S) adaptation to Virtual Reality (VR) and Augmented Reality (AR) therapies (WAI-VAR). The relationship between the therapeutic alliance (TA) with VR and AR and clinically significant change (CSC) is also explored. Seventy-five patients took part in this study (74.7% women, Mage = 34.41). Fear of flying and adjustment disorder patients received VR therapy, and cockroach phobia patients received AR therapy. Psychometric properties, CSC, one-way ANOVA, Spearman’s Correlations and Multiple Regression were calculated. The WAI-VAR showed a unidimensional structure, high internal consistency and adequate convergent validity. “Not changed” patients scored lower on the WAI-VAR than “improved” and “recovered” patients. Correlation between the WAI-VAR and CSC was moderate. The best fitting model for predicting CSC was a linear combination of the TA with therapist (WAI-S) and the TA with VR and AR (WAI-VAR), due to the latter variable slightly increased the percentage of variability accounted for in CSC. The WAI-VAR is the first validated instrument to measure the TA with VR and AR in research and clinical practice. This study reveals the importance of the quality of the TA with technologies in achieving positive outcomes in the therapy. PMID:26500589

Working alliance inventory applied to virtual and augmented reality (WAI-VAR): psychometrics and therapeutic outcomes.

PubMed

Miragall, Marta; Baños, Rosa M; Cebolla, Ausiàs; Botella, Cristina

2015-01-01

This study examines the psychometric properties of the Working Alliance Inventory-Short (WAI-S) adaptation to Virtual Reality (VR) and Augmented Reality (AR) therapies (WAI-VAR). The relationship between the therapeutic alliance (TA) with VR and AR and clinically significant change (CSC) is also explored. Seventy-five patients took part in this study (74.7% women, M age = 34.41). Fear of flying and adjustment disorder patients received VR therapy, and cockroach phobia patients received AR therapy. Psychometric properties, CSC, one-way ANOVA, Spearman's Correlations and Multiple Regression were calculated. The WAI-VAR showed a unidimensional structure, high internal consistency and adequate convergent validity. "Not changed" patients scored lower on the WAI-VAR than "improved" and "recovered" patients. Correlation between the WAI-VAR and CSC was moderate. The best fitting model for predicting CSC was a linear combination of the TA with therapist (WAI-S) and the TA with VR and AR (WAI-VAR), due to the latter variable slightly increased the percentage of variability accounted for in CSC. The WAI-VAR is the first validated instrument to measure the TA with VR and AR in research and clinical practice. This study reveals the importance of the quality of the TA with technologies in achieving positive outcomes in the therapy.

Evaluation of morpho-anatomical and chemical differences between varieties of the medicinal plant Casearia sylvestris Swartz.

PubMed

Claudino, Josiane C; Sacramento, Luis V S do; Koch, Ingrid; Santos, Helen A; Cavalheiro, Alberto J; Tininis, Aristeu G; Santos, André G dos

2013-01-01

Casearia sylvestris Swartz (Salicaceae) has been used in traditional medicine and its leaf extracts have been exhibited important pharmacological activities. The species presents morphological, chemical and genetic variation. Two varieties are considered due external morphological differences: C. sylvestris var. sylvestris and var. lingua. There are difficulties in definition of these varieties. The objective of this work is to evaluate chemical and morpho-anatomical differences between C. sylvestris varieties that can be applied in their distinction for pharmaceutical or botanical purposes. Transverse and paradermic sections of leaves were prepared for morpho-anatomical, histochemical and quantitative microscopy (stomatal and palisade index) analyses. Diterpene profiles of the specimens were obtained by HPLC-DAD and TLC. Morpho-anatomical analyses demonstrated significant differences between the varieties only in paradermic sections: var. sylvestris--polygonal epidermic cell walls and hypostomatic; var. lingua--rounded epidermic cell walls and amphistomatic. No differences were observed for stomatal index; palisade index was found 2.8 for var. lingua and 3.9 for var. sylvestris. Chromatographic analyses confirmed previous results demonstrating that diterpene profile in varieties differs, with predominance of these metabolites in var. sylvestris. In conclusion, this work indicates that chromatographic analysis besides morpho-anatomical analysis can be applied in distinction of C. sylvestris varieties.

In vitro antioxidant and anticancer effects of solvent fractions from Prunella vulgaris var. lilacina.

PubMed

Hwang, Yu-Jin; Lee, Eun-Ju; Kim, Haeng-Ran; Hwang, Kyung-A

2013-11-09

Recently, considerable attention has been focused on exploring the potential antioxidant properties of plant extracts or isolated products of plant origin. Prunella vulgaris var. lilacina is widely distributed in Korea, Japan, China, and Europe, and it continues to be used to treat inflammation, eye pain, headache, and dizziness. However, reports on the antioxidant activities of P. vulgaris var. lilacina are limited, particularly concerning the relationship between its phenolic content and antioxidant capacity. In this study, we investigated the antioxidant and anticancer activities of an ethanol extract from P. vulgaris var. lilacina and its fractions. Dried powder of P. vulgaris var. lilacina was extracted with ethanol, and the extract was fractionated to produce the hexane fraction, butanol fraction, chloroform fraction and residual water fraction. The phenolic content was assayed using the Folin-Ciocalteu colorimetric method. Subsequently, the antioxidant activities of the ethanol extract and its fractions were analyzed employing various antioxidant assay methods including DPPH, FRAP, ABTS, SOD activity and production of reactive oxygen species. Additionally, the extract and fractions were assayed for their ability to exert cytotoxic activities on various cancer cells using the MTT assay. We also investigated the expression of genes associated with apoptotic cell death by RT-PCR. The total phenolic contents of the ethanol extract and water fraction of P. vulgaris var. lilacina were 303.66 and 322.80 mg GAE/g dry weight (or fractions), respectively. The results showed that the ethanol extract and the water fraction of P. vulgaris var. lilacina had higher antioxidant content than other solvent fractions, similar to their total phenolic content. Anticancer activity was also tested using the HepG2, HT29, A549, MKN45 and HeLa cancer cell lines. The results clearly demonstrated that the P. vulgaris var. lilacina ethanol extract induced significant cytotoxic effects on the various cancer cell lines, and these effects were stronger than those induced by the P. vulgaris var. lilacina solvent fractions. We also investigated the expression of genes associated with apoptotic cell death. We confirmed that the P. vulgaris var. lilacina ethanol extract and water fraction significantly increased the expression of p53, Bax and Fas. These results suggest that the ethanol extract from P. vulgaris var. lilacina and its fractions could be applied as natural sources of antioxidants and anticancer activities in food and in the pharmaceutical industry.

Classification tree and minimum-volume ellipsoid analyses of the distribution of ponderosa pine in the western USA

USGS Publications Warehouse

Norris, Jodi R.; Jackson, Stephen T.; Betancourt, Julio L.

2006-01-01

Aim? Ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) is an economically and ecologically important conifer that has a wide geographic range in the western USA, but is mostly absent from the geographic centre of its distribution - the Great Basin and adjoining mountain ranges. Much of its modern range was achieved by migration of geographically distinct Sierra Nevada (P. ponderosa var. ponderosa) and Rocky Mountain (P. ponderosa var. scopulorum) varieties in the last 10,000 years. Previous research has confirmed genetic differences between the two varieties, and measurable genetic exchange occurs where their ranges now overlap in western Montana. A variety of approaches in bioclimatic modelling is required to explore the ecological differences between these varieties and their implications for historical biogeography and impending changes in western landscapes. Location? Western USA. Methods? We used a classification tree analysis and a minimum-volume ellipsoid as models to explain the broad patterns of distribution of ponderosa pine in modern environments using climatic and edaphic variables. Most biogeographical modelling assumes that the target group represents a single, ecologically uniform taxonomic population. Classification tree analysis does not require this assumption because it allows the creation of pathways that predict multiple positive and negative outcomes. Thus, classification tree analysis can be used to test the ecological uniformity of the species. In addition, a multidimensional ellipsoid was constructed to describe the niche of each variety of ponderosa pine, and distances from the niche were calculated and mapped on a 4-km grid for each ecological variable. Results? The resulting classification tree identified three dominant pathways predicting ponderosa pine presence. Two of these three pathways correspond roughly to the distribution of var. ponderosa, and the third pathway generally corresponds to the distribution of var. scopulorum. The classification tree and minimum-volume ellipsoid model show that both varieties have very similar temperature limitations, although var. ponderosa is more limited by the temperature extremes of the continental interior. The precipitation limitations of the two varieties are seasonally different, with var. ponderosa requiring significant winter moisture and var. scopulorum requiring significant summer moisture. Great Basin mountain ranges are too cold at higher elevations to support either variety of ponderosa pine, and at lower elevations are too dry in summer for var. scopulorum and too dry in winter for var. ponderosa. Main conclusions? The classification tree analysis indicates that var. ponderosa is ecologically as well as genetically distinct from var. scopulorum. Ecological differences may maintain genetic separation in spite of a limited zone of introgression between the two varieties in western Montana. Two hypotheses about past and future movements of ponderosa pine emerge from our analyses. The first hypothesis is that, during the last glacial period, colder and/or drier summers truncated most of the range of var. scopulorum in the central Rockies, but had less dramatic effects on the more maritime and winter-wet distribution of var. ponderosa. The second hypothesis is that, all other factors held constant, increasing summer temperatures in the future should produce changes in the distribution of var. scopulorum that are likely to involve range expansions in the central Rockies with the warming of mountain ranges currently too cold but sufficiently wet in summer for var. scopulorum. Finally, our results underscore the growing need to focus on genotypes in biogeographical modelling and ecological forecasting.

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function.

PubMed

Zhu, Xinyu; Ma, Hong; Chen, Zhiduan

2011-03-09

Plants contain numerous Su(var)3-9 homologues (SUVH) and related (SUVR) genes, some of which await functional characterization. Although there have been studies on the evolution of plant Su(var)3-9 SET genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation. Putative orthologs of plant Su(var)3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core Su(var)3-9 homologues and related (cSUVHR) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant Su(var)3-9 SET genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade. A detailed phylogenetic analysis of the plant Su(var)3-9 SET genes was performed. A novel deep phylogenetic relationship including most plant Su(var)3-9 SET genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of Physcomitrella patens (moss) from other land plants. One or multiple retroposition events might have occurred among SUVH genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant Su(var)3-9 SET genes with different functions were described, contributing to the design of further experimental studies.

Identification and Characterization of the Spodoptera Su(var) 3-9 Histone H3K9 trimethyltransferase and Its Effect in AcMNPV Infection

PubMed Central

Li, Binbin; Li, Sisi; Yin, Juan; Zhong, Jiang

2013-01-01

Histone H3-lysine9 (H3K9) trimethyltransferase gene Su(var) 3-9 was cloned and identified in three Spodoptera insects, Spodoptera frugiperda ( S . frugiperda ), S . exigua and S . litura . Sequence analysis showed that Spodoptera Su(var) 3-9 is highly conserved evolutionarily. Su(var) 3-9 protein was found to be localized in the nucleus in Sf9 cells, and interact with histone H3, and the heterochromatin protein 1a (HP1a) and HP1b. A dose-dependent enzymatic activity was found at both 27 °C and 37 °C in vitro, with higher activity at 27 °C. Addition of specific inhibitor chaetocin resulted in decreased histone methylation level and host chromatin relaxation. In contrast, overexpression of Su(var) 3-9 caused increased histone methylation level and cellular genome compaction. In AcMNV-infected Sf9 cells, the transcription of Su(var) 3-9 increased at late time of infection, although the mRNA levels of most cellular genes decreased. Pre-treatment of Sf9 cells with chaetocin speeded up viral DNA replication, and increased the transcription level of a variety of virus genes, whereas in Sf9 cells pre-transformed with Su(var) 3-9 expression vector, viral DNA replication slow down slightly. These findings suggest that Su(var) 3-9 might participate in the viral genes expression an genome replication repression during AcMNPV infection. It provided a new insight for the understanding virus–host interaction mechanism. PMID:23894480

Silence, Metaperformance, and Communication in Pedro Almodóvar's "Hable con ella"

ERIC Educational Resources Information Center

Fellie, Maria C.

2016-01-01

Many scenes in Pedro Almodóvar's "Hable con ella" (2002) include shots of metaperformances such as silent films, dances, television shows, concerts, and bullfights. Spectators often observe passive characters who are in turn observing. By presenting these performances within cinematic performance, Almodóvar highlights our role as viewers…

Water deficit induces swainsonine of some locoweed taxa, but with no swainsonine-growth trade-off

USDA-ARS?s Scientific Manuscript database

Locoweeds (Astragalus and Oxytropis spp.) contain swainsonine (SWA), an alkaloid toxic to vertebrates. In two common-garden experiments, we studied three A. mollissimus varieties that vary in SWA levels (barely detectable SWA var. ‘thompsonae’, intermediate SWA var. ‘bigelovii’, and high SWA var. ‘m...

40 CFR 180.1243 - Bacillus subtilis var. amyloliquefaciens strain FZB24; exemption from the requirement of a...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus subtilis var... EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1243 Bacillus subtilis... the requirement of a tolerance for residues of the Bacillus subtilis var. amyloliquefaciens strain...

Further elucidation of the taxonomic relationships and geographic distribution of Escobaria sneedii var. sneedii, E. sneedii var. leei, and E. guadalupensis (Cactaceae)

Treesearch

Marc A. Baker

2007-01-01

Individuals of E. sneedii var. sneedii were found to occur in greater abundance within the Guadalupe Mountains than was previously recorded. No additional populations morphologically intermediate between E. guadalupensis and E. sneedii were found. Taxonomic affiliation and geographic...

Residual Life and Strength Predictions and Life-Enhancement of Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, H.; Atluri, S.N.

1998-09-01

In this paper, a method to quantitatively evaluate the T{sub {var_epsilon}}* integral directly from the measured near-tip displacement field for laboratory specimens made of metallic materials, is presented. This is the first time that such an attempt became a success. In order to develop the procedure, we carefully examine the nature of T{sub {var_epsilon}}* Hence, the nature of T{sub {var_epsilon}}* is further revealed. Following Okada and Atluri (1997), the relationship between energy balance statements for a cracked plate and the T{sub {var_epsilon}}* is discussed. It is concluded that T{sub {var_epsilon}}* quantifies the deformation energy dissipated near crack tip region [anmore » elongating strip of height e] per unit crack extension. In the evaluation of T{sub {var_epsilon}}* integral directly from measured displacement field, the use of deformation theory plasticity (J2-D theory) and the truncation of the near crack integral path on the experimental studies of Omori et el. (1995) are presented, and these show a good agreement with the results of finite element analysis.« less

A Life Study of Ausforged, Standard Forged and Standard Machined AISI M-50 Spur Gears

NASA Technical Reports Server (NTRS)

Townsend, D. P.; Bamberger, E. N.; Zaretsky, E. V.

1975-01-01

Tests were conducted at 350 K (170 F) with three groups of 8.9 cm (3.5 in.) pitch diameter spur gears made of vacuum induction melted (VIM) consumable-electrode vacuum-arc melted (VAR), AISI M-50 steel and one group of vacuum-arc remelted (VAR) AISI 9310 steel. The pitting fatigue life of the standard forged and ausforged gears was approximately five times that of the VAR AISI 9310 gears and ten times that of the bending fatigue life of the standard machined VIM-VAR AISI M-50 gears run under identical conditions. There was a slight decrease in the 10-percent life of the ausforged gears from that for the standard forged gears, but the difference is not statistically significant. The standard machined gears failed primarily by gear tooth fracture while the forged and ausforged VIM-VAR AISI M-50 and the VAR AISI 9310 gears failed primarily by surface pitting fatigue. The ausforged gears had a slightly greater tendency to fail by tooth fracture than the standard forged gears.

Ape parasite origins of human malaria virulence genes

PubMed Central

Larremore, Daniel B.; Sundararaman, Sesh A.; Liu, Weimin; Proto, William R.; Clauset, Aaron; Loy, Dorothy E.; Speede, Sheri; Plenderleith, Lindsey J.; Sharp, Paul M.; Hahn, Beatrice H.; Rayner, Julian C.; Buckee, Caroline O.

2015-01-01

Antigens encoded by the var gene family are major virulence factors of the human malaria parasite Plasmodium falciparum, exhibiting enormous intra- and interstrain diversity. Here we use network analysis to show that var architecture and mosaicism are conserved at multiple levels across the Laverania subgenus, based on var-like sequences from eight single-species and three multi-species Plasmodium infections of wild-living or sanctuary African apes. Using select whole-genome amplification, we also find evidence of multi-domain var structure and synteny in Plasmodium gaboni, one of the ape Laverania species most distantly related to P. falciparum, as well as a new class of Duffy-binding-like domains. These findings indicate that the modular genetic architecture and sequence diversity underlying var-mediated host-parasite interactions evolved before the radiation of the Laverania subgenus, long before the emergence of P. falciparum. PMID:26456841

VAR2CSA domains expressed in Escherichia coli induce cross-reactive antibodies to native protein.

PubMed

Oleinikov, Andrew V; Francis, Susan E; Dorfman, Jeffrey R; Rossnagle, Eddie; Balcaitis, Stephanie; Getz, Tony; Avril, Marion; Gose, Severin; Smith, Joseph D; Fried, Michal; Duffy, Patrick E

2008-04-15

The variant surface antigen VAR2CSA is a pregnancy malaria vaccine candidate, but its size and polymorphism are obstacles to development. We expressed 3D7-type VAR2CSA domains in Escherichia coli as insoluble His-tagged proteins (Duffy binding-like [DBL] domains DBL1, DBL3, DBL4, and DBL5) that were denatured and refolded or as soluble glutathione S-transferase-tagged protein (DBL6). Anti-DBL5 antiserum cross-reacted with surface proteins of chondroitin sulfate A (CSA)-binding laboratory strains (3D7-CSA and FCR3-CSA) and a clinical pregnancy malaria isolate, whereas anti-DBL6 antiserum reacted only to 3D7 surface protein. This is the first report that E. coli-expressed VAR2CSA domains induce antibody to native VAR2CSA.

Cryptococcus neoformans var. grubii: Separate Varietal Status for Cryptococcus neoformans Serotype A Isolates

PubMed Central

Franzot, Sarah P.; Salkin, Ira F.; Casadevall, Arturo

1999-01-01

Cryptococcus neoformans var. neoformans presently includes isolates which have been determined by the immunologic reactivity of their capsular polysaccharides to be serotype A and those which have been determined to be serotype D. However, recent analyses of the URA5 sequences and DNA fingerprinting patterns suggest significant genetic differences between the two serotypes. Therefore, we propose to recognize these genotypic distinctions, as well as previously reported phenotypic differences, by restricting C. neoformans var. neoformans to isolates which are serotype D and describing a new variety, C. neoformans var. grubii, for serotype A isolates. PMID:9986871

Feasibility of Stochastic Voltage/VAr Optimization Considering Renewable Energy Resources for Smart Grid

NASA Astrophysics Data System (ADS)

Momoh, James A.; Salkuti, Surender Reddy

2016-06-01

This paper proposes a stochastic optimization technique for solving the Voltage/VAr control problem including the load demand and Renewable Energy Resources (RERs) variation. The RERs often take along some inputs like stochastic behavior. One of the important challenges i. e., Voltage/VAr control is a prime source for handling power system complexity and reliability, hence it is the fundamental requirement for all the utility companies. There is a need for the robust and efficient Voltage/VAr optimization technique to meet the peak demand and reduction of system losses. The voltages beyond the limit may damage costly sub-station devices and equipments at consumer end as well. Especially, the RERs introduces more disturbances and some of the RERs are not even capable enough to meet the VAr demand. Therefore, there is a strong need for the Voltage/VAr control in RERs environment. This paper aims at the development of optimal scheme for Voltage/VAr control involving RERs. In this paper, Latin Hypercube Sampling (LHS) method is used to cover full range of variables by maximally satisfying the marginal distribution. Here, backward scenario reduction technique is used to reduce the number of scenarios effectively and maximally retain the fitting accuracy of samples. The developed optimization scheme is tested on IEEE 24 bus Reliability Test System (RTS) considering the load demand and RERs variation.

[Effects of different type urban forest plantations on soil fertility].

PubMed

Sun, Hui-zhen; Chen, Ming-yue; Cai, Chun-ju; Zhu, Ning

2009-12-01

Aimed to study the effects of different urban forest plantations on soil fertility, soil samples were collected from eight mono-cultured plantations (Larix gmelinii, Pinus sylvestris var. mongolica, Pinus tabulaeformis var. mukdensis, Phellodendron amurense, Juglans mandshurica, Fraxinus mandshurica, Betula platyphylla, and Quercus mongolica) and one mixed plantation (P. sylvestris var. mongolica + F. mandshurica + Picea koraiensis + P. amurense + B. platyphylla) established in Northeast Forestry University's Urban Forestry Demonstration Research Base in the 1950s, with two sites of neighboring farmland and abandoned farmland as the control. The soils in broadleaved forest plantations except Q. mongolica were near neutral, those in mixed plantation, L. gmelinii, P. sylvestris var. mongolica, and P. tabulaeformis var. mukdensis were slightly acidic, and that in Q. mongolica was acidic. The contents of soil organic matter, total N and P, available P and K, and hydrolysable N tended to decrease with soil depth. There existed significant differences in the chemical indices of the same soil layers among different plantations. The soil fertility was decreased in the order of F. mandshurica > P. amurense > mixed plantation > J. mandshurica > B. platyphylla > abandoned farmland > farmland > P. sylvestris var. mongolica > L. gmelinii > Q. mongolica > P. tabulaeformis var. mukdensis, suggesting that the soil fertility in broadleaved forest plantations except Q. mongolica and in mixed plantation increased, while that in needle-leaved forest plantations tended to decrease.

40 CFR 80.157 - Volumetric additive reconciliation (“VAR”), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... preceding two months of VAR supporting documentation. (2) Except as provided in paragraph (g)(3) of this... immediately available to EPA, upon request, the preceding two months of VAR formula records and VAR supporting.... Detergent so used must be accurately and separately measured, either through the use of a separate storage...

40 CFR 80.157 - Volumetric additive reconciliation (“VAR”), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... preceding two months of VAR supporting documentation. (2) Except as provided in paragraph (g)(3) of this... immediately available to EPA, upon request, the preceding two months of VAR formula records and VAR supporting.... Detergent so used must be accurately and separately measured, either through the use of a separate storage...

40 CFR 80.157 - Volumetric additive reconciliation (“VAR”), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... preceding two months of VAR supporting documentation. (2) Except as provided in paragraph (g)(3) of this... immediately available to EPA, upon request, the preceding two months of VAR formula records and VAR supporting.... Detergent so used must be accurately and separately measured, either through the use of a separate storage...

40 CFR 80.157 - Volumetric additive reconciliation (“VAR”), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... preceding two months of VAR supporting documentation. (2) Except as provided in paragraph (g)(3) of this... immediately available to EPA, upon request, the preceding two months of VAR formula records and VAR supporting.... Detergent so used must be accurately and separately measured, either through the use of a separate storage...

40 CFR 80.157 - Volumetric additive reconciliation (“VAR”), equipment calibration, and recordkeeping requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... preceding two months of VAR supporting documentation. (2) Except as provided in paragraph (g)(3) of this... immediately available to EPA, upon request, the preceding two months of VAR formula records and VAR supporting.... Detergent so used must be accurately and separately measured, either through the use of a separate storage...

Diversity, virulence and 2,4-diacetylphloroglucinol sensitivity of Gaeumannomyces graminis var. tritici isolates from Washington State

USDA-ARS?s Scientific Manuscript database

We determined whether isolates of the take-all pathogen Gaeumannomyces graminis var. tritici become less sensitive to 2,4-DAPG during wheat monoculture as a result of exposure to the antibiotic over multiple growing seasons. Over 177 isolates of G. graminis var. tritici were baited from roots of nat...

Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca) populations. III. Central Idaho

Treesearch

Gerald E. Rehfeldt

1983-01-01

Rehfeldt, Gerald E. 1983. Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca) populations. III. Central Idaho. Canadian Journal of Forest Research. 13: 626-632. Growth, phenology, and cold hardiness of seedlings from 74 populations of Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) from central Idaho were compared in four...

Phylogeography of Pinus subsection Australes in the Caribbean Basin

PubMed Central

Jardón-Barbolla, Lev; Delgado-Valerio, Patricia; Geada-López, Gretel; Vázquez-Lobo, Alejandra; Piñero, Daniel

2011-01-01

Background and Aims Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas. Methods Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin. Key Results In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (RST = 0·671 > permuted RST = 0·101; P < 0·0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima. Conclusions Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8. PMID:21118838

Molecular dissection of placental malaria protein VAR2CSA interaction with a chemo-enzymatically synthesized chondroitin sulfate library.

PubMed

Sugiura, Nobuo; Clausen, Thomas Mandel; Shioiri, Tatsumasa; Gustavsson, Tobias; Watanabe, Hideto; Salanti, Ali

2016-12-01

Placental malaria, a serious infection caused by the parasite Plasmodium falciparum, is characterized by the selective accumulation of infected erythrocytes (IEs) in the placentas of the pregnant women. Placental adherence is mediated by the malarial VAR2CSA protein, which interacts with chondroitin sulfate (CS) proteoglycans present in the placental tissue. CS is a linear acidic polysaccharide composed of repeating disaccharide units of D-glucuronic acid and N-acetyl-D-galactosamine that are modified by sulfate groups at different positions. Previous reports have shown that placental-adhering IEs were associated with an unusually low sulfated form of chondroitin sulfate A (CSA) and that a partially sulfated dodecasaccharide is the minimal motif for the interaction. However, the fine molecular structure of this CS chain remains unclear. In this study, we have characterized the CS chain that interacts with a recombinant minimal CS-binding region of VAR2CSA (rVAR2) using a CS library of various defined lengths and sulfate compositions. The CS library was chemo-enzymatically synthesized with bacterial chondroitin polymerase and recombinant CS sulfotransferases. We found that C-4 sulfation of the N-acetyl-D-galactosamine residue is critical for supporting rVAR2 binding, whereas no other sulfate modifications showed effects. Interaction of rVAR2 with CS is highly correlated with the degree of C-4 sulfation and CS chain length. We confirmed that the minimum structure binding to rVAR2 is a tri-sulfated CSA dodecasaccharide, and found that a highly sulfated CSA eicosasaccharide is a more potent inhibitor of rVAR2 binding than the dodecasaccharides. These results suggest that CSA derivatives may potentially serve as targets in therapeutic strategies against placental malaria.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boerwinkle, E.; Brown, S.; Patsch, W.

To quantify the effect of the apolipoprotein (apo) E polymorphism on the magnitude of postprandial lipemia, the authors have defined its role in determining the response to a single high-fat meal in a large sample of (N = 474) individuals taking part in the biethnic Atherosclerosis Risk in Communities Study. The profile of postprandial response in plasma was monitored over 8 h by triglyceride, triglyceride-rich lipoprotein (TGRL)-triglyceride, apo B-48/apo B-100 ratio, and retinyl palmitate concentrations, and the apo E polymorphism was determined by DNA amplification and digestion. The frequency of the apo E alleles and their effects on fasting lipidmore » levels in this sample with vitamin A was significantly different among apo E genotypes, with delayed clearance in individuals with an [var epsilon]2 allele, compared with [var epsilon]3/3 and [var epsilon]3/4 individuals. In the sample of 397 Caucasians, average retinyl palmitate response was 1,489 [mu]g/dl in [var epsilon]2/3 individuals, compared with 1,037 [mu]g/dl in [var epsilon]3/3 individuals and 1,108 [mu]g/dl in [var epsilon]3/4 individuals. The apo E polymorphism accounted for 7.1% of the interindividual variation in postprandial retinyl palmitate response, a contribution proportionally greater than its well-known effect on fasting LDL-cholesterol. However, despite this effect on postprandial retinyl palmitate, the profile of postprandial triglyceride response was not significantly different among apo E genotypes. The profile of postprandial response was consistent between the sample of Caucasians and a smaller sample of black subjects. While these data indicate that the removal of remnant particles from circulation is delayed in subjects with the [var epsilon]2/3 genotype, there is no reported evidence that the [var epsilon]2 allele predisposes to coronary artery disease (CAD). 82 refs., 6 figs., 4 tabs.« less

VARS-TOOL: A Comprehensive, Efficient, and Robust Sensitivity Analysis Toolbox

NASA Astrophysics Data System (ADS)

Razavi, S.; Sheikholeslami, R.; Haghnegahdar, A.; Esfahbod, B.

2016-12-01

VARS-TOOL is an advanced sensitivity and uncertainty analysis toolbox, applicable to the full range of computer simulation models, including Earth and Environmental Systems Models (EESMs). The toolbox was developed originally around VARS (Variogram Analysis of Response Surfaces), which is a general framework for Global Sensitivity Analysis (GSA) that utilizes the variogram/covariogram concept to characterize the full spectrum of sensitivity-related information, thereby providing a comprehensive set of "global" sensitivity metrics with minimal computational cost. VARS-TOOL is unique in that, with a single sample set (set of simulation model runs), it generates simultaneously three philosophically different families of global sensitivity metrics, including (1) variogram-based metrics called IVARS (Integrated Variogram Across a Range of Scales - VARS approach), (2) variance-based total-order effects (Sobol approach), and (3) derivative-based elementary effects (Morris approach). VARS-TOOL is also enabled with two novel features; the first one being a sequential sampling algorithm, called Progressive Latin Hypercube Sampling (PLHS), which allows progressively increasing the sample size for GSA while maintaining the required sample distributional properties. The second feature is a "grouping strategy" that adaptively groups the model parameters based on their sensitivity or functioning to maximize the reliability of GSA results. These features in conjunction with bootstrapping enable the user to monitor the stability, robustness, and convergence of GSA with the increase in sample size for any given case study. VARS-TOOL has been shown to achieve robust and stable results within 1-2 orders of magnitude smaller sample sizes (fewer model runs) than alternative tools. VARS-TOOL, available in MATLAB and Python, is under continuous development and new capabilities and features are forthcoming.

Bearing and gear steels for aerospace applications

NASA Technical Reports Server (NTRS)

Zaretsky, Erwin V.

1990-01-01

Research in metallurgy and processing for bearing and gear steels has resulted in improvements in rolling-element bearing and gear life for aerospace application by a factor of approximately 200 over that obtained in the early 1940's. The selection and specification of a bearing or gear steel is dependent on the integration of multiple metallurgical and physical variables. For most aerospace bearings, through-hardened VIM-VAR AISI M-50 steel is the material of preference. For gears, the preferential material is case-carburized VAR AISI 9310. However, the VAR processing for this material is being replaced by VIM-VAR processing. Since case-carburized VIM-VAR M-50NiL incorporates the desirable qualities of both the AISI M-50 and AISI 9310 materials, optimal life and reliability can be achieved in both bearings and gears with a single steel. Hence, this material offers the promise of a common steel for both bearings and gears for future aerospace applications.

Preventing the return of smallpox: molecular modeling studies on thymidylate kinase from Variola virus.

PubMed

Guimarães, Ana Paula; Ramalho, Teodorico Castro; França, Tanos Celmar Costa

2014-01-01

Smallpox was one of the most devastating diseases in the human history and still represents a serious menace today due to its potential use by bioterrorists. Considering this threat and the non-existence of effective chemotherapy, we propose the enzyme thymidylate kinase from Variola virus (VarTMPK) as a potential target to the drug design against smallpox. We first built a homology model for VarTMPK and performed molecular docking studies on it in order to investigate the interactions with inhibitors of Vaccinia virus TMPK (VacTMPK). Subsequently, molecular dynamics (MD) simulations of these compounds inside VarTMPK and human TMPK (HssTMPK) were carried out in order to select the most promising and selective compounds as leads for the design of potential VarTMPK inhibitors. Results of the docking and MD simulations corroborated to each other, suggesting selectivity towards VarTMPK and, also, a good correlation with the experimental data.

Efficient Scores, Variance Decompositions and Monte Carlo Swindles.

DTIC Science & Technology

1984-08-28

to ;r Then a version .of Pythagoras ’ theorem gives the variance decomposition (6.1) varT var S var o(T-S) P P0 0 0 One way to see this is to note...complete sufficient statistics for (B, a) , and that the standard- ized residuals a(y - XB) 6 are ancillary. Basu’s sufficiency- ancillarity theorem

VarMod: modelling the functional effects of non-synonymous variants

PubMed Central

Pappalardo, Morena; Wass, Mark N.

2014-01-01

Unravelling the genotype–phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein interfaces and protein–ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod. PMID:24906884

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

PubMed

Allot, Alexis; Peng, Yifan; Wei, Chih-Hsuan; Lee, Kyubum; Phan, Lon; Lu, Zhiyong

2018-05-14

The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e.g. 'A146T' versus 'c.436G>A' versus 'rs121913527'). A search in PubMed using only one name usually cannot retrieve all relevant articles for the variant of interest. Hence, to help scientists, healthcare professionals, and database curators find the most up-to-date published variant research, we have developed LitVar for the search and retrieval of standardized variant information. In addition, LitVar uses advanced text mining techniques to compute and extract relationships between variants and other associated entities such as diseases and chemicals/drugs. LitVar is publicly available at https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar.

Changes in amino acid profile and metal content in seeds of Cicer arietinum L. (chickpea) grown under various fly-ash amendments.

PubMed

Gupta, D K; Tripathi, R D; Rai, U N; Dwivedi, S; Mishra, Seema; Srivastava, S; Inouhe, M

2006-11-01

Seeds of Cicer arietinum L. plants are edible and a valuable source of protein. Accumulation of toxic metals in the edible part of the plant, grown in fields close to fly-ash (FA) landfills, may pose a threat to human health. In the present study, the effects of FA and its amendments with different ameliorants viz., garden soil (GS), press mud (PM) and saw dust (SD), on total soluble protein contents, amino acid composition and metal accumulation in seeds were investigated in var. CSG-8962 and var. C-235 of C. arietinum. Plants accumulated adequate amounts of essential metals viz. Fe, Cu, Zn in seeds, while the toxic metals such as Cd and Cr were taken up in smaller quantities. The accumulation of Cr and Cd was less in var. C-235 than var. CSG-8962. Amendment of FA with PM enhanced the amount of soluble protein and amino acids in both varieties and was found to be superior among all tested ameliorants. Both quantitative and qualitative analysis of amino acids showed better response in var. C-235 as compared to var. CSG-8962. Thus var. C-235 seems to be suitable for cultivation in FA contaminated areas due to more accumulation of essential metals and less accumulation of toxic metals in seeds. Application of PM may further improve the growth of plants and nutritional quality of seeds.

Variogram Analysis of Response surfaces (VARS): A New Framework for Global Sensitivity Analysis of Earth and Environmental Systems Models

NASA Astrophysics Data System (ADS)

Razavi, S.; Gupta, H. V.

2015-12-01

Earth and environmental systems models (EESMs) are continually growing in complexity and dimensionality with continuous advances in understanding and computing power. Complexity and dimensionality are manifested by introducing many different factors in EESMs (i.e., model parameters, forcings, boundary conditions, etc.) to be identified. Sensitivity Analysis (SA) provides an essential means for characterizing the role and importance of such factors in producing the model responses. However, conventional approaches to SA suffer from (1) an ambiguous characterization of sensitivity, and (2) poor computational efficiency, particularly as the problem dimension grows. Here, we present a new and general sensitivity analysis framework (called VARS), based on an analogy to 'variogram analysis', that provides an intuitive and comprehensive characterization of sensitivity across the full spectrum of scales in the factor space. We prove, theoretically, that Morris (derivative-based) and Sobol (variance-based) methods and their extensions are limiting cases of VARS, and that their SA indices can be computed as by-products of the VARS framework. We also present a practical strategy for the application of VARS to real-world problems, called STAR-VARS, including a new sampling strategy, called "star-based sampling". Our results across several case studies show the STAR-VARS approach to provide reliable and stable assessments of "global" sensitivity across the full range of scales in the factor space, while being at least 1-2 orders of magnitude more efficient than the benchmark Morris and Sobol approaches.

Evidence for Globally Shared, Cross-Reacting Polymorphic Epitopes in the Pregnancy-Associated Malaria Vaccine Candidate VAR2CSA▿

PubMed Central

Avril, Marion; Kulasekara, Bridget R.; Gose, Severin O.; Rowe, Chris; Dahlbäck, Madeleine; Duffy, Patrick E.; Fried, Michal; Salanti, Ali; Misher, Lynda; Narum, David L.; Smith, Joseph D.

2008-01-01

Pregnancy-associated malaria (PAM) is characterized by the placental sequestration of Plasmodium falciparum-infected erythrocytes (IEs) with the ability to bind to chondroitin sulfate A (CSA). VAR2CSA is a leading candidate for a pregnancy malaria vaccine, but its large size (∼350 kDa) and extensive polymorphism may pose a challenge to vaccine development. In this study, rabbits were immunized with individual VAR2CSA Duffy binding-like (DBL) domains expressed in Pichia pastoris or var2csa plasmid DNA and sera were screened on different CSA-binding parasite lines. Rabbit antibodies to three recombinant proteins (DBL1, DBL3, and DBL6) and four plasmid DNAs (DBL1, DBL3, DBL5, and DBL6) reacted with homologous FCR3-CSA IEs. By comparison, antibodies to the DBL4 domain were unable to react with native VAR2CSA protein unless it was first partially proteolyzed with trypsin or chymotrypsin. To investigate the antigenic relationship of geographically diverse CSA-binding isolates, rabbit immune sera were screened on four heterologous CSA-binding lines from different continental origins. Antibodies did not target conserved epitopes exposed in all VAR2CSA alleles; however, antisera to several DBL domains cross-reacted on parasite isolates that had polymorphic loops in common with the homologous immunogen. This study demonstrates that VAR2CSA contains common polymorphic epitopes that are shared between geographically diverse CSA-binding lines. PMID:18250177

Evidence for globally shared, cross-reacting polymorphic epitopes in the pregnancy-associated malaria vaccine candidate VAR2CSA.

PubMed

Avril, Marion; Kulasekara, Bridget R; Gose, Severin O; Rowe, Chris; Dahlbäck, Madeleine; Duffy, Patrick E; Fried, Michal; Salanti, Ali; Misher, Lynda; Narum, David L; Smith, Joseph D

2008-04-01

Pregnancy-associated malaria (PAM) is characterized by the placental sequestration of Plasmodium falciparum-infected erythrocytes (IEs) with the ability to bind to chondroitin sulfate A (CSA). VAR2CSA is a leading candidate for a pregnancy malaria vaccine, but its large size ( approximately 350 kDa) and extensive polymorphism may pose a challenge to vaccine development. In this study, rabbits were immunized with individual VAR2CSA Duffy binding-like (DBL) domains expressed in Pichia pastoris or var2csa plasmid DNA and sera were screened on different CSA-binding parasite lines. Rabbit antibodies to three recombinant proteins (DBL1, DBL3, and DBL6) and four plasmid DNAs (DBL1, DBL3, DBL5, and DBL6) reacted with homologous FCR3-CSA IEs. By comparison, antibodies to the DBL4 domain were unable to react with native VAR2CSA protein unless it was first partially proteolyzed with trypsin or chymotrypsin. To investigate the antigenic relationship of geographically diverse CSA-binding isolates, rabbit immune sera were screened on four heterologous CSA-binding lines from different continental origins. Antibodies did not target conserved epitopes exposed in all VAR2CSA alleles; however, antisera to several DBL domains cross-reacted on parasite isolates that had polymorphic loops in common with the homologous immunogen. This study demonstrates that VAR2CSA contains common polymorphic epitopes that are shared between geographically diverse CSA-binding lines.

Acquisition of Infrared Variable Angle Spectroscopic Ellipsometer (IR-VASE)

DTIC Science & Technology

2016-04-22

External Advisory Board Meeting in Rio Piedras, PR. March 2016 Quiñonez B.*, Castilla D., Almodóvar J.; “ Polysaccharide -based polyelectrolyte...April 2016 Quiñonez B.*, Castilla D., Almodóvar J.; “ Polysaccharide -based polyelectrolyte multilayers: Physicochemical characterization and in...2016 Quiñonez B.*, Castilla D., Almodóvar J.; “ Polysaccharide -based polyelectrolyte multilayers: Physicochemical characterization and in vitro

75 FR 807 - Pesticide Tolerance Crop Grouping Program II; Revision to General Tolerance Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-06

...) Pepper, nonbell, Capsicum Chinese Jacq., C. annuum L. var. annuum , C. frutescens L., C. baccatum L., C... muricatum Aiton 8-09B, 8-09C Pepper, bell, Capsicum annuum L. var. annuum, 8-09B Capsicum spp Pepper, nonbell, Capsicum chinese Jacq., C. 8-09B, 8-08C annuum L. var. annuum, C. frutescens L., C. baccatum L...

Comparative ozone responses of cutleaf coneflowers (Rudbeckia laciniata var. digitata, var. ampla) from Rocky Mountain and Great Smoky Mountains National Parks, USA.

PubMed

Neufeld, Howard S; Johnson, Jennifer; Kohut, Robert

2018-01-01

Cutleaf coneflower (Rudbeckia laciniata L. var. digitata) is native to Great Smoky Mountains National Park (GRSM) and an ozone bioindicator species. Variety ampla, whose ozone sensitivity is less well known, is native to Rocky Mountain National Park (ROMO). In the early 2000s, researchers found putative ozone symptoms on var. ampla and rhizomes were sent to Appalachian State University to verify that the symptoms were the result of ozone exposure. In 2011, potted plants were exposed to ambient ozone from May to August. These same plants were grown in open-top chambers (OTCs) in 2012 and 2013, and exposed to charcoal-filtered (CF), non-filtered (NF), elevated ozone (EO), NF+50ppb in 2012 for 47days and NF+30/NF+50ppb ozone in 2013 for 36 and 36days, respectively. Ozone symptoms similar to those found in ROMO (blue-black adaxial stippling) were reproduced both in ambient air and in the OTCs. Both varieties exhibited foliar injury in the OTCs in an exposure-dependent manner, verifying that symptoms resulted from ozone exposure. In two of the three study years, var. digitata appeared more sensitive than var. ampla. Exposure to EO caused reductions in ambient photosynthetic rate (A) and stomatal conductance (g s ) for both varieties. Light response curves indicated that ozone reduced A, g s , and the apparent quantum yield while it increased the light compensation point. In CF air, var. ampla had higher light saturated A (18.2±1.04 vs 11.6±0.37μmolm -2 s -1 ), higher light saturation (1833±166.7 vs 1108±141.7μmolm -2 s -1 ), and lower Ci/Ca ratio (0.67±0.01 vs 0.77±0.01) than var. digitata. Coneflowers in both Parks are adversely affected by exposure to ambient ozone and if ozone concentrations increase in the Rocky Mountains, greater amounts of injury on var. ampla can be expected. Copyright © 2017 Elsevier B.V. All rights reserved.

Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae)

PubMed Central

Fossen, Erlend I.; Ekrem, Torbjørn; Nilsson, Anders N.; Bergsten, Johannes

2016-01-01

Abstract The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided. PMID:27081333

[Chemical Constituents of Paris polyphylla var. chinensis Aerial Parts].

PubMed

Yin, Wei; Song, Zu-rong; Liu, Jin-qi; Zhang, Guo-sheng

2015-09-01

To study the chemical constituents of aerial parts of Paris polyphylla var. chinensis . Aerial parts of Paris polyphylla var. chinensis was extracted with 95% EtOH, and separated and purified by silica gel, RP 18 and Sephadex LH-20 col- umn chromatography. The structures were identified by spectroscopic analysis. A total of ten compounds were isolated and iden- tified as β-sitosterol (1) ergosta-7, 22-dien-3-one (2), β-ecdysone (3), kaempferol (4), daucosterol (5) luteolin (6) calonysterone (7), luteolin-7-O-glucoside (8), quercetin (9), and 3β, 5α, 9α-trihydroxyergosta-7, 22-dien-6-one (10). Compounds 2,6 and 10 are isolated from Paris polyphylla var. chinensis for the first time.

Essential oil compositions and anticholinesterase activities of two edible plants Tragopogon latifolius var. angustifolius and Lycopsis orientalis.

PubMed

Ertaş, Abdulselam; Gören, Ahmet C; Boğa, Mehmet; Yeşil, Yeter; Kolak, Ufuk

2014-01-01

This is the first report in the literature on essential oil compositions of Tragopogon latifolius var. angustifolius and Lycopsis orientalis which were analysed by using GC-FID and GC-MS techniques. The main constituents of T. latifolius var. angustifolius were identified as α-selinene (10.5%), 2,5-di-tert octyl-p-benzoquinone (9.5%) and valencene (7.0%); however, the main components of L. orientalis were identified as heptacosane (10.5%), τ-muurolene (9.6%) and tetratetracontane (9.4%). The essential oils of T. latifolius var. angustifolius and L. orientalis species exhibited moderate inhibitory activity against acetyl- and butyryl-cholinesterase enzymes at 200 μg/mL.

Complete Genome Sequences of Salmonella enterica Serovars Anatum and Anatum var. 15+, Isolated from Retail Ground Turkey

PubMed Central

Marasini, Daya; Abo-Shama, Usama H.

2016-01-01

The complete genome sequences of two isolates of Salmonella enterica serovars Anatum and Anatum var. 15+ revealed the presence of two plasmids of 112 kb and 3 kb in size in each. The chromosome of Salmonella Anatum (4.83 Mb) was slightly smaller than that of Salmonella Anatum var. 15+ (4.88 Mb). PMID:26798111

Modeling Nonstationary Emotion Dynamics in Dyads using a Time-Varying Vector-Autoregressive Model.

PubMed

Bringmann, Laura F; Ferrer, Emilio; Hamaker, Ellen L; Borsboom, Denny; Tuerlinckx, Francis

2018-01-01

Emotion dynamics are likely to arise in an interpersonal context. Standard methods to study emotions in interpersonal interaction are limited because stationarity is assumed. This means that the dynamics, for example, time-lagged relations, are invariant across time periods. However, this is generally an unrealistic assumption. Whether caused by an external (e.g., divorce) or an internal (e.g., rumination) event, emotion dynamics are prone to change. The semi-parametric time-varying vector-autoregressive (TV-VAR) model is based on well-studied generalized additive models, implemented in the software R. The TV-VAR can explicitly model changes in temporal dependency without pre-existing knowledge about the nature of change. A simulation study is presented, showing that the TV-VAR model is superior to the standard time-invariant VAR model when the dynamics change over time. The TV-VAR model is applied to empirical data on daily feelings of positive affect (PA) from a single couple. Our analyses indicate reliable changes in the male's emotion dynamics over time, but not in the female's-which were not predicted by her own affect or that of her partner. This application illustrates the usefulness of using a TV-VAR model to detect changes in the dynamics in a system.

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

PubMed Central

Wei, Su-Juan; Lu, Yong-Bin; Ye, Quan-Qing; Tang, Shao-Qing

2017-01-01

Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns. PMID:28579991

Phytoremediation potential of Pityrogramma calomelanos var. austroamericana and Pteris vittata L. grown at a highly variable arsenic contaminated site.

PubMed

Niazi, Nabeel Khan; Singh, Balwant; Van Zwieten, Lukas; Kachenko, Anthony George

2011-10-01

This study examined the phytoextraction potential of two arsenic (As) hyperaccumulators, Pteris vittata L. and Pityrogramma calomelanos var. austroamericana at a historical As-contaminated cattle dip site in northern New South Wales (NSW), Australia. Total As concentration in the surface soil (0-20 cm) showed a better spatial structure than phosphate-extractable As in the surface and sub-surface soil at this site. P. calomelanos var. austroamericana produced greater frond dry biomass (mean = 130 g plant(-1)) than P. vittata (mean = 81 g plant(-1)) after 10 months of growth. Arsenic concentration and uptake in fronds were also significantly higher in P. calomelanos var. austroamericana (means = 887 mg kg(-1) and 124 mg plant(-1)) than in P. vittata (means = 674 mg kg(-1) and 57 mg plant(-1)). Our results showed that under the field conditions and highly variable soil As at the site, P. calomelanos var. austroamericana performed better than P. vittata. We predict that P. calomelanos var. austroamericana would take approximately 100 years to reduce the total As to below 20 mg kg(-1) at the site compared to > or =200 years estimated for P. vittata. However, long-term data are required to confirm these observations under field conditions.

Extrafloral nectaries of four varieties of Chamaecrista ramosa (Vogel) H.S.Irwin & Barneby (Fabaceae): anatomy, chemical nature, mechanisms of nectar secretion, and elimination.

PubMed

da Silva Pereira, Priscila; de Almeida Gonçalves, Letícia; da Silva, Marcos José; Rezende, Maria Helena

2018-04-27

Considering the importance of extrafloral nectaries (EFNs) in Fabaceae, the objectives of this research were to analyze (1) the anatomical and histochemical characteristics of the EFNs of Chamaecrista ramosa var. ramosa, C. ramosa var. curvifoliola, C. ramosa var. parvifoliola, and C. ramosa var. lucida and (2) the ultrastructure of the EFNs of C. ramosa var. ramosa. Standard techniques in plant anatomy and transmission electron microscopy were used. The anatomical analyses confirmed the characteristics described for extrafloral nectaries, evidencing three well-defined regions: epidermis, nectariferous, and subnectariferous parenchymas. Carbohydrates, proteins, pectins/mucilages, and lipids were detected by histochemical analyzes in all varieties. The ultrastructure of the EFNs of C. ramosa var. ramosa allowed the observation of microchannels at the external periclinal cell walls of the epidermis covering the secretory region. The nectariferous and subnectariferous parenchyma cells have periplasmic spaces, large plastids containing starch grains and plastoglobules, mitochondria, developed endoplasmic reticulum, large vacuoles with electron-dense contents, and membrane residues may be associated with the vacuole, suggesting the occurrence of autophagic processes. The anatomical, histochemical, and ultrastructural patterns revealed characteristics that confirm the glands of C. ramosa as extrafloral nectaries and suggest the eccrine mechanism of secretion.

A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters.

PubMed

Goudenège, David; Travers, Marie Agnès; Lemire, Astrid; Petton, Bruno; Haffner, Philippe; Labreuche, Yannick; Tourbiez, Delphine; Mangenot, Sophie; Calteau, Alexandra; Mazel, Didier; Nicolas, Jean Louis; Jacq, Annick; Le roux, Frédérique

2015-11-01

Oyster diseases caused by pathogenic vibrios pose a major challenge to the sustainability of oyster farming. In France, since 2012 a disease affecting specifically adult oysters has been associated with the presence of Vibrio aestuarianus. Here, by combining genome comparison, phylogenetic analyses and high-throughput infections of strains isolated before or during the recent outbreaks, we show that virulent strains cluster into two V. aestuarianus lineages independently of the sampling dates. The bacterial lethal dose was not different between strains isolated before or after 2012. Hence, the emergence of a new highly virulent clonal strain is unlikely. Each lineage comprises nearly identical strains, the majority of them being virulent, suggesting that within these phylogenetically coherent virulent lineages a few strains have lost their pathogenicity. Comparative genomics allowed the identification of a single frameshift in a non-virulent strain. This mutation affects the varS gene that codes for a signal transduction histidine-protein kinase. Genetic analyses confirmed that varS is necessary for infection of oysters and for a secreted metalloprotease expression. For the first time in a Vibrio species, we show here that VarS is a key factor of pathogenicity. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Experimental infection of European flat oyster Ostrea edulis with ostreid herpesvirus 1 microvar (OsHV-1μvar): Mortality, viral load and detection of viral transcripts by in situ hybridization.

PubMed

López Sanmartín, Monserrat; Power, Deborah M; de la Herrán, Roberto; Navas, José I; Batista, Frederico M

2016-06-02

Ostreid herpesvirus 1 (OsHV-1) infections have been reported in several bivalve species. Mortality of Pacific oyster Crassostrea gigas spat has increased considerably in Europe since 2008 linked to the spread of a variant of OsHV-1 called μvar. In the present study we demonstrated that O. edulis juveniles can be infected by OsHV-1μvar when administered as an intramuscular injection. Mortality in the oysters injected with OsHV-1μvar was first detected 4 days after injection and reached 25% mortality at day 10. Moreover, the high viral load observed and the detection of viral transcripts by in situ hybridization in several tissues of dying oysters suggested that OsHV-1μvar was the cause of mortality in the O. edulis juveniles. This is therefore the first study to provide evidence about the pathogenicity of OsHV-1μvar in a species that does not belong to the Crassostrea genus. Additionally, we present a novel method to detect OsHV-1 transcripts in infected individuals' using in situ hybridization. Copyright © 2016 Elsevier B.V. All rights reserved.

VarMod: modelling the functional effects of non-synonymous variants.

PubMed

Pappalardo, Morena; Wass, Mark N

2014-07-01

Unravelling the genotype-phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein-protein interfaces and protein-ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis.

PubMed

Mofiz, Ehtesham; Holt, Deborah C; Seemann, Torsten; Currie, Bart J; Fischer, Katja; Papenfuss, Anthony T

2016-06-02

The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans and mange in other animal species. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where secondary group A streptococcal and Staphylococcus aureus infections of scabies sores are thought to drive the high rate of rheumatic heart disease and chronic kidney disease. We sequenced the genome of two samples of Sarcoptes scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of Sarcoptes scabiei var. suis from a pig model. Because of the small size of the scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins. We have developed extensive genomic resources for the scabies mite, including reference genomes and a preliminary annotation.

An efficient assisted history matching and uncertainty quantification workflow using Gaussian processes proxy models and variogram based sensitivity analysis: GP-VARS

NASA Astrophysics Data System (ADS)

Rana, Sachin; Ertekin, Turgay; King, Gregory R.

2018-05-01

Reservoir history matching is frequently viewed as an optimization problem which involves minimizing misfit between simulated and observed data. Many gradient and evolutionary strategy based optimization algorithms have been proposed to solve this problem which typically require a large number of numerical simulations to find feasible solutions. Therefore, a new methodology referred to as GP-VARS is proposed in this study which uses forward and inverse Gaussian processes (GP) based proxy models combined with a novel application of variogram analysis of response surface (VARS) based sensitivity analysis to efficiently solve high dimensional history matching problems. Empirical Bayes approach is proposed to optimally train GP proxy models for any given data. The history matching solutions are found via Bayesian optimization (BO) on forward GP models and via predictions of inverse GP model in an iterative manner. An uncertainty quantification method using MCMC sampling in conjunction with GP model is also presented to obtain a probabilistic estimate of reservoir properties and estimated ultimate recovery (EUR). An application of the proposed GP-VARS methodology on PUNQ-S3 reservoir is presented in which it is shown that GP-VARS provides history match solutions in approximately four times less numerical simulations as compared to the differential evolution (DE) algorithm. Furthermore, a comparison of uncertainty quantification results obtained by GP-VARS, EnKF and other previously published methods shows that the P50 estimate of oil EUR obtained by GP-VARS is in close agreement to the true values for the PUNQ-S3 reservoir.

Understanding mechanisms of rarity in pteridophytes: competition and climate change threaten the rare fern Asplenium scolopendrium var. americanum (Aspleniaceae).

PubMed

Testo, Weston L; Watkins, James E

2013-11-01

Understanding the ecology of rare species can inform aspects of conservation strategies; however, the mechanisms of rarity remain elusive for most pteridophytes, which possess independent and ecologically distinct gametophyte and sporophyte generations. To elucidate factors contributing to recent declines of the rare fern Asplenium scolopendrium var. americanum, we studied the ecology and ecophysiology of its gametophyte generation, focusing on responses to competition, temperature, and water stress. Gametophytes of A. scolopendrium var. americanum, its widespread European relative A. scolopendrium var. scolopendrium, and five co-occurring fern species were grown from spores. Gametophytes were grown at 20°C and 25°C, and germination rates, intra- and interspecific competition, desiccation tolerance, and sporophyte production were determined for all species. Gametophytes of A. scolopendrium var. americanum had the lowest rates of germination and sporophyte production among all species studied and exhibited the greatest sensitivity to interspecific competition, temperature increases, and desiccation. Mature gametophytes of A. scolopendrium var. americanum grown at 25°C were 84.6% smaller than those grown at 20°C, and only 1.5% produced sporophytes after 200 d in culture. Similar responses were not observed in other species studied. The recent declines and current status of populations of A. scolopendrium var. americanum are linked to its gametophyte's limited capacity to tolerate competition and physiological stress linked to climate change. This is the first study to develop a mechanistic understanding of rarity and decline in a fern and demonstrates the importance of considering the ecology of the gametophyte in plants with independent sporophyte and gametophyte generations.

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

PubMed Central

Ronander, Elena; Bengtsson, Dominique C.; Joergensen, Louise; Jensen, Anja T. R.; Arnot, David E.

2012-01-01

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes. The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE1. Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System2 (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types. PMID:23070076

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study.

PubMed

van der Krieke, Lian; Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith Gm; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-08-07

Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher's tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use.

Evaluation of two health education interventions to improve the varicella vaccination: a randomized controlled trial from a province in the east China.

PubMed

Hu, Yu; Li, Qian; Chen, Yaping

2018-01-16

We evaluated the effect of two Elaboration Likelihood Model (ELM)-based health educational interventions on varicella vaccine (VarV) vaccination among pregnant women in a province in the east China. A prospective randomized controlled trial was conducted among 200 pregnant women with ≥12 gestation weeks to test two interventions, including a messaging video and a messaging booklet. The participants were randomly assigned into the control group, the video group or the booklet group. The VarV coverage at 12 and 24 months old was compared among the children of the three groups and relative risks (RRs) were calculated, by using the coverage of the control group as reference. The timeliness of VarV was also assessed. Furthermore, differences in the effects on the knowledge and attitude of VarV vaccination between the two interventions was evaluated. The VarV coverage of their children by 24 months of age was 86.4%, 76.1% and 56.7% for the video group, the booklet group and the control group, respectively. The relative risks (RRs) for the coverage of VarV at 24 months of age were 4.8 (95% CI: 2.06-11.3) for the video group and 2.4 (95% CI: 1.2-5.1) for the booklet group. The means of delays were 57.3 days in the video group, 76.9 days in the booklet group, and 100.6 days in the control group. The proportion of women who intended to vaccinate their children with VarV was higher in the video group than the booklet group (93.9% vs. 82.1%, p < 0.05). Our findings indicated that perinatal health education through booklet or video could improve the coverage and schedule adherence for children's VarV vaccination.

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study

PubMed Central

Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith GM; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-01-01

Background Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. Objective This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. Methods We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher’s tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). Results An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Conclusions Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use. PMID:26254160

Colour-scent associations in a tropical orchid: three colours but two odours.

PubMed

Delle-Vedove, Roxane; Juillet, Nicolas; Bessière, Jean-Marie; Grison, Claude; Barthes, Nicolas; Pailler, Thierry; Dormont, Laurent; Schatz, Bertrand

2011-06-01

Colour and scent are the major pollinator attractants to flowers, and their production may be linked by shared biosynthetic pathways. Species with polymorphic floral traits are particularly relevant to study the joint evolution of floral traits. We used in this study the tropical orchid Calanthe sylvatica from Réunion Island. Three distinct colour varieties are observed, presenting lilac, white or purple flowers, and named respectively C. sylvaticavar.lilacina (hereafter referred as var. lilacina), C. sylvaticavar. alba (var. alba) and C. sylvatica var. purpurea (var. purpurea). We investigated the composition of the floral scent produced by these colour varieties using the non-invasive SPME technique in the wild. Scent emissions are dominated by aromatic compounds. Nevertheless, the presence of the terpenoid (E)-4,8-dimethylnona-1,3,7-triène (DMNT) is diagnostic of var. purpurea, with the volatile organic compounds (VOC) produced by some individuals containing up to 60% of DMNT. We evidence specific colour-scent associations in C. sylvatica, with two distinct scent profiles in the three colour varieties: the lilacina-like profile containing no or very little DMNT (<2%) and the purpurea-like profile containing DMNT (>2%). Calanthe sylvatica var. alba individuals group with one or the other scent profile independently of their population of origin. We suggest that white-flowered individuals have evolved at least twice, once from var. lilacina and at least once from var. purpurea after the colonisation of la Réunion. White-flowered individuals may have been favoured by the particular pollinator fauna characterising the island. These flowering varieties of C. sylvatica, which display three colours but two scents profiles prove that colour is not always a good indicator of odour and that colour-scent associations may be complex, depending on pollination ecology of the populations concerned. Copyright © 2011 Elsevier Ltd. All rights reserved.

Pectic polysaccharides extracted from Rauvolfia verticillata (Lour.) Baill. var. hainanensis Tsiang increase LκB-α expression and ameliorate ulcerative colitis.

PubMed

Miao, X P; Sun, X N; Wei, H; Liu, Z J; Cui, L J; Deng, T Z

2015-02-01

The therapeutic potential of pectic polysaccharides extracted from Rauvolfia verticillata (Lour.) Baill. var. hainanensis Tsiang in ulcerative colitis were investigated. This study showed that pectic polysaccharides extracted from Rauvolfia verticillata (Lour.) Baill. var. hainanensis Tsiang ameliorated ulcerative colitis and were proposed to exhibit anti-inflammatory effects via increased expression of IκB-α proteins and suppressing NF-αB translocation.

Immunogenicity and safety of measles-mumps-rubella and varicella vaccines coadministered with a fourth dose of Haemophilus influenzae type b and Neisseria meningitidis serogroups C and Y-tetanus toxoid conjugate vaccine in toddlers: a pooled analysis of randomized trials.

PubMed

Bryant, Kristina; McVernon, Jodie; Marchant, Colin; Nolan, Terry; Marshall, Gary; Richmond, Peter; Marshall, Helen; Nissen, Michael; Lambert, Stephen; Aris, Emmanuel; Mesaros, Narcisa; Miller, Jacqueline

2012-08-01

A pooled analysis was conducted of 1257 toddlers who received a fourth dose of Haemophilus influenzae type b-Neisseria meningitidis serogroups C and Y-tetanus toxoid conjugate vaccine (HibMenCY-TT) or Hib conjugate vaccine (Hib polysaccharide conjugated to N. meningitidis outer membrane protein) coadministered with measles-mumps-rubella (MMR) and varicella (VAR) vaccines (NCT00134719/NCT00289783). Noninferiority of immunological responses to MMR and VAR was demonstrated between groups and incidences of MMR- and VAR-specific solicited symptoms were similar, indicating that HibMenCY-TT can be coadministered with MMR and VAR.

New family of pectinase genes PGU1b-PGU3b of the pectinolytic yeast Saccharomyces bayanus var. uvarum.

PubMed

Naumov, G I; Shalamitskiy, M Yu; Naumova, E S

2016-03-01

Using yeast genome databases and literature data, we have conducted a phylogenetic analysis of pectinase PGU genes from Saccharomyces strains assigned to the biological species S. arboricola, S. bayanus (var. uvarum), S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, and hybrid taxon S. pastorianus (syn. S. carlsbergensis). Single PGU genes were observed in all Saccharomyces species, except S. bayanus. The superfamily of divergent PGU genes has been documented in S. bayanus var. uvarum for the first time. Chromosomal localization of new PGU1b, PGU2b, and PGU3b genes in the yeast S. bayanus var. uvarum has been determined by molecular karyotyping and Southern hybridization.

Modified live infectious bursal disease virus (IBDV) vaccine delays infection of neonatal broiler chickens with variant IBDV compared to turkey herpesvirus (HVT)-IBDV vectored vaccine.

PubMed

Kurukulasuriya, Shanika; Ahmed, Khawaja Ashfaque; Ojkic, Davor; Gunawardana, Thushari; Goonewardene, Kalhari; Gupta, Ashish; Chow-Lockerbie, Betty; Popowich, Shelly; Willson, Philip; Tikoo, Suresh K; Gomis, Susantha

2017-02-07

Chickens are commonly processed around 35-45days of age in broiler chicken industry hence; diseases that occur at a young age are of paramount economic importance. Early age infection with infectious bursal disease virus (IBDV) results in long-lasting immunosuppression and profound economic losses. To our knowledge, this is the first study comparing the protection efficacy of modified live (MdLV) IBDV and herpesvirus turkey (HVT)-IBDV vaccines against early age variant IBDV (varIBDV) infection in chicks. Experiments were carried out in IBDV maternal antibody (MtAb) positive chicks (n=330), divided into 6 groups (n=50-60/group), namely Group 1 (saline), Group 2 (saline+varIBDV), Group 3 (HVT-IBDV), Group 4 (HVT-IBDV+varIBDV), Group 5 (MdLV) and Group 6 (MdLV+varIBDV). HVT-IBDV vaccination was given via the in ovo route to 18-day-old embryonated eggs. MdLV was administered via the subcutaneous route in day-old broilers. Group 2, Group 4 and Group 6 were orally challenged with varIBDV (SK-09, 3×10 3 EID 50 ) at day 6 post-hatch. IBDV seroconversion, bursal weight to body weight ratio (BBW) and bursal histopathology were assessed at 19 and 35days of age. Histopathological examination at day 19 revealed that varIBDV-SK09 challenge caused severe bursal atrophy and lower BBW in HVT-IBDV but not in MdLV vaccinated chicks. However by day 35, all challenged groups showed bursal atrophy and seroconversion. Interestingly, RT-qPCR analysis after varIBDV-SK09 challenge demonstrated an early (9days of age) and significantly high viral load (∼5744 folds) in HVT-IBDV vaccinated group vs unvaccinated challenged group (∼2.25 folds). Furthermore, flow cytometry analysis revealed inhibition of cytotoxic CD8 + T-cell response (CD44-downregulation) and decreased splenic lymphocytes counts in chicks after HVT-IBDV vaccination. Overall, our data suggest that MdLV delays varIBDV pathogenesis, whereas, HVT-IBDV vaccine is potentially immunosuppressive, which may increase the risk of early age varIBDV infection in broilers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Varenicline impairs extinction and enhances reinstatement across repeated cycles of nicotine self-administration in rats.

PubMed

Macnamara, Claire L; Holmes, Nathan M; Westbrook, R Fred; Clemens, Kelly J

2016-06-01

Varenicline is a partial nicotine receptor agonist widely prescribed as a smoking cessation medication. Repeated (or long-term) use of varenicline has been proposed as a treatment option for tobacco addiction. However the effect of repeated varenicline use on motivation for nicotine is unknown. Here the intravenous nicotine self-administration paradigm in rats was used to model the consequences of varenicline treatment across repeated cycles of administration, extinction and reinstatement. Rats acquired nicotine self-administration across 20 days before undergoing 6 days of extinction, where each extinction session was preceded by a single injection of varenicline or saline. This was followed by a single varenicline-free nicotine-primed reinstatement test. All rats then reacquired nicotine self-administration for 10 days followed by a second cycle of extinction. Across this period, rats either received a second cycle of varenicline (VAR-VAR) or saline (SAL-SAL), or the alternative treatment (SAL-VAR, VAR-SAL), followed by a final reinstatement test. Treatment with varenicline increased responding across the first cycle of extinction, but did not affect responding in the reinstatement test. Across the second cycle, varenicline again increased responding across extinction, and critically, rats treated with varenicline across cycle 1 and saline across cycle 2 (Group VAR-SAL) exhibited more reinstatement than rats in any other group. The effect of VAR on nicotine seeking was not due to its effects on locomotor activity. Instead, the results suggest that a history of VAR can increase vulnerability to reinstatement/relapse when its treatment is discontinued. The possible mechanisms of this increased vulnerability are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Unique Chromosomal Rearrangement in the Cryptococcus neoformans var. grubii Type Strain Enhances Key Phenotypes Associated with Virulence

PubMed Central

Morrow, Carl A.; Lee, I. Russel; Chow, Eve W. L.; Ormerod, Kate L.; Goldinger, Anita; Byrnes, Edmond J.; Nielsen, Kirsten; Heitman, Joseph; Schirra, Horst Joachim; Fraser, James A.

2012-01-01

ABSTRACT The accumulation of genomic structural variation between closely related populations over time can lead to reproductive isolation and speciation. The fungal pathogen Cryptococcus is thought to have recently diversified, forming a species complex containing members with distinct morphologies, distributions, and pathologies of infection. We have investigated structural changes in genomic architecture such as inversions and translocations that distinguish the most pathogenic variety, Cryptococcus neoformans var. grubii, from the less clinically prevalent Cryptococcus neoformans var. neoformans and Cryptococcus gattii. Synteny analysis between the genomes of the three Cryptococcus species/varieties (strains H99, JEC21, and R265) reveals that C. neoformans var. grubii possesses surprisingly few unique genomic rearrangements. All but one are relatively small and are shared by all molecular subtypes of C. neoformans var. grubii. In contrast, the large translocation peculiar to the C. neoformans var. grubii type strain is found in all tested subcultures from multiple laboratories, suggesting that it has possessed this rearrangement since its isolation from a human clinical sample. Furthermore, we find that the translocation directly disrupts two genes. The first of these encodes a novel protein involved in metabolism of glucose at human body temperature and affects intracellular levels of trehalose. The second encodes a homeodomain-containing transcription factor that modulates melanin production. Both mutations would be predicted to increase pathogenicity; however, when recreated in an alternate genetic background, these mutations do not affect virulence in animal models. The type strain of C. neoformans var. grubii in which the majority of molecular studies have been performed is therefore atypical for carbon metabolism and key virulence attributes. PMID:22375073

β-Galactomannan and Saccharomyces cerevisiae var. boulardii modulate the immune response against Salmonella enterica serovar Typhimurium in porcine intestinal epithelial and dendritic cells.

PubMed

Badia, Roger; Brufau, M Teresa; Guerrero-Zamora, Ana Maria; Lizardo, Rosil; Dobrescu, Irina; Martin-Venegas, Raquel; Ferrer, Ruth; Salmon, Henri; Martínez, Paz; Brufau, Joaquim

2012-03-01

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that causes inflammation, necrosis, and diarrhea in pigs, as well as being an important source of food-borne diseases in humans. Probiotics and prebiotics are promising alternatives to antibiotics to control and prevent intestinal infections. The present work investigated a recently developed β-galactomannan (βGM) prebiotic compared to the proven probiotic Saccharomyces cerevisiae var. boulardii on porcine ileum intestinal epithelial cells (IECs) of the IPI-2I line and monocyte-derived dendritic cells (DCs) cocultured in vitro with Salmonella. We observed that both S. cerevisiae var. boulardii and βGM inhibited the association of Salmonella with IECs in vitro. Our data indicated that βGM has a higher ability than S. cerevisiae var. boulardii to inhibit Salmonella-induced proinflammatory mRNA (cytokines tumor necrosis factor alpha [TNF-α], interleukin-1α [IL-1α], IL-6, and granulocyte-macrophage colony-stimulating factor [GM-CSF] and chemokines CCL2, CCL20, and CXCL8) and at protein levels (IL-6 and CXCL8). Additionally, βGM and S. cerevisiae var. boulardii induced some effects on DCs that were not observed on IECs: βGM and S. cerevisiae var. boulardii showed slight upregulation of mRNA for TNF-α, GM-CSF, and CCR7 receptor on porcine monocyte-derived dendritic cells (DCs). Indeed, the addition of βGM or S. cerevisiae var. boulardii on DCs cocultured with Salmonella showed higher gene expression (mRNA) for TNF-α, GM-CSF, and CXCL8 compared to that of the control with Salmonella. In conclusion, the addition of βGM inhibits Salmonella-induced proinflammatory profiles in IECs but may promote DC activation, although associated molecular mechanisms remain to be elucidated.

β-Galactomannan and Saccharomyces cerevisiae var. boulardii Modulate the Immune Response against Salmonella enterica Serovar Typhimurium in Porcine Intestinal Epithelial and Dendritic Cells

PubMed Central

Brufau, M. Teresa; Guerrero-Zamora, Ana Maria; Lizardo, Rosil; Dobrescu, Irina; Martin-Venegas, Raquel; Ferrer, Ruth; Salmon, Henri; Martínez, Paz

2012-01-01

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that causes inflammation, necrosis, and diarrhea in pigs, as well as being an important source of food-borne diseases in humans. Probiotics and prebiotics are promising alternatives to antibiotics to control and prevent intestinal infections. The present work investigated a recently developed β-galactomannan (βGM) prebiotic compared to the proven probiotic Saccharomyces cerevisiae var. boulardii on porcine ileum intestinal epithelial cells (IECs) of the IPI-2I line and monocyte-derived dendritic cells (DCs) cocultured in vitro with Salmonella. We observed that both S. cerevisiae var. boulardii and βGM inhibited the association of Salmonella with IECs in vitro. Our data indicated that βGM has a higher ability than S. cerevisiae var. boulardii to inhibit Salmonella-induced proinflammatory mRNA (cytokines tumor necrosis factor alpha [TNF-α], interleukin-1α [IL-1α], IL-6, and granulocyte-macrophage colony-stimulating factor [GM-CSF] and chemokines CCL2, CCL20, and CXCL8) and at protein levels (IL-6 and CXCL8). Additionally, βGM and S. cerevisiae var. boulardii induced some effects on DCs that were not observed on IECs: βGM and S. cerevisiae var. boulardii showed slight upregulation of mRNA for TNF-α, GM-CSF, and CCR7 receptor on porcine monocyte-derived dendritic cells (DCs). Indeed, the addition of βGM or S. cerevisiae var. boulardii on DCs cocultured with Salmonella showed higher gene expression (mRNA) for TNF-α, GM-CSF, and CXCL8 compared to that of the control with Salmonella. In conclusion, the addition of βGM inhibits Salmonella-induced proinflammatory profiles in IECs but may promote DC activation, although associated molecular mechanisms remain to be elucidated. PMID:22301691

Potential for wind extraction from 4D-Var assimilation of aerosols and moisture

NASA Astrophysics Data System (ADS)

Zaplotnik, Žiga; Žagar, Nedjeljka

2017-04-01

We discuss the potential of the four-dimensional variational data assimilation (4D-Var) to retrieve the unobserved wind field from observations of atmospheric tracers and the mass field through internal model dynamics and the multivariate relationships in the background-error term for 4D-Var. The presence of non-linear moist dynamics makes the wind retrieval from tracers very difficult. On the other hand, it has been shown that moisture observations strongly influence both tropical and mid-latitude wind field in 4D-Var. We present an intermediate complexity model that describes nonlinear interactions between the wind, temperature, aerosols and moisture including their sinks and sources in the framework of the so-called first baroclinic mode atmosphere envisaged by A. Gill. Aerosol physical processes, which are included in the model, are the non-linear advection, diffusion and sources and sinks that exist as dry and wet deposition and diffusion. Precipitation is parametrized according to the Betts-Miller scheme. The control vector for 4D-Var includes aerosols, moisture and the three dynamical variables. The former is analysed univariately whereas wind field and mass field are analysed in a multivariate fashion taking into account quasi-geostrophic and unbalanced dynamics. The OSSE type of studies are performed for the tropical region to assess the ability of 4D-Var to extract wind-field information from the time series of observations of tracers as a function of the flow nonlinearity, the observations density and the length of the assimilation window (12 hours and 24 hours), in dry and moist environment. Results show that the 4D-Var assimilation of aerosols and temperature data is beneficial for the wind analysis with analysis errors strongly dependent on the moist processes and reliable background-error covariances.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hang, Bo; Guliaev, Anton B.; Chenna, Ahmed

1,N{sup 6}-Ethanoadenine (EA) is an exocyclic adduct formed from DNA reaction with the antitumor agent, 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU). To understand the role of this adduct in the mechanism of mutagenicity or carcinogenicity by BCNU, an oligonucleotide with a site-specific EA was synthesized using phosphoramidite chemistry. We now report the in vitro miscoding properties of EA in translesion DNA synthesis catalyzed by mammalian DNA polymerases (pols) {alpha}, {beta}, {eta} and {iota}. These data were also compared with those obtained for the structurally related exocyclic adduct, 1,N{sup 6}-ethenoadenine ({var_epsilon}A). Using a primer extension assay, both pols {alpha} and {beta} were primarily blocked bymore » EA or {var_epsilon}A with very minor extension. Pol {eta} a member of the Y family of polymerases, was capable of catalyzing a significant amount of bypass across both adducts. Pol {eta} incorporated all four nucleotides opposite EA and {var_epsilon}A, but with differential preferences and mainly in an error-prone manner. Human pol {iota}, a paralog of human pol {eta}, was blocked by both adducts with a very small amount of synthesis past {var_epsilon}A. It incorporated C and, to a much lesser extent, T, opposite either adduct. In addition, the presence of an A adduct, e.g. {var_epsilon}A, could affect the specificity of pol {iota} toward the template T immediately 3 feet to the adduct. In conclusion, the four polymerases assayed on templates containing an EA or {var_epsilon}A showed differential bypass capacity and nucleotide incorporation specificity, with the two adducts not completely identical in influencing these properties. Although there was a measurable extent of error-free nucleotide incorporation, all these polymerases primarily misincorporated opposite EA, indicating that the adduct, similar to {var_epsilon}A, is a miscoding lesion.« less

Surface Fatigue Tests Of M50NiL Gears And Bars

NASA Technical Reports Server (NTRS)

Townsend, Dennis P.; Bamberger, Eric N.

1994-01-01

Report presents results of tests of steels for use in gears and bearings of advanced aircraft. Spur-gear endurance tests and rolling-element surface fatigue tests performed on gear and bar specimens of M50NiL steel processed by vacuum induction melting and vacuum arc remelting (VIM-VAR). Compares results of tests with similar tests of specimens of VIM-VAR AISI 9310 steel and of AISI 9310 steel subjected to VAR only.

A NEW SPECIES OF Bolivar Zaldívar-Riverón et Rodríguez-Jiménez (BRACONIDAE, DORYCTINAE) FROM BRAZIL, WITH NEW RECORDS OF THE AMAZONIAN B. ecuadorensis Zaldívar-Riverón et López-Estrada.

PubMed

Nunes, Juliano Fiorelini; Penteado-Dias, Angelica Maria; Souza-Gadelha, Sian De; Zaldívar-Riverón, Alejandro

2016-05-06

A new species of the doryctine genus Bolivar (Braconidae), B. brasiliensis sp. nov., is described from the Atlantic coastal region in Brazil. New records and taxonomic notes of the Amazonian B. ecuadorensis Zaldívar-Riverón et López-Estrada are also provided.

M-X Environmental Technical Report. Environmental Characteristics of Alternative Designated Deployment Areas, Protected Species.

DTIC Science & Technology

1980-12-22

RARE PLANTS LEGEND NUMBER SPECIES I Agave utabensis var. ebossspina 74 D. asperella var. ziorns, 147 Mentzela. leswophyll. 3 Angelica scabrida 75 D...cliffs Agave utahensis var. *boriapina Arctomecon merriami I Arenari a a tenomeres Gill. ripleyi Species known from bajadas of limestone mountains, with...hunters. Illegal collection of rare species of cacti or Agave . 3824-1 :Rare plants may he affected In the sa"e manner as native vegetation. See ETR

Use of Magnetic Bead Resin and Automated Liquid Handler Extraction Methods to Robotically Isolate Nucleic Acids of Biological Agent Simulates

DTIC Science & Technology

2003-09-01

concentration, and Bacillus subtilis var. niger spores were detectable at 10,000 CFU/ml. When combined with bead beating, these spores were consistently...Bioloeical Aaent Simulants. Cell suspensions of Bacillus subtilis var. niger spores (BG spores ) and Erwinia herbicola vegetative cells were prepared for...use as biological simulants. BG spores were prepared by inoculating 1 g spores of Bacillus subtilis var. niger (Merck & Co., Inc., Whitehouse Station

Antidepressant-like Effect of Kaempferol and Quercitirin, Isolated from Opuntia ficus-indica var. saboten

PubMed Central

Park, Soo-Hyun; Sim, Yun-Beom; Han, Pyung-Lim; Lee, Jin-Koo

2010-01-01

Opuntia ficus-indica var. saboten. is widely cultivated in Jeju Island (South Korea) for use in manufacture of health foods. This study described antidepressant effect of two flavonoids (kaempferol and quercitrin) isolated from the Opuntia ficus-indica var. saboten. The expression of the hypothalamic POMC mRNA or plasma β-endorphin levels were increased by extract of Opuntia ficus-indica var. saboten or its flavoniods administered orally. In addition, antidepressant activity was studied using tail suspension test (TST), forced swimming test (FST) and rota-rod test in chronically restraint immobilization stress group in mice. After restraint stress (2 hrs/day for 14 days), animals were kept in cage for 14 days without any further stress, bet with drugs. Mice were fed with a diet supplemented for 14 days and during the behavioral test period with kaempferol or quercitrin (30 mg/kg/day). POMC mRNA or plasma β-endorphin level was increased by extract of Opuntia ficus-indica var. saboten and its flavoniods. In addition, immobility time in TST and FST was significantly reduced by kaempferol or quercitrin. In rota-rod test, the time of permanence was maintained to the semblance of control group in turning at 15 rpm. Our results suggest that two flavonoids (kaempferol and quercitrin) isolated from the Opuntia ficus-indica var. saboten. show a potent antidepressant effect. PMID:22110339

Antidepressant-like Effect of Kaempferol and Quercitirin, Isolated from Opuntia ficus-indica var. saboten.

PubMed

Park, Soo-Hyun; Sim, Yun-Beom; Han, Pyung-Lim; Lee, Jin-Koo; Suh, Hong-Won

2010-06-01

Opuntia ficus-indica var. saboten. is widely cultivated in Jeju Island (South Korea) for use in manufacture of health foods. This study described antidepressant effect of two flavonoids (kaempferol and quercitrin) isolated from the Opuntia ficus-indica var. saboten. The expression of the hypothalamic POMC mRNA or plasma β-endorphin levels were increased by extract of Opuntia ficus-indica var. saboten or its flavoniods administered orally. In addition, antidepressant activity was studied using tail suspension test (TST), forced swimming test (FST) and rota-rod test in chronically restraint immobilization stress group in mice. After restraint stress (2 hrs/day for 14 days), animals were kept in cage for 14 days without any further stress, bet with drugs. Mice were fed with a diet supplemented for 14 days and during the behavioral test period with kaempferol or quercitrin (30 mg/kg/day). POMC mRNA or plasma β-endorphin level was increased by extract of Opuntia ficus-indica var. saboten and its flavoniods. In addition, immobility time in TST and FST was significantly reduced by kaempferol or quercitrin. In rota-rod test, the time of permanence was maintained to the semblance of control group in turning at 15 rpm. Our results suggest that two flavonoids (kaempferol and quercitrin) isolated from the Opuntia ficus-indica var. saboten. show a potent antidepressant effect.

Recurrence risk model for esophageal cancer after radical surgery.

PubMed

Lu, Jincheng; Tao, Hua; Song, Dan; Chen, Cheng

2013-10-01

The aim of the present study was to construct a risk assessment model which was tested by disease-free survival (DFS) of esophageal cancer after radical surgery. A total of 164 consecutive esophageal cancer patients who had undergone radical surgery between January 2005 and December 2006 were retrospectively analyzed. The cutpoint of value at risk (VaR) was inferred by stem-and-leaf plot, as well as by independent-samples t-test for recurrence-free time, further confirmed by crosstab chi-square test, univariate analysis and Cox regression analysis for DFS. The cutpoint of VaR was 0.3 on the basis of our model. The rate of recurrence was 30.3% (30/99) and 52.3% (34/65) in VaR <0.3 and VaR ≥0.3 (chi-square test, (χ) (2) =7.984, P=0.005), respectively. The 1-, 3-, and 5-year DFS of esophageal cancer after radical surgery was 70.4%, 48.7%, and 45.3%, respectively in VaR ≥0.3, whereas 91.5%, 75.8%, and 67.3%, respectively in VaR <0.3 (Log-rank test, (χ) (2) =9.59, P=0.0020), and further confirmed by Cox regression analysis [hazard ratio =2.10, 95% confidence interval (CI): 1.2649-3.4751; P=0.0041]. The model could be applied for integrated assessment of recurrence risk after radical surgery for esophageal cancer.

Recurrence risk model for esophageal cancer after radical surgery

PubMed Central

Tao, Hua; Song, Dan; Chen, Cheng

2013-01-01

Objective The aim of the present study was to construct a risk assessment model which was tested by disease-free survival (DFS) of esophageal cancer after radical surgery. Methods A total of 164 consecutive esophageal cancer patients who had undergone radical surgery between January 2005 and December 2006 were retrospectively analyzed. The cutpoint of value at risk (VaR) was inferred by stem-and-leaf plot, as well as by independent-samples t-test for recurrence-free time, further confirmed by crosstab chi-square test, univariate analysis and Cox regression analysis for DFS. Results The cutpoint of VaR was 0.3 on the basis of our model. The rate of recurrence was 30.3% (30/99) and 52.3% (34/65) in VaR <0.3 and VaR ≥0.3 (chi-square test, χ2 =7.984, P=0.005), respectively. The 1-, 3-, and 5-year DFS of esophageal cancer after radical surgery was 70.4%, 48.7%, and 45.3%, respectively in VaR ≥0.3, whereas 91.5%, 75.8%, and 67.3%, respectively in VaR <0.3 (Log-rank test, χ2 =9.59, P=0.0020), and further confirmed by Cox regression analysis [hazard ratio =2.10, 95% confidence interval (CI): 1.2649-3.4751; P=0.0041]. Conclusions The model could be applied for integrated assessment of recurrence risk after radical surgery for esophageal cancer. PMID:24255579

Functional Antibodies against VAR2CSA in Nonpregnant Populations from Colombia Exposed to Plasmodium falciparum and Plasmodium vivax

PubMed Central

Doritchamou, Justin; Arango, Eliana M.; Cabrera, Ana; Arroyo, Maria Isabel; Kain, Kevin C.; Ndam, Nicaise Tuikue; Maestre, Amanda

2014-01-01

In pregnancy, parity-dependent immunity is observed in response to placental infection with Plasmodium falciparum. Antibodies recognize the surface antigen, VAR2CSA, expressed on infected red blood cells and inhibit cytoadherence to the placental tissue. In most settings of malaria endemicity, antibodies against VAR2CSA are predominantly observed in multigravid women and infrequently in men, children, and nulligravid women. However, in Colombia, we detected antibodies against multiple constructs of VAR2CSA among men and children with acute P. falciparum and Plasmodium vivax infection. The majority of men and children (>60%) had high levels of IgGs against three recombinant domains of VAR2CSA: DBL5ε, DBL3X, and ID1-ID2. Surprisingly, these antibodies were observed only in pregnant women, men, and children exposed either to P. falciparum or to P. vivax. Moreover, the anti-VAR2CSA antibodies are of high avidity and efficiently inhibit adherence of infected red blood cells to chondroitin sulfate A in vitro, suggesting that they are specific and functional. These unexpected results suggest that there may be genotypic or phenotypic differences in the parasites of this region or in the host response to either P. falciparum or P. vivax infection outside pregnancy. These findings may hold significant clinical relevance to the pathophysiology and outcome of malaria infections in this region. PMID:24686068

Forecasting VaR and ES of stock index portfolio: A Vine copula method

NASA Astrophysics Data System (ADS)

Zhang, Bangzheng; Wei, Yu; Yu, Jiang; Lai, Xiaodong; Peng, Zhenfeng

2014-12-01

Risk measurement has both theoretical and practical significance in risk management. Using daily sample of 10 international stock indices, firstly this paper models the internal structures among different stock markets with C-Vine, D-Vine and R-Vine copula models. Secondly, the Value-at-Risk (VaR) and Expected Shortfall (ES) of the international stock markets portfolio are forecasted using Monte Carlo method based on the estimated dependence of different Vine copulas. Finally, the accuracy of VaR and ES measurements obtained from different statistical models are evaluated by UC, IND, CC and Posterior analysis. The empirical results show that the VaR forecasts at the quantile levels of 0.9, 0.95, 0.975 and 0.99 with three kinds of Vine copula models are sufficiently accurate. Several traditional methods, such as historical simulation, mean-variance and DCC-GARCH models, fail to pass the CC backtesting. The Vine copula methods can accurately forecast the ES of the portfolio on the base of VaR measurement, and D-Vine copula model is superior to other Vine copulas.

Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

PubMed

Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

2010-10-01

The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

Advanced Micro Grid Energy Management Coupled with Integrated Volt/VAR Control for Improved Energy Efficiency, Energy Security, and Power Quality at DoD Installations

DTIC Science & Technology

2016-10-28

assumptions. List of Assumptions: Price of electrical energy : $0.07/kWh flat rate for energy at the base Price of peak power: $15/MW peak power...EW-201147) Advanced Micro-Grid Energy Management Coupled with Integrated Volt/VAR Control for Improved Energy Efficiency, Energy Security, and...12-C-0002 5b. GRANT NUMBER Advanced Micro-Grid Energy Management Coupled with Integrated Volt/VAR Control for Improved Energy Efficiency, Energy

Four new synonyms and a new combination in Parnassia (Celastraceae).

PubMed

Shu, Yumin; Zhang, Zhixiang

2017-01-01

Parnassia yunnanensis had been previously described based on mixed specimens containing materials partially belonging to Parnassia cacuminum , which makes the application of Parnassia yunnanensis ambiguous. Therefore, we lectotypified Parnassia yunnanensis and meanwhile synonymized Parnassia lanceolata var. oblongipetala under it. Parnassia yunnanensis var. longistipitata was found more similar to Parnassia cacuminum rather than Parnassia yunnanensis , thus a new combination, Parnassia cacuminum var. longistipitata comb. nov. was proposed. Furthermore, other three names ( Parnassia vevusta , Parnassia degeensis and Parnassia kangdingensis ) were reduced to synonyms of Parnassia cacuminum too.

Selected aspects of modelling monetary transmission mechanism by BVAR model

NASA Astrophysics Data System (ADS)

Vaněk, Tomáš; Dobešová, Anna; Hampel, David

2013-10-01

In this paper we use the BVAR model with the specifically defined prior to evaluate data including high-lag dependencies. The results are compared to both restricted and common VAR model. The data depicts the monetary transmission mechanism in the Czech Republic and Slovakia from January 2002 to February 2013. The results point to the inadequacy of the common VAR model. The restricted VAR model and the BVAR model appear to be similar in the sense of impulse responses.

Fungal growth and the presence of sterigmatocystin in hard cheese.

PubMed

Northolt, M D; van Egmond, H P; Soentoro, P; Deijll, E

1980-01-01

Molds isolated from visibly molded cheeses in shops, households, and warehouses have been identified. Mold flora of cheeses in shops and households consisted mainly of Penicillium verrucosum var. cyclopium. On cheeses ripening in warehouses, Penicillium verrucosum var. cyclopium, Aspergillus versicolor, Aspergillus repens, and Enicillium verrucosum var. verrucosum were the dominant mold species. Cheese ripening in warehouses and molded with A. versicolor were examined for sterigmatocystin. Nine of 39 cheese samples contained sterigmatocystin in the surface layer in concentrations ranging from 5 to 600 micrograms/kg.

The COOH-terminal peptide of platelet factor-4 variant (CXCL4L1/PF-4var47-70) strongly inhibits angiogenesis and suppresses B16 melanoma growth in vivo.

PubMed

Vandercappellen, Jo; Liekens, Sandra; Bronckaers, Annelies; Noppen, Samuel; Ronsse, Isabelle; Dillen, Chris; Belleri, Mirella; Mitola, Stefania; Proost, Paul; Presta, Marco; Struyf, Sofie; Van Damme, Jo

2010-03-01

Chemokines influence tumor growth directly or indirectly via both angiogenesis and tumor-leukocyte interactions. Platelet factor-4 (CXCL4/PF-4), which is released from alpha-granules of activated platelets, is the first described angiostatic chemokine. Recently, it was found that the variant of CXCL4/PF-4 (CXCL4L1/PF-4var) could exert a more pronounced angiostatic and antitumoral effect than CXCL4/PF-4. However, the molecular mechanisms of the angiostatic activities of the PF-4 forms remain partially elusive. Here, we studied the biological properties of the chemically synthesized COOH-terminal peptides of CXCL4/PF-4 (CXCL4/PF-4(47-70)) and CXCL4L1/PF-4var (CXCL4L1/PF-4var(47-70)). Both PF-4 peptides lacked monocyte and lymphocyte chemotactic activity but equally well inhibited (25 nmol/L) endothelial cell motility and proliferation in the presence of a single stimulus (i.e., exogenous recombinant fibroblast growth factor-2). In contrast, when assayed in more complex angiogenesis test systems characterized by the presence of multiple mediators, including in vitro wound-healing (2.5 nmol/L versus 12.5 nmol/L), Matrigel (60 nmol/L versus 300 nmol/L), and chorioallantoic membrane assays, CXCL4L1/PF-4var(47-70) was found to be significantly (5-fold) more angiostatic than CXCL4/PF-4(47-70). In addition, low (7 microg total) doses of intratumoral CXCL4L1/PF-4var(47-70) inhibited B16 melanoma growth in mice more extensively than CXCL4/PF-4(47-70). This antitumoral activity was predominantly mediated through inhibition of angiogenesis (without affecting blood vessel stability) and induction of apoptosis, as evidenced by immunohistochemical and fluorescent staining of B16 tumor tissue. In conclusion, CXCL4L1/PF-4var(47-70) is a potent antitumoral and antiangiogenic peptide. These results may represent the basis for the design of CXCL4L1/PF-4var COOH-terminal-derived peptidomimetic anticancer drugs.

ClinVar miner: Demonstrating utility of a web-based tool for viewing and filtering clinvar data.

PubMed

Henrie, Alex; Hemphill, Sarah E; Ruiz-Schultz, Nicole; Cushman, Brandon; DiStefano, Marina T; Azzariti, Danielle; Harrison, Steven M; Rehm, Heidi L; Eilbeck, Karen

2018-05-23

ClinVar Miner is a web-based suite that utilizes the data held in the National Center for Biotechnology Information's ClinVar archive. The goal is to render the data more accessible to processes pertaining to conflict resolution of variant interpretation as well as tracking details of data submission and data management for detailed variant curation. Here we establish the use of these tools to address three separate use-cases and to perform analyses across submissions. We demonstrate that the ClinVar Miner tools are an effective means to browse and consolidate data for variant submitters, curation groups, and general oversight. These tools are also relevant to the variant interpretation community in general. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Volt-VAR Optimization on American Electric Power Feeders in Northeast Columbus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, Kevin P.; Weaver, T. F.

2012-05-10

In 2007 American Electric Power launched the gridSMART® initiative with the goals of increasing efficiency of the electricity delivery system and improving service to the end-use customers. As part of the initiative, a coordinated Volt-VAR system was deployed on eleven distribution feeders at five substations in the Northeast Columbus Ohio Area. The goal of the coordinated Volt-VAR system was to decrease the amount of energy necessary to provide end-use customers with the same quality of service. The evaluation of the Volt-VAR system performance was conducted in two stages. The first stage was composed of simulation, analysis, and estimation, while themore » second stage was composed of analyzing collected field data. This panel paper will examine the analysis conducted in both stages and present the estimated improvements in system efficiency.« less

Molecular and morphological evidence for Penstemon luculentus (Plantaginaceae): a replacement name for Penstemon fremontii var. glabrescens

PubMed Central

Johnson, Robert L.; Stevens, Mikel R.; Johnson, Leigh A.; Robbins, Matthew D.; Anderson, Chris D.; Ricks, Nathan J.; Farley, Kevin M.

2016-01-01

Abstract Penstemon luculentus R.L.Johnson & M.R.Stevens, nom. nov. replaces Penstemon fremontii var. glabrescens Dorn & Lichvar. The varietal name glabrescens was not elevated because it was already occupied by Penstemon glabrescens Pennell, a different species. This new arrangement is supported by molecular and morphological evidence. An analysis of genetic diversity in populations of both varieties of Penstemon fremontii Torr. & A. Gray (glabrescens and fremontii) from the Piceance Basin, Colorado, using SSR (simple sequences repeats) or microsatellites markers, revealed significant genetic differentiation between the two. Penstemon fremontii var. glabrescens was also genetically different from Penstemon gibbensii Dorn and Penstemon scariosus var. garrettii (Pennell) N.H. Holmgren. The combination of hirtellous stems, glabrous leaves, non-glandular inflorescence, and long anther hairs distinguish Penstemon luculentus from other morphologically similar species. PMID:27489478

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis).

PubMed

Hu, Guang-Fu; Liu, Xiang-Jiang; Li, Zhong; Liang, Hong-Wei; Hu, Shao-Na; Zou, Gui-Wei

2016-01-01

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp.

PubMed

Barret, Matthieu; Frey-Klett, Pascale; Guillerm-Erckelboudt, Anne-Yvonne; Boutin, Morgane; Guernec, Gregory; Sarniguet, Alain

2009-12-01

Traits contributing to the competence of biocontrol bacteria to colonize plant roots are often induced in the rhizosphere in response to plant components. These interactions have been studied using the two partners in gnotobiotic systems. However, in nature, beneficial or pathogenic fungi often colonize roots. Influence of these plant-fungus interactions on bacterial behavior remains to be investigated. Here, we have examined the influence of colonization of wheat roots by the take-all fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Bacteria were inoculated onto healthy, early G. graminis var. tritici-colonized and necrotic roots and transcriptomes were compared by shotgun DNA microarray. Pf29Arp decreased disease severity when inoculated before the onset of necrosis. Necrotic roots exerted a broader effect on gene expression compared with early G. graminis var. tritici-colonized and healthy roots. A gene encoding a putative type VI secretion system effector was only induced in necrotic conditions. A common pool of Pf29Arp genes differentially expressed on G. graminis var. tritici-colonized roots was related to carbon metabolism and oxidative stress, with a highest fold-change with necrosis. Overall, the data showed that the association of the pathogenic fungus with the roots strongly altered Pf29Arp adaptation with differences between early and late G. graminis var. tritici infection steps.

Taxonomic revision of genus Ablattaria Reitter (Coleoptera, Silphidae) using geometric morphometrics

PubMed Central

Qubaiová, Jarin; Růžička, Jan; Šípková, Hana

2015-01-01

Abstract The genus Ablattaria Reitter, 1884 (Coleoptera: Silphidae: Silphinae) is revised. Four taxa are recognized as valid species: Ablattaria arenaria (Kraatz, 1876), Ablattaria cribrata (Ménétries, 1832), Ablattaria laevigata (Fabricius, 1775) and Ablattaria subtriangula Reitter, 1905. Ablattaria laevigata var. meridionalis Ganglbauer, 1899 is newly treated as a junior subjective synonym of Ablattaria laevigata. Lectotypes are designated for Phosphuga arenaria Kraatz, 1876, Ablattaria arenaria var. punctigera Reitter, 1884, Ablattaria arenaria var. alleoni Portevin, 1926, Silpha cribrata Ménétries, 1832, Silpha laevigata Fabricius, 1775, Silpha gibba Brullé, 1832, Ablattaria gibba var. costulata Portevin, 1926, Ablattaria gibba var. distinguenda Portevin, 1926, Ablattaria gibba var. punctata Portevin, 1926 and Ablattaria subtriangula Reitter, 1905. The distribution of all taxa is mapped, based on material examined. Geometric morphometric methods were used to evaluate shape variability in Ablattaria. Results indicated sexual dimorphism in all species. Shape inconsistency was found between the sexes of all taxa when tested independently. The first two relative warp axes indicated 65.17% shape variation in males and 65.72% in females. Canonical variate analysis separated the taxa studied. There was minimal overlap between some groups in both sexes. Differences in body shape between populations of Ablattaria laevigata from Central Europe, Italy and Greece + Turkey were also examined. Relative warps implied 58.01% shape variability on both axes in males and 64.78% in females. CVA revealed noticeable overlaps between the groups, although the Italian population demonstrated a higher separation in both sexes. PMID:25685005

Polyamidoamine (PAMAM) dendrimers as potential release modulators and oral bioavailability enhancers of vardenafil hydrochloride.

PubMed

Tawfik, Mai Ahmed; Tadros, Mina Ibrahim; Mohamed, Magdy Ibrahim

2018-05-21

Vardenafil hydrochloride (VAR) is an erectile dysfunction treating drug. VAR has a short elimination half-life (4-5 h) and suffers low oral bioavailability (15%). This work aimed to explore the dual potential of VAR-dendrimer complexes as drug release modulators and oral bioavailability enhancers. VAR-dendrimer complexes were prepared by solvent evaporation technique using four dendrimer generations (G4.5, G5, G5.5 and G6) at three concentrations (190 nM, 380 nM and 950 nM). The systems were evaluated for intermolecular interactions, particle size, zeta potential, drug entrapment efficiency percentages (EE%) and drug released percentages after 2 h (Q 2h ) and 24 h (Q 24h ). The results were statistically analyzed, and the system showing the highest desirability was selected for further pharmacokinetic studies in rabbits, in comparison to Levitra ® tablets. The highest desirability (0.82) was achieved with D10 system comprising VAR (10 mg) and G6 (190 nM). It possessed small particle size (113.85 nm), low PDI (0.19), positive zeta potential (+21.53), high EE% (75.24%), promising Q 2 h (41.45%) and Q 24 h (74.05%). Compared to Levitra ® tablets, the significantly (p < 0.01) delayed T max , prolonged MRT (0-∞) and higher relative bioavailability (3.7-fold) could clarify the dual potential of D10 as a sustained release system capable of enhancing VAR oral bioavailability.

A Prototype Regional GSI-based EnKF-Variational Hybrid Data Assimilation System for the Rapid Refresh Forecasting System: Dual-Resolution Implementation and Testing Results

NASA Astrophysics Data System (ADS)

Pan, Yujie; Xue, Ming; Zhu, Kefeng; Wang, Mingjun

2018-05-01

A dual-resolution (DR) version of a regional ensemble Kalman filter (EnKF)-3D ensemble variational (3DEnVar) coupled hybrid data assimilation system is implemented as a prototype for the operational Rapid Refresh forecasting system. The DR 3DEnVar system combines a high-resolution (HR) deterministic background forecast with lower-resolution (LR) EnKF ensemble perturbations used for flow-dependent background error covariance to produce a HR analysis. The computational cost is substantially reduced by running the ensemble forecasts and EnKF analyses at LR. The DR 3DEnVar system is tested with 3-h cycles over a 9-day period using a 40/˜13-km grid spacing combination. The HR forecasts from the DR hybrid analyses are compared with forecasts launched from HR Gridpoint Statistical Interpolation (GSI) 3D variational (3DVar) analyses, and single LR hybrid analyses interpolated to the HR grid. With the DR 3DEnVar system, a 90% weight for the ensemble covariance yields the lowest forecast errors and the DR hybrid system clearly outperforms the HR GSI 3DVar. Humidity and wind forecasts are also better than those launched from interpolated LR hybrid analyses, but the temperature forecasts are slightly worse. The humidity forecasts are improved most. For precipitation forecasts, the DR 3DEnVar always outperforms HR GSI 3DVar. It also outperforms the LR 3DEnVar, except for the initial forecast period and lower thresholds.

Utilizing nanobody technology to target non-immunodominant domains of VAR2CSA.

PubMed

Ditlev, Sisse B; Florea, Raluca; Nielsen, Morten A; Theander, Thor G; Magez, Stefan; Boeuf, Philippe; Salanti, Ali

2014-01-01

Placental malaria is a major health problem for both pregnant women and their fetuses in malaria endemic regions. It is triggered by the accumulation of Plasmodium falciparum-infected erythrocytes (IE) in the intervillous spaces of the placenta and is associated with foetal growth restriction and maternal anemia. IE accumulation is supported by the binding of the parasite-expressed protein VAR2CSA to placental chondroitin sulfate A (CSA). Defining specific CSA-binding epitopes of VAR2CSA, against which to target the immune response, is essential for the development of a vaccine aimed at blocking IE adhesion. However, the development of a VAR2CSA adhesion-blocking vaccine remains challenging due to (i) the large size of VAR2CSA and (ii) the extensive immune selection for polymorphisms and thereby non-neutralizing B-cell epitopes. Camelid heavy-chain-only antibodies (HcAbs) are known to target epitopes that are less immunogenic to classical IgG and, due to their small size and protruding antigen-binding loop, able to reach and recognize cryptic, conformational epitopes which are inaccessible to conventional antibodies. The variable heavy chain (VHH) domain is the antigen-binding site of camelid HcAbs, the so called Nanobody, which represents the smallest known (15 kDa) intact, native antigen-binding fragment. In this study, we have used the Nanobody technology, an approach new to malaria research, to generate small and functional antibody fragments recognizing unique epitopes broadly distributed on VAR2CSA.

Designing a VAR2CSA-based vaccine to prevent placental malaria.

PubMed

Fried, Michal; Duffy, Patrick E

2015-12-22

Placental malaria (PM) due to Plasmodium falciparum is a major cause of maternal, fetal and infant mortality, but the mechanisms of pathogenesis and protective immunity are relatively well-understood for this condition, providing a path for vaccine development. P. falciparum parasites bind to chondroitin sulfate A (CSA) to sequester in the placenta, and women become resistant over 1-2 pregnancies as they acquire antibodies that block adhesion to CSA. The protein VAR2CSA, a member of the PfEMP1 variant surface antigen family, mediates parasite adhesion to CSA, and is the leading target for a vaccine to prevent PM. Obstacles to PM vaccine development include the large size (∼ 350 kD), high cysteine content, and sequence variation of VAR2CSA. A number of approaches have been taken to identify the combination of VAR2CSA domains and alleles that can induce broadly active antibodies that block adhesion of heterologous parasite isolates to CSA. This review summarizes these approaches, which have examined VAR2CSA fragments for binding activity, antigenicity with naturally acquired antibodies, and immunogenicity in animals for inducing anti-adhesion or surface-reactive antibodies. Two products are expected to enter human clinical studies in the near future based on N-terminal VAR2CSA fragments that have high binding affinity for CSA, and additional proteins preferentially expressed by placental parasites are also being examined for their potential contribution to a PM vaccine. Copyright © 2015. Published by Elsevier Ltd.

Genetic diversity of the DBLalpha region in Plasmodium falciparum var genes among Asia-Pacific isolates.

PubMed

Fowler, Elizabeth V; Peters, Jennifer M; Gatton, Michelle L; Chen, Nanhua; Cheng, Qin

2002-03-01

In Plasmodium falciparum a highly polymorphic multi-copy gene family, var, encodes the variant surface antigen P. falciparum erythrocyte membrane protein 1 (PfEMP1), which has an important role in cytoadherence and immune evasion. Using previously described universal PCR primers for the first Duffy binding-like domain (DBLalpha) of var we analysed the DBLalpha repertoires of Dd2 (originally from Thailand) and eight isolates from the Solomon Islands (n=4), Philippines (n=2), Papua New Guinea (n=1) and Africa (n=1). We found 15-32 unique DBLalpha sequence types among these isolates and estimated detectable DBLalpha repertoire sizes ranging from 33-38 to 52-57 copies per genome. Our data suggest that var gene repertoires generally consist of 40-50 copies per genome. Eighteen DBLalpha sequences appeared in more than one Asia-Pacific isolate with the number of sequences shared between any two isolates ranging from 0 to 6 (mean=2.0 +/-1.6). At the amino acid level DBLalpha sequence similarity within isolates ranged from 45.2 +/- 7.1 to 50.2 +/- 6.9%, and was not significantly different from the DBLalpha amino acid sequence similarity among isolates (P>0.1). Comparisons with published sequences also revealed little overlap among DBLalpha sequences from different regions. High DBLalpha sequence diversity and minimal overlap among these isolates suggest that the global var gene repertoire is immense, and may potentially be selected for by the host's protective immune response to the var gene products, PfEMP1.

A putative hybrid swarm within Oonopsis foliosa (Asteraceae: Astereae)

USGS Publications Warehouse

Hughes, J.F.; Brown, G.K.

2004-01-01

Oo??nopsis foliosa var. foliosa and var. monocephala are endemic to short-grass steppe of southeastern Colorado and until recently were considered geographically disjunct. The only known qualitative feature separating these 2 varieties is floral head type; var. foliosa has radiate heads, whereas var. monocephala heads are discoid. Sympatry between these varieties is restricted to a small area in which a range of parental types and intermediate head morphologies is observed. We used distribution mapping, morphometric analyses, chromosome cytology, and pollen stainability to characterize the sympatric zone. Morphometrics confirms that the only discrete difference between var. foliosa and var. monocephala is radiate versus discoid heads, respectively. The outer florets of putative hybrid individuals ranged from conspicuously elongated yet radially symmetric disc-floret corollas, to elongated radially asymmetric bilabiate- or deeply cleft corollas, to stunted ray florets with appendages remnant of corolla lobes. Chromosome cytology of pollen mother cells from both putative parental varieties and a series of intermediate morphological types collected at the sympatric zone reveal evidence of translocation heterozygosity. Pollen stainability shows no significant differences in viability between the parental varieties and putative hybrids. The restricted distribution of putative hybrids to a narrow zone of sympatry between the parental types and the presence of meiotic chromosome-pairing anomalies in these intermediate plants are consistent with a hybrid origin. The high stainability of putative-hybrid pollen adds to a growing body of evidence that hybrids are not universally unfit.

Dimension reduction of frequency-based direct Granger causality measures on short time series.

PubMed

Siggiridou, Elsa; Kimiskidis, Vasilios K; Kugiumtzis, Dimitris

2017-09-01

The mainstream in the estimation of effective brain connectivity relies on Granger causality measures in the frequency domain. If the measure is meant to capture direct causal effects accounting for the presence of other observed variables, as in multi-channel electroencephalograms (EEG), typically the fit of a vector autoregressive (VAR) model on the multivariate time series is required. For short time series of many variables, the estimation of VAR may not be stable requiring dimension reduction resulting in restricted or sparse VAR models. The restricted VAR obtained by the modified backward-in-time selection method (mBTS) is adapted to the generalized partial directed coherence (GPDC), termed restricted GPDC (RGPDC). Dimension reduction on other frequency based measures, such the direct directed transfer function (dDTF), is straightforward. First, a simulation study using linear stochastic multivariate systems is conducted and RGPDC is favorably compared to GPDC on short time series in terms of sensitivity and specificity. Then the two measures are tested for their ability to detect changes in brain connectivity during an epileptiform discharge (ED) from multi-channel scalp EEG. It is shown that RGPDC identifies better than GPDC the connectivity structure of the simulated systems, as well as changes in the brain connectivity, and is less dependent on the free parameter of VAR order. The proposed dimension reduction in frequency measures based on VAR constitutes an appropriate strategy to estimate reliably brain networks within short-time windows. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of the DBL3X-DBL4ε region of the VAR2CSA placental malaria vaccine candidate: insight into DBL domain interactions

PubMed Central

Gangnard, Stéphane; Lewit-Bentley, Anita; Dechavanne, Sébastien; Srivastava, Anand; Amirat, Faroudja; Bentley, Graham A.; Gamain, Benoît

2015-01-01

The human malaria parasite, Plasmodium falciparum, is able to evade spleen-mediated clearing from blood stream by sequestering in peripheral organs. This is due to the adhesive properties conferred by the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family exported by the parasite to the surface of infected erythrocytes. Expression of the VAR2CSA variant of PfEMP1 leads to pregnancy-associated malaria, which occurs when infected erythrocytes massively sequester in the placenta by binding to low-sulfated Chondroitin Sulfate A (CSA) present in the intervillous spaces. VAR2CSA is a 350 kDa protein that carries six Duffy-Binding Like (DBL) domains, one Cysteine-rich Inter-Domain Regions (CIDR) and several inter-domain regions. In the present paper, we report for the first time the crystal structure at 2.9 Å of a VAR2CSA double domain, DBL3X-DBL4ε, from the FCR3 strain. DBL3X and DBL4ε share a large contact interface formed by residues that are invariant or highly conserved in VAR2CSA variants, which suggests that these two central DBL domains (DBL3X-DBL4ε) contribute significantly to the structuring of the functional VAR2CSA extracellular region. We have also examined the antigenicity of peptides corresponding to exposed loop regions of the DBL4ε structure. PMID:26450557

Symmetry and topology code of the cluster self-assembly of framework MT structures of alumophosphates AlPO4(H2O)2 (metavariscite and variscite) and Al2(PO4)2(H2O)3 (APC)

NASA Astrophysics Data System (ADS)

Ilyushin, G. D.; Blatov, V. A.

2017-03-01

The supramolecular chemistry of alumophosphates, which form framework 3D MT structures from polyhedral AlO4(H2O)2 clusters with octahedral O coordination (of M polyhedra) and PO4 and AlO4 with tetrahedral O coordination (of T polyhedra), is considered. A combinatorial-topological modeling of the formation of possible types of linear (six types) and ring (two types) tetrapolyhedral cluster precursors M2T2 from MT monomers is carried out. Different versions of chain formation from linked (MT)2 rings (six types) are considered. The model, which has a universal character, has been used to simulate the cluster selfassembly of the crystal structure of AlPO4(H2O)2 minerals (metavariscite, m-VAR, and variscite, VAR) and zeolite [Al2(PO4)2(H2O)2] · H2O (APC). A tetrapolyhedral linear precursor is established for m-VAR and a ring precursor (MT)2 is established for VAR and APC. The symmetry and topology code of the processes of crystal structure self-assembly from cluster precursors is completely reconstructed. The functional role of the O-H···O hydrogen bonds is considered for the first time. The cluster self-assembly model explains the specific features of the morphogenesis of single crystals: m-VAR prisms, flattened VAR octahedra, and needleshaped APC square-base prisms.

Placental Sequestration of Plasmodium falciparum Malaria Parasites Is Mediated by the Interaction Between VAR2CSA and Chondroitin Sulfate A on Syndecan-1

PubMed Central

Mao, Yang; Resende, Mafalda; Daugaard, Mads; Riis Kristensen, Anders; Damm, Peter; G. Theander, Thor; R. Hansson, Stefan; Salanti, Ali

2016-01-01

During placental malaria, Plasmodium falciparum infected erythrocytes sequester in the placenta, causing health problems for both the mother and fetus. The specific adherence is mediated by the VAR2CSA protein, which binds to placental chondroitin sulfate (CS) on chondroitin sulfate proteoglycans (CSPGs) in the placental syncytium. However, the identity of the CSPG core protein and the cellular impact of the interaction have remain elusive. In this study we identified the specific CSPG core protein to which the CS is attached, and characterized its exact placental location. VAR2CSA pull-down experiments using placental extracts from whole placenta or syncytiotrophoblast microvillous cell membranes showed three distinct CSPGs available for VAR2CSA adherence. Further examination of these three CSPGs by immunofluorescence and proximity ligation assays showed that syndecan-1 is the main receptor for VAR2CSA mediated placental adherence. We further show that the commonly used placental choriocarcinoma cell line, BeWo, express a different set of proteoglycans than those present on placental syncytiotrophoblast and may not be the most biologically relevant model to study placental malaria. Syncytial fusion of the BeWo cells, triggered by forskolin treatment, caused an increased expression of placental CS-modified syndecan-1. In line with this, we show that rVAR2 binding to placental CS impairs syndecan-1-related Src signaling in forskolin treated BeWo cells, but not in untreated cells. PMID:27556547

Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.

PubMed

Cendejas-Bueno, E; Kolecka, A; Alastruey-Izquierdo, A; Theelen, B; Groenewald, M; Kostrzewa, M; Cuenca-Estrella, M; Gómez-López, A; Boekhout, T

2012-11-01

The Candida haemulonii species complex is currently known as C. haemulonii groups I and II. Here we describe C. haemulonii group II as a new species, Candida duobushaemulonii sp. nov., and C. haemulonii var. vulnera as new a variety of C. haemulonii group I using phenotypic and molecular methods. These taxa and other relatives of C. haemulonii (i.e., Candida auris and Candida pseudohaemulonii) cannot be differentiated by the commercial methods now used for yeast identification. Four isolates (C. haemulonii var. vulnera) differed from the other isolates of C. haemulonii in the sequence of the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon. The new species and the new variety have a multiresistant antifungal profile, which includes high MICs of amphotericin B (geometric mean MIC, 1.18 mg/liter for C. haemulonii var. vulnera and 2 mg/liter for C. duobushaemulonii sp. nov) and cross-resistance to azole compounds. Identification of these species should be based on molecular methods, such as sequence analysis of ITS regions and matrix-assisted laser desorption ionization-time of flight mass spectrometry.

VarDetect: a nucleotide sequence variation exploratory tool

PubMed Central

Ngamphiw, Chumpol; Kulawonganunchai, Supasak; Assawamakin, Anunchai; Jenwitheesuk, Ekachai; Tongsima, Sissades

2008-01-01

Background Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides. Results We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency. Availability VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at . PMID:19091032

[Isolation and diversity analyses of endophytic fungi from Paris polyphylla var. yunnanensis].

PubMed

Wang, Qian; Shen, Shi-Kang; Zhang, Ai-Li; Wu, Chun-Yan; Wu, Fu-Qin; Zhang, Xin-Jun; Wang, Yue-Hua

2013-11-01

The paper is aimed at studying the diversity of endophytic fungi community from Paris polyphylla var. yunnanensis, and to provide a scientific basis for the utilization value of the endophytic fungi as bioactive material resources. In the present study, endophytic fungi were isolated from roots, rhizomes and leaves of wild P. polyphylla var. yunnanensis collected from Baoshan, Heqing county and Songming city of Yunnan province, and identified and classified by morphological methods together with its ITS sequence analysis. Seven and forty-nine strains of endophytic fungi were isolated from P. polyphylla var. yunnanensis. They were identified belonging to 41 genus. In these 41 genus, 3 genus exist in root only, 12 genus only exist in rhizome and 8 genus only exist in leaf. There was difference in endophytic fungi isolated from different sample sites. Endophytic fungi diversity from rhizomes of Heqing site was the highest. Endophytic fungi similarity coefficient was low among different sites and tissues. Based on these results, it is reasonable to propose that endophytic fungi of P. polyphylla var. yannanensis from different tissue and different sample sites has a certain difference which is possibly relate to their different habitats, different structure and composition of each tissue.

Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa

PubMed Central

Litvintseva, Anastasia P.; Carbone, Ignazio; Rossouw, Jenny; Thakur, Rameshwari; Govender, Nelesh P.; Mitchell, Thomas G.

2011-01-01

Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian and arboreal habitats. This airborne, opportunistic pathogen is profoundly neurotropic and the leading cause of fungal meningitis. Patients with HIV/AIDS have been ravaged by cryptococcosis – an estimated one million new cases occur each year, and mortality approaches 50%. Using phylogenetic and population genetic analyses, we present evidence that C. neoformans var. grubii may have evolved from a diverse population in southern Africa. Our ecological studies support the hypothesis that a few of these strains acquired a new environmental reservoir, the excreta of feral pigeons (Columba livia), and were globally dispersed by the migration of birds and humans. This investigation also discovered a novel arboreal reservoir for highly diverse strains of C. neoformans var. grubii that are restricted to southern Africa, the mopane tree (Colophospermum mopane). This finding may have significant public health implications because these primal strains have optimal potential for evolution and because mopane trees contribute to the local economy as a source of timber, folkloric remedies and the edible mopane worm. PMID:21589919

A new framework for comprehensive, robust, and efficient global sensitivity analysis: 1. Theory

NASA Astrophysics Data System (ADS)

Razavi, Saman; Gupta, Hoshin V.

2016-01-01

Computer simulation models are continually growing in complexity with increasingly more factors to be identified. Sensitivity Analysis (SA) provides an essential means for understanding the role and importance of these factors in producing model responses. However, conventional approaches to SA suffer from (1) an ambiguous characterization of sensitivity, and (2) poor computational efficiency, particularly as the problem dimension grows. Here, we present a new and general sensitivity analysis framework (called VARS), based on an analogy to "variogram analysis," that provides an intuitive and comprehensive characterization of sensitivity across the full spectrum of scales in the factor space. We prove, theoretically, that Morris (derivative-based) and Sobol (variance-based) methods and their extensions are special cases of VARS, and that their SA indices can be computed as by-products of the VARS framework. Synthetic functions that resemble actual model response surfaces are used to illustrate the concepts, and show VARS to be as much as two orders of magnitude more computationally efficient than the state-of-the-art Sobol approach. In a companion paper, we propose a practical implementation strategy, and demonstrate the effectiveness, efficiency, and reliability (robustness) of the VARS framework on real-data case studies.

Annotated type catalogue of the Orthalicoidea (Mollusca, Gastropoda) in the Royal Belgian Institute of Sciences, Brussels, with descriptions of two new species

PubMed Central

Breure, Abraham S.H.

2011-01-01

Abstract The type status is described of 57 taxa from the superfamily Orthalicoidea in the collection of the Brussels museum. Two new species are described: Stenostylus perturbatus sp. n., and Suniellus adriani sp. n. New lectotypes are designated for Bulimulus (Naesiotus) amastroides Ancey, 1887; Bulimulus blanfordianus Ancey, 1903; Bulimulus montivagus chacoensis Ancey, 1897; Bulimus coloratus Nyst, 1845; Plecochilus dalmasi Dautzenberg, 1900; Placostylus porphyrostomus elata Dautzenberg, 1923; Bulimulus ephippium Ancey, 1904; Bulimus fulminans Nyst, 1843; Bulimus funckii Nyst, 1843; Orphnus thompsoni lutea Cousin, 1887; Bulimus melanocheilus Nyst, 1845; Orphnus thompsoni nigricans Cousin, 1887; Orphnus thompsoni olivacea Cousin, 1887; Bulimulus pollonerae Ancey, 1897; Orphnus thompsoni zebra Cousin, 1887. New combinations are: Bostryx borellii (Ancey, 1897); Bostryx carandaitiensis (Preston, 1907); Protoglyptus mazei (Crosse, 1874); Kuschelenia (Vermiculatus) sanborni (Haas, 1947). New synonymies are established for the following nominal taxa: Orphnus thompsoni var. lutea Cousin, 1887 = Kara thompsonii (Pfeiffer, 1845); Orphnus thompsoni var. nigricans Cousin, 1887 = Kara thompsonii (Pfeiffer, 1845); Thaumastus nystianus var. nigricans Cousin, 1887 = Drymaeus (Drymaeus) nystianus (Pfeiffer, 1853); Orphnus thompsoni var. olivacea Cousin, 1887 = Kara thompsonii (Pfeiffer, 1845); Orphnus thompsoni var. zebra Cousin, 1887 = Kara thompsonii (Pfeiffer, 1845). PMID:21747669

Revision of the Gonioctena nivosa species-group (Coleoptera, Chrysomelidae, Chrysomelinae) in the Holarctic region, with descriptions of two new species

PubMed Central

Cho, Hee-Wook; Kippenberg, Horst; Borowiec, Lech

2016-01-01

Abstract The Gonioctena nivosa species-group of the genus Gonioctena Chevrolat, 1836 is defined and reviewed. It contains six species including two new to science: Gonioctena gracilicornis (Kraatz, 1879), Gonioctena nivosa (Suffrian, 1851), Gonioctena norvegica (Strand, 1936), Gonioctena springlovae (Bechyně, 1948), Gonioctena amurensis Cho & Borowiec, sp. n. and Gonioctena jani Cho & Borowiec, sp. n. Six new synonyms are proposed: Gonioctena nivosa (= Gonioctena arctica alberta Brown, 1952, syn. n., Phytodecta linnaeana bergrothi Jacobson, 1901, syn. n., Phytodecta linnaeanus var. mutatus Achard, 1924, syn. n., Phytodecta linnaeanus var. simplex Achard, 1924, syn. n. and Phytodecta nivosa var. cedehensis Ronchetti, 1922, syn. n.) and Gonioctena norvegica (= Gonioctena janovskii Medvedev, 1976, syn. n.). Phytodecta flavicornis var. limbatipennis Achard, 1924 and Phytodecta nivosa var. bicolor Heyden, 1883 are removed from synonymy with Gonioctena nivosa (Suffrian, 1851) and are synonymized with Gonioctena flavicornis (Suffrian, 1851). Distribution maps, a key to species, color variation, geographic variation of male genitalia and host plants are provided. Ovoviviparity is newly recorded in Gonioctena gracilicornis and Gonioctena nivosa. Lectotypes are designated for Gonioctena affinis, Gonioctena arctica, Gonioctena linnaeana bergrothi and Gonioctena nivosa. PMID:27408579

American Lung Association

MedlinePlus

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Estimating seed crops of conifer and hardwood species

Treesearch

Philip M. McDonald

1992-01-01

Cone, acorn, and berry crops of ponderosa pine (Pinus ponderosa Dougl. ex Laws. var. ponderosa), sugar pine (Pinus lambertiana Dougl.), Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), California white fir (Abies concolor var. lowiana (Gord...

Mississippi River: Study of Alternatives for Rehabilitation of Lock and Dam Number 1. Minneapolis, Minnesota. Volume 4. Appendices G-M.

DTIC Science & Technology

1976-04-01

juniper (Juniperus chinensis, var. pfitzeriana), globe juniper (Juni]erus virginiana , var. globosa), dwarf Japanese yew (Taxus cuspidata, var. nana) and...excessively, compacted after planting. Heavy pruning of the tree’s upper branches is recommended at this point, to reduce the load put on root functioning...8217 5@9 BB 500.00 Shrubs-2 Juniperus chinensis 4𔃻 BB 42.00 Juniperus virginiana 31- BB 48.70 Taxus cuspidata 31 BB 38.40 *Cotoneaster apiculata 5’ BB

Determination of Effects of Designated Pollutants on Plant Species

DTIC Science & Technology

1976-10-01

grown at var Early Bird White Lompoc Barley Hordeum vuZgare Burpee Grown at Lompoc between flower var CM 67 seed crops Bean Phaseolus vulgaris Burpee...Rapid growth, widespread field var Pinto and garden cultivation, good for comparisons with other investigators Citrus Citrus sinesis UCR-PPD2 Special use...damage, 46 SI l I 90 + BARLEY CM 67 90. PINTO BEAN S8080 N, E 70 70 . zo 60 60- S50 50. - + z 0 +w o 40 40 + z + o 4-- + () 30 0 30- 0 4 EXPOSURE TIME

Effect of environmental factors on the germination and emergence of Salvia verbenaca L. cultivars (verbenaca and vernalis): An invasive species in semi-arid and arid rangeland regions

PubMed Central

Javaid, Muhammad Mansoor; Ali, Hafiz Haider; Weller, Sandra

2018-01-01

Salvia verbenaca (wild sage) is a commonly cultivated herbal medicine plant, which is native to the Mediterranean climate regions of Europe, Africa, Asia and the Middle East. However, it has become an invasive species in semi-arid and arid regions of southern Australia. Two varieties are present in this region, var. verbenaca and var. vernalis, each of which can be distinguished by differences in morphology and flowering period. Following trials to determine the optimum temperate regime for germination and response to light and dark, seeds of both varieties were tested for their response to variations in pH, moisture stress, salinity, and burial depth. The temperature and light trial was carried out using three different temperature regimes; 30/20°C, 25/15°C and 20/12°C, and two light regimes; 12 hours light/12 hours dark and 24 hours dark, with var. vernalis responding to relatively higher temperatures than var. verbenaca. The germination rate of neither species was significantly inhibited by complete darkness when compared to rates under periodic light exposure. Both varieties germinated at near optimum rates strongly to very strongly in all pH buffer solutions, from pH 5 to pH 10, but they responded most strongly at neutral pH. Var. vernalis showed slightly more tolerance to reduced moisture availability, moderate to strong salinity, and burial depth, compared to var. verbenaca. However, even a fairly shallow burial depth of 2 cm completely inhibited germination of both varieties. Thus, in circumstances where both varieties are present in a soil seedbank, var. vernalis could be expected to establish in more challenging conditions, where moisture is limited and salinity is ‘moderate to high’, implying that it is a more serious threat for invasive weed in conditions where crop plants are already challenged. PMID:29566039

Oncofetal Chondroitin Sulfate Glycosaminoglycans Are Key Players in Integrin Signaling and Tumor Cell Motility.

PubMed

Clausen, Thomas Mandel; Pereira, Marina Ayres; Al Nakouzi, Nader; Oo, Htoo Zarni; Agerbæk, Mette Ø; Lee, Sherry; Ørum-Madsen, Maj Sofie; Kristensen, Anders Riis; El-Naggar, Amal; Grandgenett, Paul M; Grem, Jean L; Hollingsworth, Michael A; Holst, Peter J; Theander, Thor; Sorensen, Poul H; Daugaard, Mads; Salanti, Ali

2016-12-01

Many tumors express proteoglycans modified with oncofetal chondroitin sulfate glycosaminoglycan chains (ofCS), which are normally restricted to the placenta. However, the role of ofCS in cancer is largely unknown. The function of ofCS in cancer was analyzed using the recombinant ofCS-binding VAR2CSA protein (rVAR2) derived from the malaria parasite, Plasmodium falciparum We demonstrate that ofCS plays a key role in tumor cell motility by affecting canonical integrin signaling pathways. Binding of rVAR2 to tumor cells inhibited the interaction of cells with extracellular matrix (ECM) components, which correlated with decreased phosphorylation of Src kinase. Moreover, rVAR2 binding decreased migration, invasion, and anchorage-independent growth of tumor cells in vitro Mass spectrometry of ofCS-modified proteoglycan complexes affinity purified from tumor cell lines on rVAR2 columns revealed an overrepresentation of proteins involved in cell motility and integrin signaling, such as integrin-β1 (ITGB1) and integrin-α4 (ITGA4). Saturating concentrations of rVAR2 inhibited downstream integrin signaling, which was mimicked by knockdown of the core chondroitin sulfate synthesis enzymes β-1,3-glucuronyltransferase 1 (B3GAT1) and chondroitin sulfate N-acetylgalactosaminyltransferase 1 (CSGALNACT1). The ofCS modification was highly expressed in both human and murine metastatic lesions in situ and preincubation or early intravenous treatment of tumor cells with rVAR2 inhibited seeding and spreading of tumor cells in mice. This was associated with a significant increase in survival of the animals. These data functionally link ofCS modifications with cancer cell motility and further highlights ofCS as a novel therapeutic cancer target. The cancer-specific expression of ofCS aids in metastatic phenotypes and is a candidate target for therapy. Mol Cancer Res; 14(12); 1288-99. ©2016 AACR. ©2016 American Association for Cancer Research.

Comparative assessment of the Euglena gracilis var. saccharophila variant strain as a producer of the β-1,3-glucan paramylon under varying light conditions.

PubMed

Sun, Angela; Hasan, Mafruha Tasnin; Hobba, Graham; Nevalainen, Helena; Te'o, Junior

2018-06-11

Euglena gracilis Z and a 'sugar loving' variant strain Euglena gracilis var. saccharophila, were investigated as producers of paramylon, a β-1,3-glucan polysaccharide with potential medicinal and industrial applications. The strains were grown under diurnal or dark growth conditions on a glucose-yeast extract medium supporting high-level paramylon production. Both strains produced the highest paramylon yields (7.4 to 8 g · L -1 , respectively) while grown in the dark, but the maximum yield was achieved faster by E. gracilis var. saccharophila (48 h vs 72 h). The glucose-to-paramylon yield coefficient Y par/glu = 0.46±0.03 in the Euglena gracilis var. saccharophila cultivation, obtained in this study, is the highest reported to date. Proteomic analysis of the metabolic pathways provided molecular clues for the strain behavior observed during cultivation. For example, overexpression of enzymes in the gluconeogenesis/glycolysis pathways including fructokinase-1 and chloroplastic fructose-1,6-bisphosphatase may have contributed to the faster rate of paramylon accumulation in E. gracilis var. saccharophila. Differentially expressed proteins in the early steps of chloroplastogenesis pathway including plastid uroporphyrinogen decarboxylases, photoreceptors, and a highly abundant (68 fold increase) plastid transketolase may have provided the E. gracilis var. saccharophila strain an advantage in paramylon production during diurnal cultivations. In conclusion, the variant strain E. gracilis var. saccharophila seems to be well suited for producing large amounts of paramylon. This work has also resulted in the identification of molecular targets for future improvement of paramylon production in E. gracilis, including the chloroplastic fructose-1,6-bisphosphatase (FBP) and phosophofructokinase 1 (PFK-1), the latter being a key regulator of glycolysis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim

PubMed Central

Marshall, B; Puthalakath, H; Caria, S; Chugh, S; Doerflinger, M; Colman, P M; Kvansakul, M

2015-01-01

Subversion of host cell apoptosis is an important survival strategy for viruses to ensure their own proliferation and survival. Certain viruses express proteins homologous in sequence, structure and function to mammalian pro-survival B-cell lymphoma 2 (Bcl-2) proteins, which prevent rapid clearance of infected host cells. In vaccinia virus (VV), the virulence factor F1L was shown to be a potent inhibitor of apoptosis that functions primarily be engaging pro-apoptotic Bim. Variola virus (VAR), the causative agent of smallpox, harbors a homolog of F1L of unknown function. We show that VAR F1L is a potent inhibitor of apoptosis, and unlike all other characterized anti-apoptotic Bcl-2 family members lacks affinity for the Bim Bcl-2 homology 3 (BH3) domain. Instead, VAR F1L engages Bid BH3 as well as Bak and Bax BH3 domains. Unlike its VV homolog, variola F1L only protects against Bax-mediated apoptosis in cellular assays. Crystal structures of variola F1L bound to Bid and Bak BH3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak BH3 in the canonical Bcl-2-binding groove, in a manner similar to VV F1L. Despite the observed conservation of structure and sequence, variola F1L inhibits apoptosis using a startlingly different mechanism compared with its VV counterpart. Our results suggest that unlike during VV infection, Bim neutralization may not be required during VAR infection. As molecular determinants for the human-specific tropism of VAR remain essentially unknown, identification of a different mechanism of action and utilization of host factors used by a VAR virulence factor compared with its VV homolog suggest that studying VAR directly may be essential to understand its unique tropism. PMID:25766319

Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim.

PubMed

Marshall, B; Puthalakath, H; Caria, S; Chugh, S; Doerflinger, M; Colman, P M; Kvansakul, M

2015-03-12

Subversion of host cell apoptosis is an important survival strategy for viruses to ensure their own proliferation and survival. Certain viruses express proteins homologous in sequence, structure and function to mammalian pro-survival B-cell lymphoma 2 (Bcl-2) proteins, which prevent rapid clearance of infected host cells. In vaccinia virus (VV), the virulence factor F1L was shown to be a potent inhibitor of apoptosis that functions primarily be engaging pro-apoptotic Bim. Variola virus (VAR), the causative agent of smallpox, harbors a homolog of F1L of unknown function. We show that VAR F1L is a potent inhibitor of apoptosis, and unlike all other characterized anti-apoptotic Bcl-2 family members lacks affinity for the Bim Bcl-2 homology 3 (BH3) domain. Instead, VAR F1L engages Bid BH3 as well as Bak and Bax BH3 domains. Unlike its VV homolog, variola F1L only protects against Bax-mediated apoptosis in cellular assays. Crystal structures of variola F1L bound to Bid and Bak BH3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak BH3 in the canonical Bcl-2-binding groove, in a manner similar to VV F1L. Despite the observed conservation of structure and sequence, variola F1L inhibits apoptosis using a startlingly different mechanism compared with its VV counterpart. Our results suggest that unlike during VV infection, Bim neutralization may not be required during VAR infection. As molecular determinants for the human-specific tropism of VAR remain essentially unknown, identification of a different mechanism of action and utilization of host factors used by a VAR virulence factor compared with its VV homolog suggest that studying VAR directly may be essential to understand its unique tropism.

Differential recognition of P. falciparum VAR2CSA domains by naturally acquired antibodies in pregnant women from a malaria endemic area.

PubMed

Brolin, Kim J M; Persson, Kristina E M; Wahlgren, Mats; Rogerson, Stephen J; Chen, Qijun

2010-02-16

Plasmodium falciparum infected red blood cells (iRBC) express variant surface antigens (VSA) of which VAR2CSA is involved in placental sequestration and causes pregnancy-associated malaria (PAM). Primigravidae are most susceptible to PAM whereas antibodies associated with protection are often present at higher levels in multigravid women. However, HIV co-infection with malaria has been shown to alter this parity-dependent acquisition of immunity, with more severe symptoms as well as more malaria episodes in HIV positive women versus HIV negative women of a similar parity. Using VAR2CSA DBL-domains expressed on the surface of CHO-745 cells we quantified levels of DBL-domain specific IgG in sera from pregnant Malawian women by flow cytometry. Dissociations constants of DBL5epsilon specific antibodies were determined using a surface plasmon resonance technique, as an indication of antibody affinities. VAR2CSA DBL5epsilon was recognized in a gender and parity-dependent manner with anti-DBL5epsilon IgG correlating significantly with IgG levels to VSA-PAM on the iRBC surface. HIV positive women had lower levels of anti-DBL5epsilon IgG than HIV negative women of similar parity. In primigravidae, antibodies in HIV positive women also showed significantly lower affinity to VAR2CSA DBL5epsilon. Pregnant women from a malaria-endemic area had increased levels of anti-DBL5epsilon IgG by parity, indicating this domain of VAR2CSA to be a promising vaccine candidate against PAM. However, it is important to consider co-infection with HIV, as this seems to change the properties of antibody response against malaria. Understanding the characteristics of antibody response against VAR2CSA is undoubtedly imperative in order to design a functional and efficient vaccine against PAM.

New phenylpropanoid glycosides from Juniperus communis var. depressa.

PubMed

Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Murata, Jin; Lang, Frank A; Tanaka, Toshiyuki; Nakanishi, Tsutomu; Inada, Akira

2010-05-01

Two new phenylpropanoid glycosides were isolated from the leaves and stems of Juniperus communis var. depressa (Cupressaceae) along with 14 known compounds. Their structures were determined by spectral analyses, in particular by 2D-NMR spectral evidence.

Endangered Species on U.S. Army Installations.

DTIC Science & Technology

1982-08-01

OLOKELEANUM x VOTOTICHIUMr VIRIDE /MFSD. x PEUCEDANUM KAIJAIEJSEL x PTERALYXIA, KAUAI x RAUVOLFIA MFLLEPI x HAD x RAUVOLFIA SArJDWICENSIS VAR...HELLERI PLANTS UNnETERMIAED SCHOFIELD BARRACKS# RAUVOLFIA SANOWICENSIS VAR, SUBACUMINATA PLANTS UINDETERMINED SCHOFIELD BARRACKS, *EMYA KAUAIENSIS /HBD

Entoloma subgenus Leptonia in boreal-temperate Eurasia: towards a phylogenetic species concept.

PubMed

Morozova, O V; Noordeloos, M E; Vila, J

2014-06-01

This study reveals the concordance, or lack thereof, between morphological and phylogenetic species concepts within Entoloma subg. Leptonia in boreal-temperate Eurasia, combining a critical morphological examination with a multigene phylogeny based on nrITS, nrLSU and mtSSU sequences. A total of 16 taxa was investigated. Emended concepts of subg. Leptonia and sect. Leptonia as well as the new sect. Dichroi are presented. Two species (Entoloma percoelestinum and E. sublaevisporum) and one variety (E. tjallingiorum var. laricinum) are described as new to science. On the basis of the morphological and phylogenetical evidence E. alnetorum is reduced to a variety of E. tjallingiorum, and E. venustum is considered a variety of E. callichroum. Accordingly, the new combinations E. tjallingiorum var. alnetorum and E. callichroum var. venustum are proposed. Entoloma lepidissimum var. pauciangulatum is now treated as a synonym of E. chytrophilum. Neotypes for E. dichroum, E. euchroum and E. lampropus are designated.

A VaR Algorithm for Warrants Portfolio

NASA Astrophysics Data System (ADS)

Dai, Jun; Ni, Liyun; Wang, Xiangrong; Chen, Weizhong

Based on Gamma Vega-Cornish Fish methodology, this paper propose the algorithm for calculating VaR via adjusting the quantile under the given confidence level using the four moments (e.g. mean, variance, skewness and kurtosis) of the warrants portfolio return and estimating the variance of portfolio by EWMA methodology. Meanwhile, the proposed algorithm considers the attenuation of the effect of history return on portfolio return of future days. Empirical study shows that, comparing with Gamma-Cornish Fish method and standard normal method, the VaR calculated by Gamma Vega-Cornish Fish can improve the effectiveness of forecasting the portfolio risk by virture of considering the Gamma risk and the Vega risk of the warrants. The significance test is conducted on the calculation results by employing two-tailed test developed by Kupiec. Test results show that the calculated VaRs of the warrants portfolio all pass the significance test under the significance level of 5%.

Extremum Seeking Control of Smart Inverters for VAR Compensation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold, Daniel; Negrete-Pincetic, Matias; Stewart, Emma

2015-09-04

Reactive power compensation is used by utilities to ensure customer voltages are within pre-defined tolerances and reduce system resistive losses. While much attention has been paid to model-based control algorithms for reactive power support and Volt Var Optimization (VVO), these strategies typically require relatively large communications capabilities and accurate models. In this work, a non-model-based control strategy for smart inverters is considered for VAR compensation. An Extremum Seeking control algorithm is applied to modulate the reactive power output of inverters based on real power information from the feeder substation, without an explicit feeder model. Simulation results using utility demand informationmore » confirm the ability of the control algorithm to inject VARs to minimize feeder head real power consumption. In addition, we show that the algorithm is capable of improving feeder voltage profiles and reducing reactive power supplied by the distribution substation.« less

Granger Causality Testing with Intensive Longitudinal Data.

PubMed

Molenaar, Peter C M

2018-06-01

The availability of intensive longitudinal data obtained by means of ambulatory assessment opens up new prospects for prevention research in that it allows the derivation of subject-specific dynamic networks of interacting variables by means of vector autoregressive (VAR) modeling. The dynamic networks thus obtained can be subjected to Granger causality testing in order to identify causal relations among the observed time-dependent variables. VARs have two equivalent representations: standard and structural. Results obtained with Granger causality testing depend upon which representation is chosen, yet no criteria exist on which this important choice can be based. A new equivalent representation is introduced called hybrid VARs with which the best representation can be chosen in a data-driven way. Partial directed coherence, a frequency-domain statistic for Granger causality testing, is shown to perform optimally when based on hybrid VARs. An application to real data is provided.

Refining value-at-risk estimates using a Bayesian Markov-switching GJR-GARCH copula-EVT model.

PubMed

Sampid, Marius Galabe; Hasim, Haslifah M; Dai, Hongsheng

2018-01-01

In this paper, we propose a model for forecasting Value-at-Risk (VaR) using a Bayesian Markov-switching GJR-GARCH(1,1) model with skewed Student's-t innovation, copula functions and extreme value theory. A Bayesian Markov-switching GJR-GARCH(1,1) model that identifies non-constant volatility over time and allows the GARCH parameters to vary over time following a Markov process, is combined with copula functions and EVT to formulate the Bayesian Markov-switching GJR-GARCH(1,1) copula-EVT VaR model, which is then used to forecast the level of risk on financial asset returns. We further propose a new method for threshold selection in EVT analysis, which we term the hybrid method. Empirical and back-testing results show that the proposed VaR models capture VaR reasonably well in periods of calm and in periods of crisis.

[Responses of Pinus sylvestris var. mongolica radial growth to climate warming in Great Xing' an Mountins: a case study in Mangui].

PubMed

Zhang, Xing-Liang; He, Xing-Yuan; Chen, Zhen-Ju; Cui, Ming-Xing; Li, Na

2011-12-01

Based on the theory and methodology of dendrochronology, the tree ring width chronology of Pinus sylvestris var. mongolica in Mangui of Great Xing' an Mountains was developed, and the relationships between the standardized tree ring width chronology and local climate factors (temperature and precipitation) as well as the effects of climate factors on the P. sylvestris var. mongolica radial growth were analyzed. In this region, the mean monthly temperature in April-August of current year was the main factor limiting the radial growth, and the increasing mean monthly temperature from April to August had negative effects to the radial growth. The simulation of the variations of the radial growth by the mean monthly temperature change in April-August showed that the radial growth of P. sylvestris var. mongolica would present a declining trend accompanied with the warmer and drier regional climate condition.

RBF neural network prediction on weak electrical signals in Aloe vera var. chinensis

NASA Astrophysics Data System (ADS)

Wang, Lanzhou; Zhao, Jiayin; Wang, Miao

2008-10-01

A Gaussian radial base function (RBF) neural network forecast on signals in the Aloe vera var. chinensis by the wavelet soft-threshold denoised as the time series and using the delayed input window chosen at 50, is set up to forecast backward. There was the maximum amplitude at 310.45μV, minimum -75.15μV, average value -2.69μV and <1.5Hz at frequency in Aloe vera var. chinensis respectively. The electrical signal in Aloe vera var. chinensis is a sort of weak, unstable and low frequency signals. A result showed that it is feasible to forecast plant electrical signals for the timing by the RBF. The forecast data can be used as the preferences for the intelligent autocontrol system based on the adaptive characteristic of plants to achieve the energy saving on the agricultural production in the plastic lookum or greenhouse.

Selection and characterization of Euglena anabaena var. minor as a new candidate Euglena species for industrial application.

PubMed

Suzuki, Kengo; Mitra, Sharbanee; Iwata, Osamu; Ishikawa, Takahiro; Kato, Sueo; Yamada, Koji

2015-01-01

Euglena gracilis is a microalgae used as a model organism. Recently, mass cultivation of this species has been achieved for industrial applications. The genus Euglena includes more than 200 species that share common useful features, but the potential industrial applications of other Euglena species have not been evaluated. Thus, we conducted a pilot screening study to identify other species that proliferate at a sufficiently rapid rate to be used for mass cultivation; we found that Euglena anabaena var. minor had a rapid growth rate. In addition, its cells accumulated more than 40% weight of carbohydrate, most of which is considered to be a euglenoid specific type of beta-1-3-glucan, paramylon. Carbohydrate is stored in E. anabaena var. minor cells during normal culture, whereas E. gracilis requires nitrogen limitation to facilitate paramylon accumulation. These results suggest the potential industrial application of E. anabaena var. minor.

[Comparison of Chemical Components of Essential Oil from Ocimum basilicum var. pilosum Extracted by Supercritical CO2 Fluid and Steam Distillation].

PubMed

Wang, Zhao-yu; Zheng, Jia-huan; Shi, Sheng-ying; Luo, Zhi-xiong; Ni, Shun-yu; Lin, Jing-ming

2015-11-01

To compare the chemical components of essential oil prepared by steam distillation extraction (SD) and supercritical CO2 fluid extraction (SFE-CO2) from Ocimum basilicum var. pilosum whole plant. The essential oil of Ocimum basilicum var. pilosum were extracted by SD and SFE-CO2. The chemical components of essential oil were separated and analyzed by gas chromatography-mass spectrometry( GC-MS). Their relative contents were determined by normalization of peak area. 40 and 42 compounds were detected in the essential oil prepared by SD and SFE-CO2 respectively. 25 compounds were common. Thereare significant differences of the chemical components between the Ocimum basilicum var. pilosum essential oil prepared by SD and thatby SFE-CO2. Different methods showed different extraction efficiency with a special compound. It might be a good idea to unite several methods in the modern traditional Chinese medicine industry.

Somatic Embryogenesis in Olive (Olea europaea L. subsp. europaea var. sativa and var. sylvestris).

PubMed

Rugini, Eddo; Silvestri, Cristian

2016-01-01

Protocols for olive somatic embryogenesis from zygotic embryos and mature tissues have been described for both Olea europaea sub. europaea var. sativa and var. sylvestris. Immature zygotic embryos (no more than 75 days old), used after fruit collection or stored at 12-14 °C for 2-3 months, are the best responsive explants and very slightly genotype dependent, and one single protocol can be effective for a wide range of genotypes. On the contrary, protocols for mature zygotic embryos and for mature tissue of cultivars are often genotype specific, so that they may require many adjustments according to genotypes. The use of thidiazuron and cefotaxime seems to be an important trigger for induction phase particularly for tissues derived from cultivars. Up to now, however, the application of this technique for large-scale propagation is hampered also by the low rate of embryo germination; it proves nonetheless very useful for genetic improvement.

The Advantages of Hybrid 4DEnVar in the Context of the Forecast Sensitivity to Initial Conditions

NASA Astrophysics Data System (ADS)

Song, Hyo-Jong; Shin, Seoleun; Ha, Ji-Hyun; Lim, Sujeong

2017-11-01

Hybrid four-dimensional ensemble variational data assimilation (hybrid 4DEnVar) is a prospective successor to three-dimensional variational data assimilation (3DVar) in operational weather prediction centers currently developing a new weather prediction model and those that do not operate adjoint models. In experiments using real observations, hybrid 4DEnVar improved Northern Hemisphere (NH; 20°N-90°N) 500 hPa geopotential height forecasts up to 5 days in a NH summer month compared to 3DVar, with statistical significance. This result is verified against ERA-Interim through a Monte Carlo test. By a regression analysis, the sensitivity of 5 day forecast is associated with the quality of the initial condition. The increased analysis skill for midtropospheric midlatitude temperature and subtropical moisture has the most apparent effect on forecast skill in the NH including a typhoon prediction case. Through attributing the analysis improvements by hybrid 4DEnVar separately to the ensemble background error covariance (BEC), its four-dimensional (4-D) extension, and climatological BEC, it is revealed that the ensemble BEC contributes to the subtropical moisture analysis, whereas the 4-D extension does to the midtropospheric midlatitude temperature. This result implies that hourly wind-mass correlation in 6 h analysis window is required to extract the potential of hybrid 4DEnVar for the midlatitude temperature analysis to the maximum. However, the temporal ensemble correlation, in hourly time scale, between moisture and another variable is invalid so that it could not work for improving the hybrid 4DEnVar analysis.

[Diversity and community structure of endophytic fungi from Taxus chinensis var. mairei].

PubMed

2014-07-01

A total of 628 endophytic fungi were isolated from 480 tissue segments of needles and branches of Taxus chinensis var. mairei. According to morphological characteristics and ITS sequences, they represented 43 taxa in 28 genera, of which 10 Hyphomycetes, 20 Coelomycetes, 12 Ascomycetes and 1 unknown fungus. Phomopsis mali was confirmed as the dominant species. In accordance with relative frequency, Alternaria alternata, Aureobasidium pullulans, Colletotrichum boninense, C. gloeosporioides, Epicoccum nigrum , Fungal sp., Fusarium lateritium, Glomerella cingulata, Magnaporthales sp. , Nigrospora oryzae, Pestalotiopsis maculiformans, P. microspora, Peyronellaea glomerata and Xylaria sp. 1 were more common in T. chinensis var. mairei. T. chinensis var. mairei were severely infected by endophytic fungi. Endophytic fungi were found in 81 percent of plant tissues with a high diversity. Distribution ranges of endophytic fungi were influenced by tissue properties. The colonization rate, richness, diversity of endophytic fungi in needles were obviously lower than in branches, and kinds of endophytic fungi between branches were more similar than those in needles, thus endophytic fungi had tissue preference. In addition, tissue age influenced the community structure of endophytic fungi. The elder branch tissues were, the higher colonization rate, richness, diversity of endophytic fungi were. Systematic studying the diversity and community structure of endophytic fungi in T. chinensis var. mairei and clarifying their distribution regularity in plant tissues would offer basic data and scientific basis for their development and utilization. Discussing the presence of fungal pathogens in healthy plant tissues would be of positive significance for source protection of T. chinensis var. mairei.

Volatile sulphur compounds and pathways of L-methionine catabolism in Williopsis yeasts.

PubMed

Tan, Amelia W J; Lee, Pin-Rou; Seow, Yi-Xin; Ong, Peter K C; Liu, Shao-Quan

2012-08-01

Volatile sulphur compounds (VSCs) are important to the food industry due to their high potency and presence in many foods. This study assessed for the first time VSC production and pathways of L: -methionine catabolism in yeasts from the genus Williopsis with a view to understanding VSC formation and their potential flavour impact. Five strains of Williopsis saturnus (var. saturnus, var. subsufficiens, var. suavolens, var. sargentensis and var. mrakii) were screened for VSC production in a synthetic medium supplemented with L: -methionine. A diverse range of VSCs were produced including dimethyl disulphide, dimethyl trisulphide, 3-(methylthio)-1-propanal (methional), 3-(methylthio)-1-propanol (methionol), 3-(methylthio)-1-propene, 3-(methylthio)-1-propyl acetate, 3-(methylthio)-1-propanoic acid (methionic acid) and ethyl 3-(methylthio)-1-propanoate, though the production of these VSCs varied between yeast strains. W. saturnus var. saturnus NCYC22 was selected for further studies due to its relatively high VSC production. VSC production was characterised step-wise with yeast strain NCYC22 in coconut cream at different L: -methionine concentrations (0.00-0.20%) and under various inorganic sulphate (0.00-0.20%) and nitrogen (ammonia) supplementation (0.00-0.20%), respectively. Optimal VSC production was obtained with 0.1% of L: -methionine, while supplementation of sulphate had no significant effect. Nitrogen supplementation showed a dramatic inhibitory effect on VSC production. Based on the production of VSCs, the study suggests that the Ehrlich pathway of L: -methionine catabolism is operative in W. saturnus yeasts and can be manipulated by adjusting certain nutrient parameters to control VSC production.

The role of the mussel Mytilus spp. in the transmission of ostreid herpesvirus-1 microVar.

PubMed

O' Reilly, A J; Laide, C; Maloy, A; Hutton, S; Bookelaar, B; O' Sullivan, K; Lynch, S A; Culloty, S C

2017-12-21

The Pacific oyster Crassostrea gigas contributes significantly to global aquaculture; however, C. gigas culture has been affected by ostreid herpesvirus-1 (OsHV-1) and variants. The dynamics of how the virus maintains itself at culture sites is unclear and the role of carriers, reservoirs or hosts is unknown. Both wild and cultured mussels Mytilus spp. (Mytilus edulis, Mytilus galloprovincialis and hybrids) are commonly found at C. gigas culture sites. The objective of this study was to investigate if Mytilus spp. can harbour the virus and if viral transmission can occur between mussels and oysters. Mytilus spp. living at oyster trestles, 400-500 m higher up the shore from the trestles and up to 26 km at non-culture sites were screened for OsHV-1 and variants by all the World Organization for Animal Health (OIE) recommended diagnostic methods including polymerase chain reaction (PCR), quantitative PCR (qPCR), histology, in situ hybridization and confirmation using direct sequencing. The particular primers that target OsHV-1 and variants, including OsHV-1 microVar (μVar), were used in the PCR and qPCR. OsHV-1 μVar was detected in wild Mytilus spp. at C. gigas culture sites and more significantly the virus was detected in mussels at non-culture sites. Cohabitation of exposed wild mussels and naïve C. gigas resulted in viral transmission after 14 days, under an elevated temperature regime. These results indicate that mussels can harbour OsHV-1 μVar; however, the impact of OsHV-1 μVar on Mytilus spp. requires further investigation.

[Effect of Astragalus membranaceus var. mongholicus seed extracts on seed germination and seedling growth of different Codonopsis pilosula caltiver].

PubMed

Guo, Feng-Xia; Wu, Zhi-Jiang; Chen, Yuan; Xi, Zhuo-Xia; Zhang, Xiao-Hu; Yao, Li-Rong; Chen, Xiang

2012-11-01

To reveal the allelopathy effect of Astragalus membranaceus var. mongholicus seeds and provide information for the intercrop production. The A. membranaceus. var. mongholicus seeds were soaked in distilled water for different time (12, 24, 36, 48, 60 h) , and then the seed extracts were used to study their effects on the seed germination, seedling growth and development of two Codonopsis pilosula. The A. membranaceus var. mongholicus seeds contained some allelopathy compounds. Their soaked liquid had significantly influence on the seed germination and seedling growth of C. pilosula. The seed germination rate, germination power, germination index and vigor index of two C. pilosula calrivar were improved and then inhabited with soaking time elongation. The extract soaking for 24 h significantly improved the germination traits but the extract for 60 h appeared different degrees of inhibiting vigor. The seed extracts soaking ranging between 12 and 60 h all significantly improved the above plant growth of C. pilosula but significant inhibited their radicle growth in length. And with the soaking time elongation the facilitation effect weakened and the inhibiting effect enhanced, especially more significant in the C. pilosula caltivar (Baitiaodangshen). The A. membranaceus var. mongholicus seeds have allelopathic compounds and the endogenous inhibitor can be extracted when soaked for more than 24 h in water with intact seeds, resulting in improvement of seed germination rate. The C. pilosula could be intercropped in A. membranaceus var. mongholicus field, however, when intercroped it should notice that the intercrop proportion should vary with the caltivar.

Immunomodulatory Activity of Xanthones from Calophyllum teysmannii var. inuphylloide.

PubMed

Gonzalez, M J; Nascimento, M S; Cidade, H M; Pinto, M M; Kijjoa, A; Anantachoke, C; Silva, A M; Herz, W

1999-05-01

Nine xanthones, including 3-(4-hydroxy-3-metnylbutyl)-4,8-dihydroxyxanthone, were isolated from the wood of a Thai collection of CALOPHYLLUM TEYSMANNII Miq. var. INUPHYLLOIDE (King) P. Stephen. Immunomodulatory activities of eight of these have been investigated.

4D Hybrid Ensemble-Variational Data Assimilation for the NCEP GFS: Outer Loops and Variable Transforms

NASA Astrophysics Data System (ADS)

Kleist, D. T.; Ide, K.; Mahajan, R.; Thomas, C.

2014-12-01

The use of hybrid error covariance models has become quite popular for numerical weather prediction (NWP). One such method for incorporating localized covariances from an ensemble within the variational framework utilizes an augmented control variable (EnVar), and has been implemented in the operational NCEP data assimilation system (GSI). By taking the existing 3D EnVar algorithm in GSI and allowing for four-dimensional ensemble perturbations, coupled with the 4DVAR infrastructure already in place, a 4D EnVar capability has been developed. The 4D EnVar algorithm has a few attractive qualities relative to 4DVAR, including the lack of need for tangent-linear and adjoint model as well as reduced computational cost. Preliminary results using real observations have been encouraging, showing forecast improvements nearly as large as were found in moving from 3DVAR to hybrid 3D EnVar. 4D EnVar is the method of choice for the next generation assimilation system for use with the operational NCEP global model, the global forecast system (GFS). The use of an outer-loop has long been the method of choice for 4DVar data assimilation to help address nonlinearity. An outer loop involves the re-running of the (deterministic) background forecast from the updated initial condition at the beginning of the assimilation window, and proceeding with another inner loop minimization. Within 4D EnVar, a similar procedure can be adopted since the solver evaluates a 4D analysis increment throughout the window, consistent with the valid times of the 4D ensemble perturbations. In this procedure, the ensemble perturbations are kept fixed and centered about the updated background state. This is analogous to the quasi-outer loop idea developed for the EnKF. Here, we present results for both toy model and real NWP systems demonstrating the impact from incorporating outer loops to address nonlinearity within the 4D EnVar context. The appropriate amplitudes for observation and background error covariances in subsequent outer loops will be explored. Lastly, variable transformations on the ensemble perturbations will be utilized to help address issues of non-Gaussianity. This may be particularly important for variables that clearly have non-Gaussian error characteristics such as water vapor and cloud condensate.

Variation in phenology and monoterpene patterns of defoliated and nondefoliated Douglas-fir (Pseudotsuga menziesii var. glauca).

Treesearch

Rose-Marie Muzika; Judith Engle; Catherine Parks; Boyd Wickman

1993-01-01

Foliage was collected from paired Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) trees characterized as either "resistant" or "susceptible" western spruce budworm (Choristoneura occidentalis Freeman (Lepidoptera: Tortricidae) attack. Resistant trees produced more...

[A new secoiridoid from the flowers of Jasminum officinale L. var. grandiflorum].

PubMed

Zhao, Gui-Qin; Yin, Zhi-Feng; Dong, Jun-Xing

2008-05-01

To study the chemical constituents of the flowers of Jasminum officinale L. var. grandiflorum, the compounds were isolated and purified by HPLC, recrystallization and chromatography on silica gel and Sephadex LH-20 column. Their structures were elucidated on the basis of physicochemical properties and spectral analysis. Six secoiridoids were identified as jasgranoside (I), jaspolyoside (II), 8-epi-kingiside (III), 10-hydroxy-oleuropein (IV), 10-hydroxy-ligstroside (V), oleoside-7, 11-dimethyl ester (VI). Compound I is a new compound. Compounds II, III, IV, V and VI were isolated from Jasminum officinale L. var. grandiflorum for the first time.

[Iridoid glycosides from buds of Jasminum officinale L. var. grandiflorum].

PubMed

Zhao, Gui-qin; Yin, Zhi-feng; Liu, Yu-cui; Li, Hong-bo

2011-10-01

The study on the buds of Jasminum officinale L. var. grandiflorum was carried out to look for anti-HBV constituents. The isolation and purification were performed by HPLC and chromatography on silica gel, polyamide and Sephadex LH-20 column. The structures were elucidated on the basis of physicochemical properties and spectral analysis. Six iridoid glycosides were identified as jasgranoside B (1), 6-O-methy-catalpol (2), deacetyl asperulosidic acid (3), aucubin (4), 8-dehydroxy shanzhiside (5), and loganin (6). Jasgranoside B (1) is a new compound. Compounds 2-6 were isolated from Jasminum officinale L. var. grandiflorum for the first time.

[Systematics and genegeography of Juniperus communis inferred from isoenzyme data].

PubMed

Khantemirova, E V; Berkutenko, A N; Semerikov, V L

2012-09-01

Using isoenzyme analysis, 35 populations of Juniperus communis L. from various parts of the Russian species range and by one population from Sweden and Alaska were studied. The total sample size was 1200 plants. As a result, the existence ofJ. communis var. oblonga in North Caucasus and J. communis var. depressa in North America was confirmed, but genetic differences between J. communis var. communis and J. communis var. saxatilis were not detected in the main part of the Russian species range (European part of Russia, Ural, Siberia). These populations proved to be genetically uniform with the same predominant allelic frequencies, which may evidence recent settling of this species from one of Central or East European refugium. J. communis var. saxatilis from northeastern Russia inhabiting the region behind Verkhoyansk mountain and Russian Far East showed considerable differentiation in frequencies of alleles at three loci and geographical subdivision. These populations also exhibit high intrapopulation variation. This can be connected with the refugium in this territory. The origin of this group is probably connected with migrations from Central Asia (Tibet) in the direction to northeastern Russia along mountains connecting Central and North Asia. It is also assumed that migrations of this species previously proceeded across the Beringian land bridge.

CP violation experiment at Fermilab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsiung, Yee B.

1990-07-01

The E731 experiment at Fermilab has searched for direct'' CP violation in K{sup 0} {yields} {pi}{pi}, which is parametrized by {var epsilon}{prime}/{var epsilon}. For the first time, in 20% of the data set, all four modes of the K{sub L,S} {yields} {pi}{sup +}{pi}{sup {minus}} ({pi}{sup 0}{pi}{sup 0}) were collected simultaneously, providing a great check on the systematic uncertainty. The result is Re({var epsilon}{prime}/{var epsilon}) = {minus}0.0004 {plus minus} 0.0014 (stat) {plus minus} 0.0006(syst), which provides no evidence for direct'' CP violation. The CPT symmetry has also been tested by measuring the phase difference {Delta}{phi} = {phi}{sub 00} {minus} {phi}{sub {plusmore » minus}} between the two CP violating parameters {eta}{sub 00} and {eta}{sub {plus minus}}. We fine {Delta}{phi} = {minus}0.3{degrees} {plus minus} 2.4{degree}(stat) {plus minus} 1.2{degree}(syst). Using this together with the world average {phi}{sub {plus minus}}, we fine that the phase of the K{sup 0}-{bar K}{sup 0} mixing parameter {var epsilon} is 44.5{degree} {plus minus} 1.5{degree}. Both of these results agree well with the predictions of CPT symmetry. 17 refs., 10 figs.« less

Comparative Proteomic Analysis of Differential Responses of Pinus massoniana and Taxus wallichiana var. mairei to Simulated Acid Rain

PubMed Central

Hu, Wen-Jun; Chen, Juan; Liu, Ting-Wu; Simon, Martin; Wang, Wen-Hua; Chen, Juan; Wu, Fei-Hua; Liu, Xiang; Shen, Zhi-Jun; Zheng, Hai-Lei

2014-01-01

Acid rain (AR), a serious environmental issue, severely affects plant growth and development. As the gymnosperms of conifer woody plants, Pinus massoniana (AR-sensitive) and Taxus wallichiana var. mairei (AR-resistant) are widely distributed in southern China. Under AR stress, significant necrosis and collapsed lesions were found in P. massoniana needles with remarkable yellowing and wilting tips, whereas T. wallichiana var. mairei did not exhibit chlorosis and visible damage. Due to the activation of a large number of stress-related genes and the synthesis of various functional proteins to counteract AR stress, it is important to study the differences in AR-tolerance mechanisms by comparative proteomic analysis of tolerant and sensitive species. This study revealed a total of 65 and 26 differentially expressed proteins that were identified in P. massoniana and T. wallichiana var. mairei, respectively. Among them, proteins involved in metabolism, photosynthesis, signal transduction and transcription were drastically down-regulated in P. massoniana, whereas most of the proteins participating in metabolism, cell structure, photosynthesis and transcription were increased in T. wallichiana var. mairei. These results suggest the distinct patterns of protein expression in the two woody species in response to AR, allowing a deeper understanding of diversity on AR tolerance in forest tree species. PMID:24625662

20 MHz Forward-imaging Single-element Beam Steering with an Internal Rotating Variable-Angle Reflecting Surface: Wire phantom and Ex vivo pilot study

PubMed Central

Raphael, David T.; Li, Xiang; Park, Jinhyoung; Chen, Ruimin; Chabok, Hamid; Barukh, Arthur; Zhou, Qifa; Elgazery, Mahmoud; Shung, K. Kirk

2012-01-01

Feasibility is demonstrated for a forward-imaging beam steering system involving a single-element 20 MHz angled-face acoustic transducer combined with an internal rotating variable-angle reflecting surface (VARS). Rotation of the VARS structure, for a fixed position of the transducer, generates a 2-D angular sector scan. If these VARS revolutions were to be accompanied by successive rotations of the single-element transducer, 3-D imaging would be achieved. In the design of this device, a single-element 20 MHz PMN-PT press-focused angled-face transducer is focused on the circle of midpoints of a micro-machined VARS within the distal end of an endoscope. The 2-D imaging system was tested in water bath experiments with phantom wire structures at a depth of 10 mm, and exhibited an axial resolution of 66 μm and a lateral resolution of 520 μm. Chirp coded excitation was used to enhance the signal-to-noise ratio, and to increase the depth of penetration. Images of an ex vivo cow eye were obtained. This VARS-based approach offers a novel forward-looking beam-steering method, which could be useful in intra-cavity imaging. PMID:23122968

20 MHz forward-imaging single-element beam steering with an internal rotating variable-angle reflecting surface: Wire phantom and ex vivo pilot study.

PubMed

Raphael, David T; Li, Xiang; Park, Jinhyoung; Chen, Ruimin; Chabok, Hamid; Barukh, Arthur; Zhou, Qifa; Elgazery, Mahmoud; Shung, K Kirk

2013-02-01

Feasibility is demonstrated for a forward-imaging beam steering system involving a single-element 20MHz angled-face acoustic transducer combined with an internal rotating variable-angle reflecting surface (VARS). Rotation of the VARS structure, for a fixed position of the transducer, generates a 2-D angular sector scan. If these VARS revolutions were to be accompanied by successive rotations of the single-element transducer, 3-D imaging would be achieved. In the design of this device, a single-element 20MHz PMN-PT press-focused angled-face transducer is focused on the circle of midpoints of a micro-machined VARS within the distal end of an endoscope. The 2-D imaging system was tested in water bath experiments with phantom wire structures at a depth of 10mm, and exhibited an axial resolution of 66μm and a lateral resolution of 520μm. Chirp coded excitation was used to enhance the signal-to-noise ratio, and to increase the depth of penetration. Images of an ex vivo cow eye were obtained. This VARS-based approach offers a novel forward-looking beam-steering method, which could be useful in intra-cavity imaging. Copyright © 2012 Elsevier B.V. All rights reserved.

Infective capacity of Cryptococcus neoformans and Cryptococcus gattii in a human astrocytoma cell line.

PubMed

Olave, M C; Vargas-Zambrano, J C; Celis, A M; Castañeda, E; González, J M

2017-07-01

Pathogenesis of cryptococcosis in the central nervous system (CNS) is a topic of ongoing research, including the mechanisms by which this fungus invades and infects the brain. Astrocytes, the most common CNS cells, play a fundamental role in the local immune response. Astrocytes might participate in cryptococcosis either as a host or by responding to fungal antigens. To determine the infectivity of Cryptococcus neoformans var. grubii and Cryptococcus gattii in a human astrocytoma cell line and the induction of major histocompatibility complex (MHC) molecules. A glioblastoma cell line was infected with C. neoformans var. grubii and C. gattii blastoconidia labelled with FUN-1 fluorescent stain. The percentage of infection and expression of HLA class I and II molecules were determined by flow cytometry. The interactions between the fungi and cells were observed by fluorescence microscopy. There was no difference between C. neoformans var. grubii and C. gattii in the percentage infection, but C. neoformans var. grubii induced higher expression of HLA class II than C. gattii. More blastoconidia were recovered from C. neoformans-infected cells than from C. gattii infected cells. Cryptococcus neoformans var. grubii may have different virulence mechanisms that allow its survival in human glia-derived cells. © 2017 Blackwell Verlag GmbH.

Data Assimilation of Lightning using 1D+3D/4D WRF Var Assimilation Schemes with Non-Linear Observation Operators

NASA Astrophysics Data System (ADS)

Navon, M. I.; Stefanescu, R.; Fuelberg, H. E.; Marchand, M.

2012-12-01

NASA's launch of the GOES-R Lightning Mapper (GLM) in 2015 will provide continuous, full disc, high resolution total lightning (IC + CG) data. The data will be available at a horizontal resolution of approximately 9 km. Compared to other types of data, the assimilation of lightning data into operational numerical models has received relatively little attention. Previous efforts of lightning assimilation mostly have employed nudging. This paper will describe the implementation of 1D+3D/4D Var assimilation schemes of existing ground-based WTLN (Worldwide Total Lightning Network) lightning observations using non-linear observation operators in the incremental WRFDA system. To mimic the expected output of GLM, the WTLN data were used to generate lightning super-observations characterized by flash rates/81 km2/20 min. A major difficulty associated with variational approaches is the complexity of the observation operator that defines the model equivalent of lightning. We use Convective Available Potential Energy (CAPE) as a proxy between lightning data and model variables. This operator is highly nonlinear. Marecal and Mahfouf (2003) have shown that nonlinearities can prevent direct assimilation of rainfall rates in the ECMWF 4D-VAR (using the incremental formulation proposed by Courtier et al. (1994)) from being successful. Using data from the 2011 Tuscaloosa, AL tornado outbreak, we have proved that the direct assimilation of lightning data into the WRF 3D/4D - Var systems is limited due to this incremental approach. Severe threshold limits must be imposed on the innovation vectors to obtain an improved analysis. We have implemented 1D+3D/4D Var schemes to assimilate lightning observations into the WRF model. Their use avoids innovation vector constrains from preventing the inclusion of a greater number of lightning observations Their use also minimizes the problem that nonlinearities in the moist convective scheme can introduce discontinuities in the cost function between inner and outer loops of the incremental 3-D/4-D VAR minimization. The first part of this paper will describe the methodology and performance analysis of the 1D-Var retrieval scheme that adjusts the WRF temperature profiles closer to an observed value as in Mahfouf et al. (2005). The second part will show the positive impact of these 1D-Var pseudo - temperature observations on both model 3D/4D-Var WRF analyses and short-range forecasts for three cases - the Tuscaloosa tornado outbreak (April 27, 2011) with intense but localized lightning, a second severe storm outbreak with more widespread but less intense lightning (June 27, 2011), and a northeaster containing much less lightning.

A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria.

PubMed

Yang, Yunpeng; Zhang, Lu; Huang, He; Yang, Chen; Yang, Sheng; Gu, Yang; Jiang, Weihong

2017-01-24

Catabolite control protein A (CcpA) is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR) and carbon catabolite activation (CCA), two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt) consensus site that is called a catabolite response element (cre) within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named cre var , has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA). It was found that the length of the intervening spacer of cre var can affect CcpA binding affinity, and moreover, the core palindromic sequence of cre var is the key structure for regulation. Such a variable architecture of cre var shows potential importance for CcpA's diverse and fine regulation. A total of 103 potential cre var sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs), and 30 sites were confirmed to be bound by CcpA. These 30 cre var sites are associated with 27 genes involved in many important pathways. Also of significance, the cre var sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria. In Gram-positive bacteria, the global regulator CcpA controls a large number of important physiological and metabolic processes. Although a typical consensus CcpA-binding site, cre, has been identified, it remains poorly explored for the diversity of CcpA-mediated catabolite regulation. Here, we discovered a novel flexible CcpA-binding site architecture (cre var ) that is highly variable in both length and base composition but follows certain principles, providing new insights into how CcpA can differentially recognize a variety of target genes to form a complicated regulatory network. A comprehensive search further revealed the wide distribution of cre var sites in Gram-positive bacteria, indicating it may have a universal function. This finding is the first to characterize such a highly flexible transcription factor-binding site architecture, which would be valuable for deeper understanding of CcpA-mediated global catabolite regulation in bacteria. Copyright © 2017 Yang et al.

Tylopilus aquarius, comb. et stat. nov., and its new variety from Brazil

Treesearch

Anderlechi Barbosa-Silva; Clark L. Ovrebo; Beatriz Ortiz-Santana; Mariana C.A. Sá; Marcelo A. Sulzbacher; Melanie Roy; Felipe. Wartchow

2017-01-01

We propose the new species and new combination, Tylopilus aquarius var. aquarius, by elevating T. potamogeton v. aquarius to species level. We also describe a new variety, T. aquarius var. megistus, from the Atlantic Forest states Paraiba and...

Grafting for Management of Southern Root-knot Nematode, Meloidogyne Incognita, in Watermelon

USDA-ARS?s Scientific Manuscript database

Four bottlegourd (Lagenaria siceraria) cultivars, one squash (Cucurbita moschata x C. maxima) hybrid, four wild watermelon (Citrullus lanatus var. citroides) germplasm lines, and one commercial wild watermelon (C. lanatus var. citroides) cultivar were evaluated as rootstocks for cultivated watermelo...

Antibacterial effects of ellagitannins from Acalypha wilkesiana var. macafeana hort.: surface morphology analysis with environmental scanning electron microscopy and synergy with antibiotics.

PubMed

Din, Wardah Mustafa; Jin, Khoo Teng; Ramli, Ramliza; Khaithir, Tzar Mohd Nizam; Wiart, Christophe

2013-09-01

The present study served to gain further insight into the bactericidal effects of ellagitannins from Acalypha wilkesiana var. macafeana hort. against pathogenic bacteria. Ellagitannins from the aerial parts of A. wilkesiana var. macafeana hort. (EAW) inhibited the growth of Bacillus cereus (ATCC 11778), Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 11632) and Methicillin-resistant Staphylococcus aureus (MRSA) clinical strain with inhibition zones equal to 11.01 ± 1.53 mm, 16.63 ± 0.11 mm, 11.40 ± 1.10 mm and 8.22 ± 0.19 mm, respectively. The minimal inhibition concentration and the minimal bactericidal concentration of ellagitannins from A. wilkesiana var. macafeana hort. (EAW) against MRSA were 750 µg/mL and 3000 µg/mL, respectively. We then examined the synergistic effect of EAW with three antibiotics, i.e. ampicillin, streptomycin and tetracycline, via the checkerboard assay and time-kill assay and observed that EAW is synergistic with ampicillin against S. aureus (ATCC 11632). Environmental electron scanning microscopy analysis showed cell lysis against S. aureus (ATCC 11632) upon treatment with the ellagitannin fraction. The ellagitannin fraction from A. wilkesiana var. macafeana hort. is bactericidal against gram-positive bacteria tested and works synergistically with ampicillin against S. aureus. Morphology analysis of the cell suggests that the bactericidal property of the ellagitannin fraction mechanism involves lysis of the cell wall. In summary, our studies demonstrate that A. wilkesiana var. macafeana hort. produces bactericidal ellagitannins of clinical and/or cosmetological value. Copyright © 2012 John Wiley & Sons, Ltd.

Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples.

PubMed

Scantlebury, C E; Pinchbeck, G L; Loughnane, P; Aklilu, N; Ashine, T; Stringer, A P; Gordon, L; Marshall, M; Christley, R M; McCarthy, A J

2016-12-01

Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum This molecular diagnostic method now permits investigation of the epidemiology of EZL. Copyright © 2016 Scantlebury et al.

Occasional hybridization between a native and invasive Senecio species in Australia is unlikely to contribute to invasive success.

PubMed

Dormontt, Eleanor E; Prentis, Peter J; Gardner, Michael G; Lowe, Andrew J

2017-01-01

Hybridization between native and invasive species can facilitate introgression of native genes that increase invasive potential by providing exotic species with pre-adapted genes suitable for new environments. In this study we assessed the outcome of hybridization between native Senecio pinnatifolius var. pinnatifolius A.Rich. (dune ecotype) and invasive Senecio madagascariensis Poir. to investigate the potential for introgression of adaptive genes to have facilitated S. madagascariensis spread in Australia. We used amplified fragment length polymorphisms (141 loci) and nuclear microsatellites (2 loci) to genotype a total of 118 adults and 223 seeds from S. pinnatifolius var. pinnatifolius and S. madagascariensis at one allopatric and two shared sites. We used model based clustering and assignment methods to establish whether hybrid seed set and mature hybrids occur in the field. We detected no adult hybrids in any population. Low incidence of hybrid seed set was found at Lennox Head where the contact zone overlapped for 20 m (6% and 22% of total seeds sampled for S. pinnatifolius var. pinnatifolius and S. madagascariensis respectively). One hybrid seed was detected at Ballina where a gap of approximately 150 m was present between species (2% of total seeds sampled for S. madagascariensis ). We found no evidence of adult hybrid plants at two shared sites. Hybrid seed set from both species was identified at low levels. Based on these findings we conclude that introgression of adaptive genes from S. pinnatifolius var. pinnatifolius is unlikely to have facilitated S. madagascariensis invasions in Australia. Revisitation of one site after two years could find no remaining S. pinnatifolius var.  pinnatifolius , suggesting that contact zones between these species are dynamic and that S. pinnatifolius var.  pinnatifolius may be at risk of displacement by S. madagascariensis in coastal areas.

Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples

PubMed Central

Pinchbeck, G. L.; Loughnane, P.; Aklilu, N.; Ashine, T.; Stringer, A. P.; Gordon, L.; Marshall, M.; Christley, R. M.

2016-01-01

Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum. This molecular diagnostic method now permits investigation of the epidemiology of EZL. PMID:27707938

Inverse Regional Modeling with Adjoint-Free Technique

NASA Astrophysics Data System (ADS)

Yaremchuk, M.; Martin, P.; Panteleev, G.; Beattie, C.

2016-02-01

The ongoing parallelization trend in computer technologies facilitates the use ensemble methods in geophysical data assimilation. Of particular interest are ensemble techniques which do not require the development of tangent linear numerical models and their adjoints for optimization. These ``adjoint-free'' methods minimize the cost function within the sequence of subspaces spanned by a carefully chosen sets perturbations of the control variables. In this presentation, an adjoint-free variational technique (a4dVar) is demonstrated in an application estimating initial conditions of two numerical models: the Navy Coastal Ocean Model (NCOM), and the surface wave model (WAM). With the NCOM, performance of both adjoint and adjoint-free 4dVar data assimilation techniques is compared in application to the hydrographic surveys and velocity observations collected in the Adriatic Sea in 2006. Numerical experiments have shown that a4dVar is capable of providing forecast skill similar to that of conventional 4dVar at comparable computational expense while being less susceptible to excitation of ageostrophic modes that are not supported by observations. Adjoint-free technique constrained by the WAM model is tested in a series of data assimilation experiments with synthetic observations in the southern Chukchi Sea. The types of considered observations are directional spectra estimated from point measurements by stationary buoys, significant wave height (SWH) observations by coastal high-frequency radars and along-track SWH observations by satellite altimeters. The a4dVar forecast skill is shown to be 30-40% better than the skill of the sequential assimilaiton method based on optimal interpolation which is currently used in operations. Prospects of further development of the a4dVar methods in regional applications are discussed.

Development of the WRF-CO2 4D-Var assimilation system v1.0

NASA Astrophysics Data System (ADS)

Zheng, Tao; French, Nancy H. F.; Baxter, Martin

2018-05-01

Regional atmospheric CO2 inversions commonly use Lagrangian particle trajectory model simulations to calculate the required influence function, which quantifies the sensitivity of a receptor to flux sources. In this paper, an adjoint-based four-dimensional variational (4D-Var) assimilation system, WRF-CO2 4D-Var, is developed to provide an alternative approach. This system is developed based on the Weather Research and Forecasting (WRF) modeling system, including the system coupled to chemistry (WRF-Chem), with tangent linear and adjoint codes (WRFPLUS), and with data assimilation (WRFDA), all in version 3.6. In WRF-CO2 4D-Var, CO2 is modeled as a tracer and its feedback to meteorology is ignored. This configuration allows most WRF physical parameterizations to be used in the assimilation system without incurring a large amount of code development. WRF-CO2 4D-Var solves for the optimized CO2 flux scaling factors in a Bayesian framework. Two variational optimization schemes are implemented for the system: the first uses the limited memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) minimization algorithm (L-BFGS-B) and the second uses the Lanczos conjugate gradient (CG) in an incremental approach. WRFPLUS forward, tangent linear, and adjoint models are modified to include the physical and dynamical processes involved in the atmospheric transport of CO2. The system is tested by simulations over a domain covering the continental United States at 48 km × 48 km grid spacing. The accuracy of the tangent linear and adjoint models is assessed by comparing against finite difference sensitivity. The system's effectiveness for CO2 inverse modeling is tested using pseudo-observation data. The results of the sensitivity and inverse modeling tests demonstrate the potential usefulness of WRF-CO2 4D-Var for regional CO2 inversions.

Loss of function mutations in VARS encoding cytoplasmic valyl-tRNA synthetase cause microcephaly, seizures, and progressive cerebral atrophy.

PubMed

Stephen, Joshi; Nampoothiri, Sheela; Banerjee, Aditi; Tolman, Nathanial J; Penninger, Josef Martin; Elling, Ullrich; Agu, Chukwuma A; Burke, John D; Devadathan, Kalpana; Kannan, Rajesh; Huang, Yan; Steinbach, Peter J; Martinis, Susan A; Gahl, William A; Malicdan, May Christine V

2018-04-01

Progressive microcephaly and neurodegeneration are genetically heterogenous conditions, largely associated with genes that are essential for the survival of neurons. In this study, we interrogate the genetic etiology of two siblings from a non-consanguineous family with severe early onset of neurological manifestations. Whole exome sequencing identified novel compound heterozygous mutations in VARS that segregated with the proband: a missense (c.3192G>A; p.Met1064Ile) and a splice site mutation (c.1577-2A>G). The VARS gene encodes cytoplasmic valyl-tRNA synthetase (ValRS), an enzyme that is essential during eukaryotic translation. cDNA analysis on patient derived fibroblasts revealed that the splice site acceptor variant allele led to nonsense mediated decay, thus resulting in a null allele. Three-dimensional modeling of ValRS predicts that the missense mutation lies in a highly conserved region and could alter side chain packing, thus affecting tRNA binding or destabilizing the interface between the catalytic and tRNA binding domains. Further quantitation of the expression of VARS showed remarkably reduced levels of mRNA and protein in skin derived fibroblasts. Aminoacylation experiments on patient derived cells showed markedly reduced enzyme activity of ValRS suggesting the mutations to be loss of function. Bi-allelic mutations in cytoplasmic amino acyl tRNA synthetases are well-known for their role in neurodegenerative disorders, yet human disorders associated with VARS mutations have not yet been clinically well characterized. Our study describes the phenotype associated with recessive VARS mutations and further functional delineation of the pathogenicity of novel variants identified, which widens the clinical and genetic spectrum of patients with progressive microcephaly.

Varenicline Reduces Alcohol Intake During Repeated Cycles of Alcohol Reaccess Following Deprivation in Alcohol-Preferring (P) Rats.

PubMed

Froehlich, Janice C; Nicholson, Emily R; Dilley, Julian E; Filosa, Nick J; Rademacher, Logan C; Smith, Teal N

2017-08-01

Most alcoholics experience periods of voluntary alcohol abstinence or imposed alcohol deprivation followed by a return to alcohol drinking. This study examined whether varenicline (VAR) reduces alcohol intake during a return to drinking after periods of alcohol deprivation in rats selectively bred for high alcohol drinking (the alcohol preferring or "P" rats). Alcohol-experienced P rats were given 24-hour access to food and water and scheduled access to alcohol (15% and 30% v/v) for 2 h/d. After 4 weeks, rats were deprived of alcohol for 2 weeks, followed by reaccess to alcohol for 2 weeks, and this pattern was repeated for a total of 3 cycles. Rats were fed either vehicle (VEH) or VAR, in doses of 0.5, 1.0, or 2.0 mg/kg BW, at 1 hour prior to onset of the daily alcohol reaccess period for the first 5 days of each of the 3 alcohol reaccess cycles. Low-dose VAR (0.5 mg/kg BW) reduced alcohol intake during the 5 days of drug treatment in alcohol reaccess cycles 1 and 2. Higher doses of VAR (1.0 mg/kg BW and 2.0 mg/kg BW) reduced alcohol intake during the 5 days of treatment in all 3 alcohol reaccess cycles. The decrease in alcohol intake disappeared with termination of VAR treatment in all alcohol reaccess cycles. The results demonstrate that VAR decreases alcohol intake during multiple cycles of alcohol reaccess following alcohol deprivation in rats and suggests that it may prevent a return to heavy alcohol drinking during a lapse from alcohol abstinence in humans with alcohol use disorder. Copyright © 2017 by the Research Society on Alcoholism.

Antioxidant properties and global metabolite screening of the probiotic yeast Saccharomyces cerevisiae var. boulardii.

PubMed

Datta, Suprama; Timson, David J; Annapure, Uday S

2017-07-01

Saccharomyces cerevisiae var. boulardii is the only yeast species with probiotic properties. It is considered to have therapeutic significance in gastrointestinal disorders. In the present study, a comparative physiological study between this yeast and Saccharomyces cerevisiae (BY4742) was performed by evaluating two prominent traits of probiotic species, responses to different stress conditions and antioxidant capacity. A global metabolite profile was also developed aiming to identify which therapeutically important secondary metabolites are produced. Saccharomyces cerevisiae var. boulardii showed no significant difference in growth patterns but greater stress tolerance compared to S. cerevisiae. It also demonstrated a six- to 10-fold greater antioxidant potential (judged by the 1,1-diphenyl-2-picrylhydrazyl assay), with a 70-fold higher total phenolic content and a 20-fold higher total flavonoid content in the extracellular fraction. These features were clearly differentiated by principal component analysis and further indicated by metabolite profiling. The extracellular fraction of the S. cerevisiae var. boulardii cultures was found to be rich in polyphenolic metabolites: vanillic acid, cinnamic acid, phenyl ethyl alcohol (rose oil), erythromycin, amphetamine and vitamin B 6 , which results in the antioxidant capacity of this strain. The present study presents a new perspective for differentiating the two genetically related strains of yeast, S. cerevisiae and S. cerevisiae var. boulardii by assessing their metabolome fingerprints. In addition to the correlation of the phenotypic properties with the secretory metabolites of these two yeasts, the present study also emphasizes the potential to exploit S. cerevisiae var. boulardii in the industrial production of these metabolites. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Mechanisms Governing Interannual Variability of Stratosphere-to-Troposphere Ozone Transport

NASA Astrophysics Data System (ADS)

Albers, John R.; Perlwitz, Judith; Butler, Amy H.; Birner, Thomas; Kiladis, George N.; Lawrence, Zachary D.; Manney, Gloria L.; Langford, Andrew O.; Dias, Juliana

2018-01-01

Factors governing the strength and frequency of stratospheric ozone intrusions over the Pacific-North American region are considered for their role in modulating tropospheric ozone on interannual timescales. The strength of the association between two major modes of climate variability—the El Niño-Southern Oscillation (ENSO) and the Northern Annular Mode (NAM)—and the amount of ozone contained in stratospheric intrusions are tested in the context of two mechanisms that modulate stratosphere-to-troposphere transport (STT) of ozone: (StratVarO3) the winter season buildup of ozone abundances in the lowermost stratosphere (LMS) and (JetVar) Pacific jet and wave breaking variability during spring. In essence, StratVarO3 corresponds to variability in the amount of ozone per intrusion, while JetVar governs the frequency of intrusions. The resulting analysis, based on two different reanalysis products, suggests that StratVarO3 is more important than JetVar for driving interannual variations in STT of ozone over the Pacific-North American region. In particular, the abundance of ozone in the LMS at the end of winter is shown to be a robust indicator of the amount of ozone that will be contained in stratospheric intrusions during the ensuing spring. Additionally, it is shown that the overall strength of the winter season stratospheric NAM is a useful predictor of ozone intrusion strength. The results also suggest a nuanced relationship between the phase of ENSO and STT of ozone. While ENSO-related jet variability is associated with STT variability, it is wave breaking frequency rather than typical ENSO teleconnection patterns that is responsible for the ENSO-STT relationship.

Harnessing Omics Big Data in Nine Vertebrate Species by Genome-Wide Prioritization of Sequence Variants with the Highest Predicted Deleterious Effect on Protein Function.

PubMed

Rozman, Vita; Kunej, Tanja

2018-05-10

Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish. The analysis was conducted using the Ensembl/BioMart tool. Genes comprising pDelVars in the highest number of examined species were identified using a Python script. Multiple genomic alignments of the selected genes were built to identify interspecies orthologous potentially deleterious variants, which we defined as the "ortho-pDelVars." Genome-wide prioritization revealed that in humans, 0.12% of the known variants are predicted to be deleterious. In seven out of nine examined vertebrate species, the genes encoding the multiple PDZ domain crumbs cell polarity complex component (MPDZ) and the transforming acidic coiled-coil containing protein 2 (TACC2) comprise pDelVars. Five interspecies ortho-pDelVars were identified in three genes. These findings offer new ways to harness genomics big data by facilitating the identification of functional polymorphisms in humans and animal models and thus provide a future basis for optimization of protocols for whole genome prioritization of pDelVars and screening of orthologous sequence variants. The approach presented here can inform various postgenomic applications such as personalized medicine and multiomics study of health interventions (iatromics).

Growth, allometry and shade tolerance of understory saplings of four subalpine conifers in central Japan.

PubMed

Takahashi, Koichi; Obata, Yoshiko

2014-03-01

The conifers Abies veitchii, A. mariesii, Picea jezoensis var. hondoensis, Tsuga diversifolia dominate in subalpine forests in central Japan. We expected that species differences in shade tolerance and in aboveground and belowground architecture are important for their coexistence. We examined net production and carbon allocation of understory saplings. Although the four species allocated similar amounts of biomass to roots at a given trunk height, the root-zone area of T. diversifolia was greater than that of the three other species. T. diversifolia often dominates shallow soil sites, such as ridge and rocky slopes, and, therefore, a wide spread of lateral roots would be an adaptation to such edaphic conditions. Crown width and leaf and branch mass were greatest for T. diversifolia and A. mariesii, followed in order by A. veitchii and P. jezoensis var. hondoensis. Although leaf mass of P. jezoensis var. hondoensis was lowest among the four species, species differences were not found in the net production per sapling because net production per leaf mass was greatest for P. jezoensis var. hondoensis. The leaf lifespan was longer in the order A. mariesii, T. diversifolia, P. jezoensis var. hondoensis and A. veitchii. The minimum rate of net production per leaf mass required to maintain the current sapling leaf mass (MRNP(LM)) was lowest in A. mariesii and T. diversifolia, and increased in the order of A. veitchii and P. jezoensis var. hondoensis. A. mariesii and T. diversifolia may survive in shade conditions by a lower MRNP(LM) than the two other species. Therefore, species differences in aboveground and belowground architecture and MRNPLM reflected their shade tolerance and regeneration strategies, which contribute to their coexistence.

Rapid Identification of Cryptococcus neoformans var. grubii, C. neoformans var. neoformans, and C. gattii by Use of Rapid Biochemical Tests, Differential Media, and DNA Sequencing ▿

PubMed Central

McTaggart, Lisa; Richardson, Susan E.; Seah, Christine; Hoang, Linda; Fothergill, Annette; Zhang, Sean X.

2011-01-01

Rapid identification of Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. neoformans, and Cryptococcus gattii is imperative for facilitation of prompt treatment of cryptococcosis and for understanding the epidemiology of the disease. Our purpose was to evaluate a test algorithm incorporating commercial rapid biochemical tests, differential media, and DNA sequence analysis that will allow us to differentiate these taxa rapidly and accurately. We assessed 147 type, reference, and clinical isolates, including 6 other Cryptococcus spp. (10 isolates) and 14 other yeast species (24 isolates), using a 4-hour urea broth test (Remel), a 24-hour urea broth test (Becton Dickinson), a 4-hour caffeic acid disk test (Hardy Diagnostics and Remel), 40- to 44-hour growth assessment on l-canavanine glycine bromothymol blue (CGB) agar, and intergenic spacer (IGS) sequence analysis. All 123 Cryptococcus isolates hydrolyzed urea, along with 7 isolates of Rhodotorula and Trichosporon. Eighty-five of 86 C. neoformans (99%) and 26 of 27 C. gattii (96%) isolates had positive caffeic acid results, unlike the other cryptococci (0/10) and yeast species (0/24). Together, these two tests positively identified virtually all C. neoformans/C. gattii isolates (98%) within 4 h. CGB agar or IGS sequencing further differentiated these isolates within 48 h. On CGB, 25 of 27 (93%) C. gattii strains induced a blue color change, in contrast to 0 of 86 C. neoformans isolates. Neighbor-joining cluster analysis of IGS sequences differentiated C. neoformans var. grubii, C. neoformans var. neoformans, and C. gattii. Based on these results, we describe a rapid identification algorithm for use in a microbiology laboratory to distinguish clinically relevant Cryptococcus spp. PMID:21593254

Rapid identification of Cryptococcus neoformans var. grubii, C. neoformans var. neoformans, and C. gattii by use of rapid biochemical tests, differential media, and DNA sequencing.

PubMed

McTaggart, Lisa; Richardson, Susan E; Seah, Christine; Hoang, Linda; Fothergill, Annette; Zhang, Sean X

2011-07-01

Rapid identification of Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. neoformans, and Cryptococcus gattii is imperative for facilitation of prompt treatment of cryptococcosis and for understanding the epidemiology of the disease. Our purpose was to evaluate a test algorithm incorporating commercial rapid biochemical tests, differential media, and DNA sequence analysis that will allow us to differentiate these taxa rapidly and accurately. We assessed 147 type, reference, and clinical isolates, including 6 other Cryptococcus spp. (10 isolates) and 14 other yeast species (24 isolates), using a 4-hour urea broth test (Remel), a 24-hour urea broth test (Becton Dickinson), a 4-hour caffeic acid disk test (Hardy Diagnostics and Remel), 40- to 44-hour growth assessment on l-canavanine glycine bromothymol blue (CGB) agar, and intergenic spacer (IGS) sequence analysis. All 123 Cryptococcus isolates hydrolyzed urea, along with 7 isolates of Rhodotorula and Trichosporon. Eighty-five of 86 C. neoformans (99%) and 26 of 27 C. gattii (96%) isolates had positive caffeic acid results, unlike the other cryptococci (0/10) and yeast species (0/24). Together, these two tests positively identified virtually all C. neoformans/C. gattii isolates (98%) within 4 h. CGB agar or IGS sequencing further differentiated these isolates within 48 h. On CGB, 25 of 27 (93%) C. gattii strains induced a blue color change, in contrast to 0 of 86 C. neoformans isolates. Neighbor-joining cluster analysis of IGS sequences differentiated C. neoformans var. grubii, C. neoformans var. neoformans, and C. gattii. Based on these results, we describe a rapid identification algorithm for use in a microbiology laboratory to distinguish clinically relevant Cryptococcus spp.

Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic nematode, Rotylenchulus reniformis.

PubMed

Nyaku, Seloame T; Sripathi, Venkateswara R; Kantety, Ramesh V; Gu, Yong Q; Lawrence, Kathy; Sharma, Govind C

2013-01-01

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene.

Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

PubMed Central

Nyaku, Seloame T.; Sripathi, Venkateswara R.; Kantety, Ramesh V.; Gu, Yong Q.; Lawrence, Kathy; Sharma, Govind C.

2013-01-01

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene. PMID:23593343

What Constitutes a "Good" Sensitivity Analysis? Elements and Tools for a Robust Sensitivity Analysis with Reduced Computational Cost

NASA Astrophysics Data System (ADS)

Razavi, Saman; Gupta, Hoshin; Haghnegahdar, Amin

2016-04-01

Global sensitivity analysis (GSA) is a systems theoretic approach to characterizing the overall (average) sensitivity of one or more model responses across the factor space, by attributing the variability of those responses to different controlling (but uncertain) factors (e.g., model parameters, forcings, and boundary and initial conditions). GSA can be very helpful to improve the credibility and utility of Earth and Environmental System Models (EESMs), as these models are continually growing in complexity and dimensionality with continuous advances in understanding and computing power. However, conventional approaches to GSA suffer from (1) an ambiguous characterization of sensitivity, and (2) poor computational efficiency, particularly as the problem dimension grows. Here, we identify several important sensitivity-related characteristics of response surfaces that must be considered when investigating and interpreting the ''global sensitivity'' of a model response (e.g., a metric of model performance) to its parameters/factors. Accordingly, we present a new and general sensitivity and uncertainty analysis framework, Variogram Analysis of Response Surfaces (VARS), based on an analogy to 'variogram analysis', that characterizes a comprehensive spectrum of information on sensitivity. We prove, theoretically, that Morris (derivative-based) and Sobol (variance-based) methods and their extensions are special cases of VARS, and that their SA indices are contained within the VARS framework. We also present a practical strategy for the application of VARS to real-world problems, called STAR-VARS, including a new sampling strategy, called "star-based sampling". Our results across several case studies show the STAR-VARS approach to provide reliable and stable assessments of "global" sensitivity, while being at least 1-2 orders of magnitude more efficient than the benchmark Morris and Sobol approaches.

Chemopreventive and Anticancer Activities of Allium victorialis var. platyphyllum Extracts

PubMed Central

Kim, Hyun-Jeong; Park, Min Jeong; Park, Hee-Juhn; Chung, Won-Yoon; Kim, Ki-Rim; Park, Kwang-Kyun

2014-01-01

Background: Allium victorialis var. platyphyllum is an edible perennial herb and has been used as a vegetable or as a Korean traditional medicine. Allium species have received much attention owing to their diverse pharmacological properties, including antioxidative, anti-inflammatory, and anticancer activities. However, A. victorialis var. platyphyllum needs more study. Methods: The chemopreventive potential of A. victorialis var. platyphyllum methanol extracts was examined by measuring 12-O-tetra-decanoylphorbol 13-acetate (TPA)-induced superoxide anion production in the differentiated HL-60 cells, TPA-induced mouse ear edema, and Ames/Salmonella mutagenicity. The apoptosis-inducing capabilities of the extracts were evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay, 4’,6-diamidino-2-phenylindole staining, and the DNA fragmentation assay in human colon cancer HT-29 cells. Antimetastatic activities of the extracts were also investigated in an experimental mouse lung metastasis model. Results: The methanol extracts of A. victorialis var. platyphyllum rhizome (AVP-R) and A. victorialis var. platyphyllum stem (AVP-S) dose-dependently inhibited the TPA-induced generation of superoxide anion in HL-60 cells and TPA-induced ear edema in mice, as well as 7,12-dimethylbenz[a]anthracene (DMBA) and tert-butyl hydroperoxide (t-BOOH) -induced bacterial mutagenesis. AVP-R and AVP-S reduced cell viability in a dose-related manner and induced apoptotic morphological changes and internucleosomal DNA fragmentation in HT-29 cells. In the experimental mouse lung metastasis model, the formation of tumor nodules in lung tissue was significantly inhibited by the treatment of the extracts. Conclusions: AVP-R and AVP-S possess antioxidative, anti-inflammatory, antimutagenic, proapoptotic, and antimetastatic activities. Therefore, these extracts can serve as a beneficial supplement for the prevention and treatment of cancer. PMID:25337587

21 CFR 173.145 - Alpha-Galactosidase derived from Mortierella vinaceae var. raffinoseutilizer.

Code of Federal Regulations, 2014 CFR

2014-04-01

... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.145 Alpha-Galactosidase derived from... following conditions: (a) The food additive is the enzyme alpha-galactosidase and the mycelia of the microorganism Mortierella vinaceae var. raffinoseutilizer which produces the enzyme. (b) The nonpathogenic...

Utility of Grafting for Managing Southern Root-knot Nematode, Meloidogyne Incognita, in Watermelon

USDA-ARS?s Scientific Manuscript database

Four bottlegourd (Lagenaria siceraria) cultivars, one squash (Cucurbita moschata x C. maxima) hybrid, four wild watermelon (Citrullus lanatus var. citroides) germplasm lines, and one commercial wild watermelon (C. lanatus var. citroides) cultivar were evaluated as rootstocks for cultivated watermelo...

Toxicity of "Bacillus thuringiensis var. Kurstaki" to the Painted Lady Butterfly, Vanessa cardui.

ERIC Educational Resources Information Center

Stalter, Richard; Nadal, Gerard; Kincaid, Dwight

2000-01-01

Reports the effects of Bacillus thuringiensis var. Kurstaki (BT), which is highly toxic, to a non-target lepidopteran, the Painted Lady butterfly. Indicates that BT kills some Painted Lady butterfly larvae at the lowest dilution tested after 48 hours. (ASK)

Analysis of sesquiterpene distributions in leaves, branches, and trunks of avocado (Persea americana Mill.)

USDA-ARS?s Scientific Manuscript database

Avocado is a commercially valuable fruit crop cultivated in tropical and subtropical climates throughout the world. Taxonomists recognize three horticultural races of avocado, consisting of Mexican (Persea americana var. drymifolia), Guatemalan (P. americana var. guatemalensis), and West Indian (P. ...

Solvency II solvency capital requirement for life insurance companies based on expected shortfall.

PubMed

Boonen, Tim J

2017-01-01

This paper examines the consequences for a life annuity insurance company if the solvency II solvency capital requirements (SCR) are calibrated based on expected shortfall (ES) instead of value-at-risk (VaR). We focus on the risk modules of the SCRs for the three risk classes equity risk, interest rate risk and longevity risk. The stress scenarios are determined using the calibration method proposed by EIOPA in 2014. We apply the stress-scenarios for these three risk classes to a fictitious life annuity insurance company. We find that for EIOPA's current quantile 99.5% of the VaR, the stress scenarios of the various risk classes based on ES are close to the stress scenarios based on VaR. Might EIOPA choose to calibrate the stress scenarios on a smaller quantile, the longevity SCR is relatively larger and the equity SCR is relatively smaller if ES is used instead of VaR. We derive the same conclusion if stress scenarios are determined with empirical stress scenarios.

Removal of methylene blue by invasive marine seaweed: Caulerpa racemosa var. cylindracea.

PubMed

Cengiz, Sevilay; Cavas, Levent

2008-05-01

Caulerpa racemosa var. cylindracea is one of the well-known invasive species in the Mediterranean Sea. In the present study, dried biomass of C. racemosa var. cylindracea was shown to have adsorption capacity for methylene blue. The adsorption reached equilibrium at 90 min for all studied concentrations (5-100mg/L). The pseudo-second-order model is well in line with our experimental results. There was a sharp increase in the adsorbed dye amount per adsorbent amount from 3.3 to 16.7 g/L, then a slight increase up to 66.7 g/L was observed. Langmuir and Freundlich's models were applied to the data related to adsorption isotherm. According to Langmuir's model data, the observed maximum adsorption capacity (qm) was 5.23 mg/g at 18 degrees C. The enthalpy of adsorption was found to be 33 kJ/mol, which indicated a chemical adsorption between dye molecules and C. racemosa var. cylindracea functional groups.

Reduced-Rank Array Modes of the California Current Observing System

NASA Astrophysics Data System (ADS)

Moore, Andrew M.; Arango, Hernan G.; Edwards, Christopher A.

2018-01-01

The information content of the ocean observing array spanning the U.S. west coast is explored using the reduced-rank array modes (RAMs) derived from a four-dimensional variational (4D-Var) data assimilation system covering a period of three decades. RAMs are an extension of the original formulation of array modes introduced by Bennett (1985) but in the reduced model state-space explored by the 4D-Var system, and reveal the extent to which this space is activated by the observations. The projection of the RAMs onto the empirical orthogonal functions (EOFs) of the 4D-Var background error correlation matrix provides a quantitative measure of the effectiveness of the measurements in observing the circulation. It is found that much of the space spanned by the background error covariance is unconstrained by the present ocean observing system. The RAM spectrum is also used to introduce a new criterion to prevent 4D-Var from overfitting the model to the observations.

GC-MS analysis and antimicrobial activity determination of Citrus medica L. var proper leaf essential oil from South Sulawesi against skin pathogen microorganism

NASA Astrophysics Data System (ADS)

Aliyah; Himawan, A.; Rante, H.; Mufidah; Ningsih, D. R.

2017-11-01

A research about Citrus medica L. var sarcodactylis had been conducted and it showed a significant antimicrobial activity, thus drive our curiosity to investigate the other variety from the same species, Citrus medica L. var proper. This research focuses in chemical compound study and antimicrobial activity screening against Staphylococcus aureus, Propionibacterium acne, and Candida albicans of Citrus medica L. var Proper leaves’ essential oil. The essential oil is distillated from fresh leaves by hydrodestillation. The chemical compound was analysed using GC-MS instrument while the antimicrobial activity was tested using disk diffusion method. The results showed that the major component of the essential oil was Z-citral, citral and limonene compounds. The antimicrobial activity test results against the test microorganism are 9.15±0.15 mm, 11.15±1.3 mm and 8.02±0.48 mm, consecutively, for Staphylococcus aureus, Propionibacterium acne and Candida albicans.

Fatty acid composition of Juniperus species (Juniperus section) native to Turkey.

PubMed

Güvenç, Aysegül; Küçükboyaci, Nurgün; Gören, Ahmet Ceyhan

2012-07-01

Fatty acid compositions of seeds of five taxa of the Juniperus section of the genus Juniperus L. (Cupressaceae), i. e. J. drupacea Lab., J. communis L. var. communis, J. communis var. saxatilis Pall., J. oxycedrus L. subsp. oxycedrus, and J. oxycedrus subsp. macrocarpa (Sibth. & Sm.) Ball, were investigated. Methyl ester derivatized fatty acids of the lipophylic extracts of the five species were comparatively analyzed by capillary gas chromatography-mass spectrometry (GC-MS). Juniperus taxa showed uniform fatty acid patterns, among which linoleic (25.8 - 32.5%), pinolenic (11.9 - 24.1%) and oleic acids (12.4 - 17.2%) were determined to be the main fractions in the seed oils. Juniperonic acid was found to be remarkably high in J. communis var. saxatilis (11.4%), J. oxycedrus subsp. oxycedrus (10.4%), and J. communis var. communis (10.1%). To the best of our knowledge, the present work discloses the first report on the fatty acid compositions of seeds of this Juniperus section grown in Turkey.

Genetic and phenological variation of tocochromanol (vitamin E) content in wild (Daucus carota L. var. carota) and domesticated carrot (D. carota L. var. sativa)

PubMed Central

Luby, Claire H; Maeda, Hiroshi A; Goldman, Irwin L

2014-01-01

Carrot roots (Daucus carota L. var. sativa) produce tocochromanol compounds, collectively known as vitamin E. However, little is known about their types and amounts. Here we determined the range and variation in types and amounts of tocochromanols in a variety of cultivated carrot accessions throughout carrot postharvest storage and reproductive stages and in wild-type roots (Daucus carota L. var. carota). Of eight possible tocochromanol compounds, we detected and quantified α-, and the combined peak for β- and γ- forms of tocopherols and tocotrienols. Significant variation in amounts of tocochromanol compounds was observed across accessions and over time. Large increases in α-tocopherol were noted during both reproductive growth and the postharvest stages. The variation of tocochromanols in carrot root tissue provides useful information for future research seeking to understand the role of these compounds in carrot root tissue or to breed varieties with increased levels of these compounds. PMID:26504534

Forecasting the value-at-risk of Chinese stock market using the HARQ model and extreme value theory

NASA Astrophysics Data System (ADS)

Liu, Guangqiang; Wei, Yu; Chen, Yongfei; Yu, Jiang; Hu, Yang

2018-06-01

Using intraday data of the CSI300 index, this paper discusses value-at-risk (VaR) forecasting of the Chinese stock market from the perspective of high-frequency volatility models. First, we measure the realized volatility (RV) with 5-minute high-frequency returns of the CSI300 index and then model it with the newly introduced heterogeneous autoregressive quarticity (HARQ) model, which can handle the time-varying coefficients of the HAR model. Second, we forecast the out-of-sample VaR of the CSI300 index by combining the HARQ model and extreme value theory (EVT). Finally, using several popular backtesting methods, we compare the VaR forecasting accuracy of HARQ model with other traditional HAR-type models, such as HAR, HAR-J, CHAR, and SHAR. The empirical results show that the novel HARQ model can beat other HAR-type models in forecasting the VaR of the Chinese stock market at various risk levels.

Rolling-element fatigue life of AMS 5749 corrosion resistant, high temperature bearing steel

NASA Technical Reports Server (NTRS)

Parker, R. J.; Hodder, R. S.

1977-01-01

The rolling element fatigue lives of AMS 5749 and AISI M-50 were compared in tests run in the five ball fatigue tester and the rolling contact fatigue tester. The effects of double vacuum melting and retained austenite on the life of AMS 5749 were determined in five ball fatigue tests. The double vacuum melting process consisted of induction vacuum melting followed by vacuum arc remelting (VIM-VAR). In the five ball tests, VIM-VAR AMS 5749 gave lives at least six times that of VIM-VAR AISI M-50. Similar tests in the rolling contact fatigue tester showed no significant difference in the lives of the two materials. The rolling element fatigue life of VIM-VAR AMS 5749 was at least 14 times that of vacuum induction melted AMS 5749. A trend toward increased rolling element fatigue life with decreased retained austenite is apparent, but the confidence that all experimental differences are significant is not great.

Data assimilation of non-conventional observations using GEOS-R flash lightning: 1D+4D-VAR approach vs. assimilation of images (Invited)

NASA Astrophysics Data System (ADS)

Navon, M. I.; Stefanescu, R.

2013-12-01

Previous assimilation of lightning used nudging approaches. We develop three approaches namely, 3D-VAR WRFDA and1D+nD-VAR (n=3,4) WRFDA . The present research uses Convective Available Potential Energy (CAPE) as a proxy between lightning data and model variables. To test performance of aforementioned schemes, we assess quality of resulting analysis and forecasts of precipitation compared to those from a control experiment and verify them against NCEP stage IV precipitation. Results demonstrate that assimilating lightning observations improves precipitation statistics during the assimilation window and for 3-7 h thereafter. The 1D+4D-VAR approach yielded the best performance significantly improving precipitation rmse errors by 25% and 27.5%,compared to control during the assimilation window for two tornadic test cases. Finally we propose a new approach to assimilate 2-D images of lightning flashes based on pixel intensity, mitigating dimensionality by a reduced order method.

Secondary bacterial symbiont community in aphids responds to plant diversity.

PubMed

Zytynska, Sharon E; Meyer, Sebastian T; Sturm, Sarah; Ullmann, Wiebke; Mehrparvar, Mohsen; Weisser, Wolfgang W

2016-03-01

Biodiversity is important for ecosystem functioning and biotic interactions. In experimental grasslands, increasing plant species richness is known to increase the diversity of associated herbivores and their predators. If these interactions can also involve endosymbionts that reside within a plant or animal host is currently unknown. In plant-feeding aphids, secondary bacterial symbionts can have strong fitness effects on the host, e.g. resistance to natural enemies or fungal pathogens. We examined the secondary symbiont community in three species of aphid, each feeding on a unique host plant across experimental plots that varied in plant species richness. Aphids were collected in May and June, and the symbiont community identified using species-specific PCR assays. Aphis fabae aphids were found to host six different symbiont species with individual aphids co-hosting up to four symbionts. Uroleucon jaceae and Macrosiphum rosae hosted two and three symbiont species, respectively. We found that, at the aphid population level, increasing plant species richness increased the diversity of the aphid symbiont community, whereas at the individual aphid level, the opposite was found. These effects are potentially driven by varying selective pressures across different plant communities of varying diversities, mediated by defensive protection responses and a changing cost-benefit trade-off to the aphid for hosting multiple secondary symbionts. Our work extends documented effects of plant diversity beyond visible biotic interactions to changes in endosymbiont communities, with potentially far-reaching consequences to related ecosystem processes.

Influence of Different Plant Species on Methane Emissions from Soil in a Restored Swiss Wetland

PubMed Central

Bhullar, Gurbir S.; Edwards, Peter J.; Olde Venterink, Harry

2014-01-01

Plants are a major factor influencing methane emissions from wetlands, along with environmental parameters such as water table, temperature, pH, nutrients and soil carbon substrate. We conducted a field experiment to study how different plant species influence methane emissions from a wetland in Switzerland. The top 0.5 m of soil at this site had been removed five years earlier, leaving a substrate with very low methanogenic activity. We found a sixfold difference among plant species in their effect on methane emission rates: Molinia caerulea and Lysimachia vulgaris caused low emission rates, whereas Senecio paludosus, Carex flava, Juncus effusus and Typha latifolia caused relatively high rates. Centaurea jacea, Iris sibirica, and Carex davalliana caused intermediate rates. However, we found no effect of either plant biomass or plant functional groups – based on life form or productivity of the habitat – upon methane emission. Emissions were much lower than those usually reported in temperate wetlands, which we attribute to reduced concentrations of labile carbon following topsoil removal. Thus, unlike most wetland sites, methane production in this site was probably fuelled chiefly by root exudation from living plants and from root decay. We conclude that in most wetlands, where concentrations of labile carbon are much higher, these sources account for only a small proportion of the methane emitted. Our study confirms that plant species composition does influence methane emission from wetlands, and should be considered when developing measures to mitigate the greenhouse gas emissions. PMID:24586894

Anti-U-like as an alloantibody in S-s-U- and S-s-U+(var) black people.

PubMed

Peyrard, Thierry; Lam, Yin; Saison, Carole; Arnaud, Lionel; Babinet, Jérôme; Rouger, Philippe; Bierling, Philippe; Janvier, Daniel

2012-03-01

S, s, and U antigens belong to the MNS system. They are carried by glycophorin B (GPB), encoded by GYPB. Black people with the low-prevalence S-s- phenotype, either U- or U+(var), can make a clinically significant anti-U. Anti-U-like, a cold immunoglobulin G autoantibody quite commonly observed in S-s+U+ black persons, was previously described to be nonreactive with ficin-, α-chymotrypsin-, and pronase-treated red blood cells (RBCs); nonreactive or weakly reactive with papain-treated RBCs; and reactive with trypsin-treated RBCs. Here we describe, in S-s- people from different molecular backgrounds, an alloantibody to a high-prevalence GPB antigen, which presents the same pattern of reactivity with proteases as autoanti-U-like. Four S-s- patients with an alloantibody to a high-prevalence GPB antigen were investigated by serologic and molecular methods. An alloantibody was observed in two S-s-U-/Del GYPB, one S-s-U+(var)/GYPB(P2), and one S-s-U+(var)/GYPB(NY) patients. As this alloantibody showed the same pattern of reactivity with proteases as autoanti-U-like, we decided to name it "anti-U-like." Anti-U-like made by the two S-s-U- patients was reactive with the S-s-U+(var) RBCs of the two other patients. S-s-U-/Del GYPB, S-s-U+(var)/GYPB(P2), and S-s-U+(var)/GYPB(NY) patients can make an alloanti-U-like. Anti-U-like made by S-s-U- people appears reactive with GYPB(P2) and GYPB(NY) RBCs, which both express a weak and partial U-like reactivity. We recommend transfusing S-s-U- RBCs in S-s-U- patients showing alloanti-U-like. Our study contributes to a better understanding of alloimmunization to GPB in black people and confirms importance of genotyping in S-s- patients, especially those with sickle cell disease to be frequently transfused. © 2011 American Association of Blood Banks.

Production and Characterization of a Monoclonal Antibody Raised Against Surface Antigens from Mycelium of Gaeumannomyces graminis var. tritici: Evidence for an Extracellular Polyphenol Oxidase.

PubMed

Thornton, C R; Dewey, F M; Gilligan, C A

1997-01-01

ABSTRACT A murine monoclonal antibody (MAb) of immunoglobulin class M (IgM) was raised against surface antigens from Gaeumannomyces graminis var. tritici and, by enzyme-linked immunosorbent assay, recognized isolates of G. graminis var. tritici, G. graminis var. avenae and G. graminis var. graminis. Characterization of the antigen by heat and protease treatments showed that the epitope recognized by the MAb was a protein. Antigen production was detected only in live mycelia. Immunofluorescence studies showed that the antigen was associated with both the broad melanized macrohyphae and hyaline mycelia of G. graminis var. tritici. Secretion of antigen into an aqueous minimal medium was promoted only by exposure of live mycelia to certain phenolic substrates, including monophenols ortho-, para-, and meta-cresol; 3,4,5-trihydroxybenzoic acid (gallic acid); and phenolic amino acid L-3-(3,4-dihydroxyphenyl) alanine (L-DOPA). Antigen secretion was not promoted by 3-(4-hydroxyphenyl) alanine (L-tyrosine). The MAb reacted strongly with purified enzyme laccase (polyphenol oxidase, EC 1.10.3.2) but did not recognize purified tyrosinase (monophenol oxidase, EC 1.14.18.1). Moreover, chemicals that bind to copper and inhibit copper-containing enzymes such as laccase completely inhibited antigen secretion in response to L-DOPA. The MAb was tested for specificity against a wide range of fungi, common yeast species, and gram positive and negative bacteria. It did not recognize antigens from a broad range of unrelated fungi, including Gliocladium roseum, Fusarium sp., Phoma exigua, Phialophora fastigiata, Penicillium crustosum, Pythium ultimum, Rhizopus stolonifer, Rhizoctonia carotae, R. oryzae, R. tuliparum, and Trichoderma viride, nor did it recognize surface antigens from yeasts or bacteria. The MAb cross-reacted with antigens from Botrytis spp., Chaetomium globosum, R. cerealis, and R. solani. However, secretion of antigen by R. solani and R. cerealis was not promoted by L-DOPA, and secretion by C. globosum in response to the phenolic amino acid was significantly less compared to G. graminis var. tritici.

Phenyl ethers from cultured lichen mycobionts of Graphis scripta var. serpentina and G. rikuzensis.

PubMed

Takenaka, Yukiko; Tanahashi, Takao; Nagakura, Naotaka; Hamada, Nobuo

2003-07-01

Spore-derived mycobionts of the lichen Graphis scripta var. serpentina and G. rikuzensis were cultivated on a malt-yeast extract medium supplemented with 10% sucrose and their metabolites were investigated. 3,3'-Dihydroxy-5,5'-dimethyldiphenyl ether was isolated from the cultures of the mycobionts of G. scripta var. serpentina, while a new phenyl ether, rikuzenol, along with two known diphenyl ethers, violaceol-I and violaceol-II, were isolated from those of G. rikuzensis. The structure of the new compound was determined by spectroscopic methods. Violaceol-I was chemically synthesized and interconversion between violaceol-I and violaceol-II was proven.

Genetic relationship and biological status of the industrially important yeast Saccharomyces eubayanus Sampaio et al.

PubMed

Naumov, G I

2017-03-01

The genomes of the recently discovered yeast Saccharomyces eubayanus and traditional S. cerevisiae are known to be found in the yeast S. pastorianus (syn. S. carlsbergensis), which are essential for brewing. The cryotolerant yeast S. bayanus var. uvarum is of great importance for production of some wines. Based on ascospore viability and meiotic recombination of the control parental markers in hybrids, we have shown that there is no complete interspecies post-zygotic isolation between the yeasts S. eubayanus, S. bayanus var. bayanus and S. bayanus var. uvarum. The genetic data presented indicate that all of the three taxa belong to the same species.

The complete chloroplast genome sequence of Dianthus superbus var. longicalycinus.

PubMed

Gurusamy, Raman; Lee, Do-Hyung; Park, SeonJoo

2016-05-01

The complete chloroplast genome (cpDNA) sequence of Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicine was reported and characterized. The cpDNA of Dianthus superbus var. longicalycinus is 149,539 bp, with 36.3% GC content. A pair of inverted repeats (IRs) of 24,803 bp is separated by a large single-copy region (LSC, 82,805 bp) and a small single-copy region (SSC, 17,128 bp). It encodes 85 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Of 129 individual genes, 13 genes encoded one intron and three genes have two introns.

Mycorrhizal colonization and plant growth affected by aqueous extract of Artemisia princeps var. orientalis and two phenolic compounds.

PubMed

Yun, K W; Choi, S K

2002-02-01

The effects of an aqueous extract of Artemisia princeps var. orientalis and two phenolic compounds on mycorrhizal colonization and plant growth have been investigated. Greenhouse studies showed that the inhibitory effect of the extract on mycorrhizal colonization and plant growth increased in proportion to the concentration of the extract. When the mycorrhizal test plants were treated with an increasing concentration of phenolic compounds, the mycorrhizal colonization in roots of the test plant and the plant growth were decreased. There were strong indications that mycorrhizal fungi mitigated the inhibitory influence of shoot extract of A. princeps var. orientalis and phenolic compounds.

Exchangeability, extreme returns and Value-at-Risk forecasts

NASA Astrophysics Data System (ADS)

Huang, Chun-Kai; North, Delia; Zewotir, Temesgen

2017-07-01

In this paper, we propose a new approach to extreme value modelling for the forecasting of Value-at-Risk (VaR). In particular, the block maxima and the peaks-over-threshold methods are generalised to exchangeable random sequences. This caters for the dependencies, such as serial autocorrelation, of financial returns observed empirically. In addition, this approach allows for parameter variations within each VaR estimation window. Empirical prior distributions of the extreme value parameters are attained by using resampling procedures. We compare the results of our VaR forecasts to that of the unconditional extreme value theory (EVT) approach and the conditional GARCH-EVT model for robust conclusions.

Thermal Inactivation of Aerosolized Bacillus subtilis var. niger Spores

PubMed Central

Mullican, Charles L.; Buchanan, Lee M.; Hoffman, Robert K.

1971-01-01

A hot-air sterilizer capable of exposing airborne microorganisms to elevated temperatures with an almost instantaneous heating time was developed and evaluated. With this apparatus, aerosolized Bacillus subtilis var. niger spores were killed in about 0.02 sec when exposed to temperatures above 260 C. This is about 500 times faster than killing times reported by others. Extrapolation and comparison of data on the time and temperature required to klll B. subtilis var. niger spores on surfaces show that approximately the same killing time is required as is necessary for spores in air, if corrections are made for the heating time of the surface. PMID:5002138

40 CFR 180.41 - Crop group tables.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... var. bulbiferum L.H. Bailey; A. cepa L. var. viviparum (Metz.) Alef.) 3-07B Onion, Welsh, tops (Allium... grains group. (19) Crop Group 17. Grass Forage, Fodder, and Hay Group. (i) Representative commodities. Bermuda grass; bluegrass; and bromegrass or fescue. (ii) Commodities. The commodities included in Crop...

Detecting the influence of ornamental Berberis thunbergii var. atropurpurea in invasive populations of Berberis thunbergii (Berberidaceae) using AFLP1.

PubMed

Lubell, Jessica D; Brand, Mark H; Lehrer, Jonathan M; Holsinger, Kent E

2008-06-01

Japanese barberry (Berberis thunbergii DC.) is a widespread invasive plant that remains an important landscape shrub represented by ornamental, purple-leaved forms of the botanical variety atropurpurea. These forms differ greatly in appearance from feral plants, bringing into question whether they contribute to invasive populations or whether the invasions represent self-sustaining populations derived from the initial introduction of the species in the late 19th century. In this study we used amplified fragment length polymorphism (AFLP) markers to determine whether genetic contributions from B. t. var. atropurpurea are found within naturalized Japanese barberry populations in southern New England. Bayesian clustering of AFLP genotypes and principal coordinate analysis distinguished B. t. var. atropurpurea genotypes from 85 plants representing five invasive populations. While a single feral plant resembled B. t. var. atropurpurea phenotypically and fell within the same genetic cluster, all other naturalized plants sampled were genetically distinct from the purple-leaved genotypes. Seven plants from two different sites possessed morphology consistent with Berberis vulgaris (common barberry) or B. ×ottawensis (B. thunbergii × B. vulgaris). Genetic analysis placed these plants in two clusters separate from B. thunbergii. Although the Bayesian analysis indicated some introgression of B. t. var. atropurpurea and B. vulgaris, these genotypes have had limited influence on extant feral populations of B. thunbergii.

Contributions of natural climate changes and human activities to the trend of extreme precipitation

NASA Astrophysics Data System (ADS)

Gao, Lu; Huang, Jie; Chen, Xingwei; Chen, Ying; Liu, Meibing

2018-06-01

This study focuses on the analysis of the nonstationarity characteristics of extreme precipitation and their attributions in the southeastern coastal region of China. The maximum daily precipitation (MDP) series is extracted from observations at 79 meteorological stations in the study area during the first flood season (April-June) from 1960 to 2012. The trends of the mean (Mn) and variance (Var) of MDP are detected using the Generalized Additive Models for Location, Scale, and Shape parameters (GAMLSS) and Mann-Kendall test. The contributions of natural climate change and human activities to the Mn and Var changes of MDP are investigated using six large-scale circulation variables and emissions of four greenhouse gases based on GAMLSS and a contribution analysis method. The results demonstrate that the nonstationarity of extreme precipitation on local scales is significant. The Mn and Var of extreme precipitation increase in the north of Zhejiang, the middle of Fujian, and the south of Guangdong. In general, natural climate change contributes more to Mn from 1960 to 2012 than to Var. However, human activities cause a greater Var in the rapid socioeconomic development period (1986-2012) than in the slow socioeconomic development period (1960-1985), especially in Zhejiang and Guangdong. The community should pay more attention to the possibility of extreme precipitation events and associated disasters triggered by human activities.

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar.

PubMed

Harrison, Steven M; Dolinsky, Jill S; Knight Johnson, Amy E; Pesaran, Tina; Azzariti, Danielle R; Bale, Sherri; Chao, Elizabeth C; Das, Soma; Vincent, Lisa; Rehm, Heidi L

2017-10-01

Data sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories. As part of a ClinGen initiative, four clinical laboratories (Ambry, GeneDx, Partners Healthcare Laboratory for Molecular Medicine, and University of Chicago Genetic Services Laboratory) collaborated to identify the basis of interpretation differences and to investigate if data sharing and reassessment resolve interpretation differences by analyzing a subset of variants. ClinVar variants with submissions from at least two of the four participating laboratories were compared. For a subset of identified differences, laboratories documented the basis for discordance, shared internal data, independently reassessed with the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines, and then compared interpretations. At least two of the participating laboratories interpreted 6,169 variants in ClinVar, of which 88.3% were initially concordant. Laboratories reassessed 242/724 initially discordant variants, of which 87.2% (211) were resolved by reassessment with current criteria and/or internal data sharing; 12.8% (31) of reassessed variants remained discordant owing to differences in the application of the ACMG-AMP guidelines. Participating laboratories increased their overall concordance from 88.3 to 91.7%, indicating that sharing variant interpretations in ClinVar-thereby allowing identification of differences and motivation to resolve those differences-is critical to moving toward more consistent variant interpretations.Genet Med advance online publication 09 March 2017.

[Susceptibility of Aedes aegypti (L.) strains from Havana to a Bacillus thuringiensis var. israelensis].

PubMed

Menéndez Díaz, Zulema; Rodríguez Rodríguez, Jinnay; Gato Armas, René; Companioni Ibañez, Ariamys; Díaz Pérez, Manuel; Bruzón Aguila, Rosa Yirian

2012-01-01

the integration of chemical and biological methods is one of the strategies for the vector control, due to the existing environmental problems and the concerns of the community as a result of the synthetic organic insecticide actions. The bacterium called Bacillus thuringiensis var. israelensis in liquid formulation has been widely used in the vector control programs in several countries and has shown high efficacy at lab in Cuba. to determine the susceptibility of Aedes aegypti collected in the municipalities of La Habana province to Bacillus thuringiensis var. israelensis. fifteen Aedes aegypti strains, one from each municipality, were used including larvae and pupas collected in 2010 and one reference strain known as Rockefeller. The aqueous formulation of Bacillus thuringiensis var. israelensis (Bactivec, Labiofam, Cuba) was used. The bioassays complied with the World Health Organization guidelines for use of bacterial larvicides in the public health sector. The larval mortality was read after 24 hours and the results were processed by the statistical system SPSS (11.0) through Probit analysis. the evaluated mosquito strains showed high susceptibility to biolarvicide, there were no significant differences in LC50 values of Ae. aegypti strains, neither in the comparison of these values with those of the reference strain. the presented results indicate that the use of Bacillus thuringiensis var. israelensis continues to be a choice for the control of Aedes aegypti larval populations in La Habana province.

[Negative air ions generated by plants upon pulsed electric field stimulation applied to soil].

PubMed

Wu, Ren-ye; Deng, Chuan-yuan; Yang, Zhi-jian; Weng, Hai-yong; Zhu, Tie-jun-rong; Zheng, Jin-gui

2015-02-01

This paper investigated the capacity of plants (Schlumbergera truncata, Aloe vera var. chinensis, Chlorophytum comosum, Schlumbergera bridgesii, Gymnocalycium mihanovichii var. friedrichii, Aspidistra elatior, Cymbidium kanran, Echinocactus grusonii, Agave americana var. marginata, Asparagus setaceus) to generate negative air ions (NAI) under pulsed electric field stimulation. The results showed that single plant generated low amounts of NAI in natural condition. The capacity of C. comosum and G. mihanovichii var. friedrichii generated most NAI among the above ten species, with a daily average of 43 ion · cm(-3). The least one was A. americana var. marginata with the value of 19 ion · cm(-3). When proper pulsed electric field stimulation was applied to soil, the NAI of ten plant species were greatly improved. The effect of pulsed electric field u3 (average voltage over the pulse period was 2.0 x 10(4) V, pulse frequency was 1 Hz, and pulse duration was 50 ms) was the greatest. The mean NAI concentration of C. kanran was the highest 1454967 ion · cm(-3), which was 48498.9 times as much as that in natural condition. The lowest one was S. truncata with the value of 34567 ion · cm(-3), which was 843.1 times as much as that in natural condition. The capacity of the same plants to generate negative air ion varied extremely under different intensity pulsed electric fields.

An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster.

PubMed

Eberle, Andrea B; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Hessle, Viktoria; Silberberg, Gilad; von Euler, Anne; Silverstein, Rebecca A; Visa, Neus

2015-09-01

RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin.

An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster

PubMed Central

Eberle, Andrea B.; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Hessle, Viktoria; Silberberg, Gilad; von Euler, Anne; Silverstein, Rebecca A.; Visa, Neus

2015-01-01

RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin. PMID:26389589

Crop candidates for the bioregenerative life support systems in China

NASA Astrophysics Data System (ADS)

Chunxiao, Xu; Hong, Liu

The use of plants for life support applications in space is appealing because of the multiple life support functions by the plants. Research on crops that were grown in the life support system to provide food and oxygen, remove carbon dioxide was begun from 1960. To select possible crops for research on the bioregenerative life support systems in China, criteria for the selection of potential crops were made, and selection of crops was carried out based on these criteria. The results showed that 14 crops including 4 food crops (wheat, rice, soybean and peanut) and 7 vegetables (Chinese cabbage, lettuce, radish, carrot, tomato, squash and pepper) won higher scores. Wheat ( Triticum aestivum L.), rice ( Oryza sativa L.), soybean ( Glycine max L.) and peanut ( Arachis hypogaea L.) are main food crops in China. Chinese cabbage ( Brassica campestris L. ssp. chinensis var. communis), lettuce ( Lactuca sativa L. var. longifolia Lam.), radish ( Raphanus sativus L.), carrot ( Daucus carota L. var. sativa DC.), tomato ( Lycopersicon escalentum L.), squash ( Cucurbita moschata Duch.) and pepper ( Capsicum frutescens L. var. longum Bailey) are 7 vegetables preferred by Chinese. Furthermore, coriander ( Coriandum sativum L.), welsh onion ( Allium fistulosum L. var. giganteum Makino) and garlic ( Allium sativum L.) were selected as condiments to improve the taste of space crew. To each crop species, several cultivars were selected for further research according to their agronomic characteristics.

Mycotoxin producing potential of some isolates of Aspergillus flavus and Eurotium groups from meat products.

PubMed

el-Kady, I; el-Maraghy, S; Zohri, A N

1994-09-01

All strains (92) of A. flavus group proved to be positive for production of aflatoxin (45 to 1200 micrograms/50 ml medium) on potato dextrose liquid medium, while 59 strains only proved to be positive (35-310 micrograms/50 ml) on 15% NaCl potato-dextrose liquid medium. Most of the strains tested of A. flavus, A. flavus var. columnaris and A. oryzae produced aflatoxins B1, B2, G1 & G2. All positive strains of A. tamarii produced aflatoxins G1 & G2 while the tested isolate of A. zonatus produced aflatoxins B1 & G1. Of 95 strains tested of Eurotium, aflatoxins B1 & G1 were produced by one strain of each of E. chevalieri var. intermedium, E. repens and E. rubrum. Gliotoxin was detected in the extract of two strains of E. chevalieri and one strain of each of E. chevalieri var. intermedium and E. pseudoglaucum on the salt-free medium, and two strains of each of E. chevalieri, E. chevalieri var. intermedium and one of E. pseudoglaucum on 15% NaCl medium. Sterigmatocystin was produced by some strains of E. chevalieri, E. chevalieri var. intermedium, E. amstelodami, E. pseudoglaucum and E. rubrum on the two experimental media. One strain only of E. repens produced ochratoxin A while citrinin was detected in the extract of one strain of E. pseudoglaucum.

Response of the Cottonwood Leaf Beetle (Coleoptera: Chrysomelidae) to Bacillus thuringiensis var. san diego

Treesearch

Leah S. Bauer

1990-01-01

A standardized laboratory bioassay was used to quantify the lethal and sub-lethal responses of larval and adult cottonwood leaf beetles, Chrysomela scripta F., to Bacillus thuringiensis var. san diego, formulated as M-One standard powder (Mycogen Corporation, San Diego). The median lethal concentration (LC

Diversity, virulence and 2,4-diacetylphloroglucinol sensitivity of Gaeumannomyces graminis var. tritici isolates from Washington State.

USDA-ARS?s Scientific Manuscript database

Populations of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens buildup in soils that have undergone continuous wheat or barley monoculture, resulting in take-all decline (TAD). We tested whether Gaeumannomyces graminis var. tritici (Ggt) isolates (causal agent of take-all) in mon...

Length and Rapid Elongation of Pedicels of the Female Flowers of Cucumis anguria L.

USDA-ARS?s Scientific Manuscript database

This report summarizes observations on the length and growth of pedicels of pollinated and unpollinated female flowers of Cucumis anguria var. anguria and C. anguria var. longaculeatus. These observations were conducted on six germplasm accessions of C. anguria conserved by the USDA-ARS North Centr...

Detection of Papaya ringspot virus type W infecting the cucurbit weed Cucumis melo var. dudaim in Florida

USDA-ARS?s Scientific Manuscript database

This is the first report of Papaya ringspot virus type W infecting Cucumis melo var. dudaim, a cucurbit weed, in Florida. It provides an overview of this virus reservoir for growers, extension workers, crop consultants and research and regulatory scientists....

40 CFR 180.41 - Crop group tables.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., Capsicum annuum L. var. annuum, Capsicum spp 8-10B Pepper, nonbell, Capsicum chinese Jacq., C. annuum L. var. annuum, C. frutescens L., C. baccatum L., C. pubescens Ruiz & Pav., Capsicum spp 8-10B, 8-10C... muricatum) Pepper (Capsicum spp.) (includes bell pepper, chili pepper, cooking pepper, pimento, sweet pepper...

40 CFR 180.41 - Crop group tables.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., Capsicum annuum L. var. annuum, Capsicum spp 8-10B Pepper, nonbell, Capsicum chinese Jacq., C. annuum L. var. annuum, C. frutescens L., C. baccatum L., C. pubescens Ruiz & Pav., Capsicum spp 8-10B, 8-10C... muricatum) Pepper (Capsicum spp.) (includes bell pepper, chili pepper, cooking pepper, pimento, sweet pepper...

40 CFR 180.41 - Crop group tables.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., Capsicum annuum L. var. annuum, Capsicum spp 8-10B Pepper, nonbell, Capsicum chinese Jacq., C. annuum L. var. annuum, C. frutescens L., C. baccatum L., C. pubescens Ruiz & Pav., Capsicum spp 8-10B, 8-10C... muricatum) Pepper (Capsicum spp.) (includes bell pepper, chili pepper, cooking pepper, pimento, sweet pepper...

Development and characterization of 12 polymorphic microsatellite loci for pityopsis graminifolia var. latifolia

USDA-ARS?s Scientific Manuscript database

Pityopsis graminifolia var. latifolia (narrowleaf silkplant), is an herbaceous perennial indigenous to northern Alabama and east Tennessee. Pityopsis graminifolia is a tetraploid (2n=4x=36) and is a sympatric species of the federally endangered plant P. ruthii, which grows along the Hiwassee and Oco...

7a-hydroxfriedelan-3one-26-OL-29-OIC acid and other constituents from Pileostegia Viburnoids VAR. Glabrescens

USDA-ARS?s Scientific Manuscript database

The preliminary phytotoxic evaluations of a n-BuOH extract from traditional Chinese medicinal plant Pileostegia viburnoides var. glabrescens showed herbicidal activity against dicot Lactuca sativa (lettuce) and monocot Agrostis stolonifera (bentgrass). In order to identify the phytotoxic constituent...

The phenolic extractives in southern red oak (Quercus falcata Michx. var. falcata)

Treesearch

Seiji Ohara; Richard W. Hemingway

1989-01-01

The bark of southern red oak (Quercus falcala Michx. var. falcala) is a rich source of quercitrin (quercetin-3-rhamnoside). It contains only low concentrations of (+)-catechin and no significant amounts of epicatechin or gallocatechin. The three major dimeric proanthocyanidins present are epicatechin-(4β→8)-...

[Analysis of protective effect of using chickenpox live attenuated vaccine among 4-17 years old children in Minhang district, Shanghai].

PubMed

Du, Yan; Yu, Feng; Zhang, Liping; Wang, Xi; Jin, Baofang; Wang, Ye; Mei, Kewen; Lu, Jia; Jiang, Lufang

2014-12-01

To survey on the vaccination of varicella live attenuated vaccine among 4-17 children in Minhang District, and analyze the protective effect against varicella. We collected outbreak chickenpox cases reported from infectious disease report system and surveillance units in Minhang district from 1st May in 2012 to 30th Apr in 2013. The 1: 3 matched case-control study was conducted to questionnaire the legal guardian of the cases and control group, and calculate the protective effect and effective term of protection. The survey included vaccination, chickenpox exposure history, previous history of varicella illness, suffering from the symptoms of chickenpox, the vaccinations brand, etc. The criteria of accepted case were those healthy students who were in the same class with those chickenpox cases. The accepted matched controlling data were those children who were from the same class with outbreak chickenpox cases without varicelliform eruption, similar live condition, the closest house, the same gender, the closest age. This study investigated 390 cases of patients and the control group included 1 170 cases. Chi-square test was used to compare the vaccination of cases and controls, as well as the incidence of chickenpox vaccination different brands VarV, Mantel-Haenzel chi-square test was applied to compare the protective effect of the two groups. VarV overall vaccination rate was 68.3% (1 065/1 560), among them, the case group coverage was 45.1% (176/390), significantly lower than the control group (76.0% (889/1 170)) (χ² = 128.55, P < 0.01). The coverage in children of 4-10 years old group was 88.4% (375/424), significantly higher than the 11-17 years old group (60.7% (690/1 136)) (χ² = 109.40, P < 0.01). The overall protective effect of VarV was 78.10% (71.82%-82.98%).Vaccinated group incidence ratio was 16.5% (176/1 065), significantly lower than the unvaccinated group (43.2% (214/495)) (χ² = 128.55, P < 0.01). The chickenpox risk of the children who were vaccinated was lower than those who were not, and the OR (95%CI) was 0.22(0.17-0.28) . Proportion of the fever and the typical symptoms of varicella zoster were 26.1% (46/176), 8.0% (14/176) in the children vaccinated VarV, significantly lower than children without VarV vaccination history (54.7% (117/214) , 18.2% (39/214) ) (χ² values were 32.33 and 8.67, respectively. P values both <0.01). The varicella incidence was 17.4% (139/797) in children vaccinated domestic VarV, and it was 13.8% (37/268) in the group of imported VarV (χ² = 1.92, P = 0.184) . The average duration of effective protection period for domestic and imported VarV was (6.2 ± 2.7), (6.3 ± 3.4) years (F = 2.24, P = 0.136). The risk of varicella incidence and the proportion of fever or typical varicella zoster were lower in the one dose of VarV vaccinated; Effective protective effect was consistent in the children with domestic or imported VarV vaccination.

Network-Cognizant Design of Decentralized Volt/VAR Controllers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, Kyri A; Bernstein, Andrey; Zhao, Changhong

This paper considers the problem of designing decentralized Volt/VAR controllers for distributed energy resources (DERs). The voltage-reactive power characteristics of individual DERs are obtained by solving a convex optimization problem, where given performance objectives (e.g., minimization of the voltage deviations from a given profile) are specified and stability constraints are enforced. The resultant Volt/VAR characteristics are network-cognizant, in the sense that they embed information on the location of the DERs and, consequently, on the effect of reactive-power adjustments on the voltages throughout the feeder. Bounds on the maximum voltage deviation incurred by the controllers are analytically established. Numerical results aremore » reported to corroborate the technical findings.« less

Ecological-floristic analysis of soil algae and cyanobacteria on the Tra-Tau and Yurak-Tau Mounts, Bashkiria

NASA Astrophysics Data System (ADS)

Bakieva, G. R.; Khaibullina, L. S.; Gaisina, L. A.; Kabirov, R. R.

2012-09-01

The species composition of the soil algae and cyanobacteria in the Tra-Tau and Yurak-Tau mountains is represented by 136 species belonging to five phyla: Cyanobacteria (56 species), Chlorophyta (52 species), Xanthophyta (13 species), Bacillariophyta (12 species), and Eustigmatophyta (3 species). Hantzschia amphioxys var. amphioxys, Hantzschia amphioxys var. constricta, Klebsormidium flaccidum, Leptolyngbya foveolarum, Luticola mutica, Navicula minima var. minima, Nostoc punctiforme, Phormidium jadinianum, Phormidium autumnale, and Pinnularia borealis were identified more often than other species. The composition of the algal flora depended on the soil properties; the higher plants also had a significant influence on the species composition of the soil algae.

Lack of gender-specific antibody recognition of products from domains of a var gene implicated in pregnancy-associated Plasmodium falciparum malaria.

PubMed

Jensen, Anja T R; Zornig, Hanne D; Buhmann, Caecilie; Salanti, Ali; Koram, Kwadwo A; Riley, Eleanor M; Theander, Thor G; Hviid, Lars; Staalsoe, Trine

2003-07-01

Gender-specific and parity-dependent acquired antibody recognition is characteristic of variant surface antigens (VSA) expressed by chondroitin sulfate A (CSA)-adherent Plasmodium falciparum involved in pregnancy-associated malaria (PAM). However, antibody recognition of recombinant products of a specific VSA gene (2O2var1) implicated in PAM and transcribed by a CSA-adhering parasite line did not have these characteristics. Furthermore, we could not demonstrate preferential transcription of 2O2var1 in the CSA-adhering line versus the unselected, parental isolate. Our data call for circumspection regarding the molecular identity of the parasite ligand mediating adhesion to CSA in PAM.

[Study on quality standard of Mucuna pruriens var. utilis].

PubMed

Wu, Shi-Hong; Jiang, Wei-Zhe; Lv, Li; Wu, Ling-Ling; Lv, Cong; Shi, Xiao-Xia; Su, Gui-Liang

2009-03-01

To provide scientific basis for the utilization and development of Mucuna pruriens var. utilis by establishing its quality control standard. The bioactive constituents were analyzed by TLC and HPLC. Moisture, ash and the extracts of Mucuna pruriens var. utilis were all determined. The TLC spots of levodopa had similar color with the control group at the same position. The results of HPLC quantitative analysis showed that the linear range of levodopa was 26.45 to approximately 132.25 microg/mL, r = 0.9992, and the average recovery rate was 103.8%, RSD = 1.85%. This method is convenient, accurate, reliable with good reproducibility, so it can be used to establish quality standard for the medicinal material.

Variation in functional ascospore parts in the ascomycetous yeast Dipodascopsis uninucleata.

PubMed

Bareetseng, A S; Kock, J L F; Pohl, C H; Pretorius, E E; Van Wyk, P W J

2004-04-01

A variation in functional ascospore morphology was detected using electron microscopy (EM) in two varieties of the yeast Dipodascopsis uninucleata, i.e., D. uninucleata var. uninucleata and D. uninucleata var. wickerhamii. It was found that the latter produces ascospores characterized by the absence of small surface hooks which have been implicated in the release and re-assembly of ascospores in D. uninucleata var. uninucleata. These varieties are closely related on the basis of their mode of sexual reproduction, ascospore morphology as observed under the light microscope, physiological characteristics as well as the extent of divergence in the variable D1/D2 domain of the large subunit 26S ribosomal DNA.

A time-parallel approach to strong-constraint four-dimensional variational data assimilation

NASA Astrophysics Data System (ADS)

Rao, Vishwas; Sandu, Adrian

2016-05-01

A parallel-in-time algorithm based on an augmented Lagrangian approach is proposed to solve four-dimensional variational (4D-Var) data assimilation problems. The assimilation window is divided into multiple sub-intervals that allows parallelization of cost function and gradient computations. The solutions to the continuity equations across interval boundaries are added as constraints. The augmented Lagrangian approach leads to a different formulation of the variational data assimilation problem than the weakly constrained 4D-Var. A combination of serial and parallel 4D-Vars to increase performance is also explored. The methodology is illustrated on data assimilation problems involving the Lorenz-96 and the shallow water models.

Germination of vegetable seeds exposed to very high pressure

NASA Astrophysics Data System (ADS)

Mori, Y.; Yokota, S.; Ono, F.

2012-07-01

Effects of high hydrostatic pressure were investigated on vegetable seeds in the GPa range to examine the potentialities of breed improvement by high-pressure processing. Specimens of several seeds of broccoli (Brassica oleracea var. italica), Turnip leaf (Brassica rapa var. perviridis) and Potherb Mustard (Brassica rapa var. nipposinica) were put in a teflon capsule with liquid high pressure medium, fluorinate, and inserted into a pyrophillite cube. By using a cubic anvil press a hydrostatic pressure of 5.5 GP a was applied to these seeds for 15 minutes. After being brought back to ambient pressure, they were seeded on humid soil in a plant pot. Many of these vegetable seeds began to germinate within 6 days after seeded.

Three new germacrane-type sesquiterpenes with NGF-potentiating activity from Valeriana officinalis var. latiofolia.

PubMed

Chen, Heng-Wen; Chen, Li; Li, Bin; Yin, Hai-Long; Tian, Ying; Wang, Qiong; Xiao, Yan-Hua; Dong, Jun-Xing

2013-11-14

Three new germacrane-type sesquiterpenoids, volvalerenal F (1), volvalerenal G (2) and volvalerenic acid D (3), along with five known compounds 4-8, were isolated from the CHCl₃ soluble partition of the ethanol extract of Valeriana officinalis var. latiofolia. The structures of the new compounds were determined on the basis of spectroscopic evidence, including their 1D- and 2D-NMR spectra, as well as mass spectrometry. The eight germacrane-type sesquiterpenoids showed nerve growth factor (NGF) potentiating activity, which mediates the neurite outgrowth in PC 12D cells. This study intends to reveal the chemical basis of the use of V. officinalis var. latiofolia as a dietary supplement.

Vector Autoregression, Structural Equation Modeling, and Their Synthesis in Neuroimaging Data Analysis

PubMed Central

Chen, Gang; Glen, Daniel R.; Saad, Ziad S.; Hamilton, J. Paul; Thomason, Moriah E.; Gotlib, Ian H.; Cox, Robert W.

2011-01-01

Vector autoregression (VAR) and structural equation modeling (SEM) are two popular brain-network modeling tools. VAR, which is a data-driven approach, assumes that connected regions exert time-lagged influences on one another. In contrast, the hypothesis-driven SEM is used to validate an existing connectivity model where connected regions have contemporaneous interactions among them. We present the two models in detail and discuss their applicability to FMRI data, and interpretational limits. We also propose a unified approach that models both lagged and contemporaneous effects. The unifying model, structural vector autoregression (SVAR), may improve statistical and explanatory power, and avoids some prevalent pitfalls that can occur when VAR and SEM are utilized separately. PMID:21975109

Malus sieversii: a diverse Central Asian apple species in the USDA-ARS National Plant Germplasm System

USDA-ARS?s Scientific Manuscript database

There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, ...

Antiparasitic and antimicrobial indolizidines from the leaves of Prosopis glandulosa var glandulosa from Nevada and Texas USA

USDA-ARS?s Scientific Manuscript database

A new indolizidine alkaloid, named (Delta) 1,6-juliprosopine (1), together with previously known indolizidine analogs (2-6), was isolated from the leaves of Prosopis glandulosa var. glandulosa, collected from Nevada, USA; while two other known indolizidines juliprosopine (6) and juliprosine (7) were...

Stomatal behavior of ozone-sensitive and -insensitive coneflowers ( Rudbeckia laciniata var. digitata ) in Great Smoky Mountains National Park

Treesearch

Nancy Grulke; H. S. Neufeld; A. W. Davison; M. Roberts; A. H. Chappelka

2006-01-01

• Morphological and physiological attributes were assessed to elucidate the underlying mechanisms of ozone (O3) sensitivity in a highly sensitive species, cutleaf coneflower (Rudbeckia laciniata var. digitata). • Foliage at the same height in the canopy on paired O3-...

Susceptibility of the endangered Karner blue butterfly (Lepidoptera: Lycaenidae) to Bacillus thuringiensis var. kurstaki used for gypsy moth suppression in Michigan

Treesearch

Catherine Papp Herms; Deborah G. McCullough; Leah S. Bauer; Robert A. Haack; Norman R. Dubois

1997-01-01

We investigated the phenological and physiological susceptibility of the endangered Karner blue butterfly (Lycaeides melissa samuelis) to Bacillus thuringiensis var. kurstaki (Bt), a product widely used for gypsy moth (Lymantria dispar) suppression in Michigan and other infested states. We...

Pollination of pima pineapple cactus (Coryphantha sheeri var. robustispina): does pollen flow limit abundance of this endangered species?

Treesearch

Christopher J. McDonald; Guy R. McPherson

2005-01-01

Pima pineapple cactus (PPC) (Coryphantha sheeri var. robustispina), a federally listed endangered species, occurs throughout southeastern Arizona and has relatively low population densities. To determine whether pollination limits reproduction of PPC we used florescent dye to quantify pollen flow between individuals in a PPC...

Planting Wetland Species On Upland Soil

Treesearch

T. A. Harrington

1965-01-01

Baldcypress (Taxodium distichum var. distichum), pondcypress (T. distichum var. nutans), and blackgum(Nyssa sylvatica) can be successfullyplanted as bare-rooted, l- 0 stock on upland soils in northeast Florida according to a study on the Olustee Experimental Forest.This research was conducted with the cooperation of the Florida Board of Forestry. After three growing...

Survival, frost susceptibility, growth, and disease resistance of corkbark and subalpine fir grown for landscape and Christmas trees

USDA-ARS?s Scientific Manuscript database

Trees from six corkbark fir (Abies lasiocarpa var. arizonica) and 10 subalpine fir (A. lasiocarpa var. lasiocarpa) seed sources were grown at the University of Idaho Sandpoint Research and Extension Center (SREC) and two commercial nurseries in Idaho and Oregon. Post transplant mortality was highest...

Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yie...

Assessing the anticancer compounds Se-methylselenocysteine and glucosinolates in Se-biofortified broccoli (brassica oleracea L. var. italica) sprouts and florets

USDA-ARS?s Scientific Manuscript database

Broccoli (Brassica oleracea L. var. italica) is a rich source of chemopreventive compounds. Here, we evaluated and compared the effect of selenium (Se) treatment on the accumulation of anticancer compound Se-methylselenocysteine (SeMSCys) and glucosinolates in broccoli sprouts and florets. Total Se ...

40 CFR 180.41 - Crop group tables.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... var. bulbiferum L.H. Bailey; A. cepa L. var. viviparum (Metz.) Alef.) 3-07B Onion, Welsh, tops (Allium... Tahiti lime, Citrus latifolia (Yu. Tanaka) Tanaka 10-10B Tangelo, Citrus x tangelo J.W. Ingram & H.E... straw of all commodities included in the group cereal grains group. (22) Crop Group 17. Grass Forage...

Optimal Placement of Dynamic Var Sources by Using Empirical Controllability Covariance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Junjian; Huang, Weihong; Sun, Kai

In this paper, the empirical controllability covariance (ECC), which is calculated around the considered operating condition of a power system, is applied to quantify the degree of controllability of system voltages under specific dynamic var source locations. An optimal dynamic var source placement method addressing fault-induced delayed voltage recovery (FIDVR) issues is further formulated as an optimization problem that maximizes the determinant of ECC. The optimization problem is effectively solved by the NOMAD solver, which implements the mesh adaptive direct search algorithm. The proposed method is tested on an NPCC 140-bus system and the results show that the proposed methodmore » with fault specified ECC can solve the FIDVR issue caused by the most severe contingency with fewer dynamic var sources than the voltage sensitivity index (VSI)-based method. The proposed method with fault unspecified ECC does not depend on the settings of the contingency and can address more FIDVR issues than the VSI method when placing the same number of SVCs under different fault durations. It is also shown that the proposed method can help mitigate voltage collapse.« less

Trypsin inhibitors from Capsicum baccatum var. pendulum leaves involved in Pepper yellow mosaic virus resistance.

PubMed

Moulin, M M; Rodrigues, R; Ribeiro, S F F; Gonçalves, L S A; Bento, C S; Sudré, C P; Vasconcelos, I M; Gomes, V M

2014-11-07

Several plant organs contain proteinase inhibitors, which are produced during normal plant development or are induced upon pathogen attack to suppress the enzymatic activity of phytopathogenic microorganisms. In this study, we examined the presence of proteinase inhibitors, specifically trypsin inhibitors, in the leaf extract of Capsicum baccatum var. pendulum inoculated with PepYMV (Pepper yellow mosaic virus). Leaf extract from plants with the accession number UENF 1624, which is resistant to PepYMV, was collected at 7 different times (0, 24, 48, 72, 96, 120, and 144 h). Seedlings inoculated with PepYMV and control seedlings were grown in a growth chamber. Protein extract from leaf samples was partially purified by reversed-phase chromatography using a C2/C18 column. Residual trypsin activity was assayed to detect inhibitors followed by Tricine-SDS-PAGE analysis to determine the N-terminal peptide sequence. Based on trypsin inhibitor assays, trypsin inhibitors are likely constitutively synthesized in C. baccatum var. pendulum leaf tissue. These inhibitors are likely a defense mechanism for the C. baccatum var. pendulum- PepYMV pathosystem.

Part I. Metabolites of Penicillium verrucosum var. cyclopium; Part II. Regioselective deuteriations of deoxyribose and incorporation into deoxynucleosides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hodge, R.P.

1988-01-01

Penicillium verrucosum var. cyclopium is the fungus responsible for several outbreaks of neurotoxicoses among cattle in Tennessee beginning in 1979. Verrucosidin isolated from samples of P. verrucosum var. cyclopium was later shown to be a powerful neurotoxin capable of paralyzing its victims and was also said to cause tremoring in some cases. Part I of this dissertation describes the re-investigation of metabolites of P. verrucosum var. cyclopium and tremorgenicity of verrucosidin. Verrucosidin has been shown in this study to be non-tremorgenic. This research also describes development of efficient synthetic methods for incorporation of deuterium into the deoxyribose moiety of deoxyribonucleosides.more » Deuteriated deoxynucleosides are presently being considered for synthesis of deuteriated sequences of DNA to be utilized in {sup 1}H NMR studies of solution conformation and dynamics, as well as interactions with proteins, drugs, metals and carcinogens. A route for synthesizing 2-deoxy-D-ribose from D-ribonic-acid-{gamma}-lactone incorporating deuterium at the C-1, C-2 or C-5 positions is presented.« less

[Simultaneous determination of 4 diterpenoids in Rabdosia japonica var.glaucocalyx by HPLC-ESI-MS/MS and cluster analysis].

PubMed

Tian, Ting-Ting; Ma, Ying-Hua; Xie, Wei-Wei; Jin, Yi-Ran; Xu, Hui-Jun; Zhang, Lan-Tong; Du, Ying-Feng

2016-01-01

A quick HPLC-ESI-MS/MS method was established for simultaneous determination of four major diterpenoids in Rabdosia japonica var.glaucocalyx, including glaucocalyxin A, oridonin, hebeirubesensin and enmenol. Analysis was performed on an Agilent ZORBAX SB-C18(4.6 mm×250 mm, 5 μm ) column eluted in a gradient program with methanol and water. The flow rate was 0.8 mL•min⁻¹. Multiple reaction monitoring (MRM) scanning mode was performed in negative ion switching mode to apply for the quantitative determination. The calibration curves for the above four compounds were linear in corresponding injection amount. The average recoveries of the compounds ranged from 92.40% to 105.9%, with RSDs of 1.7%-6.5%. The method is simple, rapid, accurate with good repeatability, which can provide a reference for overcalling evaluation the quality of R. japonica var.glaucocalyx. The result of cluster analysis- showed that the quality of R. japonica glaucocalyx var. greatly varied between areas and parts. Copyright© by the Chinese Pharmaceutical Association.

Analysis of the relationship between Chalcone Isomerase gene expression level and rutin production in Ficus deltoidea var. deltoidea and F. deltoidea var. angustifolia

NASA Astrophysics Data System (ADS)

Najid, Najihah Mohd; Zain, Che Radziah Che Mohd; Zainal, Zamri

2016-11-01

Ficus deltoidea (moraceae) is a herbal plant with medicinal values. Previous studies reported that the F. deltoidea contains a high level of bioactive compounds such as flavonoids. A cDNA encodes for chalcone isomerase was identified from F. deltoidea, designated as FdCHI, which involved in the isomerization of naringenin chalcone to naringenin. Naringenin is a key branch point for the synthesis of rutin, which is believed involved in defense mechanism in the plant. Therefore, we hypothesized that there might be a direct relationship between FdCHI expression level and rutin production in leaves of F. deltoidea var. deltoidea (FDD) and F. deltoidea var. angustifolia (FDA). Our result showed that expression level of FdCHI in leaves FDD was greater than FDA. Analysis of High Performance Liquid Chromatography (HPLC) revealed that rutin was only detected in FDA leaves. Based on the results between FdCHI expression and rutin production, this study concluded that there is no relationship between FdCHI expression and rutin production in leaves of FDA and FDD.

Estimation of value at risk in currency exchange rate portfolio using asymmetric GJR-GARCH Copula

NASA Astrophysics Data System (ADS)

Nurrahmat, Mohamad Husein; Noviyanti, Lienda; Bachrudin, Achmad

2017-03-01

In this study, we discuss the problem in measuring the risk in a portfolio based on value at risk (VaR) using asymmetric GJR-GARCH Copula. The approach based on the consideration that the assumption of normality over time for the return can not be fulfilled, and there is non-linear correlation for dependent model structure among the variables that lead to the estimated VaR be inaccurate. Moreover, the leverage effect also causes the asymmetric effect of dynamic variance and shows the weakness of the GARCH models due to its symmetrical effect on conditional variance. Asymmetric GJR-GARCH models are used to filter the margins while the Copulas are used to link them together into a multivariate distribution. Then, we use copulas to construct flexible multivariate distributions with different marginal and dependence structure, which is led to portfolio joint distribution does not depend on the assumptions of normality and linear correlation. VaR obtained by the analysis with confidence level 95% is 0.005586. This VaR derived from the best Copula model, t-student Copula with marginal distribution of t distribution.

Nutritional and anti-nutritional potential of three accessions of itching bean (Mucuna pruriens (L.) DC var. pruriens): an under-utilized tribal pulse.

PubMed

Kala, Balasubiramanian Kamatchi; Mohan, Veerabahu Ramasamy

2010-08-01

Three accessions of the under-utilized legume itching bean (Mucuna pruriens var. pruriens) were analysed for proximate composition, mineral profiles, vitamins (niacin and ascorbic acid), fatty acid profiles, amino acid profiles of total seed protein, in vitro protein digestibility and certain anti-nutritional factors. All three accessions of M. pruriens var. pruriens contained higher amounts of crude protein and crude lipid when compared with most of the commonly consumed pulses. The fatty acid profiles revealed that the seed lipids contained a higher concentration of palmitic acid and linoleic acids. Amino acid profiles of M. pruriens var. pruriens revealed that the seed protein contained relatively higher levels of certain essential amino acids compared with the FAO/WHO requirement pattern. The investigated seeds are rich in minerals such as potassium, calcium, magnesium, phosphorus, iron and manganese. Anti nutritional substances such as total free phenolics, tannins, 3,4-dihydroxyphenylalanine, phytic acid, hydrogen cyanide, trypsin inhibitor activity, oligosaccharides and phytohaemagglutinating activity were investigated. The anti-nutritional fatty acid, behenic acid, also was detected in the present study.

The distinct proteome of placental malaria parasites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fried, Michal; Hixson, Kim K.; Anderson, Lori

Malaria proteins expressed on the surface of Plasmodium falciparum infected erythrocytes (IE) mediate adhesion and are targeted by protective immune responses. During pregnancy, IE sequester in the placenta. Placental IE bind to the molecule chondroitin sulfate A (CSA) and preferentially transcribe the gene that encodes VAR2CSA, a member of the PfEMP1 variant surface antigen family. Over successive pregnancies women develop specific immunity to CSA-binding IE and antibodies to VAR2CSA. We used tandem mass spectrometry together with accurate mass and time tag technology to study IE membrane fractions of placental parasites. VAR2CSA peptides were detected in placental IE and in IEmore » from children, but the MC variant of VAR2CSA was specifically associated with placental IE. We identified six conserved hypothetical proteins with putative TM or signal peptides that were exclusively expressed by the placental IE, and 11 such proteins that were significantly more abundant in placental IE. One of these hypothetical proteins, PFI1785w, is a 42kDa molecule detected by Western blot in parasites infecting pregnant women but not those infecting children.« less

Total alpha-globin gene cluster deletion has high frequency in Filipinos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunt, J.A.; Haruyama, A.Z.; Chu, B.M.

1994-09-01

Most {alpha}-thalassemias [Thal] are due to large deletions. In Southeast Asians, the (--{sup SEA}) double {alpha}-globin gene deletion is common, 3 (--{sup Tot}) total {alpha}-globin cluster deletions are known: Filipino (--{sup Fil}), Thai (--{sup Thai}), and Chinese (--{sup Chin}). In a Hawaii Thal project, provisional diagnosis of {alpha}-Thal-1 heterozygotes was based on microcytosis, normal isoelectric focusing, and no iron deficiency. One in 10 unselected Filipinos was an {alpha}-Thal-1 heterozygote, 2/3 of these had a (--{sup Tot}) deletion: a {var_sigma}-cDNA probe consistently showed fainter intensity of the constant 5.5 kb {var_sigma}{sub 2} BamHI band, with no heterzygosity for {var_sigma}-globin region polymorphisms;more » {alpha}-cDNA or {var_sigma}-cDNA probes showed no BamHI or BglII bands diagnostic of the (--{sup SEA}) deletion; bands for the (-{alpha}) {alpha}-Thal-2 single {alpha}-globin deletions were only seen in Hb H cases. A reliable monoclonal anti-{var_sigma}-peptide antibody test for the (--{sup SEA}) deletion was always negative in (--{sup Tot}) samples. Southern digests with the Lo probe, a gift from D. Higgs of Oxford Univ., confirmed that 49 of 50 (--{sup Tot}) chromosomes in Filipinos were (--{sup Fil}). Of 20 {alpha}-Thal-1 hydrops born to Filipinos, 11 were (--{sup Fil}/--{sup SEA}) compound heterozygotes; 9 were (--{sup SEA}/--{sup SEA}) homozygotes, but none was a (--{sup Fil}/--{sup Fil}).« less

Diverse Functional Outcomes of Plasmodium falciparum Ligation of EPCR: Potential Implications for Malarial Pathogenesis

PubMed Central

Gillrie, Mark R.; Avril, Marion; Brazier, Andrew J.; Davis, Shevaun P.; Stins, Monique F.; Smith, Joseph D.; Ho, May

2015-01-01

Summary P. falciparum-infected erythrocytes (IRBC) expressing the domain cassettes (DC) 8 and 13 of the cytoadherent ligand PfEMP1 adhere to the endothelial protein C receptor (EPCR). By interfering with EPCR anti-coagulant and pro-endothelial barrier functions, IRBC adhesion could promote coagulation and vascular permeability that contribute to the pathogenesis of cerebral malaria. In this study, we examined adhesion of DC8- and DC13-expressing parasite lines to endothelial cells from different microvasculature, and the consequences of EPCR engagement on endothelial cell function. We found that IRBC from IT4var19 (DC8) and IT4var07 (DC13) parasite lines adhered to human brain, lung, and dermal endothelial cells under shear stress. However, the relative contribution of EPCR to parasite cytoadherence on the different types of endothelial cell varied. We also observed divergent functional outcomes for DC8 CIDRα1.1 and DC13 CIDRα1.4 domains. IT4var07 CIDRα1.4 inhibited generation of activated protein C (APC) on lung and dermal endothelial cells and blocked the APC-EPCR binding interaction on brain endothelial cells. IT4var19 CIDRα1.1 inhibited thrombin-induced endothelial barrier dysfunction in lung endothelial cells, while IT4var07 CIDRα1.4- inhibited the protective effect of APC on thrombin-induced permeability. Overall, these findings reveal a much greater complexity of how CIDRα1-expressing parasites may modulate malaria pathogenesis through EPCR adhesion. PMID:26119044

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

PubMed Central

Jia, Peilin; Zhao, Zhongming

2014-01-01

A major challenge in interpreting the large volume of mutation data identified by next-generation sequencing (NGS) is to distinguish driver mutations from neutral passenger mutations to facilitate the identification of targetable genes and new drugs. Current approaches are primarily based on mutation frequencies of single-genes, which lack the power to detect infrequently mutated driver genes and ignore functional interconnection and regulation among cancer genes. We propose a novel mutation network method, VarWalker, to prioritize driver genes in large scale cancer mutation data. VarWalker fits generalized additive models for each sample based on sample-specific mutation profiles and builds on the joint frequency of both mutation genes and their close interactors. These interactors are selected and optimized using the Random Walk with Restart algorithm in a protein-protein interaction network. We applied the method in >300 tumor genomes in two large-scale NGS benchmark datasets: 183 lung adenocarcinoma samples and 121 melanoma samples. In each cancer, we derived a consensus mutation subnetwork containing significantly enriched consensus cancer genes and cancer-related functional pathways. These cancer-specific mutation networks were then validated using independent datasets for each cancer. Importantly, VarWalker prioritizes well-known, infrequently mutated genes, which are shown to interact with highly recurrently mutated genes yet have been ignored by conventional single-gene-based approaches. Utilizing VarWalker, we demonstrated that network-assisted approaches can be effectively adapted to facilitate the detection of cancer driver genes in NGS data. PMID:24516372

VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.

PubMed

Jia, Peilin; Zhao, Zhongming

2014-02-01

A major challenge in interpreting the large volume of mutation data identified by next-generation sequencing (NGS) is to distinguish driver mutations from neutral passenger mutations to facilitate the identification of targetable genes and new drugs. Current approaches are primarily based on mutation frequencies of single-genes, which lack the power to detect infrequently mutated driver genes and ignore functional interconnection and regulation among cancer genes. We propose a novel mutation network method, VarWalker, to prioritize driver genes in large scale cancer mutation data. VarWalker fits generalized additive models for each sample based on sample-specific mutation profiles and builds on the joint frequency of both mutation genes and their close interactors. These interactors are selected and optimized using the Random Walk with Restart algorithm in a protein-protein interaction network. We applied the method in >300 tumor genomes in two large-scale NGS benchmark datasets: 183 lung adenocarcinoma samples and 121 melanoma samples. In each cancer, we derived a consensus mutation subnetwork containing significantly enriched consensus cancer genes and cancer-related functional pathways. These cancer-specific mutation networks were then validated using independent datasets for each cancer. Importantly, VarWalker prioritizes well-known, infrequently mutated genes, which are shown to interact with highly recurrently mutated genes yet have been ignored by conventional single-gene-based approaches. Utilizing VarWalker, we demonstrated that network-assisted approaches can be effectively adapted to facilitate the detection of cancer driver genes in NGS data.

Chloroethyinitrosourea-derived ethano cytosine and adenine adducts are substrates for escherichia coli glycosylases excising analogous etheno adducts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guliaev, Anton B.; Singer, B.; Hang, Bo

2004-05-05

Exocyclic ethano DNA adducts are saturated etheno ring derivatives formed mainly by therapeutic chloroethylnitrosoureas (CNUs), which are also mutagenic and carcinogenic. In this work, we report that two of the ethano adducts, 3,N{sup 4}-ethanocytosine (EC) and 1,N{sup 6}-ethanoadenine (EA), are novel substrates for the Escherichia coli mismatch-specific uracil-DNA glycosylase (Mug) and 3-methyladenine DNA glycosylase II (AlkA), respectively. It has been shown previously that Mug excises 3,N{sup 4}-ethenocytosine ({var_epsilon}C) and AlkA releases 1,N{sup 6}-ethenoadenine ({var_epsilon}A). Using synthetic oligonucleotides containing a single ethano or etheno adduct, we found that both glycosylases had a {approx}20-fold lower excision activity toward EC or EA thanmore » that toward their structurally analogous {var_epsilon}C or {var_epsilon}A adduct. Both enzymes were capable of excising the ethano base paired with any of the four natural bases, but with varying efficiencies. The Mug activity toward EC could be stimulated by E. coli endonuclease IV and, more efficiently, by exonuclease III. Molecular dynamics (MD) simulations showed similar structural features of the etheno and ethano derivatives when present in DNA duplexes. However, also as shown by MD, the stacking interaction between the EC base and Phe 30 in the Mug active site is reduced as compared to the {var_epsilon}C base, which could account for the lower EC activity observed in this study.« less

Callus induction of leaf explant Piper betle L. Var Nigra with combination of plant growth regulators indole-3-acetic acid (IAA), benzyl amino purin (BAP) and kinetin

NASA Astrophysics Data System (ADS)

Junairiah, Zuraidassanaaz, Nabilah Istighfari; Izdihar, Fairuz Nabil; Manuhara, Yosephine Sri Wulan

2017-09-01

The purpose of this research was to determine the combination of plant growth regulators IAA, BAP and kinetin towards callus induction and growth of leaf explants Piper betle L. VarNigra. Explants from leaf of Piper betle L. VarNigra was cultured on MS medium with 24 treatment combinations of plant growth regulators IAA and BAP and 24 treatment combinations of plant growth regulators IAA and kinetin with 0.0;0.5;1.0;1.5;2.0 mg/L concentration respectively, the observed variable were the length of time the formation of callus, callus morphology, fresh and dry weight of callus. The results of this research showed that the combination of growth regulators IAA with BAP and kinetin had effects on leaf growth of Piper betle L. VarNigra. During 8 weeks observation, it indicated that the combination of concentration IAA 0.5 mg/L and BAP 2.0 mg/L showed fastest callus formation at 8.5 days. Combination of concentration IAA 1.0 mg/L and BAP 1.5 mg/L showed the highest of fresh weight at 0.6596 grams, and the highest dry weight was obtained from the combination of concentration IAA 0.5 mg/L and BAP 0.5 mg/L at 0.0727 grams. Combination of concentration IAA 1.0 mg/L and kinetin 1.5 mg/L had the highest of fresh weight at 0.2972 grams and the highest dry weight at 0.1660 grams. Callus of Piper betle L. VarNigra had two textures, that were compact and friable, and also showed various kind of colors, like white, greenish white, yellowish white, tanned white, brown and black. Based on this research, that concentration IAA 1.0 mg/L and 1.5 mg/L kinetin was the best combination for induction of callus from leaf of Piper betle L. Var Nigra.

[Regeneration characteristics of woody plant seedlings in typical secondary forests in Qinling Mountains].

PubMed

Kang, Bing; Liu, Shi-Rong; Wang, De-Xiang; Zhang, Ying; Liu, Hong-Ru; Du, Yan-Ling

2011-12-01

By using sampling plot method, an investigation was conducted on the regeneration characteristics of woody plant seedlings in five kinds of typical secondary forests (Pinus tabulaeformis, Quercus valiena var. acuteserrata, Betula albo-sinensis, Picea asperata, and Pinus armandii) in Qinling Mountains. There was an obvious species differentiation of woody plant seedlings and saplings in the forests. Except for Q. valiena var. acuteserrata and P. armandii forests, the similarity coefficient of the seedlings and saplings species in the forests was lower. The seedlings and saplings quantity, species richness index, Simpson dominance index, and evenness index were higher in P. tabulaeformis and Q. valiena var. acuteserrata forests, the lowest in B. albo-sinensis forest, and basically the same in P. asperata and P. armandii forests. The percentages of the seedlings and saplings in the five forests had significant differences (P < 0.05). Except in B. albo-sinensis forest where the percentage of the saplings was higher, the percentage of the seedlings in the other stands was larger, and in the order of P. asperata forest > P. tabulaeformis forest > Q. valiena var. acuteserrata forest > P. armandii forest, respectively. The sprouting percentage of the seedlings in different forests had significant difference (P < 0.05), and was in the sequence of P. armandii forest > P. asperata forest > B. albo-sinensis forest > Q. valiena var. acuteserrata forest > P. tabulaeformis forest. In Q. valiena var. acuteserrata and P. tabulaeformis forests, the percentage of tree seedlings was the highest, occupying 68% and 51.4% of the total number of woody seedlings, respectively, and their communities were in the medium succession period, with a stronger persistent regeneration capability; in P. asperata and P. armandii forests, the percentage of tree seedlings was 40% and 15%, respectively, and their communities were in the late succession period, with a rather poor regeneration capability; while in B. albo-sinensis forest, the seedlings were difficult to develop into saplings, and thus, its continuous persistent regeneration capability was lack.

Combined varenicline and naltrexone treatment reduces smoking topography intensity in heavy-drinking smokers.

PubMed

Roche, Daniel J O; Bujarski, Spencer; Hartwell, Emily; Green, ReJoyce; Ray, Lara A

2015-07-01

Heavy drinking smokers constitute a distinct sub-population of smokers for whom traditional smoking cessation therapies may not be effective. Recent evidence suggested that combined varenicline (VAR) and naltrexone (NTX) therapy may be more efficacious than either monotherapy alone in reducing smoking and drinking-related behavior in this population. The manner in which individuals smoke a cigarette (i.e., smoking topography) may be predictive of smoking cessation outcomes, yet the effects of smoking pharmacotherapies on puffing behavior have not been thoroughly examined. Therefore, the current double-blind medication study examined the effects of VAR alone (1mg BID), low dose NTX alone (25mg QD), the combination of VAR+NTX, and placebo on smoking topography measures in heavy drinking, non-treatment seeking daily smokers (n=120). After a 9-day titration period, participants completed a laboratory session in which they smoked their first cigarette of the day using a smoking topography device following 12h of nicotine abstinence and consumption of an alcoholic beverage (BrAC=0.06g/dl). The primary measures were puff count, volume, duration, and velocity and inter-puff interval (IPI). Independent of medication group, puff velocity and IPI increased, while puff volume and duration decreased, over the course of the cigarette. The active medication groups, vs. the placebo group, had significantly blunted puff duration and velocity slopes over the course of the cigarette, and this effect was particularly evident in the VAR+NTX group. Additionally, the VAR+NTX group demonstrated lower average IPI than the monotherapy groups and lower average puff volume than all other groups. These results suggest that smoking pharmacotherapies, particularly the combination of VAR+NTX, alter smoking topography in heavy drinking smokers, producing a pattern of less intense puffing behavior. As smoking topography has been predictive of the ability to quit smoking, future studies should examine how smoking pharmacotherapies' effects on puffing behavior relate to smoking cessation outcomes. Copyright © 2015. Published by Elsevier Inc.

Combined Varenicline and naltrexone treatment reduces smoking topography intensity in heavy-drinking smokers

PubMed Central

Roche, Daniel J.O.; Bujarski, Spencer; Hartwell, Emily; Green, ReJoyce; Ray, Lara A.

2015-01-01

Heavy drinking smokers constitute a distinct sub-population of smokers for whom traditional smoking cessation therapies may not be effective. Recent evidence suggested that combined varenicline (VAR) and naltrexone (NTX) therapy may be more efficacious than either monotherapy alone in reducing smoking and drinking-related behavior in this population. The manner in which individuals smoke a cigarette (i.e., smoking topography) may be predictive of smoking cessation outcomes, yet the effects of smoking pharmacotherapies on puffing behavior have not been thoroughly examined. Therefore, the current double-blind medication study examined the effects of VAR alone (1mg BID), low dose NTX alone (25mg QD), the combination of VAR+NTX, and placebo on smoking topography measures in heavy drinking, non-treatment seeking daily smokers (n=120). After a 9-day titration period, participants completed a laboratory session in which they smoked their first cigarette of the day using a smoking topography device following 12-hrs of nicotine abstinence and consumption of an alcoholic beverage (BrAC = 0.06 g/dl). The primary measures were puff count, volume, duration, and velocity and inter-puff interval (IPI). Independent of medication group, puff velocity and IPI increased, while puff volume and duration decreased, over the course of the cigarette. The active medication groups, vs. the placebo group, had significantly blunted puff duration and velocity slopes over the course of the cigarette, and this effect was particularly evident in the VAR+NTX group. Additionally, the VAR+NTX group demonstrated lower average IPI than the monotherapy groups and lower average puff volume than all other groups. These results suggest that smoking pharmacotherapies, particularly the combination of VAR+NTX, alter smoking topography in heavy drinking smokers, producing a pattern of less intense puffing behavior. As smoking topography has been predictive of the ability to quit smoking, future studies should examine how smoking pharmacotherapies’ effects on puffing behavior relate to smoking cessation outcomes. PMID:25933795

B-Cell Responses to Pregnancy-Restricted and -Unrestricted Plasmodium falciparum Erythrocyte Membrane Protein 1 Antigens in Ghanaian Women Naturally Exposed to Malaria Parasites

PubMed Central

Ampomah, Paulina; Stevenson, Liz; Ofori, Michael F.; Barfod, Lea

2014-01-01

Protective immunity to Plasmodium falciparum malaria acquired after natural exposure is largely antibody mediated. IgG-specific P. falciparum EMP1 (PfEMP1) proteins on the infected erythrocyte surface are particularly important. The transient antibody responses and the slowly acquired protective immunity probably reflect the clonal antigenic variation and allelic polymorphism of PfEMP1. However, it is likely that other immune-evasive mechanisms are also involved, such as interference with formation and maintenance of immunological memory. We measured PfEMP1-specific antibody levels by enzyme-linked immunosorbent assay (ELISA) and memory B-cell frequencies by enzyme-linked immunosorbent spot (ELISPOT) assay in a cohort of P. falciparum-exposed nonpregnant Ghanaian women. The antigens used were a VAR2CSA-type PfEMP1 (IT4VAR04) with expression restricted to parasites infecting the placenta, as well as two commonly recognized PfEMP1 proteins (HB3VAR06 and IT4VAR60) implicated in rosetting and not pregnancy restricted. This enabled, for the first time, a direct comparison in the same individuals of immune responses specific for a clinically important parasite antigen expressed only during well-defined periods (pregnancy) to responses specific for comparable antigens expressed independent of pregnancy. Our data indicate that PfEMP1-specific B-cell memory is adequately acquired even when antigen exposure is infrequent (e.g., VAR2CSA-type PfEMP1). Furthermore, immunological memory specific for VAR2CSA-type PfEMP1 can be maintained for many years without antigen reexposure and after circulating antigen-specific IgG has disappeared. The study provides evidence that natural exposure to P. falciparum leads to formation of durable B-cell immunity to clinically important PfEMP1 antigens. This has encouraging implications for current efforts to develop PfEMP1-based vaccines. PMID:24566620

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)

PubMed Central

Shih, Kai-Ming; Chang, Chung-Te; Chung, Jeng-Der; Chiang, Yu-Chung; Hwang, Shih-Ying

2018-01-01

Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana. PMID:29449860

[Chemical constituents of Pileostegia viburnoides var. glabrescens].

PubMed

Zou, Ju-ying; Chen, Sheng-huang; Li, Qin-wen; Ou, Yang-wen; Chen, Han-jun; Wang, Wei

2012-05-01

To study the chemical constituents of Pileostegia viburnoides var. glabrescens. The compounds were isolated and purified by various techniques. Their structures were determined by physicochemical properties and spectral analysis. Five compounds were isolated and identified as friedelin (1), beta-sitosterol (2), umbelliferone (3), daucosterol (4) and skimmin (5). All the compounds were isolated from this genus for the first time.

Combined effect of seaweed (Sargassum wightii) and Bacillus thuringiensis var. israelensis on the coastal mosquito,Anopheles sundaicus, in Tamil Nadu, India

USDA-ARS?s Scientific Manuscript database

Studies were made of the extract of Sargassum wightii combined with Bacillus thuringiensis var. israelensis (Bti) for control of the malaria vector Anopheles sundaicus. Treatment of mosquito larvae with 0.001% S. wightii extract indicated median lethal concentrations (LC50) of 88, 73, 134, 156, and...

Geographical Variation in the Terpene Composition of the Leaf Oil of Douglas Fir,

DTIC Science & Technology

The two forms of Douglas fir, Pseudotsuga menziesii var. menziesii and var. glauca, differ quite considerably with regard to the monoterpenes of...their leaf oils. Several chemical races, differing quantitatively in certain monoterpenes , appear to exist in each variety and the leaf oil composition seems to be particularly useful in classifying intermediate forms. (Author)

Rauniticine-allo-oxindole B and rauniticinic-allo acid B, new heteroyohimbine-type oxindole alkaloids from the stems of Malaysian Uncaria longiflora var. pteropoda.

PubMed

Salim, Fatimah; Ismail, Nor Hadiani; Awang, Khalijah; Ahmad, Rohaya

2011-08-04

Two new heteroyohimbine-type oxindole alkaloids, rauniticine-allo-oxindole B and rauniticinic-allo acid B, have been successfully isolated from the stems extract of Malaysian Uncaria longiflora var. pteropoda. The structures of the two new alkaloids were determined by spectroscopic analysis.

[The benthic red alga Ceramium ciliatum var. robustum (J.Ag.) G. Mazoyer is a remarkable biological indicator of littoral mercury pollution].

PubMed

Augier, H; Gilles, G; Ramonda, G

1977-02-07

The study of mercury composition of red Algae Ceranium ciliatum var. robustum, comparatively with other marine organisms and considering its growth and the extent of pollution at various harvesting points: reveals that this seaweed constitutes a conspicuous biological indicator for the littoral mercury pollution.

Differences in volatile profiles between populations of Ceratoides lanata var. subspinosa (Rydb.)

Treesearch

J.T. Howell; Mary Lucero; Rick Estell; Dean Anderson; Ed Fredrickson; Marta Remmenga

2007-01-01

Ceratoides lanata (Rydb.) J.T. Howell, common winterfat, is valued for its nutrient content and palatability to livestock; however, the subspecies Ceratoides lanata var. subspinosa (Rydb.) J.T. Howell, (‘subspinosa’) is considered unpalatable. Curiously, observations of ‘subspinosa’ revealed several populations...

HYDROLOGICAL AND CLIMATIC RESPONSES OF OLD-GROWTH PINUS ELLIOTTII VAR. DENSA IN MESIC PINE FLATWOODS FLORIDA, USA

EPA Science Inventory

Pinus elliottii Englem. var. densa Little & Dorman (Southern Slash Pine) is unique in that it is the only native sub-tropical pine in the USA. Once occupying much of the south Florida landscape, it is now restricted to an estimated 3% of its pre human settlement area. Land manag...

Family differences in equations for predicting biomass and leaf area in Douglas-fir (Pseudotsuga menziesii var. menziesii).

Treesearch

J.B. St. Clair

1993-01-01

Logarithmic regression equations were developed to predict component biomass and leaf area for an 18-yr-old genetic test of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco var. menziesii) based on stem diameter or cross-sectional sapwood area. Equations did not differ among open-pollinated families in slope, but intercepts...

Composition, mosquito larvicidal, biting deterrent and antifungal activity of essential oils of different plant parts of Cupressus arizonica var. glabra (Carolina Sapphire)

USDA-ARS?s Scientific Manuscript database

Essential oils obtained from the hydrodistillation of female cones (FC), male cones (MC), needles-twigs (NT) and wood barks (WB) of ‘Carolina Sapphire’ [Cupressus arizonica var glabra (Sudw.) Little] were analyzed simultaneously by gas chromatography (GC) and gas chromatography–mass spectrometry (GC...

Morphology and accumulation of epicuticular wax on needles of Douglas-fir (Pseudotsuga menziesii var. menziesii)

Treesearch

Constance A. Harrington; William C. Carlson

2015-01-01

Past studies have documented differences in epicuticular wax among several tree species but little attention has been paid to changes in accumulation of foliar wax that can occur during the year. We sampled current-year needles from the terminal shoots of Douglas-fir (Pseudotsuga menziesii var. menziesii) in late June/early...

First Report of Soybean Rust, Caused by Phakopsora pachyrhizi, on Kudzu (Pueraria montana var. lobata) in Illinois

USDA-ARS?s Scientific Manuscript database

Soybean rust, caused by Phakopsora pachyrhizi, was first observed on soybean (Glycine max) in the continental United States in Louisiana in 2004, and on kudzu (Pueraria montana var. lobata) in the United States in 2005. Kudzu is a leguminous weed that is prevalent in the southern United States with ...

First report of downy mildew disease caused by Plasmopara halstedii on the native Rudbeckia fulgida Aiton var. speciosa (Wender.)

USDA-ARS?s Scientific Manuscript database

The showy black-eyed Susan Rudbeckia fulgida Aiton var. speciosa (Wender.) is an important perennial wildflower native to the Northeast and Midwest regions of the United States. Besides its aesthetic value in the landscape, this native plant attracts pollinators and provides seeds for birds during t...

Characterization of the pH-Mediated solubility of Bacillus thuringiensis var. san diego native δ-endotoxin crystals

Treesearch

C. N. Koller; L. S. Bauer; R. M. Hollingworth

1992-01-01

Native crystals of Bacillus thuringiensis var. san diego, a coleopteran-specific δ-endotoxin, were metabolically labeled with [35S]methionine. Specific activity was 82,000 CPM/μg (2.44 Ci/mmol). Using a universal buffer formulated with the same ionic strength at every pH, we determined that...

Mycena sect. Hygrocyboideae in the mountains of the Dominican Republic

Treesearch

D. Jean Lodge; B.A. Perry; D.E. Desjardin

2004-01-01

A collection of Mycena epipterygia from montane cloud forest in the Dominican Republic was found to have one-fourth to one-half monosporous basidia mixed with bisporous basidia. It is described as a new variety, M. epipterygia var. domingensis Lodge, differing from M. epipterygia var. epipterygioides and other two-spored varieties in having smaller dimensions of spores...

Seed Source Significantly Influences Growth Rates and Disease Resistance of Abies Lasiocarpa Grown for Ornamental Nursery Stock and Christmas Trees

USDA-ARS?s Scientific Manuscript database

Trees from six corkbark fir (Abies lasiocarpa var. arizonica) and 10 subalpine fir (Abies lasiocarpa var. lasiocarpa) seed sources were grown at the University of Idaho (SREC) and three commercial nurseries in northern Idaho and northeastern Oregon. Post transplant mortality was highest during the f...

Disseminated Nosocomial Fungal Infection by Aureobasidium pullulans var. melanigenum: a Case Report

PubMed Central

Bolignano, Giuseppe; Criseo, Giuseppe

2003-01-01

We report on a rare case of disseminated nosocomial fungal infection due to Aureobasidium pullulans var. melanigenum in a severely traumatized patient. Repeated blood and urine cultures yielded multicellular filamentous hyphal structures of varying size accompanied by budding yeast-like-cells of ellipsoidal morphology. The patient became asymptomatic after fluconazole therapy. PMID:12958301

Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca). IV. Montana and Idaho near the Continental Divide

Treesearch

Gerald Rehfeldt

1988-01-01

Seventy-seven seedling populations of Douglas-fir (Pseudotsuga menziesii var. glauca) sampled from near the Continental Divide in Idaho and Montana exhibited pronounced genetic differences when compared in three common environments. Differentiation involved several traits that are components of an annual developmental cycle that must be completed within a growing...

Genome Sequence of the Thermotolerant Yeast Kluyveromyces marxianus var. marxianus KCTC 17555

PubMed Central

Jeong, Haeyoung; Lee, Dae-Hee; Kim, Sun Hong; Kim, Hyun-Jin; Lee, Kyusang; Song, Ju Yeon; Kim, Byung Kwon; Sung, Bong Hyun; Sohn, Jung Hoon; Koo, Hyun Min

2012-01-01

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548). PMID:23193140

Chemical Composition and Mosquitocidal activity of n-Hexane and Methanol Extracts from Euphorbia anacampseros var. tmolea, an endemic species of Turkey, against Aedes aegypti

USDA-ARS?s Scientific Manuscript database

New and safe mosquito control agents are necessary due to increasing resistance to synthetic insecticides and environmental change. The mosquito larvicidal and adulticidal activity and chemical composition of Euphorbia anacampseros var. tmolea extracts are investigated in this article for the first ...

Transcriptome analysis and identification of genes associated with omega-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

USDA-ARS?s Scientific Manuscript database

Background: Perilla (Perilla frutescens (L.) var frutescens) produces high levels of a-linolenic acid (ALA), an omega-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cD...

The Chilling Optimum of Idaho and Arizona Ponderosa Pine Buds

Treesearch

David L. Wenny; Daniel J. Swanson; R. Kasten Dumroese

2002-01-01

Ponderosa pine (Pinus ponderosa) seedlings from Idaho (var. ponderosa) and Arizona (var. scopulorum) grown in a container nursery received optimum chilling [2,010 hr (84 days) of temperatures below 5°C]. While seedlings were in the greenhouse, days required for 50% of the population to break bud were similar for both seed sources...

Tolerance of subzero winter cold in kudzu (Pueraria montana var. lobata) and its implications for northward migration in a warming climate

USDA-ARS?s Scientific Manuscript database

Kudzu (Pueraria montana var. lobata) is an important invasive species that was planted throughout southeastern North America until the mid-20th century. Winter survival is commonly assumed to control its distribution; however, its cold tolerance thresholds have not been determined. Here, we used bio...

Application of Autonomous Smart Inverter Volt-VAR Function for Voltage Reduction Energy Savings and Power Quality in Electric Distribution Systems: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Fei; Nagarajan, Adarsh; Baggu, Murali

This paper evaluated the impact of smart inverter Volt-VAR function on voltage reduction energy saving and power quality in electric power distribution systems. A methodology to implement the voltage reduction optimization was developed by controlling the substation LTC and capacitor banks, and having smart inverters participate through their autonomous Volt-VAR control. In addition, a power quality scoring methodology was proposed and utilized to quantify the effect on power distribution system power quality. All of these methodologies were applied to a utility distribution system model to evaluate the voltage reduction energy saving and power quality under various PV penetrations and smartmore » inverter densities.« less

Isolation of Cryptococcus neoformans var. neoformans from bird droppings, fruits and vegetables in Mexico City.

PubMed

López-Martínez, R; Castañón-Olivares, L R

1995-01-01

The presence of Cryptococcus neoformans in various natural sources, such as bird droppings, fruits and vegetables, was investigated. A total of 711 samples were analyzed; C. neoformans var. neoformans was isolated from seven out of 74 bird droppings (9.5%), with parrots as one of the most significant sources. Fruits were positive in 9.5% of the 169 samples studied, specially citrus fruits, particularly grapefruit, in which the highest frequency was found. From the 468 vegetable samples, only 20 were positive (4.2%). It is emphasized that five of the positive vegetables species are autochthonous to Mexico: avocado (Nectandra salicifolia), beet (Beta vulgaris var. quinopodiace), chayote (Sechium edule), stringbean (Cassia sp), and nopal (Opuntia ficus-indica).

Pigment production on L-tryptophan medium by Cryptococcus gattii and Cryptococcus neoformans.

PubMed

Chaskes, Stuart; Cammer, Michael; Nieves, Edward; Casadevall, Arturo

2014-01-01

In recent years strains previously grouped within Cryptococcus neoformans have been divided into two species C. neoformans and C. gattii, with Cryptococcus neoformans comprising serotypes A, D, and AD and C. gattii comprising serotypes B and C. Cryptococcus neoformans have also been subdivided into two varieties C. neoformans var. grubii, serotype A, and C. neoformans var. neoformans, serotype D. We analyzed the growth and pigment production characteristics of 139 strains of Cryptococcus spp. in L-tryptophan containing media. Nearly all strains of Cryptococcus, including each variety and serotype tested produced a pink water-soluble pigment (molecular weight of 535.2 Da) from L-tryptophan. Consequently, the partial separation of the species was based on whether the pink pigment was secreted into the medium (extracellular) or retained as an intracellular pigment. On L-tryptophan medium C. neoformans var. grubii and serotype AD produced a pink extracellular pigment. In contrast, for C. gattii, the pink pigment was localized intracellularly and masked by heavy production of brown pigments. Pigment production by C. neoformans var. neoformans was variable with some strains producing the pink extracellular pigment and others retained the pink pigment intracellularly. The pink intracellular pigment produced by strains of C. neoformans var. neoformans was masked by production of brown pigments. Cryptococcus laccase mutants failed to produce pigments from L-tryptophan. This is the first report that the enzyme laccase is involved in tryptophan metabolism. Prior to this report Cryptococcus laccase produced melanin or melanin like-pigments from heterocyclic compounds that contained ortho or para diphenols, diaminobenzenes and aminophenol compounds. The pigments produced from L-tryptophan were not melanin.

Chemical composition and some biological activities of the essential oils from basil Ocimum different cultivars.

PubMed

Avetisyan, Arpi; Markosian, Anahit; Petrosyan, Margarit; Sahakyan, Naira; Babayan, Anush; Aloyan, Samvel; Trchounian, Armen

2017-01-19

The plants belonging to the Ocimum genus of the Lamiaceae family are considered to be a rich source of essential oils which have expressed biological activity and use in different area of human activity. There is a great variety of chemotypes within the same basil species. Essential oils from three different cultivars of basil, O. basilicum var. purpureum, O. basilicum var. thyrsiflora, and O. citriodorum Vis. were the subjects of our investigations. The oils were obtained by steam distillation in a Clevenger-type apparatus. The gas chromatography mass selective analysis was used to determine their chemical composition. The antioxidant activities of these essential oils were measured using 1,1-diphenyl-2-picrylhydrazyl assays; the tyrosinase inhibition abilities of the given group of oils were also assessed spectophotometrically, and the antimicrobial activity of the essential oils was determined by the agar diffusion method, minimal inhibitory concentrations were expressed. According to the results, the qualitative and quantitative composition of essential oils was quite different: O. basilicum var. purpureum essential oil contained 57.3% methyl-chavicol (estragol); O. basilicum var. thyrsiflora oil had 68.0% linalool. The main constituents of O. citriodorum oil were nerol (23.0%) and citral (20.7%). The highest antioxidant activity was demonstrated by O. basilicum var. thyrsiflora essential oil. This oil has also exhibited the highest tyrosinase inhibition level, whereas the oil from O. citriodorum cultivar demonstrated the highest antimicrobial activity. The results obtained indicate that these essential oils have antioxidant, antibacterial and antifungal activity and can be used as natural antioxidant and antimicrobial agents in medicine, food industry and cosmetics.

Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.

PubMed

Rhodes, Johanna; Desjardins, Christopher A; Sykes, Sean M; Beale, Mathew A; Vanhove, Mathieu; Sakthikumar, Sharadha; Chen, Yuan; Gujja, Sharvari; Saif, Sakina; Chowdhary, Anuradha; Lawson, Daniel John; Ponzio, Vinicius; Colombo, Arnaldo Lopes; Meyer, Wieland; Engelthaler, David M; Hagen, Ferry; Illnait-Zaragozi, Maria Teresa; Alanio, Alexandre; Vreulink, Jo-Marie; Heitman, Joseph; Perfect, John R; Litvintseva, Anastasia P; Bicanic, Tihana; Harrison, Thomas S; Fisher, Matthew C; Cuomo, Christina A

2017-09-01

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically human immunodeficiency virus/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterize the major subdivisions, their relative diversity, and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii ( serotype AA) and of hybrids with C. neoformans var. neoformans (serotype AD) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil reveal that the previously "African" VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions; demonstrating the highly dispersive nature of this pathogen. Copyright © 2017 Rhodes et al.

Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands.

PubMed

Wallace, Lisa E; Wheeler, Gregory L; McGlaughlin, Mitchell E; Bresowar, Gerald; Helenurm, Kaius

2017-05-01

Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. DNA sequences were collected from nuclear (ADH) and plastid genomes ( rpL16 , ndhA , psbD-trnT ) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus , we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems. © 2017 Botanical Society of America.

Dry Heat Inactivation of Bacillus subtilis var. niger Spores as a Function of Relative Humidity

PubMed Central

Brannen, J. P.; Garst, D. M.

1972-01-01

Dry heat sterilization of Bacillus subtilis var. niger spores at 105 C is enhanced in the relative humidity range 0.03 to 0.2%. D-values of 115 and 125 C are predicted by a kinetic model with parameters set from 105 C data. These predictions are compared to observations. Images PMID:4625341

Responses of Wound-Inoculated Seedlings of Pinus elliottii var. elliottii and Pinus taeda to Mycelial Cultures Derived from Multople and Singel Basidiospores of Cronartium quercuum f. sp. fusiforme

Treesearch

T. Miller; K.P. Gramacho; R.A. Schmidt; H.V. Amerson; E.G. Kuhlman

1998-01-01

In 1991, a series of experiments was initiated to examine the effectiveness and research value of inoculating 6-week-old seedlings of slash (Pinus elliottii var. elliottii) and loblolly pine (P. raeda) with suspensions of basidiospores of Cronartium quercuum f. sp. fusiforme...

76 FR 53162 - Acceptance of Public Submissions Regarding the Study of Stable Value Contracts

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-25

... the risk of a run on a SVF? To the extent that SVC providers use value-at-risk (``VaR'') models, do such VaR models adequately assess the risk of loss resulting from such events or other possible but extremely unlikely events? Do other loss models more adequately assess the risk of loss, such as the...

A sex-averaged genetic linkage map in coastal Douglas-fir (Pseudotsuga menziesii [Mirb] Franco var menziesii) based on RFLP and RAPD markers

Treesearch

K.D. Jermstad; D.L. Bassoni; N.C. Wheeler; D.B. Neale

1998-01-01

We have constructed a sex-averaged genetic linkage map in coastal Douglas-fir ( Pseudotsuga menziesii [Mirb.] Franco var menziesii) using a three-generation outcrossed pedigree and molecular markers. Our research objectives are to learn about genome organization and to identify markers associated with adaptive traits. The map...

The relationship between Swiss needle cast symptom severity and level of Phaeocryptopus gaeumannii colonization in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii).

Treesearch

F. Temel; G.R. Johnson; J.K. Stone

2004-01-01

This study examined 108 15-year-old Douglas-fir (Pseudotsuga menziesii var. menziesii trees to investigate whether trees exhibiting less severe Swiss needle cast (SNC) symptoms were more resistant (had less fungal colonization) or more tolerant (maintained healthy foliage under similar infection levels). Trees were sampled from...

Neolignan and flavonoid glycosides in Juniperus communis var. depressa.

PubMed

Nakanishi, Tsutomu; Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Inada, Akira; Murata, Jin; Lang, Frank A; Iinuma, Munekazu; Tanaka, Toshiyuki

2004-01-01

Two neolignan glycosides (junipercomnosides A and B) were isolated from aerial parts of Juniperus communis var. depressa along with two known neolignan glycosides and seven flavonoid glycosides. The structures of the isolated compounds were determined by spectral analysis, in particular by 2D-NMR analysis. The significance of distribution of flavonoids in the chemotaxonomy of genus Juniperus was also discussed.

Primary Attraction of Ips latidens (LeConte) and Hylastes Gracilis LeConte (Coleoptera: Scolytidae) to High-Girdled Lodgepole Pine, Pinus Contorta var. Latifolia Engelmann

Treesearch

D.R. Miller; J.L. Madden; J.H. Borden

1986-01-01

In the absence of secondary attraction, 2 species of Scolytidae, Ips latidens (LeConte) and Hylastes gracilis LeConte, showed significant preference while in flight for high-girdled over non-girdled lodgepole pines, Pinus contorta var. latifolia Engelmann. In contrast, beetles in 2 genera...

Long- and short-term flooding effects on survival and sink-source relationships of swamp-adapted tree species

Treesearch

M.N. Angelov; Shi-Jean S. Sung; R.L. Doong; W.R. Harms; Paul P. Kormanik; C.C. Black

1995-01-01

About 95% of swamp tupelo (Nyssa sylvatica var. biflora (Walt.) Sarg.) And sweetgum (Liquidambar styraciflua L.) seedlings survived continuous root flooding for more than two years, whereas none of the swamp chestnut oak (Quercus michauxii Nutt.) And cherrybark oak (Q. falcata var. pagodifolia Ell.) Seedlings survived one year of flooding.Flooding caused increases in...

17 CFR 240.15c3-1f - Optional market and credit risk requirements for OTC derivatives dealers (Appendix F to 17 CFR...

Code of Federal Regulations, 2010 CFR

2010-04-01

... charges. An OTC derivatives dealer shall provide a description of all statistical models used for pricing... controls over those models, and a statement regarding whether the firm has developed its own internal VAR models. If the OTC derivatives dealer's VAR model incorporates empirical correlations across risk...

40 CFR 180.1154 - CryIA(c) and CryIC derived delta-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated...

Code of Federal Regulations, 2010 CFR

2010-07-01

...-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated in killed Pseudomonas fluorescens, and the... RESIDUES IN FOOD Exemptions From Tolerances § 180.1154 CryIA(c) and CryIC derived delta-endotoxins of... plasmid and cloning vector genetic constructs. CryIA(c) and CryIC derived delta-endotoxins of Bacillus...

40 CFR 180.1154 - CryIA(c) and CryIC derived delta-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated...

Code of Federal Regulations, 2011 CFR

2011-07-01

...-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated in killed Pseudomonas fluorescens, and the... RESIDUES IN FOOD Exemptions From Tolerances § 180.1154 CryIA(c) and CryIC derived delta-endotoxins of... plasmid and cloning vector genetic constructs. CryIA(c) and CryIC derived delta-endotoxins of Bacillus...

Composition of Pteryxia terebinthina var. californica (Coult. and Rose) Mathias essential oils

USGS Publications Warehouse

Beauchamp, Philip E.; Dev, Vasu; Munevar-Mendoza, Elsa; Moore, Peggy E.

2000-01-01

β-Pinene (35.0%, 53.8%) was the major component of both the aerial parts and the root oils of Pteryxia terebinthina var. californica, respectively. β-Phellandrene (12.2%) was the other most abundant component of the oil from aeial parts while δ-3-carene (14.2%) was the second abundant component of the root oil.

40 CFR 180.1154 - CryIA(c) and CryIC derived delta-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated...

Code of Federal Regulations, 2013 CFR

2013-07-01

...-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated in killed Pseudomonas fluorescens, and the... RESIDUES IN FOOD Exemptions From Tolerances § 180.1154 CryIA(c) and CryIC derived delta-endotoxins of... plasmid and cloning vector genetic constructs. CryIA(c) and CryIC derived delta-endotoxins of Bacillus...

40 CFR 180.1154 - CryIA(c) and CryIC derived delta-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated...

Code of Federal Regulations, 2012 CFR

2012-07-01

...-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated in killed Pseudomonas fluorescens, and the... RESIDUES IN FOOD Exemptions From Tolerances § 180.1154 CryIA(c) and CryIC derived delta-endotoxins of... plasmid and cloning vector genetic constructs. CryIA(c) and CryIC derived delta-endotoxins of Bacillus...

40 CFR 180.1154 - CryIA(c) and CryIC derived delta-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated...

Code of Federal Regulations, 2014 CFR

2014-07-01

...-endotoxins of Bacillus thuringiensis var. kurstaki encapsulated in killed Pseudomonas fluorescens, and the... RESIDUES IN FOOD Exemptions From Tolerances § 180.1154 CryIA(c) and CryIC derived delta-endotoxins of... plasmid and cloning vector genetic constructs. CryIA(c) and CryIC derived delta-endotoxins of Bacillus...

Dynamic Relationship between Gross Domestic Product and Domestic Investment in Rwanda

ERIC Educational Resources Information Center

Ocaya, Bruno; Ruranga, Charles; Kaberuka, William

2012-01-01

This study uses a VAR model to analyse the dynamic relationship between gross domestic product (GDP) and domestic investment (DI) in Rwanda for the period 1970 to 2011. Several selection lag criteria chose a maximum lag of one, and a bivariate VAR(1) model specification in levels was adopted. Unit root tests show that both GDP and DI series are…

Effects of fire and restoration seeding on establishment of squarrose knapweed (Centaurea virgata var. squarrosa)

Treesearch

Alison Whittaker; Scott L. Jensen

2008-01-01

Squarrose knapweed (Centaurea virgata var. squarrosa), herein referred to simply as knapweed, is a noxious weed that invades both disturbed and healthy sagebrush communities. Fire, grazing, mining, recreation, and farming have all played a large part in the establishment of knapweed in Tintic Valley, Utah. This study was designed to look at the...

The Gaussian Graphical Model in Cross-Sectional and Time-Series Data.

PubMed

Epskamp, Sacha; Waldorp, Lourens J; Mõttus, René; Borsboom, Denny

2018-04-16

We discuss the Gaussian graphical model (GGM; an undirected network of partial correlation coefficients) and detail its utility as an exploratory data analysis tool. The GGM shows which variables predict one-another, allows for sparse modeling of covariance structures, and may highlight potential causal relationships between observed variables. We describe the utility in three kinds of psychological data sets: data sets in which consecutive cases are assumed independent (e.g., cross-sectional data), temporally ordered data sets (e.g., n = 1 time series), and a mixture of the 2 (e.g., n > 1 time series). In time-series analysis, the GGM can be used to model the residual structure of a vector-autoregression analysis (VAR), also termed graphical VAR. Two network models can then be obtained: a temporal network and a contemporaneous network. When analyzing data from multiple subjects, a GGM can also be formed on the covariance structure of stationary means-the between-subjects network. We discuss the interpretation of these models and propose estimation methods to obtain these networks, which we implement in the R packages graphicalVAR and mlVAR. The methods are showcased in two empirical examples, and simulation studies on these methods are included in the supplementary materials.

Argania spinosa var. mutica and var. apiculata: variation of fatty-acid composition, phenolic content, and antioxidant and α-amylase-inhibitory activities among varieties, organs, and development stages.

PubMed

El Adib, Saifeddine; Aissi, Oumayma; Charrouf, Zoubida; Ben Jeddi, Fayçal; Messaoud, Chokri

2015-09-01

Argania spinosa includes two varieties, var. apiculata and var. mutica. These argan varieties were introduced into Tunisia in ancient times and are actually cultivated in some botanic gardens. Little is known about the chemical differentiation among these argan varieties. Hence, the aim of this study was to determine the fatty-acid composition, the total phenolic and flavonoid contents, and the antioxidant and α-amylase-inhibitory activities of leaf, seed, and pulp extracts of both argan varieties harvested during the months of January to April. The fatty-acid distribution was found to depend on the argan variety, the plant organ, and the harvest time. Significant variations in the phenolic contents were observed between the investigated varieties as well as between leaves, pulps, and seeds of each variety. As expected, phenolic compounds were found to be contributors to the antioxidant and α-amylase-inhibitory activities of both argan varieties. The chemical differentiation observed among the two argan varieties, based mainly on the fatty-acid composition, might have some chemotaxonomic value. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

Value-at-Risk analysis using ARMAX GARCHX approach for estimating risk of banking subsector stock return’s

NASA Astrophysics Data System (ADS)

Dewi Ratih, Iis; Sutijo Supri Ulama, Brodjol; Prastuti, Mike

2018-03-01

Value at Risk (VaR) is one of the statistical methods used to measure market risk by estimating the worst losses in a given time period and level of confidence. The accuracy of this measuring tool is very important in determining the amount of capital that must be provided by the company to cope with possible losses. Because there is a greater losses to be faced with a certain degree of probability by the greater risk. Based on this, VaR calculation analysis is of particular concern to researchers and practitioners of the stock market to be developed, thus getting more accurate measurement estimates. In this research, risk analysis of stocks in four banking sub-sector, Bank Rakyat Indonesia, Bank Mandiri, Bank Central Asia and Bank Negara Indonesia will be done. Stock returns are expected to be influenced by exogenous variables, namely ICI and exchange rate. Therefore, in this research, stock risk estimation are done by using VaR ARMAX-GARCHX method. Calculating the VaR value with the ARMAX-GARCHX approach using window 500 gives more accurate results. Overall, Bank Central Asia is the only bank had the estimated maximum loss in the 5% quantile.

Quantum work fluctuations in connection with the Jarzynski equality.

PubMed

Jaramillo, Juan D; Deng, Jiawen; Gong, Jiangbin

2017-10-01

A result of great theoretical and experimental interest, the Jarzynski equality predicts a free energy change ΔF of a system at inverse temperature β from an ensemble average of nonequilibrium exponential work, i.e., 〈e^{-βW}〉=e^{-βΔF}. The number of experimental work values needed to reach a given accuracy of ΔF is determined by the variance of e^{-βW}, denoted var(e^{-βW}). We discover in this work that var(e^{-βW}) in both harmonic and anharmonic Hamiltonian systems can systematically diverge in nonadiabatic work protocols, even when the adiabatic protocols do not suffer from such divergence. This divergence may be regarded as a type of dynamically induced phase transition in work fluctuations. For a quantum harmonic oscillator with time-dependent trapping frequency as a working example, any nonadiabatic work protocol is found to yield a diverging var(e^{-βW}) at sufficiently low temperatures, markedly different from the classical behavior. The divergence of var(e^{-βW}) indicates the too-far-from-equilibrium nature of a nonadiabatic work protocol and makes it compulsory to apply designed control fields to suppress the quantum work fluctuations in order to test the Jarzynski equality.

Effects of Cd, Pb, Zn, Cu-resistant endophytic Enterobacter sr CBSB1 and Rhodotorula sp. CBSB79 on the growth and phytoextraction of Brassica plants in multimetal contaminated soils.

PubMed

Wang, Wenfeng; Deng, Zujun; Tan, Hongming; Cao, Lixiang

2013-01-01

To survey the effects of endophytic Enterobacter sp. CBSB1 and Rhodotorula sp. CBSB79 resistant to Cd2+, Pb2+, Zn2+, and Cu2+ on the growth and phytoextraction of Brassica, the endophytes were isolated by surface- sterilized methods and characterized. The CBSB1 significantly increased 44.2% of the dry weight of Brassica napus in the multimetal contaminated soil (P < 0.05) and showed no effect or declined the dry weight of B. alboglabra, B. campestris ssp. chinensis var. cummunis, B. campestris ssp. chinensis var. utilis cv. Youqing12, B. campestris ssp. chinensis var. utilis cv. Lvbao701 plants. The dry weights of B. napus, B. campestris ssp. chinensis var. utilis, and B. alboglabra showed a significant increase when the CBSB79 was inoculated (P < 0.05). In general, inoculation with bacteria and yeast did not greatly alter the metal concentration in plant tissues. Compared to Enterobacter sp. CBSB1, the yeast Rhodotorula sp CBSB79 showed higher potentials to improve extraction efficacy of Cd, Pb, Zn, and Cu by Brassica seedlings in the field.

Evaluation of volatiles from Ampelopsis brevipedunculata var. heterophylla using GC-olfactometry, GC-MS and GC-pulsed flame photometric detector.

PubMed

Nakamura, Atsuhiko; Miyazawa, Mitsuo

2013-01-01

Ampelopsis brevipedunculata var. heterophylla is extensively cultivated in Asia, and the dried leaves and branches have a characteristic odor and have been used as a tea. To investigate the odorants contributing to the characteristic odor of A. brevipedunculata var. heterophylla, the aroma extraction dilution analysis method was performed through gas chromatography olfactometry. In addition, volatile sulfur compounds were evaluated using pulsed flame photometric detector. As a result, 86 compounds were identified in the oils of leaves and 78 in branches, accounting for 80.0% and 68.3%, respectively, of the compounds identified. The main compounds in the essential oil of leaves were palmitic acid (12.5%), phenylacetaldehyde (4.1%) and hexahydrofarnesyl acetone (3.9%). On the other hand, the essential oil of branches contained palmitic acid (12.7%), terpinen-4-ol (4.4%) and α-cadinol (3.7%). The total number of odor-active compounds identified in the leaf and branch oils was 39. The most odorous compounds of leaves and branches of A. brevipedunculata var. heterophylla were (E, Z)-2,6-nonadienal (melon, green odor), (E)-2-nonenal (grassy odor), phenylacetaldehyde (honey-like) and (E)-linalool oxide (woody odor).

An empirical study on information spillover effects between the Chinese copper futures market and spot market

NASA Astrophysics Data System (ADS)

Liu, Xiangli; Cheng, Siwei; Wang, Shouyang; Hong, Yongmiao; Li, Yi

2008-02-01

This study employs a parametric approach based on TGARCH and GARCH models to estimate the VaR of the copper futures market and spot market in China. Considering the short selling mechanism in the futures market, the paper introduces two new notions: upside VaR and extreme upside risk spillover. And downside VaR and upside VaR are examined by using the above approach. Also, we use Kupiec’s [P.H. Kupiec, Techniques for verifying the accuracy of risk measurement models, Journal of Derivatives 3 (1995) 73-84] backtest to test the power of our approaches. In addition, we investigate information spillover effects between the futures market and the spot market by employing a linear Granger causality test, and Granger causality tests in mean, volatility and risk respectively. Moreover, we also investigate the relationship between the futures market and the spot market by using a test based on a kernel function. Empirical results indicate that there exist significant two-way spillovers between the futures market and the spot market, and the spillovers from the futures market to the spot market are much more striking.

Application of HS-SPME and GC-MS to characterization of volatile compounds emitted from Osmanthus flowers.

PubMed

Deng, Chunhui; Song, Guoxin; Hu, Yaoming

2004-12-01

Headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS) was developed for characterization of volatile compounds emitted from two varieties Osmanthus flowers of O. fragrans var. latifolius and O. fragrans var. thunbergii. The SPME parameters were studied, the optimum conditions of a 65 microm carbowax/divinylbenzene (CW/DVB), extraction temperature of 22 degrees C and extraction time of 10 min were obtained and applied to extraction of the volatile emissions. Fourteen compounds released from both varieties of Osmanthus flowers were separated and identified by GC-MS, which mainly included alpha-linalool, beta-linalool, trans-linalool oxide, cis-linalool oxide, alpha-lonone, beta-lonone, capraldehyde and decalactone. By comparing their peak areas, we found that the sums of the fourteen compounds from the two Osmanthus flowers were very close, while the relative contents of individual volatile compounds in the two emissions were very different. The relative content of alpha-linalool and beta-linalool in O. fragrans var. latifolius were 39.46% and 0.51%, while in O. fragrans var. thunbergii were 9.53% and 27.71%. Due to their different relative contents, the two varieties of flower have different fragrances.

Inheritance of the complete mitochondrial genomes Cyprinus capio furong(♀) × Cyprinus carpio var.singguonensis(♂).

PubMed

Peng, Huizhen; Liu, Qiaolin; Xiao, Tiaoyi

2016-09-01

In this study, 15 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of C. capio furong(♀) × C. carpio var.singguonensis(♂) in order to characterize and compare their mitochondrial genomes. The total length of the mitochondrial genome was 16,581 bp and deposited in the GenBank with the accession number KP210473. The organization of the mitochondrial genomes contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region which was similar to those reported mitochondrial genomes. Most genes were encoded on the H-strand, except for the ND6 and 8 tRNA genes, encoding on the L-strand. The nucleotide skewness for the coding strands of C. capio furong(♀) × C. carpio var.singguonensis(♂) (AT-skew = 0.12, GC-skew = -0.27) were biased toward T and G. The complete mitogenome may provide important date for the study of genetic mechanism of C. capio furong(♀) × C. carpio var.singguonensis(♂).

Considerations for Using Hybrid Ensemble-Variational Data Assimilation in NASA-GMAO's Next Reanalysis System

NASA Technical Reports Server (NTRS)

El Akkraoui, Amal; Todling, Ricardo

2017-01-01

The Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) is the latest reanalysis produced by GMAO, and provides global data spanning the period 1980-present. The atmospheric data assimilation component of MERRA-2 used a 3D-Var scheme, which was operational at the time of its design. Since then, a Hybrid 3D-Var, then a Hybrid 4D-EnVar were implemented, adding an ensemble component to the data assimilation scheme. In this work, we will be examining the benefits of using hybrid ensemble flow-dependent covariances to represent errors and uncertainties in historic periods. Specifically, periods of pre- and post-satellites, as well as periods of active tropical cyclone seasons. Finally, we will also be exploring the use of adaptive localization scales.

[Glycosides from flowers of Jasminum officinale L. var. grandiflorum].

PubMed

Zhao, Gui-qin; Xia, Jing-jing; Dong, Jun-xing

2007-10-01

To study the chemical constituents of the flower of Jasminum officinale L. var. grandiflorum. The compounds were isolated and purified by re-crystallization and chromatography on silica gel and Sephadex LH-20 column. Their structures were elucidated on the physicochemical properties and spectral analysis. Seven glycosides were identified as kaempferol-3-O-alpha-L-rhamnopyranosyl (1-->3)-[alpha-L-rhamnopyranosyl (1-->6)]-beta-D-galactopyranoside (I), kaempferol-3-O-rutinoside (II), 7-ketologanin (III), oleoside-11-methyl ester (IV), 7-glucosyl-l1-methyl oleoside (V), ligstroside (VI), oleuropein (VII). Compound I is a new compound. Compounds III and V were isolated from the family of Jasminum for the first time and compounds II, IV and VI were isolated from Jasminum officinale L. var. grandiflorum for the first time.

In vitro study of antioxidant activity and phenolic content of Chrysanthemum balsamita varieties.

PubMed

Benedec, Daniela; Filip, Lorena; Vlase, Laurian; Bele, Constantin; Sevastre, Bogdan; Raita, Oana; Olah, Neli-Kinga; Hanganu, Daniela

2016-07-01

The purpose of our study was to identify the phenolic substances of two varieties of Chrysanthemum balsamita (balsamita and tanacetoides) and to measure the overall antioxidant activity. The phenolic compounds were determined by HPLC. The evaluation of the polyphenolic content was performed by colorimetric analysis. The antioxidant activity was measured by three in vitro assay models: the DPPH, the silver nanoparticles antioxidant capacity (SNPAC) and EPR radical detection. Using HPLC-MS analysis, phenolic acids, flavonoids and flavonoid aglycone were detected. The highest antioxidant activity was showed by Chrysanthemum balsamita var. balsamita, while the lowest for the Chrysanthemum balsamita var. tanacetoides extract, in accord with the polyphenolic content. The results show that Chrysanthemum balsamita var. balsamita might be a source of antioxidant flavonoids, especially rutin and isoquercitrin.

The influence of auxins on the biosynthesis of isoprene derivatives in callus cultures of Vaccinium corymbosum var. bluecrop.

PubMed

Migas, Piotr; Luczkiewicz, Maria; Cisowski, Wojciech

2006-01-01

Callus cultures of Vaccinium corymbosum var. bluecrop were optimized for their isoprene derivatives production by supplementing Schenk-Hildebrandt (SH) medium with constant concentration of kinetin (2.32 microM) and two different amounts of selected auxins. Every auxin, except for IBA, used in 10-time higher concentration (2,4D, NAA, IAA, NOA) stimulated biosynthesis of beta-sitosterol and inhibited triterpene synthesis. Quantitative analysis of isoprene derivatives in callus biomass collected on the 25th day of the experiment proved that the analyzed callus of Vaccinium corymbosum var. bluecrop synthesized the highest amount of isoprene derivatives after subculturing on SH medium modified with 22.6 microM of 2,4D and 2.32 microM of kinetin.

Local Voltage Control in Distribution Networks: A Game-Theoretic Perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xinyang; Tian, Jie; Chen, Lijun

Inverter-based voltage regulation is gaining importance to alleviate emerging reliability and power-quality concerns related to distribution systems with high penetration of photovoltaic (PV) systems. This paper seeks contribution in the domain of reactive power compensation by establishing stability of local Volt/VAr controllers. In lieu of the approximate linear surrogate used in the existing work, the paper establishes existence and uniqueness of an equilibrium point using nonlinear AC power flow model. Key to this end is to consider a nonlinear dynamical system with non-incremental local Volt/VAr control, cast the Volt/VAr dynamics as a game, and leverage the fixed-point theorem as wellmore » as pertinent contraction mapping argument. Numerical examples are provided to complement the analytical results.« less

Local Voltage Control in Distribution Networks: A Game-Theoretic Perspective: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xinyang; Tian, Jie; Chen, Lijun

Inverter-based voltage regulation is gaining importance to alleviate emerging reliability and power-quality concerns related to distribution systems with high penetration of photovoltaic (PV) systems. This paper seeks contribution in the domain of reactive power compensation by establishing stability of local Volt/VAr controllers. In lieu of the approximate linear surrogate used in the existing work, the paper establishes existence and uniqueness of an equilibrium point using nonlinear AC power flow model. Key to this end is to consider a nonlinear dynamical system with non-incremental local Volt/VAr control, cast the Volt/VAr dynamics as a game, and leverage the fixed-point theorem as wellmore » as pertinent contraction mapping argument. Numerical examples are provided to complement the analytical results.« less

Analysis of concentration-dependent effects of copper and PCB on different Chattonella spp. microalgae (raphidophyceae) cultivated in artificial seawater medium

PubMed Central

Niestroy, Jeanette; Martínez, Alfonso Bárbara; Band-Schmidt, Christine J.

2014-01-01

In the present study, the effect on the chlorophyll a and the total protein content as well as the Chattonella spp. cell viability were examined after concentration-dependent exposure to CuCl2 and Aroclor 1242. The comparison between various raphidophyte strains provides an insight into the different susceptibilities to contaminants of Chattonella subsalsa (CSNAV-1), C. marina var. marina (CMCV-1) and C. marina var. ovata (COPV-2). The microalgae were cultivated in artificial seawater medium. Exponentially growing microalgae (8-10 days in culture) were used for exposure experiments. We observed in all three raphidophyte species cytotoxicity-mediated modifications beginning at concentrations of 150 and 200 µM of the heavy metal copper after 24 hours exposure. But interestingly, the three strains exhibited only slight differences in their susceptibility to CuCl2. C. subsalsa and C. marina var. marina cells were first affected at the chlorophyll a level and in cell viability. The total protein amount was reduced significantly only after exposure to 300 µM of CuCl2. However, C. marina var. ovata microalgae showed similar reduction curves for all three analysed cytotoxicity endpoints after heavy metal exposure. On the other hand, after Aroclor 1242 incubation the cytotoxic modification pattern indicated clearly the different susceptibilities of the three raphidophyte strains. C. subsalsa cells noticeably exhibited a decrease in the analysed pigment amount (30-20 % compared to that of the control) already after 0.007 mg/L PCB exposure. In contrast, cell viability and total protein content were slightly reduced and fell below the 50 % threshold after 0.7 and 3.3 mg/L of Aroclor 1242, respectively. Interestingly, C. marina var. ovata showed almost no cytotoxic modification caused by the PCB mixture. Only the concentration of 0.7 mg/L Aroclor 1242 clearly affected the cell viability. As opposed to that we observed a concentration-dependent decrease of cell viability and chlorophyll a amount in CMCV-1 microalgae. These observations confirmed that the susceptibility of the raphidophytes strains CSNAV-1, CMCV-1 and COPV-2 is contaminant-dependent. We showed differences even between two variants of Chattonella (Chattonella marina var. marina and C. marina var. ovata). Furthermore, we were able to show the different mode of action of two common pollutants by simple cytotoxic parameters like total protein and chlorophyll a content as well as by cell counting analysis. PMID:26417254

Analysis of concentration-dependent effects of copper and PCB on different Chattonella spp. microalgae (raphidophyceae) cultivated in artificial seawater medium.

PubMed

Niestroy, Jeanette; Martínez, Alfonso Bárbara; Band-Schmidt, Christine J

2014-01-01

In the present study, the effect on the chlorophyll a and the total protein content as well as the Chattonella spp. cell viability were examined after concentration-dependent exposure to CuCl2 and Aroclor 1242. The comparison between various raphidophyte strains provides an insight into the different susceptibilities to contaminants of Chattonella subsalsa (CSNAV-1), C. marina var. marina (CMCV-1) and C. marina var. ovata (COPV-2). The microalgae were cultivated in artificial seawater medium. Exponentially growing microalgae (8-10 days in culture) were used for exposure experiments. We observed in all three raphidophyte species cytotoxicity-mediated modifications beginning at concentrations of 150 and 200 µM of the heavy metal copper after 24 hours exposure. But interestingly, the three strains exhibited only slight differences in their susceptibility to CuCl2. C. subsalsa and C. marina var. marina cells were first affected at the chlorophyll a level and in cell viability. The total protein amount was reduced significantly only after exposure to 300 µM of CuCl2. However, C. marina var. ovata microalgae showed similar reduction curves for all three analysed cytotoxicity endpoints after heavy metal exposure. On the other hand, after Aroclor 1242 incubation the cytotoxic modification pattern indicated clearly the different susceptibilities of the three raphidophyte strains. C. subsalsa cells noticeably exhibited a decrease in the analysed pigment amount (30-20 % compared to that of the control) already after 0.007 mg/L PCB exposure. In contrast, cell viability and total protein content were slightly reduced and fell below the 50 % threshold after 0.7 and 3.3 mg/L of Aroclor 1242, respectively. Interestingly, C. marina var. ovata showed almost no cytotoxic modification caused by the PCB mixture. Only the concentration of 0.7 mg/L Aroclor 1242 clearly affected the cell viability. As opposed to that we observed a concentration-dependent decrease of cell viability and chlorophyll a amount in CMCV-1 microalgae. These observations confirmed that the susceptibility of the raphidophytes strains CSNAV-1, CMCV-1 and COPV-2 is contaminant-dependent. We showed differences even between two variants of Chattonella (Chattonella marina var. marina and C. marina var. ovata). Furthermore, we were able to show the different mode of action of two common pollutants by simple cytotoxic parameters like total protein and chlorophyll a content as well as by cell counting analysis.

Distribution and taxonomic discussion of Tetraneuris verdiensis, an apparently rare edaphic endemic from the Verde Valley of Arizona

Treesearch

Daniel J. Godec

2001-01-01

Tetraneuris verdiensis was first published in 1996. It appears to be closely related to Tetraneuris acaulis var. arizonica. The closest known location of T. acaulis var. arizonica is approximately 7 miles northwest of the known T. verdiensis locations, which are 5 miles east of Camp Verde. Tetraneuris verdiensis is significant in that no other entirely discoid...

Literature-Related Discovery: Potential Treatments and Preventives for SARS

DTIC Science & Technology

2010-01-01

evaluated the immunomodulatory effects of probiotic Bacillus cereus var. toyoi on the systemic immunity of piglets……Blood samples of probiotic ...and IFN-gamma production of polyclonally stimulated PBMCs was on average higher in the probiotic group. Specific proliferative responses of PBMCs...average higher in the probiotic group. In conclusion, B. cereus var. toyoi therefore alters the immune status of piglets as indicated by changes in

Recurrent prosthetic valve endocarditis caused by Aspergillus delacroxii (formerly Aspergillus nidulans var. echinulatus)

PubMed Central

Uhrin, Gábor Balázs; Jensen, Rasmus Hare; Korup, Eva; Grønlund, Jens; Hjort, Ulla; Moser, Claus; Arendrup, Maiken Cavling; Schønheyder, Henrik Carl

2015-01-01

We report Aspergillus delacroxii (formerly Aspergillus nidulans var. echinulatus) causing recurrent prosthetic valve endocarditis. The fungus was the sole agent detected during replacement of a mechanical aortic valve conduit due to abscess formation. Despite extensive surgery and anti-fungal treatment, the patient had a cerebral hemorrhage 4 months post-surgery prompting a diagnosis of recurrent prosthetic valve endocarditis and fungemia. PMID:26909244

A novel indole-diterpenoid, JBIR-03 with anti-MRSA activity from Dichotomomyces cejpii var. cejpii NBRC 103559.

PubMed

Ogata, Masahiro; Ueda, Jun-ya; Hoshi, Midori; Hashimoto, Junko; Nakashima, Takuji; Anzai, Kozue; Takagi, Motoki; Shin-ya, Kazuo

2007-10-01

A new indole-diterpene, JBIR-03 (1), was isolated from the fungus Dichotomomyces cejpii var. cejpii NBRC 103559 and its structure was determined based on the spectroscopic data. 1 exhibited anti-MRSA (methicillin-resistant Staphylococcus aureus) activity and antifungal activity against apple Valsa canker-causing fungus, Valsa ceratosperma, while it exhibited no toxicity towards human cancer cells.

Environmental Impact Analysis Process. Environmental Assessment Proposed SMC Military Family Housing, San Pedro, California

DTIC Science & Technology

1998-12-01

paint conditions to be 98 percent intact, with cracking, flaking, and peeling noted on various exterior components of the units tested. The survey...paradisiaca var. seminifera Musa spp. banana bananas MYOPORACEAE Myoporum laetum Myoporum spp. myoporum myoporums MYRICACEAE Myrica...Chinese banyan common fig rubber plant Indian laurel fig rustyleaf fig white mulberry MUSACEAE Musa paradisiaca var. seminifera Musa spp. banana

Pest risk assessment of the importation into the United States of unprocessed Pinus logs and chips from Australia

Treesearch

John T Kliejunas; Harold H. Burdsall; Gregg A. DeNitto; Andris Eglitis; Dennis A. Haugen; Michael I. Haverty; Jessie A. Micales-Glaeser

2006-01-01

The unmitigated pest risk potential for the importation of unprocessed logs and chips of species of Pinus (Pinus radiata, P. elliottii Engelm. var. elliottii, P. taeda L., and P. caribaea var. hondurensis, principally) from Australia into the United States was assessed by estimating the likelihood and consequences of introduction of representative insects and pathogens...

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Campbell, J. E.

1972-01-01

A set of conditions in which 90 C was a more lethal temperature than 125 C for the destruction of Bacillus subtilis var. niger was identified as a function of relative humidity, with maximum effectiveness at 100% R.H. A systematic study of the influence of head-space moisture and temperature on the destruction of B. subtilis var. niger is reported.

75 FR 76284 - Pesticide Tolerance Crop Grouping Program II; Revisions to General Tolerance Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-08

............ 8-10B, 8-10C Pepper, bell, Capsicum annuum L. var. 8-10B annuum, Capsicum spp. Pepper, nonbell, Capsicum chinese Jacq., 8-10B, 8-10C C. annuum L. var. annuum, C. frutescens L., C. baccatum L., C. pubescens Ruiz & Pav., Capsicum spp. Roselle, Hibiscus sabdariffa L 8-10B, 8-10C Scarlet eggplant, Solanum...

Ecological adaptations in Douglas-fir (Pseudotsuga menziesii var. glauca) populations: I. North Idaho and North-East Washington

Treesearch

Gerald E. Rehfeldt

1979-01-01

Growth, phenology and frost tolerance of seedlings from 50 populations of Douglas-fir (Pseudotsuga menziesii var. glauca) were compared in 12 environments. Statistical analyses of six variables (bud burst, bud set, 3-year height, spring and fall frost injuries, and deviation from regression of 3-year height on 2-year height) showed that populations not only differed in...

Withanolides from Jaborosa caulescens var. bipinnatifida

PubMed Central

Zhang, Huaping; Cao, Cong-Mei; Gallagher, Robert J.; Day, Victor W.; Montenegro, Gloria; Timmermann, Barbara N.

2013-01-01

Two new withanolides 2,3-dihydrotrechonolide A (1) and 2,3-dihydro-21-hydroxytrechonolide A (2) were isolated along with two known withanolides trechonolide A (3) and jaborosalactone 39 (4) from Jaborosa caulescens var. bipinnatifida (Solanaceae). The structures of 1-2 were elucidated through 2D NMR and other spectroscopic techniques. In addition, the structure of withanolide 1 was confirmed by X-ray crystallographic analysis. PMID:24314746

Genetic differentiation of two California red oak species, Quercus parvula var. shreveii and Q. wislizeni, based on AFLP genetic markers

Treesearch

Nasser Kashani; Richard S. Dodd

2002-01-01

Oaks are renowned for posing problems in defining species boundaries. One example is the case of the interior live oak complex that is usually taken to include two varieties of Quercus wislizeni from the Coast Ranges of California and the Sierra Nevada, and Q. parvula var. shreveii from the central coast of...

Isoprene derivatives from the leaves and callus cultures of Vaccinium corymbosum var. bluecrop.

PubMed

Migas, Piotr; Cisowski, Wojciech; Dembińska-Migas, Wanda

2005-01-01

The phytochemical analysis of Vaccinium corymbosum var bluecrop leaves and callus biomass revealed ursolic acid, oleanolic acid, alpha-amyrin and beta-amyrin in both plant materials. Beta-sitosterol was determined only in callus biomass. The structure of isolated compounds was elucidated by TLC co-chromatography with standards and with spectroscopic methods (1H NMR, 13C NMR, EI-MS).

Germacrane-type sesquiterpenoids from the roots of Valeriana officinalis var. latifolia.

PubMed

Wang, Peng-Cheng; Ran, Xin-Hui; Chen, Rui; Luo, Huai-Rong; Liu, Yu-Qing; Zhou, Jun; Zhao, You-Xing

2010-09-24

Eight new germacrane-type sesquiterpenoids, volvalerenals A-E (2-6) and volvalerenic acids A-C (7-9), along with four known compounds, were isolated from a chloroform extract of the roots of Valeriana officinalis var. latifolia. The structures and relative configurations of 2-9 were elucidated on the basis of spectroscopic data interpretation. The effects of all compounds isolated on acetylcholinesterase were evaluated.

Bauer ketones 23 and 24 from Echinacea paradoxa var. paradoxa inhibit lipopolysaccharide-induced nitric oxide, prostaglandin E2 and cytokines in RAW 264.7 mouse macrophages

USDA-ARS?s Scientific Manuscript database

Among the nine Echinacea species, E. purpurea, E. angustifolia and E. pallida, have been widely used to treat the common cold, flu and other infections. In our study, ethanol extracts of these three Echinacea species and E. paradoxa, including its typical variety, E. paradoxa var. paradoxa, were scr...

Rhizomucor variabilis var. regularior and Hormographiella aspergillata infections in a leukemic bone marrow transplant recipient with refractory neutropenia.

PubMed

Abuali, Mayssa M; Posada, Roberto; Del Toro, Gustavo; Roman, Elizabeth; Ramani, Rama; Chaturvedi, Sudha; Chaturvedi, Vishnu; LaBombardi, Vincent J

2009-12-01

Rhizomucor variabilis and Hormographiella aspergillata rarely cause human infections. This report details a fatal case of a 14-year-old female with leukemia posthematopoietic cell transplant and relapse with refractory pancytopenia. The patient first developed an R. variabilis var. regularior palate infection and later developed a cutaneous H. aspergillata infection while on posaconazole and caspofungin therapy.

Combining Varenicline (Chantix) with Naltrexone Decreases Alcohol Drinking More Effectively Than Does Either Drug Alone in a Rodent Model of Alcoholism.

PubMed

Froehlich, Janice C; Fischer, Stephen M; Dilley, Julian E; Nicholson, Emily R; Smith, Teal N; Filosa, Nick J; Rademacher, Logan C

2016-09-01

This study examined whether varenicline (VAR), or naltrexone (NTX), alone or in combination, reduces alcohol drinking in alcohol-preferring (P) rats with a genetic predisposition toward high voluntary alcohol intake. Alcohol-experienced P rats that had been drinking alcohol (15% v/v) for 2 h/d for 4 weeks were fed either vehicle (VEH), VAR alone (0.5, 1.0, or 2.0 mg/kg body weight [BW]), NTX alone (10.0, 15.0, or 20.0 mg/kg BW), or VAR + NTX in 1 of 4 dose combinations (0.5 VAR + 10.0 NTX, 0.5 VAR + 15.0 NTX, 1.0 VAR + 10.0 NTX, or 1.0 VAR + 15.0 NTX) at 1 hour prior to alcohol access for 10 consecutive days, and the effects on alcohol intake were assessed. When administered alone, VAR in doses of 0.5 or 1.0 mg/kg BW did not alter alcohol intake but a dose of 2.0 mg/kg BW decreased alcohol intake. This effect disappeared when drug treatment was terminated. NTX in doses of 10.0 and 15.0 mg/kg BW did not alter alcohol intake but a dose of 20.0 mg/kg BW decreased alcohol intake. Combining low doses of VAR and NTX into a single medication reduced alcohol intake as well as did high doses of each drug alone. Reduced alcohol intake occurred immediately after onset of treatment with the combined medication and continued throughout prolonged treatment. Low doses of VAR and NTX, when combined in a single medication, reduce alcohol intake in a rodent model of alcoholism. This approach has the advantage of reducing potential side effects associated with each drug. Lowering the dose of NTX and VAR in a combined treatment approach that maintains efficacy while reducing the incidence of negative side effects may increase patient compliance and improve clinical outcomes for alcoholics and heavy drinkers who want to reduce their alcohol intake. Copyright © 2016 by the Research Society on Alcoholism.

Assimilation of Atmospheric InfraRed Sounder (AIRS) Profiles using WRF-Var

NASA Technical Reports Server (NTRS)

Zavodsky, Brad; Jedlovec, Gary J.; Lapenta, William

2008-01-01

The Weather Research and Forecasting (WRF) model contains a three-dimensional variational (3DVAR) assimilation system (WRF-Var), which allows a user to join data from multiple sources into one coherent analysis. WRF-Var combines observations with a background field traditionally generated using a previous model forecast through minimization of a cost function. In data sparse regions, remotely-sensed observations may be able to improve analyses and produce improved forecasts. One such source comes from the Atmospheric Infrared Sounder (AIRS), which together with the Advanced Microwave Sounding Unit (AMSU), represents one of the most advanced space-based atmospheric sounding systems. The combined AIRS/AMSU system provides radiance measurements used as input to a sophisticated retrieval scheme which has been shown to produce temperature profiles with an accuracy of 1 K over 1 km layers and humidity profiles with accuracy of 15% in 2 km layers in both clear and partly cloudy conditions. The retrieval algorithm also provides estimates of the accuracy of the retrieved values at each pressure level, allowing the user to select profiles based on the required error tolerances of the application. The purpose of this paper is to describe a procedure to optimally assimilate high-resolution AIRS profile data into a regional configuration of the Advanced Research WRF (ARW) version 2.2 using WRF-Var. The paper focuses on development of background error covariances for the regional domain and background field type using gen_be and an optimal methodology for ingesting AIRS temperature and moisture profiles as separate overland and overwater retrievals with different error characteristics in the WRF-Var. The AIRS thermodynamic profiles are obtained from the version 5.0 Earth Observing System (EOS) science team retrieval algorithm and contain information about the quality of each temperature layer. The quality indicators are used to select the highest quality temperature and moisture data for each profile location and pressure level. Analyses are run to produce quasi-real-time regional weather forecasts over the continental U.S. The preliminary assessment of the impact of the AIRS profiles will focus on intelligent use of the quality indicators, optimized tuning of the WRF-Var, and comparison of analysis soundings to radiosondes.

Multiplexing detection of IgG against Plasmodium falciparum pregnancy-specific antigens

PubMed Central

Fonseca, Ana Maria; Quinto, Llorenç; Jiménez, Alfons; González, Raquel; Bardají, Azucena; Maculuve, Sonia; Dobaño, Carlota; Rupérez, Maria; Vala, Anifa; Aponte, John J.; Sevene, Esperanza; Macete, Eusebio; Menéndez, Clara

2017-01-01

Background Pregnant women exposed to Plasmodium falciparum generate antibodies against VAR2CSA, the parasite protein that mediates adhesion of infected erythrocytes to the placenta. There is a need of high-throughput tools to determine the fine specificity of these antibodies that can be used to identify immune correlates of protection and exposure. Here we aimed at developing a multiplex-immunoassay to detect antibodies against VAR2CSA antigens. Methods and findings We constructed two multiplex-bead arrays, one composed of 3 VAR2CSA recombinant-domains (DBL3X, DBL5Ɛ and DBL6Ɛ) and another composed of 46 new peptides covering VAR2CSA conserved and semi-conserved regions. IgG reactivity was similar in multiplexed and singleplexed determinations (Pearson correlation, protein array: R2 = 0.99 and peptide array: R2 = 0.87). IgG recognition of 25 out of 46 peptides and all recombinant-domains was higher in pregnant Mozambican women (n = 106) than in Mozambican men (n = 102) and Spanish individuals (n = 101; p<0.05). Agreement of IgG levels detected in cryopreserved plasma and in elutions from dried blood spots was good after exclusion of inappropriate filter papers. Under heterogeneous levels of exposure to malaria, similar seropositivity cutoffs were obtained using finite mixture models applied to antibodies measured on pregnant Mozambican women and average of antibodies measured on pregnant Spanish women never exposed to malaria. The application of the multiplex-bead array developed here, allowed the assessment of higher IgG levels and seroprevalences against VAR2CSA-derived antigens in women pregnant during 2003–2005 than during 2010–2012, in accordance with the levels of malaria transmission reported for these years in Mozambique. Conclusions The multiplex bead-based immunoassay to detect antibodies against selected 25 VAR2CSA new-peptides and recombinant-domains was successfully implemented. Analysis of field samples showed that responses were specific among pregnant women and dependent on the level of exposure to malaria. This platform provides a high-throughput approach to investigating correlates of protection and identifying serological markers of exposure for malaria in pregnancy. PMID:28715465

Organic acids on the growth, anatomical structure, biochemical parameters and heavy metal accumulation of Iris lactea var. chinensis seedling growing in Pb mine tailings.

PubMed

Han, Yu-Lin; Huang, Su-Zhen; Yuan, Hai-Yan; Zhao, Jiu-Zhou; Gu, Ji-Guang

2013-08-01

The effect of citric acid (CA) and ethylene diamine tetraacetic acid (EDTA) on the growth, anatomical structure, physiological responses and lead (Pb) accumulation of Iris lactea var. chinensis seedling growing in Pb mine tailings for 30 days were studied. Results showed that the dry weights (DW) of roots decreased significantly under both levels of CA. The DWs of leaves and roots treated with 2 mmol/kg EDTA decreased significantly and were 23 and 54 %, respectively, lower than those of the control. The tolerant indexes of I. lactea var. chinensis under all treatments of organic acids were lower than control. The root tip anatomical structure was little affected under the treatments of 2 mmol/kg CA and 2 mmol/kg EDTA compared with control. However, the formation of photosynthesizing cells was inhibited by the treatment of 2 mmol/kg EDTA. The concentrations of chlorophyll a, chlorophyll b and total carotenoids in the leaves treated with 2 mmol/kg EDTA significantly decreased. Higher CA level and lower EDTA level could trigger the synthesis of ascorbic acid and higher level of EDTA could trigger the synthesis of glutathione. CA and EDTA could promote Pb accumulation of I. lactea var. chinensis and Pb concentration in the leaves and roots at 2 mmol/kg EDTA treatment increased significantly and reached to 160.44 and 936.08 μg/g DW, respectively, and 1.8 and 1.6 times higher than those of the control. The results indicated that I. lactea var. chinensis could be used to remediate Pb tailing and the role of EDTA in promoting Pb accumulation was better than CA did.

A Stimulus-Locked Vector Autoregressive Model for Slow Event-Related fMRI Designs

PubMed Central

Siegle, Greg

2009-01-01

Summary Neuroscientists have become increasingly interested in exploring dynamic relationships among brain regions. Such a relationship, when directed from one region toward another, is denoted by “effective connectivity.” An fMRI experimental paradigm which is well-suited for examination of effective connectivity is the slow event-related design. This design presents stimuli at sufficient temporal spacing for determining within-trial trajectories of BOLD activation, allowing for the analysis of stimulus-locked temporal covariation of brain responses in multiple regions. This may be especially important for emotional stimuli processing, which can evolve over the course of several seconds, if not longer. However, while several methods have been devised for determining fMRI effective connectivity, few are adapted to event-related designs, which include non-stationary BOLD responses and multiple levels of nesting. We propose a model tailored for exploring effective connectivity of multiple brain regions in event-related fMRI designs - a semi-parametric adaptation of vector autoregressive (VAR) models, termed “stimulus-locked VAR” (SloVAR). Connectivity coefficients vary as a function of time relative to stimulus onset, are regularized via basis expansions, and vary randomly across subjects. SloVAR obtains flexible, data-driven estimates of effective connectivity and hence is useful for building connectivity models when prior information on dynamic regional relationships is sparse. Indices derived from the coefficient estimates can also be used to relate effective connectivity estimates to behavioral or clinical measures. We demonstrate the SloVAR model on a sample of clinically depressed and normal controls, showing that early but not late cortico-amygdala connectivity appears crucial to emotional control and early but not late cortico-cortico connectivity predicts depression severity in the depressed group, relationships that would have been missed in a more traditional VAR analysis. PMID:19236927

PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes

PubMed Central

2014-01-01

Background We propose a phenotype-driven analysis of encrypted exome data to facilitate the widespread implementation of exome sequencing as a clinical genetic screening test. Twenty test-patients with varied syndromes were selected from the literature. For each patient, the mutation, phenotypic data, and genetic diagnosis were available. Next, control exome-files, each modified to include one of these twenty mutations, were assigned to the corresponding test-patients. These data were used by a geneticist blinded to the diagnoses to test the efficiency of our software, PhenoVar. The score assigned by PhenoVar to any genetic diagnosis listed in OMIM (Online Mendelian Inheritance in Man) took into consideration both the patient’s phenotype and all variations present in the corresponding exome. The physician did not have access to the individual mutations. PhenoVar filtered the search using a cut-off phenotypic match threshold to prevent undesired discovery of incidental findings and ranked the OMIM entries according to diagnostic score. Results When assigning the same weight to all variants in the exome, PhenoVar predicted the correct diagnosis in 10/20 patients, while in 15/20 the correct diagnosis was among the 4 highest ranked diagnoses. When assigning a higher weight to variants known, or bioinformatically predicted, to cause disease, PhenoVar’s yield increased to 14/20 (18/20 in top 4). No incidental findings were identified using our cut-off phenotypic threshold. Conclusion The phenotype-driven approach described could render widespread use of ES more practical, ethical and clinically useful. The implications about novel disease identification, advancement of complex diseases and personalized medicine are discussed. PMID:24884844

High Levels of Antibodies to Multiple Domains and Strains of VAR2CSA Correlate with the Absence of Placental Malaria in Cameroonian Women Living in an Area of High Plasmodium falciparum Transmission

PubMed Central

Tutterrow, Yeung L.; Avril, Marion; Singh, Kavita; Long, Carole A.; Leke, Robert J.; Sama, Grace; Salanti, Ali; Smith, Joseph D.; Leke, Rose G. F.

2012-01-01

Placental malaria, caused by sequestration of Plasmodium falciparum-infected erythrocytes in the placenta, is associated with increased risk of maternal morbidity and poor birth outcomes. The parasite antigen VAR2CSA (variant surface antigen 2-chondroitin sulfate A) is expressed on infected erythrocytes and mediates binding to chondroitin sulfate A, initiating inflammation and disrupting homeostasis at the maternal-fetal interface. Although antibodies can prevent sequestration, it is unclear whether parasite clearance is due to antibodies to a single Duffy binding-like (DBL) domain or to an extensive repertoire of antibodies to multiple DBL domains and allelic variants. Accordingly, plasma samples collected longitudinally from pregnant women were screened for naturally acquired antibodies against an extensive panel of VAR2CSA proteins, including 2 to 3 allelic variants for each of 5 different DBL domains. Analyses were performed on plasma samples collected from 3 to 9 months of pregnancy from women living in areas in Cameroon with high and low malaria transmission. The results demonstrate that high antibody levels to multiple VAR2CSA domains, rather than a single domain, were associated with the absence of placental malaria when antibodies were present from early in the second trimester until term. Absence of placental malaria was associated with increasing antibody breadth to different DBL domains and allelic variants in multigravid women. Furthermore, the antibody responses of women in the lower-transmission site had both lower magnitude and lesser breadth than those in the high-transmission site. These data suggest that immunity to placental malaria results from high antibody levels to multiple VAR2CSA domains and allelic variants and that antibody breadth is influenced by malaria transmission intensity. PMID:22331427

Grapefruit extract activity in the control of rose powdery mildew and black spot.

PubMed

Wojdyła, A T

2001-01-01

Efficacy of grapefruit extract (a.i. of Biosept 33 SL) in the control of Sphaerotheca pannosa var. rosae and Diplocarpon rosae on roses was investigated during 1998-1999. The extract was applied as plant spray in concentrations from 0.017 to 0.099%. First treatment of rose shrubs was done when visible disease symptoms occurred on leaves and spraying was repeated 3 (in plastic tunnel) or 10-times (in the field) at weekly intervals. In the second experiment roses with visible powdery mildew symptoms were sprayed once with grapefruit extract. Leaves were sampled one or 7 days after the extract application and germination of spores of S. pannosa var. rosae on potato dextrose agar was evaluated. In the next experiment roses grown under plastic tunnel were sprayed once with the tested preparation. After 24 hours leaves were collected and appearance of fungal hyphae and spores of S. pannosa var. rosae was studied in scanning electron microscope. In the control of S. pannosa var. rosae grapefruit extract at conc. 0.066% was as effective as triforine (standard) applied at 0.027%. Reduction of concentration resulted in the decreased efficacy of the tested preparation. Spores of S. pannosa var. rosae collected one day after grapefruit extract application germinated in about 5%. Analyses of spore vitality 6 days letter showed that only about 15% of conidia could germinated on PDA agar. In contrary, spores from untreated leaves germinated in about 95%. Scanning electrone microscope analysis of leaves taken from plants protected with grapefruit extract showed that most of hyphae were separated from leaf surface. Almost all hyphae and spores were degenerated. In the control of D. rosae the preparation in all tested concentrations gave satisfactory results but was less effective than triforine.

On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation.

PubMed

Pérez-Través, Laura; Lopes, Christian A; Querol, Amparo; Barrio, Eladio

2014-01-01

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99-100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.

On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation

PubMed Central

Pérez-Través, Laura; Lopes, Christian A.; Querol, Amparo; Barrio, Eladio

2014-01-01

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains. PMID:24705561

Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

PubMed

Ma, S J; Sa, K J; Hong, T K; Lee, J K

2017-09-21

In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

Oil biosynthesis and transcriptome profiles in developing endosperm and oil characteristic analyses in Paeonia ostii var. lishizhenii.

PubMed

Xiu, Yu; Wu, Guodong; Tang, Wensi; Peng, Zhengfeng; Bu, Xiangpan; Chao, Longjun; Yin, Xue; Xiong, Jiannan; Zhang, Haiwu; Zhao, Xiaoqing; Ding, Jing; Ma, Lvyi; Wang, Huafang; van Staden, Johannes

2018-06-04

Paeonia ostii var. lishizhenii, a well-known medicinal and horticultural plant, is indigenous to China. Recent studies have shown that its seed has a high oil content, and it was approved as a novel resource of edible oil with a high level of α-linolenic acid by the Chinese Government. This study measured the seed oil contents and fatty acid components of P. ostii var. lishizhenii and six other peonies, P. suffruticosa, P. ludlowii, P. decomposita, P. rockii, and P. lactiflora Pall. 'Heze' and 'Gansu'. The results show that P. ostii var. lishizhenii exhibits the average oil characteristics of tested peonies, with an oil content of 21.3%, α-linolenic acid 43.8%, and unsaturated fatty acids around 92.1%. Hygiene indicators for the seven peony seed oils met the Chinese national food standards. P. ostii var. lishizhenii seeds were used to analyze transcriptome gene regulation networks on endosperm development and oil biosynthesis. In total, 124,117 transcripts were obtained from six endosperm developing stages (S0-S5). The significant changes in differential expression genes (DEGs) clarify three peony endosperm developmental phases: the endosperm cell mitotic phase (S0-S1), the TAG biosynthesis phase (S1-S4), and the mature phase (S5). The DEGs in plant hormone signal transduction, DNA replication, cell division, differentiation, transcription factors, and seed dormancy pathways regulate the endosperm development process. Another 199 functional DEGs participate in glycolysis, pentose phosphate pathway, citrate cycle, FA biosynthesis, TAG assembly, and other pathways. A key transcription factor (WRI1) and some important target genes (ACCase, FATA, LPCAT, FADs, and DGAT etc.) were found in the comprehensive genetic networks of oil biosynthesis. Copyright © 2018 Elsevier GmbH. All rights reserved.

A network approach to analyzing highly recombinant malaria parasite genes.

PubMed

Larremore, Daniel B; Clauset, Aaron; Buckee, Caroline O

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences.

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

PubMed Central

Larremore, Daniel B.; Clauset, Aaron; Buckee, Caroline O.

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. PMID:24130474

Dominance of an alien shrub Rhus typhina over a native shrub Vitex negundo var. heterophylla under variable water supply patterns

PubMed Central

Du, Ning; Tan, Xiangfeng; Li, Qiang; Liu, Xiao; Zhang, Wenxin; Wang, Renqing; Liu, Jian; Guo, Weihua

2017-01-01

Temporal heterogeneity of a resource supply can have a profound effect on the interactions between alien and native plant species and their potential invasiveness. Precipitation patterns may be variable and result in a higher heterogeneity of water supply with global climate change. In this study, an alien shrub species, Rhus typhina, introduced to China from North America and a native shrub species, Vitex negundo var. heterophylla, were grown in monoculture and mixed culture under different water supply regimes, with four levels of water supply frequencies but with a constant level of total supplied water. After 60 days of treatments, the alien species was found to be the superior competitor in the mixed culture and was unaffected by changes in the water supply pattern. The dominance of R. typhina was mainly owing to its greater biomass and effective modulation of leaf physiology. However, in the mixed culture, V. negundo var. heterophylla exhibited both leaf- and whole-plant-level acclimations, including higher leaf length to petiole length and root to shoot biomass ratios, and lower specific leaf weight and leaf length to leaf width ratio. Plant height of V. negundo var. heterophylla was comparable to that of R. typhina in the mixed culture, which is a strategy to escape shading. Although water treatments had little effect on most traits in both species, the possible influence of water regimes should not be neglected. Compared with high-frequency water supply treatments, more individuals of V. negundo var. heterophylla died in low-water-frequency treatments when in competition with R. typhina, which may lead to species turnover in the field. The authors recommended that caution should be exercised when introducing R. typhina to non-native areas in the context of global climate change. PMID:28445505

Ethnopharmacological evaluation of some Scorzonera species: in vivo anti-inflammatory and antinociceptive effects.

PubMed

Küpeli Akkol, Esra; Bahadır Acıkara, Ozlem; Süntar, Ipek; Ergene, Burçin; Saltan Çitoğlu, Gülçin

2012-03-27

Scorzonera species are mainly used against inflammation and to relieve pain in Turkish traditional medicine. Therefore, we aimed to assess in vivo anti-inflammatory and antinociceptive activities of the aerial part and root extracts of Scorzonera acuminata, Scorzonera cana var. alpina, Scorzonera cana var. jacquiniana, Scorzonera cana var. radicosa, Scorzonera cinerea, Scorzonera eriophora, Scorzonera incisa, Scorzonera laciniata ssp. laciniata, Scorzonera parviflora and Scorzonera sublanata. For the anti-inflammatory activity evaluation carrageenan, PGE(2) and serotonin-induced hind paw edema and 12-O-tetradecanoyl-13-acetate (TPA)-induced mouse ear edema models were used. p-Benzoquinone-induced abdominal constriction test was employed in mice for the assessment of antinociceptive activity. Furthermore chemical composition of the tested extracts was investigated qualitatively and quantitatively by using RP-HPLC method. Some phenolic acids and flavonoids were used as standards. Extracts prepared from the aerial parts of Scorzonera cana var. jacquiniana, Scorzonera cinerea, Scorzonera eriophora, Scorzonera incisa and Scorzonera parviflora showed significant inhibitory effect on carrageenan and PGE(2)-induced hind paw edema model as well as on p-benzoquinone-induced abdominal constriction test. The extracts did not show any remarkable activity on serotonin-induced hind paw edema and TPA-induced mouse ear edema models. Chlorogenic acid was detected as major compounds in all the species investigated. Additionally, among the tested flavonoids, luteolin-7-glucoside, hyperoside and rutin were found to be in different amounts in Scorzonera species. The experimental data revealed that Scorzonera cana var. jacquiniana, Scorzonera cinerea, Scorzonera eriophora, Scorzonera incisa and Scorzonera parviflora possess significant anti-inflammatory and antinociceptive activity. It has been suggested that flavonoids and chlorogenic acid are partly responsible for mentioned activities of Scorzonera species. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Pigment Production on L-Tryptophan Medium by Cryptococcus gattii and Cryptococcus neoformans

PubMed Central

Chaskes, Stuart; Cammer, Michael; Nieves, Edward; Casadevall, Arturo

2014-01-01

In recent years strains previously grouped within Cryptococcus neoformans have been divided into two species C. neoformans and C. gattii, with Cryptococcus neoformans comprising serotypes A, D, and AD and C. gattii comprising serotypes B and C. Cryptococcus neoformans have also been subdivided into two varieties C. neoformans var. grubii, serotype A, and C. neoformans var. neoformans, serotype D. We analyzed the growth and pigment production characteristics of 139 strains of Cryptococcus spp. in L-tryptophan containing media. Nearly all strains of Cryptococcus, including each variety and serotype tested produced a pink water-soluble pigment (molecular weight of 535.2 Da) from L-tryptophan. Consequently, the partial separation of the species was based on whether the pink pigment was secreted into the medium (extracellular) or retained as an intracellular pigment. On L-tryptophan medium C. neoformans var. grubii and serotype AD produced a pink extracellular pigment. In contrast, for C. gattii, the pink pigment was localized intracellularly and masked by heavy production of brown pigments. Pigment production by C. neoformans var. neoformans was variable with some strains producing the pink extracellular pigment and others retained the pink pigment intracellularly. The pink intracellular pigment produced by strains of C. neoformans var. neoformans was masked by production of brown pigments. Cryptococcus laccase mutants failed to produce pigments from L-tryptophan. This is the first report that the enzyme laccase is involved in tryptophan metabolism. Prior to this report Cryptococcus laccase produced melanin or melanin like-pigments from heterocyclic compounds that contained ortho or para diphenols, diaminobenzenes and aminophenol compounds. The pigments produced from L-tryptophan were not melanin. PMID:24736553

Dominance of an alien shrub Rhus typhina over a native shrub Vitex negundo var. heterophylla under variable water supply patterns.

PubMed

Du, Ning; Tan, Xiangfeng; Li, Qiang; Liu, Xiao; Zhang, Wenxin; Wang, Renqing; Liu, Jian; Guo, Weihua

2017-01-01

Temporal heterogeneity of a resource supply can have a profound effect on the interactions between alien and native plant species and their potential invasiveness. Precipitation patterns may be variable and result in a higher heterogeneity of water supply with global climate change. In this study, an alien shrub species, Rhus typhina, introduced to China from North America and a native shrub species, Vitex negundo var. heterophylla, were grown in monoculture and mixed culture under different water supply regimes, with four levels of water supply frequencies but with a constant level of total supplied water. After 60 days of treatments, the alien species was found to be the superior competitor in the mixed culture and was unaffected by changes in the water supply pattern. The dominance of R. typhina was mainly owing to its greater biomass and effective modulation of leaf physiology. However, in the mixed culture, V. negundo var. heterophylla exhibited both leaf- and whole-plant-level acclimations, including higher leaf length to petiole length and root to shoot biomass ratios, and lower specific leaf weight and leaf length to leaf width ratio. Plant height of V. negundo var. heterophylla was comparable to that of R. typhina in the mixed culture, which is a strategy to escape shading. Although water treatments had little effect on most traits in both species, the possible influence of water regimes should not be neglected. Compared with high-frequency water supply treatments, more individuals of V. negundo var. heterophylla died in low-water-frequency treatments when in competition with R. typhina, which may lead to species turnover in the field. The authors recommended that caution should be exercised when introducing R. typhina to non-native areas in the context of global climate change.

FBST for Cointegration Problems

NASA Astrophysics Data System (ADS)

Diniz, M.; Pereira, C. A. B.; Stern, J. M.

2008-11-01

In order to estimate causal relations, the time series econometrics has to be aware of spurious correlation, a problem first mentioned by Yule [21]. To solve the problem, one can work with differenced series or use multivariate models like VAR or VEC models. In this case, the analysed series are going to present a long run relation i.e. a cointegration relation. Even though the Bayesian literature about inference on VAR/VEC models is quite advanced, Bauwens et al. [2] highlight that "the topic of selecting the cointegrating rank has not yet given very useful and convincing results." This paper presents the Full Bayesian Significance Test applied to cointegration rank selection tests in multivariate (VAR/VEC) time series models and shows how to implement it using available in the literature and simulated data sets. A standard non-informative prior is assumed.

PURIFICATION AND ACTIVITY OF PROTEINASE OF STREPTOCOCCUS FAECALIS VAR. LIQUEFACIENS

PubMed Central

Shugart, Lee R.; Beck, Raymond W.

1964-01-01

Shugart, Lee R. (University of Tennessee, Knoxville) and Raymond W. Beck. Purification and activity of proteinase of Streptococcus faecalis var. liquefaciens. J. Bacteriol. 88:586–590. 1964.—A proteolytic enzyme from Streptococcus faecalis var. liquefaciens was purified 480-fold by ammonium sulfate fractionation and treatment with calcium phosphate gel. Approximately 20% of the original enzyme activity was recovered in the purified fraction. Optimal enzyme activity was found to be at pH 7.6 and 35 C. The enzyme is apparently more susceptible to heat denaturation when complexed with substrate than when heated in the absence of substrate. Michaelis-Menten constants were found to be 0.655% for hemoglobin and 0.133% for casein. Apparent energies of activation on these substrates were calculated to be 9,060 and 12,020 cal, respectively. PMID:14208492

Effect of double vacuum melting and retained austenite on rolling-element fatigue life of AMS 5749 bearing steel

NASA Technical Reports Server (NTRS)

Parker, R. J.; Hodder, R. S.

1977-01-01

AMS 5749 steel combines the tempering, hot hardness, and hardness retention characteristics of AISI M-50 steel with the corrosion and oxidation resistance of AISI 440C stainless steel. The five-ball fatigue tester was used to evaluate the rolling-element fatigue life of AMS 5749. Double vacuum melting (vacuum induction melting plus vacuum arc remelting, VIM-VAR) produced AMS 5749 material with a rolling-element fatigue life at least 14 times that of vacuum induction melting alone. The VIM-VAR AMS 5749 steel balls gave lives from 6 to 12 times greater than VIM-VAR AISI M-50 steel balls. The highest level of retained austenite, 14.6 percent, was significantly detrimental to rolling-element fatigue life relative to the intermediate level of 11.1 percent.

Phase Diagram of Spin-1/2 Alternating Ferromagnetic Chain with XY-Like Anisotropy

NASA Astrophysics Data System (ADS)

Yoshida, Satoru; Okamoto, Kiyomi

1989-12-01

By the use of the numerical method we investigate the ground state phase diagram of spin-1/2 alternating ferromagnetic chain. We numerically diagonalized the Hamiltonian of finite systems (up to 20 spins) and analyzed the numerical data for various physical quantities using the finite size scaling and the extrapolation methods. The ground state is either the effective singlet (ES) state or the spin fluid (SF) state depending on the value of the alternation parameter δ and the anisotropy parameter \\varDelta{\\equiv}Jz/J\\bot(\\varDelta{=}{-}1 for the isotropic ferromagnetic case and \\varDelta{=}0 for the XY case). The phase diagram obtained in this work strongly stupports the theoretical studies of Kohmoto-den Nijs-Kadanoff and Okamoto-Sugiyama. We also discuss the critical properties near the ES-SF transition line.

Medicinal activities of the leaves of Musa sapientum var. sylvesteris in vitro

PubMed Central

Sahaa, Repon Kumer; Acharyaa, Srijan; Shovon, Syed Sohidul Haque; Royb, Priyanka

2013-01-01

Objective This study is to investigate the medicinal value of methanolic extract of the leaves of Musa sapientum var. sylvesteris in Bangladesh. Methods Several biochemical assays, thin layer chormatogarphy and ultra-violet spectroscopy were used to detect the presence of various types of compounds in this extract. Antioxidant effects were measured by DPPH scavenging assay, total reducing assay and hydrogen peroxide scavenging assay. Receptor binding activities and hydrogen peroxide induced hemolysis assay were performed by hemagglutination assay and hemolysis assay using erythrocytes. Disk diffusion assay was performed to show the antibacterial effect of the extract. Results Methanolic extract of the leaves showed antioxidant and antibacterial activity in vitro. The extract showed hemaglutination inhibition activities and hydrogen peroxide induced hemolysis inhibition activity of human red blood cells. Conclusion Musa sapientum var. sylvesteris can be an useful medicinal plant. PMID:23730561

Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae).

PubMed

Li, Zhi-Zhong; Lu, Meng-Xue; Saina, Josphat K; Gichira, Andrew W; Wang, Qing-Feng; Chen, Jin-Ming

2017-11-01

Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis . One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata , and 12 amplified in each of the other three varieties of O. acuminata . These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata .

Vegetative Analysis of the Flookplain of the Trinity River, Texas,

DTIC Science & Technology

1974-09-30

humilis var. longiflora (Gray) Fern. Ruellia Ruellia nudiflora (Gray)1*~ n_ __ Rush Juncus nodatus Coy.f Rush Juncus Torreyi Coy. Rush-foil...scurfpea Psoralea rhombifolia T. & G.J Royal fern Osmunda reai var. §pectabilis (Willd.) Gray Ruellia Ruellia caroliniensis (Walt.) Steud. Ruellia Ruellia ...o’clock Mirabilis nyctaginea (Michx.) 1 Wild indigo Baptisia Nuttalliana, SmallJ Wild onion Allium canadense L. Wild petunia Ruellia Corzoi Tharp & Barkl

Patterns of growth and mortality in the endangered Nichol's Turk's Head Cactus (Echinocactus horizonthalonius var. nicholii L. Benson; Cactaceae) in Southeastern Arizona

Treesearch

M. E. McIntosh; L. A. McDade; A. E. Boyd; P. D. Jenkins

2007-01-01

Nichol’s Turk’s Head Cactus (Echinocactus horizonthalonius var. nicholii L. Benson; Cactaceae) occurs in a few isolated populations in the Sonoran desert of southcentral Arizona (Pima and Pinal counties). The populations of this variety are disjunct from the more widespread variety that occurs in the Chihuahuan desert of Texas and...

Environmental Assessment for a Taxiway M Bypass Road at Travis Air Force Base, California

DTIC Science & Technology

2011-10-01

California Species Scientific Name Species Common Name Protection Status Presence Plants Astragalus tener var. tener Alkali milk -vetch CNPS 1B...Downingia pusilla Dwarf downingia CNPS 2.2 Potential Astragalus tener var. ferrisiae Ferris’ milk -vetch CNPS 1B.1 Potential Fritillaria liliacea...Bypass Road and C Bunker Access Road improvements. Use of raw building materials for construction would be an irretrievable commitment of

A monoterpene glucoside and three megastigmane glycosides from Juniperus communis var. depressa.

PubMed

Nakanishi, Tsutomu; Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Inada, Akira; Murata, Jin; Lang, Frank A; Iinuma, Munekazu; Tanaka, Toshiyuki; Sakagami, Yoshikazu

2005-07-01

A new monoterpene glucoside (1) and three new natural megastigmane glycosides (2-4) were isolated along with a known megastigmane glucoside (5) from twigs with leaves of Juniperus communis var. depressa (Cupressaceae) collected in Oregon, U.S.A., and their structures were determined on the basis of spectral and chemical evidence. In addition, the antibacterial activities of the isolated components against Helicobacter pylori were also investigated.

Biology and control of Eriophyid mites with a case study of Aceria sp. on New Mexico olive (Forestiera pubescens Nutt. var. pubescens)

Treesearch

Tessa R. Grasswitz

2012-01-01

The biology, recognition, and impact of eriophyid mites (with emphasis on species associated with trees and shrubs) are briefly reviewed. A case study of a leaf-curling eriophyid mite (Aceria sp.) attacking New Mexico olive (Forestiera pubescens Nutt. var. pubescens) is used to illustrate the complexities of developing control strategies for eriophyids in native plant...

Withanolides from Jaborosa caulescens var. bipinnatifida.

PubMed

Zhang, Huaping; Cao, Cong-Mei; Gallagher, Robert J; Day, Victor W; Montenegro, Gloria; Timmermann, Barbara N

2014-02-01

Withanolides 2,3-dihydrotrechonolide A (1) and 2,3-dihydro-21-hydroxytrechonolide A (2) were isolated along with two known withanolides trechonolide A (3) and jaborosalactone 39 (4) from Jaborosa caulescens var. bipinnatifida (Solanaceae). The structures of 1-2 were elucidated through 2D NMR and other spectroscopic techniques. In addition, the structure of withanolide 1 was confirmed by X-ray crystallographic analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Rhizomucor variabilis var. regularior and Hormographiella aspergillata Infections in a Leukemic Bone Marrow Transplant Recipient with Refractory Neutropenia ▿

PubMed Central

Abuali, Mayssa M.; Posada, Roberto; Del Toro, Gustavo; Roman, Elizabeth; Ramani, Rama; Chaturvedi, Sudha; Chaturvedi, Vishnu; LaBombardi, Vincent J.

2009-01-01

Rhizomucor variabilis and Hormographiella aspergillata rarely cause human infections. This report details a fatal case of a 14-year-old female with leukemia posthematopoietic cell transplant and relapse with refractory pancytopenia. The patient first developed an R. variabilis var. regularior palate infection and later developed a cutaneous H. aspergillata infection while on posaconazole and caspofungin therapy. PMID:19846651

[Development of cysticercoid larva of Hymenolepis nana var. fraterna in Tenebrio molitor and Leucophaea maderae haemoceles (author's transl)].

PubMed

Pesson, B; Leger, N; Bouchet, P

1978-01-01

When embryos of Hymenolepis nana var. fraterna are injected abdominally, they are able to reach the cysticercoid stage in the haemocele of Leucophaea maderae which naturally resist to infection by ingestion of the eggs. The haemocytic defence reaction of the cockroach and the structure of the surface of larvae are examined and compared with development in a natural host Tenebrio molitor.

Effects of Fermentation Temperature and Aeration on Production of Natural Isoamyl Acetate by Williopsis saturnus var. saturnus

PubMed Central

Yilmaztekin, Murat; Cabaroglu, Turgut; Erten, Huseyin

2013-01-01

Isoamyl acetate is a natural flavour ester, widely used as a source of banana flavour by the food industry. Williopsis saturnus var. saturnus is a yeast which can produce isoamyl acetate by esterification of amyl alcohols with acetyl coenzyme A via fermentation. The evaluation of this kind of production as an alternative way to obtain natural banana flavour could be possible, if the levels produced were high enough to make a commercial product. In this study, the effects of temperature (15°C and 25°C) and aeration (aerobic, semiaerobic, and anaerobic) on the production of isoamyl acetate by Williopsis saturnus var. saturnus from sugar beet molasses were examined. According to the results obtained, isoamyl acetate production rate and specific productivity were higher at 25°C than at 15°C and at semiaerobic condition than aerobic and anaerobic conditions. Williopsis saturnus var. saturnus showed a production rate of 0.703 mg L−1 h−1 and a specific productivity of 0.0297 mg L−1 cell−1 h−1 isoamyl acetate with semiaerobic condition at 25°C. The maximum amount of isoamyl acetate reached with these conditions was 118 mg/L. PMID:23862159

Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables

PubMed Central

Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

2016-01-01

Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops. PMID:26727246

Reactive power planning under high penetration of wind energy using Benders decomposition

DOE PAGES

Xu, Yan; Wei, Yanli; Fang, Xin; ...

2015-11-05

This study addresses the optimal allocation of reactive power volt-ampere reactive (VAR) sources under the paradigm of high penetration of wind energy. Reactive power planning (RPP) in this particular condition involves a high level of uncertainty because of wind power characteristic. To properly model wind generation uncertainty, a multi-scenario framework optimal power flow that considers the voltage stability constraint under the worst wind scenario and transmission N 1 contingency is developed. The objective of RPP in this study is to minimise the total cost including the VAR investment cost and the expected generation cost. Therefore RPP under this condition ismore » modelled as a two-stage stochastic programming problem to optimise the VAR location and size in one stage, then to minimise the fuel cost in the other stage, and eventually, to find the global optimal RPP results iteratively. Benders decomposition is used to solve this model with an upper level problem (master problem) for VAR allocation optimisation and a lower problem (sub-problem) for generation cost minimisation. Impact of the potential reactive power support from doubly-fed induction generator (DFIG) is also analysed. Lastly, case studies on the IEEE 14-bus and 118-bus systems are provided to verify the proposed method.« less

Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables.

PubMed

Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

2016-01-04

Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops.

An arbuscular mycorrhizal fungus and Epichloë festucae var. lolii reduce Bipolaris sorokiniana disease incidence and improve perennial ryegrass growth.

PubMed

Li, Fang; Guo, Yan'e; Christensen, Michael J; Gao, Ping; Li, Yanzhong; Duan, Tingyu

2018-02-01

Leaf spot of perennial ryegrass (Lolium perenne) caused by Bipolaris sorokiniana is an important disease in temperate regions of the world. We designed this experiment to test for the combined effects of the arbuscular mycorrhizal (AM) fungus Claroideoglomus etunicatum and the grass endophyte fungus Epichloë festucae var. lolii on growth and disease occurrence in perennial ryegrass. The results show that C. etunicatum increased plant P uptake and total dry weight and that this beneficial effect was slightly enhanced when in association with the grass endophyte. The presence in plants of both the endophyte and B. sorokiniana decreased AM fungal colonization. Plants inoculated with B. sorokiniana showed the typical leaf spot symptoms 2 weeks after inoculation and the lowest disease incidence was with plants that were host to both C. etunicatum and E. festucae var. lolii. Plants with these two fungi had much higher activity of peroxidases (POD), superoxide dismutase (SOD) and catalase (CAT) and lower values of malondialdehyde (MDA) and hydrogen peroxide (H 2 O 2 ). The AM fungus C. etunicatum and the grass endophyte fungus E. festucae var. lolii have the potential to promote perennial ryegrass growth and resistance to B. sorokiniana leaf spot.

Two Different Points of View through Artificial Intelligence and Vector Autoregressive Models for Ex Post and Ex Ante Forecasting

PubMed Central

Aydin, Alev Dilek; Caliskan Cavdar, Seyma

2015-01-01

The ANN method has been applied by means of multilayered feedforward neural networks (MLFNs) by using different macroeconomic variables such as the exchange rate of USD/TRY, gold prices, and the Borsa Istanbul (BIST) 100 index based on monthly data over the period of January 2000 and September 2014 for Turkey. Vector autoregressive (VAR) method has also been applied with the same variables for the same period of time. In this study, different from other studies conducted up to the present, ENCOG machine learning framework has been used along with JAVA programming language in order to constitute the ANN. The training of network has been done by resilient propagation method. The ex post and ex ante estimates obtained by the ANN method have been compared with the results obtained by the econometric forecasting method of VAR. Strikingly, our findings based on the ANN method reveal that there is a possibility of financial distress or a financial crisis in Turkey starting from October 2017. The results which were obtained with the method of VAR also support the results of ANN method. Additionally, our results indicate that the ANN approach has more superior prediction performance than the VAR method. PMID:26550010

Estimation of Confidence Intervals for Multiplication and Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verbeke, J

2009-07-17

Helium-3 tubes are used to detect thermal neutrons by charge collection using the {sup 3}He(n,p) reaction. By analyzing the time sequence of neutrons detected by these tubes, one can determine important features about the constitution of a measured object: Some materials such as Cf-252 emit several neutrons simultaneously, while others such as uranium and plutonium isotopes multiply the number of neutrons to form bursts. This translates into unmistakable signatures. To determine the type of materials measured, one compares the measured count distribution with the one generated by a theoretical fission chain model. When the neutron background is negligible, the theoreticalmore » count distributions can be completely characterized by a pair of parameters, the multiplication M and the detection efficiency {var_epsilon}. While the optimal pair of M and {var_epsilon} can be determined by existing codes such as BigFit, the uncertainty on these parameters has not yet been fully studied. The purpose of this work is to precisely compute the uncertainties on the parameters M and {var_epsilon}, given the uncertainties in the count distribution. By considering different lengths of time tagged data, we will determine how the uncertainties on M and {var_epsilon} vary with the different count distributions.« less

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

PubMed Central

Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

2014-01-01

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

Effects of losartan on experimental varicocele-induced testicular germ cell apoptosis.

PubMed

Bolat, D; Oltulu, F; Uysal, A; Kose, T; Gunlusoy, B; Yigitturk, G; Turk, N S; Turan, T

2016-09-01

To investigate the potential protective effects of losartan on varicocele-induced germ cell apoptosis, 24 adult male Sprague Dawley rats were divided into three groups: a sham operation was performed in SHAM group, and experimental left varicocele was created in VAR and VAR + LOS groups. Additionally, in VAR + LOS group, losartan was administered for 30 days starting on the day of surgery. At the end of 30 days, all animals were sacrificed and left orchiectomy was performed. Testicular injury and spermatogenesis were evaluated according to Johnsen scoring system. To assess the nitrosative stress, immunohistochemical staining for endothelial nitric oxide synthase was used and evaluated by H-score and apoptotic index (AI) of germ cells was analysed by TUNEL method. A significant decrease in the mean Johnsen score (JS) was observed in VAR group compared with SHAM (p < .001). The mean H-score and AI were significantly higher in VAR group compared with SHAM (p < .001). After losartan administration, mean JS was significantly increased (p < .001) and mean H-score and AI were significantly decreased compared with VAR group (p < .001 and .01, respectively). Findings of this suggest that losartan acts as a potent protective agent against varicocele-induced germ cell apoptosis. © 2016 Blackwell Verlag GmbH.

Two Different Points of View through Artificial Intelligence and Vector Autoregressive Models for Ex Post and Ex Ante Forecasting.

PubMed

Aydin, Alev Dilek; Caliskan Cavdar, Seyma

2015-01-01

The ANN method has been applied by means of multilayered feedforward neural networks (MLFNs) by using different macroeconomic variables such as the exchange rate of USD/TRY, gold prices, and the Borsa Istanbul (BIST) 100 index based on monthly data over the period of January 2000 and September 2014 for Turkey. Vector autoregressive (VAR) method has also been applied with the same variables for the same period of time. In this study, different from other studies conducted up to the present, ENCOG machine learning framework has been used along with JAVA programming language in order to constitute the ANN. The training of network has been done by resilient propagation method. The ex post and ex ante estimates obtained by the ANN method have been compared with the results obtained by the econometric forecasting method of VAR. Strikingly, our findings based on the ANN method reveal that there is a possibility of financial distress or a financial crisis in Turkey starting from October 2017. The results which were obtained with the method of VAR also support the results of ANN method. Additionally, our results indicate that the ANN approach has more superior prediction performance than the VAR method.